From 789acd9981ba7043ef59c21351208a68f2eba73a Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Wed, 11 Nov 2015 13:30:50 -0700 Subject: [PATCH] removed c_numpy.pxd and replaced with 'cimport numpy' - 'cimport c_numpy; c_numpy.import_array()' replaced with 'import numpy; cimport numpy' - replaced ndarray.dimensions --> ndarray.shape - re-ran cython to generate C files --- .../MDAnalysis/coordinates/dcdtimeseries.c | 4602 +++++++-- .../MDAnalysis/coordinates/dcdtimeseries.pyx | 12 +- package/MDAnalysis/lib/distances.c | 9033 ++++++++++++----- package/MDAnalysis/lib/distances.pyx | 176 +- package/MDAnalysis/lib/distances_openmp.c | 4877 +++++++-- package/MDAnalysis/lib/distances_openmp.pyx | 175 +- package/include/c_numpy.pxd | 33 - 7 files changed, 15015 insertions(+), 3893 deletions(-) delete mode 100644 package/include/c_numpy.pxd diff --git a/package/MDAnalysis/coordinates/dcdtimeseries.c b/package/MDAnalysis/coordinates/dcdtimeseries.c index 9e0c73c4b89..b15825e6f94 100644 --- a/package/MDAnalysis/coordinates/dcdtimeseries.c +++ b/package/MDAnalysis/coordinates/dcdtimeseries.c @@ -1,25 +1,13 @@ -/* Generated by Cython 0.22.1 */ +/* Generated by Cython 0.23.4 */ #define PY_SSIZE_T_CLEAN -#ifndef CYTHON_USE_PYLONG_INTERNALS -#ifdef PYLONG_BITS_IN_DIGIT -#define CYTHON_USE_PYLONG_INTERNALS 0 -#else -#include "pyconfig.h" -#ifdef PYLONG_BITS_IN_DIGIT -#define CYTHON_USE_PYLONG_INTERNALS 1 -#else -#define CYTHON_USE_PYLONG_INTERNALS 0 -#endif -#endif -#endif #include "Python.h" #ifndef Py_PYTHON_H #error Python headers needed to compile C extensions, please install development version of Python. #elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03020000) #error Cython requires Python 2.6+ or Python 3.2+. #else -#define CYTHON_ABI "0_22_1" +#define CYTHON_ABI "0_23_4" #include #ifndef offsetof #define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) @@ -54,6 +42,9 @@ #define CYTHON_COMPILING_IN_PYPY 0 #define CYTHON_COMPILING_IN_CPYTHON 1 #endif +#if !defined(CYTHON_USE_PYLONG_INTERNALS) && CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x02070000 +#define CYTHON_USE_PYLONG_INTERNALS 1 +#endif #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 && !defined(Py_OptimizeFlag) #define Py_OptimizeFlag 0 #endif @@ -61,12 +52,12 @@ #define CYTHON_FORMAT_SSIZE_T "z" #if PY_MAJOR_VERSION < 3 #define __Pyx_BUILTIN_MODULE_NAME "__builtin__" - #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \ + #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) \ + #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 @@ -84,7 +75,7 @@ #endif #if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND) #define CYTHON_PEP393_ENABLED 1 - #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \ + #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) @@ -103,12 +94,10 @@ #if CYTHON_COMPILING_IN_PYPY #define __Pyx_PyUnicode_Concat(a, b) PyNumber_Add(a, b) #define __Pyx_PyUnicode_ConcatSafe(a, b) PyNumber_Add(a, b) - #define __Pyx_PyFrozenSet_Size(s) PyObject_Size(s) #else #define __Pyx_PyUnicode_Concat(a, b) PyUnicode_Concat(a, b) - #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ? \ + #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ?\ PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b)) - #define __Pyx_PyFrozenSet_Size(s) PySet_Size(s) #endif #if CYTHON_COMPILING_IN_PYPY && !defined(PyUnicode_Contains) #define PyUnicode_Contains(u, s) PySequence_Contains(u, s) @@ -176,16 +165,18 @@ #else #define __Pyx_PyMethod_New(func, self, klass) PyMethod_New(func, self, klass) #endif -#ifndef CYTHON_INLINE - #if defined(__GNUC__) - #define CYTHON_INLINE __inline__ - #elif defined(_MSC_VER) - #define CYTHON_INLINE __inline - #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L - #define CYTHON_INLINE inline - #else - #define CYTHON_INLINE - #endif +#if PY_VERSION_HEX >= 0x030500B1 +#define __Pyx_PyAsyncMethodsStruct PyAsyncMethods +#define __Pyx_PyType_AsAsync(obj) (Py_TYPE(obj)->tp_as_async) +#elif CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 +typedef struct { + unaryfunc am_await; + unaryfunc am_aiter; + unaryfunc am_anext; +} __Pyx_PyAsyncMethodsStruct; +#define __Pyx_PyType_AsAsync(obj) ((__Pyx_PyAsyncMethodsStruct*) (Py_TYPE(obj)->tp_reserved)) +#else +#define __Pyx_PyType_AsAsync(obj) NULL #endif #ifndef CYTHON_RESTRICT #if defined(__GNUC__) @@ -198,35 +189,33 @@ #define CYTHON_RESTRICT #endif #endif +#define __Pyx_void_to_None(void_result) ((void)(void_result), Py_INCREF(Py_None), Py_None) + +#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 + +#if defined(WIN32) || defined(MS_WINDOWS) + #define _USE_MATH_DEFINES +#endif +#include #ifdef NAN #define __PYX_NAN() ((float) NAN) #else static CYTHON_INLINE float __PYX_NAN() { - /* Initialize NaN. The sign is irrelevant, an exponent with all bits 1 and - a nonzero mantissa means NaN. If the first bit in the mantissa is 1, it is - a quiet NaN. */ float value; memset(&value, 0xFF, sizeof(value)); return value; } #endif -#define __Pyx_void_to_None(void_result) (void_result, Py_INCREF(Py_None), Py_None) -#ifdef __cplusplus -template -void __Pyx_call_destructor(T* x) { - x->~T(); -} -template -class __Pyx_FakeReference { - public: - __Pyx_FakeReference() : ptr(NULL) { } - __Pyx_FakeReference(T& ref) : ptr(&ref) { } - T *operator->() { return ptr; } - operator T&() { return *ptr; } - private: - T *ptr; -}; -#endif #if PY_MAJOR_VERSION >= 3 @@ -245,13 +234,13 @@ class __Pyx_FakeReference { #endif #endif -#if defined(WIN32) || defined(MS_WINDOWS) -#define _USE_MATH_DEFINES -#endif -#include #define __PYX_HAVE__coordinates__dcdtimeseries #define __PYX_HAVE_API__coordinates__dcdtimeseries +#include "string.h" +#include "stdio.h" +#include "stdlib.h" #include "numpy/arrayobject.h" +#include "numpy/ufuncobject.h" #include "readdcd.h" #include "correl.h" #ifdef _OPENMP @@ -290,16 +279,34 @@ typedef struct {PyObject **p; char *s; const Py_ssize_t n; const char* encoding; #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 || \ +#define __Pyx_uchar_cast(c) ((unsigned char)c) +#define __Pyx_long_cast(x) ((long)x) +#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))) ) +#if defined (__cplusplus) && __cplusplus >= 201103L + #include + #define __Pyx_sst_abs(value) std::abs(value) +#elif SIZEOF_INT >= SIZEOF_SIZE_T + #define __Pyx_sst_abs(value) abs(value) +#elif SIZEOF_LONG >= SIZEOF_SIZE_T + #define __Pyx_sst_abs(value) labs(value) +#elif defined (_MSC_VER) && defined (_M_X64) + #define __Pyx_sst_abs(value) _abs64(value) +#elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L + #define __Pyx_sst_abs(value) llabs(value) +#elif defined (__GNUC__) + #define __Pyx_sst_abs(value) __builtin_llabs(value) +#else + #define __Pyx_sst_abs(value) ((value<0) ? -value : value) +#endif 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)) @@ -334,8 +341,9 @@ static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) #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)) +#define __Pyx_NewRef(obj) (Py_INCREF(obj), obj) +#define __Pyx_Owned_Py_None(b) __Pyx_NewRef(Py_None) +#define __Pyx_PyBool_FromLong(b) ((b) ? __Pyx_NewRef(Py_True) : __Pyx_NewRef(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*); @@ -441,26 +449,293 @@ 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[] = { "MDAnalysis/coordinates/dcdtimeseries.pyx", - "include/c_numpy.pxd", + "__init__.pxd", + "type.pxd", }; -/* "coordinates/dcdtimeseries.pyx":21 - * c_numpy.import_array() +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":725 + * # 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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":726 + * + * 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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":727 + * ctypedef npy_int8 int8_t + * ctypedef npy_int16 int16_t + * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< + * ctypedef npy_int64 int64_t + * #ctypedef npy_int96 int96_t + */ +typedef npy_int32 __pyx_t_5numpy_int32_t; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":728 + * 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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":732 + * #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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":733 + * + * 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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":734 + * ctypedef npy_uint8 uint8_t + * ctypedef npy_uint16 uint16_t + * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< + * ctypedef npy_uint64 uint64_t + * #ctypedef npy_uint96 uint96_t + */ +typedef npy_uint32 __pyx_t_5numpy_uint32_t; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":735 + * 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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":739 + * #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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":740 + * + * 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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":749 + * # 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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":750 + * # 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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":751 + * 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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":753 + * 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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":754 + * + * ctypedef npy_ulong uint_t + * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<< + * ctypedef npy_ulonglong ulonglong_t + * + */ +typedef npy_ulonglong __pyx_t_5numpy_ulong_t; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":755 + * 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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":757 + * ctypedef npy_ulonglong ulonglong_t + * + * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< + * ctypedef npy_uintp uintp_t + * + */ +typedef npy_intp __pyx_t_5numpy_intp_t; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":758 + * + * ctypedef npy_intp intp_t + * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< + * + * ctypedef npy_double float_t + */ +typedef npy_uintp __pyx_t_5numpy_uintp_t; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":760 + * 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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":761 + * + * ctypedef npy_double float_t + * ctypedef npy_double double_t # <<<<<<<<<<<<<< + * ctypedef npy_longdouble longdouble_t + * + */ +typedef npy_double __pyx_t_5numpy_double_t; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":762 + * 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; + +/* "coordinates/dcdtimeseries.pyx":20 + * cimport numpy * * ctypedef int size_t # <<<<<<<<<<<<<< * * cdef extern from "Python.h": */ typedef int __pyx_t_11coordinates_13dcdtimeseries_size_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 ---*/ + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":764 + * 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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":765 + * + * ctypedef npy_cfloat cfloat_t + * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<< + * ctypedef npy_clongdouble clongdouble_t + * + */ +typedef npy_cdouble __pyx_t_5numpy_cdouble_t; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":766 + * 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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":768 + * 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_t_11coordinates_13dcdtimeseries_dcdhandle; typedef struct __pyx_t_11coordinates_13dcdtimeseries_dcdhandle __pyx_t_11coordinates_13dcdtimeseries_dcdhandle; -/* "coordinates/dcdtimeseries.pyx":40 +/* "coordinates/dcdtimeseries.pyx":39 * int jump_to_dcdstep(fio_fd fd, int natoms, int nsets, int nfixed, int charmm, int header_size, int step) * * ctypedef struct dcdhandle: # <<<<<<<<<<<<<< @@ -502,19 +777,19 @@ struct __pyx_t_11coordinates_13dcdtimeseries_dcdhandle { static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname); #define __Pyx_RefNannyDeclarations void *__pyx_refnanny = NULL; #ifdef WITH_THREAD - #define __Pyx_RefNannySetupContext(name, acquire_gil) \ - if (acquire_gil) { \ - PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure(); \ - __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__); \ - PyGILState_Release(__pyx_gilstate_save); \ - } else { \ - __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__); \ + #define __Pyx_RefNannySetupContext(name, acquire_gil)\ + if (acquire_gil) {\ + PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure();\ + __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__);\ + PyGILState_Release(__pyx_gilstate_save);\ + } else {\ + __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__);\ } #else - #define __Pyx_RefNannySetupContext(name, acquire_gil) \ + #define __Pyx_RefNannySetupContext(name, acquire_gil)\ __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__) #endif - #define __Pyx_RefNannyFinishContext() \ + #define __Pyx_RefNannyFinishContext()\ __Pyx_RefNanny->FinishContext(&__pyx_refnanny) #define __Pyx_INCREF(r) __Pyx_RefNanny->INCREF(__pyx_refnanny, (PyObject *)(r), __LINE__) #define __Pyx_DECREF(r) __Pyx_RefNanny->DECREF(__pyx_refnanny, (PyObject *)(r), __LINE__) @@ -537,13 +812,13 @@ struct __pyx_t_11coordinates_13dcdtimeseries_dcdhandle { #define __Pyx_XGOTREF(r) #define __Pyx_XGIVEREF(r) #endif -#define __Pyx_XDECREF_SET(r, v) do { \ - PyObject *tmp = (PyObject *) r; \ - r = v; __Pyx_XDECREF(tmp); \ +#define __Pyx_XDECREF_SET(r, v) do {\ + PyObject *tmp = (PyObject *) r;\ + r = v; __Pyx_XDECREF(tmp);\ } while (0) -#define __Pyx_DECREF_SET(r, v) do { \ - PyObject *tmp = (PyObject *) r; \ - r = v; __Pyx_DECREF(tmp); \ +#define __Pyx_DECREF_SET(r, v) do {\ + PyObject *tmp = (PyObject *) r;\ + r = v; __Pyx_DECREF(tmp);\ } while (0) #define __Pyx_CLEAR(r) do { PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);} while(0) #define __Pyx_XCLEAR(r) do { if((r) != NULL) {PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);}} while(0) @@ -570,17 +845,14 @@ static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact, static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); -static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], \ - PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, \ +static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[],\ + PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args,\ const char* function_name); -static CYTHON_INLINE long __Pyx_div_long(long, long); /* proto */ - -#ifndef __PYX_FORCE_INIT_THREADS - #define __PYX_FORCE_INIT_THREADS 0 -#endif +static CYTHON_INLINE long __Pyx_div_long(long, long); -#define UNARY_NEG_WOULD_OVERFLOW(x) (((x) < 0) & ((unsigned long)(x) == 0-(unsigned long)(x))) +#define UNARY_NEG_WOULD_OVERFLOW(x)\ + (((x) < 0) & ((unsigned long)(x) == 0-(unsigned long)(x))) #if CYTHON_COMPILING_IN_CPYTHON static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw); @@ -597,9 +869,9 @@ static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name); static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); -static CYTHON_INLINE int __Pyx_mod_int(int, int); /* proto */ +static CYTHON_INLINE int __Pyx_mod_int(int, int); -static CYTHON_INLINE int __Pyx_div_int(int, int); /* proto */ +static CYTHON_INLINE int __Pyx_div_int(int, int); #if CYTHON_COMPILING_IN_CPYTHON static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg); @@ -607,20 +879,20 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg); -#define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \ - (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \ - __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) : \ - (is_list ? (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL) : \ +#define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ + __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) :\ + (is_list ? (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL) :\ __Pyx_GetItemInt_Generic(o, to_py_func(i)))) -#define __Pyx_GetItemInt_List(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \ - (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \ - __Pyx_GetItemInt_List_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) : \ +#define __Pyx_GetItemInt_List(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ + __Pyx_GetItemInt_List_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\ (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL)) static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, int wraparound, int boundscheck); -#define __Pyx_GetItemInt_Tuple(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \ - (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \ - __Pyx_GetItemInt_Tuple_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) : \ +#define __Pyx_GetItemInt_Tuple(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ + __Pyx_GetItemInt_Tuple_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\ (PyErr_SetString(PyExc_IndexError, "tuple index out of range"), (PyObject*)NULL)) static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, int wraparound, int boundscheck); @@ -628,6 +900,34 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, int is_list, int wraparound, int boundscheck); +#if PY_MAJOR_VERSION >= 3 && !CYTHON_COMPILING_IN_PYPY +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 CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); + +static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index); + +static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void); + +static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); + typedef struct { int code_line; PyCodeObject* code_object; @@ -645,14 +945,112 @@ 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); -static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); - static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long 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 CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__NPY_TYPES(enum NPY_TYPES value); + static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *); static int __Pyx_check_binary_version(void); @@ -672,10 +1070,34 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); +/* Module declarations from 'cpython.buffer' */ + +/* Module declarations from 'libc.string' */ + +/* Module declarations from 'libc.stdio' */ + +/* Module declarations from '__builtin__' */ + +/* Module declarations from 'cpython.type' */ +static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0; + +/* Module declarations from 'cpython' */ + +/* Module declarations from 'cpython.object' */ + +/* Module declarations from 'cpython.ref' */ + +/* Module declarations from 'libc.stdlib' */ + /* Module declarations from 'numpy' */ -/* Module declarations from 'c_numpy' */ -static PyTypeObject *__pyx_ptype_7c_numpy_ndarray = 0; +/* 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 'coordinates.dcdtimeseries' */ #define __Pyx_MODULE_NAME "coordinates.dcdtimeseries" @@ -684,10 +1106,27 @@ int __pyx_module_is_main_coordinates__dcdtimeseries = 0; /* Implementation of 'coordinates.dcdtimeseries' */ static PyObject *__pyx_builtin_Exception; static PyObject *__pyx_builtin_IOError; -static PyObject *__pyx_pf_11coordinates_13dcdtimeseries___read_timecorrel(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_atoms, PyObject *__pyx_v_atomcounts, PyObject *__pyx_v_format, PyObject *__pyx_v_auxdata, int __pyx_v_sizedata, int __pyx_v_lowerb, int __pyx_v_upperb, int __pyx_v_start, int __pyx_v_stop, int __pyx_v_skip); /* proto */ -static PyObject *__pyx_pf_11coordinates_13dcdtimeseries_2__read_timeseries(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_atoms, int __pyx_v_skip); /* proto */ +static PyObject *__pyx_builtin_ValueError; +static PyObject *__pyx_builtin_range; +static PyObject *__pyx_builtin_RuntimeError; +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_j[] = "j"; +static char __pyx_k_l[] = "l"; +static char __pyx_k_q[] = "q"; +static char __pyx_k_Zd[] = "Zd"; +static char __pyx_k_Zf[] = "Zf"; +static char __pyx_k_Zg[] = "Zg"; static char __pyx_k_np[] = "np"; static char __pyx_k_rc[] = "rc"; static char __pyx_k_dcd[] = "dcd"; @@ -729,24 +1168,37 @@ static char __pyx_k_sizedata[] = "sizedata"; static char __pyx_k_unitcell[] = "unitcell"; static char __pyx_k_Exception[] = "Exception"; static char __pyx_k_dcd_C_ptr[] = "_dcd_C_ptr"; +static char __pyx_k_ValueError[] = "ValueError"; static char __pyx_k_atomcounts[] = "atomcounts"; +static char __pyx_k_RuntimeError[] = "RuntimeError"; static char __pyx_k_atomcountslist[] = "atomcountslist"; static char __pyx_k_read_timecorrel[] = "__read_timecorrel"; static char __pyx_k_read_timeseries[] = "__read_timeseries"; static char __pyx_k_coordinates_dcdtimeseries[] = "coordinates.dcdtimeseries"; +static char __pyx_k_ndarray_is_not_C_contiguous[] = "ndarray is not C contiguous"; static char __pyx_k_Error_jumping_to_starting_frame[] = "Error jumping to starting frame"; static char __pyx_k_No_data_requested_timeseries_is[] = "No data requested, timeseries is empty"; -static char __pyx_k_home_richard_code_mdanalysis_pa[] = "/home/richard/code/mdanalysis/package/MDAnalysis/coordinates/dcdtimeseries.pyx"; +static char __pyx_k_nfs_homes2_oliver_Library_pytho[] = "/nfs/homes2/oliver/Library/python/mdanalysis/package/MDAnalysis/coordinates/dcdtimeseries.pyx"; +static char __pyx_k_unknown_dtype_code_in_numpy_pxd[] = "unknown dtype code in numpy.pxd (%d)"; static char __pyx_k_Error_reading_frame_from_DCD_fil[] = "Error reading frame from DCD file"; static char __pyx_k_Error_skipping_frame_from_DCD_fi[] = "Error skipping frame from DCD file"; +static char __pyx_k_Format_string_allocated_too_shor[] = "Format string allocated too short, see comment in numpy.pxd"; static char __pyx_k_No_atoms_passed_into___read_time[] = "No atoms passed into __read_timeseries function"; +static char __pyx_k_Non_native_byte_order_not_suppor[] = "Non-native byte order not supported"; +static char __pyx_k_ndarray_is_not_Fortran_contiguou[] = "ndarray is not Fortran contiguous"; +static char __pyx_k_Format_string_allocated_too_shor_2[] = "Format string allocated too short."; static PyObject *__pyx_kp_s_Error_jumping_to_starting_frame; static PyObject *__pyx_kp_s_Error_reading_frame_from_DCD_fil; static PyObject *__pyx_kp_s_Error_skipping_frame_from_DCD_fi; static PyObject *__pyx_n_s_Exception; +static PyObject *__pyx_kp_u_Format_string_allocated_too_shor; +static PyObject *__pyx_kp_u_Format_string_allocated_too_shor_2; static PyObject *__pyx_n_s_IOError; static PyObject *__pyx_kp_s_No_atoms_passed_into___read_time; static PyObject *__pyx_kp_s_No_data_requested_timeseries_is; +static PyObject *__pyx_kp_u_Non_native_byte_order_not_suppor; +static PyObject *__pyx_n_s_RuntimeError; +static PyObject *__pyx_n_s_ValueError; static PyObject *__pyx_n_s_array; static PyObject *__pyx_n_s_atomcounts; static PyObject *__pyx_n_s_atomcountslist; @@ -763,7 +1215,6 @@ static PyObject *__pyx_n_s_float32; static PyObject *__pyx_n_s_float64; static PyObject *__pyx_n_s_fmtstr; static PyObject *__pyx_n_s_format; -static PyObject *__pyx_kp_s_home_richard_code_mdanalysis_pa; static PyObject *__pyx_n_s_i; static PyObject *__pyx_n_s_import; static PyObject *__pyx_n_s_index; @@ -773,6 +1224,9 @@ static PyObject *__pyx_n_s_lowerb; static PyObject *__pyx_n_s_main; static PyObject *__pyx_n_s_n_atoms; static PyObject *__pyx_n_s_n_frames; +static PyObject *__pyx_kp_u_ndarray_is_not_C_contiguous; +static PyObject *__pyx_kp_u_ndarray_is_not_Fortran_contiguou; +static PyObject *__pyx_kp_s_nfs_homes2_oliver_Library_pytho; static PyObject *__pyx_n_s_np; static PyObject *__pyx_n_s_numdata; static PyObject *__pyx_n_s_numpy; @@ -792,8 +1246,13 @@ static PyObject *__pyx_n_s_tempY; static PyObject *__pyx_n_s_tempZ; static PyObject *__pyx_n_s_test; static PyObject *__pyx_n_s_unitcell; +static PyObject *__pyx_kp_u_unknown_dtype_code_in_numpy_pxd; static PyObject *__pyx_n_s_upperb; static PyObject *__pyx_n_s_zeros; +static PyObject *__pyx_pf_11coordinates_13dcdtimeseries___read_timecorrel(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_atoms, PyObject *__pyx_v_atomcounts, PyObject *__pyx_v_format, PyObject *__pyx_v_auxdata, int __pyx_v_sizedata, int __pyx_v_lowerb, int __pyx_v_upperb, int __pyx_v_start, int __pyx_v_stop, int __pyx_v_skip); /* proto */ +static PyObject *__pyx_pf_11coordinates_13dcdtimeseries_2__read_timeseries(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_atoms, int __pyx_v_skip); /* 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_int_3; static PyObject *__pyx_tuple_; static PyObject *__pyx_tuple__2; @@ -803,16 +1262,22 @@ static PyObject *__pyx_tuple__5; static PyObject *__pyx_tuple__6; static PyObject *__pyx_tuple__7; static PyObject *__pyx_tuple__8; +static PyObject *__pyx_tuple__9; static PyObject *__pyx_tuple__10; -static PyObject *__pyx_codeobj__9; -static PyObject *__pyx_codeobj__11; - -/* "coordinates/dcdtimeseries.pyx":62 +static PyObject *__pyx_tuple__11; +static PyObject *__pyx_tuple__12; +static PyObject *__pyx_tuple__13; +static PyObject *__pyx_tuple__14; +static PyObject *__pyx_tuple__16; +static PyObject *__pyx_codeobj__15; +static PyObject *__pyx_codeobj__17; + +/* "coordinates/dcdtimeseries.pyx":61 * import numpy as np * * def __read_timecorrel(object self, object atoms, object atomcounts, object format, object auxdata, int sizedata, int lowerb, int upperb, int start, int stop, int skip): # <<<<<<<<<<<<<< * cdef dcdhandle* dcd - * cdef c_numpy.ndarray atomlist, atomcountslist, auxlist + * cdef numpy.ndarray atomlist, atomcountslist, auxlist */ /* Python wrapper */ @@ -865,56 +1330,56 @@ static PyObject *__pyx_pw_11coordinates_13dcdtimeseries_1__read_timecorrel(PyObj case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_atoms)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("__read_timecorrel", 1, 11, 11, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__read_timecorrel", 1, 11, 11, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_atomcounts)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("__read_timecorrel", 1, 11, 11, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__read_timecorrel", 1, 11, 11, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 3: if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_format)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("__read_timecorrel", 1, 11, 11, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__read_timecorrel", 1, 11, 11, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 4: if (likely((values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_auxdata)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("__read_timecorrel", 1, 11, 11, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__read_timecorrel", 1, 11, 11, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 5: if (likely((values[5] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_sizedata)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("__read_timecorrel", 1, 11, 11, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__read_timecorrel", 1, 11, 11, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 6: if (likely((values[6] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_lowerb)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("__read_timecorrel", 1, 11, 11, 6); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__read_timecorrel", 1, 11, 11, 6); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 7: if (likely((values[7] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_upperb)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("__read_timecorrel", 1, 11, 11, 7); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__read_timecorrel", 1, 11, 11, 7); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 8: if (likely((values[8] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_start)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("__read_timecorrel", 1, 11, 11, 8); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__read_timecorrel", 1, 11, 11, 8); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 9: if (likely((values[9] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_stop)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("__read_timecorrel", 1, 11, 11, 9); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__read_timecorrel", 1, 11, 11, 9); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 10: if (likely((values[10] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_skip)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("__read_timecorrel", 1, 11, 11, 10); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__read_timecorrel", 1, 11, 11, 10); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__read_timecorrel") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__read_timecorrel") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else if (PyTuple_GET_SIZE(__pyx_args) != 11) { goto __pyx_L5_argtuple_error; @@ -936,16 +1401,16 @@ static PyObject *__pyx_pw_11coordinates_13dcdtimeseries_1__read_timecorrel(PyObj __pyx_v_atomcounts = values[2]; __pyx_v_format = values[3]; __pyx_v_auxdata = values[4]; - __pyx_v_sizedata = __Pyx_PyInt_As_int(values[5]); if (unlikely((__pyx_v_sizedata == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - __pyx_v_lowerb = __Pyx_PyInt_As_int(values[6]); if (unlikely((__pyx_v_lowerb == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - __pyx_v_upperb = __Pyx_PyInt_As_int(values[7]); if (unlikely((__pyx_v_upperb == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - __pyx_v_start = __Pyx_PyInt_As_int(values[8]); if (unlikely((__pyx_v_start == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - __pyx_v_stop = __Pyx_PyInt_As_int(values[9]); if (unlikely((__pyx_v_stop == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - __pyx_v_skip = __Pyx_PyInt_As_int(values[10]); if (unlikely((__pyx_v_skip == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_sizedata = __Pyx_PyInt_As_int(values[5]); if (unlikely((__pyx_v_sizedata == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_lowerb = __Pyx_PyInt_As_int(values[6]); if (unlikely((__pyx_v_lowerb == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_upperb = __Pyx_PyInt_As_int(values[7]); if (unlikely((__pyx_v_upperb == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_start = __Pyx_PyInt_As_int(values[8]); if (unlikely((__pyx_v_start == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_stop = __Pyx_PyInt_As_int(values[9]); if (unlikely((__pyx_v_stop == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_skip = __Pyx_PyInt_As_int(values[10]); if (unlikely((__pyx_v_skip == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("__read_timecorrel", 1, 11, 11, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__read_timecorrel", 1, 11, 11, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; __Pyx_AddTraceback("coordinates.dcdtimeseries.__read_timecorrel", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); @@ -993,34 +1458,32 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries___read_timecorrel(CYTHON int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__read_timecorrel", 0); - /* "coordinates/dcdtimeseries.pyx":70 + /* "coordinates/dcdtimeseries.pyx":69 * cdef char* fmtstr * * dcd = PyCObject_AsVoidPtr(self._dcd_C_ptr) # <<<<<<<<<<<<<< * cdef int n_frames * if (stop == -1): stop = dcd.nsets */ - __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_dcd_C_ptr); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_dcd_C_ptr); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_v_dcd = ((__pyx_t_11coordinates_13dcdtimeseries_dcdhandle *)PyCObject_AsVoidPtr(__pyx_t_1)); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "coordinates/dcdtimeseries.pyx":72 + /* "coordinates/dcdtimeseries.pyx":71 * dcd = PyCObject_AsVoidPtr(self._dcd_C_ptr) * cdef int n_frames * if (stop == -1): stop = dcd.nsets # <<<<<<<<<<<<<< * n_frames = (stop-start+1) / skip * cdef int numdata */ - __pyx_t_2 = ((__pyx_v_stop == -1) != 0); + __pyx_t_2 = ((__pyx_v_stop == -1L) != 0); if (__pyx_t_2) { __pyx_t_3 = __pyx_v_dcd->nsets; __pyx_v_stop = __pyx_t_3; - goto __pyx_L3; } - __pyx_L3:; - /* "coordinates/dcdtimeseries.pyx":73 + /* "coordinates/dcdtimeseries.pyx":72 * cdef int n_frames * if (stop == -1): stop = dcd.nsets * n_frames = (stop-start+1) / skip # <<<<<<<<<<<<<< @@ -1029,38 +1492,26 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries___read_timecorrel(CYTHON */ __pyx_t_4 = ((__pyx_v_stop - __pyx_v_start) + 1); if (unlikely(__pyx_v_skip == 0)) { - #ifdef WITH_THREAD - PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure(); - #endif PyErr_SetString(PyExc_ZeroDivisionError, "integer division or modulo by zero"); - #ifdef WITH_THREAD - PyGILState_Release(__pyx_gilstate_save); - #endif - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 73; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } else if (sizeof(long) == sizeof(long) && (!(((int)-1) > 0)) && unlikely(__pyx_v_skip == (int)-1) && unlikely(UNARY_NEG_WOULD_OVERFLOW(__pyx_t_4))) { - #ifdef WITH_THREAD - PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure(); - #endif PyErr_SetString(PyExc_OverflowError, "value too large to perform division"); - #ifdef WITH_THREAD - PyGILState_Release(__pyx_gilstate_save); - #endif - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 73; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_v_n_frames = __Pyx_div_long(__pyx_t_4, __pyx_v_skip); - /* "coordinates/dcdtimeseries.pyx":75 + /* "coordinates/dcdtimeseries.pyx":74 * n_frames = (stop-start+1) / skip * cdef int numdata * numdata = len(format) # <<<<<<<<<<<<<< * if numdata==0: * raise Exception("No data requested, timeseries is empty") */ - __pyx_t_5 = PyObject_Length(__pyx_v_format); if (unlikely(__pyx_t_5 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyObject_Length(__pyx_v_format); if (unlikely(__pyx_t_5 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_numdata = __pyx_t_5; - /* "coordinates/dcdtimeseries.pyx":76 + /* "coordinates/dcdtimeseries.pyx":75 * cdef int numdata * numdata = len(format) * if numdata==0: # <<<<<<<<<<<<<< @@ -1070,21 +1521,29 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries___read_timecorrel(CYTHON __pyx_t_2 = ((__pyx_v_numdata == 0) != 0); if (__pyx_t_2) { - /* "coordinates/dcdtimeseries.pyx":77 + /* "coordinates/dcdtimeseries.pyx":76 * numdata = len(format) * if numdata==0: * raise Exception("No data requested, timeseries is empty") # <<<<<<<<<<<<<< * fmtstr = PyString_AsString(format) * */ - __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_Exception, __pyx_tuple_, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_Exception, __pyx_tuple_, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_Raise(__pyx_t_1, 0, 0, 0); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "coordinates/dcdtimeseries.pyx":75 + * cdef int numdata + * numdata = len(format) + * if numdata==0: # <<<<<<<<<<<<<< + * raise Exception("No data requested, timeseries is empty") + * fmtstr = PyString_AsString(format) + */ } - /* "coordinates/dcdtimeseries.pyx":78 + /* "coordinates/dcdtimeseries.pyx":77 * if numdata==0: * raise Exception("No data requested, timeseries is empty") * fmtstr = PyString_AsString(format) # <<<<<<<<<<<<<< @@ -1093,21 +1552,21 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries___read_timecorrel(CYTHON */ __pyx_v_fmtstr = PyString_AsString(__pyx_v_format); - /* "coordinates/dcdtimeseries.pyx":80 + /* "coordinates/dcdtimeseries.pyx":79 * fmtstr = PyString_AsString(format) * * atomlist = np.array(atoms, np.int32) # <<<<<<<<<<<<<< * atomcountslist = np.array(atomcounts, np.int32) * 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__pyx_L1_error;} + __pyx_t_9 = PyTuple_New(2+__pyx_t_5); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); if (__pyx_t_6) { __Pyx_GIVEREF(__pyx_t_6); PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_6); __pyx_t_6 = NULL; @@ -1133,29 +1592,29 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries___read_timecorrel(CYTHON __Pyx_GIVEREF(__pyx_t_8); PyTuple_SET_ITEM(__pyx_t_9, 1+__pyx_t_5, __pyx_t_8); __pyx_t_8 = 0; - __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_7, __pyx_t_9, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_7, __pyx_t_9, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; - if 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__pyx_t_8 = __Pyx_PyInt_From_int(__pyx_v_n_frames); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_8); - __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 90; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); __Pyx_GIVEREF(__pyx_t_6); PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_6); @@ -1270,9 +1729,9 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries___read_timecorrel(CYTHON PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_t_8); __pyx_t_6 = 0; __pyx_t_8 = 0; - __pyx_t_8 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 90; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_8 = 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__pyx_ptype_7c_numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 90; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_data = ((PyArrayObject *)__pyx_t_1); __pyx_t_1 = 0; - /* "coordinates/dcdtimeseries.pyx":91 + /* "coordinates/dcdtimeseries.pyx":90 * #data = np.zeros((n_frames, sizedata), np.float64) * data = np.zeros((sizedata, n_frames), np.float64) * temp = np.zeros((3, range), np.float32) # <<<<<<<<<<<<<< * tempX = (temp.data+0*temp.strides[0]) * tempY = (temp.data+1*temp.strides[0]) */ - __pyx_t_7 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 91; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_7)) {__pyx_filename = 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{__pyx_filename = __pyx_f[0]; __pyx_lineno = 91; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 90; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_INCREF(__pyx_int_3); __Pyx_GIVEREF(__pyx_int_3); @@ -1328,9 +1787,9 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries___read_timecorrel(CYTHON __Pyx_GIVEREF(__pyx_t_7); PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_7); __pyx_t_7 = 0; - __pyx_t_7 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 91; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 90; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); - __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_t_7, __pyx_n_s_float32); if (unlikely(!__pyx_t_9)) 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__pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_temp = ((PyArrayObject *)__pyx_t_1); __pyx_t_1 = 0; - /* "coordinates/dcdtimeseries.pyx":92 + /* "coordinates/dcdtimeseries.pyx":91 * data = np.zeros((sizedata, n_frames), np.float64) * temp = np.zeros((3, range), np.float32) * tempX = (temp.data+0*temp.strides[0]) # <<<<<<<<<<<<<< @@ -1373,7 +1832,7 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries___read_timecorrel(CYTHON */ __pyx_v_tempX = ((float *)(__pyx_v_temp->data + (0 * (__pyx_v_temp->strides[0])))); - /* "coordinates/dcdtimeseries.pyx":93 + /* "coordinates/dcdtimeseries.pyx":92 * temp = np.zeros((3, range), np.float32) * tempX = (temp.data+0*temp.strides[0]) * tempY = (temp.data+1*temp.strides[0]) # <<<<<<<<<<<<<< @@ -1382,7 +1841,7 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries___read_timecorrel(CYTHON */ __pyx_v_tempY = ((float *)(__pyx_v_temp->data + (1 * (__pyx_v_temp->strides[0])))); - /* "coordinates/dcdtimeseries.pyx":94 + /* 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*__pyx_pf_11coordinates_13dcdtimeseries___read_timecorrel(CYTHON */ __pyx_v_dcd->setsread = 0; - /* "coordinates/dcdtimeseries.pyx":99 + /* "coordinates/dcdtimeseries.pyx":98 * rc = fio_fseek(dcd.fd, dcd.header_size, 0) #FIO_SEEK_SET * dcd.setsread = 0 * dcd.first = 1 # <<<<<<<<<<<<<< @@ -1418,7 +1877,7 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries___read_timecorrel(CYTHON */ __pyx_v_dcd->first = 1; - /* "coordinates/dcdtimeseries.pyx":102 + /* "coordinates/dcdtimeseries.pyx":101 * * # Jump to frame * if (start > 0): # <<<<<<<<<<<<<< @@ -1428,7 +1887,7 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries___read_timecorrel(CYTHON __pyx_t_2 = ((__pyx_v_start > 0) != 0); if (__pyx_t_2) { - /* "coordinates/dcdtimeseries.pyx":103 + /* "coordinates/dcdtimeseries.pyx":102 * # Jump to frame * if (start > 0): * rc = jump_to_dcdstep(dcd.fd, dcd.natoms, dcd.nsets, dcd.nfixed, dcd.charmm, dcd.header_size, start) # <<<<<<<<<<<<<< @@ -1437,7 +1896,7 @@ static PyObject 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__pyx_tuple__2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 105; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_tuple__2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 104; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_Raise(__pyx_t_1, 0, 0, 0); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 105; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 104; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "coordinates/dcdtimeseries.pyx":103 + * if (start > 0): + * rc = jump_to_dcdstep(dcd.fd, dcd.natoms, dcd.nsets, dcd.nfixed, dcd.charmm, dcd.header_size, start) + * if (rc < 0): # <<<<<<<<<<<<<< + * raise IOError("Error jumping to starting frame") + * dcd.first = 0 + */ } - /* "coordinates/dcdtimeseries.pyx":106 + /* "coordinates/dcdtimeseries.pyx":105 * if (rc < 0): * raise IOError("Error jumping to starting frame") * dcd.first = 0 # <<<<<<<<<<<<<< @@ -1470,7 +1937,7 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries___read_timecorrel(CYTHON */ __pyx_v_dcd->first = 0; - /* "coordinates/dcdtimeseries.pyx":107 + /* "coordinates/dcdtimeseries.pyx":106 * raise IOError("Error jumping to starting frame") * dcd.first = 0 * dcd.setsread = start # <<<<<<<<<<<<<< @@ -1478,11 +1945,17 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries___read_timecorrel(CYTHON * cdef int index, numskip */ __pyx_v_dcd->setsread = __pyx_v_start; - goto __pyx_L5; + + /* "coordinates/dcdtimeseries.pyx":101 + * + * # Jump to frame + * if (start > 0): # <<<<<<<<<<<<<< + * rc = jump_to_dcdstep(dcd.fd, dcd.natoms, dcd.nsets, dcd.nfixed, dcd.charmm, dcd.header_size, start) + * if (rc < 0): + */ } - __pyx_L5:; - /* "coordinates/dcdtimeseries.pyx":112 + /* "coordinates/dcdtimeseries.pyx":111 * cdef int i, j * cdef float unitcell[6] * for i from 0 <= i < n_frames: # <<<<<<<<<<<<<< @@ -1492,7 +1965,7 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries___read_timecorrel(CYTHON __pyx_t_3 = __pyx_v_n_frames; for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_3; __pyx_v_i++) { - /* "coordinates/dcdtimeseries.pyx":113 + /* "coordinates/dcdtimeseries.pyx":112 * cdef float unitcell[6] * for i from 0 <= i < n_frames: * if (skip > 1): # <<<<<<<<<<<<<< @@ -1502,7 +1975,7 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries___read_timecorrel(CYTHON __pyx_t_2 = ((__pyx_v_skip > 1) != 0); if (__pyx_t_2) { - /* "coordinates/dcdtimeseries.pyx":116 + /* "coordinates/dcdtimeseries.pyx":115 * # Check if we have fixed atoms * # XXX not done * numskip = skip - (dcd.setsread % skip) - 1 # <<<<<<<<<<<<<< @@ -1510,18 +1983,12 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries___read_timecorrel(CYTHON * if (rc < 0): */ if (unlikely(__pyx_v_skip == 0)) { - #ifdef WITH_THREAD - PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure(); - #endif PyErr_SetString(PyExc_ZeroDivisionError, "integer division or modulo by zero"); - #ifdef WITH_THREAD - PyGILState_Release(__pyx_gilstate_save); - #endif - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 116; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 115; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_v_numskip = ((__pyx_v_skip - __Pyx_mod_int(__pyx_v_dcd->setsread, __pyx_v_skip)) - 1); - /* "coordinates/dcdtimeseries.pyx":117 + /* "coordinates/dcdtimeseries.pyx":116 * # XXX not done * numskip = skip - (dcd.setsread % skip) - 1 * rc = skip_dcdstep(dcd.fd, dcd.natoms, dcd.nfixed, dcd.charmm, numskip) # <<<<<<<<<<<<<< @@ -1530,7 +1997,7 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries___read_timecorrel(CYTHON */ __pyx_v_rc = skip_dcdstep(__pyx_v_dcd->fd, __pyx_v_dcd->natoms, __pyx_v_dcd->nfixed, __pyx_v_dcd->charmm, __pyx_v_numskip); - /* "coordinates/dcdtimeseries.pyx":118 + /* "coordinates/dcdtimeseries.pyx":117 * numskip = skip - (dcd.setsread % skip) - 1 * rc = skip_dcdstep(dcd.fd, dcd.natoms, dcd.nfixed, dcd.charmm, numskip) * if (rc < 0): # <<<<<<<<<<<<<< @@ -1540,33 +2007,47 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries___read_timecorrel(CYTHON __pyx_t_2 = ((__pyx_v_rc < 0) != 0); if (__pyx_t_2) { - /* "coordinates/dcdtimeseries.pyx":119 + /* "coordinates/dcdtimeseries.pyx":118 * rc = skip_dcdstep(dcd.fd, dcd.natoms, dcd.nfixed, dcd.charmm, numskip) * if (rc < 0): * raise IOError("Error skipping frame from DCD file") # <<<<<<<<<<<<<< * dcd.setsread = dcd.setsread + numskip * rc = read_dcdsubset(dcd.fd, dcd.natoms, lowerb, upperb, tempX, tempY, tempZ, unitcell, dcd.nfixed, dcd.first, dcd.freeind, dcd.fixedcoords, dcd.reverse, dcd.charmm) */ - __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_tuple__3, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 119; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_tuple__3, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 118; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_Raise(__pyx_t_1, 0, 0, 0); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 119; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - } + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 118; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "coordinates/dcdtimeseries.pyx":120 - * if (rc < 0): + /* "coordinates/dcdtimeseries.pyx":117 + * numskip = skip - (dcd.setsread % skip) - 1 + * rc = skip_dcdstep(dcd.fd, dcd.natoms, dcd.nfixed, dcd.charmm, numskip) + * if (rc < 0): # <<<<<<<<<<<<<< + * raise IOError("Error skipping frame from DCD file") + * dcd.setsread = dcd.setsread + numskip + */ + } + + /* "coordinates/dcdtimeseries.pyx":119 + * if (rc < 0): * raise IOError("Error skipping frame from DCD file") * dcd.setsread = dcd.setsread + numskip # <<<<<<<<<<<<<< * rc = read_dcdsubset(dcd.fd, dcd.natoms, lowerb, upperb, tempX, tempY, tempZ, unitcell, dcd.nfixed, dcd.first, dcd.freeind, dcd.fixedcoords, dcd.reverse, dcd.charmm) * dcd.first=0 */ __pyx_v_dcd->setsread = (__pyx_v_dcd->setsread + __pyx_v_numskip); - goto __pyx_L9; + + /* "coordinates/dcdtimeseries.pyx":112 + * cdef float unitcell[6] + * for i from 0 <= i < n_frames: + * if (skip > 1): # <<<<<<<<<<<<<< + * # Check if we have fixed atoms + * # XXX not done + */ } - __pyx_L9:; - /* "coordinates/dcdtimeseries.pyx":121 + /* "coordinates/dcdtimeseries.pyx":120 * raise IOError("Error skipping frame from DCD file") * dcd.setsread = dcd.setsread + numskip * rc = read_dcdsubset(dcd.fd, dcd.natoms, lowerb, upperb, tempX, tempY, tempZ, unitcell, dcd.nfixed, dcd.first, dcd.freeind, dcd.fixedcoords, dcd.reverse, dcd.charmm) # <<<<<<<<<<<<<< @@ -1575,7 +2056,7 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries___read_timecorrel(CYTHON */ __pyx_v_rc = read_dcdsubset(__pyx_v_dcd->fd, __pyx_v_dcd->natoms, __pyx_v_lowerb, __pyx_v_upperb, __pyx_v_tempX, __pyx_v_tempY, __pyx_v_tempZ, __pyx_v_unitcell, __pyx_v_dcd->nfixed, __pyx_v_dcd->first, __pyx_v_dcd->freeind, __pyx_v_dcd->fixedcoords, __pyx_v_dcd->reverse, __pyx_v_dcd->charmm); - /* "coordinates/dcdtimeseries.pyx":122 + /* "coordinates/dcdtimeseries.pyx":121 * dcd.setsread = dcd.setsread + numskip * rc = read_dcdsubset(dcd.fd, dcd.natoms, lowerb, upperb, tempX, tempY, tempZ, unitcell, dcd.nfixed, dcd.first, dcd.freeind, dcd.fixedcoords, dcd.reverse, dcd.charmm) * dcd.first=0 # <<<<<<<<<<<<<< @@ -1584,7 +2065,7 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries___read_timecorrel(CYTHON */ __pyx_v_dcd->first = 0; - /* "coordinates/dcdtimeseries.pyx":123 + /* "coordinates/dcdtimeseries.pyx":122 * rc = read_dcdsubset(dcd.fd, dcd.natoms, lowerb, upperb, tempX, tempY, tempZ, unitcell, dcd.nfixed, dcd.first, dcd.freeind, dcd.fixedcoords, dcd.reverse, dcd.charmm) * dcd.first=0 * dcd.setsread = dcd.setsread + 1 # <<<<<<<<<<<<<< @@ -1593,7 +2074,7 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries___read_timecorrel(CYTHON */ __pyx_v_dcd->setsread = (__pyx_v_dcd->setsread + 1); - /* "coordinates/dcdtimeseries.pyx":124 + /* "coordinates/dcdtimeseries.pyx":123 * dcd.first=0 * dcd.setsread = dcd.setsread + 1 * if (rc < 0): # <<<<<<<<<<<<<< @@ -1603,21 +2084,29 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries___read_timecorrel(CYTHON __pyx_t_2 = ((__pyx_v_rc < 0) != 0); if (__pyx_t_2) { - /* "coordinates/dcdtimeseries.pyx":125 + /* "coordinates/dcdtimeseries.pyx":124 * dcd.setsread = dcd.setsread + 1 * if (rc < 0): * raise IOError("Error reading frame from DCD file") # <<<<<<<<<<<<<< * # Copy into data array based on format * copyseries(i, data.data, data.strides, tempX, tempY, tempZ, fmtstr, numdata, atomlist.data, atomcountslist.data, lowerb, auxlist.data); */ - __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_tuple__4, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 125; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_tuple__4, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 124; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_Raise(__pyx_t_1, 0, 0, 0); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 125; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 124; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "coordinates/dcdtimeseries.pyx":123 + * dcd.first=0 + * dcd.setsread = dcd.setsread + 1 + * if (rc < 0): # <<<<<<<<<<<<<< + * raise IOError("Error reading frame from DCD file") + * # Copy into data array based on format + */ } - /* "coordinates/dcdtimeseries.pyx":127 + /* "coordinates/dcdtimeseries.pyx":126 * raise IOError("Error reading frame from DCD file") * # Copy into data array based on format * copyseries(i, data.data, data.strides, tempX, tempY, tempZ, fmtstr, numdata, atomlist.data, atomcountslist.data, lowerb, auxlist.data); # <<<<<<<<<<<<<< @@ -1626,7 +2115,7 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries___read_timecorrel(CYTHON */ copyseries(__pyx_v_i, ((char *)__pyx_v_data->data), __pyx_v_data->strides, __pyx_v_tempX, __pyx_v_tempY, __pyx_v_tempZ, __pyx_v_fmtstr, __pyx_v_numdata, ((int *)__pyx_v_atomlist->data), ((int *)__pyx_v_atomcountslist->data), __pyx_v_lowerb, ((double *)__pyx_v_auxlist->data)); - /* "coordinates/dcdtimeseries.pyx":128 + /* "coordinates/dcdtimeseries.pyx":127 * # Copy into data array based on format * copyseries(i, data.data, data.strides, tempX, tempY, tempZ, fmtstr, numdata, atomlist.data, atomcountslist.data, lowerb, auxlist.data); * PyErr_CheckSignals() # <<<<<<<<<<<<<< @@ -1636,7 +2125,7 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries___read_timecorrel(CYTHON PyErr_CheckSignals(); } - /* "coordinates/dcdtimeseries.pyx":131 + /* "coordinates/dcdtimeseries.pyx":130 * * # Reset trajectory * rc = fio_fseek(dcd.fd, dcd.header_size, 0) #FIO_SEEK_SET # <<<<<<<<<<<<<< @@ -1645,7 +2134,7 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries___read_timecorrel(CYTHON */ __pyx_v_rc = fio_fseek(__pyx_v_dcd->fd, __pyx_v_dcd->header_size, 0); - /* "coordinates/dcdtimeseries.pyx":132 + /* "coordinates/dcdtimeseries.pyx":131 * # Reset trajectory * rc = fio_fseek(dcd.fd, dcd.header_size, 0) #FIO_SEEK_SET * dcd.setsread = 0 # <<<<<<<<<<<<<< @@ -1654,7 +2143,7 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries___read_timecorrel(CYTHON */ __pyx_v_dcd->setsread = 0; - /* "coordinates/dcdtimeseries.pyx":133 + /* "coordinates/dcdtimeseries.pyx":132 * rc = fio_fseek(dcd.fd, dcd.header_size, 0) #FIO_SEEK_SET * dcd.setsread = 0 * dcd.first = 1 # <<<<<<<<<<<<<< @@ -1663,7 +2152,7 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries___read_timecorrel(CYTHON */ __pyx_v_dcd->first = 1; - /* "coordinates/dcdtimeseries.pyx":134 + /* "coordinates/dcdtimeseries.pyx":133 * dcd.setsread = 0 * dcd.first = 1 * return data # <<<<<<<<<<<<<< @@ -1675,12 +2164,12 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries___read_timecorrel(CYTHON __pyx_r = ((PyObject *)__pyx_v_data); goto __pyx_L0; - /* "coordinates/dcdtimeseries.pyx":62 + /* "coordinates/dcdtimeseries.pyx":61 * import numpy as np * * def __read_timecorrel(object self, object atoms, object atomcounts, object format, object auxdata, int sizedata, int lowerb, int upperb, int start, int stop, int skip): # <<<<<<<<<<<<<< * cdef dcdhandle* dcd - * cdef c_numpy.ndarray atomlist, atomcountslist, auxlist + * cdef numpy.ndarray atomlist, atomcountslist, auxlist */ /* function exit code */ @@ -1704,12 +2193,12 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries___read_timecorrel(CYTHON return __pyx_r; } -/* "coordinates/dcdtimeseries.pyx":136 +/* "coordinates/dcdtimeseries.pyx":135 * return data * * def __read_timeseries(object self, object atoms, int skip): # <<<<<<<<<<<<<< * cdef dcdhandle* dcd - * cdef c_numpy.ndarray atomlist + * cdef numpy.ndarray atomlist */ /* Python wrapper */ @@ -1746,16 +2235,16 @@ static PyObject *__pyx_pw_11coordinates_13dcdtimeseries_3__read_timeseries(PyObj case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_atoms)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("__read_timeseries", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 136; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__read_timeseries", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_skip)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("__read_timeseries", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 136; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__read_timeseries", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__read_timeseries") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 136; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__read_timeseries") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else if (PyTuple_GET_SIZE(__pyx_args) != 3) { goto __pyx_L5_argtuple_error; @@ -1766,11 +2255,11 @@ static PyObject *__pyx_pw_11coordinates_13dcdtimeseries_3__read_timeseries(PyObj } __pyx_v_self = values[0]; __pyx_v_atoms = values[1]; - __pyx_v_skip = __Pyx_PyInt_As_int(values[2]); if (unlikely((__pyx_v_skip == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 136; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_skip = __Pyx_PyInt_As_int(values[2]); if (unlikely((__pyx_v_skip == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("__read_timeseries", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 136; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__read_timeseries", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; __Pyx_AddTraceback("coordinates.dcdtimeseries.__read_timeseries", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); @@ -1819,19 +2308,19 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries_2__read_timeseries(CYTHO int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__read_timeseries", 0); - /* "coordinates/dcdtimeseries.pyx":143 + /* "coordinates/dcdtimeseries.pyx":142 * cdef int rc * * dcd = PyCObject_AsVoidPtr(self._dcd_C_ptr) # <<<<<<<<<<<<<< * cdef int n_frames * n_frames = dcd.nsets / skip */ - __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_dcd_C_ptr); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 143; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_dcd_C_ptr); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_v_dcd = ((__pyx_t_11coordinates_13dcdtimeseries_dcdhandle *)PyCObject_AsVoidPtr(__pyx_t_1)); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "coordinates/dcdtimeseries.pyx":145 + /* "coordinates/dcdtimeseries.pyx":144 * dcd = PyCObject_AsVoidPtr(self._dcd_C_ptr) * cdef int n_frames * n_frames = dcd.nsets / skip # <<<<<<<<<<<<<< @@ -1839,38 +2328,26 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries_2__read_timeseries(CYTHO * n_atoms = len(atoms) */ if (unlikely(__pyx_v_skip == 0)) { - #ifdef WITH_THREAD - PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure(); - #endif PyErr_SetString(PyExc_ZeroDivisionError, "integer division or modulo by zero"); - #ifdef WITH_THREAD - PyGILState_Release(__pyx_gilstate_save); - #endif - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 145; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 144; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } else if (sizeof(int) == sizeof(long) && (!(((int)-1) > 0)) && unlikely(__pyx_v_skip == (int)-1) && unlikely(UNARY_NEG_WOULD_OVERFLOW(__pyx_v_dcd->nsets))) { - #ifdef WITH_THREAD - PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure(); - #endif PyErr_SetString(PyExc_OverflowError, "value too large to perform division"); - #ifdef WITH_THREAD - PyGILState_Release(__pyx_gilstate_save); - #endif - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 145; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 144; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_v_n_frames = __Pyx_div_int(__pyx_v_dcd->nsets, __pyx_v_skip); - /* "coordinates/dcdtimeseries.pyx":147 + /* "coordinates/dcdtimeseries.pyx":146 * n_frames = dcd.nsets / skip * cdef int n_atoms * n_atoms = len(atoms) # <<<<<<<<<<<<<< * if n_atoms==0: * raise Exception("No atoms passed into __read_timeseries function") */ - __pyx_t_2 = PyObject_Length(__pyx_v_atoms); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 147; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_Length(__pyx_v_atoms); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 146; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_n_atoms = __pyx_t_2; - /* "coordinates/dcdtimeseries.pyx":148 + /* "coordinates/dcdtimeseries.pyx":147 * cdef int n_atoms * n_atoms = len(atoms) * if n_atoms==0: # <<<<<<<<<<<<<< @@ -1880,30 +2357,38 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries_2__read_timeseries(CYTHO __pyx_t_3 = ((__pyx_v_n_atoms == 0) != 0); if (__pyx_t_3) { - /* "coordinates/dcdtimeseries.pyx":149 + /* "coordinates/dcdtimeseries.pyx":148 * n_atoms = len(atoms) * if n_atoms==0: * raise Exception("No atoms passed into __read_timeseries function") # <<<<<<<<<<<<<< * atomlist = np.array(atoms) * cdef int lowerb, upperb, range */ - __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_Exception, __pyx_tuple__5, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 149; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_Exception, __pyx_tuple__5, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 148; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_Raise(__pyx_t_1, 0, 0, 0); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 149; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 148; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "coordinates/dcdtimeseries.pyx":147 + * cdef int n_atoms + * n_atoms = len(atoms) + * if n_atoms==0: # <<<<<<<<<<<<<< + * raise Exception("No atoms passed into __read_timeseries function") + * atomlist = np.array(atoms) + */ } - /* "coordinates/dcdtimeseries.pyx":150 + /* "coordinates/dcdtimeseries.pyx":149 * if n_atoms==0: * raise Exception("No atoms passed into __read_timeseries function") * atomlist = np.array(atoms) # <<<<<<<<<<<<<< * cdef int lowerb, upperb, range * lowerb = atoms[0] */ - __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 150; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 149; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_array); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 150; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_array); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 149; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __pyx_t_4 = NULL; @@ -1917,51 +2402,51 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries_2__read_timeseries(CYTHO } } if (!__pyx_t_4) { - __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_v_atoms); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 150; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 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__Pyx_GOTREF(__pyx_t_6); - __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 156; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_INCREF(__pyx_int_3); __Pyx_GIVEREF(__pyx_int_3); @@ -2055,9 +2540,9 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries_2__read_timeseries(CYTHO __Pyx_GIVEREF(__pyx_t_6); PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_6); __pyx_t_6 = 0; - __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 156; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - __pyx_t_8 = __Pyx_PyObject_GetAttrStr(__pyx_t_6, __pyx_n_s_float32); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_8 = __Pyx_PyObject_GetAttrStr(__pyx_t_6, __pyx_n_s_float32); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 156; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_8); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __pyx_t_6 = NULL; @@ -2072,7 +2557,7 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries_2__read_timeseries(CYTHO __pyx_t_2 = 1; } } - __pyx_t_4 = PyTuple_New(2+__pyx_t_2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyTuple_New(2+__pyx_t_2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 156; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); if (__pyx_t_6) { __Pyx_GIVEREF(__pyx_t_6); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_6); __pyx_t_6 = NULL; @@ -2083,15 +2568,15 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries_2__read_timeseries(CYTHO PyTuple_SET_ITEM(__pyx_t_4, 1+__pyx_t_2, __pyx_t_8); __pyx_t_5 = 0; __pyx_t_8 = 0; - __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_9, __pyx_t_4, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_9, __pyx_t_4, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 156; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_7c_numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 156; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_temp = ((PyArrayObject *)__pyx_t_1); __pyx_t_1 = 0; - /* "coordinates/dcdtimeseries.pyx":158 + /* "coordinates/dcdtimeseries.pyx":157 * coord = np.zeros((n_atoms, n_frames, 3), np.float64) * temp = np.zeros((3, range), np.float32) * tempX = (temp.data+0*temp.strides[0]) # <<<<<<<<<<<<<< @@ -2100,7 +2585,7 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries_2__read_timeseries(CYTHO */ __pyx_v_tempX = ((float *)(__pyx_v_temp->data + (0 * (__pyx_v_temp->strides[0])))); - /* "coordinates/dcdtimeseries.pyx":159 + /* "coordinates/dcdtimeseries.pyx":158 * temp = np.zeros((3, range), np.float32) * tempX = (temp.data+0*temp.strides[0]) * tempY = (temp.data+1*temp.strides[0]) # <<<<<<<<<<<<<< @@ -2109,7 +2594,7 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries_2__read_timeseries(CYTHO */ __pyx_v_tempY = ((float *)(__pyx_v_temp->data + (1 * (__pyx_v_temp->strides[0])))); - /* "coordinates/dcdtimeseries.pyx":160 + /* "coordinates/dcdtimeseries.pyx":159 * tempX = (temp.data+0*temp.strides[0]) * tempY = (temp.data+1*temp.strides[0]) * tempZ = (temp.data+2*temp.strides[0]) # <<<<<<<<<<<<<< @@ -2118,7 +2603,7 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries_2__read_timeseries(CYTHO */ __pyx_v_tempZ = ((float *)(__pyx_v_temp->data + (2 * (__pyx_v_temp->strides[0])))); - /* "coordinates/dcdtimeseries.pyx":162 + /* "coordinates/dcdtimeseries.pyx":161 * tempZ = (temp.data+2*temp.strides[0]) * # Jump to the beginning of the trajectory file * rc = fio_fseek(dcd.fd, dcd.header_size, 0) #FIO_SEEK_SET # <<<<<<<<<<<<<< @@ -2127,7 +2612,7 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries_2__read_timeseries(CYTHO */ __pyx_v_rc = fio_fseek(__pyx_v_dcd->fd, __pyx_v_dcd->header_size, 0); - /* "coordinates/dcdtimeseries.pyx":163 + /* "coordinates/dcdtimeseries.pyx":162 * # Jump to the beginning of the trajectory file * rc = fio_fseek(dcd.fd, dcd.header_size, 0) #FIO_SEEK_SET * dcd.setsread = 0 # <<<<<<<<<<<<<< @@ -2136,7 +2621,7 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries_2__read_timeseries(CYTHO */ __pyx_v_dcd->setsread = 0; - /* "coordinates/dcdtimeseries.pyx":164 + /* "coordinates/dcdtimeseries.pyx":163 * rc = fio_fseek(dcd.fd, dcd.header_size, 0) #FIO_SEEK_SET * dcd.setsread = 0 * dcd.first = 1 # <<<<<<<<<<<<<< @@ -2145,7 +2630,7 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries_2__read_timeseries(CYTHO */ __pyx_v_dcd->first = 1; - /* "coordinates/dcdtimeseries.pyx":169 + /* "coordinates/dcdtimeseries.pyx":168 * cdef int i, j * cdef float unitcell[6] * for i from 0 <= i < n_frames: # <<<<<<<<<<<<<< @@ -2155,7 +2640,7 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries_2__read_timeseries(CYTHO __pyx_t_7 = __pyx_v_n_frames; for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_7; __pyx_v_i++) { - /* "coordinates/dcdtimeseries.pyx":170 + /* "coordinates/dcdtimeseries.pyx":169 * cdef float unitcell[6] * for i from 0 <= i < n_frames: * if (skip > 1): # <<<<<<<<<<<<<< @@ -2165,7 +2650,7 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries_2__read_timeseries(CYTHO __pyx_t_3 = ((__pyx_v_skip > 1) != 0); if (__pyx_t_3) { - /* "coordinates/dcdtimeseries.pyx":173 + /* "coordinates/dcdtimeseries.pyx":172 * # Check if we have fixed atoms * # XXX not done * numskip = skip - (dcd.setsread % skip) - 1 # <<<<<<<<<<<<<< @@ -2173,18 +2658,12 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries_2__read_timeseries(CYTHO * if (rc < 0): */ if (unlikely(__pyx_v_skip == 0)) { - #ifdef WITH_THREAD - PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure(); - #endif PyErr_SetString(PyExc_ZeroDivisionError, "integer division or modulo by zero"); - #ifdef WITH_THREAD - PyGILState_Release(__pyx_gilstate_save); - #endif - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 173; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_v_numskip = ((__pyx_v_skip - __Pyx_mod_int(__pyx_v_dcd->setsread, __pyx_v_skip)) - 1); - /* "coordinates/dcdtimeseries.pyx":174 + /* "coordinates/dcdtimeseries.pyx":173 * # XXX not done * numskip = skip - (dcd.setsread % skip) - 1 * rc = skip_dcdstep(dcd.fd, dcd.natoms, dcd.nfixed, dcd.charmm, numskip) # <<<<<<<<<<<<<< @@ -2193,7 +2672,7 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries_2__read_timeseries(CYTHO */ __pyx_v_rc = skip_dcdstep(__pyx_v_dcd->fd, __pyx_v_dcd->natoms, __pyx_v_dcd->nfixed, __pyx_v_dcd->charmm, __pyx_v_numskip); - /* "coordinates/dcdtimeseries.pyx":175 + /* "coordinates/dcdtimeseries.pyx":174 * numskip = skip - (dcd.setsread % skip) - 1 * rc = skip_dcdstep(dcd.fd, dcd.natoms, dcd.nfixed, dcd.charmm, numskip) * if (rc < 0): # <<<<<<<<<<<<<< @@ -2203,21 +2682,29 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries_2__read_timeseries(CYTHO __pyx_t_3 = ((__pyx_v_rc < 0) != 0); if (__pyx_t_3) { - /* "coordinates/dcdtimeseries.pyx":176 + /* "coordinates/dcdtimeseries.pyx":175 * rc = skip_dcdstep(dcd.fd, dcd.natoms, dcd.nfixed, dcd.charmm, numskip) * if (rc < 0): * raise IOError("Error skipping frame from DCD file") # <<<<<<<<<<<<<< * dcd.setsread = dcd.setsread + numskip * rc = read_dcdsubset(dcd.fd, dcd.natoms, lowerb, upperb, tempX, tempY, tempZ, unitcell, dcd.nfixed, dcd.first, dcd.freeind, dcd.fixedcoords, dcd.reverse, dcd.charmm) */ - __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_tuple__6, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 176; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_tuple__6, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 175; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_Raise(__pyx_t_1, 0, 0, 0); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 176; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 175; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "coordinates/dcdtimeseries.pyx":174 + * numskip = skip - (dcd.setsread % skip) - 1 + * rc = skip_dcdstep(dcd.fd, dcd.natoms, dcd.nfixed, dcd.charmm, numskip) + * if (rc < 0): # <<<<<<<<<<<<<< + * raise IOError("Error skipping frame from DCD file") + * dcd.setsread = dcd.setsread + numskip + */ } - /* "coordinates/dcdtimeseries.pyx":177 + /* "coordinates/dcdtimeseries.pyx":176 * if (rc < 0): * raise IOError("Error skipping frame from DCD file") * dcd.setsread = dcd.setsread + numskip # <<<<<<<<<<<<<< @@ -2225,11 +2712,17 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries_2__read_timeseries(CYTHO * dcd.first=0 */ __pyx_v_dcd->setsread = (__pyx_v_dcd->setsread + __pyx_v_numskip); - goto __pyx_L6; + + /* "coordinates/dcdtimeseries.pyx":169 + * cdef float unitcell[6] + * for i from 0 <= i < n_frames: + * if (skip > 1): # <<<<<<<<<<<<<< + * # Check if we have fixed atoms + * # XXX not done + */ } - __pyx_L6:; - /* "coordinates/dcdtimeseries.pyx":178 + /* "coordinates/dcdtimeseries.pyx":177 * raise IOError("Error skipping frame from DCD file") * dcd.setsread = dcd.setsread + numskip * rc = read_dcdsubset(dcd.fd, dcd.natoms, lowerb, upperb, tempX, tempY, tempZ, unitcell, dcd.nfixed, dcd.first, dcd.freeind, dcd.fixedcoords, dcd.reverse, dcd.charmm) # <<<<<<<<<<<<<< @@ -2238,7 +2731,7 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries_2__read_timeseries(CYTHO */ __pyx_v_rc = read_dcdsubset(__pyx_v_dcd->fd, __pyx_v_dcd->natoms, __pyx_v_lowerb, __pyx_v_upperb, __pyx_v_tempX, __pyx_v_tempY, __pyx_v_tempZ, __pyx_v_unitcell, __pyx_v_dcd->nfixed, __pyx_v_dcd->first, __pyx_v_dcd->freeind, __pyx_v_dcd->fixedcoords, __pyx_v_dcd->reverse, __pyx_v_dcd->charmm); - /* "coordinates/dcdtimeseries.pyx":179 + /* "coordinates/dcdtimeseries.pyx":178 * dcd.setsread = dcd.setsread + numskip * rc = read_dcdsubset(dcd.fd, dcd.natoms, lowerb, upperb, tempX, tempY, tempZ, unitcell, dcd.nfixed, dcd.first, dcd.freeind, dcd.fixedcoords, dcd.reverse, dcd.charmm) * dcd.first=0 # <<<<<<<<<<<<<< @@ -2247,7 +2740,7 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries_2__read_timeseries(CYTHO */ __pyx_v_dcd->first = 0; - /* "coordinates/dcdtimeseries.pyx":180 + /* "coordinates/dcdtimeseries.pyx":179 * rc = read_dcdsubset(dcd.fd, dcd.natoms, lowerb, upperb, tempX, tempY, tempZ, unitcell, dcd.nfixed, dcd.first, dcd.freeind, dcd.fixedcoords, dcd.reverse, dcd.charmm) * dcd.first=0 * dcd.setsread = dcd.setsread + 1 # <<<<<<<<<<<<<< @@ -2256,7 +2749,7 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries_2__read_timeseries(CYTHO */ __pyx_v_dcd->setsread = (__pyx_v_dcd->setsread + 1); - /* "coordinates/dcdtimeseries.pyx":181 + /* "coordinates/dcdtimeseries.pyx":180 * dcd.first=0 * dcd.setsread = dcd.setsread + 1 * if (rc < 0): # <<<<<<<<<<<<<< @@ -2266,21 +2759,29 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries_2__read_timeseries(CYTHO __pyx_t_3 = ((__pyx_v_rc < 0) != 0); if (__pyx_t_3) { - /* "coordinates/dcdtimeseries.pyx":182 + /* "coordinates/dcdtimeseries.pyx":181 * dcd.setsread = dcd.setsread + 1 * if (rc < 0): * raise IOError("Error reading frame from DCD file") # <<<<<<<<<<<<<< * # Copy into numeric array * for j from 0 <= j < n_atoms: */ - __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_tuple__7, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 182; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_tuple__7, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_Raise(__pyx_t_1, 0, 0, 0); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 182; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "coordinates/dcdtimeseries.pyx":180 + * dcd.first=0 + * dcd.setsread = dcd.setsread + 1 + * if (rc < 0): # <<<<<<<<<<<<<< + * raise IOError("Error reading frame from DCD file") + * # Copy into numeric array + */ } - /* "coordinates/dcdtimeseries.pyx":184 + /* "coordinates/dcdtimeseries.pyx":183 * raise IOError("Error reading frame from DCD file") * # Copy into numeric array * for j from 0 <= j < n_atoms: # <<<<<<<<<<<<<< @@ -2290,7 +2791,7 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries_2__read_timeseries(CYTHO __pyx_t_10 = __pyx_v_n_atoms; for (__pyx_v_j = 0; __pyx_v_j < __pyx_t_10; __pyx_v_j++) { - /* "coordinates/dcdtimeseries.pyx":185 + /* "coordinates/dcdtimeseries.pyx":184 * # Copy into numeric array * for j from 0 <= j < n_atoms: * index = (atomlist.data)[j]-lowerb # <<<<<<<<<<<<<< @@ -2299,7 +2800,7 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries_2__read_timeseries(CYTHO */ __pyx_v_index = ((((int *)__pyx_v_atomlist->data)[__pyx_v_j]) - __pyx_v_lowerb); - /* "coordinates/dcdtimeseries.pyx":186 + /* "coordinates/dcdtimeseries.pyx":185 * for j from 0 <= j < n_atoms: * index = (atomlist.data)[j]-lowerb * ( (coord.data+j*coord.strides[0]+i*coord.strides[1]+0*coord.strides[2]))[0] = tempX[index] # <<<<<<<<<<<<<< @@ -2308,7 +2809,7 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries_2__read_timeseries(CYTHO */ (((double *)(((__pyx_v_coord->data + (__pyx_v_j * (__pyx_v_coord->strides[0]))) + (__pyx_v_i * (__pyx_v_coord->strides[1]))) + (0 * (__pyx_v_coord->strides[2]))))[0]) = (__pyx_v_tempX[__pyx_v_index]); - /* "coordinates/dcdtimeseries.pyx":187 + /* "coordinates/dcdtimeseries.pyx":186 * index = (atomlist.data)[j]-lowerb * ( (coord.data+j*coord.strides[0]+i*coord.strides[1]+0*coord.strides[2]))[0] = tempX[index] * ( (coord.data+j*coord.strides[0]+i*coord.strides[1]+1*coord.strides[2]))[0] = tempY[index] # <<<<<<<<<<<<<< @@ -2317,7 +2818,7 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries_2__read_timeseries(CYTHO */ (((double *)(((__pyx_v_coord->data + (__pyx_v_j * (__pyx_v_coord->strides[0]))) + (__pyx_v_i * (__pyx_v_coord->strides[1]))) + (1 * (__pyx_v_coord->strides[2]))))[0]) = (__pyx_v_tempY[__pyx_v_index]); - /* "coordinates/dcdtimeseries.pyx":188 + /* "coordinates/dcdtimeseries.pyx":187 * ( (coord.data+j*coord.strides[0]+i*coord.strides[1]+0*coord.strides[2]))[0] = tempX[index] * ( (coord.data+j*coord.strides[0]+i*coord.strides[1]+1*coord.strides[2]))[0] = tempY[index] * ( (coord.data+j*coord.strides[0]+i*coord.strides[1]+2*coord.strides[2]))[0] = tempZ[index] # <<<<<<<<<<<<<< @@ -2327,7 +2828,7 @@ static PyObject *__pyx_pf_11coordinates_13dcdtimeseries_2__read_timeseries(CYTHO } } - /* "coordinates/dcdtimeseries.pyx":189 + /* "coordinates/dcdtimeseries.pyx":188 * ( 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__Pyx_GIVEREF(__pyx_tuple__16); + __pyx_codeobj__17 = (PyObject*)__Pyx_PyCode_New(3, 0, 21, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__16, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_nfs_homes2_oliver_Library_pytho, __pyx_n_s_read_timeseries, 135, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__17)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_RefNannyFinishContext(); return 0; __pyx_L1_error:; @@ -2593,18 +5314,24 @@ PyMODINIT_FUNC PyInit_dcdtimeseries(void) } #endif __Pyx_RefNannySetupContext("PyMODINIT_FUNC PyInit_dcdtimeseries(void)", 0); - if ( __Pyx_check_binary_version() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_check_binary_version() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_empty_tuple = PyTuple_New(0); if (unlikely(!__pyx_empty_tuple)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_empty_bytes = PyBytes_FromStringAndSize("", 0); if (unlikely(!__pyx_empty_bytes)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #ifdef __Pyx_CyFunction_USED - if (__Pyx_CyFunction_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__pyx_CyFunction_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #endif #ifdef __Pyx_FusedFunction_USED if (__pyx_FusedFunction_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #endif + #ifdef __Pyx_Coroutine_USED + if (__pyx_Coroutine_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif #ifdef __Pyx_Generator_USED if (__pyx_Generator_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #endif + #ifdef __Pyx_StopAsyncIteration_USED + if (__pyx_StopAsyncIteration_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif /*--- Library function declarations ---*/ /*--- Threads initialization code ---*/ #if defined(__PYX_FORCE_INIT_THREADS) && __PYX_FORCE_INIT_THREADS @@ -2627,12 +5354,12 @@ PyMODINIT_FUNC PyInit_dcdtimeseries(void) #endif if (PyObject_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; /*--- Initialize various global constants etc. ---*/ - if (unlikely(__Pyx_InitGlobals() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_InitGlobals() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #if PY_MAJOR_VERSION < 3 && 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__pyx_clineno = __LINE__; goto __pyx_L1_error;} /*--- Constants init code ---*/ - if (unlikely(__Pyx_InitCachedConstants() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_InitCachedConstants() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} /*--- Global init code ---*/ /*--- Variable export code ---*/ /*--- Function export code ---*/ /*--- Type init code ---*/ /*--- Type import code ---*/ - __pyx_ptype_7c_numpy_ndarray = __Pyx_ImportType("numpy", "ndarray", sizeof(PyArrayObject), 0); if (unlikely(!__pyx_ptype_7c_numpy_ndarray)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_7cpython_4type_type = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "type", + #if CYTHON_COMPILING_IN_PYPY + sizeof(PyTypeObject), + #else + sizeof(PyHeapTypeObject), + #endif + 0); if (unlikely(!__pyx_ptype_7cpython_4type_type)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 9; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5numpy_dtype = __Pyx_ImportType("numpy", "dtype", sizeof(PyArray_Descr), 0); if (unlikely(!__pyx_ptype_5numpy_dtype)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 155; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5numpy_flatiter = __Pyx_ImportType("numpy", "flatiter", sizeof(PyArrayIterObject), 0); if (unlikely(!__pyx_ptype_5numpy_flatiter)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 168; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5numpy_broadcast = __Pyx_ImportType("numpy", "broadcast", sizeof(PyArrayMultiIterObject), 0); if (unlikely(!__pyx_ptype_5numpy_broadcast)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5numpy_ndarray = __Pyx_ImportType("numpy", "ndarray", sizeof(PyArrayObject), 0); if (unlikely(!__pyx_ptype_5numpy_ndarray)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5numpy_ufunc = __Pyx_ImportType("numpy", "ufunc", sizeof(PyUFuncObject), 0); if (unlikely(!