From c2b8b5d9de51aa61b58fd6d9a85f9bf9c092ed1f Mon Sep 17 00:00:00 2001
From: Lars Buitinck <larsmans@gmail.com>
Date: Wed, 7 Aug 2013 14:16:56 +0200
Subject: [PATCH] FIX integer types in Ward clustering
Use np.npy_intp, aka np.intp in Python, for all indices.
Also added mode='c' declarations where NumPy would permit
and made some small improvements to the docs and code style.
---
sklearn/cluster/_hierarchical.c | 2015 ++++++++++++++++++-----------
sklearn/cluster/_hierarchical.pyx | 84 +-
sklearn/cluster/hierarchical.py | 24 +-
3 files changed, 1284 insertions(+), 839 deletions(-)
diff --git a/sklearn/cluster/_hierarchical.c b/sklearn/cluster/_hierarchical.c
index f62b8ad1c1..ecf30f0ab2 100644
--- a/sklearn/cluster/_hierarchical.c
+++ b/sklearn/cluster/_hierarchical.c
@@ -1,6 +1,18 @@
-/* Generated by Cython 0.17.4 on Thu Jan 10 17:59:48 2013 */
+/* Generated by Cython 0.19.1 on Wed Aug 7 14:16:15 2013 */
#define PY_SSIZE_T_CLEAN
+#ifndef CYTHON_USE_PYLONG_INTERNALS
+#ifdef PYLONG_BITS_IN_DIGIT
+#define CYTHON_USE_PYLONG_INTERNALS 0
+#else
+#include "pyconfig.h"
+#ifdef PYLONG_BITS_IN_DIGIT
+#define CYTHON_USE_PYLONG_INTERNALS 1
+#else
+#define CYTHON_USE_PYLONG_INTERNALS 0
+#endif
+#endif
+#endif
#include "Python.h"
#ifndef Py_PYTHON_H
#error Python headers needed to compile C extensions, please install development version of Python.
@@ -116,6 +128,9 @@
#if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3)
#define Py_TPFLAGS_HAVE_NEWBUFFER 0
#endif
+#if PY_VERSION_HEX < 0x02060000
+ #define Py_TPFLAGS_HAVE_VERSION_TAG 0
+#endif
#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
#define CYTHON_PEP393_ENABLED 1
#define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \
@@ -155,6 +170,14 @@
#define PyBytes_Concat PyString_Concat
#define PyBytes_ConcatAndDel PyString_ConcatAndDel
#endif
+#if PY_MAJOR_VERSION >= 3
+ #define __Pyx_PyBaseString_Check(obj) PyUnicode_Check(obj)
+ #define __Pyx_PyBaseString_CheckExact(obj) PyUnicode_CheckExact(obj)
+#else
+ #define __Pyx_PyBaseString_Check(obj) (PyString_CheckExact(obj) || PyUnicode_CheckExact(obj) || \
+ PyString_Check(obj) || PyUnicode_Check(obj))
+ #define __Pyx_PyBaseString_CheckExact(obj) (Py_TYPE(obj) == &PyBaseString_Type)
+#endif
#if PY_VERSION_HEX < 0x02060000
#define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type)
#define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type)
@@ -227,6 +250,40 @@
#define __Pyx_NAMESTR(n) (n)
#define __Pyx_DOCSTR(n) (n)
#endif
+#ifndef CYTHON_INLINE
+ #if defined(__GNUC__)
+ #define CYTHON_INLINE __inline__
+ #elif defined(_MSC_VER)
+ #define CYTHON_INLINE __inline
+ #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
+ #define CYTHON_INLINE inline
+ #else
+ #define CYTHON_INLINE
+ #endif
+#endif
+#ifndef CYTHON_RESTRICT
+ #if defined(__GNUC__)
+ #define CYTHON_RESTRICT __restrict__
+ #elif defined(_MSC_VER)
+ #define CYTHON_RESTRICT __restrict
+ #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
+ #define CYTHON_RESTRICT restrict
+ #else
+ #define CYTHON_RESTRICT
+ #endif
+#endif
+#ifdef NAN
+#define __PYX_NAN() ((float) NAN)
+#else
+static CYTHON_INLINE float __PYX_NAN() {
+ /* Initialize NaN. The sign is irrelevant, an exponent with all bits 1 and
+ a nonzero mantissa means NaN. If the first bit in the mantissa is 1, it is
+ a quiet NaN. */
+ float value;
+ memset(&value, 0xFF, sizeof(value));
+ return value;
+}
+#endif
#if PY_MAJOR_VERSION >= 3
@@ -251,6 +308,7 @@
#include <math.h>
#define __PYX_HAVE__sklearn__cluster___hierarchical
#define __PYX_HAVE_API__sklearn__cluster___hierarchical
+#include "string.h"
#include "stdio.h"
#include "stdlib.h"
#include "numpy/arrayobject.h"
@@ -263,21 +321,6 @@
#define CYTHON_WITHOUT_ASSERTIONS
#endif
-
-/* inline attribute */
-#ifndef CYTHON_INLINE
- #if defined(__GNUC__)
- #define CYTHON_INLINE __inline__
- #elif defined(_MSC_VER)
- #define CYTHON_INLINE __inline
- #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
- #define CYTHON_INLINE inline
- #else
- #define CYTHON_INLINE
- #endif
-#endif
-
-/* unused attribute */
#ifndef CYTHON_UNUSED
# if defined(__GNUC__)
# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
@@ -291,30 +334,130 @@
# define CYTHON_UNUSED
# endif
#endif
-
-typedef struct {PyObject **p; char *s; const long n; const char* encoding; const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; /*proto*/
-
-
-/* Type Conversion Predeclarations */
-
-#define __Pyx_PyBytes_FromUString(s) PyBytes_FromString((char*)s)
-#define __Pyx_PyBytes_AsUString(s) ((unsigned char*) PyBytes_AsString(s))
-
+typedef struct {PyObject **p; char *s; const Py_ssize_t n; const char* encoding;
+ const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; /*proto*/
+
+#define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0
+#define __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT 0
+#define __PYX_DEFAULT_STRING_ENCODING ""
+#define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString
+#define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
+static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject*);
+static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length);
+#define __Pyx_PyBytes_FromString PyBytes_FromString
+#define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize
+static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(char*);
+#if PY_MAJOR_VERSION < 3
+ #define __Pyx_PyStr_FromString __Pyx_PyBytes_FromString
+ #define __Pyx_PyStr_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
+#else
+ #define __Pyx_PyStr_FromString __Pyx_PyUnicode_FromString
+ #define __Pyx_PyStr_FromStringAndSize __Pyx_PyUnicode_FromStringAndSize
+#endif
+#define __Pyx_PyObject_AsUString(s) ((unsigned char*) __Pyx_PyObject_AsString(s))
+#define __Pyx_PyObject_FromUString(s) __Pyx_PyObject_FromString((char*)s)
+#define __Pyx_PyBytes_FromUString(s) __Pyx_PyBytes_FromString((char*)s)
+#define __Pyx_PyStr_FromUString(s) __Pyx_PyStr_FromString((char*)s)
+#define __Pyx_PyUnicode_FromUString(s) __Pyx_PyUnicode_FromString((char*)s)
+#if PY_MAJOR_VERSION < 3
+static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u)
+{
+ const Py_UNICODE *u_end = u;
+ while (*u_end++) ;
+ return u_end - u - 1;
+}
+#else
+#define __Pyx_Py_UNICODE_strlen Py_UNICODE_strlen
+#endif
+#define __Pyx_PyUnicode_FromUnicode(u) PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u))
+#define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode
+#define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode
#define __Pyx_Owned_Py_None(b) (Py_INCREF(Py_None), Py_None)
#define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False))
static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*);
static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x);
-
static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*);
-
#if CYTHON_COMPILING_IN_CPYTHON
#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
#else
#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x)
#endif
#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x))
+#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
+static int __Pyx_sys_getdefaultencoding_not_ascii;
+static int __Pyx_init_sys_getdefaultencoding_params() {
+ PyObject* sys = NULL;
+ PyObject* default_encoding = NULL;
+ PyObject* ascii_chars_u = NULL;
+ PyObject* ascii_chars_b = NULL;
+ sys = PyImport_ImportModule("sys");
+ if (sys == NULL) goto bad;
+ default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL);
+ if (default_encoding == NULL) goto bad;
+ if (strcmp(PyBytes_AsString(default_encoding), "ascii") == 0) {
+ __Pyx_sys_getdefaultencoding_not_ascii = 0;
+ } else {
+ const char* default_encoding_c = PyBytes_AS_STRING(default_encoding);
+ char ascii_chars[128];
+ int c;
+ for (c = 0; c < 128; c++) {
+ ascii_chars[c] = c;
+ }
+ __Pyx_sys_getdefaultencoding_not_ascii = 1;
+ ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL);
+ if (ascii_chars_u == NULL) goto bad;
+ ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL);
+ if (ascii_chars_b == NULL || strncmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) {
+ PyErr_Format(
+ PyExc_ValueError,
+ "This module compiled with c_string_encoding=ascii, but default encoding '%s' is not a superset of ascii.",
+ default_encoding_c);
+ goto bad;
+ }
+ }
+ Py_XDECREF(sys);
+ Py_XDECREF(default_encoding);
+ Py_XDECREF(ascii_chars_u);
+ Py_XDECREF(ascii_chars_b);
+ return 0;
+bad:
+ Py_XDECREF(sys);
+ Py_XDECREF(default_encoding);
+ Py_XDECREF(ascii_chars_u);
+ Py_XDECREF(ascii_chars_b);
+ return -1;
+}
+#endif
+#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT && PY_MAJOR_VERSION >= 3
+#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_DecodeUTF8(c_str, size, NULL)
+#else
+#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_Decode(c_str, size, __PYX_DEFAULT_STRING_ENCODING, NULL)
+#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
+static char* __PYX_DEFAULT_STRING_ENCODING;
+static int __Pyx_init_sys_getdefaultencoding_params() {
+ PyObject* sys = NULL;
+ PyObject* default_encoding = NULL;
+ char* default_encoding_c;
+ sys = PyImport_ImportModule("sys");
+ if (sys == NULL) goto bad;
+ default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL);
+ if (default_encoding == NULL) goto bad;
+ default_encoding_c = PyBytes_AS_STRING(default_encoding);
+ __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c));
+ strcpy(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c);
+ Py_DECREF(sys);
+ Py_DECREF(default_encoding);
+ return 0;
+bad:
+ Py_XDECREF(sys);
+ Py_XDECREF(default_encoding);
+ return -1;
+}
+#endif
+#endif
+
#ifdef __GNUC__
/* Test for GCC > 2.95 */
@@ -329,8 +472,9 @@ static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*);
#define likely(x) (x)
#define unlikely(x) (x)
#endif /* __GNUC__ */
-
+
static PyObject *__pyx_m;
+static PyObject *__pyx_d;
static PyObject *__pyx_b;
static PyObject *__pyx_empty_tuple;
static PyObject *__pyx_empty_bytes;
@@ -591,27 +735,27 @@ typedef npy_double __pyx_t_5numpy_double_t;
*/
typedef npy_longdouble __pyx_t_5numpy_longdouble_t;
-/* "sklearn/cluster/_hierarchical.pyx":4
- * cimport numpy as np
+/* "sklearn/cluster/_hierarchical.pyx":7
* cimport cython
+ *
* ctypedef np.float64_t DOUBLE # <<<<<<<<<<<<<<
- * ctypedef np.int_t INT
+ * ctypedef np.npy_intp INTP
* ctypedef np.int8_t INT8
*/
typedef __pyx_t_5numpy_float64_t __pyx_t_7sklearn_7cluster_13_hierarchical_DOUBLE;
-/* "sklearn/cluster/_hierarchical.pyx":5
- * cimport cython
+/* "sklearn/cluster/_hierarchical.pyx":8
+ *
* ctypedef np.float64_t DOUBLE
- * ctypedef np.int_t INT # <<<<<<<<<<<<<<
+ * ctypedef np.npy_intp INTP # <<<<<<<<<<<<<<
* ctypedef np.int8_t INT8
*
*/
-typedef __pyx_t_5numpy_int_t __pyx_t_7sklearn_7cluster_13_hierarchical_INT;
+typedef npy_intp __pyx_t_7sklearn_7cluster_13_hierarchical_INTP;
-/* "sklearn/cluster/_hierarchical.pyx":6
