[Scipy-svn] r4795 - in branches/spatial/scipy/spatial: . tests
scipy-svn at scipy.org
scipy-svn at scipy.org
Sun Oct 12 09:24:15 EDT 2008
Author: peridot
Date: 2008-10-12 08:23:48 -0500 (Sun, 12 Oct 2008)
New Revision: 4795
Added:
branches/spatial/scipy/spatial/ckdtree.c
branches/spatial/scipy/spatial/ckdtree.pyx
Modified:
branches/spatial/scipy/spatial/__init__.py
branches/spatial/scipy/spatial/setup.py
branches/spatial/scipy/spatial/tests/test_kdtree.py
Log:
kd-tree implementation in compiled (cython) code. Note that the c is not automatically built.
Modified: branches/spatial/scipy/spatial/__init__.py
===================================================================
--- branches/spatial/scipy/spatial/__init__.py 2008-10-12 13:06:54 UTC (rev 4794)
+++ branches/spatial/scipy/spatial/__init__.py 2008-10-12 13:23:48 UTC (rev 4795)
@@ -5,6 +5,7 @@
from info import __doc__
from kdtree import *
+from ckdtree import *
__all__ = filter(lambda s:not s.startswith('_'),dir())
Added: branches/spatial/scipy/spatial/ckdtree.c
===================================================================
--- branches/spatial/scipy/spatial/ckdtree.c 2008-10-12 13:06:54 UTC (rev 4794)
+++ branches/spatial/scipy/spatial/ckdtree.c 2008-10-12 13:23:48 UTC (rev 4795)
@@ -0,0 +1,5995 @@
+/* Generated by Cython 0.9.8.1.1 on Sun Oct 12 09:20:26 2008 */
+
+#define PY_SSIZE_T_CLEAN
+#include "Python.h"
+#include "structmember.h"
+#ifndef PY_LONG_LONG
+ #define PY_LONG_LONG LONG_LONG
+#endif
+#ifndef DL_EXPORT
+ #define DL_EXPORT(t) t
+#endif
+#if PY_VERSION_HEX < 0x02040000
+ #define METH_COEXIST 0
+#endif
+#if PY_VERSION_HEX < 0x02050000
+ typedef int Py_ssize_t;
+ #define PY_SSIZE_T_MAX INT_MAX
+ #define PY_SSIZE_T_MIN INT_MIN
+ #define PyInt_FromSsize_t(z) PyInt_FromLong(z)
+ #define PyInt_AsSsize_t(o) PyInt_AsLong(o)
+ #define PyNumber_Index(o) PyNumber_Int(o)
+ #define PyIndex_Check(o) PyNumber_Check(o)
+#endif
+#if PY_VERSION_HEX < 0x02060000
+ #define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt)
+ #define Py_TYPE(ob) (((PyObject*)(ob))->ob_type)
+ #define Py_SIZE(ob) (((PyVarObject*)(ob))->ob_size)
+ #define PyVarObject_HEAD_INIT(type, size) \
+ PyObject_HEAD_INIT(type) size,
+ #define PyType_Modified(t)
+
+ typedef struct {
+ void *buf;
+ Py_ssize_t len;
+ int readonly;
+ const char *format;
+ int ndim;
+ Py_ssize_t *shape;
+ Py_ssize_t *strides;
+ Py_ssize_t *suboffsets;
+ Py_ssize_t itemsize;
+ void *internal;
+ } Py_buffer;
+
+ #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)
+ #define PyBUF_C_CONTIGUOUS (0x0020 | PyBUF_STRIDES)
+ #define PyBUF_F_CONTIGUOUS (0x0040 | PyBUF_STRIDES)
+ #define PyBUF_ANY_CONTIGUOUS (0x0080 | PyBUF_STRIDES)
+ #define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES)
+
+#endif
+#if PY_MAJOR_VERSION < 3
+ #define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
+#else
+ #define __Pyx_BUILTIN_MODULE_NAME "builtins"
+#endif
+#if PY_MAJOR_VERSION >= 3
+ #define Py_TPFLAGS_CHECKTYPES 0
+ #define Py_TPFLAGS_HAVE_INDEX 0
+#endif
+#if PY_MAJOR_VERSION >= 3
+ #define PyBaseString_Type PyUnicode_Type
+ #define PyString_Type PyBytes_Type
+ #define PyInt_Type PyLong_Type
+ #define PyInt_Check(op) PyLong_Check(op)
+ #define PyInt_CheckExact(op) PyLong_CheckExact(op)
+ #define PyInt_FromString PyLong_FromString
+ #define PyInt_FromUnicode PyLong_FromUnicode
+ #define PyInt_FromLong PyLong_FromLong
+ #define PyInt_FromSize_t PyLong_FromSize_t
+ #define PyInt_FromSsize_t PyLong_FromSsize_t
+ #define PyInt_AsLong PyLong_AsLong
+ #define PyInt_AS_LONG PyLong_AS_LONG
+ #define PyInt_AsSsize_t PyLong_AsSsize_t
+ #define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask
+ #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask
+ #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y)
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+ #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y)
+ #define PyBytes_Type PyString_Type
+#endif
+#if PY_MAJOR_VERSION >= 3
+ #define PyMethod_New(func, self, klass) PyInstanceMethod_New(func)
+#endif
+#if !defined(WIN32) && !defined(MS_WINDOWS)
+ #ifndef __stdcall
+ #define __stdcall
+ #endif
+ #ifndef __cdecl
+ #define __cdecl
+ #endif
+#else
+ #define _USE_MATH_DEFINES
+#endif
+#ifdef __cplusplus
+#define __PYX_EXTERN_C extern "C"
+#else
+#define __PYX_EXTERN_C extern
+#endif
+#include <math.h>
+#define __PYX_HAVE_API__scipy__spatial__ckdtree
+#include "numpy/arrayobject.h"
+#include "stdlib.h"
+
+
+#ifdef __GNUC__
+#define INLINE __inline__
+#elif _WIN32
+#define INLINE __inline
+#else
+#define INLINE
+#endif
+
+typedef struct {PyObject **p; char *s; long n; char is_unicode; char intern; char is_identifier;} __Pyx_StringTabEntry; /*proto*/
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+/* Type Conversion Predeclarations */
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+#define __Pyx_PyBytes_FromString PyString_FromString
+#define __Pyx_PyBytes_AsString PyString_AsString
+#else
+#define __Pyx_PyBytes_FromString PyBytes_FromString
+#define __Pyx_PyBytes_AsString PyBytes_AsString
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+
+#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))
+#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
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+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);
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+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))
+#define likely(x) __builtin_expect(!!(x), 1)
+#define unlikely(x) __builtin_expect(!!(x), 0)
+#else /* __GNUC__ > 2 ... */
+#define likely(x) (x)
+#define unlikely(x) (x)
+#endif /* __GNUC__ > 2 ... */
+#else /* __GNUC__ */
+#define likely(x) (x)
+#define unlikely(x) (x)
+#endif /* __GNUC__ */
+
+static PyObject *__pyx_m;
+static PyObject *__pyx_b;
+static PyObject *__pyx_empty_tuple;
+static int __pyx_lineno;
+static int __pyx_clineno = 0;
+static const char * __pyx_cfilenm= __FILE__;
+static const char *__pyx_filename;
+static const char **__pyx_f;
+static INLINE void __Pyx_SafeReleaseBuffer(PyObject* obj, Py_buffer* info);
+static INLINE void __Pyx_ZeroBuffer(Py_buffer* buf); /*proto*/
+static INLINE const char* __Pyx_ConsumeWhitespace(const char* ts); /*proto*/
+static INLINE const char* __Pyx_BufferTypestringCheckEndian(const char* ts); /*proto*/
+static void __Pyx_BufferNdimError(Py_buffer* buffer, int expected_ndim); /*proto*/
+static const char* __Pyx_BufferTypestringCheck_item_double(const char* ts); /*proto*/
+
+static int __Pyx_GetBuffer_double(PyObject* obj, Py_buffer* buf, int flags, int nd); /*proto*/
+
+static void __Pyx_RaiseBufferFallbackError(void); /*proto*/
+static const char* __Pyx_BufferTypestringCheck_item_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); /*proto*/
+static const char* __Pyx_BufferTypestringCheck_item_int(const char* ts); /*proto*/
+
+static int __Pyx_GetBuffer_int(PyObject* obj, Py_buffer* buf, int flags, int nd); /*proto*/
+static void __Pyx_RaiseBufferIndexError(int axis); /*proto*/
+#define __Pyx_BufPtrStrided2d(buf, i0, s0, i1, s1) ((char*)buf + i0 * s0 + i1 * s1)
+
+static INLINE void __Pyx_RaiseArgtupleTooLong(Py_ssize_t num_expected, Py_ssize_t num_found); /*proto*/
+#if (PY_MAJOR_VERSION < 3) && !(Py_TPFLAGS_DEFAULT & Py_TPFLAGS_HAVE_NEWBUFFER)
+static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags);
+static void __Pyx_ReleaseBuffer(PyObject *obj, Py_buffer *view);
+#else
+#define __Pyx_GetBuffer PyObject_GetBuffer
+#define __Pyx_ReleaseBuffer PyObject_ReleaseBuffer
+#endif
+
+Py_ssize_t __Pyx_zeros[] = {0, 0};
+Py_ssize_t __Pyx_minusones[] = {-1, -1};
+
+static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list); /*proto*/
+
+static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/
+
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
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+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*/
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+static int __Pyx_Print(PyObject *, int); /*proto*/
+#if PY_MAJOR_VERSION >= 3
+static PyObject* __pyx_print = 0;
+static PyObject* __pyx_print_kwargs = 0;
+#endif
+
+static INLINE PyObject *__Pyx_GetItemInt(PyObject *o, Py_ssize_t i, int is_unsigned) {
+ 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)) {
+ 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))
+ 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);
+ }
+ return r;
+}
+
+static void __Pyx_WriteUnraisable(const char *name); /*proto*/
+
+static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/
+
+static PyTypeObject *__Pyx_ImportType(char *module_name, char *class_name, long size); /*proto*/
+
+static PyObject *__Pyx_ImportModule(char *name); /*proto*/
+
+static void __Pyx_AddTraceback(const char *funcname); /*proto*/
+
+static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/
+
+/* Type declarations */
+
+typedef npy_int8 __pyx_t_5numpy_int8_t;
+
+typedef npy_int16 __pyx_t_5numpy_int16_t;
+
+typedef npy_int32 __pyx_t_5numpy_int32_t;
+
+typedef npy_int64 __pyx_t_5numpy_int64_t;
+
+typedef npy_uint8 __pyx_t_5numpy_uint8_t;
+
+typedef npy_uint16 __pyx_t_5numpy_uint16_t;
+
+typedef npy_uint32 __pyx_t_5numpy_uint32_t;
+
+typedef npy_uint64 __pyx_t_5numpy_uint64_t;
+
+typedef npy_float32 __pyx_t_5numpy_float32_t;
+
+typedef npy_float64 __pyx_t_5numpy_float64_t;
+
+typedef npy_long __pyx_t_5numpy_int_t;
+
+typedef npy_longlong __pyx_t_5numpy_long_t;
+
+typedef npy_ulong __pyx_t_5numpy_uint_t;
+
+typedef npy_ulonglong __pyx_t_5numpy_ulong_t;
+
+typedef npy_double __pyx_t_5numpy_float_t;
+
+typedef npy_double __pyx_t_5numpy_double_t;
+
+typedef npy_longdouble __pyx_t_5numpy_longdouble_t;
+
+/* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":15
+ *
+ * # priority queue
+ * cdef union heapcontents: # <<<<<<<<<<<<<<
+ * int intdata
+ * char* ptrdata
+ */
+
+union __pyx_t_5scipy_7spatial_7ckdtree_heapcontents {
+ int intdata;
+ char *ptrdata;
+};
+
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+ * char* ptrdata
+ *
+ * cdef struct heapitem: # <<<<<<<<<<<<<<
+ * double priority
+ * heapcontents contents
+ */
+
+struct __pyx_t_5scipy_7spatial_7ckdtree_heapitem {
+ double priority;
+ union __pyx_t_5scipy_7spatial_7ckdtree_heapcontents contents;
+};
+
+/* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":23
+ * heapcontents contents
+ *
+ * cdef struct heap: # <<<<<<<<<<<<<<
+ * int n
+ * heapitem* heap
+ */
+
+struct __pyx_t_5scipy_7spatial_7ckdtree_heap {
+ int n;
+ struct __pyx_t_5scipy_7spatial_7ckdtree_heapitem *heap;
+ int space;
+};
+
+/* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":139
+ *
+ * # Tree structure
+ * cdef struct innernode: # <<<<<<<<<<<<<<
+ * int split_dim
+ * int n_points
+ */
+
+struct __pyx_t_5scipy_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;
+};
+
+/* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":145
+ * innernode* less
+ * innernode* greater
+ * cdef struct leafnode: # <<<<<<<<<<<<<<
+ * int split_dim
+ * int n_points
+ */
+
+struct __pyx_t_5scipy_7spatial_7ckdtree_leafnode {
+ int split_dim;
+ int n_points;
+ int start_idx;
+ int end_idx;
+};
+
+/* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":153
+ * # this is the standard trick for variable-size arrays:
+ * # malloc sizeof(nodeinfo)+self.m*sizeof(double) bytes.
