# HG changeset patch # User Stephen Skory # Date 1247710118 25200 # Branch hopwrap # Node ID abd1d707fd2b9ec045adce896e079aff5eb8504e # Parent 60615619173287c363a6f12088c6361c45735deb Periodized spatial, and commented out the testing stuff in spatial. diff -r 60615619173287c363a6f12088c6361c45735deb -r abd1d707fd2b9ec045adce896e079aff5eb8504e yt/extensions/kdtree/fKD.v --- a/yt/extensions/kdtree/fKD.v Wed Jul 15 11:59:56 2009 -0400 +++ b/yt/extensions/kdtree/fKD.v Wed Jul 15 19:08:38 2009 -0700 @@ -19,7 +19,6 @@ sort logical /.false./ rearrange logical /.true./ - %%%% interval: lower real upper real diff -r 60615619173287c363a6f12088c6361c45735deb -r abd1d707fd2b9ec045adce896e079aff5eb8504e yt/extensions/spatial/__init__.py --- a/yt/extensions/spatial/__init__.py Wed Jul 15 11:59:56 2009 -0400 +++ b/yt/extensions/spatial/__init__.py Wed Jul 15 19:08:38 2009 -0700 @@ -10,5 +10,5 @@ __all__ += ['distance'] import distance -from numpy.testing import Tester -test = Tester().test +#from numpy.testing import Tester +#test = Tester().test diff -r 60615619173287c363a6f12088c6361c45735deb -r abd1d707fd2b9ec045adce896e079aff5eb8504e yt/extensions/spatial/ckdtree.c --- a/yt/extensions/spatial/ckdtree.c Wed Jul 15 11:59:56 2009 -0400 +++ b/yt/extensions/spatial/ckdtree.c Wed Jul 15 19:08:38 2009 -0700 @@ -1,8 +1,11 @@ -/* Generated by Cython 0.10.3 on Thu Mar 12 23:38:09 2009 */ +/* Generated by Cython 0.11.2 on Wed Jul 15 19:06:02 2009 */ #define PY_SSIZE_T_CLEAN #include "Python.h" #include "structmember.h" +#ifndef Py_PYTHON_H + #error Python headers needed to compile C extensions, please install development version of Python. +#endif #ifndef PY_LONG_LONG #define PY_LONG_LONG LONG_LONG #endif @@ -11,11 +14,13 @@ #endif #if PY_VERSION_HEX < 0x02040000 #define METH_COEXIST 0 + #define PyDict_CheckExact(op) (Py_TYPE(op) == &PyDict_Type) #endif #if PY_VERSION_HEX < 0x02050000 typedef int Py_ssize_t; #define PY_SSIZE_T_MAX INT_MAX #define PY_SSIZE_T_MIN INT_MIN + #define PY_FORMAT_SIZE_T "" #define PyInt_FromSsize_t(z) PyInt_FromLong(z) #define PyInt_AsSsize_t(o) PyInt_AsLong(o) #define PyNumber_Index(o) PyNumber_Int(o) @@ -45,7 +50,6 @@ #define PyBUF_SIMPLE 0 #define PyBUF_WRITABLE 0x0001 - #define PyBUF_LOCK 0x0002 #define PyBUF_FORMAT 0x0004 #define PyBUF_ND 0x0008 #define PyBUF_STRIDES (0x0010 | PyBUF_ND) @@ -70,6 +74,7 @@ #if PY_MAJOR_VERSION >= 3 #define PyBaseString_Type PyUnicode_Type #define PyString_Type PyBytes_Type + #define PyString_CheckExact PyBytes_CheckExact #define PyInt_Type PyLong_Type #define PyInt_Check(op) PyLong_Check(op) #define PyInt_CheckExact(op) PyLong_CheckExact(op) @@ -98,18 +103,38 @@ #ifndef __cdecl #define __cdecl #endif + #ifndef __fastcall + #define __fastcall + #endif #else #define _USE_MATH_DEFINES #endif +#if PY_VERSION_HEX < 0x02050000 + #define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),((char *)(n))) + #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),((char *)(n)),(a)) + #define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),((char *)(n))) +#else + #define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),(n)) + #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),(n),(a)) + #define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),(n)) +#endif +#if PY_VERSION_HEX < 0x02050000 + #define __Pyx_NAMESTR(n) ((char *)(n)) + #define __Pyx_DOCSTR(n) ((char *)(n)) +#else + #define __Pyx_NAMESTR(n) (n) + #define __Pyx_DOCSTR(n) (n) +#endif #ifdef __cplusplus #define __PYX_EXTERN_C extern "C" #else #define __PYX_EXTERN_C extern #endif #include -#define __PYX_HAVE_API__scipy__spatial__ckdtree +#define __PYX_HAVE_API__yt__extensions__spatial__ckdtree #include "stdlib.h" #include "numpy/arrayobject.h" +#define __PYX_USE_C99_COMPLEX defined(_Complex_I) #ifdef __GNUC__ @@ -130,33 +155,54 @@ /* Type Conversion Predeclarations */ #if PY_MAJOR_VERSION < 3 -#define __Pyx_PyBytes_FromString PyString_FromString -#define __Pyx_PyBytes_AsString PyString_AsString +#define __Pyx_PyBytes_FromString PyString_FromString +#define __Pyx_PyBytes_FromStringAndSize PyString_FromStringAndSize +#define __Pyx_PyBytes_AsString PyString_AsString #else -#define __Pyx_PyBytes_FromString PyBytes_FromString -#define __Pyx_PyBytes_AsString PyBytes_AsString +#define __Pyx_PyBytes_FromString PyBytes_FromString +#define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize +#define __Pyx_PyBytes_AsString PyBytes_AsString #endif #define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False)) -static INLINE int __Pyx_PyObject_IsTrue(PyObject* x); -static INLINE PY_LONG_LONG __pyx_PyInt_AsLongLong(PyObject* x); -static INLINE unsigned PY_LONG_LONG __pyx_PyInt_AsUnsignedLongLong(PyObject* x); -static INLINE Py_ssize_t __pyx_PyIndex_AsSsize_t(PyObject* b); - -#define __pyx_PyInt_AsLong(x) (PyInt_CheckExact(x) ? PyInt_AS_LONG(x) : PyInt_AsLong(x)) +static INLINE int __Pyx_PyObject_IsTrue(PyObject*); +static INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x); + +#if !defined(T_PYSSIZET) +#if PY_VERSION_HEX < 0x02050000 +#define T_PYSSIZET T_INT +#elif !defined(T_LONGLONG) +#define T_PYSSIZET \ + ((sizeof(Py_ssize_t) == sizeof(int)) ? T_INT : \ + ((sizeof(Py_ssize_t) == sizeof(long)) ? T_LONG : -1)) +#else +#define T_PYSSIZET \ + ((sizeof(Py_ssize_t) == sizeof(int)) ? T_INT : \ + ((sizeof(Py_ssize_t) == sizeof(long)) ? T_LONG : \ + ((sizeof(Py_ssize_t) == sizeof(PY_LONG_LONG)) ? T_LONGLONG : -1))) +#endif +#endif + +#if !defined(T_SIZET) +#if !defined(T_ULONGLONG) +#define T_SIZET \ + ((sizeof(size_t) == sizeof(unsigned int)) ? T_UINT : \ + ((sizeof(size_t) == sizeof(unsigned long)) ? T_ULONG : -1)) +#else +#define T_SIZET \ + ((sizeof(size_t) == sizeof(unsigned int)) ? T_UINT : \ + ((sizeof(size_t) == sizeof(unsigned long)) ? T_ULONG : \ + ((sizeof(size_t) == sizeof(unsigned PY_LONG_LONG)) ? T_ULONGLONG : -1))) +#endif +#endif + +static INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*); +static INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t); +static INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*); + #define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x)) -static INLINE unsigned char __pyx_PyInt_unsigned_char(PyObject* x); -static INLINE unsigned short __pyx_PyInt_unsigned_short(PyObject* x); -static INLINE char __pyx_PyInt_char(PyObject* x); -static INLINE short __pyx_PyInt_short(PyObject* x); -static INLINE int __pyx_PyInt_int(PyObject* x); -static INLINE long __pyx_PyInt_long(PyObject* x); -static INLINE signed char __pyx_PyInt_signed_char(PyObject* x); -static INLINE signed short __pyx_PyInt_signed_short(PyObject* x); -static INLINE signed int __pyx_PyInt_signed_int(PyObject* x); -static INLINE signed long __pyx_PyInt_signed_long(PyObject* x); -static INLINE long double __pyx_PyInt_long_double(PyObject* x); + #ifdef __GNUC__ /* Test for GCC > 2.95 */ #if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95)) @@ -180,6 +226,37 @@ static const char *__pyx_filename; static const char **__pyx_f; + +#ifdef CYTHON_REFNANNY +typedef struct { + void (*INCREF)(void*, PyObject*, int); + void (*DECREF)(void*, PyObject*, int); + void (*GOTREF)(void*, PyObject*, int); + void (*GIVEREF)(void*, PyObject*, int); + void* (*NewContext)(const char*, int, const char*); + void (*FinishContext)(void**); +} __Pyx_RefnannyAPIStruct; +static __Pyx_RefnannyAPIStruct *__Pyx_Refnanny = NULL; +#define __Pyx_ImportRefcountAPI(name) (__Pyx_RefnannyAPIStruct *) PyCObject_Import((char *)name, (char *)"RefnannyAPI") +#define __Pyx_INCREF(r) __Pyx_Refnanny->INCREF(__pyx_refchk, (PyObject *)(r), __LINE__) +#define __Pyx_DECREF(r) __Pyx_Refnanny->DECREF(__pyx_refchk, (PyObject *)(r), __LINE__) +#define __Pyx_GOTREF(r) __Pyx_Refnanny->GOTREF(__pyx_refchk, (PyObject *)(r), __LINE__) +#define __Pyx_GIVEREF(r) __Pyx_Refnanny->GIVEREF(__pyx_refchk, (PyObject *)(r), __LINE__) +#define __Pyx_XDECREF(r) if((r) == NULL) ; else __Pyx_DECREF(r) +#define __Pyx_SetupRefcountContext(name) void* __pyx_refchk = __Pyx_Refnanny->NewContext((name), __LINE__, __FILE__) +#define __Pyx_FinishRefcountContext() __Pyx_Refnanny->FinishContext(&__pyx_refchk) +#else +#define __Pyx_INCREF(r) Py_INCREF(r) +#define __Pyx_DECREF(r) Py_DECREF(r) +#define __Pyx_GOTREF(r) +#define __Pyx_GIVEREF(r) +#define __Pyx_XDECREF(r) Py_XDECREF(r) +#define __Pyx_SetupRefcountContext(name) +#define __Pyx_FinishRefcountContext() +#endif /* CYTHON_REFNANNY */ +#define __Pyx_XGIVEREF(r) if((r) == NULL) ; else __Pyx_GIVEREF(r) +#define __Pyx_XGOTREF(r) if((r) == NULL) ; else __Pyx_GOTREF(r) + static void __Pyx_RaiseDoubleKeywordsError( const char* func_name, PyObject* kw_name); /*proto*/ @@ -187,47 +264,112 @@ Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); /*proto*/ static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, const char* function_name); /*proto*/ + +static int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); /*proto*/ + +/* Run-time type information about structs used with buffers */ +struct __Pyx_StructField_; + +typedef struct { + const char* name; /* for error messages only */ + struct __Pyx_StructField_* fields; + size_t size; /* sizeof(type) */ + char typegroup; /* _R_eal, _C_omplex, Signed _I_nt, _U_nsigned int, _S_truct, _P_ointer, _O_bject */ +} __Pyx_TypeInfo; + +typedef struct __Pyx_StructField_ { + __Pyx_TypeInfo* type; + const char* name; + size_t offset; +} __Pyx_StructField; + +typedef struct { + __Pyx_StructField* field; + size_t parent_offset; +} __Pyx_BufFmt_StackElem; + + static INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info); -static INLINE void __Pyx_ZeroBuffer(Py_buffer* buf); /*proto*/ -static INLINE const char* __Pyx_ConsumeWhitespace(const char* ts); /*proto*/ -static void __Pyx_BufferNdimError(Py_buffer* buffer, int expected_ndim); /*proto*/ -static const char* __Pyx_DescribeTokenInFormatString(const char* ts); /*proto*/ -static const char* __Pyx_CheckTypestring_double(const char* ts); /*proto*/ - -static int __Pyx_GetBuffer_double(PyObject* obj, Py_buffer* buf, int flags, int nd, int cast); /*proto*/ +static int __Pyx_GetBufferAndValidate(Py_buffer* buf, PyObject* obj, __Pyx_TypeInfo* dtype, int flags, int nd, int cast, __Pyx_BufFmt_StackElem* stack); static void __Pyx_RaiseBufferFallbackError(void); /*proto*/ -static const char* __Pyx_CheckTypestring_nn___pyx_t_5numpy_int32_t(const char* ts); /*proto*/ - -static int __Pyx_GetBuffer_nn___pyx_t_5numpy_int32_t(PyObject* obj, Py_buffer* buf, int flags, int nd, int cast); /*proto*/ static INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/ static INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); /*proto*/ -static INLINE PyObject *__Pyx_GetItemInt(PyObject *o, Py_ssize_t i, int is_unsigned) { + +static INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) { PyObject *r; - if (PyList_CheckExact(o) && 0 <= i && i < PyList_GET_SIZE(o)) { + if (!j) return NULL; + r = PyObject_GetItem(o, j); + Py_DECREF(j); + return r; +} + + +#define __Pyx_GetItemInt_List(o, i, size, to_py_func) ((size <= sizeof(Py_ssize_t)) ? \ + __Pyx_GetItemInt_List_Fast(o, i, size <= sizeof(long)) : \ + __Pyx_GetItemInt_Generic(o, to_py_func(i))) + +static INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, int fits_long) { + if (likely(o != Py_None)) { + if (likely((0 <= i) & (i < PyList_GET_SIZE(o)))) { + PyObject *r = PyList_GET_ITEM(o, i); + Py_INCREF(r); + return r; + } + else if ((-PyList_GET_SIZE(o) <= i) & (i < 0)) { + PyObject *r = PyList_GET_ITEM(o, PyList_GET_SIZE(o) + i); + Py_INCREF(r); + return r; + } + } + return __Pyx_GetItemInt_Generic(o, fits_long ? PyInt_FromLong(i) : PyLong_FromLongLong(i)); +} + +#define __Pyx_GetItemInt_Tuple(o, i, size, to_py_func) ((size <= sizeof(Py_ssize_t)) ? \ + __Pyx_GetItemInt_Tuple_Fast(o, i, size <= sizeof(long)) : \ + __Pyx_GetItemInt_Generic(o, to_py_func(i))) + +static INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, int fits_long) { + if (likely(o != Py_None)) { + if (likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) { + PyObject *r = PyTuple_GET_ITEM(o, i); + Py_INCREF(r); + return r; + } + else if ((-PyTuple_GET_SIZE(o) <= i) & (i < 0)) { + PyObject *r = PyTuple_GET_ITEM(o, PyTuple_GET_SIZE(o) + i); + Py_INCREF(r); + return r; + } + } + return __Pyx_GetItemInt_Generic(o, fits_long ? PyInt_FromLong(i) : PyLong_FromLongLong(i)); +} + + +#define __Pyx_GetItemInt(o, i, size, to_py_func) ((size <= sizeof(Py_ssize_t)) ? \ + __Pyx_GetItemInt_Fast(o, i, size <= sizeof(long)) : \ + __Pyx_GetItemInt_Generic(o, to_py_func(i))) + +static INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, int fits_long) { + PyObject *r; + if (PyList_CheckExact(o) && ((0 <= i) & (i < PyList_GET_SIZE(o)))) { r = PyList_GET_ITEM(o, i); Py_INCREF(r); } - else if (PyTuple_CheckExact(o) && 0 <= i && i < PyTuple_GET_SIZE(o)) { + else if (PyTuple_CheckExact(o) && ((0 <= i) & (i < PyTuple_GET_SIZE(o)))) { r = PyTuple_GET_ITEM(o, i); Py_INCREF(r); } - else if (Py_TYPE(o)->tp_as_sequence && Py_TYPE(o)->tp_as_sequence->sq_item && (likely(i >= 0) || !is_unsigned)) + else if (Py_TYPE(o)->tp_as_sequence && Py_TYPE(o)->tp_as_sequence->sq_item && (likely(i >= 0))) { r = PySequence_GetItem(o, i); + } else { - PyObject *j = (likely(i >= 0) || !is_unsigned) ? PyInt_FromLong(i) : PyLong_FromUnsignedLongLong((sizeof(unsigned long long) > sizeof(Py_ssize_t) ? (1ULL << (sizeof(Py_ssize_t)*8)) : 0) + i); - if (!j) - return 0; - r = PyObject_GetItem(o, j); - Py_DECREF(j); + r = __Pyx_GetItemInt_Generic(o, fits_long ? PyInt_FromLong(i) : PyLong_FromLongLong(i)); } return r; } -static const char* __Pyx_CheckTypestring_int(const char* ts); /*proto*/ - -static int __Pyx_GetBuffer_int(PyObject* obj, Py_buffer* buf, int flags, int nd, int cast); /*proto*/ static void __Pyx_RaiseBufferIndexError(int axis); /*proto*/ #define __Pyx_BufPtrStrided2d(type, buf, i0, s0, i1, s1) (type)((char*)buf + i0 * s0 + i1 * s1) #if PY_MAJOR_VERSION < 3 @@ -247,15 +389,258 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb); /*proto*/ +static INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index); + +static INLINE void __Pyx_RaiseTooManyValuesError(void); + static PyObject *__Pyx_UnpackItem(PyObject *, Py_ssize_t index); /*proto*/ static int __Pyx_EndUnpack(PyObject *); /*proto*/ -static int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); /*proto*/ - -static INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); /*proto*/ -static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); /*proto*/ - -static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); /*proto*/ +#if __PYX_USE_C99_COMPLEX + #define __Pyx_REAL_PART(z) __real__(z) + #define __Pyx_IMAG_PART(z) __imag__(z) +#else + #define __Pyx_REAL_PART(z) ((z).real) + #define __Pyx_IMAG_PART(z) ((z).imag) +#endif + +#define __pyx_PyObject_from_complex(z) PyComplex_FromDoubles((double)__Pyx_REAL_PART(z), (double)__Pyx_IMAG_PART(z)) + +#if __PYX_USE_C99_COMPLEX + + typedef float _Complex __pyx_t_float_complex; + static INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + return x + y*(__pyx_t_float_complex)_Complex_I; + } + + #define __pyx_t_float_complex_is_zero(a) ((a) == 0) + #define __pyx_t_float_complex_eq(a, b) ((a) == (b)) + #define __pyx_t_float_complex_add(a, b) ((a)+(b)) + #define __pyx_t_float_complex_sub(a, b) ((a)-(b)) + #define __pyx_t_float_complex_mul(a, b) ((a)*(b)) + #define __pyx_t_float_complex_div(a, b) ((a)/(b)) + #define __pyx_t_float_complex_neg(a) (-(a)) + +#else + + typedef struct { float real, imag; } __pyx_t_float_complex; + static INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + __pyx_t_float_complex c; c.real = x; c.imag = y; return c; + } + + static INLINE int __pyx_t_float_complex_is_zero(__pyx_t_float_complex a) { + return (a.real == 0) & (a.imag == 0); + } + + static INLINE int __pyx_t_float_complex_eq(__pyx_t_float_complex a, __pyx_t_float_complex b) { + return (a.real == b.real) & (a.imag == b.imag); + } + + static INLINE __pyx_t_float_complex __pyx_t_float_complex_add(__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 INLINE __pyx_t_float_complex __pyx_t_float_complex_sub(__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 INLINE __pyx_t_float_complex __pyx_t_float_complex_mul(__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 INLINE __pyx_t_float_complex __pyx_t_float_complex_div(__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 INLINE __pyx_t_float_complex __pyx_t_float_complex_neg(__pyx_t_float_complex a) { + __pyx_t_float_complex z; + z.real = -a.real; + z.imag = -a.imag; + return z; + } + +#endif + +#if __PYX_USE_C99_COMPLEX + + typedef double _Complex __pyx_t_double_complex; + static INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + return x + y*(__pyx_t_double_complex)_Complex_I; + } + + #define __pyx_t_double_complex_is_zero(a) ((a) == 0) + #define __pyx_t_double_complex_eq(a, b) ((a) == (b)) + #define __pyx_t_double_complex_add(a, b) ((a)+(b)) + #define __pyx_t_double_complex_sub(a, b) ((a)-(b)) + #define __pyx_t_double_complex_mul(a, b) ((a)*(b)) + #define __pyx_t_double_complex_div(a, b) ((a)/(b)) + #define __pyx_t_double_complex_neg(a) (-(a)) + +#else + + typedef struct { double real, imag; } __pyx_t_double_complex; + static INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + __pyx_t_double_complex c; c.real = x; c.imag = y; return c; + } + + static INLINE int __pyx_t_double_complex_is_zero(__pyx_t_double_complex a) { + return (a.real == 0) & (a.imag == 0); + } + + static INLINE int __pyx_t_double_complex_eq(__pyx_t_double_complex a, __pyx_t_double_complex b) { + return (a.real == b.real) & (a.imag == b.imag); + } + + static INLINE __pyx_t_double_complex __pyx_t_double_complex_add(__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 INLINE __pyx_t_double_complex __pyx_t_double_complex_sub(__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 INLINE __pyx_t_double_complex __pyx_t_double_complex_mul(__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 INLINE __pyx_t_double_complex __pyx_t_double_complex_div(__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 INLINE __pyx_t_double_complex __pyx_t_double_complex_neg(__pyx_t_double_complex a) { + __pyx_t_double_complex z; + z.real = -a.real; + z.imag = -a.imag; + return z; + } + +#endif + +#if __PYX_USE_C99_COMPLEX + + typedef long double _Complex __pyx_t_long__double_complex; + static INLINE __pyx_t_long__double_complex __pyx_t_long__double_complex_from_parts(long double x, long double y) { + return x + y*(__pyx_t_long__double_complex)_Complex_I; + } + + #define __pyx_t_long__double_complex_is_zero(a) ((a) == 0) + #define __pyx_t_long__double_complex_eq(a, b) ((a) == (b)) + #define __pyx_t_long__double_complex_add(a, b) ((a)+(b)) + #define __pyx_t_long__double_complex_sub(a, b) ((a)-(b)) + #define __pyx_t_long__double_complex_mul(a, b) ((a)*(b)) + #define __pyx_t_long__double_complex_div(a, b) ((a)/(b)) + #define __pyx_t_long__double_complex_neg(a) (-(a)) + +#else + + typedef struct { long double real, imag; } __pyx_t_long__double_complex; + static INLINE __pyx_t_long__double_complex __pyx_t_long__double_complex_from_parts(long double x, long double y) { + __pyx_t_long__double_complex c; c.real = x; c.imag = y; return c; + } + + static INLINE int __pyx_t_long__double_complex_is_zero(__pyx_t_long__double_complex a) { + return (a.real == 0) & (a.imag == 0); + } + + static INLINE int __pyx_t_long__double_complex_eq(__pyx_t_long__double_complex a, __pyx_t_long__double_complex b) { + return (a.real == b.real) & (a.imag == b.imag); + } + + static INLINE __pyx_t_long__double_complex __pyx_t_long__double_complex_add(__pyx_t_long__double_complex a, __pyx_t_long__double_complex b) { + __pyx_t_long__double_complex z; + z.real = a.real + b.real; + z.imag = a.imag + b.imag; + return z; + } + + static INLINE __pyx_t_long__double_complex __pyx_t_long__double_complex_sub(__pyx_t_long__double_complex a, __pyx_t_long__double_complex b) { + __pyx_t_long__double_complex z; + z.real = a.real - b.real; + z.imag = a.imag - b.imag; + return z; + } + + static INLINE __pyx_t_long__double_complex __pyx_t_long__double_complex_mul(__pyx_t_long__double_complex a, __pyx_t_long__double_complex b) { + __pyx_t_long__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 INLINE __pyx_t_long__double_complex __pyx_t_long__double_complex_div(__pyx_t_long__double_complex a, __pyx_t_long__double_complex b) { + __pyx_t_long__double_complex z; + long 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 INLINE __pyx_t_long__double_complex __pyx_t_long__double_complex_neg(__pyx_t_long__double_complex a) { + __pyx_t_long__double_complex z; + z.real = -a.real; + z.imag = -a.imag; + return z; + } + +#endif + +static INLINE int __Pyx_StrEq(const char *, const char *); /*proto*/ + +static INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject *); + +static INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject *); + +static INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject *); + +static INLINE char __Pyx_PyInt_AsChar(PyObject *); + +static INLINE short __Pyx_PyInt_AsShort(PyObject *); + +static INLINE int __Pyx_PyInt_AsInt(PyObject *); + +static INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject *); + +static INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject *); + +static INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject *); + +static INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject *); + +static INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject *); + +static INLINE long __Pyx_PyInt_AsLong(PyObject *); + +static INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject *); + +static INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject *); + +static INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject *); static void __Pyx_WriteUnraisable(const char *name); /*proto*/ @@ -291,6 +676,10 @@ typedef npy_float64 __pyx_t_5numpy_float64_t; +typedef npy_complex64 __pyx_t_5numpy_complex64_t; + +typedef npy_complex128 __pyx_t_5numpy_complex128_t; + typedef npy_long __pyx_t_5numpy_int_t; typedef npy_longlong __pyx_t_5numpy_long_t; @@ -311,7 +700,9 @@ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; -/* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":15 +typedef npy_cdouble __pyx_t_5numpy_complex_t; + +/* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":15 * * # priority queue * cdef union heapcontents: # <<<<<<<<<<<<<< @@ -319,12 +710,12 @@ * char* ptrdata */ -union __pyx_t_5scipy_7spatial_7ckdtree_heapcontents { +union __pyx_t_2yt_10extensions_7spatial_7ckdtree_heapcontents { int intdata; char *ptrdata; }; -/* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":19 +/* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":19 * char* ptrdata * * cdef struct heapitem: # <<<<<<<<<<<<<< @@ -332,12 +723,12 @@ * heapcontents contents */ -struct __pyx_t_5scipy_7spatial_7ckdtree_heapitem { +struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_heapitem { double priority; - union __pyx_t_5scipy_7spatial_7ckdtree_heapcontents contents; + union __pyx_t_2yt_10extensions_7spatial_7ckdtree_heapcontents contents; }; -/* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":23 +/* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":23 * heapcontents contents * * cdef struct heap: # <<<<<<<<<<<<<< @@ -345,13 +736,13 @@ * heapitem* heap */ -struct __pyx_t_5scipy_7spatial_7ckdtree_heap { +struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_heap { int n; - struct __pyx_t_5scipy_7spatial_7ckdtree_heapitem *heap; + struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_heapitem *heap; int space; }; -/* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":139 +/* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":149 * * # Tree structure * cdef struct innernode: # <<<<<<<<<<<<<< @@ -359,15 +750,17 @@ * int n_points */ -struct __pyx_t_5scipy_7spatial_7ckdtree_innernode { +struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_innernode { int split_dim; int n_points; double split; - struct __pyx_t_5scipy_7spatial_7ckdtree_innernode *less; - struct __pyx_t_5scipy_7spatial_7ckdtree_innernode *greater; + double *maxes; + double *mins; + struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_innernode *less; + struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_innernode *greater; }; -/* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":145 +/* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":157 * innernode* less * innernode* greater * cdef struct leafnode: # <<<<<<<<<<<<<< @@ -375,14 +768,16 @@ * int n_points */ -struct __pyx_t_5scipy_7spatial_7ckdtree_leafnode { +struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_leafnode { int split_dim; int n_points; int start_idx; int end_idx; + double *maxes; + double *mins; }; -/* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":153 +/* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":167 * # this is the standard trick for variable-size arrays: * # malloc sizeof(nodeinfo)+self.m*sizeof(double) bytes. * cdef struct nodeinfo: # <<<<<<<<<<<<<< @@ -390,12 +785,12 @@ * double side_distances[0] */ -struct __pyx_t_5scipy_7spatial_7ckdtree_nodeinfo { - struct __pyx_t_5scipy_7spatial_7ckdtree_innernode *node; +struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_nodeinfo { + struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_innernode *node; double side_distances[0]; }; -/* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":157 +/* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":171 * double side_distances[0] * * cdef class cKDTree: # <<<<<<<<<<<<<< @@ -403,10 +798,10 @@ * */ -struct __pyx_obj_5scipy_7spatial_7ckdtree_cKDTree { +struct __pyx_obj_2yt_10extensions_7spatial_7ckdtree_cKDTree { PyObject_HEAD - struct __pyx_vtabstruct_5scipy_7spatial_7ckdtree_cKDTree *__pyx_vtab; - struct __pyx_t_5scipy_7spatial_7ckdtree_innernode *tree; + struct __pyx_vtabstruct_2yt_10extensions_7spatial_7ckdtree_cKDTree *__pyx_vtab; + struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_innernode *tree; PyObject *data; double *raw_data; int n; @@ -421,12 +816,12 @@ }; -struct __pyx_vtabstruct_5scipy_7spatial_7ckdtree_cKDTree { - struct __pyx_t_5scipy_7spatial_7ckdtree_innernode *(*__build)(struct __pyx_obj_5scipy_7spatial_7ckdtree_cKDTree *, int, int, double *, double *); - PyObject *(*__free_tree)(struct __pyx_obj_5scipy_7spatial_7ckdtree_cKDTree *, struct __pyx_t_5scipy_7spatial_7ckdtree_innernode *); - void (*__query)(struct __pyx_obj_5scipy_7spatial_7ckdtree_cKDTree *, double *, int *, double *, int, double, double, double); +struct __pyx_vtabstruct_2yt_10extensions_7spatial_7ckdtree_cKDTree { + struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_innernode *(*__build)(struct __pyx_obj_2yt_10extensions_7spatial_7ckdtree_cKDTree *, int, int, double *, double *); + PyObject *(*__free_tree)(struct __pyx_obj_2yt_10extensions_7spatial_7ckdtree_cKDTree *, struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_innernode *); + void (*__query)(struct __pyx_obj_2yt_10extensions_7spatial_7ckdtree_cKDTree *, double *, int *, double *, int, double, double, double, double *); }; -static struct __pyx_vtabstruct_5scipy_7spatial_7ckdtree_cKDTree *__pyx_vtabptr_5scipy_7spatial_7ckdtree_cKDTree; +static struct __pyx_vtabstruct_2yt_10extensions_7spatial_7ckdtree_cKDTree *__pyx_vtabptr_2yt_10extensions_7spatial_7ckdtree_cKDTree; /* Module declarations from python_buffer */ /* Module declarations from stdlib */ @@ -437,25 +832,34 @@ static PyTypeObject *__pyx_ptype_5numpy_dtype = 0; static PyTypeObject *__pyx_ptype_5numpy_ndarray = 0; -/* Module declarations from scipy.spatial.ckdtree */ - -static PyTypeObject *__pyx_ptype_5scipy_7spatial_7ckdtree_cKDTree = 0; -static double __pyx_v_5scipy_7spatial_7ckdtree_infinity; -static double __pyx_k_24; -static PyObject *__pyx_f_5scipy_7spatial_7ckdtree_heapcreate(struct __pyx_t_5scipy_7spatial_7ckdtree_heap *, int); /*proto*/ -static PyObject *__pyx_f_5scipy_7spatial_7ckdtree_heapdestroy(struct __pyx_t_5scipy_7spatial_7ckdtree_heap *); /*proto*/ -static PyObject *__pyx_f_5scipy_7spatial_7ckdtree_heapresize(struct __pyx_t_5scipy_7spatial_7ckdtree_heap *, int); /*proto*/ -static PyObject *__pyx_f_5scipy_7spatial_7ckdtree_heappush(struct __pyx_t_5scipy_7spatial_7ckdtree_heap *, struct __pyx_t_5scipy_7spatial_7ckdtree_heapitem); /*proto*/ -static struct __pyx_t_5scipy_7spatial_7ckdtree_heapitem __pyx_f_5scipy_7spatial_7ckdtree_heappeek(struct __pyx_t_5scipy_7spatial_7ckdtree_heap *); /*proto*/ -static PyObject *__pyx_f_5scipy_7spatial_7ckdtree_heapremove(struct __pyx_t_5scipy_7spatial_7ckdtree_heap *); /*proto*/ -static struct __pyx_t_5scipy_7spatial_7ckdtree_heapitem __pyx_f_5scipy_7spatial_7ckdtree_heappop(struct __pyx_t_5scipy_7spatial_7ckdtree_heap *); /*proto*/ -static double __pyx_f_5scipy_7spatial_7ckdtree_dmax(double, double); /*proto*/ -static double __pyx_f_5scipy_7spatial_7ckdtree_dabs(double); /*proto*/ -static double __pyx_f_5scipy_7spatial_7ckdtree__distance_p(double *, double *, double, int, double); /*proto*/ - - -/* Implementation of scipy.spatial.ckdtree */ +static INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *, char *, char *, int *); /*proto*/ +/* Module declarations from yt.extensions.spatial.ckdtree */ + +static PyTypeObject *__pyx_ptype_2yt_10extensions_7spatial_7ckdtree_cKDTree = 0; +static double __pyx_v_2yt_10extensions_7spatial_7ckdtree_infinity; +static double __pyx_k_32; +static INLINE PyObject *__pyx_f_2yt_10extensions_7spatial_7ckdtree_heapcreate(struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_heap *, int); /*proto*/ +static INLINE PyObject *__pyx_f_2yt_10extensions_7spatial_7ckdtree_heapdestroy(struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_heap *); /*proto*/ +static INLINE PyObject *__pyx_f_2yt_10extensions_7spatial_7ckdtree_heapresize(struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_heap *, int); /*proto*/ +static INLINE PyObject *__pyx_f_2yt_10extensions_7spatial_7ckdtree_heappush(struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_heap *, struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_heapitem); /*proto*/ +static struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_heapitem __pyx_f_2yt_10extensions_7spatial_7ckdtree_heappeek(struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_heap *); /*proto*/ +static PyObject *__pyx_f_2yt_10extensions_7spatial_7ckdtree_heapremove(struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_heap *); /*proto*/ +static struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_heapitem __pyx_f_2yt_10extensions_7spatial_7ckdtree_heappop(struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_heap *); /*proto*/ +static INLINE double __pyx_f_2yt_10extensions_7spatial_7ckdtree_dmax(double, double); /*proto*/ +static INLINE double __pyx_f_2yt_10extensions_7spatial_7ckdtree_dabs(double); /*proto*/ +static INLINE double __pyx_f_2yt_10extensions_7spatial_7ckdtree_dmin(double, double); /*proto*/ +static INLINE double __pyx_f_2yt_10extensions_7spatial_7ckdtree__distance_p(double *, double *, double, int, double, double *); /*proto*/ +static __Pyx_TypeInfo __Pyx_TypeInfo_double = { "double", NULL, sizeof(double), 'R' }; +static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_5numpy_int32_t = { "numpy.int32_t", NULL, sizeof(__pyx_t_5numpy_int32_t), 'I' }; +static __Pyx_TypeInfo __Pyx_TypeInfo_int = { "int", NULL, sizeof(int), 'I' }; +#define __Pyx_MODULE_NAME "yt.extensions.spatial.ckdtree" +int __pyx_module_is_main_yt__extensions__spatial__ckdtree = 0; + +/* Implementation of yt.extensions.spatial.ckdtree */ static PyObject *__pyx_int_0; +static PyObject *__pyx_int_neg_1; +static char __pyx_k___main__[] = "__main__"; +static PyObject *__pyx_kp___main__; static char __pyx_k___init__[] = "__init__"; static PyObject *__pyx_kp___init__; static char __pyx_k___dealloc__[] = "__dealloc__"; @@ -474,8 +878,10 @@ static PyObject *__pyx_kp_eps; static char __pyx_k_p[] = "p"; static PyObject *__pyx_kp_p; -static char __pyx_k_23[] = "distance_upper_bound"; -static PyObject *__pyx_kp_23; +static char __pyx_k_31[] = "distance_upper_bound"; +static PyObject *__pyx_kp_31; +static char __pyx_k_period[] = "period"; +static PyObject *__pyx_kp_period; static char __pyx_k_numpy[] = "numpy"; static PyObject *__pyx_kp_numpy; static char __pyx_k_np[] = "np"; @@ -486,6 +892,8 @@ static PyObject *__pyx_kp_inf; static char __pyx_k_ValueError[] = "ValueError"; static PyObject *__pyx_kp_ValueError; +static char __pyx_k_range[] = "range"; +static PyObject *__pyx_kp_range; static char __pyx_k_ascontiguousarray[] = "ascontiguousarray"; static PyObject *__pyx_kp_ascontiguousarray; static char __pyx_k_dtype[] = "dtype"; @@ -502,12 +910,14 @@ static PyObject *__pyx_kp_amin; static char __pyx_k_arange[] = "arange"; static PyObject *__pyx_kp_arange; -static char __pyx_k_27[] = "int32"; -static PyObject *__pyx_kp_27; +static char __pyx_k_35[] = "int32"; +static PyObject *__pyx_kp_35; static char __pyx_k_asarray[] = "asarray"; static PyObject *__pyx_kp_asarray; static char __pyx_k_astype[] = "astype"; static PyObject *__pyx_kp_astype; +static char __pyx_k_array[] = "array"; +static PyObject *__pyx_kp_array; static char __pyx_k_newaxis[] = "newaxis"; static PyObject *__pyx_kp_newaxis; static char __pyx_k_prod[] = "prod"; @@ -518,17 +928,19 @@ static PyObject *__pyx_kp_empty; static char __pyx_k_fill[] = "fill"; static PyObject *__pyx_kp_fill; -static char __pyx_k_30[] = "i"; -static PyObject *__pyx_kp_30; +static char __pyx_k_38[] = "i"; +static PyObject *__pyx_kp_38; static PyObject *__pyx_builtin_ValueError; -static PyObject *__pyx_kp_25; -static char __pyx_k_25[] = "Heap containing %d items cannot be resized to %d"; -static PyObject *__pyx_kp_26; -static char __pyx_k_26[] = "leafsize must be at least 1"; -static PyObject *__pyx_kp_28; -static PyObject *__pyx_kp_29; -static char __pyx_k_28[] = "x must consist of vectors of length %d but has shape %s"; -static char __pyx_k_29[] = "Only p-norms with 1<=p<=infinity permitted"; +static PyObject *__pyx_builtin_range; +static PyObject *__pyx_kp_33; +static char __pyx_k_33[] = "Heap containing %d items cannot be resized to %d"; +static PyObject *__pyx_kp_34; +static char __pyx_k_34[] = "leafsize must be at least 1"; +static PyObject *__pyx_kp_36; +static PyObject *__pyx_kp_37; +static char __pyx_k_36[] = "x must consist of vectors of length %d but has shape %s"; +static char __pyx_k_37[] = "Only p-norms with 1<=p<=infinity permitted"; +static PyObject *__pyx_int_15; static char __pyx_k___getbuffer__[] = "__getbuffer__"; static PyObject *__pyx_kp___getbuffer__; static char __pyx_k___releasebuffer__[] = "__releasebuffer__"; @@ -537,47 +949,51 @@ static PyObject *__pyx_kp_info; static char __pyx_k_flags[] = "flags"; static PyObject *__pyx_kp_flags; -static char __pyx_k_iteritems[] = "iteritems"; -static PyObject *__pyx_kp_iteritems; -static char __pyx_k_next[] = "next"; -static PyObject *__pyx_kp_next; -static char __pyx_k_StopIteration[] = "StopIteration"; -static PyObject *__pyx_kp_StopIteration; -static char __pyx_k_pop[] = "pop"; -static PyObject *__pyx_kp_pop; +static char __pyx_k_itervalues[] = "itervalues"; +static PyObject *__pyx_kp_itervalues; static char __pyx_k_RuntimeError[] = "RuntimeError"; static PyObject *__pyx_kp_RuntimeError; static PyObject *__pyx_kp_1; static PyObject *__pyx_kp_2; -static PyObject *__pyx_kp_20; -static PyObject *__pyx_kp_21; -static PyObject *__pyx_kp_22; -static PyObject *__pyx_builtin_StopIteration; +static PyObject *__pyx_kp_5; +static PyObject *__pyx_kp_23; static PyObject *__pyx_builtin_RuntimeError; static char __pyx_k_1[] = "ndarray is not C contiguous"; static char __pyx_k_2[] = "ndarray is not Fortran contiguous"; -static char __pyx_k_3[] = "b"; -static char __pyx_k_4[] = "B"; -static char __pyx_k_5[] = "h"; 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- - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":29 +static INLINE PyObject *__pyx_f_2yt_10extensions_7spatial_7ckdtree_heapcreate(struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_heap *__pyx_v_self, int __pyx_v_initial_size) { + PyObject *__pyx_r = NULL; + __Pyx_SetupRefcountContext("heapcreate"); + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":29 * * cdef inline heapcreate(heap* self,int initial_size): * self.space = initial_size # <<<<<<<<<<<<<< @@ -597,16 +1014,16 @@ */ __pyx_v_self->space = __pyx_v_initial_size; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":30 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":30 * cdef inline heapcreate(heap* self,int initial_size): * self.space = initial_size * self.heap = stdlib.malloc(sizeof(heapitem)*self.space) # <<<<<<<<<<<<<< * self.n=0 * */ - __pyx_v_self->heap = ((struct __pyx_t_5scipy_7spatial_7ckdtree_heapitem *)malloc(((sizeof(struct __pyx_t_5scipy_7spatial_7ckdtree_heapitem)) * __pyx_v_self->space))); - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":31 + __pyx_v_self->heap = ((struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_heapitem *)malloc(((sizeof(struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_heapitem)) * __pyx_v_self->space))); + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":31 * self.space = initial_size * self.heap = stdlib.malloc(sizeof(heapitem)*self.space) * self.n=0 # <<<<<<<<<<<<<< @@ -615,11 +1032,13 @@ */ __pyx_v_self->n = 0; - __pyx_r = Py_None; Py_INCREF(Py_None); + __pyx_r = Py_None; __Pyx_INCREF(Py_None); + __Pyx_XGIVEREF(__pyx_r); + __Pyx_FinishRefcountContext(); return __pyx_r; } -/* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":33 +/* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":33 * self.n=0 * * cdef inline heapdestroy(heap* self): # <<<<<<<<<<<<<< @@ -627,10 +1046,11 @@ * */ -static INLINE PyObject *__pyx_f_5scipy_7spatial_7ckdtree_heapdestroy(struct __pyx_t_5scipy_7spatial_7ckdtree_heap *__pyx_v_self) { - PyObject *__pyx_r; - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":34 +static INLINE PyObject *__pyx_f_2yt_10extensions_7spatial_7ckdtree_heapdestroy(struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_heap *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_SetupRefcountContext("heapdestroy"); + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":34 * * cdef inline heapdestroy(heap* self): * stdlib.free(self.heap) # <<<<<<<<<<<<<< @@ -639,11 +1059,13 @@ */ free(__pyx_v_self->heap); - __pyx_r = Py_None; Py_INCREF(Py_None); + __pyx_r = Py_None; __Pyx_INCREF(Py_None); + __Pyx_XGIVEREF(__pyx_r); + __Pyx_FinishRefcountContext(); return __pyx_r; } -/* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":36 +/* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":36 * stdlib.free(self.heap) * * cdef inline heapresize(heap* self, int new_space): # <<<<<<<<<<<<<< @@ -651,53 +1073,62 @@ * raise ValueError("Heap containing %d items cannot be resized to %d" % (self.n, new_space)) */ -static INLINE PyObject *__pyx_f_5scipy_7spatial_7ckdtree_heapresize(struct __pyx_t_5scipy_7spatial_7ckdtree_heap *__pyx_v_self, int __pyx_v_new_space) { - PyObject *__pyx_r; - int __pyx_1; - PyObject *__pyx_2 = 0; - PyObject *__pyx_3 = 0; - PyObject *__pyx_4 = 0; - PyObject *__pyx_t_1 = NULL; - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":37 +static INLINE PyObject *__pyx_f_2yt_10extensions_7spatial_7ckdtree_heapresize(struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_heap *__pyx_v_self, int __pyx_v_new_space) { + PyObject *__pyx_r = NULL; + int __pyx_t_1; + PyObject *__pyx_t_2 = NULL; + PyObject *__pyx_t_3 = NULL; + PyObject *__pyx_t_4 = NULL; + __Pyx_SetupRefcountContext("heapresize"); + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":37 * * cdef inline heapresize(heap* self, int new_space): * if new_spacen); - if (__pyx_1) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":38 + __pyx_t_1 = (__pyx_v_new_space < __pyx_v_self->n); + if (__pyx_t_1) { + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":38 * cdef inline heapresize(heap* self, int new_space): * if new_spacestdlib.realloc(self.heap,new_space*sizeof(heapitem)) */ - __pyx_2 = PyInt_FromLong(__pyx_v_self->n); 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__pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;} goto __pyx_L3; } __pyx_L3:; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":39 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":39 * if new_spacespace = __pyx_v_new_space; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":40 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":40 * raise ValueError("Heap containing %d items cannot be resized to %d" % (self.n, new_space)) * self.space = new_space * self.heap = stdlib.realloc(self.heap,new_space*sizeof(heapitem)) # <<<<<<<<<<<<<< * * cdef inline heappush(heap* self, heapitem item): */ - __pyx_v_self->heap = ((struct __pyx_t_5scipy_7spatial_7ckdtree_heapitem *)realloc(((void *)__pyx_v_self->heap), (__pyx_v_new_space * (sizeof(struct __pyx_t_5scipy_7spatial_7ckdtree_heapitem))))); - - __pyx_r = Py_None; Py_INCREF(Py_None); + __pyx_v_self->heap = ((struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_heapitem *)realloc(((void *)__pyx_v_self->heap), (__pyx_v_new_space * (sizeof(struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_heapitem))))); + + __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; __pyx_L1_error:; - Py_XDECREF(__pyx_2); - Py_XDECREF(__pyx_3); - Py_XDECREF(__pyx_4); - __Pyx_AddTraceback("scipy.spatial.ckdtree.heapresize"); + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_XDECREF(__pyx_t_4); + __Pyx_AddTraceback("yt.extensions.spatial.ckdtree.heapresize"); __pyx_r = 0; __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_FinishRefcountContext(); return __pyx_r; } -/* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":42 +/* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":42 * self.heap = stdlib.realloc(self.heap,new_space*sizeof(heapitem)) * * cdef inline heappush(heap* self, heapitem item): # <<<<<<<<<<<<<< @@ -735,14 +1168,15 @@ * cdef heapitem t */ -static INLINE PyObject *__pyx_f_5scipy_7spatial_7ckdtree_heappush(struct __pyx_t_5scipy_7spatial_7ckdtree_heap *__pyx_v_self, struct __pyx_t_5scipy_7spatial_7ckdtree_heapitem __pyx_v_item) { +static INLINE PyObject *__pyx_f_2yt_10extensions_7spatial_7ckdtree_heappush(struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_heap *__pyx_v_self, struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_heapitem __pyx_v_item) { int __pyx_v_i; 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+ if (__pyx_t_1) { + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":48 * self.n += 1 * if self.n>self.space: * heapresize(self,2*self.space+1) # <<<<<<<<<<<<<< * * i = self.n-1 */ - __pyx_2 = __pyx_f_5scipy_7spatial_7ckdtree_heapresize(__pyx_v_self, ((2 * __pyx_v_self->space) + 1)); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - Py_DECREF(__pyx_2); __pyx_2 = 0; + __pyx_t_2 = __pyx_f_2yt_10extensions_7spatial_7ckdtree_heapresize(__pyx_v_self, ((2 * __pyx_v_self->space) + 1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; goto __pyx_L3; } __pyx_L3:; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":50 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":50 * heapresize(self,2*self.space+1) * * i = self.n-1 # <<<<<<<<<<<<<< @@ -783,7 +1218,7 @@ */ __pyx_v_i = (__pyx_v_self->n - 1); - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":51 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":51 * * i = self.n-1 * self.heap[i] = item # <<<<<<<<<<<<<< @@ -792,7 +1227,7 @@ */ (__pyx_v_self->heap[__pyx_v_i]) = __pyx_v_item; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":52 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":52 * i = self.n-1 * self.heap[i] = item * while i>0 and self.heap[i].priority 0); - if (__pyx_1) { - __pyx_1 = ((__pyx_v_self->heap[__pyx_v_i]).priority < (__pyx_v_self->heap[((__pyx_v_i - 1) / 2)]).priority); - } - if (!__pyx_1) break; - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":53 + if ((__pyx_v_i > 0)) { + __pyx_t_1 = ((__pyx_v_self->heap[__pyx_v_i]).priority < (__pyx_v_self->heap[((__pyx_v_i - 1) / 2)]).priority); + } else { + __pyx_t_1 = (__pyx_v_i > 0); + } + if (!__pyx_t_1) break; + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":53 * self.heap[i] = item * while i>0 and self.heap[i].priorityheap[((__pyx_v_i - 1) / 2)]); - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":54 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":54 * while i>0 and self.heap[i].priorityheap[((__pyx_v_i - 1) / 2)]) = (__pyx_v_self->heap[__pyx_v_i]); - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":55 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":55 * t = self.heap[(i-1)//2] * self.heap[(i-1)//2] = self.heap[i] * self.heap[i] = t # <<<<<<<<<<<<<< @@ -833,7 +1269,7 @@ */ (__pyx_v_self->heap[__pyx_v_i]) = __pyx_v_t; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":56 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":56 * self.heap[(i-1)//2] = self.heap[i] * self.heap[i] = t * i = (i-1)//2 # <<<<<<<<<<<<<< @@ -843,17 +1279,19 @@ __pyx_v_i = ((__pyx_v_i - 1) / 2); } - __pyx_r = Py_None; Py_INCREF(Py_None); + __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; __pyx_L1_error:; - Py_XDECREF(__pyx_2); - __Pyx_AddTraceback("scipy.spatial.ckdtree.heappush"); + __Pyx_XDECREF(__pyx_t_2); + __Pyx_AddTraceback("yt.extensions.spatial.ckdtree.heappush"); __pyx_r = 0; __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_FinishRefcountContext(); return __pyx_r; } -/* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":58 +/* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":58 * i = (i-1)//2 * * cdef heapitem heappeek(heap* self): # <<<<<<<<<<<<<< @@ -861,10 +1299,11 @@ * */ -static struct __pyx_t_5scipy_7spatial_7ckdtree_heapitem __pyx_f_5scipy_7spatial_7ckdtree_heappeek(struct __pyx_t_5scipy_7spatial_7ckdtree_heap *__pyx_v_self) { - struct __pyx_t_5scipy_7spatial_7ckdtree_heapitem __pyx_r; - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":59 +static struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_heapitem __pyx_f_2yt_10extensions_7spatial_7ckdtree_heappeek(struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_heap *__pyx_v_self) { + struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_heapitem __pyx_r; + __Pyx_SetupRefcountContext("heappeek"); + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":59 * * cdef heapitem heappeek(heap* self): * return self.heap[0] # <<<<<<<<<<<<<< @@ -875,10 +1314,11 @@ goto __pyx_L0; __pyx_L0:; + __Pyx_FinishRefcountContext(); return __pyx_r; } -/* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":61 +/* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":61 * return self.heap[0] * * cdef heapremove(heap* self): # <<<<<<<<<<<<<< @@ -886,17 +1326,20 @@ * cdef int i, j, k, l */ -static PyObject *__pyx_f_5scipy_7spatial_7ckdtree_heapremove(struct __pyx_t_5scipy_7spatial_7ckdtree_heap *__pyx_v_self) { - struct __pyx_t_5scipy_7spatial_7ckdtree_heapitem __pyx_v_t; +static PyObject *__pyx_f_2yt_10extensions_7spatial_7ckdtree_heapremove(struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_heap *__pyx_v_self) { + struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_heapitem __pyx_v_t; int __pyx_v_i; int __pyx_v_j; int __pyx_v_k; int __pyx_v_l; - PyObject *__pyx_r; - int __pyx_1; - PyObject *__pyx_2 = 0; - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":65 + PyObject *__pyx_r = NULL; + int __pyx_t_1; + PyObject *__pyx_t_2 = NULL; + int __pyx_t_3; + int __pyx_t_4; + __Pyx_SetupRefcountContext("heapremove"); + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":65 * cdef int i, j, k, l * * self.heap[0] = self.heap[self.n-1] # <<<<<<<<<<<<<< @@ -905,7 +1348,7 @@ */ (__pyx_v_self->heap[0]) = (__pyx_v_self->heap[(__pyx_v_self->n - 1)]); - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":66 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":66 * * self.heap[0] = self.heap[self.n-1] * self.n -= 1 # <<<<<<<<<<<<<< @@ -914,33 +1357,35 @@ */ __pyx_v_self->n -= 1; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":67 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":67 * self.heap[0] = self.heap[self.n-1] * self.n -= 1 * if self.n < self.space//4 and self.space>40: #FIXME: magic number # <<<<<<<<<<<<<< * heapresize(self,self.space//2+1) * */ - __pyx_1 = (__pyx_v_self->n < (__pyx_v_self->space / 4)); - if (__pyx_1) { - __pyx_1 = (__pyx_v_self->space > 40); + if ((__pyx_v_self->n < (__pyx_v_self->space / 4))) { + __pyx_t_1 = (__pyx_v_self->space > 40); + } else { + __pyx_t_1 = (__pyx_v_self->n < (__pyx_v_self->space / 4)); } - if (__pyx_1) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":68 + if (__pyx_t_1) { + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":68 * self.n -= 1 * if self.n < self.space//4 and self.space>40: #FIXME: magic number * heapresize(self,self.space//2+1) # <<<<<<<<<<<<<< * * i=0 */ - __pyx_2 = __pyx_f_5scipy_7spatial_7ckdtree_heapresize(__pyx_v_self, ((__pyx_v_self->space / 2) + 1)); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - Py_DECREF(__pyx_2); __pyx_2 = 0; + __pyx_t_2 = __pyx_f_2yt_10extensions_7spatial_7ckdtree_heapresize(__pyx_v_self, ((__pyx_v_self->space / 2) + 1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; goto __pyx_L3; } __pyx_L3:; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":70 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":70 * heapresize(self,self.space//2+1) * * i=0 # <<<<<<<<<<<<<< @@ -949,7 +1394,7 @@ */ __pyx_v_i = 0; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":71 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":71 * * i=0 * j=1 # <<<<<<<<<<<<<< @@ -958,7 +1403,7 @@ */ __pyx_v_j = 1; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":72 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":72 * i=0 * j=1 * k=2 # <<<<<<<<<<<<<< @@ -967,7 +1412,7 @@ */ __pyx_v_k = 2; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":73 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":73 * j=1 * k=2 * while ((jn); - if (__pyx_1) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":74 + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":74 * k=2 * while ((j self.heap[j].priority or # <<<<<<<<<<<<<< * k self.heap[k].priority)): */ - __pyx_1 = ((__pyx_v_self->heap[__pyx_v_i]).priority > (__pyx_v_self->heap[__pyx_v_j]).priority); - } - if (!__pyx_1) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":75 + if ((__pyx_v_j < __pyx_v_self->n)) { + __pyx_t_1 = ((__pyx_v_self->heap[__pyx_v_i]).priority > (__pyx_v_self->heap[__pyx_v_j]).priority); + } else { + __pyx_t_1 = (__pyx_v_j < __pyx_v_self->n); + } + if (!__pyx_t_1) { + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":75 * while ((j self.heap[j].priority or * k self.heap[k].priority)): * if kself.heap[k].priority: */ - __pyx_1 = (__pyx_v_k < __pyx_v_self->n); - if (__pyx_1) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":76 + if ((__pyx_v_k < __pyx_v_self->n)) { + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":76 * self.heap[i].priority > self.heap[j].priority or * k self.heap[k].priority)): # <<<<<<<<<<<<<< * if kself.heap[k].priority: * l = k */ - __pyx_1 = ((__pyx_v_self->heap[__pyx_v_i]).priority > (__pyx_v_self->heap[__pyx_v_k]).priority); + __pyx_t_3 = ((__pyx_v_self->heap[__pyx_v_i]).priority > (__pyx_v_self->heap[__pyx_v_k]).priority); + } else { + __pyx_t_3 = (__pyx_v_k < __pyx_v_self->n); } - } - if (!__pyx_1) break; - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":77 + __pyx_t_4 = __pyx_t_3; + } else { + __pyx_t_4 = __pyx_t_1; + } + if (!__pyx_t_4) break; + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":77 * k self.heap[k].priority)): * if kself.heap[k].priority: # <<<<<<<<<<<<<< * l = k * else: */ - __pyx_1 = (__pyx_v_k < __pyx_v_self->n); - if (__pyx_1) { - __pyx_1 = ((__pyx_v_self->heap[__pyx_v_j]).priority > (__pyx_v_self->heap[__pyx_v_k]).priority); - } - if (__pyx_1) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":78 + if ((__pyx_v_k < __pyx_v_self->n)) { + __pyx_t_4 = ((__pyx_v_self->heap[__pyx_v_j]).priority > (__pyx_v_self->heap[__pyx_v_k]).priority); + } else { + __pyx_t_4 = (__pyx_v_k < __pyx_v_self->n); + } + if (__pyx_t_4) { + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":78 * self.heap[i].priority > self.heap[k].priority)): * if kself.heap[k].priority: * l = k # <<<<<<<<<<<<<< @@ -1036,7 +1487,7 @@ } /*else*/ { - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":80 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":80 * l = k * else: * l = j # <<<<<<<<<<<<<< @@ -1047,7 +1498,7 @@ } __pyx_L6:; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":81 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":81 * else: * l = j * t = self.heap[l] # <<<<<<<<<<<<<< @@ -1056,7 +1507,7 @@ */ __pyx_v_t = (__pyx_v_self->heap[__pyx_v_l]); - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":82 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":82 * l = j * t = self.heap[l] * self.heap[l] = self.heap[i] # <<<<<<<<<<<<<< @@ -1065,7 +1516,7 @@ */ (__pyx_v_self->heap[__pyx_v_l]) = (__pyx_v_self->heap[__pyx_v_i]); - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":83 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":83 * t = self.heap[l] * self.heap[l] = self.heap[i] * self.heap[i] = t # <<<<<<<<<<<<<< @@ -1074,7 +1525,7 @@ */ (__pyx_v_self->heap[__pyx_v_i]) = __pyx_v_t; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":84 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":84 * self.heap[l] = self.heap[i] * self.heap[i] = t * i = l # <<<<<<<<<<<<<< @@ -1083,7 +1534,7 @@ */ __pyx_v_i = __pyx_v_l; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":85 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":85 * self.heap[i] = t * i = l * j = 2*i+1 # <<<<<<<<<<<<<< @@ -1092,7 +1543,7 @@ */ __pyx_v_j = ((2 * __pyx_v_i) + 1); - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":86 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":86 * i = l * j = 2*i+1 * k = 2*i+2 # <<<<<<<<<<<<<< @@ -1102,17 +1553,19 @@ __pyx_v_k = ((2 * __pyx_v_i) + 2); } - __pyx_r = Py_None; Py_INCREF(Py_None); + __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; __pyx_L1_error:; - Py_XDECREF(__pyx_2); - __Pyx_AddTraceback("scipy.spatial.ckdtree.heapremove"); + __Pyx_XDECREF(__pyx_t_2); + __Pyx_AddTraceback("yt.extensions.spatial.ckdtree.heapremove"); __pyx_r = 0; __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_FinishRefcountContext(); return __pyx_r; } -/* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":88 +/* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":88 * k = 2*i+2 * * cdef heapitem heappop(heap* self): # <<<<<<<<<<<<<< @@ -1120,31 +1573,33 @@ * it = heappeek(self) */ -static struct __pyx_t_5scipy_7spatial_7ckdtree_heapitem __pyx_f_5scipy_7spatial_7ckdtree_heappop(struct __pyx_t_5scipy_7spatial_7ckdtree_heap *__pyx_v_self) { - struct __pyx_t_5scipy_7spatial_7ckdtree_heapitem __pyx_v_it; - struct __pyx_t_5scipy_7spatial_7ckdtree_heapitem __pyx_r; - PyObject *__pyx_1 = 0; - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":90 +static struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_heapitem __pyx_f_2yt_10extensions_7spatial_7ckdtree_heappop(struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_heap *__pyx_v_self) { + struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_heapitem __pyx_v_it; + struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_heapitem __pyx_r; + PyObject *__pyx_t_1 = NULL; + __Pyx_SetupRefcountContext("heappop"); + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":90 * cdef heapitem heappop(heap* self): * cdef heapitem it * it = heappeek(self) # <<<<<<<<<<<<<< * heapremove(self) * return it */ - __pyx_v_it = __pyx_f_5scipy_7spatial_7ckdtree_heappeek(__pyx_v_self); - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":91 + __pyx_v_it = __pyx_f_2yt_10extensions_7spatial_7ckdtree_heappeek(__pyx_v_self); + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":91 * cdef heapitem it * it = heappeek(self) * heapremove(self) # <<<<<<<<<<<<<< * return it * */ - __pyx_1 = __pyx_f_5scipy_7spatial_7ckdtree_heapremove(__pyx_v_self); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 91; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - Py_DECREF(__pyx_1); __pyx_1 = 0; - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":92 + __pyx_t_1 = __pyx_f_2yt_10extensions_7spatial_7ckdtree_heapremove(__pyx_v_self); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 91; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":92 * it = heappeek(self) * heapremove(self) * return it # <<<<<<<<<<<<<< @@ -1156,13 +1611,14 @@ goto __pyx_L0; __pyx_L1_error:; - Py_XDECREF(__pyx_1); - __Pyx_WriteUnraisable("scipy.spatial.ckdtree.heappop"); + __Pyx_XDECREF(__pyx_t_1); + __Pyx_WriteUnraisable("yt.extensions.spatial.ckdtree.heappop"); __pyx_L0:; + __Pyx_FinishRefcountContext(); return __pyx_r; } -/* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":99 +/* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":99 * * # utility functions * cdef inline double dmax(double x, double