+/* "sklearn/cluster/_hierarchical.pyx":9
* ctypedef np.float64_t DOUBLE
- * ctypedef np.int_t INT
+ * ctypedef np.npy_intp INTP
* ctypedef np.int8_t INT8 # <<<<<<<<<<<<<<
*
* np.import_array()
@@ -729,7 +873,22 @@ typedef npy_cdouble __pyx_t_5numpy_complex_t;
#define __Pyx_CLEAR(r) do { PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);} while(0)
#define __Pyx_XCLEAR(r) do { if((r) != NULL) {PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);}} while(0)
-static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/
+#if CYTHON_COMPILING_IN_CPYTHON
+static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject* attr_name) {
+ PyTypeObject* tp = Py_TYPE(obj);
+ if (likely(tp->tp_getattro))
+ return tp->tp_getattro(obj, attr_name);
+#if PY_MAJOR_VERSION < 3
+ if (likely(tp->tp_getattr))
+ return tp->tp_getattr(obj, PyString_AS_STRING(attr_name));
+#endif
+ return PyObject_GetAttr(obj, attr_name);
+}
+#else
+#define __Pyx_PyObject_GetAttrStr(o,n) PyObject_GetAttr(o,n)
+#endif
+
+static PyObject *__Pyx_GetBuiltinName(PyObject *name); /*proto*/
static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact,
Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); /*proto*/
@@ -747,131 +906,77 @@ static CYTHON_INLINE int __Pyx_GetBufferAndValidate(Py_buffer* buf, PyObject* o
__Pyx_TypeInfo* dtype, int flags, int nd, int cast, __Pyx_BufFmt_StackElem* stack);
static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info);
-#define __Pyx_BufPtrStrided1d(type, buf, i0, s0) (type)((char*)buf + i0 * s0)
-#define __Pyx_BufPtrStrided2d(type, buf, i0, s0, i1, s1) (type)((char*)buf + i0 * s0 + i1 * s1)
+#define __Pyx_BufPtrCContig1d(type, buf, i0, s0) ((type)buf + i0)
+#define __Pyx_BufPtrCContig2d(type, buf, i0, s0, i1, s1) ((type)((char*)buf + i0 * s0) + i1)
static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
-static CYTHON_INLINE PyObject* __Pyx_PyObject_Pop(PyObject* L) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x02040000
- if (likely(PyList_CheckExact(L))
- && likely(PyList_GET_SIZE(L) > (((PyListObject*)L)->allocated >> 1))) {
- Py_SIZE(L) -= 1;
- return PyList_GET_ITEM(L, PyList_GET_SIZE(L));
- }
-#if PY_VERSION_HEX >= 0x02050000
- else if (Py_TYPE(L) == (&PySet_Type)) {
- return PySet_Pop(L);
- }
-#endif
-#endif
- return PyObject_CallMethod(L, (char*)"pop", NULL);
+static PyObject* __Pyx_PyObject_CallMethodTuple(PyObject* obj, PyObject* method_name, PyObject* args) {
+ PyObject *method, *result = NULL;
+ if (unlikely(!args)) return NULL;
+ method = __Pyx_PyObject_GetAttrStr(obj, method_name);
+ if (unlikely(!method)) goto bad;
+ result = PyObject_Call(method, args, NULL);
+ Py_DECREF(method);
+bad:
+ Py_DECREF(args);
+ return result;
}
+#define __Pyx_PyObject_CallMethod3(obj, name, arg1, arg2, arg3) \
+ __Pyx_PyObject_CallMethodTuple(obj, name, PyTuple_Pack(3, arg1, arg2, arg3))
+#define __Pyx_PyObject_CallMethod2(obj, name, arg1, arg2) \
+ __Pyx_PyObject_CallMethodTuple(obj, name, PyTuple_Pack(2, arg1, arg2))
+#define __Pyx_PyObject_CallMethod1(obj, name, arg1) \
+ __Pyx_PyObject_CallMethodTuple(obj, name, PyTuple_Pack(1, arg1))
+#define __Pyx_PyObject_CallMethod0(obj, name) \
+ __Pyx_PyObject_CallMethodTuple(obj, name, (Py_INCREF(__pyx_empty_tuple), __pyx_empty_tuple))
+
+static CYTHON_INLINE PyObject* __Pyx_PyObject_Pop(PyObject* L); /*proto*/
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) {
- PyObject *r;
- if (!j) return NULL;
- r = PyObject_GetItem(o, j);
- Py_DECREF(j);
- return r;
-}
-#define __Pyx_GetItemInt_List(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
- __Pyx_GetItemInt_List_Fast(o, i) : \
- __Pyx_GetItemInt_Generic(o, to_py_func(i)))
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i) {
-#if CYTHON_COMPILING_IN_CPYTHON
- if (likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
- PyObject *r = PyList_GET_ITEM(o, i);
- Py_INCREF(r);
- return r;
- }
- else if ((-PyList_GET_SIZE(o) <= i) & (i < 0)) {
- PyObject *r = PyList_GET_ITEM(o, PyList_GET_SIZE(o) + i);
- Py_INCREF(r);
- return r;
- }
- return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
-#else
- return PySequence_GetItem(o, i);
-#endif
-}
-#define __Pyx_GetItemInt_Tuple(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
- __Pyx_GetItemInt_Tuple_Fast(o, i) : \
- __Pyx_GetItemInt_Generic(o, to_py_func(i)))
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) {
#if CYTHON_COMPILING_IN_CPYTHON
- if (likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
- PyObject *r = PyTuple_GET_ITEM(o, i);
- Py_INCREF(r);
- return r;
- }
- else if ((-PyTuple_GET_SIZE(o) <= i) & (i < 0)) {
- PyObject *r = PyTuple_GET_ITEM(o, PyTuple_GET_SIZE(o) + i);
- Py_INCREF(r);
- return r;
+static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) {
+ PyListObject* L = (PyListObject*) list;
+ Py_ssize_t len = Py_SIZE(list);
+ if (likely(L->allocated > len) & likely(len > (L->allocated >> 1))) {
+ Py_INCREF(x);
+ PyList_SET_ITEM(list, len, x);
+ Py_SIZE(list) = len+1;
+ return 0;
}
- return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
-#else
- return PySequence_GetItem(o, i);
-#endif
+ return PyList_Append(list, x);
}
-#define __Pyx_GetItemInt(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
- __Pyx_GetItemInt_Fast(o, i) : \
- __Pyx_GetItemInt_Generic(o, to_py_func(i)))
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i) {
-#if CYTHON_COMPILING_IN_CPYTHON
- if (PyList_CheckExact(o)) {
- Py_ssize_t n = (likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
- if (likely((n >= 0) & (n < PyList_GET_SIZE(o)))) {
- PyObject *r = PyList_GET_ITEM(o, n);
- Py_INCREF(r);
- return r;
- }
- }
- else if (PyTuple_CheckExact(o)) {
- Py_ssize_t n = (likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o);
- if (likely((n >= 0) & (n < PyTuple_GET_SIZE(o)))) {
- PyObject *r = PyTuple_GET_ITEM(o, n);
- Py_INCREF(r);
- return r;
- }
- } else { /* inlined PySequence_GetItem() */
- PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
- if (likely(m && m->sq_item)) {
- if (unlikely(i < 0) && likely(m->sq_length)) {
- Py_ssize_t l = m->sq_length(o);
- if (unlikely(l < 0)) return NULL;
- i += l;
- }
- return m->sq_item(o, i);
- }
- }
#else
- if (PySequence_Check(o)) {
- return PySequence_GetItem(o, i);
- }
+#define __Pyx_PyList_Append(L,x) PyList_Append(L,x)
#endif
- return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
-}
+
+#define __Pyx_GetItemInt(o, i, size, to_py_func, is_list, wraparound, boundscheck) \
+ (((size) <= sizeof(Py_ssize_t)) ? \
+ __Pyx_GetItemInt_Fast(o, i, is_list, wraparound, boundscheck) : \
+ __Pyx_GetItemInt_Generic(o, to_py_func(i)))
+#define __Pyx_GetItemInt_List(o, i, size, to_py_func, is_list, wraparound, boundscheck) \
+ (((size) <= sizeof(Py_ssize_t)) ? \
+ __Pyx_GetItemInt_List_Fast(o, i, wraparound, boundscheck) : \
+ __Pyx_GetItemInt_Generic(o, to_py_func(i)))
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
+ int wraparound, int boundscheck);
+#define __Pyx_GetItemInt_Tuple(o, i, size, to_py_func, is_list, wraparound, boundscheck) \
+ (((size) <= sizeof(Py_ssize_t)) ? \
+ __Pyx_GetItemInt_Tuple_Fast(o, i, wraparound, boundscheck) : \
+ __Pyx_GetItemInt_Generic(o, to_py_func(i)))
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
+ int wraparound, int boundscheck);
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j);
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i,
+ int is_list, int wraparound, int boundscheck);
+
+static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name); /*proto*/
static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); /*proto*/
static void __Pyx_RaiseBufferFallbackError(void); /*proto*/
-static CYTHON_INLINE PyObject* __Pyx_PyObject_Append(PyObject* L, PyObject* x) {
- if (likely(PyList_CheckExact(L))) {
- if (unlikely(PyList_Append(L, x) < 0)) return NULL;
- Py_INCREF(Py_None);
- return Py_None; /* this is just to have an accurate signature */
- } else {
- PyObject *r, *m;
- m = __Pyx_GetAttrString(L, "append");
- if (!m) return NULL;
- r = PyObject_CallFunctionObjArgs(m, x, NULL);
- Py_DECREF(m);
- return r;
- }
-}
+#define __Pyx_BufPtrStrided1d(type, buf, i0, s0) (type)((char*)buf + i0 * s0)
+static CYTHON_INLINE PyObject* __Pyx_PyObject_Append(PyObject* L, PyObject* x); /*proto*/
static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); /*proto*/
@@ -910,7 +1015,11 @@ typedef struct {
static Py_ssize_t __Pyx_zeros[] = {0, 0, 0, 0, 0, 0, 0, 0};
static Py_ssize_t __Pyx_minusones[] = {-1, -1, -1, -1, -1, -1, -1, -1};
-static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level); /*proto*/
+static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); /*proto*/
+
+static CYTHON_INLINE Py_intptr_t __Pyx_PyInt_from_py_Py_intptr_t(PyObject *);
+
+static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_Py_intptr_t(Py_intptr_t);
#if CYTHON_CCOMPLEX
#ifdef __cplusplus
@@ -1080,6 +1189,8 @@ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/
/* Module declarations from 'cpython.ref' */
+/* Module declarations from 'libc.string' */
+
/* Module declarations from 'libc.stdio' */
/* Module declarations from 'cpython.object' */
@@ -1105,7 +1216,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *, cha
/* Module declarations from 'sklearn.cluster._hierarchical' */
static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_7sklearn_7cluster_13_hierarchical_DOUBLE = { "DOUBLE", NULL, sizeof(__pyx_t_7sklearn_7cluster_13_hierarchical_DOUBLE), { 0 }, 0, 'R', 0, 0 };
-static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_7sklearn_7cluster_13_hierarchical_INT = { "INT", NULL, sizeof(__pyx_t_7sklearn_7cluster_13_hierarchical_INT), { 0 }, 0, IS_UNSIGNED(__pyx_t_7sklearn_7cluster_13_hierarchical_INT) ? 'U' : 'I', IS_UNSIGNED(__pyx_t_7sklearn_7cluster_13_hierarchical_INT), 0 };
+static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_7sklearn_7cluster_13_hierarchical_INTP = { "INTP", NULL, sizeof(__pyx_t_7sklearn_7cluster_13_hierarchical_INTP), { 0 }, 0, IS_UNSIGNED(__pyx_t_7sklearn_7cluster_13_hierarchical_INTP) ? 'U' : 'I', IS_UNSIGNED(__pyx_t_7sklearn_7cluster_13_hierarchical_INTP), 0 };
static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_7sklearn_7cluster_13_hierarchical_INT8 = { "INT8", NULL, sizeof(__pyx_t_7sklearn_7cluster_13_hierarchical_INT8), { 0 }, 0, IS_UNSIGNED(__pyx_t_7sklearn_7cluster_13_hierarchical_INT8) ? 'U' : 'I', IS_UNSIGNED(__pyx_t_7sklearn_7cluster_13_hierarchical_INT8), 0 };
#define __Pyx_MODULE_NAME "sklearn.cluster._hierarchical"
int __pyx_module_is_main_sklearn__cluster___hierarchical = 0;
@@ -1115,7 +1226,7 @@ static PyObject *__pyx_builtin_range;
static PyObject *__pyx_builtin_ValueError;
static PyObject *__pyx_builtin_RuntimeError;