__pyx_ptype_5numpy_ufunc)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;} /*--- Variable import code ---*/ /*--- Function import code ---*/ /*--- Execution code ---*/ + #if defined(__Pyx_Generator_USED) || defined(__Pyx_Coroutine_USED) + if (__Pyx_patch_abc() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif - /* "coordinates/dcdtimeseries.pyx":19 - * - * cimport c_numpy - * c_numpy.import_array() # <<<<<<<<<<<<<< - * - * ctypedef int size_t - */ - import_array(); - - /* "coordinates/dcdtimeseries.pyx":60 + /* "coordinates/dcdtimeseries.pyx":59 * void copyseries(int frame, char *data, int *strides, float *tempX, float *tempY, float *tempZ, char* datacode, int numdata, int* atomlist, int* atomcounts, int lowerb, double 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"coordinates/dcdtimeseries.pyx":61 * import numpy as np * * def __read_timecorrel(object self, object atoms, object atomcounts, object format, object auxdata, int sizedata, int lowerb, int upperb, int start, int stop, int skip): # <<<<<<<<<<<<<< * cdef dcdhandle* dcd - * cdef c_numpy.ndarray atomlist, atomcountslist, auxlist + * cdef numpy.ndarray atomlist, atomcountslist, auxlist */ - __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_11coordinates_13dcdtimeseries_1__read_timecorrel, NULL, __pyx_n_s_coordinates_dcdtimeseries); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_11coordinates_13dcdtimeseries_1__read_timecorrel, NULL, __pyx_n_s_coordinates_dcdtimeseries); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - if (PyDict_SetItem(__pyx_d, __pyx_n_s_read_timecorrel, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_d, __pyx_n_s_read_timecorrel, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "coordinates/dcdtimeseries.pyx":136 + /* "coordinates/dcdtimeseries.pyx":135 * return data * * def __read_timeseries(object self, object atoms, int skip): # <<<<<<<<<<<<<< * cdef dcdhandle* dcd - * cdef c_numpy.ndarray atomlist + * cdef numpy.ndarray atomlist */ - __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_11coordinates_13dcdtimeseries_3__read_timeseries, NULL, __pyx_n_s_coordinates_dcdtimeseries); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 136; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_11coordinates_13dcdtimeseries_3__read_timeseries, NULL, __pyx_n_s_coordinates_dcdtimeseries); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - if (PyDict_SetItem(__pyx_d, __pyx_n_s_read_timeseries, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 136; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_d, __pyx_n_s_read_timeseries, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; /* "coordinates/dcdtimeseries.pyx":1 @@ -2711,6 +5443,14 @@ PyMODINIT_FUNC PyInit_dcdtimeseries(void) if (PyDict_SetItem(__pyx_d, __pyx_n_s_test, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + /* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":976 + * arr.base = baseptr + * + * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< + * if arr.base is NULL: + * return None + */ + /*--- Wrapped vars code ---*/ goto __pyx_L0; @@ -3205,8 +5945,12 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObjec } #else static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { - PyObject* args = PyTuple_Pack(1, arg); - return (likely(args)) ? __Pyx_PyObject_Call(func, args, NULL) : NULL; + PyObject *result; + PyObject *args = PyTuple_Pack(1, arg); + if (unlikely(!args)) return NULL; + result = __Pyx_PyObject_Call(func, args, NULL); + Py_DECREF(args); + return result; } #endif @@ -3280,15 +6024,103 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, return NULL; } } - return m->sq_item(o, i); + return m->sq_item(o, i); + } + } +#else + if (is_list || PySequence_Check(o)) { + return PySequence_GetItem(o, i); + } +#endif + return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); +} + +static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { + PyErr_Format(PyExc_ValueError, + "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected); +} + +static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { + PyErr_Format(PyExc_ValueError, + "need more than %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack", + index, (index == 1) ? "" : "s"); +} + +static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); +} + +static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { + PyObject *empty_list = 0; + PyObject *module = 0; + PyObject *global_dict = 0; + PyObject *empty_dict = 0; + PyObject *list; + #if PY_VERSION_HEX < 0x03030000 + PyObject *py_import; + py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import); + if (!py_import) + goto bad; + #endif + if (from_list) + list = from_list; + else { + empty_list = PyList_New(0); + if (!empty_list) + goto bad; + list = empty_list; + } + global_dict = PyModule_GetDict(__pyx_m); + if (!global_dict) + goto bad; + empty_dict = PyDict_New(); + if (!empty_dict) + goto bad; + { + #if PY_MAJOR_VERSION >= 3 + if (level == -1) { + if (strchr(__Pyx_MODULE_NAME, '.')) { + #if PY_VERSION_HEX < 0x03030000 + PyObject *py_level = PyInt_FromLong(1); + if (!py_level) + goto bad; + module = PyObject_CallFunctionObjArgs(py_import, + name, global_dict, empty_dict, list, py_level, NULL); + Py_DECREF(py_level); + #else + module = PyImport_ImportModuleLevelObject( + name, global_dict, empty_dict, list, 1); + #endif + if (!module) { + if (!PyErr_ExceptionMatches(PyExc_ImportError)) + goto bad; + PyErr_Clear(); + } + } + level = 0; + } + #endif + if (!module) { + #if PY_VERSION_HEX < 0x03030000 + PyObject *py_level = PyInt_FromLong(level); + if (!py_level) + goto bad; + module = PyObject_CallFunctionObjArgs(py_import, + name, global_dict, empty_dict, list, py_level, NULL); + Py_DECREF(py_level); + #else + module = PyImport_ImportModuleLevelObject( + name, global_dict, empty_dict, list, level); + #endif } } -#else - if (is_list || PySequence_Check(o)) { - return PySequence_GetItem(o, i); - } -#endif - return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); +bad: + #if PY_VERSION_HEX < 0x03030000 + Py_XDECREF(py_import); + #endif + Py_XDECREF(empty_list); + Py_XDECREF(empty_dict); + return module; } static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { @@ -3297,7 +6129,7 @@ static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int co return count; } while (start < end) { - mid = (start + end) / 2; + mid = start + (end - start) / 2; if (code_line < entries[mid].code_line) { end = mid; } else if (code_line > entries[mid].code_line) { @@ -3450,102 +6282,33 @@ static void __Pyx_AddTraceback(const char *funcname, int c_line, Py_XDECREF(py_frame); } -static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { - PyObject *empty_list = 0; - PyObject *module = 0; - PyObject *global_dict = 0; - PyObject *empty_dict = 0; - PyObject *list; - #if PY_VERSION_HEX < 0x03030000 - PyObject *py_import; - py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import); - if (!py_import) - goto bad; - #endif - if (from_list) - list = from_list; - else { - empty_list = PyList_New(0); - if (!empty_list) - goto bad; - list = empty_list; - } - global_dict = PyModule_GetDict(__pyx_m); - if (!global_dict) - goto bad; - empty_dict = PyDict_New(); - if (!empty_dict) - goto bad; - { - #if PY_MAJOR_VERSION >= 3 - if (level == -1) { - if (strchr(__Pyx_MODULE_NAME, '.')) { - #if PY_VERSION_HEX < 0x03030000 - PyObject *py_level = PyInt_FromLong(1); - if (!py_level) - goto bad; - module = PyObject_CallFunctionObjArgs(py_import, - name, global_dict, empty_dict, list, py_level, NULL); - Py_DECREF(py_level); - #else - module = PyImport_ImportModuleLevelObject( - name, global_dict, empty_dict, list, 1); - #endif - if (!module) { - if (!PyErr_ExceptionMatches(PyExc_ImportError)) - goto bad; - PyErr_Clear(); - } - } - level = 0; - } - #endif - if (!module) { - #if PY_VERSION_HEX < 0x03030000 - PyObject *py_level = PyInt_FromLong(level); - if (!py_level) - goto bad; - module = PyObject_CallFunctionObjArgs(py_import, - name, global_dict, empty_dict, list, py_level, NULL); - Py_DECREF(py_level); - #else - module = PyImport_ImportModuleLevelObject( - name, global_dict, empty_dict, list, level); - #endif - } - } -bad: - #if PY_VERSION_HEX < 0x03030000 - Py_XDECREF(py_import); - #endif - Py_XDECREF(empty_list); - Py_XDECREF(empty_dict); - return module; -} - -#define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value) \ - { \ - func_type value = func_value; \ - if (sizeof(target_type) < sizeof(func_type)) { \ - if (unlikely(value != (func_type) (target_type) value)) { \ - func_type zero = 0; \ - if (is_unsigned && unlikely(value < zero)) \ - goto raise_neg_overflow; \ - else \ - goto raise_overflow; \ - } \ - } \ - return (target_type) value; \ +#define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\ + __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0) +#define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\ + __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1) +#define __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, exc)\ + {\ + func_type value = func_value;\ + if (sizeof(target_type) < sizeof(func_type)) {\ + if (unlikely(value != (func_type) (target_type) value)) {\ + func_type zero = 0;\ + if (exc && unlikely(value == (func_type)-1 && PyErr_Occurred()))\ + return (target_type) -1;\ + if (is_unsigned && unlikely(value < zero))\ + goto raise_neg_overflow;\ + else\ + goto raise_overflow;\ + }\ + }\ + return (target_type) value;\ } -#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 - #if CYTHON_USE_PYLONG_INTERNALS +#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 neg_one = (int) -1, const_zero = (int) 0; const int is_unsigned = neg_one > const_zero; #if PY_MAJOR_VERSION < 3 if (likely(PyInt_Check(x))) { @@ -3562,13 +6325,39 @@ static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { -#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 - #if CYTHON_USE_PYLONG_INTERNALS +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; switch (Py_SIZE(x)) { - case 0: return 0; - case 1: __PYX_VERIFY_RETURN_INT(int, digit, ((PyLongObject*)x)->ob_digit[0]); + case 0: return (int) 0; + case 1: __PYX_VERIFY_RETURN_INT(int, digit, digits[0]) + case 2: + if (8 * sizeof(int) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) >= 2 * PyLong_SHIFT) { + return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); + } + } + break; + case 3: + if (8 * sizeof(int) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) >= 3 * PyLong_SHIFT) { + return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); + } + } + break; + case 4: + if (8 * sizeof(int) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) >= 4 * PyLong_SHIFT) { + return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); + } + } + break; } - #endif #endif #if CYTHON_COMPILING_IN_CPYTHON if (unlikely(Py_SIZE(x) < 0)) { @@ -3584,24 +6373,77 @@ static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { } #endif if (sizeof(int) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, PyLong_AsUnsignedLong(x)) + __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x)) } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) + __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) } } else { -#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 - #if CYTHON_USE_PYLONG_INTERNALS +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; switch (Py_SIZE(x)) { - case 0: return 0; - case 1: __PYX_VERIFY_RETURN_INT(int, digit, +(((PyLongObject*)x)->ob_digit[0])); - case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]); + case 0: return (int) 0; + case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, -(sdigit) digits[0]) + case 1: __PYX_VERIFY_RETURN_INT(int, digit, +digits[0]) + case -2: + if (8 * sizeof(int) - 1 > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { + return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case 2: + if (8 * sizeof(int) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { + return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case -3: + if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { + return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case 3: + if (8 * sizeof(int) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { + return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case -4: + if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { + return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case 4: + if (8 * sizeof(int) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { + return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; } - #endif #endif if (sizeof(int) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT(int, long, PyLong_AsLong(x)) + __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x)) } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT(int, PY_LONG_LONG, PyLong_AsLongLong(x)) + __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x)) } } { @@ -3650,7 +6492,7 @@ static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { } static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { - const int neg_one = (int) -1, const_zero = 0; + const int neg_one = (int) -1, const_zero = (int) 0; const int is_unsigned = neg_one > const_zero; if (is_unsigned) { if (sizeof(int) < sizeof(long)) { @@ -3676,7 +6518,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { } static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { - const long neg_one = (long) -1, const_zero = 0; + const long neg_one = (long) -1, const_zero = (long) 0; const int is_unsigned = neg_one > const_zero; if (is_unsigned) { if (sizeof(long) < sizeof(long)) { @@ -3701,8 +6543,274 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { } } +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + return ::std::complex< float >(x, y); + } + #else + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + return x + y*(__pyx_t_float_complex)_Complex_I; + } + #endif +#else + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + __pyx_t_float_complex z; + z.real = x; + z.imag = y; + return z; + } +#endif + +#if CYTHON_CCOMPLEX +#else + static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + return (a.real == b.real) && (a.imag == b.imag); + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real + b.real; + z.imag = a.imag + b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real - b.real; + z.imag = a.imag - b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prodf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real * b.real - a.imag * b.imag; + z.imag = a.real * b.imag + a.imag * b.real; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + float denom = b.real * b.real + b.imag * b.imag; + z.real = (a.real * b.real + a.imag * b.imag) / denom; + z.imag = (a.imag * b.real - a.real * b.imag) / denom; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex a) { + __pyx_t_float_complex z; + z.real = -a.real; + z.imag = -a.imag; + return z; + } + static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex a) { + return (a.real == 0) && (a.imag == 0); + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex a) { + __pyx_t_float_complex z; + z.real = a.real; + z.imag = -a.imag; + return z; + } + #if 1 + static CYTHON_INLINE float __Pyx_c_absf(__pyx_t_float_complex z) { + #if !defined(HAVE_HYPOT) || defined(_MSC_VER) + return sqrtf(z.real*z.real + z.imag*z.imag); + #else + return hypotf(z.real, z.imag); + #endif + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + float r, lnr, theta, z_r, z_theta; + if (b.imag == 0 && b.real == (int)b.real) { + if (b.real < 0) { + float denom = a.real * a.real + a.imag * a.imag; + a.real = a.real / denom; + a.imag = -a.imag / denom; + b.real = -b.real; + } + switch ((int)b.real) { + case 0: + z.real = 1; + z.imag = 0; + return z; + case 1: + return a; + case 2: + z = __Pyx_c_prodf(a, a); + return __Pyx_c_prodf(a, a); + case 3: + z = __Pyx_c_prodf(a, a); + return __Pyx_c_prodf(z, a); + case 4: + z = __Pyx_c_prodf(a, a); + return __Pyx_c_prodf(z, z); + } + } + if (a.imag == 0) { + if (a.real == 0) { + return a; + } + r = a.real; + theta = 0; + } else { + r = __Pyx_c_absf(a); + theta = atan2f(a.imag, a.real); + } + lnr = logf(r); + z_r = expf(lnr * b.real - theta * b.imag); + z_theta = theta * b.real + lnr * b.imag; + z.real = z_r * cosf(z_theta); + z.imag = z_r * sinf(z_theta); + return z; + } + #endif +#endif + +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + return ::std::complex< double >(x, y); + } + #else + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + return x + y*(__pyx_t_double_complex)_Complex_I; + } + #endif +#else + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + __pyx_t_double_complex z; + z.real = x; + z.imag = y; + return z; + } +#endif + +#if CYTHON_CCOMPLEX +#else + static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex a, __pyx_t_double_complex b) { + return (a.real == b.real) && (a.imag == b.imag); + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real + b.real; + z.imag = a.imag + b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real - b.real; + z.imag = a.imag - b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real * b.real - a.imag * b.imag; + z.imag = a.real * b.imag + a.imag * b.real; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + double denom = b.real * b.real + b.imag * b.imag; + z.real = (a.real * b.real + a.imag * b.imag) / denom; + z.imag = (a.imag * b.real - a.real * b.imag) / denom; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex a) { + __pyx_t_double_complex z; + z.real = -a.real; + z.imag = -a.imag; + return z; + } + static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex a) { + return (a.real == 0) && (a.imag == 0); + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex a) { + __pyx_t_double_complex z; + z.real = a.real; + z.imag = -a.imag; + return z; + } + #if 1 + static CYTHON_INLINE double __Pyx_c_abs(__pyx_t_double_complex z) { + #if !defined(HAVE_HYPOT) || defined(_MSC_VER) + return sqrt(z.real*z.real + z.imag*z.imag); + #else + return hypot(z.real, z.imag); + #endif + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + double r, lnr, theta, z_r, z_theta; + if (b.imag == 0 && b.real == (int)b.real) { + if (b.real < 0) { + double denom = a.real * a.real + a.imag * a.imag; + a.real = a.real / denom; + a.imag = -a.imag / denom; + b.real = -b.real; + } + switch ((int)b.real) { + case 0: + z.real = 1; + z.imag = 0; + return z; + case 1: + return a; + case 2: + z = __Pyx_c_prod(a, a); + return __Pyx_c_prod(a, a); + case 3: + z = __Pyx_c_prod(a, a); + return __Pyx_c_prod(z, a); + case 4: + z = __Pyx_c_prod(a, a); + return __Pyx_c_prod(z, z); + } + } + if (a.imag == 0) { + if (a.real == 0) { + return a; + } + r = a.real; + theta = 0; + } else { + r = __Pyx_c_abs(a); + theta = atan2(a.imag, a.real); + } + lnr = log(r); + z_r = exp(lnr * b.real - theta * b.imag); + z_theta = theta * b.real + lnr * b.imag; + z.real = z_r * cos(z_theta); + z.imag = z_r * sin(z_theta); + return z; + } + #endif +#endif + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__NPY_TYPES(enum NPY_TYPES value) { + const enum NPY_TYPES neg_one = (enum NPY_TYPES) -1, const_zero = (enum NPY_TYPES) 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(enum NPY_TYPES) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(enum NPY_TYPES) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); + } else if (sizeof(enum NPY_TYPES) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); + } + } else { + if (sizeof(enum NPY_TYPES) <= sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(enum NPY_TYPES) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(enum NPY_TYPES), + little, !is_unsigned); + } +} + static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { - const long neg_one = (long) -1, const_zero = 0; + const long neg_one = (long) -1, const_zero = (long) 0; const int is_unsigned = neg_one > const_zero; #if PY_MAJOR_VERSION < 3 if (likely(PyInt_Check(x))) { @@ -3719,13 +6827,39 @@ static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { -#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 - #if CYTHON_USE_PYLONG_INTERNALS +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; switch (Py_SIZE(x)) { - case 0: return 0; - case 1: __PYX_VERIFY_RETURN_INT(long, digit, ((PyLongObject*)x)->ob_digit[0]); + case 0: return (long) 0; + case 1: __PYX_VERIFY_RETURN_INT(long, digit, digits[0]) + case 2: + if (8 * sizeof(long) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) >= 2 * PyLong_SHIFT) { + return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); + } + } + break; + case 3: + if (8 * sizeof(long) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) >= 3 * PyLong_SHIFT) { + return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); + } + } + break; + case 4: + if (8 * sizeof(long) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) >= 4 * PyLong_SHIFT) { + return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); + } + } + break; } - #endif #endif #if CYTHON_COMPILING_IN_CPYTHON if (unlikely(Py_SIZE(x) < 0)) { @@ -3741,24 +6875,77 @@ static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { } #endif if (sizeof(long) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, PyLong_AsUnsignedLong(x)) + __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x)) } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) + __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) } } else { -#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 - #if CYTHON_USE_PYLONG_INTERNALS +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; switch (Py_SIZE(x)) { - case 0: return 0; - case 1: __PYX_VERIFY_RETURN_INT(long, digit, +(((PyLongObject*)x)->ob_digit[0])); - case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]); + case 0: return (long) 0; + case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, -(sdigit) digits[0]) + case 1: __PYX_VERIFY_RETURN_INT(long, digit, +digits[0]) + case -2: + if (8 * sizeof(long) - 1 > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case 2: + if (8 * sizeof(long) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case -3: + if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case 3: + if (8 * sizeof(long) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case -4: + if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { + return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case 4: + if (8 * sizeof(long) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { + return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; } - #endif #endif if (sizeof(long) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT(long, long, PyLong_AsLong(x)) + __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x)) } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT(long, PY_LONG_LONG, PyLong_AsLongLong(x)) + __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x)) } } { @@ -3940,7 +7127,7 @@ static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) { 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 CYTHON_COMPILING_IN_CPYTHON && (__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 && @@ -3981,7 +7168,7 @@ static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_ #endif } else #endif -#if !CYTHON_COMPILING_IN_PYPY +#if (!CYTHON_COMPILING_IN_PYPY) || (defined(PyByteArray_AS_STRING) && defined(PyByteArray_GET_SIZE)) if (PyByteArray_Check(o)) { *length = PyByteArray_GET_SIZE(o); return PyByteArray_AS_STRING(o); @@ -4011,7 +7198,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) { #else if (PyLong_Check(x)) #endif - return Py_INCREF(x), x; + return __Pyx_NewRef(x); m = Py_TYPE(x)->tp_as_number; #if PY_MAJOR_VERSION < 3 if (m && m->nb_int) { @@ -4051,18 +7238,55 @@ 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); + if (likely(PyInt_CheckExact(b))) { + if (sizeof(Py_ssize_t) >= sizeof(long)) + return PyInt_AS_LONG(b); + else + return PyInt_AsSsize_t(x); + } #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 + #if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)b)->ob_digit; + const Py_ssize_t size = Py_SIZE(b); + if (likely(__Pyx_sst_abs(size) <= 1)) { + ival = likely(size) ? digits[0] : 0; + if (size == -1) ival = -ival; + return ival; + } else { + switch (size) { + case 2: + if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { + return (Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case -2: + if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { + return -(Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case 3: + if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { + return (Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case -3: + if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { + return -(Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case 4: + if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { + return (Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case -4: + if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { + return -(Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + } + } #endif return PyLong_AsSsize_t(b); } diff --git a/package/MDAnalysis/coordinates/dcdtimeseries.pyx b/package/MDAnalysis/coordinates/dcdtimeseries.pyx index 366fd1e88bc..c60e20589c8 100644 --- a/package/MDAnalysis/coordinates/dcdtimeseries.pyx +++ b/package/MDAnalysis/coordinates/dcdtimeseries.pyx @@ -15,8 +15,8 @@ # doi:10.1002/jcc.21787 # -cimport c_numpy -c_numpy.import_array() +import numpy +cimport numpy ctypedef int size_t @@ -61,8 +61,8 @@ import numpy as np def __read_timecorrel(object self, object atoms, object atomcounts, object format, object auxdata, int sizedata, int lowerb, int upperb, int start, int stop, int skip): cdef dcdhandle* dcd - cdef c_numpy.ndarray atomlist, atomcountslist, auxlist - cdef c_numpy.ndarray data, temp + cdef numpy.ndarray atomlist, atomcountslist, auxlist + cdef numpy.ndarray data, temp cdef float *tempX, *tempY, *tempZ cdef int rc cdef char* fmtstr @@ -135,8 +135,8 @@ def __read_timecorrel(object self, object atoms, object atomcounts, object forma def __read_timeseries(object self, object atoms, int skip): cdef dcdhandle* dcd - cdef c_numpy.ndarray atomlist - cdef c_numpy.ndarray coord, temp + cdef numpy.ndarray atomlist + cdef numpy.ndarray coord, temp cdef float *tempX, *tempY, *tempZ cdef int rc diff --git a/package/MDAnalysis/lib/distances.c b/package/MDAnalysis/lib/distances.c index 9e20a7db0d9..c37ef430e60 100644 --- a/package/MDAnalysis/lib/distances.c +++ b/package/MDAnalysis/lib/distances.c @@ -1,25 +1,13 @@ -/* Generated by Cython 0.22.1 */ +/* Generated by Cython 0.23.4 */ #define PY_SSIZE_T_CLEAN -#ifndef CYTHON_USE_PYLONG_INTERNALS -#ifdef PYLONG_BITS_IN_DIGIT -#define CYTHON_USE_PYLONG_INTERNALS 0 -#else -#include "pyconfig.h" -#ifdef PYLONG_BITS_IN_DIGIT -#define CYTHON_USE_PYLONG_INTERNALS 1 -#else -#define CYTHON_USE_PYLONG_INTERNALS 0 -#endif -#endif -#endif #include "Python.h" #ifndef Py_PYTHON_H #error Python headers needed to compile C extensions, please install development version of Python. #elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03020000) #error Cython requires Python 2.6+ or Python 3.2+. #else -#define CYTHON_ABI "0_22_1" +#define CYTHON_ABI "0_23_4" #include #ifndef offsetof #define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) @@ -54,6 +42,9 @@ #define CYTHON_COMPILING_IN_PYPY 0 #define CYTHON_COMPILING_IN_CPYTHON 1 #endif +#if !defined(CYTHON_USE_PYLONG_INTERNALS) && CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x02070000 +#define CYTHON_USE_PYLONG_INTERNALS 1 +#endif #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 && !defined(Py_OptimizeFlag) #define Py_OptimizeFlag 0 #endif @@ -61,12 +52,12 @@ #define CYTHON_FORMAT_SSIZE_T "z" #if PY_MAJOR_VERSION < 3 #define __Pyx_BUILTIN_MODULE_NAME "__builtin__" - #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \ + #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) \ + #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 @@ -84,7 +75,7 @@ #endif #if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND) #define CYTHON_PEP393_ENABLED 1 - #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \ + #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) @@ -103,12 +94,10 @@ #if CYTHON_COMPILING_IN_PYPY #define __Pyx_PyUnicode_Concat(a, b) PyNumber_Add(a, b) #define __Pyx_PyUnicode_ConcatSafe(a, b) PyNumber_Add(a, b) - #define __Pyx_PyFrozenSet_Size(s) PyObject_Size(s) #else #define __Pyx_PyUnicode_Concat(a, b) PyUnicode_Concat(a, b) - #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ? \ + #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ?\ PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b)) - #define __Pyx_PyFrozenSet_Size(s) PySet_Size(s) #endif #if CYTHON_COMPILING_IN_PYPY && !defined(PyUnicode_Contains) #define PyUnicode_Contains(u, s) PySequence_Contains(u, s) @@ -176,16 +165,18 @@ #else #define __Pyx_PyMethod_New(func, self, klass) PyMethod_New(func, self, klass) #endif -#ifndef CYTHON_INLINE - #if defined(__GNUC__) - #define CYTHON_INLINE __inline__ - #elif defined(_MSC_VER) - #define CYTHON_INLINE __inline - #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L - #define CYTHON_INLINE inline - #else - #define CYTHON_INLINE - #endif +#if PY_VERSION_HEX >= 0x030500B1 +#define __Pyx_PyAsyncMethodsStruct PyAsyncMethods +#define __Pyx_PyType_AsAsync(obj) (Py_TYPE(obj)->tp_as_async) +#elif CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 +typedef struct { + unaryfunc am_await; + unaryfunc am_aiter; + unaryfunc am_anext; +} __Pyx_PyAsyncMethodsStruct; +#define __Pyx_PyType_AsAsync(obj) ((__Pyx_PyAsyncMethodsStruct*) (Py_TYPE(obj)->tp_reserved)) +#else +#define __Pyx_PyType_AsAsync(obj) NULL #endif #ifndef CYTHON_RESTRICT #if defined(__GNUC__) @@ -198,35 +189,33 @@ #define CYTHON_RESTRICT #endif #endif +#define __Pyx_void_to_None(void_result) ((void)(void_result), Py_INCREF(Py_None), Py_None) + +#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 + +#if defined(WIN32) || defined(MS_WINDOWS) + #define _USE_MATH_DEFINES +#endif +#include #ifdef NAN #define __PYX_NAN() ((float) NAN) #else static CYTHON_INLINE float __PYX_NAN() { - /* Initialize NaN. The sign is irrelevant, an exponent with all bits 1 and - a nonzero mantissa means NaN. If the first bit in the mantissa is 1, it is - a quiet NaN. */ float value; memset(&value, 0xFF, sizeof(value)); return value; } #endif -#define __Pyx_void_to_None(void_result) (void_result, Py_INCREF(Py_None), Py_None) -#ifdef __cplusplus -template -void __Pyx_call_destructor(T* x) { - x->~T(); -} -template -class __Pyx_FakeReference { - public: - __Pyx_FakeReference() : ptr(NULL) { } - __Pyx_FakeReference(T& ref) : ptr(&ref) { } - T *operator->() { return ptr; } - operator T&() { return *ptr; } - private: - T *ptr; -}; -#endif #if PY_MAJOR_VERSION >= 3 @@ -245,18 +234,15 @@ class __Pyx_FakeReference { #endif #endif -#if defined(WIN32) || defined(MS_WINDOWS) -#define _USE_MATH_DEFINES -#endif -#include #define __PYX_HAVE__lib___distances #define __PYX_HAVE_API__lib___distances -#include "numpy/arrayobject.h" #include "string.h" +#include "stdio.h" +#include "stdlib.h" +#include "numpy/arrayobject.h" +#include "numpy/ufuncobject.h" #include "calc_distances.h" #include "pythread.h" -#include "stdlib.h" -#include "stdio.h" #include "pystate.h" #ifdef _OPENMP #include @@ -294,16 +280,34 @@ typedef struct {PyObject **p; char *s; const Py_ssize_t n; const char* encoding; #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 || \ +#define __Pyx_uchar_cast(c) ((unsigned char)c) +#define __Pyx_long_cast(x) ((long)x) +#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))) ) +#if defined (__cplusplus) && __cplusplus >= 201103L + #include + #define __Pyx_sst_abs(value) std::abs(value) +#elif SIZEOF_INT >= SIZEOF_SIZE_T + #define __Pyx_sst_abs(value) abs(value) +#elif SIZEOF_LONG >= SIZEOF_SIZE_T + #define __Pyx_sst_abs(value) labs(value) +#elif defined (_MSC_VER) && defined (_M_X64) + #define __Pyx_sst_abs(value) _abs64(value) +#elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L + #define __Pyx_sst_abs(value) llabs(value) +#elif defined (__GNUC__) + #define __Pyx_sst_abs(value) __builtin_llabs(value) +#else + #define __Pyx_sst_abs(value) ((value<0) ? -value : value) +#endif 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)) @@ -338,8 +342,9 @@ static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) #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)) +#define __Pyx_NewRef(obj) (Py_INCREF(obj), obj) +#define __Pyx_Owned_Py_None(b) __Pyx_NewRef(Py_None) +#define __Pyx_PyBool_FromLong(b) ((b) ? __Pyx_NewRef(Py_True) : __Pyx_NewRef(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*); @@ -445,11 +450,33 @@ 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[] = { "MDAnalysis/lib/distances.pyx", + "__init__.pxd", "stringsource", - "include/c_numpy.pxd", + "type.pxd", }; struct __pyx_memoryview_obj; typedef struct { @@ -500,21 +527,22 @@ typedef struct { #define CYTHON_ATOMICS 1 #endif #define __pyx_atomic_int_type int -#if CYTHON_ATOMICS && __GNUC__ >= 4 && (__GNUC_MINOR__ > 1 || \ - (__GNUC_MINOR__ == 1 && __GNUC_PATCHLEVEL >= 2)) && \ +#if CYTHON_ATOMICS && __GNUC__ >= 4 && (__GNUC_MINOR__ > 1 ||\ + (__GNUC_MINOR__ == 1 && __GNUC_PATCHLEVEL >= 2)) &&\ !defined(__i386__) #define __pyx_atomic_incr_aligned(value, lock) __sync_fetch_and_add(value, 1) #define __pyx_atomic_decr_aligned(value, lock) __sync_fetch_and_sub(value, 1) #ifdef __PYX_DEBUG_ATOMICS #warning "Using GNU atomics" #endif -#elif CYTHON_ATOMICS && MSC_VER +#elif CYTHON_ATOMICS && defined(_MSC_VER) && 0 #include + #undef __pyx_atomic_int_type #define __pyx_atomic_int_type LONG #define __pyx_atomic_incr_aligned(value, lock) InterlockedIncrement(value) #define __pyx_atomic_decr_aligned(value, lock) InterlockedDecrement(value) #ifdef __PYX_DEBUG_ATOMICS - #warning "Using MSVC atomics" + #pragma message ("Using MSVC atomics") #endif #elif CYTHON_ATOMICS && (defined(__ICC) || defined(__INTEL_COMPILER)) && 0 #define __pyx_atomic_incr_aligned(value, lock) _InterlockedIncrement(value) @@ -531,25 +559,270 @@ typedef struct { #endif typedef volatile __pyx_atomic_int_type __pyx_atomic_int; #if CYTHON_ATOMICS - #define __pyx_add_acquisition_count(memview) \ + #define __pyx_add_acquisition_count(memview)\ __pyx_atomic_incr_aligned(__pyx_get_slice_count_pointer(memview), memview->lock) - #define __pyx_sub_acquisition_count(memview) \ + #define __pyx_sub_acquisition_count(memview)\ __pyx_atomic_decr_aligned(__pyx_get_slice_count_pointer(memview), memview->lock) #else - #define __pyx_add_acquisition_count(memview) \ + #define __pyx_add_acquisition_count(memview)\ __pyx_add_acquisition_count_locked(__pyx_get_slice_count_pointer(memview), memview->lock) - #define __pyx_sub_acquisition_count(memview) \ + #define __pyx_sub_acquisition_count(memview)\ __pyx_sub_acquisition_count_locked(__pyx_get_slice_count_pointer(memview), memview->lock) #endif +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":725 + * # 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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":726 + * + * 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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":727 + * ctypedef npy_int8 int8_t + * ctypedef npy_int16 int16_t + * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< + * ctypedef npy_int64 int64_t + * #ctypedef npy_int96 int96_t + */ +typedef npy_int32 __pyx_t_5numpy_int32_t; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":728 + * 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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":732 + * #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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":733 + * + * 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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":734 + * ctypedef npy_uint8 uint8_t + * ctypedef npy_uint16 uint16_t + * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< + * ctypedef npy_uint64 uint64_t + * #ctypedef npy_uint96 uint96_t + */ +typedef npy_uint32 __pyx_t_5numpy_uint32_t; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":735 + * 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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":739 + * #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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":740 + * + * 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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":749 + * # 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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":750 + * # 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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":751 + * 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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":753 + * 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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":754 + * + * ctypedef npy_ulong uint_t + * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<< + * ctypedef npy_ulonglong ulonglong_t + * + */ +typedef npy_ulonglong __pyx_t_5numpy_ulong_t; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":755 + * 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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":757 + * ctypedef npy_ulonglong ulonglong_t + * + * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< + * ctypedef npy_uintp uintp_t + * + */ +typedef npy_intp __pyx_t_5numpy_intp_t; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":758 + * + * ctypedef npy_intp intp_t + * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< + * + * ctypedef npy_double float_t + */ +typedef npy_uintp __pyx_t_5numpy_uintp_t; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":760 + * 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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":761 + * + * ctypedef npy_double float_t + * ctypedef npy_double double_t # <<<<<<<<<<<<<< + * ctypedef npy_longdouble longdouble_t + * + */ +typedef npy_double __pyx_t_5numpy_double_t; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":762 + * 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_array_obj; struct __pyx_MemviewEnum_obj; struct __pyx_memoryview_obj; struct __pyx_memoryviewslice_obj; -/* "View.MemoryView":99 +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":764 + * 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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":765 + * + * ctypedef npy_cfloat cfloat_t + * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<< + * ctypedef npy_clongdouble clongdouble_t + * + */ +typedef npy_cdouble __pyx_t_5numpy_cdouble_t; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":766 + * 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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":768 + * ctypedef npy_clongdouble clongdouble_t + * + * ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<< + * + * cdef inline object PyArray_MultiIterNew1(a): + */ +typedef npy_cdouble __pyx_t_5numpy_complex_t; + +/* "View.MemoryView":101 * * @cname("__pyx_array") * cdef class array: # <<<<<<<<<<<<<< @@ -573,7 +846,7 @@ struct __pyx_array_obj { }; -/* "View.MemoryView":269 +/* "View.MemoryView":271 * * @cname('__pyx_MemviewEnum') * cdef class Enum(object): # <<<<<<<<<<<<<< @@ -586,7 +859,7 @@ struct __pyx_MemviewEnum_obj { }; -/* "View.MemoryView":302 +/* "View.MemoryView":304 * * @cname('__pyx_memoryview') * cdef class memoryview(object): # <<<<<<<<<<<<<< @@ -609,7 +882,7 @@ struct __pyx_memoryview_obj { }; -/* "View.MemoryView":921 +/* "View.MemoryView":923 * * @cname('__pyx_memoryviewslice') * cdef class _memoryviewslice(memoryview): # <<<<<<<<<<<<<< @@ -626,7 +899,7 @@ struct __pyx_memoryviewslice_obj { -/* "View.MemoryView":302 +/* "View.MemoryView":304 * * @cname('__pyx_memoryview') * cdef class memoryview(object): # <<<<<<<<<<<<<< @@ -646,7 +919,7 @@ struct __pyx_vtabstruct_memoryview { static struct __pyx_vtabstruct_memoryview *__pyx_vtabptr_memoryview; -/* "View.MemoryView":921 +/* "View.MemoryView":923 * * @cname('__pyx_memoryviewslice') * cdef class _memoryviewslice(memoryview): # <<<<<<<<<<<<<< @@ -676,19 +949,19 @@ static struct __pyx_vtabstruct__memoryviewslice *__pyx_vtabptr__memoryviewslice; static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname); #define __Pyx_RefNannyDeclarations void *__pyx_refnanny = NULL; #ifdef WITH_THREAD - #define __Pyx_RefNannySetupContext(name, acquire_gil) \ - if (acquire_gil) { \ - PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure(); \ - __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__); \ - PyGILState_Release(__pyx_gilstate_save); \ - } else { \ - __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__); \ + #define __Pyx_RefNannySetupContext(name, acquire_gil)\ + if (acquire_gil) {\ + PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure();\ + __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__);\ + PyGILState_Release(__pyx_gilstate_save);\ + } else {\ + __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__);\ } #else - #define __Pyx_RefNannySetupContext(name, acquire_gil) \ + #define __Pyx_RefNannySetupContext(name, acquire_gil)\ __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__) #endif - #define __Pyx_RefNannyFinishContext() \ + #define __Pyx_RefNannyFinishContext()\ __Pyx_RefNanny->FinishContext(&__pyx_refnanny) #define __Pyx_INCREF(r) __Pyx_RefNanny->INCREF(__pyx_refnanny, (PyObject *)(r), __LINE__) #define __Pyx_DECREF(r) __Pyx_RefNanny->DECREF(__pyx_refnanny, (PyObject *)(r), __LINE__) @@ -711,13 +984,13 @@ static struct __pyx_vtabstruct__memoryviewslice *__pyx_vtabptr__memoryviewslice; #define __Pyx_XGOTREF(r) #define __Pyx_XGIVEREF(r) #endif -#define __Pyx_XDECREF_SET(r, v) do { \ - PyObject *tmp = (PyObject *) r; \ - r = v; __Pyx_XDECREF(tmp); \ +#define __Pyx_XDECREF_SET(r, v) do {\ + PyObject *tmp = (PyObject *) r;\ + r = v; __Pyx_XDECREF(tmp);\ } while (0) -#define __Pyx_DECREF_SET(r, v) do { \ - PyObject *tmp = (PyObject *) r; \ - r = v; __Pyx_DECREF(tmp); \ +#define __Pyx_DECREF_SET(r, v) do {\ + PyObject *tmp = (PyObject *) r;\ + r = v; __Pyx_DECREF(tmp);\ } while (0) #define __Pyx_CLEAR(r) do { PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);} while(0) #define __Pyx_XCLEAR(r) do { if((r) != NULL) {PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);}} while(0) @@ -744,14 +1017,14 @@ static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact, static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); -static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], \ - PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, \ +static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[],\ + PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args,\ const char* function_name); static CYTHON_INLINE int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed, const char *name, int exact); -static CYTHON_INLINE long __Pyx_div_long(long, long); /* proto */ +static CYTHON_INLINE long __Pyx_div_long(long, long); static CYTHON_INLINE int __Pyx_GetBufferAndValidate(Py_buffer* buf, PyObject* obj, __Pyx_TypeInfo* dtype, int flags, int nd, int cast, __Pyx_BufFmt_StackElem* stack); @@ -782,6 +1055,13 @@ static CYTHON_INLINE int __pyx_sub_acquisition_count_locked( static CYTHON_INLINE void __Pyx_INC_MEMVIEW(__Pyx_memviewslice *, int, int); static CYTHON_INLINE void __Pyx_XDEC_MEMVIEW(__Pyx_memviewslice *, int, int); +#if CYTHON_COMPILING_IN_CPYTHON +static PyObject* __Pyx_PyFloat_DivideCObj(PyObject *op1, PyObject *op2, double floatval, int inplace); +#else +#define __Pyx_PyFloat_DivideCObj(op1, op2, floatval, inplace)\ + ((inplace ? __Pyx_PyNumber_InPlaceDivide(op1, op2) : __Pyx_PyNumber_Divide(op1, op2))) + #endif + #if CYTHON_COMPILING_IN_CPYTHON static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw); #else @@ -793,6 +1073,34 @@ static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyOb static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); +#if PY_MAJOR_VERSION >= 3 && !CYTHON_COMPILING_IN_PYPY +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 CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); + +static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index); + +static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void); + +static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); + #include static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals); @@ -805,13 +1113,10 @@ static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int #define __Pyx_PyString_Equals __Pyx_PyBytes_Equals #endif -static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t, Py_ssize_t); /* proto */ - -#ifndef __PYX_FORCE_INIT_THREADS - #define __PYX_FORCE_INIT_THREADS 0 -#endif +static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t, Py_ssize_t); -#define UNARY_NEG_WOULD_OVERFLOW(x) (((x) < 0) & ((unsigned long)(x) == 0-(unsigned long)(x))) +#define UNARY_NEG_WOULD_OVERFLOW(x)\ + (((x) < 0) & ((unsigned long)(x) == 0-(unsigned long)(x))) static CYTHON_UNUSED int __pyx_array_getbuffer(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /*proto*/ static PyObject *get_memview(PyObject *__pyx_v_self); /*proto*/ @@ -822,14 +1127,6 @@ static CYTHON_INLINE PyObject* __Pyx_decode_c_string( const char* encoding, const char* errors, PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)); -static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); - -static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index); - -static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void); - -static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); - static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); @@ -837,20 +1134,22 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb); -#define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \ - (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \ - __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) : \ - (is_list ? (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL) : \ +static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); + +#define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ + __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) :\ + (is_list ? (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL) :\ __Pyx_GetItemInt_Generic(o, to_py_func(i)))) -#define __Pyx_GetItemInt_List(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \ - (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \ - __Pyx_GetItemInt_List_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) : \ +#define __Pyx_GetItemInt_List(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ + __Pyx_GetItemInt_List_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\ (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL)) static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, int wraparound, int boundscheck); -#define __Pyx_GetItemInt_Tuple(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \ - (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \ - __Pyx_GetItemInt_Tuple_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) : \ +#define __Pyx_GetItemInt_Tuple(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ + __Pyx_GetItemInt_Tuple_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\ (PyErr_SetString(PyExc_IndexError, "tuple index out of range"), (PyObject*)NULL)) static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, int wraparound, int boundscheck); @@ -884,6 +1183,13 @@ static PyObject *__pyx_memoryview_get_ndim(PyObject *__pyx_v_self); /*proto*/ static PyObject *__pyx_memoryview_get_itemsize(PyObject *__pyx_v_self); /*proto*/ static PyObject *__pyx_memoryview_get_nbytes(PyObject *__pyx_v_self); /*proto*/ static PyObject *__pyx_memoryview_get_size(PyObject *__pyx_v_self); /*proto*/ +#if CYTHON_COMPILING_IN_CPYTHON +static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, long intval, int inplace); +#else +#define __Pyx_PyInt_AddObjC(op1, op2, intval, inplace)\ + (inplace ? PyNumber_InPlaceAdd(op1, op2) : PyNumber_Add(op1, op2)) +#endif + static CYTHON_INLINE int __Pyx_PyList_Extend(PyObject* L, PyObject* v) { #if CYTHON_COMPILING_IN_CPYTHON PyObject* none = _PyList_Extend((PyListObject*)L, v); @@ -914,6 +1220,10 @@ static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) { static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname); +#ifndef __PYX_FORCE_INIT_THREADS + #define __PYX_FORCE_INIT_THREADS 0 +#endif + static PyObject *__pyx_memoryviewslice__get__base(PyObject *__pyx_v_self); /*proto*/ static void __Pyx_WriteUnraisable(const char *name, int clineno, int lineno, const char *filename, @@ -975,6 +1285,106 @@ static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long 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 CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__NPY_TYPES(enum NPY_TYPES value); + static int __pyx_memviewslice_is_contig(const __Pyx_memviewslice *mvs, char order, int ndim); @@ -990,8 +1400,6 @@ __pyx_memoryview_copy_new_contig(const __Pyx_memviewslice *from_mvs, static CYTHON_INLINE PyObject *__pyx_capsule_create(void *p, const char *sig); -static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); - static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *); static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *); @@ -1042,10 +1450,34 @@ static PyObject *__pyx_memoryviewslice_assign_item_from_object(struct __pyx_memo /* Module declarations from 'cython' */ +/* Module declarations from 'cpython.buffer' */ + +/* Module declarations from 'libc.string' */ + +/* Module declarations from 'libc.stdio' */ + +/* Module declarations from '__builtin__' */ + +/* Module declarations from 'cpython.type' */ +static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0; + +/* Module declarations from 'cpython' */ + +/* Module declarations from 'cpython.object' */ + +/* Module declarations from 'cpython.ref' */ + +/* Module declarations from 'libc.stdlib' */ + /* Module declarations from 'numpy' */ -/* Module declarations from 'c_numpy' */ -static PyTypeObject *__pyx_ptype_7c_numpy_ndarray = 0; +/* 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 'lib._distances' */ static PyTypeObject *__pyx_array_type = 0; @@ -1096,72 +1528,32 @@ int __pyx_module_is_main_lib___distances = 0; /* Implementation of 'lib._distances' */ static PyObject *__pyx_builtin_range; static PyObject *__pyx_builtin_ValueError; +static PyObject *__pyx_builtin_RuntimeError; static PyObject *__pyx_builtin_MemoryError; static PyObject *__pyx_builtin_enumerate; static PyObject *__pyx_builtin_Ellipsis; static PyObject *__pyx_builtin_TypeError; static PyObject *__pyx_builtin_id; static PyObject *__pyx_builtin_IndexError; -static PyObject *__pyx_pf_3lib_10_distances_calc_distance_array(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_ref, PyArrayObject *__pyx_v_conf, PyArrayObject *__pyx_v_result); /* proto */ -static PyObject *__pyx_pf_3lib_10_distances_2calc_distance_array_ortho(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_ref, PyArrayObject *__pyx_v_conf, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_result); /* proto */ -static PyObject *__pyx_pf_3lib_10_distances_4calc_distance_array_triclinic(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_ref, PyArrayObject *__pyx_v_conf, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_result); /* proto */ -static PyObject *__pyx_pf_3lib_10_distances_6calc_self_distance_array(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_ref, PyArrayObject *__pyx_v_result); /* proto */ -static PyObject *__pyx_pf_3lib_10_distances_8calc_self_distance_array_ortho(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_ref, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_result); /* proto */ -static PyObject *__pyx_pf_3lib_10_distances_10calc_self_distance_array_triclinic(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_ref, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_result); /* proto */ -static PyObject *__pyx_pf_3lib_10_distances_12coord_transform(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords, PyArrayObject *__pyx_v_box); /* proto */ -static PyObject *__pyx_pf_3lib_10_distances_14calc_bond_distance(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_results); /* proto */ -static PyObject *__pyx_pf_3lib_10_distances_16calc_bond_distance_ortho(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_results); /* proto */ -static PyObject *__pyx_pf_3lib_10_distances_18calc_bond_distance_triclinic(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_results); /* proto */ -static PyObject *__pyx_pf_3lib_10_distances_20calc_angle(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_coords3, PyArrayObject *__pyx_v_results); /* proto */ -static PyObject *__pyx_pf_3lib_10_distances_22calc_angle_ortho(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_coords3, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_results); /* proto */ -static PyObject *__pyx_pf_3lib_10_distances_24calc_angle_triclinic(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_coords3, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_results); /* proto */ -static PyObject *__pyx_pf_3lib_10_distances_26calc_dihedral(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_coords3, PyArrayObject *__pyx_v_coords4, PyArrayObject *__pyx_v_results); /* proto */ -static PyObject *__pyx_pf_3lib_10_distances_28calc_dihedral_ortho(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_coords3, PyArrayObject *__pyx_v_coords4, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_results); /* proto */ -static PyObject *__pyx_pf_3lib_10_distances_30calc_dihedral_triclinic(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_coords3, PyArrayObject *__pyx_v_coords4, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_results); /* proto */ -static PyObject *__pyx_pf_3lib_10_distances_32ortho_pbc(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_box_inverse); /* proto */ -static PyObject *__pyx_pf_3lib_10_distances_34triclinic_pbc(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_box_inverse); /* proto */ -static PyObject *__pyx_pf_3lib_10_distances_36contact_matrix_no_pbc(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_coord, PyObject *__pyx_v_sparse_contacts, PyObject *__pyx_v_cutoff); /* proto */ -static PyObject *__pyx_pf_3lib_10_distances_38contact_matrix_pbc(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_coord, PyObject *__pyx_v_sparse_contacts, PyObject *__pyx_v_box, PyObject *__pyx_v_cutoff); /* proto */ -static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array___cinit__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_shape, Py_ssize_t __pyx_v_itemsize, PyObject *__pyx_v_format, PyObject *__pyx_v_mode, int __pyx_v_allocate_buffer); /* proto */ -static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_2__getbuffer__(struct __pyx_array_obj *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ -static void __pyx_array___pyx_pf_15View_dot_MemoryView_5array_4__dealloc__(struct __pyx_array_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_5array_7memview___get__(struct __pyx_array_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_array___pyx_pf_15View_dot_MemoryView_5array_6__getattr__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_attr); /* proto */ -static PyObject *__pyx_array___pyx_pf_15View_dot_MemoryView_5array_8__getitem__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_item); /* proto */ -static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_10__setitem__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_item, PyObject *__pyx_v_value); /* proto */ -static int __pyx_MemviewEnum___pyx_pf_15View_dot_MemoryView_4Enum___init__(struct __pyx_MemviewEnum_obj *__pyx_v_self, PyObject *__pyx_v_name); /* proto */ -static PyObject *__pyx_MemviewEnum___pyx_pf_15View_dot_MemoryView_4Enum_2__repr__(struct __pyx_MemviewEnum_obj *__pyx_v_self); /* proto */ -static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview___cinit__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_obj, int __pyx_v_flags, int __pyx_v_dtype_is_object); /* proto */ -static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__dealloc__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_4__getitem__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index); /* proto */ -static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_6__setitem__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value); /* proto */ -static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_8__getbuffer__(struct __pyx_memoryview_obj *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_1T___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_4base___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_5shape___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_7strides___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_10suboffsets___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_4ndim___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_8itemsize___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_6nbytes___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_4size___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static Py_ssize_t __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_10__len__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_12__repr__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_14__str__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_16is_c_contig(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_18is_f_contig(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_20copy(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_22copy_fortran(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static void __pyx_memoryviewslice___pyx_pf_15View_dot_MemoryView_16_memoryviewslice___dealloc__(struct __pyx_memoryviewslice_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_15View_dot_MemoryView_16_memoryviewslice_4base___get__(struct __pyx_memoryviewslice_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_tp_new_array(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ -static PyObject *__pyx_tp_new_Enum(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ -static PyObject *__pyx_tp_new_memoryview(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ -static PyObject *__pyx_tp_new__memoryviewslice(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +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_c[] = "c"; +static char __pyx_k_d[] = "d"; +static char __pyx_k_f[] = "f"; +static char __pyx_k_g[] = "g"; +static char __pyx_k_h[] = "h"; static char __pyx_k_i[] = "i"; static char __pyx_k_j[] = "j"; +static char __pyx_k_l[] = "l"; +static char __pyx_k_q[] = "q"; +static char __pyx_k_Zd[] = "Zd"; +static char __pyx_k_Zf[] = "Zf"; +static char __pyx_k_Zg[] = "Zg"; static char __pyx_k_id[] = "id"; static char __pyx_k_rr[] = "rr"; static char __pyx_k_box[] = "box"; @@ -1180,15 +1572,18 @@ static char __pyx_k_size[] = "size"; static char __pyx_k_step[] = "step"; static char __pyx_k_stop[] = "stop"; static char __pyx_k_test[] = "__test__"; +static char __pyx_k_ASCII[] = "ASCII"; static char __pyx_k_class[] = "__class__"; static char __pyx_k_coord[] = "coord"; static char __pyx_k_error[] = "error"; static char __pyx_k_flags[] = "flags"; +static char __pyx_k_numpy[] = "numpy"; static char __pyx_k_range[] = "range"; static char __pyx_k_shape[] = "shape"; static char __pyx_k_start[] = "start"; static char __pyx_k_coords[] = "coords"; static char __pyx_k_cutoff[] = "cutoff"; +static char __pyx_k_encode[] = "encode"; static char __pyx_k_format[] = "format"; static char __pyx_k_import[] = "__import__"; static char __pyx_k_name_2[] = "__name__"; @@ -1221,6 +1616,7 @@ static char __pyx_k_coord_view[] = "coord_view"; static char __pyx_k_pyx_vtable[] = "__pyx_vtable__"; static char __pyx_k_MemoryError[] = "MemoryError"; static char __pyx_k_box_inverse[] = "box_inverse"; +static char __pyx_k_RuntimeError[] = "RuntimeError"; static char __pyx_k_calc_dihedral[] = "calc_dihedral"; static char __pyx_k_pyx_getbuffer[] = "__pyx_getbuffer"; static char __pyx_k_triclinic_pbc[] = "triclinic_pbc"; @@ -1253,30 +1649,39 @@ static char __pyx_k_calc_distance_array_ortho[] = "calc_distance_array_ortho"; static char __pyx_k_Index_out_of_bounds_axis_d[] = "Index out of bounds (axis %d)"; static char __pyx_k_Step_may_not_be_zero_axis_d[] = "Step may not be zero (axis %d)"; static char __pyx_k_itemsize_0_for_cython_array[] = "itemsize <= 0 for cython.array"; +static char __pyx_k_ndarray_is_not_C_contiguous[] = "ndarray is not C contiguous"; static char __pyx_k_calc_bond_distance_triclinic[] = "calc_bond_distance_triclinic"; static char __pyx_k_calc_distance_array_triclinic[] = "calc_distance_array_triclinic"; static char __pyx_k_unable_to_allocate_array_data[] = "unable to allocate array data."; static char __pyx_k_calc_self_distance_array_ortho[] = "calc_self_distance_array_ortho"; static char __pyx_k_strided_and_direct_or_indirect[] = ""; static char __pyx_k_Distance_calculation_library_mo[] = "\nDistance calculation library --- :mod:`MDAnalysis.lib._distances`\n=================================================================\n\nSerial versions of all distance calculations\n"; -static char __pyx_k_home_richard_code_mdanalysis_pa[] = "/home/richard/code/mdanalysis/package/MDAnalysis/lib/distances.pyx"; +static char __pyx_k_nfs_homes2_oliver_Library_pytho[] = "/nfs/homes2/oliver/Library/python/mdanalysis/package/MDAnalysis/lib/distances.pyx"; +static char __pyx_k_unknown_dtype_code_in_numpy_pxd[] = "unknown dtype code in numpy.pxd (%d)"; static char __pyx_k_All_dimensions_preceding_dimensi[] = "All dimensions preceding dimension %d must be indexed and not sliced"; static char __pyx_k_Buffer_view_does_not_expose_stri[] = "Buffer view does not expose strides"; static char __pyx_k_Can_only_create_a_buffer_that_is[] = "Can only create a buffer that is contiguous in memory."; static char __pyx_k_Cannot_transpose_memoryview_with[] = "Cannot transpose memoryview with indirect dimensions"; static char __pyx_k_Empty_shape_tuple_for_cython_arr[] = "Empty shape tuple for cython.array"; +static char __pyx_k_Format_string_allocated_too_shor[] = "Format string allocated too short, see comment in numpy.pxd"; static char __pyx_k_Indirect_dimensions_not_supporte[] = "Indirect dimensions not supported"; static char __pyx_k_Invalid_mode_expected_c_or_fortr[] = "Invalid mode, expected 'c' or 'fortran', got %s"; +static char __pyx_k_Non_native_byte_order_not_suppor[] = "Non-native byte order not supported"; static char __pyx_k_Out_of_bounds_on_buffer_access_a[] = "Out of bounds on buffer access (axis %d)"; static char __pyx_k_Unable_to_convert_item_to_object[] = "Unable to convert item to object"; static char __pyx_k_calc_self_distance_array_triclin[] = "calc_self_distance_array_triclinic"; static char __pyx_k_got_differing_extents_in_dimensi[] = "got differing extents in dimension %d (got %d and %d)"; +static char __pyx_k_ndarray_is_not_Fortran_contiguou[] = "ndarray is not Fortran contiguous"; static char __pyx_k_unable_to_allocate_shape_and_str[] = "unable to allocate shape and strides."; +static char __pyx_k_Format_string_allocated_too_shor_2[] = "Format string allocated too short."; +static PyObject *__pyx_n_s_ASCII; static PyObject *__pyx_kp_s_Buffer_view_does_not_expose_stri; static PyObject *__pyx_kp_s_Can_only_create_a_buffer_that_is; static PyObject *__pyx_kp_s_Cannot_index_with_type_s; static PyObject *__pyx_n_s_Ellipsis; static PyObject *__pyx_kp_s_Empty_shape_tuple_for_cython_arr; +static PyObject *__pyx_kp_u_Format_string_allocated_too_shor; +static PyObject *__pyx_kp_u_Format_string_allocated_too_shor_2; static PyObject *__pyx_n_s_IndexError; static PyObject *__pyx_kp_s_Indirect_dimensions_not_supporte; static PyObject *__pyx_kp_s_Invalid_mode_expected_c_or_fortr; @@ -1284,8 +1689,10 @@ static PyObject *__pyx_kp_s_Invalid_shape_in_axis_d_d; static PyObject *__pyx_n_s_MemoryError; static PyObject *__pyx_kp_s_MemoryView_of_r_at_0x_x; static PyObject *__pyx_kp_s_MemoryView_of_r_object; +static PyObject *__pyx_kp_u_Non_native_byte_order_not_suppor; static PyObject *__pyx_n_b_O; static PyObject *__pyx_kp_s_Out_of_bounds_on_buffer_access_a; +static PyObject *__pyx_n_s_RuntimeError; static PyObject *__pyx_n_s_TypeError; static PyObject *__pyx_kp_s_Unable_to_convert_item_to_object; static PyObject *__pyx_n_s_ValueError; @@ -1332,6 +1739,7 @@ static PyObject *__pyx_n_s_cutoff2; static PyObject *__pyx_n_s_dist; static PyObject *__pyx_n_s_distnum; static PyObject *__pyx_n_s_dtype_is_object; +static PyObject *__pyx_n_s_encode; static PyObject *__pyx_n_s_enumerate; static PyObject *__pyx_n_s_error; static PyObject *__pyx_n_s_flags; @@ -1339,7 +1747,6 @@ static PyObject *__pyx_n_s_format; static PyObject *__pyx_n_s_fortran; static PyObject *__pyx_n_u_fortran; static PyObject *__pyx_kp_s_got_differing_extents_in_dimensi; -static PyObject *__pyx_kp_s_home_richard_code_mdanalysis_pa; static PyObject *__pyx_n_s_i; static PyObject *__pyx_n_s_id; static PyObject *__pyx_n_s_import; @@ -1352,8 +1759,12 @@ static PyObject *__pyx_n_s_memview; static PyObject *__pyx_n_s_mode; static PyObject *__pyx_n_s_name; static PyObject *__pyx_n_s_name_2; +static PyObject *__pyx_kp_u_ndarray_is_not_C_contiguous; +static PyObject *__pyx_kp_u_ndarray_is_not_Fortran_contiguou; static PyObject *__pyx_n_s_ndim; +static PyObject *__pyx_kp_s_nfs_homes2_oliver_Library_pytho; static PyObject *__pyx_n_s_numcoords; +static PyObject *__pyx_n_s_numpy; static PyObject *__pyx_n_s_obj; static PyObject *__pyx_n_s_ortho_pbc; static PyObject *__pyx_n_s_pack; @@ -1380,14 +1791,72 @@ static PyObject *__pyx_n_s_test; static PyObject *__pyx_n_s_triclinic_pbc; static PyObject *__pyx_kp_s_unable_to_allocate_array_data; static PyObject *__pyx_kp_s_unable_to_allocate_shape_and_str; +static PyObject *__pyx_kp_u_unknown_dtype_code_in_numpy_pxd; static PyObject *__pyx_n_s_unpack; +static PyObject *__pyx_pf_3lib_10_distances_calc_distance_array(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_ref, PyArrayObject *__pyx_v_conf, PyArrayObject *__pyx_v_result); /* proto */ +static PyObject *__pyx_pf_3lib_10_distances_2calc_distance_array_ortho(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_ref, PyArrayObject *__pyx_v_conf, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_result); /* proto */ +static PyObject *__pyx_pf_3lib_10_distances_4calc_distance_array_triclinic(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_ref, PyArrayObject *__pyx_v_conf, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_result); /* proto */ +static PyObject *__pyx_pf_3lib_10_distances_6calc_self_distance_array(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_ref, PyArrayObject *__pyx_v_result); /* proto */ +static PyObject *__pyx_pf_3lib_10_distances_8calc_self_distance_array_ortho(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_ref, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_result); /* proto */ +static PyObject *__pyx_pf_3lib_10_distances_10calc_self_distance_array_triclinic(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_ref, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_result); /* proto */ +static PyObject *__pyx_pf_3lib_10_distances_12coord_transform(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords, PyArrayObject *__pyx_v_box); /* proto */ +static PyObject *__pyx_pf_3lib_10_distances_14calc_bond_distance(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_results); /* proto */ +static PyObject *__pyx_pf_3lib_10_distances_16calc_bond_distance_ortho(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_results); /* proto */ +static PyObject *__pyx_pf_3lib_10_distances_18calc_bond_distance_triclinic(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_results); /* proto */ +static PyObject *__pyx_pf_3lib_10_distances_20calc_angle(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_coords3, PyArrayObject *__pyx_v_results); /* proto */ +static PyObject *__pyx_pf_3lib_10_distances_22calc_angle_ortho(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_coords3, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_results); /* proto */ +static PyObject *__pyx_pf_3lib_10_distances_24calc_angle_triclinic(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_coords3, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_results); /* proto */ +static PyObject *__pyx_pf_3lib_10_distances_26calc_dihedral(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_coords3, PyArrayObject *__pyx_v_coords4, PyArrayObject *__pyx_v_results); /* proto */ +static PyObject *__pyx_pf_3lib_10_distances_28calc_dihedral_ortho(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_coords3, PyArrayObject *__pyx_v_coords4, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_results); /* proto */ +static PyObject *__pyx_pf_3lib_10_distances_30calc_dihedral_triclinic(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_coords3, PyArrayObject *__pyx_v_coords4, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_results); /* proto */ +static PyObject *__pyx_pf_3lib_10_distances_32ortho_pbc(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_box_inverse); /* proto */ +static PyObject *__pyx_pf_3lib_10_distances_34triclinic_pbc(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_box_inverse); /* proto */ +static PyObject *__pyx_pf_3lib_10_distances_36contact_matrix_no_pbc(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_coord, PyObject *__pyx_v_sparse_contacts, PyObject *__pyx_v_cutoff); /* proto */ +static PyObject *__pyx_pf_3lib_10_distances_38contact_matrix_pbc(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_coord, PyObject *__pyx_v_sparse_contacts, PyObject *__pyx_v_box, PyObject *__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 int __pyx_array___pyx_pf_15View_dot_MemoryView_5array___cinit__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_shape, Py_ssize_t __pyx_v_itemsize, PyObject *__pyx_v_format, PyObject *__pyx_v_mode, int __pyx_v_allocate_buffer); /* proto */ +static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_2__getbuffer__(struct __pyx_array_obj *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ +static void __pyx_array___pyx_pf_15View_dot_MemoryView_5array_4__dealloc__(struct __pyx_array_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_5array_7memview___get__(struct __pyx_array_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_array___pyx_pf_15View_dot_MemoryView_5array_6__getattr__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_attr); /* proto */ +static PyObject *__pyx_array___pyx_pf_15View_dot_MemoryView_5array_8__getitem__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_item); /* proto */ +static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_10__setitem__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_item, PyObject *__pyx_v_value); /* proto */ +static int __pyx_MemviewEnum___pyx_pf_15View_dot_MemoryView_4Enum___init__(struct __pyx_MemviewEnum_obj *__pyx_v_self, PyObject *__pyx_v_name); /* proto */ +static PyObject *__pyx_MemviewEnum___pyx_pf_15View_dot_MemoryView_4Enum_2__repr__(struct __pyx_MemviewEnum_obj *__pyx_v_self); /* proto */ +static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview___cinit__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_obj, int __pyx_v_flags, int __pyx_v_dtype_is_object); /* proto */ +static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__dealloc__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_4__getitem__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index); /* proto */ +static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_6__setitem__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value); /* proto */ +static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_8__getbuffer__(struct __pyx_memoryview_obj *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_1T___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_4base___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_5shape___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_7strides___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_10suboffsets___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_4ndim___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_8itemsize___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_6nbytes___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_4size___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static Py_ssize_t __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_10__len__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_12__repr__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_14__str__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_16is_c_contig(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_18is_f_contig(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_20copy(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_22copy_fortran(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static void __pyx_memoryviewslice___pyx_pf_15View_dot_MemoryView_16_memoryviewslice___dealloc__(struct __pyx_memoryviewslice_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_16_memoryviewslice_4base___get__(struct __pyx_memoryviewslice_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_tp_new_array(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_tp_new_Enum(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_tp_new_memoryview(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_tp_new__memoryviewslice(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ static PyObject *__pyx_float_1_; static PyObject *__pyx_int_0; static PyObject *__pyx_int_1; static PyObject *__pyx_int_2; static PyObject *__pyx_int_neg_1; static PyObject *__pyx_tuple_; -static PyObject *__pyx_slice__9; static PyObject *__pyx_tuple__2; static PyObject *__pyx_tuple__3; static PyObject *__pyx_tuple__4; @@ -1395,60 +1864,68 @@ static PyObject *__pyx_tuple__5; static PyObject *__pyx_tuple__6; static PyObject *__pyx_tuple__7; static PyObject *__pyx_tuple__8; -static PyObject *__pyx_slice__10; -static PyObject *__pyx_slice__11; +static PyObject *__pyx_tuple__9; +static PyObject *__pyx_slice__16; +static PyObject *__pyx_slice__17; +static PyObject *__pyx_slice__18; +static PyObject *__pyx_tuple__10; +static PyObject *__pyx_tuple__11; static PyObject *__pyx_tuple__12; static PyObject *__pyx_tuple__13; +static PyObject *__pyx_tuple__14; static PyObject *__pyx_tuple__15; -static PyObject *__pyx_tuple__17; static PyObject *__pyx_tuple__19; -static PyObject *__pyx_tuple__21; -static PyObject *__pyx_tuple__23; -static PyObject *__pyx_tuple__25; -static PyObject *__pyx_tuple__27; -static PyObject *__pyx_tuple__29; -static PyObject *__pyx_tuple__31; -static PyObject *__pyx_tuple__33; 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static PyObject *__pyx_tuple__56; -static PyObject *__pyx_tuple__57; -static PyObject *__pyx_codeobj__14; -static PyObject *__pyx_codeobj__16; -static PyObject *__pyx_codeobj__18; -static PyObject *__pyx_codeobj__20; -static PyObject *__pyx_codeobj__22; -static PyObject *__pyx_codeobj__24; -static PyObject *__pyx_codeobj__26; -static PyObject *__pyx_codeobj__28; -static PyObject *__pyx_codeobj__30; -static PyObject *__pyx_codeobj__32; -static PyObject *__pyx_codeobj__34; -static PyObject *__pyx_codeobj__36; -static PyObject *__pyx_codeobj__38; -static PyObject *__pyx_codeobj__40; -static PyObject *__pyx_codeobj__42; -static PyObject *__pyx_codeobj__44; -static PyObject *__pyx_codeobj__46; -static PyObject *__pyx_codeobj__48; -static PyObject *__pyx_codeobj__50; -static PyObject *__pyx_codeobj__52; +static PyObject *__pyx_tuple__58; +static PyObject *__pyx_tuple__60; +static PyObject *__pyx_tuple__61; +static PyObject *__pyx_tuple__62; +static PyObject *__pyx_tuple__63; +static PyObject *__pyx_tuple__64; +static PyObject *__pyx_codeobj__21; +static PyObject *__pyx_codeobj__23; +static PyObject *__pyx_codeobj__25; +static PyObject *__pyx_codeobj__27; +static PyObject *__pyx_codeobj__29; +static PyObject *__pyx_codeobj__31; +static PyObject *__pyx_codeobj__33; +static PyObject *__pyx_codeobj__35; +static PyObject *__pyx_codeobj__37; +static PyObject *__pyx_codeobj__39; +static PyObject *__pyx_codeobj__41; +static PyObject *__pyx_codeobj__43; +static PyObject *__pyx_codeobj__45; +static PyObject *__pyx_codeobj__47; +static PyObject *__pyx_codeobj__49; +static PyObject *__pyx_codeobj__51; +static PyObject *__pyx_codeobj__53; +static PyObject *__pyx_codeobj__55; +static PyObject *__pyx_codeobj__57; +static PyObject *__pyx_codeobj__59; /* "MDAnalysis/lib/distances.pyx":55 * void minimum_image(double *x, float *box, float *inverse_box) * - * def calc_distance_array(c_numpy.ndarray ref, c_numpy.ndarray conf, # <<<<<<<<<<<<<< - * c_numpy.ndarray result): + * def calc_distance_array(numpy.ndarray ref, numpy.ndarray conf, # <<<<<<<<<<<<<< + * numpy.ndarray result): * cdef int confnum, refnum */ @@ -1516,9 +1993,9 @@ static PyObject *__pyx_pw_3lib_10_distances_1calc_distance_array(PyObject *__pyx __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_ref), __pyx_ptype_7c_numpy_ndarray, 1, "ref", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_conf), __pyx_ptype_7c_numpy_ndarray, 1, "conf", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_result), __pyx_ptype_7c_numpy_ndarray, 1, "result", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_ref), __pyx_ptype_5numpy_ndarray, 1, "ref", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_conf), __pyx_ptype_5numpy_ndarray, 1, "conf", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_result), __pyx_ptype_5numpy_ndarray, 1, "result", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_pf_3lib_10_distances_calc_distance_array(__pyx_self, __pyx_v_ref, __pyx_v_conf, __pyx_v_result); /* function exit code */ @@ -1538,25 +2015,25 @@ static PyObject *__pyx_pf_3lib_10_distances_calc_distance_array(CYTHON_UNUSED Py __Pyx_RefNannySetupContext("calc_distance_array", 0); /* "MDAnalysis/lib/distances.pyx":58 - * c_numpy.ndarray result): + * numpy.ndarray result): * cdef int confnum, refnum - * confnum = conf.dimensions[0] # <<<<<<<<<<<<<< - * refnum = ref.dimensions[0] + * confnum = conf.shape[0] # <<<<<<<<<<<<<< + * refnum = ref.shape[0] * */ __pyx_v_confnum = (__pyx_v_conf->dimensions[0]); /* "MDAnalysis/lib/distances.pyx":59 * cdef int confnum, refnum - * confnum = conf.dimensions[0] - * refnum = ref.dimensions[0] # <<<<<<<<<<<<<< + * confnum = conf.shape[0] + * refnum = ref.shape[0] # <<<<<<<<<<<<<< * * _calc_distance_array(ref.data, refnum, */ __pyx_v_refnum = (__pyx_v_ref->dimensions[0]); /* "MDAnalysis/lib/distances.pyx":61 - * refnum = ref.dimensions[0] + * refnum = ref.shape[0] * * _calc_distance_array(ref.data, refnum, # <<<<<<<<<<<<<< * conf.data, confnum, @@ -1567,8 +2044,8 @@ static PyObject *__pyx_pf_3lib_10_distances_calc_distance_array(CYTHON_UNUSED Py /* "MDAnalysis/lib/distances.pyx":55 * void minimum_image(double *x, float *box, float *inverse_box) * - * def calc_distance_array(c_numpy.ndarray ref, c_numpy.ndarray conf, # <<<<<<<<<<<<<< - * c_numpy.ndarray result): + * def calc_distance_array(numpy.ndarray ref, numpy.ndarray conf, # <<<<<<<<<<<<<< + * numpy.ndarray result): * cdef int confnum, refnum */ @@ -1582,9 +2059,9 @@ static PyObject *__pyx_pf_3lib_10_distances_calc_distance_array(CYTHON_UNUSED Py /* "MDAnalysis/lib/distances.pyx":65 * result.data) * - * def calc_distance_array_ortho(c_numpy.ndarray ref, c_numpy.ndarray conf, # <<<<<<<<<<<<<< - * c_numpy.ndarray box, - * c_numpy.ndarray result): + * def calc_distance_array_ortho(numpy.ndarray