y): # <<<<<<<<<<<<<< @@ -1170,21 +1626,22 @@ * return x */ -static INLINE double __pyx_f_5scipy_7spatial_7ckdtree_dmax(double __pyx_v_x, double __pyx_v_y) { +static INLINE double __pyx_f_2yt_10extensions_7spatial_7ckdtree_dmax(double __pyx_v_x, double __pyx_v_y) { double __pyx_r; - int __pyx_1; - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":100 + int __pyx_t_1; + __Pyx_SetupRefcountContext("dmax"); + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":100 * # utility functions * cdef inline double dmax(double x, double y): * if x>y: # <<<<<<<<<<<<<< * return x * else: */ - __pyx_1 = (__pyx_v_x > __pyx_v_y); - if (__pyx_1) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":101 + __pyx_t_1 = (__pyx_v_x > __pyx_v_y); + if (__pyx_t_1) { + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":101 * cdef inline double dmax(double x, double y): * if x>y: * return x # <<<<<<<<<<<<<< @@ -1197,7 +1654,7 @@ } /*else*/ { - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":103 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":103 * return x * else: * return y # <<<<<<<<<<<<<< @@ -1211,10 +1668,11 @@ __pyx_r = 0; __pyx_L0:; + __Pyx_FinishRefcountContext(); return __pyx_r; } -/* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":104 +/* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":104 * else: * return y * cdef inline double dabs(double x): # <<<<<<<<<<<<<< @@ -1222,21 +1680,22 @@ * return x */ -static INLINE double __pyx_f_5scipy_7spatial_7ckdtree_dabs(double __pyx_v_x) { +static INLINE double __pyx_f_2yt_10extensions_7spatial_7ckdtree_dabs(double __pyx_v_x) { double __pyx_r; - int __pyx_1; - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":105 + int __pyx_t_1; + __Pyx_SetupRefcountContext("dabs"); + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":105 * return y * cdef inline double dabs(double x): * if x>0: # <<<<<<<<<<<<<< * return x * else: */ - __pyx_1 = (__pyx_v_x > 0); - if (__pyx_1) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":106 + __pyx_t_1 = (__pyx_v_x > 0); + if (__pyx_t_1) { + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":106 * cdef inline double dabs(double x): * if x>0: * return x # <<<<<<<<<<<<<< @@ -1249,12 +1708,12 @@ } /*else*/ { - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":108 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":108 * return x * else: * return -x # <<<<<<<<<<<<<< - * cdef inline double _distance_p(double*x,double*y,double p,int k,double upperbound): - * """Compute the distance between x and y + * cdef inline double dmin(double x, double y): + * if xupperbound: - */ - for (__pyx_v_i = 0; __pyx_v_i < __pyx_v_k; __pyx_v_i+=1) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":121 + * m = dmin(dabs(x[i] - y[i]), period[i] - dabs(x[i] - y[i])) + * r = dmax(r,m) + */ + for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_v_k; __pyx_t_2+=1) { + __pyx_v_i = __pyx_t_2; + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":128 * if p==infinity: * for i in range(k): - * r = dmax(r,dabs(x[i]-y[i])) # <<<<<<<<<<<<<< + * m = dmin(dabs(x[i] - y[i]), period[i] - dabs(x[i] - y[i])) # <<<<<<<<<<<<<< + * r = dmax(r,m) + * if r>upperbound: + */ + __pyx_v_m = __pyx_f_2yt_10extensions_7spatial_7ckdtree_dmin(__pyx_f_2yt_10extensions_7spatial_7ckdtree_dabs(((__pyx_v_x[__pyx_v_i]) - (__pyx_v_y[__pyx_v_i]))), ((__pyx_v_period[__pyx_v_i]) - __pyx_f_2yt_10extensions_7spatial_7ckdtree_dabs(((__pyx_v_x[__pyx_v_i]) - (__pyx_v_y[__pyx_v_i]))))); + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":129 + * for i in range(k): + * m = dmin(dabs(x[i] - y[i]), period[i] - dabs(x[i] - y[i])) + * r = dmax(r,m) # <<<<<<<<<<<<<< * if r>upperbound: * return r */ - __pyx_v_r = __pyx_f_5scipy_7spatial_7ckdtree_dmax(__pyx_v_r, __pyx_f_5scipy_7spatial_7ckdtree_dabs(((__pyx_v_x[__pyx_v_i]) - (__pyx_v_y[__pyx_v_i])))); - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":122 - * for i in range(k): - * r = dmax(r,dabs(x[i]-y[i])) + __pyx_v_r = __pyx_f_2yt_10extensions_7spatial_7ckdtree_dmax(__pyx_v_r, __pyx_v_m); + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":130 + * m = dmin(dabs(x[i] - y[i]), period[i] - dabs(x[i] - y[i])) + * r = dmax(r,m) * if r>upperbound: # <<<<<<<<<<<<<< * return r * elif p==1: */ - __pyx_1 = (__pyx_v_r > __pyx_v_upperbound); - if (__pyx_1) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":123 - * r = dmax(r,dabs(x[i]-y[i])) + __pyx_t_1 = (__pyx_v_r > __pyx_v_upperbound); + if (__pyx_t_1) { + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":131 + * r = dmax(r,m) * if r>upperbound: * return r # <<<<<<<<<<<<<< * elif p==1: @@ -1343,46 +1870,56 @@ goto __pyx_L3; } - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":124 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":132 * if r>upperbound: * return r * elif p==1: # <<<<<<<<<<<<<< * for i in range(k): - * r += dabs(x[i]-y[i]) - */ - __pyx_1 = (__pyx_v_p == 1); - if (__pyx_1) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":125 + * m = dmin(dabs(x[i] - y[i]), period[i] - dabs(x[i] - y[i])) + */ + __pyx_t_1 = (__pyx_v_p == 1); + if (__pyx_t_1) { + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":133 * return r * elif p==1: * for i in range(k): # <<<<<<<<<<<<<< - * r += dabs(x[i]-y[i]) - * if r>upperbound: - */ - for (__pyx_v_i = 0; __pyx_v_i < __pyx_v_k; __pyx_v_i+=1) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":126 + * m = dmin(dabs(x[i] - y[i]), period[i] - dabs(x[i] - y[i])) + * r += m + */ + for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_v_k; __pyx_t_2+=1) { + __pyx_v_i = __pyx_t_2; + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":134 * elif p==1: * for i in range(k): - * r += dabs(x[i]-y[i]) # <<<<<<<<<<<<<< + * m = dmin(dabs(x[i] - y[i]), period[i] - dabs(x[i] - y[i])) # <<<<<<<<<<<<<< + * r += m + * if r>upperbound: + */ + __pyx_v_m = __pyx_f_2yt_10extensions_7spatial_7ckdtree_dmin(__pyx_f_2yt_10extensions_7spatial_7ckdtree_dabs(((__pyx_v_x[__pyx_v_i]) - (__pyx_v_y[__pyx_v_i]))), ((__pyx_v_period[__pyx_v_i]) - __pyx_f_2yt_10extensions_7spatial_7ckdtree_dabs(((__pyx_v_x[__pyx_v_i]) - (__pyx_v_y[__pyx_v_i]))))); + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":135 + * for i in range(k): + * m = dmin(dabs(x[i] - y[i]), period[i] - dabs(x[i] - y[i])) + * r += m # <<<<<<<<<<<<<< * if r>upperbound: * return r */ - __pyx_v_r += __pyx_f_5scipy_7spatial_7ckdtree_dabs(((__pyx_v_x[__pyx_v_i]) - (__pyx_v_y[__pyx_v_i]))); - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":127 - * for i in range(k): - * r += dabs(x[i]-y[i]) + __pyx_v_r += __pyx_v_m; + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":136 + * m = dmin(dabs(x[i] - y[i]), period[i] - dabs(x[i] - y[i])) + * r += m * if r>upperbound: # <<<<<<<<<<<<<< * return r * else: */ - __pyx_1 = (__pyx_v_r > __pyx_v_upperbound); - if (__pyx_1) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":128 - * r += dabs(x[i]-y[i]) + __pyx_t_1 = (__pyx_v_r > __pyx_v_upperbound); + if (__pyx_t_1) { + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":137 + * r += m * if r>upperbound: * return r # <<<<<<<<<<<<<< * else: @@ -1398,36 +1935,46 @@ } /*else*/ { - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":130 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":139 * return r * else: * for i in range(k): # <<<<<<<<<<<<<< - * r += dabs(x[i]-y[i])**p - * if r>upperbound: - */ - for (__pyx_v_i = 0; __pyx_v_i < __pyx_v_k; __pyx_v_i+=1) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":131 + * m = dmin(dabs(x[i] - y[i]), period[i] - dabs(x[i] - y[i])) + * r += m**p + */ + for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_v_k; __pyx_t_2+=1) { + __pyx_v_i = __pyx_t_2; + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":140 * else: * for i in range(k): - * r += dabs(x[i]-y[i])**p # <<<<<<<<<<<<<< + * m = dmin(dabs(x[i] - y[i]), period[i] - dabs(x[i] - y[i])) # <<<<<<<<<<<<<< + * r += m**p + * if r>upperbound: + */ + __pyx_v_m = __pyx_f_2yt_10extensions_7spatial_7ckdtree_dmin(__pyx_f_2yt_10extensions_7spatial_7ckdtree_dabs(((__pyx_v_x[__pyx_v_i]) - (__pyx_v_y[__pyx_v_i]))), ((__pyx_v_period[__pyx_v_i]) - __pyx_f_2yt_10extensions_7spatial_7ckdtree_dabs(((__pyx_v_x[__pyx_v_i]) - (__pyx_v_y[__pyx_v_i]))))); + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":141 + * for i in range(k): + * m = dmin(dabs(x[i] - y[i]), period[i] - dabs(x[i] - y[i])) + * r += m**p # <<<<<<<<<<<<<< * if r>upperbound: * return r */ - __pyx_v_r += pow(__pyx_f_5scipy_7spatial_7ckdtree_dabs(((__pyx_v_x[__pyx_v_i]) - (__pyx_v_y[__pyx_v_i]))), __pyx_v_p); - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":132 - * for i in range(k): - * r += dabs(x[i]-y[i])**p + __pyx_v_r += pow(__pyx_v_m, __pyx_v_p); + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":142 + * m = dmin(dabs(x[i] - y[i]), period[i] - dabs(x[i] - y[i])) + * r += m**p * if r>upperbound: # <<<<<<<<<<<<<< * return r * return r */ - __pyx_1 = (__pyx_v_r > __pyx_v_upperbound); - if (__pyx_1) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":133 - * r += dabs(x[i]-y[i])**p + __pyx_t_1 = (__pyx_v_r > __pyx_v_upperbound); + if (__pyx_t_1) { + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":143 + * r += m**p * if r>upperbound: * return r # <<<<<<<<<<<<<< * return r @@ -1442,7 +1989,7 @@ } __pyx_L3:; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":134 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":144 * if r>upperbound: * return r * return r # <<<<<<<<<<<<<< @@ -1454,10 +2001,11 @@ __pyx_r = 0; __pyx_L0:; + __Pyx_FinishRefcountContext(); return __pyx_r; } -/* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":195 +/* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":209 * cdef object indices * cdef np.int32_t* raw_indices * def __init__(cKDTree self, data, int leafsize=10): # <<<<<<<<<<<<<< @@ -1465,9 +2013,9 @@ * */ -static int __pyx_pf_5scipy_7spatial_7ckdtree_7cKDTree___init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_5scipy_7spatial_7ckdtree_7cKDTree___init__[] = "Construct a kd-tree.\n\n Parameters:\n ===========\n\n data : array-like, shape (n,m)\n The n data points of dimension mto be indexed. This array is \n not copied unless this is necessary to produce a contiguous \n array of doubles, and so modifying this data will result in \n bogus results.\n leafsize : positive integer\n The number of points at which the algorithm switches over to\n brute-force.\n "; -static int __pyx_pf_5scipy_7spatial_7ckdtree_7cKDTree___init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static int __pyx_pf_2yt_10extensions_7spatial_7ckdtree_7cKDTree___init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_2yt_10extensions_7spatial_7ckdtree_7cKDTree___init__[] = "Construct a kd-tree.\n\n Parameters:\n ===========\n\n data : array-like, shape (n,m)\n The n data points of dimension mto be indexed. This array is \n not copied unless this is necessary to produce a contiguous \n array of doubles, and so modifying this data will result in \n bogus results.\n leafsize : positive integer\n The number of points at which the algorithm switches over to\n brute-force.\n "; +static int __pyx_pf_2yt_10extensions_7spatial_7ckdtree_7cKDTree___init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_data = 0; int __pyx_v_leafsize; PyArrayObject *__pyx_v_inner_data; @@ -1491,25 +2039,25 @@ int __pyx_r; PyObject *__pyx_1 = 0; PyObject *__pyx_2 = 0; - PyObject *__pyx_3 = 0; - PyObject *__pyx_4 = 0; - PyObject *__pyx_5 = 0; - int __pyx_6; - int __pyx_7; - PyObject *__pyx_8 = 0; - PyArrayObject *__pyx_t_1 = NULL; - int __pyx_t_2; + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; PyObject *__pyx_t_3 = NULL; - PyObject *__pyx_t_4 = NULL; - PyObject *__pyx_t_5 = NULL; - PyArrayObject *__pyx_t_6 = NULL; - PyArrayObject *__pyx_t_7 = NULL; + int __pyx_t_4; 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kw_args--; } + } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 195; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } __pyx_v_data = values[0]; if (values[1]) { - __pyx_v_leafsize = __pyx_PyInt_int(values[1]); if (unlikely((__pyx_v_leafsize == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 195; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_leafsize = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_leafsize == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + } else { + __pyx_v_leafsize = 10; 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- if (__pyx_1) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":241 + * # Skory + */ + __pyx_t_1 = ((__pyx_v_end_idx - __pyx_v_start_idx) <= __pyx_v_self->leafsize); + if (__pyx_t_1) { + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":255 * cdef double*mids * if end_idx-start_idx<=self.leafsize: * n = stdlib.malloc(sizeof(leafnode)) # <<<<<<<<<<<<<< + * # Skory + * n.maxes = stdlib.malloc(sizeof(double)*self.m) + */ + __pyx_v_n = ((struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_leafnode *)malloc((sizeof(struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_leafnode)))); + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":257 + * n = stdlib.malloc(sizeof(leafnode)) + * # Skory + * n.maxes = stdlib.malloc(sizeof(double)*self.m) # <<<<<<<<<<<<<< + * n.mins = stdlib.malloc(sizeof(double)*self.m) + * for i in range(self.m): + */ + __pyx_v_n->maxes = ((double *)malloc(((sizeof(double)) * __pyx_v_self->m))); + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":258 + * # Skory + * n.maxes = stdlib.malloc(sizeof(double)*self.m) + * n.mins = stdlib.malloc(sizeof(double)*self.m) # <<<<<<<<<<<<<< + * for i in range(self.m): + * n.maxes[i] = maxes[i] + */ + __pyx_v_n->mins = ((double *)malloc(((sizeof(double)) * __pyx_v_self->m))); + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":259 + * n.maxes = stdlib.malloc(sizeof(double)*self.m) + * n.mins = stdlib.malloc(sizeof(double)*self.m) + * for i in range(self.m): # <<<<<<<<<<<<<< + * n.maxes[i] = maxes[i] + * n.mins[i] = mins[i] + */ + for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_v_self->m; __pyx_t_2+=1) { + __pyx_v_i = __pyx_t_2; + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":260 + * n.mins = stdlib.malloc(sizeof(double)*self.m) + * for i in range(self.m): + * n.maxes[i] = maxes[i] # <<<<<<<<<<<<<< + * n.mins[i] = mins[i] + * n.split_dim = -1 + */ + (__pyx_v_n->maxes[__pyx_v_i]) = (__pyx_v_maxes[__pyx_v_i]); + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":261 + * for i in range(self.m): + * n.maxes[i] = maxes[i] + * n.mins[i] = mins[i] # <<<<<<<<<<<<<< * n.split_dim = -1 * n.start_idx = start_idx */ - __pyx_v_n = ((struct __pyx_t_5scipy_7spatial_7ckdtree_leafnode *)malloc((sizeof(struct __pyx_t_5scipy_7spatial_7ckdtree_leafnode)))); - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":242 - * if end_idx-start_idx<=self.leafsize: - * n = stdlib.malloc(sizeof(leafnode)) + (__pyx_v_n->mins[__pyx_v_i]) = (__pyx_v_mins[__pyx_v_i]); + } + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":262 + * n.maxes[i] = maxes[i] + * n.mins[i] = mins[i] * n.split_dim = -1 # <<<<<<<<<<<<<< * n.start_idx = start_idx * n.end_idx = end_idx */ __pyx_v_n->split_dim = -1; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":243 - * n = stdlib.malloc(sizeof(leafnode)) + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":263 + * n.mins[i] = mins[i] * n.split_dim = -1 * n.start_idx = start_idx # <<<<<<<<<<<<<< * n.end_idx = end_idx @@ -2021,7 +2693,7 @@ */ __pyx_v_n->start_idx = __pyx_v_start_idx; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":244 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":264 * n.split_dim = -1 * n.start_idx = start_idx * n.end_idx = end_idx # <<<<<<<<<<<<<< @@ -2030,20 +2702,20 @@ */ __pyx_v_n->end_idx = __pyx_v_end_idx; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":245 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":265 * n.start_idx = start_idx * n.end_idx = end_idx * return n # <<<<<<<<<<<<<< * else: * d = 0 */ - __pyx_r = ((struct __pyx_t_5scipy_7spatial_7ckdtree_innernode *)__pyx_v_n); + __pyx_r = ((struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_innernode *)__pyx_v_n); goto __pyx_L0; goto __pyx_L3; } /*else*/ { - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":247 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":267 * return n * else: * d = 0 # <<<<<<<<<<<<<< @@ -2052,7 +2724,7 @@ */ __pyx_v_d = 0; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":248 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":268 * else: * d = 0 * size = 0 # <<<<<<<<<<<<<< @@ -2061,27 +2733,27 @@ */ __pyx_v_size = 0; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":249 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":269 * d = 0 * size = 0 * for i in range(self.m): # <<<<<<<<<<<<<< * if maxes[i]-mins[i] > size: * d = i */ - __pyx_2 = __pyx_v_self->m; - for (__pyx_v_i = 0; __pyx_v_i < __pyx_2; __pyx_v_i+=1) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":250 + for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_v_self->m; __pyx_t_2+=1) { + __pyx_v_i = __pyx_t_2; + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":270 * size = 0 * for i in range(self.m): * if maxes[i]-mins[i] > size: # <<<<<<<<<<<<<< * d = i * size = maxes[i]-mins[i] */ - __pyx_1 = (((__pyx_v_maxes[__pyx_v_i]) - (__pyx_v_mins[__pyx_v_i])) > __pyx_v_size); - if (__pyx_1) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":251 + __pyx_t_1 = (((__pyx_v_maxes[__pyx_v_i]) - (__pyx_v_mins[__pyx_v_i])) > __pyx_v_size); + if (__pyx_t_1) { + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":271 * for i in range(self.m): * if maxes[i]-mins[i] > size: * d = i # <<<<<<<<<<<<<< @@ -2090,7 +2762,7 @@ */ __pyx_v_d = __pyx_v_i; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":252 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":272 * if maxes[i]-mins[i] > size: * d = i * size = maxes[i]-mins[i] # <<<<<<<<<<<<<< @@ -2098,12 +2770,12 @@ * minval = mins[d] */ __pyx_v_size = ((__pyx_v_maxes[__pyx_v_i]) - (__pyx_v_mins[__pyx_v_i])); - goto __pyx_L6; + goto __pyx_L8; } - __pyx_L6:; - } - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":253 + __pyx_L8:; + } + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":273 * d = i * size = maxes[i]-mins[i] * maxval = maxes[d] # <<<<<<<<<<<<<< @@ -2112,7 +2784,7 @@ */ __pyx_v_maxval = (__pyx_v_maxes[__pyx_v_d]); - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":254 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":274 * size = maxes[i]-mins[i] * maxval = maxes[d] * minval = mins[d] # <<<<<<<<<<<<<< @@ -2121,26 +2793,26 @@ */ __pyx_v_minval = (__pyx_v_mins[__pyx_v_d]); - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":255 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":275 * maxval = maxes[d] * minval = mins[d] * if maxval==minval: # <<<<<<<<<<<<<< * # all points are identical; warn user? * n = stdlib.malloc(sizeof(leafnode)) */ - __pyx_1 = (__pyx_v_maxval == __pyx_v_minval); - if (__pyx_1) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":257 + __pyx_t_1 = (__pyx_v_maxval == __pyx_v_minval); + if (__pyx_t_1) { + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":277 * if maxval==minval: * # all points are identical; warn user? * n = stdlib.malloc(sizeof(leafnode)) # <<<<<<<<<<<<<< * n.split_dim = -1 * n.start_idx = start_idx */ - __pyx_v_n = ((struct __pyx_t_5scipy_7spatial_7ckdtree_leafnode *)malloc((sizeof(struct __pyx_t_5scipy_7spatial_7ckdtree_leafnode)))); - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":258 + __pyx_v_n = ((struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_leafnode *)malloc((sizeof(struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_leafnode)))); + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":278 * # all points are identical; warn user? * n = stdlib.malloc(sizeof(leafnode)) * n.split_dim = -1 # <<<<<<<<<<<<<< @@ -2149,7 +2821,7 @@ */ __pyx_v_n->split_dim = -1; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":259 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":279 * n = stdlib.malloc(sizeof(leafnode)) * n.split_dim = -1 * n.start_idx = start_idx # <<<<<<<<<<<<<< @@ -2158,7 +2830,7 @@ */ __pyx_v_n->start_idx = __pyx_v_start_idx; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":260 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":280 * n.split_dim = -1 * n.start_idx = start_idx * n.end_idx = end_idx # <<<<<<<<<<<<<< @@ -2167,20 +2839,20 @@ */ __pyx_v_n->end_idx = __pyx_v_end_idx; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":261 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":281 * n.start_idx = start_idx * n.end_idx = end_idx * return n # <<<<<<<<<<<<<< * * split = (maxval+minval)/2 */ - __pyx_r = ((struct __pyx_t_5scipy_7spatial_7ckdtree_innernode *)__pyx_v_n); + __pyx_r = ((struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_innernode *)__pyx_v_n); goto __pyx_L0; - goto __pyx_L7; - } - __pyx_L7:; - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":263 + goto __pyx_L9; + } + __pyx_L9:; + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":283 * return n * * split = (maxval+minval)/2 # <<<<<<<<<<<<<< @@ -2189,7 +2861,7 @@ */ __pyx_v_split = ((__pyx_v_maxval + __pyx_v_minval) / 2); - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":265 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":285 * split = (maxval+minval)/2 * * p = start_idx # <<<<<<<<<<<<<< @@ -2198,7 +2870,7 @@ */ __pyx_v_p = __pyx_v_start_idx; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":266 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":286 * * p = start_idx * q = end_idx-1 # <<<<<<<<<<<<<< @@ -2207,7 +2879,7 @@ */ __pyx_v_q = (__pyx_v_end_idx - 1); - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":267 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":287 * p = start_idx * q = end_idx-1 * while p<=q: # <<<<<<<<<<<<<< @@ -2215,20 +2887,20 @@ * p+=1 */ while (1) { - __pyx_1 = (__pyx_v_p <= __pyx_v_q); - if (!__pyx_1) break; - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":268 + __pyx_t_1 = (__pyx_v_p <= __pyx_v_q); + if (!__pyx_t_1) break; + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":288 * q = end_idx-1 * while p<=q: * if self.raw_data[self.raw_indices[p]*self.m+d]=split: */ - __pyx_1 = ((__pyx_v_self->raw_data[(((__pyx_v_self->raw_indices[__pyx_v_p]) * __pyx_v_self->m) + __pyx_v_d)]) < __pyx_v_split); - if (__pyx_1) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":269 + __pyx_t_1 = ((__pyx_v_self->raw_data[(((__pyx_v_self->raw_indices[__pyx_v_p]) * __pyx_v_self->m) + __pyx_v_d)]) < __pyx_v_split); + if (__pyx_t_1) { + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":289 * while p<=q: * if self.raw_data[self.raw_indices[p]*self.m+d]=split: # <<<<<<<<<<<<<< * q-=1 * else: */ - __pyx_1 = ((__pyx_v_self->raw_data[(((__pyx_v_self->raw_indices[__pyx_v_q]) * __pyx_v_self->m) + __pyx_v_d)]) >= __pyx_v_split); - if (__pyx_1) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":271 + __pyx_t_1 = ((__pyx_v_self->raw_data[(((__pyx_v_self->raw_indices[__pyx_v_q]) * __pyx_v_self->m) + __pyx_v_d)]) >= __pyx_v_split); + if (__pyx_t_1) { + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":291 * p+=1 * elif self.raw_data[self.raw_indices[q]*self.m+d]>=split: * q-=1 # <<<<<<<<<<<<<< @@ -2257,11 +2929,11 @@ * t = self.raw_indices[p] */ __pyx_v_q -= 1; - goto __pyx_L10; + goto __pyx_L12; } /*else*/ { - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":273 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":293 * q-=1 * else: * t = self.raw_indices[p] # <<<<<<<<<<<<<< @@ -2270,7 +2942,7 @@ */ __pyx_v_t = (__pyx_v_self->raw_indices[__pyx_v_p]); - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":274 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":294 * else: * t = self.raw_indices[p] * self.raw_indices[p] = self.raw_indices[q] # <<<<<<<<<<<<<< @@ -2279,7 +2951,7 @@ */ (__pyx_v_self->raw_indices[__pyx_v_p]) = (__pyx_v_self->raw_indices[__pyx_v_q]); - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":275 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":295 * t = self.raw_indices[p] * self.raw_indices[p] = self.raw_indices[q] * self.raw_indices[q] = t # <<<<<<<<<<<<<< @@ -2288,7 +2960,7 @@ */ (__pyx_v_self->raw_indices[__pyx_v_q]) = __pyx_v_t; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":276 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":296 * self.raw_indices[p] = self.raw_indices[q] * self.raw_indices[q] = t * p+=1 # <<<<<<<<<<<<<< @@ -2297,7 +2969,7 @@ */ __pyx_v_p += 1; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":277 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":297 * self.raw_indices[q] = t * p+=1 * q-=1 # <<<<<<<<<<<<<< @@ -2306,20 +2978,20 @@ */ __pyx_v_q -= 1; } - __pyx_L10:; - } - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":280 + __pyx_L12:; + } + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":300 * * # slide midpoint if necessary * if p==start_idx: # <<<<<<<<<<<<<< * # no points less than split * j = start_idx */ - __pyx_1 = (__pyx_v_p == __pyx_v_start_idx); - if (__pyx_1) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":282 + __pyx_t_1 = (__pyx_v_p == __pyx_v_start_idx); + if (__pyx_t_1) { + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":302 * if p==start_idx: * # no points less than split * j = start_idx # <<<<<<<<<<<<<< @@ -2328,7 +3000,7 @@ */ __pyx_v_j = __pyx_v_start_idx; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":283 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":303 * # no points less than split * j = start_idx * split = self.raw_data[self.raw_indices[j]*self.m+d] # <<<<<<<<<<<<<< @@ -2337,26 +3009,27 @@ */ __pyx_v_split = (__pyx_v_self->raw_data[(((__pyx_v_self->raw_indices[__pyx_v_j]) * __pyx_v_self->m) + __pyx_v_d)]); - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":284 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":304 * j = start_idx * split = self.raw_data[self.raw_indices[j]*self.m+d] * for i in range(start_idx+1, end_idx): # <<<<<<<<<<<<<< * if self.raw_data[self.raw_indices[i]*self.m+d]raw_data[(((__pyx_v_self->raw_indices[__pyx_v_i]) * __pyx_v_self->m) + __pyx_v_d)]) < __pyx_v_split); - if (__pyx_1) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":286 + __pyx_t_1 = ((__pyx_v_self->raw_data[(((__pyx_v_self->raw_indices[__pyx_v_i]) * __pyx_v_self->m) + __pyx_v_d)]) < __pyx_v_split); + if (__pyx_t_1) { + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":306 * for i in range(start_idx+1, end_idx): * if self.raw_data[self.raw_indices[i]*self.m+d]raw_data[(((__pyx_v_self->raw_indices[__pyx_v_j]) * __pyx_v_self->m) + __pyx_v_d)]); - goto __pyx_L14; + goto __pyx_L16; } - __pyx_L14:; + __pyx_L16:; } - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":288 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":308 * j = i * split = self.raw_data[self.raw_indices[j]*self.m+d] * t = self.raw_indices[start_idx] # <<<<<<<<<<<<<< @@ -2387,7 +3060,7 @@ */ __pyx_v_t = (__pyx_v_self->raw_indices[__pyx_v_start_idx]); - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":289 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":309 * split = self.raw_data[self.raw_indices[j]*self.m+d] * t = self.raw_indices[start_idx] * self.raw_indices[start_idx] = self.raw_indices[j] # <<<<<<<<<<<<<< @@ -2396,7 +3069,7 @@ */ (__pyx_v_self->raw_indices[__pyx_v_start_idx]) = (__pyx_v_self->raw_indices[__pyx_v_j]); - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":290 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":310 * t = self.raw_indices[start_idx] * self.raw_indices[start_idx] = self.raw_indices[j] * self.raw_indices[j] = t # <<<<<<<<<<<<<< @@ -2405,7 +3078,7 @@ */ (__pyx_v_self->raw_indices[__pyx_v_j]) = __pyx_v_t; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":291 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":311 * self.raw_indices[start_idx] = self.raw_indices[j] * self.raw_indices[j] = t * p = start_idx+1 # <<<<<<<<<<<<<< @@ -2414,7 +3087,7 @@ */ __pyx_v_p = (__pyx_v_start_idx + 1); - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":292 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":312 * self.raw_indices[j] = t * p = start_idx+1 * q = start_idx # <<<<<<<<<<<<<< @@ -2422,20 +3095,20 @@ * # no points greater than split */ __pyx_v_q = __pyx_v_start_idx; - goto __pyx_L11; - } - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":293 + goto __pyx_L13; + } + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":313 * p = start_idx+1 * q = start_idx * elif p==end_idx: # <<<<<<<<<<<<<< * # no points greater