static PyObject *__pyx_pf_7sklearn_7cluster_13_hierarchical_compute_ward_dist(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_m_1, PyArrayObject *__pyx_v_m_2, PyArrayObject *__pyx_v_coord_row, PyArrayObject *__pyx_v_coord_col, PyArrayObject *__pyx_v_res); /* proto */
-static PyObject *__pyx_pf_7sklearn_7cluster_13_hierarchical_2_hc_get_descendent(CYTHON_UNUSED PyObject *__pyx_self, int __pyx_v_node, PyObject *__pyx_v_children, int __pyx_v_n_leaves); /* proto */
+static PyObject *__pyx_pf_7sklearn_7cluster_13_hierarchical_2_hc_get_descendent(CYTHON_UNUSED PyObject *__pyx_self, __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_v_node, PyObject *__pyx_v_children, __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_v_n_leaves); /* proto */
static PyObject *__pyx_pf_7sklearn_7cluster_13_hierarchical_4hc_get_heads(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_parents, PyObject *__pyx_v_copy); /* proto */
static PyObject *__pyx_pf_7sklearn_7cluster_13_hierarchical_6_get_parents(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_nodes, PyObject *__pyx_v_heads, PyArrayObject *__pyx_v_parents, PyArrayObject *__pyx_v_not_visited); /* proto */
static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */
@@ -1126,7 +1237,7 @@ static char __pyx_k_6[] = "Non-native byte order not supported";
static char __pyx_k_8[] = "unknown dtype code in numpy.pxd (%d)";
static char __pyx_k_9[] = "Format string allocated too short, see comment in numpy.pxd";
static char __pyx_k_12[] = "Format string allocated too short.";
-static char __pyx_k_16[] = "/scratch/apps/src/scikit-learn/sklearn/cluster/_hierarchical.pyx";
+static char __pyx_k_16[] = "/home/lars/src/scikit-learn/sklearn/cluster/_hierarchical.pyx";
static char __pyx_k_17[] = "sklearn.cluster._hierarchical";
static char __pyx_k__B[] = "B";
static char __pyx_k__H[] = "H";
@@ -1153,6 +1264,7 @@ static char __pyx_k__col[] = "col";
static char __pyx_k__ind[] = "ind";
static char __pyx_k__m_1[] = "m_1";
static char __pyx_k__m_2[] = "m_2";
+static char __pyx_k__pop[] = "pop";
static char __pyx_k__res[] = "res";
static char __pyx_k__row[] = "row";
static char __pyx_k__copy[] = "copy";
@@ -1163,6 +1275,7 @@ static char __pyx_k__node0[] = "node0";
static char __pyx_k__nodes[] = "nodes";
static char __pyx_k__numpy[] = "numpy";
static char __pyx_k__range[] = "range";
+static char __pyx_k__append[] = "append";
static char __pyx_k__extend[] = "extend";
static char __pyx_k__parent[] = "parent";
static char __pyx_k__parents[] = "parents";
@@ -1175,14 +1288,17 @@ static char __pyx_k__coord_col[] = "coord_col";
static char __pyx_k__coord_row[] = "coord_row";
static char __pyx_k__n_indices[] = "n_indices";
static char __pyx_k__ValueError[] = "ValueError";
+static char __pyx_k____import__[] = "__import__";
static char __pyx_k__descendent[] = "descendent";
static char __pyx_k__n_features[] = "n_features";
static char __pyx_k__not_visited[] = "not_visited";
static char __pyx_k__RuntimeError[] = "RuntimeError";
static char __pyx_k___get_parents[] = "_get_parents";
static char __pyx_k__hc_get_heads[] = "hc_get_heads";
+static char __pyx_k____pyx_getbuffer[] = "__pyx_getbuffer";
static char __pyx_k__compute_ward_dist[] = "compute_ward_dist";
static char __pyx_k___hc_get_descendent[] = "_hc_get_descendent";
+static char __pyx_k____pyx_releasebuffer[] = "__pyx_releasebuffer";
static PyObject *__pyx_kp_u_12;
static PyObject *__pyx_kp_s_16;
static PyObject *__pyx_n_s_17;
@@ -1193,10 +1309,14 @@ static PyObject *__pyx_kp_u_8;
static PyObject *__pyx_kp_u_9;
static PyObject *__pyx_n_s__RuntimeError;
static PyObject *__pyx_n_s__ValueError;
+static PyObject *__pyx_n_s____import__;
static PyObject *__pyx_n_s____main__;
+static PyObject *__pyx_n_s____pyx_getbuffer;
+static PyObject *__pyx_n_s____pyx_releasebuffer;
static PyObject *__pyx_n_s____test__;
static PyObject *__pyx_n_s___get_parents;
static PyObject *__pyx_n_s___hc_get_descendent;
+static PyObject *__pyx_n_s__append;
static PyObject *__pyx_n_s__children;
static PyObject *__pyx_n_s__col;
static PyObject *__pyx_n_s__compute_ward_dist;
@@ -1225,6 +1345,7 @@ static PyObject *__pyx_n_s__numpy;
static PyObject *__pyx_n_s__pa;
static PyObject *__pyx_n_s__parent;
static PyObject *__pyx_n_s__parents;
+static PyObject *__pyx_n_s__pop;
static PyObject *__pyx_n_s__range;
static PyObject *__pyx_n_s__res;
static PyObject *__pyx_n_s__row;
@@ -1256,6 +1377,9 @@ static PyObject *__pyx_pw_7sklearn_7cluster_13_hierarchical_1compute_ward_dist(P
PyArrayObject *__pyx_v_coord_row = 0;
PyArrayObject *__pyx_v_coord_col = 0;
PyArrayObject *__pyx_v_res = 0;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("compute_ward_dist (wrapper)", 0);
@@ -1282,26 +1406,26 @@ static PyObject *__pyx_pw_7sklearn_7cluster_13_hierarchical_1compute_ward_dist(P
case 1:
if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__m_2)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("compute_ward_dist", 1, 5, 5, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 14; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("compute_ward_dist", 1, 5, 5, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 17; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__coord_row)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("compute_ward_dist", 1, 5, 5, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 14; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("compute_ward_dist", 1, 5, 5, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 17; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 3:
if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__coord_col)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("compute_ward_dist", 1, 5, 5, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 14; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("compute_ward_dist", 1, 5, 5, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 17; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 4:
if (likely((values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__res)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("compute_ward_dist", 1, 5, 5, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 14; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("compute_ward_dist", 1, 5, 5, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 17; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "compute_ward_dist") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 14; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "compute_ward_dist") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 17; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 5) {
goto __pyx_L5_argtuple_error;
@@ -1320,17 +1444,17 @@ static PyObject *__pyx_pw_7sklearn_7cluster_13_hierarchical_1compute_ward_dist(P
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("compute_ward_dist", 1, 5, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 14; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("compute_ward_dist", 1, 5, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 17; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("sklearn.cluster._hierarchical.compute_ward_dist", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_m_1), __pyx_ptype_5numpy_ndarray, 1, "m_1", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 14; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_m_2), __pyx_ptype_5numpy_ndarray, 1, "m_2", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coord_row), __pyx_ptype_5numpy_ndarray, 1, "coord_row", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 16; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coord_col), __pyx_ptype_5numpy_ndarray, 1, "coord_col", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 17; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_res), __pyx_ptype_5numpy_ndarray, 1, "res", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 18; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_m_1), __pyx_ptype_5numpy_ndarray, 1, "m_1", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 17; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_m_2), __pyx_ptype_5numpy_ndarray, 1, "m_2", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 18; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coord_row), __pyx_ptype_5numpy_ndarray, 1, "coord_row", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 19; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coord_col), __pyx_ptype_5numpy_ndarray, 1, "coord_col", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 20; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_res), __pyx_ptype_5numpy_ndarray, 1, "res", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_r = __pyx_pf_7sklearn_7cluster_13_hierarchical_compute_ward_dist(__pyx_self, __pyx_v_m_1, __pyx_v_m_2, __pyx_v_coord_row, __pyx_v_coord_col, __pyx_v_res);
goto __pyx_L0;
__pyx_L1_error:;
@@ -1340,21 +1464,21 @@ static PyObject *__pyx_pw_7sklearn_7cluster_13_hierarchical_1compute_ward_dist(P
return __pyx_r;
}
-/* "sklearn/cluster/_hierarchical.pyx":14
+/* "sklearn/cluster/_hierarchical.pyx":17
* @cython.wraparound(False)
* @cython.cdivision(True)
- * def compute_ward_dist(np.ndarray[DOUBLE, ndim=1] m_1,\ # <<<<<<<<<<<<<<
- * np.ndarray[DOUBLE, ndim=2] m_2,\
- * np.ndarray[INT, ndim=1] coord_row,
+ * def compute_ward_dist(np.ndarray[DOUBLE, ndim=1, mode='c'] m_1, # <<<<<<<<<<<<<<
+ * np.ndarray[DOUBLE, ndim=2, mode='c'] m_2,
+ * np.ndarray[INTP, ndim=1, mode='c'] coord_row,
*/
static PyObject *__pyx_pf_7sklearn_7cluster_13_hierarchical_compute_ward_dist(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_m_1, PyArrayObject *__pyx_v_m_2, PyArrayObject *__pyx_v_coord_row, PyArrayObject *__pyx_v_coord_col, PyArrayObject *__pyx_v_res) {
- int __pyx_v_size_max;
- int __pyx_v_n_features;
- int __pyx_v_i;
- int __pyx_v_j;
- int __pyx_v_row;
- int __pyx_v_col;
+ __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_v_size_max;
+ __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_v_n_features;
+ __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_v_i;
+ __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_v_j;
+ __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_v_row;
+ __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_v_col;
__pyx_t_7sklearn_7cluster_13_hierarchical_DOUBLE __pyx_v_pa;
__pyx_t_7sklearn_7cluster_13_hierarchical_DOUBLE __pyx_v_n;
__Pyx_LocalBuf_ND __pyx_pybuffernd_coord_col;
@@ -1369,22 +1493,22 @@ static PyObject *__pyx_pf_7sklearn_7cluster_13_hierarchical_compute_ward_dist(CY
__Pyx_Buffer __pyx_pybuffer_res;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- int __pyx_t_1;
- int __pyx_t_2;
- int __pyx_t_3;
- int __pyx_t_4;
- int __pyx_t_5;
- int __pyx_t_6;
- int __pyx_t_7;
- int __pyx_t_8;
- int __pyx_t_9;
- int __pyx_t_10;
- int __pyx_t_11;
- int __pyx_t_12;
- int __pyx_t_13;
- int __pyx_t_14;
- int __pyx_t_15;
- int __pyx_t_16;
+ __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_t_1;