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+ * innernode* node
+ * double side_distances[0]
+ */
+
+struct __pyx_t_5scipy_7spatial_7ckdtree_nodeinfo {
+ struct __pyx_t_5scipy_7spatial_7ckdtree_innernode *node;
+ double side_distances[0];
+};
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+ * double side_distances[0]
+ *
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+ *
+ */
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+ PyObject *data;
+ double *raw_data;
+ int n;
+ int m;
+ int leafsize;
+ PyObject *maxes;
+ double *raw_maxes;
+ PyObject *mins;
+ double *raw_mins;
+ PyObject *indices;
+ __pyx_t_5numpy_int32_t *raw_indices;
+};
+
+
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+ 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);
+};
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+
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+static double __pyx_k_17;
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+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 PyObject *__pyx_int_0;
+static char __pyx_k___init__[] = "__init__";
+static PyObject *__pyx_kp___init__;
+static char __pyx_k___del__[] = "__del__";
+static PyObject *__pyx_kp___del__;
+static char __pyx_k_query[] = "query";
+static PyObject *__pyx_kp_query;
+static char __pyx_k_numpy[] = "numpy";
+static PyObject *__pyx_kp_numpy;
+static char __pyx_k_np[] = "np";
+static PyObject *__pyx_kp_np;
+static char __pyx_k_kdtree[] = "kdtree";
+static PyObject *__pyx_kp_kdtree;
+static char __pyx_k_inf[] = "inf";
+static PyObject *__pyx_kp_inf;
+static char __pyx_k_ValueError[] = "ValueError";
+static PyObject *__pyx_kp_ValueError;
+static char __pyx_k_ascontiguousarray[] = "ascontiguousarray";
+static PyObject *__pyx_kp_ascontiguousarray;
+static char __pyx_k_dtype[] = "dtype";
+static PyObject *__pyx_kp_dtype;
+static char __pyx_k_float[] = "float";
+static PyObject *__pyx_kp_float;
+static char __pyx_k_shape[] = "shape";
+static PyObject *__pyx_kp_shape;
+static char __pyx_k_amax[] = "amax";
+static PyObject *__pyx_kp_amax;
+static char __pyx_k_axis[] = "axis";
+static PyObject *__pyx_kp_axis;
+static char __pyx_k_amin[] = "amin";
+static PyObject *__pyx_kp_amin;
+static char __pyx_k_arange[] = "arange";
+static PyObject *__pyx_kp_arange;
+static char __pyx_k_int[] = "int";
+static PyObject *__pyx_kp_int;
+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_newaxis[] = "newaxis";
+static PyObject *__pyx_kp_newaxis;
+static char __pyx_k_prod[] = "prod";
+static PyObject *__pyx_kp_prod;
+static char __pyx_k_reshape[] = "reshape";
+static PyObject *__pyx_kp_reshape;
+static char __pyx_k_empty[] = "empty";
+static PyObject *__pyx_kp_empty;
+static char __pyx_k_fill[] = "fill";
+static PyObject *__pyx_kp_fill;
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+ PyObject *__pyx_r;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":29
+ *
+ * cdef inline heapcreate(heap* self,int initial_size):
+ * self.space = initial_size # <<<<<<<<<<<<<<
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+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":30
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+ *
+ */
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+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":31
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+ *
+ * cdef inline heapdestroy(heap* self):
+ */
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+
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+}
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+ *
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+}
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+ PyObject *__pyx_r;
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+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":37
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+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":38
+ * cdef inline heapresize(heap* self, int new_space):
+ * if new_space<self.n:
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+}
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+ * self.heap = <heapitem*>stdlib.realloc(<void*>self.heap,new_space*sizeof(heapitem))
+ *
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+ * cdef int i
+ * cdef heapitem t
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+ PyObject *__pyx_r;
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+ *
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+ */
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+ * i = self.n-1
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+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":54
+ * while i>0 and self.heap[i].priority<self.heap[(i-1)//2].priority:
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+ * i = (i-1)//2
+ */
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+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":55
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+ *
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+ */
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+}
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+/* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":58
+ * i = (i-1)//2
+ *
+ * cdef heapitem heappeek(heap* self): # <<<<<<<<<<<<<<
+ * return self.heap[0]
+ *
+ */
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+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;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":59
+ *
+ * cdef heapitem heappeek(heap* self):
+ * return self.heap[0] # <<<<<<<<<<<<<<
+ *
+ * cdef heapremove(heap* self):
+ */
+ __pyx_r = (__pyx_v_self->heap[0]);
+ goto __pyx_L0;
+
+ __pyx_L0:;
+ return __pyx_r;
+}
+
+/* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":61
+ * return self.heap[0]
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+ * cdef heapitem t
+ * cdef int i, j, k, l
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+ int __pyx_v_j;
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+ int __pyx_v_l;
+ PyObject *__pyx_r;
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+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":65
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+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":67
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+ * self.n -= 1
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+ * heapresize(self,self.space//2+1)
+ *
+ */
+ __pyx_1 = (__pyx_v_self->n < (__pyx_v_self->space / 4));
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+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":68
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+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":70
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+ * j=1
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+ *
+ * i=0
+ * j=1 # <<<<<<<<<<<<<<
+ * k=2
+ * while ((j<self.n and
+ */
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+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":72
+ * i=0
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+ * j=1
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+ * self.heap[i].priority > self.heap[j].priority or
+ * k<self.n and
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+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":74
+ * k=2
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+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":75
+ * while ((j<self.n and
+ * self.heap[i].priority > self.heap[j].priority or
+ * k<self.n and # <<<<<<<<<<<<<<
+ * self.heap[i].priority > self.heap[k].priority)):
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+ */
+ __pyx_1 = (__pyx_v_k < __pyx_v_self->n);
+ if (__pyx_1) {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":76
+ * self.heap[i].priority > self.heap[j].priority or
+ * k<self.n and
+ * self.heap[i].priority > self.heap[k].priority)): # <<<<<<<<<<<<<<
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+ }
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+ if (!__pyx_1) break;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":77
+ * k<self.n and
+ * self.heap[i].priority > self.heap[k].priority)):
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+ * 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);
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+ if (__pyx_1) {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":78
+ * self.heap[i].priority > self.heap[k].priority)):
+ * if k<self.n and self.heap[j].priority>self.heap[k].priority:
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+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":80
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+ */
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+
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+ * k = 2*i+2 # <<<<<<<<<<<<<<
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+ * cdef heapitem heappop(heap* self):
+ */
+ __pyx_v_k = ((2 * __pyx_v_i) + 2);
+ }
+
+ __pyx_r = Py_None; Py_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ Py_XDECREF(__pyx_2);
+ __Pyx_AddTraceback("scipy.spatial.ckdtree.heapremove");
+ __pyx_r = 0;
+ __pyx_L0:;
+ return __pyx_r;
+}
+
+/* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":88
+ * k = 2*i+2
+ *
+ * cdef heapitem heappop(heap* self): # <<<<<<<<<<<<<<
+ * cdef heapitem it
+ * it = heappeek(self)
+ */
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+ struct __pyx_t_5scipy_7spatial_7ckdtree_heapitem __pyx_v_it;
+ struct __pyx_t_5scipy_7spatial_7ckdtree_heapitem __pyx_r;
+ PyObject *__pyx_1 = 0;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/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);
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":91
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+ Py_DECREF(__pyx_1); __pyx_1 = 0;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":92
+ * it = heappeek(self)
+ * heapremove(self)
+ * return it # <<<<<<<<<<<<<<
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+ *
+ */
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+
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+}
+
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+ *
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+ * return x
+ */
+
+static INLINE double __pyx_f_5scipy_7spatial_7ckdtree_dmax(double __pyx_v_x, double __pyx_v_y) {
+ double __pyx_r;
+ int __pyx_1;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/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) {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":101
+ * cdef inline double dmax(double x, double y):
+ * if x>y:
+ * return x # <<<<<<<<<<<<<<
+ * else:
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+ */
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+ goto __pyx_L3;
+ }
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+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":103
+ * return x
+ * else:
+ * return y # <<<<<<<<<<<<<<
+ * cdef inline double dabs(double x):
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+ */
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+ goto __pyx_L0;
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+ __pyx_L3:;
+
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+ __pyx_L0:;
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+}
+
+/* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":104
+ * else:
+ * return y
+ * cdef inline double dabs(double x): # <<<<<<<<<<<<<<
+ * if x>0:
+ * return x
+ */
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+ double __pyx_r;
+ int __pyx_1;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":105
+ * return y
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+ * if x>0: # <<<<<<<<<<<<<<
+ * return x
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+ */
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+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":106
+ * cdef inline double dabs(double x):
+ * if x>0:
+ * return x # <<<<<<<<<<<<<<
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+ */
+ __pyx_r = __pyx_v_x;
+ goto __pyx_L0;
+ goto __pyx_L3;
+ }
+ /*else*/ {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":108
+ * return x
+ * else:
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+ }
+ __pyx_L3:;
+
+ __pyx_r = 0;
+ __pyx_L0:;
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+}
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+ * else:
+ * return -x
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+ int __pyx_v_i;
+ double __pyx_v_r;
+ double __pyx_r;
+ int __pyx_1;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":118
+ * cdef int i
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+ * r = 0 # <<<<<<<<<<<<<<
+ * if p==infinity:
+ * for i in range(k):
+ */
+ __pyx_v_r = 0;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":119
+ * cdef double r
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+ * if p==infinity: # <<<<<<<<<<<<<<
+ * for i in range(k):
+ * r = dmax(r,dabs(x[i]-y[i]))
+ */
+ __pyx_1 = (__pyx_v_p == __pyx_v_5scipy_7spatial_7ckdtree_infinity);
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+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":120
+ * r = 0
+ * if p==infinity:
+ * for i in range(k): # <<<<<<<<<<<<<<
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+ * if r>upperbound:
+ */
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+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":121
+ * if p==infinity:
+ * for i in range(k):
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+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":122
+ * for i in range(k):
+ * r = dmax(r,dabs(x[i]-y[i]))
+ * if r>upperbound: # <<<<<<<<<<<<<<
+ * return r
+ * elif p==1:
+ */
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+ if (__pyx_1) {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":123
+ * r = dmax(r,dabs(x[i]-y[i]))
+ * if r>upperbound:
+ * return r # <<<<<<<<<<<<<<
+ * elif p==1:
+ * for i in range(k):
+ */
+ __pyx_r = __pyx_v_r;
+ goto __pyx_L0;
+ goto __pyx_L6;
+ }
+ __pyx_L6:;
+ }
+ goto __pyx_L3;
+ }
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":124
+ * 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) {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":125
+ * 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) {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":126
+ * elif p==1:
+ * for i in range(k):
+ * r += dabs(x[i]-y[i]) # <<<<<<<<<<<<<<
+ * 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])));
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":127
+ * for i in range(k):
+ * r += dabs(x[i]-y[i])
+ * if r>upperbound: # <<<<<<<<<<<<<<
+ * return r
+ * else:
+ */
+ __pyx_1 = (__pyx_v_r > __pyx_v_upperbound);
+ if (__pyx_1) {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":128
+ * r += dabs(x[i]-y[i])
+ * if r>upperbound:
+ * return r # <<<<<<<<<<<<<<
+ * else:
+ * for i in range(k):
+ */
+ __pyx_r = __pyx_v_r;
+ goto __pyx_L0;
+ goto __pyx_L9;
+ }
+ __pyx_L9:;
+ }
+ goto __pyx_L3;
+ }
+ /*else*/ {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":130
+ * 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) {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":131
+ * else:
+ * for i in range(k):
+ * r += dabs(x[i]-y[i])**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);
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":132
+ * for i in range(k):
+ * r += dabs(x[i]-y[i])**p
+ * if r>upperbound: # <<<<<<<<<<<<<<
+ * return r
+ * return r
+ */
+ __pyx_1 = (__pyx_v_r > __pyx_v_upperbound);
+ if (__pyx_1) {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":133
+ * r += dabs(x[i]-y[i])**p
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+ goto __pyx_L0;
+ goto __pyx_L12;
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+ }
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+ __pyx_L3:;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":134
+ * if r>upperbound:
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+ * return r # <<<<<<<<<<<<<<
+ *
+ *
+ */
+ __pyx_r = __pyx_v_r;
+ goto __pyx_L0;
+
+ __pyx_r = 0;
+ __pyx_L0:;
+ return __pyx_r;
+}
+
+/* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":195
+ * cdef object indices
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+ Py_buffer __pyx_bstruct_inner_indices;
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+ * d = i
+ * size = maxes[i]-mins[i]
+ * maxval = maxes[d] # <<<<<<<<<<<<<<
+ * minval = mins[d]
+ * if maxval==minval:
+ */
+ __pyx_v_maxval = (__pyx_v_maxes[__pyx_v_d]);
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":254
+ * size = maxes[i]-mins[i]
+ * maxval = maxes[d]
+ * minval = mins[d] # <<<<<<<<<<<<<<
+ * if maxval==minval:
+ * # all points are identical; warn user?
+ */
+ __pyx_v_minval = (__pyx_v_mins[__pyx_v_d]);
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":255
+ * maxval = maxes[d]
+ * minval = mins[d]
+ * if maxval==minval: # <<<<<<<<<<<<<<
+ * # all points are identical; warn user?
+ * n = <leafnode*>stdlib.malloc(sizeof(leafnode))
+ */
+ __pyx_1 = (__pyx_v_maxval == __pyx_v_minval);
+ if (__pyx_1) {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":257
+ * if maxval==minval:
+ * # all points are identical; warn user?
+ * n = <leafnode*>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))));
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":258
+ * # all points are identical; warn user?