than split * j = end_idx-1 */ - __pyx_1 = (__pyx_v_p == __pyx_v_end_idx); - if (__pyx_1) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":295 + __pyx_t_1 = (__pyx_v_p == __pyx_v_end_idx); + if (__pyx_t_1) { + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":315 * elif p==end_idx: * # no points greater than split * j = end_idx-1 # <<<<<<<<<<<<<< @@ -2444,7 +3117,7 @@ */ __pyx_v_j = (__pyx_v_end_idx - 1); - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":296 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":316 * # no points greater than split * j = end_idx-1 * split = self.raw_data[self.raw_indices[j]*self.m+d] # <<<<<<<<<<<<<< @@ -2453,27 +3126,27 @@ */ __pyx_v_split = (__pyx_v_self->raw_data[(((__pyx_v_self->raw_indices[__pyx_v_j]) * __pyx_v_self->m) + __pyx_v_d)]); - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":297 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":317 * j = end_idx-1 * split = self.raw_data[self.raw_indices[j]*self.m+d] * for i in range(start_idx, end_idx-1): # <<<<<<<<<<<<<< * if self.raw_data[self.raw_indices[i]*self.m+d]>split: * j = i */ - __pyx_3 = (__pyx_v_end_idx - 1); - for (__pyx_v_i = __pyx_v_start_idx; __pyx_v_i < __pyx_3; __pyx_v_i+=1) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":298 + for (__pyx_t_2 = __pyx_v_start_idx; __pyx_t_2 < (__pyx_v_end_idx - 1); __pyx_t_2+=1) { + __pyx_v_i = __pyx_t_2; + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":318 * split = self.raw_data[self.raw_indices[j]*self.m+d] * for i in range(start_idx, end_idx-1): * if self.raw_data[self.raw_indices[i]*self.m+d]>split: # <<<<<<<<<<<<<< * j = i * split = self.raw_data[self.raw_indices[j]*self.m+d] */ - __pyx_1 = ((__pyx_v_self->raw_data[(((__pyx_v_self->raw_indices[__pyx_v_i]) * __pyx_v_self->m) + __pyx_v_d)]) > __pyx_v_split); - if (__pyx_1) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":299 + __pyx_t_1 = ((__pyx_v_self->raw_data[(((__pyx_v_self->raw_indices[__pyx_v_i]) * __pyx_v_self->m) + __pyx_v_d)]) > __pyx_v_split); + if (__pyx_t_1) { + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":319 * for i in range(start_idx, end_idx-1): * if self.raw_data[self.raw_indices[i]*self.m+d]>split: * j = i # <<<<<<<<<<<<<< @@ -2482,7 +3155,7 @@ */ __pyx_v_j = __pyx_v_i; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":300 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":320 * if self.raw_data[self.raw_indices[i]*self.m+d]>split: * j = i * split = self.raw_data[self.raw_indices[j]*self.m+d] # <<<<<<<<<<<<<< @@ -2490,12 +3163,12 @@ * self.raw_indices[end_idx-1] = self.raw_indices[j] */ __pyx_v_split = (__pyx_v_self->raw_data[(((__pyx_v_self->raw_indices[__pyx_v_j]) * __pyx_v_self->m) + __pyx_v_d)]); - goto __pyx_L17; + goto __pyx_L19; } - __pyx_L17:; + __pyx_L19:; } - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":301 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":321 * j = i * split = self.raw_data[self.raw_indices[j]*self.m+d] * t = self.raw_indices[end_idx-1] # <<<<<<<<<<<<<< @@ -2504,7 +3177,7 @@ */ __pyx_v_t = (__pyx_v_self->raw_indices[(__pyx_v_end_idx - 1)]); - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":302 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":322 * split = self.raw_data[self.raw_indices[j]*self.m+d] * t = self.raw_indices[end_idx-1] * self.raw_indices[end_idx-1] = self.raw_indices[j] # <<<<<<<<<<<<<< @@ -2513,7 +3186,7 @@ */ (__pyx_v_self->raw_indices[(__pyx_v_end_idx - 1)]) = (__pyx_v_self->raw_indices[__pyx_v_j]); - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":303 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":323 * t = self.raw_indices[end_idx-1] * self.raw_indices[end_idx-1] = self.raw_indices[j] * self.raw_indices[j] = t # <<<<<<<<<<<<<< @@ -2522,7 +3195,7 @@ */ (__pyx_v_self->raw_indices[__pyx_v_j]) = __pyx_v_t; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":304 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":324 * self.raw_indices[end_idx-1] = self.raw_indices[j] * self.raw_indices[j] = t * p = end_idx-1 # <<<<<<<<<<<<<< @@ -2531,7 +3204,7 @@ */ __pyx_v_p = (__pyx_v_end_idx - 1); - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":305 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":325 * self.raw_indices[j] = t * p = end_idx-1 * q = end_idx-2 # <<<<<<<<<<<<<< @@ -2539,20 +3212,20 @@ * # construct new node representation */ __pyx_v_q = (__pyx_v_end_idx - 2); - goto __pyx_L11; - } - __pyx_L11:; - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":308 + goto __pyx_L13; + } + __pyx_L13:; + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":328 * * # construct new node representation * ni = stdlib.malloc(sizeof(innernode)) # <<<<<<<<<<<<<< * * mids = stdlib.malloc(sizeof(double)*self.m) */ - __pyx_v_ni = ((struct __pyx_t_5scipy_7spatial_7ckdtree_innernode *)malloc((sizeof(struct __pyx_t_5scipy_7spatial_7ckdtree_innernode)))); - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":310 + __pyx_v_ni = ((struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_innernode *)malloc((sizeof(struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_innernode)))); + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":330 * ni = stdlib.malloc(sizeof(innernode)) * * mids = stdlib.malloc(sizeof(double)*self.m) # <<<<<<<<<<<<<< @@ -2561,17 +3234,17 @@ */ __pyx_v_mids = ((double *)malloc(((sizeof(double)) * __pyx_v_self->m))); - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":311 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":331 * * mids = stdlib.malloc(sizeof(double)*self.m) * for i in range(self.m): # <<<<<<<<<<<<<< * mids[i] = maxes[i] * mids[d] = split */ - __pyx_2 = __pyx_v_self->m; - for (__pyx_v_i = 0; __pyx_v_i < __pyx_2; __pyx_v_i+=1) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":312 + for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_v_self->m; __pyx_t_2+=1) { + __pyx_v_i = __pyx_t_2; + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":332 * mids = stdlib.malloc(sizeof(double)*self.m) * for i in range(self.m): * mids[i] = maxes[i] # <<<<<<<<<<<<<< @@ -2581,7 +3254,7 @@ (__pyx_v_mids[__pyx_v_i]) = (__pyx_v_maxes[__pyx_v_i]); } - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":313 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":333 * for i in range(self.m): * mids[i] = maxes[i] * mids[d] = split # <<<<<<<<<<<<<< @@ -2590,26 +3263,26 @@ */ (__pyx_v_mids[__pyx_v_d]) = __pyx_v_split; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":314 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":334 * mids[i] = maxes[i] * mids[d] = split * ni.less = self.__build(start_idx,p,mids,mins) # <<<<<<<<<<<<<< * * for i in range(self.m): */ - __pyx_v_ni->less = ((struct __pyx_vtabstruct_5scipy_7spatial_7ckdtree_cKDTree *)__pyx_v_self->__pyx_vtab)->__build(__pyx_v_self, __pyx_v_start_idx, __pyx_v_p, __pyx_v_mids, __pyx_v_mins); - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":316 + __pyx_v_ni->less = ((struct __pyx_vtabstruct_2yt_10extensions_7spatial_7ckdtree_cKDTree *)__pyx_v_self->__pyx_vtab)->__build(__pyx_v_self, __pyx_v_start_idx, __pyx_v_p, __pyx_v_mids, __pyx_v_mins); + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":336 * ni.less = self.__build(start_idx,p,mids,mins) * * for i in range(self.m): # <<<<<<<<<<<<<< * mids[i] = mins[i] * mids[d] = split */ - __pyx_2 = __pyx_v_self->m; - for (__pyx_v_i = 0; __pyx_v_i < __pyx_2; __pyx_v_i+=1) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":317 + for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_v_self->m; __pyx_t_2+=1) { + __pyx_v_i = __pyx_t_2; + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":337 * * for i in range(self.m): * mids[i] = mins[i] # <<<<<<<<<<<<<< @@ -2619,7 +3292,7 @@ (__pyx_v_mids[__pyx_v_i]) = (__pyx_v_mins[__pyx_v_i]); } - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":318 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":338 * for i in range(self.m): * mids[i] = mins[i] * mids[d] = split # <<<<<<<<<<<<<< @@ -2628,16 +3301,16 @@ */ (__pyx_v_mids[__pyx_v_d]) = __pyx_v_split; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":319 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":339 * mids[i] = mins[i] * mids[d] = split * ni.greater = self.__build(p,end_idx,maxes,mids) # <<<<<<<<<<<<<< * * stdlib.free(mids) */ - __pyx_v_ni->greater = ((struct __pyx_vtabstruct_5scipy_7spatial_7ckdtree_cKDTree *)__pyx_v_self->__pyx_vtab)->__build(__pyx_v_self, __pyx_v_p, __pyx_v_end_idx, __pyx_v_maxes, __pyx_v_mids); - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":321 + __pyx_v_ni->greater = ((struct __pyx_vtabstruct_2yt_10extensions_7spatial_7ckdtree_cKDTree *)__pyx_v_self->__pyx_vtab)->__build(__pyx_v_self, __pyx_v_p, __pyx_v_end_idx, __pyx_v_maxes, __pyx_v_mids); + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":341 * ni.greater = self.__build(p,end_idx,maxes,mids) * * stdlib.free(mids) # <<<<<<<<<<<<<< @@ -2646,26 +3319,73 @@ */ free(__pyx_v_mids); - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":323 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":343 * stdlib.free(mids) * * ni.split_dim = d # <<<<<<<<<<<<<< * ni.split = split - * + * # Skory */ __pyx_v_ni->split_dim = __pyx_v_d; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":324 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":344 * * ni.split_dim = d * ni.split = split # <<<<<<<<<<<<<< + * # Skory + * ni.maxes = stdlib.malloc(sizeof(double)*self.m) + */ + __pyx_v_ni->split = __pyx_v_split; + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":346 + * ni.split = split + * # Skory + * ni.maxes = stdlib.malloc(sizeof(double)*self.m) # <<<<<<<<<<<<<< + * ni.mins = stdlib.malloc(sizeof(double)*self.m) + * for i in range(self.m): + */ + __pyx_v_ni->maxes = ((double *)malloc(((sizeof(double)) * __pyx_v_self->m))); + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":347 + * # Skory + * ni.maxes = stdlib.malloc(sizeof(double)*self.m) + * ni.mins = stdlib.malloc(sizeof(double)*self.m) # <<<<<<<<<<<<<< + * for i in range(self.m): + * ni.maxes[i] = maxes[i] + */ + __pyx_v_ni->mins = ((double *)malloc(((sizeof(double)) * __pyx_v_self->m))); + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":348 + * ni.maxes = stdlib.malloc(sizeof(double)*self.m) + * ni.mins = stdlib.malloc(sizeof(double)*self.m) + * for i in range(self.m): # <<<<<<<<<<<<<< + * ni.maxes[i] = maxes[i] + * ni.mins[i] = mins[i] + */ + for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_v_self->m; __pyx_t_2+=1) { + __pyx_v_i = __pyx_t_2; + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":349 + * ni.mins = stdlib.malloc(sizeof(double)*self.m) + * for i in range(self.m): + * ni.maxes[i] = maxes[i] # <<<<<<<<<<<<<< + * ni.mins[i] = mins[i] + * + */ + (__pyx_v_ni->maxes[__pyx_v_i]) = (__pyx_v_maxes[__pyx_v_i]); + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":350 + * for i in range(self.m): + * ni.maxes[i] = maxes[i] + * ni.mins[i] = mins[i] # <<<<<<<<<<<<<< * * return ni */ - __pyx_v_ni->split = __pyx_v_split; - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":326 - * ni.split = split + (__pyx_v_ni->mins[__pyx_v_i]) = (__pyx_v_mins[__pyx_v_i]); + } + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":352 + * ni.mins[i] = mins[i] * * return ni # <<<<<<<<<<<<<< * @@ -2678,10 +3398,11 @@ __pyx_r = 0; __pyx_L0:; + __Pyx_FinishRefcountContext(); return __pyx_r; } -/* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":328 +/* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":354 * return ni * * cdef __free_tree(cKDTree self, innernode* node): # <<<<<<<<<<<<<< @@ -2689,64 +3410,87 @@ * self.__free_tree(node.less) */ -static PyObject *__pyx_f_5scipy_7spatial_7ckdtree_7cKDTree___free_tree(struct __pyx_obj_5scipy_7spatial_7ckdtree_cKDTree *__pyx_v_self, struct __pyx_t_5scipy_7spatial_7ckdtree_innernode *__pyx_v_node) { - PyObject *__pyx_r; - int __pyx_1; - PyObject *__pyx_2 = 0; - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":329 +static PyObject *__pyx_f_2yt_10extensions_7spatial_7ckdtree_7cKDTree___free_tree(struct __pyx_obj_2yt_10extensions_7spatial_7ckdtree_cKDTree *__pyx_v_self, struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_innernode *__pyx_v_node) { + PyObject *__pyx_r = NULL; + int __pyx_t_1; + PyObject *__pyx_t_2 = NULL; + __Pyx_SetupRefcountContext("__free_tree"); + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":355 * * cdef __free_tree(cKDTree self, innernode* node): * if node.split_dim!=-1: # <<<<<<<<<<<<<< * self.__free_tree(node.less) * self.__free_tree(node.greater) */ - __pyx_1 = (__pyx_v_node->split_dim != -1); - if (__pyx_1) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":330 + __pyx_t_1 = (__pyx_v_node->split_dim != -1); + if (__pyx_t_1) { + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":356 * cdef __free_tree(cKDTree self, innernode* node): * if node.split_dim!=-1: * self.__free_tree(node.less) # <<<<<<<<<<<<<< * self.__free_tree(node.greater) - * stdlib.free(node) - */ - __pyx_2 = ((struct __pyx_vtabstruct_5scipy_7spatial_7ckdtree_cKDTree *)__pyx_v_self->__pyx_vtab)->__free_tree(__pyx_v_self, __pyx_v_node->less); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 330; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - Py_DECREF(__pyx_2); __pyx_2 = 0; - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":331 + * stdlib.free(node.maxes) # Skory + */ + __pyx_t_2 = ((struct __pyx_vtabstruct_2yt_10extensions_7spatial_7ckdtree_cKDTree *)__pyx_v_self->__pyx_vtab)->__free_tree(__pyx_v_self, __pyx_v_node->less); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 356; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":357 * if node.split_dim!=-1: * self.__free_tree(node.less) * self.__free_tree(node.greater) # <<<<<<<<<<<<<< - * stdlib.free(node) - * - */ - __pyx_2 = ((struct __pyx_vtabstruct_5scipy_7spatial_7ckdtree_cKDTree *)__pyx_v_self->__pyx_vtab)->__free_tree(__pyx_v_self, __pyx_v_node->greater); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 331; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - Py_DECREF(__pyx_2); __pyx_2 = 0; + * stdlib.free(node.maxes) # Skory + * stdlib.free(node.mins) + */ + __pyx_t_2 = ((struct __pyx_vtabstruct_2yt_10extensions_7spatial_7ckdtree_cKDTree *)__pyx_v_self->__pyx_vtab)->__free_tree(__pyx_v_self, __pyx_v_node->greater); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; goto __pyx_L3; } __pyx_L3:; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":332 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":358 * self.__free_tree(node.less) * self.__free_tree(node.greater) + * stdlib.free(node.maxes) # Skory # <<<<<<<<<<<<<< + * stdlib.free(node.mins) + * stdlib.free(node) + */ + free(__pyx_v_node->maxes); + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":359 + * self.__free_tree(node.greater) + * stdlib.free(node.maxes) # Skory + * stdlib.free(node.mins) # <<<<<<<<<<<<<< + * stdlib.free(node) + * + */ + free(__pyx_v_node->mins); + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":360 + * stdlib.free(node.maxes) # Skory + * stdlib.free(node.mins) * stdlib.free(node) # <<<<<<<<<<<<<< * * def __dealloc__(cKDTree self): */ free(__pyx_v_node); - __pyx_r = Py_None; Py_INCREF(Py_None); + __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; __pyx_L1_error:; - Py_XDECREF(__pyx_2); - __Pyx_AddTraceback("scipy.spatial.ckdtree.cKDTree.__free_tree"); + __Pyx_XDECREF(__pyx_t_2); + __Pyx_AddTraceback("yt.extensions.spatial.ckdtree.cKDTree.__free_tree"); __pyx_r = 0; __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_FinishRefcountContext(); return __pyx_r; } -/* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":334 +/* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":362 * stdlib.free(node) * * def __dealloc__(cKDTree self): # <<<<<<<<<<<<<< @@ -2754,22 +3498,23 @@ * # should happen only if __init__ was never called */ -static void __pyx_pf_5scipy_7spatial_7ckdtree_7cKDTree___dealloc__(PyObject *__pyx_v_self); /*proto*/ -static void __pyx_pf_5scipy_7spatial_7ckdtree_7cKDTree___dealloc__(PyObject *__pyx_v_self) { - int __pyx_1; - PyObject *__pyx_2 = 0; - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":335 +static void __pyx_pf_2yt_10extensions_7spatial_7ckdtree_7cKDTree___dealloc__(PyObject *__pyx_v_self); /*proto*/ +static void __pyx_pf_2yt_10extensions_7spatial_7ckdtree_7cKDTree___dealloc__(PyObject *__pyx_v_self) { + int __pyx_t_1; + PyObject *__pyx_t_2 = NULL; + __Pyx_SetupRefcountContext("__dealloc__"); + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":363 * * def __dealloc__(cKDTree self): * if (self.tree) == 0: # <<<<<<<<<<<<<< * # should happen only if __init__ was never called * return */ - __pyx_1 = (((int)((struct __pyx_obj_5scipy_7spatial_7ckdtree_cKDTree *)__pyx_v_self)->tree) == 0); - if (__pyx_1) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":337 + __pyx_t_1 = (((int)((struct __pyx_obj_2yt_10extensions_7spatial_7ckdtree_cKDTree *)__pyx_v_self)->tree) == 0); + if (__pyx_t_1) { + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":365 * if (self.tree) == 0: * # should happen only if __init__ was never called * return # <<<<<<<<<<<<<< @@ -2781,24 +3526,26 @@ } __pyx_L5:; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":338 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":366 * # should happen only if __init__ was never called * return * self.__free_tree(self.tree) # <<<<<<<<<<<<<< * * cdef void __query(cKDTree self, */ - __pyx_2 = ((struct __pyx_vtabstruct_5scipy_7spatial_7ckdtree_cKDTree *)((struct __pyx_obj_5scipy_7spatial_7ckdtree_cKDTree *)__pyx_v_self)->__pyx_vtab)->__free_tree(((struct __pyx_obj_5scipy_7spatial_7ckdtree_cKDTree *)__pyx_v_self), ((struct __pyx_obj_5scipy_7spatial_7ckdtree_cKDTree *)__pyx_v_self)->tree); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - Py_DECREF(__pyx_2); __pyx_2 = 0; + __pyx_t_2 = ((struct __pyx_vtabstruct_2yt_10extensions_7spatial_7ckdtree_cKDTree *)((struct __pyx_obj_2yt_10extensions_7spatial_7ckdtree_cKDTree *)__pyx_v_self)->__pyx_vtab)->__free_tree(((struct __pyx_obj_2yt_10extensions_7spatial_7ckdtree_cKDTree *)__pyx_v_self), ((struct __pyx_obj_2yt_10extensions_7spatial_7ckdtree_cKDTree *)__pyx_v_self)->tree); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 366; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; goto __pyx_L0; __pyx_L1_error:; - Py_XDECREF(__pyx_2); - __Pyx_AddTraceback("scipy.spatial.ckdtree.cKDTree.__dealloc__"); + __Pyx_XDECREF(__pyx_t_2); + __Pyx_AddTraceback("yt.extensions.spatial.ckdtree.cKDTree.__dealloc__"); __pyx_L0:; + __Pyx_FinishRefcountContext(); } -/* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":340 +/* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":368 * self.__free_tree(self.tree) * * cdef void __query(cKDTree self, # <<<<<<<<<<<<<< @@ -2806,58 +3553,64 @@ * int*result_indices, */ -static void __pyx_f_5scipy_7spatial_7ckdtree_7cKDTree___query(struct __pyx_obj_5scipy_7spatial_7ckdtree_cKDTree *__pyx_v_self, double *__pyx_v_result_distances, int *__pyx_v_result_indices, double *__pyx_v_x, int __pyx_v_k, double __pyx_v_eps, double __pyx_v_p, double __pyx_v_distance_upper_bound) { - struct __pyx_t_5scipy_7spatial_7ckdtree_heap __pyx_v_q; - struct __pyx_t_5scipy_7spatial_7ckdtree_heap __pyx_v_neighbors; +static void __pyx_f_2yt_10extensions_7spatial_7ckdtree_7cKDTree___query(struct __pyx_obj_2yt_10extensions_7spatial_7ckdtree_cKDTree *__pyx_v_self, double *__pyx_v_result_distances, int *__pyx_v_result_indices, double *__pyx_v_x, int __pyx_v_k, double __pyx_v_eps, double __pyx_v_p, double __pyx_v_distance_upper_bound, double *__pyx_v_period) { + struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_heap __pyx_v_q; + struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_heap __pyx_v_neighbors; int __pyx_v_i; double __pyx_v_t; - struct __pyx_t_5scipy_7spatial_7ckdtree_nodeinfo *__pyx_v_inf; - struct __pyx_t_5scipy_7spatial_7ckdtree_nodeinfo *__pyx_v_inf2; + struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_nodeinfo *__pyx_v_inf; + struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_nodeinfo *__pyx_v_inf2; double __pyx_v_d; + double __pyx_v_m_left; + double __pyx_v_m_right; + double __pyx_v_m; double __pyx_v_epsfac; double __pyx_v_min_distance; double __pyx_v_far_min_distance; - struct __pyx_t_5scipy_7spatial_7ckdtree_heapitem __pyx_v_it; - struct __pyx_t_5scipy_7spatial_7ckdtree_heapitem __pyx_v_it2; - struct __pyx_t_5scipy_7spatial_7ckdtree_heapitem __pyx_v_neighbor; - struct __pyx_t_5scipy_7spatial_7ckdtree_leafnode *__pyx_v_node; - struct __pyx_t_5scipy_7spatial_7ckdtree_innernode *__pyx_v_inode; - struct __pyx_t_5scipy_7spatial_7ckdtree_innernode *__pyx_v_near; - struct __pyx_t_5scipy_7spatial_7ckdtree_innernode *__pyx_v_far; - PyObject *__pyx_1 = 0; - int __pyx_2; - int __pyx_3; - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":371 + struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_heapitem __pyx_v_it; + struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_heapitem __pyx_v_it2; + struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_heapitem __pyx_v_neighbor; + struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_leafnode *__pyx_v_node; + struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_innernode *__pyx_v_inode; + struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_innernode *__pyx_v_near; + struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_innernode *__pyx_v_far; + PyObject *__pyx_t_1 = NULL; + int __pyx_t_2; + int __pyx_t_3; + __Pyx_SetupRefcountContext("__query"); + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":401 * # distances between the nearest side of the cell and the target * # the head node of the cell * heapcreate(&q,12) # <<<<<<<<<<<<<< * * # priority queue for the nearest neighbors */ - __pyx_1 = __pyx_f_5scipy_7spatial_7ckdtree_heapcreate((&__pyx_v_q), 12); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 371; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - Py_DECREF(__pyx_1); __pyx_1 = 0; - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":376 + __pyx_t_1 = __pyx_f_2yt_10extensions_7spatial_7ckdtree_heapcreate((&__pyx_v_q), 12); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 401; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":406 * # furthest known neighbor first * # entries are (-distance**p, i) * heapcreate(&neighbors,k) # <<<<<<<<<<<<<< * * # set up first nodeinfo */ - __pyx_1 = __pyx_f_5scipy_7spatial_7ckdtree_heapcreate((&__pyx_v_neighbors), __pyx_v_k); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 376; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - Py_DECREF(__pyx_1); __pyx_1 = 0; - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":379 + __pyx_t_1 = __pyx_f_2yt_10extensions_7spatial_7ckdtree_heapcreate((&__pyx_v_neighbors), __pyx_v_k); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 406; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":409 * * # set up first nodeinfo * inf = stdlib.malloc(sizeof(nodeinfo)+self.m*sizeof(double)) # <<<<<<<<<<<<<< * inf.node = self.tree * for i in range(self.m): */ - __pyx_v_inf = ((struct __pyx_t_5scipy_7spatial_7ckdtree_nodeinfo *)malloc(((sizeof(struct __pyx_t_5scipy_7spatial_7ckdtree_nodeinfo)) + (__pyx_v_self->m * (sizeof(double)))))); - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":380 + __pyx_v_inf = ((struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_nodeinfo *)malloc(((sizeof(struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_nodeinfo)) + (__pyx_v_self->m * (sizeof(double)))))); + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":410 * # set up first nodeinfo * inf = stdlib.malloc(sizeof(nodeinfo)+self.m*sizeof(double)) * inf.node = self.tree # <<<<<<<<<<<<<< @@ -2866,17 +3619,17 @@ */ __pyx_v_inf->node = __pyx_v_self->tree; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":381 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":411 * inf = stdlib.malloc(sizeof(nodeinfo)+self.m*sizeof(double)) * inf.node = self.tree * for i in range(self.m): # <<<<<<<<<<<<<< * inf.side_distances[i] = 0 * t = x[i]-self.raw_maxes[i] */ - __pyx_2 = __pyx_v_self->m; - for (__pyx_v_i = 0; __pyx_v_i < __pyx_2; __pyx_v_i+=1) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":382 + for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_v_self->m; __pyx_t_2+=1) { + __pyx_v_i = __pyx_t_2; + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":412 * inf.node = self.tree * for i in range(self.m): * inf.side_distances[i] = 0 # <<<<<<<<<<<<<< @@ -2885,7 +3638,7 @@ */ (__pyx_v_inf->side_distances[__pyx_v_i]) = 0; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":383 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":413 * for i in range(self.m): * inf.side_distances[i] = 0 * t = x[i]-self.raw_maxes[i] # <<<<<<<<<<<<<< @@ -2894,48 +3647,48 @@ */ __pyx_v_t = ((__pyx_v_x[__pyx_v_i]) - (__pyx_v_self->raw_maxes[__pyx_v_i])); - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":384 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":414 * inf.side_distances[i] = 0 * t = x[i]-self.raw_maxes[i] * if t>inf.side_distances[i]: # <<<<<<<<<<<<<< * inf.side_distances[i] = t * else: */ - __pyx_3 = (__pyx_v_t > (__pyx_v_inf->side_distances[__pyx_v_i])); - if (__pyx_3) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":385 + __pyx_t_3 = (__pyx_v_t > (__pyx_v_inf->side_distances[__pyx_v_i])); + if (__pyx_t_3) { + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":415 * t = x[i]-self.raw_maxes[i] * if t>inf.side_distances[i]: * inf.side_distances[i] = t # <<<<<<<<<<<<<< * else: - * t = self.raw_mins[i]-x[i] + * #t = dmin( dabs(self.raw_mins[i]-x[i]), 1 - dabs(self.raw_mins[i]-x[i])) */ (__pyx_v_inf->side_distances[__pyx_v_i]) = __pyx_v_t; goto __pyx_L5; } /*else*/ { - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":387 - * inf.side_distances[i] = t + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":418 * else: + * #t = dmin( dabs(self.raw_mins[i]-x[i]), 1 - dabs(self.raw_mins[i]-x[i])) * t = self.raw_mins[i]-x[i] # <<<<<<<<<<<<<< * if t>inf.side_distances[i]: * inf.side_distances[i] = t */ __pyx_v_t = ((__pyx_v_self->raw_mins[__pyx_v_i]) - (__pyx_v_x[__pyx_v_i])); - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":388 - * else: + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":419 + * #t = dmin( dabs(self.raw_mins[i]-x[i]), 1 - dabs(self.raw_mins[i]-x[i])) * t = self.raw_mins[i]-x[i] * if t>inf.side_distances[i]: # <<<<<<<<<<<<<< * inf.side_distances[i] = t * if p!=1 and p!=infinity: */ - __pyx_3 = (__pyx_v_t > (__pyx_v_inf->side_distances[__pyx_v_i])); - if (__pyx_3) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":389 + __pyx_t_3 = (__pyx_v_t > (__pyx_v_inf->side_distances[__pyx_v_i])); + if (__pyx_t_3) { + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":420 * t = self.raw_mins[i]-x[i] * if t>inf.side_distances[i]: * inf.side_distances[i] = t # <<<<<<<<<<<<<< @@ -2949,20 +3702,21 @@ } __pyx_L5:; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":390 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":421 * if t>inf.side_distances[i]: * inf.side_distances[i] = t * if p!=1 and p!=infinity: # <<<<<<<<<<<<<< * inf.side_distances[i]=inf.side_distances[i]**p * */ - __pyx_3 = (__pyx_v_p != 1); - if (__pyx_3) { - __pyx_3 = (__pyx_v_p != __pyx_v_5scipy_7spatial_7ckdtree_infinity); - } - if (__pyx_3) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":391 + if ((__pyx_v_p != 1)) { + __pyx_t_3 = (__pyx_v_p != __pyx_v_2yt_10extensions_7spatial_7ckdtree_infinity); + } else { + __pyx_t_3 = (__pyx_v_p != 1); + } + if (__pyx_t_3) { + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":422 * inf.side_distances[i] = t * if p!=1 and p!