+ __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_t_2;
+ __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_t_3;
+ __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_t_4;
+ __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_t_5;
+ __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_t_6;
+ __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_t_7;
+ __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_t_8;
+ __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_t_9;
+ __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_t_10;
+ __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_t_11;
+ __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_t_12;
+ __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_t_13;
+ __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_t_14;
+ __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_t_15;
+ __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_t_16;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
@@ -1411,51 +1535,51 @@ static PyObject *__pyx_pf_7sklearn_7cluster_13_hierarchical_compute_ward_dist(CY
__pyx_pybuffernd_res.rcbuffer = &__pyx_pybuffer_res;
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
- if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m_1.rcbuffer->pybuffer, (PyObject*)__pyx_v_m_1, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_7cluster_13_hierarchical_DOUBLE, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 14; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m_1.rcbuffer->pybuffer, (PyObject*)__pyx_v_m_1, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_7cluster_13_hierarchical_DOUBLE, PyBUF_FORMAT| PyBUF_C_CONTIGUOUS, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 17; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_pybuffernd_m_1.diminfo[0].strides = __pyx_pybuffernd_m_1.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_m_1.diminfo[0].shape = __pyx_pybuffernd_m_1.rcbuffer->pybuffer.shape[0];
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
- if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m_2.rcbuffer->pybuffer, (PyObject*)__pyx_v_m_2, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_7cluster_13_hierarchical_DOUBLE, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 14; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_m_2.rcbuffer->pybuffer, (PyObject*)__pyx_v_m_2, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_7cluster_13_hierarchical_DOUBLE, PyBUF_FORMAT| PyBUF_C_CONTIGUOUS, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 17; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_pybuffernd_m_2.diminfo[0].strides = __pyx_pybuffernd_m_2.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_m_2.diminfo[0].shape = __pyx_pybuffernd_m_2.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_m_2.diminfo[1].strides = __pyx_pybuffernd_m_2.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_m_2.diminfo[1].shape = __pyx_pybuffernd_m_2.rcbuffer->pybuffer.shape[1];
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
- if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_coord_row.rcbuffer->pybuffer, (PyObject*)__pyx_v_coord_row, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_7cluster_13_hierarchical_INT, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 14; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_coord_row.rcbuffer->pybuffer, (PyObject*)__pyx_v_coord_row, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_7cluster_13_hierarchical_INTP, PyBUF_FORMAT| PyBUF_C_CONTIGUOUS, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 17; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_pybuffernd_coord_row.diminfo[0].strides = __pyx_pybuffernd_coord_row.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_coord_row.diminfo[0].shape = __pyx_pybuffernd_coord_row.rcbuffer->pybuffer.shape[0];
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
- if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_coord_col.rcbuffer->pybuffer, (PyObject*)__pyx_v_coord_col, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_7cluster_13_hierarchical_INT, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 14; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_coord_col.rcbuffer->pybuffer, (PyObject*)__pyx_v_coord_col, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_7cluster_13_hierarchical_INTP, PyBUF_FORMAT| PyBUF_C_CONTIGUOUS, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 17; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_pybuffernd_coord_col.diminfo[0].strides = __pyx_pybuffernd_coord_col.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_coord_col.diminfo[0].shape = __pyx_pybuffernd_coord_col.rcbuffer->pybuffer.shape[0];
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
- if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_res.rcbuffer->pybuffer, (PyObject*)__pyx_v_res, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_7cluster_13_hierarchical_DOUBLE, PyBUF_FORMAT| PyBUF_STRIDES| PyBUF_WRITABLE, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 14; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_res.rcbuffer->pybuffer, (PyObject*)__pyx_v_res, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_7cluster_13_hierarchical_DOUBLE, PyBUF_FORMAT| PyBUF_C_CONTIGUOUS| PyBUF_WRITABLE, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 17; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_pybuffernd_res.diminfo[0].strides = __pyx_pybuffernd_res.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_res.diminfo[0].shape = __pyx_pybuffernd_res.rcbuffer->pybuffer.shape[0];
- /* "sklearn/cluster/_hierarchical.pyx":19
- * np.ndarray[INT, ndim=1] coord_col,\
- * np.ndarray[DOUBLE, ndim=1] res):
- * cdef int size_max = coord_row.shape[0] # <<<<<<<<<<<<<<
- * cdef int n_features = m_2.shape[1]
- * cdef int i, j, row, col
+ /* "sklearn/cluster/_hierarchical.pyx":22
+ * np.ndarray[INTP, ndim=1, mode='c'] coord_col,
+ * np.ndarray[DOUBLE, ndim=1, mode='c'] res):
+ * cdef INTP size_max = coord_row.shape[0] # <<<<<<<<<<<<<<
+ * cdef INTP n_features = m_2.shape[1]
+ * cdef INTP i, j, row, col
*/
__pyx_v_size_max = (__pyx_v_coord_row->dimensions[0]);
- /* "sklearn/cluster/_hierarchical.pyx":20
- * np.ndarray[DOUBLE, ndim=1] res):
- * cdef int size_max = coord_row.shape[0]
- * cdef int n_features = m_2.shape[1] # <<<<<<<<<<<<<<
- * cdef int i, j, row, col
+ /* "sklearn/cluster/_hierarchical.pyx":23
+ * np.ndarray[DOUBLE, ndim=1, mode='c'] res):
+ * cdef INTP size_max = coord_row.shape[0]
+ * cdef INTP n_features = m_2.shape[1] # <<<<<<<<<<<<<<
+ * cdef INTP i, j, row, col
* cdef DOUBLE pa, n
*/
__pyx_v_n_features = (__pyx_v_m_2->dimensions[1]);
- /* "sklearn/cluster/_hierarchical.pyx":23
- * cdef int i, j, row, col
+ /* "sklearn/cluster/_hierarchical.pyx":27
* cdef DOUBLE pa, n
+ *
* for i in range(size_max): # <<<<<<<<<<<<<<
* row = coord_row[i]
* col = coord_col[i]
@@ -1464,17 +1588,17 @@ static PyObject *__pyx_pf_7sklearn_7cluster_13_hierarchical_compute_ward_dist(CY
for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) {
__pyx_v_i = __pyx_t_2;
- /* "sklearn/cluster/_hierarchical.pyx":24
- * cdef DOUBLE pa, n
+ /* "sklearn/cluster/_hierarchical.pyx":28
+ *
* for i in range(size_max):
* row = coord_row[i] # <<<<<<<<<<<<<<
* col = coord_col[i]
* n = (m_1[row] * m_1[col]) / (m_1[row] + m_1[col])
*/
__pyx_t_3 = __pyx_v_i;
- __pyx_v_row = (*__Pyx_BufPtrStrided1d(__pyx_t_7sklearn_7cluster_13_hierarchical_INT *, __pyx_pybuffernd_coord_row.rcbuffer->pybuffer.buf, __pyx_t_3, __pyx_pybuffernd_coord_row.diminfo[0].strides));
+ __pyx_v_row = (*__Pyx_BufPtrCContig1d(__pyx_t_7sklearn_7cluster_13_hierarchical_INTP *, __pyx_pybuffernd_coord_row.rcbuffer->pybuffer.buf, __pyx_t_3, __pyx_pybuffernd_coord_row.diminfo[0].strides));
- /* "sklearn/cluster/_hierarchical.pyx":25
+ /* "sklearn/cluster/_hierarchical.pyx":29
* for i in range(size_max):
* row = coord_row[i]
* col = coord_col[i] # <<<<<<<<<<<<<<
@@ -1482,9 +1606,9 @@ static PyObject *__pyx_pf_7sklearn_7cluster_13_hierarchical_compute_ward_dist(CY
* pa = 0.
*/
__pyx_t_4 = __pyx_v_i;
- __pyx_v_col = (*__Pyx_BufPtrStrided1d(__pyx_t_7sklearn_7cluster_13_hierarchical_INT *, __pyx_pybuffernd_coord_col.rcbuffer->pybuffer.buf, __pyx_t_4, __pyx_pybuffernd_coord_col.diminfo[0].strides));
+ __pyx_v_col = (*__Pyx_BufPtrCContig1d(__pyx_t_7sklearn_7cluster_13_hierarchical_INTP *, __pyx_pybuffernd_coord_col.rcbuffer->pybuffer.buf, __pyx_t_4, __pyx_pybuffernd_coord_col.diminfo[0].strides));
- /* "sklearn/cluster/_hierarchical.pyx":26
+ /* "sklearn/cluster/_hierarchical.pyx":30
* row = coord_row[i]
* col = coord_col[i]
* n = (m_1[row] * m_1[col]) / (m_1[row] + m_1[col]) # <<<<<<<<<<<<<<
@@ -1495,32 +1619,32 @@ static PyObject *__pyx_pf_7sklearn_7cluster_13_hierarchical_compute_ward_dist(CY
__pyx_t_6 = __pyx_v_col;
__pyx_t_7 = __pyx_v_row;
__pyx_t_8 = __pyx_v_col;
- __pyx_v_n = (((*__Pyx_BufPtrStrided1d(__pyx_t_7sklearn_7cluster_13_hierarchical_DOUBLE *, __pyx_pybuffernd_m_1.rcbuffer->pybuffer.buf, __pyx_t_5, __pyx_pybuffernd_m_1.diminfo[0].strides)) * (*__Pyx_BufPtrStrided1d(__pyx_t_7sklearn_7cluster_13_hierarchical_DOUBLE *, __pyx_pybuffernd_m_1.rcbuffer->pybuffer.buf, __pyx_t_6, __pyx_pybuffernd_m_1.diminfo[0].strides))) / ((*__Pyx_BufPtrStrided1d(__pyx_t_7sklearn_7cluster_13_hierarchical_DOUBLE *, __pyx_pybuffernd_m_1.rcbuffer->pybuffer.buf, __pyx_t_7, __pyx_pybuffernd_m_1.diminfo[0].strides)) + (*__Pyx_BufPtrStrided1d(__pyx_t_7sklearn_7cluster_13_hierarchical_DOUBLE *, __pyx_pybuffernd_m_1.rcbuffer->pybuffer.buf, __pyx_t_8, __pyx_pybuffernd_m_1.diminfo[0].strides))));
+ __pyx_v_n = (((*__Pyx_BufPtrCContig1d(__pyx_t_7sklearn_7cluster_13_hierarchical_DOUBLE *, __pyx_pybuffernd_m_1.rcbuffer->pybuffer.buf, __pyx_t_5, __pyx_pybuffernd_m_1.diminfo[0].strides)) * (*__Pyx_BufPtrCContig1d(__pyx_t_7sklearn_7cluster_13_hierarchical_DOUBLE *, __pyx_pybuffernd_m_1.rcbuffer->pybuffer.buf, __pyx_t_6, __pyx_pybuffernd_m_1.diminfo[0].strides))) / ((*__Pyx_BufPtrCContig1d(__pyx_t_7sklearn_7cluster_13_hierarchical_DOUBLE *, __pyx_pybuffernd_m_1.rcbuffer->pybuffer.buf, __pyx_t_7, __pyx_pybuffernd_m_1.diminfo[0].strides)) + (*__Pyx_BufPtrCContig1d(__pyx_t_7sklearn_7cluster_13_hierarchical_DOUBLE *, __pyx_pybuffernd_m_1.rcbuffer->pybuffer.buf, __pyx_t_8, __pyx_pybuffernd_m_1.diminfo[0].strides))));
- /* "sklearn/cluster/_hierarchical.pyx":27
+ /* "sklearn/cluster/_hierarchical.pyx":31
* col = coord_col[i]
* n = (m_1[row] * m_1[col]) / (m_1[row] + m_1[col])
* pa = 0. # <<<<<<<<<<<<<<
* for j in range(n_features):
- * pa += (m_2[row, j] / m_1[row] - m_2[col, j] / m_1[col])**2
+ * pa += (m_2[row, j] / m_1[row] - m_2[col, j] / m_1[col]) ** 2
*/
__pyx_v_pa = 0.;
- /* "sklearn/cluster/_hierarchical.pyx":28
+ /* "sklearn/cluster/_hierarchical.pyx":32
* n = (m_1[row] * m_1[col]) / (m_1[row] + m_1[col])
* pa = 0.