+ * n = <leafnode*>stdlib.malloc(sizeof(leafnode))
+ * n.split_dim = -1 # <<<<<<<<<<<<<<
+ * n.start_idx = start_idx
+ * n.end_idx = end_idx
+ */
+ __pyx_v_n->split_dim = -1;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":259
+ * n = <leafnode*>stdlib.malloc(sizeof(leafnode))
+ * n.split_dim = -1
+ * n.start_idx = start_idx # <<<<<<<<<<<<<<
+ * n.end_idx = end_idx
+ * return <innernode*>n
+ */
+ __pyx_v_n->start_idx = __pyx_v_start_idx;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":260
+ * n.split_dim = -1
+ * n.start_idx = start_idx
+ * n.end_idx = end_idx # <<<<<<<<<<<<<<
+ * return <innernode*>n
+ *
+ */
+ __pyx_v_n->end_idx = __pyx_v_end_idx;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":261
+ * n.start_idx = start_idx
+ * n.end_idx = end_idx
+ * return <innernode*>n # <<<<<<<<<<<<<<
+ *
+ * split = (maxval+minval)/2
+ */
+ __pyx_r = ((struct __pyx_t_5scipy_7spatial_7ckdtree_innernode *)__pyx_v_n);
+ goto __pyx_L0;
+ goto __pyx_L7;
+ }
+ __pyx_L7:;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":263
+ * return <innernode*>n
+ *
+ * split = (maxval+minval)/2 # <<<<<<<<<<<<<<
+ *
+ * p = start_idx
+ */
+ __pyx_v_split = ((__pyx_v_maxval + __pyx_v_minval) / 2);
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":265
+ * split = (maxval+minval)/2
+ *
+ * p = start_idx # <<<<<<<<<<<<<<
+ * q = end_idx-1
+ * while p<=q:
+ */
+ __pyx_v_p = __pyx_v_start_idx;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":266
+ *
+ * p = start_idx
+ * q = end_idx-1 # <<<<<<<<<<<<<<
+ * while p<=q:
+ * if self.raw_data[self.raw_indices[p]*self.m+d]<split:
+ */
+ __pyx_v_q = (__pyx_v_end_idx - 1);
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":267
+ * p = start_idx
+ * q = end_idx-1
+ * while p<=q: # <<<<<<<<<<<<<<
+ * if self.raw_data[self.raw_indices[p]*self.m+d]<split:
+ * p+=1
+ */
+ while (1) {
+ __pyx_1 = (__pyx_v_p <= __pyx_v_q);
+ if (!__pyx_1) break;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":268
+ * q = end_idx-1
+ * while p<=q:
+ * if self.raw_data[self.raw_indices[p]*self.m+d]<split: # <<<<<<<<<<<<<<
+ * p+=1
+ * elif self.raw_data[self.raw_indices[q]*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) {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":269
+ * while p<=q:
+ * if self.raw_data[self.raw_indices[p]*self.m+d]<split:
+ * p+=1 # <<<<<<<<<<<<<<
+ * elif self.raw_data[self.raw_indices[q]*self.m+d]>=split:
+ * q-=1
+ */
+ __pyx_v_p += 1;
+ goto __pyx_L10;
+ }
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":270
+ * if self.raw_data[self.raw_indices[p]*self.m+d]<split:
+ * p+=1
+ * elif self.raw_data[self.raw_indices[q]*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) {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":271
+ * p+=1
+ * elif self.raw_data[self.raw_indices[q]*self.m+d]>=split:
+ * q-=1 # <<<<<<<<<<<<<<
+ * else:
+ * t = self.raw_indices[p]
+ */
+ __pyx_v_q -= 1;
+ goto __pyx_L10;
+ }
+ /*else*/ {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":273
+ * q-=1
+ * else:
+ * t = self.raw_indices[p] # <<<<<<<<<<<<<<
+ * self.raw_indices[p] = self.raw_indices[q]
+ * self.raw_indices[q] = t
+ */
+ __pyx_v_t = (__pyx_v_self->raw_indices[__pyx_v_p]);
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":274
+ * else:
+ * t = self.raw_indices[p]
+ * self.raw_indices[p] = self.raw_indices[q] # <<<<<<<<<<<<<<
+ * self.raw_indices[q] = t
+ * p+=1
+ */
+ (__pyx_v_self->raw_indices[__pyx_v_p]) = (__pyx_v_self->raw_indices[__pyx_v_q]);
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":275
+ * t = self.raw_indices[p]
+ * self.raw_indices[p] = self.raw_indices[q]
+ * self.raw_indices[q] = t # <<<<<<<<<<<<<<
+ * p+=1
+ * q-=1
+ */
+ (__pyx_v_self->raw_indices[__pyx_v_q]) = __pyx_v_t;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":276
+ * self.raw_indices[p] = self.raw_indices[q]
+ * self.raw_indices[q] = t
+ * p+=1 # <<<<<<<<<<<<<<
+ * q-=1
+ *
+ */
+ __pyx_v_p += 1;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":277
+ * self.raw_indices[q] = t
+ * p+=1
+ * q-=1 # <<<<<<<<<<<<<<
+ *
+ * # slide midpoint if necessary
+ */
+ __pyx_v_q -= 1;
+ }
+ __pyx_L10:;
+ }
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":280
+ *
+ * # 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) {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":282
+ * if p==start_idx:
+ * # no points less than split
+ * j = start_idx # <<<<<<<<<<<<<<
+ * split = self.raw_data[self.raw_indices[j]*self.m+d]
+ * for i in range(start_idx+1, end_idx):
+ */
+ __pyx_v_j = __pyx_v_start_idx;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":283
+ * # no points less than split
+ * 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]<split:
+ */
+ __pyx_v_split = (__pyx_v_self->raw_data[(((__pyx_v_self->raw_indices[__pyx_v_j]) * __pyx_v_self->m) + __pyx_v_d)]);
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":284
+ * 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]<split:
+ * j = i
+ */
+ for (__pyx_v_i = (__pyx_v_start_idx + 1); __pyx_v_i < __pyx_v_end_idx; __pyx_v_i+=1) {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":285
+ * 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]<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) {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":286
+ * for i in range(start_idx+1, end_idx):
+ * 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]
+ * t = self.raw_indices[start_idx]
+ */
+ __pyx_v_j = __pyx_v_i;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":287
+ * 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] # <<<<<<<<<<<<<<
+ * t = self.raw_indices[start_idx]
+ * self.raw_indices[start_idx] = 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_L14;
+ }
+ __pyx_L14:;
+ }
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":288
+ * j = i
+ * 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]
+ * self.raw_indices[j] = t
+ */
+ __pyx_v_t = (__pyx_v_self->raw_indices[__pyx_v_start_idx]);
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":289
+ * 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] # <<<<<<<<<<<<<<
+ * self.raw_indices[j] = t
+ * p = start_idx+1
+ */
+ (__pyx_v_self->raw_indices[__pyx_v_start_idx]) = (__pyx_v_self->raw_indices[__pyx_v_j]);
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":290
+ * t = self.raw_indices[start_idx]
+ * self.raw_indices[start_idx] = self.raw_indices[j]
+ * self.raw_indices[j] = t # <<<<<<<<<<<<<<
+ * p = start_idx+1
+ * q = start_idx
+ */
+ (__pyx_v_self->raw_indices[__pyx_v_j]) = __pyx_v_t;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":291
+ * self.raw_indices[start_idx] = self.raw_indices[j]
+ * self.raw_indices[j] = t
+ * p = start_idx+1 # <<<<<<<<<<<<<<
+ * q = start_idx
+ * elif p==end_idx:
+ */
+ __pyx_v_p = (__pyx_v_start_idx + 1);
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":292
+ * self.raw_indices[j] = t
+ * p = start_idx+1
+ * q = start_idx # <<<<<<<<<<<<<<
+ * elif p==end_idx:
+ * # no points greater than split
+ */
+ __pyx_v_q = __pyx_v_start_idx;
+ goto __pyx_L11;
+ }
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":293
+ * 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) {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":295
+ * elif p==end_idx:
+ * # no points greater than split
+ * j = end_idx-1 # <<<<<<<<<<<<<<
+ * split = self.raw_data[self.raw_indices[j]*self.m+d]
+ * for i in range(start_idx, end_idx-1):
+ */
+ __pyx_v_j = (__pyx_v_end_idx - 1);
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":296
+ * # no points greater than split
+ * 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:
+ */
+ __pyx_v_split = (__pyx_v_self->raw_data[(((__pyx_v_self->raw_indices[__pyx_v_j]) * __pyx_v_self->m) + __pyx_v_d)]);
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":297
+ * 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) {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":298
+ * 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) {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":299
+ * 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]
+ * t = self.raw_indices[end_idx-1]
+ */
+ __pyx_v_j = __pyx_v_i;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":300
+ * 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] # <<<<<<<<<<<<<<
+ * t = self.raw_indices[end_idx-1]
+ * 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;
+ }
+ __pyx_L17:;
+ }
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":301
+ * j = i
+ * 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]
+ * self.raw_indices[j] = t
+ */
+ __pyx_v_t = (__pyx_v_self->raw_indices[(__pyx_v_end_idx - 1)]);
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":302
+ * 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] # <<<<<<<<<<<<<<
+ * self.raw_indices[j] = t
+ * p = end_idx-1
+ */
+ (__pyx_v_self->raw_indices[(__pyx_v_end_idx - 1)]) = (__pyx_v_self->raw_indices[__pyx_v_j]);
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":303
+ * t = self.raw_indices[end_idx-1]
+ * self.raw_indices[end_idx-1] = self.raw_indices[j]
+ * self.raw_indices[j] = t # <<<<<<<<<<<<<<
+ * p = end_idx-1
+ * q = end_idx-2
+ */
+ (__pyx_v_self->raw_indices[__pyx_v_j]) = __pyx_v_t;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":304
+ * self.raw_indices[end_idx-1] = self.raw_indices[j]
+ * self.raw_indices[j] = t
+ * p = end_idx-1 # <<<<<<<<<<<<<<
+ * q = end_idx-2
+ *
+ */
+ __pyx_v_p = (__pyx_v_end_idx - 1);
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":305
+ * self.raw_indices[j] = t
+ * p = end_idx-1
+ * q = end_idx-2 # <<<<<<<<<<<<<<
+ *
+ * # construct new node representation
+ */
+ __pyx_v_q = (__pyx_v_end_idx - 2);
+ goto __pyx_L11;
+ }
+ __pyx_L11:;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":308
+ *
+ * # construct new node representation
+ * ni = <innernode*>stdlib.malloc(sizeof(innernode)) # <<<<<<<<<<<<<<
+ *
+ * mids = <double*>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))));
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":310
+ * ni = <innernode*>stdlib.malloc(sizeof(innernode))
+ *
+ * mids = <double*>stdlib.malloc(sizeof(double)*self.m) # <<<<<<<<<<<<<<
+ * for i in range(self.m):
+ * mids[i] = maxes[i]
+ */
+ __pyx_v_mids = ((double *)malloc(((sizeof(double)) * __pyx_v_self->m)));
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":311
+ *
+ * mids = <double*>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) {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":312
+ * mids = <double*>stdlib.malloc(sizeof(double)*self.m)
+ * for i in range(self.m):
+ * mids[i] = maxes[i] # <<<<<<<<<<<<<<
+ * mids[d] = split
+ * ni.less = self.__build(start_idx,p,mids,mins)
+ */
+ (__pyx_v_mids[__pyx_v_i]) = (__pyx_v_maxes[__pyx_v_i]);
+ }
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":313
+ * for i in range(self.m):
+ * mids[i] = maxes[i]
+ * mids[d] = split # <<<<<<<<<<<<<<
+ * ni.less = self.__build(start_idx,p,mids,mins)
+ *
+ */
+ (__pyx_v_mids[__pyx_v_d]) = __pyx_v_split;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":314
+ * 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);
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":316
+ * 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) {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":317
+ *
+ * for i in range(self.m):
+ * mids[i] = mins[i] # <<<<<<<<<<<<<<
+ * mids[d] = split
+ * ni.greater = self.__build(p,end_idx,maxes,mids)
+ */
+ (__pyx_v_mids[__pyx_v_i]) = (__pyx_v_mins[__pyx_v_i]);
+ }
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":318
+ * for i in range(self.m):
+ * mids[i] = mins[i]
+ * mids[d] = split # <<<<<<<<<<<<<<
+ * ni.greater = self.__build(p,end_idx,maxes,mids)
+ *
+ */
+ (__pyx_v_mids[__pyx_v_d]) = __pyx_v_split;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":319
+ * 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);
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":321
+ * ni.greater = self.__build(p,end_idx,maxes,mids)
+ *
+ * stdlib.free(mids) # <<<<<<<<<<<<<<
+ *
+ * ni.split_dim = d
+ */
+ free(__pyx_v_mids);
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":323
+ * stdlib.free(mids)
+ *
+ * ni.split_dim = d # <<<<<<<<<<<<<<
+ * ni.split = split
+ *
+ */
+ __pyx_v_ni->split_dim = __pyx_v_d;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":324
+ *
+ * ni.split_dim = d
+ * ni.split = split # <<<<<<<<<<<<<<