=infinity: * inf.side_distances[i]=inf.side_distances[i]**p # <<<<<<<<<<<<<< @@ -2975,48 +3729,48 @@ __pyx_L7:; } - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":394 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":425 * * # compute first distance * min_distance = 0. # <<<<<<<<<<<<<< * for i in range(self.m): * if p==infinity: */ - __pyx_v_min_distance = 0.; - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":395 + __pyx_v_min_distance = 0.0; + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":426 * # compute first distance * min_distance = 0. * for i in range(self.m): # <<<<<<<<<<<<<< * if p==infinity: * min_distance = dmax(min_distance,inf.side_distances[i]) */ - __pyx_2 = __pyx_v_self->m; - for (__pyx_v_i = 0; __pyx_v_i < __pyx_2; __pyx_v_i+=1) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":396 + for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_v_self->m; __pyx_t_2+=1) { + __pyx_v_i = __pyx_t_2; + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":427 * min_distance = 0. * for i in range(self.m): * if p==infinity: # <<<<<<<<<<<<<< * min_distance = dmax(min_distance,inf.side_distances[i]) * else: */ - __pyx_3 = (__pyx_v_p == __pyx_v_5scipy_7spatial_7ckdtree_infinity); - if (__pyx_3) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":397 + __pyx_t_3 = (__pyx_v_p == __pyx_v_2yt_10extensions_7spatial_7ckdtree_infinity); + if (__pyx_t_3) { + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":428 * for i in range(self.m): * if p==infinity: * min_distance = dmax(min_distance,inf.side_distances[i]) # <<<<<<<<<<<<<< * else: * min_distance += inf.side_distances[i] */ - __pyx_v_min_distance = __pyx_f_5scipy_7spatial_7ckdtree_dmax(__pyx_v_min_distance, (__pyx_v_inf->side_distances[__pyx_v_i])); + __pyx_v_min_distance = __pyx_f_2yt_10extensions_7spatial_7ckdtree_dmax(__pyx_v_min_distance, (__pyx_v_inf->side_distances[__pyx_v_i])); goto __pyx_L10; } /*else*/ { - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":399 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":430 * min_distance = dmax(min_distance,inf.side_distances[i]) * else: * min_distance += inf.side_distances[i] # <<<<<<<<<<<<<< @@ -3028,17 +3782,17 @@ __pyx_L10:; } - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":402 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":433 * * # fiddle approximation factor * if eps==0: # <<<<<<<<<<<<<< * epsfac=1 * elif p==infinity: */ - __pyx_3 = (__pyx_v_eps == 0); - if (__pyx_3) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":403 + __pyx_t_3 = (__pyx_v_eps == 0); + if (__pyx_t_3) { + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":434 * # fiddle approximation factor * if eps==0: * epsfac=1 # <<<<<<<<<<<<<< @@ -3049,17 +3803,17 @@ goto __pyx_L11; } - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":404 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":435 * if eps==0: * epsfac=1 * elif p==infinity: # <<<<<<<<<<<<<< * epsfac = 1/(1+eps) * else: */ - __pyx_3 = (__pyx_v_p == __pyx_v_5scipy_7spatial_7ckdtree_infinity); - if (__pyx_3) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":405 + __pyx_t_3 = (__pyx_v_p == __pyx_v_2yt_10extensions_7spatial_7ckdtree_infinity); + if (__pyx_t_3) { + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":436 * epsfac=1 * elif p==infinity: * epsfac = 1/(1+eps) # <<<<<<<<<<<<<< @@ -3071,7 +3825,7 @@ } /*else*/ { - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":407 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":438 * epsfac = 1/(1+eps) * else: * epsfac = 1/(1+eps)**p # <<<<<<<<<<<<<< @@ -3082,20 +3836,21 @@ } __pyx_L11:; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":410 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":441 * * # internally we represent all distances as distance**p * if p!=infinity and distance_upper_bound!=infinity: # <<<<<<<<<<<<<< * distance_upper_bound = distance_upper_bound**p * */ - __pyx_3 = (__pyx_v_p != __pyx_v_5scipy_7spatial_7ckdtree_infinity); - if (__pyx_3) { - __pyx_3 = (__pyx_v_distance_upper_bound != __pyx_v_5scipy_7spatial_7ckdtree_infinity); + if ((__pyx_v_p != __pyx_v_2yt_10extensions_7spatial_7ckdtree_infinity)) { + __pyx_t_3 = (__pyx_v_distance_upper_bound != __pyx_v_2yt_10extensions_7spatial_7ckdtree_infinity); + } else { + __pyx_t_3 = (__pyx_v_p != __pyx_v_2yt_10extensions_7spatial_7ckdtree_infinity); } - if (__pyx_3) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":411 + if (__pyx_t_3) { + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":442 * # internally we represent all distances as distance**p * if p!=infinity and distance_upper_bound!=infinity: * distance_upper_bound = distance_upper_bound**p # <<<<<<<<<<<<<< @@ -3107,7 +3862,7 @@ } __pyx_L12:; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":413 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":444 * distance_upper_bound = distance_upper_bound**p * * while True: # <<<<<<<<<<<<<< @@ -3115,81 +3870,82 @@ * node = inf.node */ while (1) { - __pyx_3 = 1; - if (!__pyx_3) break; - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":414 + __pyx_t_3 = 1; + if (!__pyx_t_3) break; + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":445 * * while True: * if inf.node.split_dim==-1: # <<<<<<<<<<<<<< * node = inf.node * */ - __pyx_3 = (__pyx_v_inf->node->split_dim == -1); - if (__pyx_3) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":415 + __pyx_t_3 = (__pyx_v_inf->node->split_dim == -1); + if (__pyx_t_3) { + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":446 * while True: * if inf.node.split_dim==-1: * node = inf.node # <<<<<<<<<<<<<< * * # brute-force */ - __pyx_v_node = ((struct __pyx_t_5scipy_7spatial_7ckdtree_leafnode *)__pyx_v_inf->node); - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":418 + __pyx_v_node = ((struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_leafnode *)__pyx_v_inf->node); + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":449 * * # brute-force * for i in range(node.start_idx,node.end_idx): # <<<<<<<<<<<<<< * d = _distance_p( * self.raw_data+self.raw_indices[i]*self.m, */ - __pyx_2 = __pyx_v_node->end_idx; - for (__pyx_v_i = __pyx_v_node->start_idx; __pyx_v_i < __pyx_2; __pyx_v_i+=1) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":421 + for (__pyx_t_2 = __pyx_v_node->start_idx; __pyx_t_2 < __pyx_v_node->end_idx; __pyx_t_2+=1) { + __pyx_v_i = __pyx_t_2; + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":452 * d = _distance_p( * self.raw_data+self.raw_indices[i]*self.m, - * x,p,self.m,distance_upper_bound) # <<<<<<<<<<<<<< + * x,p,self.m,distance_upper_bound,period) # <<<<<<<<<<<<<< * * if draw_data + ((__pyx_v_self->raw_indices[__pyx_v_i]) * __pyx_v_self->m)), __pyx_v_x, __pyx_v_p, __pyx_v_self->m, __pyx_v_distance_upper_bound); - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":423 - * x,p,self.m,distance_upper_bound) + __pyx_v_d = __pyx_f_2yt_10extensions_7spatial_7ckdtree__distance_p((__pyx_v_self->raw_data + ((__pyx_v_self->raw_indices[__pyx_v_i]) * __pyx_v_self->m)), __pyx_v_x, __pyx_v_p, __pyx_v_self->m, __pyx_v_distance_upper_bound, __pyx_v_period); + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":454 + * x,p,self.m,distance_upper_bound,period) * * if draw_indices[__pyx_v_i]); - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":429 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":460 * neighbor.priority = -d * neighbor.contents.intdata = self.raw_indices[i] * heappush(&neighbors,neighbor) # <<<<<<<<<<<<<< * * # adjust upper bound for efficiency */ - __pyx_1 = __pyx_f_5scipy_7spatial_7ckdtree_heappush((&__pyx_v_neighbors), __pyx_v_neighbor); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 429; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - Py_DECREF(__pyx_1); __pyx_1 = 0; - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":432 + __pyx_t_1 = __pyx_f_2yt_10extensions_7spatial_7ckdtree_heappush((&__pyx_v_neighbors), __pyx_v_neighbor); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 460; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":463 * * # adjust upper bound for efficiency * if neighbors.n==k: # <<<<<<<<<<<<<< * distance_upper_bound = -heappeek(&neighbors).priority * # done with this node, get another */ - __pyx_3 = (__pyx_v_neighbors.n == __pyx_v_k); - if (__pyx_3) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":433 + __pyx_t_3 = (__pyx_v_neighbors.n == __pyx_v_k); + if (__pyx_t_3) { + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":464 * # adjust upper bound for efficiency * if neighbors.n==k: * distance_upper_bound = -heappeek(&neighbors).priority # <<<<<<<<<<<<<< * # done with this node, get another * stdlib.free(inf) */ - __pyx_v_distance_upper_bound = (-__pyx_f_5scipy_7spatial_7ckdtree_heappeek((&__pyx_v_neighbors)).priority); + __pyx_v_distance_upper_bound = (-__pyx_f_2yt_10extensions_7spatial_7ckdtree_heappeek((&__pyx_v_neighbors)).priority); goto __pyx_L20; } __pyx_L20:; @@ -3243,7 +4000,7 @@ __pyx_L18:; } - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":435 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":466 * distance_upper_bound = -heappeek(&neighbors).priority * # done with this node, get another * stdlib.free(inf) # <<<<<<<<<<<<<< @@ -3252,47 +4009,47 @@ */ free(__pyx_v_inf); - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":436 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":467 * # done with this node, get another * stdlib.free(inf) * if q.n==0: # <<<<<<<<<<<<<< * # no more nodes to visit * break */ - __pyx_3 = (__pyx_v_q.n == 0); - if (__pyx_3) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":438 + __pyx_t_3 = (__pyx_v_q.n == 0); + if (__pyx_t_3) { + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":469 * if q.n==0: * # no more nodes to visit * break # <<<<<<<<<<<<<< * else: * it = heappop(&q) */ - goto __pyx_L14; + goto __pyx_L14_break; goto __pyx_L21; } /*else*/ { - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":440 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":471 * break * else: * it = heappop(&q) # <<<<<<<<<<<<<< * inf = it.contents.ptrdata * min_distance = it.priority */ - __pyx_v_it = __pyx_f_5scipy_7spatial_7ckdtree_heappop((&__pyx_v_q)); - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":441 + __pyx_v_it = __pyx_f_2yt_10extensions_7spatial_7ckdtree_heappop((&__pyx_v_q)); + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":472 * else: * it = heappop(&q) * inf = it.contents.ptrdata # <<<<<<<<<<<<<< * min_distance = it.priority * else: */ - __pyx_v_inf = ((struct __pyx_t_5scipy_7spatial_7ckdtree_nodeinfo *)__pyx_v_it.contents.ptrdata); - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":442 + __pyx_v_inf = ((struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_nodeinfo *)__pyx_v_it.contents.ptrdata); + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":473 * it = heappop(&q) * inf = it.contents.ptrdata * min_distance = it.priority # <<<<<<<<<<<<<< @@ -3306,26 +4063,26 @@ } /*else*/ { - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":444 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":475 * min_distance = it.priority * else: * inode = inf.node # <<<<<<<<<<<<<< * * # we don't push cells that are too far onto the queue at all, */ - __pyx_v_inode = ((struct __pyx_t_5scipy_7spatial_7ckdtree_innernode *)__pyx_v_inf->node); - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":449 + __pyx_v_inode = ((struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_innernode *)__pyx_v_inf->node); + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":480 * # but since the distance_upper_bound decreases, we might get * # here even if the cell's too far * if min_distance>distance_upper_bound*epsfac: # <<<<<<<<<<<<<< * # since this is the nearest cell, we're done, bail out * stdlib.free(inf) */ - __pyx_3 = (__pyx_v_min_distance > (__pyx_v_distance_upper_bound * __pyx_v_epsfac)); - if (__pyx_3) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":451 + __pyx_t_3 = (__pyx_v_min_distance > (__pyx_v_distance_upper_bound * __pyx_v_epsfac)); + if (__pyx_t_3) { + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":482 * if min_distance>distance_upper_bound*epsfac: * # since this is the nearest cell, we're done, bail out * stdlib.free(inf) # <<<<<<<<<<<<<< @@ -3334,17 +4091,17 @@ */ free(__pyx_v_inf); - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":453 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":484 * stdlib.free(inf) * # free all the nodes still on the heap * for i in range(q.n): # <<<<<<<<<<<<<< * stdlib.free(q.heap[i].contents.ptrdata) * break */ - __pyx_2 = __pyx_v_q.n; - for (__pyx_v_i = 0; __pyx_v_i < __pyx_2; __pyx_v_i+=1) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":454 + for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_v_q.n; __pyx_t_2+=1) { + __pyx_v_i = __pyx_t_2; + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":485 * # free all the nodes still on the heap * for i in range(q.n): * stdlib.free(q.heap[i].contents.ptrdata) # <<<<<<<<<<<<<< @@ -3354,29 +4111,29 @@ free((__pyx_v_q.heap[__pyx_v_i]).contents.ptrdata); } - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":455 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":486 * for i in range(q.n): * stdlib.free(q.heap[i].contents.ptrdata) * break # <<<<<<<<<<<<<< * * # set up children for searching */ - goto __pyx_L14; + goto __pyx_L14_break; goto __pyx_L22; } __pyx_L22:; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":458 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":489 * * # set up children for searching * if x[inode.split_dim]split_dim]) < __pyx_v_inode->split); - if (__pyx_3) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":459 + __pyx_t_3 = ((__pyx_v_x[__pyx_v_inode->split_dim]) < __pyx_v_inode->split); + if (__pyx_t_3) { + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":490 * # set up children for searching * if x[inode.split_dim]less; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":460 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":491 * if x[inode.split_dim]greater; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":463 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":494 * else: * near = inode.greater * far = inode.less # <<<<<<<<<<<<<< @@ -3417,7 +4174,7 @@ } __pyx_L25:; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":468 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":499 * # we're going here next, so no point pushing it on the queue * # no need to recompute the distance or the side_distances * inf.node = near # <<<<<<<<<<<<<< @@ -3426,44 +4183,71 @@ */ __pyx_v_inf->node = __pyx_v_near; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":473 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":504 * # on the split value; compute its distance and side_distances * # and push it on the queue if it's near enough * inf2 = stdlib.malloc(sizeof(nodeinfo)+self.m*sizeof(double)) # <<<<<<<<<<<<<< * it2.contents.ptrdata = inf2 * inf2.node = far */ - __pyx_v_inf2 = ((struct __pyx_t_5scipy_7spatial_7ckdtree_nodeinfo *)malloc(((sizeof(struct __pyx_t_5scipy_7spatial_7ckdtree_nodeinfo)) + (__pyx_v_self->m * (sizeof(double)))))); - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":474 + __pyx_v_inf2 = ((struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_nodeinfo *)malloc(((sizeof(struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_nodeinfo)) + (__pyx_v_self->m * (sizeof(double)))))); + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":505 * # and push it on the queue if it's near enough * inf2 = stdlib.malloc(sizeof(nodeinfo)+self.m*sizeof(double)) * it2.contents.ptrdata = inf2 # <<<<<<<<<<<<<< * inf2.node = far - * # most side distances unchanged + * */ __pyx_v_it2.contents.ptrdata = ((char *)__pyx_v_inf2); - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":475 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":506 * inf2 = stdlib.malloc(sizeof(nodeinfo)+self.m*sizeof(double)) * it2.contents.ptrdata = inf2 * inf2.node = far # <<<<<<<<<<<<<< + * + * # Periodicity added by S Skory + */ + __pyx_v_inf2->node = __pyx_v_far; + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":510 + * # Periodicity added by S Skory + * m_left = dmin( dabs(far.mins[inode.split_dim] - x[inode.split_dim]), \ + * 1 - dabs(far.mins[inode.split_dim] - x[inode.split_dim])) # <<<<<<<<<<<<<< + * m_right = dmin( dabs(far.maxes[inode.split_dim] - x[inode.split_dim]), \ + * 1 - dabs(far.maxes[inode.split_dim] - x[inode.split_dim])) + */ + __pyx_v_m_left = __pyx_f_2yt_10extensions_7spatial_7ckdtree_dmin(__pyx_f_2yt_10extensions_7spatial_7ckdtree_dabs(((__pyx_v_far->mins[__pyx_v_inode->split_dim]) - (__pyx_v_x[__pyx_v_inode->split_dim]))), (1 - __pyx_f_2yt_10extensions_7spatial_7ckdtree_dabs(((__pyx_v_far->mins[__pyx_v_inode->split_dim]) - (__pyx_v_x[__pyx_v_inode->split_dim]))))); + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":512 + * 1 - dabs(far.mins[inode.split_dim] - x[inode.split_dim])) + * m_right = dmin( dabs(far.maxes[inode.split_dim] - x[inode.split_dim]), \ + * 1 - dabs(far.maxes[inode.split_dim] - x[inode.split_dim])) # <<<<<<<<<<<<<< + * m = dmin(m_left,m_right) + * + */ + __pyx_v_m_right = __pyx_f_2yt_10extensions_7spatial_7ckdtree_dmin(__pyx_f_2yt_10extensions_7spatial_7ckdtree_dabs(((__pyx_v_far->maxes[__pyx_v_inode->split_dim]) - (__pyx_v_x[__pyx_v_inode->split_dim]))), (1 - __pyx_f_2yt_10extensions_7spatial_7ckdtree_dabs(((__pyx_v_far->maxes[__pyx_v_inode->split_dim]) - (__pyx_v_x[__pyx_v_inode->split_dim]))))); + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":513 + * m_right = dmin( dabs(far.maxes[inode.split_dim] - x[inode.split_dim]), \ + * 1 - dabs(far.maxes[inode.split_dim] - x[inode.split_dim])) + * m = dmin(m_left,m_right) # <<<<<<<<<<<<<< + * * # most side distances unchanged - * for i in range(self.m): - */ - __pyx_v_inf2->node = __pyx_v_far; - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":477 - * inf2.node = far + */ + __pyx_v_m = __pyx_f_2yt_10extensions_7spatial_7ckdtree_dmin(__pyx_v_m_left, __pyx_v_m_right); + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":516 + * * # most side distances unchanged * for i in range(self.m): # <<<<<<<<<<<<<< * inf2.side_distances[i] = inf.side_distances[i] * */ - __pyx_2 = __pyx_v_self->m; - for (__pyx_v_i = 0; __pyx_v_i < __pyx_2; __pyx_v_i+=1) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":478 + for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_v_self->m; __pyx_t_2+=1) { + __pyx_v_i = __pyx_t_2; + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":517 * # most side distances unchanged * for i in range(self.m): * inf2.side_distances[i] = inf.side_distances[i] # <<<<<<<<<<<<<< @@ -3473,80 +4257,80 @@ (__pyx_v_inf2->side_distances[__pyx_v_i]) = (__pyx_v_inf->side_distances[__pyx_v_i]); } - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":482 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":521 * # one side distance changes * # we can adjust the minimum distance without recomputing * if p == infinity: # <<<<<<<<<<<<<< * # we never use side_distances in the l_infinity case * # inf2.side_distances[inode.split_dim] = dabs(inode.split-x[inode.split_dim]) */ - __pyx_3 = (__pyx_v_p == __pyx_v_5scipy_7spatial_7ckdtree_infinity); - if (__pyx_3) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":485 + __pyx_t_3 = (__pyx_v_p == __pyx_v_2yt_10extensions_7spatial_7ckdtree_infinity); + if (__pyx_t_3) { + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":524 * # we never use side_distances in the l_infinity case * # inf2.side_distances[inode.split_dim] = dabs(inode.split-x[inode.split_dim]) - * far_min_distance = dmax(min_distance, dabs(inode.split-x[inode.split_dim])) # <<<<<<<<<<<<<< + * far_min_distance = dmax(min_distance, m) # <<<<<<<<<<<<<< * elif p == 1: - * inf2.side_distances[inode.split_dim] = dabs(inode.split-x[inode.split_dim]) - */ - __pyx_v_far_min_distance = __pyx_f_5scipy_7spatial_7ckdtree_dmax(__pyx_v_min_distance, __pyx_f_5scipy_7spatial_7ckdtree_dabs((__pyx_v_inode->split - (__pyx_v_x[__pyx_v_inode->split_dim])))); + * inf2.side_distances[inode.split_dim] = m + */ + __pyx_v_far_min_distance = __pyx_f_2yt_10extensions_7spatial_7ckdtree_dmax(__pyx_v_min_distance, __pyx_v_m); goto __pyx_L28; } - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":486 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":525 * # inf2.side_distances[inode.split_dim] = dabs(inode.split-x[inode.split_dim]) - * far_min_distance = dmax(min_distance, dabs(inode.split-x[inode.split_dim])) + * far_min_distance = dmax(min_distance, m) * elif p == 1: # <<<<<<<<<<<<<< - * inf2.side_distances[inode.split_dim] = dabs(inode.split-x[inode.split_dim]) - * far_min_distance = min_distance - inf.side_distances[inode.split_dim] + inf2.side_distances[inode.split_dim] - */ - __pyx_3 = (__pyx_v_p == 1); - if (__pyx_3) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":487 - * far_min_distance = dmax(min_distance, dabs(inode.split-x[inode.split_dim])) + * inf2.side_distances[inode.split_dim] = m + * far_min_distance = dmax(min_distance, m) + */ + __pyx_t_3 = (__pyx_v_p == 1); + if (__pyx_t_3) { + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":526 + * far_min_distance = dmax(min_distance, m) * elif p == 1: - * inf2.side_distances[inode.split_dim] = dabs(inode.split-x[inode.split_dim]) # <<<<<<<<<<<<<< - * far_min_distance = min_distance - inf.side_distances[inode.split_dim] + inf2.side_distances[inode.split_dim] + * inf2.side_distances[inode.split_dim] = m # <<<<<<<<<<<<<< + * far_min_distance = dmax(min_distance, m) * else: */ - (__pyx_v_inf2->side_distances[__pyx_v_inode->split_dim]) = __pyx_f_5scipy_7spatial_7ckdtree_dabs((__pyx_v_inode->split - (__pyx_v_x[__pyx_v_inode->split_dim]))); - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":488 + (__pyx_v_inf2->side_distances[__pyx_v_inode->split_dim]) = __pyx_v_m; + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":527 * elif p == 1: - * inf2.side_distances[inode.split_dim] = dabs(inode.split-x[inode.split_dim]) - * far_min_distance = min_distance - inf.side_distances[inode.split_dim] + inf2.side_distances[inode.split_dim] # <<<<<<<<<<<<<< + * inf2.side_distances[inode.split_dim] = m + * far_min_distance = dmax(min_distance, m) # <<<<<<<<<<<<<< * else: - * inf2.side_distances[inode.split_dim] = dabs(inode.split-x[inode.split_dim])**p - */ - __pyx_v_far_min_distance = ((__pyx_v_min_distance - (__pyx_v_inf->side_distances[__pyx_v_inode->split_dim])) + (__pyx_v_inf2->side_distances[__pyx_v_inode->split_dim])); + * inf2.side_distances[inode.split_dim] = m**p + */ + __pyx_v_far_min_distance = __pyx_f_2yt_10extensions_7spatial_7ckdtree_dmax(__pyx_v_min_distance, __pyx_v_m); goto __pyx_L28; } /*else*/ { - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":490 - * far_min_distance = min_distance - inf.side_distances[inode.split_dim] + inf2.side_distances[inode.split_dim] + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":529 + * far_min_distance = dmax(min_distance, m) * else: - * inf2.side_distances[inode.split_dim] = dabs(inode.split-x[inode.split_dim])**p # <<<<<<<<<<<<<< - * far_min_distance = min_distance - inf.side_distances[inode.split_dim] + inf2.side_distances[inode.split_dim] - * - */ - (__pyx_v_inf2->side_distances[__pyx_v_inode->split_dim]) = pow(__pyx_f_5scipy_7spatial_7ckdtree_dabs((__pyx_v_inode->split - (__pyx_v_x[__pyx_v_inode->split_dim]))), __pyx_v_p); - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":491 - * else: - * inf2.side_distances[inode.split_dim] = dabs(inode.split-x[inode.split_dim])**p - * far_min_distance = min_distance - inf.side_distances[inode.split_dim] + inf2.side_distances[inode.split_dim] # <<<<<<<<<<<<<< + * inf2.side_distances[inode.split_dim] = m**p # <<<<<<<<<<<<<< + * #far_min_distance = min_distance - inf.side_distances[inode.split_dim] + inf2.side_distances[inode.split_dim] + * far_min_distance = m**p + */ + (__pyx_v_inf2->side_distances[__pyx_v_inode->split_dim]) = pow(__pyx_v_m, __pyx_v_p); + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":531 + * inf2.side_distances[inode.split_dim] = m**p + * #far_min_distance = min_distance - inf.side_distances[inode.split_dim] + inf2.side_distances[inode.split_dim] + * far_min_distance = m**p # <<<<<<<<<<<<<< * * it2.priority = far_min_distance */ - __pyx_v_far_min_distance = ((__pyx_v_min_distance - (__pyx_v_inf->side_distances[__pyx_v_inode->split_dim])) + (__pyx_v_inf2->side_distances[__pyx_v_inode->split_dim])); + __pyx_v_far_min_distance = pow(__pyx_v_m, __pyx_v_p); } __pyx_L28:; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":493 - * far_min_distance = min_distance - inf.side_distances[inode.split_dim] + inf2.side_distances[inode.split_dim] + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":533 + * far_min_distance = m**p * * it2.priority = far_min_distance # <<<<<<<<<<<<<< * @@ -3554,30 +4338,31 @@ */ __pyx_v_it2.priority = __pyx_v_far_min_distance; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":497 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":537 * * # far child might be too far, if so, don't bother pushing it * if far_min_distance<=distance_upper_bound*epsfac: # <<<<<<<<<<<<<< * heappush(&q,it2) * else: */ - __pyx_3 = (__pyx_v_far_min_distance <= (__pyx_v_distance_upper_bound * __pyx_v_epsfac)); - if (__pyx_3) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":498 + __pyx_t_3 = (__pyx_v_far_min_distance <= (__pyx_v_distance_upper_bound * __pyx_v_epsfac)); + if (__pyx_t_3) { + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":538 * # far child might be too far, if so, don't bother pushing it * if far_min_distance<=distance_upper_bound*epsfac: * heappush(&q,it2) # <<<<<<<<<<<<<< * else: * stdlib.free(inf2) */ - __pyx_1 = __pyx_f_5scipy_7spatial_7ckdtree_heappush((&__pyx_v_q), __pyx_v_it2); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 498; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - Py_DECREF(__pyx_1); __pyx_1 = 0; + __pyx_t_1 = __pyx_f_2yt_10extensions_7spatial_7ckdtree_heappush((&__pyx_v_q), __pyx_v_it2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 538; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; goto __pyx_L29; } /*else*/ { - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":500 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":540 * heappush(&q,it2) * else: * stdlib.free(inf2) # <<<<<<<<<<<<<< @@ -3586,7 +4371,7 @@ */ free(__pyx_v_inf2); - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":502 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":542 * stdlib.free(inf2) * # just in case * it2.contents.ptrdata = 0 # <<<<<<<<<<<<<< @@ -3599,27 +4384,28 @@ } __pyx_L15:; } - __pyx_L14:; - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":505 + __pyx_L14_break:; + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":545 * * # fill output arrays with sorted neighbors * for i in range(neighbors.n-1,-1,-1): # <<<<<<<<<<<<<< * neighbor = heappop(&neighbors) # FIXME: neighbors may be realloced * result_indices[i] = neighbor.contents.intdata */ - for (__pyx_v_i = (__pyx_v_neighbors.n - 1); __pyx_v_i > -1; __pyx_v_i-=1) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":506 + for (__pyx_t_2 = (__pyx_v_neighbors.n - 1); __pyx_t_2 > -1; __pyx_t_2-=1) { + __pyx_v_i = __pyx_t_2; + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":546 * # fill output arrays with sorted neighbors * for i in range(neighbors.n-1,-1,-1): * neighbor = heappop(&neighbors) # FIXME: neighbors may be realloced # <<<<<<<<<<<<<< * result_indices[i] = neighbor.contents.intdata * if p==1 or p==infinity: */ - __pyx_v_neighbor = __pyx_f_5scipy_7spatial_7ckdtree_heappop((&__pyx_v_neighbors)); - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":507 + __pyx_v_neighbor = __pyx_f_2yt_10extensions_7spatial_7ckdtree_heappop((&__pyx_v_neighbors)); + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":547 * for i in range(neighbors.n-1,-1,-1): * neighbor = heappop(&neighbors) # FIXME: neighbors may be realloced * result_indices[i] = neighbor.contents.intdata # <<<<<<<<<<<<<< @@ -3628,20 +4414,21 @@ */ (__pyx_v_result_indices[__pyx_v_i]) = __pyx_v_neighbor.contents.intdata; - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":508 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":548 * neighbor = heappop(&neighbors) # FIXME: neighbors may be realloced * result_indices[i] = neighbor.contents.intdata * if p==1 or p==infinity: # <<<<<<<<<<<<<< * result_distances[i] = -neighbor.priority * else: */ - __pyx_3 = (__pyx_v_p == 1); - if (!__pyx_3) { - __pyx_3 = (__pyx_v_p == __pyx_v_5scipy_7spatial_7ckdtree_infinity); - } - if (__pyx_3) { - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":509 + if (!