ref, numpy.ndarray conf, # <<<<<<<<<<<<<< + * numpy.ndarray box, + * numpy.ndarray result): */ /* Python wrapper */ @@ -1660,10 +2137,10 @@ static PyObject *__pyx_pw_3lib_10_distances_3calc_distance_array_ortho(PyObject __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_ref), __pyx_ptype_7c_numpy_ndarray, 1, "ref", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 65; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_conf), __pyx_ptype_7c_numpy_ndarray, 1, "conf", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 65; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_7c_numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_result), __pyx_ptype_7c_numpy_ndarray, 1, "result", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_ref), __pyx_ptype_5numpy_ndarray, 1, "ref", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 65; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_conf), __pyx_ptype_5numpy_ndarray, 1, "conf", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 65; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_5numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_result), __pyx_ptype_5numpy_ndarray, 1, "result", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_pf_3lib_10_distances_2calc_distance_array_ortho(__pyx_self, __pyx_v_ref, __pyx_v_conf, __pyx_v_box, __pyx_v_result); /* function exit code */ @@ -1683,25 +2160,25 @@ static PyObject *__pyx_pf_3lib_10_distances_2calc_distance_array_ortho(CYTHON_UN __Pyx_RefNannySetupContext("calc_distance_array_ortho", 0); /* "MDAnalysis/lib/distances.pyx":69 - * c_numpy.ndarray result): + * numpy.ndarray result): * cdef int confnum, refnum - * confnum = conf.dimensions[0] # <<<<<<<<<<<<<< - * refnum = ref.dimensions[0] + * confnum = conf.shape[0] # <<<<<<<<<<<<<< + * refnum = ref.shape[0] * */ __pyx_v_confnum = (__pyx_v_conf->dimensions[0]); /* "MDAnalysis/lib/distances.pyx":70 * cdef int confnum, refnum - * confnum = conf.dimensions[0] - * refnum = ref.dimensions[0] # <<<<<<<<<<<<<< + * confnum = conf.shape[0] + * refnum = ref.shape[0] # <<<<<<<<<<<<<< * * _calc_distance_array_ortho(ref.data, refnum, */ __pyx_v_refnum = (__pyx_v_ref->dimensions[0]); /* "MDAnalysis/lib/distances.pyx":72 - * refnum = ref.dimensions[0] + * refnum = ref.shape[0] * * _calc_distance_array_ortho(ref.data, refnum, # <<<<<<<<<<<<<< * conf.data, confnum, @@ -1712,9 +2189,9 @@ static PyObject *__pyx_pf_3lib_10_distances_2calc_distance_array_ortho(CYTHON_UN /* "MDAnalysis/lib/distances.pyx":65 * result.data) * - * def calc_distance_array_ortho(c_numpy.ndarray ref, c_numpy.ndarray conf, # <<<<<<<<<<<<<< - * c_numpy.ndarray box, - * c_numpy.ndarray result): + * def calc_distance_array_ortho(numpy.ndarray ref, numpy.ndarray conf, # <<<<<<<<<<<<<< + * numpy.ndarray box, + * numpy.ndarray result): */ /* function exit code */ @@ -1727,9 +2204,9 @@ static PyObject *__pyx_pf_3lib_10_distances_2calc_distance_array_ortho(CYTHON_UN /* "MDAnalysis/lib/distances.pyx":77 * result.data) * - * def calc_distance_array_triclinic(c_numpy.ndarray ref, c_numpy.ndarray conf, # <<<<<<<<<<<<<< - * c_numpy.ndarray box, - * c_numpy.ndarray result): + * def calc_distance_array_triclinic(numpy.ndarray ref, numpy.ndarray conf, # <<<<<<<<<<<<<< + * numpy.ndarray box, + * numpy.ndarray result): */ /* Python wrapper */ @@ -1805,10 +2282,10 @@ static PyObject *__pyx_pw_3lib_10_distances_5calc_distance_array_triclinic(PyObj __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_ref), __pyx_ptype_7c_numpy_ndarray, 1, "ref", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_conf), __pyx_ptype_7c_numpy_ndarray, 1, "conf", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_7c_numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_result), __pyx_ptype_7c_numpy_ndarray, 1, "result", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_ref), __pyx_ptype_5numpy_ndarray, 1, "ref", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_conf), __pyx_ptype_5numpy_ndarray, 1, "conf", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_5numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_result), __pyx_ptype_5numpy_ndarray, 1, "result", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_pf_3lib_10_distances_4calc_distance_array_triclinic(__pyx_self, __pyx_v_ref, __pyx_v_conf, __pyx_v_box, __pyx_v_result); /* function exit code */ @@ -1828,25 +2305,25 @@ static PyObject *__pyx_pf_3lib_10_distances_4calc_distance_array_triclinic(CYTHO __Pyx_RefNannySetupContext("calc_distance_array_triclinic", 0); /* "MDAnalysis/lib/distances.pyx":81 - * c_numpy.ndarray result): + * numpy.ndarray result): * cdef int confnum, refnum - * confnum = conf.dimensions[0] # <<<<<<<<<<<<<< - * refnum = ref.dimensions[0] + * confnum = conf.shape[0] # <<<<<<<<<<<<<< + * refnum = ref.shape[0] * */ __pyx_v_confnum = (__pyx_v_conf->dimensions[0]); /* "MDAnalysis/lib/distances.pyx":82 * cdef int confnum, refnum - * confnum = conf.dimensions[0] - * refnum = ref.dimensions[0] # <<<<<<<<<<<<<< + * confnum = conf.shape[0] + * refnum = ref.shape[0] # <<<<<<<<<<<<<< * * _calc_distance_array_triclinic(ref.data, refnum, */ __pyx_v_refnum = (__pyx_v_ref->dimensions[0]); /* "MDAnalysis/lib/distances.pyx":84 - * refnum = ref.dimensions[0] + * refnum = ref.shape[0] * * _calc_distance_array_triclinic(ref.data, refnum, # <<<<<<<<<<<<<< * conf.data, confnum, @@ -1857,9 +2334,9 @@ static PyObject *__pyx_pf_3lib_10_distances_4calc_distance_array_triclinic(CYTHO /* "MDAnalysis/lib/distances.pyx":77 * result.data) * - * def calc_distance_array_triclinic(c_numpy.ndarray ref, c_numpy.ndarray conf, # <<<<<<<<<<<<<< - * c_numpy.ndarray box, - * c_numpy.ndarray result): + * def calc_distance_array_triclinic(numpy.ndarray ref, numpy.ndarray conf, # <<<<<<<<<<<<<< + * numpy.ndarray box, + * numpy.ndarray result): */ /* function exit code */ @@ -1872,8 +2349,8 @@ static PyObject *__pyx_pf_3lib_10_distances_4calc_distance_array_triclinic(CYTHO /* "MDAnalysis/lib/distances.pyx":89 * result.data) * - * def calc_self_distance_array(c_numpy.ndarray ref, # <<<<<<<<<<<<<< - * c_numpy.ndarray result): + * def calc_self_distance_array(numpy.ndarray ref, # <<<<<<<<<<<<<< + * numpy.ndarray result): * cdef int refnum, distnum */ @@ -1932,8 +2409,8 @@ static PyObject *__pyx_pw_3lib_10_distances_7calc_self_distance_array(PyObject * __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_ref), __pyx_ptype_7c_numpy_ndarray, 1, "ref", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_result), __pyx_ptype_7c_numpy_ndarray, 1, "result", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 90; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_ref), __pyx_ptype_5numpy_ndarray, 1, "ref", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_result), __pyx_ptype_5numpy_ndarray, 1, "result", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 90; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_pf_3lib_10_distances_6calc_self_distance_array(__pyx_self, __pyx_v_ref, __pyx_v_result); /* function exit code */ @@ -1953,9 +2430,9 @@ static PyObject *__pyx_pf_3lib_10_distances_6calc_self_distance_array(CYTHON_UNU __Pyx_RefNannySetupContext("calc_self_distance_array", 0); /* "MDAnalysis/lib/distances.pyx":92 - * c_numpy.ndarray result): + * numpy.ndarray result): * cdef int refnum, distnum - * refnum = ref.dimensions[0] # <<<<<<<<<<<<<< + * refnum = ref.shape[0] # <<<<<<<<<<<<<< * distnum = (refnum*(refnum-1))/2 * */ @@ -1963,7 +2440,7 @@ static PyObject *__pyx_pf_3lib_10_distances_6calc_self_distance_array(CYTHON_UNU /* "MDAnalysis/lib/distances.pyx":93 * cdef int refnum, distnum - * refnum = ref.dimensions[0] + * refnum = ref.shape[0] * distnum = (refnum*(refnum-1))/2 # <<<<<<<<<<<<<< * * _calc_self_distance_array(ref.data, refnum, @@ -1982,8 +2459,8 @@ static PyObject *__pyx_pf_3lib_10_distances_6calc_self_distance_array(CYTHON_UNU /* "MDAnalysis/lib/distances.pyx":89 * result.data) * - * def calc_self_distance_array(c_numpy.ndarray ref, # <<<<<<<<<<<<<< - * c_numpy.ndarray result): + * def calc_self_distance_array(numpy.ndarray ref, # <<<<<<<<<<<<<< + * numpy.ndarray result): * cdef int refnum, distnum */ @@ -1997,9 +2474,9 @@ static PyObject *__pyx_pf_3lib_10_distances_6calc_self_distance_array(CYTHON_UNU /* "MDAnalysis/lib/distances.pyx":98 * result.data, distnum) * - * def calc_self_distance_array_ortho(c_numpy.ndarray ref, # <<<<<<<<<<<<<< - * c_numpy.ndarray box, - * c_numpy.ndarray result): + * def calc_self_distance_array_ortho(numpy.ndarray ref, # <<<<<<<<<<<<<< + * numpy.ndarray box, + * numpy.ndarray result): */ /* Python wrapper */ @@ -2066,9 +2543,9 @@ static PyObject *__pyx_pw_3lib_10_distances_9calc_self_distance_array_ortho(PyOb __Pyx_RefNannyFinishContext(); 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__pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_result), __pyx_ptype_5numpy_ndarray, 1, "result", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 100; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_pf_3lib_10_distances_8calc_self_distance_array_ortho(__pyx_self, __pyx_v_ref, __pyx_v_box, __pyx_v_result); /* function exit code */ @@ -2088,9 +2565,9 @@ static PyObject *__pyx_pf_3lib_10_distances_8calc_self_distance_array_ortho(CYTH __Pyx_RefNannySetupContext("calc_self_distance_array_ortho", 0); /* "MDAnalysis/lib/distances.pyx":102 - * c_numpy.ndarray result): + * numpy.ndarray result): * cdef int refnum, distnum - * refnum = ref.dimensions[0] # <<<<<<<<<<<<<< + * refnum = ref.shape[0] # <<<<<<<<<<<<<< * distnum = (refnum*(refnum-1))/2 * */ @@ -2098,7 +2575,7 @@ static PyObject *__pyx_pf_3lib_10_distances_8calc_self_distance_array_ortho(CYTH /* "MDAnalysis/lib/distances.pyx":103 * cdef int refnum, distnum - * refnum = ref.dimensions[0] + * refnum = ref.shape[0] * distnum = (refnum*(refnum-1))/2 # <<<<<<<<<<<<<< * * _calc_self_distance_array_ortho(ref.data, refnum, @@ -2117,9 +2594,9 @@ static PyObject *__pyx_pf_3lib_10_distances_8calc_self_distance_array_ortho(CYTH /* "MDAnalysis/lib/distances.pyx":98 * result.data, distnum) * - * def calc_self_distance_array_ortho(c_numpy.ndarray ref, # <<<<<<<<<<<<<< - * c_numpy.ndarray box, - * c_numpy.ndarray result): + * def calc_self_distance_array_ortho(numpy.ndarray ref, # <<<<<<<<<<<<<< + * numpy.ndarray box, + * numpy.ndarray result): */ /* function exit code */ @@ -2132,9 +2609,9 @@ static PyObject *__pyx_pf_3lib_10_distances_8calc_self_distance_array_ortho(CYTH /* "MDAnalysis/lib/distances.pyx":109 * result.data, distnum) * - * def calc_self_distance_array_triclinic(c_numpy.ndarray ref, # <<<<<<<<<<<<<< - * c_numpy.ndarray box, - * c_numpy.ndarray result): + * def calc_self_distance_array_triclinic(numpy.ndarray ref, # <<<<<<<<<<<<<< + * numpy.ndarray box, + * numpy.ndarray result): */ /* Python wrapper */ @@ -2201,9 +2678,9 @@ static PyObject *__pyx_pw_3lib_10_distances_11calc_self_distance_array_triclinic __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_ref), __pyx_ptype_7c_numpy_ndarray, 1, "ref", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 109; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_7c_numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_result), __pyx_ptype_7c_numpy_ndarray, 1, "result", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 111; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_ref), __pyx_ptype_5numpy_ndarray, 1, "ref", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 109; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_5numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_result), __pyx_ptype_5numpy_ndarray, 1, "result", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 111; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_pf_3lib_10_distances_10calc_self_distance_array_triclinic(__pyx_self, __pyx_v_ref, __pyx_v_box, __pyx_v_result); /* function exit code */ @@ -2223,9 +2700,9 @@ static PyObject *__pyx_pf_3lib_10_distances_10calc_self_distance_array_triclinic __Pyx_RefNannySetupContext("calc_self_distance_array_triclinic", 0); /* "MDAnalysis/lib/distances.pyx":113 - * c_numpy.ndarray result): + * numpy.ndarray result): * cdef int refnum, distnum - * refnum = ref.dimensions[0] # <<<<<<<<<<<<<< + * refnum = ref.shape[0] # <<<<<<<<<<<<<< * distnum = (refnum*(refnum-1))/2 * */ @@ -2233,7 +2710,7 @@ static PyObject *__pyx_pf_3lib_10_distances_10calc_self_distance_array_triclinic /* "MDAnalysis/lib/distances.pyx":114 * cdef int refnum, distnum - * refnum = ref.dimensions[0] + * refnum = ref.shape[0] * distnum = (refnum*(refnum-1))/2 # <<<<<<<<<<<<<< * * _calc_self_distance_array_triclinic(ref.data, refnum, @@ -2252,9 +2729,9 @@ static PyObject *__pyx_pf_3lib_10_distances_10calc_self_distance_array_triclinic /* "MDAnalysis/lib/distances.pyx":109 * result.data, distnum) * - * def calc_self_distance_array_triclinic(c_numpy.ndarray ref, # <<<<<<<<<<<<<< - * c_numpy.ndarray box, - * c_numpy.ndarray result): + * def calc_self_distance_array_triclinic(numpy.ndarray ref, # <<<<<<<<<<<<<< + * numpy.ndarray box, + * numpy.ndarray result): */ /* function exit code */ @@ -2267,8 +2744,8 @@ static PyObject *__pyx_pf_3lib_10_distances_10calc_self_distance_array_triclinic /* "MDAnalysis/lib/distances.pyx":120 * result.data, distnum) * - * def coord_transform(c_numpy.ndarray coords, # <<<<<<<<<<<<<< - * c_numpy.ndarray box): + * def coord_transform(numpy.ndarray coords, # <<<<<<<<<<<<<< + * numpy.ndarray box): * cdef int numcoords */ @@ -2327,8 +2804,8 @@ static PyObject *__pyx_pw_3lib_10_distances_13coord_transform(PyObject *__pyx_se __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords), __pyx_ptype_7c_numpy_ndarray, 1, "coords", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 120; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_7c_numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 121; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords), __pyx_ptype_5numpy_ndarray, 1, "coords", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 120; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_5numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 121; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_pf_3lib_10_distances_12coord_transform(__pyx_self, __pyx_v_coords, __pyx_v_box); /* function exit code */ @@ -2347,16 +2824,16 @@ static PyObject *__pyx_pf_3lib_10_distances_12coord_transform(CYTHON_UNUSED PyOb __Pyx_RefNannySetupContext("coord_transform", 0); /* "MDAnalysis/lib/distances.pyx":123 - * c_numpy.ndarray box): + * numpy.ndarray box): * cdef int numcoords - * numcoords = coords.dimensions[0] # <<<<<<<<<<<<<< + * numcoords = coords.shape[0] # <<<<<<<<<<<<<< * * _coord_transform( coords.data, numcoords, */ __pyx_v_numcoords = (__pyx_v_coords->dimensions[0]); /* "MDAnalysis/lib/distances.pyx":125 - * numcoords = coords.dimensions[0] + * numcoords = coords.shape[0] * * _coord_transform( coords.data, numcoords, # <<<<<<<<<<<<<< * box.data) @@ -2367,8 +2844,8 @@ static PyObject *__pyx_pf_3lib_10_distances_12coord_transform(CYTHON_UNUSED PyOb /* "MDAnalysis/lib/distances.pyx":120 * result.data, distnum) * - * def coord_transform(c_numpy.ndarray coords, # <<<<<<<<<<<<<< - * c_numpy.ndarray box): + * def coord_transform(numpy.ndarray coords, # <<<<<<<<<<<<<< + * numpy.ndarray box): * cdef int numcoords */ @@ -2382,9 +2859,9 @@ static PyObject *__pyx_pf_3lib_10_distances_12coord_transform(CYTHON_UNUSED PyOb /* "MDAnalysis/lib/distances.pyx":128 * box.data) * - * def calc_bond_distance(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray results): + * def calc_bond_distance(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray results): */ /* Python wrapper */ @@ -2451,9 +2928,9 @@ static PyObject *__pyx_pw_3lib_10_distances_15calc_bond_distance(PyObject *__pyx __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords1), __pyx_ptype_7c_numpy_ndarray, 1, "coords1", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 128; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords2), __pyx_ptype_7c_numpy_ndarray, 1, "coords2", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 129; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_results), __pyx_ptype_7c_numpy_ndarray, 1, "results", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 130; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords1), __pyx_ptype_5numpy_ndarray, 1, "coords1", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 128; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords2), __pyx_ptype_5numpy_ndarray, 1, "coords2", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 129; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_results), __pyx_ptype_5numpy_ndarray, 1, "results", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 130; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_pf_3lib_10_distances_14calc_bond_distance(__pyx_self, __pyx_v_coords1, __pyx_v_coords2, __pyx_v_results); /* function exit code */ @@ -2472,16 +2949,16 @@ static PyObject *__pyx_pf_3lib_10_distances_14calc_bond_distance(CYTHON_UNUSED P __Pyx_RefNannySetupContext("calc_bond_distance", 0); /* "MDAnalysis/lib/distances.pyx":132 - * c_numpy.ndarray results): + * numpy.ndarray results): * cdef int numcoords - * numcoords = coords1.dimensions[0] # <<<<<<<<<<<<<< + * numcoords = coords1.shape[0] # <<<<<<<<<<<<<< * * _calc_bond_distance( coords1.data, coords2.data, */ __pyx_v_numcoords = (__pyx_v_coords1->dimensions[0]); /* "MDAnalysis/lib/distances.pyx":134 - * numcoords = coords1.dimensions[0] + * numcoords = coords1.shape[0] * * _calc_bond_distance( coords1.data, coords2.data, # <<<<<<<<<<<<<< * numcoords, @@ -2492,9 +2969,9 @@ static PyObject *__pyx_pf_3lib_10_distances_14calc_bond_distance(CYTHON_UNUSED P /* "MDAnalysis/lib/distances.pyx":128 * box.data) * - * def calc_bond_distance(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray results): + * def calc_bond_distance(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray results): */ /* function exit code */ @@ -2507,9 +2984,9 @@ static PyObject *__pyx_pf_3lib_10_distances_14calc_bond_distance(CYTHON_UNUSED P /* "MDAnalysis/lib/distances.pyx":138 * results.data) * - * def calc_bond_distance_ortho(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray box, + * def calc_bond_distance_ortho(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray box, */ /* Python wrapper */ @@ -2585,10 +3062,10 @@ static PyObject *__pyx_pw_3lib_10_distances_17calc_bond_distance_ortho(PyObject __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords1), __pyx_ptype_7c_numpy_ndarray, 1, "coords1", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 138; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords2), __pyx_ptype_7c_numpy_ndarray, 1, "coords2", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 139; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_7c_numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_results), __pyx_ptype_7c_numpy_ndarray, 1, "results", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 141; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords1), __pyx_ptype_5numpy_ndarray, 1, "coords1", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 138; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords2), __pyx_ptype_5numpy_ndarray, 1, "coords2", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 139; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_5numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_results), __pyx_ptype_5numpy_ndarray, 1, "results", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 141; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_pf_3lib_10_distances_16calc_bond_distance_ortho(__pyx_self, __pyx_v_coords1, __pyx_v_coords2, __pyx_v_box, __pyx_v_results); /* function exit code */ @@ -2607,16 +3084,16 @@ static PyObject *__pyx_pf_3lib_10_distances_16calc_bond_distance_ortho(CYTHON_UN __Pyx_RefNannySetupContext("calc_bond_distance_ortho", 0); /* "MDAnalysis/lib/distances.pyx":143 - * c_numpy.ndarray results): + * numpy.ndarray results): * cdef int numcoords - * numcoords = coords1.dimensions[0] # <<<<<<<<<<<<<< + * numcoords = coords1.shape[0] # <<<<<<<<<<<<<< * * _calc_bond_distance_ortho( coords1.data, coords2.data, */ __pyx_v_numcoords = (__pyx_v_coords1->dimensions[0]); /* "MDAnalysis/lib/distances.pyx":145 - * numcoords = coords1.dimensions[0] + * numcoords = coords1.shape[0] * * _calc_bond_distance_ortho( coords1.data, coords2.data, # <<<<<<<<<<<<<< * numcoords, @@ -2627,9 +3104,9 @@ static PyObject *__pyx_pf_3lib_10_distances_16calc_bond_distance_ortho(CYTHON_UN /* "MDAnalysis/lib/distances.pyx":138 * results.data) * - * def calc_bond_distance_ortho(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray box, + * def calc_bond_distance_ortho(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray box, */ /* function exit code */ @@ -2642,9 +3119,9 @@ static PyObject *__pyx_pf_3lib_10_distances_16calc_bond_distance_ortho(CYTHON_UN /* "MDAnalysis/lib/distances.pyx":150 * results.data) * - * def calc_bond_distance_triclinic(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray box, + * def calc_bond_distance_triclinic(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray box, */ /* Python wrapper */ @@ -2720,10 +3197,10 @@ static PyObject *__pyx_pw_3lib_10_distances_19calc_bond_distance_triclinic(PyObj __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords1), __pyx_ptype_7c_numpy_ndarray, 1, "coords1", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 150; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords2), __pyx_ptype_7c_numpy_ndarray, 1, "coords2", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 151; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_7c_numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 152; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_results), __pyx_ptype_7c_numpy_ndarray, 1, "results", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 153; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords1), __pyx_ptype_5numpy_ndarray, 1, "coords1", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 150; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords2), __pyx_ptype_5numpy_ndarray, 1, "coords2", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 151; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_5numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 152; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_results), __pyx_ptype_5numpy_ndarray, 1, "results", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 153; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_pf_3lib_10_distances_18calc_bond_distance_triclinic(__pyx_self, __pyx_v_coords1, __pyx_v_coords2, __pyx_v_box, __pyx_v_results); /* function exit code */ @@ -2742,16 +3219,16 @@ static PyObject *__pyx_pf_3lib_10_distances_18calc_bond_distance_triclinic(CYTHO __Pyx_RefNannySetupContext("calc_bond_distance_triclinic", 0); /* "MDAnalysis/lib/distances.pyx":155 - * c_numpy.ndarray results): + * numpy.ndarray results): * cdef int numcoords - * numcoords = coords1.dimensions[0] # <<<<<<<<<<<<<< + * numcoords = coords1.shape[0] # <<<<<<<<<<<<<< * * _calc_bond_distance_triclinic( coords1.data, coords2.data, */ __pyx_v_numcoords = (__pyx_v_coords1->dimensions[0]); /* "MDAnalysis/lib/distances.pyx":157 - * numcoords = coords1.dimensions[0] + * numcoords = coords1.shape[0] * * _calc_bond_distance_triclinic( coords1.data, coords2.data, # <<<<<<<<<<<<<< * numcoords, @@ -2762,9 +3239,9 @@ static PyObject *__pyx_pf_3lib_10_distances_18calc_bond_distance_triclinic(CYTHO /* "MDAnalysis/lib/distances.pyx":150 * results.data) * - * def calc_bond_distance_triclinic(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray box, + * def calc_bond_distance_triclinic(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray box, */ /* function exit code */ @@ -2777,9 +3254,9 @@ static PyObject *__pyx_pf_3lib_10_distances_18calc_bond_distance_triclinic(CYTHO /* "MDAnalysis/lib/distances.pyx":162 * results.data) * - * def calc_angle(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray coords3, + * def calc_angle(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray coords3, */ /* Python wrapper */ @@ -2855,10 +3332,10 @@ static PyObject *__pyx_pw_3lib_10_distances_21calc_angle(PyObject *__pyx_self, P __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords1), __pyx_ptype_7c_numpy_ndarray, 1, "coords1", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 162; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords2), __pyx_ptype_7c_numpy_ndarray, 1, "coords2", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 163; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords3), __pyx_ptype_7c_numpy_ndarray, 1, "coords3", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 164; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_results), __pyx_ptype_7c_numpy_ndarray, 1, "results", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 165; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords1), __pyx_ptype_5numpy_ndarray, 1, "coords1", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 162; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords2), __pyx_ptype_5numpy_ndarray, 1, "coords2", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 163; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords3), __pyx_ptype_5numpy_ndarray, 1, "coords3", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 164; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_results), __pyx_ptype_5numpy_ndarray, 1, "results", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 165; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_pf_3lib_10_distances_20calc_angle(__pyx_self, __pyx_v_coords1, __pyx_v_coords2, __pyx_v_coords3, __pyx_v_results); /* function exit code */ @@ -2877,16 +3354,16 @@ static PyObject *__pyx_pf_3lib_10_distances_20calc_angle(CYTHON_UNUSED PyObject __Pyx_RefNannySetupContext("calc_angle", 0); /* "MDAnalysis/lib/distances.pyx":167 - * c_numpy.ndarray results): + * numpy.ndarray results): * cdef int numcoords - * numcoords = coords1.dimensions[0] # <<<<<<<<<<<<<< + * numcoords = coords1.shape[0] # <<<<<<<<<<<<<< * * _calc_angle( coords1.data, coords2.data, */ __pyx_v_numcoords = (__pyx_v_coords1->dimensions[0]); /* "MDAnalysis/lib/distances.pyx":169 - * numcoords = coords1.dimensions[0] + * numcoords = coords1.shape[0] * * _calc_angle( coords1.data, coords2.data, # <<<<<<<<<<<<<< * coords3.data, @@ -2897,9 +3374,9 @@ static PyObject *__pyx_pf_3lib_10_distances_20calc_angle(CYTHON_UNUSED PyObject /* "MDAnalysis/lib/distances.pyx":162 * results.data) * - * def calc_angle(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray coords3, + * def calc_angle(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray coords3, */ /* function exit code */ @@ -2912,9 +3389,9 @@ static PyObject *__pyx_pf_3lib_10_distances_20calc_angle(CYTHON_UNUSED PyObject /* "MDAnalysis/lib/distances.pyx":174 * results.data) * - * def calc_angle_ortho(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray coords3, + * def calc_angle_ortho(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray coords3, */ /* Python wrapper */ @@ -2999,11 +3476,11 @@ static PyObject *__pyx_pw_3lib_10_distances_23calc_angle_ortho(PyObject *__pyx_s __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords1), __pyx_ptype_7c_numpy_ndarray, 1, "coords1", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 174; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords2), __pyx_ptype_7c_numpy_ndarray, 1, "coords2", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 175; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords3), __pyx_ptype_7c_numpy_ndarray, 1, "coords3", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 176; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_7c_numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 177; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_results), __pyx_ptype_7c_numpy_ndarray, 1, "results", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 178; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords1), __pyx_ptype_5numpy_ndarray, 1, "coords1", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 174; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords2), __pyx_ptype_5numpy_ndarray, 1, "coords2", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 175; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords3), __pyx_ptype_5numpy_ndarray, 1, "coords3", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 176; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_5numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 177; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_results), __pyx_ptype_5numpy_ndarray, 1, "results", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 178; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_pf_3lib_10_distances_22calc_angle_ortho(__pyx_self, __pyx_v_coords1, __pyx_v_coords2, __pyx_v_coords3, __pyx_v_box, __pyx_v_results); /* function exit code */ @@ -3022,16 +3499,16 @@ static PyObject *__pyx_pf_3lib_10_distances_22calc_angle_ortho(CYTHON_UNUSED PyO __Pyx_RefNannySetupContext("calc_angle_ortho", 0); /* "MDAnalysis/lib/distances.pyx":180 - * c_numpy.ndarray results): + * numpy.ndarray results): * cdef int numcoords - * numcoords = coords1.dimensions[0] # <<<<<<<<<<<<<< + * numcoords = coords1.shape[0] # <<<<<<<<<<<<<< * * _calc_angle_ortho( coords1.data, coords2.data, */ __pyx_v_numcoords = (__pyx_v_coords1->dimensions[0]); /* "MDAnalysis/lib/distances.pyx":182 - * numcoords = coords1.dimensions[0] + * numcoords = coords1.shape[0] * * _calc_angle_ortho( coords1.data, coords2.data, # <<<<<<<<<<<<<< * coords3.data, @@ -3042,9 +3519,9 @@ static PyObject *__pyx_pf_3lib_10_distances_22calc_angle_ortho(CYTHON_UNUSED PyO /* "MDAnalysis/lib/distances.pyx":174 * results.data) * - * def calc_angle_ortho(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray coords3, + * def calc_angle_ortho(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray coords3, */ /* function exit code */ @@ -3057,9 +3534,9 @@ static PyObject *__pyx_pf_3lib_10_distances_22calc_angle_ortho(CYTHON_UNUSED PyO /* "MDAnalysis/lib/distances.pyx":188 * results.data) * - * def calc_angle_triclinic(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray coords3, + * def calc_angle_triclinic(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray coords3, */ /* Python wrapper */ @@ -3144,11 +3621,11 @@ static PyObject *__pyx_pw_3lib_10_distances_25calc_angle_triclinic(PyObject *__p __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords1), __pyx_ptype_7c_numpy_ndarray, 1, "coords1", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 188; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords2), __pyx_ptype_7c_numpy_ndarray, 1, "coords2", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords3), __pyx_ptype_7c_numpy_ndarray, 1, "coords3", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 190; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_7c_numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 191; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_results), __pyx_ptype_7c_numpy_ndarray, 1, "results", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 192; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords1), __pyx_ptype_5numpy_ndarray, 1, "coords1", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 188; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords2), __pyx_ptype_5numpy_ndarray, 1, "coords2", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords3), __pyx_ptype_5numpy_ndarray, 1, "coords3", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 190; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_5numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 191; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_results), __pyx_ptype_5numpy_ndarray, 1, "results", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 192; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_pf_3lib_10_distances_24calc_angle_triclinic(__pyx_self, __pyx_v_coords1, __pyx_v_coords2, __pyx_v_coords3, __pyx_v_box, __pyx_v_results); /* function exit code */ @@ -3167,16 +3644,16 @@ static PyObject *__pyx_pf_3lib_10_distances_24calc_angle_triclinic(CYTHON_UNUSED __Pyx_RefNannySetupContext("calc_angle_triclinic", 0); /* "MDAnalysis/lib/distances.pyx":194 - * c_numpy.ndarray results): + * numpy.ndarray results): * cdef int numcoords - * numcoords = coords1.dimensions[0] # <<<<<<<<<<<<<< + * numcoords = coords1.shape[0] # <<<<<<<<<<<<<< * * _calc_angle_triclinic( coords1.data, coords2.data, */ __pyx_v_numcoords = (__pyx_v_coords1->dimensions[0]); /* "MDAnalysis/lib/distances.pyx":196 - * numcoords = coords1.dimensions[0] + * numcoords = coords1.shape[0] * * _calc_angle_triclinic( coords1.data, coords2.data, # <<<<<<<<<<<<<< * coords3.data, @@ -3187,9 +3664,9 @@ static PyObject *__pyx_pf_3lib_10_distances_24calc_angle_triclinic(CYTHON_UNUSED /* "MDAnalysis/lib/distances.pyx":188 * results.data) * - * def calc_angle_triclinic(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray coords3, + * def calc_angle_triclinic(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray coords3, */ /* function exit code */ @@ -3202,9 +3679,9 @@ static PyObject *__pyx_pf_3lib_10_distances_24calc_angle_triclinic(CYTHON_UNUSED /* "MDAnalysis/lib/distances.pyx":202 * results.data) * - * def calc_dihedral(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray coords3, + * def calc_dihedral(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray coords3, */ /* Python wrapper */ @@ -3289,11 +3766,11 @@ static PyObject *__pyx_pw_3lib_10_distances_27calc_dihedral(PyObject *__pyx_self __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords1), __pyx_ptype_7c_numpy_ndarray, 1, "coords1", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords2), __pyx_ptype_7c_numpy_ndarray, 1, "coords2", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 203; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords3), __pyx_ptype_7c_numpy_ndarray, 1, "coords3", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 204; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords4), __pyx_ptype_7c_numpy_ndarray, 1, "coords4", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_results), __pyx_ptype_7c_numpy_ndarray, 1, "results", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 206; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords1), __pyx_ptype_5numpy_ndarray, 1, "coords1", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords2), __pyx_ptype_5numpy_ndarray, 1, "coords2", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 203; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords3), __pyx_ptype_5numpy_ndarray, 1, "coords3", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 204; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords4), __pyx_ptype_5numpy_ndarray, 1, "coords4", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_results), __pyx_ptype_5numpy_ndarray, 1, "results", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 206; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_pf_3lib_10_distances_26calc_dihedral(__pyx_self, __pyx_v_coords1, __pyx_v_coords2, __pyx_v_coords3, __pyx_v_coords4, __pyx_v_results); /* function exit code */ @@ -3312,16 +3789,16 @@ static PyObject *__pyx_pf_3lib_10_distances_26calc_dihedral(CYTHON_UNUSED PyObje __Pyx_RefNannySetupContext("calc_dihedral", 0); /* "MDAnalysis/lib/distances.pyx":208 - * c_numpy.ndarray results): + * numpy.ndarray results): * cdef int numcoords - * numcoords = coords1.dimensions[0] # <<<<<<<<<<<<<< + * numcoords = coords1.shape[0] # <<<<<<<<<<<<<< * * _calc_dihedral( coords1.data, coords2.data, */ __pyx_v_numcoords = (__pyx_v_coords1->dimensions[0]); /* "MDAnalysis/lib/distances.pyx":210 - * numcoords = coords1.dimensions[0] + * numcoords = coords1.shape[0] * * _calc_dihedral( coords1.data, coords2.data, # <<<<<<<<<<<<<< * coords3.data, coords4.data, @@ -3332,9 +3809,9 @@ static PyObject *__pyx_pf_3lib_10_distances_26calc_dihedral(CYTHON_UNUSED PyObje /* "MDAnalysis/lib/distances.pyx":202 * results.data) * - * def calc_dihedral(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray coords3, + * def calc_dihedral(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray coords3, */ /* function exit code */ @@ -3347,9 +3824,9 @@ static PyObject *__pyx_pf_3lib_10_distances_26calc_dihedral(CYTHON_UNUSED PyObje /* "MDAnalysis/lib/distances.pyx":215 * results.data) * - * def calc_dihedral_ortho(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray coords3, + * def calc_dihedral_ortho(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray coords3, */ /* Python wrapper */ @@ -3443,12 +3920,12 @@ static PyObject *__pyx_pw_3lib_10_distances_29calc_dihedral_ortho(PyObject *__py __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords1), __pyx_ptype_7c_numpy_ndarray, 1, "coords1", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords2), __pyx_ptype_7c_numpy_ndarray, 1, "coords2", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 216; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords3), __pyx_ptype_7c_numpy_ndarray, 1, "coords3", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords4), __pyx_ptype_7c_numpy_ndarray, 1, "coords4", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_7c_numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_results), __pyx_ptype_7c_numpy_ndarray, 1, "results", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords1), __pyx_ptype_5numpy_ndarray, 1, "coords1", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords2), __pyx_ptype_5numpy_ndarray, 1, "coords2", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 216; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords3), __pyx_ptype_5numpy_ndarray, 1, "coords3", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords4), __pyx_ptype_5numpy_ndarray, 1, "coords4", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_5numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_results), __pyx_ptype_5numpy_ndarray, 1, "results", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_pf_3lib_10_distances_28calc_dihedral_ortho(__pyx_self, __pyx_v_coords1, __pyx_v_coords2, __pyx_v_coords3, __pyx_v_coords4, __pyx_v_box, __pyx_v_results); /* function exit code */ @@ -3467,16 +3944,16 @@ static PyObject *__pyx_pf_3lib_10_distances_28calc_dihedral_ortho(CYTHON_UNUSED __Pyx_RefNannySetupContext("calc_dihedral_ortho", 0); /* "MDAnalysis/lib/distances.pyx":222 - * c_numpy.ndarray results): + * numpy.ndarray results): * cdef int numcoords - * numcoords = coords1.dimensions[0] # <<<<<<<<<<<<<< + * numcoords = coords1.shape[0] # <<<<<<<<<<<<<< * * _calc_dihedral_ortho( coords1.data, coords2.data, */ __pyx_v_numcoords = (__pyx_v_coords1->dimensions[0]); /* "MDAnalysis/lib/distances.pyx":224 - * numcoords = coords1.dimensions[0] + * numcoords = coords1.shape[0] * * _calc_dihedral_ortho( coords1.data, coords2.data, # <<<<<<<<<<<<<< * coords3.data, coords4.data, @@ -3487,9 +3964,9 @@ static PyObject *__pyx_pf_3lib_10_distances_28calc_dihedral_ortho(CYTHON_UNUSED /* "MDAnalysis/lib/distances.pyx":215 * results.data) * - * def calc_dihedral_ortho(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray coords3, + * def calc_dihedral_ortho(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray coords3, */ /* function exit code */ @@ -3502,9 +3979,9 @@ static PyObject *__pyx_pf_3lib_10_distances_28calc_dihedral_ortho(CYTHON_UNUSED /* "MDAnalysis/lib/distances.pyx":230 * results.data) * - * def calc_dihedral_triclinic(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray coords3, + * def calc_dihedral_triclinic(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray coords3, */ /* Python wrapper */ @@ -3598,12 +4075,12 @@ static PyObject *__pyx_pw_3lib_10_distances_31calc_dihedral_triclinic(PyObject * __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords1), __pyx_ptype_7c_numpy_ndarray, 1, "coords1", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 230; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords2), __pyx_ptype_7c_numpy_ndarray, 1, "coords2", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 231; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords3), __pyx_ptype_7c_numpy_ndarray, 1, "coords3", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 232; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords4), __pyx_ptype_7c_numpy_ndarray, 1, "coords4", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 233; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_7c_numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 234; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_results), __pyx_ptype_7c_numpy_ndarray, 1, "results", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 235; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords1), __pyx_ptype_5numpy_ndarray, 1, "coords1", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 230; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords2), __pyx_ptype_5numpy_ndarray, 1, "coords2", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 231; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords3), __pyx_ptype_5numpy_ndarray, 1, "coords3", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 232; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords4), __pyx_ptype_5numpy_ndarray, 1, "coords4", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 233; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_5numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 234; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_results), __pyx_ptype_5numpy_ndarray, 1, "results", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 235; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_pf_3lib_10_distances_30calc_dihedral_triclinic(__pyx_self, __pyx_v_coords1, __pyx_v_coords2, __pyx_v_coords3, __pyx_v_coords4, __pyx_v_box, __pyx_v_results); /* function exit code */ @@ -3622,16 +4099,16 @@ static PyObject *__pyx_pf_3lib_10_distances_30calc_dihedral_triclinic(CYTHON_UNU __Pyx_RefNannySetupContext("calc_dihedral_triclinic", 0); /* "MDAnalysis/lib/distances.pyx":237 - * c_numpy.ndarray results): + * numpy.ndarray results): * cdef int numcoords - * numcoords = coords1.dimensions[0] # <<<<<<<<<<<<<< + * numcoords = coords1.shape[0] # <<<<<<<<<<<<<< * * _calc_dihedral_triclinic( coords1.data, coords2.data, */ __pyx_v_numcoords = (__pyx_v_coords1->dimensions[0]); /* "MDAnalysis/lib/distances.pyx":239 - * numcoords = coords1.dimensions[0] + * numcoords = coords1.shape[0] * * _calc_dihedral_triclinic( coords1.data, coords2.data, # <<<<<<<<<<<<<< * coords3.data, coords4.data, @@ -3642,9 +4119,9 @@ static PyObject *__pyx_pf_3lib_10_distances_30calc_dihedral_triclinic(CYTHON_UNU /* "MDAnalysis/lib/distances.pyx":230 * results.data) * - * def calc_dihedral_triclinic(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray coords3, + * def calc_dihedral_triclinic(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray coords3, */ /* function exit code */ @@ -3657,8 +4134,8 @@ static PyObject *__pyx_pf_3lib_10_distances_30calc_dihedral_triclinic(CYTHON_UNU /* "MDAnalysis/lib/distances.pyx":245 * results.data) * - * def ortho_pbc(c_numpy.ndarray coords, # <<<<<<<<<<<<<< - * c_numpy.ndarray box, c_numpy.ndarray box_inverse): + * def ortho_pbc(numpy.ndarray coords, # <<<<<<<<<<<<<< + * numpy.ndarray box, numpy.ndarray box_inverse): * cdef int numcoords */ @@ -3726,9 +4203,9 @@ static PyObject *__pyx_pw_3lib_10_distances_33ortho_pbc(PyObject *__pyx_self, Py __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords), __pyx_ptype_7c_numpy_ndarray, 1, "coords", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 245; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_7c_numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 246; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box_inverse), __pyx_ptype_7c_numpy_ndarray, 1, "box_inverse", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 246; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords), __pyx_ptype_5numpy_ndarray, 1, "coords", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 245; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_5numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 246; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box_inverse), __pyx_ptype_5numpy_ndarray, 1, "box_inverse", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 246; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_pf_3lib_10_distances_32ortho_pbc(__pyx_self, __pyx_v_coords, __pyx_v_box, __pyx_v_box_inverse); /* function exit code */ @@ -3747,16 +4224,16 @@ static PyObject *__pyx_pf_3lib_10_distances_32ortho_pbc(CYTHON_UNUSED PyObject * __Pyx_RefNannySetupContext("ortho_pbc", 0); /* "MDAnalysis/lib/distances.pyx":248 - * c_numpy.ndarray box, c_numpy.ndarray box_inverse): + * numpy.ndarray box, numpy.ndarray box_inverse): * cdef int numcoords - * numcoords = coords.dimensions[0] # <<<<<<<<<<<<<< + * numcoords = coords.shape[0] # <<<<<<<<<<<<<< * * _ortho_pbc( coords.data, numcoords, */ __pyx_v_numcoords = (__pyx_v_coords->dimensions[0]); /* "MDAnalysis/lib/distances.pyx":250 - * numcoords = coords.dimensions[0] + * numcoords = coords.shape[0] * * _ortho_pbc( coords.data, numcoords, # <<<<<<<<<<<<<< * box.data, box_inverse.data) @@ -3767,8 +4244,8 @@ static PyObject *__pyx_pf_3lib_10_distances_32ortho_pbc(CYTHON_UNUSED PyObject * /* "MDAnalysis/lib/distances.pyx":245 * results.data) * - * def ortho_pbc(c_numpy.ndarray coords, # <<<<<<<<<<<<<< - * c_numpy.ndarray box, c_numpy.ndarray box_inverse): + * def ortho_pbc(numpy.ndarray coords, # <<<<<<<<<<<<<< + * numpy.ndarray box, numpy.ndarray box_inverse): * cdef int numcoords */ @@ -3782,8 +4259,8 @@ static PyObject *__pyx_pf_3lib_10_distances_32ortho_pbc(CYTHON_UNUSED PyObject * /* "MDAnalysis/lib/distances.pyx":253 * box.data, box_inverse.data) * - * def triclinic_pbc(c_numpy.ndarray coords, # <<<<<<<<<<<<<< - * c_numpy.ndarray box, c_numpy.ndarray box_inverse): + * def triclinic_pbc(numpy.ndarray coords, # <<<<<<<<<<<<<< + * numpy.ndarray box, numpy.ndarray box_inverse): * cdef int numcoords */ @@ -3851,9 +4328,9 @@ static PyObject *__pyx_pw_3lib_10_distances_35triclinic_pbc(PyObject *__pyx_self __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords), __pyx_ptype_7c_numpy_ndarray, 1, "coords", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 253; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_7c_numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 254; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box_inverse), __pyx_ptype_7c_numpy_ndarray, 1, "box_inverse", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 254; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords), __pyx_ptype_5numpy_ndarray, 1, "coords", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 253; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_5numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 254; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box_inverse), __pyx_ptype_5numpy_ndarray, 1, "box_inverse", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 254; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_pf_3lib_10_distances_34triclinic_pbc(__pyx_self, __pyx_v_coords, __pyx_v_box, __pyx_v_box_inverse); /* function exit code */ @@ -3872,16 +4349,16 @@ static PyObject *__pyx_pf_3lib_10_distances_34triclinic_pbc(CYTHON_UNUSED PyObje __Pyx_RefNannySetupContext("triclinic_pbc", 0); /* "MDAnalysis/lib/distances.pyx":256 - * c_numpy.ndarray box, c_numpy.ndarray box_inverse): + * numpy.ndarray box, numpy.ndarray box_inverse): * cdef int numcoords - * numcoords = coords.dimensions[0] # <<<<<<<<<<<<<< + * numcoords = coords.shape[0] # <<<<<<<<<<<<<< * * _triclinic_pbc( coords.data, numcoords, */ __pyx_v_numcoords = (__pyx_v_coords->dimensions[0]); /* "MDAnalysis/lib/distances.pyx":258 - * numcoords = coords.dimensions[0] + * numcoords = coords.shape[0] * * _triclinic_pbc( coords.data, numcoords, # <<<<<<<<<<<<<< * box.data, box_inverse.data) @@ -3892,8 +4369,8 @@ static PyObject *__pyx_pf_3lib_10_distances_34triclinic_pbc(CYTHON_UNUSED PyObje /* "MDAnalysis/lib/distances.pyx":253 * box.data, box_inverse.data) * - * def triclinic_pbc(c_numpy.ndarray coords, # <<<<<<<<<<<<<< - * c_numpy.ndarray box, c_numpy.ndarray box_inverse): + * def triclinic_pbc(numpy.ndarray coords, # <<<<<<<<<<<<<< + * numpy.ndarray box, numpy.ndarray box_inverse): * cdef int numcoords */ @@ -4003,18 +4480,19 @@ static PyObject *__pyx_pf_3lib_10_distances_36contact_matrix_no_pbc(CYTHON_UNUSE PyObject *__pyx_t_8 = NULL; int __pyx_t_9; int __pyx_t_10; - int __pyx_t_11; - int __pyx_t_12; + Py_ssize_t __pyx_t_11; + Py_ssize_t __pyx_t_12; Py_ssize_t __pyx_t_13; - int __pyx_t_14; + Py_ssize_t __pyx_t_14; Py_ssize_t __pyx_t_15; - int __pyx_t_16; + Py_ssize_t __pyx_t_16; Py_ssize_t __pyx_t_17; - int __pyx_t_18; + Py_ssize_t __pyx_t_18; Py_ssize_t __pyx_t_19; - int __pyx_t_20; + Py_ssize_t __pyx_t_20; Py_ssize_t __pyx_t_21; - int __pyx_t_22; + Py_ssize_t __pyx_t_22; + int __pyx_t_23; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; @@ -4108,14 +4586,14 @@ static PyObject *__pyx_pf_3lib_10_distances_36contact_matrix_no_pbc(CYTHON_UNUSE * rr[2] = coord_view[i, 2] - coord_view[j, 2] */ __pyx_t_11 = __pyx_v_i; - __pyx_t_1 = 0; + __pyx_t_12 = 0; if (__pyx_t_11 < 0) __pyx_t_11 += __pyx_v_coord_view.shape[0]; - if (__pyx_t_1 < 0) __pyx_t_1 += __pyx_v_coord_view.shape[1]; - __pyx_t_12 = __pyx_v_j; - __pyx_t_13 = 0; - if (__pyx_t_12 < 0) __pyx_t_12 += __pyx_v_coord_view.shape[0]; - if (__pyx_t_13 < 0) __pyx_t_13 += __pyx_v_coord_view.shape[1]; - (__pyx_v_rr[0]) = ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_coord_view.data + __pyx_t_11 * __pyx_v_coord_view.strides[0]) )) + __pyx_t_1)) ))) - (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_coord_view.data + __pyx_t_12 * __pyx_v_coord_view.strides[0]) )) + __pyx_t_13)) )))); + if (__pyx_t_12 < 0) __pyx_t_12 += __pyx_v_coord_view.shape[1]; + __pyx_t_13 = __pyx_v_j; + __pyx_t_14 = 0; + if (__pyx_t_13 < 0) __pyx_t_13 += __pyx_v_coord_view.shape[0]; + if (__pyx_t_14 < 0) __pyx_t_14 += __pyx_v_coord_view.shape[1]; + (__pyx_v_rr[0]) = ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_coord_view.data + __pyx_t_11 * __pyx_v_coord_view.strides[0]) )) + __pyx_t_12)) ))) - (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_coord_view.data + __pyx_t_13 * __pyx_v_coord_view.strides[0]) )) + __pyx_t_14)) )))); /* "MDAnalysis/lib/distances.pyx":275 * for j in range(i+1, rows): @@ -4124,15 +4602,15 @@ static PyObject *__pyx_pf_3lib_10_distances_36contact_matrix_no_pbc(CYTHON_UNUSE * rr[2] = coord_view[i, 2] - coord_view[j, 2] * dist = rr[0]*rr[0] + rr[1]*rr[1] + rr[2]*rr[2] */ - __pyx_t_14 = __pyx_v_i; - __pyx_t_15 = 1; - if (__pyx_t_14 < 0) __pyx_t_14 += __pyx_v_coord_view.shape[0]; - if (__pyx_t_15 < 0) __pyx_t_15 += __pyx_v_coord_view.shape[1]; - __pyx_t_16 = __pyx_v_j; - __pyx_t_17 = 1; - if (__pyx_t_16 < 0) __pyx_t_16 += __pyx_v_coord_view.shape[0]; - if (__pyx_t_17 < 0) __pyx_t_17 += __pyx_v_coord_view.shape[1]; - (__pyx_v_rr[1]) = ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_coord_view.data + __pyx_t_14 * __pyx_v_coord_view.strides[0]) )) + __pyx_t_15)) ))) - (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_coord_view.data + __pyx_t_16 * __pyx_v_coord_view.strides[0]) )) + __pyx_t_17)) )))); + __pyx_t_15 = __pyx_v_i; + __pyx_t_16 = 1; + if (__pyx_t_15 < 0) __pyx_t_15 += __pyx_v_coord_view.shape[0]; + if (__pyx_t_16 < 0) __pyx_t_16 += __pyx_v_coord_view.shape[1]; + __pyx_t_17 = __pyx_v_j; + __pyx_t_18 = 1; + if (__pyx_t_17 < 0) __pyx_t_17 += __pyx_v_coord_view.shape[0]; + if (__pyx_t_18 < 0) __pyx_t_18 += __pyx_v_coord_view.shape[1]; + (__pyx_v_rr[1]) = ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_coord_view.data + __pyx_t_15 * __pyx_v_coord_view.strides[0]) )) + __pyx_t_16)) ))) - (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_coord_view.data + __pyx_t_17 * __pyx_v_coord_view.strides[0]) )) + __pyx_t_18)) )))); /* "MDAnalysis/lib/distances.pyx":276 * rr[0] = coord_view[i, 0] - coord_view[j, 0] @@ -4141,15 +4619,15 @@ static PyObject *__pyx_pf_3lib_10_distances_36contact_matrix_no_pbc(CYTHON_UNUSE * dist = rr[0]*rr[0] + rr[1]*rr[1] + rr[2]*rr[2] * if dist < cutoff2: */ - __pyx_t_18 = __pyx_v_i; - __pyx_t_19 = 2; - if (__pyx_t_18 < 0) __pyx_t_18 += __pyx_v_coord_view.shape[0]; - if (__pyx_t_19 < 0) __pyx_t_19 += __pyx_v_coord_view.shape[1]; - __pyx_t_20 = __pyx_v_j; - __pyx_t_21 = 2; - if (__pyx_t_20 < 0) __pyx_t_20 += __pyx_v_coord_view.shape[0]; - if (__pyx_t_21 < 0) __pyx_t_21 += __pyx_v_coord_view.shape[1]; - (__pyx_v_rr[2]) = ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_coord_view.data + __pyx_t_18 * __pyx_v_coord_view.strides[0]) )) + __pyx_t_19)) ))) - (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_coord_view.data + __pyx_t_20 * __pyx_v_coord_view.strides[0]) )) + __pyx_t_21)) )))); + __pyx_t_19 = __pyx_v_i; + __pyx_t_20 = 2; + if (__pyx_t_19 < 0) __pyx_t_19 += __pyx_v_coord_view.shape[0]; + if (__pyx_t_20 < 0) __pyx_t_20 += __pyx_v_coord_view.shape[1]; + __pyx_t_21 = __pyx_v_j; + __pyx_t_22 = 2; + if (__pyx_t_21 < 0) __pyx_t_21 += __pyx_v_coord_view.shape[0]; + if (__pyx_t_22 < 0) __pyx_t_22 += __pyx_v_coord_view.shape[1]; + (__pyx_v_rr[2]) = ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_coord_view.data + __pyx_t_19 * __pyx_v_coord_view.strides[0]) )) + __pyx_t_20)) ))) - (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_coord_view.data + __pyx_t_21 * __pyx_v_coord_view.strides[0]) )) + __pyx_t_22)) )))); /* "MDAnalysis/lib/distances.pyx":277 * rr[1] = coord_view[i, 1] - coord_view[j, 1] @@ -4167,8 +4645,8 @@ static PyObject *__pyx_pf_3lib_10_distances_36contact_matrix_no_pbc(CYTHON_UNUSE * sparse_contacts[i, j] = True * sparse_contacts[j, i] = True */ - __pyx_t_22 = ((__pyx_v_dist < __pyx_v_cutoff2) != 0); - if (__pyx_t_22) { + __pyx_t_23 = ((__pyx_v_dist < __pyx_v_cutoff2) != 0); + if (__pyx_t_23) { /* "MDAnalysis/lib/distances.pyx":279 * dist = rr[0]*rr[0] + rr[1]*rr[1] + rr[2]*rr[2] @@ -4213,9 +4691,15 @@ static PyObject *__pyx_pf_3lib_10_distances_36contact_matrix_no_pbc(CYTHON_UNUSE __pyx_t_7 = 0; if (unlikely(PyObject_SetItem(__pyx_v_sparse_contacts, __pyx_t_8, Py_True) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 280; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - goto __pyx_L7; + + /* "MDAnalysis/lib/distances.pyx":278 + * rr[2] = coord_view[i, 2] - coord_view[j, 2] + * dist = rr[0]*rr[0] + rr[1]*rr[1] + rr[2]*rr[2] + * if dist < cutoff2: # <<<<<<<<<<<<<< + * sparse_contacts[i, j] = True + * sparse_contacts[j, i] = True + */ } - __pyx_L7:; } } @@ -4355,20 +4839,21 @@ static PyObject *__pyx_pf_3lib_10_distances_38contact_matrix_pbc(CYTHON_UNUSED P PyObject *__pyx_t_9 = NULL; int __pyx_t_10; int __pyx_t_11; - int __pyx_t_12; - int __pyx_t_13; + Py_ssize_t __pyx_t_12; + Py_ssize_t __pyx_t_13; Py_ssize_t __pyx_t_14; - int __pyx_t_15; + Py_ssize_t __pyx_t_15; Py_ssize_t __pyx_t_16; - int __pyx_t_17; + Py_ssize_t __pyx_t_17; Py_ssize_t __pyx_t_18; - int __pyx_t_19; + Py_ssize_t __pyx_t_19; Py_ssize_t __pyx_t_20; - int __pyx_t_21; + Py_ssize_t __pyx_t_21; Py_ssize_t __pyx_t_22; Py_ssize_t __pyx_t_23; Py_ssize_t __pyx_t_24; - int __pyx_t_25; + Py_ssize_t __pyx_t_25; + int __pyx_t_26; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; @@ -4430,7 +4915,7 @@ static PyObject *__pyx_pf_3lib_10_distances_38contact_matrix_pbc(CYTHON_UNUSED P * * cdef int i, j */ - __pyx_t_2 = __Pyx_PyNumber_Divide(__pyx_float_1_, __pyx_v_box); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 289; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyFloat_DivideCObj(__pyx_float_1_, __pyx_v_box, 1., 0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 289; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_t_5 = __Pyx_PyObject_to_MemoryviewSlice_dc_float(__pyx_t_2); if (unlikely(!__pyx_t_5.memview)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 289; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -4491,14 +4976,14 @@ static PyObject *__pyx_pf_3lib_10_distances_38contact_matrix_pbc(CYTHON_UNUSED P * rr[2] = coord_view[i, 2] - coord_view[j, 2] */ __pyx_t_12 = __pyx_v_i; - __pyx_t_1 = 0; + __pyx_t_13 = 0; if (__pyx_t_12 < 0) __pyx_t_12 += __pyx_v_coord_view.shape[0]; - if (__pyx_t_1 < 0) __pyx_t_1 += __pyx_v_coord_view.shape[1]; - __pyx_t_13 = __pyx_v_j; - __pyx_t_14 = 0; - if (__pyx_t_13 < 0) __pyx_t_13 += __pyx_v_coord_view.shape[0]; - if (__pyx_t_14 < 0) __pyx_t_14 += __pyx_v_coord_view.shape[1]; - (__pyx_v_rr[0]) = ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_coord_view.data + __pyx_t_12 * __pyx_v_coord_view.strides[0]) )) + __pyx_t_1)) ))) - (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_coord_view.data + __pyx_t_13 * __pyx_v_coord_view.strides[0]) )) + __pyx_t_14)) )))); + if (__pyx_t_13 < 0) __pyx_t_13 += __pyx_v_coord_view.shape[1]; + __pyx_t_14 = __pyx_v_j; + __pyx_t_15 = 0; + if (__pyx_t_14 < 0) __pyx_t_14 += __pyx_v_coord_view.shape[0]; + if (__pyx_t_15 < 0) __pyx_t_15 += __pyx_v_coord_view.shape[1]; + (__pyx_v_rr[0]) = ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_coord_view.data + __pyx_t_12 * __pyx_v_coord_view.strides[0]) )) + __pyx_t_13)) ))) - (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_coord_view.data + __pyx_t_14 * __pyx_v_coord_view.strides[0]) )) + __pyx_t_15)) )))); /* "MDAnalysis/lib/distances.pyx":298 * for j in range(i+1, rows): @@ -4507,15 +4992,15 @@ static PyObject *__pyx_pf_3lib_10_distances_38contact_matrix_pbc(CYTHON_UNUSED P * rr[2] = coord_view[i, 2] - coord_view[j, 2] * */ - __pyx_t_15 = __pyx_v_i; - __pyx_t_16 = 1; - if (__pyx_t_15 < 0) __pyx_t_15 += __pyx_v_coord_view.shape[0]; - if (__pyx_t_16 < 0) __pyx_t_16 += __pyx_v_coord_view.shape[1]; - __pyx_t_17 = __pyx_v_j; - __pyx_t_18 = 1; - if (__pyx_t_17 < 0) __pyx_t_17 += __pyx_v_coord_view.shape[0]; - if (__pyx_t_18 < 0) __pyx_t_18 += __pyx_v_coord_view.shape[1]; - (__pyx_v_rr[1]) = ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_coord_view.data + __pyx_t_15 * __pyx_v_coord_view.strides[0]) )) + __pyx_t_16)) ))) - (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_coord_view.data + __pyx_t_17 * __pyx_v_coord_view.strides[0]) )) + __pyx_t_18)) )))); + __pyx_t_16 = __pyx_v_i; + __pyx_t_17 = 1; + if (__pyx_t_16 < 0) __pyx_t_16 += __pyx_v_coord_view.shape[0]; + if (__pyx_t_17 < 0) __pyx_t_17 += __pyx_v_coord_view.shape[1]; + __pyx_t_18 = __pyx_v_j; + __pyx_t_19 = 1; + if (__pyx_t_18 < 0) __pyx_t_18 += __pyx_v_coord_view.shape[0]; + if (__pyx_t_19 < 0) __pyx_t_19 += __pyx_v_coord_view.shape[1]; + (__pyx_v_rr[1]) = ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_coord_view.data + __pyx_t_16 * __pyx_v_coord_view.strides[0]) )) + __pyx_t_17)) ))) - (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_coord_view.data + __pyx_t_18 * __pyx_v_coord_view.strides[0]) )) + __pyx_t_19)) )))); /* "MDAnalysis/lib/distances.pyx":299 * rr[0] = coord_view[i, 0] - coord_view[j, 0] @@ -4524,15 +5009,15 @@ static PyObject *__pyx_pf_3lib_10_distances_38contact_matrix_pbc(CYTHON_UNUSED P * * minimum_image(rr, &box_view[0], &box_inv[0]) */ - __pyx_t_19 = __pyx_v_i; - __pyx_t_20 = 2; - if (__pyx_t_19 < 0) __pyx_t_19 += __pyx_v_coord_view.shape[0]; - if (__pyx_t_20 < 0) __pyx_t_20 += __pyx_v_coord_view.shape[1]; - __pyx_t_21 = __pyx_v_j; - __pyx_t_22 = 2; - if (__pyx_t_21 < 0) __pyx_t_21 += __pyx_v_coord_view.shape[0]; - if (__pyx_t_22 < 0) __pyx_t_22 += __pyx_v_coord_view.shape[1]; - (__pyx_v_rr[2]) = ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_coord_view.data + __pyx_t_19 * __pyx_v_coord_view.strides[0]) )) + __pyx_t_20)) ))) - (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_coord_view.data + __pyx_t_21 * __pyx_v_coord_view.strides[0]) )) + __pyx_t_22)) )))); + __pyx_t_20 = __pyx_v_i; + __pyx_t_21 = 2; + if (__pyx_t_20 < 0) __pyx_t_20 += __pyx_v_coord_view.shape[0]; 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PyTuple_GET_ITEM(__pyx_args, 2); + case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = PyDict_Size(__pyx_kwds); + switch (pos_args) { + case 0: + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_shape)) != 0)) kw_args--; + else goto __pyx_L5_argtuple_error; + case 1: + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_itemsize)) != 0)) kw_args--; + else { + __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 3, 5, 1); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 118; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + } + case 2: + if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_format)) != 0)) kw_args--; + else { + __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 3, 5, 2); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 118; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + } + case 3: + if (kw_args > 0) { PyObject* value = 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__pyx_v_self->data = ((char *)malloc(__pyx_v_self->len)); - /* "View.MemoryView":169 + /* "View.MemoryView":171 * * self.data = malloc(self.len) * if not self.data: # <<<<<<<<<<<<<< @@ -5198,21 +7885,29 @@ static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array___cinit__(struct __ __pyx_t_4 = ((!(__pyx_v_self->data != 0)) != 0); if (__pyx_t_4) { - /* "View.MemoryView":170 + /* "View.MemoryView":172 * self.data = malloc(self.len) * if not self.data: * raise MemoryError("unable to allocate array data.") # <<<<<<<<<<<<<< * * if self.dtype_is_object: */ - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_MemoryError, __pyx_tuple__4, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 170; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_3); - __Pyx_Raise(__pyx_t_3, 0, 0, 0); - __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - {__pyx_filename = __pyx_f[1]; __pyx_lineno = 170; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_MemoryError, __pyx_tuple__11, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_5); + __Pyx_Raise(__pyx_t_5, 0, 0, 0); + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + {__pyx_filename = __pyx_f[2]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "View.MemoryView":171 + * + * self.data = malloc(self.len) + * if not self.data: # <<<<<<<<<<<<<< + * raise MemoryError("unable to allocate array data.") + * + */ } - /* "View.MemoryView":172 + /* "View.MemoryView":174 * raise MemoryError("unable to allocate array data.") * * if self.dtype_is_object: # <<<<<<<<<<<<<< @@ -5222,7 +7917,7 @@ static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array___cinit__(struct __ __pyx_t_4 = (__pyx_v_self->dtype_is_object != 0); if (__pyx_t_4) { - /* "View.MemoryView":173 + /* "View.MemoryView":175 * * if self.dtype_is_object: * p = self.data # 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unlikely(__pyx_v_itemsize == -1) && unlikely(UNARY_NEG_WOULD_OVERFLOW(__pyx_v_self->len))) { - #ifdef WITH_THREAD - PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure(); - #endif + else if (sizeof(Py_ssize_t) == sizeof(long) && (!(((Py_ssize_t)-1) > 0)) && unlikely(__pyx_v_itemsize == (Py_ssize_t)-1) && unlikely(UNARY_NEG_WOULD_OVERFLOW(__pyx_v_self->len))) { PyErr_SetString(PyExc_OverflowError, "value too large to perform division"); - #ifdef WITH_THREAD - PyGILState_Release(__pyx_gilstate_save); - #endif - {__pyx_filename = __pyx_f[1]; __pyx_lineno = 174; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[2]; __pyx_lineno = 176; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_t_1 = __Pyx_div_Py_ssize_t(__pyx_v_self->len, __pyx_v_itemsize); for (__pyx_t_8 = 0; __pyx_t_8 < __pyx_t_1; __pyx_t_8+=1) { __pyx_v_i = __pyx_t_8; - /* "View.MemoryView":175 + /* "View.MemoryView":177 * p = self.data * for i in range(self.len / itemsize): * p[i] = Py_None # <<<<<<<<<<<<<< @@ -5271,7 +7954,7 @@ static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array___cinit__(struct __ */ (__pyx_v_p[__pyx_v_i]) = Py_None; - /* "View.MemoryView":176 + /* "View.MemoryView":178 * for i in range(self.len / itemsize): * p[i] = Py_None * Py_INCREF(Py_None) # <<<<<<<<<<<<<< @@ -5280,14 +7963,26 @@ static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array___cinit__(struct __ */ Py_INCREF(Py_None); } - goto __pyx_L13; + + /* "View.MemoryView":174 + * raise MemoryError("unable to allocate array data.") + * + * if self.dtype_is_object: # <<<<<<<<<<<<<< + * p = self.data + * for i in range(self.len / itemsize): + */ } - __pyx_L13:; - goto __pyx_L11; + + /* "View.MemoryView":167 + * self.free_data = allocate_buffer + * self.dtype_is_object = format == b'O' + * if allocate_buffer: # <<<<<<<<<<<<<< + * + * + */ } - __pyx_L11:; - /* "View.MemoryView":116 + /* "View.MemoryView":118 * cdef bint dtype_is_object * * def __cinit__(array self, tuple shape, Py_ssize_t itemsize, format not None, # <<<<<<<<<<<<<< @@ -5300,7 +7995,7 @@ static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array___cinit__(struct __ goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_3); - __Pyx_XDECREF(__pyx_t_7); + __Pyx_XDECREF(__pyx_t_5); __Pyx_XDECREF(__pyx_t_9); __Pyx_XDECREF(__pyx_t_10); __Pyx_AddTraceback("View.MemoryView.array.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename); @@ -5311,7 +8006,7 @@ static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array___cinit__(struct __ return __pyx_r; } -/* "View.MemoryView":179 +/* "View.MemoryView":181 * * @cname('getbuffer') * def __getbuffer__(self, Py_buffer *info, int flags): # <<<<<<<<<<<<<< @@ -5352,7 +8047,7 @@ static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_2__getbuffer__(stru __Pyx_GIVEREF(__pyx_v_info->obj); } - /* "View.MemoryView":180 + /* "View.MemoryView":182 * @cname('getbuffer') * def __getbuffer__(self, Py_buffer *info, int flags): * cdef int bufmode = -1 # <<<<<<<<<<<<<< @@ -5361,18 +8056,18 @@ static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_2__getbuffer__(stru */ __pyx_v_bufmode = -1; - /* "View.MemoryView":181 + /* "View.MemoryView":183 * def __getbuffer__(self, Py_buffer *info, int flags): * cdef int bufmode = -1 * if self.mode == u"c": # <<<<<<<<<<<<<< * bufmode = PyBUF_C_CONTIGUOUS | PyBUF_ANY_CONTIGUOUS * elif self.mode == u"fortran": */ - __pyx_t_1 = (__Pyx_PyUnicode_Equals(__pyx_v_self->mode, __pyx_n_u_c, Py_EQ)); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = (__Pyx_PyUnicode_Equals(__pyx_v_self->mode, __pyx_n_u_c, Py_EQ)); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 183; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_2 = (__pyx_t_1 != 0); if (__pyx_t_2) { - /* "View.MemoryView":182 + /* "View.MemoryView":184 * cdef int bufmode = -1 * if self.mode == u"c": * bufmode = PyBUF_C_CONTIGUOUS | PyBUF_ANY_CONTIGUOUS # <<<<<<<<<<<<<< @@ -5380,21 +8075,29 @@ static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_2__getbuffer__(stru * bufmode = PyBUF_F_CONTIGUOUS | PyBUF_ANY_CONTIGUOUS */ __pyx_v_bufmode = (PyBUF_C_CONTIGUOUS | PyBUF_ANY_CONTIGUOUS); + + /* "View.MemoryView":183 + * def __getbuffer__(self, Py_buffer *info, int flags): + * cdef int bufmode = -1 + * if self.mode == u"c": # <<<<<<<<<<<<<< + * bufmode = PyBUF_C_CONTIGUOUS | PyBUF_ANY_CONTIGUOUS + * elif self.mode == u"fortran": + */ goto __pyx_L3; } - /* "View.MemoryView":183 + /* "View.MemoryView":185 * if self.mode == u"c": * bufmode = PyBUF_C_CONTIGUOUS | PyBUF_ANY_CONTIGUOUS * elif self.mode == u"fortran": # <<<<<<<<<<<<<< * bufmode = PyBUF_F_CONTIGUOUS | PyBUF_ANY_CONTIGUOUS * if not (flags & bufmode): */ - __pyx_t_2 = (__Pyx_PyUnicode_Equals(__pyx_v_self->mode, __pyx_n_u_fortran, Py_EQ)); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 183; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = (__Pyx_PyUnicode_Equals(__pyx_v_self->mode, __pyx_n_u_fortran, Py_EQ)); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 185; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_1 = (__pyx_t_2 != 0); if (__pyx_t_1) { - /* "View.MemoryView":184 + /* "View.MemoryView":186 * bufmode = PyBUF_C_CONTIGUOUS | PyBUF_ANY_CONTIGUOUS * elif self.mode == u"fortran": * bufmode = PyBUF_F_CONTIGUOUS | PyBUF_ANY_CONTIGUOUS # <<<<<<<<<<<<<< @@ -5402,11 +8105,18 @@ static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_2__getbuffer__(stru * raise ValueError("Can only create a buffer that is contiguous in memory.") */ __pyx_v_bufmode = (PyBUF_F_CONTIGUOUS | PyBUF_ANY_CONTIGUOUS); - goto __pyx_L3; + + /* "View.MemoryView":185 + * if self.mode == u"c": + * bufmode = PyBUF_C_CONTIGUOUS | PyBUF_ANY_CONTIGUOUS + * elif self.mode == u"fortran": # <<<<<<<<<<<<<< + * bufmode = PyBUF_F_CONTIGUOUS | PyBUF_ANY_CONTIGUOUS + * if not (flags & bufmode): + */ } __pyx_L3:; - /* "View.MemoryView":185 + /* "View.MemoryView":187 * elif self.mode == u"fortran": * bufmode = PyBUF_F_CONTIGUOUS | PyBUF_ANY_CONTIGUOUS * if not (flags & bufmode): # <<<<<<<<<<<<<< @@ -5416,21 +8126,29 @@ static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_2__getbuffer__(stru __pyx_t_1 = ((!((__pyx_v_flags & __pyx_v_bufmode) != 0)) != 0); if (__pyx_t_1) { - /* "View.MemoryView":186 + /* "View.MemoryView":188 * bufmode = PyBUF_F_CONTIGUOUS | PyBUF_ANY_CONTIGUOUS * if not (flags & bufmode): * raise ValueError("Can only create a buffer that is contiguous in memory.") # <<<<<<<<<<<<<< * info.buf = self.data * info.len = self.len */ - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__5, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 186; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__12, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 188; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_Raise(__pyx_t_3, 0, 0, 0); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - {__pyx_filename = __pyx_f[1]; __pyx_lineno = 186; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[2]; __pyx_lineno = 188; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "View.MemoryView":187 + * elif self.mode == u"fortran": + * bufmode = PyBUF_F_CONTIGUOUS | PyBUF_ANY_CONTIGUOUS + * if not (flags & bufmode): # <<<<<<<<<<<<<< + * raise ValueError("Can only create a buffer that is contiguous in memory.") + * info.buf = self.data + */ } - /* "View.MemoryView":187 + /* "View.MemoryView":189 * if not (flags & bufmode): * raise ValueError("Can only create a buffer that is contiguous in memory.") * info.buf = self.data # <<<<<<<<<<<<<< @@ -5440,7 +8158,7 @@ static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_2__getbuffer__(stru __pyx_t_4 = __pyx_v_self->data; __pyx_v_info->buf = __pyx_t_4; - /* "View.MemoryView":188 + /* "View.MemoryView":190 * raise ValueError("Can only create a buffer that is contiguous in memory.") * info.buf = self.data * info.len = self.len # <<<<<<<<<<<<<< @@ -5450,7 +8168,7 @@ static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_2__getbuffer__(stru __pyx_t_5 = __pyx_v_self->len; __pyx_v_info->len = __pyx_t_5; - /* "View.MemoryView":189 + /* "View.MemoryView":191 * info.buf = self.data * info.len = self.len * info.ndim = self.ndim # <<<<<<<<<<<<<< @@ -5460,7 +8178,7 @@ static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_2__getbuffer__(stru __pyx_t_6 = __pyx_v_self->ndim; __pyx_v_info->ndim = __pyx_t_6; - /* "View.MemoryView":190 + /* "View.MemoryView":192 * info.len = self.len * info.ndim = self.ndim * info.shape = self._shape # <<<<<<<<<<<<<< @@ -5470,7 +8188,7 @@ static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_2__getbuffer__(stru __pyx_t_7 = __pyx_v_self->_shape; __pyx_v_info->shape = __pyx_t_7; - /* "View.MemoryView":191 + /* "View.MemoryView":193 * info.ndim = self.ndim * info.shape = self._shape * info.strides = self._strides # <<<<<<<<<<<<<< @@ -5480,7 +8198,7 @@ static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_2__getbuffer__(stru __pyx_t_7 = __pyx_v_self->_strides; __pyx_v_info->strides = __pyx_t_7; - /* "View.MemoryView":192 + /* "View.MemoryView":194 * info.shape = self._shape * info.strides = self._strides * info.suboffsets = NULL # <<<<<<<<<<<<<< @@ -5489,7 +8207,7 @@ static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_2__getbuffer__(stru */ __pyx_v_info->suboffsets = NULL; - /* "View.MemoryView":193 + /* "View.MemoryView":195 * info.strides = self._strides * info.suboffsets = NULL * info.itemsize = self.itemsize # <<<<<<<<<<<<<< @@ -5499,7 +8217,7 @@ static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_2__getbuffer__(stru __pyx_t_5 = __pyx_v_self->itemsize; __pyx_v_info->itemsize = __pyx_t_5; - /* "View.MemoryView":194 + /* 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__pyx_L5; } - /*else*/ { - /* "View.MemoryView":199 + /* "View.MemoryView":201 * info.format = self.format * else: * info.format = NULL # <<<<<<<<<<<<<< * * info.obj = self */ + /*else*/ { __pyx_v_info->format = NULL; } __pyx_L5:; - /* "View.MemoryView":201 + /* "View.MemoryView":203 * info.format = NULL * * info.obj = self # <<<<<<<<<<<<<< @@ -5555,7 +8281,7 @@ static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_2__getbuffer__(stru __Pyx_DECREF(__pyx_v_info->obj); __pyx_v_info->obj = ((PyObject *)__pyx_v_self); - /* "View.MemoryView":179 + /* "View.MemoryView":181 * * @cname('getbuffer') * def __getbuffer__(self, Py_buffer *info, int flags): # <<<<<<<<<<<<<< @@ -5585,7 +8311,7 @@ static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_2__getbuffer__(stru return __pyx_r; } -/* "View.MemoryView":205 +/* "View.MemoryView":207 * __pyx_getbuffer = capsule( &__pyx_array_getbuffer, "getbuffer(obj, view, flags)") * * def __dealloc__(array self): # <<<<<<<<<<<<<< @@ -5609,7 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self.callback_free_data(self.data) + * elif self.free_data: + */ goto __pyx_L3; } - /* "View.MemoryView":208 + /* "View.MemoryView":210 * if self.callback_free_data != NULL: * self.callback_free_data(self.data) * elif self.free_data: # <<<<<<<<<<<<<< @@ -5640,7 +8374,7 @@ static void __pyx_array___pyx_pf_15View_dot_MemoryView_5array_4__dealloc__(struc __pyx_t_1 = (__pyx_v_self->free_data != 0); if (__pyx_t_1) { - /* "View.MemoryView":209 + /* "View.MemoryView":211 * self.callback_free_data(self.data) * elif self.free_data: * if self.dtype_is_object: # <<<<<<<<<<<<<< @@ -5650,7 +8384,7 @@ static void __pyx_array___pyx_pf_15View_dot_MemoryView_5array_4__dealloc__(struc __pyx_t_1 = (__pyx_v_self->dtype_is_object != 0); if (__pyx_t_1) { - /* "View.MemoryView":210 + /* "View.MemoryView":212 * elif self.free_data: * if self.dtype_is_object: * refcount_objects_in_slice(self.data, self._shape, # <<<<<<<<<<<<<< @@ -5658,23 +8392,36 @@ static void 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/*else*/ { + __pyx_t_4 = PyInt_FromSsize_t(__pyx_v_itemsize); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 243; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_5 = __Pyx_PyBytes_FromString(__pyx_v_format); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 241; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_PyBytes_FromString(__pyx_v_format); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 243; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - __pyx_t_3 = __Pyx_decode_c_string(__pyx_v_mode, 0, strlen(__pyx_v_mode), NULL, NULL, PyUnicode_DecodeASCII); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 241; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_decode_c_string(__pyx_v_mode, 0, strlen(__pyx_v_mode), NULL, NULL, PyUnicode_DecodeASCII); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; 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__pyx_L1_error;} + __pyx_t_5 = __Pyx_PyObject_Call(((PyObject *)__pyx_array_type), __pyx_t_2, __pyx_t_3); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 243; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_v_result = ((struct __pyx_array_obj *)__pyx_t_5); __pyx_t_5 = 0; - /* "View.MemoryView":243 + /* "View.MemoryView":245 * result = array(shape, itemsize, format, mode.decode('ASCII'), * allocate_buffer=False) * result.data = buf # <<<<<<<<<<<<<< @@ -6118,7 +8873,7 @@ static struct __pyx_array_obj *__pyx_array_new(PyObject *__pyx_v_shape, Py_ssize } __pyx_L3:; - /* "View.MemoryView":245 + /* "View.MemoryView":247 * result.data = buf * * return result # <<<<<<<<<<<<<< @@ -6130,7 +8885,7 @@ static struct __pyx_array_obj *__pyx_array_new(PyObject *__pyx_v_shape, Py_ssize __pyx_r = __pyx_v_result; goto __pyx_L0; - /* "View.MemoryView":234 + /* "View.MemoryView":236 * * @cname("__pyx_array_new") * cdef array array_cwrapper(tuple shape, Py_ssize_t itemsize, char *format, # <<<<<<<<<<<<<< @@ -6153,7 +8908,7 @@ static struct __pyx_array_obj *__pyx_array_new(PyObject *__pyx_v_shape, Py_ssize return __pyx_r; } -/* "View.MemoryView":271 +/* "View.MemoryView":273 * cdef class Enum(object): * cdef object name * def __init__(self, name): # <<<<<<<<<<<<<< @@ -6189,7 +8944,7 @@ static int __pyx_MemviewEnum___init__(PyObject *__pyx_v_self, PyObject *__pyx_ar else goto __pyx_L5_argtuple_error; } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 271; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 273; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else if (PyTuple_GET_SIZE(__pyx_args) != 1) { goto __pyx_L5_argtuple_error; @@ -6200,7 +8955,7 @@ static int __pyx_MemviewEnum___init__(PyObject *__pyx_v_self, PyObject *__pyx_ar } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("__init__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[1]; __pyx_lineno = 271; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__init__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 273; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; __Pyx_AddTraceback("View.MemoryView.Enum.