+ *
+ * return ni
+ */
+ __pyx_v_ni->split = __pyx_v_split;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":326
+ * ni.split = split
+ *
+ * return ni # <<<<<<<<<<<<<<
+ *
+ * cdef __free_tree(cKDTree self, innernode* node):
+ */
+ __pyx_r = __pyx_v_ni;
+ goto __pyx_L0;
+ }
+ __pyx_L3:;
+
+ __pyx_r = 0;
+ __pyx_L0:;
+ return __pyx_r;
+}
+
+/* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":328
+ * return ni
+ *
+ * cdef __free_tree(cKDTree self, innernode* node): # <<<<<<<<<<<<<<
+ * if node.split_dim!=-1:
+ * 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;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":329
+ *
+ * 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) {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":330
+ * 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;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":331
+ * 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;
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":332
+ * self.__free_tree(node.less)
+ * self.__free_tree(node.greater)
+ * stdlib.free(node) # <<<<<<<<<<<<<<
+ *
+ * def __del__(cKDTree self):
+ */
+ free(__pyx_v_node);
+
+ __pyx_r = Py_None; Py_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ Py_XDECREF(__pyx_2);
+ __Pyx_AddTraceback("scipy.spatial.ckdtree.cKDTree.__free_tree");
+ __pyx_r = 0;
+ __pyx_L0:;
+ return __pyx_r;
+}
+
+/* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":334
+ * stdlib.free(node)
+ *
+ * def __del__(cKDTree self): # <<<<<<<<<<<<<<
+ * print "freeing cKDTree"
+ * self.__free_tree(self.tree)
+ */
+
+static PyObject *__pyx_pf_5scipy_7spatial_7ckdtree_7cKDTree___del__(PyObject *__pyx_v_self, PyObject *unused); /*proto*/
+static PyObject *__pyx_pf_5scipy_7spatial_7ckdtree_7cKDTree___del__(PyObject *__pyx_v_self, PyObject *unused) {
+ PyObject *__pyx_r;
+ PyObject *__pyx_1 = 0;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":335
+ *
+ * def __del__(cKDTree self):
+ * print "freeing cKDTree" # <<<<<<<<<<<<<<
+ * self.__free_tree(self.tree)
+ *
+ */
+ __pyx_1 = PyTuple_New(1); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ Py_INCREF(__pyx_kp_20);
+ PyTuple_SET_ITEM(__pyx_1, 0, __pyx_kp_20);
+ if (__Pyx_Print(((PyObject *)__pyx_1), 1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ Py_DECREF(((PyObject *)__pyx_1)); __pyx_1 = 0;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":336
+ * def __del__(cKDTree self):
+ * print "freeing cKDTree"
+ * self.__free_tree(self.tree) # <<<<<<<<<<<<<<
+ *
+ * cdef void __query(cKDTree self,
+ */
+ __pyx_1 = ((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_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ Py_DECREF(__pyx_1); __pyx_1 = 0;
+
+ __pyx_r = Py_None; Py_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ Py_XDECREF(__pyx_1);
+ __Pyx_AddTraceback("scipy.spatial.ckdtree.cKDTree.__del__");
+ __pyx_r = NULL;
+ __pyx_L0:;
+ return __pyx_r;
+}
+
+/* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":338
+ * self.__free_tree(self.tree)
+ *
+ * cdef void __query(cKDTree self, # <<<<<<<<<<<<<<
+ * double*result_distances,
+ * 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;
+ 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;
+ double __pyx_v_d;
+ 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;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":369
+ * # 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 = 369; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ Py_DECREF(__pyx_1); __pyx_1 = 0;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":374
+ * # 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 = 374; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ Py_DECREF(__pyx_1); __pyx_1 = 0;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":377
+ *
+ * # set up first nodeinfo
+ * inf = <nodeinfo*>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))))));
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":378
+ * # set up first nodeinfo
+ * inf = <nodeinfo*>stdlib.malloc(sizeof(nodeinfo)+self.m*sizeof(double))
+ * inf.node = self.tree # <<<<<<<<<<<<<<
+ * for i in range(self.m):
+ * inf.side_distances[i] = 0
+ */
+ __pyx_v_inf->node = __pyx_v_self->tree;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":379
+ * inf = <nodeinfo*>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) {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":380
+ * inf.node = self.tree
+ * for i in range(self.m):
+ * inf.side_distances[i] = 0 # <<<<<<<<<<<<<<
+ * t = x[i]-self.raw_maxes[i]
+ * if t>inf.side_distances[i]:
+ */
+ (__pyx_v_inf->side_distances[__pyx_v_i]) = 0;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":381
+ * for i in range(self.m):
+ * inf.side_distances[i] = 0
+ * t = x[i]-self.raw_maxes[i] # <<<<<<<<<<<<<<
+ * if t>inf.side_distances[i]:
+ * inf.side_distances[i] = t
+ */
+ __pyx_v_t = ((__pyx_v_x[__pyx_v_i]) - (__pyx_v_self->raw_maxes[__pyx_v_i]));
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":382
+ * 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) {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":383
+ * 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]
+ */
+ (__pyx_v_inf->side_distances[__pyx_v_i]) = __pyx_v_t;
+ goto __pyx_L5;
+ }
+ /*else*/ {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":385
+ * inf.side_distances[i] = t
+ * else:
+ * 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]));
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":386
+ * else:
+ * 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) {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":387
+ * t = self.raw_mins[i]-x[i]
+ * 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_v_inf->side_distances[__pyx_v_i]) = __pyx_v_t;
+ goto __pyx_L6;
+ }
+ __pyx_L6:;
+ }
+ __pyx_L5:;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":388
+ * 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) {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":389
+ * inf.side_distances[i] = t
+ * if p!=1 and p!=infinity:
+ * inf.side_distances[i]=inf.side_distances[i]**p # <<<<<<<<<<<<<<
+ *
+ * # compute first distance
+ */
+ (__pyx_v_inf->side_distances[__pyx_v_i]) = pow((__pyx_v_inf->side_distances[__pyx_v_i]), __pyx_v_p);
+ goto __pyx_L7;
+ }
+ __pyx_L7:;
+ }
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":392
+ *
+ * # compute first distance
+ * min_distance = 0. # <<<<<<<<<<<<<<
+ * for i in range(self.m):
+ * if p==infinity:
+ */
+ __pyx_v_min_distance = 0.;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":393
+ * # 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) {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":394
+ * 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) {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":395
+ * 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]));
+ goto __pyx_L10;
+ }
+ /*else*/ {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":397
+ * min_distance = dmax(min_distance,inf.side_distances[i])
+ * else:
+ * min_distance += inf.side_distances[i] # <<<<<<<<<<<<<<
+ *
+ * # fiddle approximation factor
+ */
+ __pyx_v_min_distance += (__pyx_v_inf->side_distances[__pyx_v_i]);
+ }
+ __pyx_L10:;
+ }
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":400
+ *
+ * # fiddle approximation factor
+ * if eps==0: # <<<<<<<<<<<<<<
+ * epsfac=1
+ * elif p==infinity:
+ */
+ __pyx_3 = (__pyx_v_eps == 0);
+ if (__pyx_3) {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":401
+ * # fiddle approximation factor
+ * if eps==0:
+ * epsfac=1 # <<<<<<<<<<<<<<
+ * elif p==infinity:
+ * epsfac = 1/(1+eps)
+ */
+ __pyx_v_epsfac = 1;
+ goto __pyx_L11;
+ }
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":402
+ * 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) {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":403
+ * epsfac=1
+ * elif p==infinity:
+ * epsfac = 1/(1+eps) # <<<<<<<<<<<<<<
+ * else:
+ * epsfac = 1/(1+eps)**p
+ */
+ __pyx_v_epsfac = (1 / (1 + __pyx_v_eps));
+ goto __pyx_L11;
+ }
+ /*else*/ {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":405
+ * epsfac = 1/(1+eps)
+ * else:
+ * epsfac = 1/(1+eps)**p # <<<<<<<<<<<<<<
+ *
+ * # internally we represent all distances as distance**p
+ */
+ __pyx_v_epsfac = (1 / pow((1 + __pyx_v_eps), __pyx_v_p));
+ }
+ __pyx_L11:;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":408
+ *
+ * # 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_3) {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":409
+ * # internally we represent all distances as distance**p
+ * if p!=infinity and distance_upper_bound!=infinity:
+ * distance_upper_bound = distance_upper_bound**p # <<<<<<<<<<<<<<
+ *
+ * while True:
+ */
+ __pyx_v_distance_upper_bound = pow(__pyx_v_distance_upper_bound, __pyx_v_p);
+ goto __pyx_L12;
+ }
+ __pyx_L12:;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":411
+ * distance_upper_bound = distance_upper_bound**p
+ *
+ * while True: # <<<<<<<<<<<<<<
+ * if inf.node.split_dim==-1:
+ * node = <leafnode*>inf.node
+ */
+ while (1) {
+ __pyx_3 = 1;
+ if (!__pyx_3) break;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":412
+ *
+ * while True:
+ * if inf.node.split_dim==-1: # <<<<<<<<<<<<<<
+ * node = <leafnode*>inf.node
+ *
+ */
+ __pyx_3 = (__pyx_v_inf->node->split_dim == -1);
+ if (__pyx_3) {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":413
+ * while True:
+ * if inf.node.split_dim==-1:
+ * node = <leafnode*>inf.node # <<<<<<<<<<<<<<
+ *
+ * # brute-force
+ */
+ __pyx_v_node = ((struct __pyx_t_5scipy_7spatial_7ckdtree_leafnode *)__pyx_v_inf->node);
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":416
+ *
+ * # 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) {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":419
+ * d = _distance_p(
+ * self.raw_data+self.raw_indices[i]*self.m,
+ * x,p,self.m,distance_upper_bound) # <<<<<<<<<<<<<<
+ *
+ * if d<distance_upper_bound:
+ */
+ __pyx_v_d = __pyx_f_5scipy_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);
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":421
+ * x,p,self.m,distance_upper_bound)
+ *
+ * if d<distance_upper_bound: # <<<<<<<<<<<<<<
+ * # replace furthest neighbor
+ * if neighbors.n==k:
+ */
+ __pyx_3 = (__pyx_v_d < __pyx_v_distance_upper_bound);
+ if (__pyx_3) {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":423
+ * if d<distance_upper_bound:
+ * # replace furthest neighbor
+ * if neighbors.n==k: # <<<<<<<<<<<<<<
+ * heapremove(&neighbors)
+ * neighbor.priority = -d
+ */
+ __pyx_3 = (__pyx_v_neighbors.n == __pyx_v_k);
+ if (__pyx_3) {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":424
+ * # replace furthest neighbor
+ * if neighbors.n==k:
+ * heapremove(&neighbors) # <<<<<<<<<<<<<<
+ * neighbor.priority = -d
+ * neighbor.contents.intdata = self.raw_indices[i]
+ */
+ __pyx_1 = __pyx_f_5scipy_7spatial_7ckdtree_heapremove((&__pyx_v_neighbors)); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 424; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ Py_DECREF(__pyx_1); __pyx_1 = 0;
+ goto __pyx_L19;
+ }
+ __pyx_L19:;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":425
+ * if neighbors.n==k:
+ * heapremove(&neighbors)
+ * neighbor.priority = -d # <<<<<<<<<<<<<<
+ * neighbor.contents.intdata = self.raw_indices[i]
+ * heappush(&neighbors,neighbor)
+ */
+ __pyx_v_neighbor.priority = (-__pyx_v_d);
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":426
+ * heapremove(&neighbors)
+ * neighbor.priority = -d
+ * neighbor.contents.intdata = self.raw_indices[i] # <<<<<<<<<<<<<<
+ * heappush(&neighbors,neighbor)
+ *
+ */
+ __pyx_v_neighbor.contents.intdata = (__pyx_v_self->raw_indices[__pyx_v_i]);
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":427
+ * 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 = 427; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ Py_DECREF(__pyx_1); __pyx_1 = 0;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":430
+ *
+ * # 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) {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":431
+ * # 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);
+ goto __pyx_L20;
+ }
+ __pyx_L20:;
+ goto __pyx_L18;
+ }
+ __pyx_L18:;
+ }
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":433
+ * distance_upper_bound = -heappeek(&neighbors).priority
+ * # done with this node, get another
+ * stdlib.free(inf) # <<<<<<<<<<<<<<