(__pyx_v_p == 1)) { + __pyx_t_3 = (__pyx_v_p == __pyx_v_2yt_10extensions_7spatial_7ckdtree_infinity); + } else { + __pyx_t_3 = (__pyx_v_p == 1); + } + if (__pyx_t_3) { + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":549 * result_indices[i] = neighbor.contents.intdata * if p==1 or p==infinity: * result_distances[i] = -neighbor.priority # <<<<<<<<<<<<<< @@ -3653,68 +4440,76 @@ } /*else*/ { - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":511 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":551 * result_distances[i] = -neighbor.priority * else: * result_distances[i] = (-neighbor.priority)**(1./p) # <<<<<<<<<<<<<< * * heapdestroy(&q) */ - (__pyx_v_result_distances[__pyx_v_i]) = pow((-__pyx_v_neighbor.priority), (1. / __pyx_v_p)); + (__pyx_v_result_distances[__pyx_v_i]) = pow((-__pyx_v_neighbor.priority), (1.0 / __pyx_v_p)); } __pyx_L32:; } - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":513 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":553 * result_distances[i] = (-neighbor.priority)**(1./p) * * heapdestroy(&q) # <<<<<<<<<<<<<< * heapdestroy(&neighbors) * */ - __pyx_1 = __pyx_f_5scipy_7spatial_7ckdtree_heapdestroy((&__pyx_v_q)); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 513; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - Py_DECREF(__pyx_1); __pyx_1 = 0; - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":514 + __pyx_t_1 = __pyx_f_2yt_10extensions_7spatial_7ckdtree_heapdestroy((&__pyx_v_q)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 553; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":554 * * heapdestroy(&q) * heapdestroy(&neighbors) # <<<<<<<<<<<<<< * * def query(cKDTree self, object x, int k=1, double eps=0, double p=2, */ - __pyx_1 = __pyx_f_5scipy_7spatial_7ckdtree_heapdestroy((&__pyx_v_neighbors)); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - Py_DECREF(__pyx_1); __pyx_1 = 0; + __pyx_t_1 = __pyx_f_2yt_10extensions_7spatial_7ckdtree_heapdestroy((&__pyx_v_neighbors)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 554; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; goto __pyx_L0; __pyx_L1_error:; - Py_XDECREF(__pyx_1); - __Pyx_WriteUnraisable("scipy.spatial.ckdtree.cKDTree.__query"); + __Pyx_XDECREF(__pyx_t_1); + __Pyx_WriteUnraisable("yt.extensions.spatial.ckdtree.cKDTree.__query"); __pyx_L0:; + __Pyx_FinishRefcountContext(); } -/* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":516 +/* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":556 * heapdestroy(&neighbors) * * def query(cKDTree self, object x, int k=1, double eps=0, double p=2, # <<<<<<<<<<<<<< - * double distance_upper_bound=infinity): + * double distance_upper_bound=infinity, object period=None): * """query the kd-tree for nearest neighbors */ -static PyObject *__pyx_pf_5scipy_7spatial_7ckdtree_7cKDTree_query(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_5scipy_7spatial_7ckdtree_7cKDTree_query[] = "query the kd-tree for nearest neighbors\n\n Parameters:\n ===========\n\n x : array-like, last dimension self.m\n An array of points to query.\n k : integer\n The number of nearest neighbors to return.\n eps : nonnegative float\n Return approximate nearest neighbors; the kth returned value \n is guaranteed to be no further than (1+eps) times the \n distance to the real kth nearest neighbor.\n p : float, 1<=p<=infinity\n Which Minkowski p-norm to use. \n 1 is the sum-of-absolute-values \"Manhattan\" distance\n 2 is the usual Euclidean distance\n infinity is the maximum-coordinate-difference distance\n distance_upper_bound : nonnegative float\n Return only neighbors within this distance. This is used to prune\n tree searches, so if you are doing a series of nearest-neighbor\n queries, it may help to supply the distance to the nearest neighbor\n of the most recent point.\n\n Returns:\n ========\n \n d : array of floats\n The distances to the nearest neighbors. \n If x has shape tuple+(self.m,), then d has shape tuple+(k,).\n Missing neighbors are indicated with infinite distances.\n i : array of integers\n The locations of the neighbors in self.data.\n If x has shape tuple+(self.m,), then i has shape tuple+(k,).\n Missing neighbors are indicated with self.n.\n "; -static PyObject *__pyx_pf_5scipy_7spatial_7ckdtree_7cKDTree_query(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pf_2yt_10extensions_7spatial_7ckdtree_7cKDTree_query(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_2yt_10extensions_7spatial_7ckdtree_7cKDTree_query[] = "query the kd-tree for nearest neighbors\n\n Parameters:\n ===========\n\n x : array-like, last dimension self.m\n An array of points to query.\n k : integer\n The number of nearest neighbors to return.\n eps : nonnegative float\n Return approximate nearest neighbors; the kth returned value \n is guaranteed to be no further than (1+eps) times the \n distance to the real kth nearest neighbor.\n p : float, 1<=p<=infinity\n Which Minkowski p-norm to use. \n 1 is the sum-of-absolute-values \"Manhattan\" distance\n 2 is the usual Euclidean distance\n infinity is the maximum-coordinate-difference distance\n distance_upper_bound : nonnegative float\n Return only neighbors within this distance. This is used to prune\n tree searches, so if you are doing a series of nearest-neighbor\n queries, it may help to supply the distance to the nearest neighbor\n of the most recent point.\n\n Returns:\n ========\n \n d : array of floats\n The distances to the nearest neighbors. \n If x has shape tuple+(self.m,), then d has shape tuple+(k,).\n Missing neighbors are indicated with infinite distances.\n i : array of integers\n The locations of the neighbors in self.data.\n If x has shape tuple+(self.m,), then i has shape tuple+(k,).\n Missing neighbors are indicated with self.n.\n "; +static PyObject *__pyx_pf_2yt_10extensions_7spatial_7ckdtree_7cKDTree_query(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_x = 0; int __pyx_v_k; double __pyx_v_eps; double __pyx_v_p; double __pyx_v_distance_upper_bound; + PyObject *__pyx_v_period = 0; PyArrayObject *__pyx_v_ii; PyArrayObject *__pyx_v_dd; PyArrayObject *__pyx_v_xx; + PyArrayObject *__pyx_v_cperiod; int __pyx_v_c; PyObject *__pyx_v_single; PyObject *__pyx_v_retshape; PyObject *__pyx_v_n; + Py_buffer __pyx_bstruct_cperiod; + Py_ssize_t __pyx_bstride_0_cperiod = 0; + Py_ssize_t __pyx_bshape_0_cperiod = 0; Py_buffer __pyx_bstruct_ii; Py_ssize_t __pyx_bstride_0_ii = 0; Py_ssize_t __pyx_bstride_1_ii = 0; @@ -3730,35 +4525,35 @@ Py_ssize_t __pyx_bstride_1_dd = 0; Py_ssize_t __pyx_bshape_0_dd = 0; Py_ssize_t __pyx_bshape_1_dd = 0; - PyObject *__pyx_r; + PyObject *__pyx_r = NULL; PyObject *__pyx_1 = 0; PyObject *__pyx_2 = 0; - PyObject *__pyx_3 = 0; - int __pyx_4; - PyObject *__pyx_5 = 0; - Py_ssize_t __pyx_6 = 0; - PyObject *__pyx_7 = 0; - int __pyx_8; PyObject *__pyx_t_1 = NULL; - PyArrayObject *__pyx_t_2 = NULL; - int __pyx_t_3; - PyObject *__pyx_t_4 = NULL; + PyObject *__pyx_t_2 = NULL; + PyObject *__pyx_t_3 = NULL; + int __pyx_t_4; PyObject *__pyx_t_5 = NULL; PyArrayObject *__pyx_t_6 = NULL; - PyArrayObject *__pyx_t_7 = NULL; - long __pyx_t_8; - long __pyx_t_9; - long __pyx_t_10; - long __pyx_t_11; - static PyObject **__pyx_pyargnames[] = {&__pyx_kp_x,&__pyx_kp_k,&__pyx_kp_eps,&__pyx_kp_p,&__pyx_kp_23,0}; - __pyx_v_k = 1; - __pyx_v_eps = ((double)0); - __pyx_v_p = ((double)2); - __pyx_v_distance_upper_bound = __pyx_k_24; + int __pyx_t_7; + PyObject *__pyx_t_8 = NULL; + PyObject *__pyx_t_9 = NULL; + PyObject *__pyx_t_10 = NULL; + Py_ssize_t __pyx_t_11; + PyArrayObject *__pyx_t_12 = NULL; + PyArrayObject *__pyx_t_13 = NULL; + PyArrayObject *__pyx_t_14 = NULL; + long __pyx_t_15; + long __pyx_t_16; + long __pyx_t_17; + long __pyx_t_18; + static PyObject **__pyx_pyargnames[] = {&__pyx_kp_x,&__pyx_kp_k,&__pyx_kp_eps,&__pyx_kp_p,&__pyx_kp_31,&__pyx_kp_period,0}; + __Pyx_SetupRefcountContext("query"); if (unlikely(__pyx_kwds)) { - PyObject* values[5] = {0,0,0,0,0}; Py_ssize_t kw_args = PyDict_Size(__pyx_kwds); + PyObject* values[6] = {0,0,0,0,0,0}; + values[5] = Py_None; switch (PyTuple_GET_SIZE(__pyx_args)) { + case 6: values[5] = PyTuple_GET_ITEM(__pyx_args, 5); case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4); case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3); case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); @@ -3772,29 +4567,69 @@ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_kp_x); if (likely(values[0])) kw_args--; else goto __pyx_L5_argtuple_error; + case 1: + if (kw_args > 1) { + PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_kp_k); + if (unlikely(value)) { values[1] = value; kw_args--; } + } + case 2: + if (kw_args > 1) { + PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_kp_eps); + if (unlikely(value)) { values[2] = value; kw_args--; } + } + case 3: + if (kw_args > 1) { + PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_kp_p); + if (unlikely(value)) { values[3] = value; kw_args--; } + } + case 4: + if (kw_args > 1) { + PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_kp_31); + if (unlikely(value)) { values[4] = value; kw_args--; } + } + case 5: + if (kw_args > 1) { + PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_kp_period); + if (unlikely(value)) { values[5] = value; kw_args--; } + } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "query") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 516; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "query") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 556; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } __pyx_v_x = values[0]; if (values[1]) { - __pyx_v_k = __pyx_PyInt_int(values[1]); if (unlikely((__pyx_v_k == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 516; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_k = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_k == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 556; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + } else { + __pyx_v_k = 1; } if (values[2]) { - __pyx_v_eps = __pyx_PyFloat_AsDouble(values[2]); if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 516; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_eps = __pyx_PyFloat_AsDouble(values[2]); if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 556; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + } else { + __pyx_v_eps = ((double)0); } if (values[3]) { - __pyx_v_p = __pyx_PyFloat_AsDouble(values[3]); if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 516; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_p = __pyx_PyFloat_AsDouble(values[3]); if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 556; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + } else { + __pyx_v_p = ((double)2); } if (values[4]) { - __pyx_v_distance_upper_bound = __pyx_PyFloat_AsDouble(values[4]); if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 517; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - } + __pyx_v_distance_upper_bound = __pyx_PyFloat_AsDouble(values[4]); if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 557; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + } else { + __pyx_v_distance_upper_bound = __pyx_k_32; + } + __pyx_v_period = values[5]; } else { + __pyx_v_k = 1; + __pyx_v_eps = ((double)0); + __pyx_v_p = ((double)2); + __pyx_v_distance_upper_bound = __pyx_k_32; + __pyx_v_period = Py_None; switch (PyTuple_GET_SIZE(__pyx_args)) { - case 5: __pyx_v_distance_upper_bound = __pyx_PyFloat_AsDouble(PyTuple_GET_ITEM(__pyx_args, 4)); if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 517; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - case 4: __pyx_v_p = __pyx_PyFloat_AsDouble(PyTuple_GET_ITEM(__pyx_args, 3)); if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 516; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - case 3: __pyx_v_eps = __pyx_PyFloat_AsDouble(PyTuple_GET_ITEM(__pyx_args, 2)); if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 516; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - case 2: __pyx_v_k = __pyx_PyInt_int(PyTuple_GET_ITEM(__pyx_args, 1)); if (unlikely((__pyx_v_k == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 516; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + case 6: __pyx_v_period = PyTuple_GET_ITEM(__pyx_args, 5); + case 5: __pyx_v_distance_upper_bound = __pyx_PyFloat_AsDouble(PyTuple_GET_ITEM(__pyx_args, 4)); if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 557; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + case 4: __pyx_v_p = __pyx_PyFloat_AsDouble(PyTuple_GET_ITEM(__pyx_args, 3)); if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 556; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + case 3: __pyx_v_eps = __pyx_PyFloat_AsDouble(PyTuple_GET_ITEM(__pyx_args, 2)); if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 556; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + case 2: __pyx_v_k = __Pyx_PyInt_AsInt(PyTuple_GET_ITEM(__pyx_args, 1)); 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+ __pyx_t_1 = (!PyArray_CHKFLAGS(((PyArrayObject *)__pyx_v_self), NPY_F_CONTIGUOUS)); + } else { + __pyx_t_1 = ((__pyx_v_flags & PyBUF_F_CONTIGUOUS) == PyBUF_F_CONTIGUOUS); } - if (__pyx_1) { - - /* "/usr/data/david/local/lib64/python2.4/site-packages/Cython/Includes/numpy.pxd":69 + if (__pyx_t_1) { + + /* "/Library/Frameworks/Python.framework/Versions/4.1.30101/lib/python2.5/site-packages/Cython-0.11.2-py2.5-macosx-10.3-i386.egg/Cython/Includes/numpy.pxd":87 * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): * raise ValueError("ndarray is not Fortran contiguous") # <<<<<<<<<<<<<< * * info.buf = PyArray_DATA(self) */ - __pyx_2 = PyTuple_New(1); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - Py_INCREF(__pyx_kp_2); - PyTuple_SET_ITEM(__pyx_2, 0, __pyx_kp_2); - __pyx_3 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_2), NULL); if (unlikely(!__pyx_3)) {__pyx_filename = __pyx_f[1]; 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+ +static PyObject *__pyx_tp_new_2yt_10extensions_7spatial_7ckdtree_cKDTree(PyTypeObject *t, PyObject *a, PyObject *k) { + struct __pyx_obj_2yt_10extensions_7spatial_7ckdtree_cKDTree *p; PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; - p = ((struct __pyx_obj_5scipy_7spatial_7ckdtree_cKDTree *)o); - p->__pyx_vtab = __pyx_vtabptr_5scipy_7spatial_7ckdtree_cKDTree; + p = ((struct __pyx_obj_2yt_10extensions_7spatial_7ckdtree_cKDTree *)o); + p->__pyx_vtab = __pyx_vtabptr_2yt_10extensions_7spatial_7ckdtree_cKDTree; p->data = Py_None; Py_INCREF(Py_None); p->maxes = Py_None; Py_INCREF(Py_None); p->mins = Py_None; Py_INCREF(Py_None); @@ -5782,13 +7252,13 @@ return o; } -static void __pyx_tp_dealloc_5scipy_7spatial_7ckdtree_cKDTree(PyObject *o) { - struct __pyx_obj_5scipy_7spatial_7ckdtree_cKDTree *p = (struct __pyx_obj_5scipy_7spatial_7ckdtree_cKDTree *)o; +static void __pyx_tp_dealloc_2yt_10extensions_7spatial_7ckdtree_cKDTree(PyObject *o) { + struct __pyx_obj_2yt_10extensions_7spatial_7ckdtree_cKDTree *p = (struct __pyx_obj_2yt_10extensions_7spatial_7ckdtree_cKDTree *)o; { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); ++Py_REFCNT(o); - __pyx_pf_5scipy_7spatial_7ckdtree_7cKDTree___dealloc__(o); + __pyx_pf_2yt_10extensions_7spatial_7ckdtree_7cKDTree___dealloc__(o); if (PyErr_Occurred()) PyErr_WriteUnraisable(o); --Py_REFCNT(o); PyErr_Restore(etype, eval, etb); @@ -5800,9 +7270,9 @@ (*Py_TYPE(o)->tp_free)(o); } -static int __pyx_tp_traverse_5scipy_7spatial_7ckdtree_cKDTree(PyObject *o, visitproc v, void *a) { +static int __pyx_tp_traverse_2yt_10extensions_7spatial_7ckdtree_cKDTree(PyObject *o, visitproc v, void *a) { int e; - struct __pyx_obj_5scipy_7spatial_7ckdtree_cKDTree *p = (struct __pyx_obj_5scipy_7spatial_7ckdtree_cKDTree *)o; + struct __pyx_obj_2yt_10extensions_7spatial_7ckdtree_cKDTree *p = (struct __pyx_obj_2yt_10extensions_7spatial_7ckdtree_cKDTree *)o; if (p->data) { e = (*v)(p->data, a); if (e) return e; } @@ -5818,8 +7288,8 @@ return 0; } -static int __pyx_tp_clear_5scipy_7spatial_7ckdtree_cKDTree(PyObject *o) { - struct __pyx_obj_5scipy_7spatial_7ckdtree_cKDTree *p = (struct __pyx_obj_5scipy_7spatial_7ckdtree_cKDTree *)o; +static int __pyx_tp_clear_2yt_10extensions_7spatial_7ckdtree_cKDTree(PyObject *o) { + struct __pyx_obj_2yt_10extensions_7spatial_7ckdtree_cKDTree *p = (struct __pyx_obj_2yt_10extensions_7spatial_7ckdtree_cKDTree *)o; PyObject* tmp; tmp = ((PyObject*)p->data); p->data = Py_None; Py_INCREF(Py_None); @@ -5836,18 +7306,18 @@ return 0; } -static struct PyMethodDef __pyx_methods_5scipy_7spatial_7ckdtree_cKDTree[] = { - {"query", (PyCFunction)__pyx_pf_5scipy_7spatial_7ckdtree_7cKDTree_query, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5scipy_7spatial_7ckdtree_7cKDTree_query}, +static struct PyMethodDef __pyx_methods_2yt_10extensions_7spatial_7ckdtree_cKDTree[] = { + {__Pyx_NAMESTR("query"), (PyCFunction)__pyx_pf_2yt_10extensions_7spatial_7ckdtree_7cKDTree_query, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_2yt_10extensions_7spatial_7ckdtree_7cKDTree_query)}, {0, 0, 0, 0} }; -static struct PyMemberDef __pyx_members_5scipy_7spatial_7ckdtree_cKDTree[] = { - {"data", T_OBJECT, offsetof(struct __pyx_obj_5scipy_7spatial_7ckdtree_cKDTree, data), READONLY, 0}, - {"n", T_INT, offsetof(struct __pyx_obj_5scipy_7spatial_7ckdtree_cKDTree, n), READONLY, 0}, - {"m", T_INT, offsetof(struct __pyx_obj_5scipy_7spatial_7ckdtree_cKDTree, m), READONLY, 0}, - {"leafsize", T_INT, offsetof(struct __pyx_obj_5scipy_7spatial_7ckdtree_cKDTree, leafsize), READONLY, 0}, - {"maxes", T_OBJECT, offsetof(struct __pyx_obj_5scipy_7spatial_7ckdtree_cKDTree, maxes), READONLY, 0}, - {"mins", T_OBJECT, offsetof(struct __pyx_obj_5scipy_7spatial_7ckdtree_cKDTree, mins), READONLY, 0}, +static struct PyMemberDef __pyx_members_2yt_10extensions_7spatial_7ckdtree_cKDTree[] = { + {(char *)"data", T_OBJECT, offsetof(struct __pyx_obj_2yt_10extensions_7spatial_7ckdtree_cKDTree, data), READONLY, 0}, + {(char *)"n", T_INT, offsetof(struct __pyx_obj_2yt_10extensions_7spatial_7ckdtree_cKDTree, n), READONLY, 0}, + {(char *)"m", T_INT, offsetof(struct __pyx_obj_2yt_10extensions_7spatial_7ckdtree_cKDTree, m), READONLY, 0}, + {(char *)"leafsize", T_INT, offsetof(struct __pyx_obj_2yt_10extensions_7spatial_7ckdtree_cKDTree, leafsize), READONLY, 0}, + {(char *)"maxes", T_OBJECT, offsetof(struct __pyx_obj_2yt_10extensions_7spatial_7ckdtree_cKDTree, maxes), READONLY, 0}, + {(char *)"mins", T_OBJECT, offsetof(struct __pyx_obj_2yt_10extensions_7spatial_7ckdtree_cKDTree, mins), READONLY, 0}, {0, 0, 0, 0, 0} }; @@ -5875,7 +7345,11 @@ 0, /*nb_coerce*/ #endif 0, /*nb_int*/ + #if PY_MAJOR_VERSION >= 3 + 0, /*reserved*/ + #else 0, /*nb_long*/ + #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ @@ -5945,12 +7419,12 @@ #endif }; -PyTypeObject __pyx_type_5scipy_7spatial_7ckdtree_cKDTree = { +PyTypeObject __pyx_type_2yt_10extensions_7spatial_7ckdtree_cKDTree = { PyVarObject_HEAD_INIT(0, 0) - "scipy.spatial.ckdtree.cKDTree", /*tp_name*/ - sizeof(struct __pyx_obj_5scipy_7spatial_7ckdtree_cKDTree), /*tp_basicsize*/ + __Pyx_NAMESTR("yt.extensions.spatial.ckdtree.cKDTree"), /*tp_name*/ + sizeof(struct __pyx_obj_2yt_10extensions_7spatial_7ckdtree_cKDTree), /*tp_basicsize*/ 0, /*tp_itemsize*/ - __pyx_tp_dealloc_5scipy_7spatial_7ckdtree_cKDTree, /*tp_dealloc*/ + __pyx_tp_dealloc_2yt_10extensions_7spatial_7ckdtree_cKDTree, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ @@ -5966,24 +7440,24 @@ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_cKDTree, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ - "kd-tree for quick nearest-neighbor lookup\n\n This class provides an index into a set of k-dimensional points\n which can be used to rapidly look up the nearest neighbors of any\n point. \n\n The algorithm used is described in Maneewongvatana and Mount 1999. \n The general idea is that the kd-tree is a binary trie, each of whose\n nodes represents an axis-aligned hyperrectangle. Each node specifies\n an axis and splits the set of points based on whether their coordinate\n along that axis is greater than or less than a particular value. \n\n During construction, the axis and splitting point are chosen by the \n \"sliding midpoint\" rule, which ensures that the cells do not all\n become long and thin. \n\n The tree can be queried for the r closest neighbors of any given point \n (optionally returning only those within some maximum distance of the \n point). It can also be queried, with a substantial gain in efficiency, \n for the r approximate closest neighbors.\n\n For large dimensions (20 is already large) do not expect this to run \n significantly faster than brute force. High-dimensional nearest-neighbor\n queries are a substantial open problem in computer science.\n ", /*tp_doc*/ - __pyx_tp_traverse_5scipy_7spatial_7ckdtree_cKDTree, /*tp_traverse*/ - __pyx_tp_clear_5scipy_7spatial_7ckdtree_cKDTree, /*tp_clear*/ + __Pyx_DOCSTR("kd-tree for quick nearest-neighbor lookup\n\n This class provides an index into a set of k-dimensional points\n which can be used to rapidly look up the nearest neighbors of any\n point. \n\n The algorithm used is described in Maneewongvatana and Mount 1999. \n The general idea is that the kd-tree is a binary trie, each of whose\n nodes represents an axis-aligned hyperrectangle. Each node specifies\n an axis and splits the set of points based on whether their coordinate\n along that axis is greater than or less than a particular value. \n\n During construction, the axis and splitting point are chosen by the \n \"sliding midpoint\" rule, which ensures that the cells do not all\n become long and thin. \n\n The tree can be queried for the r closest neighbors of any given point \n (optionally returning only those within some maximum distance of the \n point). It can also be queried, with a substantial gain in efficiency, \n for the r approximate closest neighbors.\n\n For large dimensions (20 is already large) do not expect this to run \n significantly faster than brute force. High-dimensional nearest-neighbor\n queries are a substantial open problem in computer science.\n "), /*tp_doc*/ + __pyx_tp_traverse_2yt_10extensions_7spatial_7ckdtree_cKDTree, /*tp_traverse*/ + __pyx_tp_clear_2yt_10extensions_7spatial_7ckdtree_cKDTree, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ - __pyx_methods_5scipy_7spatial_7ckdtree_cKDTree, /*tp_methods*/ - __pyx_members_5scipy_7spatial_7ckdtree_cKDTree, /*tp_members*/ + __pyx_methods_2yt_10extensions_7spatial_7ckdtree_cKDTree, /*tp_methods*/ + __pyx_members_2yt_10extensions_7spatial_7ckdtree_cKDTree, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ - __pyx_pf_5scipy_7spatial_7ckdtree_7cKDTree___init__, /*tp_init*/ + __pyx_pf_2yt_10extensions_7spatial_7ckdtree_7cKDTree___init__, /*tp_init*/ 0, /*tp_alloc*/ - __pyx_tp_new_5scipy_7spatial_7ckdtree_cKDTree, /*tp_new*/ + __pyx_tp_new_2yt_10extensions_7spatial_7ckdtree_cKDTree, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ @@ -6002,7 +7476,7 @@ #if PY_MAJOR_VERSION >= 3 static struct PyModuleDef __pyx_moduledef = { PyModuleDef_HEAD_INIT, - "ckdtree", + __Pyx_NAMESTR("ckdtree"), 0, /* m_doc */ -1, /* m_size */ __pyx_methods /* m_methods */, @@ -6014,6 +7488,7 @@ #endif static __Pyx_StringTabEntry __pyx_string_tab[] = { + {&__pyx_kp___main__, __pyx_k___main__, sizeof(__pyx_k___main__), 1, 1, 1}, {&__pyx_kp___init__, __pyx_k___init__, sizeof(__pyx_k___init__), 1, 1, 1}, {&__pyx_kp___dealloc__, __pyx_k___dealloc__, sizeof(__pyx_k___dealloc__), 1, 1, 1}, {&__pyx_kp_query, __pyx_k_query, sizeof(__pyx_k_query), 1, 1, 1}, @@ -6023,12 +7498,14 @@ {&__pyx_kp_k, __pyx_k_k, sizeof(__pyx_k_k), 1, 1, 1}, {&__pyx_kp_eps, __pyx_k_eps, sizeof(__pyx_k_eps), 1, 1, 1}, {&__pyx_kp_p, __pyx_k_p, sizeof(__pyx_k_p), 1, 1, 1}, - {&__pyx_kp_23, __pyx_k_23, sizeof(__pyx_k_23), 1, 1, 1}, + {&__pyx_kp_31, __pyx_k_31, sizeof(__pyx_k_31), 1, 1, 1}, + {&__pyx_kp_period, __pyx_k_period, sizeof(__pyx_k_period), 1, 1, 1}, {&__pyx_kp_numpy, __pyx_k_numpy, sizeof(__pyx_k_numpy), 1, 1, 1}, {&__pyx_kp_np, __pyx_k_np, sizeof(__pyx_k_np), 0, 1, 1}, {&__pyx_kp_kdtree, __pyx_k_kdtree, sizeof(__pyx_k_kdtree), 1, 1, 1}, {&__pyx_kp_inf, __pyx_k_inf, sizeof(__pyx_k_inf), 1, 1, 1}, {&__pyx_kp_ValueError, __pyx_k_ValueError, sizeof(__pyx_k_ValueError), 1, 1, 1}, + {&__pyx_kp_range, __pyx_k_range, sizeof(__pyx_k_range), 1, 1, 1}, {&__pyx_kp_ascontiguousarray, __pyx_k_ascontiguousarray, sizeof(__pyx_k_ascontiguousarray), 1, 1, 1}, {&__pyx_kp_dtype, __pyx_k_dtype, sizeof(__pyx_k_dtype), 1, 1, 1}, {&__pyx_kp_float, __pyx_k_float, sizeof(__pyx_k_float), 1, 1, 1}, @@ -6037,39 +7514,40 @@ {&__pyx_kp_axis, __pyx_k_axis, sizeof(__pyx_k_axis), 1, 1, 1}, {&__pyx_kp_amin, __pyx_k_amin, sizeof(__pyx_k_amin), 1, 1, 1}, {&__pyx_kp_arange, __pyx_k_arange, sizeof(__pyx_k_arange), 1, 1, 1}, - {&__pyx_kp_27, __pyx_k_27, sizeof(__pyx_k_27), 1, 1, 1}, + {&__pyx_kp_35, __pyx_k_35, sizeof(__pyx_k_35), 1, 1, 1}, {&__pyx_kp_asarray, __pyx_k_asarray, sizeof(__pyx_k_asarray), 1, 1, 1}, {&__pyx_kp_astype, __pyx_k_astype, sizeof(__pyx_k_astype), 1, 1, 1}, + {&__pyx_kp_array, __pyx_k_array, sizeof(__pyx_k_array), 1, 1, 1}, {&__pyx_kp_newaxis, __pyx_k_newaxis, sizeof(__pyx_k_newaxis), 1, 1, 1}, {&__pyx_kp_prod, __pyx_k_prod, sizeof(__pyx_k_prod), 1, 1, 1}, {&__pyx_kp_reshape, __pyx_k_reshape, sizeof(__pyx_k_reshape), 1, 1, 1}, {&__pyx_kp_empty, __pyx_k_empty, sizeof(__pyx_k_empty), 1, 1, 1}, {&__pyx_kp_fill, __pyx_k_fill, sizeof(__pyx_k_fill), 1, 1, 1}, - {&__pyx_kp_30, __pyx_k_30, sizeof(__pyx_k_30), 0, 1, 0}, - {&__pyx_kp_25, __pyx_k_25, sizeof(__pyx_k_25), 0, 0, 0}, - {&__pyx_kp_26, __pyx_k_26, sizeof(__pyx_k_26), 0, 0, 0}, - {&__pyx_kp_28, __pyx_k_28, sizeof(__pyx_k_28), 0, 0, 0}, - {&__pyx_kp_29, __pyx_k_29, sizeof(__pyx_k_29), 0, 0, 0}, + {&__pyx_kp_38, __pyx_k_38, sizeof(__pyx_k_38), 0, 1, 0}, + {&__pyx_kp_33, __pyx_k_33, sizeof(__pyx_k_33), 0, 0, 0}, + {&__pyx_kp_34, __pyx_k_34, sizeof(__pyx_k_34), 0, 0, 0}, + {&__pyx_kp_36, __pyx_k_36, sizeof(__pyx_k_36), 0, 0, 0}, + {&__pyx_kp_37, __pyx_k_37, sizeof(__pyx_k_37), 0, 0, 0}, {&__pyx_kp___getbuffer__, __pyx_k___getbuffer__, sizeof(__pyx_k___getbuffer__), 1, 1, 1}, {&__pyx_kp___releasebuffer__, __pyx_k___releasebuffer__, sizeof(__pyx_k___releasebuffer__), 1, 1, 1}, {&__pyx_kp_info, __pyx_k_info, sizeof(__pyx_k_info), 1, 1, 1}, {&__pyx_kp_flags, __pyx_k_flags, sizeof(__pyx_k_flags), 1, 1, 1}, - {&__pyx_kp_iteritems, __pyx_k_iteritems, sizeof(__pyx_k_iteritems), 1, 1, 1}, - {&__pyx_kp_next, __pyx_k_next, sizeof(__pyx_k_next), 1, 1, 1}, - {&__pyx_kp_StopIteration, __pyx_k_StopIteration, sizeof(__pyx_k_StopIteration), 1, 1, 1}, - {&__pyx_kp_pop, __pyx_k_pop, sizeof(__pyx_k_pop), 1, 1, 1}, + {&__pyx_kp_itervalues, __pyx_k_itervalues, sizeof(__pyx_k_itervalues), 1, 1, 1}, {&__pyx_kp_RuntimeError, __pyx_k_RuntimeError, sizeof(__pyx_k_RuntimeError), 1, 1, 1}, {&__pyx_kp_1, __pyx_k_1, sizeof(__pyx_k_1), 0, 0, 0}, {&__pyx_kp_2, __pyx_k_2, sizeof(__pyx_k_2), 0, 0, 0}, - {&__pyx_kp_20, __pyx_k_20, sizeof(__pyx_k_20), 0, 0, 0}, - {&__pyx_kp_21, __pyx_k_21, sizeof(__pyx_k_21), 0, 0, 0}, - {&__pyx_kp_22, __pyx_k_22, sizeof(__pyx_k_22), 0, 0, 0}, + {&__pyx_kp_5, __pyx_k_5, sizeof(__pyx_k_5), 0, 0, 0}, + {&__pyx_kp_23, __pyx_k_23, sizeof(__pyx_k_23), 0, 0, 0}, + {&__pyx_kp_25, __pyx_k_25, sizeof(__pyx_k_25), 0, 0, 0}, + {&__pyx_kp_28, __pyx_k_28, sizeof(__pyx_k_28), 0, 0, 0}, + {&__pyx_kp_29, __pyx_k_29, sizeof(__pyx_k_29), 0, 0, 0}, + {&__pyx_kp_30, __pyx_k_30, sizeof(__pyx_k_30), 0, 0, 0}, {0, 0, 0, 0, 0, 0} }; static int __Pyx_InitCachedBuiltins(void) { __pyx_builtin_ValueError = __Pyx_GetName(__pyx_b, __pyx_kp_ValueError); if (!__pyx_builtin_ValueError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_builtin_StopIteration = __Pyx_GetName(__pyx_b, __pyx_kp_StopIteration); if (!__pyx_builtin_StopIteration) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 144; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_builtin_RuntimeError = __Pyx_GetName(__pyx_b, __pyx_kp_RuntimeError); if (!__pyx_builtin_RuntimeError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 158; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_range = __Pyx_GetName(__pyx_b, __pyx_kp_range); if (!__pyx_builtin_range) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 127; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_RuntimeError = __Pyx_GetName(__pyx_b, __pyx_kp_RuntimeError); if (!__pyx_builtin_RuntimeError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 292; __pyx_clineno = __LINE__; goto __pyx_L1_error;} return 0; __pyx_L1_error:; return -1; @@ -6077,6 +7555,8 @@ static int __Pyx_InitGlobals(void) { __pyx_int_0 = PyInt_FromLong(0); if (unlikely(!__pyx_int_0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_int_neg_1 = PyInt_FromLong(-1); if (unlikely(!__pyx_int_neg_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_int_15 = PyInt_FromLong(15); if (unlikely(!__pyx_int_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; if (__Pyx_InitStrings(__pyx_string_tab) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; return 0; __pyx_L1_error:; @@ -6092,16 +7572,33 @@ #endif { PyObject *__pyx_1 = 0; - PyObject *__pyx_2 = 0; - double __pyx_3; + PyObject *__pyx_t_1 = NULL; + double __pyx_t_2; + #ifdef CYTHON_REFNANNY + void* __pyx_refchk = NULL; + __Pyx_Refnanny = __Pyx_ImportRefcountAPI("refnanny"); + if (!