* for j in range(n_features): # <<<<<<<<<<<<<<
- * pa += (m_2[row, j] / m_1[row] - m_2[col, j] / m_1[col])**2
+ * pa += (m_2[row, j] / m_1[row] - m_2[col, j] / m_1[col]) ** 2
* res[i] = pa * n
*/
__pyx_t_9 = __pyx_v_n_features;
for (__pyx_t_10 = 0; __pyx_t_10 < __pyx_t_9; __pyx_t_10+=1) {
__pyx_v_j = __pyx_t_10;
- /* "sklearn/cluster/_hierarchical.pyx":29
+ /* "sklearn/cluster/_hierarchical.pyx":33
* pa = 0.
* for j in range(n_features):
- * pa += (m_2[row, j] / m_1[row] - m_2[col, j] / m_1[col])**2 # <<<<<<<<<<<<<<
+ * pa += (m_2[row, j] / m_1[row] - m_2[col, j] / m_1[col]) ** 2 # <<<<<<<<<<<<<<
* res[i] = pa * n
* return res
*/
@@ -1530,22 +1654,22 @@ static PyObject *__pyx_pf_7sklearn_7cluster_13_hierarchical_compute_ward_dist(CY
__pyx_t_14 = __pyx_v_col;
__pyx_t_15 = __pyx_v_j;
__pyx_t_16 = __pyx_v_col;
- __pyx_v_pa = (__pyx_v_pa + pow((((*__Pyx_BufPtrStrided2d(__pyx_t_7sklearn_7cluster_13_hierarchical_DOUBLE *, __pyx_pybuffernd_m_2.rcbuffer->pybuffer.buf, __pyx_t_11, __pyx_pybuffernd_m_2.diminfo[0].strides, __pyx_t_12, __pyx_pybuffernd_m_2.diminfo[1].strides)) / (*__Pyx_BufPtrStrided1d(__pyx_t_7sklearn_7cluster_13_hierarchical_DOUBLE *, __pyx_pybuffernd_m_1.rcbuffer->pybuffer.buf, __pyx_t_13, __pyx_pybuffernd_m_1.diminfo[0].strides))) - ((*__Pyx_BufPtrStrided2d(__pyx_t_7sklearn_7cluster_13_hierarchical_DOUBLE *, __pyx_pybuffernd_m_2.rcbuffer->pybuffer.buf, __pyx_t_14, __pyx_pybuffernd_m_2.diminfo[0].strides, __pyx_t_15, __pyx_pybuffernd_m_2.diminfo[1].strides)) / (*__Pyx_BufPtrStrided1d(__pyx_t_7sklearn_7cluster_13_hierarchical_DOUBLE *, __pyx_pybuffernd_m_1.rcbuffer->pybuffer.buf, __pyx_t_16, __pyx_pybuffernd_m_1.diminfo[0].strides)))), 2.0));
+ __pyx_v_pa = (__pyx_v_pa + pow((((*__Pyx_BufPtrCContig2d(__pyx_t_7sklearn_7cluster_13_hierarchical_DOUBLE *, __pyx_pybuffernd_m_2.rcbuffer->pybuffer.buf, __pyx_t_11, __pyx_pybuffernd_m_2.diminfo[0].strides, __pyx_t_12, __pyx_pybuffernd_m_2.diminfo[1].strides)) / (*__Pyx_BufPtrCContig1d(__pyx_t_7sklearn_7cluster_13_hierarchical_DOUBLE *, __pyx_pybuffernd_m_1.rcbuffer->pybuffer.buf, __pyx_t_13, __pyx_pybuffernd_m_1.diminfo[0].strides))) - ((*__Pyx_BufPtrCContig2d(__pyx_t_7sklearn_7cluster_13_hierarchical_DOUBLE *, __pyx_pybuffernd_m_2.rcbuffer->pybuffer.buf, __pyx_t_14, __pyx_pybuffernd_m_2.diminfo[0].strides, __pyx_t_15, __pyx_pybuffernd_m_2.diminfo[1].strides)) / (*__Pyx_BufPtrCContig1d(__pyx_t_7sklearn_7cluster_13_hierarchical_DOUBLE *, __pyx_pybuffernd_m_1.rcbuffer->pybuffer.buf, __pyx_t_16, __pyx_pybuffernd_m_1.diminfo[0].strides)))), 2.0));
}
- /* "sklearn/cluster/_hierarchical.pyx":30
+ /* "sklearn/cluster/_hierarchical.pyx":34
* for j in range(n_features):
- * pa += (m_2[row, j] / m_1[row] - m_2[col, j] / m_1[col])**2
+ * pa += (m_2[row, j] / m_1[row] - m_2[col, j] / m_1[col]) ** 2
* res[i] = pa * n # <<<<<<<<<<<<<<
* return res
*
*/
__pyx_t_9 = __pyx_v_i;
- *__Pyx_BufPtrStrided1d(__pyx_t_7sklearn_7cluster_13_hierarchical_DOUBLE *, __pyx_pybuffernd_res.rcbuffer->pybuffer.buf, __pyx_t_9, __pyx_pybuffernd_res.diminfo[0].strides) = (__pyx_v_pa * __pyx_v_n);
+ *__Pyx_BufPtrCContig1d(__pyx_t_7sklearn_7cluster_13_hierarchical_DOUBLE *, __pyx_pybuffernd_res.rcbuffer->pybuffer.buf, __pyx_t_9, __pyx_pybuffernd_res.diminfo[0].strides) = (__pyx_v_pa * __pyx_v_n);
}
- /* "sklearn/cluster/_hierarchical.pyx":31
- * pa += (m_2[row, j] / m_1[row] - m_2[col, j] / m_1[col])**2
+ /* "sklearn/cluster/_hierarchical.pyx":35
+ * pa += (m_2[row, j] / m_1[row] - m_2[col, j] / m_1[col]) ** 2
* res[i] = pa * n
* return res # <<<<<<<<<<<<<<
*
@@ -1584,12 +1708,15 @@ static PyObject *__pyx_pf_7sklearn_7cluster_13_hierarchical_compute_ward_dist(CY
/* Python wrapper */
static PyObject *__pyx_pw_7sklearn_7cluster_13_hierarchical_3_hc_get_descendent(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_7sklearn_7cluster_13_hierarchical_2_hc_get_descendent[] = "\n Function returning all the descendent leaves of a set of nodes in the tree.\n\n Parameters\n ----------\n node : int\n The node for which we want the descendents.\n\n children : list of pairs. Length of n_nodes\n List of the children of each nodes.\n This is not defined for leaves.\n\n n_leaves : int\n Number of leaves.\n\n Return\n ------\n descendent : list of int\n ";
+static char __pyx_doc_7sklearn_7cluster_13_hierarchical_2_hc_get_descendent[] = "\n Function returning all the descendent leaves of a set of nodes in the tree.\n\n Parameters\n ----------\n node : integer\n The node for which we want the descendents.\n\n children : list of pairs, length n_nodes\n The children of each non-leaf node. Values less than `n_samples` refer\n to leaves of the tree. A greater value `i` indicates a node with\n children `children[i - n_samples]`.\n\n n_leaves : integer\n Number of leaves.\n\n Returns\n -------\n descendent : list of int\n ";
static PyMethodDef __pyx_mdef_7sklearn_7cluster_13_hierarchical_3_hc_get_descendent = {__Pyx_NAMESTR("_hc_get_descendent"), (PyCFunction)__pyx_pw_7sklearn_7cluster_13_hierarchical_3_hc_get_descendent, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_7sklearn_7cluster_13_hierarchical_2_hc_get_descendent)};
static PyObject *__pyx_pw_7sklearn_7cluster_13_hierarchical_3_hc_get_descendent(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- int __pyx_v_node;
+ __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_v_node;
PyObject *__pyx_v_children = 0;
- int __pyx_v_n_leaves;
+ __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_v_n_leaves;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("_hc_get_descendent (wrapper)", 0);
@@ -1614,16 +1741,16 @@ static PyObject *__pyx_pw_7sklearn_7cluster_13_hierarchical_3_hc_get_descendent(
case 1:
if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__children)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("_hc_get_descendent", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("_hc_get_descendent", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__n_leaves)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("_hc_get_descendent", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("_hc_get_descendent", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "_hc_get_descendent") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "_hc_get_descendent") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 3) {
goto __pyx_L5_argtuple_error;
@@ -1632,13 +1759,13 @@ static PyObject *__pyx_pw_7sklearn_7cluster_13_hierarchical_3_hc_get_descendent(
values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
}
- __pyx_v_node = __Pyx_PyInt_AsInt(values[0]); if (unlikely((__pyx_v_node == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_node = __Pyx_PyInt_from_py_Py_intptr_t(values[0]); if (unlikely((__pyx_v_node == (npy_intp)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_v_children = values[1];
- __pyx_v_n_leaves = __Pyx_PyInt_AsInt(values[2]); if (unlikely((__pyx_v_n_leaves == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_n_leaves = __Pyx_PyInt_from_py_Py_intptr_t(values[2]); if (unlikely((__pyx_v_n_leaves == (npy_intp)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("_hc_get_descendent", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("_hc_get_descendent", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("sklearn.cluster._hierarchical._hc_get_descendent", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -1649,65 +1776,66 @@ static PyObject *__pyx_pw_7sklearn_7cluster_13_hierarchical_3_hc_get_descendent(
return __pyx_r;
}
-/* "sklearn/cluster/_hierarchical.pyx":34
+/* "sklearn/cluster/_hierarchical.pyx":38
*
*
- * def _hc_get_descendent(int node, children, int n_leaves): # <<<<<<<<<<<<<<
+ * def _hc_get_descendent(INTP node, children, INTP n_leaves): # <<<<<<<<<<<<<<
* """
* Function returning all the descendent leaves of a set of nodes in the tree.