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); @@ -6218,7 +8973,7 @@ static int __pyx_MemviewEnum___pyx_pf_15View_dot_MemoryView_4Enum___init__(struc __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__init__", 0); - /* "View.MemoryView":272 + /* "View.MemoryView":274 * cdef object name * def __init__(self, name): * self.name = name # <<<<<<<<<<<<<< @@ -6231,7 +8986,7 @@ static int __pyx_MemviewEnum___pyx_pf_15View_dot_MemoryView_4Enum___init__(struc __Pyx_DECREF(__pyx_v_self->name); __pyx_v_self->name = __pyx_v_name; - /* "View.MemoryView":271 + /* "View.MemoryView":273 * cdef class Enum(object): * cdef object name * def __init__(self, name): # <<<<<<<<<<<<<< @@ -6245,7 +9000,7 @@ static int __pyx_MemviewEnum___pyx_pf_15View_dot_MemoryView_4Enum___init__(struc return __pyx_r; } -/* "View.MemoryView":273 +/* "View.MemoryView":275 * def __init__(self, name): * self.name = name * def __repr__(self): # <<<<<<<<<<<<<< @@ -6271,7 +9026,7 @@ static PyObject *__pyx_MemviewEnum___pyx_pf_15View_dot_MemoryView_4Enum_2__repr_ __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__repr__", 0); - /* "View.MemoryView":274 + /* "View.MemoryView":276 * self.name = name * def __repr__(self): * return self.name # <<<<<<<<<<<<<< @@ -6283,7 +9038,7 @@ static PyObject *__pyx_MemviewEnum___pyx_pf_15View_dot_MemoryView_4Enum_2__repr_ __pyx_r = __pyx_v_self->name; goto __pyx_L0; - /* "View.MemoryView":273 + /* "View.MemoryView":275 * def __init__(self, name): * self.name = name * def __repr__(self): # <<<<<<<<<<<<<< @@ -6298,7 +9053,7 @@ static PyObject *__pyx_MemviewEnum___pyx_pf_15View_dot_MemoryView_4Enum_2__repr_ return __pyx_r; } -/* "View.MemoryView":288 +/* "View.MemoryView":290 * * @cname('__pyx_align_pointer') * cdef void *align_pointer(void *memory, size_t alignment) nogil: # <<<<<<<<<<<<<< @@ -6312,7 +9067,7 @@ static void *__pyx_align_pointer(void *__pyx_v_memory, size_t __pyx_v_alignment) void *__pyx_r; int __pyx_t_1; - /* "View.MemoryView":290 + /* "View.MemoryView":292 * cdef void *align_pointer(void *memory, size_t alignment) nogil: * "Align pointer memory on a given boundary" * cdef Py_intptr_t aligned_p = memory # <<<<<<<<<<<<<< @@ -6321,7 +9076,7 @@ static void *__pyx_align_pointer(void *__pyx_v_memory, size_t __pyx_v_alignment) */ __pyx_v_aligned_p = ((Py_intptr_t)__pyx_v_memory); - /* "View.MemoryView":294 + /* "View.MemoryView":296 * * with cython.cdivision(True): * offset = aligned_p % alignment # <<<<<<<<<<<<<< @@ -6330,7 +9085,7 @@ static void *__pyx_align_pointer(void *__pyx_v_memory, size_t __pyx_v_alignment) */ __pyx_v_offset = (__pyx_v_aligned_p % __pyx_v_alignment); - /* "View.MemoryView":296 + /* "View.MemoryView":298 * offset = aligned_p % alignment * * if offset > 0: # <<<<<<<<<<<<<< @@ -6340,7 +9095,7 @@ static void *__pyx_align_pointer(void *__pyx_v_memory, size_t __pyx_v_alignment) __pyx_t_1 = ((__pyx_v_offset > 0) != 0); if (__pyx_t_1) { - /* "View.MemoryView":297 + /* "View.MemoryView":299 * * if offset > 0: * aligned_p += alignment - offset # <<<<<<<<<<<<<< @@ -6348,11 +9103,17 @@ static void *__pyx_align_pointer(void *__pyx_v_memory, size_t __pyx_v_alignment) * return aligned_p */ __pyx_v_aligned_p = (__pyx_v_aligned_p + (__pyx_v_alignment - __pyx_v_offset)); - goto __pyx_L3; + + /* "View.MemoryView":298 + * offset = aligned_p % alignment + * + * if offset > 0: # <<<<<<<<<<<<<< + * aligned_p += alignment - offset + * + */ } - __pyx_L3:; - /* "View.MemoryView":299 + /* "View.MemoryView":301 * aligned_p += alignment - offset * * return aligned_p # <<<<<<<<<<<<<< @@ -6362,7 +9123,7 @@ static void *__pyx_align_pointer(void *__pyx_v_memory, size_t __pyx_v_alignment) __pyx_r = ((void *)__pyx_v_aligned_p); goto __pyx_L0; - /* "View.MemoryView":288 + /* "View.MemoryView":290 * * @cname('__pyx_align_pointer') * cdef void *align_pointer(void *memory, size_t alignment) nogil: # <<<<<<<<<<<<<< @@ -6375,7 +9136,7 @@ static void *__pyx_align_pointer(void *__pyx_v_memory, size_t __pyx_v_alignment) return __pyx_r; } -/* "View.MemoryView":317 +/* "View.MemoryView":319 * cdef __Pyx_TypeInfo *typeinfo * * def __cinit__(memoryview self, object obj, int flags, bint dtype_is_object=False): # <<<<<<<<<<<<<< @@ -6416,7 +9177,7 @@ static int __pyx_memoryview___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_ar case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_flags)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 2, 3, 1); {__pyx_filename = __pyx_f[1]; __pyx_lineno = 317; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 2, 3, 1); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: if (kw_args > 0) { @@ -6425,7 +9186,7 @@ static int __pyx_memoryview___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_ar } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 317; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else { switch (PyTuple_GET_SIZE(__pyx_args)) { @@ -6437,16 +9198,16 @@ static int __pyx_memoryview___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_ar } } __pyx_v_obj = values[0]; - __pyx_v_flags = __Pyx_PyInt_As_int(values[1]); if (unlikely((__pyx_v_flags == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 317; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_flags = __Pyx_PyInt_As_int(values[1]); if (unlikely((__pyx_v_flags == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L3_error;} if (values[2]) { - __pyx_v_dtype_is_object = __Pyx_PyObject_IsTrue(values[2]); if (unlikely((__pyx_v_dtype_is_object == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 317; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_dtype_is_object = __Pyx_PyObject_IsTrue(values[2]); if (unlikely((__pyx_v_dtype_is_object == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } else { __pyx_v_dtype_is_object = ((int)0); } } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 2, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[1]; __pyx_lineno = 317; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 2, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; __Pyx_AddTraceback("View.MemoryView.memoryview.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); @@ -6473,7 +9234,7 @@ static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview___cinit_ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__cinit__", 0); - /* "View.MemoryView":318 + /* "View.MemoryView":320 * * def __cinit__(memoryview self, object obj, int flags, bint dtype_is_object=False): * self.obj = obj # <<<<<<<<<<<<<< @@ -6486,7 +9247,7 @@ static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview___cinit_ __Pyx_DECREF(__pyx_v_self->obj); __pyx_v_self->obj = __pyx_v_obj; - /* "View.MemoryView":319 + /* "View.MemoryView":321 * def __cinit__(memoryview self, object obj, int flags, bint dtype_is_object=False): * self.obj = obj * self.flags = flags # <<<<<<<<<<<<<< @@ -6495,14 +9256,14 @@ static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview___cinit_ */ __pyx_v_self->flags = __pyx_v_flags; - /* "View.MemoryView":320 + /* "View.MemoryView":322 * self.obj = obj * self.flags = flags * if type(self) is memoryview or obj is not None: # <<<<<<<<<<<<<< * __Pyx_GetBuffer(obj, &self.view, flags) * if self.view.obj == NULL: */ - __pyx_t_2 = (((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))) == ((PyObject *)((PyObject *)__pyx_memoryview_type))); + __pyx_t_2 = (((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))) == ((PyObject *)__pyx_memoryview_type)); __pyx_t_3 = (__pyx_t_2 != 0); if (!__pyx_t_3) { } else { @@ -6515,16 +9276,16 @@ static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview___cinit_ __pyx_L4_bool_binop_done:; if (__pyx_t_1) { - /* "View.MemoryView":321 + /* "View.MemoryView":323 * self.flags = flags * if type(self) is memoryview or obj is not None: * __Pyx_GetBuffer(obj, &self.view, flags) # <<<<<<<<<<<<<< * if self.view.obj == NULL: * (<__pyx_buffer *> &self.view).obj = Py_None */ - __pyx_t_4 = __Pyx_GetBuffer(__pyx_v_obj, (&__pyx_v_self->view), __pyx_v_flags); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 321; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_GetBuffer(__pyx_v_obj, (&__pyx_v_self->view), __pyx_v_flags); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 323; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "View.MemoryView":322 + /* "View.MemoryView":324 * if type(self) is memoryview or obj is not None: * __Pyx_GetBuffer(obj, &self.view, flags) * if self.view.obj == NULL: # <<<<<<<<<<<<<< @@ -6534,7 +9295,7 @@ static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview___cinit_ __pyx_t_1 = ((((PyObject *)__pyx_v_self->view.obj) == NULL) != 0); if (__pyx_t_1) { - /* "View.MemoryView":323 + /* "View.MemoryView":325 * __Pyx_GetBuffer(obj, &self.view, flags) * if self.view.obj == NULL: * (<__pyx_buffer *> &self.view).obj = Py_None # <<<<<<<<<<<<<< @@ -6543,7 +9304,7 @@ static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview___cinit_ */ ((Py_buffer *)(&__pyx_v_self->view))->obj = Py_None; - /* "View.MemoryView":324 + /* "View.MemoryView":326 * if self.view.obj == NULL: * (<__pyx_buffer *> &self.view).obj = Py_None * Py_INCREF(Py_None) # <<<<<<<<<<<<<< @@ -6551,14 +9312,26 @@ static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview___cinit_ * self.lock = PyThread_allocate_lock() */ Py_INCREF(Py_None); - goto __pyx_L6; + + /* "View.MemoryView":324 + * if type(self) is memoryview or obj is not None: + * __Pyx_GetBuffer(obj, &self.view, flags) + * if self.view.obj == NULL: # <<<<<<<<<<<<<< + * (<__pyx_buffer *> &self.view).obj = Py_None + * Py_INCREF(Py_None) + */ } - __pyx_L6:; - goto __pyx_L3; + + /* "View.MemoryView":322 + * self.obj = obj + * self.flags = flags + * if type(self) is memoryview or obj is not None: # <<<<<<<<<<<<<< + * __Pyx_GetBuffer(obj, &self.view, flags) + * if self.view.obj == NULL: + */ } - __pyx_L3:; - /* "View.MemoryView":326 + /* "View.MemoryView":328 * Py_INCREF(Py_None) * * self.lock = PyThread_allocate_lock() # <<<<<<<<<<<<<< @@ -6567,7 +9340,7 @@ static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview___cinit_ */ __pyx_v_self->lock = PyThread_allocate_lock(); - /* "View.MemoryView":327 + /* "View.MemoryView":329 * * self.lock = PyThread_allocate_lock() * if self.lock == NULL: # <<<<<<<<<<<<<< @@ -6577,17 +9350,25 @@ static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview___cinit_ __pyx_t_1 = ((__pyx_v_self->lock == NULL) != 0); if (__pyx_t_1) { - /* "View.MemoryView":328 + /* "View.MemoryView":330 * self.lock = PyThread_allocate_lock() * if self.lock == NULL: * raise MemoryError # <<<<<<<<<<<<<< * * if flags & PyBUF_FORMAT: */ - PyErr_NoMemory(); {__pyx_filename = __pyx_f[1]; __pyx_lineno = 328; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + PyErr_NoMemory(); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 330; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "View.MemoryView":329 + * + * self.lock = PyThread_allocate_lock() + * if self.lock == NULL: # <<<<<<<<<<<<<< + * raise MemoryError + * + */ } - /* "View.MemoryView":330 + /* "View.MemoryView":332 * raise MemoryError * * if flags & PyBUF_FORMAT: # <<<<<<<<<<<<<< @@ -6597,36 +9378,44 @@ static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview___cinit_ __pyx_t_1 = ((__pyx_v_flags & PyBUF_FORMAT) != 0); if (__pyx_t_1) { - /* "View.MemoryView":331 + /* "View.MemoryView":333 * * if flags & PyBUF_FORMAT: * self.dtype_is_object = self.view.format == b'O' # <<<<<<<<<<<<<< * else: * self.dtype_is_object = dtype_is_object */ - __pyx_t_5 = __Pyx_PyBytes_FromString(__pyx_v_self->view.format); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 331; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_PyBytes_FromString(__pyx_v_self->view.format); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 333; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - __pyx_t_6 = PyObject_RichCompare(__pyx_t_5, __pyx_n_b_O, Py_EQ); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 331; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyObject_RichCompare(__pyx_t_5, __pyx_n_b_O, Py_EQ); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 333; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 331; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 333; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __pyx_v_self->dtype_is_object = __pyx_t_1; + + /* "View.MemoryView":332 + * raise MemoryError + * + * if flags & PyBUF_FORMAT: # <<<<<<<<<<<<<< + * self.dtype_is_object = self.view.format == b'O' + * else: + */ goto __pyx_L8; } - /*else*/ { - /* "View.MemoryView":333 + /* "View.MemoryView":335 * self.dtype_is_object = self.view.format == b'O' * else: * self.dtype_is_object = dtype_is_object # <<<<<<<<<<<<<< * * self.acquisition_count_aligned_p = <__pyx_atomic_int *> align_pointer( */ + /*else*/ { __pyx_v_self->dtype_is_object = __pyx_v_dtype_is_object; } __pyx_L8:; - /* "View.MemoryView":335 + /* "View.MemoryView":337 * self.dtype_is_object = dtype_is_object * * self.acquisition_count_aligned_p = <__pyx_atomic_int *> align_pointer( # <<<<<<<<<<<<<< @@ -6635,7 +9424,7 @@ static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview___cinit_ */ __pyx_v_self->acquisition_count_aligned_p = ((__pyx_atomic_int *)__pyx_align_pointer(((void *)(&(__pyx_v_self->acquisition_count[0]))), (sizeof(__pyx_atomic_int)))); - /* "View.MemoryView":337 + /* "View.MemoryView":339 * self.acquisition_count_aligned_p = <__pyx_atomic_int *> align_pointer( * &self.acquisition_count[0], sizeof(__pyx_atomic_int)) * self.typeinfo = NULL # <<<<<<<<<<<<<< @@ -6644,7 +9433,7 @@ static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview___cinit_ */ __pyx_v_self->typeinfo = NULL; - /* 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None: * __Pyx_ReleaseBuffer(&self.view) # <<<<<<<<<<<<<< @@ -6709,11 +9498,17 @@ static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__deal * if self.lock != NULL: */ __Pyx_ReleaseBuffer((&__pyx_v_self->view)); - goto __pyx_L3; + + /* "View.MemoryView":342 + * + * def __dealloc__(memoryview self): + * if self.obj is not None: # <<<<<<<<<<<<<< + * __Pyx_ReleaseBuffer(&self.view) + * + */ } - __pyx_L3:; - /* "View.MemoryView":343 + /* "View.MemoryView":345 * __Pyx_ReleaseBuffer(&self.view) * * if self.lock != NULL: # <<<<<<<<<<<<<< @@ -6723,7 +9518,7 @@ static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__deal __pyx_t_2 = ((__pyx_v_self->lock != NULL) != 0); if (__pyx_t_2) { - /* "View.MemoryView":344 + /* "View.MemoryView":346 * * if self.lock != NULL: * PyThread_free_lock(self.lock) # <<<<<<<<<<<<<< @@ -6731,11 +9526,17 @@ static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__deal * cdef char *get_item_pointer(memoryview self, object index) except NULL: */ PyThread_free_lock(__pyx_v_self->lock); - goto __pyx_L4; + + /* "View.MemoryView":345 + * __Pyx_ReleaseBuffer(&self.view) + * + * if self.lock != NULL: # <<<<<<<<<<<<<< + * PyThread_free_lock(self.lock) + * + */ } - __pyx_L4:; - /* "View.MemoryView":339 + /* "View.MemoryView":341 * self.typeinfo = NULL * * def __dealloc__(memoryview self): # <<<<<<<<<<<<<< @@ -6747,7 +9548,7 @@ static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__deal __Pyx_RefNannyFinishContext(); } -/* "View.MemoryView":346 +/* "View.MemoryView":348 * PyThread_free_lock(self.lock) * * cdef char *get_item_pointer(memoryview self, object index) except NULL: # <<<<<<<<<<<<<< @@ -6773,7 +9574,7 @@ static char *__pyx_memoryview_get_item_pointer(struct __pyx_memoryview_obj *__py int __pyx_clineno = 0; __Pyx_RefNannySetupContext("get_item_pointer", 0); - /* "View.MemoryView":348 + /* "View.MemoryView":350 * cdef char 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__pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_4 = Py_TYPE(__pyx_t_2)->tp_iternext; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 350; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = Py_TYPE(__pyx_t_2)->tp_iternext; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 352; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } for (;;) { if (likely(!__pyx_t_4)) { if (likely(PyList_CheckExact(__pyx_t_2))) { if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_2)) break; #if CYTHON_COMPILING_IN_CPYTHON - __pyx_t_5 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_5); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 350; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_5); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 352; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #else - __pyx_t_5 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 350; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 352; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); #endif } else { if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_2)) break; #if CYTHON_COMPILING_IN_CPYTHON - __pyx_t_5 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_5); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 350; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_5); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 352; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #else - __pyx_t_5 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 350; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 352; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); #endif } @@ -6823,7 +9624,7 @@ static char *__pyx_memoryview_get_item_pointer(struct __pyx_memoryview_obj *__py PyObject* exc_type = PyErr_Occurred(); if (exc_type) { if (likely(exc_type == PyExc_StopIteration || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear(); - else {__pyx_filename = __pyx_f[1]; __pyx_lineno = 350; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + else {__pyx_filename = __pyx_f[2]; __pyx_lineno = 352; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } break; } @@ -6834,18 +9635,18 @@ static char *__pyx_memoryview_get_item_pointer(struct __pyx_memoryview_obj *__py __pyx_v_dim = __pyx_t_1; __pyx_t_1 = (__pyx_t_1 + 1); - /* "View.MemoryView":351 + /* "View.MemoryView":353 * * for dim, idx in enumerate(index): * itemp = pybuffer_index(&self.view, itemp, idx, dim) # <<<<<<<<<<<<<< * * return itemp */ - __pyx_t_6 = __Pyx_PyIndex_AsSsize_t(__pyx_v_idx); if (unlikely((__pyx_t_6 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 351; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_7 = __pyx_pybuffer_index((&__pyx_v_self->view), __pyx_v_itemp, __pyx_t_6, __pyx_v_dim); if (unlikely(__pyx_t_7 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 351; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_PyIndex_AsSsize_t(__pyx_v_idx); if (unlikely((__pyx_t_6 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 353; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = __pyx_pybuffer_index((&__pyx_v_self->view), __pyx_v_itemp, __pyx_t_6, __pyx_v_dim); if (unlikely(__pyx_t_7 == NULL)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 353; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_itemp = __pyx_t_7; - /* "View.MemoryView":350 + /* "View.MemoryView":352 * cdef char *itemp = self.view.buf * * for dim, idx in enumerate(index): # <<<<<<<<<<<<<< @@ -6855,7 +9656,7 @@ static char *__pyx_memoryview_get_item_pointer(struct __pyx_memoryview_obj *__py } __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "View.MemoryView":353 + /* "View.MemoryView":355 * itemp = pybuffer_index(&self.view, itemp, idx, dim) * * return itemp # <<<<<<<<<<<<<< @@ -6865,7 +9666,7 @@ static char *__pyx_memoryview_get_item_pointer(struct __pyx_memoryview_obj *__py __pyx_r = __pyx_v_itemp; goto __pyx_L0; - /* "View.MemoryView":346 + /* "View.MemoryView":348 * PyThread_free_lock(self.lock) * * cdef char *get_item_pointer(memoryview self, object index) except NULL: # <<<<<<<<<<<<<< @@ -6885,7 +9686,7 @@ static char *__pyx_memoryview_get_item_pointer(struct __pyx_memoryview_obj *__py return __pyx_r; } -/* "View.MemoryView":356 +/* "View.MemoryView":358 * * * def __getitem__(memoryview self, object index): # <<<<<<<<<<<<<< @@ -6923,7 +9724,7 @@ static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_4_ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__getitem__", 0); - /* "View.MemoryView":357 + /* "View.MemoryView":359 * * def __getitem__(memoryview self, object index): * if index is Ellipsis: # <<<<<<<<<<<<<< @@ -6934,7 +9735,7 @@ static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_4_ __pyx_t_2 = (__pyx_t_1 != 0); if (__pyx_t_2) { - /* "View.MemoryView":358 + /* "View.MemoryView":360 * def __getitem__(memoryview self, object index): * if index is Ellipsis: * return self # <<<<<<<<<<<<<< @@ -6945,16 +9746,24 @@ static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_4_ __Pyx_INCREF(((PyObject *)__pyx_v_self)); __pyx_r = ((PyObject *)__pyx_v_self); goto __pyx_L0; + + /* "View.MemoryView":359 + * + * def __getitem__(memoryview self, object index): + * if index is Ellipsis: # <<<<<<<<<<<<<< + * return self + * + */ } - /* "View.MemoryView":360 + /* "View.MemoryView":362 * return self * * have_slices, indices = _unellipsify(index, self.view.ndim) # <<<<<<<<<<<<<< * * cdef char *itemp */ - __pyx_t_3 = _unellipsify(__pyx_v_index, __pyx_v_self->view.ndim); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = _unellipsify(__pyx_v_index, __pyx_v_self->view.ndim); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 362; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); if (likely(__pyx_t_3 != Py_None)) { PyObject* sequence = __pyx_t_3; @@ -6966,7 +9775,7 @@ static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_4_ if (unlikely(size != 2)) { if (size > 2) __Pyx_RaiseTooManyValuesError(2); else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); - {__pyx_filename = __pyx_f[1]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[2]; __pyx_lineno = 362; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } #if CYTHON_COMPILING_IN_CPYTHON __pyx_t_4 = PyTuple_GET_ITEM(sequence, 0); @@ -6974,31 +9783,31 @@ static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_4_ __Pyx_INCREF(__pyx_t_4); __Pyx_INCREF(__pyx_t_5); #else - __pyx_t_4 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 362; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_5 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 362; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); #endif __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; } else { - __Pyx_RaiseNoneNotIterableError(); {__pyx_filename = __pyx_f[1]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_RaiseNoneNotIterableError(); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 362; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_v_have_slices = __pyx_t_4; __pyx_t_4 = 0; __pyx_v_indices = __pyx_t_5; __pyx_t_5 = 0; - /* "View.MemoryView":363 + /* "View.MemoryView":365 * * cdef char *itemp * if have_slices: # <<<<<<<<<<<<<< * return memview_slice(self, indices) * else: */ - __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_have_slices); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 363; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_have_slices); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 365; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__pyx_t_2) { - /* "View.MemoryView":364 + /* "View.MemoryView":366 * cdef char *itemp * if have_slices: * return memview_slice(self, indices) # <<<<<<<<<<<<<< @@ -7006,25 +9815,33 @@ static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_4_ * itemp = self.get_item_pointer(indices) */ __Pyx_XDECREF(__pyx_r); - __pyx_t_3 = ((PyObject *)__pyx_memview_slice(__pyx_v_self, __pyx_v_indices)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = ((PyObject *)__pyx_memview_slice(__pyx_v_self, __pyx_v_indices)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 366; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_r = __pyx_t_3; __pyx_t_3 = 0; goto __pyx_L0; + + /* "View.MemoryView":365 + * + * cdef char *itemp + * if have_slices: # <<<<<<<<<<<<<< + * return memview_slice(self, indices) + * else: + */ } - /*else*/ { - /* "View.MemoryView":366 + /* "View.MemoryView":368 * return memview_slice(self, indices) * else: * itemp = self.get_item_pointer(indices) # <<<<<<<<<<<<<< * return self.convert_item_to_object(itemp) * */ - __pyx_t_6 = ((struct __pyx_vtabstruct_memoryview *)__pyx_v_self->__pyx_vtab)->get_item_pointer(__pyx_v_self, __pyx_v_indices); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 366; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + /*else*/ { + __pyx_t_6 = ((struct __pyx_vtabstruct_memoryview *)__pyx_v_self->__pyx_vtab)->get_item_pointer(__pyx_v_self, __pyx_v_indices); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 368; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_itemp = __pyx_t_6; - /* "View.MemoryView":367 + /* "View.MemoryView":369 * else: * itemp = self.get_item_pointer(indices) * return self.convert_item_to_object(itemp) # <<<<<<<<<<<<<< @@ -7032,14 +9849,14 @@ static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_4_ * def __setitem__(memoryview self, object index, object value): */ __Pyx_XDECREF(__pyx_r); - __pyx_t_3 = ((struct __pyx_vtabstruct_memoryview *)__pyx_v_self->__pyx_vtab)->convert_item_to_object(__pyx_v_self, __pyx_v_itemp); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 367; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = ((struct __pyx_vtabstruct_memoryview *)__pyx_v_self->__pyx_vtab)->convert_item_to_object(__pyx_v_self, __pyx_v_itemp); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 369; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_r = __pyx_t_3; __pyx_t_3 = 0; goto __pyx_L0; } - /* "View.MemoryView":356 + /* "View.MemoryView":358 * * * def __getitem__(memoryview self, object index): # <<<<<<<<<<<<<< @@ -7062,7 +9879,7 @@ static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_4_ return __pyx_r; } -/* "View.MemoryView":369 +/* "View.MemoryView":371 * return self.convert_item_to_object(itemp) * * def __setitem__(memoryview self, object index, object value): # <<<<<<<<<<<<<< @@ -7098,14 +9915,14 @@ static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_6__setit __Pyx_RefNannySetupContext("__setitem__", 0); __Pyx_INCREF(__pyx_v_index); - /* "View.MemoryView":370 + /* "View.MemoryView":372 * * def __setitem__(memoryview self, object index, object value): * have_slices, index = _unellipsify(index, self.view.ndim) # <<<<<<<<<<<<<< * * if have_slices: */ - __pyx_t_1 = _unellipsify(__pyx_v_index, __pyx_v_self->view.ndim); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 370; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = _unellipsify(__pyx_v_index, __pyx_v_self->view.ndim); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 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__pyx_t_2 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 372; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_3 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 370; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 372; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); #endif __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; } else { - __Pyx_RaiseNoneNotIterableError(); {__pyx_filename = __pyx_f[1]; __pyx_lineno = 370; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_RaiseNoneNotIterableError(); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 372; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_v_have_slices = __pyx_t_2; __pyx_t_2 = 0; __Pyx_DECREF_SET(__pyx_v_index, __pyx_t_3); __pyx_t_3 = 0; - /* "View.MemoryView":372 + /* "View.MemoryView":374 * have_slices, index = _unellipsify(index, self.view.ndim) * * if have_slices: # <<<<<<<<<<<<<< * obj = self.is_slice(value) * if obj: */ - __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_v_have_slices); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 372; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_v_have_slices); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 374; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__pyx_t_4) { - /* "View.MemoryView":373 + /* "View.MemoryView":375 * * if have_slices: * obj = self.is_slice(value) # <<<<<<<<<<<<<< * if obj: * self.setitem_slice_assignment(self[index], obj) */ - __pyx_t_1 = ((struct __pyx_vtabstruct_memoryview *)__pyx_v_self->__pyx_vtab)->is_slice(__pyx_v_self, __pyx_v_value); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 373; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = ((struct __pyx_vtabstruct_memoryview *)__pyx_v_self->__pyx_vtab)->is_slice(__pyx_v_self, __pyx_v_value); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_v_obj = __pyx_t_1; __pyx_t_1 = 0; - /* "View.MemoryView":374 + /* "View.MemoryView":376 * if have_slices: * obj = self.is_slice(value) * if obj: # <<<<<<<<<<<<<< * self.setitem_slice_assignment(self[index], obj) * else: */ - __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_v_obj); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 374; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_v_obj); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 376; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__pyx_t_4) { - /* "View.MemoryView":375 + /* "View.MemoryView":377 * obj = self.is_slice(value) * if obj: * self.setitem_slice_assignment(self[index], obj) # <<<<<<<<<<<<<< * else: * self.setitem_slice_assign_scalar(self[index], value) */ - __pyx_t_1 = PyObject_GetItem(((PyObject *)__pyx_v_self), __pyx_v_index); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_t_1 = PyObject_GetItem(((PyObject *)__pyx_v_self), __pyx_v_index); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 377; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __Pyx_GOTREF(__pyx_t_1); - __pyx_t_3 = ((struct __pyx_vtabstruct_memoryview *)__pyx_v_self->__pyx_vtab)->setitem_slice_assignment(__pyx_v_self, __pyx_t_1, __pyx_v_obj); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = ((struct __pyx_vtabstruct_memoryview *)__pyx_v_self->__pyx_vtab)->setitem_slice_assignment(__pyx_v_self, __pyx_t_1, __pyx_v_obj); if 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{__pyx_filename = __pyx_f[2]; __pyx_lineno = 379; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __Pyx_GOTREF(__pyx_t_3); - if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_memoryview_type))))) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 377; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_1 = ((struct __pyx_vtabstruct_memoryview *)__pyx_v_self->__pyx_vtab)->setitem_slice_assign_scalar(__pyx_v_self, ((struct __pyx_memoryview_obj *)__pyx_t_3), __pyx_v_value); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 377; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_memoryview_type))))) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 379; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = ((struct __pyx_vtabstruct_memoryview *)__pyx_v_self->__pyx_vtab)->setitem_slice_assign_scalar(__pyx_v_self, ((struct __pyx_memoryview_obj *)__pyx_t_3), __pyx_v_value); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 379; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; } __pyx_L4:; + + /* "View.MemoryView":374 + * have_slices, index = _unellipsify(index, self.view.ndim) + * + * if have_slices: # <<<<<<<<<<<<<< + * obj = self.is_slice(value) + * if obj: + */ goto __pyx_L3; } - /*else*/ { - /* "View.MemoryView":379 + /* "View.MemoryView":381 * self.setitem_slice_assign_scalar(self[index], value) * else: * self.setitem_indexed(index, value) # <<<<<<<<<<<<<< * * cdef is_slice(self, obj): */ - __pyx_t_1 = ((struct __pyx_vtabstruct_memoryview *)__pyx_v_self->__pyx_vtab)->setitem_indexed(__pyx_v_self, __pyx_v_index, __pyx_v_value); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 379; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + /*else*/ { + __pyx_t_1 = ((struct __pyx_vtabstruct_memoryview *)__pyx_v_self->__pyx_vtab)->setitem_indexed(__pyx_v_self, __pyx_v_index, __pyx_v_value); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 381; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; } __pyx_L3:; - /* "View.MemoryView":369 + /* "View.MemoryView":371 * return self.convert_item_to_object(itemp) * * def __setitem__(memoryview self, object index, object value): # <<<<<<<<<<<<<< @@ -7246,7 +10079,7 @@ static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_6__setit return __pyx_r; } -/* "View.MemoryView":381 +/* "View.MemoryView":383 * self.setitem_indexed(index, value) * * cdef is_slice(self, obj): # <<<<<<<<<<<<<< @@ -7272,18 +10105,18 @@ static PyObject *__pyx_memoryview_is_slice(struct __pyx_memoryview_obj *__pyx_v_ __Pyx_RefNannySetupContext("is_slice", 0); __Pyx_INCREF(__pyx_v_obj); - /* "View.MemoryView":382 + /* "View.MemoryView":384 * * cdef is_slice(self, obj): * if not isinstance(obj, memoryview): # <<<<<<<<<<<<<< * try: * obj = memoryview(obj, self.flags|PyBUF_ANY_CONTIGUOUS, */ - __pyx_t_1 = __Pyx_TypeCheck(__pyx_v_obj, ((PyObject *)__pyx_memoryview_type)); + __pyx_t_1 = __Pyx_TypeCheck(__pyx_v_obj, __pyx_memoryview_type); __pyx_t_2 = ((!(__pyx_t_1 != 0)) != 0); if (__pyx_t_2) { - /* "View.MemoryView":383 + /* "View.MemoryView":385 * cdef is_slice(self, obj): * if not isinstance(obj, memoryview): * try: # <<<<<<<<<<<<<< @@ -7297,34 +10130,34 @@ static PyObject *__pyx_memoryview_is_slice(struct __pyx_memoryview_obj *__pyx_v_ __Pyx_XGOTREF(__pyx_t_5); /*try:*/ { - /* "View.MemoryView":384 + /* "View.MemoryView":386 * if not isinstance(obj, memoryview): * try: * obj = memoryview(obj, self.flags|PyBUF_ANY_CONTIGUOUS, # <<<<<<<<<<<<<< * self.dtype_is_object) * except TypeError: */ - __pyx_t_6 = __Pyx_PyInt_From_int((__pyx_v_self->flags | PyBUF_ANY_CONTIGUOUS)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 384; __pyx_clineno = __LINE__; goto __pyx_L4_error;} + __pyx_t_6 = __Pyx_PyInt_From_int((__pyx_v_self->flags | PyBUF_ANY_CONTIGUOUS)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L4_error;} __Pyx_GOTREF(__pyx_t_6); - /* "View.MemoryView":385 + /* "View.MemoryView":387 * try: * obj = memoryview(obj, self.flags|PyBUF_ANY_CONTIGUOUS, * self.dtype_is_object) # <<<<<<<<<<<<<< * except TypeError: * return None */ - __pyx_t_7 = __Pyx_PyBool_FromLong(__pyx_v_self->dtype_is_object); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 385; __pyx_clineno = __LINE__; goto __pyx_L4_error;} + __pyx_t_7 = __Pyx_PyBool_FromLong(__pyx_v_self->dtype_is_object); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 387; __pyx_clineno = __LINE__; goto __pyx_L4_error;} __Pyx_GOTREF(__pyx_t_7); - /* "View.MemoryView":384 + /* "View.MemoryView":386 * if not isinstance(obj, memoryview): * try: * obj = memoryview(obj, 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(unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L4_error;} __Pyx_GOTREF(__pyx_t_7); __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; __Pyx_DECREF_SET(__pyx_v_obj, __pyx_t_7); __pyx_t_7 = 0; + + /* "View.MemoryView":385 + * cdef is_slice(self, obj): + * if not isinstance(obj, memoryview): + * try: # <<<<<<<<<<<<<< + * obj = memoryview(obj, self.flags|PyBUF_ANY_CONTIGUOUS, + * self.dtype_is_object) + */ } __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0; @@ -7350,7 +10191,7 @@ static PyObject *__pyx_memoryview_is_slice(struct __pyx_memoryview_obj *__pyx_v_ __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0; __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0; - /* "View.MemoryView":386 + /* "View.MemoryView":388 * obj = memoryview(obj, self.flags|PyBUF_ANY_CONTIGUOUS, * self.dtype_is_object) * except TypeError: # <<<<<<<<<<<<<< @@ -7360,12 +10201,12 @@ static PyObject *__pyx_memoryview_is_slice(struct __pyx_memoryview_obj 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{__pyx_filename = __pyx_f[2]; __pyx_lineno = 397; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "View.MemoryView":396 + /* "View.MemoryView":398 * * memoryview_copy_contents(get_slice_from_memview(src, &src_slice)[0], * get_slice_from_memview(dst, &dst_slice)[0], # <<<<<<<<<<<<<< * src.ndim, dst.ndim, self.dtype_is_object) * */ - if (!(likely(((__pyx_v_dst) == Py_None) || likely(__Pyx_TypeTest(__pyx_v_dst, __pyx_memoryview_type))))) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 396; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_v_dst) == Py_None) || likely(__Pyx_TypeTest(__pyx_v_dst, __pyx_memoryview_type))))) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 398; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "View.MemoryView":397 + /* "View.MemoryView":399 * memoryview_copy_contents(get_slice_from_memview(src, &src_slice)[0], * get_slice_from_memview(dst, &dst_slice)[0], * src.ndim, dst.ndim, self.dtype_is_object) # <<<<<<<<<<<<<< * * cdef 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(unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 397; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_dst, __pyx_n_s_ndim); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 399; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_3 = __Pyx_PyInt_As_int(__pyx_t_1); if (unlikely((__pyx_t_3 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 397; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyInt_As_int(__pyx_t_1); if (unlikely((__pyx_t_3 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 399; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "View.MemoryView":395 + /* "View.MemoryView":397 * cdef __Pyx_memviewslice src_slice * * memoryview_copy_contents(get_slice_from_memview(src, &src_slice)[0], # <<<<<<<<<<<<<< * get_slice_from_memview(dst, 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PyErr_NoMemory(); {__pyx_filename = __pyx_f[1]; __pyx_lineno = 411; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + PyErr_NoMemory(); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 413; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "View.MemoryView":412 + * if self.view.itemsize > sizeof(array): + * tmp = PyMem_Malloc(self.view.itemsize) + * if tmp == NULL: # <<<<<<<<<<<<<< + * raise MemoryError + * item = tmp + */ } - /* "View.MemoryView":412 + /* "View.MemoryView":414 * if tmp == NULL: * raise MemoryError * item = tmp # <<<<<<<<<<<<<< @@ -7616,22 +10479,30 @@ static PyObject *__pyx_memoryview_setitem_slice_assign_scalar(struct __pyx_memor * item = array */ __pyx_v_item = __pyx_v_tmp; + + /* "View.MemoryView":410 + * dst_slice = get_slice_from_memview(dst, &tmp_slice) + * + * if self.view.itemsize > sizeof(array): # <<<<<<<<<<<<<< + * tmp = PyMem_Malloc(self.view.itemsize) + * if tmp == NULL: + */ goto __pyx_L3; } - /*else*/ { - /* "View.MemoryView":414 + /* 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__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - goto __pyx_L9; + + /* "View.MemoryView":426 + * + * + * if self.view.suboffsets != NULL: # <<<<<<<<<<<<<< + * assert_direct_dimensions(self.view.suboffsets, self.view.ndim) + * slice_assign_scalar(dst_slice, dst.view.ndim, self.view.itemsize, + */ } - __pyx_L9:; - /* "View.MemoryView":426 + /* "View.MemoryView":428 * if self.view.suboffsets != NULL: * assert_direct_dimensions(self.view.suboffsets, self.view.ndim) * slice_assign_scalar(dst_slice, dst.view.ndim, self.view.itemsize, # <<<<<<<<<<<<<< @@ -7709,7 +10594,7 @@ static PyObject *__pyx_memoryview_setitem_slice_assign_scalar(struct __pyx_memor __pyx_memoryview_slice_assign_scalar(__pyx_v_dst_slice, __pyx_v_dst->view.ndim, __pyx_v_self->view.itemsize, __pyx_v_item, __pyx_v_self->dtype_is_object); } - /* "View.MemoryView":429 + /* "View.MemoryView":431 * item, self.dtype_is_object) * finally: * PyMem_Free(tmp) # <<<<<<<<<<<<<< @@ -7754,7 +10639,7 @@ static PyObject 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__LINE__; goto __pyx_L1_error;} + __pyx_t_2 = ((struct __pyx_vtabstruct_memoryview *)__pyx_v_self->__pyx_vtab)->assign_item_from_object(__pyx_v_self, __pyx_v_itemp, __pyx_v_value); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 435; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "View.MemoryView":431 + /* "View.MemoryView":433 * PyMem_Free(tmp) * * cdef setitem_indexed(self, index, value): # <<<<<<<<<<<<<< @@ -7836,7 +10721,7 @@ static PyObject *__pyx_memoryview_setitem_indexed(struct __pyx_memoryview_obj *_ return __pyx_r; } -/* "View.MemoryView":435 +/* "View.MemoryView":437 * self.assign_item_from_object(itemp, value) * * cdef convert_item_to_object(self, char *itemp): # <<<<<<<<<<<<<< @@ -7867,31 +10752,31 @@ static PyObject *__pyx_memoryview_convert_item_to_object(struct __pyx_memoryview int __pyx_clineno = 0; __Pyx_RefNannySetupContext("convert_item_to_object", 0); - /* 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__pyx_lineno = 441; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyBytes_FromStringAndSize(__pyx_v_itemp + 0, __pyx_v_self->view.itemsize - 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 443; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_v_bytesitem = ((PyObject*)__pyx_t_1); __pyx_t_1 = 0; - /* "View.MemoryView":442 + /* "View.MemoryView":444 * * bytesitem = itemp[:self.view.itemsize] * try: # <<<<<<<<<<<<<< @@ -7905,16 +10790,16 @@ static PyObject *__pyx_memoryview_convert_item_to_object(struct __pyx_memoryview __Pyx_XGOTREF(__pyx_t_4); /*try:*/ { - /* "View.MemoryView":443 + /* "View.MemoryView":445 * bytesitem = itemp[:self.view.itemsize] * try: * result = struct.unpack(self.view.format, bytesitem) # <<<<<<<<<<<<<< * except struct.error: * raise ValueError("Unable to convert item to object") */ - __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_struct, __pyx_n_s_unpack); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 443; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_struct, __pyx_n_s_unpack); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 445; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __Pyx_GOTREF(__pyx_t_5); - __pyx_t_6 = __Pyx_PyBytes_FromString(__pyx_v_self->view.format); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 443; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_t_6 = __Pyx_PyBytes_FromString(__pyx_v_self->view.format); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 445; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __Pyx_GOTREF(__pyx_t_6); __pyx_t_7 = NULL; __pyx_t_8 = 0; @@ -7928,7 +10813,7 @@ static PyObject *__pyx_memoryview_convert_item_to_object(struct __pyx_memoryview __pyx_t_8 = 1; } } - __pyx_t_9 = PyTuple_New(2+__pyx_t_8); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 443; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_t_9 = PyTuple_New(2+__pyx_t_8); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 445; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __Pyx_GOTREF(__pyx_t_9); if (__pyx_t_7) { __Pyx_GIVEREF(__pyx_t_7); PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_7); __pyx_t_7 = NULL; @@ -7939,27 +10824,35 @@ static PyObject *__pyx_memoryview_convert_item_to_object(struct __pyx_memoryview __Pyx_GIVEREF(__pyx_v_bytesitem); PyTuple_SET_ITEM(__pyx_t_9, 1+__pyx_t_8, __pyx_v_bytesitem); __pyx_t_6 = 0; - __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_5, __pyx_t_9, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 443; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_5, __pyx_t_9, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 445; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __pyx_v_result = __pyx_t_1; __pyx_t_1 = 0; + + /* "View.MemoryView":444 + * + * bytesitem = itemp[:self.view.itemsize] + * try: # <<<<<<<<<<<<<< + * result = struct.unpack(self.view.format, bytesitem) + * except struct.error: + */ } - /*else:*/ { - /* "View.MemoryView":447 + /* "View.MemoryView":449 * raise ValueError("Unable to convert item to object") * else: * if len(self.view.format) == 1: # <<<<<<<<<<<<<< * return result[0] * return result */ + /*else:*/ { __pyx_t_10 = strlen(__pyx_v_self->view.format); __pyx_t_11 = ((__pyx_t_10 == 1) != 0); if (__pyx_t_11) { - /* "View.MemoryView":448 + /* "View.MemoryView":450 * else: * if len(self.view.format) == 1: * return result[0] # <<<<<<<<<<<<<< @@ -7967,14 +10860,22 @@ static PyObject *__pyx_memoryview_convert_item_to_object(struct __pyx_memoryview * */ __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_result, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 448; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;}; + __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_result, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 450; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;}; __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; goto __pyx_L6_except_return; + + /* "View.MemoryView":449 + * raise ValueError("Unable to convert item to object") + * else: + * if len(self.view.format) == 1: # <<<<<<<<<<<<<< + * return result[0] + * return result + */ } - /* "View.MemoryView":449 + /* "View.MemoryView":451 * if len(self.view.format) == 1: * return result[0] * return result # <<<<<<<<<<<<<< @@ -7993,39 +10894,47 @@ static PyObject *__pyx_memoryview_convert_item_to_object(struct __pyx_memoryview __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0; __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "View.MemoryView":444 + /* "View.MemoryView":446 * try: * result = struct.unpack(self.view.format, bytesitem) * except struct.error: # <<<<<<<<<<<<<< * raise ValueError("Unable to convert item to object") * else: */ - __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_struct, __pyx_n_s_error); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 444; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;} + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_struct, __pyx_n_s_error); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 446; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_12 = PyErr_ExceptionMatches(__pyx_t_1); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; if (__pyx_t_12) { __Pyx_AddTraceback("View.MemoryView.memoryview.convert_item_to_object", __pyx_clineno, __pyx_lineno, __pyx_filename); - if (__Pyx_GetException(&__pyx_t_1, &__pyx_t_5, &__pyx_t_9) < 0) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 444; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;} + if (__Pyx_GetException(&__pyx_t_1, &__pyx_t_5, &__pyx_t_9) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 446; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_GOTREF(__pyx_t_5); __Pyx_GOTREF(__pyx_t_9); - /* "View.MemoryView":445 + /* "View.MemoryView":447 * result = struct.unpack(self.view.format, bytesitem) * except struct.error: * raise ValueError("Unable to convert item to object") # <<<<<<<<<<<<<< * else: * if len(self.view.format) == 1: */ - __pyx_t_6 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__6, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 445; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;} + __pyx_t_6 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__13, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 447; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_Raise(__pyx_t_6, 0, 0, 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__pyx_t_1 = 0; __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - if (!(likely(PyBytes_CheckExact(__pyx_t_4))||((__pyx_t_4) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "bytes", Py_TYPE(__pyx_t_4)->tp_name), 0))) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 460; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(PyBytes_CheckExact(__pyx_t_4))||((__pyx_t_4) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "bytes", Py_TYPE(__pyx_t_4)->tp_name), 0))) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 462; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_bytesvalue = ((PyObject*)__pyx_t_4); __pyx_t_4 = 0; + + /* "View.MemoryView":461 + * cdef Py_ssize_t i + * + * if isinstance(value, tuple): # <<<<<<<<<<<<<< + * bytesvalue = struct.pack(self.view.format, *value) + * else: + */ goto __pyx_L3; } - /*else*/ { - /* "View.MemoryView":462 + /* "View.MemoryView":464 * bytesvalue = struct.pack(self.view.format, *value) * else: * bytesvalue 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PyObject *__pyx_memoryview_assign_item_from_object(struct __pyx_memoryvie __pyx_t_7 = 1; } } - __pyx_t_8 = PyTuple_New(2+__pyx_t_7); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 462; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_8 = PyTuple_New(2+__pyx_t_7); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 464; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_8); if (__pyx_t_5) { __Pyx_GIVEREF(__pyx_t_5); PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_5); __pyx_t_5 = NULL; @@ -8188,17 +11105,17 @@ static PyObject *__pyx_memoryview_assign_item_from_object(struct __pyx_memoryvie __Pyx_GIVEREF(__pyx_v_value); PyTuple_SET_ITEM(__pyx_t_8, 1+__pyx_t_7, __pyx_v_value); __pyx_t_1 = 0; - __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_t_8, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 462; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_t_8, 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"View.MemoryView":466 * bytesvalue = struct.pack(self.view.format, value) * * for i, c in enumerate(bytesvalue): # <<<<<<<<<<<<<< @@ -8236,7 +11153,7 @@ static PyObject *__pyx_memoryview_assign_item_from_object(struct __pyx_memoryvie */ __pyx_t_7 = (__pyx_t_7 + 1); - /* "View.MemoryView":465 + /* "View.MemoryView":467 * * for i, c in enumerate(bytesvalue): * itemp[i] = c # <<<<<<<<<<<<<< @@ -8247,7 +11164,7 @@ static PyObject *__pyx_memoryview_assign_item_from_object(struct __pyx_memoryvie } __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - /* "View.MemoryView":451 + /* "View.MemoryView":453 * return result * * cdef assign_item_from_object(self, char *itemp, object value): # <<<<<<<<<<<<<< @@ -8275,7 +11192,7 @@ static PyObject *__pyx_memoryview_assign_item_from_object(struct __pyx_memoryvie return __pyx_r; } -/* "View.MemoryView":468 +/* "View.MemoryView":470 * * @cname('getbuffer') * def __getbuffer__(self, Py_buffer *info, int flags): # <<<<<<<<<<<<<< @@ -8311,7 +11228,7 @@ static int 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self.view.shape + * else: + */ goto __pyx_L3; } - /*else*/ { - /* "View.MemoryView":472 + /* "View.MemoryView":474 * info.shape = self.view.shape * else: * info.shape = NULL # <<<<<<<<<<<<<< * * if flags & PyBUF_STRIDES: */ + /*else*/ { __pyx_v_info->shape = NULL; } __pyx_L3:; - /* "View.MemoryView":474 + /* "View.MemoryView":476 * info.shape = NULL * * if flags & PyBUF_STRIDES: # <<<<<<<<<<<<<< @@ -8355,7 +11280,7 @@ static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_8__getbu __pyx_t_1 = ((__pyx_v_flags & PyBUF_STRIDES) != 0); if (__pyx_t_1) { - /* "View.MemoryView":475 + /* "View.MemoryView":477 * * if flags & PyBUF_STRIDES: * info.strides = self.view.strides # <<<<<<<<<<<<<< @@ -8364,22 +11289,30 @@ static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_8__getbu */ __pyx_t_2 = __pyx_v_self->view.strides; __pyx_v_info->strides = __pyx_t_2; + + /* "View.MemoryView":476 + * info.shape = NULL + * + * if flags & PyBUF_STRIDES: # <<<<<<<<<<<<<< + * info.strides = self.view.strides + * else: + */ goto __pyx_L4; } - /*else*/ { - /* "View.MemoryView":477 + /* "View.MemoryView":479 * info.strides = self.view.strides * else: * info.strides = NULL # <<<<<<<<<<<<<< * * if flags & PyBUF_INDIRECT: */ + /*else*/ { __pyx_v_info->strides = NULL; } __pyx_L4:; - /* "View.MemoryView":479 + /* "View.MemoryView":481 * info.strides = NULL * * if flags & PyBUF_INDIRECT: # <<<<<<<<<<<<<< @@ -8389,7 +11322,7 @@ static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_8__getbu __pyx_t_1 = ((__pyx_v_flags & PyBUF_INDIRECT) != 0); if (__pyx_t_1) { - /* "View.MemoryView":480 + /* "View.MemoryView":482 * * if flags & PyBUF_INDIRECT: * info.suboffsets = self.view.suboffsets # <<<<<<<<<<<<<< @@ -8398,22 +11331,30 @@ static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_8__getbu */ __pyx_t_2 = __pyx_v_self->view.suboffsets; __pyx_v_info->suboffsets = __pyx_t_2; + + /* "View.MemoryView":481 + * info.strides = NULL + * + * if flags & PyBUF_INDIRECT: # <<<<<<<<<<<<<< + * info.suboffsets = self.view.suboffsets + * else: + */ goto __pyx_L5; } - /*else*/ { - /* "View.MemoryView":482 + /* "View.MemoryView":484 * info.suboffsets = self.view.suboffsets * else: * info.suboffsets = NULL # <<<<<<<<<<<<<< * * if flags & PyBUF_FORMAT: */ + /*else*/ { __pyx_v_info->suboffsets = NULL; } __pyx_L5:; - /* "View.MemoryView":484 + /* "View.MemoryView":486 * info.suboffsets = NULL * * if flags & PyBUF_FORMAT: # <<<<<<<<<<<<<< @@ -8423,7 +11364,7 @@ static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_8__getbu __pyx_t_1 = ((__pyx_v_flags & PyBUF_FORMAT) != 0); if (__pyx_t_1) { - /* "View.MemoryView":485 + /* "View.MemoryView":487 * * if flags & PyBUF_FORMAT: * info.format = self.view.format # <<<<<<<<<<<<<< @@ -8432,22 +11373,30 @@ static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_8__getbu */ __pyx_t_3 = __pyx_v_self->view.format; __pyx_v_info->format = __pyx_t_3; + + /* 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__pyx_t_1 = 0; - /* "View.MemoryView":503 + /* "View.MemoryView":505 * def __get__(self): * cdef _memoryviewslice result = memoryview_copy(self) * transpose_memslice(&result.from_slice) # <<<<<<<<<<<<<< * return result * */ - __pyx_t_2 = __pyx_memslice_transpose((&__pyx_v_result->from_slice)); if (unlikely(__pyx_t_2 == 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 503; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __pyx_memslice_transpose((&__pyx_v_result->from_slice)); if (unlikely(__pyx_t_2 == 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 505; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "View.MemoryView":504 + /* "View.MemoryView":506 * cdef _memoryviewslice result = memoryview_copy(self) * transpose_memslice(&result.from_slice) * return result # <<<<<<<<<<<<<< @@ -8593,7 +11542,7 @@ static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_1T___get__(struct _ __pyx_r = ((PyObject *)__pyx_v_result); goto __pyx_L0; - /* "View.MemoryView":501 + /* 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(unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 516; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_3 = (__pyx_v_self->view.shape + __pyx_v_self->view.ndim); for (__pyx_t_4 = __pyx_v_self->view.shape; __pyx_t_4 < __pyx_t_3; __pyx_t_4++) { __pyx_t_2 = __pyx_t_4; __pyx_v_length = (__pyx_t_2[0]); - __pyx_t_5 = PyInt_FromSsize_t(__pyx_v_length); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyInt_FromSsize_t(__pyx_v_length); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 516; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - if (unlikely(__Pyx_ListComp_Append(__pyx_t_1, (PyObject*)__pyx_t_5))) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_ListComp_Append(__pyx_t_1, (PyObject*)__pyx_t_5))) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 516; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; } - __pyx_t_5 = PyList_AsTuple(((PyObject*)__pyx_t_1)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyList_AsTuple(((PyObject*)__pyx_t_1)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 516; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_r = __pyx_t_5; __pyx_t_5 = 0; goto __pyx_L0; - /* "View.MemoryView":513 + /* "View.MemoryView":515 * property shape: * @cname('__pyx_memoryview_get_shape') * def __get__(self): # <<<<<<<<<<<<<< @@ -8747,7 +11696,7 @@ static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_5shape___get__(stru return __pyx_r; } -/* "View.MemoryView":518 +/* "View.MemoryView":520 * property strides: * @cname('__pyx_memoryview_get_strides') * def __get__(self): # 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__pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_4, __pyx_t_5); __Pyx_INCREF(__pyx_t_7); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 637; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #else - __pyx_t_7 = PySequence_ITEM(__pyx_t_4, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 635; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = PySequence_ITEM(__pyx_t_4, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 637; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); #endif } @@ -10170,7 +13157,7 @@ static PyObject *_unellipsify(PyObject *__pyx_v_index, int __pyx_v_ndim) { PyObject* exc_type = PyErr_Occurred(); if (exc_type) { if (likely(exc_type == PyExc_StopIteration || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear(); - else {__pyx_filename = __pyx_f[1]; 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= __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = __Pyx_PyList_Extend(__pyx_v_result, __pyx_t_7); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 640; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; - /* "View.MemoryView":639 + /* "View.MemoryView":641 * if not seen_ellipsis: * result.extend([slice(None)] * (ndim - len(tup) + 1)) * seen_ellipsis = True # <<<<<<<<<<<<<< @@ -10235,22 +13222,30 @@ static PyObject *_unellipsify(PyObject *__pyx_v_index, int __pyx_v_ndim) { * result.append(slice(None)) */ __pyx_v_seen_ellipsis = 1; + + /* "View.MemoryView":639 + * for idx, item in enumerate(tup): + * if item is Ellipsis: + * if not seen_ellipsis: # <<<<<<<<<<<<<< + * result.extend([slice(None)] * (ndim - len(tup) + 1)) + * seen_ellipsis = True + */ goto __pyx_L7; } - /*else*/ { - /* "View.MemoryView":641 + /* "View.MemoryView":643 * seen_ellipsis = True * else: * result.append(slice(None)) # <<<<<<<<<<<<<< * have_slices = True 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__Pyx_PyString_Format(__pyx_kp_s_Cannot_index_with_type_s, ((PyObject *)Py_TYPE(__pyx_v_item))); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); - __pyx_t_11 = PyTuple_New(1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 645; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_11 = PyTuple_New(1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_11); __Pyx_GIVEREF(__pyx_t_7); PyTuple_SET_ITEM(__pyx_t_11, 0, __pyx_t_7); __pyx_t_7 = 0; - __pyx_t_7 = __Pyx_PyObject_Call(__pyx_builtin_TypeError, __pyx_t_11, NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 645; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = __Pyx_PyObject_Call(__pyx_builtin_TypeError, __pyx_t_11, NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0; __Pyx_Raise(__pyx_t_7, 0, 0, 0); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; - {__pyx_filename = __pyx_f[1]; __pyx_lineno = 645; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[2]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "View.MemoryView":646 + * have_slices = True + * else: + * if not isinstance(item, slice) and not PyIndex_Check(item): # <<<<<<<<<<<<<< + * raise TypeError("Cannot index with type '%s'" % type(item)) + * + */ } - /* "View.MemoryView":647 + /* "View.MemoryView":649 * raise TypeError("Cannot index with type '%s'" % type(item)) * * have_slices = have_slices or isinstance(item, slice) # <<<<<<<<<<<<<< @@ -10322,18 +13333,18 @@ static PyObject *_unellipsify(PyObject *__pyx_v_index, int __pyx_v_ndim) { __pyx_L11_bool_binop_done:; __pyx_v_have_slices = __pyx_t_1; - /* 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__pyx_t_3); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 654; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - goto __pyx_L13; + + /* "View.MemoryView":653 + * + * nslices = ndim - len(result) + * if nslices: # <<<<<<<<<<<<<< + * result.extend([slice(None)] * nslices) + * + */ } - __pyx_L13:; - /* "View.MemoryView":654 + /* "View.MemoryView":656 * result.extend([slice(None)] * nslices) * * return have_slices or nslices, tuple(result) # <<<<<<<<<<<<<< @@ -10396,20 +13413,20 @@ static PyObject *_unellipsify(PyObject *__pyx_v_index, int __pyx_v_ndim) { __Pyx_XDECREF(__pyx_r); if (!__pyx_v_have_slices) { } else { - __pyx_t_4 = __Pyx_PyBool_FromLong(__pyx_v_have_slices); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 654; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyBool_FromLong(__pyx_v_have_slices); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 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(unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 654; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 656; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); __Pyx_GIVEREF(__pyx_t_3); PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_3); @@ -10421,7 +13438,7 @@ static PyObject *_unellipsify(PyObject *__pyx_v_index, int __pyx_v_ndim) { __pyx_t_7 = 0; goto __pyx_L0; - /* "View.MemoryView":622 + /* "View.MemoryView":624 * return isinstance(o, memoryview) * * cdef tuple _unellipsify(object index, int ndim): # <<<<<<<<<<<<<< @@ -10447,7 +13464,7 @@ static PyObject *_unellipsify(PyObject *__pyx_v_index, int __pyx_v_ndim) { return __pyx_r; } -/* "View.MemoryView":656 +/* "View.MemoryView":658 * return have_slices or nslices, tuple(result) * * cdef assert_direct_dimensions(Py_ssize_t *suboffsets, int ndim): # <<<<<<<<<<<<<< @@ -10469,7 +13486,7 @@ static PyObject 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dimensions not supported") # <<<<<<<<<<<<<< * * */ - __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__12, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 659; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__19, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 661; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_Raise(__pyx_t_5, 0, 0, 0); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - {__pyx_filename = __pyx_f[1]; __pyx_lineno = 659; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[2]; __pyx_lineno = 661; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "View.MemoryView":660 + * cdef assert_direct_dimensions(Py_ssize_t *suboffsets, int ndim): + * for suboffset in suboffsets[:ndim]: + * if suboffset >= 0: # <<<<<<<<<<<<<< + * raise ValueError("Indirect dimensions not supported") + * + */ } } - /* "View.MemoryView":656 + /* "View.MemoryView":658 * return have_slices or nslices, tuple(result) * * cdef assert_direct_dimensions(Py_ssize_t *suboffsets, int ndim): # <<<<<<<<<<<<<< @@ -10527,7 +13552,7 @@ static PyObject *assert_direct_dimensions(Py_ssize_t *__pyx_v_suboffsets, int __ return __pyx_r; } -/* "View.MemoryView":666 +/* "View.MemoryView":668 * * @cname('__pyx_memview_slice') * cdef memoryview memview_slice(memoryview memview, object indices): # <<<<<<<<<<<<<< @@ -10571,7 +13596,7 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("memview_slice", 0); - /* "View.MemoryView":667 + /* "View.MemoryView":669 * @cname('__pyx_memview_slice') * cdef memoryview memview_slice(memoryview memview, object indices): * cdef int new_ndim = 0, suboffset_dim = -1, dim # <<<<<<<<<<<<<< @@ -10581,7 +13606,7 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ __pyx_v_new_ndim = 0; __pyx_v_suboffset_dim = -1; - /* "View.MemoryView":674 + /* "View.MemoryView":676 * * * memset(&dst, 0, sizeof(dst)) # <<<<<<<<<<<<<< @@ -10590,7 +13615,7 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ */ memset((&__pyx_v_dst), 0, (sizeof(__pyx_v_dst))); - /* "View.MemoryView":678 + /* "View.MemoryView":680 * cdef _memoryviewslice memviewsliceobj * * assert memview.view.ndim > 0 # <<<<<<<<<<<<<< @@ -10601,36 +13626,36 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ if (unlikely(!Py_OptimizeFlag)) { if (unlikely(!((__pyx_v_memview->view.ndim > 0) != 0))) { PyErr_SetNone(PyExc_AssertionError); - {__pyx_filename = __pyx_f[1]; __pyx_lineno = 678; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[2]; __pyx_lineno = 680; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } } #endif - /* "View.MemoryView":680 + /* "View.MemoryView":682 * assert memview.view.ndim > 0 * * if 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683; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_3 = ((PyObject *)__pyx_v_memview); __Pyx_INCREF(__pyx_t_3); __pyx_v_memviewsliceobj = ((struct __pyx_memoryviewslice_obj *)__pyx_t_3); __pyx_t_3 = 0; - /* "View.MemoryView":682 + /* "View.MemoryView":684 * if isinstance(memview, _memoryviewslice): * memviewsliceobj = memview * p_src = &memviewsliceobj.from_slice # <<<<<<<<<<<<<< @@ -10638,20 +13663,28 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ * slice_copy(memview, &src) */ __pyx_v_p_src = (&__pyx_v_memviewsliceobj->from_slice); + + /* "View.MemoryView":682 + * assert memview.view.ndim > 0 + * + * if isinstance(memview, _memoryviewslice): # <<<<<<<<<<<<<< + * memviewsliceobj = memview + * p_src = &memviewsliceobj.from_slice + */ goto __pyx_L3; } - /*else*/ { - /* "View.MemoryView":684 + /* "View.MemoryView":686 * p_src = &memviewsliceobj.from_slice * else: * slice_copy(memview, &src) # <<<<<<<<<<<<<< * p_src = &src * */ + /*else*/ { __pyx_memoryview_slice_copy(__pyx_v_memview, (&__pyx_v_src)); - /* "View.MemoryView":685 + /* "View.MemoryView":687 * else: * slice_copy(memview, &src) * p_src = &src # <<<<<<<<<<<<<< @@ -10662,7 +13695,7 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ } __pyx_L3:; - /* "View.MemoryView":691 + /* "View.MemoryView":693 * * * dst.memview = p_src.memview # <<<<<<<<<<<<<< @@ -10672,7 +13705,7 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ __pyx_t_4 = __pyx_v_p_src->memview; __pyx_v_dst.memview = __pyx_t_4; - /* "View.MemoryView":692 + /* "View.MemoryView":694 * * dst.memview = p_src.memview * dst.data = p_src.data # <<<<<<<<<<<<<< @@ -10682,7 +13715,7 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ __pyx_t_5 = __pyx_v_p_src->data; __pyx_v_dst.data = __pyx_t_5; - /* "View.MemoryView":697 + /* "View.MemoryView":699 * * * cdef __Pyx_memviewslice *p_dst = &dst # <<<<<<<<<<<<<< @@ -10691,7 +13724,7 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ */ __pyx_v_p_dst = (&__pyx_v_dst); - /* "View.MemoryView":698 + /* "View.MemoryView":700 * * cdef __Pyx_memviewslice *p_dst = &dst * cdef int *p_suboffset_dim = &suboffset_dim # <<<<<<<<<<<<<< @@ -10700,7 +13733,7 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ */ __pyx_v_p_suboffset_dim = (&__pyx_v_suboffset_dim); - /* "View.MemoryView":702 + /* "View.MemoryView":704 * cdef bint have_start, have_stop, have_step * * for dim, index in enumerate(indices): # <<<<<<<<<<<<<< @@ -10712,26 +13745,26 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ __pyx_t_3 = __pyx_v_indices; __Pyx_INCREF(__pyx_t_3); __pyx_t_7 = 0; __pyx_t_8 = NULL; } else { - __pyx_t_7 = -1; __pyx_t_3 = PyObject_GetIter(__pyx_v_indices); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = -1; __pyx_t_3 = PyObject_GetIter(__pyx_v_indices); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 704; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_8 = Py_TYPE(__pyx_t_3)->tp_iternext; if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_8 = Py_TYPE(__pyx_t_3)->tp_iternext; if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 704; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } for (;;) { if (likely(!__pyx_t_8)) { if (likely(PyList_CheckExact(__pyx_t_3))) { if (__pyx_t_7 >= PyList_GET_SIZE(__pyx_t_3)) break; #if CYTHON_COMPILING_IN_CPYTHON - __pyx_t_9 = PyList_GET_ITEM(__pyx_t_3, __pyx_t_7); __Pyx_INCREF(__pyx_t_9); __pyx_t_7++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = PyList_GET_ITEM(__pyx_t_3, __pyx_t_7); __Pyx_INCREF(__pyx_t_9); __pyx_t_7++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 704; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #else - __pyx_t_9 = PySequence_ITEM(__pyx_t_3, __pyx_t_7); __pyx_t_7++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = PySequence_ITEM(__pyx_t_3, __pyx_t_7); __pyx_t_7++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 704; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); #endif } else { if (__pyx_t_7 >= PyTuple_GET_SIZE(__pyx_t_3)) break; #if CYTHON_COMPILING_IN_CPYTHON - __pyx_t_9 = PyTuple_GET_ITEM(__pyx_t_3, __pyx_t_7); __Pyx_INCREF(__pyx_t_9); __pyx_t_7++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = PyTuple_GET_ITEM(__pyx_t_3, __pyx_t_7); __Pyx_INCREF(__pyx_t_9); __pyx_t_7++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 704; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #else - __pyx_t_9 = PySequence_ITEM(__pyx_t_3, __pyx_t_7); __pyx_t_7++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = PySequence_ITEM(__pyx_t_3, __pyx_t_7); __pyx_t_7++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 704; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); #endif } @@ -10741,7 +13774,7 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ PyObject* exc_type = PyErr_Occurred(); if (exc_type) { if (likely(exc_type == PyExc_StopIteration || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear(); - else {__pyx_filename = __pyx_f[1]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + else {__pyx_filename = __pyx_f[2]; __pyx_lineno = 704; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } break; } @@ -10752,7 +13785,7 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ __pyx_v_dim = __pyx_t_6; __pyx_t_6 = (__pyx_t_6 + 1); - /* "View.MemoryView":703 + /* "View.MemoryView":705 * * for dim, index in enumerate(indices): * if PyIndex_Check(index): # <<<<<<<<<<<<<< @@ -10762,27 +13795,35 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ __pyx_t_2 = (PyIndex_Check(__pyx_v_index) != 0); if (__pyx_t_2) { - /* "View.MemoryView":707 + /* "View.MemoryView":709 * p_dst, p_src.shape[dim], p_src.strides[dim], p_src.suboffsets[dim], * dim, new_ndim, p_suboffset_dim, * index, 0, 0, # start, stop, step # <<<<<<<<<<<<<< * 0, 0, 0, # have_{start,stop,step} * False) */ - __pyx_t_10 = __Pyx_PyIndex_AsSsize_t(__pyx_v_index); if (unlikely((__pyx_t_10 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 707; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = __Pyx_PyIndex_AsSsize_t(__pyx_v_index); if (unlikely((__pyx_t_10 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "View.MemoryView":704 + /* "View.MemoryView":706 * for dim, index in enumerate(indices): * if PyIndex_Check(index): * slice_memviewslice( # <<<<<<<<<<<<<< * p_dst, p_src.shape[dim], p_src.strides[dim], p_src.suboffsets[dim], * dim, new_ndim, p_suboffset_dim, */ - __pyx_t_11 = __pyx_memoryview_slice_memviewslice(__pyx_v_p_dst, (__pyx_v_p_src->shape[__pyx_v_dim]), (__pyx_v_p_src->strides[__pyx_v_dim]), (__pyx_v_p_src->suboffsets[__pyx_v_dim]), __pyx_v_dim, __pyx_v_new_ndim, __pyx_v_p_suboffset_dim, __pyx_t_10, 0, 0, 0, 0, 0, 0); if (unlikely(__pyx_t_11 == -1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 704; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_11 = __pyx_memoryview_slice_memviewslice(__pyx_v_p_dst, (__pyx_v_p_src->shape[__pyx_v_dim]), (__pyx_v_p_src->strides[__pyx_v_dim]), (__pyx_v_p_src->suboffsets[__pyx_v_dim]), __pyx_v_dim, __pyx_v_new_ndim, __pyx_v_p_suboffset_dim, __pyx_t_10, 0, 0, 0, 0, 0, 0); if (unlikely(__pyx_t_11 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 706; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "View.MemoryView":705 + * + * for dim, index in enumerate(indices): + * if PyIndex_Check(index): # <<<<<<<<<<<<<< + * slice_memviewslice( + * p_dst, p_src.shape[dim], p_src.strides[dim], p_src.suboffsets[dim], + */ goto __pyx_L6; } - /* "View.MemoryView":710 + /* "View.MemoryView":712 * 0, 0, 0, # have_{start,stop,step} * False) * elif index is None: # <<<<<<<<<<<<<< @@ -10793,7 +13834,7 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ __pyx_t_1 = (__pyx_t_2 != 0); if (__pyx_t_1) { - /* "View.MemoryView":711 + /* "View.MemoryView":713 * False) * elif index is None: * p_dst.shape[new_ndim] = 1 # <<<<<<<<<<<<<< @@ -10802,7 +13843,7 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ */ (__pyx_v_p_dst->shape[__pyx_v_new_ndim]) = 1; - /* "View.MemoryView":712 + /* "View.MemoryView":714 * elif index is None: * p_dst.shape[new_ndim] = 1 * p_dst.strides[new_ndim] = 0 # <<<<<<<<<<<<<< @@ -10811,16 +13852,16 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ */ (__pyx_v_p_dst->strides[__pyx_v_new_ndim]) = 0; - /* "View.MemoryView":713 + /* "View.MemoryView":715 * p_dst.shape[new_ndim] = 1 * p_dst.strides[new_ndim] = 0 * p_dst.suboffsets[new_ndim] = -1 # <<<<<<<<<<<<<< * new_ndim += 1 * else: */ - (__pyx_v_p_dst->suboffsets[__pyx_v_new_ndim]) = -1; + (__pyx_v_p_dst->suboffsets[__pyx_v_new_ndim]) = -1L; - /* "View.MemoryView":714 + /* "View.MemoryView":716 * p_dst.strides[new_ndim] = 0 * p_dst.suboffsets[new_ndim] = -1 * new_ndim += 1 # <<<<<<<<<<<<<< @@ -10828,24 +13869,32 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ * start = index.start or 0 */ __pyx_v_new_ndim = (__pyx_v_new_ndim + 1); + + /* "View.MemoryView":712 + * 0, 0, 0, # have_{start,stop,step} + * False) + * elif index is None: # <<<<<<<<<<<<<< + * p_dst.shape[new_ndim] = 1 + * p_dst.strides[new_ndim] = 0 + */ goto __pyx_L6; } - /*else*/ { - /* "View.MemoryView":716 + /* "View.MemoryView":718 * new_ndim += 1 * else: * start = index.start or 0 # <<<<<<<<<<<<<< * stop = index.stop or 0 * step = index.step or 0 */ - __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_index, __pyx_n_s_start); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 716; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + /*else*/ { + __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_index, __pyx_n_s_start); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 718; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); - __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 716; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 718; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (!__pyx_t_1) { __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; } else { - __pyx_t_12 = __Pyx_PyIndex_AsSsize_t(__pyx_t_9); if (unlikely((__pyx_t_12 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 716; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_12 = __Pyx_PyIndex_AsSsize_t(__pyx_t_9); if (unlikely((__pyx_t_12 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 718; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_10 = __pyx_t_12; __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; goto __pyx_L7_bool_binop_done; @@ -10854,20 +13903,20 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ __pyx_L7_bool_binop_done:; __pyx_v_start = __pyx_t_10; - /* "View.MemoryView":717 + /* "View.MemoryView":719 * else: * start = index.start or 0 * stop = index.stop or 0 # <<<<<<<<<<<<<< * step = index.step or 0 * */ - __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_index, __pyx_n_s_stop); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 717; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_index, __pyx_n_s_stop); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); - __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 717; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (!__pyx_t_1) { __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; } else { - __pyx_t_12 = __Pyx_PyIndex_AsSsize_t(__pyx_t_9); if (unlikely((__pyx_t_12 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 717; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_12 = __Pyx_PyIndex_AsSsize_t(__pyx_t_9); if (unlikely((__pyx_t_12 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_10 = __pyx_t_12; __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; goto __pyx_L9_bool_binop_done; @@ -10876,20 +13925,20 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ __pyx_L9_bool_binop_done:; __pyx_v_stop = __pyx_t_10; - /* "View.MemoryView":718 + /* "View.MemoryView":720 * start = index.start or 0 * stop = index.stop or 0 * step = index.step or 0 # <<<<<<<<<<<<<< * * have_start = index.start is not None */ - __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_index, __pyx_n_s_step); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 718; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_index, __pyx_n_s_step); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 720; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); - __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 718; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 720; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (!__pyx_t_1) { __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; } else { - __pyx_t_12 = __Pyx_PyIndex_AsSsize_t(__pyx_t_9); if (unlikely((__pyx_t_12 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 718; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_12 = __Pyx_PyIndex_AsSsize_t(__pyx_t_9); if (unlikely((__pyx_t_12 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 720; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_10 = __pyx_t_12; __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; goto __pyx_L11_bool_binop_done; @@ -10898,55 +13947,55 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ __pyx_L11_bool_binop_done:; __pyx_v_step = __pyx_t_10; - /* "View.MemoryView":720 + /* "View.MemoryView":722 * step = index.step or 0 * * have_start = index.start is not None # <<<<<<<<<<<<<< * have_stop = index.stop is not None * have_step = index.step is not None */ - __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_index, __pyx_n_s_start); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 720; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_index, __pyx_n_s_start); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 722; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); __pyx_t_1 = (__pyx_t_9 != Py_None); __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __pyx_v_have_start = __pyx_t_1; - /* "View.MemoryView":721 + /* "View.MemoryView":723 * * have_start = index.start is not None * have_stop = index.stop is not None # <<<<<<<<<<<<<< * have_step = index.step is not None * */ - __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_index, __pyx_n_s_stop); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 721; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_index, __pyx_n_s_stop); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 723; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); __pyx_t_1 = (__pyx_t_9 != Py_None); __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __pyx_v_have_stop = __pyx_t_1; - /* "View.MemoryView":722 + /* "View.MemoryView":724 * have_start = index.start is not None * have_stop = index.stop is not None * have_step = index.step is not None # <<<<<<<<<<<<<< * * slice_memviewslice( */ - __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_index, __pyx_n_s_step); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 722; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_index, __pyx_n_s_step); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 724; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); __pyx_t_1 = (__pyx_t_9 != Py_None); __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __pyx_v_have_step = __pyx_t_1; - /* "View.MemoryView":724 + /* "View.MemoryView":726 * have_step = index.step is not None * * slice_memviewslice( # <<<<<<<<<<<<<< * p_dst, p_src.shape[dim], p_src.strides[dim], p_src.suboffsets[dim], * dim, new_ndim, p_suboffset_dim, */ - __pyx_t_11 = __pyx_memoryview_slice_memviewslice(__pyx_v_p_dst, (__pyx_v_p_src->shape[__pyx_v_dim]), (__pyx_v_p_src->strides[__pyx_v_dim]), (__pyx_v_p_src->suboffsets[__pyx_v_dim]), __pyx_v_dim, __pyx_v_new_ndim, __pyx_v_p_suboffset_dim, __pyx_v_start, __pyx_v_stop, __pyx_v_step, __pyx_v_have_start, __pyx_v_have_stop, __pyx_v_have_step, 1); if (unlikely(__pyx_t_11 == -1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 724; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_11 = __pyx_memoryview_slice_memviewslice(__pyx_v_p_dst, (__pyx_v_p_src->shape[__pyx_v_dim]), (__pyx_v_p_src->strides[__pyx_v_dim]), (__pyx_v_p_src->suboffsets[__pyx_v_dim]), __pyx_v_dim, __pyx_v_new_ndim, __pyx_v_p_suboffset_dim, __pyx_v_start, __pyx_v_stop, __pyx_v_step, __pyx_v_have_start, __pyx_v_have_stop, __pyx_v_have_step, 1); if (unlikely(__pyx_t_11 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 726; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "View.MemoryView":730 + /* "View.MemoryView":732 * have_start, have_stop, have_step, * True) * new_ndim += 1 # <<<<<<<<<<<<<< @@ -10957,7 +14006,7 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ } __pyx_L6:; - /* "View.MemoryView":702 + /* "View.MemoryView":704 * cdef bint have_start, have_stop, have_step * * for dim, index in enumerate(indices): # <<<<<<<<<<<<<< @@ -10967,18 +14016,18 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ } __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - /* "View.MemoryView":732 + /* "View.MemoryView":734 * new_ndim += 1 * * if isinstance(memview, _memoryviewslice): # <<<<<<<<<<<<<< * return memoryview_fromslice(dst, new_ndim, * memviewsliceobj.to_object_func, */ - __pyx_t_1 = __Pyx_TypeCheck(((PyObject *)__pyx_v_memview), ((PyObject *)__pyx_memoryviewslice_type)); + __pyx_t_1 = __Pyx_TypeCheck(((PyObject *)__pyx_v_memview), __pyx_memoryviewslice_type); __pyx_t_2 = (__pyx_t_1 != 0); if (__pyx_t_2) { - /* "View.MemoryView":733 + /* "View.MemoryView":735 * * if isinstance(memview, _memoryviewslice): * return memoryview_fromslice(dst, new_ndim, # <<<<<<<<<<<<<< @@ -10987,73 +14036,81 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ */ __Pyx_XDECREF(((PyObject *)__pyx_r)); - /* "View.MemoryView":734 + /* "View.MemoryView":736 * if isinstance(memview, _memoryviewslice): * return memoryview_fromslice(dst, new_ndim, * memviewsliceobj.to_object_func, # <<<<<<<<<<<<<< * memviewsliceobj.to_dtype_func, * memview.dtype_is_object) */ - if (unlikely(!