__Pyx_Refnanny) { + PyErr_Clear(); + __Pyx_Refnanny = __Pyx_ImportRefcountAPI("Cython.Runtime.refnanny"); + if (!__Pyx_Refnanny) + Py_FatalError("failed to import refnanny module"); + } + __pyx_refchk = __Pyx_Refnanny->NewContext("PyMODINIT_FUNC PyInit_ckdtree(void)", __LINE__, __FILE__); + #endif __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;} /*--- Library function declarations ---*/ __pyx_init_filenames(); + /*--- Threads initialization code ---*/ + #if defined(__PYX_FORCE_INIT_THREADS) && __PYX_FORCE_INIT_THREADS + #ifdef WITH_THREAD /* Python build with threading support? */ + PyEval_InitThreads(); + #endif + #endif /*--- 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;} /*--- Module creation code ---*/ #if PY_MAJOR_VERSION < 3 - __pyx_m = Py_InitModule4("ckdtree", __pyx_methods, 0, 0, PYTHON_API_VERSION); + __pyx_m = Py_InitModule4(__Pyx_NAMESTR("ckdtree"), __pyx_methods, 0, 0, PYTHON_API_VERSION); #else __pyx_m = PyModule_Create(&__pyx_moduledef); #endif @@ -6109,30 +7606,39 @@ #if PY_MAJOR_VERSION < 3 Py_INCREF(__pyx_m); #endif - __pyx_b = PyImport_AddModule(__Pyx_BUILTIN_MODULE_NAME); + __pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__Pyx_BUILTIN_MODULE_NAME)); if (!__pyx_b) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; - if (PyObject_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + if (__Pyx_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + if (__pyx_module_is_main_yt__extensions__spatial__ckdtree) { + if (__Pyx_SetAttrString(__pyx_m, "__name__", __pyx_kp___main__) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + } /*--- Builtin init code ---*/ if (unlikely(__Pyx_InitCachedBuiltins() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_skip_dispatch = 0; /*--- Global init code ---*/ /*--- Function export code ---*/ /*--- Type init code ---*/ - __pyx_vtabptr_5scipy_7spatial_7ckdtree_cKDTree = &__pyx_vtable_5scipy_7spatial_7ckdtree_cKDTree; - *(void(**)(void))&__pyx_vtable_5scipy_7spatial_7ckdtree_cKDTree.__build = (void(*)(void))__pyx_f_5scipy_7spatial_7ckdtree_7cKDTree___build; - *(void(**)(void))&__pyx_vtable_5scipy_7spatial_7ckdtree_cKDTree.__free_tree = (void(*)(void))__pyx_f_5scipy_7spatial_7ckdtree_7cKDTree___free_tree; - *(void(**)(void))&__pyx_vtable_5scipy_7spatial_7ckdtree_cKDTree.__query = (void(*)(void))__pyx_f_5scipy_7spatial_7ckdtree_7cKDTree___query; - if (PyType_Ready(&__pyx_type_5scipy_7spatial_7ckdtree_cKDTree) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (__Pyx_SetVtable(__pyx_type_5scipy_7spatial_7ckdtree_cKDTree.tp_dict, __pyx_vtabptr_5scipy_7spatial_7ckdtree_cKDTree) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyObject_SetAttrString(__pyx_m, "cKDTree", (PyObject *)&__pyx_type_5scipy_7spatial_7ckdtree_cKDTree) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_5scipy_7spatial_7ckdtree_cKDTree = &__pyx_type_5scipy_7spatial_7ckdtree_cKDTree; + __pyx_vtabptr_2yt_10extensions_7spatial_7ckdtree_cKDTree = &__pyx_vtable_2yt_10extensions_7spatial_7ckdtree_cKDTree; + #if PY_MAJOR_VERSION >= 3 + __pyx_vtable_2yt_10extensions_7spatial_7ckdtree_cKDTree.__build = (struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_innernode *(*)(struct __pyx_obj_2yt_10extensions_7spatial_7ckdtree_cKDTree *, int, int, double *, double *))__pyx_f_2yt_10extensions_7spatial_7ckdtree_7cKDTree___build; + __pyx_vtable_2yt_10extensions_7spatial_7ckdtree_cKDTree.__free_tree = (PyObject *(*)(struct __pyx_obj_2yt_10extensions_7spatial_7ckdtree_cKDTree *, struct __pyx_t_2yt_10extensions_7spatial_7ckdtree_innernode *))__pyx_f_2yt_10extensions_7spatial_7ckdtree_7cKDTree___free_tree; + __pyx_vtable_2yt_10extensions_7spatial_7ckdtree_cKDTree.__query = (void (*)(struct __pyx_obj_2yt_10extensions_7spatial_7ckdtree_cKDTree *, double *, int *, double *, int, double, double, double, double *))__pyx_f_2yt_10extensions_7spatial_7ckdtree_7cKDTree___query; + #else + *(void(**)(void))&__pyx_vtable_2yt_10extensions_7spatial_7ckdtree_cKDTree.__build = (void(*)(void))__pyx_f_2yt_10extensions_7spatial_7ckdtree_7cKDTree___build; + *(void(**)(void))&__pyx_vtable_2yt_10extensions_7spatial_7ckdtree_cKDTree.__free_tree = (void(*)(void))__pyx_f_2yt_10extensions_7spatial_7ckdtree_7cKDTree___free_tree; + *(void(**)(void))&__pyx_vtable_2yt_10extensions_7spatial_7ckdtree_cKDTree.__query = (void(*)(void))__pyx_f_2yt_10extensions_7spatial_7ckdtree_7cKDTree___query; + #endif + if (PyType_Ready(&__pyx_type_2yt_10extensions_7spatial_7ckdtree_cKDTree) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 171; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_SetVtable(__pyx_type_2yt_10extensions_7spatial_7ckdtree_cKDTree.tp_dict, __pyx_vtabptr_2yt_10extensions_7spatial_7ckdtree_cKDTree) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 171; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_SetAttrString(__pyx_m, "cKDTree", (PyObject *)&__pyx_type_2yt_10extensions_7spatial_7ckdtree_cKDTree) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 171; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_2yt_10extensions_7spatial_7ckdtree_cKDTree = &__pyx_type_2yt_10extensions_7spatial_7ckdtree_cKDTree; /*--- Type import code ---*/ - __pyx_ptype_5numpy_dtype = __Pyx_ImportType("numpy", "dtype", sizeof(PyArray_Descr)); if (unlikely(!__pyx_ptype_5numpy_dtype)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 30; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_5numpy_ndarray = __Pyx_ImportType("numpy", "ndarray", sizeof(PyArrayObject)); if (unlikely(!__pyx_ptype_5numpy_ndarray)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5numpy_dtype = __Pyx_ImportType("numpy", "dtype", sizeof(PyArray_Descr)); if (unlikely(!__pyx_ptype_5numpy_dtype)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5numpy_ndarray = __Pyx_ImportType("numpy", "ndarray", sizeof(PyArrayObject)); if (unlikely(!__pyx_ptype_5numpy_ndarray)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 51; __pyx_clineno = __LINE__; goto __pyx_L1_error;} /*--- Function import code ---*/ /*--- Execution code ---*/ - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":3 + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":3 * # Copyright Anne M. Archibald 2008 * # Released under the scipy license * import numpy as np # <<<<<<<<<<<<<< @@ -6140,10 +7646,11 @@ * cimport stdlib */ __pyx_1 = __Pyx_Import(__pyx_kp_numpy, 0); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_1); if (PyObject_SetAttr(__pyx_m, __pyx_kp_np, __pyx_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - Py_DECREF(__pyx_1); __pyx_1 = 0; - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":7 + __Pyx_DECREF(__pyx_1); __pyx_1 = 0; + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":7 * cimport stdlib * * import kdtree # <<<<<<<<<<<<<< @@ -6151,10 +7658,11 @@ * cdef double infinity = np.inf */ __pyx_1 = __Pyx_Import(__pyx_kp_kdtree, 0); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 7; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_1); if (PyObject_SetAttr(__pyx_m, __pyx_kp_kdtree, __pyx_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 7; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - Py_DECREF(__pyx_1); __pyx_1 = 0; - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":9 + __Pyx_DECREF(__pyx_1); __pyx_1 = 0; + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":9 * import kdtree * * cdef double infinity = np.inf # <<<<<<<<<<<<<< @@ -6162,39 +7670,42 @@ * */ __pyx_1 = __Pyx_GetName(__pyx_m, __pyx_kp_np); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 9; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_2 = PyObject_GetAttr(__pyx_1, __pyx_kp_inf); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 9; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - Py_DECREF(__pyx_1); __pyx_1 = 0; - __pyx_3 = __pyx_PyFloat_AsDouble(__pyx_2); if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 9; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - Py_DECREF(__pyx_2); __pyx_2 = 0; - __pyx_v_5scipy_7spatial_7ckdtree_infinity = __pyx_3; - - /* "/usr/data/david/src/dsp/scipy/trunk/scipy/spatial/ckdtree.pyx":517 + __Pyx_GOTREF(__pyx_1); + __pyx_t_1 = PyObject_GetAttr(__pyx_1, __pyx_kp_inf); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 9; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_1); __pyx_1 = 0; + __pyx_t_2 = __pyx_PyFloat_AsDouble(__pyx_t_1); if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 9; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_v_2yt_10extensions_7spatial_7ckdtree_infinity = __pyx_t_2; + + /* "/Users/sskory/Documents/yt-devel/yt/extensions/spatial/ckdtree.pyx":557 * * def query(cKDTree self, object x, int k=1, double eps=0, double p=2, - * double distance_upper_bound=infinity): # <<<<<<<<<<<<<< + * double distance_upper_bound=infinity, object period=None): # <<<<<<<<<<<<<< * """query the kd-tree for nearest neighbors * */ - __pyx_k_24 = __pyx_v_5scipy_7spatial_7ckdtree_infinity; - - /* "/usr/data/david/local/lib64/python2.4/site-packages/Cython/Includes/stdlib.pxd":2 - * - * cdef extern from "stdlib.h": # <<<<<<<<<<<<<< - * ctypedef unsigned long size_t + __pyx_k_32 = __pyx_v_2yt_10extensions_7spatial_7ckdtree_infinity; + + /* "/Library/Frameworks/Python.framework/Versions/4.1.30101/lib/python2.5/site-packages/Cython-0.11.2-py2.5-macosx-10.3-i386.egg/Cython/Includes/stdlib.pxd":2 + * + * cdef extern from "stdlib.h" nogil: # <<<<<<<<<<<<<< * void free(void *ptr) - */ + * void *malloc(size_t size) + */ + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_1); + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("yt.extensions.spatial.ckdtree"); + Py_DECREF(__pyx_m); __pyx_m = 0; + __pyx_L0:; + __Pyx_FinishRefcountContext(); #if PY_MAJOR_VERSION < 3 return; #else return __pyx_m; #endif - __pyx_L1_error:; - Py_XDECREF(__pyx_1); - Py_XDECREF(__pyx_2); - __Pyx_AddTraceback("scipy.spatial.ckdtree"); - #if PY_MAJOR_VERSION >= 3 - return NULL; - #endif } static const char *__pyx_filenames[] = { @@ -6265,18 +7776,17 @@ PyObject*** first_kw_arg = argnames + num_pos_args; while (PyDict_Next(kwds, &pos, &key, &value)) { - #if PY_MAJOR_VERSION < 3 - if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key))) { - #else - if (unlikely(!PyUnicode_CheckExact(key)) && unlikely(!PyUnicode_Check(key))) { - #endif - goto invalid_keyword_type; + name = first_kw_arg; + while (*name && (**name != key)) name++; + if (*name) { + values[name-argnames] = value; } else { - name = argnames; - while (*name && (**name != key)) name++; - if (*name) { - if (name < first_kw_arg) goto arg_passed_twice; - values[name-argnames] = value; + #if PY_MAJOR_VERSION < 3 + if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key))) { + #else + if (unlikely(!PyUnicode_CheckExact(key)) && unlikely(!PyUnicode_Check(key))) { + #endif + goto invalid_keyword_type; } else { for (name = first_kw_arg; *name; name++) { #if PY_MAJOR_VERSION >= 3 @@ -6284,8 +7794,7 @@ PyUnicode_Compare(**name, key) == 0) break; #else if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) && - strcmp(PyString_AS_STRING(**name), - PyString_AS_STRING(key)) == 0) break; + _PyString_Eq(**name, key)) break; #endif } if (*name) { @@ -6299,8 +7808,7 @@ PyUnicode_Compare(**name, key) == 0) goto arg_passed_twice; #else if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) && - strcmp(PyString_AS_STRING(**name), - PyString_AS_STRING(key)) == 0) goto arg_passed_twice; + _PyString_Eq(**name, key)) goto arg_passed_twice; #endif } if (kwds2) { @@ -6333,10 +7841,413 @@ return -1; } -static INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info) { - if (info->buf == NULL) return; - if (info->suboffsets == __Pyx_minusones) info->suboffsets = NULL; - __Pyx_ReleaseBuffer(info); +static int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { + if (!type) { + PyErr_Format(PyExc_SystemError, "Missing type object"); + return 0; + } + if (obj == Py_None || PyObject_TypeCheck(obj, type)) + return 1; + PyErr_Format(PyExc_TypeError, "Cannot convert %s to %s", + Py_TYPE(obj)->tp_name, type->tp_name); + return 0; +} + +static INLINE int __Pyx_IsLittleEndian(void) { + unsigned int n = 1; + return *(unsigned char*)(&n) != 0; +} + +typedef struct { + __Pyx_StructField root; + __Pyx_BufFmt_StackElem* head; + size_t fmt_offset; + int new_count, enc_count; + int is_complex; + char enc_type; + char packmode; +} __Pyx_BufFmt_Context; + +static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx, + __Pyx_BufFmt_StackElem* stack, + __Pyx_TypeInfo* type) { + stack[0].field = &ctx->root; + stack[0].parent_offset = 0; + ctx->root.type = type; + ctx->root.name = "buffer dtype"; + ctx->root.offset = 0; + ctx->head = stack; + ctx->head->field = &ctx->root; + ctx->fmt_offset = 0; + ctx->head->parent_offset = 0; + ctx->packmode = '@'; + ctx->new_count = 1; + ctx->enc_count = 0; + ctx->enc_type = 0; + ctx->is_complex = 0; + while (type->typegroup == 'S') { + ++ctx->head; + ctx->head->field = type->fields; + ctx->head->parent_offset = 0; + type = type->fields->type; + } +} + +static int __Pyx_BufFmt_ParseNumber(const char** ts) { + int count; + const char* t = *ts; + if (*t < '0' || *t > '9') { + return -1; + } else { + count = *t++ - '0'; + while (*t >= '0' && *t < '9') { + count *= 10; + count += *t++ - '0'; + } + } + *ts = t; + return count; +} + +static void __Pyx_BufFmt_RaiseUnexpectedChar(char ch) { + char msg[] = {ch, 0}; + PyErr_Format(PyExc_ValueError, "Unexpected format string character: '%s'", msg); +} + +static const char* __Pyx_BufFmt_DescribeTypeChar(char ch, int is_complex) { + switch (ch) { + case 'b': return "'char'"; + case 'B': return "'unsigned char'"; + case 'h': return "'short'"; + case 'H': return "'unsigned short'"; + case 'i': return "'int'"; + case 'I': return "'unsigned int'"; + case 'l': return "'long'"; + case 'L': return "'unsigned long'"; + case 'q': return "'long long'"; + case 'Q': return "'unsigned long long'"; + case 'f': return (is_complex ? "'complex float'" : "'float'"); + case 'd': return (is_complex ? "'complex double'" : "'double'"); + case 'g': return (is_complex ? "'complex long double'" : "'long double'"); + case 'T': return "a struct"; + case 'O': return "Python object"; + case 'P': return "a pointer"; + case 0: return "end"; + default: return "unparseable format string"; + } +} + +static size_t __Pyx_BufFmt_TypeCharToStandardSize(char ch, int is_complex) { + switch (ch) { + case '?': case 'c': case 'b': case 'B': return 1; + case 'h': case 'H': return 2; + case 'i': case 'I': case 'l': case 'L': return 4; + case 'q': case 'Q': return 8; + case 'f': return (is_complex ? 8 : 4); + case 'd': return (is_complex ? 16 : 8); + case 'g': { + PyErr_SetString(PyExc_ValueError, "Python does not define a standard format string size for long double ('g').."); + return 0; + } + case 'O': case 'P': return sizeof(void*); + default: + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } +} + +static size_t __Pyx_BufFmt_TypeCharToNativeSize(char ch, int is_complex) { + switch (ch) { + case 'c': case 'b': case 'B': return 1; + case 'h': case 'H': return sizeof(short); + case 'i': case 'I': return sizeof(int); + case 'l': case 'L': return sizeof(long); + #ifdef HAVE_LONG_LONG + case 'q': case 'Q': return sizeof(PY_LONG_LONG); + #endif + case 'f': return sizeof(float) * (is_complex ? 2 : 1); + case 'd': return sizeof(double) * (is_complex ? 2 : 1); + case 'g': return sizeof(long double) * (is_complex ? 2 : 1); + case 'O': case 'P': return sizeof(void*); + default: { + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } + } +} + +typedef struct { char c; short x; } __Pyx_st_short; +typedef struct { char c; int x; } __Pyx_st_int; +typedef struct { char c; long x; } __Pyx_st_long; +typedef struct { char c; float x; } __Pyx_st_float; +typedef struct { char c; double x; } __Pyx_st_double; +typedef struct { char c; long double x; } __Pyx_st_longdouble; +typedef struct { char c; void *x; } __Pyx_st_void_p; +#ifdef HAVE_LONG_LONG +typedef struct { char c; PY_LONG_LONG x; } __Pyx_s_long_long; +#endif + +static size_t __Pyx_BufFmt_TypeCharToAlignment(char ch, int is_complex) { + switch (ch) { + case '?': case 'c': case 'b': case 'B': return 1; + case 'h': case 'H': return sizeof(__Pyx_st_short) - sizeof(short); + case 'i': case 'I': return sizeof(__Pyx_st_int) - sizeof(int); + case 'l': case 'L': return sizeof(__Pyx_st_long) - sizeof(long); +#ifdef HAVE_LONG_LONG + case 'q': case 'Q': return sizeof(__Pyx_s_long_long) - sizeof(PY_LONG_LONG); +#endif + case 'f': return sizeof(__Pyx_st_float) - sizeof(float); + case 'd': return sizeof(__Pyx_st_double) - sizeof(double); + case 'g': return sizeof(__Pyx_st_longdouble) - sizeof(long double); + case 'P': case 'O': return sizeof(__Pyx_st_void_p) - sizeof(void*); + default: + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } +} + +static size_t __Pyx_BufFmt_TypeCharToGroup(char ch, int is_complex) { + switch (ch) { + case 'c': case 'b': case 'h': case 'i': case 'l': case 'q': return 'I'; + case 'B': case 'H': case 'I': case 'L': case 'Q': return 'U'; + case 'f': case 'd': case 'g': return (is_complex ? 'C' : 'R'); + case 'O': return 'O'; + case 'P': return 'P'; + default: { + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } + } +} + +static void __Pyx_BufFmt_RaiseExpected(__Pyx_BufFmt_Context* ctx) { + if (ctx->head == NULL || ctx->head->field == &ctx->root) { + const char* expected; + const char* quote; + if (ctx->head == NULL) { + expected = "end"; + quote = ""; + } else { + expected = ctx->head->field->type->name; + quote = "'"; + } + PyErr_Format(PyExc_ValueError, + "Buffer dtype mismatch, expected %s%s%s but got %s", + quote, expected, quote, + __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex)); + } else { + __Pyx_StructField* field = ctx->head->field; + __Pyx_StructField* parent = (ctx->head - 1)->field; + PyErr_Format(PyExc_ValueError, + "Buffer dtype mismatch, expected '%s' but got %s in '%s.%s'", + field->type->name, __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex), + parent->type->name, field->name); + } +} + +static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) { + char group; + size_t size, offset; + if (ctx->enc_type == 0) return 0; + group = __Pyx_BufFmt_TypeCharToGroup(ctx->enc_type, ctx->is_complex); + do { + __Pyx_StructField* field = ctx->head->field; + __Pyx_TypeInfo* type = field->type; + + if (ctx->packmode == '@' || ctx->packmode == '^') { + size = __Pyx_BufFmt_TypeCharToNativeSize(ctx->enc_type, ctx->is_complex); + } else { + size = __Pyx_BufFmt_TypeCharToStandardSize(ctx->enc_type, ctx->is_complex); + } + if (ctx->packmode == '@') { + int align_at = __Pyx_BufFmt_TypeCharToAlignment(ctx->enc_type, ctx->is_complex); + int align_mod_offset; + if (align_at == 0) return -1; + align_mod_offset = ctx->fmt_offset % align_at; + if (align_mod_offset > 0) ctx->fmt_offset += align_at - align_mod_offset; + } + + if (type->size != size || type->typegroup != group) { + if (type->typegroup == 'C' && type->fields != NULL) { + /* special case -- treat as struct rather than complex number */ + size_t parent_offset = ctx->head->parent_offset + field->offset; + ++ctx->head; + ctx->head->field = type->fields; + ctx->head->parent_offset = parent_offset; + continue; + } + + __Pyx_BufFmt_RaiseExpected(ctx); + return -1; + } + + offset = ctx->head->parent_offset + field->offset; + if (ctx->fmt_offset != offset) { + PyErr_Format(PyExc_ValueError, + "Buffer dtype mismatch; next field is at offset %"PY_FORMAT_SIZE_T"d " + "but %"PY_FORMAT_SIZE_T"d expected", ctx->fmt_offset, offset); + return -1; + } + + ctx->fmt_offset += size; + + --ctx->enc_count; /* Consume from buffer string */ + + /* Done checking, move to next field, pushing or popping struct stack if needed */ + while (1) { + if (field == &ctx->root) { + ctx->head = NULL; + if (ctx->enc_count != 0) { + __Pyx_BufFmt_RaiseExpected(ctx); + return -1; + } + break; /* breaks both loops as ctx->enc_count == 0 */ + } + ctx->head->field = ++field; + if (field->type == NULL) { + --ctx->head; + field = ctx->head->field; + continue; + } else if (field->type->typegroup == 'S') { + size_t parent_offset = ctx->head->parent_offset + field->offset; + if (field->type->fields->type == NULL) continue; /* empty struct */ + field = field->type->fields; + ++ctx->head; + ctx->head->field = field; + ctx->head->parent_offset = parent_offset; + break; + } else { + break; + } + } + } while (ctx->enc_count); + ctx->enc_type = 0; + ctx->is_complex = 0; + return 0; +} + +static int __Pyx_BufFmt_FirstPack(__Pyx_BufFmt_Context* ctx) { + if (ctx->enc_type != 0 || ctx->packmode != '@') { + PyErr_SetString(PyExc_ValueError, "Buffer packing mode currently only allowed at beginning of format string (this is a defect)"); + return -1; + } + return 0; +} + +static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts) { + int got_Z = 0; + while (1) { + switch(*ts) { + case 0: + if (ctx->enc_type != 0 && ctx->head == NULL) { + __Pyx_BufFmt_RaiseExpected(ctx); + return NULL; + } + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + if (ctx->head != NULL) { + __Pyx_BufFmt_RaiseExpected(ctx); + return NULL; + } + return ts; + case ' ': + case 10: + case 13: + ++ts; + break; + case '<': + if (!__Pyx_IsLittleEndian()) { + PyErr_SetString(PyExc_ValueError, "Little-endian buffer not supported on big-endian compiler"); + return NULL; + } + if (__Pyx_BufFmt_FirstPack(ctx) == -1) return NULL; + ctx->packmode = '='; + ++ts; + break; + case '>': + case '!': + if (__Pyx_IsLittleEndian()) { + PyErr_SetString(PyExc_ValueError, "Big-endian buffer not supported on little-endian compiler"); + return NULL; + } + if (__Pyx_BufFmt_FirstPack(ctx) == -1) return NULL; + ctx->packmode = '='; + ++ts; + break; + case '=': + case '@': + case '^': + if (__Pyx_BufFmt_FirstPack(ctx) == -1) return NULL; + ctx->packmode = *ts++; + break; + case 'T': /* substruct */ + { + int i; + const char* ts_after_sub; + int struct_count = ctx->new_count; + ctx->new_count = 1; + ++ts; + if (*ts != '{') { + PyErr_SetString(PyExc_ValueError, "Buffer acquisition: Expected '{' after 'T'"); + return NULL; + } + ++ts; + ts_after_sub = ts; + for (i = 0; i != struct_count; ++i) { + ts_after_sub = __Pyx_BufFmt_CheckString(ctx, ts); + if (!ts_after_sub) return NULL; + } + ts = ts_after_sub; + } + break; + case '}': /* end of substruct; either repeat or move on */ + ++ts; + return ts; + case 'x': + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->fmt_offset += ctx->new_count; + ctx->new_count = 1; + ctx->enc_count = 0; + ctx->enc_type = 0; + ++ts; + break; + case 'Z': + got_Z = 1; + ++ts; + if (*ts != 'f' && *ts != 'd' && *ts != 'g') { + __Pyx_BufFmt_RaiseUnexpectedChar('Z'); + return NULL; + } /* fall through */ + case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I': + case 'l': case 'L': case 'q': case 'Q': + case 'f': case 'd': case 'g': + case 'O': + if (ctx->enc_type == *ts && got_Z == ctx->is_complex) { + /* Continue pooling same type */ + ctx->enc_count += ctx->new_count; + } else { + /* New type */ + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->enc_count = ctx->new_count; + ctx->enc_type = *ts; + ctx->is_complex = got_Z; + } + ++ts; + ctx->new_count = 1; + got_Z = 0; + break; + default: + { + ctx->new_count = __Pyx_BufFmt_ParseNumber(&ts); + if (ctx->new_count == -1) { /* First char was not a digit */ + char msg[2] = { *ts, 0 }; + PyErr_Format(PyExc_ValueError, + "Does not understand character buffer dtype format string ('%s')", msg); + return NULL; + } + } + + } + } } static INLINE void __Pyx_ZeroBuffer(Py_buffer* buf) { @@ -6347,81 +8258,7 @@ buf->suboffsets = __Pyx_minusones; } -static INLINE const char* __Pyx_ConsumeWhitespace(const char* ts) { - while (1) { - switch (*ts) { - case '@': - case 10: - case 13: - case ' ': - ++ts; - break; - case '=': - case '<': - case '>': - case '!': - PyErr_SetString(PyExc_ValueError, "Buffer acquisition error: Only native byte order, size and alignment supported."); - return NULL; - default: - return ts; - } - } -} - -static void __Pyx_BufferNdimError(Py_buffer* buffer, int expected_ndim) { - PyErr_Format(PyExc_ValueError, - "Buffer has wrong number of dimensions (expected %d, got %d)", - expected_ndim, buffer->ndim); -} - -static const char* __Pyx_DescribeTokenInFormatString(const char* ts) { - switch (*ts) { - case 'b': return "char"; - case 'B': return "unsigned char"; - case 'h': return "short"; - case 'H': return "unsigned short"; - case 'i': return "int"; - case 'I': return "unsigned int"; - case 'l': return "long"; - case 'L': return "unsigned long"; - case 'q': return "long long"; - case 'Q': return "unsigned long long"; - case 'f': return "float"; - case 'd': return "double"; - case 'g': return "long double"; - case 'Z': switch (*(ts+1)) { - case 'f': return "complex float"; - case 'd': return "complex double"; - case 'g': return "complex long double"; - default: return "unparseable format string"; - } - case 'T': return "a struct"; - case 'O': return "Python object"; - case 'P': return "a pointer"; - default: return "unparseable format string"; - } -} - -static const char* __Pyx_CheckTypestring_double(const char* ts) { - int ok; - ts = __Pyx_ConsumeWhitespace(ts); if (!ts) return NULL; - if (*ts == '1') ++ts; - switch (*ts) { - case 'f': ok = (sizeof(double) == sizeof(float) && (double)-1 < 0); break; - case 'd': ok = (sizeof(double) == sizeof(double) && (double)-1 < 0); break; - case 'g': ok = (sizeof(double) == sizeof(long double) && (double)-1 < 0); break; - default: ok = 0; - } - if (!(ok)) { - PyErr_Format(PyExc_ValueError, "Buffer dtype mismatch (expected double, got %s)", __Pyx_DescribeTokenInFormatString(ts)); - return NULL; - } - ++ts; - return ts; - } - -static int __Pyx_GetBuffer_double(PyObject* obj, Py_buffer* buf, int flags, int nd, int cast) { - const char* ts; +static int __Pyx_GetBufferAndValidate(Py_buffer* buf, PyObject* obj, __Pyx_TypeInfo* dtype, int flags, int nd, int cast, __Pyx_BufFmt_StackElem* stack) { if (obj == Py_None) { __Pyx_ZeroBuffer(buf); return 0; @@ -6429,29 +8266,23 @@ buf->buf = NULL; if (__Pyx_GetBuffer(obj, buf, flags) == -1) goto fail; if (buf->ndim != nd) { - __Pyx_BufferNdimError(buf, nd); + PyErr_Format(PyExc_ValueError, + "Buffer has wrong number of dimensions (expected %d, got %d)", + nd, buf->ndim); goto fail; } if (!cast) { - ts = buf->format; - ts = __Pyx_ConsumeWhitespace(ts); - if (!ts) goto fail; - ts = __Pyx_CheckTypestring_double(ts); - if (!ts) goto fail; - ts = __Pyx_ConsumeWhitespace(ts); - if (!ts) goto fail; - if (*ts != 0) { - PyErr_Format(PyExc_ValueError, - "Buffer dtype mismatch (expected end, got %s)", - __Pyx_DescribeTokenInFormatString(ts)); - goto fail; - } - } else { - if (buf->itemsize != sizeof(double)) { - PyErr_SetString(PyExc_ValueError, - "Attempted cast of buffer to datatype of different size."); - goto fail; - } + __Pyx_BufFmt_Context ctx; + __Pyx_BufFmt_Init(&ctx, stack, dtype); + if (!__Pyx_BufFmt_CheckString(&ctx, buf->format)) goto fail; + } + if ((unsigned)buf->itemsize != dtype->size) { + PyErr_Format(PyExc_ValueError, + "Item size of buffer (%"PY_FORMAT_SIZE_T"d byte%s) does not match size of '%s' (%"PY_FORMAT_SIZE_T"d byte%s)", + buf->itemsize, (buf->itemsize > 1) ? "s" : "", + dtype->name, + dtype->size, (dtype->size > 1) ? "s" : ""); + goto fail; } if (buf->suboffsets == NULL) buf->suboffsets = __Pyx_minusones; return 0; @@ -6459,74 +8290,40 @@ __Pyx_ZeroBuffer(buf); return -1; } + +static INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info) { + if (info->buf == NULL) return; + if (info->suboffsets == __Pyx_minusones) info->suboffsets = NULL; + __Pyx_ReleaseBuffer(info); +} + static void __Pyx_RaiseBufferFallbackError(void) { PyErr_Format(PyExc_ValueError, "Buffer acquisition failed on assignment; and then reacquiring the old buffer failed too!"); } -static const char* __Pyx_CheckTypestring_nn___pyx_t_5numpy_int32_t(const char* ts) { - int ok; - ts = __Pyx_ConsumeWhitespace(ts); if (!ts) return NULL; - if (*ts == '1') ++ts; - switch (*ts) { - case 'b': ok = (sizeof(__pyx_t_5numpy_int32_t) == sizeof(char) && (__pyx_t_5numpy_int32_t)-1 < 0); break; - case 'h': ok = (sizeof(__pyx_t_5numpy_int32_t) == sizeof(short) && (__pyx_t_5numpy_int32_t)-1 < 0); break; - case 'i': ok = (sizeof(__pyx_t_5numpy_int32_t) == sizeof(int) && (__pyx_t_5numpy_int32_t)-1 < 0); break; - case 'l': ok = (sizeof(__pyx_t_5numpy_int32_t) == sizeof(long) && (__pyx_t_5numpy_int32_t)-1 < 0); break; - case 'q': ok = (sizeof(__pyx_t_5numpy_int32_t) == sizeof(long long) && (__pyx_t_5numpy_int32_t)-1 < 0); break; - default: ok = 0; - } - if (!