*/
-static PyObject *__pyx_pf_7sklearn_7cluster_13_hierarchical_2_hc_get_descendent(CYTHON_UNUSED PyObject *__pyx_self, int __pyx_v_node, PyObject *__pyx_v_children, int __pyx_v_n_leaves) {
+static PyObject *__pyx_pf_7sklearn_7cluster_13_hierarchical_2_hc_get_descendent(CYTHON_UNUSED PyObject *__pyx_self, __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_v_node, PyObject *__pyx_v_children, __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_v_n_leaves) {
PyObject *__pyx_v_ind = NULL;
PyObject *__pyx_v_descendent = NULL;
- int __pyx_v_n_indices;
- int __pyx_v_i;
+ __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_v_i;
+ __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_v_n_indices;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
int __pyx_t_3;
- int __pyx_t_4;
+ __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_t_4;
int __pyx_t_5;
- PyObject *__pyx_t_6 = NULL;
+ int __pyx_t_6;
+ PyObject *__pyx_t_7 = NULL;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("_hc_get_descendent", 0);
- /* "sklearn/cluster/_hierarchical.pyx":54
+ /* "sklearn/cluster/_hierarchical.pyx":59
* descendent : list of int
* """
* ind = [node] # <<<<<<<<<<<<<<
* if node < n_leaves:
* return ind
*/
- __pyx_t_1 = PyInt_FromLong(__pyx_v_node); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_Py_intptr_t(__pyx_v_node); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyList_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyList_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
PyList_SET_ITEM(__pyx_t_2, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
- __pyx_v_ind = __pyx_t_2;
+ __pyx_v_ind = ((PyObject*)__pyx_t_2);
__pyx_t_2 = 0;
- /* "sklearn/cluster/_hierarchical.pyx":55
+ /* "sklearn/cluster/_hierarchical.pyx":60
* """
* ind = [node]
* if node < n_leaves: # <<<<<<<<<<<<<<
* return ind
* descendent = []
*/
- __pyx_t_3 = (__pyx_v_node < __pyx_v_n_leaves);
+ __pyx_t_3 = ((__pyx_v_node < __pyx_v_n_leaves) != 0);
if (__pyx_t_3) {
- /* "sklearn/cluster/_hierarchical.pyx":56
+ /* "sklearn/cluster/_hierarchical.pyx":61
* ind = [node]
* if node < n_leaves:
* return ind # <<<<<<<<<<<<<<
* descendent = []
- * # It is actually faster to do the accounting of the number of
+ *
*/
__Pyx_XDECREF(__pyx_r);
__Pyx_INCREF(((PyObject *)__pyx_v_ind));
@@ -1717,73 +1845,74 @@ static PyObject *__pyx_pf_7sklearn_7cluster_13_hierarchical_2_hc_get_descendent(
}
__pyx_L3:;
- /* "sklearn/cluster/_hierarchical.pyx":57
+ /* "sklearn/cluster/_hierarchical.pyx":62
* if node < n_leaves:
* return ind
* descendent = [] # <<<<<<<<<<<<<<
+ *
* # It is actually faster to do the accounting of the number of
- * # elements is the list ourselves: len is a lengthy operation on a
*/
- __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_v_descendent = __pyx_t_2;
+ __pyx_v_descendent = ((PyObject*)__pyx_t_2);
__pyx_t_2 = 0;
- /* "sklearn/cluster/_hierarchical.pyx":61
+ /* "sklearn/cluster/_hierarchical.pyx":67
* # elements is the list ourselves: len is a lengthy operation on a
* # chained list
- * cdef int n_indices = 1 # <<<<<<<<<<<<<<
- * cdef int i
+ * cdef INTP i, n_indices = 1 # <<<<<<<<<<<<<<
+ *
* while n_indices:
*/
__pyx_v_n_indices = 1;
- /* "sklearn/cluster/_hierarchical.pyx":63
- * cdef int n_indices = 1
- * cdef int i
+ /* "sklearn/cluster/_hierarchical.pyx":69
+ * cdef INTP i, n_indices = 1
+ *
* while n_indices: # <<<<<<<<<<<<<<
* i = ind.pop()
* if i < n_leaves:
*/
while (1) {
- if (!__pyx_v_n_indices) break;
+ __pyx_t_3 = (__pyx_v_n_indices != 0);
+ if (!__pyx_t_3) break;
- /* "sklearn/cluster/_hierarchical.pyx":64
- * cdef int i
+ /* "sklearn/cluster/_hierarchical.pyx":70
+ *
* while n_indices:
* i = ind.pop() # <<<<<<<<<<<<<<
* if i < n_leaves:
* descendent.append(i)
*/
- __pyx_t_2 = __Pyx_PyObject_Pop(((PyObject *)__pyx_v_ind)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_Pop(((PyObject *)__pyx_v_ind)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_4 = __Pyx_PyInt_AsInt(__pyx_t_2); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyInt_from_py_Py_intptr_t(__pyx_t_2); if (unlikely((__pyx_t_4 == (npy_intp)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_v_i = __pyx_t_4;
- /* "sklearn/cluster/_hierarchical.pyx":65
+ /* "sklearn/cluster/_hierarchical.pyx":71
* while n_indices:
* i = ind.pop()
* if i < n_leaves: # <<<<<<<<<<<<<<
* descendent.append(i)
* n_indices -= 1
*/
- __pyx_t_3 = (__pyx_v_i < __pyx_v_n_leaves);
+ __pyx_t_3 = ((__pyx_v_i < __pyx_v_n_leaves) != 0);
if (__pyx_t_3) {
- /* "sklearn/cluster/_hierarchical.pyx":66
+ /* "sklearn/cluster/_hierarchical.pyx":72
* i = ind.pop()
* if i < n_leaves:
* descendent.append(i) # <<<<<<<<<<<<<<
* n_indices -= 1
* else:
*/
- __pyx_t_2 = PyInt_FromLong(__pyx_v_i); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyInt_to_py_Py_intptr_t(__pyx_v_i); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_5 = PyList_Append(__pyx_v_descendent, __pyx_t_2); if (unlikely(__pyx_t_5 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyList_Append(__pyx_v_descendent, __pyx_t_2); if (unlikely(__pyx_t_5 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "sklearn/cluster/_hierarchical.pyx":67
+ /* "sklearn/cluster/_hierarchical.pyx":73
* if i < n_leaves:
* descendent.append(i)
* n_indices -= 1 # <<<<<<<<<<<<<<
@@ -1795,30 +1924,30 @@ static PyObject *__pyx_pf_7sklearn_7cluster_13_hierarchical_2_hc_get_descendent(
}
/*else*/ {
- /* "sklearn/cluster/_hierarchical.pyx":69
+ /* "sklearn/cluster/_hierarchical.pyx":75
* n_indices -= 1
* else:
* ind.extend(children[i - n_leaves]) # <<<<<<<<<<<<<<
* n_indices += 1
* return descendent
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_ind), __pyx_n_s__extend); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_ind), __pyx_n_s__extend); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_4 = (__pyx_v_i - __pyx_v_n_leaves);
- __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_children, __pyx_t_4, sizeof(int), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = (__pyx_v_i - __pyx_v_n_leaves);
+ __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_children, __pyx_t_6, sizeof(int), PyInt_FromLong, 0, 1, 1); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_1);
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "sklearn/cluster/_hierarchical.pyx":70
+ /* "sklearn/cluster/_hierarchical.pyx":76
* else:
* ind.extend(children[i - n_leaves])
* n_indices += 1 # <<<<<<<<<<<<<<
@@ -1830,7 +1959,7 @@ static PyObject *__pyx_pf_7sklearn_7cluster_13_hierarchical_2_hc_get_descendent(
__pyx_L6:;
}
- /* "sklearn/cluster/_hierarchical.pyx":71
+ /* "sklearn/cluster/_hierarchical.pyx":77
* ind.extend(children[i - n_leaves])
* n_indices += 1
* return descendent # <<<<<<<<<<<<<<
@@ -1847,7 +1976,7 @@ static PyObject *__pyx_pf_7sklearn_7cluster_13_hierarchical_2_hc_get_descendent(
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_6);
+ __Pyx_XDECREF(__pyx_t_7);
__Pyx_AddTraceback("sklearn.cluster._hierarchical._hc_get_descendent", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
@@ -1860,11 +1989,14 @@ static PyObject *__pyx_pf_7sklearn_7cluster_13_hierarchical_2_hc_get_descendent(
/* Python wrapper */
static PyObject *__pyx_pw_7sklearn_7cluster_13_hierarchical_5hc_get_heads(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_7sklearn_7cluster_13_hierarchical_4hc_get_heads[] = " Return the heads of the forest, as defined by parents\n \n Parameters\n ===========\n parents: array of integers\n The parent structure defining the forest (ensemble of trees)\n copy: boolean\n If copy is False, the input 'parents' array is modified inplace\n\n Returns\n =======\n heads: array of integers of same shape as parents\n The indices in the 'parents' of the tree heads\n\n ";
+static char __pyx_doc_7sklearn_7cluster_13_hierarchical_4hc_get_heads[] = "Returns the heads of the forest, as defined by parents.\n\n Parameters\n ----------\n parents : array of integers\n The parent structure defining the forest (ensemble of trees)\n copy : boolean\n If copy is False, the input 'parents' array is modified inplace\n\n Returns\n -------\n heads : array of integers of same shape as parents\n The indices in the 'parents' of the tree heads\n\n ";
static PyMethodDef __pyx_mdef_7sklearn_7cluster_13_hierarchical_5hc_get_heads = {__Pyx_NAMESTR("hc_get_heads"), (PyCFunction)__pyx_pw_7sklearn_7cluster_13_hierarchical_5hc_get_heads, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_7sklearn_7cluster_13_hierarchical_4hc_get_heads)};
static PyObject *__pyx_pw_7sklearn_7cluster_13_hierarchical_5hc_get_heads(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyArrayObject *__pyx_v_parents = 0;
PyObject *__pyx_v_copy = 0;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("hc_get_heads (wrapper)", 0);
@@ -1893,7 +2025,7 @@ static PyObject *__pyx_pw_7sklearn_7cluster_13_hierarchical_5hc_get_heads(PyObje
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "hc_get_heads") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "hc_get_heads") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -1908,13 +2040,13 @@ static PyObject *__pyx_pw_7sklearn_7cluster_13_hierarchical_5hc_get_heads(PyObje
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("hc_get_heads", 0, 1, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("hc_get_heads", 0, 1, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("sklearn.cluster._hierarchical.hc_get_heads", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_parents), __pyx_ptype_5numpy_ndarray, 1, "parents", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_parents), __pyx_ptype_5numpy_ndarray, 1, "parents", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_r = __pyx_pf_7sklearn_7cluster_13_hierarchical_4hc_get_heads(__pyx_self, __pyx_v_parents, __pyx_v_copy);
goto __pyx_L0;
__pyx_L1_error:;
@@ -1924,19 +2056,19 @@ static PyObject *__pyx_pw_7sklearn_7cluster_13_hierarchical_5hc_get_heads(PyObje
return __pyx_r;
}
-/* "sklearn/cluster/_hierarchical.pyx":76
+/* "sklearn/cluster/_hierarchical.pyx":82
* @cython.boundscheck(False)
* @cython.wraparound(False)
- * def hc_get_heads(np.ndarray[INT, ndim=1] parents, copy=True): # <<<<<<<<<<<<<<
- * """ Return the heads of the forest, as defined by parents
+ * def hc_get_heads(np.ndarray[INTP, ndim=1] parents, copy=True): # <<<<<<<<<<<<<<
+ * """Returns the heads of the forest, as defined by parents.