__pyx_v_memviewsliceobj)) { __Pyx_RaiseUnboundLocalError("memviewsliceobj"); {__pyx_filename = __pyx_f[1]; __pyx_lineno = 734; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } + if (unlikely(!__pyx_v_memviewsliceobj)) { __Pyx_RaiseUnboundLocalError("memviewsliceobj"); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - /* "View.MemoryView":735 + /* "View.MemoryView":737 * return memoryview_fromslice(dst, new_ndim, * memviewsliceobj.to_object_func, * memviewsliceobj.to_dtype_func, # <<<<<<<<<<<<<< * memview.dtype_is_object) * else: */ - if (unlikely(!__pyx_v_memviewsliceobj)) { __Pyx_RaiseUnboundLocalError("memviewsliceobj"); {__pyx_filename = __pyx_f[1]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } + if (unlikely(!__pyx_v_memviewsliceobj)) { __Pyx_RaiseUnboundLocalError("memviewsliceobj"); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - /* "View.MemoryView":733 + /* "View.MemoryView":735 * * if isinstance(memview, _memoryviewslice): * return memoryview_fromslice(dst, new_ndim, # <<<<<<<<<<<<<< * memviewsliceobj.to_object_func, * memviewsliceobj.to_dtype_func, */ - __pyx_t_3 = __pyx_memoryview_fromslice(__pyx_v_dst, __pyx_v_new_ndim, __pyx_v_memviewsliceobj->to_object_func, __pyx_v_memviewsliceobj->to_dtype_func, __pyx_v_memview->dtype_is_object); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __pyx_memoryview_fromslice(__pyx_v_dst, __pyx_v_new_ndim, __pyx_v_memviewsliceobj->to_object_func, __pyx_v_memviewsliceobj->to_dtype_func, __pyx_v_memview->dtype_is_object); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_memoryview_type))))) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_memoryview_type))))) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = ((struct __pyx_memoryview_obj *)__pyx_t_3); __pyx_t_3 = 0; goto __pyx_L0; + + /* "View.MemoryView":734 + * new_ndim += 1 + * + * if isinstance(memview, _memoryviewslice): # <<<<<<<<<<<<<< + * return memoryview_fromslice(dst, new_ndim, + * memviewsliceobj.to_object_func, + */ } - /*else*/ { - /* "View.MemoryView":738 + /* "View.MemoryView":740 * memview.dtype_is_object) * else: * return memoryview_fromslice(dst, new_ndim, NULL, NULL, # <<<<<<<<<<<<<< * memview.dtype_is_object) * */ + /*else*/ { __Pyx_XDECREF(((PyObject *)__pyx_r)); - /* "View.MemoryView":739 + /* "View.MemoryView":741 * else: * return memoryview_fromslice(dst, new_ndim, NULL, NULL, * memview.dtype_is_object) # <<<<<<<<<<<<<< * * */ - __pyx_t_3 = __pyx_memoryview_fromslice(__pyx_v_dst, __pyx_v_new_ndim, NULL, NULL, __pyx_v_memview->dtype_is_object); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __pyx_memoryview_fromslice(__pyx_v_dst, __pyx_v_new_ndim, NULL, NULL, __pyx_v_memview->dtype_is_object); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - /* "View.MemoryView":738 + /* "View.MemoryView":740 * memview.dtype_is_object) * else: * return memoryview_fromslice(dst, new_ndim, NULL, NULL, # <<<<<<<<<<<<<< * memview.dtype_is_object) * */ - if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_memoryview_type))))) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_memoryview_type))))) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = ((struct __pyx_memoryview_obj *)__pyx_t_3); __pyx_t_3 = 0; goto __pyx_L0; } - /* "View.MemoryView":666 + /* "View.MemoryView":668 * * @cname('__pyx_memview_slice') * cdef memoryview memview_slice(memoryview memview, object indices): # <<<<<<<<<<<<<< @@ -11075,7 +14132,7 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ return __pyx_r; } -/* "View.MemoryView":763 +/* "View.MemoryView":765 * * @cname('__pyx_memoryview_slice_memviewslice') * cdef int slice_memviewslice( # <<<<<<<<<<<<<< @@ -11094,7 +14151,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, const char *__pyx_filename = NULL; int __pyx_clineno = 0; - /* "View.MemoryView":783 + /* "View.MemoryView":785 * cdef bint negative_step * * if not is_slice: # <<<<<<<<<<<<<< @@ -11104,7 +14161,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_1 = ((!(__pyx_v_is_slice != 0)) != 0); if (__pyx_t_1) { - /* "View.MemoryView":785 + /* "View.MemoryView":787 * if not is_slice: * * if start < 0: # <<<<<<<<<<<<<< @@ -11114,7 +14171,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_1 = ((__pyx_v_start < 0) != 0); if (__pyx_t_1) { - /* "View.MemoryView":786 + /* "View.MemoryView":788 * * if start < 0: * start += shape # <<<<<<<<<<<<<< @@ -11122,11 +14179,17 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, * _err_dim(IndexError, "Index out of bounds (axis %d)", dim) */ __pyx_v_start = (__pyx_v_start + __pyx_v_shape); - goto __pyx_L4; + + /* "View.MemoryView":787 + * if not is_slice: + * + * if start < 0: # <<<<<<<<<<<<<< + * start += shape + * if not 0 <= start < shape: + */ } - __pyx_L4:; - /* "View.MemoryView":787 + /* "View.MemoryView":789 * if start < 0: * start += shape * if not 0 <= start < shape: # <<<<<<<<<<<<<< @@ -11140,28 +14203,42 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((!(__pyx_t_1 != 0)) != 0); if (__pyx_t_2) { - /* "View.MemoryView":788 + /* "View.MemoryView":790 * start += shape * if not 0 <= start < shape: * _err_dim(IndexError, "Index out of bounds (axis %d)", dim) # <<<<<<<<<<<<<< * else: * */ - __pyx_t_3 = __pyx_memoryview_err_dim(__pyx_builtin_IndexError, __pyx_k_Index_out_of_bounds_axis_d, __pyx_v_dim); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 788; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L5; + __pyx_t_3 = __pyx_memoryview_err_dim(__pyx_builtin_IndexError, __pyx_k_Index_out_of_bounds_axis_d, __pyx_v_dim); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "View.MemoryView":789 + * if start < 0: + * start += shape + * if not 0 <= start < shape: # <<<<<<<<<<<<<< + * _err_dim(IndexError, "Index out of bounds (axis %d)", dim) + * else: + */ } - __pyx_L5:; + + /* "View.MemoryView":785 + * cdef bint negative_step + * + * if not is_slice: # <<<<<<<<<<<<<< + * + * if start < 0: + */ goto __pyx_L3; } - /*else*/ { - /* "View.MemoryView":791 + /* "View.MemoryView":793 * else: * * negative_step = have_step != 0 and step < 0 # <<<<<<<<<<<<<< * * if have_step and step == 0: */ + /*else*/ { __pyx_t_1 = ((__pyx_v_have_step != 0) != 0); if (__pyx_t_1) { } else { @@ -11173,7 +14250,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_L6_bool_binop_done:; __pyx_v_negative_step = __pyx_t_2; - /* "View.MemoryView":793 + /* "View.MemoryView":795 * negative_step = have_step != 0 and step < 0 * * if have_step and step == 0: # <<<<<<<<<<<<<< @@ -11191,19 +14268,25 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_L9_bool_binop_done:; if (__pyx_t_2) { - /* "View.MemoryView":794 + /* "View.MemoryView":796 * * if have_step and step == 0: * _err_dim(ValueError, "Step may not be zero (axis %d)", dim) # <<<<<<<<<<<<<< * * */ - __pyx_t_3 = __pyx_memoryview_err_dim(__pyx_builtin_ValueError, __pyx_k_Step_may_not_be_zero_axis_d, __pyx_v_dim); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 794; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L8; + __pyx_t_3 = __pyx_memoryview_err_dim(__pyx_builtin_ValueError, __pyx_k_Step_may_not_be_zero_axis_d, __pyx_v_dim); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "View.MemoryView":795 + * negative_step = have_step != 0 and step < 0 + * + * if have_step and step == 0: # <<<<<<<<<<<<<< + * _err_dim(ValueError, "Step may not be zero (axis %d)", dim) + * + */ } - __pyx_L8:; - /* "View.MemoryView":797 + /* "View.MemoryView":799 * * * if have_start: # <<<<<<<<<<<<<< @@ -11213,7 +14296,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = (__pyx_v_have_start != 0); if (__pyx_t_2) { - /* "View.MemoryView":798 + /* "View.MemoryView":800 * * if have_start: * if start < 0: # <<<<<<<<<<<<<< @@ -11223,7 +14306,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_start < 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":799 + /* "View.MemoryView":801 * if have_start: * if start < 0: * start += shape # <<<<<<<<<<<<<< @@ -11232,7 +14315,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_start = (__pyx_v_start + __pyx_v_shape); - /* "View.MemoryView":800 + /* "View.MemoryView":802 * if start < 0: * start += shape * if start < 0: # <<<<<<<<<<<<<< @@ -11242,7 +14325,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_start < 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":801 + /* "View.MemoryView":803 * start += shape * if start < 0: * start = 0 # <<<<<<<<<<<<<< @@ -11250,13 +14333,27 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, * if negative_step: */ __pyx_v_start = 0; - goto __pyx_L13; + + /* "View.MemoryView":802 + * if start < 0: + * start += shape + * if start < 0: # <<<<<<<<<<<<<< + * start = 0 + * elif start >= shape: + */ } - __pyx_L13:; + + /* "View.MemoryView":800 + * + * if have_start: + * if start < 0: # <<<<<<<<<<<<<< + * start += shape + * if start < 0: + */ goto __pyx_L12; } - /* "View.MemoryView":802 + /* "View.MemoryView":804 * if start < 0: * start = 0 * elif start >= shape: # <<<<<<<<<<<<<< @@ -11266,7 +14363,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_start >= __pyx_v_shape) != 0); if (__pyx_t_2) { - /* "View.MemoryView":803 + /* "View.MemoryView":805 * start = 0 * elif start >= shape: * if negative_step: # <<<<<<<<<<<<<< @@ -11276,7 +14373,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = (__pyx_v_negative_step != 0); if (__pyx_t_2) { - /* "View.MemoryView":804 + /* "View.MemoryView":806 * elif start >= shape: * if negative_step: * start = shape - 1 # <<<<<<<<<<<<<< @@ -11284,38 +14381,61 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, * start = shape */ __pyx_v_start = (__pyx_v_shape - 1); + + /* "View.MemoryView":805 + * start = 0 + * elif start >= shape: + * if negative_step: # <<<<<<<<<<<<<< + * start = shape - 1 + * else: + */ goto __pyx_L14; } - /*else*/ { - /* "View.MemoryView":806 + /* "View.MemoryView":808 * start = shape - 1 * else: * start = shape # <<<<<<<<<<<<<< * else: * if negative_step: */ + /*else*/ { __pyx_v_start = __pyx_v_shape; } __pyx_L14:; - goto __pyx_L12; + + /* "View.MemoryView":804 + * if start < 0: + * start = 0 + * elif start >= shape: # <<<<<<<<<<<<<< + * if negative_step: + * start = shape - 1 + */ } __pyx_L12:; + + /* "View.MemoryView":799 + * + * + * if have_start: # <<<<<<<<<<<<<< + * if start < 0: + * start += shape + */ goto __pyx_L11; } - /*else*/ { - /* "View.MemoryView":808 + /* "View.MemoryView":810 * start = shape * else: * if negative_step: # <<<<<<<<<<<<<< * start = shape - 1 * else: */ + /*else*/ { __pyx_t_2 = (__pyx_v_negative_step != 0); if (__pyx_t_2) { - /* "View.MemoryView":809 + /* "View.MemoryView":811 * else: * if negative_step: * start = shape - 1 # <<<<<<<<<<<<<< @@ -11323,24 +14443,32 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, * start = 0 */ __pyx_v_start = (__pyx_v_shape - 1); + + /* "View.MemoryView":810 + * start = shape + * else: + * if negative_step: # <<<<<<<<<<<<<< + * start = shape - 1 + * else: + */ goto __pyx_L15; } - /*else*/ { - /* "View.MemoryView":811 + /* "View.MemoryView":813 * start = shape - 1 * else: * start = 0 # <<<<<<<<<<<<<< * * if have_stop: */ + /*else*/ { __pyx_v_start = 0; } __pyx_L15:; } __pyx_L11:; - /* "View.MemoryView":813 + /* "View.MemoryView":815 * start = 0 * * if have_stop: # <<<<<<<<<<<<<< @@ -11350,7 +14478,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = (__pyx_v_have_stop != 0); if (__pyx_t_2) { - /* "View.MemoryView":814 + /* "View.MemoryView":816 * * if have_stop: * if stop < 0: # <<<<<<<<<<<<<< @@ -11360,7 +14488,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_stop < 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":815 + /* "View.MemoryView":817 * if have_stop: * if stop < 0: * stop += shape # <<<<<<<<<<<<<< @@ -11369,7 +14497,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_stop = (__pyx_v_stop + __pyx_v_shape); - /* "View.MemoryView":816 + /* "View.MemoryView":818 * if stop < 0: * stop += shape * if stop < 0: # <<<<<<<<<<<<<< @@ -11379,7 +14507,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_stop < 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":817 + /* "View.MemoryView":819 * stop += shape * if stop < 0: * stop = 0 # <<<<<<<<<<<<<< @@ -11387,13 +14515,27 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, * stop = shape */ __pyx_v_stop = 0; - goto __pyx_L18; + + /* "View.MemoryView":818 + * if stop < 0: + * stop += shape + * if stop < 0: # <<<<<<<<<<<<<< + * stop = 0 + * elif stop > shape: + */ } - __pyx_L18:; + + /* "View.MemoryView":816 + * + * if have_stop: + * if stop < 0: # <<<<<<<<<<<<<< + * stop += shape + * if stop < 0: + */ goto __pyx_L17; } - /* "View.MemoryView":818 + /* "View.MemoryView":820 * if stop < 0: * stop = 0 * elif stop > shape: # <<<<<<<<<<<<<< @@ -11403,7 +14545,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_stop > __pyx_v_shape) != 0); if (__pyx_t_2) { - /* "View.MemoryView":819 + /* "View.MemoryView":821 * stop = 0 * elif stop > shape: * stop = shape # <<<<<<<<<<<<<< @@ -11411,49 +14553,72 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, * if negative_step: */ __pyx_v_stop = __pyx_v_shape; - goto __pyx_L17; + + /* "View.MemoryView":820 + * if stop < 0: + * stop = 0 + * elif stop > shape: # <<<<<<<<<<<<<< + * stop = shape + * else: + */ } __pyx_L17:; + + /* "View.MemoryView":815 + * start = 0 + * + * if have_stop: # <<<<<<<<<<<<<< + * if stop < 0: + * stop += shape + */ goto __pyx_L16; } - /*else*/ { - /* "View.MemoryView":821 + /* "View.MemoryView":823 * stop = shape * else: * if negative_step: # <<<<<<<<<<<<<< * stop = -1 * else: */ + /*else*/ { __pyx_t_2 = (__pyx_v_negative_step != 0); if (__pyx_t_2) { - /* "View.MemoryView":822 + /* "View.MemoryView":824 * else: * if negative_step: * stop = -1 # <<<<<<<<<<<<<< * else: * stop = shape */ - __pyx_v_stop = -1; + __pyx_v_stop = -1L; + + /* "View.MemoryView":823 + * stop = shape + * else: + * if negative_step: # <<<<<<<<<<<<<< + * stop = -1 + * else: + */ goto __pyx_L19; } - /*else*/ { - /* "View.MemoryView":824 + /* "View.MemoryView":826 * stop = -1 * else: * stop = shape # <<<<<<<<<<<<<< * * if not have_step: */ + /*else*/ { __pyx_v_stop = __pyx_v_shape; } __pyx_L19:; } __pyx_L16:; - /* "View.MemoryView":826 + /* "View.MemoryView":828 * stop = shape * * if not have_step: # <<<<<<<<<<<<<< @@ -11463,7 +14628,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((!(__pyx_v_have_step != 0)) != 0); if (__pyx_t_2) { - /* "View.MemoryView":827 + /* "View.MemoryView":829 * * if not have_step: * step = 1 # <<<<<<<<<<<<<< @@ -11471,11 +14636,17 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, * */ __pyx_v_step = 1; - goto __pyx_L20; + + /* "View.MemoryView":828 + * stop = shape + * + * if not have_step: # <<<<<<<<<<<<<< + * step = 1 + * + */ } - __pyx_L20:; - /* "View.MemoryView":831 + /* "View.MemoryView":833 * * with cython.cdivision(True): * new_shape = (stop - start) // step # <<<<<<<<<<<<<< @@ -11484,7 +14655,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_new_shape = ((__pyx_v_stop - __pyx_v_start) / __pyx_v_step); - /* "View.MemoryView":833 + /* "View.MemoryView":835 * new_shape = (stop - start) // step * * if (stop - start) - step * new_shape: # <<<<<<<<<<<<<< @@ -11494,7 +14665,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = (((__pyx_v_stop - __pyx_v_start) - (__pyx_v_step * __pyx_v_new_shape)) != 0); if (__pyx_t_2) { - /* "View.MemoryView":834 + /* "View.MemoryView":836 * * if (stop - start) - step * new_shape: * new_shape += 1 # <<<<<<<<<<<<<< @@ -11502,11 +14673,17 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, * if new_shape < 0: */ __pyx_v_new_shape = (__pyx_v_new_shape + 1); - goto __pyx_L21; + + /* "View.MemoryView":835 + * new_shape = (stop - start) // step + * + * if (stop - start) - step * new_shape: # <<<<<<<<<<<<<< + * new_shape += 1 + * + */ } - __pyx_L21:; - /* "View.MemoryView":836 + /* "View.MemoryView":838 * new_shape += 1 * * if new_shape < 0: # <<<<<<<<<<<<<< @@ -11516,7 +14693,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_new_shape < 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":837 + /* "View.MemoryView":839 * * if new_shape < 0: * new_shape = 0 # <<<<<<<<<<<<<< @@ -11524,11 +14701,17 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, * */ __pyx_v_new_shape = 0; - goto __pyx_L22; + + /* "View.MemoryView":838 + * new_shape += 1 + * + * if new_shape < 0: # <<<<<<<<<<<<<< + * new_shape = 0 + * + */ } - __pyx_L22:; - /* "View.MemoryView":840 + /* "View.MemoryView":842 * * * dst.strides[new_ndim] = stride * step # <<<<<<<<<<<<<< @@ -11537,7 +14720,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ (__pyx_v_dst->strides[__pyx_v_new_ndim]) = (__pyx_v_stride * __pyx_v_step); - /* "View.MemoryView":841 + /* "View.MemoryView":843 * * dst.strides[new_ndim] = stride * step * dst.shape[new_ndim] = new_shape # <<<<<<<<<<<<<< @@ -11546,7 +14729,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ (__pyx_v_dst->shape[__pyx_v_new_ndim]) = __pyx_v_new_shape; - /* "View.MemoryView":842 + /* "View.MemoryView":844 * dst.strides[new_ndim] = stride * step * dst.shape[new_ndim] = new_shape * dst.suboffsets[new_ndim] = suboffset # <<<<<<<<<<<<<< @@ -11557,7 +14740,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, } __pyx_L3:; - /* "View.MemoryView":845 + /* "View.MemoryView":847 * * * if suboffset_dim[0] < 0: # <<<<<<<<<<<<<< @@ -11567,7 +14750,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = (((__pyx_v_suboffset_dim[0]) < 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":846 + /* "View.MemoryView":848 * * if suboffset_dim[0] < 0: * dst.data += start * stride # <<<<<<<<<<<<<< @@ -11575,23 +14758,31 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, * dst.suboffsets[suboffset_dim[0]] += start * stride */ __pyx_v_dst->data = (__pyx_v_dst->data + (__pyx_v_start * __pyx_v_stride)); + + /* "View.MemoryView":847 + * + * + * if suboffset_dim[0] < 0: # <<<<<<<<<<<<<< + * dst.data += start * stride + * else: + */ goto __pyx_L23; } - /*else*/ { - /* "View.MemoryView":848 + /* "View.MemoryView":850 * dst.data += start * stride * else: * dst.suboffsets[suboffset_dim[0]] += start * stride # <<<<<<<<<<<<<< * * if suboffset >= 0: */ + /*else*/ { __pyx_t_3 = (__pyx_v_suboffset_dim[0]); (__pyx_v_dst->suboffsets[__pyx_t_3]) = ((__pyx_v_dst->suboffsets[__pyx_t_3]) + (__pyx_v_start * __pyx_v_stride)); } __pyx_L23:; - /* "View.MemoryView":850 + /* "View.MemoryView":852 * dst.suboffsets[suboffset_dim[0]] += start * stride * * if suboffset >= 0: # <<<<<<<<<<<<<< @@ -11601,7 +14792,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_suboffset >= 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":851 + /* "View.MemoryView":853 * * if suboffset >= 0: * if not is_slice: # <<<<<<<<<<<<<< @@ -11611,7 +14802,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((!(__pyx_v_is_slice != 0)) != 0); if (__pyx_t_2) { - /* "View.MemoryView":852 + /* "View.MemoryView":854 * if suboffset >= 0: * if not is_slice: * if new_ndim == 0: # <<<<<<<<<<<<<< @@ -11621,7 +14812,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_new_ndim == 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":853 + /* "View.MemoryView":855 * if not is_slice: * if new_ndim == 0: * dst.data = ( dst.data)[0] + suboffset # <<<<<<<<<<<<<< @@ -11629,39 +14820,69 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, * _err_dim(IndexError, "All dimensions preceding dimension %d " */ __pyx_v_dst->data = ((((char **)__pyx_v_dst->data)[0]) + __pyx_v_suboffset); + + /* "View.MemoryView":854 + * if suboffset >= 0: + * if not is_slice: + * if new_ndim == 0: # <<<<<<<<<<<<<< + * dst.data = ( dst.data)[0] + suboffset + * else: + */ goto __pyx_L26; } - /*else*/ { - /* "View.MemoryView":855 + /* "View.MemoryView":857 * dst.data = ( dst.data)[0] + suboffset * else: * _err_dim(IndexError, "All dimensions preceding dimension %d " # <<<<<<<<<<<<<< * "must be indexed and not sliced", dim) * else: */ - __pyx_t_3 = __pyx_memoryview_err_dim(__pyx_builtin_IndexError, __pyx_k_All_dimensions_preceding_dimensi, __pyx_v_dim); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 855; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + /*else*/ { + + /* "View.MemoryView":858 + * else: + * _err_dim(IndexError, "All dimensions preceding dimension %d " + * "must be indexed and not sliced", dim) # <<<<<<<<<<<<<< + * else: + * suboffset_dim[0] = new_ndim + */ + __pyx_t_3 = __pyx_memoryview_err_dim(__pyx_builtin_IndexError, __pyx_k_All_dimensions_preceding_dimensi, __pyx_v_dim); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_L26:; + + /* "View.MemoryView":853 + * + * if suboffset >= 0: + * if not is_slice: # <<<<<<<<<<<<<< + * if new_ndim == 0: + * dst.data = ( dst.data)[0] + suboffset + */ goto __pyx_L25; } - /*else*/ { - /* "View.MemoryView":858 + /* "View.MemoryView":860 * "must be indexed and not sliced", dim) * else: * suboffset_dim[0] = new_ndim # <<<<<<<<<<<<<< * * return 0 */ + /*else*/ { (__pyx_v_suboffset_dim[0]) = __pyx_v_new_ndim; } __pyx_L25:; - goto __pyx_L24; + + /* "View.MemoryView":852 + * dst.suboffsets[suboffset_dim[0]] += start * stride + * + * if suboffset >= 0: # <<<<<<<<<<<<<< + * if not is_slice: + * if new_ndim == 0: + */ } - __pyx_L24:; - /* "View.MemoryView":860 + /* "View.MemoryView":862 * suboffset_dim[0] = new_ndim * * return 0 # <<<<<<<<<<<<<< @@ -11671,7 +14892,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_r = 0; goto __pyx_L0; - /* "View.MemoryView":763 + /* "View.MemoryView":765 * * @cname('__pyx_memoryview_slice_memviewslice') * cdef int slice_memviewslice( # <<<<<<<<<<<<<< @@ -11695,7 +14916,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, return __pyx_r; } -/* "View.MemoryView":866 +/* "View.MemoryView":868 * * @cname('__pyx_pybuffer_index') * cdef char *pybuffer_index(Py_buffer *view, char *bufp, Py_ssize_t index, # <<<<<<<<<<<<<< @@ -11720,16 +14941,16 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P int __pyx_clineno = 0; __Pyx_RefNannySetupContext("pybuffer_index", 0); - /* "View.MemoryView":868 + /* "View.MemoryView":870 * cdef char *pybuffer_index(Py_buffer *view, char *bufp, Py_ssize_t index, * Py_ssize_t dim) except NULL: * cdef Py_ssize_t shape, stride, suboffset = -1 # <<<<<<<<<<<<<< * cdef Py_ssize_t itemsize = view.itemsize * cdef char *resultp */ - __pyx_v_suboffset = -1; + __pyx_v_suboffset = -1L; - /* "View.MemoryView":869 + /* "View.MemoryView":871 * Py_ssize_t dim) except NULL: * cdef Py_ssize_t shape, stride, suboffset = -1 * cdef Py_ssize_t itemsize = view.itemsize # <<<<<<<<<<<<<< @@ -11739,7 +14960,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P __pyx_t_1 = __pyx_v_view->itemsize; __pyx_v_itemsize = __pyx_t_1; - /* "View.MemoryView":872 + /* "View.MemoryView":874 * cdef char *resultp * * if view.ndim == 0: # <<<<<<<<<<<<<< @@ -11749,7 +14970,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P __pyx_t_2 = ((__pyx_v_view->ndim == 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":873 + /* "View.MemoryView":875 * * if view.ndim == 0: * shape = view.len / itemsize # <<<<<<<<<<<<<< @@ -11757,28 +14978,16 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P * else: */ if (unlikely(__pyx_v_itemsize == 0)) { - #ifdef WITH_THREAD - PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure(); - #endif PyErr_SetString(PyExc_ZeroDivisionError, "integer division or modulo by zero"); - #ifdef WITH_THREAD - PyGILState_Release(__pyx_gilstate_save); - #endif - {__pyx_filename = __pyx_f[1]; __pyx_lineno = 873; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[2]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - else if (sizeof(Py_ssize_t) == sizeof(long) && unlikely(__pyx_v_itemsize == -1) && unlikely(UNARY_NEG_WOULD_OVERFLOW(__pyx_v_view->len))) { - #ifdef WITH_THREAD - PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure(); - #endif + else if (sizeof(Py_ssize_t) == sizeof(long) && (!(((Py_ssize_t)-1) > 0)) && unlikely(__pyx_v_itemsize == (Py_ssize_t)-1) && unlikely(UNARY_NEG_WOULD_OVERFLOW(__pyx_v_view->len))) { PyErr_SetString(PyExc_OverflowError, "value too large to perform division"); - #ifdef WITH_THREAD - PyGILState_Release(__pyx_gilstate_save); - #endif - {__pyx_filename = __pyx_f[1]; __pyx_lineno = 873; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[2]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_v_shape = __Pyx_div_Py_ssize_t(__pyx_v_view->len, __pyx_v_itemsize); - /* "View.MemoryView":874 + /* "View.MemoryView":876 * if view.ndim == 0: * shape = view.len / itemsize * stride = itemsize # <<<<<<<<<<<<<< @@ -11786,20 +14995,28 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P * shape = view.shape[dim] */ __pyx_v_stride = __pyx_v_itemsize; + + /* "View.MemoryView":874 + * cdef char *resultp + * + * if view.ndim == 0: # <<<<<<<<<<<<<< + * shape = view.len / itemsize + * stride = itemsize + */ goto __pyx_L3; } - /*else*/ { - /* "View.MemoryView":876 + /* "View.MemoryView":878 * stride = itemsize * else: * shape = view.shape[dim] # <<<<<<<<<<<<<< * stride = view.strides[dim] * if view.suboffsets != NULL: */ + /*else*/ { __pyx_v_shape = (__pyx_v_view->shape[__pyx_v_dim]); - /* "View.MemoryView":877 + /* "View.MemoryView":879 * else: * shape = view.shape[dim] * stride = view.strides[dim] # <<<<<<<<<<<<<< @@ -11808,7 +15025,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P */ __pyx_v_stride = (__pyx_v_view->strides[__pyx_v_dim]); - /* "View.MemoryView":878 + /* "View.MemoryView":880 * shape = view.shape[dim] * stride = view.strides[dim] * if view.suboffsets != NULL: # <<<<<<<<<<<<<< @@ -11818,7 +15035,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P __pyx_t_2 = ((__pyx_v_view->suboffsets != NULL) != 0); if (__pyx_t_2) { - /* "View.MemoryView":879 + /* "View.MemoryView":881 * stride = view.strides[dim] * if view.suboffsets != NULL: * suboffset = view.suboffsets[dim] # <<<<<<<<<<<<<< @@ -11826,13 +15043,19 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P * if index < 0: */ __pyx_v_suboffset = (__pyx_v_view->suboffsets[__pyx_v_dim]); - goto __pyx_L4; + + /* "View.MemoryView":880 + * shape = view.shape[dim] + * stride = view.strides[dim] + * if view.suboffsets != NULL: # <<<<<<<<<<<<<< + * suboffset = view.suboffsets[dim] + * + */ } - __pyx_L4:; } __pyx_L3:; - /* "View.MemoryView":881 + /* "View.MemoryView":883 * suboffset = view.suboffsets[dim] * * if index < 0: # <<<<<<<<<<<<<< @@ -11842,7 +15065,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P __pyx_t_2 = ((__pyx_v_index < 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":882 + /* "View.MemoryView":884 * * if index < 0: * index += view.shape[dim] # <<<<<<<<<<<<<< @@ -11851,7 +15074,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P */ __pyx_v_index = (__pyx_v_index + (__pyx_v_view->shape[__pyx_v_dim])); - /* "View.MemoryView":883 + /* "View.MemoryView":885 * if index < 0: * index += view.shape[dim] * if index < 0: # <<<<<<<<<<<<<< @@ -11861,35 +15084,49 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P __pyx_t_2 = ((__pyx_v_index < 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":884 + /* "View.MemoryView":886 * index += view.shape[dim] * if index < 0: * raise IndexError("Out of bounds on buffer access (axis %d)" % dim) # <<<<<<<<<<<<<< * * if index >= shape: */ - __pyx_t_3 = PyInt_FromSsize_t(__pyx_v_dim); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 884; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyInt_FromSsize_t(__pyx_v_dim); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 886; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_4 = __Pyx_PyString_Format(__pyx_kp_s_Out_of_bounds_on_buffer_access_a, __pyx_t_3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 884; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyString_Format(__pyx_kp_s_Out_of_bounds_on_buffer_access_a, __pyx_t_3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 886; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 884; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = 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0; goto __pyx_L0; + + /* "View.MemoryView":938 + * + * cdef convert_item_to_object(self, char *itemp): + * if self.to_object_func != NULL: # <<<<<<<<<<<<<< + * return self.to_object_func(itemp) + * else: + */ } - /*else*/ { - /* "View.MemoryView":939 + /* "View.MemoryView":941 * return self.to_object_func(itemp) * else: * return memoryview.convert_item_to_object(self, itemp) # <<<<<<<<<<<<<< * * cdef assign_item_from_object(self, char *itemp, object value): */ + /*else*/ { __Pyx_XDECREF(__pyx_r); - __pyx_t_2 = __pyx_memoryview_convert_item_to_object(((struct __pyx_memoryview_obj *)__pyx_v_self), __pyx_v_itemp); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 939; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __pyx_memoryview_convert_item_to_object(((struct __pyx_memoryview_obj *)__pyx_v_self), __pyx_v_itemp); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 941; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_r = __pyx_t_2; __pyx_t_2 = 0; goto __pyx_L0; } - /* "View.MemoryView":935 + /* "View.MemoryView":937 * __PYX_XDEC_MEMVIEW(&self.from_slice, 1) * * cdef convert_item_to_object(self, char *itemp): # <<<<<<<<<<<<<< @@ -12272,7 +15537,7 @@ static PyObject *__pyx_memoryviewslice_convert_item_to_object(struct __pyx_memor return __pyx_r; } -/* "View.MemoryView":941 +/* "View.MemoryView":943 * return memoryview.convert_item_to_object(self, itemp) * * cdef assign_item_from_object(self, char *itemp, object value): # <<<<<<<<<<<<<< @@ -12291,7 +15556,7 @@ static PyObject *__pyx_memoryviewslice_assign_item_from_object(struct __pyx_memo int __pyx_clineno = 0; __Pyx_RefNannySetupContext("assign_item_from_object", 0); - /* "View.MemoryView":942 + /* "View.MemoryView":944 * * cdef assign_item_from_object(self, char *itemp, object value): * if self.to_dtype_func != NULL: # <<<<<<<<<<<<<< @@ -12301,32 +15566,40 @@ static PyObject 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value) + * else: + */ goto __pyx_L3; } - /*else*/ { - /* "View.MemoryView":945 + /* "View.MemoryView":947 * self.to_dtype_func(itemp, value) * else: * memoryview.assign_item_from_object(self, itemp, value) # <<<<<<<<<<<<<< * * property base: */ - __pyx_t_3 = __pyx_memoryview_assign_item_from_object(((struct __pyx_memoryview_obj *)__pyx_v_self), __pyx_v_itemp, __pyx_v_value); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 945; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + /*else*/ { + __pyx_t_3 = __pyx_memoryview_assign_item_from_object(((struct __pyx_memoryview_obj *)__pyx_v_self), __pyx_v_itemp, __pyx_v_value); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 947; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; } __pyx_L3:; - /* "View.MemoryView":941 + /* "View.MemoryView":943 * return memoryview.convert_item_to_object(self, itemp) * * cdef assign_item_from_object(self, char *itemp, object value): # <<<<<<<<<<<<<< @@ -12347,7 +15620,7 @@ static PyObject *__pyx_memoryviewslice_assign_item_from_object(struct __pyx_memo return __pyx_r; } -/* "View.MemoryView":949 +/* "View.MemoryView":951 * property base: * @cname('__pyx_memoryviewslice__get__base') * def __get__(self): # <<<<<<<<<<<<<< @@ -12373,7 +15646,7 @@ static PyObject *__pyx_pf_15View_dot_MemoryView_16_memoryviewslice_4base___get__ __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__get__", 0); - /* "View.MemoryView":950 + /* "View.MemoryView":952 * @cname('__pyx_memoryviewslice__get__base') * def __get__(self): * return self.from_object # <<<<<<<<<<<<<< @@ -12385,7 +15658,7 @@ static PyObject *__pyx_pf_15View_dot_MemoryView_16_memoryviewslice_4base___get__ __pyx_r = __pyx_v_self->from_object; goto __pyx_L0; - /* "View.MemoryView":949 + /* "View.MemoryView":951 * property base: * @cname('__pyx_memoryviewslice__get__base') * def __get__(self): # <<<<<<<<<<<<<< @@ -12400,7 +15673,7 @@ static PyObject *__pyx_pf_15View_dot_MemoryView_16_memoryviewslice_4base___get__ return __pyx_r; } -/* "View.MemoryView":956 +/* "View.MemoryView":958 * * @cname('__pyx_memoryview_fromslice') * cdef memoryview_fromslice(__Pyx_memviewslice memviewslice, # <<<<<<<<<<<<<< @@ -12428,7 +15701,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl int __pyx_clineno = 0; __Pyx_RefNannySetupContext("memoryview_fromslice", 0); - /* "View.MemoryView":964 + /* "View.MemoryView":966 * cdef _memoryviewslice result * * if memviewslice.memview == Py_None: # <<<<<<<<<<<<<< @@ -12438,7 +15711,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl __pyx_t_1 = ((((PyObject *)__pyx_v_memviewslice.memview) == Py_None) != 0); if (__pyx_t_1) { - /* "View.MemoryView":965 + /* "View.MemoryView":967 * * if memviewslice.memview == Py_None: * return None # <<<<<<<<<<<<<< @@ -12449,18 +15722,26 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl __Pyx_INCREF(Py_None); __pyx_r = Py_None; goto __pyx_L0; + + /* "View.MemoryView":966 + * cdef _memoryviewslice result + * + * if memviewslice.memview == Py_None: # <<<<<<<<<<<<<< + * return None + * + */ } - /* "View.MemoryView":970 + /* "View.MemoryView":972 * * * result = _memoryviewslice(None, 0, dtype_is_object) # <<<<<<<<<<<<<< * * result.from_slice = memviewslice */ - __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_dtype_is_object); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_dtype_is_object); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 972; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_3 = PyTuple_New(3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyTuple_New(3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 972; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_INCREF(Py_None); __Pyx_GIVEREF(Py_None); @@ -12471,13 +15752,13 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl __Pyx_GIVEREF(__pyx_t_2); PyTuple_SET_ITEM(__pyx_t_3, 2, __pyx_t_2); __pyx_t_2 = 0; - __pyx_t_2 = __Pyx_PyObject_Call(((PyObject *)((PyObject *)__pyx_memoryviewslice_type)), __pyx_t_3, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(((PyObject *)__pyx_memoryviewslice_type), __pyx_t_3, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 972; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_v_result = ((struct __pyx_memoryviewslice_obj *)__pyx_t_2); __pyx_t_2 = 0; - /* "View.MemoryView":972 + /* 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= __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_memviewslice.memview), __pyx_n_s_base); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 977; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_GIVEREF(__pyx_t_2); __Pyx_GOTREF(__pyx_v_result->from_object); @@ -12510,7 +15791,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl __pyx_v_result->from_object = __pyx_t_2; __pyx_t_2 = 0; - /* "View.MemoryView":976 + /* "View.MemoryView":978 * * result.from_object = ( memviewslice.memview).base * result.typeinfo = memviewslice.memview.typeinfo # <<<<<<<<<<<<<< @@ -12520,7 +15801,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl __pyx_t_4 = __pyx_v_memviewslice.memview->typeinfo; __pyx_v_result->__pyx_base.typeinfo = __pyx_t_4; - /* "View.MemoryView":978 + /* "View.MemoryView":980 * result.typeinfo = memviewslice.memview.typeinfo * * result.view = memviewslice.memview.view # <<<<<<<<<<<<<< @@ -12530,7 +15811,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl __pyx_t_5 = __pyx_v_memviewslice.memview->view; __pyx_v_result->__pyx_base.view = __pyx_t_5; - /* "View.MemoryView":979 + /* "View.MemoryView":981 * * result.view = memviewslice.memview.view * result.view.buf = memviewslice.data # <<<<<<<<<<<<<< @@ -12539,7 +15820,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl */ __pyx_v_result->__pyx_base.view.buf = ((void *)__pyx_v_memviewslice.data); - /* "View.MemoryView":980 + /* "View.MemoryView":982 * result.view = memviewslice.memview.view * result.view.buf = memviewslice.data * result.view.ndim = ndim # <<<<<<<<<<<<<< @@ -12548,7 +15829,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl */ __pyx_v_result->__pyx_base.view.ndim = __pyx_v_ndim; - /* "View.MemoryView":981 + /* "View.MemoryView":983 * result.view.buf = memviewslice.data * result.view.ndim = ndim * (<__pyx_buffer *> &result.view).obj = Py_None # <<<<<<<<<<<<<< @@ -12557,7 +15838,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl */ ((Py_buffer *)(&__pyx_v_result->__pyx_base.view))->obj = Py_None; - /* "View.MemoryView":982 + /* "View.MemoryView":984 * result.view.ndim = ndim * (<__pyx_buffer *> &result.view).obj = Py_None * Py_INCREF(Py_None) # <<<<<<<<<<<<<< @@ -12566,7 +15847,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl */ Py_INCREF(Py_None); - /* "View.MemoryView":984 + /* "View.MemoryView":986 * Py_INCREF(Py_None) * * result.flags = PyBUF_RECORDS # <<<<<<<<<<<<<< @@ -12575,7 +15856,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl */ __pyx_v_result->__pyx_base.flags = PyBUF_RECORDS; - /* "View.MemoryView":986 + /* "View.MemoryView":988 * result.flags = PyBUF_RECORDS * * result.view.shape = result.from_slice.shape # <<<<<<<<<<<<<< @@ -12584,7 +15865,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl */ __pyx_v_result->__pyx_base.view.shape = ((Py_ssize_t *)__pyx_v_result->from_slice.shape); - /* "View.MemoryView":987 + /* "View.MemoryView":989 * * result.view.shape = result.from_slice.shape * result.view.strides = result.from_slice.strides # <<<<<<<<<<<<<< @@ -12593,7 +15874,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl */ __pyx_v_result->__pyx_base.view.strides = ((Py_ssize_t *)__pyx_v_result->from_slice.strides); - /* "View.MemoryView":990 + /* "View.MemoryView":992 * * * result.view.suboffsets = NULL # <<<<<<<<<<<<<< @@ -12602,7 +15883,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl */ __pyx_v_result->__pyx_base.view.suboffsets = NULL; - /* "View.MemoryView":991 + /* "View.MemoryView":993 * * result.view.suboffsets = NULL * for suboffset in result.from_slice.suboffsets[:ndim]: # <<<<<<<<<<<<<< @@ -12614,7 +15895,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl __pyx_t_6 = __pyx_t_8; __pyx_v_suboffset = (__pyx_t_6[0]); - /* "View.MemoryView":992 + /* "View.MemoryView":994 * result.view.suboffsets = NULL * for suboffset in result.from_slice.suboffsets[:ndim]: * if suboffset >= 0: # <<<<<<<<<<<<<< @@ -12624,7 +15905,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl __pyx_t_1 = ((__pyx_v_suboffset >= 0) != 0); if (__pyx_t_1) { - /* "View.MemoryView":993 + /* "View.MemoryView":995 * for suboffset in result.from_slice.suboffsets[:ndim]: * if suboffset >= 0: * result.view.suboffsets = result.from_slice.suboffsets # <<<<<<<<<<<<<< @@ -12633,7 +15914,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl */ __pyx_v_result->__pyx_base.view.suboffsets = ((Py_ssize_t *)__pyx_v_result->from_slice.suboffsets); - /* 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result.view.itemsize * for length in result.view.shape[:ndim]: # <<<<<<<<<<<<<< @@ -12665,29 +15954,29 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl __pyx_t_7 = (__pyx_v_result->__pyx_base.view.shape + __pyx_v_ndim); for (__pyx_t_8 = __pyx_v_result->__pyx_base.view.shape; __pyx_t_8 < __pyx_t_7; __pyx_t_8++) { __pyx_t_6 = __pyx_t_8; - __pyx_t_2 = PyInt_FromSsize_t((__pyx_t_6[0])); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 997; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyInt_FromSsize_t((__pyx_t_6[0])); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 999; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_XDECREF_SET(__pyx_v_length, __pyx_t_2); __pyx_t_2 = 0; - /* "View.MemoryView":998 + /* "View.MemoryView":1000 * result.view.len = result.view.itemsize * for length in result.view.shape[:ndim]: * result.view.len *= length # <<<<<<<<<<<<<< * * result.to_object_func = to_object_func */ - __pyx_t_2 = PyInt_FromSsize_t(__pyx_v_result->__pyx_base.view.len); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 998; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyInt_FromSsize_t(__pyx_v_result->__pyx_base.view.len); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1000; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_3 = PyNumber_InPlaceMultiply(__pyx_t_2, __pyx_v_length); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 998; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyNumber_InPlaceMultiply(__pyx_t_2, __pyx_v_length); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1000; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __pyx_t_9 = __Pyx_PyIndex_AsSsize_t(__pyx_t_3); if (unlikely((__pyx_t_9 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 998; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = __Pyx_PyIndex_AsSsize_t(__pyx_t_3); if (unlikely((__pyx_t_9 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1000; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_v_result->__pyx_base.view.len = __pyx_t_9; } - /* "View.MemoryView":1000 + /* "View.MemoryView":1002 * result.view.len *= length * * result.to_object_func = to_object_func # <<<<<<<<<<<<<< @@ -12696,7 +15985,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl */ __pyx_v_result->to_object_func = __pyx_v_to_object_func; - /* "View.MemoryView":1001 + /* "View.MemoryView":1003 * * result.to_object_func = to_object_func * result.to_dtype_func = to_dtype_func # <<<<<<<<<<<<<< @@ -12705,7 +15994,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl */ __pyx_v_result->to_dtype_func = __pyx_v_to_dtype_func; - /* "View.MemoryView":1003 + /* "View.MemoryView":1005 * result.to_dtype_func = to_dtype_func * * return result # <<<<<<<<<<<<<< @@ -12717,7 +16006,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl __pyx_r = ((PyObject *)__pyx_v_result); goto __pyx_L0; - /* "View.MemoryView":956 + /* "View.MemoryView":958 * * @cname('__pyx_memoryview_fromslice') * cdef memoryview_fromslice(__Pyx_memviewslice memviewslice, # <<<<<<<<<<<<<< @@ -12739,7 +16028,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl return __pyx_r; } -/* "View.MemoryView":1006 +/* "View.MemoryView":1008 * * @cname('__pyx_memoryview_get_slice_from_memoryview') * cdef __Pyx_memviewslice *get_slice_from_memview(memoryview memview, # <<<<<<<<<<<<<< @@ -12759,31 +16048,31 @@ static __Pyx_memviewslice *__pyx_memoryview_get_slice_from_memoryview(struct __p int __pyx_clineno = 0; __Pyx_RefNannySetupContext("get_slice_from_memview", 0); - /* "View.MemoryView":1009 + /* "View.MemoryView":1011 * __Pyx_memviewslice *mslice): * cdef _memoryviewslice obj * if isinstance(memview, _memoryviewslice): # <<<<<<<<<<<<<< * obj = memview * return &obj.from_slice */ - __pyx_t_1 = __Pyx_TypeCheck(((PyObject *)__pyx_v_memview), ((PyObject *)__pyx_memoryviewslice_type)); + __pyx_t_1 = __Pyx_TypeCheck(((PyObject *)__pyx_v_memview), __pyx_memoryviewslice_type); __pyx_t_2 = (__pyx_t_1 != 0); if (__pyx_t_2) { - /* "View.MemoryView":1010 + /* "View.MemoryView":1012 * cdef _memoryviewslice obj * if isinstance(memview, _memoryviewslice): * obj = memview # <<<<<<<<<<<<<< * return &obj.from_slice * else: */ - if (!(likely(((((PyObject *)__pyx_v_memview)) == Py_None) || likely(__Pyx_TypeTest(((PyObject *)__pyx_v_memview), __pyx_memoryviewslice_type))))) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 1010; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((((PyObject *)__pyx_v_memview)) == Py_None) || likely(__Pyx_TypeTest(((PyObject *)__pyx_v_memview), __pyx_memoryviewslice_type))))) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1012; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_3 = ((PyObject *)__pyx_v_memview); __Pyx_INCREF(__pyx_t_3); __pyx_v_obj = ((struct __pyx_memoryviewslice_obj *)__pyx_t_3); __pyx_t_3 = 0; - /* "View.MemoryView":1011 + /* "View.MemoryView":1013 * if isinstance(memview, _memoryviewslice): * obj = memview * return &obj.from_slice # <<<<<<<<<<<<<< @@ -12792,19 +16081,27 @@ static __Pyx_memviewslice *__pyx_memoryview_get_slice_from_memoryview(struct __p */ __pyx_r = (&__pyx_v_obj->from_slice); goto __pyx_L0; + + /* "View.MemoryView":1011 + * __Pyx_memviewslice *mslice): + * cdef _memoryviewslice obj + * if isinstance(memview, _memoryviewslice): # <<<<<<<<<<<<<< + * obj = memview + * return &obj.from_slice + */ } - /*else*/ { - /* "View.MemoryView":1013 + /* "View.MemoryView":1015 * return &obj.from_slice * else: * slice_copy(memview, mslice) # <<<<<<<<<<<<<< * return mslice * */ + /*else*/ { __pyx_memoryview_slice_copy(__pyx_v_memview, __pyx_v_mslice); - /* "View.MemoryView":1014 + /* "View.MemoryView":1016 * else: * slice_copy(memview, mslice) * return mslice # <<<<<<<<<<<<<< @@ -12815,7 +16112,7 @@ static __Pyx_memviewslice *__pyx_memoryview_get_slice_from_memoryview(struct __p goto __pyx_L0; } - /* "View.MemoryView":1006 + /* "View.MemoryView":1008 * * @cname('__pyx_memoryview_get_slice_from_memoryview') * cdef __Pyx_memviewslice *get_slice_from_memview(memoryview memview, # <<<<<<<<<<<<<< @@ -12834,7 +16131,7 @@ static __Pyx_memviewslice *__pyx_memoryview_get_slice_from_memoryview(struct __p return __pyx_r; } -/* "View.MemoryView":1017 +/* "View.MemoryView":1019 * * @cname('__pyx_memoryview_slice_copy') * cdef void slice_copy(memoryview memview, __Pyx_memviewslice *dst): # <<<<<<<<<<<<<< @@ -12854,7 +16151,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem Py_ssize_t __pyx_t_4; __Pyx_RefNannySetupContext("slice_copy", 0); - /* "View.MemoryView":1021 + /* "View.MemoryView":1023 * cdef (Py_ssize_t*) shape, strides, suboffsets * * shape = memview.view.shape # <<<<<<<<<<<<<< @@ -12864,7 +16161,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem __pyx_t_1 = __pyx_v_memview->view.shape; __pyx_v_shape = __pyx_t_1; - /* "View.MemoryView":1022 + /* "View.MemoryView":1024 * * shape = memview.view.shape * strides = memview.view.strides # <<<<<<<<<<<<<< @@ -12874,7 +16171,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem __pyx_t_1 = __pyx_v_memview->view.strides; __pyx_v_strides = __pyx_t_1; - /* "View.MemoryView":1023 + /* "View.MemoryView":1025 * shape = memview.view.shape * strides = memview.view.strides * suboffsets = memview.view.suboffsets # <<<<<<<<<<<<<< @@ -12884,7 +16181,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem __pyx_t_1 = __pyx_v_memview->view.suboffsets; __pyx_v_suboffsets = __pyx_t_1; - /* "View.MemoryView":1025 + /* "View.MemoryView":1027 * suboffsets = memview.view.suboffsets * * dst.memview = <__pyx_memoryview *> memview # <<<<<<<<<<<<<< @@ -12893,7 +16190,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem */ __pyx_v_dst->memview = ((struct __pyx_memoryview_obj *)__pyx_v_memview); - /* "View.MemoryView":1026 + /* "View.MemoryView":1028 * * dst.memview = <__pyx_memoryview *> memview * dst.data = memview.view.buf # <<<<<<<<<<<<<< @@ -12902,7 +16199,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem */ __pyx_v_dst->data = ((char *)__pyx_v_memview->view.buf); - /* "View.MemoryView":1028 + /* "View.MemoryView":1030 * dst.data = memview.view.buf * * for dim in range(memview.view.ndim): # <<<<<<<<<<<<<< @@ -12913,7 +16210,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { __pyx_v_dim = __pyx_t_3; - /* "View.MemoryView":1029 + /* "View.MemoryView":1031 * * for dim in range(memview.view.ndim): * dst.shape[dim] = shape[dim] # <<<<<<<<<<<<<< @@ -12922,7 +16219,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem */ (__pyx_v_dst->shape[__pyx_v_dim]) = (__pyx_v_shape[__pyx_v_dim]); - /* "View.MemoryView":1030 + /* "View.MemoryView":1032 * for dim in range(memview.view.ndim): * dst.shape[dim] = shape[dim] * dst.strides[dim] = strides[dim] # <<<<<<<<<<<<<< @@ -12931,7 +16228,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem */ (__pyx_v_dst->strides[__pyx_v_dim]) = (__pyx_v_strides[__pyx_v_dim]); - /* "View.MemoryView":1031 + /* "View.MemoryView":1033 * dst.shape[dim] = shape[dim] * dst.strides[dim] = strides[dim] * dst.suboffsets[dim] = suboffsets[dim] if suboffsets else -1 # <<<<<<<<<<<<<< @@ -12941,12 +16238,12 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem if ((__pyx_v_suboffsets != 0)) { __pyx_t_4 = (__pyx_v_suboffsets[__pyx_v_dim]); } else { - __pyx_t_4 = -1; + __pyx_t_4 = -1L; } (__pyx_v_dst->suboffsets[__pyx_v_dim]) = __pyx_t_4; } - /* "View.MemoryView":1017 + /* "View.MemoryView":1019 * * @cname('__pyx_memoryview_slice_copy') * cdef void slice_copy(memoryview memview, __Pyx_memviewslice *dst): # <<<<<<<<<<<<<< @@ -12958,7 +16255,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem __Pyx_RefNannyFinishContext(); } -/* "View.MemoryView":1034 +/* "View.MemoryView":1036 * * @cname('__pyx_memoryview_copy_object') * cdef memoryview_copy(memoryview memview): # <<<<<<<<<<<<<< @@ -12976,7 +16273,7 @@ static PyObject *__pyx_memoryview_copy_object(struct __pyx_memoryview_obj *__pyx int __pyx_clineno = 0; __Pyx_RefNannySetupContext("memoryview_copy", 0); - /* "View.MemoryView":1037 + /* "View.MemoryView":1039 * "Create a new memoryview object" * cdef __Pyx_memviewslice memviewslice * slice_copy(memview, &memviewslice) # <<<<<<<<<<<<<< @@ -12985,7 +16282,7 @@ static PyObject *__pyx_memoryview_copy_object(struct __pyx_memoryview_obj *__pyx */ __pyx_memoryview_slice_copy(__pyx_v_memview, (&__pyx_v_memviewslice)); - /* "View.MemoryView":1038 + /* "View.MemoryView":1040 * cdef __Pyx_memviewslice memviewslice * slice_copy(memview, &memviewslice) * return memoryview_copy_from_slice(memview, &memviewslice) # <<<<<<<<<<<<<< @@ -12993,13 +16290,13 @@ static PyObject *__pyx_memoryview_copy_object(struct __pyx_memoryview_obj *__pyx * @cname('__pyx_memoryview_copy_object_from_slice') */ __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = __pyx_memoryview_copy_object_from_slice(__pyx_v_memview, (&__pyx_v_memviewslice)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 1038; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __pyx_memoryview_copy_object_from_slice(__pyx_v_memview, (&__pyx_v_memviewslice)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1040; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; goto __pyx_L0; - /* "View.MemoryView":1034 + /* "View.MemoryView":1036 * * @cname('__pyx_memoryview_copy_object') * cdef memoryview_copy(memoryview memview): # <<<<<<<<<<<<<< @@ -13018,7 +16315,7 @@ static PyObject *__pyx_memoryview_copy_object(struct __pyx_memoryview_obj *__pyx return __pyx_r; } -/* "View.MemoryView":1041 +/* "View.MemoryView":1043 * * @cname('__pyx_memoryview_copy_object_from_slice') * cdef memoryview_copy_from_slice(memoryview memview, __Pyx_memviewslice *memviewslice): # <<<<<<<<<<<<<< @@ -13041,18 +16338,18 @@ static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview int __pyx_clineno = 0; __Pyx_RefNannySetupContext("memoryview_copy_from_slice", 0); - /* "View.MemoryView":1048 + /* "View.MemoryView":1050 * cdef int (*to_dtype_func)(char *, object) except 0 * * if isinstance(memview, _memoryviewslice): # <<<<<<<<<<<<<< * to_object_func = (<_memoryviewslice> memview).to_object_func * to_dtype_func = (<_memoryviewslice> memview).to_dtype_func */ - __pyx_t_1 = __Pyx_TypeCheck(((PyObject *)__pyx_v_memview), ((PyObject *)__pyx_memoryviewslice_type)); + __pyx_t_1 = __Pyx_TypeCheck(((PyObject *)__pyx_v_memview), __pyx_memoryviewslice_type); __pyx_t_2 = (__pyx_t_1 != 0); if (__pyx_t_2) { - /* "View.MemoryView":1049 + /* "View.MemoryView":1051 * * if isinstance(memview, _memoryviewslice): * to_object_func = (<_memoryviewslice> memview).to_object_func # <<<<<<<<<<<<<< @@ -13062,7 +16359,7 @@ static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview __pyx_t_3 = ((struct __pyx_memoryviewslice_obj *)__pyx_v_memview)->to_object_func; __pyx_v_to_object_func = __pyx_t_3; - /* "View.MemoryView":1050 + /* "View.MemoryView":1052 * if isinstance(memview, _memoryviewslice): * to_object_func = (<_memoryviewslice> memview).to_object_func * to_dtype_func = (<_memoryviewslice> memview).to_dtype_func # <<<<<<<<<<<<<< @@ -13071,20 +16368,28 @@ static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview */ __pyx_t_4 = ((struct __pyx_memoryviewslice_obj *)__pyx_v_memview)->to_dtype_func; __pyx_v_to_dtype_func = __pyx_t_4; + + /* "View.MemoryView":1050 + * cdef int (*to_dtype_func)(char *, object) except 0 + * + * if isinstance(memview, _memoryviewslice): # <<<<<<<<<<<<<< + * to_object_func = (<_memoryviewslice> memview).to_object_func + * to_dtype_func = (<_memoryviewslice> memview).to_dtype_func + */ goto __pyx_L3; } - /*else*/ { - /* "View.MemoryView":1052 + /* "View.MemoryView":1054 * to_dtype_func = (<_memoryviewslice> memview).to_dtype_func * else: * to_object_func = NULL # <<<<<<<<<<<<<< * to_dtype_func = NULL * */ + /*else*/ { __pyx_v_to_object_func = NULL; - /* "View.MemoryView":1053 + /* "View.MemoryView":1055 * else: * to_object_func = NULL * to_dtype_func = NULL # <<<<<<<<<<<<<< @@ -13095,7 +16400,7 @@ static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview } __pyx_L3:; - /* "View.MemoryView":1055 + /* "View.MemoryView":1057 * to_dtype_func = NULL * * return memoryview_fromslice(memviewslice[0], memview.view.ndim, # <<<<<<<<<<<<<< @@ -13104,20 +16409,20 @@ static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview */ __Pyx_XDECREF(__pyx_r); - /* "View.MemoryView":1057 + /* "View.MemoryView":1059 * return memoryview_fromslice(memviewslice[0], memview.view.ndim, * to_object_func, to_dtype_func, * memview.dtype_is_object) # <<<<<<<<<<<<<< * * */ - __pyx_t_5 = __pyx_memoryview_fromslice((__pyx_v_memviewslice[0]), __pyx_v_memview->view.ndim, __pyx_v_to_object_func, __pyx_v_to_dtype_func, __pyx_v_memview->dtype_is_object); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 1055; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __pyx_memoryview_fromslice((__pyx_v_memviewslice[0]), __pyx_v_memview->view.ndim, __pyx_v_to_object_func, __pyx_v_to_dtype_func, __pyx_v_memview->dtype_is_object); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1057; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __pyx_r = __pyx_t_5; __pyx_t_5 = 0; goto __pyx_L0; - /* "View.MemoryView":1041 + /* "View.MemoryView":1043 * * @cname('__pyx_memoryview_copy_object_from_slice') * cdef memoryview_copy_from_slice(memoryview memview, __Pyx_memviewslice *memviewslice): # <<<<<<<<<<<<<< @@ -13136,7 +16441,7 @@ static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview return __pyx_r; } -/* "View.MemoryView":1063 +/* "View.MemoryView":1065 * * * cdef Py_ssize_t abs_py_ssize_t(Py_ssize_t arg) nogil: # <<<<<<<<<<<<<< @@ -13148,7 +16453,7 @@ static Py_ssize_t abs_py_ssize_t(Py_ssize_t __pyx_v_arg) { Py_ssize_t __pyx_r; int __pyx_t_1; - /* "View.MemoryView":1064 + /* "View.MemoryView":1066 * * cdef Py_ssize_t abs_py_ssize_t(Py_ssize_t arg) nogil: * if arg < 0: # <<<<<<<<<<<<<< @@ -13158,7 +16463,7 @@ static Py_ssize_t abs_py_ssize_t(Py_ssize_t __pyx_v_arg) { __pyx_t_1 = ((__pyx_v_arg < 0) != 0); if (__pyx_t_1) { - /* "View.MemoryView":1065 + /* "View.MemoryView":1067 * cdef Py_ssize_t abs_py_ssize_t(Py_ssize_t arg) nogil: * if arg < 0: * return -arg # <<<<<<<<<<<<<< @@ -13167,21 +16472,29 @@ static Py_ssize_t abs_py_ssize_t(Py_ssize_t __pyx_v_arg) { */ __pyx_r = (-__pyx_v_arg); goto __pyx_L0; + + /* "View.MemoryView":1066 + * + * cdef Py_ssize_t abs_py_ssize_t(Py_ssize_t arg) nogil: + * if arg < 0: # <<<<<<<<<<<<<< + * return -arg + * else: + */ } - /*else*/ { - /* "View.MemoryView":1067 + /* "View.MemoryView":1069 * return -arg * else: * return arg # <<<<<<<<<<<<<< * * @cname('__pyx_get_best_slice_order') */ + /*else*/ { __pyx_r = __pyx_v_arg; goto __pyx_L0; } - /* "View.MemoryView":1063 + /* "View.MemoryView":1065 * * * cdef Py_ssize_t abs_py_ssize_t(Py_ssize_t arg) nogil: # <<<<<<<<<<<<<< @@ -13194,7 +16507,7 @@ static Py_ssize_t abs_py_ssize_t(Py_ssize_t __pyx_v_arg) { return __pyx_r; } -/* "View.MemoryView":1070 +/* "View.MemoryView":1072 * * @cname('__pyx_get_best_slice_order') * cdef char get_best_order(__Pyx_memviewslice *mslice, int ndim) nogil: # <<<<<<<<<<<<<< @@ -13211,7 +16524,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ int __pyx_t_2; int __pyx_t_3; - /* "View.MemoryView":1075 + /* "View.MemoryView":1077 * """ * cdef int i * cdef Py_ssize_t c_stride = 0 # <<<<<<<<<<<<<< @@ -13220,7 +16533,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ */ __pyx_v_c_stride = 0; - /* "View.MemoryView":1076 + /* "View.MemoryView":1078 * cdef int i * cdef Py_ssize_t c_stride = 0 * cdef Py_ssize_t f_stride = 0 # <<<<<<<<<<<<<< @@ -13229,17 +16542,17 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ */ __pyx_v_f_stride = 0; - /* "View.MemoryView":1078 + /* "View.MemoryView":1080 * cdef Py_ssize_t f_stride = 0 * * for i in range(ndim - 1, -1, -1): # <<<<<<<<<<<<<< * if mslice.shape[i] > 1: * c_stride = mslice.strides[i] */ - for (__pyx_t_1 = (__pyx_v_ndim - 1); __pyx_t_1 > -1; __pyx_t_1-=1) { + for (__pyx_t_1 = (__pyx_v_ndim - 1); __pyx_t_1 > -1L; __pyx_t_1-=1) { __pyx_v_i = __pyx_t_1; - /* "View.MemoryView":1079 + /* "View.MemoryView":1081 * * for i in range(ndim - 1, -1, -1): * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< @@ -13249,7 +16562,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ __pyx_t_2 = (((__pyx_v_mslice->shape[__pyx_v_i]) > 1) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1080 + /* "View.MemoryView":1082 * for i in range(ndim - 1, -1, -1): * if mslice.shape[i] > 1: * c_stride = mslice.strides[i] # <<<<<<<<<<<<<< @@ -13258,7 +16571,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ */ __pyx_v_c_stride = (__pyx_v_mslice->strides[__pyx_v_i]); - /* "View.MemoryView":1081 + /* "View.MemoryView":1083 * if mslice.shape[i] > 1: * c_stride = mslice.strides[i] * break # <<<<<<<<<<<<<< @@ -13266,11 +16579,19 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ * for i in range(ndim): */ goto __pyx_L4_break; + + /* "View.MemoryView":1081 + * + * for i in range(ndim - 1, -1, -1): + * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< + * c_stride = mslice.strides[i] + * break + */ } } __pyx_L4_break:; - /* "View.MemoryView":1083 + /* "View.MemoryView":1085 * break * * for i in range(ndim): # <<<<<<<<<<<<<< @@ -13281,7 +16602,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_1; __pyx_t_3+=1) { __pyx_v_i = __pyx_t_3; - /* "View.MemoryView":1084 + /* "View.MemoryView":1086 * * for i in range(ndim): * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< @@ -13291,7 +16612,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ __pyx_t_2 = (((__pyx_v_mslice->shape[__pyx_v_i]) > 1) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1085 + /* "View.MemoryView":1087 * for i in range(ndim): * if mslice.shape[i] > 1: * f_stride = mslice.strides[i] # <<<<<<<<<<<<<< @@ -13300,7 +16621,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ */ __pyx_v_f_stride = (__pyx_v_mslice->strides[__pyx_v_i]); - /* "View.MemoryView":1086 + /* "View.MemoryView":1088 * if mslice.shape[i] > 1: * f_stride = mslice.strides[i] * break # <<<<<<<<<<<<<< @@ -13308,11 +16629,19 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): */ goto __pyx_L7_break; + + /* "View.MemoryView":1086 + * + * for i in range(ndim): + * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< + * f_stride = mslice.strides[i] + * break + */ } } __pyx_L7_break:; - /* "View.MemoryView":1088 + /* "View.MemoryView":1090 * break * * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): # <<<<<<<<<<<<<< @@ -13322,7 +16651,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ __pyx_t_2 = ((abs_py_ssize_t(__pyx_v_c_stride) <= abs_py_ssize_t(__pyx_v_f_stride)) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1089 + /* "View.MemoryView":1091 * * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): * return 'C' # <<<<<<<<<<<<<< @@ -13331,21 +16660,29 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ */ __pyx_r = 'C'; goto __pyx_L0; + + /* "View.MemoryView":1090 + * break + * + * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): # <<<<<<<<<<<<<< + * return 'C' + * else: + */ } - /*else*/ { - /* "View.MemoryView":1091 + /* "View.MemoryView":1093 * return 'C' * else: * return 'F' # <<<<<<<<<<<<<< * * @cython.cdivision(True) */ + /*else*/ { __pyx_r = 'F'; goto __pyx_L0; } - /* "View.MemoryView":1070 + /* "View.MemoryView":1072 * * @cname('__pyx_get_best_slice_order') * cdef char get_best_order(__Pyx_memviewslice *mslice, int ndim) nogil: # <<<<<<<<<<<<<< @@ -13358,7 +16695,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ return __pyx_r; } -/* "View.MemoryView":1094 +/* "View.MemoryView":1096 * * @cython.cdivision(True) * cdef void _copy_strided_to_strided(char *src_data, Py_ssize_t *src_strides, # <<<<<<<<<<<<<< @@ -13378,7 +16715,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v Py_ssize_t __pyx_t_4; Py_ssize_t __pyx_t_5; - /* "View.MemoryView":1101 + /* "View.MemoryView":1103 * * cdef Py_ssize_t i * cdef Py_ssize_t src_extent = src_shape[0] # <<<<<<<<<<<<<< @@ -13387,7 +16724,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ __pyx_v_src_extent = (__pyx_v_src_shape[0]); - /* "View.MemoryView":1102 + /* "View.MemoryView":1104 * cdef Py_ssize_t i * cdef Py_ssize_t src_extent = src_shape[0] * cdef Py_ssize_t dst_extent = dst_shape[0] # <<<<<<<<<<<<<< @@ -13396,7 +16733,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ __pyx_v_dst_extent = (__pyx_v_dst_shape[0]); - /* "View.MemoryView":1103 + /* "View.MemoryView":1105 * cdef Py_ssize_t src_extent = src_shape[0] * cdef Py_ssize_t dst_extent = dst_shape[0] * cdef Py_ssize_t src_stride = src_strides[0] # <<<<<<<<<<<<<< @@ -13405,7 +16742,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ __pyx_v_src_stride = (__pyx_v_src_strides[0]); - /* "View.MemoryView":1104 + /* "View.MemoryView":1106 * cdef Py_ssize_t dst_extent = dst_shape[0] * cdef Py_ssize_t src_stride = src_strides[0] * cdef Py_ssize_t dst_stride = dst_strides[0] # <<<<<<<<<<<<<< @@ -13414,7 +16751,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ __pyx_v_dst_stride = (__pyx_v_dst_strides[0]); - /* "View.MemoryView":1106 + /* "View.MemoryView":1108 * cdef Py_ssize_t dst_stride = dst_strides[0] * * if ndim == 1: # <<<<<<<<<<<<<< @@ -13424,7 +16761,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v __pyx_t_1 = ((__pyx_v_ndim == 1) != 0); if (__pyx_t_1) { - /* "View.MemoryView":1107 + /* "View.MemoryView":1109 * * if ndim == 1: * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<< @@ -13444,7 +16781,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v goto __pyx_L5_bool_binop_done; } - /* "View.MemoryView":1108 + /* "View.MemoryView":1110 * if ndim == 1: * if (src_stride > 0 and dst_stride > 0 and * src_stride == itemsize == dst_stride): # <<<<<<<<<<<<<< @@ -13458,9 +16795,17 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v __pyx_t_3 = (__pyx_t_2 != 0); __pyx_t_1 = __pyx_t_3; __pyx_L5_bool_binop_done:; + + /* "View.MemoryView":1109 + * + * if ndim == 1: + * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<< + * src_stride == itemsize == dst_stride): + * memcpy(dst_data, src_data, itemsize * dst_extent) + */ if (__pyx_t_1) { - /* "View.MemoryView":1109 + /* "View.MemoryView":1111 * if (src_stride > 0 and dst_stride > 0 and * src_stride == itemsize == dst_stride): * memcpy(dst_data, src_data, itemsize * dst_extent) # <<<<<<<<<<<<<< @@ -13468,22 +16813,30 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v * for i in range(dst_extent): */ memcpy(__pyx_v_dst_data, __pyx_v_src_data, (__pyx_v_itemsize * __pyx_v_dst_extent)); + + /* "View.MemoryView":1109 + * + * if ndim == 1: + * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<< + * src_stride == itemsize == dst_stride): + * memcpy(dst_data, src_data, itemsize * dst_extent) + */ goto __pyx_L4; } - /*else*/ { - /* "View.MemoryView":1111 + /* "View.MemoryView":1113 * memcpy(dst_data, src_data, itemsize * dst_extent) * else: * for i in range(dst_extent): # <<<<<<<<<<<<<< * memcpy(dst_data, src_data, itemsize) * src_data += src_stride */ + /*else*/ { __pyx_t_4 = __pyx_v_dst_extent; for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { __pyx_v_i = __pyx_t_5; - /* "View.MemoryView":1112 + /* "View.MemoryView":1114 * else: * for i in range(dst_extent): * memcpy(dst_data, src_data, itemsize) # <<<<<<<<<<<<<< @@ -13492,7 +16845,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ memcpy(__pyx_v_dst_data, __pyx_v_src_data, __pyx_v_itemsize); - /* "View.MemoryView":1113 + /* "View.MemoryView":1115 * for i in range(dst_extent): * memcpy(dst_data, src_data, itemsize) * src_data += src_stride # <<<<<<<<<<<<<< @@ -13501,33 +16854,41 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ __pyx_v_src_data = (__pyx_v_src_data + __pyx_v_src_stride); - /* "View.MemoryView":1114 + /* "View.MemoryView":1116 * memcpy(dst_data, src_data, itemsize) * src_data += src_stride * dst_data += dst_stride # <<<<<<<<<<<<<< * else: * for i in range(dst_extent): */ - __pyx_v_dst_data = (__pyx_v_dst_data + __pyx_v_dst_stride); - } - } - __pyx_L4:; + __pyx_v_dst_data = (__pyx_v_dst_data + __pyx_v_dst_stride); + } + } + __pyx_L4:; + + /* "View.MemoryView":1108 + * cdef Py_ssize_t dst_stride = dst_strides[0] + * + * if ndim == 1: # <<<<<<<<<<<<<< + * if (src_stride > 0 and dst_stride > 0 and + * src_stride == itemsize == dst_stride): + */ goto __pyx_L3; } - /*else*/ { - /* "View.MemoryView":1116 + /* "View.MemoryView":1118 * dst_data += dst_stride * else: * for i in range(dst_extent): # <<<<<<<<<<<<<< * _copy_strided_to_strided(src_data, src_strides + 1, * dst_data, dst_strides + 1, */ + /*else*/ { __pyx_t_4 = __pyx_v_dst_extent; for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { __pyx_v_i = __pyx_t_5; - /* "View.MemoryView":1117 + /* "View.MemoryView":1119 * else: * for i in range(dst_extent): * _copy_strided_to_strided(src_data, src_strides + 1, # <<<<<<<<<<<<<< @@ -13536,7 +16897,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ _copy_strided_to_strided(__pyx_v_src_data, (__pyx_v_src_strides + 1), __pyx_v_dst_data, (__pyx_v_dst_strides + 1), (__pyx_v_src_shape + 1), (__pyx_v_dst_shape + 1), (__pyx_v_ndim - 1), __pyx_v_itemsize); - /* "View.MemoryView":1121 + /* "View.MemoryView":1123 * src_shape + 1, dst_shape + 1, * ndim - 1, itemsize) * src_data += src_stride # <<<<<<<<<<<<<< @@ -13545,7 +16906,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ __pyx_v_src_data = (__pyx_v_src_data + __pyx_v_src_stride); - /* "View.MemoryView":1122 + /* "View.MemoryView":1124 * ndim - 1, itemsize) * src_data += src_stride * dst_data += dst_stride # <<<<<<<<<<<<<< @@ -13557,7 +16918,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v } __pyx_L3:; - /* "View.MemoryView":1094 + /* "View.MemoryView":1096 * * @cython.cdivision(True) * cdef void _copy_strided_to_strided(char *src_data, Py_ssize_t *src_strides, # <<<<<<<<<<<<<< @@ -13568,7 +16929,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v /* function exit code */ } -/* "View.MemoryView":1124 +/* "View.MemoryView":1126 * dst_data += dst_stride * * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< @@ -13578,7 +16939,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v static void copy_strided_to_strided(__Pyx_memviewslice *__pyx_v_src, __Pyx_memviewslice *__pyx_v_dst, int __pyx_v_ndim, size_t __pyx_v_itemsize) { - /* "View.MemoryView":1127 + /* "View.MemoryView":1129 * __Pyx_memviewslice *dst, * int ndim, size_t itemsize) nogil: * _copy_strided_to_strided(src.data, src.strides, dst.data, dst.strides, # <<<<<<<<<<<<<< @@ -13587,7 +16948,7 @@ static void copy_strided_to_strided(__Pyx_memviewslice *__pyx_v_src, __Pyx_memvi */ _copy_strided_to_strided(__pyx_v_src->data, __pyx_v_src->strides, __pyx_v_dst->data, __pyx_v_dst->strides, __pyx_v_src->shape, __pyx_v_dst->shape, __pyx_v_ndim, __pyx_v_itemsize); - /* "View.MemoryView":1124 + /* "View.MemoryView":1126 * dst_data += dst_stride * * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< @@ -13598,7 +16959,7 @@ static void copy_strided_to_strided(__Pyx_memviewslice *__pyx_v_src, __Pyx_memvi /* function exit code */ } -/* "View.MemoryView":1131 +/* "View.MemoryView":1133 * * @cname('__pyx_memoryview_slice_get_size') * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: # <<<<<<<<<<<<<< @@ -13614,7 +16975,7 @@ static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *__pyx_v_sr int __pyx_t_2; int __pyx_t_3; - /* "View.MemoryView":1134 + /* "View.MemoryView":1136 * "Return the size of the memory occupied by the slice in number of bytes" * cdef int i * cdef Py_ssize_t size = src.memview.view.itemsize # <<<<<<<<<<<<<< @@ -13624,7 +16985,7 @@ static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *__pyx_v_sr __pyx_t_1 = __pyx_v_src->memview->view.itemsize; __pyx_v_size = __pyx_t_1; - /* "View.MemoryView":1136 + /* "View.MemoryView":1138 * cdef Py_ssize_t size = src.memview.view.itemsize * * for i in range(ndim): # <<<<<<<<<<<<<< @@ -13635,7 +16996,7 @@ static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *__pyx_v_sr for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { __pyx_v_i = __pyx_t_3; - /* "View.MemoryView":1137 + /* "View.MemoryView":1139 * * for i in range(ndim): * size *= src.shape[i] # <<<<<<<<<<<<<< @@ -13645,7 +17006,7 @@ static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *__pyx_v_sr __pyx_v_size = (__pyx_v_size * (__pyx_v_src->shape[__pyx_v_i])); } - /* "View.MemoryView":1139 + /* "View.MemoryView":1141 * size *= src.shape[i] * * return size # <<<<<<<<<<<<<< @@ -13655,7 +17016,7 @@ static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *__pyx_v_sr __pyx_r = __pyx_v_size; goto __pyx_L0; - /* "View.MemoryView":1131 + /* "View.MemoryView":1133 * * @cname('__pyx_memoryview_slice_get_size') * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: # <<<<<<<<<<<<<< @@ -13668,7 +17029,7 @@ static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *__pyx_v_sr return __pyx_r; } -/* "View.MemoryView":1142 +/* "View.MemoryView":1144 * * @cname('__pyx_fill_contig_strides_array') * cdef Py_ssize_t fill_contig_strides_array( # <<<<<<<<<<<<<< @@ -13683,7 +17044,7 @@ static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ int __pyx_t_2; int __pyx_t_3; - /* "View.MemoryView":1151 + /* "View.MemoryView":1153 * cdef int idx * * if order == 'F': # <<<<<<<<<<<<<< @@ -13693,7 +17054,7 @@ static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ __pyx_t_1 = ((__pyx_v_order == 'F') != 0); if (__pyx_t_1) { - /* "View.MemoryView":1152 + /* "View.MemoryView":1154 * * if order == 'F': * for idx in range(ndim): # <<<<<<<<<<<<<< @@ -13704,7 +17065,7 @@ static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { __pyx_v_idx = __pyx_t_3; - /* "View.MemoryView":1153 + /* "View.MemoryView":1155 * if order == 'F': * for idx in range(ndim): * strides[idx] = stride # <<<<<<<<<<<<<< @@ -13713,7 +17074,7 @@ static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ */ (__pyx_v_strides[__pyx_v_idx]) = __pyx_v_stride; - /* "View.MemoryView":1154 + /* "View.MemoryView":1156 * for idx in range(ndim): * strides[idx] = stride * stride = stride * shape[idx] # <<<<<<<<<<<<<< @@ -13722,21 +17083,29 @@ static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ */ __pyx_v_stride = (__pyx_v_stride * (__pyx_v_shape[__pyx_v_idx])); } + + /* "View.MemoryView":1153 + * cdef int idx + * + * if order == 'F': # <<<<<<<<<<<<<< + * for idx in range(ndim): + * strides[idx] = stride + */ goto __pyx_L3; } - /*else*/ { - /* "View.MemoryView":1156 + /* "View.MemoryView":1158 * stride = stride * shape[idx] * else: * for idx in range(ndim - 1, -1, -1): # <<<<<<<<<<<<<< * strides[idx] = stride * stride = stride * shape[idx] */ - for (__pyx_t_2 = (__pyx_v_ndim - 1); __pyx_t_2 > -1; __pyx_t_2-=1) { + /*else*/ { + for (__pyx_t_2 = (__pyx_v_ndim - 1); __pyx_t_2 > -1L; __pyx_t_2-=1) { __pyx_v_idx = __pyx_t_2; - /* "View.MemoryView":1157 + /* "View.MemoryView":1159 * else: * for idx in range(ndim - 1, -1, -1): * strides[idx] = stride # <<<<<<<<<<<<<< @@ -13745,7 +17114,7 @@ static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ */ (__pyx_v_strides[__pyx_v_idx]) = __pyx_v_stride; - /* "View.MemoryView":1158 + /* "View.MemoryView":1160 * for idx in range(ndim - 1, -1, -1): * strides[idx] = stride * stride = stride * shape[idx] # <<<<<<<<<<<<<< @@ -13757,7 +17126,7 @@ static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ } __pyx_L3:; - /* "View.MemoryView":1160 + /* "View.MemoryView":1162 * stride = stride * shape[idx] * * return stride # <<<<<<<<<<<<<< @@ -13767,7 +17136,7 @@ static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ __pyx_r = __pyx_v_stride; goto __pyx_L0; - /* "View.MemoryView":1142 + /* "View.MemoryView":1144 * * @cname('__pyx_fill_contig_strides_array') * cdef Py_ssize_t fill_contig_strides_array( # <<<<<<<<<<<<<< @@ -13780,7 +17149,7 @@ static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ return __pyx_r; } -/* "View.MemoryView":1163 +/* "View.MemoryView":1165 * * @cname('__pyx_memoryview_copy_data_to_temp') * cdef void *copy_data_to_temp(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< @@ -13803,7 +17172,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, const char *__pyx_filename = NULL; int __pyx_clineno = 0; - /* "View.MemoryView":1174 + /* "View.MemoryView":1176 * cdef void *result * * cdef size_t itemsize = src.memview.view.itemsize # <<<<<<<<<<<<<< @@ -13813,7 +17182,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, __pyx_t_1 = __pyx_v_src->memview->view.itemsize; __pyx_v_itemsize = __pyx_t_1; - /* "View.MemoryView":1175 + /* "View.MemoryView":1177 * * cdef size_t itemsize = src.memview.view.itemsize * cdef size_t size = slice_get_size(src, ndim) # <<<<<<<<<<<<<< @@ -13822,7 +17191,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, */ __pyx_v_size = __pyx_memoryview_slice_get_size(__pyx_v_src, __pyx_v_ndim); - /* "View.MemoryView":1177 + /* "View.MemoryView":1179 * cdef size_t size = slice_get_size(src, ndim) * * result = malloc(size) # <<<<<<<<<<<<<< @@ -13831,7 +17200,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, */ __pyx_v_result = malloc(__pyx_v_size); - /* "View.MemoryView":1178 + /* "View.MemoryView":1180 * * result = malloc(size) * if not result: # <<<<<<<<<<<<<< @@ -13841,19 +17210,25 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, __pyx_t_2 = ((!(__pyx_v_result != 0)) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1179 + /* "View.MemoryView":1181 * result = malloc(size) * if not result: * _err(MemoryError, NULL) # <<<<<<<<<<<<<< * * */ - __pyx_t_3 = __pyx_memoryview_err(__pyx_builtin_MemoryError, NULL); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 1179; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L3; + __pyx_t_3 = __pyx_memoryview_err(__pyx_builtin_MemoryError, NULL); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1181; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "View.MemoryView":1180 + * + * result = malloc(size) + * if not result: # <<<<<<<<<<<<<< + * _err(MemoryError, NULL) + * + */ } - __pyx_L3:; - /* "View.MemoryView":1182 + /* "View.MemoryView":1184 * * * tmpslice.data = result # <<<<<<<<<<<<<< @@ -13862,7 +17237,7 @@ static void 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-14258,39 +17647,47 @@ static int __pyx_memoryview_err(PyObject *__pyx_v_error, char *__pyx_v_msg) { } } if (!