(ok)) { - PyErr_Format(PyExc_ValueError, "Buffer dtype mismatch (expected numpy.int32_t, got %s)", __Pyx_DescribeTokenInFormatString(ts)); - return NULL; - } - ++ts; - return ts; - } - -static int __Pyx_GetBuffer_nn___pyx_t_5numpy_int32_t(PyObject* obj, Py_buffer* buf, int flags, int nd, int cast) { - const char* ts; - if (obj == Py_None) { - __Pyx_ZeroBuffer(buf); - return 0; - } - buf->buf = NULL; - if (__Pyx_GetBuffer(obj, buf, flags) == -1) goto fail; - if (buf->ndim != nd) { - __Pyx_BufferNdimError(buf, nd); - goto fail; - } - if (!cast) { - ts = buf->format; - ts = __Pyx_ConsumeWhitespace(ts); - if (!ts) goto fail; - ts = __Pyx_CheckTypestring_nn___pyx_t_5numpy_int32_t(ts); - if (!ts) goto fail; - ts = __Pyx_ConsumeWhitespace(ts); - if (!ts) goto fail; - if (*ts != 0) { - PyErr_Format(PyExc_ValueError, - "Buffer dtype mismatch (expected end, got %s)", - __Pyx_DescribeTokenInFormatString(ts)); - goto fail; - } - } else { - if (buf->itemsize != sizeof(__pyx_t_5numpy_int32_t)) { - PyErr_SetString(PyExc_ValueError, - "Attempted cast of buffer to datatype of different size."); - goto fail; - } - } - if (buf->suboffsets == NULL) buf->suboffsets = __Pyx_minusones; - return 0; -fail:; - __Pyx_ZeroBuffer(buf); - return -1; -} + static INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) { PyObject *tmp_type, *tmp_value, *tmp_tb; PyThreadState *tstate = PyThreadState_GET(); +#if PY_MAJOR_VERSION >= 3 + /* Note: this is a temporary work-around to prevent crashes in Python 3.0 */ + if ((tstate->exc_type != NULL) & (tstate->exc_type != Py_None)) { + tmp_type = tstate->exc_type; + tmp_value = tstate->exc_value; + tmp_tb = tstate->exc_traceback; + PyErr_NormalizeException(&type, &value, &tb); + PyErr_NormalizeException(&tmp_type, &tmp_value, &tmp_tb); + tstate->exc_type = 0; + tstate->exc_value = 0; + tstate->exc_traceback = 0; + PyException_SetContext(value, tmp_value); + Py_DECREF(tmp_type); + Py_XDECREF(tmp_tb); + } +#endif + tmp_type = tstate->curexc_type; tmp_value = tstate->curexc_value; tmp_tb = tstate->curexc_traceback; @@ -6550,65 +8347,7 @@ } -static const char* __Pyx_CheckTypestring_int(const char* ts) { - int ok; - ts = __Pyx_ConsumeWhitespace(ts); if (!ts) return NULL; - if (*ts == '1') ++ts; - switch (*ts) { - case 'b': ok = (sizeof(int) == sizeof(char) && (int)-1 < 0); break; - case 'h': ok = (sizeof(int) == sizeof(short) && (int)-1 < 0); break; - case 'i': ok = (sizeof(int) == sizeof(int) && (int)-1 < 0); break; - case 'l': ok = (sizeof(int) == sizeof(long) && (int)-1 < 0); break; - case 'q': ok = (sizeof(int) == sizeof(long long) && (int)-1 < 0); break; - default: ok = 0; - } - if (!(ok)) { - PyErr_Format(PyExc_ValueError, "Buffer dtype mismatch (expected int, got %s)", __Pyx_DescribeTokenInFormatString(ts)); - return NULL; - } - ++ts; - return ts; - } - -static int __Pyx_GetBuffer_int(PyObject* obj, Py_buffer* buf, int flags, int nd, int cast) { - const char* ts; - if (obj == Py_None) { - __Pyx_ZeroBuffer(buf); - return 0; - } - buf->buf = NULL; - if (__Pyx_GetBuffer(obj, buf, flags) == -1) goto fail; - if (buf->ndim != nd) { - __Pyx_BufferNdimError(buf, nd); - goto fail; - } - if (!cast) { - ts = buf->format; - ts = __Pyx_ConsumeWhitespace(ts); - if (!ts) goto fail; - ts = __Pyx_CheckTypestring_int(ts); - if (!ts) goto fail; - ts = __Pyx_ConsumeWhitespace(ts); - if (!ts) goto fail; - if (*ts != 0) { - PyErr_Format(PyExc_ValueError, - "Buffer dtype mismatch (expected end, got %s)", - __Pyx_DescribeTokenInFormatString(ts)); - goto fail; - } - } else { - if (buf->itemsize != sizeof(int)) { - PyErr_SetString(PyExc_ValueError, - "Attempted cast of buffer to datatype of different size."); - goto fail; - } - } - if (buf->suboffsets == NULL) buf->suboffsets = __Pyx_minusones; - return 0; -fail:; - __Pyx_ZeroBuffer(buf); - return -1; -}static void __Pyx_RaiseBufferIndexError(int axis) { +static void __Pyx_RaiseBufferIndexError(int axis) { PyErr_Format(PyExc_IndexError, "Out of bounds on buffer access (axis %d)", axis); } @@ -6645,7 +8384,7 @@ PyObject *global_dict = 0; PyObject *empty_dict = 0; PyObject *list; - __import__ = PyObject_GetAttrString(__pyx_b, "__import__"); + __import__ = __Pyx_GetAttrString(__pyx_b, "__import__"); if (!__import__) goto bad; if (from_list) @@ -6662,8 +8401,8 @@ empty_dict = PyDict_New(); if (!empty_dict) goto bad; - module = PyObject_CallFunction(__import__, "OOOO", - name, global_dict, empty_dict, list); + module = PyObject_CallFunctionObjArgs(__import__, + name, global_dict, empty_dict, list, NULL); bad: Py_XDECREF(empty_list); Py_XDECREF(__import__); @@ -6743,16 +8482,25 @@ return; } +static INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { + PyErr_Format(PyExc_ValueError, + #if PY_VERSION_HEX < 0x02050000 + "need more than %d value%s to unpack", (int)index, + #else + "need more than %zd value%s to unpack", index, + #endif + (index == 1) ? "" : "s"); +} + +static INLINE void __Pyx_RaiseTooManyValuesError(void) { + PyErr_SetString(PyExc_ValueError, "too many values to unpack"); +} + static PyObject *__Pyx_UnpackItem(PyObject *iter, Py_ssize_t index) { PyObject *item; if (!(item = PyIter_Next(iter))) { if (!PyErr_Occurred()) { - PyErr_Format(PyExc_ValueError, - #if PY_VERSION_HEX < 0x02050000 - "need more than %d values to unpack", (int)index); - #else - "need more than %zd values to unpack", index); - #endif + __Pyx_RaiseNeedMoreValuesError(index); } } return item; @@ -6762,7 +8510,7 @@ PyObject *item; if ((item = PyIter_Next(iter))) { Py_DECREF(item); - PyErr_SetString(PyExc_ValueError, "too many values to unpack"); + __Pyx_RaiseTooManyValuesError(); return -1; } else if (!PyErr_Occurred()) @@ -6771,71 +8519,294 @@ return -1; } -static int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { - if (!type) { - PyErr_Format(PyExc_SystemError, "Missing type object"); - return 0; - } - if (obj == Py_None || PyObject_TypeCheck(obj, type)) - return 1; - PyErr_Format(PyExc_TypeError, "Cannot convert %s to %s", - Py_TYPE(obj)->tp_name, type->tp_name); - return 0; +static INLINE int __Pyx_StrEq(const char *s1, const char *s2) { + while (*s1 != '\0' && *s1 == *s2) { s1++; s2++; } + return *s1 == *s2; } -static INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) { - PyThreadState *tstate = PyThreadState_GET(); - *type = tstate->exc_type; - *value = tstate->exc_value; - *tb = tstate->exc_traceback; - Py_XINCREF(*type); - Py_XINCREF(*value); - Py_XINCREF(*tb); +static INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { + if (sizeof(unsigned char) < sizeof(long)) { + long val = __Pyx_PyInt_AsLong(x); + if (unlikely(val != (long)(unsigned char)val)) { + if (unlikely(val == -1 && PyErr_Occurred())) + return (unsigned char)-1; + if (unlikely(val < 0)) { + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to unsigned char"); + return (unsigned char)-1; + } + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to unsigned char"); + return (unsigned char)-1; + } + return (unsigned char)val; + } + return (unsigned char)__Pyx_PyInt_AsUnsignedLong(x); } -static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - PyThreadState *tstate = PyThreadState_GET(); - tmp_type = tstate->exc_type; - tmp_value = tstate->exc_value; - tmp_tb = tstate->exc_traceback; - tstate->exc_type = type; - tstate->exc_value = value; - tstate->exc_traceback = tb; - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); +static INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) { + if (sizeof(unsigned short) < sizeof(long)) { + long val = __Pyx_PyInt_AsLong(x); + if (unlikely(val != (long)(unsigned short)val)) { + if (unlikely(val == -1 && PyErr_Occurred())) + return (unsigned short)-1; + if (unlikely(val < 0)) { + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to unsigned short"); + return (unsigned short)-1; + } + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to unsigned short"); + return (unsigned short)-1; + } + return (unsigned short)val; + } + return (unsigned short)__Pyx_PyInt_AsUnsignedLong(x); } -static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - PyThreadState *tstate = PyThreadState_GET(); - __Pyx_ErrFetch(type, value, tb); - PyErr_NormalizeException(type, value, tb); - if (PyErr_Occurred()) - goto bad; - Py_INCREF(*type); - Py_INCREF(*value); - Py_INCREF(*tb); - tmp_type = tstate->exc_type; - tmp_value = tstate->exc_value; - tmp_tb = tstate->exc_traceback; - tstate->exc_type = *type; - tstate->exc_value = *value; - tstate->exc_traceback = *tb; - /* Make sure tstate is in a consistent state when we XDECREF - these objects (XDECREF may run arbitrary code). */ - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); - return 0; -bad: - Py_XDECREF(*type); - Py_XDECREF(*value); - Py_XDECREF(*tb); - return -1; +static INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) { + if (sizeof(unsigned int) < sizeof(long)) { + long val = __Pyx_PyInt_AsLong(x); + if (unlikely(val != (long)(unsigned int)val)) { + if (unlikely(val == -1 && PyErr_Occurred())) + return (unsigned int)-1; + if (unlikely(val < 0)) { + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to unsigned int"); + return (unsigned int)-1; + } + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to unsigned int"); + return (unsigned int)-1; + } + return (unsigned int)val; + } + return (unsigned int)__Pyx_PyInt_AsUnsignedLong(x); } +static INLINE char __Pyx_PyInt_AsChar(PyObject* x) { + if (sizeof(char) < sizeof(long)) { + long val = __Pyx_PyInt_AsLong(x); + if (unlikely(val != (long)(char)val)) { + if (unlikely(val == -1 && PyErr_Occurred())) + return (char)-1; + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to char"); + return (char)-1; + } + return (char)val; + } + return (char)__Pyx_PyInt_AsLong(x); +} + +static INLINE short __Pyx_PyInt_AsShort(PyObject* x) { + if (sizeof(short) < sizeof(long)) { + long val = __Pyx_PyInt_AsLong(x); + if (unlikely(val != (long)(short)val)) { + if (unlikely(val == -1 && PyErr_Occurred())) + return (short)-1; + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to short"); + return (short)-1; + } + return (short)val; + } + return (short)__Pyx_PyInt_AsLong(x); +} + +static INLINE int __Pyx_PyInt_AsInt(PyObject* x) { + if (sizeof(int) < sizeof(long)) { + long val = __Pyx_PyInt_AsLong(x); + if (unlikely(val != (long)(int)val)) { + if (unlikely(val == -1 && PyErr_Occurred())) + return (int)-1; + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to int"); + return (int)-1; + } + return (int)val; + } + return (int)__Pyx_PyInt_AsLong(x); +} + +static INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) { + if (sizeof(signed char) < sizeof(long)) { + long val = __Pyx_PyInt_AsLong(x); + if (unlikely(val != (long)(signed char)val)) { + if (unlikely(val == -1 && PyErr_Occurred())) + return (signed char)-1; + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to signed char"); + return (signed char)-1; + } + return (signed char)val; + } + return (signed char)__Pyx_PyInt_AsSignedLong(x); +} + +static INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) { + if (sizeof(signed short) < sizeof(long)) { + long val = __Pyx_PyInt_AsLong(x); + if (unlikely(val != (long)(signed short)val)) { + if (unlikely(val == -1 && PyErr_Occurred())) + return (signed short)-1; + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to signed short"); + return (signed short)-1; + } + return (signed short)val; + } + return (signed short)__Pyx_PyInt_AsSignedLong(x); +} + +static INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) { + if (sizeof(signed int) < sizeof(long)) { + long val = __Pyx_PyInt_AsLong(x); + if (unlikely(val != (long)(signed int)val)) { + if (unlikely(val == -1 && PyErr_Occurred())) + return (signed int)-1; + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to signed int"); + return (signed int)-1; + } + return (signed int)val; + } + return (signed int)__Pyx_PyInt_AsSignedLong(x); +} + +static INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) { +#if PY_VERSION_HEX < 0x03000000 + if (likely(PyInt_CheckExact(x) || PyInt_Check(x))) { + long val = PyInt_AS_LONG(x); + if (unlikely(val < 0)) { + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to unsigned long"); + return (unsigned long)-1; + } + return (unsigned long)val; + } else +#endif + if (likely(PyLong_CheckExact(x) || PyLong_Check(x))) { + if (unlikely(Py_SIZE(x) < 0)) { + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to unsigned long"); + return (unsigned long)-1; + } + return PyLong_AsUnsignedLong(x); + } else { + unsigned long val; + PyObject *tmp = __Pyx_PyNumber_Int(x); + if (!tmp) return (unsigned long)-1; + val = __Pyx_PyInt_AsUnsignedLong(tmp); + Py_DECREF(tmp); + return val; + } +} + +static INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) { +#if PY_VERSION_HEX < 0x03000000 + if (likely(PyInt_CheckExact(x) || PyInt_Check(x))) { + long val = PyInt_AS_LONG(x); + if (unlikely(val < 0)) { + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to unsigned PY_LONG_LONG"); + return (unsigned PY_LONG_LONG)-1; + } + return (unsigned PY_LONG_LONG)val; + } else +#endif + if (likely(PyLong_CheckExact(x) || PyLong_Check(x))) { + if (unlikely(Py_SIZE(x) < 0)) { + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to unsigned PY_LONG_LONG"); + return (unsigned PY_LONG_LONG)-1; + } + return PyLong_AsUnsignedLongLong(x); + } else { + unsigned PY_LONG_LONG val; + PyObject *tmp = __Pyx_PyNumber_Int(x); + if (!tmp) return (unsigned PY_LONG_LONG)-1; + val = __Pyx_PyInt_AsUnsignedLongLong(tmp); + Py_DECREF(tmp); + return val; + } +} + +static INLINE long __Pyx_PyInt_AsLong(PyObject* x) { +#if PY_VERSION_HEX < 0x03000000 + if (likely(PyInt_CheckExact(x) || PyInt_Check(x))) { + long val = PyInt_AS_LONG(x); + return (long)val; + } else +#endif + if (likely(PyLong_CheckExact(x) || PyLong_Check(x))) { + return PyLong_AsLong(x); + } else { + long val; + PyObject *tmp = __Pyx_PyNumber_Int(x); + if (!tmp) return (long)-1; + val = __Pyx_PyInt_AsLong(tmp); + Py_DECREF(tmp); + return val; + } +} + +static INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { +#if PY_VERSION_HEX < 0x03000000 + if (likely(PyInt_CheckExact(x) || PyInt_Check(x))) { + long val = PyInt_AS_LONG(x); + return (PY_LONG_LONG)val; + } else +#endif + if (likely(PyLong_CheckExact(x) || PyLong_Check(x))) { + return PyLong_AsLongLong(x); + } else { + PY_LONG_LONG val; + PyObject *tmp = __Pyx_PyNumber_Int(x); + if (!tmp) return (PY_LONG_LONG)-1; + val = __Pyx_PyInt_AsLongLong(tmp); + Py_DECREF(tmp); + return val; + } +} + +static INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) { +#if PY_VERSION_HEX < 0x03000000 + if (likely(PyInt_CheckExact(x) || PyInt_Check(x))) { + long val = PyInt_AS_LONG(x); + return (signed long)val; + } else +#endif + if (likely(PyLong_CheckExact(x) || PyLong_Check(x))) { + return PyLong_AsLong(x); + } else { + signed long val; + PyObject *tmp = __Pyx_PyNumber_Int(x); + if (!tmp) return (signed long)-1; + val = __Pyx_PyInt_AsSignedLong(tmp); + Py_DECREF(tmp); + return val; + } +} + +static INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) { +#if PY_VERSION_HEX < 0x03000000 + if (likely(PyInt_CheckExact(x) || PyInt_Check(x))) { + long val = PyInt_AS_LONG(x); + return (signed PY_LONG_LONG)val; + } else +#endif + if (likely(PyLong_CheckExact(x) || PyLong_Check(x))) { + return PyLong_AsLongLong(x); + } else { + signed PY_LONG_LONG val; + PyObject *tmp = __Pyx_PyNumber_Int(x); + if (!tmp) return (signed PY_LONG_LONG)-1; + val = __Pyx_PyInt_AsSignedLongLong(tmp); + Py_DECREF(tmp); + return val; + } +} static void __Pyx_WriteUnraisable(const char *name) { PyObject *old_exc, *old_val, *old_tb; @@ -7048,7 +9019,59 @@ /* Type Conversion Functions */ -static INLINE Py_ssize_t __pyx_PyIndex_AsSsize_t(PyObject* b) { +static INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { + if (x == Py_True) return 1; + else if ((x == Py_False) | (x == Py_None)) return 0; + else return PyObject_IsTrue(x); +} + +static INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) { + PyNumberMethods *m; + const char *name = NULL; + PyObject *res = NULL; +#if PY_VERSION_HEX < 0x03000000 + if (PyInt_Check(x) || PyLong_Check(x)) +#else + if (PyLong_Check(x)) +#endif + return Py_INCREF(x), x; + m = Py_TYPE(x)->tp_as_number; +#if PY_VERSION_HEX < 0x03000000 + if (m && m->nb_int) { + name = "int"; + res = PyNumber_Int(x); + } + else if (m && m->nb_long) { + name = "long"; + res = PyNumber_Long(x); + } +#else + if (m && m->nb_int) { + name = "int"; + res = PyNumber_Long(x); + } +#endif + if (res) { +#if PY_VERSION_HEX < 0x03000000 + if (!PyInt_Check(res) && !PyLong_Check(res)) { +#else + if (!PyLong_Check(res)) { +#endif + PyErr_Format(PyExc_TypeError, + "__%s__ returned non-%s (type %.200s)", + name, name, Py_TYPE(res)->tp_name); + Py_DECREF(res); + return NULL; + } + } + else if (!PyErr_Occurred()) { + PyErr_SetString(PyExc_TypeError, + "an integer is required"); + } + return res; +} + +static INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { Py_ssize_t ival; PyObject* x = PyNumber_Index(b); if (!x) return -1; @@ -7057,212 +9080,30 @@ return ival; } -static INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { - if (x == Py_True) return 1; - else if (x == Py_False) return 0; - else return PyObject_IsTrue(x); +static INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { +#if PY_VERSION_HEX < 0x02050000 + if (ival <= LONG_MAX) + return PyInt_FromLong((long)ival); + else { + unsigned char *bytes = (unsigned char *) &ival; + int one = 1; int little = (int)*(unsigned char*)&one; + return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0); + } +#else + return PyInt_FromSize_t(ival); +#endif } -static INLINE PY_LONG_LONG __pyx_PyInt_AsLongLong(PyObject* x) { - if (PyInt_CheckExact(x)) { - return PyInt_AS_LONG(x); - } - else if (PyLong_CheckExact(x)) { - return PyLong_AsLongLong(x); - } - else { - PY_LONG_LONG val; - PyObject* tmp = PyNumber_Int(x); if (!tmp) return (PY_LONG_LONG)-1; - val = __pyx_PyInt_AsLongLong(tmp); - Py_DECREF(tmp); - return val; - } +static INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { + unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x); + if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) { + return (size_t)-1; + } else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) { + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to size_t"); + return (size_t)-1; + } + return (size_t)val; } -static INLINE unsigned PY_LONG_LONG __pyx_PyInt_AsUnsignedLongLong(PyObject* x) { - if (PyInt_CheckExact(x)) { - long val = PyInt_AS_LONG(x); - if (unlikely(val < 0)) { - PyErr_SetString(PyExc_TypeError, "Negative assignment to unsigned type."); - return (unsigned PY_LONG_LONG)-1; - } - return val; - } - else if (PyLong_CheckExact(x)) { - return PyLong_AsUnsignedLongLong(x); - } - else { - PY_LONG_LONG val; - PyObject* tmp = PyNumber_Int(x); if (!tmp) return (PY_LONG_LONG)-1; - val = __pyx_PyInt_AsUnsignedLongLong(tmp); - Py_DECREF(tmp); - return val; - } -} - - -static INLINE unsigned char __pyx_PyInt_unsigned_char(PyObject* x) { - if (sizeof(unsigned char) < sizeof(long)) { - long long_val = __pyx_PyInt_AsLong(x); - unsigned char val = (unsigned char)long_val; - if (unlikely((val != long_val) || (long_val < 0))) { - PyErr_SetString(PyExc_OverflowError, "value too large to convert to unsigned char"); - return (unsigned char)-1; - } - return val; - } - else { - return __pyx_PyInt_AsLong(x); - } -} - -static INLINE unsigned short __pyx_PyInt_unsigned_short(PyObject* x) { - if (sizeof(unsigned short) < sizeof(long)) { - long long_val = __pyx_PyInt_AsLong(x); - unsigned short val = (unsigned short)long_val; - if (unlikely((val != long_val) || (long_val < 0))) { - PyErr_SetString(PyExc_OverflowError, "value too large to convert to unsigned short"); - return (unsigned short)-1; - } - return val; - } - else { - return __pyx_PyInt_AsLong(x); - } -} - -static INLINE char __pyx_PyInt_char(PyObject* x) { - if (sizeof(char) < sizeof(long)) { - long long_val = __pyx_PyInt_AsLong(x); - char val = (char)long_val; - if (unlikely((val != long_val) )) { - PyErr_SetString(PyExc_OverflowError, "value too large to convert to char"); - return (char)-1; - } - return val; - } - else { - return __pyx_PyInt_AsLong(x); - } -} - -static INLINE short __pyx_PyInt_short(PyObject* x) { - if (sizeof(short) < sizeof(long)) { - long long_val = __pyx_PyInt_AsLong(x); - short val = (short)long_val; - if (unlikely((val != long_val) )) { - PyErr_SetString(PyExc_OverflowError, "value too large to convert to short"); - return (short)-1; - } - return val; - } - else { - return __pyx_PyInt_AsLong(x); - } -} - -static INLINE int __pyx_PyInt_int(PyObject* x) { - if (sizeof(int) < sizeof(long)) { - long long_val = __pyx_PyInt_AsLong(x); - int val = (int)long_val; - if (unlikely((val != long_val) )) { - PyErr_SetString(PyExc_OverflowError, "value too large to convert to int"); - return (int)-1; - } - return val; - } - else { - return __pyx_PyInt_AsLong(x); - } -} - -static INLINE long __pyx_PyInt_long(PyObject* x) { - if (sizeof(long) < sizeof(long)) { - long long_val = __pyx_PyInt_AsLong(x); - long val = (long)long_val; - if (unlikely((val != long_val) )) { - PyErr_SetString(PyExc_OverflowError, "value too large to convert to long"); - return (long)-1; - } - return val; - } - else { - return __pyx_PyInt_AsLong(x); - } -} - -static INLINE signed char __pyx_PyInt_signed_char(PyObject* x) { - if (sizeof(signed char) < sizeof(long)) { - long long_val = __pyx_PyInt_AsLong(x); - signed char val = (signed char)long_val; - if (unlikely((val != long_val) )) { - PyErr_SetString(PyExc_OverflowError, "value too large to convert to signed char"); - return (signed char)-1; - } - return val; - } - else { - return __pyx_PyInt_AsLong(x); - } -} - -static INLINE signed short __pyx_PyInt_signed_short(PyObject* x) { - if (sizeof(signed short) < sizeof(long)) { - long long_val = __pyx_PyInt_AsLong(x); - signed short val = (signed short)long_val; - if (unlikely((val != long_val) )) { - PyErr_SetString(PyExc_OverflowError, "value too large to convert to signed short"); - return (signed short)-1; - } - return val; - } - else { - return __pyx_PyInt_AsLong(x); - } -} - -static INLINE signed int __pyx_PyInt_signed_int(PyObject* x) { - if (sizeof(signed int) < sizeof(long)) { - long long_val = __pyx_PyInt_AsLong(x); - signed int val = (signed int)long_val; - if (unlikely((val != long_val) )) { - PyErr_SetString(PyExc_OverflowError, "value too large to convert to signed int"); - return (signed int)-1; - } - return val; - } - else { - return __pyx_PyInt_AsLong(x); - } -} - -static INLINE signed long __pyx_PyInt_signed_long(PyObject* x) { - if (sizeof(signed long) < sizeof(long)) { - long long_val = __pyx_PyInt_AsLong(x); - signed long val = (signed long)long_val; - if (unlikely((val != long_val) )) { - PyErr_SetString(PyExc_OverflowError, "value too large to convert to signed long"); - return (signed long)-1; - } - return val; - } - else { - return __pyx_PyInt_AsLong(x); - } -} - -static INLINE long double __pyx_PyInt_long_double(PyObject* x) { - if (sizeof(long double) < sizeof(long)) { - long long_val = __pyx_PyInt_AsLong(x); - long double val = (long double)long_val; - if (unlikely((val != long_val) )) { - PyErr_SetString(PyExc_OverflowError, "value too large to convert to long double"); - return (long double)-1; - } - return val; - } - else { - return __pyx_PyInt_AsLong(x); - } -} - + diff -r 60615619173287c363a6f12088c6361c45735deb -r abd1d707fd2b9ec045adce896e079aff5eb8504e yt/extensions/spatial/ckdtree.pyx --- a/yt/extensions/spatial/ckdtree.pyx Wed Jul 15 11:59:56 2009 -0400 +++ b/yt/extensions/spatial/ckdtree.pyx Wed Jul 15 19:08:38 2009 -0700 @@ -106,29 +106,39 @@ return x else: return -x -cdef inline double _distance_p(double*x,double*y,double p,int k,double upperbound): +cdef inline double dmin(double x, double y): + if xupperbound: return r elif p==1: for i in range(k): - r += dabs(x[i]-y[i]) + m = dmin(dabs(x[i] - y[i]), period[i] - dabs(x[i] - y[i])) + r += m if r>upperbound: return r else: for i in range(k): - r += dabs(x[i]-y[i])**p + m = dmin(dabs(x[i] - y[i]), period[i] - dabs(x[i] - y[i])) + r += m**p if r>upperbound: return r return r @@ -140,6 +150,8 @@ int split_dim int n_points double split + double* maxes + double* mins innernode* less innernode* greater cdef struct leafnode: @@ -147,6 +159,8 @@ int n_points int start_idx int end_idx + double* maxes + double* mins # this is the standard trick for variable-size arrays: # malloc sizeof(nodeinfo)+self.m*sizeof(double) bytes. @@ -239,6 +253,12 @@ cdef double*mids if end_idx-start_idx<=self.leafsize: n = stdlib.malloc(sizeof(leafnode)) + # Skory + n.maxes = stdlib.malloc(sizeof(double)*self.m) + n.mins = stdlib.malloc(sizeof(double)*self.m) + for i in range(self.m): + n.maxes[i] = maxes[i] + n.mins[i] = mins[i] n.split_dim = -1 n.start_idx = start_idx n.end_idx = end_idx @@ -322,6 +342,12 @@ ni.split_dim = d ni.split = split + # Skory + ni.maxes = stdlib.malloc(sizeof(double)*self.m) + ni.mins = stdlib.malloc(sizeof(double)*self.m) + for i in range(self.m): + ni.maxes[i] = maxes[i] + ni.mins[i] = mins[i] return ni @@ -329,6 +355,8 @@ if node.split_dim!=-1: self.__free_tree(node.less) self.__free_tree(node.greater) + stdlib.free(node.maxes) # Skory + stdlib.free(node.mins) stdlib.free(node) def __dealloc__(cKDTree self): @@ -344,7 +372,8 @@ int k, double eps, double p, - double distance_upper_bound): + double distance_upper_bound, + double*period): cdef heap q cdef heap neighbors @@ -353,6 +382,7 @@ cdef nodeinfo* inf cdef nodeinfo* inf2 cdef double d + cdef double m_left, m_right, m cdef double epsfac cdef double min_distance cdef double far_min_distance @@ -384,6 +414,7 @@ if t>inf.side_distances[i]: inf.side_distances[i] = t else: + #t = dmin( dabs(self.raw_mins[i]-x[i]), 1 - dabs(self.raw_mins[i]-x[i])) t = self.raw_mins[i]-x[i] if t>inf.side_distances[i]: inf.side_distances[i] = t @@ -418,7 +449,7 @@ for i in range(node.start_idx,node.end_idx): d = _distance_p( self.raw_data+self.raw_indices[i]*self.m, - x,p,self.m,distance_upper_bound) + x,p,self.m,distance_upper_bound,period) if dstdlib.malloc(sizeof(nodeinfo)+self.m*sizeof(double)) it2.contents.ptrdata = inf2 inf2.node = far + + # Periodicity added by S Skory + m_left = dmin( dabs(far.mins[inode.split_dim] - x[inode.split_dim]), \ + 1 - dabs(far.mins[inode.split_dim] - x[inode.split_dim])) + m_right = dmin( dabs(far.maxes[inode.split_dim] - x[inode.split_dim]), \ + 1 - dabs(far.maxes[inode.split_dim] - x[inode.split_dim])) + m = dmin(m_left,m_right) + # most side distances unchanged for i in range(self.m): inf2.side_distances[i] = inf.side_distances[i] @@ -482,13 +521,14 @@ if p == infinity: # we never use side_distances in the l_infinity case # inf2.side_distances[inode.split_dim] = dabs(inode.split-x[inode.split_dim]) - far_min_distance = dmax(min_distance, dabs(inode.split-x[inode.split_dim])) + far_min_distance = dmax(min_distance, m) elif p == 1: - inf2.side_distances[inode.split_dim] = dabs(inode.split-x[inode.split_dim]) - far_min_distance = min_distance - inf.side_distances[inode.split_dim] + inf2.side_distances[inode.split_dim] + inf2.side_distances[inode.split_dim] = m + far_min_distance = dmax(min_distance, m) else: - inf2.side_distances[inode.split_dim] = dabs(inode.split-x[inode.split_dim])**p - far_min_distance = min_distance - inf.side_distances[inode.split_dim] + inf2.side_distances[inode.split_dim] + inf2.side_distances[inode.split_dim] = m**p + #far_min_distance = min_distance - inf.side_distances[inode.split_dim] + inf2.side_distances[inode.split_dim] + far_min_distance = m**p it2.priority = far_min_distance @@ -514,7 +554,7 @@ heapdestroy(&neighbors) def query(cKDTree self, object x, int k=1, double eps=0, double p=2, - double distance_upper_bound=infinity): + double distance_upper_bound=infinity, object period=None): """query the kd-tree for nearest neighbors Parameters: @@ -554,8 +594,14 @@ cdef np.ndarray[int, ndim=2] ii cdef np.ndarray[double, ndim=2] dd cdef np.ndarray[double, ndim=2] xx + cdef np.ndarray[double, ndim=1] cperiod cdef int c x = np.asarray(x).astype(np.float) + if period is None: + period = np.array([np.inf]*self.m) + else: + period = np.asarray(period).astype(np.float) + cperiod = np.ascontiguousarray(period) if np.shape(x)[-1] != self.m: raise ValueError("x must consist of vectors of length %d but has shape %s" % (self.m, np.shape(x))) if p<1: @@ -581,7 +627,8 @@ k, eps, p, - distance_upper_bound) + distance_upper_bound, + cperiod.data) if single: if k==1: return dd[0,0], ii[0,0]