+ * if q.n==0:
+ * # no more nodes to visit
+ */
+ free(__pyx_v_inf);
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":434
+ * # 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) {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":436
+ * if q.n==0:
+ * # no more nodes to visit
+ * break # <<<<<<<<<<<<<<
+ * else:
+ * it = heappop(&q)
+ */
+ goto __pyx_L14;
+ goto __pyx_L21;
+ }
+ /*else*/ {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":438
+ * break
+ * else:
+ * it = heappop(&q) # <<<<<<<<<<<<<<
+ * inf = <nodeinfo*>it.contents.ptrdata
+ * min_distance = it.priority
+ */
+ __pyx_v_it = __pyx_f_5scipy_7spatial_7ckdtree_heappop((&__pyx_v_q));
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":439
+ * else:
+ * it = heappop(&q)
+ * inf = <nodeinfo*>it.contents.ptrdata # <<<<<<<<<<<<<<
+ * min_distance = it.priority
+ * else:
+ */
+ __pyx_v_inf = ((struct __pyx_t_5scipy_7spatial_7ckdtree_nodeinfo *)__pyx_v_it.contents.ptrdata);
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":440
+ * it = heappop(&q)
+ * inf = <nodeinfo*>it.contents.ptrdata
+ * min_distance = it.priority # <<<<<<<<<<<<<<
+ * else:
+ * inode = <innernode*>inf.node
+ */
+ __pyx_v_min_distance = __pyx_v_it.priority;
+ }
+ __pyx_L21:;
+ goto __pyx_L15;
+ }
+ /*else*/ {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":442
+ * min_distance = it.priority
+ * else:
+ * inode = <innernode*>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);
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":447
+ * # 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) {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":449
+ * if min_distance>distance_upper_bound*epsfac:
+ * # since this is the nearest cell, we're done, bail out
+ * stdlib.free(inf) # <<<<<<<<<<<<<<
+ * # free all the nodes still on the heap
+ * for i in range(q.n):
+ */
+ free(__pyx_v_inf);
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":451
+ * 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) {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":452
+ * # free all the nodes still on the heap
+ * for i in range(q.n):
+ * stdlib.free(q.heap[i].contents.ptrdata) # <<<<<<<<<<<<<<
+ * break
+ *
+ */
+ free((__pyx_v_q.heap[__pyx_v_i]).contents.ptrdata);
+ }
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":453
+ * for i in range(q.n):
+ * stdlib.free(q.heap[i].contents.ptrdata)
+ * break # <<<<<<<<<<<<<<
+ *
+ * # set up children for searching
+ */
+ goto __pyx_L14;
+ goto __pyx_L22;
+ }
+ __pyx_L22:;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":456
+ *
+ * # set up children for searching
+ * if x[inode.split_dim]<inode.split: # <<<<<<<<<<<<<<
+ * near = inode.less
+ * far = inode.greater
+ */
+ __pyx_3 = ((__pyx_v_x[__pyx_v_inode->split_dim]) < __pyx_v_inode->split);
+ if (__pyx_3) {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":457
+ * # set up children for searching
+ * if x[inode.split_dim]<inode.split:
+ * near = inode.less # <<<<<<<<<<<<<<
+ * far = inode.greater
+ * else:
+ */
+ __pyx_v_near = __pyx_v_inode->less;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":458
+ * if x[inode.split_dim]<inode.split:
+ * near = inode.less
+ * far = inode.greater # <<<<<<<<<<<<<<
+ * else:
+ * near = inode.greater
+ */
+ __pyx_v_far = __pyx_v_inode->greater;
+ goto __pyx_L25;
+ }
+ /*else*/ {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":460
+ * far = inode.greater
+ * else:
+ * near = inode.greater # <<<<<<<<<<<<<<
+ * far = inode.less
+ *
+ */
+ __pyx_v_near = __pyx_v_inode->greater;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":461
+ * else:
+ * near = inode.greater
+ * far = inode.less # <<<<<<<<<<<<<<
+ *
+ * # near child is at the same distance as the current node
+ */
+ __pyx_v_far = __pyx_v_inode->less;
+ }
+ __pyx_L25:;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":466
+ * # 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 # <<<<<<<<<<<<<<
+ *
+ * # far child is further by an amount depending only
+ */
+ __pyx_v_inf->node = __pyx_v_near;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":471
+ * # on the split value; compute its distance and side_distances
+ * # and push it on the queue if it's near enough
+ * inf2 = <nodeinfo*>stdlib.malloc(sizeof(nodeinfo)+self.m*sizeof(double)) # <<<<<<<<<<<<<<
+ * it2.contents.ptrdata = <char*> 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))))));
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":472
+ * # and push it on the queue if it's near enough
+ * inf2 = <nodeinfo*>stdlib.malloc(sizeof(nodeinfo)+self.m*sizeof(double))
+ * it2.contents.ptrdata = <char*> inf2 # <<<<<<<<<<<<<<
+ * inf2.node = far
+ * # most side distances unchanged
+ */
+ __pyx_v_it2.contents.ptrdata = ((char *)__pyx_v_inf2);
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":473
+ * inf2 = <nodeinfo*>stdlib.malloc(sizeof(nodeinfo)+self.m*sizeof(double))
+ * it2.contents.ptrdata = <char*> inf2
+ * inf2.node = far # <<<<<<<<<<<<<<
+ * # most side distances unchanged
+ * for i in range(self.m):
+ */
+ __pyx_v_inf2->node = __pyx_v_far;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":475
+ * inf2.node = far
+ * # 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) {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":476
+ * # most side distances unchanged
+ * for i in range(self.m):
+ * inf2.side_distances[i] = inf.side_distances[i] # <<<<<<<<<<<<<<
+ *
+ * # one side distance changes
+ */
+ (__pyx_v_inf2->side_distances[__pyx_v_i]) = (__pyx_v_inf->side_distances[__pyx_v_i]);
+ }
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":480
+ * # 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) {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":483
+ * # 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])) # <<<<<<<<<<<<<<
+ * 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]))));
+ goto __pyx_L28;
+ }
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":484
+ * # 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]))
+ * 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) {
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":485
+ * far_min_distance = dmax(min_distance, dabs(inode.split-x[inode.split_dim]))
+ * 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]
+ * 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])));
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":486
+ * 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] # <<<<<<<<<<<<<<
+ * 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]));
+ goto __pyx_L28;
+ }
+ /*else*/ {
+
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+ __pyx_L6:;
+
+ /* "/home/peridot/devlib/lib/python2.5/site-packages/Cython-0.9.8.1.1-py2.5-linux-i686.egg/Cython/Includes/numpy.pxd":74
+ * if f == NULL:
+ * raise ValueError("only objects, int and float dtypes supported for ndarray buffer access so far (dtype is %d)" % t)
+ * info.format = f # <<<<<<<<<<<<<<
+ *
+ *
+ */
+ __pyx_v_info->format = __pyx_v_f;
+
+ __pyx_r = 0;
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ Py_XDECREF(__pyx_2);
+ Py_XDECREF(__pyx_3);
+ __Pyx_AddTraceback("numpy.ndarray.__getbuffer__");
+ __pyx_r = -1;
+ __pyx_L0:;
+ return __pyx_r;
+}
+static struct __pyx_vtabstruct_5scipy_7spatial_7ckdtree_cKDTree __pyx_vtable_5scipy_7spatial_7ckdtree_cKDTree;
+
+static PyObject *__pyx_tp_new_5scipy_7spatial_7ckdtree_cKDTree(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_5scipy_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->data = Py_None; Py_INCREF(Py_None);
+ p->maxes = Py_None; Py_INCREF(Py_None);
+ p->mins = Py_None; Py_INCREF(Py_None);
+ p->indices = Py_None; Py_INCREF(Py_None);
+ 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;
+ Py_XDECREF(p->data);
+ Py_XDECREF(p->maxes);
+ Py_XDECREF(p->mins);
+ Py_XDECREF(p->indices);
+ (*Py_TYPE(o)->tp_free)(o);
+}
+
+static int __pyx_tp_traverse_5scipy_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;
+ if (p->data) {
+ e = (*v)(p->data, a); if (e) return e;
+ }
+ if (p->maxes) {
+ e = (*v)(p->maxes, a); if (e) return e;
+ }
+ if (p->mins) {
+ e = (*v)(p->mins, a); if (e) return e;
+ }
+ if (p->indices) {
+ e = (*v)(p->indices, a); if (e) return e;
+ }
+ 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;
+ PyObject* tmp;
+ tmp = ((PyObject*)p->data);
+ p->data = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ tmp = ((PyObject*)p->maxes);
+ p->maxes = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ tmp = ((PyObject*)p->mins);
+ p->mins = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ tmp = ((PyObject*)p->indices);
+ p->indices = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ return 0;
+}
+
+static struct PyMethodDef __pyx_methods_5scipy_7spatial_7ckdtree_cKDTree[] = {
+ {"__del__", (PyCFunction)__pyx_pf_5scipy_7spatial_7ckdtree_7cKDTree___del__, METH_NOARGS, 0},
+ {"query", (PyCFunction)__pyx_pf_5scipy_7spatial_7ckdtree_7cKDTree_query, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5scipy_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},
+ {0, 0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number_cKDTree = {
+ 0, /*nb_add*/
+ 0, /*nb_subtract*/
+ 0, /*nb_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_divide*/
+ #endif
+ 0, /*nb_remainder*/
+ 0, /*nb_divmod*/
+ 0, /*nb_power*/
+ 0, /*nb_negative*/
+ 0, /*nb_positive*/
+ 0, /*nb_absolute*/
+ 0, /*nb_nonzero*/
+ 0, /*nb_invert*/
+ 0, /*nb_lshift*/
+ 0, /*nb_rshift*/
+ 0, /*nb_and*/
+ 0, /*nb_xor*/
+ 0, /*nb_or*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_coerce*/
+ #endif
+ 0, /*nb_int*/
+ 0, /*nb_long*/
+ 0, /*nb_float*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_oct*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_hex*/
+ #endif
+ 0, /*nb_inplace_add*/
+ 0, /*nb_inplace_subtract*/
+ 0, /*nb_inplace_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_inplace_divide*/
+ #endif
+ 0, /*nb_inplace_remainder*/
+ 0, /*nb_inplace_power*/
+ 0, /*nb_inplace_lshift*/
+ 0, /*nb_inplace_rshift*/
+ 0, /*nb_inplace_and*/
+ 0, /*nb_inplace_xor*/
+ 0, /*nb_inplace_or*/
+ 0, /*nb_floor_divide*/
+ 0, /*nb_true_divide*/
+ 0, /*nb_inplace_floor_divide*/
+ 0, /*nb_inplace_true_divide*/
+ #if (PY_MAJOR_VERSION >= 3) || (Py_TPFLAGS_DEFAULT & Py_TPFLAGS_HAVE_INDEX)
+ 0, /*nb_index*/
+ #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence_cKDTree = {
+ 0, /*sq_length*/
+ 0, /*sq_concat*/
+ 0, /*sq_repeat*/
+ 0, /*sq_item*/
+ 0, /*sq_slice*/
+ 0, /*sq_ass_item*/
+ 0, /*sq_ass_slice*/
+ 0, /*sq_contains*/
+ 0, /*sq_inplace_concat*/
+ 0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping_cKDTree = {
+ 0, /*mp_length*/
+ 0, /*mp_subscript*/
+ 0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer_cKDTree = {
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getreadbuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getwritebuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getsegcount*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getcharbuffer*/
+ #endif
+ #if (PY_MAJOR_VERSION >= 3) || (Py_TPFLAGS_DEFAULT & Py_TPFLAGS_HAVE_NEWBUFFER)
+ 0, /*bf_getbuffer*/
+ #endif
+ #if (PY_MAJOR_VERSION >= 3) || (Py_TPFLAGS_DEFAULT & Py_TPFLAGS_HAVE_NEWBUFFER)
+ 0, /*bf_releasebuffer*/
+ #endif
+};
+
+PyTypeObject __pyx_type_5scipy_7spatial_7ckdtree_cKDTree = {
+ PyVarObject_HEAD_INIT(0, 0)
+ "scipy.spatial.ckdtree.cKDTree", /*tp_name*/
+ sizeof(struct __pyx_obj_5scipy_7spatial_7ckdtree_cKDTree), /*tp_basicsize*/
+ 0, /*tp_itemsize*/
+ __pyx_tp_dealloc_5scipy_7spatial_7ckdtree_cKDTree, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+ 0, /*tp_compare*/
+ 0, /*tp_repr*/
+ &__pyx_tp_as_number_cKDTree, /*tp_as_number*/
+ &__pyx_tp_as_sequence_cKDTree, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_cKDTree, /*tp_as_mapping*/
+ 0, /*tp_hash*/
+ 0, /*tp_call*/
+ 0, /*tp_str*/
+ 0, /*tp_getattro*/
+ 0, /*tp_setattro*/
+ &__pyx_tp_as_buffer_cKDTree, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|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*/
+ 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*/
+ 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*/
+ 0, /*tp_alloc*/
+ __pyx_tp_new_5scipy_7spatial_7ckdtree_cKDTree, /*tp_new*/
+ 0, /*tp_free*/
+ 0, /*tp_is_gc*/
+ 0, /*tp_bases*/
+ 0, /*tp_mro*/
+ 0, /*tp_cache*/
+ 0, /*tp_subclasses*/
+ 0, /*tp_weaklist*/
+};
+
+static struct PyMethodDef __pyx_methods[] = {
+ {0, 0, 0, 0}