*
*/
static PyObject *__pyx_pf_7sklearn_7cluster_13_hierarchical_4hc_get_heads(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_parents, PyObject *__pyx_v_copy) {
- unsigned int __pyx_v_parent;
- unsigned int __pyx_v_node0;
- unsigned int __pyx_v_node;
- unsigned int __pyx_v_size;
+ __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_v_parent;
+ __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_v_node0;
+ __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_v_node;
+ __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_v_size;
__Pyx_LocalBuf_ND __pyx_pybuffernd_parents;
__Pyx_Buffer __pyx_pybuffer_parents;
PyObject *__pyx_r = NULL;
@@ -1950,11 +2082,10 @@ static PyObject *__pyx_pf_7sklearn_7cluster_13_hierarchical_4hc_get_heads(CYTHON
PyObject *__pyx_t_7 = NULL;
PyObject *__pyx_t_8 = NULL;
PyObject *__pyx_t_9 = NULL;
- unsigned int __pyx_t_10;
- unsigned int __pyx_t_11;
- unsigned int __pyx_t_12;
- unsigned int __pyx_t_13;
- unsigned int __pyx_t_14;
+ __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_t_10;
+ __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_t_11;
+ __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_t_12;
+ __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_t_13;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
@@ -1966,50 +2097,50 @@ static PyObject *__pyx_pf_7sklearn_7cluster_13_hierarchical_4hc_get_heads(CYTHON
__pyx_pybuffernd_parents.rcbuffer = &__pyx_pybuffer_parents;
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
- if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_parents.rcbuffer->pybuffer, (PyObject*)__pyx_v_parents, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_7cluster_13_hierarchical_INT, PyBUF_FORMAT| PyBUF_STRIDES| PyBUF_WRITABLE, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_parents.rcbuffer->pybuffer, (PyObject*)__pyx_v_parents, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_7cluster_13_hierarchical_INTP, PyBUF_FORMAT| PyBUF_STRIDES| PyBUF_WRITABLE, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_pybuffernd_parents.diminfo[0].strides = __pyx_pybuffernd_parents.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_parents.diminfo[0].shape = __pyx_pybuffernd_parents.rcbuffer->pybuffer.shape[0];
- /* "sklearn/cluster/_hierarchical.pyx":93
+ /* "sklearn/cluster/_hierarchical.pyx":99
* """
- * cdef unsigned int parent, node0, node, size
+ * cdef INTP parent, node0, node, size
* if copy: # <<<<<<<<<<<<<<
* parents = np.copy(parents)
* size = parents.size
*/
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_copy); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 93; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_copy); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 99; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_1) {
- /* "sklearn/cluster/_hierarchical.pyx":94
- * cdef unsigned int parent, node0, node, size
+ /* "sklearn/cluster/_hierarchical.pyx":100
+ * cdef INTP parent, node0, node, size
* if copy:
* parents = np.copy(parents) # <<<<<<<<<<<<<<
* size = parents.size
- * for node0 in range(size):
+ *
*/
- __pyx_t_2 = __Pyx_GetName(__pyx_m, __pyx_n_s__np); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 94; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s__np); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 100; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__copy); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 94; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s__copy); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 100; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 94; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 100; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(((PyObject *)__pyx_v_parents));
PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_v_parents));
__Pyx_GIVEREF(((PyObject *)__pyx_v_parents));
- __pyx_t_4 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 94; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 100; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 94; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 100; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_5 = ((PyArrayObject *)__pyx_t_4);
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
__Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_parents.rcbuffer->pybuffer);
- __pyx_t_6 = __Pyx_GetBufferAndValidate(&__pyx_pybuffernd_parents.rcbuffer->pybuffer, (PyObject*)__pyx_t_5, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_7cluster_13_hierarchical_INT, PyBUF_FORMAT| PyBUF_STRIDES| PyBUF_WRITABLE, 1, 0, __pyx_stack);
+ __pyx_t_6 = __Pyx_GetBufferAndValidate(&__pyx_pybuffernd_parents.rcbuffer->pybuffer, (PyObject*)__pyx_t_5, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_7cluster_13_hierarchical_INTP, PyBUF_FORMAT| PyBUF_STRIDES| PyBUF_WRITABLE, 1, 0, __pyx_stack);
if (unlikely(__pyx_t_6 < 0)) {
PyErr_Fetch(&__pyx_t_7, &__pyx_t_8, &__pyx_t_9);
- if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_parents.rcbuffer->pybuffer, (PyObject*)__pyx_v_parents, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_7cluster_13_hierarchical_INT, PyBUF_FORMAT| PyBUF_STRIDES| PyBUF_WRITABLE, 1, 0, __pyx_stack) == -1)) {
+ if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_parents.rcbuffer->pybuffer, (PyObject*)__pyx_v_parents, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_7cluster_13_hierarchical_INTP, PyBUF_FORMAT| PyBUF_STRIDES| PyBUF_WRITABLE, 1, 0, __pyx_stack) == -1)) {
Py_XDECREF(__pyx_t_7); Py_XDECREF(__pyx_t_8); Py_XDECREF(__pyx_t_9);
__Pyx_RaiseBufferFallbackError();
} else {
@@ -2017,7 +2148,7 @@ static PyObject *__pyx_pf_7sklearn_7cluster_13_hierarchical_4hc_get_heads(CYTHON
}
}
__pyx_pybuffernd_parents.diminfo[0].strides = __pyx_pybuffernd_parents.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_parents.diminfo[0].shape = __pyx_pybuffernd_parents.rcbuffer->pybuffer.shape[0];
- if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 94; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 100; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_5 = 0;
__Pyx_DECREF(((PyObject *)__pyx_v_parents));
@@ -2027,59 +2158,49 @@ static PyObject *__pyx_pf_7sklearn_7cluster_13_hierarchical_4hc_get_heads(CYTHON
}
__pyx_L3:;
- /* "sklearn/cluster/_hierarchical.pyx":95
+ /* "sklearn/cluster/_hierarchical.pyx":101
* if copy:
* parents = np.copy(parents)
* size = parents.size # <<<<<<<<<<<<<<
- * for node0 in range(size):
- * # Start from the top of the tree and go down
+ *
+ * # Start from the top of the tree and go down
*/
- __pyx_t_4 = PyObject_GetAttr(((PyObject *)__pyx_v_parents), __pyx_n_s__size); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 95; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_parents), __pyx_n_s__size); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 101; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_10 = __Pyx_PyInt_AsUnsignedInt(__pyx_t_4); if (unlikely((__pyx_t_10 == (unsigned int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 95; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_PyInt_from_py_Py_intptr_t(__pyx_t_4); if (unlikely((__pyx_t_10 == (npy_intp)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 101; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__pyx_v_size = __pyx_t_10;
- /* "sklearn/cluster/_hierarchical.pyx":96
- * parents = np.copy(parents)
- * size = parents.size
- * for node0 in range(size): # <<<<<<<<<<<<<<
- * # Start from the top of the tree and go down
- * node0 = size - node0 - 1
- */
- __pyx_t_10 = __pyx_v_size;
- for (__pyx_t_11 = 0; __pyx_t_11 < __pyx_t_10; __pyx_t_11+=1) {
- __pyx_v_node0 = __pyx_t_11;
-
- /* "sklearn/cluster/_hierarchical.pyx":98
- * for node0 in range(size):
- * # Start from the top of the tree and go down
- * node0 = size - node0 - 1 # <<<<<<<<<<<<<<
+ /* "sklearn/cluster/_hierarchical.pyx":104
+ *
+ * # Start from the top of the tree and go down
+ * for node0 in range(size - 1, -1, -1): # <<<<<<<<<<<<<<
* node = node0
* parent = parents[node]
*/
- __pyx_v_node0 = ((__pyx_v_size - __pyx_v_node0) - 1);
+ for (__pyx_t_10 = (__pyx_v_size - 1); __pyx_t_10 > -1; __pyx_t_10-=1) {
+ __pyx_v_node0 = __pyx_t_10;
- /* "sklearn/cluster/_hierarchical.pyx":99
- * # Start from the top of the tree and go down
- * node0 = size - node0 - 1
+ /* "sklearn/cluster/_hierarchical.pyx":105
+ * # Start from the top of the tree and go down
+ * for node0 in range(size - 1, -1, -1):
* node = node0 # <<<<<<<<<<<<<<
* parent = parents[node]
* while parent != node:
*/
__pyx_v_node = __pyx_v_node0;
- /* "sklearn/cluster/_hierarchical.pyx":100
- * node0 = size - node0 - 1
+ /* "sklearn/cluster/_hierarchical.pyx":106
+ * for node0 in range(size - 1, -1, -1):
* node = node0
* parent = parents[node] # <<<<<<<<<<<<<<
* while parent != node:
* parents[node0] = parent
*/
- __pyx_t_12 = __pyx_v_node;
- __pyx_v_parent = (*__Pyx_BufPtrStrided1d(__pyx_t_7sklearn_7cluster_13_hierarchical_INT *, __pyx_pybuffernd_parents.rcbuffer->pybuffer.buf, __pyx_t_12, __pyx_pybuffernd_parents.diminfo[0].strides));
+ __pyx_t_11 = __pyx_v_node;
+ __pyx_v_parent = (*__Pyx_BufPtrStrided1d(__pyx_t_7sklearn_7cluster_13_hierarchical_INTP *, __pyx_pybuffernd_parents.rcbuffer->pybuffer.buf, __pyx_t_11, __pyx_pybuffernd_parents.diminfo[0].strides));
- /* "sklearn/cluster/_hierarchical.pyx":101
+ /* "sklearn/cluster/_hierarchical.pyx":107
* node = node0
* parent = parents[node]
* while parent != node: # <<<<<<<<<<<<<<
@@ -2087,20 +2208,20 @@ static PyObject *__pyx_pf_7sklearn_7cluster_13_hierarchical_4hc_get_heads(CYTHON
* node = parent
*/
while (1) {
- __pyx_t_1 = (__pyx_v_parent != __pyx_v_node);
+ __pyx_t_1 = ((__pyx_v_parent != __pyx_v_node) != 0);
if (!__pyx_t_1) break;
- /* "sklearn/cluster/_hierarchical.pyx":102
+ /* "sklearn/cluster/_hierarchical.pyx":108
* parent = parents[node]
* while parent != node:
* parents[node0] = parent # <<<<<<<<<<<<<<
* node = parent
* parent = parents[node]
*/
- __pyx_t_13 = __pyx_v_node0;
- *__Pyx_BufPtrStrided1d(__pyx_t_7sklearn_7cluster_13_hierarchical_INT *, __pyx_pybuffernd_parents.rcbuffer->pybuffer.buf, __pyx_t_13, __pyx_pybuffernd_parents.diminfo[0].strides) = __pyx_v_parent;
+ __pyx_t_12 = __pyx_v_node0;
+ *__Pyx_BufPtrStrided1d(__pyx_t_7sklearn_7cluster_13_hierarchical_INTP *, __pyx_pybuffernd_parents.rcbuffer->pybuffer.buf, __pyx_t_12, __pyx_pybuffernd_parents.diminfo[0].strides) = __pyx_v_parent;
- /* "sklearn/cluster/_hierarchical.pyx":103
+ /* "sklearn/cluster/_hierarchical.pyx":109
* while parent != node:
* parents[node0] = parent
* node = parent # <<<<<<<<<<<<<<
@@ -2109,19 +2230,19 @@ static PyObject *__pyx_pf_7sklearn_7cluster_13_hierarchical_4hc_get_heads(CYTHON
*/
__pyx_v_node = __pyx_v_parent;
- /* "sklearn/cluster/_hierarchical.pyx":104
+ /* "sklearn/cluster/_hierarchical.pyx":110
* parents[node0] = parent
* node = parent
* parent = parents[node] # <<<<<<<<<<<<<<
* return parents
*
*/
- __pyx_t_14 = __pyx_v_node;