__pyx_t_5) { - __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 1218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1220; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_GOTREF(__pyx_t_2); } else { - __pyx_t_6 = PyTuple_New(1+1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 1218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyTuple_New(1+1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1220; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_GIVEREF(__pyx_t_5); PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_5); __pyx_t_5 = NULL; __Pyx_GIVEREF(__pyx_t_3); PyTuple_SET_ITEM(__pyx_t_6, 0+1, __pyx_t_3); __pyx_t_3 = 0; - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_6, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 1218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_6, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1220; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; } __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - {__pyx_filename = __pyx_f[1]; __pyx_lineno = 1218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1220; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "View.MemoryView":1219 + * @cname('__pyx_memoryview_err') + * cdef int _err(object error, char *msg) except -1 with gil: + * if msg != NULL: # <<<<<<<<<<<<<< + * raise error(msg.decode('ascii')) + * else: + */ } - /*else*/ { - /* "View.MemoryView":1220 + /* "View.MemoryView":1222 * raise error(msg.decode('ascii')) * else: * raise error # <<<<<<<<<<<<<< * * @cname('__pyx_memoryview_copy_contents') */ + /*else*/ { __Pyx_Raise(__pyx_v_error, 0, 0, 0); - {__pyx_filename = __pyx_f[1]; __pyx_lineno = 1220; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - /* "View.MemoryView":1216 + /* "View.MemoryView":1218 * * @cname('__pyx_memoryview_err') * cdef int _err(object error, char *msg) except -1 with gil: # <<<<<<<<<<<<<< @@ -14315,7 +17712,7 @@ static int __pyx_memoryview_err(PyObject *__pyx_v_error, char *__pyx_v_msg) { return __pyx_r; } -/* "View.MemoryView":1223 +/* "View.MemoryView":1225 * * @cname('__pyx_memoryview_copy_contents') * cdef int memoryview_copy_contents(__Pyx_memviewslice src, # <<<<<<<<<<<<<< @@ -14344,7 +17741,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ const char *__pyx_filename = NULL; int __pyx_clineno = 0; - /* "View.MemoryView":1231 + /* "View.MemoryView":1233 * Check for overlapping memory and verify the shapes. * """ * cdef void *tmpdata = NULL # <<<<<<<<<<<<<< @@ -14353,7 +17750,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_v_tmpdata = NULL; - /* "View.MemoryView":1232 + /* "View.MemoryView":1234 * """ * cdef void *tmpdata = NULL * cdef size_t itemsize = src.memview.view.itemsize # <<<<<<<<<<<<<< @@ -14363,7 +17760,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_1 = __pyx_v_src.memview->view.itemsize; __pyx_v_itemsize = __pyx_t_1; - /* "View.MemoryView":1234 + /* "View.MemoryView":1236 * cdef size_t itemsize = src.memview.view.itemsize * cdef int i * cdef char order = get_best_order(&src, src_ndim) # <<<<<<<<<<<<<< @@ -14372,7 +17769,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_v_order = __pyx_get_best_slice_order((&__pyx_v_src), __pyx_v_src_ndim); - /* "View.MemoryView":1235 + /* "View.MemoryView":1237 * cdef int i * cdef char order = get_best_order(&src, src_ndim) * cdef bint broadcasting = False # <<<<<<<<<<<<<< @@ -14381,7 +17778,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_v_broadcasting = 0; - /* "View.MemoryView":1236 + /* "View.MemoryView":1238 * cdef char order = get_best_order(&src, src_ndim) * cdef bint broadcasting = False * cdef bint direct_copy = False # <<<<<<<<<<<<<< @@ -14390,7 +17787,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_v_direct_copy = 0; - /* "View.MemoryView":1239 + /* "View.MemoryView":1241 * cdef __Pyx_memviewslice tmp * * if src_ndim < dst_ndim: # <<<<<<<<<<<<<< @@ -14400,7 +17797,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = ((__pyx_v_src_ndim < __pyx_v_dst_ndim) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1240 + /* "View.MemoryView":1242 * * if src_ndim < dst_ndim: * broadcast_leading(&src, src_ndim, dst_ndim) # <<<<<<<<<<<<<< @@ -14408,10 +17805,18 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ * broadcast_leading(&dst, dst_ndim, src_ndim) */ __pyx_memoryview_broadcast_leading((&__pyx_v_src), __pyx_v_src_ndim, __pyx_v_dst_ndim); + + /* "View.MemoryView":1241 + * cdef __Pyx_memviewslice tmp + * + * if src_ndim < dst_ndim: # <<<<<<<<<<<<<< + * broadcast_leading(&src, src_ndim, dst_ndim) + * elif dst_ndim < src_ndim: + */ goto __pyx_L3; } - /* "View.MemoryView":1241 + /* "View.MemoryView":1243 * if src_ndim < dst_ndim: * broadcast_leading(&src, src_ndim, dst_ndim) * elif dst_ndim < src_ndim: # <<<<<<<<<<<<<< @@ -14421,7 +17826,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = ((__pyx_v_dst_ndim < __pyx_v_src_ndim) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1242 + /* "View.MemoryView":1244 * broadcast_leading(&src, src_ndim, dst_ndim) * elif dst_ndim < src_ndim: * broadcast_leading(&dst, dst_ndim, src_ndim) # <<<<<<<<<<<<<< @@ -14429,11 +17834,18 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ * cdef int ndim = max(src_ndim, dst_ndim) */ __pyx_memoryview_broadcast_leading((&__pyx_v_dst), __pyx_v_dst_ndim, __pyx_v_src_ndim); - goto __pyx_L3; + + /* "View.MemoryView":1243 + * if src_ndim < dst_ndim: + * broadcast_leading(&src, src_ndim, dst_ndim) + * elif dst_ndim < src_ndim: # <<<<<<<<<<<<<< + * broadcast_leading(&dst, dst_ndim, src_ndim) + * + */ } __pyx_L3:; - /* "View.MemoryView":1244 + /* "View.MemoryView":1246 * broadcast_leading(&dst, dst_ndim, src_ndim) * * cdef int ndim = max(src_ndim, dst_ndim) # <<<<<<<<<<<<<< @@ -14449,7 +17861,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ } __pyx_v_ndim = __pyx_t_5; - /* "View.MemoryView":1246 + /* "View.MemoryView":1248 * cdef int ndim = max(src_ndim, dst_ndim) * * for i in range(ndim): # <<<<<<<<<<<<<< @@ -14460,7 +17872,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_5; __pyx_t_3+=1) { __pyx_v_i = __pyx_t_3; - /* "View.MemoryView":1247 + /* "View.MemoryView":1249 * * for i in range(ndim): * if src.shape[i] != dst.shape[i]: # <<<<<<<<<<<<<< @@ -14470,7 +17882,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = (((__pyx_v_src.shape[__pyx_v_i]) != (__pyx_v_dst.shape[__pyx_v_i])) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1248 + /* "View.MemoryView":1250 * for i in range(ndim): * if src.shape[i] != dst.shape[i]: * if src.shape[i] == 1: # <<<<<<<<<<<<<< @@ -14480,7 +17892,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = (((__pyx_v_src.shape[__pyx_v_i]) == 1) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1249 + /* "View.MemoryView":1251 * if src.shape[i] != dst.shape[i]: * if src.shape[i] == 1: * broadcasting = True # <<<<<<<<<<<<<< @@ -14489,7 +17901,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_v_broadcasting = 1; - /* "View.MemoryView":1250 + /* "View.MemoryView":1252 * if src.shape[i] == 1: * broadcasting = True * src.strides[i] = 0 # <<<<<<<<<<<<<< @@ -14497,25 +17909,39 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ * _err_extents(i, dst.shape[i], src.shape[i]) */ (__pyx_v_src.strides[__pyx_v_i]) = 0; + + /* "View.MemoryView":1250 + * for i in range(ndim): + * if src.shape[i] != dst.shape[i]: + * if src.shape[i] == 1: # <<<<<<<<<<<<<< + * broadcasting = True + * src.strides[i] = 0 + */ goto __pyx_L7; } - /*else*/ { - /* "View.MemoryView":1252 + /* "View.MemoryView":1254 * src.strides[i] = 0 * else: * _err_extents(i, dst.shape[i], src.shape[i]) # <<<<<<<<<<<<<< * * if src.suboffsets[i] >= 0: */ - __pyx_t_4 = __pyx_memoryview_err_extents(__pyx_v_i, (__pyx_v_dst.shape[__pyx_v_i]), (__pyx_v_src.shape[__pyx_v_i])); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 1252; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + /*else*/ { + __pyx_t_4 = __pyx_memoryview_err_extents(__pyx_v_i, (__pyx_v_dst.shape[__pyx_v_i]), (__pyx_v_src.shape[__pyx_v_i])); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1254; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_L7:; - goto __pyx_L6; + + /* "View.MemoryView":1249 + * + * for i in range(ndim): + * if src.shape[i] != dst.shape[i]: # <<<<<<<<<<<<<< + * if src.shape[i] == 1: + * broadcasting = True + */ } - __pyx_L6:; - /* "View.MemoryView":1254 + /* "View.MemoryView":1256 * _err_extents(i, dst.shape[i], src.shape[i]) * * if src.suboffsets[i] >= 0: # <<<<<<<<<<<<<< @@ -14525,20 +17951,26 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = (((__pyx_v_src.suboffsets[__pyx_v_i]) >= 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1255 + /* "View.MemoryView":1257 * * if src.suboffsets[i] >= 0: * _err_dim(ValueError, "Dimension %d is not direct", i) # <<<<<<<<<<<<<< * * if slices_overlap(&src, &dst, ndim, itemsize): */ - __pyx_t_4 = __pyx_memoryview_err_dim(__pyx_builtin_ValueError, __pyx_k_Dimension_d_is_not_direct, __pyx_v_i); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 1255; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L8; + __pyx_t_4 = __pyx_memoryview_err_dim(__pyx_builtin_ValueError, __pyx_k_Dimension_d_is_not_direct, __pyx_v_i); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1257; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "View.MemoryView":1256 + * _err_extents(i, dst.shape[i], src.shape[i]) + * + * if src.suboffsets[i] >= 0: # <<<<<<<<<<<<<< + * _err_dim(ValueError, "Dimension %d is not direct", i) + * + */ } - __pyx_L8:; } - /* "View.MemoryView":1257 + /* "View.MemoryView":1259 * _err_dim(ValueError, "Dimension %d is not direct", i) * * if slices_overlap(&src, &dst, ndim, itemsize): # <<<<<<<<<<<<<< @@ -14548,7 +17980,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = (__pyx_slices_overlap((&__pyx_v_src), (&__pyx_v_dst), __pyx_v_ndim, __pyx_v_itemsize) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1259 + /* "View.MemoryView":1261 * if slices_overlap(&src, &dst, ndim, itemsize): * * if not slice_is_contig(&src, order, ndim): # <<<<<<<<<<<<<< @@ -14558,7 +17990,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = ((!(__pyx_memviewslice_is_contig((&__pyx_v_src), __pyx_v_order, __pyx_v_ndim) != 0)) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1260 + /* "View.MemoryView":1262 * * if not slice_is_contig(&src, order, ndim): * order = get_best_order(&dst, ndim) # <<<<<<<<<<<<<< @@ -14566,21 +17998,27 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ * tmpdata = copy_data_to_temp(&src, &tmp, order, ndim) */ __pyx_v_order = __pyx_get_best_slice_order((&__pyx_v_dst), __pyx_v_ndim); - goto __pyx_L10; + + /* "View.MemoryView":1261 + * if slices_overlap(&src, &dst, ndim, itemsize): + * + * if not slice_is_contig(&src, order, ndim): # <<<<<<<<<<<<<< + * order = get_best_order(&dst, ndim) + * + */ } - __pyx_L10:; - /* "View.MemoryView":1262 + /* "View.MemoryView":1264 * order = get_best_order(&dst, ndim) * * tmpdata = copy_data_to_temp(&src, &tmp, order, ndim) # <<<<<<<<<<<<<< * src = tmp * */ - __pyx_t_6 = __pyx_memoryview_copy_data_to_temp((&__pyx_v_src), (&__pyx_v_tmp), __pyx_v_order, __pyx_v_ndim); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 1262; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __pyx_memoryview_copy_data_to_temp((&__pyx_v_src), (&__pyx_v_tmp), __pyx_v_order, __pyx_v_ndim); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1264; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_tmpdata = __pyx_t_6; - /* "View.MemoryView":1263 + /* "View.MemoryView":1265 * * tmpdata = copy_data_to_temp(&src, &tmp, order, ndim) * src = tmp # <<<<<<<<<<<<<< @@ -14588,11 +18026,17 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ * if not broadcasting: */ __pyx_v_src = __pyx_v_tmp; - goto __pyx_L9; + + /* "View.MemoryView":1259 + * _err_dim(ValueError, "Dimension %d is not direct", i) + * + * if slices_overlap(&src, &dst, ndim, itemsize): # <<<<<<<<<<<<<< + * + * if not slice_is_contig(&src, order, ndim): + */ } - __pyx_L9:; - /* "View.MemoryView":1265 + /* "View.MemoryView":1267 * src = tmp * * if not broadcasting: # <<<<<<<<<<<<<< @@ -14602,7 +18046,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = ((!(__pyx_v_broadcasting != 0)) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1268 + /* "View.MemoryView":1270 * * * if slice_is_contig(&src, 'C', ndim): # <<<<<<<<<<<<<< @@ -14612,7 +18056,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = (__pyx_memviewslice_is_contig((&__pyx_v_src), 'C', __pyx_v_ndim) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1269 + /* "View.MemoryView":1271 * * if slice_is_contig(&src, 'C', ndim): * direct_copy = slice_is_contig(&dst, 'C', ndim) # <<<<<<<<<<<<<< @@ -14620,10 +18064,18 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ * direct_copy = slice_is_contig(&dst, 'F', ndim) */ __pyx_v_direct_copy = __pyx_memviewslice_is_contig((&__pyx_v_dst), 'C', __pyx_v_ndim); + + /* "View.MemoryView":1270 + * + * + * if slice_is_contig(&src, 'C', ndim): # <<<<<<<<<<<<<< + * direct_copy = slice_is_contig(&dst, 'C', ndim) + * elif slice_is_contig(&src, 'F', ndim): + */ goto __pyx_L12; } - /* "View.MemoryView":1270 + /* "View.MemoryView":1272 * if slice_is_contig(&src, 'C', ndim): * direct_copy = slice_is_contig(&dst, 'C', ndim) * elif slice_is_contig(&src, 'F', ndim): # <<<<<<<<<<<<<< @@ -14633,7 +18085,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = (__pyx_memviewslice_is_contig((&__pyx_v_src), 'F', __pyx_v_ndim) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1271 + /* "View.MemoryView":1273 * direct_copy = slice_is_contig(&dst, 'C', ndim) * elif slice_is_contig(&src, 'F', ndim): * direct_copy = slice_is_contig(&dst, 'F', ndim) # <<<<<<<<<<<<<< @@ -14641,11 +18093,18 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ * if direct_copy: */ __pyx_v_direct_copy = __pyx_memviewslice_is_contig((&__pyx_v_dst), 'F', __pyx_v_ndim); - goto __pyx_L12; + + /* "View.MemoryView":1272 + * if slice_is_contig(&src, 'C', ndim): + * direct_copy = slice_is_contig(&dst, 'C', ndim) + * elif slice_is_contig(&src, 'F', ndim): # <<<<<<<<<<<<<< + * direct_copy = slice_is_contig(&dst, 'F', ndim) + * + */ } __pyx_L12:; - /* "View.MemoryView":1273 + /* "View.MemoryView":1275 * direct_copy = slice_is_contig(&dst, 'F', ndim) * * if direct_copy: # <<<<<<<<<<<<<< @@ -14655,7 +18114,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = (__pyx_v_direct_copy != 0); if (__pyx_t_2) { - /* "View.MemoryView":1275 + /* "View.MemoryView":1277 * if direct_copy: * * refcount_copying(&dst, dtype_is_object, ndim, False) # <<<<<<<<<<<<<< @@ -14664,7 +18123,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 0); - /* "View.MemoryView":1276 + /* "View.MemoryView":1278 * * refcount_copying(&dst, dtype_is_object, ndim, False) * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) # <<<<<<<<<<<<<< @@ -14673,7 +18132,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ memcpy(__pyx_v_dst.data, __pyx_v_src.data, __pyx_memoryview_slice_get_size((&__pyx_v_src), __pyx_v_ndim)); - /* "View.MemoryView":1277 + /* "View.MemoryView":1279 * refcount_copying(&dst, dtype_is_object, ndim, False) * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) * refcount_copying(&dst, dtype_is_object, ndim, True) # <<<<<<<<<<<<<< @@ -14682,7 +18141,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 1); - /* "View.MemoryView":1278 + /* "View.MemoryView":1280 * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) * refcount_copying(&dst, dtype_is_object, ndim, True) * free(tmpdata) # <<<<<<<<<<<<<< @@ -14691,7 +18150,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ free(__pyx_v_tmpdata); - /* "View.MemoryView":1279 + /* "View.MemoryView":1281 * refcount_copying(&dst, dtype_is_object, ndim, True) * free(tmpdata) * return 0 # <<<<<<<<<<<<<< @@ -14700,12 +18159,26 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_r = 0; goto __pyx_L0; + + /* "View.MemoryView":1275 + * direct_copy = slice_is_contig(&dst, 'F', ndim) + * + * if direct_copy: # <<<<<<<<<<<<<< + * + * refcount_copying(&dst, dtype_is_object, ndim, False) + */ } - goto __pyx_L11; + + /* "View.MemoryView":1267 + * src = tmp + * + * if not broadcasting: # <<<<<<<<<<<<<< + * + * + */ } - __pyx_L11:; - /* "View.MemoryView":1281 + /* "View.MemoryView":1283 * return 0 * * if order == 'F' == get_best_order(&dst, ndim): # <<<<<<<<<<<<<< @@ -14719,28 +18192,34 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_7 = (__pyx_t_2 != 0); if (__pyx_t_7) { - /* "View.MemoryView":1284 + /* "View.MemoryView":1286 * * * transpose_memslice(&src) # <<<<<<<<<<<<<< * transpose_memslice(&dst) * */ - __pyx_t_5 = __pyx_memslice_transpose((&__pyx_v_src)); if (unlikely(__pyx_t_5 == 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 1284; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __pyx_memslice_transpose((&__pyx_v_src)); if (unlikely(__pyx_t_5 == 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1286; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "View.MemoryView":1285 + /* "View.MemoryView":1287 * * transpose_memslice(&src) * transpose_memslice(&dst) # <<<<<<<<<<<<<< * * refcount_copying(&dst, dtype_is_object, ndim, False) */ - __pyx_t_5 = __pyx_memslice_transpose((&__pyx_v_dst)); if (unlikely(__pyx_t_5 == 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 1285; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L14; + __pyx_t_5 = __pyx_memslice_transpose((&__pyx_v_dst)); if (unlikely(__pyx_t_5 == 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1287; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "View.MemoryView":1283 + * return 0 + * + * if order == 'F' == get_best_order(&dst, ndim): # <<<<<<<<<<<<<< + * + * + */ } - __pyx_L14:; - /* "View.MemoryView":1287 + /* "View.MemoryView":1289 * transpose_memslice(&dst) * * refcount_copying(&dst, dtype_is_object, ndim, False) # <<<<<<<<<<<<<< @@ -14749,7 +18228,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 0); - /* "View.MemoryView":1288 + /* "View.MemoryView":1290 * * refcount_copying(&dst, dtype_is_object, ndim, False) * copy_strided_to_strided(&src, &dst, ndim, itemsize) # <<<<<<<<<<<<<< @@ -14758,7 +18237,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ copy_strided_to_strided((&__pyx_v_src), (&__pyx_v_dst), __pyx_v_ndim, __pyx_v_itemsize); - /* "View.MemoryView":1289 + /* "View.MemoryView":1291 * refcount_copying(&dst, dtype_is_object, ndim, False) * copy_strided_to_strided(&src, &dst, ndim, itemsize) * refcount_copying(&dst, dtype_is_object, ndim, True) # <<<<<<<<<<<<<< @@ -14767,7 +18246,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 1); - /* "View.MemoryView":1291 + /* "View.MemoryView":1293 * refcount_copying(&dst, dtype_is_object, ndim, True) * * free(tmpdata) # <<<<<<<<<<<<<< @@ -14776,7 +18255,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ free(__pyx_v_tmpdata); - /* "View.MemoryView":1292 + /* "View.MemoryView":1294 * * free(tmpdata) * return 0 # <<<<<<<<<<<<<< @@ -14786,7 +18265,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_r = 0; goto __pyx_L0; - /* "View.MemoryView":1223 + /* "View.MemoryView":1225 * * @cname('__pyx_memoryview_copy_contents') * cdef int memoryview_copy_contents(__Pyx_memviewslice src, # <<<<<<<<<<<<<< @@ -14810,7 +18289,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ return __pyx_r; } -/* "View.MemoryView":1295 +/* "View.MemoryView":1297 * * @cname('__pyx_memoryview_broadcast_leading') * cdef void broadcast_leading(__Pyx_memviewslice *mslice, # <<<<<<<<<<<<<< @@ -14824,7 +18303,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic int __pyx_t_1; int __pyx_t_2; - /* "View.MemoryView":1299 + /* "View.MemoryView":1301 * int ndim_other) nogil: * cdef int i * cdef int offset = ndim_other - ndim # <<<<<<<<<<<<<< @@ -14833,17 +18312,17 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic */ __pyx_v_offset = (__pyx_v_ndim_other - __pyx_v_ndim); - /* "View.MemoryView":1301 + /* "View.MemoryView":1303 * cdef int offset = ndim_other - ndim * * for i in range(ndim - 1, -1, -1): # <<<<<<<<<<<<<< * mslice.shape[i + offset] = mslice.shape[i] * mslice.strides[i + offset] = mslice.strides[i] */ - for (__pyx_t_1 = (__pyx_v_ndim - 1); __pyx_t_1 > -1; __pyx_t_1-=1) { + for (__pyx_t_1 = (__pyx_v_ndim - 1); __pyx_t_1 > -1L; __pyx_t_1-=1) { __pyx_v_i = __pyx_t_1; - /* "View.MemoryView":1302 + /* "View.MemoryView":1304 * * for i in range(ndim - 1, -1, -1): * mslice.shape[i + offset] = mslice.shape[i] # <<<<<<<<<<<<<< @@ -14852,7 +18331,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic */ (__pyx_v_mslice->shape[(__pyx_v_i + __pyx_v_offset)]) = (__pyx_v_mslice->shape[__pyx_v_i]); - /* "View.MemoryView":1303 + /* "View.MemoryView":1305 * for i in range(ndim - 1, -1, -1): * mslice.shape[i + offset] = mslice.shape[i] * mslice.strides[i + offset] = mslice.strides[i] # <<<<<<<<<<<<<< @@ -14861,7 +18340,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic */ (__pyx_v_mslice->strides[(__pyx_v_i + __pyx_v_offset)]) = (__pyx_v_mslice->strides[__pyx_v_i]); - /* "View.MemoryView":1304 + /* "View.MemoryView":1306 * mslice.shape[i + offset] = mslice.shape[i] * mslice.strides[i + offset] = mslice.strides[i] * mslice.suboffsets[i + offset] = mslice.suboffsets[i] # <<<<<<<<<<<<<< @@ -14871,7 +18350,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic (__pyx_v_mslice->suboffsets[(__pyx_v_i + __pyx_v_offset)]) = (__pyx_v_mslice->suboffsets[__pyx_v_i]); } - /* "View.MemoryView":1306 + /* "View.MemoryView":1308 * mslice.suboffsets[i + offset] = mslice.suboffsets[i] * * for i in range(offset): # <<<<<<<<<<<<<< @@ -14882,7 +18361,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) { __pyx_v_i = __pyx_t_2; - /* "View.MemoryView":1307 + /* "View.MemoryView":1309 * * for i in range(offset): * mslice.shape[i] = 1 # <<<<<<<<<<<<<< @@ -14891,7 +18370,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic */ (__pyx_v_mslice->shape[__pyx_v_i]) = 1; - /* "View.MemoryView":1308 + /* "View.MemoryView":1310 * for i in range(offset): * mslice.shape[i] = 1 * mslice.strides[i] = mslice.strides[0] # <<<<<<<<<<<<<< @@ -14900,17 +18379,17 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic */ (__pyx_v_mslice->strides[__pyx_v_i]) = (__pyx_v_mslice->strides[0]); - /* "View.MemoryView":1309 + /* "View.MemoryView":1311 * mslice.shape[i] = 1 * mslice.strides[i] = mslice.strides[0] * mslice.suboffsets[i] = -1 # <<<<<<<<<<<<<< * * */ - (__pyx_v_mslice->suboffsets[__pyx_v_i]) = -1; + (__pyx_v_mslice->suboffsets[__pyx_v_i]) = -1L; } - /* "View.MemoryView":1295 + /* "View.MemoryView":1297 * * @cname('__pyx_memoryview_broadcast_leading') * cdef void broadcast_leading(__Pyx_memviewslice *mslice, # <<<<<<<<<<<<<< @@ -14921,7 +18400,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic /* function exit code */ } -/* "View.MemoryView":1317 +/* "View.MemoryView":1319 * * @cname('__pyx_memoryview_refcount_copying') * cdef void refcount_copying(__Pyx_memviewslice *dst, bint dtype_is_object, # <<<<<<<<<<<<<< @@ -14932,7 +18411,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic static void __pyx_memoryview_refcount_copying(__Pyx_memviewslice *__pyx_v_dst, int __pyx_v_dtype_is_object, int __pyx_v_ndim, int __pyx_v_inc) { int __pyx_t_1; - /* "View.MemoryView":1321 + /* "View.MemoryView":1323 * * * if dtype_is_object: # <<<<<<<<<<<<<< @@ -14942,7 +18421,7 @@ static void __pyx_memoryview_refcount_copying(__Pyx_memviewslice *__pyx_v_dst, i __pyx_t_1 = (__pyx_v_dtype_is_object != 0); if (__pyx_t_1) { - /* "View.MemoryView":1322 + /* "View.MemoryView":1324 * * if dtype_is_object: * refcount_objects_in_slice_with_gil(dst.data, dst.shape, # <<<<<<<<<<<<<< @@ -14950,11 +18429,17 @@ static void __pyx_memoryview_refcount_copying(__Pyx_memviewslice *__pyx_v_dst, i * */ __pyx_memoryview_refcount_objects_in_slice_with_gil(__pyx_v_dst->data, __pyx_v_dst->shape, __pyx_v_dst->strides, __pyx_v_ndim, __pyx_v_inc); - goto __pyx_L3; + + /* "View.MemoryView":1323 + * + * + * if dtype_is_object: # <<<<<<<<<<<<<< + * refcount_objects_in_slice_with_gil(dst.data, dst.shape, + * dst.strides, ndim, inc) + */ } - __pyx_L3:; - /* "View.MemoryView":1317 + /* "View.MemoryView":1319 * * @cname('__pyx_memoryview_refcount_copying') * cdef void refcount_copying(__Pyx_memviewslice *dst, bint dtype_is_object, # <<<<<<<<<<<<<< @@ -14965,7 +18450,7 @@ static void __pyx_memoryview_refcount_copying(__Pyx_memviewslice *__pyx_v_dst, i /* function exit code */ } -/* "View.MemoryView":1326 +/* "View.MemoryView":1328 * * @cname('__pyx_memoryview_refcount_objects_in_slice_with_gil') * cdef void refcount_objects_in_slice_with_gil(char *data, Py_ssize_t *shape, # <<<<<<<<<<<<<< @@ -14980,7 +18465,7 @@ static void __pyx_memoryview_refcount_objects_in_slice_with_gil(char *__pyx_v_da #endif __Pyx_RefNannySetupContext("refcount_objects_in_slice_with_gil", 0); - /* "View.MemoryView":1329 + /* "View.MemoryView":1331 * Py_ssize_t *strides, int ndim, * bint inc) with gil: * refcount_objects_in_slice(data, shape, strides, ndim, inc) # <<<<<<<<<<<<<< @@ -14989,7 +18474,7 @@ static void __pyx_memoryview_refcount_objects_in_slice_with_gil(char *__pyx_v_da */ __pyx_memoryview_refcount_objects_in_slice(__pyx_v_data, __pyx_v_shape, __pyx_v_strides, __pyx_v_ndim, __pyx_v_inc); - /* "View.MemoryView":1326 + /* "View.MemoryView":1328 * * @cname('__pyx_memoryview_refcount_objects_in_slice_with_gil') * cdef void refcount_objects_in_slice_with_gil(char *data, Py_ssize_t *shape, # <<<<<<<<<<<<<< @@ -15004,7 +18489,7 @@ static void __pyx_memoryview_refcount_objects_in_slice_with_gil(char *__pyx_v_da #endif } -/* "View.MemoryView":1332 +/* "View.MemoryView":1334 * * @cname('__pyx_memoryview_refcount_objects_in_slice') * cdef void refcount_objects_in_slice(char *data, Py_ssize_t *shape, # <<<<<<<<<<<<<< @@ -15020,7 +18505,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss int __pyx_t_3; __Pyx_RefNannySetupContext("refcount_objects_in_slice", 0); - /* "View.MemoryView":1336 + /* "View.MemoryView":1338 * cdef Py_ssize_t i * * for i in range(shape[0]): # <<<<<<<<<<<<<< @@ -15031,7 +18516,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) { __pyx_v_i = __pyx_t_2; - /* "View.MemoryView":1337 + /* "View.MemoryView":1339 * * for i in range(shape[0]): * if ndim == 1: # <<<<<<<<<<<<<< @@ -15041,7 +18526,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss __pyx_t_3 = ((__pyx_v_ndim == 1) != 0); if (__pyx_t_3) { - /* "View.MemoryView":1338 + /* "View.MemoryView":1340 * for i in range(shape[0]): * if ndim == 1: * if inc: # <<<<<<<<<<<<<< @@ -15051,7 +18536,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss __pyx_t_3 = (__pyx_v_inc != 0); if (__pyx_t_3) { - /* "View.MemoryView":1339 + /* "View.MemoryView":1341 * if ndim == 1: * if inc: * Py_INCREF(( data)[0]) # <<<<<<<<<<<<<< @@ -15059,36 +18544,60 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss * Py_DECREF(( data)[0]) */ Py_INCREF((((PyObject **)__pyx_v_data)[0])); + + /* "View.MemoryView":1340 + * for i in range(shape[0]): + * if ndim == 1: + * if inc: # <<<<<<<<<<<<<< + * Py_INCREF(( data)[0]) + * else: + */ goto __pyx_L6; } - /*else*/ { - /* "View.MemoryView":1341 + /* "View.MemoryView":1343 * Py_INCREF(( data)[0]) * else: * Py_DECREF(( data)[0]) # <<<<<<<<<<<<<< * else: * refcount_objects_in_slice(data, shape + 1, strides + 1, */ + /*else*/ { Py_DECREF((((PyObject **)__pyx_v_data)[0])); } __pyx_L6:; + + /* "View.MemoryView":1339 + * + * for i in range(shape[0]): + * if ndim == 1: # <<<<<<<<<<<<<< + * if inc: + * Py_INCREF(( data)[0]) + */ goto __pyx_L5; } - /*else*/ { - /* "View.MemoryView":1343 + /* "View.MemoryView":1345 * Py_DECREF(( data)[0]) * else: * refcount_objects_in_slice(data, shape + 1, strides + 1, # <<<<<<<<<<<<<< * ndim - 1, inc) * + */ + /*else*/ { + + /* "View.MemoryView":1346 + * else: + * refcount_objects_in_slice(data, shape + 1, strides + 1, + * ndim - 1, inc) # <<<<<<<<<<<<<< + * + * data += strides[0] */ __pyx_memoryview_refcount_objects_in_slice(__pyx_v_data, (__pyx_v_shape + 1), (__pyx_v_strides + 1), (__pyx_v_ndim - 1), __pyx_v_inc); } __pyx_L5:; - /* "View.MemoryView":1346 + /* "View.MemoryView":1348 * ndim - 1, inc) * * data += strides[0] # <<<<<<<<<<<<<< @@ -15098,7 +18607,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss __pyx_v_data = (__pyx_v_data + (__pyx_v_strides[0])); } - /* "View.MemoryView":1332 + /* "View.MemoryView":1334 * * @cname('__pyx_memoryview_refcount_objects_in_slice') * cdef void refcount_objects_in_slice(char *data, Py_ssize_t *shape, # <<<<<<<<<<<<<< @@ -15110,7 +18619,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss __Pyx_RefNannyFinishContext(); } -/* "View.MemoryView":1352 +/* "View.MemoryView":1354 * * @cname('__pyx_memoryview_slice_assign_scalar') * cdef void slice_assign_scalar(__Pyx_memviewslice *dst, int ndim, # <<<<<<<<<<<<<< @@ -15120,7 +18629,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss static void __pyx_memoryview_slice_assign_scalar(__Pyx_memviewslice *__pyx_v_dst, int __pyx_v_ndim, size_t __pyx_v_itemsize, void *__pyx_v_item, int __pyx_v_dtype_is_object) { - /* "View.MemoryView":1355 + /* "View.MemoryView":1357 * size_t itemsize, void *item, * bint dtype_is_object) nogil: * refcount_copying(dst, dtype_is_object, ndim, False) # <<<<<<<<<<<<<< @@ -15129,7 +18638,7 @@ static void __pyx_memoryview_slice_assign_scalar(__Pyx_memviewslice *__pyx_v_dst */ __pyx_memoryview_refcount_copying(__pyx_v_dst, __pyx_v_dtype_is_object, __pyx_v_ndim, 0); - /* "View.MemoryView":1356 + /* "View.MemoryView":1358 * bint dtype_is_object) nogil: * refcount_copying(dst, dtype_is_object, ndim, False) * _slice_assign_scalar(dst.data, dst.shape, dst.strides, ndim, # <<<<<<<<<<<<<< @@ -15138,7 +18647,7 @@ static void __pyx_memoryview_slice_assign_scalar(__Pyx_memviewslice *__pyx_v_dst */ __pyx_memoryview__slice_assign_scalar(__pyx_v_dst->data, __pyx_v_dst->shape, __pyx_v_dst->strides, __pyx_v_ndim, __pyx_v_itemsize, __pyx_v_item); - /* "View.MemoryView":1358 + /* "View.MemoryView":1360 * _slice_assign_scalar(dst.data, dst.shape, dst.strides, ndim, * itemsize, item) * refcount_copying(dst, dtype_is_object, ndim, True) # <<<<<<<<<<<<<< @@ -15147,7 +18656,7 @@ static void __pyx_memoryview_slice_assign_scalar(__Pyx_memviewslice *__pyx_v_dst */ __pyx_memoryview_refcount_copying(__pyx_v_dst, __pyx_v_dtype_is_object, __pyx_v_ndim, 1); - /* "View.MemoryView":1352 + /* "View.MemoryView":1354 * * @cname('__pyx_memoryview_slice_assign_scalar') * cdef void slice_assign_scalar(__Pyx_memviewslice *dst, int ndim, # <<<<<<<<<<<<<< @@ -15158,7 +18667,7 @@ static void __pyx_memoryview_slice_assign_scalar(__Pyx_memviewslice *__pyx_v_dst /* function exit code */ } -/* "View.MemoryView":1362 +/* "View.MemoryView":1364 * * @cname('__pyx_memoryview__slice_assign_scalar') * cdef void _slice_assign_scalar(char *data, Py_ssize_t *shape, # <<<<<<<<<<<<<< @@ -15174,7 +18683,7 @@ static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t Py_ssize_t __pyx_t_2; Py_ssize_t __pyx_t_3; - /* "View.MemoryView":1366 + /* "View.MemoryView":1368 * size_t itemsize, void *item) nogil: * cdef Py_ssize_t i * cdef Py_ssize_t stride = strides[0] # <<<<<<<<<<<<<< @@ -15183,7 +18692,7 @@ static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t */ __pyx_v_stride = (__pyx_v_strides[0]); - /* "View.MemoryView":1367 + /* "View.MemoryView":1369 * cdef Py_ssize_t i * cdef Py_ssize_t stride = strides[0] * cdef Py_ssize_t extent = shape[0] # <<<<<<<<<<<<<< @@ -15192,7 +18701,7 @@ static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t */ __pyx_v_extent = (__pyx_v_shape[0]); - /* "View.MemoryView":1369 + /* "View.MemoryView":1371 * cdef Py_ssize_t extent = shape[0] * * if ndim == 1: # <<<<<<<<<<<<<< @@ -15202,7 +18711,7 @@ static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t __pyx_t_1 = ((__pyx_v_ndim == 1) != 0); if (__pyx_t_1) { - /* "View.MemoryView":1370 + /* "View.MemoryView":1372 * * if ndim == 1: * for i in range(extent): # <<<<<<<<<<<<<< @@ -15213,7 +18722,7 @@ static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { __pyx_v_i = __pyx_t_3; - /* "View.MemoryView":1371 + /* "View.MemoryView":1373 * if ndim == 1: * for i in range(extent): * memcpy(data, item, itemsize) # <<<<<<<<<<<<<< @@ -15222,7 +18731,7 @@ static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t */ memcpy(__pyx_v_data, __pyx_v_item, __pyx_v_itemsize); - /* "View.MemoryView":1372 + /* "View.MemoryView":1374 * for i in range(extent): * memcpy(data, item, itemsize) * data += stride # <<<<<<<<<<<<<< @@ -15231,22 +18740,30 @@ static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t */ __pyx_v_data = (__pyx_v_data + __pyx_v_stride); } + + /* "View.MemoryView":1371 + * cdef Py_ssize_t extent = shape[0] + * + * if ndim == 1: # <<<<<<<<<<<<<< + * for i in range(extent): + * memcpy(data, item, itemsize) + */ goto __pyx_L3; } - /*else*/ { - /* "View.MemoryView":1374 + /* "View.MemoryView":1376 * data += stride * else: * for i in range(extent): # <<<<<<<<<<<<<< * _slice_assign_scalar(data, shape + 1, strides + 1, * ndim - 1, itemsize, item) */ + /*else*/ { __pyx_t_2 = __pyx_v_extent; for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { __pyx_v_i = __pyx_t_3; - /* "View.MemoryView":1375 + /* "View.MemoryView":1377 * else: * for i in range(extent): * _slice_assign_scalar(data, shape + 1, strides + 1, # <<<<<<<<<<<<<< @@ -15255,7 +18772,7 @@ static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t */ __pyx_memoryview__slice_assign_scalar(__pyx_v_data, (__pyx_v_shape + 1), (__pyx_v_strides + 1), (__pyx_v_ndim - 1), __pyx_v_itemsize, __pyx_v_item); - /* "View.MemoryView":1377 + /* "View.MemoryView":1379 * _slice_assign_scalar(data, shape + 1, strides + 1, * ndim - 1, itemsize, item) * data += stride # <<<<<<<<<<<<<< @@ -15267,7 +18784,7 @@ static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t } __pyx_L3:; - /* "View.MemoryView":1362 + /* "View.MemoryView":1364 * * @cname('__pyx_memoryview__slice_assign_scalar') * cdef void _slice_assign_scalar(char *data, Py_ssize_t *shape, # <<<<<<<<<<<<<< @@ -15404,8 +18921,9 @@ static PyTypeObject __pyx_type___pyx_array = { 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ - #else - 0, /*reserved*/ + #endif + #if PY_MAJOR_VERSION >= 3 + 0, /*tp_as_async*/ #endif 0, /*tp_repr*/ 0, /*tp_as_number*/ @@ -15509,8 +19027,9 @@ static PyTypeObject __pyx_type___pyx_MemviewEnum = { 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ - #else - 0, /*reserved*/ + #endif + #if PY_MAJOR_VERSION >= 3 + 0, /*tp_as_async*/ #endif __pyx_MemviewEnum___repr__, /*tp_repr*/ 0, /*tp_as_number*/ @@ -15755,8 +19274,9 @@ static PyTypeObject __pyx_type___pyx_memoryview = { 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ - #else - 0, /*reserved*/ + #endif + #if PY_MAJOR_VERSION >= 3 + 0, /*tp_as_async*/ #endif __pyx_memoryview___repr__, /*tp_repr*/ 0, /*tp_as_number*/ @@ -15879,8 +19399,9 @@ static PyTypeObject __pyx_type___pyx_memoryviewslice = { 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ - #else - 0, /*reserved*/ + #endif + #if PY_MAJOR_VERSION >= 3 + 0, /*tp_as_async*/ #endif #if CYTHON_COMPILING_IN_PYPY __pyx_memoryview___repr__, /*tp_repr*/ @@ -15956,11 +19477,14 @@ static struct PyModuleDef __pyx_moduledef = { #endif static __Pyx_StringTabEntry __pyx_string_tab[] = { + {&__pyx_n_s_ASCII, __pyx_k_ASCII, sizeof(__pyx_k_ASCII), 0, 0, 1, 1}, {&__pyx_kp_s_Buffer_view_does_not_expose_stri, __pyx_k_Buffer_view_does_not_expose_stri, sizeof(__pyx_k_Buffer_view_does_not_expose_stri), 0, 0, 1, 0}, {&__pyx_kp_s_Can_only_create_a_buffer_that_is, __pyx_k_Can_only_create_a_buffer_that_is, sizeof(__pyx_k_Can_only_create_a_buffer_that_is), 0, 0, 1, 0}, {&__pyx_kp_s_Cannot_index_with_type_s, __pyx_k_Cannot_index_with_type_s, sizeof(__pyx_k_Cannot_index_with_type_s), 0, 0, 1, 0}, {&__pyx_n_s_Ellipsis, __pyx_k_Ellipsis, sizeof(__pyx_k_Ellipsis), 0, 0, 1, 1}, {&__pyx_kp_s_Empty_shape_tuple_for_cython_arr, __pyx_k_Empty_shape_tuple_for_cython_arr, sizeof(__pyx_k_Empty_shape_tuple_for_cython_arr), 0, 0, 1, 0}, + {&__pyx_kp_u_Format_string_allocated_too_shor, __pyx_k_Format_string_allocated_too_shor, sizeof(__pyx_k_Format_string_allocated_too_shor), 0, 1, 0, 0}, + {&__pyx_kp_u_Format_string_allocated_too_shor_2, __pyx_k_Format_string_allocated_too_shor_2, sizeof(__pyx_k_Format_string_allocated_too_shor_2), 0, 1, 0, 0}, {&__pyx_n_s_IndexError, __pyx_k_IndexError, sizeof(__pyx_k_IndexError), 0, 0, 1, 1}, {&__pyx_kp_s_Indirect_dimensions_not_supporte, __pyx_k_Indirect_dimensions_not_supporte, sizeof(__pyx_k_Indirect_dimensions_not_supporte), 0, 0, 1, 0}, {&__pyx_kp_s_Invalid_mode_expected_c_or_fortr, __pyx_k_Invalid_mode_expected_c_or_fortr, sizeof(__pyx_k_Invalid_mode_expected_c_or_fortr), 0, 0, 1, 0}, @@ -15968,8 +19492,10 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_MemoryError, __pyx_k_MemoryError, sizeof(__pyx_k_MemoryError), 0, 0, 1, 1}, {&__pyx_kp_s_MemoryView_of_r_at_0x_x, __pyx_k_MemoryView_of_r_at_0x_x, sizeof(__pyx_k_MemoryView_of_r_at_0x_x), 0, 0, 1, 0}, {&__pyx_kp_s_MemoryView_of_r_object, __pyx_k_MemoryView_of_r_object, sizeof(__pyx_k_MemoryView_of_r_object), 0, 0, 1, 0}, + {&__pyx_kp_u_Non_native_byte_order_not_suppor, __pyx_k_Non_native_byte_order_not_suppor, sizeof(__pyx_k_Non_native_byte_order_not_suppor), 0, 1, 0, 0}, {&__pyx_n_b_O, __pyx_k_O, sizeof(__pyx_k_O), 0, 0, 0, 1}, {&__pyx_kp_s_Out_of_bounds_on_buffer_access_a, __pyx_k_Out_of_bounds_on_buffer_access_a, sizeof(__pyx_k_Out_of_bounds_on_buffer_access_a), 0, 0, 1, 0}, + {&__pyx_n_s_RuntimeError, __pyx_k_RuntimeError, sizeof(__pyx_k_RuntimeError), 0, 0, 1, 1}, {&__pyx_n_s_TypeError, __pyx_k_TypeError, sizeof(__pyx_k_TypeError), 0, 0, 1, 1}, {&__pyx_kp_s_Unable_to_convert_item_to_object, __pyx_k_Unable_to_convert_item_to_object, sizeof(__pyx_k_Unable_to_convert_item_to_object), 0, 0, 1, 0}, {&__pyx_n_s_ValueError, __pyx_k_ValueError, sizeof(__pyx_k_ValueError), 0, 0, 1, 1}, @@ -16016,6 +19542,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_dist, __pyx_k_dist, sizeof(__pyx_k_dist), 0, 0, 1, 1}, {&__pyx_n_s_distnum, __pyx_k_distnum, sizeof(__pyx_k_distnum), 0, 0, 1, 1}, {&__pyx_n_s_dtype_is_object, __pyx_k_dtype_is_object, sizeof(__pyx_k_dtype_is_object), 0, 0, 1, 1}, + {&__pyx_n_s_encode, __pyx_k_encode, sizeof(__pyx_k_encode), 0, 0, 1, 1}, {&__pyx_n_s_enumerate, __pyx_k_enumerate, sizeof(__pyx_k_enumerate), 0, 0, 1, 1}, {&__pyx_n_s_error, __pyx_k_error, sizeof(__pyx_k_error), 0, 0, 1, 1}, {&__pyx_n_s_flags, __pyx_k_flags, sizeof(__pyx_k_flags), 0, 0, 1, 1}, @@ -16023,7 +19550,6 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_fortran, __pyx_k_fortran, sizeof(__pyx_k_fortran), 0, 0, 1, 1}, {&__pyx_n_u_fortran, __pyx_k_fortran, sizeof(__pyx_k_fortran), 0, 1, 0, 1}, {&__pyx_kp_s_got_differing_extents_in_dimensi, __pyx_k_got_differing_extents_in_dimensi, sizeof(__pyx_k_got_differing_extents_in_dimensi), 0, 0, 1, 0}, - {&__pyx_kp_s_home_richard_code_mdanalysis_pa, __pyx_k_home_richard_code_mdanalysis_pa, sizeof(__pyx_k_home_richard_code_mdanalysis_pa), 0, 0, 1, 0}, {&__pyx_n_s_i, __pyx_k_i, sizeof(__pyx_k_i), 0, 0, 1, 1}, {&__pyx_n_s_id, __pyx_k_id, sizeof(__pyx_k_id), 0, 0, 1, 1}, {&__pyx_n_s_import, __pyx_k_import, sizeof(__pyx_k_import), 0, 0, 1, 1}, @@ -16036,8 +19562,12 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_mode, __pyx_k_mode, sizeof(__pyx_k_mode), 0, 0, 1, 1}, {&__pyx_n_s_name, __pyx_k_name, sizeof(__pyx_k_name), 0, 0, 1, 1}, {&__pyx_n_s_name_2, __pyx_k_name_2, sizeof(__pyx_k_name_2), 0, 0, 1, 1}, + {&__pyx_kp_u_ndarray_is_not_C_contiguous, __pyx_k_ndarray_is_not_C_contiguous, sizeof(__pyx_k_ndarray_is_not_C_contiguous), 0, 1, 0, 0}, + {&__pyx_kp_u_ndarray_is_not_Fortran_contiguou, __pyx_k_ndarray_is_not_Fortran_contiguou, sizeof(__pyx_k_ndarray_is_not_Fortran_contiguou), 0, 1, 0, 0}, {&__pyx_n_s_ndim, __pyx_k_ndim, sizeof(__pyx_k_ndim), 0, 0, 1, 1}, + {&__pyx_kp_s_nfs_homes2_oliver_Library_pytho, __pyx_k_nfs_homes2_oliver_Library_pytho, sizeof(__pyx_k_nfs_homes2_oliver_Library_pytho), 0, 0, 1, 0}, {&__pyx_n_s_numcoords, __pyx_k_numcoords, sizeof(__pyx_k_numcoords), 0, 0, 1, 1}, + {&__pyx_n_s_numpy, __pyx_k_numpy, sizeof(__pyx_k_numpy), 0, 0, 1, 1}, {&__pyx_n_s_obj, __pyx_k_obj, sizeof(__pyx_k_obj), 0, 0, 1, 1}, {&__pyx_n_s_ortho_pbc, __pyx_k_ortho_pbc, sizeof(__pyx_k_ortho_pbc), 0, 0, 1, 1}, {&__pyx_n_s_pack, __pyx_k_pack, sizeof(__pyx_k_pack), 0, 0, 1, 1}, @@ -16064,18 +19594,20 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_triclinic_pbc, __pyx_k_triclinic_pbc, sizeof(__pyx_k_triclinic_pbc), 0, 0, 1, 1}, {&__pyx_kp_s_unable_to_allocate_array_data, __pyx_k_unable_to_allocate_array_data, sizeof(__pyx_k_unable_to_allocate_array_data), 0, 0, 1, 0}, {&__pyx_kp_s_unable_to_allocate_shape_and_str, __pyx_k_unable_to_allocate_shape_and_str, sizeof(__pyx_k_unable_to_allocate_shape_and_str), 0, 0, 1, 0}, + {&__pyx_kp_u_unknown_dtype_code_in_numpy_pxd, __pyx_k_unknown_dtype_code_in_numpy_pxd, sizeof(__pyx_k_unknown_dtype_code_in_numpy_pxd), 0, 1, 0, 0}, {&__pyx_n_s_unpack, __pyx_k_unpack, sizeof(__pyx_k_unpack), 0, 0, 1, 1}, {0, 0, 0, 0, 0, 0, 0} }; static int __Pyx_InitCachedBuiltins(void) { __pyx_builtin_range = __Pyx_GetBuiltinName(__pyx_n_s_range); if (!__pyx_builtin_range) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 271; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_builtin_ValueError = __Pyx_GetBuiltinName(__pyx_n_s_ValueError); if (!__pyx_builtin_ValueError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 127; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_builtin_MemoryError = __Pyx_GetBuiltinName(__pyx_n_s_MemoryError); if (!__pyx_builtin_MemoryError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_builtin_enumerate = __Pyx_GetBuiltinName(__pyx_n_s_enumerate); if (!__pyx_builtin_enumerate) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 145; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_builtin_Ellipsis = __Pyx_GetBuiltinName(__pyx_n_s_Ellipsis); if (!__pyx_builtin_Ellipsis) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_builtin_TypeError = __Pyx_GetBuiltinName(__pyx_n_s_TypeError); if (!__pyx_builtin_TypeError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_builtin_id = __Pyx_GetBuiltinName(__pyx_n_s_id); if (!__pyx_builtin_id) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 569; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_builtin_IndexError = __Pyx_GetBuiltinName(__pyx_n_s_IndexError); if (!__pyx_builtin_IndexError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 788; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_ValueError = __Pyx_GetBuiltinName(__pyx_n_s_ValueError); if (!__pyx_builtin_ValueError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_RuntimeError = 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{__pyx_filename = __pyx_f[0]; __pyx_lineno = 253; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__54); + __Pyx_GIVEREF(__pyx_tuple__54); + __pyx_codeobj__55 = (PyObject*)__Pyx_PyCode_New(3, 0, 4, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__54, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_nfs_homes2_oliver_Library_pytho, __pyx_n_s_triclinic_pbc, 253, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__55)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 253; __pyx_clineno = __LINE__; goto __pyx_L1_error;} /* "MDAnalysis/lib/distances.pyx":263 * @@ -16443,10 +20052,10 @@ static int __Pyx_InitCachedConstants(void) { * cdef int rows = len(coord) * cdef double cutoff2 = cutoff ** 2 */ - __pyx_tuple__49 = PyTuple_Pack(10, __pyx_n_s_coord, __pyx_n_s_sparse_contacts, __pyx_n_s_cutoff, __pyx_n_s_rows, __pyx_n_s_cutoff2, __pyx_n_s_coord_view, __pyx_n_s_i, __pyx_n_s_j, __pyx_n_s_rr, __pyx_n_s_dist); if (unlikely(!__pyx_tuple__49)) 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__pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__60); + __Pyx_GIVEREF(__pyx_tuple__60); - /* "View.MemoryView":277 + /* "View.MemoryView":279 * * cdef generic = Enum("") * cdef strided = Enum("") # default # <<<<<<<<<<<<<< * cdef indirect = Enum("") * */ - __pyx_tuple__54 = PyTuple_Pack(1, __pyx_kp_s_strided_and_direct); if (unlikely(!__pyx_tuple__54)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 277; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__54); - __Pyx_GIVEREF(__pyx_tuple__54); + __pyx_tuple__61 = PyTuple_Pack(1, __pyx_kp_s_strided_and_direct); if (unlikely(!__pyx_tuple__61)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__61); + __Pyx_GIVEREF(__pyx_tuple__61); - /* "View.MemoryView":278 + /* "View.MemoryView":280 * cdef generic = Enum("") * cdef strided = Enum("") # default * cdef indirect = Enum("") # <<<<<<<<<<<<<< * * */ - __pyx_tuple__55 = PyTuple_Pack(1, 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(unlikely(!__pyx_tuple__63)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 283; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__63); + __Pyx_GIVEREF(__pyx_tuple__63); - /* "View.MemoryView":282 + /* "View.MemoryView":284 * * cdef contiguous = Enum("") * cdef indirect_contiguous = Enum("") # <<<<<<<<<<<<<< * * */ - __pyx_tuple__57 = PyTuple_Pack(1, __pyx_kp_s_contiguous_and_indirect); if (unlikely(!__pyx_tuple__57)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 282; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__57); - __Pyx_GIVEREF(__pyx_tuple__57); + __pyx_tuple__64 = PyTuple_Pack(1, __pyx_kp_s_contiguous_and_indirect); if (unlikely(!__pyx_tuple__64)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 284; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__64); + __Pyx_GIVEREF(__pyx_tuple__64); __Pyx_RefNannyFinishContext(); return 0; __pyx_L1_error:; @@ -16556,18 +20165,24 @@ PyMODINIT_FUNC 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goto __pyx_L1_error;} #endif #ifdef __Pyx_FusedFunction_USED if (__pyx_FusedFunction_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #endif + #ifdef __Pyx_Coroutine_USED + if (__pyx_Coroutine_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif #ifdef __Pyx_Generator_USED if (__pyx_Generator_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #endif + #ifdef __Pyx_StopAsyncIteration_USED + if (__pyx_StopAsyncIteration_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif /*--- Library function declarations ---*/ /*--- Threads initialization code ---*/ #if defined(__PYX_FORCE_INIT_THREADS) && __PYX_FORCE_INIT_THREADS @@ -16590,12 +20205,12 @@ PyMODINIT_FUNC PyInit__distances(void) #endif if (PyObject_SetAttrString(__pyx_m, "__builtins__", __pyx_b) 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__pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } #if PY_MAJOR_VERSION >= 3 { @@ -16606,9 +20221,9 @@ PyMODINIT_FUNC PyInit__distances(void) } #endif /*--- Builtin init code ---*/ - if (unlikely(__Pyx_InitCachedBuiltins() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_InitCachedBuiltins() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} /*--- Constants init code ---*/ - if (unlikely(__Pyx_InitCachedConstants() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_InitCachedConstants() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} /*--- Global init code ---*/ generic = Py_None; Py_INCREF(Py_None); strided = Py_None; Py_INCREF(Py_None); @@ -16618,10 +20233,10 @@ PyMODINIT_FUNC PyInit__distances(void) /*--- Variable export code ---*/ /*--- 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__pyx_vtabptr_memoryview) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_memoryview_type = &__pyx_type___pyx_memoryview; __pyx_vtabptr__memoryviewslice = &__pyx_vtable__memoryviewslice; __pyx_vtable__memoryviewslice.__pyx_base = *__pyx_vtabptr_memoryview; __pyx_vtable__memoryviewslice.__pyx_base.convert_item_to_object = (PyObject *(*)(struct __pyx_memoryview_obj *, char *))__pyx_memoryviewslice_convert_item_to_object; __pyx_vtable__memoryviewslice.__pyx_base.assign_item_from_object = (PyObject *(*)(struct __pyx_memoryview_obj *, char *, PyObject *))__pyx_memoryviewslice_assign_item_from_object; __pyx_type___pyx_memoryviewslice.tp_base = __pyx_memoryview_type; - if (PyType_Ready(&__pyx_type___pyx_memoryviewslice) < 0) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 921; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyType_Ready(&__pyx_type___pyx_memoryviewslice) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 923; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_type___pyx_memoryviewslice.tp_print = 0; - if (__Pyx_SetVtable(__pyx_type___pyx_memoryviewslice.tp_dict, __pyx_vtabptr__memoryviewslice) < 0) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 921; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_SetVtable(__pyx_type___pyx_memoryviewslice.tp_dict, __pyx_vtabptr__memoryviewslice) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 923; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_memoryviewslice_type = &__pyx_type___pyx_memoryviewslice; /*--- Type import code ---*/ - __pyx_ptype_7c_numpy_ndarray = __Pyx_ImportType("numpy", "ndarray", sizeof(PyArrayObject), 0); if (unlikely(!__pyx_ptype_7c_numpy_ndarray)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_7cpython_4type_type = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "type", + #if CYTHON_COMPILING_IN_PYPY + sizeof(PyTypeObject), + #else + sizeof(PyHeapTypeObject), + #endif + 0); if (unlikely(!__pyx_ptype_7cpython_4type_type)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 9; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5numpy_dtype = __Pyx_ImportType("numpy", "dtype", sizeof(PyArray_Descr), 0); if (unlikely(!__pyx_ptype_5numpy_dtype)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 155; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5numpy_flatiter = __Pyx_ImportType("numpy", "flatiter", sizeof(PyArrayIterObject), 0); if (unlikely(!__pyx_ptype_5numpy_flatiter)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 168; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5numpy_broadcast = __Pyx_ImportType("numpy", "broadcast", sizeof(PyArrayMultiIterObject), 0); if (unlikely(!__pyx_ptype_5numpy_broadcast)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5numpy_ndarray = __Pyx_ImportType("numpy", "ndarray", sizeof(PyArrayObject), 0); if (unlikely(!__pyx_ptype_5numpy_ndarray)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5numpy_ufunc = __Pyx_ImportType("numpy", "ufunc", sizeof(PyUFuncObject), 0); if (unlikely(!__pyx_ptype_5numpy_ufunc)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;} /*--- Variable import code ---*/ /*--- Function import code ---*/ /*--- Execution code ---*/ + #if defined(__Pyx_Generator_USED) || defined(__Pyx_Coroutine_USED) + if (__Pyx_patch_abc() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif - /* "MDAnalysis/lib/distances.pyx":27 + /* "MDAnalysis/lib/distances.pyx":26 + * * cimport cython - * cimport c_numpy - * c_numpy.import_array() # <<<<<<<<<<<<<< + * import numpy # <<<<<<<<<<<<<< + * cimport numpy * - * cdef extern from "string.h": */ - import_array(); + __pyx_t_1 = __Pyx_Import(__pyx_n_s_numpy, 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_numpy, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; /* "MDAnalysis/lib/distances.pyx":55 * void minimum_image(double *x, float *box, float *inverse_box) * - * def calc_distance_array(c_numpy.ndarray ref, c_numpy.ndarray conf, # <<<<<<<<<<<<<< - * c_numpy.ndarray result): + * def calc_distance_array(numpy.ndarray ref, numpy.ndarray conf, # <<<<<<<<<<<<<< + * numpy.ndarray result): * cdef int confnum, refnum */ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3lib_10_distances_1calc_distance_array, NULL, __pyx_n_s_lib__distances); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -16675,9 +20307,9 @@ PyMODINIT_FUNC PyInit__distances(void) /* "MDAnalysis/lib/distances.pyx":65 * result.data) * - * def calc_distance_array_ortho(c_numpy.ndarray ref, c_numpy.ndarray conf, # <<<<<<<<<<<<<< - * c_numpy.ndarray box, - * c_numpy.ndarray result): + * def calc_distance_array_ortho(numpy.ndarray ref, numpy.ndarray conf, # <<<<<<<<<<<<<< + * numpy.ndarray box, + * numpy.ndarray result): */ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3lib_10_distances_3calc_distance_array_ortho, NULL, __pyx_n_s_lib__distances); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 65; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); @@ -16687,9 +20319,9 @@ PyMODINIT_FUNC PyInit__distances(void) /* "MDAnalysis/lib/distances.pyx":77 * result.data) * - * def calc_distance_array_triclinic(c_numpy.ndarray ref, c_numpy.ndarray conf, # <<<<<<<<<<<<<< - * c_numpy.ndarray box, - * c_numpy.ndarray result): + * def calc_distance_array_triclinic(numpy.ndarray ref, numpy.ndarray conf, # <<<<<<<<<<<<<< + * numpy.ndarray box, + * numpy.ndarray result): */ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3lib_10_distances_5calc_distance_array_triclinic, NULL, __pyx_n_s_lib__distances); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); @@ -16699,8 +20331,8 @@ PyMODINIT_FUNC PyInit__distances(void) /* "MDAnalysis/lib/distances.pyx":89 * result.data) * - * def calc_self_distance_array(c_numpy.ndarray ref, # <<<<<<<<<<<<<< - * c_numpy.ndarray result): + * def calc_self_distance_array(numpy.ndarray ref, # <<<<<<<<<<<<<< + * numpy.ndarray result): * cdef int refnum, distnum */ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3lib_10_distances_7calc_self_distance_array, NULL, __pyx_n_s_lib__distances); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -16711,9 +20343,9 @@ PyMODINIT_FUNC PyInit__distances(void) /* "MDAnalysis/lib/distances.pyx":98 * result.data, distnum) * - * def calc_self_distance_array_ortho(c_numpy.ndarray ref, # <<<<<<<<<<<<<< - * c_numpy.ndarray box, - * c_numpy.ndarray result): + * def calc_self_distance_array_ortho(numpy.ndarray ref, # <<<<<<<<<<<<<< + * numpy.ndarray box, + * numpy.ndarray result): */ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3lib_10_distances_9calc_self_distance_array_ortho, NULL, __pyx_n_s_lib__distances); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 98; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); @@ -16723,9 +20355,9 @@ PyMODINIT_FUNC PyInit__distances(void) /* "MDAnalysis/lib/distances.pyx":109 * result.data, distnum) * - * def calc_self_distance_array_triclinic(c_numpy.ndarray ref, # <<<<<<<<<<<<<< - * c_numpy.ndarray box, - * c_numpy.ndarray result): + * def calc_self_distance_array_triclinic(numpy.ndarray ref, # <<<<<<<<<<<<<< + * numpy.ndarray box, + * numpy.ndarray result): */ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3lib_10_distances_11calc_self_distance_array_triclinic, NULL, __pyx_n_s_lib__distances); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 109; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); @@ -16735,8 +20367,8 @@ PyMODINIT_FUNC PyInit__distances(void) /* "MDAnalysis/lib/distances.pyx":120 * result.data, distnum) * - * def coord_transform(c_numpy.ndarray coords, # <<<<<<<<<<<<<< - * c_numpy.ndarray box): + * def coord_transform(numpy.ndarray coords, # <<<<<<<<<<<<<< + * numpy.ndarray box): * cdef int numcoords */ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3lib_10_distances_13coord_transform, NULL, __pyx_n_s_lib__distances); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 120; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -16747,9 +20379,9 @@ PyMODINIT_FUNC PyInit__distances(void) /* "MDAnalysis/lib/distances.pyx":128 * box.data) * - * def calc_bond_distance(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray results): + * def calc_bond_distance(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray results): */ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3lib_10_distances_15calc_bond_distance, NULL, __pyx_n_s_lib__distances); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 128; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); @@ -16759,9 +20391,9 @@ PyMODINIT_FUNC PyInit__distances(void) /* "MDAnalysis/lib/distances.pyx":138 * results.data) * - * def calc_bond_distance_ortho(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray box, + * def calc_bond_distance_ortho(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray box, */ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3lib_10_distances_17calc_bond_distance_ortho, NULL, __pyx_n_s_lib__distances); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 138; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); @@ -16771,9 +20403,9 @@ PyMODINIT_FUNC PyInit__distances(void) /* "MDAnalysis/lib/distances.pyx":150 * results.data) * - * def calc_bond_distance_triclinic(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray box, + * def calc_bond_distance_triclinic(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray box, */ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3lib_10_distances_19calc_bond_distance_triclinic, NULL, __pyx_n_s_lib__distances); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 150; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); @@ -16783,9 +20415,9 @@ PyMODINIT_FUNC PyInit__distances(void) /* "MDAnalysis/lib/distances.pyx":162 * results.data) * - * def calc_angle(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray coords3, + * def calc_angle(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray coords3, */ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3lib_10_distances_21calc_angle, NULL, __pyx_n_s_lib__distances); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 162; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); @@ -16795,9 +20427,9 @@ PyMODINIT_FUNC PyInit__distances(void) /* "MDAnalysis/lib/distances.pyx":174 * results.data) * - * def calc_angle_ortho(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray coords3, + * def calc_angle_ortho(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray coords3, */ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3lib_10_distances_23calc_angle_ortho, NULL, __pyx_n_s_lib__distances); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 174; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); @@ -16807,9 +20439,9 @@ PyMODINIT_FUNC PyInit__distances(void) /* "MDAnalysis/lib/distances.pyx":188 * results.data) * - * def calc_angle_triclinic(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray coords3, + * def calc_angle_triclinic(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray coords3, */ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3lib_10_distances_25calc_angle_triclinic, NULL, __pyx_n_s_lib__distances); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 188; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); @@ -16819,9 +20451,9 @@ PyMODINIT_FUNC PyInit__distances(void) /* "MDAnalysis/lib/distances.pyx":202 * results.data) * - * def calc_dihedral(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray coords3, + * def calc_dihedral(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray coords3, */ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3lib_10_distances_27calc_dihedral, NULL, __pyx_n_s_lib__distances); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); @@ -16831,9 +20463,9 @@ PyMODINIT_FUNC PyInit__distances(void) /* "MDAnalysis/lib/distances.pyx":215 * results.data) * - * def calc_dihedral_ortho(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray coords3, + * def calc_dihedral_ortho(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray coords3, */ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3lib_10_distances_29calc_dihedral_ortho, NULL, __pyx_n_s_lib__distances); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); @@ -16843,9 +20475,9 @@ PyMODINIT_FUNC PyInit__distances(void) /* 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__Pyx_PyObject_Call(((PyObject *)((PyObject *)__pyx_MemviewEnum_type)), __pyx_tuple__55, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 278; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_Call(((PyObject *)__pyx_MemviewEnum_type), __pyx_tuple__62, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 280; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_XGOTREF(indirect); __Pyx_DECREF_SET(indirect, __pyx_t_1); __Pyx_GIVEREF(__pyx_t_1); __pyx_t_1 = 0; - /* "View.MemoryView":281 + /* "View.MemoryView":283 * * * cdef contiguous = Enum("") # <<<<<<<<<<<<<< * cdef indirect_contiguous = Enum("") * */ - __pyx_t_1 = __Pyx_PyObject_Call(((PyObject *)((PyObject *)__pyx_MemviewEnum_type)), __pyx_tuple__56, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 281; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_Call(((PyObject *)__pyx_MemviewEnum_type), __pyx_tuple__63, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 283; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_XGOTREF(contiguous); __Pyx_DECREF_SET(contiguous, __pyx_t_1); __Pyx_GIVEREF(__pyx_t_1); __pyx_t_1 = 0; - /* "View.MemoryView":282 + /* "View.MemoryView":284 * * cdef contiguous = Enum("") * cdef indirect_contiguous = Enum("") # <<<<<<<<<<<<<< * * */ - __pyx_t_1 = __Pyx_PyObject_Call(((PyObject *)((PyObject *)__pyx_MemviewEnum_type)), __pyx_tuple__57, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 282; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_Call(((PyObject *)__pyx_MemviewEnum_type), __pyx_tuple__64, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 284; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_XGOTREF(indirect_contiguous); __Pyx_DECREF_SET(indirect_contiguous, __pyx_t_1); __Pyx_GIVEREF(__pyx_t_1); __pyx_t_1 = 0; - /* "View.MemoryView":496 + /* "View.MemoryView":498 * info.obj = self * * __pyx_getbuffer = capsule( &__pyx_memoryview_getbuffer, "getbuffer(obj, view, flags)") # <<<<<<<<<<<<<< * * */ - __pyx_t_1 = __pyx_capsule_create(((void *)(&__pyx_memoryview_getbuffer)), __pyx_k_getbuffer_obj_view_flags); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 496; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __pyx_capsule_create(((void *)(&__pyx_memoryview_getbuffer)), __pyx_k_getbuffer_obj_view_flags); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 498; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - if (PyDict_SetItem(__pyx_memoryview_type->tp_dict, __pyx_n_s_pyx_getbuffer, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 496; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_memoryview_type->tp_dict, __pyx_n_s_pyx_getbuffer, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 498; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; PyType_Modified(__pyx_memoryview_type); - /* "View.MemoryView":952 + /* "View.MemoryView":954 * return self.from_object * * __pyx_getbuffer = capsule( &__pyx_memoryview_getbuffer, "getbuffer(obj, view, flags)") # <<<<<<<<<<<<<< * * */ - __pyx_t_1 = __pyx_capsule_create(((void *)(&__pyx_memoryview_getbuffer)), __pyx_k_getbuffer_obj_view_flags); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 952; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __pyx_capsule_create(((void *)(&__pyx_memoryview_getbuffer)), __pyx_k_getbuffer_obj_view_flags); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 954; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - if (PyDict_SetItem(__pyx_memoryviewslice_type->tp_dict, __pyx_n_s_pyx_getbuffer, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 952; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_memoryviewslice_type->tp_dict, __pyx_n_s_pyx_getbuffer, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 954; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; PyType_Modified(__pyx_memoryviewslice_type); - /* "View.MemoryView":1362 + /* "View.MemoryView":1364 * * @cname('__pyx_memoryview__slice_assign_scalar') * cdef void _slice_assign_scalar(char *data, Py_ssize_t *shape, # <<<<<<<<<<<<<< @@ -17856,7 +21488,6 @@ __Pyx_init_memviewslice(struct __pyx_memoryview_obj *memview, static CYTHON_INLINE void __pyx_fatalerror(const char *fmt, ...) { va_list vargs; char msg[200]; - va_start(vargs, fmt); #ifdef HAVE_STDARG_PROTOTYPES va_start(vargs, fmt); #else @@ -17935,6 +21566,77 @@ static CYTHON_INLINE void __Pyx_XDEC_MEMVIEW(__Pyx_memviewslice *memslice, } } +#if CYTHON_USE_PYLONG_INTERNALS + #include "longintrepr.h" +#endif + +#if CYTHON_COMPILING_IN_CPYTHON +static PyObject* __Pyx_PyFloat_DivideCObj(PyObject *op1, PyObject *op2, double floatval, CYTHON_UNUSED int inplace) { + const double a = floatval; + double b, result; + if (likely(PyFloat_CheckExact(op2))) { + b = PyFloat_AS_DOUBLE(op2); + } else + #if PY_MAJOR_VERSION < 3 + if (likely(PyInt_CheckExact(op2))) { + b = (double) PyInt_AS_LONG(op2); + } else + #endif + if (likely(PyLong_CheckExact(op2))) { + #if CYTHON_USE_PYLONG_INTERNALS && PY_MAJOR_VERSION >= 3 + const digit* digits = ((PyLongObject*)op2)->ob_digit; + const Py_ssize_t size = Py_SIZE(op2); + switch (size) { + case 0: b = 0.0; break; + case -1: b = -(double) digits[0]; break; + case 1: b = (double) digits[0]; break; + case -2: + case 2: + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT && ((8 * sizeof(unsigned long) < 53) || (1 * PyLong_SHIFT < 53))) { + b = (double) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + if ((8 * sizeof(unsigned long) < 53) || (2 * PyLong_SHIFT < 53) || (b < (double) (1L<<53))) { + if (size == -2) + b = -b; + break; + } + } + case -3: + case 3: + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT && ((8 * sizeof(unsigned long) < 53) || (2 * PyLong_SHIFT < 53))) { + b = (double) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + if ((8 * sizeof(unsigned long) < 53) || (3 * PyLong_SHIFT < 53) || (b < (double) (1L<<53))) { + if (size == -3) + b = -b; + break; + } + } + case -4: + case 4: + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT && ((8 * sizeof(unsigned long) < 53) || (3 * PyLong_SHIFT < 53))) { + b = (double) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + if ((8 * sizeof(unsigned long) < 53) || (4 * PyLong_SHIFT < 53) || (b < (double) (1L<<53))) { + if (size == -4) + b = -b; + break; + } + } + default: + #else + { + #endif + b = PyLong_AsDouble(op2); + if (unlikely(b == -1.0 && PyErr_Occurred())) return NULL; + } + } else { + return (inplace ? __Pyx_PyNumber_InPlaceDivide(op1, op2) : __Pyx_PyNumber_Divide(op1, op2)); + } + PyFPE_START_PROTECT("divide", return NULL) + result = a / b; + PyFPE_END_PROTECT(result) + return PyFloat_FromDouble(result); +} +#endif + #if CYTHON_COMPILING_IN_CPYTHON static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw) { PyObject *result; @@ -18145,6 +21847,33 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject } #endif +static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { + PyErr_Format(PyExc_ValueError, + "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected); +} + +static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { + PyErr_Format(PyExc_ValueError, + "need more than %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack", + index, (index == 1) ? "" : "s"); +} + +static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); +} + +static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { + if (unlikely(!type)) { + PyErr_SetString(PyExc_SystemError, "Missing type object"); + return 0; + } + if (likely(PyObject_TypeCheck(obj, type))) + return 1; + PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s", + Py_TYPE(obj)->tp_name, type->tp_name); + return 0; +} + static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) { #if CYTHON_COMPILING_IN_PYPY return PyObject_RichCompareBool(s1, s2, equals); @@ -18290,7 +22019,13 @@ static CYTHON_INLINE PyObject* __Pyx_decode_c_string( PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)) { Py_ssize_t length; if (unlikely((start < 0) | (stop < 0))) { - length = strlen(cstring); + size_t slen = strlen(cstring); + if (unlikely(slen > (size_t) PY_SSIZE_T_MAX)) { + PyErr_SetString(PyExc_OverflowError, + "c-string too long to convert to Python"); + return NULL; + } + length = (Py_ssize_t) slen; if (start < 0) { start += length; if (start < 0) @@ -18310,33 +22045,6 @@ static CYTHON_INLINE PyObject* __Pyx_decode_c_string( } } -static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { - PyErr_Format(PyExc_ValueError, - "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected); -} - -static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { - PyErr_Format(PyExc_ValueError, - "need more than %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack", - index, (index == 1) ? "" : "s"); -} - -static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { - PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); -} - -static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { - if (unlikely(!type)) { - PyErr_SetString(PyExc_SystemError, "Missing type object"); - return 0; - } - if (likely(PyObject_TypeCheck(obj, type))) - return 1; - PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s", - Py_TYPE(obj)->tp_name, type->tp_name); - return 0; -} - static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) { #if CYTHON_COMPILING_IN_CPYTHON PyThreadState *tstate = PyThreadState_GET(); @@ -18444,6 +22152,79 @@ static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, *tb = tmp_tb; } +static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { + PyObject *empty_list = 0; + PyObject *module = 0; + PyObject *global_dict = 0; + PyObject *empty_dict = 0; + PyObject *list; + #if PY_VERSION_HEX < 0x03030000 + PyObject *py_import; + py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import); + if (!py_import) + goto bad; + #endif + if (from_list) + list = from_list; + else { + empty_list = PyList_New(0); + if (!empty_list) + goto bad; + list = empty_list; + } + global_dict = PyModule_GetDict(__pyx_m); + if (!global_dict) + goto bad; + empty_dict = PyDict_New(); + if (!empty_dict) + goto bad; + { + #if PY_MAJOR_VERSION >= 3 + if (level == -1) { + if (strchr(__Pyx_MODULE_NAME, '.')) { + #if PY_VERSION_HEX < 0x03030000 + PyObject *py_level = PyInt_FromLong(1); + if (!py_level) + goto bad; + module = PyObject_CallFunctionObjArgs(py_import, + name, global_dict, empty_dict, list, py_level, NULL); + Py_DECREF(py_level); + #else + module = PyImport_ImportModuleLevelObject( + name, global_dict, empty_dict, list, 1); + #endif + if (!module) { + if (!PyErr_ExceptionMatches(PyExc_ImportError)) + goto bad; + PyErr_Clear(); + } + } + level = 0; + } + #endif + if (!module) { + #if PY_VERSION_HEX < 0x03030000 + PyObject *py_level = PyInt_FromLong(level); + if (!py_level) + goto bad; + module = PyObject_CallFunctionObjArgs(py_import, + name, global_dict, empty_dict, list, py_level, NULL); + Py_DECREF(py_level); + #else + module = PyImport_ImportModuleLevelObject( + name, global_dict, empty_dict, list, level); + #endif + } + } +bad: + #if PY_VERSION_HEX < 0x03030000 + Py_XDECREF(py_import); + #endif + Py_XDECREF(empty_list); + Py_XDECREF(empty_dict); + return module; +} + static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) { PyObject *r; if (!j) return NULL; @@ -18525,6 +22306,103 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); } +#if CYTHON_COMPILING_IN_CPYTHON +static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED long intval, CYTHON_UNUSED int inplace) { + #if PY_MAJOR_VERSION < 3 + if (likely(PyInt_CheckExact(op1))) { + const long b = intval; + long x; + long a = PyInt_AS_LONG(op1); + x = (long)((unsigned long)a + b); + if (likely((x^a) >= 0 || (x^b) >= 0)) + return PyInt_FromLong(x); + return PyLong_Type.tp_as_number->nb_add(op1, op2); + } + #endif + #if CYTHON_USE_PYLONG_INTERNALS && PY_MAJOR_VERSION >= 3 + if (likely(PyLong_CheckExact(op1))) { + const long b = intval; + long a, x; + const PY_LONG_LONG llb = intval; + PY_LONG_LONG lla, llx; + const digit* digits = ((PyLongObject*)op1)->ob_digit; + const Py_ssize_t size = Py_SIZE(op1); + if (likely(__Pyx_sst_abs(size) <= 1)) { + a = likely(size) ? digits[0] : 0; + if (size == -1) a = -a; + } else { + switch (size) { + case -2: + if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + break; + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { + lla = -(PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); + goto long_long; + } + case 2: + if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + break; + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { + lla = (PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); + goto long_long; + } + case -3: + if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + break; + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { + lla = -(PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); + goto long_long; + } + case 3: + if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + break; + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { + lla = (PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); + goto long_long; + } + case -4: + if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { + a = -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + break; + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { + lla = -(PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); + goto long_long; + } + case 4: + if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { + a = (long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + break; + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { + lla = (PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); + goto long_long; + } + default: return PyLong_Type.tp_as_number->nb_add(op1, op2); + } + } + x = a + b; + return PyLong_FromLong(x); + long_long: + llx = lla + llb; + return PyLong_FromLongLong(llx); + } + #endif + if (PyFloat_CheckExact(op1)) { + const long b = intval; + double a = PyFloat_AS_DOUBLE(op1); + double result; + PyFPE_START_PROTECT("add", return NULL) + result = ((double)a) + (double)b; + PyFPE_END_PROTECT(result) + return PyFloat_FromDouble(result); + } + return (inplace ? PyNumber_InPlaceAdd : PyNumber_Add)(op1, op2); +} +#endif + static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) { PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname); } @@ -18609,8 +22487,12 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObjec } #else static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { - PyObject* args = PyTuple_Pack(1, arg); - return (likely(args)) ? __Pyx_PyObject_Call(func, args, NULL) : NULL; + PyObject *result; + PyObject *args = PyTuple_Pack(1, arg); + if (unlikely(!args)) return NULL; + result = __Pyx_PyObject_Call(func, args, NULL); + Py_DECREF(args); + return result; } #endif @@ -18637,7 +22519,7 @@ static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int co return count; } while (start < end) { - mid = (start + end) / 2; + mid = start + (end - start) / 2; if (code_line < entries[mid].code_line) { end = mid; } else if (code_line > entries[mid].code_line) { @@ -18793,6 +22675,7 @@ static void __Pyx_AddTraceback(const char *funcname, int c_line, #if PY_MAJOR_VERSION < 3 static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) { if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags); + if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) return __pyx_pw_5numpy_7ndarray_1__getbuffer__(obj, view, flags); if (PyObject_TypeCheck(obj, __pyx_array_type)) return __pyx_array_getbuffer(obj, view, flags); if (PyObject_TypeCheck(obj, __pyx_memoryview_type)) return __pyx_memoryview_getbuffer(obj, view, flags); PyErr_Format(PyExc_TypeError, "'%.200s' does not have the buffer interface", Py_TYPE(obj)->tp_name); @@ -18805,14 +22688,15 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { PyBuffer_Release(view); return; } + if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) { __pyx_pw_5numpy_7ndarray_3__releasebuffer__(obj, view); return; } Py_DECREF(obj); view->obj = NULL; } #endif - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { - const int neg_one = (int) -1, const_zero = 0; + static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { + const int neg_one = (int) -1, const_zero = (int) 0; const int is_unsigned = neg_one > const_zero; if (is_unsigned) { if (sizeof(int) < sizeof(long)) { @@ -18837,29 +22721,29 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { } } -#define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value) \ - { \ - func_type value = func_value; \ - if (sizeof(target_type) < sizeof(func_type)) { \ - if (unlikely(value != (func_type) (target_type) value)) { \ - func_type zero = 0; \ - if (is_unsigned && unlikely(value < zero)) \ - goto raise_neg_overflow; \ - else \ - goto raise_overflow; \ - } \ - } \ - return (target_type) value; \ +#define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\ + __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0) +#define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\ + __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1) +#define __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, exc)\ + {\ + func_type value = func_value;\ + if (sizeof(target_type) < sizeof(func_type)) {\ + if (unlikely(value != (func_type) (target_type) value)) {\ + func_type zero = 0;\ + if (exc && unlikely(value == (func_type)-1 && PyErr_Occurred()))\ + return (target_type) -1;\ + if (is_unsigned && unlikely(value < zero))\ + goto raise_neg_overflow;\ + else\ + goto raise_overflow;\ + }\ + }\ + return (target_type) value;\ } -#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 - #if CYTHON_USE_PYLONG_INTERNALS - #include "longintrepr.h" - #endif -#endif - static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { - const int neg_one = (int) -1, const_zero = 0; + const int neg_one = (int) -1, const_zero = (int) 0; const int is_unsigned = neg_one > const_zero; #if PY_MAJOR_VERSION < 3 if (likely(PyInt_Check(x))) { @@ -18876,13 +22760,39 @@ static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { -#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 - #if CYTHON_USE_PYLONG_INTERNALS +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; switch (Py_SIZE(x)) { - case 0: return 0; - case 1: __PYX_VERIFY_RETURN_INT(int, digit, ((PyLongObject*)x)->ob_digit[0]); + case 0: return (int) 0; + case 1: __PYX_VERIFY_RETURN_INT(int, digit, digits[0]) + case 2: + if (8 * sizeof(int) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) >= 2 * PyLong_SHIFT) { + return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); + } + } + break; + case 3: + if (8 * sizeof(int) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) >= 3 * PyLong_SHIFT) { + return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); + } + } + break; + case 4: + if (8 * sizeof(int) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) >= 4 * PyLong_SHIFT) { + return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); + } + } + break; } - #endif #endif #if CYTHON_COMPILING_IN_CPYTHON if (unlikely(Py_SIZE(x) < 0)) { @@ -18898,24 +22808,77 @@ static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { } #endif if (sizeof(int) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, PyLong_AsUnsignedLong(x)) + __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x)) } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) + __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) } } else { -#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 - #if CYTHON_USE_PYLONG_INTERNALS +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; switch (Py_SIZE(x)) { - case 0: return 0; - case 1: __PYX_VERIFY_RETURN_INT(int, digit, +(((PyLongObject*)x)->ob_digit[0])); - case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]); + case 0: return (int) 0; + case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, -(sdigit) digits[0]) + case 1: __PYX_VERIFY_RETURN_INT(int, digit, +digits[0]) + case -2: + if (8 * sizeof(int) - 1 > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { + return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case 2: + if (8 * sizeof(int) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { + return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case -3: + if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { + return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case 3: + if (8 * sizeof(int) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { + return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case -4: + if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { + return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case 4: + if (8 * sizeof(int) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { + return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; } - #endif #endif if (sizeof(int) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT(int, long, PyLong_AsLong(x)) + __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x)) } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT(int, PY_LONG_LONG, PyLong_AsLongLong(x)) + __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x)) } } { @@ -18964,7 +22927,7 @@ static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { } static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { - const long neg_one = (long) -1, const_zero = 0; + const long neg_one = (long) -1, const_zero = (long) 0; const int is_unsigned = neg_one > const_zero; if (is_unsigned) { if (sizeof(long) < sizeof(long)) { @@ -18989,6 +22952,272 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { } } +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + return ::std::complex< float >(x, y); + } + #else + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + return x + y*(__pyx_t_float_complex)_Complex_I; + } + #endif +#else + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + __pyx_t_float_complex z; + z.real = x; + z.imag = y; + return z; + } +#endif + +#if CYTHON_CCOMPLEX +#else + static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + return (a.real == b.real) && (a.imag == b.imag); + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real + b.real; + z.imag = a.imag + b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real - b.real; + z.imag = a.imag - b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prodf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real * b.real - a.imag * b.imag; + z.imag = a.real * b.imag + a.imag * b.real; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + float denom = b.real * b.real + b.imag * b.imag; + z.real = (a.real * b.real + a.imag * b.imag) / denom; + z.imag = (a.imag * b.real - a.real * b.imag) / denom; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex a) { + __pyx_t_float_complex z; + z.real = -a.real; + z.imag = -a.imag; + return z; + } + static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex a) { + return (a.real == 0) && (a.imag == 0); + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex a) { + __pyx_t_float_complex z; + z.real = a.real; + z.imag = -a.imag; + return z; + } + #if 1 + static CYTHON_INLINE float __Pyx_c_absf(__pyx_t_float_complex z) { + #if !defined(HAVE_HYPOT) || defined(_MSC_VER) + return sqrtf(z.real*z.real + z.imag*z.imag); + #else + return hypotf(z.real, z.imag); + #endif + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + float r, lnr, theta, z_r, z_theta; + if (b.imag == 0 && b.real == (int)b.real) { + if (b.real < 0) { + float denom = a.real * a.real + a.imag * a.imag; + a.real = a.real / denom; + a.imag = -a.imag / denom; + b.real = -b.real; + } + switch ((int)b.real) { + case 0: + z.real = 1; + z.imag = 0; + return z; + case 1: + return a; + case 2: + z = __Pyx_c_prodf(a, a); + return __Pyx_c_prodf(a, a); + case 3: + z = __Pyx_c_prodf(a, a); + return __Pyx_c_prodf(z, a); + case 4: + z = __Pyx_c_prodf(a, a); + return __Pyx_c_prodf(z, z); + } + } + if (a.imag == 0) { + if (a.real == 0) { + return a; + } + r = a.real; + theta = 0; + } else { + r = __Pyx_c_absf(a); + theta = atan2f(a.imag, a.real); + } + lnr = logf(r); + z_r = expf(lnr * b.real - theta * b.imag); + z_theta = theta * b.real + lnr * b.imag; + z.real = z_r * cosf(z_theta); + z.imag = z_r * sinf(z_theta); + return z; + } + #endif +#endif + +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + return ::std::complex< double >(x, y); + } + #else + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + return x + y*(__pyx_t_double_complex)_Complex_I; + } + #endif +#else + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + __pyx_t_double_complex z; + z.real = x; + z.imag = y; + return z; + } +#endif + +#if CYTHON_CCOMPLEX +#else + static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex a, __pyx_t_double_complex b) { + return (a.real == b.real) && (a.imag == b.imag); + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real + b.real; + z.imag = a.imag + b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real - b.real; + z.imag = a.imag - b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real * b.real - a.imag * b.imag; + z.imag = a.real * b.imag + a.imag * b.real; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + double denom = b.real * b.real + b.imag * b.imag; + z.real = (a.real * b.real + a.imag * b.imag) / denom; + z.imag = (a.imag * b.real - a.real * b.imag) / denom; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex a) { + __pyx_t_double_complex z; + z.real = -a.real; + z.imag = -a.imag; + return z; + } + static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex a) { + return (a.real == 0) && (a.imag == 0); + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex a) { + __pyx_t_double_complex z; + z.real = a.real; + z.imag = -a.imag; + return z; + } + #if 1 + static CYTHON_INLINE double __Pyx_c_abs(__pyx_t_double_complex z) { + #if !defined(HAVE_HYPOT) || defined(_MSC_VER) + return sqrt(z.real*z.real + z.imag*z.imag); + #else + return hypot(z.real, z.imag); + #endif + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + double r, lnr, theta, z_r, z_theta; + if (b.imag == 0 && b.real == (int)b.real) { + if (b.real < 0) { + double denom = a.real * a.real + a.imag * a.imag; + a.real = a.real / denom; + a.imag = -a.imag / denom; + b.real = -b.real; + } + switch ((int)b.real) { + case 0: + z.real = 1; + z.imag = 0; + return z; + case 1: + return a; + case 2: + z = __Pyx_c_prod(a, a); + return __Pyx_c_prod(a, a); + case 3: + z = __Pyx_c_prod(a, a); + return __Pyx_c_prod(z, a); + case 4: + z = __Pyx_c_prod(a, a); + return __Pyx_c_prod(z, z); + } + } + if (a.imag == 0) { + if (a.real == 0) { + return a; + } + r = a.real; + theta = 0; + } else { + r = __Pyx_c_abs(a); + theta = atan2(a.imag, a.real); + } + lnr = log(r); + z_r = exp(lnr * b.real - theta * b.imag); + z_theta = theta * b.real + lnr * b.imag; + z.real = z_r * cos(z_theta); + z.imag = z_r * sin(z_theta); + return z; + } + #endif +#endif + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__NPY_TYPES(enum NPY_TYPES value) { + const enum NPY_TYPES neg_one = (enum NPY_TYPES) -1, const_zero = (enum NPY_TYPES) 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(enum NPY_TYPES) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(enum NPY_TYPES) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); + } else if (sizeof(enum NPY_TYPES) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); + } + } else { + if (sizeof(enum NPY_TYPES) <= sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(enum NPY_TYPES) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(enum NPY_TYPES), + little, !is_unsigned); + } +} + static int __pyx_memviewslice_is_contig(const __Pyx_memviewslice *mvs, char order, int ndim) @@ -19124,81 +23353,8 @@ __pyx_capsule_create(void *p, CYTHON_UNUSED const char *sig) return cobj; } -static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { - PyObject *empty_list = 0; - PyObject *module = 0; - PyObject *global_dict = 0; - PyObject *empty_dict = 0; - PyObject *list; - #if PY_VERSION_HEX < 0x03030000 - PyObject *py_import; - py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import); - if (!py_import) - goto bad; - #endif - if (from_list) - list = from_list; - else { - empty_list = PyList_New(0); - if (!empty_list) - goto bad; - list = empty_list; - } - global_dict = PyModule_GetDict(__pyx_m); - if (!global_dict) - goto bad; - empty_dict = PyDict_New(); - if (!empty_dict) - goto bad; - { - #if PY_MAJOR_VERSION >= 3 - if (level == -1) { - if (strchr(__Pyx_MODULE_NAME, '.')) { - #if PY_VERSION_HEX < 0x03030000 - PyObject *py_level = PyInt_FromLong(1); - if (!py_level) - goto bad; - module = PyObject_CallFunctionObjArgs(py_import, - name, global_dict, empty_dict, list, py_level, NULL); - Py_DECREF(py_level); - #else - module = PyImport_ImportModuleLevelObject( - name, global_dict, empty_dict, list, 1); - #endif - if (!module) { - if (!PyErr_ExceptionMatches(PyExc_ImportError)) - goto bad; - PyErr_Clear(); - } - } - level = 0; - } - #endif - if (!module) { - #if PY_VERSION_HEX < 0x03030000 - PyObject *py_level = PyInt_FromLong(level); - if (!py_level) - goto bad; - module = PyObject_CallFunctionObjArgs(py_import, - name, global_dict, empty_dict, list, py_level, NULL); - Py_DECREF(py_level); - #else - module = PyImport_ImportModuleLevelObject( - name, global_dict, empty_dict, list, level); - #endif - } - } -bad: - #if PY_VERSION_HEX < 0x03030000 - Py_XDECREF(py_import); - #endif - Py_XDECREF(empty_list); - Py_XDECREF(empty_dict); - return module; -} - static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *x) { - const char neg_one = (char) -1, const_zero = 0; + const char neg_one = (char) -1, const_zero = (char) 0; const int is_unsigned = neg_one > const_zero; #if PY_MAJOR_VERSION < 3 if (likely(PyInt_Check(x))) { @@ -19215,13 +23371,39 @@ static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *x) { #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { -#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 - #if CYTHON_USE_PYLONG_INTERNALS +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; switch (Py_SIZE(x)) { - case 0: return 0; - case 1: __PYX_VERIFY_RETURN_INT(char, digit, ((PyLongObject*)x)->ob_digit[0]); + case 0: return (char) 0; + case 1: __PYX_VERIFY_RETURN_INT(char, digit, digits[0]) + case 2: + if (8 * sizeof(char) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) >= 2 * PyLong_SHIFT) { + return (char) (((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); + } + } + break; + case 3: + if (8 * sizeof(char) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) >= 3 * PyLong_SHIFT) { + return (char) (((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); + } + } + break; + case 4: + if (8 * sizeof(char) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) >= 4 * PyLong_SHIFT) { + return (char) (((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); + } + } + break; } - #endif #endif #if CYTHON_COMPILING_IN_CPYTHON if (unlikely(Py_SIZE(x) < 0)) { @@ -19237,24 +23419,77 @@ static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *x) { } #endif if (sizeof(char) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, PyLong_AsUnsignedLong(x)) + __PYX_VERIFY_RETURN_INT_EXC(char, unsigned long, PyLong_AsUnsignedLong(x)) } else if (sizeof(char) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT(char, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) + __PYX_VERIFY_RETURN_INT_EXC(char, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) } } else { -#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 - #if CYTHON_USE_PYLONG_INTERNALS +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; switch (Py_SIZE(x)) { - case 0: return 0; - case 1: __PYX_VERIFY_RETURN_INT(char, digit, +(((PyLongObject*)x)->ob_digit[0])); - case -1: __PYX_VERIFY_RETURN_INT(char, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]); + case 0: return (char) 0; + case -1: __PYX_VERIFY_RETURN_INT(char, sdigit, -(sdigit) digits[0]) + case 1: __PYX_VERIFY_RETURN_INT(char, digit, +digits[0]) + case -2: + if (8 * sizeof(char) - 1 > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { + return (char) (((char)-1)*(((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); + } + } + break; + case 2: + if (8 * sizeof(char) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { + return (char) ((((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); + } + } + break; + case -3: + if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { + return (char) (((char)-1)*(((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); + } + } + break; + case 3: + if (8 * sizeof(char) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { + return (char) ((((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); + } + } + break; + case -4: + if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) - 1 > 4 * PyLong_SHIFT) { + return (char) (((char)-1)*(((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); + } + } + break; + case 4: + if (8 * sizeof(char) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(char) - 1 > 4 * PyLong_SHIFT) { + return (char) ((((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); + } + } + break; } - #endif #endif if (sizeof(char) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT(char, long, PyLong_AsLong(x)) + __PYX_VERIFY_RETURN_INT_EXC(char, long, PyLong_AsLong(x)) } else if (sizeof(char) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT(char, PY_LONG_LONG, PyLong_AsLongLong(x)) + __PYX_VERIFY_RETURN_INT_EXC(char, PY_LONG_LONG, PyLong_AsLongLong(x)) } } { @@ -19303,7 +23538,7 @@ static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *x) { } static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { - const long neg_one = (long) -1, const_zero = 0; + const long neg_one = (long) -1, const_zero = (long) 0; const int is_unsigned = neg_one > const_zero; #if PY_MAJOR_VERSION < 3 if (likely(PyInt_Check(x))) { @@ -19320,13 +23555,39 @@ static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { -#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 - #if CYTHON_USE_PYLONG_INTERNALS +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; switch (Py_SIZE(x)) { - case 0: return 0; - case 1: __PYX_VERIFY_RETURN_INT(long, digit, ((PyLongObject*)x)->ob_digit[0]); + case 0: return (long) 0; + case 1: __PYX_VERIFY_RETURN_INT(long, digit, digits[0]) + case 2: + if (8 * sizeof(long) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) >= 2 * PyLong_SHIFT) { + return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); + } + } + break; + case 3: + if (8 * sizeof(long) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) >= 3 * PyLong_SHIFT) { + return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); + } + } + break; + case 4: + if (8 * sizeof(long) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) >= 4 * PyLong_SHIFT) { + return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); + } + } + break; } - #endif #endif #if CYTHON_COMPILING_IN_CPYTHON if (unlikely(Py_SIZE(x) < 0)) { @@ -19342,24 +23603,77 @@ static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { } #endif if (sizeof(long) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, PyLong_AsUnsignedLong(x)) + __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x)) } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) + __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) } } else { -#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 - #if CYTHON_USE_PYLONG_INTERNALS +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; switch (Py_SIZE(x)) { - case 0: return 0; - case 1: __PYX_VERIFY_RETURN_INT(long, digit, +(((PyLongObject*)x)->ob_digit[0])); - case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]); + case 0: return (long) 0; + case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, -(sdigit) digits[0]) + case 1: __PYX_VERIFY_RETURN_INT(long, digit, +digits[0]) + case -2: + if (8 * sizeof(long) - 1 > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case 2: + if (8 * sizeof(long) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case -3: + if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case 3: + if (8 * sizeof(long) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case -4: + if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { + return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case 4: + if (8 * sizeof(long) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { + return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; } - #endif #endif if (sizeof(long) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT(long, long, PyLong_AsLong(x)) + __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x)) } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT(long, PY_LONG_LONG, PyLong_AsLongLong(x)) + __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x)) } } { @@ -19806,7 +24120,7 @@ static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) { 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 CYTHON_COMPILING_IN_CPYTHON && (__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 && @@ -19847,7 +24161,7 @@ static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_ #endif } else #endif -#if !CYTHON_COMPILING_IN_PYPY +#if (!CYTHON_COMPILING_IN_PYPY) || (defined(PyByteArray_AS_STRING) && defined(PyByteArray_GET_SIZE)) if (PyByteArray_Check(o)) { *length = PyByteArray_GET_SIZE(o); return PyByteArray_AS_STRING(o); @@ -19877,7 +24191,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) { #else if (PyLong_Check(x)) #endif - return Py_INCREF(x), x; + return __Pyx_NewRef(x); m = Py_TYPE(x)->tp_as_number; #if PY_MAJOR_VERSION < 3 if (m && m->nb_int) { @@ -19917,18 +24231,55 @@ 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); + if (likely(PyInt_CheckExact(b))) { + if (sizeof(Py_ssize_t) >= sizeof(long)) + return PyInt_AS_LONG(b); + else + return PyInt_AsSsize_t(x); + } #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 + #if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)b)->ob_digit; + const Py_ssize_t size = Py_SIZE(b); + if (likely(__Pyx_sst_abs(size) <= 1)) { + ival = likely(size) ? digits[0] : 0; + if (size == -1) ival = -ival; + return ival; + } else { + switch (size) { + case 2: + if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { + return (Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case -2: + if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { + return -(Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case 3: + if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { + return (Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case -3: + if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { + return -(Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case 4: + if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { + return (Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case -4: + if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { + return -(Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + } + } #endif return PyLong_AsSsize_t(b); } diff --git a/package/MDAnalysis/lib/distances.pyx b/package/MDAnalysis/lib/distances.pyx index 0b5f5d885d9..f714291566b 100644 --- a/package/MDAnalysis/lib/distances.pyx +++ b/package/MDAnalysis/lib/distances.pyx @@ -23,8 +23,8 @@ Serial versions of all distance calculations """ cimport cython -cimport c_numpy -c_numpy.import_array() +import numpy +cimport numpy cdef extern from "string.h": void* memcpy(void *dst, void *src, int len) @@ -52,132 +52,132 @@ cdef extern from "calc_distances.h": void _triclinic_pbc(coordinate* coords, int numcoords, coordinate* box, float* box_inverse) void minimum_image(double *x, float *box, float *inverse_box) -def calc_distance_array(c_numpy.ndarray ref, c_numpy.ndarray conf, - c_numpy.ndarray result): +def calc_distance_array(numpy.ndarray ref, numpy.ndarray conf, + numpy.ndarray result): cdef int confnum, refnum - confnum = conf.dimensions[0] - refnum = ref.dimensions[0] + confnum = conf.shape[0] + refnum = ref.shape[0] _calc_distance_array(ref.data, refnum, conf.data, confnum, result.data) -def calc_distance_array_ortho(c_numpy.ndarray ref, c_numpy.ndarray conf, - c_numpy.ndarray box, - c_numpy.ndarray result): +def calc_distance_array_ortho(numpy.ndarray ref, numpy.ndarray conf, + numpy.ndarray box, + numpy.ndarray result): cdef int confnum, refnum - confnum = conf.dimensions[0] - refnum = ref.dimensions[0] + confnum = conf.shape[0] + refnum = ref.shape[0] _calc_distance_array_ortho(ref.data, refnum, conf.data, confnum, box.data, result.data) -def calc_distance_array_triclinic(c_numpy.ndarray ref, c_numpy.ndarray conf, - c_numpy.ndarray box, - c_numpy.ndarray result): +def calc_distance_array_triclinic(numpy.ndarray ref, numpy.ndarray conf, + numpy.ndarray box, + numpy.ndarray result): cdef int confnum, refnum - confnum = conf.dimensions[0] - refnum = ref.dimensions[0] + confnum = conf.shape[0] + refnum = ref.shape[0] _calc_distance_array_triclinic(ref.data, refnum, conf.data, confnum, box.data, - result.data) + result.data) -def calc_self_distance_array(c_numpy.ndarray ref, - c_numpy.ndarray result): +def calc_self_distance_array(numpy.ndarray ref, + numpy.ndarray result): cdef int refnum, distnum - refnum = ref.dimensions[0] + refnum = ref.shape[0] distnum = (refnum*(refnum-1))/2 _calc_self_distance_array(ref.data, refnum, result.data, distnum) -def calc_self_distance_array_ortho(c_numpy.ndarray ref, - c_numpy.ndarray box, - c_numpy.ndarray result): +def calc_self_distance_array_ortho(numpy.ndarray ref, + numpy.ndarray box, + numpy.ndarray result): cdef int refnum, distnum - refnum = ref.dimensions[0] + refnum = ref.shape[0] distnum = (refnum*(refnum-1))/2 _calc_self_distance_array_ortho(ref.data, refnum, box.data, result.data, distnum) -def calc_self_distance_array_triclinic(c_numpy.ndarray ref, - c_numpy.ndarray box, - c_numpy.ndarray result): +def calc_self_distance_array_triclinic(numpy.ndarray ref, + numpy.ndarray box, + numpy.ndarray result): cdef int refnum, distnum - refnum = ref.dimensions[0] + refnum = ref.shape[0] distnum = (refnum*(refnum-1))/2 _calc_self_distance_array_triclinic(ref.data, refnum, box.data, result.data, distnum) -def coord_transform(c_numpy.ndarray coords, - c_numpy.ndarray box): +def coord_transform(numpy.ndarray coords, + numpy.ndarray box): cdef int numcoords - numcoords = coords.dimensions[0] + numcoords = coords.shape[0] _coord_transform( coords.data, numcoords, box.data) -def calc_bond_distance(c_numpy.ndarray coords1, - c_numpy.ndarray coords2, - c_numpy.ndarray results): +def calc_bond_distance(numpy.ndarray coords1, + numpy.ndarray coords2, + numpy.ndarray results): cdef int numcoords - numcoords = coords1.dimensions[0] + numcoords = coords1.shape[0] _calc_bond_distance( coords1.data, coords2.data, numcoords, results.data) -def calc_bond_distance_ortho(c_numpy.ndarray coords1, - c_numpy.ndarray coords2, - c_numpy.ndarray box, - c_numpy.ndarray results): +def calc_bond_distance_ortho(numpy.ndarray coords1, + numpy.ndarray coords2, + numpy.ndarray box, + numpy.ndarray results): cdef int numcoords - numcoords = coords1.dimensions[0] + numcoords = coords1.shape[0] _calc_bond_distance_ortho( coords1.data, coords2.data, numcoords, box.data, results.data) -def calc_bond_distance_triclinic(c_numpy.ndarray coords1, - c_numpy.ndarray coords2, - c_numpy.ndarray box, - c_numpy.ndarray results): +def calc_bond_distance_triclinic(numpy.ndarray coords1, + numpy.ndarray coords2, + numpy.ndarray box, + numpy.ndarray results): cdef int numcoords - numcoords = coords1.dimensions[0] + numcoords = coords1.shape[0] _calc_bond_distance_triclinic( coords1.data, coords2.data, numcoords, box.data, results.data) -def calc_angle(c_numpy.ndarray coords1, - c_numpy.ndarray coords2, - c_numpy.ndarray coords3, - c_numpy.ndarray results): +def calc_angle(numpy.ndarray coords1, + numpy.ndarray coords2, + numpy.ndarray coords3, + numpy.ndarray results): cdef int numcoords - numcoords = coords1.dimensions[0] + numcoords = coords1.shape[0] _calc_angle( coords1.data, coords2.data, coords3.data, numcoords, results.data) -def calc_angle_ortho(c_numpy.ndarray coords1, - c_numpy.ndarray coords2, - c_numpy.ndarray coords3, - c_numpy.ndarray box, - c_numpy.ndarray results): +def calc_angle_ortho(numpy.ndarray coords1, + numpy.ndarray coords2, + numpy.ndarray coords3, + numpy.ndarray box, + numpy.ndarray results): cdef int numcoords - numcoords = coords1.dimensions[0] + numcoords = coords1.shape[0] _calc_angle_ortho( coords1.data, coords2.data, coords3.data, @@ -185,13 +185,13 @@ def calc_angle_ortho(c_numpy.ndarray coords1, box.data, results.data) -def calc_angle_triclinic(c_numpy.ndarray coords1, - c_numpy.ndarray coords2, - c_numpy.ndarray coords3, - c_numpy.ndarray box, - c_numpy.ndarray results): +def calc_angle_triclinic(numpy.ndarray coords1, + numpy.ndarray coords2, + numpy.ndarray coords3, + numpy.ndarray box, + numpy.ndarray results): cdef int numcoords - numcoords = coords1.dimensions[0] + numcoords = coords1.shape[0] _calc_angle_triclinic( coords1.data, coords2.data, coords3.data, @@ -199,27 +199,27 @@ def calc_angle_triclinic(c_numpy.ndarray coords1, box.data, results.data) -def calc_dihedral(c_numpy.ndarray coords1, - c_numpy.ndarray coords2, - c_numpy.ndarray coords3, - c_numpy.ndarray coords4, - c_numpy.ndarray results): +def calc_dihedral(numpy.ndarray coords1, + numpy.ndarray coords2, + numpy.ndarray coords3, + numpy.ndarray coords4, + numpy.ndarray results): cdef int numcoords - numcoords = coords1.dimensions[0] + numcoords = coords1.shape[0] _calc_dihedral( coords1.data, coords2.data, coords3.data, coords4.data, numcoords, results.data) -def calc_dihedral_ortho(c_numpy.ndarray coords1, - c_numpy.ndarray coords2, - c_numpy.ndarray coords3, - c_numpy.ndarray coords4, - c_numpy.ndarray box, - c_numpy.ndarray results): +def calc_dihedral_ortho(numpy.ndarray coords1, + numpy.ndarray coords2, + numpy.ndarray coords3, + numpy.ndarray coords4, + numpy.ndarray box, + numpy.ndarray results): cdef int numcoords - numcoords = coords1.dimensions[0] + numcoords = coords1.shape[0] _calc_dihedral_ortho( coords1.data, coords2.data, coords3.data, coords4.data, @@ -227,14 +227,14 @@ def calc_dihedral_ortho(c_numpy.ndarray coords1, box.data, results.data) -def calc_dihedral_triclinic(c_numpy.ndarray coords1, - c_numpy.ndarray coords2, - c_numpy.ndarray coords3, - c_numpy.ndarray coords4, - c_numpy.ndarray box, - c_numpy.ndarray results): +def calc_dihedral_triclinic(numpy.ndarray coords1, + numpy.ndarray coords2, + numpy.ndarray coords3, + numpy.ndarray coords4, + numpy.ndarray box, + numpy.ndarray results): cdef int numcoords - numcoords = coords1.dimensions[0] + numcoords = coords1.shape[0] _calc_dihedral_triclinic( coords1.data, coords2.data, coords3.data, coords4.data, @@ -242,18 +242,18 @@ def calc_dihedral_triclinic(c_numpy.ndarray coords1, box.data, results.data) -def ortho_pbc(c_numpy.ndarray coords, - c_numpy.ndarray box, c_numpy.ndarray box_inverse): +def ortho_pbc(numpy.ndarray coords, + numpy.ndarray box, numpy.ndarray box_inverse): cdef int numcoords - numcoords = coords.dimensions[0] + numcoords = coords.shape[0] _ortho_pbc( coords.data, numcoords, box.data, box_inverse.data) -def triclinic_pbc(c_numpy.ndarray coords, - c_numpy.ndarray box, c_numpy.ndarray box_inverse): +def triclinic_pbc(numpy.ndarray coords, + numpy.ndarray box, numpy.ndarray box_inverse): cdef int numcoords - numcoords = coords.dimensions[0] + numcoords = coords.shape[0] _triclinic_pbc( coords.data, numcoords, box.data, box_inverse.data) diff --git a/package/MDAnalysis/lib/distances_openmp.c b/package/MDAnalysis/lib/distances_openmp.c index 317238da098..0a675c1f562 100644 --- a/package/MDAnalysis/lib/distances_openmp.c +++ b/package/MDAnalysis/lib/distances_openmp.c @@ -1,25 +1,13 @@ -/* Generated by Cython 0.22.1 */ +/* Generated by Cython 0.23.4 */ #define PY_SSIZE_T_CLEAN -#ifndef CYTHON_USE_PYLONG_INTERNALS -#ifdef PYLONG_BITS_IN_DIGIT -#define CYTHON_USE_PYLONG_INTERNALS 0 -#else -#include "pyconfig.h" -#ifdef PYLONG_BITS_IN_DIGIT -#define CYTHON_USE_PYLONG_INTERNALS 1 -#else -#define CYTHON_USE_PYLONG_INTERNALS 0 -#endif -#endif -#endif #include "Python.h" #ifndef Py_PYTHON_H #error Python headers needed to compile C extensions, please install development version of Python. #elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03020000) #error Cython requires Python 2.6+ or Python 3.2+. #else -#define CYTHON_ABI "0_22_1" +#define CYTHON_ABI "0_23_4" #include #ifndef offsetof #define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) @@ -54,6 +42,9 @@ #define CYTHON_COMPILING_IN_PYPY 0 #define CYTHON_COMPILING_IN_CPYTHON 1 #endif +#if !defined(CYTHON_USE_PYLONG_INTERNALS) && CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x02070000 +#define CYTHON_USE_PYLONG_INTERNALS 1 +#endif #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 && !defined(Py_OptimizeFlag) #define Py_OptimizeFlag 0 #endif @@ -61,12 +52,12 @@ #define CYTHON_FORMAT_SSIZE_T "z" #if PY_MAJOR_VERSION < 3 #define __Pyx_BUILTIN_MODULE_NAME "__builtin__" - #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \ + #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) \ + #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 @@ -84,7 +75,7 @@ #endif #if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND) #define CYTHON_PEP393_ENABLED 1 - #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \ + #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) @@ -103,12 +94,10 @@ #if CYTHON_COMPILING_IN_PYPY #define __Pyx_PyUnicode_Concat(a, b) PyNumber_Add(a, b) #define __Pyx_PyUnicode_ConcatSafe(a, b) PyNumber_Add(a, b) - #define __Pyx_PyFrozenSet_Size(s) PyObject_Size(s) #else #define __Pyx_PyUnicode_Concat(a, b) PyUnicode_Concat(a, b) - #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ? \ + #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ?\ PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b)) - #define __Pyx_PyFrozenSet_Size(s) PySet_Size(s) #endif #if CYTHON_COMPILING_IN_PYPY && !defined(PyUnicode_Contains) #define PyUnicode_Contains(u, s) PySequence_Contains(u, s) @@ -176,16 +165,18 @@ #else #define __Pyx_PyMethod_New(func, self, klass) PyMethod_New(func, self, klass) #endif -#ifndef CYTHON_INLINE - #if defined(__GNUC__) - #define CYTHON_INLINE __inline__ - #elif defined(_MSC_VER) - #define CYTHON_INLINE __inline - #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L - #define CYTHON_INLINE inline - #else - #define CYTHON_INLINE - #endif +#if PY_VERSION_HEX >= 0x030500B1 +#define __Pyx_PyAsyncMethodsStruct PyAsyncMethods +#define __Pyx_PyType_AsAsync(obj) (Py_TYPE(obj)->tp_as_async) +#elif CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 +typedef struct { + unaryfunc am_await; + unaryfunc am_aiter; + unaryfunc am_anext; +} __Pyx_PyAsyncMethodsStruct; +#define __Pyx_PyType_AsAsync(obj) ((__Pyx_PyAsyncMethodsStruct*) (Py_TYPE(obj)->tp_reserved)) +#else +#define __Pyx_PyType_AsAsync(obj) NULL #endif #ifndef CYTHON_RESTRICT #if defined(__GNUC__) @@ -198,35 +189,33 @@ #define CYTHON_RESTRICT #endif #endif +#define __Pyx_void_to_None(void_result) ((void)(void_result), Py_INCREF(Py_None), Py_None) + +#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 + +#if defined(WIN32) || defined(MS_WINDOWS) + #define _USE_MATH_DEFINES +#endif +#include #ifdef NAN #define __PYX_NAN() ((float) NAN) #else static CYTHON_INLINE float __PYX_NAN() { - /* Initialize NaN. The sign is irrelevant, an exponent with all bits 1 and - a nonzero mantissa means NaN. If the first bit in the mantissa is 1, it is - a quiet NaN. */ float value; memset(&value, 0xFF, sizeof(value)); return value; } #endif -#define __Pyx_void_to_None(void_result) (void_result, Py_INCREF(Py_None), Py_None) -#ifdef __cplusplus -template -void __Pyx_call_destructor(T* x) { - x->~T(); -} -template -class __Pyx_FakeReference { - public: - __Pyx_FakeReference() : ptr(NULL) { } - __Pyx_FakeReference(T& ref) : ptr(&ref) { } - T *operator->() { return ptr; } - operator T&() { return *ptr; } - private: - T *ptr; -}; -#endif #if PY_MAJOR_VERSION >= 3 @@ -245,14 +234,13 @@ class __Pyx_FakeReference { #endif #endif -#if defined(WIN32) || defined(MS_WINDOWS) -#define _USE_MATH_DEFINES -#endif -#include #define __PYX_HAVE__lib___distances_openmp #define __PYX_HAVE_API__lib___distances_openmp -#include "numpy/arrayobject.h" #include "string.h" +#include "stdio.h" +#include "stdlib.h" +#include "numpy/arrayobject.h" +#include "numpy/ufuncobject.h" #include "calc_distances.h" #ifdef _OPENMP #include @@ -290,16 +278,34 @@ typedef struct {PyObject **p; char *s; const Py_ssize_t n; const char* encoding; #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 || \ +#define __Pyx_uchar_cast(c) ((unsigned char)c) +#define __Pyx_long_cast(x) ((long)x) +#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))) ) +#if defined (__cplusplus) && __cplusplus >= 201103L + #include + #define __Pyx_sst_abs(value) std::abs(value) +#elif SIZEOF_INT >= SIZEOF_SIZE_T + #define __Pyx_sst_abs(value) abs(value) +#elif SIZEOF_LONG >= SIZEOF_SIZE_T + #define __Pyx_sst_abs(value) labs(value) +#elif defined (_MSC_VER) && defined (_M_X64) + #define __Pyx_sst_abs(value) _abs64(value) +#elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L + #define __Pyx_sst_abs(value) llabs(value) +#elif defined (__GNUC__) + #define __Pyx_sst_abs(value) __builtin_llabs(value) +#else + #define __Pyx_sst_abs(value) ((value<0) ? -value : value) +#endif 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)) @@ -334,8 +340,9 @@ static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) #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)) +#define __Pyx_NewRef(obj) (Py_INCREF(obj), obj) +#define __Pyx_Owned_Py_None(b) __Pyx_NewRef(Py_None) +#define __Pyx_PyBool_FromLong(b) ((b) ? __Pyx_NewRef(Py_True) : __Pyx_NewRef(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*); @@ -441,14 +448,281 @@ 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[] = { "MDAnalysis/lib/distances_openmp.pyx", - "include/c_numpy.pxd", + "__init__.pxd", + "type.pxd", }; +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":725 + * # 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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":726 + * + * 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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":727 + * ctypedef npy_int8 int8_t + * ctypedef npy_int16 int16_t + * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< + * ctypedef npy_int64 int64_t + * #ctypedef npy_int96 int96_t + */ +typedef npy_int32 __pyx_t_5numpy_int32_t; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":728 + * 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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":732 + * #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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":733 + * + * 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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":734 + * ctypedef npy_uint8 uint8_t + * ctypedef npy_uint16 uint16_t + * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< + * ctypedef npy_uint64 uint64_t + * #ctypedef npy_uint96 uint96_t + */ +typedef npy_uint32 __pyx_t_5numpy_uint32_t; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":735 + * 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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":739 + * #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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":740 + * + * 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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":749 + * # 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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":750 + * # 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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":751 + * 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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":753 + * 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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":754 + * + * ctypedef npy_ulong uint_t + * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<< + * ctypedef npy_ulonglong ulonglong_t + * + */ +typedef npy_ulonglong __pyx_t_5numpy_ulong_t; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":755 + * 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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":757 + * ctypedef npy_ulonglong ulonglong_t + * + * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< + * ctypedef npy_uintp uintp_t + * + */ +typedef npy_intp __pyx_t_5numpy_intp_t; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":758 + * + * ctypedef npy_intp intp_t + * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< + * + * ctypedef npy_double float_t + */ +typedef npy_uintp __pyx_t_5numpy_uintp_t; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":760 + * 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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":761 + * + * ctypedef npy_double float_t + * ctypedef npy_double double_t # <<<<<<<<<<<<<< + * ctypedef npy_longdouble longdouble_t + * + */ +typedef npy_double __pyx_t_5numpy_double_t; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":762 + * 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 ---*/ +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":764 + * 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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":765 + * + * ctypedef npy_cfloat cfloat_t + * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<< + * ctypedef npy_clongdouble clongdouble_t + * + */ +typedef npy_cdouble __pyx_t_5numpy_cdouble_t; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":766 + * 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; + +/* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":768 + * ctypedef npy_clongdouble clongdouble_t + * + * ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<< + * + * cdef inline object PyArray_MultiIterNew1(a): + */ +typedef npy_cdouble __pyx_t_5numpy_complex_t; + /* --- Runtime support code (head) --- */ #ifndef CYTHON_REFNANNY #define CYTHON_REFNANNY 0 @@ -466,19 +740,19 @@ static const char *__pyx_f[] = { static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname); #define __Pyx_RefNannyDeclarations void *__pyx_refnanny = NULL; #ifdef WITH_THREAD - #define __Pyx_RefNannySetupContext(name, acquire_gil) \ - if (acquire_gil) { \ - PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure(); \ - __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__); \ - PyGILState_Release(__pyx_gilstate_save); \ - } else { \ - __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__); \ + #define __Pyx_RefNannySetupContext(name, acquire_gil)\ + if (acquire_gil) {\ + PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure();\ + __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__);\ + PyGILState_Release(__pyx_gilstate_save);\ + } else {\ + __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__);\ } #else - #define __Pyx_RefNannySetupContext(name, acquire_gil) \ + #define __Pyx_RefNannySetupContext(name, acquire_gil)\ __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__) #endif - #define __Pyx_RefNannyFinishContext() \ + #define __Pyx_RefNannyFinishContext()\ __Pyx_RefNanny->FinishContext(&__pyx_refnanny) #define __Pyx_INCREF(r) __Pyx_RefNanny->INCREF(__pyx_refnanny, (PyObject *)(r), __LINE__) #define __Pyx_DECREF(r) __Pyx_RefNanny->DECREF(__pyx_refnanny, (PyObject *)(r), __LINE__) @@ -501,13 +775,13 @@ static const char *__pyx_f[] = { #define __Pyx_XGOTREF(r) #define __Pyx_XGIVEREF(r) #endif -#define __Pyx_XDECREF_SET(r, v) do { \ - PyObject *tmp = (PyObject *) r; \ - r = v; __Pyx_XDECREF(tmp); \ +#define __Pyx_XDECREF_SET(r, v) do {\ + PyObject *tmp = (PyObject *) r;\ + r = v; __Pyx_XDECREF(tmp);\ } while (0) -#define __Pyx_DECREF_SET(r, v) do { \ - PyObject *tmp = (PyObject *) r; \ - r = v; __Pyx_DECREF(tmp); \ +#define __Pyx_DECREF_SET(r, v) do {\ + PyObject *tmp = (PyObject *) r;\ + r = v; __Pyx_DECREF(tmp);\ } while (0) #define __Pyx_CLEAR(r) do { PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);} while(0) #define __Pyx_XCLEAR(r) do { if((r) != NULL) {PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);}} while(0) @@ -517,14 +791,72 @@ static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact, static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); -static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], \ - PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, \ +static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[],\ + PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args,\ const char* function_name); static CYTHON_INLINE int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed, const char *name, int exact); -static CYTHON_INLINE long __Pyx_div_long(long, long); /* proto */ +static CYTHON_INLINE long __Pyx_div_long(long, long); + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject* attr_name) { + PyTypeObject* tp = Py_TYPE(obj); + if (likely(tp->tp_getattro)) + return tp->tp_getattro(obj, attr_name); +#if PY_MAJOR_VERSION < 3 + if (likely(tp->tp_getattr)) + return tp->tp_getattr(obj, PyString_AS_STRING(attr_name)); +#endif + return PyObject_GetAttr(obj, attr_name); +} +#else +#define __Pyx_PyObject_GetAttrStr(o,n) PyObject_GetAttr(o,n) +#endif + +static PyObject *__Pyx_GetBuiltinName(PyObject *name); + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw); +#else +#define __Pyx_PyObject_Call(func, arg, kw) PyObject_Call(func, arg, kw) +#endif + +static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); +static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); + +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); + +#if PY_MAJOR_VERSION >= 3 && !CYTHON_COMPILING_IN_PYPY +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 CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); + +static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index); + +static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void); + +static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); + +static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); typedef struct { int code_line; @@ -543,12 +875,114 @@ 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); -static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long 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 long __Pyx_PyInt_As_long(PyObject *); +static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float, float); + +#if CYTHON_CCOMPLEX + #define __Pyx_c_eqf(a, b) ((a)==(b)) + #define __Pyx_c_sumf(a, b) ((a)+(b)) + #define __Pyx_c_difff(a, b) ((a)-(b)) + #define __Pyx_c_prodf(a, b) ((a)*(b)) + #define __Pyx_c_quotf(a, b) ((a)/(b)) + #define __Pyx_c_negf(a) (-(a)) + #ifdef __cplusplus + #define __Pyx_c_is_zerof(z) ((z)==(float)0) + #define __Pyx_c_conjf(z) (::std::conj(z)) + #if 1 + #define __Pyx_c_absf(z) (::std::abs(z)) + #define __Pyx_c_powf(a, b) (::std::pow(a, b)) + #endif + #else + #define __Pyx_c_is_zerof(z) ((z)==0) + #define __Pyx_c_conjf(z) (conjf(z)) + #if 1 + #define __Pyx_c_absf(z) (cabsf(z)) + #define __Pyx_c_powf(a, b) (cpowf(a, b)) + #endif + #endif +#else + static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prodf(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex); + static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex); + #if 1 + static CYTHON_INLINE float __Pyx_c_absf(__pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex, __pyx_t_float_complex); + #endif +#endif + +static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double, double); + +#if CYTHON_CCOMPLEX + #define __Pyx_c_eq(a, b) ((a)==(b)) + #define __Pyx_c_sum(a, b) ((a)+(b)) + #define __Pyx_c_diff(a, b) ((a)-(b)) + #define __Pyx_c_prod(a, b) ((a)*(b)) + #define __Pyx_c_quot(a, b) ((a)/(b)) + #define __Pyx_c_neg(a) (-(a)) + #ifdef __cplusplus + #define __Pyx_c_is_zero(z) ((z)==(double)0) + #define __Pyx_c_conj(z) (::std::conj(z)) + #if 1 + #define __Pyx_c_abs(z) (::std::abs(z)) + #define __Pyx_c_pow(a, b) (::std::pow(a, b)) + #endif + #else + #define __Pyx_c_is_zero(z) ((z)==0) + #define __Pyx_c_conj(z) (conj(z)) + #if 1 + #define __Pyx_c_abs(z) (cabs(z)) + #define __Pyx_c_pow(a, b) (cpow(a, b)) + #endif + #endif +#else + static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex); + static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex); + #if 1 + static CYTHON_INLINE double __Pyx_c_abs(__pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex, __pyx_t_double_complex); + #endif +#endif + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__NPY_TYPES(enum NPY_TYPES value); + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value); + +static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *); + static int __Pyx_check_binary_version(void); #if !defined(__Pyx_PyIdentifier_FromString) @@ -566,40 +1000,69 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); +/* Module declarations from 'cpython.buffer' */ + +/* Module declarations from 'libc.string' */ + +/* Module declarations from 'libc.stdio' */ + +/* Module declarations from '__builtin__' */ + +/* Module declarations from 'cpython.type' */ +static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0; + +/* Module declarations from 'cpython' */ + +/* Module declarations from 'cpython.object' */ + +/* Module declarations from 'cpython.ref' */ + +/* Module declarations from 'libc.stdlib' */ + /* Module declarations from 'numpy' */ -/* Module declarations from 'c_numpy' */ -static PyTypeObject *__pyx_ptype_7c_numpy_ndarray = 0; +/* 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 'lib._distances_openmp' */ #define __Pyx_MODULE_NAME "lib._distances_openmp" int __pyx_module_is_main_lib___distances_openmp = 0; /* Implementation of 'lib._distances_openmp' */ -static PyObject *__pyx_pf_3lib_17_distances_openmp_calc_distance_array(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_ref, PyArrayObject *__pyx_v_conf, PyArrayObject *__pyx_v_result); /* proto */ -static PyObject *__pyx_pf_3lib_17_distances_openmp_2calc_distance_array_ortho(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_ref, PyArrayObject *__pyx_v_conf, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_result); /* proto */ -static PyObject *__pyx_pf_3lib_17_distances_openmp_4calc_distance_array_triclinic(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_ref, PyArrayObject *__pyx_v_conf, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_result); /* proto */ -static PyObject *__pyx_pf_3lib_17_distances_openmp_6calc_self_distance_array(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_ref, PyArrayObject *__pyx_v_result); /* proto */ -static PyObject *__pyx_pf_3lib_17_distances_openmp_8calc_self_distance_array_ortho(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_ref, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_result); /* proto */ -static PyObject *__pyx_pf_3lib_17_distances_openmp_10calc_self_distance_array_triclinic(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_ref, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_result); /* proto */ -static PyObject *__pyx_pf_3lib_17_distances_openmp_12coord_transform(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords, PyArrayObject *__pyx_v_box); /* proto */ -static PyObject *__pyx_pf_3lib_17_distances_openmp_14calc_bond_distance(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_results); /* proto */ -static PyObject *__pyx_pf_3lib_17_distances_openmp_16calc_bond_distance_ortho(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_results); /* proto */ -static PyObject *__pyx_pf_3lib_17_distances_openmp_18calc_bond_distance_triclinic(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_results); /* proto */ -static PyObject *__pyx_pf_3lib_17_distances_openmp_20calc_angle(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_coords3, PyArrayObject *__pyx_v_results); /* proto */ -static PyObject *__pyx_pf_3lib_17_distances_openmp_22calc_angle_ortho(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_coords3, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_results); /* proto */ -static PyObject *__pyx_pf_3lib_17_distances_openmp_24calc_angle_triclinic(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_coords3, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_results); /* proto */ -static PyObject *__pyx_pf_3lib_17_distances_openmp_26calc_dihedral(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_coords3, PyArrayObject *__pyx_v_coords4, PyArrayObject *__pyx_v_results); /* proto */ -static PyObject *__pyx_pf_3lib_17_distances_openmp_28calc_dihedral_ortho(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_coords3, PyArrayObject *__pyx_v_coords4, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_results); /* proto */ -static PyObject *__pyx_pf_3lib_17_distances_openmp_30calc_dihedral_triclinic(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_coords3, PyArrayObject *__pyx_v_coords4, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_results); /* proto */ -static PyObject *__pyx_pf_3lib_17_distances_openmp_32ortho_pbc(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_box_inverse); /* proto */ -static PyObject *__pyx_pf_3lib_17_distances_openmp_34triclinic_pbc(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_box_inverse); /* proto */ +static PyObject *__pyx_builtin_ValueError; +static PyObject *__pyx_builtin_range; +static PyObject *__pyx_builtin_RuntimeError; +static char __pyx_k_B[] = "B"; +static char __pyx_k_H[] = "H"; +static char __pyx_k_I[] = "I"; +static char __pyx_k_L[] = "L"; +static char __pyx_k_O[] = "O"; +static char __pyx_k_Q[] = "Q"; +static char __pyx_k_b[] = "b"; +static char __pyx_k_d[] = "d"; +static char __pyx_k_f[] = "f"; +static char __pyx_k_g[] = "g"; +static char __pyx_k_h[] = "h"; +static char __pyx_k_i[] = "i"; +static char __pyx_k_l[] = "l"; +static char __pyx_k_q[] = "q"; +static char __pyx_k_Zd[] = "Zd"; +static char __pyx_k_Zf[] = "Zf"; +static char __pyx_k_Zg[] = "Zg"; static char __pyx_k_box[] = "box"; static char __pyx_k_ref[] = "ref"; static char __pyx_k_conf[] = "conf"; static char __pyx_k_main[] = "__main__"; static char __pyx_k_test[] = "__test__"; +static char __pyx_k_numpy[] = "numpy"; +static char __pyx_k_range[] = "range"; static char __pyx_k_coords[] = "coords"; +static char __pyx_k_import[] = "__import__"; static char __pyx_k_refnum[] = "refnum"; static char __pyx_k_result[] = "result"; static char __pyx_k_confnum[] = "confnum"; @@ -611,8 +1074,10 @@ static char __pyx_k_distnum[] = "distnum"; static char __pyx_k_results[] = "results"; static char __pyx_k_numcoords[] = "numcoords"; static char __pyx_k_ortho_pbc[] = "ortho_pbc"; +static char __pyx_k_ValueError[] = "ValueError"; static char __pyx_k_calc_angle[] = "calc_angle"; static char __pyx_k_box_inverse[] = "box_inverse"; +static char __pyx_k_RuntimeError[] = "RuntimeError"; static char __pyx_k_calc_dihedral[] = "calc_dihedral"; static char __pyx_k_triclinic_pbc[] = "triclinic_pbc"; static char __pyx_k_coord_transform[] = "coord_transform"; @@ -626,12 +1091,23 @@ static char __pyx_k_calc_dihedral_triclinic[] = "calc_dihedral_triclinic"; static char __pyx_k_calc_bond_distance_ortho[] = "calc_bond_distance_ortho"; static char __pyx_k_calc_self_distance_array[] = "calc_self_distance_array"; static char __pyx_k_calc_distance_array_ortho[] = "calc_distance_array_ortho"; +static char __pyx_k_ndarray_is_not_C_contiguous[] = "ndarray is not C contiguous"; static char __pyx_k_calc_bond_distance_triclinic[] = "calc_bond_distance_triclinic"; static char __pyx_k_calc_distance_array_triclinic[] = "calc_distance_array_triclinic"; static char __pyx_k_calc_self_distance_array_ortho[] = "calc_self_distance_array_ortho"; static char __pyx_k_Parallel_distance_calculation_l[] = "\nParallel distance calculation library --- :mod:`MDAnalysis.lib._distances_openmp`\n=================================================================================\n\n\nContains OpenMP versions of the contents of \"calc_distances.h\"\n"; -static char __pyx_k_home_richard_code_mdanalysis_pa[] = "/home/richard/code/mdanalysis/package/MDAnalysis/lib/distances_openmp.pyx"; +static char __pyx_k_nfs_homes2_oliver_Library_pytho[] = "/nfs/homes2/oliver/Library/python/mdanalysis/package/MDAnalysis/lib/distances_openmp.pyx"; +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_Non_native_byte_order_not_suppor[] = "Non-native byte order not supported"; static char __pyx_k_calc_self_distance_array_triclin[] = "calc_self_distance_array_triclinic"; +static char __pyx_k_ndarray_is_not_Fortran_contiguou[] = "ndarray is not Fortran contiguous"; +static char __pyx_k_Format_string_allocated_too_shor_2[] = "Format string allocated too short."; +static PyObject *__pyx_kp_u_Format_string_allocated_too_shor; +static PyObject *__pyx_kp_u_Format_string_allocated_too_shor_2; +static PyObject *__pyx_kp_u_Non_native_byte_order_not_suppor; +static PyObject *__pyx_n_s_RuntimeError; +static PyObject *__pyx_n_s_ValueError; static PyObject *__pyx_n_s_box; static PyObject *__pyx_n_s_box_inverse; static PyObject *__pyx_n_s_calc_angle; @@ -658,20 +1134,49 @@ static PyObject *__pyx_n_s_coords2; static PyObject *__pyx_n_s_coords3; static PyObject *__pyx_n_s_coords4; static PyObject *__pyx_n_s_distnum; -static PyObject *__pyx_kp_s_home_richard_code_mdanalysis_pa; +static PyObject *__pyx_n_s_import; static PyObject *__pyx_n_s_lib__distances_openmp; static PyObject *__pyx_n_s_main; +static PyObject *__pyx_kp_u_ndarray_is_not_C_contiguous; +static PyObject *__pyx_kp_u_ndarray_is_not_Fortran_contiguou; +static PyObject *__pyx_kp_s_nfs_homes2_oliver_Library_pytho; static PyObject *__pyx_n_s_numcoords; +static PyObject *__pyx_n_s_numpy; static PyObject *__pyx_n_s_ortho_pbc; +static PyObject *__pyx_n_s_range; static PyObject *__pyx_n_s_ref; static PyObject *__pyx_n_s_refnum; static PyObject *__pyx_n_s_result; static PyObject *__pyx_n_s_results; static PyObject *__pyx_n_s_test; static PyObject *__pyx_n_s_triclinic_pbc; +static PyObject *__pyx_kp_u_unknown_dtype_code_in_numpy_pxd; +static PyObject *__pyx_pf_3lib_17_distances_openmp_calc_distance_array(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_ref, PyArrayObject *__pyx_v_conf, PyArrayObject *__pyx_v_result); /* proto */ +static PyObject *__pyx_pf_3lib_17_distances_openmp_2calc_distance_array_ortho(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_ref, PyArrayObject *__pyx_v_conf, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_result); /* proto */ +static PyObject *__pyx_pf_3lib_17_distances_openmp_4calc_distance_array_triclinic(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_ref, PyArrayObject *__pyx_v_conf, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_result); /* proto */ +static PyObject *__pyx_pf_3lib_17_distances_openmp_6calc_self_distance_array(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_ref, PyArrayObject *__pyx_v_result); /* proto */ +static PyObject *__pyx_pf_3lib_17_distances_openmp_8calc_self_distance_array_ortho(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_ref, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_result); /* proto */ +static PyObject *__pyx_pf_3lib_17_distances_openmp_10calc_self_distance_array_triclinic(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_ref, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_result); /* proto */ +static PyObject *__pyx_pf_3lib_17_distances_openmp_12coord_transform(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords, PyArrayObject *__pyx_v_box); /* proto */ +static PyObject *__pyx_pf_3lib_17_distances_openmp_14calc_bond_distance(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_results); /* proto */ +static PyObject *__pyx_pf_3lib_17_distances_openmp_16calc_bond_distance_ortho(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_results); /* proto */ +static PyObject *__pyx_pf_3lib_17_distances_openmp_18calc_bond_distance_triclinic(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_results); /* proto */ +static PyObject *__pyx_pf_3lib_17_distances_openmp_20calc_angle(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_coords3, PyArrayObject *__pyx_v_results); /* proto */ +static PyObject *__pyx_pf_3lib_17_distances_openmp_22calc_angle_ortho(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_coords3, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_results); /* proto */ +static PyObject *__pyx_pf_3lib_17_distances_openmp_24calc_angle_triclinic(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_coords3, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_results); /* proto */ +static PyObject *__pyx_pf_3lib_17_distances_openmp_26calc_dihedral(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_coords3, PyArrayObject *__pyx_v_coords4, PyArrayObject *__pyx_v_results); /* proto */ +static PyObject *__pyx_pf_3lib_17_distances_openmp_28calc_dihedral_ortho(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_coords3, PyArrayObject *__pyx_v_coords4, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_results); /* proto */ +static PyObject *__pyx_pf_3lib_17_distances_openmp_30calc_dihedral_triclinic(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords1, PyArrayObject *__pyx_v_coords2, PyArrayObject *__pyx_v_coords3, PyArrayObject *__pyx_v_coords4, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_results); /* proto */ +static PyObject *__pyx_pf_3lib_17_distances_openmp_32ortho_pbc(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_box_inverse); /* proto */ +static PyObject *__pyx_pf_3lib_17_distances_openmp_34triclinic_pbc(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_coords, PyArrayObject *__pyx_v_box, PyArrayObject *__pyx_v_box_inverse); /* 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_tuple_; +static PyObject *__pyx_tuple__2; static PyObject *__pyx_tuple__3; +static PyObject *__pyx_tuple__4; static PyObject *__pyx_tuple__5; +static PyObject *__pyx_tuple__6; static PyObject *__pyx_tuple__7; static PyObject *__pyx_tuple__9; static PyObject *__pyx_tuple__11; @@ -687,9 +1192,9 @@ static PyObject *__pyx_tuple__29; static PyObject *__pyx_tuple__31; static PyObject *__pyx_tuple__33; static PyObject *__pyx_tuple__35; -static PyObject *__pyx_codeobj__2; -static PyObject *__pyx_codeobj__4; -static PyObject *__pyx_codeobj__6; +static PyObject *__pyx_tuple__37; +static PyObject *__pyx_tuple__39; +static PyObject *__pyx_tuple__41; static PyObject *__pyx_codeobj__8; static PyObject *__pyx_codeobj__10; static PyObject *__pyx_codeobj__12; @@ -705,12 +1210,15 @@ static PyObject *__pyx_codeobj__30; static PyObject *__pyx_codeobj__32; static PyObject *__pyx_codeobj__34; static PyObject *__pyx_codeobj__36; +static PyObject *__pyx_codeobj__38; +static PyObject *__pyx_codeobj__40; +static PyObject *__pyx_codeobj__42; /* "MDAnalysis/lib/distances_openmp.pyx":54 * void _triclinic_pbc(coordinate* coords, int numcoords, coordinate* box, float* box_inverse) * - * def calc_distance_array(c_numpy.ndarray ref, c_numpy.ndarray conf, # <<<<<<<<<<<<<< - * c_numpy.ndarray result): + * def calc_distance_array(numpy.ndarray ref, numpy.ndarray conf, # <<<<<<<<<<<<<< + * numpy.ndarray result): * cdef int confnum, refnum */ @@ -778,9 +1286,9 @@ static PyObject *__pyx_pw_3lib_17_distances_openmp_1calc_distance_array(PyObject __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_ref), __pyx_ptype_7c_numpy_ndarray, 1, "ref", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_conf), __pyx_ptype_7c_numpy_ndarray, 1, "conf", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_result), __pyx_ptype_7c_numpy_ndarray, 1, "result", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_ref), __pyx_ptype_5numpy_ndarray, 1, "ref", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_conf), __pyx_ptype_5numpy_ndarray, 1, "conf", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_result), __pyx_ptype_5numpy_ndarray, 1, "result", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_pf_3lib_17_distances_openmp_calc_distance_array(__pyx_self, __pyx_v_ref, __pyx_v_conf, __pyx_v_result); /* function exit code */ @@ -800,25 +1308,25 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_calc_distance_array(CYTHON_UN __Pyx_RefNannySetupContext("calc_distance_array", 0); /* "MDAnalysis/lib/distances_openmp.pyx":57 - * c_numpy.ndarray result): + * numpy.ndarray result): * cdef int confnum, refnum - * confnum = conf.dimensions[0] # <<<<<<<<<<<<<< - * refnum = ref.dimensions[0] + * confnum = conf.shape[0] # <<<<<<<<<<<<<< + * refnum = ref.shape[0] * */ __pyx_v_confnum = (__pyx_v_conf->dimensions[0]); /* "MDAnalysis/lib/distances_openmp.pyx":58 * cdef int confnum, refnum - * confnum = conf.dimensions[0] - * refnum = ref.dimensions[0] # <<<<<<<<<<<<<< + * confnum = conf.shape[0] + * refnum = ref.shape[0] # <<<<<<<<<<<<<< * * _calc_distance_array(ref.data, refnum, */ __pyx_v_refnum = (__pyx_v_ref->dimensions[0]); /* "MDAnalysis/lib/distances_openmp.pyx":60 - * refnum = ref.dimensions[0] + * refnum = ref.shape[0] * * _calc_distance_array(ref.data, refnum, # <<<<<<<<<<<<<< * conf.data, confnum, @@ -829,8 +1337,8 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_calc_distance_array(CYTHON_UN /* "MDAnalysis/lib/distances_openmp.pyx":54 * void _triclinic_pbc(coordinate* coords, int numcoords, coordinate* box, float* box_inverse) * - * def calc_distance_array(c_numpy.ndarray ref, c_numpy.ndarray conf, # <<<<<<<<<<<<<< - * c_numpy.ndarray result): + * def calc_distance_array(numpy.ndarray ref, numpy.ndarray conf, # <<<<<<<<<<<<<< + * numpy.ndarray result): * cdef int confnum, refnum */ @@ -844,9 +1352,9 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_calc_distance_array(CYTHON_UN /* "MDAnalysis/lib/distances_openmp.pyx":64 * result.data) * - * def calc_distance_array_ortho(c_numpy.ndarray ref, c_numpy.ndarray conf, # <<<<<<<<<<<<<< - * c_numpy.ndarray box, - * c_numpy.ndarray result): + * def calc_distance_array_ortho(numpy.ndarray ref, numpy.ndarray conf, # <<<<<<<<<<<<<< + * numpy.ndarray box, + * numpy.ndarray result): */ /* Python wrapper */ @@ -922,10 +1430,10 @@ static PyObject *__pyx_pw_3lib_17_distances_openmp_3calc_distance_array_ortho(Py __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_ref), __pyx_ptype_7c_numpy_ndarray, 1, "ref", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_conf), __pyx_ptype_7c_numpy_ndarray, 1, "conf", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_7c_numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 65; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_result), __pyx_ptype_7c_numpy_ndarray, 1, "result", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_ref), __pyx_ptype_5numpy_ndarray, 1, "ref", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_conf), __pyx_ptype_5numpy_ndarray, 1, "conf", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_5numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 65; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_result), __pyx_ptype_5numpy_ndarray, 1, "result", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_pf_3lib_17_distances_openmp_2calc_distance_array_ortho(__pyx_self, __pyx_v_ref, __pyx_v_conf, __pyx_v_box, __pyx_v_result); /* function exit code */ @@ -945,25 +1453,25 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_2calc_distance_array_ortho(CY __Pyx_RefNannySetupContext("calc_distance_array_ortho", 0); /* "MDAnalysis/lib/distances_openmp.pyx":68 - * c_numpy.ndarray result): + * numpy.ndarray result): * cdef int confnum, refnum - * confnum = conf.dimensions[0] # <<<<<<<<<<<<<< - * refnum = ref.dimensions[0] + * confnum = conf.shape[0] # <<<<<<<<<<<<<< + * refnum = ref.shape[0] * */ __pyx_v_confnum = (__pyx_v_conf->dimensions[0]); /* "MDAnalysis/lib/distances_openmp.pyx":69 * cdef int confnum, refnum - * confnum = conf.dimensions[0] - * refnum = ref.dimensions[0] # <<<<<<<<<<<<<< + * confnum = conf.shape[0] + * refnum = ref.shape[0] # <<<<<<<<<<<<<< * * _calc_distance_array_ortho(ref.data, refnum, */ __pyx_v_refnum = (__pyx_v_ref->dimensions[0]); /* "MDAnalysis/lib/distances_openmp.pyx":71 - * refnum = ref.dimensions[0] + * refnum = ref.shape[0] * * _calc_distance_array_ortho(ref.data, refnum, # <<<<<<<<<<<<<< * conf.data, confnum, @@ -974,9 +1482,9 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_2calc_distance_array_ortho(CY /* "MDAnalysis/lib/distances_openmp.pyx":64 * result.data) * - * def calc_distance_array_ortho(c_numpy.ndarray ref, c_numpy.ndarray conf, # <<<<<<<<<<<<<< - * c_numpy.ndarray box, - * c_numpy.ndarray result): + * def calc_distance_array_ortho(numpy.ndarray ref, numpy.ndarray conf, # <<<<<<<<<<<<<< + * numpy.ndarray box, + * numpy.ndarray result): */ /* function exit code */ @@ -989,9 +1497,9 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_2calc_distance_array_ortho(CY /* "MDAnalysis/lib/distances_openmp.pyx":76 * result.data) * - * def calc_distance_array_triclinic(c_numpy.ndarray ref, c_numpy.ndarray conf, # <<<<<<<<<<<<<< - * c_numpy.ndarray box, - * c_numpy.ndarray result): + * def calc_distance_array_triclinic(numpy.ndarray ref, numpy.ndarray conf, # <<<<<<<<<<<<<< + * numpy.ndarray box, + * numpy.ndarray result): */ /* Python wrapper */ @@ -1067,10 +1575,10 @@ static PyObject *__pyx_pw_3lib_17_distances_openmp_5calc_distance_array_triclini __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_ref), __pyx_ptype_7c_numpy_ndarray, 1, "ref", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_conf), __pyx_ptype_7c_numpy_ndarray, 1, "conf", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_7c_numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_result), __pyx_ptype_7c_numpy_ndarray, 1, "result", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_ref), __pyx_ptype_5numpy_ndarray, 1, "ref", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_conf), __pyx_ptype_5numpy_ndarray, 1, "conf", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_5numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_result), __pyx_ptype_5numpy_ndarray, 1, "result", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_pf_3lib_17_distances_openmp_4calc_distance_array_triclinic(__pyx_self, __pyx_v_ref, __pyx_v_conf, __pyx_v_box, __pyx_v_result); /* function exit code */ @@ -1090,25 +1598,25 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_4calc_distance_array_triclini __Pyx_RefNannySetupContext("calc_distance_array_triclinic", 0); /* "MDAnalysis/lib/distances_openmp.pyx":80 - * c_numpy.ndarray result): + * numpy.ndarray result): * cdef int confnum, refnum - * confnum = conf.dimensions[0] # <<<<<<<<<<<<<< - * refnum = ref.dimensions[0] + * confnum = conf.shape[0] # <<<<<<<<<<<<<< + * refnum = ref.shape[0] * */ __pyx_v_confnum = (__pyx_v_conf->dimensions[0]); /* "MDAnalysis/lib/distances_openmp.pyx":81 * cdef int confnum, refnum - * confnum = conf.dimensions[0] - * refnum = ref.dimensions[0] # <<<<<<<<<<<<<< + * confnum = conf.shape[0] + * refnum = ref.shape[0] # <<<<<<<<<<<<<< * * _calc_distance_array_triclinic(ref.data, refnum, */ __pyx_v_refnum = (__pyx_v_ref->dimensions[0]); /* "MDAnalysis/lib/distances_openmp.pyx":83 - * refnum = ref.dimensions[0] + * refnum = ref.shape[0] * * _calc_distance_array_triclinic(ref.data, refnum, # <<<<<<<<<<<<<< * conf.data, confnum, @@ -1119,9 +1627,9 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_4calc_distance_array_triclini /* "MDAnalysis/lib/distances_openmp.pyx":76 * result.data) * - * def calc_distance_array_triclinic(c_numpy.ndarray ref, c_numpy.ndarray conf, # <<<<<<<<<<<<<< - * c_numpy.ndarray box, - * c_numpy.ndarray result): + * def calc_distance_array_triclinic(numpy.ndarray ref, numpy.ndarray conf, # <<<<<<<<<<<<<< + * numpy.ndarray box, + * numpy.ndarray result): */ /* function exit code */ @@ -1134,8 +1642,8 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_4calc_distance_array_triclini /* "MDAnalysis/lib/distances_openmp.pyx":88 * result.data) * - * def calc_self_distance_array(c_numpy.ndarray ref, # <<<<<<<<<<<<<< - * c_numpy.ndarray result): + * def calc_self_distance_array(numpy.ndarray ref, # <<<<<<<<<<<<<< + * numpy.ndarray result): * cdef int refnum, distnum */ @@ -1194,8 +1702,8 @@ static PyObject *__pyx_pw_3lib_17_distances_openmp_7calc_self_distance_array(PyO __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_ref), __pyx_ptype_7c_numpy_ndarray, 1, "ref", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_result), __pyx_ptype_7c_numpy_ndarray, 1, "result", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_ref), __pyx_ptype_5numpy_ndarray, 1, "ref", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_result), __pyx_ptype_5numpy_ndarray, 1, "result", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_pf_3lib_17_distances_openmp_6calc_self_distance_array(__pyx_self, __pyx_v_ref, __pyx_v_result); /* function exit code */ @@ -1215,9 +1723,9 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_6calc_self_distance_array(CYT __Pyx_RefNannySetupContext("calc_self_distance_array", 0); /* "MDAnalysis/lib/distances_openmp.pyx":91 - * c_numpy.ndarray result): + * numpy.ndarray result): * cdef int refnum, distnum - * refnum = ref.dimensions[0] # <<<<<<<<<<<<<< + * refnum = ref.shape[0] # <<<<<<<<<<<<<< * distnum = (refnum*(refnum-1))/2 * */ @@ -1225,7 +1733,7 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_6calc_self_distance_array(CYT /* "MDAnalysis/lib/distances_openmp.pyx":92 * cdef int refnum, distnum - * refnum = ref.dimensions[0] + * refnum = ref.shape[0] * distnum = (refnum*(refnum-1))/2 # <<<<<<<<<<<<<< * * _calc_self_distance_array(ref.data, refnum, @@ -1244,8 +1752,8 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_6calc_self_distance_array(CYT /* "MDAnalysis/lib/distances_openmp.pyx":88 * result.data) * - * def calc_self_distance_array(c_numpy.ndarray ref, # <<<<<<<<<<<<<< - * c_numpy.ndarray result): + * def calc_self_distance_array(numpy.ndarray ref, # <<<<<<<<<<<<<< + * numpy.ndarray result): * cdef int refnum, distnum */ @@ -1259,9 +1767,9 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_6calc_self_distance_array(CYT /* "MDAnalysis/lib/distances_openmp.pyx":97 * result.data, distnum) * - * def calc_self_distance_array_ortho(c_numpy.ndarray ref, # <<<<<<<<<<<<<< - * c_numpy.ndarray box, - * c_numpy.ndarray result): + * def calc_self_distance_array_ortho(numpy.ndarray ref, # <<<<<<<<<<<<<< + * numpy.ndarray box, + * numpy.ndarray result): */ /* Python wrapper */ @@ -1328,9 +1836,9 @@ static PyObject *__pyx_pw_3lib_17_distances_openmp_9calc_self_distance_array_ort __Pyx_RefNannyFinishContext(); 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__pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_result), __pyx_ptype_5numpy_ndarray, 1, "result", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 99; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_pf_3lib_17_distances_openmp_8calc_self_distance_array_ortho(__pyx_self, __pyx_v_ref, __pyx_v_box, __pyx_v_result); /* function exit code */ @@ -1350,9 +1858,9 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_8calc_self_distance_array_ort __Pyx_RefNannySetupContext("calc_self_distance_array_ortho", 0); /* "MDAnalysis/lib/distances_openmp.pyx":101 - * c_numpy.ndarray result): + * numpy.ndarray result): * cdef int refnum, distnum - * refnum = ref.dimensions[0] # <<<<<<<<<<<<<< + * refnum = ref.shape[0] # <<<<<<<<<<<<<< * distnum = (refnum*(refnum-1))/2 * */ @@ -1360,7 +1868,7 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_8calc_self_distance_array_ort /* "MDAnalysis/lib/distances_openmp.pyx":102 * cdef int refnum, distnum - * refnum = ref.dimensions[0] + * refnum = ref.shape[0] * distnum = (refnum*(refnum-1))/2 # <<<<<<<<<<<<<< * * _calc_self_distance_array_ortho(ref.data, refnum, @@ -1379,9 +1887,9 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_8calc_self_distance_array_ort /* "MDAnalysis/lib/distances_openmp.pyx":97 * result.data, distnum) * - * def calc_self_distance_array_ortho(c_numpy.ndarray ref, # <<<<<<<<<<<<<< - * c_numpy.ndarray box, - * c_numpy.ndarray result): + * def calc_self_distance_array_ortho(numpy.ndarray ref, # <<<<<<<<<<<<<< + * numpy.ndarray box, + * numpy.ndarray result): */ /* function exit code */ @@ -1394,9 +1902,9 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_8calc_self_distance_array_ort /* "MDAnalysis/lib/distances_openmp.pyx":108 * result.data, distnum) * - * def calc_self_distance_array_triclinic(c_numpy.ndarray ref, # <<<<<<<<<<<<<< - * c_numpy.ndarray box, - * c_numpy.ndarray result): + * def calc_self_distance_array_triclinic(numpy.ndarray ref, # <<<<<<<<<<<<<< + * numpy.ndarray box, + * numpy.ndarray result): */ /* Python wrapper */ @@ -1463,9 +1971,9 @@ static PyObject *__pyx_pw_3lib_17_distances_openmp_11calc_self_distance_array_tr __Pyx_RefNannyFinishContext(); 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__pyx_lineno = 109; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_result), __pyx_ptype_5numpy_ndarray, 1, "result", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_pf_3lib_17_distances_openmp_10calc_self_distance_array_triclinic(__pyx_self, __pyx_v_ref, __pyx_v_box, __pyx_v_result); /* function exit code */ @@ -1485,9 +1993,9 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_10calc_self_distance_array_tr __Pyx_RefNannySetupContext("calc_self_distance_array_triclinic", 0); /* "MDAnalysis/lib/distances_openmp.pyx":112 - * c_numpy.ndarray result): + * numpy.ndarray result): * cdef int refnum, distnum - * refnum = ref.dimensions[0] # <<<<<<<<<<<<<< + * refnum = ref.shape[0] # <<<<<<<<<<<<<< * distnum = (refnum*(refnum-1))/2 * */ @@ -1495,7 +2003,7 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_10calc_self_distance_array_tr /* "MDAnalysis/lib/distances_openmp.pyx":113 * cdef int refnum, distnum - * refnum = ref.dimensions[0] + * refnum = ref.shape[0] * distnum = (refnum*(refnum-1))/2 # <<<<<<<<<<<<<< * * _calc_self_distance_array_triclinic(ref.data, refnum, @@ -1514,9 +2022,9 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_10calc_self_distance_array_tr /* "MDAnalysis/lib/distances_openmp.pyx":108 * result.data, distnum) * - * def calc_self_distance_array_triclinic(c_numpy.ndarray ref, # <<<<<<<<<<<<<< - * c_numpy.ndarray box, - * c_numpy.ndarray result): + * def calc_self_distance_array_triclinic(numpy.ndarray ref, # <<<<<<<<<<<<<< + * numpy.ndarray box, + * numpy.ndarray result): */ /* function exit code */ @@ -1529,8 +2037,8 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_10calc_self_distance_array_tr /* "MDAnalysis/lib/distances_openmp.pyx":119 * result.data, distnum) * - * def coord_transform(c_numpy.ndarray coords, # <<<<<<<<<<<<<< - * c_numpy.ndarray box): + * def coord_transform(numpy.ndarray coords, # <<<<<<<<<<<<<< + * numpy.ndarray box): * cdef int numcoords */ @@ -1589,8 +2097,8 @@ static PyObject *__pyx_pw_3lib_17_distances_openmp_13coord_transform(PyObject *_ __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords), __pyx_ptype_7c_numpy_ndarray, 1, "coords", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 119; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_7c_numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 120; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords), __pyx_ptype_5numpy_ndarray, 1, "coords", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 119; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_5numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 120; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_pf_3lib_17_distances_openmp_12coord_transform(__pyx_self, __pyx_v_coords, __pyx_v_box); /* function exit code */ @@ -1609,16 +2117,16 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_12coord_transform(CYTHON_UNUS __Pyx_RefNannySetupContext("coord_transform", 0); /* "MDAnalysis/lib/distances_openmp.pyx":122 - * c_numpy.ndarray box): + * numpy.ndarray box): * cdef int numcoords - * numcoords = coords.dimensions[0] # <<<<<<<<<<<<<< + * numcoords = coords.shape[0] # <<<<<<<<<<<<<< * * _coord_transform( coords.data, numcoords, */ __pyx_v_numcoords = (__pyx_v_coords->dimensions[0]); /* "MDAnalysis/lib/distances_openmp.pyx":124 - * numcoords = coords.dimensions[0] + * numcoords = coords.shape[0] * * _coord_transform( coords.data, numcoords, # <<<<<<<<<<<<<< * box.data) @@ -1629,8 +2137,8 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_12coord_transform(CYTHON_UNUS /* "MDAnalysis/lib/distances_openmp.pyx":119 * result.data, distnum) * - * def coord_transform(c_numpy.ndarray coords, # <<<<<<<<<<<<<< - * c_numpy.ndarray box): + * def coord_transform(numpy.ndarray coords, # <<<<<<<<<<<<<< + * numpy.ndarray box): * cdef int numcoords */ @@ -1644,9 +2152,9 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_12coord_transform(CYTHON_UNUS /* "MDAnalysis/lib/distances_openmp.pyx":127 * box.data) * - * def calc_bond_distance(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray results): + * def calc_bond_distance(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray results): */ /* Python wrapper */ @@ -1713,9 +2221,9 @@ static PyObject *__pyx_pw_3lib_17_distances_openmp_15calc_bond_distance(PyObject __Pyx_RefNannyFinishContext(); 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__pyx_lineno = 128; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_results), __pyx_ptype_5numpy_ndarray, 1, "results", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 129; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_pf_3lib_17_distances_openmp_14calc_bond_distance(__pyx_self, __pyx_v_coords1, __pyx_v_coords2, __pyx_v_results); /* function exit code */ @@ -1734,16 +2242,16 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_14calc_bond_distance(CYTHON_U __Pyx_RefNannySetupContext("calc_bond_distance", 0); /* "MDAnalysis/lib/distances_openmp.pyx":131 - * c_numpy.ndarray results): + * numpy.ndarray results): * cdef int numcoords - * numcoords = coords1.dimensions[0] # <<<<<<<<<<<<<< + * numcoords = coords1.shape[0] # <<<<<<<<<<<<<< * * _calc_bond_distance( coords1.data, coords2.data, */ __pyx_v_numcoords = (__pyx_v_coords1->dimensions[0]); /* "MDAnalysis/lib/distances_openmp.pyx":133 - * numcoords = coords1.dimensions[0] + * numcoords = coords1.shape[0] * * _calc_bond_distance( coords1.data, coords2.data, # <<<<<<<<<<<<<< * numcoords, @@ -1754,9 +2262,9 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_14calc_bond_distance(CYTHON_U /* "MDAnalysis/lib/distances_openmp.pyx":127 * box.data) * - * def calc_bond_distance(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray results): + * def calc_bond_distance(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray results): */ /* function exit code */ @@ -1769,9 +2277,9 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_14calc_bond_distance(CYTHON_U /* "MDAnalysis/lib/distances_openmp.pyx":137 * results.data) * - * def calc_bond_distance_ortho(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray box, + * def calc_bond_distance_ortho(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray box, */ /* Python wrapper */ @@ -1847,10 +2355,10 @@ static PyObject *__pyx_pw_3lib_17_distances_openmp_17calc_bond_distance_ortho(Py __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords1), __pyx_ptype_7c_numpy_ndarray, 1, "coords1", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 137; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords2), __pyx_ptype_7c_numpy_ndarray, 1, "coords2", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 138; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_7c_numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 139; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_results), __pyx_ptype_7c_numpy_ndarray, 1, "results", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords1), __pyx_ptype_5numpy_ndarray, 1, "coords1", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 137; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords2), __pyx_ptype_5numpy_ndarray, 1, "coords2", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 138; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_5numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 139; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_results), __pyx_ptype_5numpy_ndarray, 1, "results", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_pf_3lib_17_distances_openmp_16calc_bond_distance_ortho(__pyx_self, __pyx_v_coords1, __pyx_v_coords2, __pyx_v_box, __pyx_v_results); /* function exit code */ @@ -1869,16 +2377,16 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_16calc_bond_distance_ortho(CY __Pyx_RefNannySetupContext("calc_bond_distance_ortho", 0); /* "MDAnalysis/lib/distances_openmp.pyx":142 - * c_numpy.ndarray results): + * numpy.ndarray results): * cdef int numcoords - * numcoords = coords1.dimensions[0] # <<<<<<<<<<<<<< + * numcoords = coords1.shape[0] # <<<<<<<<<<<<<< * * _calc_bond_distance_ortho( coords1.data, coords2.data, */ __pyx_v_numcoords = (__pyx_v_coords1->dimensions[0]); /* "MDAnalysis/lib/distances_openmp.pyx":144 - * numcoords = coords1.dimensions[0] + * numcoords = coords1.shape[0] * * _calc_bond_distance_ortho( coords1.data, coords2.data, # <<<<<<<<<<<<<< * numcoords, @@ -1889,9 +2397,9 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_16calc_bond_distance_ortho(CY /* "MDAnalysis/lib/distances_openmp.pyx":137 * results.data) * - * def calc_bond_distance_ortho(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray box, + * def calc_bond_distance_ortho(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray box, */ /* function exit code */ @@ -1904,9 +2412,9 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_16calc_bond_distance_ortho(CY /* "MDAnalysis/lib/distances_openmp.pyx":149 * results.data) * - * def calc_bond_distance_triclinic(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray box, + * def calc_bond_distance_triclinic(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray box, */ /* Python wrapper */ @@ -1982,10 +2490,10 @@ static PyObject *__pyx_pw_3lib_17_distances_openmp_19calc_bond_distance_triclini __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords1), __pyx_ptype_7c_numpy_ndarray, 1, "coords1", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 149; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords2), __pyx_ptype_7c_numpy_ndarray, 1, "coords2", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 150; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_7c_numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 151; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_results), __pyx_ptype_7c_numpy_ndarray, 1, "results", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 152; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords1), __pyx_ptype_5numpy_ndarray, 1, "coords1", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 149; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords2), __pyx_ptype_5numpy_ndarray, 1, "coords2", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 150; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_5numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 151; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_results), __pyx_ptype_5numpy_ndarray, 1, "results", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 152; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_pf_3lib_17_distances_openmp_18calc_bond_distance_triclinic(__pyx_self, __pyx_v_coords1, __pyx_v_coords2, __pyx_v_box, __pyx_v_results); /* function exit code */ @@ -2004,16 +2512,16 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_18calc_bond_distance_triclini __Pyx_RefNannySetupContext("calc_bond_distance_triclinic", 0); /* "MDAnalysis/lib/distances_openmp.pyx":154 - * c_numpy.ndarray results): + * numpy.ndarray results): * cdef int numcoords - * numcoords = coords1.dimensions[0] # <<<<<<<<<<<<<< + * numcoords = coords1.shape[0] # <<<<<<<<<<<<<< * * _calc_bond_distance_triclinic( coords1.data, coords2.data, */ __pyx_v_numcoords = (__pyx_v_coords1->dimensions[0]); /* "MDAnalysis/lib/distances_openmp.pyx":156 - * numcoords = coords1.dimensions[0] + * numcoords = coords1.shape[0] * * _calc_bond_distance_triclinic( coords1.data, coords2.data, # <<<<<<<<<<<<<< * numcoords, @@ -2024,9 +2532,9 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_18calc_bond_distance_triclini /* "MDAnalysis/lib/distances_openmp.pyx":149 * results.data) * - * def calc_bond_distance_triclinic(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray box, + * def calc_bond_distance_triclinic(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray box, */ /* function exit code */ @@ -2039,9 +2547,9 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_18calc_bond_distance_triclini /* "MDAnalysis/lib/distances_openmp.pyx":161 * results.data) * - * def calc_angle(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray coords3, + * def calc_angle(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray coords3, */ /* Python wrapper */ @@ -2117,10 +2625,10 @@ static PyObject *__pyx_pw_3lib_17_distances_openmp_21calc_angle(PyObject *__pyx_ __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords1), __pyx_ptype_7c_numpy_ndarray, 1, "coords1", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 161; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords2), __pyx_ptype_7c_numpy_ndarray, 1, "coords2", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 162; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords3), __pyx_ptype_7c_numpy_ndarray, 1, "coords3", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 163; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_results), __pyx_ptype_7c_numpy_ndarray, 1, "results", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 164; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords1), __pyx_ptype_5numpy_ndarray, 1, "coords1", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 161; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords2), __pyx_ptype_5numpy_ndarray, 1, "coords2", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 162; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords3), __pyx_ptype_5numpy_ndarray, 1, "coords3", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 163; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_results), __pyx_ptype_5numpy_ndarray, 1, "results", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 164; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_pf_3lib_17_distances_openmp_20calc_angle(__pyx_self, __pyx_v_coords1, __pyx_v_coords2, __pyx_v_coords3, __pyx_v_results); /* function exit code */ @@ -2139,16 +2647,16 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_20calc_angle(CYTHON_UNUSED Py __Pyx_RefNannySetupContext("calc_angle", 0); /* "MDAnalysis/lib/distances_openmp.pyx":166 - * c_numpy.ndarray results): + * numpy.ndarray results): * cdef int numcoords - * numcoords = coords1.dimensions[0] # <<<<<<<<<<<<<< + * numcoords = coords1.shape[0] # <<<<<<<<<<<<<< * * _calc_angle( coords1.data, coords2.data, */ __pyx_v_numcoords = (__pyx_v_coords1->dimensions[0]); /* "MDAnalysis/lib/distances_openmp.pyx":168 - * numcoords = coords1.dimensions[0] + * numcoords = coords1.shape[0] * * _calc_angle( coords1.data, coords2.data, # <<<<<<<<<<<<<< * coords3.data, @@ -2159,9 +2667,9 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_20calc_angle(CYTHON_UNUSED Py /* "MDAnalysis/lib/distances_openmp.pyx":161 * results.data) * - * def calc_angle(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray coords3, + * def calc_angle(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray coords3, */ /* function exit code */ @@ -2174,9 +2682,9 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_20calc_angle(CYTHON_UNUSED Py /* "MDAnalysis/lib/distances_openmp.pyx":173 * results.data) * - * def calc_angle_ortho(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray coords3, + * def calc_angle_ortho(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray coords3, */ /* Python wrapper */ @@ -2261,11 +2769,11 @@ static PyObject *__pyx_pw_3lib_17_distances_openmp_23calc_angle_ortho(PyObject * __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords1), __pyx_ptype_7c_numpy_ndarray, 1, "coords1", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 173; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords2), __pyx_ptype_7c_numpy_ndarray, 1, "coords2", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 174; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords3), __pyx_ptype_7c_numpy_ndarray, 1, "coords3", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 175; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_7c_numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 176; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_results), __pyx_ptype_7c_numpy_ndarray, 1, "results", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 177; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords1), __pyx_ptype_5numpy_ndarray, 1, "coords1", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 173; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords2), __pyx_ptype_5numpy_ndarray, 1, "coords2", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 174; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords3), __pyx_ptype_5numpy_ndarray, 1, "coords3", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 175; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_5numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 176; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_results), __pyx_ptype_5numpy_ndarray, 1, "results", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 177; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_pf_3lib_17_distances_openmp_22calc_angle_ortho(__pyx_self, __pyx_v_coords1, __pyx_v_coords2, __pyx_v_coords3, __pyx_v_box, __pyx_v_results); /* function exit code */ @@ -2284,16 +2792,16 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_22calc_angle_ortho(CYTHON_UNU __Pyx_RefNannySetupContext("calc_angle_ortho", 0); /* "MDAnalysis/lib/distances_openmp.pyx":179 - * c_numpy.ndarray results): + * numpy.ndarray results): * cdef int numcoords - * numcoords = coords1.dimensions[0] # <<<<<<<<<<<<<< + * numcoords = coords1.shape[0] # <<<<<<<<<<<<<< * * _calc_angle_ortho( coords1.data, coords2.data, */ __pyx_v_numcoords = (__pyx_v_coords1->dimensions[0]); /* "MDAnalysis/lib/distances_openmp.pyx":181 - * numcoords = coords1.dimensions[0] + * numcoords = coords1.shape[0] * * _calc_angle_ortho( coords1.data, coords2.data, # <<<<<<<<<<<<<< * coords3.data, @@ -2304,9 +2812,9 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_22calc_angle_ortho(CYTHON_UNU /* "MDAnalysis/lib/distances_openmp.pyx":173 * results.data) * - * def calc_angle_ortho(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray coords3, + * def calc_angle_ortho(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray coords3, */ /* function exit code */ @@ -2319,9 +2827,9 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_22calc_angle_ortho(CYTHON_UNU /* "MDAnalysis/lib/distances_openmp.pyx":187 * results.data) * - * def calc_angle_triclinic(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray coords3, + * def calc_angle_triclinic(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray coords3, */ /* Python wrapper */ @@ -2406,11 +2914,11 @@ static PyObject *__pyx_pw_3lib_17_distances_openmp_25calc_angle_triclinic(PyObje __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords1), __pyx_ptype_7c_numpy_ndarray, 1, "coords1", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 187; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords2), __pyx_ptype_7c_numpy_ndarray, 1, "coords2", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 188; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords3), __pyx_ptype_7c_numpy_ndarray, 1, "coords3", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_7c_numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 190; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_results), __pyx_ptype_7c_numpy_ndarray, 1, "results", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 191; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords1), __pyx_ptype_5numpy_ndarray, 1, "coords1", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 187; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords2), __pyx_ptype_5numpy_ndarray, 1, "coords2", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 188; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords3), __pyx_ptype_5numpy_ndarray, 1, "coords3", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_5numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 190; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_results), __pyx_ptype_5numpy_ndarray, 1, "results", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 191; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_pf_3lib_17_distances_openmp_24calc_angle_triclinic(__pyx_self, __pyx_v_coords1, __pyx_v_coords2, __pyx_v_coords3, __pyx_v_box, __pyx_v_results); /* function exit code */ @@ -2429,16 +2937,16 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_24calc_angle_triclinic(CYTHON __Pyx_RefNannySetupContext("calc_angle_triclinic", 0); /* "MDAnalysis/lib/distances_openmp.pyx":193 - * c_numpy.ndarray results): + * numpy.ndarray results): * cdef int numcoords - * numcoords = coords1.dimensions[0] # <<<<<<<<<<<<<< + * numcoords = coords1.shape[0] # <<<<<<<<<<<<<< * * _calc_angle_triclinic( coords1.data, coords2.data, */ __pyx_v_numcoords = (__pyx_v_coords1->dimensions[0]); /* "MDAnalysis/lib/distances_openmp.pyx":195 - * numcoords = coords1.dimensions[0] + * numcoords = coords1.shape[0] * * _calc_angle_triclinic( coords1.data, coords2.data, # <<<<<<<<<<<<<< * coords3.data, @@ -2449,9 +2957,9 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_24calc_angle_triclinic(CYTHON /* "MDAnalysis/lib/distances_openmp.pyx":187 * results.data) * - * def calc_angle_triclinic(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray coords3, + * def calc_angle_triclinic(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray coords3, */ /* function exit code */ @@ -2464,9 +2972,9 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_24calc_angle_triclinic(CYTHON /* "MDAnalysis/lib/distances_openmp.pyx":201 * results.data) * - * def calc_dihedral(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray coords3, + * def calc_dihedral(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray coords3, */ /* Python wrapper */ @@ -2551,11 +3059,11 @@ static PyObject *__pyx_pw_3lib_17_distances_openmp_27calc_dihedral(PyObject *__p __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords1), __pyx_ptype_7c_numpy_ndarray, 1, "coords1", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 201; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords2), __pyx_ptype_7c_numpy_ndarray, 1, "coords2", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords3), __pyx_ptype_7c_numpy_ndarray, 1, "coords3", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 203; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords4), __pyx_ptype_7c_numpy_ndarray, 1, "coords4", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 204; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_results), __pyx_ptype_7c_numpy_ndarray, 1, "results", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords1), __pyx_ptype_5numpy_ndarray, 1, "coords1", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 201; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords2), __pyx_ptype_5numpy_ndarray, 1, "coords2", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords3), __pyx_ptype_5numpy_ndarray, 1, "coords3", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 203; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords4), __pyx_ptype_5numpy_ndarray, 1, "coords4", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 204; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_results), __pyx_ptype_5numpy_ndarray, 1, "results", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_pf_3lib_17_distances_openmp_26calc_dihedral(__pyx_self, __pyx_v_coords1, __pyx_v_coords2, __pyx_v_coords3, __pyx_v_coords4, __pyx_v_results); /* function exit code */ @@ -2574,16 +3082,16 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_26calc_dihedral(CYTHON_UNUSED __Pyx_RefNannySetupContext("calc_dihedral", 0); /* "MDAnalysis/lib/distances_openmp.pyx":207 - * c_numpy.ndarray results): + * numpy.ndarray results): * cdef int numcoords - * numcoords = coords1.dimensions[0] # <<<<<<<<<<<<<< + * numcoords = coords1.shape[0] # <<<<<<<<<<<<<< * * _calc_dihedral( coords1.data, coords2.data, */ __pyx_v_numcoords = (__pyx_v_coords1->dimensions[0]); /* "MDAnalysis/lib/distances_openmp.pyx":209 - * numcoords = coords1.dimensions[0] + * numcoords = coords1.shape[0] * * _calc_dihedral( coords1.data, coords2.data, # <<<<<<<<<<<<<< * coords3.data, coords4.data, @@ -2594,9 +3102,9 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_26calc_dihedral(CYTHON_UNUSED /* "MDAnalysis/lib/distances_openmp.pyx":201 * results.data) * - * def calc_dihedral(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray coords3, + * def calc_dihedral(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray coords3, */ /* function exit code */ @@ -2609,9 +3117,9 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_26calc_dihedral(CYTHON_UNUSED /* "MDAnalysis/lib/distances_openmp.pyx":214 * results.data) * - * def calc_dihedral_ortho(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray coords3, + * def calc_dihedral_ortho(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray coords3, */ /* Python wrapper */ @@ -2705,12 +3213,12 @@ static PyObject *__pyx_pw_3lib_17_distances_openmp_29calc_dihedral_ortho(PyObjec __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords1), __pyx_ptype_7c_numpy_ndarray, 1, "coords1", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords2), __pyx_ptype_7c_numpy_ndarray, 1, "coords2", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords3), __pyx_ptype_7c_numpy_ndarray, 1, "coords3", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 216; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords4), __pyx_ptype_7c_numpy_ndarray, 1, "coords4", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_7c_numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_results), __pyx_ptype_7c_numpy_ndarray, 1, "results", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords1), __pyx_ptype_5numpy_ndarray, 1, "coords1", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords2), __pyx_ptype_5numpy_ndarray, 1, "coords2", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords3), __pyx_ptype_5numpy_ndarray, 1, "coords3", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 216; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords4), __pyx_ptype_5numpy_ndarray, 1, "coords4", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_5numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_results), __pyx_ptype_5numpy_ndarray, 1, "results", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_pf_3lib_17_distances_openmp_28calc_dihedral_ortho(__pyx_self, __pyx_v_coords1, __pyx_v_coords2, __pyx_v_coords3, __pyx_v_coords4, __pyx_v_box, __pyx_v_results); /* function exit code */ @@ -2729,16 +3237,16 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_28calc_dihedral_ortho(CYTHON_ __Pyx_RefNannySetupContext("calc_dihedral_ortho", 0); /* "MDAnalysis/lib/distances_openmp.pyx":221 - * c_numpy.ndarray results): + * numpy.ndarray results): * cdef int numcoords - * numcoords = coords1.dimensions[0] # <<<<<<<<<<<<<< + * numcoords = coords1.shape[0] # <<<<<<<<<<<<<< * * _calc_dihedral_ortho( coords1.data, coords2.data, */ __pyx_v_numcoords = (__pyx_v_coords1->dimensions[0]); /* "MDAnalysis/lib/distances_openmp.pyx":223 - * numcoords = coords1.dimensions[0] + * numcoords = coords1.shape[0] * * _calc_dihedral_ortho( coords1.data, coords2.data, # <<<<<<<<<<<<<< * coords3.data, coords4.data, @@ -2749,9 +3257,9 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_28calc_dihedral_ortho(CYTHON_ /* "MDAnalysis/lib/distances_openmp.pyx":214 * results.data) * - * def calc_dihedral_ortho(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray coords3, + * def calc_dihedral_ortho(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray coords3, */ /* function exit code */ @@ -2764,9 +3272,9 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_28calc_dihedral_ortho(CYTHON_ /* "MDAnalysis/lib/distances_openmp.pyx":229 * results.data) * - * def calc_dihedral_triclinic(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray coords3, + * def calc_dihedral_triclinic(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray coords3, */ /* Python wrapper */ @@ -2860,12 +3368,12 @@ static PyObject *__pyx_pw_3lib_17_distances_openmp_31calc_dihedral_triclinic(PyO __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords1), __pyx_ptype_7c_numpy_ndarray, 1, "coords1", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 229; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords2), __pyx_ptype_7c_numpy_ndarray, 1, "coords2", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 230; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords3), __pyx_ptype_7c_numpy_ndarray, 1, "coords3", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 231; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords4), __pyx_ptype_7c_numpy_ndarray, 1, "coords4", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 232; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_7c_numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 233; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_results), __pyx_ptype_7c_numpy_ndarray, 1, "results", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 234; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords1), __pyx_ptype_5numpy_ndarray, 1, "coords1", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 229; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords2), __pyx_ptype_5numpy_ndarray, 1, "coords2", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 230; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords3), __pyx_ptype_5numpy_ndarray, 1, "coords3", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 231; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords4), __pyx_ptype_5numpy_ndarray, 1, "coords4", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 232; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_5numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 233; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_results), __pyx_ptype_5numpy_ndarray, 1, "results", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 234; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_pf_3lib_17_distances_openmp_30calc_dihedral_triclinic(__pyx_self, __pyx_v_coords1, __pyx_v_coords2, __pyx_v_coords3, __pyx_v_coords4, __pyx_v_box, __pyx_v_results); /* function exit code */ @@ -2884,16 +3392,16 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_30calc_dihedral_triclinic(CYT __Pyx_RefNannySetupContext("calc_dihedral_triclinic", 0); /* "MDAnalysis/lib/distances_openmp.pyx":236 - * c_numpy.ndarray results): + * numpy.ndarray results): * cdef int numcoords - * numcoords = coords1.dimensions[0] # <<<<<<<<<<<<<< + * numcoords = coords1.shape[0] # <<<<<<<<<<<<<< * * _calc_dihedral_triclinic( coords1.data, coords2.data, */ __pyx_v_numcoords = (__pyx_v_coords1->dimensions[0]); /* "MDAnalysis/lib/distances_openmp.pyx":238 - * numcoords = coords1.dimensions[0] + * numcoords = coords1.shape[0] * * _calc_dihedral_triclinic( coords1.data, coords2.data, # <<<<<<<<<<<<<< * coords3.data, coords4.data, @@ -2904,9 +3412,9 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_30calc_dihedral_triclinic(CYT /* "MDAnalysis/lib/distances_openmp.pyx":229 * results.data) * - * def calc_dihedral_triclinic(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray coords3, + * def calc_dihedral_triclinic(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray coords3, */ /* function exit code */ @@ -2919,8 +3427,8 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_30calc_dihedral_triclinic(CYT /* "MDAnalysis/lib/distances_openmp.pyx":244 * results.data) * - * def ortho_pbc(c_numpy.ndarray coords, # <<<<<<<<<<<<<< - * c_numpy.ndarray box, c_numpy.ndarray box_inverse): + * def ortho_pbc(numpy.ndarray coords, # <<<<<<<<<<<<<< + * numpy.ndarray box, numpy.ndarray box_inverse): * cdef int numcoords */ @@ -2988,9 +3496,9 @@ static PyObject *__pyx_pw_3lib_17_distances_openmp_33ortho_pbc(PyObject *__pyx_s __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords), __pyx_ptype_7c_numpy_ndarray, 1, "coords", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 244; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_7c_numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 245; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box_inverse), __pyx_ptype_7c_numpy_ndarray, 1, "box_inverse", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 245; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords), __pyx_ptype_5numpy_ndarray, 1, "coords", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 244; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box), __pyx_ptype_5numpy_ndarray, 1, "box", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 245; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_box_inverse), __pyx_ptype_5numpy_ndarray, 1, "box_inverse", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 245; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_pf_3lib_17_distances_openmp_32ortho_pbc(__pyx_self, __pyx_v_coords, __pyx_v_box, __pyx_v_box_inverse); /* function exit code */ @@ -3009,16 +3517,16 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_32ortho_pbc(CYTHON_UNUSED PyO __Pyx_RefNannySetupContext("ortho_pbc", 0); /* "MDAnalysis/lib/distances_openmp.pyx":247 - * c_numpy.ndarray box, c_numpy.ndarray box_inverse): + * numpy.ndarray box, numpy.ndarray box_inverse): * cdef int numcoords - * numcoords = coords.dimensions[0] # <<<<<<<<<<<<<< + * numcoords = coords.shape[0] # <<<<<<<<<<<<<< * * _ortho_pbc( coords.data, numcoords, */ __pyx_v_numcoords = (__pyx_v_coords->dimensions[0]); /* "MDAnalysis/lib/distances_openmp.pyx":249 - * numcoords = coords.dimensions[0] + * numcoords = coords.shape[0] * * _ortho_pbc( coords.data, numcoords, # <<<<<<<<<<<<<< * box.data, box_inverse.data) @@ -3029,8 +3537,8 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_32ortho_pbc(CYTHON_UNUSED PyO /* "MDAnalysis/lib/distances_openmp.pyx":244 * results.data) * - * def ortho_pbc(c_numpy.ndarray coords, # <<<<<<<<<<<<<< - * c_numpy.ndarray box, c_numpy.ndarray box_inverse): + * def ortho_pbc(numpy.ndarray coords, # <<<<<<<<<<<<<< + * numpy.ndarray box, numpy.ndarray box_inverse): * cdef int numcoords */ @@ -3044,8 +3552,8 @@ static PyObject *__pyx_pf_3lib_17_distances_openmp_32ortho_pbc(CYTHON_UNUSED PyO /* "MDAnalysis/lib/distances_openmp.pyx":252 * box.data, box_inverse.data) * - * def triclinic_pbc(c_numpy.ndarray coords, # <<<<<<<<<<<<<< - * c_numpy.ndarray box, c_numpy.ndarray box_inverse): + * def triclinic_pbc(numpy.ndarray coords, # <<<<<<<<<<<<<< + * numpy.ndarray box, numpy.ndarray box_inverse): * cdef int numcoords */ @@ -3113,9 +3621,9 @@ static PyObject *__pyx_pw_3lib_17_distances_openmp_35triclinic_pbc(PyObject *__p __Pyx_RefNannyFinishContext(); 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__pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_InitGlobals() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #if PY_MAJOR_VERSION < 3 && (__PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT) if (__Pyx_init_sys_getdefaultencoding_params() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #endif if (__pyx_module_is_main_lib___distances_openmp) { - if (PyObject_SetAttrString(__pyx_m, "__name__", __pyx_n_s_main) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + if (PyObject_SetAttrString(__pyx_m, "__name__", __pyx_n_s_main) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } #if PY_MAJOR_VERSION >= 3 { @@ -3537,33 +6277,50 @@ PyMODINIT_FUNC PyInit__distances_openmp(void) } #endif /*--- Builtin init code ---*/ - if (unlikely(__Pyx_InitCachedBuiltins() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_InitCachedBuiltins() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} /*--- Constants init code ---*/ - if (unlikely(__Pyx_InitCachedConstants() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_InitCachedConstants() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} /*--- Global init code ---*/ /*--- Variable export code ---*/ /*--- Function export code ---*/ /*--- Type init code ---*/ /*--- Type import code ---*/ - __pyx_ptype_7c_numpy_ndarray = __Pyx_ImportType("numpy", "ndarray", sizeof(PyArrayObject), 0); if (unlikely(!__pyx_ptype_7c_numpy_ndarray)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_7cpython_4type_type = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "type", + #if CYTHON_COMPILING_IN_PYPY + sizeof(PyTypeObject), + #else + sizeof(PyHeapTypeObject), + #endif + 0); if (unlikely(!__pyx_ptype_7cpython_4type_type)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 9; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5numpy_dtype = __Pyx_ImportType("numpy", "dtype", sizeof(PyArray_Descr), 0); if (unlikely(!__pyx_ptype_5numpy_dtype)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 155; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5numpy_flatiter = __Pyx_ImportType("numpy", "flatiter", sizeof(PyArrayIterObject), 0); if (unlikely(!__pyx_ptype_5numpy_flatiter)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 168; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5numpy_broadcast = __Pyx_ImportType("numpy", "broadcast", sizeof(PyArrayMultiIterObject), 0); if (unlikely(!__pyx_ptype_5numpy_broadcast)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5numpy_ndarray = __Pyx_ImportType("numpy", "ndarray", sizeof(PyArrayObject), 0); if (unlikely(!__pyx_ptype_5numpy_ndarray)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5numpy_ufunc = __Pyx_ImportType("numpy", "ufunc", sizeof(PyUFuncObject), 0); if (unlikely(!__pyx_ptype_5numpy_ufunc)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;} /*--- Variable import code ---*/ /*--- Function import code ---*/ /*--- Execution code ---*/ + #if defined(__Pyx_Generator_USED) || defined(__Pyx_Coroutine_USED) + if (__Pyx_patch_abc() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif - /* "MDAnalysis/lib/distances_openmp.pyx":27 + /* "MDAnalysis/lib/distances_openmp.pyx":26 + * """ * - * cimport c_numpy - * c_numpy.import_array() # <<<<<<<<<<<<<< + * import numpy # <<<<<<<<<<<<<< + * cimport numpy * - * cdef extern from "string.h": */ - import_array(); + __pyx_t_1 = __Pyx_Import(__pyx_n_s_numpy, 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_numpy, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; /* "MDAnalysis/lib/distances_openmp.pyx":54 * void _triclinic_pbc(coordinate* coords, int numcoords, coordinate* box, float* box_inverse) * - * def calc_distance_array(c_numpy.ndarray ref, c_numpy.ndarray conf, # <<<<<<<<<<<<<< - * c_numpy.ndarray result): + * def calc_distance_array(numpy.ndarray ref, numpy.ndarray conf, # <<<<<<<<<<<<<< + * numpy.ndarray result): * cdef int confnum, refnum */ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3lib_17_distances_openmp_1calc_distance_array, NULL, __pyx_n_s_lib__distances_openmp); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -3574,9 +6331,9 @@ PyMODINIT_FUNC PyInit__distances_openmp(void) /* "MDAnalysis/lib/distances_openmp.pyx":64 * result.data) * - * def calc_distance_array_ortho(c_numpy.ndarray ref, c_numpy.ndarray conf, # <<<<<<<<<<<<<< - * c_numpy.ndarray box, - * c_numpy.ndarray result): + * def calc_distance_array_ortho(numpy.ndarray ref, numpy.ndarray conf, # <<<<<<<<<<<<<< + * numpy.ndarray box, + * numpy.ndarray result): */ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3lib_17_distances_openmp_3calc_distance_array_ortho, NULL, __pyx_n_s_lib__distances_openmp); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); @@ -3586,9 +6343,9 @@ PyMODINIT_FUNC PyInit__distances_openmp(void) /* "MDAnalysis/lib/distances_openmp.pyx":76 * result.data) * - * def calc_distance_array_triclinic(c_numpy.ndarray ref, c_numpy.ndarray conf, # <<<<<<<<<<<<<< - * c_numpy.ndarray box, - * c_numpy.ndarray result): + * def calc_distance_array_triclinic(numpy.ndarray ref, numpy.ndarray conf, # <<<<<<<<<<<<<< + * numpy.ndarray box, + * numpy.ndarray result): */ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3lib_17_distances_openmp_5calc_distance_array_triclinic, NULL, __pyx_n_s_lib__distances_openmp); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); @@ -3598,8 +6355,8 @@ PyMODINIT_FUNC PyInit__distances_openmp(void) /* "MDAnalysis/lib/distances_openmp.pyx":88 * result.data) * - * def calc_self_distance_array(c_numpy.ndarray ref, # <<<<<<<<<<<<<< - * c_numpy.ndarray result): + * def calc_self_distance_array(numpy.ndarray ref, # <<<<<<<<<<<<<< + * numpy.ndarray result): * cdef int refnum, distnum */ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3lib_17_distances_openmp_7calc_self_distance_array, NULL, __pyx_n_s_lib__distances_openmp); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -3610,9 +6367,9 @@ PyMODINIT_FUNC PyInit__distances_openmp(void) /* "MDAnalysis/lib/distances_openmp.pyx":97 * result.data, distnum) * - * def calc_self_distance_array_ortho(c_numpy.ndarray ref, # <<<<<<<<<<<<<< - * c_numpy.ndarray box, - * c_numpy.ndarray result): + * def calc_self_distance_array_ortho(numpy.ndarray ref, # <<<<<<<<<<<<<< + * numpy.ndarray box, + * numpy.ndarray result): */ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3lib_17_distances_openmp_9calc_self_distance_array_ortho, NULL, __pyx_n_s_lib__distances_openmp); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 97; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); @@ -3622,9 +6379,9 @@ PyMODINIT_FUNC PyInit__distances_openmp(void) /* "MDAnalysis/lib/distances_openmp.pyx":108 * result.data, distnum) * - * def calc_self_distance_array_triclinic(c_numpy.ndarray ref, # <<<<<<<<<<<<<< - * c_numpy.ndarray box, - * c_numpy.ndarray result): + * def calc_self_distance_array_triclinic(numpy.ndarray ref, # <<<<<<<<<<<<<< + * numpy.ndarray box, + * numpy.ndarray result): */ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3lib_17_distances_openmp_11calc_self_distance_array_triclinic, NULL, __pyx_n_s_lib__distances_openmp); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 108; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); @@ -3634,8 +6391,8 @@ PyMODINIT_FUNC PyInit__distances_openmp(void) /* "MDAnalysis/lib/distances_openmp.pyx":119 * result.data, distnum) * - * def coord_transform(c_numpy.ndarray coords, # <<<<<<<<<<<<<< - * c_numpy.ndarray box): + * def coord_transform(numpy.ndarray coords, # <<<<<<<<<<<<<< + * numpy.ndarray box): * cdef int numcoords */ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3lib_17_distances_openmp_13coord_transform, NULL, __pyx_n_s_lib__distances_openmp); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 119; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -3646,9 +6403,9 @@ PyMODINIT_FUNC PyInit__distances_openmp(void) /* "MDAnalysis/lib/distances_openmp.pyx":127 * box.data) * - * def calc_bond_distance(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray results): + * def calc_bond_distance(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray results): */ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3lib_17_distances_openmp_15calc_bond_distance, NULL, __pyx_n_s_lib__distances_openmp); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 127; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); @@ -3658,9 +6415,9 @@ PyMODINIT_FUNC PyInit__distances_openmp(void) /* "MDAnalysis/lib/distances_openmp.pyx":137 * results.data) * - * def calc_bond_distance_ortho(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray box, + * def calc_bond_distance_ortho(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray box, */ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3lib_17_distances_openmp_17calc_bond_distance_ortho, NULL, __pyx_n_s_lib__distances_openmp); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 137; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); @@ -3670,9 +6427,9 @@ PyMODINIT_FUNC PyInit__distances_openmp(void) /* "MDAnalysis/lib/distances_openmp.pyx":149 * results.data) * - * def calc_bond_distance_triclinic(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray box, + * def calc_bond_distance_triclinic(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray box, */ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3lib_17_distances_openmp_19calc_bond_distance_triclinic, NULL, __pyx_n_s_lib__distances_openmp); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 149; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); @@ -3682,9 +6439,9 @@ PyMODINIT_FUNC PyInit__distances_openmp(void) /* "MDAnalysis/lib/distances_openmp.pyx":161 * results.data) * - * def calc_angle(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray coords3, + * def calc_angle(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray coords3, */ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3lib_17_distances_openmp_21calc_angle, NULL, __pyx_n_s_lib__distances_openmp); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 161; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); @@ -3694,9 +6451,9 @@ PyMODINIT_FUNC PyInit__distances_openmp(void) /* "MDAnalysis/lib/distances_openmp.pyx":173 * results.data) * - * def calc_angle_ortho(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray coords3, + * def calc_angle_ortho(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray coords3, */ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3lib_17_distances_openmp_23calc_angle_ortho, NULL, __pyx_n_s_lib__distances_openmp); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 173; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); @@ -3706,9 +6463,9 @@ PyMODINIT_FUNC PyInit__distances_openmp(void) /* "MDAnalysis/lib/distances_openmp.pyx":187 * results.data) * - * def calc_angle_triclinic(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray coords3, + * def calc_angle_triclinic(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray coords3, */ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3lib_17_distances_openmp_25calc_angle_triclinic, NULL, __pyx_n_s_lib__distances_openmp); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 187; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); @@ -3718,9 +6475,9 @@ PyMODINIT_FUNC PyInit__distances_openmp(void) /* "MDAnalysis/lib/distances_openmp.pyx":201 * results.data) * - * def calc_dihedral(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray coords3, + * def calc_dihedral(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray coords3, */ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3lib_17_distances_openmp_27calc_dihedral, NULL, __pyx_n_s_lib__distances_openmp); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 201; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); @@ -3730,9 +6487,9 @@ PyMODINIT_FUNC PyInit__distances_openmp(void) /* "MDAnalysis/lib/distances_openmp.pyx":214 * results.data) * - * def calc_dihedral_ortho(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray coords3, + * def calc_dihedral_ortho(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray coords3, */ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3lib_17_distances_openmp_29calc_dihedral_ortho, NULL, __pyx_n_s_lib__distances_openmp); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); @@ -3742,9 +6499,9 @@ PyMODINIT_FUNC PyInit__distances_openmp(void) /* "MDAnalysis/lib/distances_openmp.pyx":229 * results.data) * - * def calc_dihedral_triclinic(c_numpy.ndarray coords1, # <<<<<<<<<<<<<< - * c_numpy.ndarray coords2, - * c_numpy.ndarray coords3, + * def calc_dihedral_triclinic(numpy.ndarray coords1, # <<<<<<<<<<<<<< + * numpy.ndarray coords2, + * numpy.ndarray coords3, */ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3lib_17_distances_openmp_31calc_dihedral_triclinic, NULL, __pyx_n_s_lib__distances_openmp); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 229; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); @@ -3754,8 +6511,8 @@ PyMODINIT_FUNC PyInit__distances_openmp(void) /* "MDAnalysis/lib/distances_openmp.pyx":244 * results.data) * - * def ortho_pbc(c_numpy.ndarray coords, # <<<<<<<<<<<<<< - * c_numpy.ndarray box, c_numpy.ndarray box_inverse): + * def ortho_pbc(numpy.ndarray coords, # <<<<<<<<<<<<<< + * numpy.ndarray box, numpy.ndarray box_inverse): * cdef int numcoords */ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3lib_17_distances_openmp_33ortho_pbc, NULL, __pyx_n_s_lib__distances_openmp); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 244; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -3766,8 +6523,8 @@ PyMODINIT_FUNC PyInit__distances_openmp(void) /* "MDAnalysis/lib/distances_openmp.pyx":252 * box.data, box_inverse.data) * - * def triclinic_pbc(c_numpy.ndarray coords, # <<<<<<<<<<<<<< - * c_numpy.ndarray box, c_numpy.ndarray box_inverse): + * def triclinic_pbc(numpy.ndarray coords, # <<<<<<<<<<<<<< + * numpy.ndarray box, numpy.ndarray box_inverse): * cdef int numcoords */ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3lib_17_distances_openmp_35triclinic_pbc, NULL, __pyx_n_s_lib__distances_openmp); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 252; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -3785,6 +6542,14 @@ PyMODINIT_FUNC PyInit__distances_openmp(void) if (PyDict_SetItem(__pyx_d, __pyx_n_s_test, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + /* "../../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":976 + * arr.base = baseptr + * + * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< + * if arr.base is NULL: + * return None + */ + /*--- Wrapped vars code ---*/ goto __pyx_L0; @@ -3985,15 +6750,338 @@ static CYTHON_INLINE int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, in else { if (likely(PyObject_TypeCheck(obj, type))) return 1; } - __Pyx_RaiseArgumentTypeInvalid(name, obj, type); + __Pyx_RaiseArgumentTypeInvalid(name, obj, type); + return 0; +} + +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 PyObject *__Pyx_GetBuiltinName(PyObject *name) { + PyObject* result = __Pyx_PyObject_GetAttrStr(__pyx_b, name); + if (unlikely(!result)) { + PyErr_Format(PyExc_NameError, +#if PY_MAJOR_VERSION >= 3 + "name '%U' is not defined", name); +#else + "name '%.200s' is not defined", PyString_AS_STRING(name)); +#endif + } + return result; +} + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw) { + PyObject *result; + ternaryfunc call = func->ob_type->tp_call; + if (unlikely(!call)) + return PyObject_Call(func, arg, kw); + if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) + return NULL; + result = (*call)(func, arg, kw); + Py_LeaveRecursiveCall(); + if (unlikely(!result) && unlikely(!PyErr_Occurred())) { + PyErr_SetString( + PyExc_SystemError, + "NULL result without error in PyObject_Call"); + } + return result; +} +#endif + +static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) { +#if CYTHON_COMPILING_IN_CPYTHON + PyObject *tmp_type, *tmp_value, *tmp_tb; + PyThreadState *tstate = PyThreadState_GET(); + tmp_type = tstate->curexc_type; + tmp_value = tstate->curexc_value; + tmp_tb = tstate->curexc_traceback; + tstate->curexc_type = type; + tstate->curexc_value = value; + tstate->curexc_traceback = tb; + Py_XDECREF(tmp_type); + Py_XDECREF(tmp_value); + Py_XDECREF(tmp_tb); +#else + PyErr_Restore(type, value, tb); +#endif +} +static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) { +#if CYTHON_COMPILING_IN_CPYTHON + PyThreadState *tstate = PyThreadState_GET(); + *type = tstate->curexc_type; + *value = tstate->curexc_value; + *tb = tstate->curexc_traceback; + tstate->curexc_type = 0; + tstate->curexc_value = 0; + tstate->curexc_traceback = 0; +#else + PyErr_Fetch(type, value, tb); +#endif +} + +#if PY_MAJOR_VERSION < 3 +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, + CYTHON_UNUSED PyObject *cause) { + Py_XINCREF(type); + if (!value || value == Py_None) + value = NULL; + else + Py_INCREF(value); + if (!tb || tb == Py_None) + tb = NULL; + else { + Py_INCREF(tb); + if (!PyTraceBack_Check(tb)) { + PyErr_SetString(PyExc_TypeError, + "raise: arg 3 must be a traceback or None"); + goto raise_error; + } + } + if (PyType_Check(type)) { +#if CYTHON_COMPILING_IN_PYPY + if (!value) { + Py_INCREF(Py_None); + value = Py_None; + } +#endif + PyErr_NormalizeException(&type, &value, &tb); + } else { + if (value) { + PyErr_SetString(PyExc_TypeError, + "instance exception may not have a separate value"); + goto raise_error; + } + value = type; + type = (PyObject*) Py_TYPE(type); + Py_INCREF(type); + if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) { + PyErr_SetString(PyExc_TypeError, + "raise: exception class must be a subclass of BaseException"); + goto raise_error; + } + } + __Pyx_ErrRestore(type, value, tb); + return; +raise_error: + Py_XDECREF(value); + Py_XDECREF(type); + Py_XDECREF(tb); + return; +} +#else +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { + PyObject* owned_instance = NULL; + if (tb == Py_None) { + tb = 0; + } else if (tb && !PyTraceBack_Check(tb)) { + PyErr_SetString(PyExc_TypeError, + "raise: arg 3 must be a traceback or None"); + goto bad; + } + if (value == Py_None) + value = 0; + if (PyExceptionInstance_Check(type)) { + if (value) { + PyErr_SetString(PyExc_TypeError, + "instance exception may not have a separate value"); + goto bad; + } + value = type; + type = (PyObject*) Py_TYPE(value); + } else if (PyExceptionClass_Check(type)) { + PyObject *instance_class = NULL; + if (value && PyExceptionInstance_Check(value)) { + instance_class = (PyObject*) Py_TYPE(value); + if (instance_class != type) { + int is_subclass = PyObject_IsSubclass(instance_class, type); + if (!is_subclass) { + instance_class = NULL; + } else if (unlikely(is_subclass == -1)) { + goto bad; + } else { + type = instance_class; + } + } + } + if (!instance_class) { + PyObject *args; + if (!value) + args = PyTuple_New(0); + else if (PyTuple_Check(value)) { + Py_INCREF(value); + args = value; + } else + args = PyTuple_Pack(1, value); + if (!args) + goto bad; + owned_instance = PyObject_Call(type, args, NULL); + Py_DECREF(args); + if (!owned_instance) + goto bad; + value = owned_instance; + if (!PyExceptionInstance_Check(value)) { + PyErr_Format(PyExc_TypeError, + "calling %R should have returned an instance of " + "BaseException, not %R", + type, Py_TYPE(value)); + goto bad; + } + } + } else { + PyErr_SetString(PyExc_TypeError, + "raise: exception class must be a subclass of BaseException"); + goto bad; + } +#if PY_VERSION_HEX >= 0x03030000 + if (cause) { +#else + if (cause && cause != Py_None) { +#endif + PyObject *fixed_cause; + if (cause == Py_None) { + fixed_cause = NULL; + } else if (PyExceptionClass_Check(cause)) { + fixed_cause = PyObject_CallObject(cause, NULL); + if (fixed_cause == NULL) + goto bad; + } else if (PyExceptionInstance_Check(cause)) { + fixed_cause = cause; + Py_INCREF(fixed_cause); + } else { + PyErr_SetString(PyExc_TypeError, + "exception causes must derive from " + "BaseException"); + goto bad; + } + PyException_SetCause(value, fixed_cause); + } + PyErr_SetObject(type, value); + if (tb) { +#if CYTHON_COMPILING_IN_PYPY + PyObject *tmp_type, *tmp_value, *tmp_tb; + PyErr_Fetch(&tmp_type, &tmp_value, &tmp_tb); + Py_INCREF(tb); + PyErr_Restore(tmp_type, tmp_value, tb); + Py_XDECREF(tmp_tb); +#else + PyThreadState *tstate = PyThreadState_GET(); + PyObject* tmp_tb = tstate->curexc_traceback; + if (tb != tmp_tb) { + Py_INCREF(tb); + tstate->curexc_traceback = tb; + Py_XDECREF(tmp_tb); + } +#endif + } +bad: + Py_XDECREF(owned_instance); + return; +} +#endif + +static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { + PyErr_Format(PyExc_ValueError, + "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected); +} + +static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { + PyErr_Format(PyExc_ValueError, + "need more than %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack", + index, (index == 1) ? "" : "s"); +} + +static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); +} + +static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { + if (unlikely(!type)) { + PyErr_SetString(PyExc_SystemError, "Missing type object"); + return 0; + } + if (likely(PyObject_TypeCheck(obj, type))) + return 1; + PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s", + Py_TYPE(obj)->tp_name, type->tp_name); return 0; } -static 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 PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { + PyObject *empty_list = 0; + PyObject *module = 0; + PyObject *global_dict = 0; + PyObject *empty_dict = 0; + PyObject *list; + #if PY_VERSION_HEX < 0x03030000 + PyObject *py_import; + py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import); + if (!py_import) + goto bad; + #endif + if (from_list) + list = from_list; + else { + empty_list = PyList_New(0); + if (!empty_list) + goto bad; + list = empty_list; + } + global_dict = PyModule_GetDict(__pyx_m); + if (!global_dict) + goto bad; + empty_dict = PyDict_New(); + if (!empty_dict) + goto bad; + { + #if PY_MAJOR_VERSION >= 3 + if (level == -1) { + if (strchr(__Pyx_MODULE_NAME, '.')) { + #if PY_VERSION_HEX < 0x03030000 + PyObject *py_level = PyInt_FromLong(1); + if (!py_level) + goto bad; + module = PyObject_CallFunctionObjArgs(py_import, + name, global_dict, empty_dict, list, py_level, NULL); + Py_DECREF(py_level); + #else + module = PyImport_ImportModuleLevelObject( + name, global_dict, empty_dict, list, 1); + #endif + if (!module) { + if (!PyErr_ExceptionMatches(PyExc_ImportError)) + goto bad; + PyErr_Clear(); + } + } + level = 0; + } + #endif + if (!module) { + #if PY_VERSION_HEX < 0x03030000 + PyObject *py_level = PyInt_FromLong(level); + if (!py_level) + goto bad; + module = PyObject_CallFunctionObjArgs(py_import, + name, global_dict, empty_dict, list, py_level, NULL); + Py_DECREF(py_level); + #else + module = PyImport_ImportModuleLevelObject( + name, global_dict, empty_dict, list, level); + #endif + } + } +bad: + #if PY_VERSION_HEX < 0x03030000 + Py_XDECREF(py_import); + #endif + Py_XDECREF(empty_list); + Py_XDECREF(empty_dict); + return module; } static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { @@ -4002,7 +7090,7 @@ static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int co return count; } while (start < end) { - mid = (start + end) / 2; + mid = start + (end - start) / 2; if (code_line < entries[mid].code_line) { end = mid; } else if (code_line > entries[mid].code_line) { @@ -4155,78 +7243,348 @@ static void __Pyx_AddTraceback(const char *funcname, int c_line, Py_XDECREF(py_frame); } -static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { - const long neg_one = (long) -1, const_zero = 0; +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + return ::std::complex< float >(x, y); + } + #else + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + return x + y*(__pyx_t_float_complex)_Complex_I; + } + #endif +#else + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + __pyx_t_float_complex z; + z.real = x; + z.imag = y; + return z; + } +#endif + +#if CYTHON_CCOMPLEX +#else + static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + return (a.real == b.real) && (a.imag == b.imag); + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real + b.real; + z.imag = a.imag + b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real - b.real; + z.imag = a.imag - b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prodf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real * b.real - a.imag * b.imag; + z.imag = a.real * b.imag + a.imag * b.real; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + float denom = b.real * b.real + b.imag * b.imag; + z.real = (a.real * b.real + a.imag * b.imag) / denom; + z.imag = (a.imag * b.real - a.real * b.imag) / denom; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex a) { + __pyx_t_float_complex z; + z.real = -a.real; + z.imag = -a.imag; + return z; + } + static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex a) { + return (a.real == 0) && (a.imag == 0); + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex a) { + __pyx_t_float_complex z; + z.real = a.real; + z.imag = -a.imag; + return z; + } + #if 1 + static CYTHON_INLINE float __Pyx_c_absf(__pyx_t_float_complex z) { + #if !defined(HAVE_HYPOT) || defined(_MSC_VER) + return sqrtf(z.real*z.real + z.imag*z.imag); + #else + return hypotf(z.real, z.imag); + #endif + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + float r, lnr, theta, z_r, z_theta; + if (b.imag == 0 && b.real == (int)b.real) { + if (b.real < 0) { + float denom = a.real * a.real + a.imag * a.imag; + a.real = a.real / denom; + a.imag = -a.imag / denom; + b.real = -b.real; + } + switch ((int)b.real) { + case 0: + z.real = 1; + z.imag = 0; + return z; + case 1: + return a; + case 2: + z = __Pyx_c_prodf(a, a); + return __Pyx_c_prodf(a, a); + case 3: + z = __Pyx_c_prodf(a, a); + return __Pyx_c_prodf(z, a); + case 4: + z = __Pyx_c_prodf(a, a); + return __Pyx_c_prodf(z, z); + } + } + if (a.imag == 0) { + if (a.real == 0) { + return a; + } + r = a.real; + theta = 0; + } else { + r = __Pyx_c_absf(a); + theta = atan2f(a.imag, a.real); + } + lnr = logf(r); + z_r = expf(lnr * b.real - theta * b.imag); + z_theta = theta * b.real + lnr * b.imag; + z.real = z_r * cosf(z_theta); + z.imag = z_r * sinf(z_theta); + return z; + } + #endif +#endif + +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + return ::std::complex< double >(x, y); + } + #else + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + return x + y*(__pyx_t_double_complex)_Complex_I; + } + #endif +#else + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + __pyx_t_double_complex z; + z.real = x; + z.imag = y; + return z; + } +#endif + +#if CYTHON_CCOMPLEX +#else + static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex a, __pyx_t_double_complex b) { + return (a.real == b.real) && (a.imag == b.imag); + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real + b.real; + z.imag = a.imag + b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real - b.real; + z.imag = a.imag - b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real * b.real - a.imag * b.imag; + z.imag = a.real * b.imag + a.imag * b.real; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + double denom = b.real * b.real + b.imag * b.imag; + z.real = (a.real * b.real + a.imag * b.imag) / denom; + z.imag = (a.imag * b.real - a.real * b.imag) / denom; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex a) { + __pyx_t_double_complex z; + z.real = -a.real; + z.imag = -a.imag; + return z; + } + static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex a) { + return (a.real == 0) && (a.imag == 0); + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex a) { + __pyx_t_double_complex z; + z.real = a.real; + z.imag = -a.imag; + return z; + } + #if 1 + static CYTHON_INLINE double __Pyx_c_abs(__pyx_t_double_complex z) { + #if !defined(HAVE_HYPOT) || defined(_MSC_VER) + return sqrt(z.real*z.real + z.imag*z.imag); + #else + return hypot(z.real, z.imag); + #endif + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + double r, lnr, theta, z_r, z_theta; + if (b.imag == 0 && b.real == (int)b.real) { + if (b.real < 0) { + double denom = a.real * a.real + a.imag * a.imag; + a.real = a.real / denom; + a.imag = -a.imag / denom; + b.real = -b.real; + } + switch ((int)b.real) { + case 0: + z.real = 1; + z.imag = 0; + return z; + case 1: + return a; + case 2: + z = __Pyx_c_prod(a, a); + return __Pyx_c_prod(a, a); + case 3: + z = __Pyx_c_prod(a, a); + return __Pyx_c_prod(z, a); + case 4: + z = __Pyx_c_prod(a, a); + return __Pyx_c_prod(z, z); + } + } + if (a.imag == 0) { + if (a.real == 0) { + return a; + } + r = a.real; + theta = 0; + } else { + r = __Pyx_c_abs(a); + theta = atan2(a.imag, a.real); + } + lnr = log(r); + z_r = exp(lnr * b.real - theta * b.imag); + z_theta = theta * b.real + lnr * b.imag; + z.real = z_r * cos(z_theta); + z.imag = z_r * sin(z_theta); + return z; + } + #endif +#endif + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { + const int neg_one = (int) -1, const_zero = (int) 0; const int is_unsigned = neg_one > const_zero; if (is_unsigned) { - if (sizeof(long) < sizeof(long)) { + if (sizeof(int) < sizeof(long)) { return PyInt_FromLong((long) value); - } else if (sizeof(long) <= sizeof(unsigned long)) { + } else if (sizeof(int) <= sizeof(unsigned long)) { return PyLong_FromUnsignedLong((unsigned long) value); - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { + } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); } } else { - if (sizeof(long) <= sizeof(long)) { + if (sizeof(int) <= sizeof(long)) { return PyInt_FromLong((long) value); - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { + } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { return PyLong_FromLongLong((PY_LONG_LONG) value); } } { int one = 1; int little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(long), + return _PyLong_FromByteArray(bytes, sizeof(int), little, !is_unsigned); } } -#define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value) \ - { \ - func_type value = func_value; \ - if (sizeof(target_type) < sizeof(func_type)) { \ - if (unlikely(value != (func_type) (target_type) value)) { \ - func_type zero = 0; \ - if (is_unsigned && unlikely(value < zero)) \ - goto raise_neg_overflow; \ - else \ - goto raise_overflow; \ - } \ - } \ - return (target_type) value; \ +#define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\ + __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0) +#define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\ + __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1) +#define __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, exc)\ + {\ + func_type value = func_value;\ + if (sizeof(target_type) < sizeof(func_type)) {\ + if (unlikely(value != (func_type) (target_type) value)) {\ + func_type zero = 0;\ + if (exc && unlikely(value == (func_type)-1 && PyErr_Occurred()))\ + return (target_type) -1;\ + if (is_unsigned && unlikely(value < zero))\ + goto raise_neg_overflow;\ + else\ + goto raise_overflow;\ + }\ + }\ + return (target_type) value;\ } -#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 - #if CYTHON_USE_PYLONG_INTERNALS +#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; +static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { + const int neg_one = (int) -1, const_zero = (int) 0; const int is_unsigned = neg_one > const_zero; #if PY_MAJOR_VERSION < 3 if (likely(PyInt_Check(x))) { - if (sizeof(long) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) + if (sizeof(int) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x)) } else { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { goto raise_neg_overflow; } - return (long) val; + 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 CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; switch (Py_SIZE(x)) { - case 0: return 0; - case 1: __PYX_VERIFY_RETURN_INT(long, digit, ((PyLongObject*)x)->ob_digit[0]); + case 0: return (int) 0; + case 1: __PYX_VERIFY_RETURN_INT(int, digit, digits[0]) + case 2: + if (8 * sizeof(int) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) >= 2 * PyLong_SHIFT) { + return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); + } + } + break; + case 3: + if (8 * sizeof(int) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) >= 3 * PyLong_SHIFT) { + return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); + } + } + break; + case 4: + if (8 * sizeof(int) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) >= 4 * PyLong_SHIFT) { + return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); + } + } + break; } - #endif #endif #if CYTHON_COMPILING_IN_CPYTHON if (unlikely(Py_SIZE(x) < 0)) { @@ -4236,30 +7594,83 @@ static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { { int result = PyObject_RichCompareBool(x, Py_False, Py_LT); if (unlikely(result < 0)) - return (long) -1; + return (int) -1; if (unlikely(result == 1)) goto raise_neg_overflow; } #endif - if (sizeof(long) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, PyLong_AsUnsignedLong(x)) - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) + if (sizeof(int) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x)) + } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) } } else { -#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 - #if CYTHON_USE_PYLONG_INTERNALS +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; switch (Py_SIZE(x)) { - case 0: return 0; - case 1: __PYX_VERIFY_RETURN_INT(long, digit, +(((PyLongObject*)x)->ob_digit[0])); - case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]); + case 0: return (int) 0; + case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, -(sdigit) digits[0]) + case 1: __PYX_VERIFY_RETURN_INT(int, digit, +digits[0]) + case -2: + if (8 * sizeof(int) - 1 > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { + return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case 2: + if (8 * sizeof(int) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { + return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case -3: + if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { + return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case 3: + if (8 * sizeof(int) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { + return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case -4: + if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { + return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case 4: + if (8 * sizeof(int) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { + return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; } - #endif #endif - if (sizeof(long) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT(long, long, PyLong_AsLong(x)) - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT(long, PY_LONG_LONG, PyLong_AsLongLong(x)) + if (sizeof(int) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x)) + } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x)) } } { @@ -4267,7 +7678,7 @@ static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { PyErr_SetString(PyExc_RuntimeError, "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); #else - long val; + int val; PyObject *v = __Pyx_PyNumber_Int(x); #if PY_MAJOR_VERSION < 3 if (likely(v) && !PyLong_Check(v)) { @@ -4287,51 +7698,129 @@ static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { return val; } #endif - return (long) -1; + return (int) -1; } } else { - long val; + int val; PyObject *tmp = __Pyx_PyNumber_Int(x); - if (!tmp) return (long) -1; - val = __Pyx_PyInt_As_long(tmp); + if (!tmp) return (int) -1; + val = __Pyx_PyInt_As_int(tmp); Py_DECREF(tmp); return val; } raise_overflow: PyErr_SetString(PyExc_OverflowError, - "value too large to convert to long"); - return (long) -1; + "value too large to convert to int"); + return (int) -1; raise_neg_overflow: PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to long"); - return (long) -1; + "can't convert negative value to int"); + return (int) -1; } -static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { - const int neg_one = (int) -1, const_zero = 0; +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__NPY_TYPES(enum NPY_TYPES value) { + const enum NPY_TYPES neg_one = (enum NPY_TYPES) -1, const_zero = (enum NPY_TYPES) 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(enum NPY_TYPES) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(enum NPY_TYPES) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); + } else if (sizeof(enum NPY_TYPES) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); + } + } else { + if (sizeof(enum NPY_TYPES) <= sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(enum NPY_TYPES) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(enum NPY_TYPES), + little, !is_unsigned); + } +} + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { + const long neg_one = (long) -1, const_zero = (long) 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 PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); + } + } else { + if (sizeof(long) <= sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_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 long __Pyx_PyInt_As_long(PyObject *x) { + const long neg_one = (long) -1, const_zero = (long) 0; const int is_unsigned = neg_one > const_zero; #if PY_MAJOR_VERSION < 3 if (likely(PyInt_Check(x))) { - if (sizeof(int) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x)) + if (sizeof(long) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) } else { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { goto raise_neg_overflow; } - return (int) val; + 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 CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; switch (Py_SIZE(x)) { - case 0: return 0; - case 1: __PYX_VERIFY_RETURN_INT(int, digit, ((PyLongObject*)x)->ob_digit[0]); + case 0: return (long) 0; + case 1: __PYX_VERIFY_RETURN_INT(long, digit, digits[0]) + case 2: + if (8 * sizeof(long) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) >= 2 * PyLong_SHIFT) { + return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); + } + } + break; + case 3: + if (8 * sizeof(long) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) >= 3 * PyLong_SHIFT) { + return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); + } + } + break; + case 4: + if (8 * sizeof(long) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) >= 4 * PyLong_SHIFT) { + return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); + } + } + break; } - #endif #endif #if CYTHON_COMPILING_IN_CPYTHON if (unlikely(Py_SIZE(x) < 0)) { @@ -4341,30 +7830,83 @@ static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { { int result = PyObject_RichCompareBool(x, Py_False, Py_LT); if (unlikely(result < 0)) - return (int) -1; + return (long) -1; if (unlikely(result == 1)) goto raise_neg_overflow; } #endif - if (sizeof(int) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, PyLong_AsUnsignedLong(x)) - } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) + if (sizeof(long) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x)) + } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) } } else { -#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 - #if CYTHON_USE_PYLONG_INTERNALS +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; switch (Py_SIZE(x)) { - case 0: return 0; - case 1: __PYX_VERIFY_RETURN_INT(int, digit, +(((PyLongObject*)x)->ob_digit[0])); - case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]); + case 0: return (long) 0; + case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, -(sdigit) digits[0]) + case 1: __PYX_VERIFY_RETURN_INT(long, digit, +digits[0]) + case -2: + if (8 * sizeof(long) - 1 > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case 2: + if (8 * sizeof(long) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case -3: + if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case 3: + if (8 * sizeof(long) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case -4: + if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { + return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case 4: + if (8 * sizeof(long) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { + return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; } - #endif #endif - if (sizeof(int) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT(int, long, PyLong_AsLong(x)) - } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT(int, PY_LONG_LONG, PyLong_AsLongLong(x)) + if (sizeof(long) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x)) + } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x)) } } { @@ -4372,7 +7914,7 @@ static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { PyErr_SetString(PyExc_RuntimeError, "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); #else - int val; + long val; PyObject *v = __Pyx_PyNumber_Int(x); #if PY_MAJOR_VERSION < 3 if (likely(v) && !PyLong_Check(v)) { @@ -4392,24 +7934,24 @@ static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { return val; } #endif - return (int) -1; + return (long) -1; } } else { - int val; + long val; PyObject *tmp = __Pyx_PyNumber_Int(x); - if (!tmp) return (int) -1; - val = __Pyx_PyInt_As_int(tmp); + if (!tmp) return (long) -1; + val = __Pyx_PyInt_As_long(tmp); Py_DECREF(tmp); return val; } raise_overflow: PyErr_SetString(PyExc_OverflowError, - "value too large to convert to int"); - return (int) -1; + "value too large to convert to long"); + return (long) -1; raise_neg_overflow: PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to int"); - return (int) -1; + "can't convert negative value to long"); + return (long) -1; } static int __Pyx_check_binary_version(void) { @@ -4546,7 +8088,7 @@ static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) { 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 CYTHON_COMPILING_IN_CPYTHON && (__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 && @@ -4587,7 +8129,7 @@ static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_ #endif } else #endif -#if !CYTHON_COMPILING_IN_PYPY +#if (!CYTHON_COMPILING_IN_PYPY) || (defined(PyByteArray_AS_STRING) && defined(PyByteArray_GET_SIZE)) if (PyByteArray_Check(o)) { *length = PyByteArray_GET_SIZE(o); return PyByteArray_AS_STRING(o); @@ -4617,7 +8159,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) { #else if (PyLong_Check(x)) #endif - return Py_INCREF(x), x; + return __Pyx_NewRef(x); m = Py_TYPE(x)->tp_as_number; #if PY_MAJOR_VERSION < 3 if (m && m->nb_int) { @@ -4657,18 +8199,55 @@ 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); + if (likely(PyInt_CheckExact(b))) { + if (sizeof(Py_ssize_t) >= sizeof(long)) + return PyInt_AS_LONG(b); + else + return PyInt_AsSsize_t(x); + } #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 + #if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)b)->ob_digit; + const Py_ssize_t size = Py_SIZE(b); + if (likely(__Pyx_sst_abs(size) <= 1)) { + ival = likely(size) ? digits[0] : 0; + if (size == -1) ival = -ival; + return ival; + } else { + switch (size) { + case 2: + if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { + return (Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case -2: + if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { + return -(Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case 3: + if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { + return (Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case -3: + if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { + return -(Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case 4: + if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { + return (Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case -4: + if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { + return -(Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + } + } #endif return PyLong_AsSsize_t(b); } diff --git a/package/MDAnalysis/lib/distances_openmp.pyx b/package/MDAnalysis/lib/distances_openmp.pyx index 6a317490b19..6b46208ee83 100644 --- a/package/MDAnalysis/lib/distances_openmp.pyx +++ b/package/MDAnalysis/lib/distances_openmp.pyx @@ -23,8 +23,8 @@ Parallel distance calculation library --- :mod:`MDAnalysis.lib._distances_openmp Contains OpenMP versions of the contents of "calc_distances.h" """ -cimport c_numpy -c_numpy.import_array() +import numpy +cimport numpy cdef extern from "string.h": void* memcpy(void *dst, void *src, int len) @@ -51,132 +51,132 @@ cdef extern from "calc_distances.h": void _ortho_pbc(coordinate* coords, int numcoords, float* box, float* box_inverse) void _triclinic_pbc(coordinate* coords, int numcoords, coordinate* box, float* box_inverse) -def calc_distance_array(c_numpy.ndarray ref, c_numpy.ndarray conf, - c_numpy.ndarray result): +def calc_distance_array(numpy.ndarray ref, numpy.ndarray conf, + numpy.ndarray result): cdef int confnum, refnum - confnum = conf.dimensions[0] - refnum = ref.dimensions[0] + confnum = conf.shape[0] + refnum = ref.shape[0] _calc_distance_array(ref.data, refnum, conf.data, confnum, result.data) -def calc_distance_array_ortho(c_numpy.ndarray ref, c_numpy.ndarray conf, - c_numpy.ndarray box, - c_numpy.ndarray result): +def calc_distance_array_ortho(numpy.ndarray ref, numpy.ndarray conf, + numpy.ndarray box, + numpy.ndarray result): cdef int confnum, refnum - confnum = conf.dimensions[0] - refnum = ref.dimensions[0] + confnum = conf.shape[0] + refnum = ref.shape[0] _calc_distance_array_ortho(ref.data, refnum, conf.data, confnum, box.data, result.data) -def calc_distance_array_triclinic(c_numpy.ndarray ref, c_numpy.ndarray conf, - c_numpy.ndarray box, - c_numpy.ndarray result): +def calc_distance_array_triclinic(numpy.ndarray ref, numpy.ndarray conf, + numpy.ndarray box, + numpy.ndarray result): cdef int confnum, refnum - confnum = conf.dimensions[0] - refnum = ref.dimensions[0] + confnum = conf.shape[0] + refnum = ref.shape[0] _calc_distance_array_triclinic(ref.data, refnum, conf.data, confnum, box.data, result.data) -def calc_self_distance_array(c_numpy.ndarray ref, - c_numpy.ndarray result): +def calc_self_distance_array(numpy.ndarray ref, + numpy.ndarray result): cdef int refnum, distnum - refnum = ref.dimensions[0] + refnum = ref.shape[0] distnum = (refnum*(refnum-1))/2 _calc_self_distance_array(ref.data, refnum, result.data, distnum) -def calc_self_distance_array_ortho(c_numpy.ndarray ref, - c_numpy.ndarray box, - c_numpy.ndarray result): +def calc_self_distance_array_ortho(numpy.ndarray ref, + numpy.ndarray box, + numpy.ndarray result): cdef int refnum, distnum - refnum = ref.dimensions[0] + refnum = ref.shape[0] distnum = (refnum*(refnum-1))/2 _calc_self_distance_array_ortho(ref.data, refnum, box.data, result.data, distnum) -def calc_self_distance_array_triclinic(c_numpy.ndarray ref, - c_numpy.ndarray box, - c_numpy.ndarray result): +def calc_self_distance_array_triclinic(numpy.ndarray ref, + numpy.ndarray box, + numpy.ndarray result): cdef int refnum, distnum - refnum = ref.dimensions[0] + refnum = ref.shape[0] distnum = (refnum*(refnum-1))/2 _calc_self_distance_array_triclinic(ref.data, refnum, box.data, result.data, distnum) -def coord_transform(c_numpy.ndarray coords, - c_numpy.ndarray box): +def coord_transform(numpy.ndarray coords, + numpy.ndarray box): cdef int numcoords - numcoords = coords.dimensions[0] + numcoords = coords.shape[0] _coord_transform( coords.data, numcoords, box.data) -def calc_bond_distance(c_numpy.ndarray coords1, - c_numpy.ndarray coords2, - c_numpy.ndarray results): +def calc_bond_distance(numpy.ndarray coords1, + numpy.ndarray coords2, + numpy.ndarray results): cdef int numcoords - numcoords = coords1.dimensions[0] + numcoords = coords1.shape[0] _calc_bond_distance( coords1.data, coords2.data, numcoords, results.data) -def calc_bond_distance_ortho(c_numpy.ndarray coords1, - c_numpy.ndarray coords2, - c_numpy.ndarray box, - c_numpy.ndarray results): +def calc_bond_distance_ortho(numpy.ndarray coords1, + numpy.ndarray coords2, + numpy.ndarray box, + numpy.ndarray results): cdef int numcoords - numcoords = coords1.dimensions[0] + numcoords = coords1.shape[0] _calc_bond_distance_ortho( coords1.data, coords2.data, numcoords, box.data, results.data) -def calc_bond_distance_triclinic(c_numpy.ndarray coords1, - c_numpy.ndarray coords2, - c_numpy.ndarray box, - c_numpy.ndarray results): +def calc_bond_distance_triclinic(numpy.ndarray coords1, + numpy.ndarray coords2, + numpy.ndarray box, + numpy.ndarray results): cdef int numcoords - numcoords = coords1.dimensions[0] + numcoords = coords1.shape[0] _calc_bond_distance_triclinic( coords1.data, coords2.data, numcoords, box.data, results.data) -def calc_angle(c_numpy.ndarray coords1, - c_numpy.ndarray coords2, - c_numpy.ndarray coords3, - c_numpy.ndarray results): +def calc_angle(numpy.ndarray coords1, + numpy.ndarray coords2, + numpy.ndarray coords3, + numpy.ndarray results): cdef int numcoords - numcoords = coords1.dimensions[0] + numcoords = coords1.shape[0] _calc_angle( coords1.data, coords2.data, coords3.data, numcoords, results.data) -def calc_angle_ortho(c_numpy.ndarray coords1, - c_numpy.ndarray coords2, - c_numpy.ndarray coords3, - c_numpy.ndarray box, - c_numpy.ndarray results): +def calc_angle_ortho(numpy.ndarray coords1, + numpy.ndarray coords2, + numpy.ndarray coords3, + numpy.ndarray box, + numpy.ndarray results): cdef int numcoords - numcoords = coords1.dimensions[0] + numcoords = coords1.shape[0] _calc_angle_ortho( coords1.data, coords2.data, coords3.data, @@ -184,13 +184,13 @@ def calc_angle_ortho(c_numpy.ndarray coords1, box.data, results.data) -def calc_angle_triclinic(c_numpy.ndarray coords1, - c_numpy.ndarray coords2, - c_numpy.ndarray coords3, - c_numpy.ndarray box, - c_numpy.ndarray results): +def calc_angle_triclinic(numpy.ndarray coords1, + numpy.ndarray coords2, + numpy.ndarray coords3, + numpy.ndarray box, + numpy.ndarray results): cdef int numcoords - numcoords = coords1.dimensions[0] + numcoords = coords1.shape[0] _calc_angle_triclinic( coords1.data, coords2.data, coords3.data, @@ -198,27 +198,27 @@ def calc_angle_triclinic(c_numpy.ndarray coords1, box.data, results.data) -def calc_dihedral(c_numpy.ndarray coords1, - c_numpy.ndarray coords2, - c_numpy.ndarray coords3, - c_numpy.ndarray coords4, - c_numpy.ndarray results): +def calc_dihedral(numpy.ndarray coords1, + numpy.ndarray coords2, + numpy.ndarray coords3, + numpy.ndarray coords4, + numpy.ndarray results): cdef int numcoords - numcoords = coords1.dimensions[0] + numcoords = coords1.shape[0] _calc_dihedral( coords1.data, coords2.data, coords3.data, coords4.data, numcoords, results.data) -def calc_dihedral_ortho(c_numpy.ndarray coords1, - c_numpy.ndarray coords2, - c_numpy.ndarray coords3, - c_numpy.ndarray coords4, - c_numpy.ndarray box, - c_numpy.ndarray results): +def calc_dihedral_ortho(numpy.ndarray coords1, + numpy.ndarray coords2, + numpy.ndarray coords3, + numpy.ndarray coords4, + numpy.ndarray box, + numpy.ndarray results): cdef int numcoords - numcoords = coords1.dimensions[0] + numcoords = coords1.shape[0] _calc_dihedral_ortho( coords1.data, coords2.data, coords3.data, coords4.data, @@ -226,14 +226,14 @@ def calc_dihedral_ortho(c_numpy.ndarray coords1, box.data, results.data) -def calc_dihedral_triclinic(c_numpy.ndarray coords1, - c_numpy.ndarray coords2, - c_numpy.ndarray coords3, - c_numpy.ndarray coords4, - c_numpy.ndarray box, - c_numpy.ndarray results): +def calc_dihedral_triclinic(numpy.ndarray coords1, + numpy.ndarray coords2, + numpy.ndarray coords3, + numpy.ndarray coords4, + numpy.ndarray box, + numpy.ndarray results): cdef int numcoords - numcoords = coords1.dimensions[0] + numcoords = coords1.shape[0] _calc_dihedral_triclinic( coords1.data, coords2.data, coords3.data, coords4.data, @@ -241,18 +241,19 @@ def calc_dihedral_triclinic(c_numpy.ndarray coords1, box.data, results.data) -def ortho_pbc(c_numpy.ndarray coords, - c_numpy.ndarray box, c_numpy.ndarray box_inverse): +def ortho_pbc(numpy.ndarray coords, + numpy.ndarray box, numpy.ndarray box_inverse): cdef int numcoords - numcoords = coords.dimensions[0] + numcoords = coords.shape[0] _ortho_pbc( coords.data, numcoords, box.data, box_inverse.data) -def triclinic_pbc(c_numpy.ndarray coords, - c_numpy.ndarray box, c_numpy.ndarray box_inverse): +def triclinic_pbc(numpy.ndarray coords, + numpy.ndarray box, numpy.ndarray box_inverse): cdef int numcoords - numcoords = coords.dimensions[0] + numcoords = coords.shape[0] _triclinic_pbc( coords.data, numcoords, box.data, box_inverse.data) + diff --git a/package/include/c_numpy.pxd b/package/include/c_numpy.pxd deleted file mode 100644 index 2f282740b67..00000000000 --- a/package/include/c_numpy.pxd +++ /dev/null @@ -1,33 +0,0 @@ -# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; -*- -# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 -# -# MDAnalysis --- http://mdanalysis.googlecode.com -# Copyright (c) 2006-2014 Naveen Michaud-Agrawal, -# Elizabeth J. Denning, Oliver Beckstein, -# and contributors (see AUTHORS for the full list) -# Released under the GNU Public Licence, v2 or any higher version -# -# Please cite your use of MDAnalysis in published work: -# -# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and -# O. Beckstein. MDAnalysis: A Toolkit for the Analysis of -# Molecular Dynamics Simulations. J. Comput. Chem. 32 (2011), 2319--2327, -# doi:10.1002/jcc.21787 -# - -cdef extern from "Python.h": - ctypedef int Py_intptr_t - -cdef extern from "numpy/arrayobject.h": - ctypedef class numpy.ndarray [object PyArrayObject]: - cdef char *data - cdef int nd - cdef Py_intptr_t *dimensions - cdef Py_intptr_t *strides - cdef object base - # descr not implemented yet here... - cdef int flags - cdef int itemsize - cdef object weakreflist - - cdef void import_array()