+};
+
+static void __pyx_init_filenames(void); /*proto*/
+
+#if PY_MAJOR_VERSION >= 3
+static struct PyModuleDef __pyx_moduledef = {
+ PyModuleDef_HEAD_INIT,
+ "ckdtree",
+ 0, /* m_doc */
+ -1, /* m_size */
+ __pyx_methods /* m_methods */,
+ NULL, /* m_reload */
+ NULL, /* m_traverse */
+ NULL, /* m_clear */
+ NULL /* m_free */
+};
+#endif
+
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+ {&__pyx_kp___del__, __pyx_k___del__, sizeof(__pyx_k___del__), 0, 1, 1},
+ {&__pyx_kp_query, __pyx_k_query, sizeof(__pyx_k_query), 0, 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},
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+ {&__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},
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+ {&__pyx_kp_empty, __pyx_k_empty, sizeof(__pyx_k_empty), 1, 1, 1},
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+ {&__pyx_kp___getbuffer__, __pyx_k___getbuffer__, sizeof(__pyx_k___getbuffer__), 0, 1, 1},
+ {&__pyx_kp_RuntimeError, __pyx_k_RuntimeError, sizeof(__pyx_k_RuntimeError), 1, 1, 1},
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+ __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_RuntimeError = __Pyx_GetName(__pyx_b, __pyx_kp_RuntimeError); if (!__pyx_builtin_RuntimeError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ return 0;
+ __pyx_L1_error:;
+ return -1;
+}
+
+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;};
+ 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:;
+ return -1;
+}
+
+#if PY_MAJOR_VERSION < 3
+PyMODINIT_FUNC initckdtree(void); /*proto*/
+PyMODINIT_FUNC initckdtree(void)
+#else
+PyMODINIT_FUNC PyInit_ckdtree(void); /*proto*/
+PyMODINIT_FUNC PyInit_ckdtree(void)
+#endif
+{
+ PyObject *__pyx_1 = 0;
+ PyObject *__pyx_2 = 0;
+ double __pyx_3;
+ __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;}
+ /*--- Libary function declarations ---*/
+ __pyx_init_filenames();
+ /*--- 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);
+ #else
+ __pyx_m = PyModule_Create(&__pyx_moduledef);
+ #endif
+ if (!__pyx_m) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ #if PY_MAJOR_VERSION < 3
+ Py_INCREF(__pyx_m);
+ #endif
+ __pyx_b = PyImport_AddModule(__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;};
+ /*--- 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;
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+ *(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;
+ /*--- Type import code ---*/
+ __pyx_ptype_5numpy_ndarray = __Pyx_ImportType("numpy", "ndarray", sizeof(PyArrayObject)); if (unlikely(!__pyx_ptype_5numpy_ndarray)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 24; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ /*--- Function import code ---*/
+ /*--- Execution code ---*/
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":3
+ * # Copyright Anne M. Archibald 2008
+ * # Released under the scipy license
+ * import numpy as np # <<<<<<<<<<<<<<
+ * cimport numpy as np
+ * 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;}
+ 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;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":7
+ * cimport stdlib
+ *
+ * import kdtree # <<<<<<<<<<<<<<
+ *
+ * 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;}
+ 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;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":9
+ * import kdtree
+ *
+ * cdef double infinity = np.inf # <<<<<<<<<<<<<<
+ *
+ *
+ */
+ __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;
+
+ /* "/home/peridot/software/scipy/svn/spatial/scipy/spatial/ckdtree.pyx":515
+ *
+ * def query(cKDTree self, object x, int k=1, double eps=0, double p=2,
+ * double distance_upper_bound=infinity): # <<<<<<<<<<<<<<
+ * """query the kd-tree for nearest neighbors
+ *
+ */
+ __pyx_k_17 = __pyx_v_5scipy_7spatial_7ckdtree_infinity;
+
+ /* "/home/peridot/devlib/lib/python2.5/site-packages/Cython-0.9.8.1.1-py2.5-linux-i686.egg/Cython/Includes/stdlib.pxd":2
+ *
+ * cdef extern from "stdlib.h": # <<<<<<<<<<<<<<
+ * ctypedef unsigned long size_t
+ * void free(void *ptr)
+ */
+ #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[] = {
+ "ckdtree.pyx",
+ "numpy.pxd",
+};
+
+/* Runtime support code */
+
+static void __pyx_init_filenames(void) {
+ __pyx_f = __pyx_filenames;
+}
+
+static INLINE void __Pyx_SafeReleaseBuffer(PyObject* obj, Py_buffer* info) {
+ if (info->buf == NULL) return;
+ if (info->suboffsets == __Pyx_minusones) info->suboffsets = NULL;
+ __Pyx_ReleaseBuffer(obj, info);
+}
+
+static INLINE void __Pyx_ZeroBuffer(Py_buffer* buf) {
+ buf->buf = NULL;
+ buf->strides = __Pyx_zeros;
+ buf->shape = __Pyx_zeros;
+ buf->suboffsets = __Pyx_minusones;
+}
+
+static INLINE const char* __Pyx_ConsumeWhitespace(const char* ts) {
+ while (1) {
+ switch (*ts) {
+ case 10:
+ case 13:
+ case ' ':
+ ++ts;
+ default:
+ return ts;
+ }
+ }
+}
+
+static INLINE const char* __Pyx_BufferTypestringCheckEndian(const char* ts) {
+ int num = 1;
+ int little_endian = ((char*)&num)[0];
+ int ok = 1;
+ switch (*ts) {
+ case '@':
+ case '=':
+ ++ts; break;
+ case '<':
+ if (little_endian) ++ts;
+ else ok = 0;
+ break;
+ case '>':
+ case '!':
+ if (!little_endian) ++ts;
+ else ok = 0;
+ break;
+ }
+ if (!ok) {
+ PyErr_Format(PyExc_ValueError, "Buffer has wrong endianness (rejecting on '%s')", ts);
+ return NULL;
+ }
+ 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_BufferTypestringCheck_item_double(const char* ts) {
+ if (*ts == '1') ++ts;
+ if (*ts != 'd') {
+ PyErr_Format(PyExc_ValueError, "Buffer datatype mismatch (expected 'd', got '%s')", ts);
+ return NULL;
+ } else return ts + 1;
+
+}
+
+static int __Pyx_GetBuffer_double(PyObject* obj, Py_buffer* buf, int flags, int nd) {
+ 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;
+ }
+ ts = buf->format;
+ ts = __Pyx_ConsumeWhitespace(ts);
+ ts = __Pyx_BufferTypestringCheckEndian(ts);
+ if (!ts) goto fail;
+ ts = __Pyx_ConsumeWhitespace(ts);
+ ts = __Pyx_BufferTypestringCheck_item_double(ts);
+ if (!ts) goto fail;
+ ts = __Pyx_ConsumeWhitespace(ts);
+ if (*ts != 0) {
+ PyErr_Format(PyExc_ValueError,
+ "Expected non-struct buffer data type (expected end, got '%s')", ts);
+ goto fail;
+ }
+ if (buf->suboffsets == NULL) buf->suboffsets = __Pyx_minusones;
+ return 0;
+fail:;
+ __Pyx_ZeroBuffer(buf);
+ return -1;
+}
+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_BufferTypestringCheck_item_nn___pyx_t_5numpy_int32_t(const char* ts) {
+ int ok;
+ 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 datatype mismatch (rejecting on '%s')", ts);
+ return NULL;
+ } else return ts + 1;
+
+}
+
+static int __Pyx_GetBuffer_nn___pyx_t_5numpy_int32_t(PyObject* obj, Py_buffer* buf, int flags, int nd) {
+ 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;
+ }
+ ts = buf->format;
+ ts = __Pyx_ConsumeWhitespace(ts);
+ ts = __Pyx_BufferTypestringCheckEndian(ts);
+ if (!ts) goto fail;
+ ts = __Pyx_ConsumeWhitespace(ts);
+ ts = __Pyx_BufferTypestringCheck_item_nn___pyx_t_5numpy_int32_t(ts);
+ if (!ts) goto fail;
+ ts = __Pyx_ConsumeWhitespace(ts);
+ if (*ts != 0) {
+ PyErr_Format(PyExc_ValueError,
+ "Expected non-struct buffer data type (expected end, got '%s')", ts);
+ goto fail;
+ }
+ if (buf->suboffsets == NULL) buf->suboffsets = __Pyx_minusones;
+ return 0;
+fail:;
+ __Pyx_ZeroBuffer(buf);
+ return -1;
+}
+static const char* __Pyx_BufferTypestringCheck_item_int(const char* ts) {
+ if (*ts == '1') ++ts;
+ if (*ts != 'i') {
+ PyErr_Format(PyExc_ValueError, "Buffer datatype mismatch (expected 'i', got '%s')", ts);
+ return NULL;
+ } else return ts + 1;
+
+}
+
+static int __Pyx_GetBuffer_int(PyObject* obj, Py_buffer* buf, int flags, int nd) {
+ 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;
+ }
+ ts = buf->format;
+ ts = __Pyx_ConsumeWhitespace(ts);
+ ts = __Pyx_BufferTypestringCheckEndian(ts);
+ if (!ts) goto fail;
+ ts = __Pyx_ConsumeWhitespace(ts);
+ ts = __Pyx_BufferTypestringCheck_item_int(ts);
+ if (!ts) goto fail;
+ ts = __Pyx_ConsumeWhitespace(ts);
+ if (*ts != 0) {
+ PyErr_Format(PyExc_ValueError,
+ "Expected non-struct buffer data type (expected end, got '%s')", ts);
+ goto fail;
+ }
+ if (buf->suboffsets == NULL) buf->suboffsets = __Pyx_minusones;
+ return 0;
+fail:;
+ __Pyx_ZeroBuffer(buf);
+ return -1;
+}static void __Pyx_RaiseBufferIndexError(int axis) {
+ PyErr_Format(PyExc_IndexError,
+ "Out of bounds on buffer access (axis %d)", axis);
+}
+
+
+static INLINE void __Pyx_RaiseArgtupleTooLong(
+ Py_ssize_t num_expected,
+ Py_ssize_t num_found)
+{
+ const char* error_message =
+ #if PY_VERSION_HEX < 0x02050000
+ "function takes at most %d positional arguments (%d given)";
+ #else
+ "function takes at most %zd positional arguments (%zd given)";
+ #endif
+ PyErr_Format(PyExc_TypeError, error_message, num_expected, num_found);
+}
+
+#if (PY_MAJOR_VERSION < 3) && !(Py_TPFLAGS_DEFAULT & Py_TPFLAGS_HAVE_NEWBUFFER)
+static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) {
+ if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) return __pyx_pf_5numpy_7ndarray___getbuffer__(obj, view, flags);
+ else {
+ PyErr_Format(PyExc_TypeError, "'%100s' does not have the buffer interface", Py_TYPE(obj)->tp_name);
+ return -1;
+ }
+}
+
+static void __Pyx_ReleaseBuffer(PyObject *obj, Py_buffer *view) {
+
+}
+
+#endif
+
+static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list) {
+ PyObject *__import__ = 0;
+ PyObject *empty_list = 0;
+ PyObject *module = 0;
+ PyObject *global_dict = 0;
+ PyObject *empty_dict = 0;
+ PyObject *list;
+ __import__ = PyObject_GetAttrString(__pyx_b, "__import__");
+ if (!__import__)
+ goto bad;
+ if (from_list)
+ list = from_list;
+ else {
+ empty_list = PyList_New(0);
+ if (!empty_list)
+ goto bad;
+ list = empty_list;
+ }
+ global_dict = PyModule_GetDict(__pyx_m);
+ if (!global_dict)
+ goto bad;
+ empty_dict = PyDict_New();
+ if (!empty_dict)
+ goto bad;
+ module = PyObject_CallFunction(__import__, "OOOO",
+ name, global_dict, empty_dict, list);
+bad:
+ Py_XDECREF(empty_list);
+ Py_XDECREF(__import__);
+ Py_XDECREF(empty_dict);
+ return module;
+}
+
+static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name) {
+ PyObject *result;
+ result = PyObject_GetAttr(dict, name);
+ if (!result)
+ PyErr_SetObject(PyExc_NameError, name);
+ return result;
+}
+
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
+ Py_XINCREF(type);
+ Py_XINCREF(value);
+ Py_XINCREF(tb);
+ /* First, check the traceback argument, replacing None with NULL. */
+ if (tb == Py_None) {
+ Py_DECREF(tb);
+ tb = 0;
+ }
+ else if (tb != NULL && !PyTraceBack_Check(tb)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: arg 3 must be a traceback or None");
+ goto raise_error;
+ }
+ /* Next, replace a missing value with None */
+ if (value == NULL) {
+ value = Py_None;
+ Py_INCREF(value);
+ }
+ #if PY_VERSION_HEX < 0x02050000
+ if (!PyClass_Check(type))
+ #else
+ if (!PyType_Check(type))
+ #endif
+ {
+ /* Raising an instance. The value should be a dummy. */
+ if (value != Py_None) {
+ PyErr_SetString(PyExc_TypeError,
+ "instance exception may not have a separate value");
+ goto raise_error;
+ }
+ /* Normalize to raise <class>, <instance> */
+ Py_DECREF(value);
+ value = type;
+ #if PY_VERSION_HEX < 0x02050000
+ if (PyInstance_Check(type)) {
+ type = (PyObject*) ((PyInstanceObject*)type)->in_class;
+ Py_INCREF(type);
+ }
+ else {
+ type = 0;
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception must be an old-style class or instance");
+ goto raise_error;
+ }
+ #else
+ type = (PyObject*) Py_TYPE(type);
+ Py_INCREF(type);
+ if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception class must be a subclass of BaseException");
+ goto raise_error;
+ }
+ #endif
+ }
+ PyErr_Restore(type, value, tb);
+ return;
+raise_error:
+ Py_XDECREF(value);
+ Py_XDECREF(type);
+ Py_XDECREF(tb);
+ return;
+}
+
+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
+ }
+ }
+ return item;
+}
+
+static int __Pyx_EndUnpack(PyObject *iter) {
+ PyObject *item;
+ if ((item = PyIter_Next(iter))) {
+ Py_DECREF(item);
+ PyErr_SetString(PyExc_ValueError, "too many values to unpack");
+ return -1;
+ }
+ else if (!PyErr_Occurred())
+ return 0;
+ else
+ 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;
+}
+
+#if PY_MAJOR_VERSION < 3
+static PyObject *__Pyx_GetStdout(void) {
+ PyObject *f = PySys_GetObject("stdout");
+ if (!f) {
+ PyErr_SetString(PyExc_RuntimeError, "lost sys.stdout");
+ }
+ return f;
+}
+
+static int __Pyx_Print(PyObject *arg_tuple, int newline) {
+ PyObject *f;
+ PyObject* v;
+ int i;
+
+ if (!(f = __Pyx_GetStdout()))
+ return -1;
+ for (i=0; i < PyTuple_GET_SIZE(arg_tuple); i++) {
+ if (PyFile_SoftSpace(f, 1)) {
+ if (PyFile_WriteString(" ", f) < 0)
+ return -1;
+ }
+ v = PyTuple_GET_ITEM(arg_tuple, i);
+ if (PyFile_WriteObject(v, f, Py_PRINT_RAW) < 0)
+ return -1;
+ if (PyString_Check(v)) {
+ char *s = PyString_AsString(v);
+ Py_ssize_t len = PyString_Size(v);
+ if (len > 0 &&
+ isspace(Py_CHARMASK(s[len-1])) &&
+ s[len-1] != ' ')
+ PyFile_SoftSpace(f, 0);
+ }
+ }
+ if (newline) {
+ if (PyFile_WriteString("\n", f) < 0)
+ return -1;
+ PyFile_SoftSpace(f, 0);
+ }
+ return 0;
+}
+
+#else /* Python 3 has a print function */
+static int __Pyx_Print(PyObject *arg_tuple, int newline) {
+ PyObject* kwargs = 0;
+ PyObject* result = 0;
+ PyObject* end_string;
+ if (!__pyx_print) {
+ __pyx_print = PyObject_GetAttrString(__pyx_b, "print");
+ if (!__pyx_print)
+ return -1;
+ }
+ if (!newline) {
+ if (!__pyx_print_kwargs) {
+ __pyx_print_kwargs = PyDict_New();
+ if (!__pyx_print_kwargs)
+ return -1;
+ end_string = PyUnicode_FromStringAndSize(" ", 1);
+ if (!end_string)
+ return -1;
+ if (PyDict_SetItemString(__pyx_print_kwargs, "end", end_string) < 0) {
+ Py_DECREF(end_string);
+ return -1;
+ }
+ Py_DECREF(end_string);
+ }
+ kwargs = __pyx_print_kwargs;
+ }
+ result = PyObject_Call(__pyx_print, arg_tuple, kwargs);
+ if (!result)
+ return -1;
+ Py_DECREF(result);
+ return 0;
+}
+#endif
+
+
+static void __Pyx_WriteUnraisable(const char *name) {
+ PyObject *old_exc, *old_val, *old_tb;
+ PyObject *ctx;
+ PyErr_Fetch(&old_exc, &old_val, &old_tb);
+ #if PY_MAJOR_VERSION < 3
+ ctx = PyString_FromString(name);
+ #else
+ ctx = PyUnicode_FromString(name);
+ #endif
+ PyErr_Restore(old_exc, old_val, old_tb);
+ if (!ctx)
+ ctx = Py_None;
+ PyErr_WriteUnraisable(ctx);
+}
+
+static int __Pyx_SetVtable(PyObject *dict, void *vtable) {
+ PyObject *pycobj = 0;
+ int result;
+
+ pycobj = PyCObject_FromVoidPtr(vtable, 0);
+ if (!pycobj)
+ goto bad;
+ if (PyDict_SetItemString(dict, "__pyx_vtable__", pycobj) < 0)
+ goto bad;
+ result = 0;
+ goto done;
+
+bad:
+ result = -1;
+done:
+ Py_XDECREF(pycobj);
+ return result;
+}
+
+#ifndef __PYX_HAVE_RT_ImportType
+#define __PYX_HAVE_RT_ImportType
+static PyTypeObject *__Pyx_ImportType(char *module_name, char *class_name,
+ long size)
+{
+ PyObject *py_module = 0;
+ PyObject *result = 0;
+ PyObject *py_name = 0;
+
+ #if PY_MAJOR_VERSION < 3
+ py_name = PyString_FromString(module_name);
+ #else
+ py_name = PyUnicode_FromString(module_name);
+ #endif
+ if (!py_name)
+ goto bad;
+
+ py_module = __Pyx_ImportModule(module_name);
+ if (!py_module)
+ goto bad;
+ result = PyObject_GetAttrString(py_module, class_name);
+ if (!result)
+ goto bad;
+ if (!PyType_Check(result)) {
+ PyErr_Format(PyExc_TypeError,
+ "%s.%s is not a type object",
+ module_name, class_name);
+ goto bad;
+ }
+ if (((PyTypeObject *)result)->tp_basicsize != size) {
+ PyErr_Format(PyExc_ValueError,
+ "%s.%s does not appear to be the correct type object",
+ module_name, class_name);
+ goto bad;
+ }
+ return (PyTypeObject *)result;
+bad:
+ Py_XDECREF(py_name);
+ Py_XDECREF(result);
+ return 0;
+}
+#endif
+
+#ifndef __PYX_HAVE_RT_ImportModule
+#define __PYX_HAVE_RT_ImportModule
+static PyObject *__Pyx_ImportModule(char *name) {
+ PyObject *py_name = 0;
+ PyObject *py_module = 0;
+
+ #if PY_MAJOR_VERSION < 3
+ py_name = PyString_FromString(name);
+ #else
+ py_name = PyUnicode_FromString(name);
+ #endif
+ if (!py_name)
+ goto bad;
+ py_module = PyImport_Import(py_name);
+ Py_DECREF(py_name);
+ return py_module;
+bad:
+ Py_XDECREF(py_name);
+ return 0;
+}
+#endif
+
+#include "compile.h"
+#include "frameobject.h"
+#include "traceback.h"
+
+static void __Pyx_AddTraceback(const char *funcname) {
+ PyObject *py_srcfile = 0;
+ PyObject *py_funcname = 0;
+ PyObject *py_globals = 0;
+ PyObject *empty_string = 0;
+ PyCodeObject *py_code = 0;
+ PyFrameObject *py_frame = 0;
+
+ #if PY_MAJOR_VERSION < 3
+ py_srcfile = PyString_FromString(__pyx_filename);
+ #else
+ py_srcfile = PyUnicode_FromString(__pyx_filename);
+ #endif
+ if (!py_srcfile) goto bad;
+ if (__pyx_clineno) {
+ #if PY_MAJOR_VERSION < 3
+ py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno);
+ #else
+ py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno);
+ #endif
+ }
+ else {
+ #if PY_MAJOR_VERSION < 3
+ py_funcname = PyString_FromString(funcname);
+ #else
+ py_funcname = PyUnicode_FromString(funcname);
+ #endif
+ }
+ if (!py_funcname) goto bad;
+ py_globals = PyModule_GetDict(__pyx_m);
+ if (!py_globals) goto bad;
+ #if PY_MAJOR_VERSION < 3
+ empty_string = PyString_FromStringAndSize("", 0);
+ #else
+ empty_string = PyBytes_FromStringAndSize("", 0);
+ #endif
+ if (!empty_string) goto bad;
+ py_code = PyCode_New(
+ 0, /*int argcount,*/
+ #if PY_MAJOR_VERSION >= 3
+ 0, /*int kwonlyargcount,*/
+ #endif
+ 0, /*int nlocals,*/
+ 0, /*int stacksize,*/
+ 0, /*int flags,*/
+ empty_string, /*PyObject *code,*/
+ __pyx_empty_tuple, /*PyObject *consts,*/
+ __pyx_empty_tuple, /*PyObject *names,*/
+ __pyx_empty_tuple, /*PyObject *varnames,*/
+ __pyx_empty_tuple, /*PyObject *freevars,*/
+ __pyx_empty_tuple, /*PyObject *cellvars,*/
+ py_srcfile, /*PyObject *filename,*/
+ py_funcname, /*PyObject *name,*/
+ __pyx_lineno, /*int firstlineno,*/
+ empty_string /*PyObject *lnotab*/
+ );
+ if (!py_code) goto bad;
+ py_frame = PyFrame_New(
+ PyThreadState_Get(), /*PyThreadState *tstate,*/
+ py_code, /*PyCodeObject *code,*/
+ py_globals, /*PyObject *globals,*/
+ 0 /*PyObject *locals*/
+ );
+ if (!py_frame) goto bad;
+ py_frame->f_lineno = __pyx_lineno;
+ PyTraceBack_Here(py_frame);
+bad:
+ Py_XDECREF(py_srcfile);
+ Py_XDECREF(py_funcname);
+ Py_XDECREF(empty_string);
+ Py_XDECREF(py_code);
+ Py_XDECREF(py_frame);
+}
+
+static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
+ while (t->p) {
+ #if PY_MAJOR_VERSION < 3
+ if (t->is_unicode && (!t->is_identifier)) {
+ *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
+ } else if (t->intern) {
+ *t->p = PyString_InternFromString(t->s);
+ } else {
+ *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
+ }
+ #else /* Python 3+ has unicode identifiers */
+ if (t->is_identifier || (t->is_unicode && t->intern)) {
+ *t->p = PyUnicode_InternFromString(t->s);
+ } else if (t->is_unicode) {
+ *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
+ } else {
+ *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
+ }
+ #endif
+ if (!*t->p)
+ return -1;
+ ++t;
+ }
+ return 0;
+}
+
+/* Type Conversion Functions */
+
+static INLINE Py_ssize_t __pyx_PyIndex_AsSsize_t(PyObject* b) {
+ Py_ssize_t ival;
+ PyObject* x = PyNumber_Index(b);
+ if (!x) return -1;
+ ival = PyInt_AsSsize_t(x);
+ Py_DECREF(x);
+ return ival;
+}
+
+static 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 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 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);
+ }
+}
+
Copied: branches/spatial/scipy/spatial/ckdtree.pyx (from rev 4794, branches/spatial/scipy/spatial/kdtree.py)
===================================================================
--- branches/spatial/scipy/spatial/kdtree.py 2008-10-12 13:06:54 UTC (rev 4794)
+++ branches/spatial/scipy/spatial/ckdtree.pyx 2008-10-12 13:23:48 UTC (rev 4795)
@@ -0,0 +1,592 @@
+# Copyright Anne M. Archibald 2008
+# Released under the scipy license
+import numpy as np
+cimport numpy as np
+cimport stdlib
+
+import kdtree
+
+cdef double infinity = np.inf
+
+
+
+
+# priority queue
+cdef union heapcontents:
+ int intdata
+ char* ptrdata
+
+cdef struct heapitem:
+ double priority
+ heapcontents contents
+
+cdef struct heap:
+ int n
+ heapitem* heap
+ int space
+
+cdef inline heapcreate(heap* self,int initial_size):
+ self.space = initial_size
+ self.heap = <heapitem*>stdlib.malloc(sizeof(heapitem)*self.space)
+ self.n=0
+
+cdef inline heapdestroy(heap* self):
+ stdlib.free(self.heap)
+
+cdef inline heapresize(heap* self, int new_space):
+ if new_space<self.n:
+ raise ValueError("Heap containing %d items cannot be resized to %d" % (self.n, new_space))
+ self.space = new_space
+ self.heap = <heapitem*>stdlib.realloc(<void*>self.heap,new_space*sizeof(heapitem))
+
+cdef inline heappush(heap* self, heapitem item):
+ cdef int i
+ cdef heapitem t
+
+ self.n += 1
+ if self.n>self.space:
+ heapresize(self,2*self.space+1)
+
+ i = self.n-1
+ self.heap[i] = item
+ while i>0 and self.heap[i].priority<self.heap[(i-1)//2].priority:
+ t = self.heap[(i-1)//2]
+ self.heap[(i-1)//2] = self.heap[i]
+ self.heap[i] = t
+ i = (i-1)//2
+
+cdef heapitem heappeek(heap* self):
+ return self.heap[0]
+
+cdef heapremove(heap* self):
+ cdef heapitem t
+ cdef int i, j, k, l
+
+ 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)
+
+ i=0
+ j=1
+ k=2
+ while ((j<self.n and
+ self.heap[i].priority > self.heap[j].priority or
+ k<self.n and
+ self.heap[i].priority > self.heap[k].priority)):
+ if k<self.n and self.heap[j].priority>self.heap[k].priority:
+ l = k
+ else:
+ l = j
+ t = self.heap[l]
+ self.heap[l] = self.heap[i]
+ self.heap[i] = t
+ i = l
+ j = 2*i+1
+ k = 2*i+2
+
+cdef heapitem heappop(heap* self):
+ cdef heapitem it
+ it = heappeek(self)
+ heapremove(self)
+ return it
+
+
+
+
+
+# utility functions
+cdef inline double dmax(double x, double y):
+ if x>y:
+ return x
+ else:
+ return y
+cdef inline double dabs(double x):
+ if x>0:
+ 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
+
+ Computes the Minkowski p-distance to the power p between two points.
+ If the distance**p is larger than upperbound, then any number larger
+ than upperbound may be returned (the calculation is truncated).
+ """
+ cdef int i
+ cdef double r
+ r = 0
+ if p==infinity:
+ for i in range(k):
+ r = dmax(r,dabs(x[i]-y[i]))
+ if r>upperbound:
+ return r
+ elif p==1:
+ for i in range(k):
+ r += dabs(x[i]-y[i])
+ if r>upperbound:
+ return r
+ else:
+ for i in range(k):
+ r += dabs(x[i]-y[i])**p
+ if r>upperbound:
+ return r
+ return r
+
+
+
+# Tree structure
+cdef struct innernode:
+ int split_dim
+ int n_points
+ double split
+ innernode* less
+ innernode* greater
+cdef struct leafnode:
+ int split_dim
+ int n_points
+ int start_idx
+ int end_idx
+
+# this is the standard trick for variable-size arrays:
+# malloc sizeof(nodeinfo)+self.m*sizeof(double) bytes.
+cdef struct nodeinfo:
+ innernode* node
+ double side_distances[0]
+
+cdef class cKDTree:
+ """kd-tree for quick nearest-neighbor lookup
+
+ This class provides an index into a set of k-dimensional points
+ which can be used to rapidly look up the nearest neighbors of any
+ point.
+
+ The algorithm used is described in Maneewongvatana and Mount 1999.
+ The general idea is that the kd-tree is a binary trie, each of whose
+ nodes represents an axis-aligned hyperrectangle. Each node specifies
+ an axis and splits the set of points based on whether their coordinate
+ along that axis is greater than or less than a particular value.
+
+ During construction, the axis and splitting point are chosen by the
+ "sliding midpoint" rule, which ensures that the cells do not all
+ become long and thin.
+
+ The tree can be queried for the r closest neighbors of any given point
+ (optionally returning only those within some maximum distance of the
+ point). It can also be queried, with a substantial gain in efficiency,
+ for the r approximate closest neighbors.
+
+ For large dimensions (20 is already large) do not expect this to run
+ significantly faster than brute force. High-dimensional nearest-neighbor
+ queries are a substantial open problem in computer science.
+ """
+
+ cdef innernode* tree
+ cdef readonly object data
+ cdef double* raw_data
+ cdef readonly int n, m
+ cdef readonly int leafsize
+ cdef readonly object maxes
+ cdef double* raw_maxes
+ cdef readonly object mins
+ cdef double* raw_mins
+ cdef object indices
+ cdef np.int32_t* raw_indices
+ def __init__(cKDTree self, data, int leafsize=10):
+ """Construct a kd-tree.
+
+ Parameters:
+ ===========
+
+ data : array-like, shape (n,m)
+ The n data points of dimension mto be indexed. This array is
+ not copied unless this is necessary to produce a contiguous
+ array of doubles, and so modifying this data will result in
+ bogus results.
+ leafsize : positive integer
+ The number of points at which the algorithm switches over to
+ brute-force.
+ """
+ cdef np.ndarray[double, ndim=2] inner_data
+ cdef np.ndarray[double, ndim=1] inner_maxes
+ cdef np.ndarray[double, ndim=1] inner_mins
+ cdef np.ndarray[np.int32_t, ndim=1] inner_indices
+ self.data = np.ascontiguousarray(data,dtype=np.float)
+ self.n, self.m = np.shape(self.data)
+ self.leafsize = leafsize
+ if self.leafsize<1:
+ raise ValueError("leafsize must be at least 1")
+ self.maxes = np.ascontiguousarray(np.amax(self.data,axis=0))
+ self.mins = np.ascontiguousarray(np.amin(self.data,axis=0))
+ self.indices = np.ascontiguousarray(np.arange(self.n,dtype=np.int))
+
+ inner_data = self.data
+ self.raw_data = <double*>inner_data.data
+ inner_maxes = self.maxes
+ self.raw_maxes = <double*>inner_maxes.data
+ inner_mins = self.mins
+ self.raw_mins = <double*>inner_mins.data
+ inner_indices = self.indices
+ self.raw_indices = <np.int32_t*>inner_indices.data
+
+ self.tree = self.__build(0, self.n, self.raw_maxes, self.raw_mins)
+
+ cdef innernode* __build(cKDTree self, int start_idx, int end_idx, double* maxes, double* mins):
+ cdef leafnode* n
+ cdef innernode* ni
+ cdef int i, j, t, p, q, d
+ cdef double size, split, minval, maxval
+ cdef double*mids
+ if end_idx-start_idx<=self.leafsize:
+ n = <leafnode*>stdlib.malloc(sizeof(leafnode))
+ n.split_dim = -1
+ n.start_idx = start_idx
+ n.end_idx = end_idx
+ return <innernode*>n
+ else:
+ d = 0
+ size = 0
+ for i in range(self.m):
+ if maxes[i]-mins[i] > size:
+ d = i
+ size = maxes[i]-mins[i]
+ maxval = maxes[d]
+ minval = mins[d]
+ if maxval==minval:
+ # all points are identical; warn user?
+ n = <leafnode*>stdlib.malloc(sizeof(leafnode))
+ n.split_dim = -1
+ n.start_idx = start_idx
+ n.end_idx = end_idx
+ return <innernode*>n
+
+ split = (maxval+minval)/2
+
+ p = start_idx
+ q = end_idx-1
+ while p<=q:
+ if self.raw_data[self.raw_indices[p]*self.m+d]<split:
+ p+=1
+ elif self.raw_data[self.raw_indices[q]*self.m+d]>=split:
+ q-=1
+ else:
+ t = self.raw_indices[p]
+ self.raw_indices[p] = self.raw_indices[q]
+ self.raw_indices[q] = t
+ p+=1
+ q-=1
+
+ # slide midpoint if necessary
+ if p==start_idx:
+ # no points less than split
+ 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]<split:
+ j = i
+ 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]
+ self.raw_indices[j] = t
+ p = start_idx+1
+ q = start_idx
+ elif p==end_idx:
+ # no points greater than split
+ 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
+ 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]
+ self.raw_indices[j] = t
+ p = end_idx-1
+ q = end_idx-2
+
+ # construct new node representation
+ ni = <innernode*>stdlib.malloc(sizeof(innernode))
+
+ mids = <double*>stdlib.malloc(sizeof(double)*self.m)
+ for i in range(self.m):
+ mids[i] = maxes[i]
+ mids[d] = split
+ ni.less = self.__build(start_idx,p,mids,mins)
+
+ for i in range(self.m):
+ mids[i] = mins[i]
+ mids[d] = split
+ ni.greater = self.__build(p,end_idx,maxes,mids)
+
+ stdlib.free(mids)
+
+ ni.split_dim = d
+ ni.split = split
+
+ return ni
+
+ 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)
+
+ def __del__(cKDTree self):
+ print "freeing cKDTree"
+ self.__free_tree(self.tree)
+
+ cdef void __query(cKDTree self,
+ double*result_distances,
+ int*result_indices,
+ double*x,
+ int k,
+ double eps,
+ double p,
+ double distance_upper_bound):
+ cdef heap q
+ cdef heap neighbors
+
+ cdef int i, j
+ cdef double t
+ cdef nodeinfo* inf
+ cdef nodeinfo* inf2
+ cdef double d
+ cdef double epsfac
+ cdef double min_distance
+ cdef double far_min_distance
+ cdef heapitem it, it2, neighbor
+ cdef leafnode* node
+ cdef innernode* inode
+ cdef innernode* near
+ cdef innernode* far
+ cdef double* side_distances
+
+ # priority queue for chasing nodes
+ # entries are:
+ # minimum distance between the cell and the target
+ # 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
+ # furthest known neighbor first
+ # entries are (-distance**p, i)
+ heapcreate(&neighbors,k)
+
+ # set up first nodeinfo
+ inf = <nodeinfo*>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]
+ if t>inf.side_distances[i]:
+ inf.side_distances[i] = t
+ else:
+ t = self.raw_mins[i]-x[i]
+ 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
+
+ # compute first distance
+ min_distance = 0.
+ 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]
+
+ # fiddle approximation factor
+ if eps==0:
+ epsfac=1
+ elif p==infinity:
+ epsfac = 1/(1+eps)
+ else:
+ epsfac = 1/(1+eps)**p
+
+ # internally we represent all distances as distance**p
+ if p!=infinity and distance_upper_bound!=infinity:
+ distance_upper_bound = distance_upper_bound**p
+
+ while True:
+ if inf.node.split_dim==-1:
+ node = <leafnode*>inf.node
+
+ # brute-force
+ 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)
+
+ if d<distance_upper_bound:
+ # replace furthest neighbor
+ if neighbors.n==k:
+ heapremove(&neighbors)
+ neighbor.priority = -d
+ neighbor.contents.intdata = self.raw_indices[i]
+ heappush(&neighbors,neighbor)
+
+ # adjust upper bound for efficiency
+ if neighbors.n==k:
+ distance_upper_bound = -heappeek(&neighbors).priority
+ # done with this node, get another
+ stdlib.free(inf)
+ if q.n==0:
+ # no more nodes to visit
+ break
+ else:
+ it = heappop(&q)
+ inf = <nodeinfo*>it.contents.ptrdata
+ min_distance = it.priority
+ else:
+ inode = <innernode*>inf.node
+
+ # we don't push cells that are too far onto the queue at all,
+ # 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)
+ # free all the nodes still on the heap
+ for i in range(q.n):
+ stdlib.free(q.heap[i].contents.ptrdata)
+ break
+
+ # set up children for searching
+ if x[inode.split_dim]<inode.split:
+ near = inode.less
+ far = inode.greater
+ else:
+ near = inode.greater
+ far = inode.less
+
+ # near child is at the same distance as the current node
+ # 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
+
+ # far child is further by an amount depending only
+ # on the split value; compute its distance and side_distances
+ # and push it on the queue if it's near enough
+ inf2 = <nodeinfo*>stdlib.malloc(sizeof(nodeinfo)+self.m*sizeof(double))
+ it2.contents.ptrdata = <char*> inf2
+ inf2.node = far
+ # most side distances unchanged
+ for i in range(self.m):
+ inf2.side_distances[i] = inf.side_distances[i]
+
+ # 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])
+ far_min_distance = dmax(min_distance, dabs(inode.split-x[inode.split_dim]))
+ 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]
+ 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]
+
+ it2.priority = far_min_distance
+
+
+ # 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)
+ # just in case
+ it2.contents.ptrdata = <char*> 0
+
+ # 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:
+ result_distances[i] = -neighbor.priority
+ else:
+ result_distances[i] = (-neighbor.priority)**(1./p)
+
+ heapdestroy(&q)
+ heapdestroy(&neighbors)
+
+ def query(cKDTree self, object x, int k=1, double eps=0, double p=2,
+ double distance_upper_bound=infinity):
+ """query the kd-tree for nearest neighbors
+
+ Parameters:
+ ===========
+
+ x : array-like, last dimension self.m
+ An array of points to query.
+ k : integer
+ The number of nearest neighbors to return.
+ eps : nonnegative float
+ Return approximate nearest neighbors; the kth returned value
+ is guaranteed to be no further than (1+eps) times the
+ distance to the real kth nearest neighbor.
+ p : float, 1<=p<=infinity
+ Which Minkowski p-norm to use.
+ 1 is the sum-of-absolute-values "Manhattan" distance
+ 2 is the usual Euclidean distance
+ infinity is the maximum-coordinate-difference distance
+ distance_upper_bound : nonnegative float
+ Return only neighbors within this distance. This is used to prune
+ tree searches, so if you are doing a series of nearest-neighbor
+ queries, it may help to supply the distance to the nearest neighbor
+ of the most recent point.
+
+ Returns:
+ ========
+
+ d : array of floats
+ The distances to the nearest neighbors.
+ If x has shape tuple+(self.m,), then d has shape tuple+(k,).
+ Missing neighbors are indicated with infinite distances.
+ i : array of integers
+ The locations of the neighbors in self.data.
+ If x has shape tuple+(self.m,), then i has shape tuple+(k,).
+ Missing neighbors are indicated with self.n+1.
+ """
+ cdef np.ndarray[int, ndim=2] ii
+ cdef np.ndarray[double, ndim=2] dd
+ cdef np.ndarray[double, ndim=2] xx
+ cdef int c
+ x = np.asarray(x).astype(np.float)
+ 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:
+ raise ValueError("Only p-norms with 1<=p<=infinity permitted")
+ if len(x.shape)==1:
+ single = True
+ x = x[np.newaxis,:]
+ else:
+ single = False
+ retshape = np.shape(x)[:-1]
+ n = np.prod(retshape)
+ xx = np.reshape(x,(n,self.m))
+ dd = np.empty((n,k),dtype=np.float)
+ dd.fill(infinity)
+ ii = np.empty((n,k),dtype='i')
+ ii.fill(self.n)
+ for c in range(n):
+ self.__query(
+ (<double*>dd.data)+c*k,
+ (<int*>ii.data)+c*k,
+ (<double*>xx.data)+c*self.m,
+ k,
+ eps,
+ p,
+ distance_upper_bound)
+ if single:
+ if k==1:
+ return dd[0,0], ii[0,0]
+ else:
+ return dd[0], ii[0]
+ else:
+ if k==1:
+ return np.reshape(dd[...,0],retshape), np.reshape(ii[...,0],retshape)
+ else:
+ return np.reshape(dd,retshape+(k,)), np.reshape(ii,retshape+(k,))
+
Property changes on: branches/spatial/scipy/spatial/ckdtree.pyx
___________________________________________________________________
Name: svn:mergeinfo
+
Modified: branches/spatial/scipy/spatial/setup.py
===================================================================
--- branches/spatial/scipy/spatial/setup.py 2008-10-12 13:06:54 UTC (rev 4794)
+++ branches/spatial/scipy/spatial/setup.py 2008-10-12 13:23:48 UTC (rev 4795)
@@ -8,6 +8,7 @@
config = Configuration('spatial', parent_package, top_path)
config.add_data_dir('tests')
+ config.add_extension('ckdtree', sources=['ckdtree.c']) # FIXME: cython
return config
Modified: branches/spatial/scipy/spatial/tests/test_kdtree.py
===================================================================
--- branches/spatial/scipy/spatial/tests/test_kdtree.py 2008-10-12 13:06:54 UTC (rev 4794)
+++ branches/spatial/scipy/spatial/tests/test_kdtree.py 2008-10-12 13:23:48 UTC (rev 4795)
@@ -3,7 +3,7 @@
from numpy.testing import *
import numpy as np
-from scipy.spatial import KDTree, distance, Rectangle, distance_matrix
+from scipy.spatial import KDTree, distance, Rectangle, distance_matrix, cKDTree
class ConsistencyTests:
def test_nearest(self):
@@ -115,21 +115,25 @@
([0.1,0.9],[0,1]))
class test_small_nonleaf(test_small):
def setUp(self):
- self.data = np.array([[0,0,0],
- [0,0,1],
- [0,1,0],
- [0,1,1],
- [1,0,0],
- [1,0,1],
- [1,1,0],
- [1,1,1]])
+ test_small.setUp(self)
self.kdtree = KDTree(self.data,leafsize=1)
- self.n = self.kdtree.n
- self.m = self.kdtree.m
- self.x = np.random.randn(self.m)
- self.d = 0.5
- self.k = 4
+class test_small_compiled(test_small):
+ def setUp(self):
+ test_small.setUp(self)
+ self.kdtree = cKDTree(self.data)
+class test_small_nonleaf_compiled(test_small):
+ def setUp(self):
+ test_small.setUp(self)
+ self.kdtree = cKDTree(self.data,leafsize=1)
+class test_random_compiled(test_random):
+ def setUp(self):
+ test_random.setUp(self)
+ self.kdtree = cKDTree(self.data)
+class test_random_far_compiled(test_random_far):
+ def setUp(self):
+ test_random_far.setUp(self)
+ self.kdtree = cKDTree(self.data)
class test_vectorization:
def setUp(self):
@@ -181,6 +185,45 @@
assert isinstance(d[0,0],list)
assert isinstance(i[0,0],list)
+class test_vectorization_compiled:
+ def setUp(self):
+ self.data = np.array([[0,0,0],
+ [0,0,1],
+ [0,1,0],
+ [0,1,1],
+ [1,0,0],
+ [1,0,1],
+ [1,1,0],
+ [1,1,1]])
+ self.kdtree = KDTree(self.data)
+
+ def test_single_query(self):
+ d, i = self.kdtree.query([0,0,0])
+ assert isinstance(d,float)
+ assert isinstance(i,int)
+
+ def test_vectorized_query(self):
+ d, i = self.kdtree.query(np.zeros((2,4,3)))
+ assert_equal(np.shape(d),(2,4))
+ assert_equal(np.shape(i),(2,4))
+
+ def test_single_query_multiple_neighbors(self):
+ s = 23
+ kk = self.kdtree.n+s
+ d, i = self.kdtree.query([0,0,0],k=kk)
+ assert_equal(np.shape(d),(kk,))
+ assert_equal(np.shape(i),(kk,))
+ assert np.all(~np.isfinite(d[-s:]))
+ assert np.all(i[-s:]==self.kdtree.n)
+ def test_vectorized_query_multiple_neighbors(self):
+ s = 23
+ kk = self.kdtree.n+s
+ d, i = self.kdtree.query(np.zeros((2,4,3)),k=kk)
+ assert_equal(np.shape(d),(2,4,kk))
+ assert_equal(np.shape(i),(2,4,kk))
+ assert np.all(~np.isfinite(d[:,:,-s:]))
+ assert np.all(i[:,:,-s:]==self.kdtree.n)
+
class ball_consistency:
def test_in_ball(self):
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