- __pyx_v_parent = (*__Pyx_BufPtrStrided1d(__pyx_t_7sklearn_7cluster_13_hierarchical_INT *, __pyx_pybuffernd_parents.rcbuffer->pybuffer.buf, __pyx_t_14, __pyx_pybuffernd_parents.diminfo[0].strides));
+ __pyx_t_13 = __pyx_v_node;
+ __pyx_v_parent = (*__Pyx_BufPtrStrided1d(__pyx_t_7sklearn_7cluster_13_hierarchical_INTP *, __pyx_pybuffernd_parents.rcbuffer->pybuffer.buf, __pyx_t_13, __pyx_pybuffernd_parents.diminfo[0].strides));
}
}
- /* "sklearn/cluster/_hierarchical.pyx":105
+ /* "sklearn/cluster/_hierarchical.pyx":111
* node = parent
* parent = parents[node]
* return parents # <<<<<<<<<<<<<<
@@ -2157,13 +2278,16 @@ static PyObject *__pyx_pf_7sklearn_7cluster_13_hierarchical_4hc_get_heads(CYTHON
/* Python wrapper */
static PyObject *__pyx_pw_7sklearn_7cluster_13_hierarchical_7_get_parents(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_7sklearn_7cluster_13_hierarchical_6_get_parents[] = " Return the heads of the given nodes, as defined by parents\n \n Modifies in-place 'heads' and 'not_visited'\n\n Parameters\n ===========\n nodes: list of integers\n The nodes to start from\n heads: list of integers\n A list to hold the results (modified inplace)\n parents: array of integers\n The parent structure defining the tree\n not_visited:\n The tree nodes to consider (modified inplace)\n\n ";
+static char __pyx_doc_7sklearn_7cluster_13_hierarchical_6_get_parents[] = "Returns the heads of the given nodes, as defined by parents.\n\n Modifies 'heads' and 'not_visited' in-place.\n\n Parameters\n ----------\n nodes : list of integers\n The nodes to start from\n heads : list of integers\n A list to hold the results (modified inplace)\n parents : array of integers\n The parent structure defining the tree\n not_visited\n The tree nodes to consider (modified inplace)\n\n ";
static PyMethodDef __pyx_mdef_7sklearn_7cluster_13_hierarchical_7_get_parents = {__Pyx_NAMESTR("_get_parents"), (PyCFunction)__pyx_pw_7sklearn_7cluster_13_hierarchical_7_get_parents, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_7sklearn_7cluster_13_hierarchical_6_get_parents)};
static PyObject *__pyx_pw_7sklearn_7cluster_13_hierarchical_7_get_parents(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_nodes = 0;
PyObject *__pyx_v_heads = 0;
PyArrayObject *__pyx_v_parents = 0;
PyArrayObject *__pyx_v_not_visited = 0;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("_get_parents (wrapper)", 0);
@@ -2189,21 +2313,21 @@ static PyObject *__pyx_pw_7sklearn_7cluster_13_hierarchical_7_get_parents(PyObje
case 1:
if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__heads)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("_get_parents", 1, 4, 4, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("_get_parents", 1, 4, 4, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 116; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__parents)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("_get_parents", 1, 4, 4, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("_get_parents", 1, 4, 4, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 116; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 3:
if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__not_visited)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("_get_parents", 1, 4, 4, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("_get_parents", 1, 4, 4, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 116; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "_get_parents") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "_get_parents") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 116; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 4) {
goto __pyx_L5_argtuple_error;
@@ -2220,14 +2344,14 @@ static PyObject *__pyx_pw_7sklearn_7cluster_13_hierarchical_7_get_parents(PyObje
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("_get_parents", 1, 4, 4, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("_get_parents", 1, 4, 4, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 116; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("sklearn.cluster._hierarchical._get_parents", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_parents), __pyx_ptype_5numpy_ndarray, 1, "parents", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_not_visited), __pyx_ptype_5numpy_ndarray, 1, "not_visited", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 111; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_parents), __pyx_ptype_5numpy_ndarray, 1, "parents", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 116; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_not_visited), __pyx_ptype_5numpy_ndarray, 1, "not_visited", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 117; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_r = __pyx_pf_7sklearn_7cluster_13_hierarchical_6_get_parents(__pyx_self, __pyx_v_nodes, __pyx_v_heads, __pyx_v_parents, __pyx_v_not_visited);
goto __pyx_L0;
__pyx_L1_error:;
@@ -2237,17 +2361,17 @@ static PyObject *__pyx_pw_7sklearn_7cluster_13_hierarchical_7_get_parents(PyObje
return __pyx_r;
}
-/* "sklearn/cluster/_hierarchical.pyx":110
+/* "sklearn/cluster/_hierarchical.pyx":116
* @cython.boundscheck(False)
* @cython.wraparound(False)
- * def _get_parents(nodes, heads, np.ndarray[INT, ndim=1] parents, # <<<<<<<<<<<<<<
- * np.ndarray[INT8, ndim=1] not_visited):
- * """ Return the heads of the given nodes, as defined by parents
+ * def _get_parents(nodes, heads, np.ndarray[INTP, ndim=1] parents, # <<<<<<<<<<<<<<
+ * np.ndarray[INT8, ndim=1, mode='c'] not_visited):
+ * """Returns the heads of the given nodes, as defined by parents.
*/
static PyObject *__pyx_pf_7sklearn_7cluster_13_hierarchical_6_get_parents(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_nodes, PyObject *__pyx_v_heads, PyArrayObject *__pyx_v_parents, PyArrayObject *__pyx_v_not_visited) {
- unsigned int __pyx_v_parent;
- unsigned int __pyx_v_node;
+ __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_v_parent;
+ __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_v_node;
__Pyx_LocalBuf_ND __pyx_pybuffernd_not_visited;
__Pyx_Buffer __pyx_pybuffer_not_visited;
__Pyx_LocalBuf_ND __pyx_pybuffernd_parents;
@@ -2258,13 +2382,12 @@ static PyObject *__pyx_pf_7sklearn_7cluster_13_hierarchical_6_get_parents(CYTHON
Py_ssize_t __pyx_t_2;
PyObject *(*__pyx_t_3)(PyObject *);
PyObject *__pyx_t_4 = NULL;
- unsigned int __pyx_t_5;
+ __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_t_5;
int __pyx_t_6;
- unsigned int __pyx_t_7;
- unsigned int __pyx_t_8;
- __pyx_t_7sklearn_7cluster_13_hierarchical_INT8 __pyx_t_9;
- unsigned int __pyx_t_10;
- PyObject *__pyx_t_11 = NULL;
+ __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_t_7;
+ __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_t_8;
+ __pyx_t_7sklearn_7cluster_13_hierarchical_INTP __pyx_t_9;
+ PyObject *__pyx_t_10 = NULL;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
@@ -2279,18 +2402,18 @@ static PyObject *__pyx_pf_7sklearn_7cluster_13_hierarchical_6_get_parents(CYTHON
__pyx_pybuffernd_not_visited.rcbuffer = &__pyx_pybuffer_not_visited;
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
- if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_parents.rcbuffer->pybuffer, (PyObject*)__pyx_v_parents, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_7cluster_13_hierarchical_INT, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_parents.rcbuffer->pybuffer, (PyObject*)__pyx_v_parents, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_7cluster_13_hierarchical_INTP, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 116; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_pybuffernd_parents.diminfo[0].strides = __pyx_pybuffernd_parents.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_parents.diminfo[0].shape = __pyx_pybuffernd_parents.rcbuffer->pybuffer.shape[0];
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
- if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_not_visited.rcbuffer->pybuffer, (PyObject*)__pyx_v_not_visited, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_7cluster_13_hierarchical_INT8, PyBUF_FORMAT| PyBUF_STRIDES| PyBUF_WRITABLE, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_not_visited.rcbuffer->pybuffer, (PyObject*)__pyx_v_not_visited, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_7cluster_13_hierarchical_INT8, PyBUF_FORMAT| PyBUF_C_CONTIGUOUS| PyBUF_WRITABLE, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 116; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_pybuffernd_not_visited.diminfo[0].strides = __pyx_pybuffernd_not_visited.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_not_visited.diminfo[0].shape = __pyx_pybuffernd_not_visited.rcbuffer->pybuffer.shape[0];
- /* "sklearn/cluster/_hierarchical.pyx":129
- * """
- * cdef unsigned int parent, node
+ /* "sklearn/cluster/_hierarchical.pyx":136
+ * cdef INTP parent, node
+ *
* for node in nodes: # <<<<<<<<<<<<<<
* parent = parents[node]
* while parent != node:
@@ -2299,7 +2422,7 @@ static PyObject *__pyx_pf_7sklearn_7cluster_13_hierarchical_6_get_parents(CYTHON
__pyx_t_1 = __pyx_v_nodes; __Pyx_INCREF(__pyx_t_1); __pyx_t_2 = 0;
__pyx_t_3 = NULL;
} else {
- __pyx_t_2 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_nodes); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 129; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_nodes); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_3 = Py_TYPE(__pyx_t_1)->tp_iternext;
}
@@ -2307,43 +2430,43 @@ static PyObject *__pyx_pf_7sklearn_7cluster_13_hierarchical_6_get_parents(CYTHON
if (!__pyx_t_3 && PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_2 >= PyList_GET_SIZE(__pyx_t_1)) break;
#if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 129; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#else
- __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 129; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#endif
} else if (!__pyx_t_3 && PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_2 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
#if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 129; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#else
- __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 129; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#endif
} else {
__pyx_t_4 = __pyx_t_3(__pyx_t_1);
if (unlikely(!__pyx_t_4)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 129; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
__Pyx_GOTREF(__pyx_t_4);
}
- __pyx_t_5 = __Pyx_PyInt_AsUnsignedInt(__pyx_t_4); if (unlikely((__pyx_t_5 == (unsigned int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 129; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyInt_from_py_Py_intptr_t(__pyx_t_4); if (unlikely((__pyx_t_5 == (npy_intp)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__pyx_v_node = __pyx_t_5;
- /* "sklearn/cluster/_hierarchical.pyx":130
- * cdef unsigned int parent, node
+ /* "sklearn/cluster/_hierarchical.pyx":137
+ *
* for node in nodes:
* parent = parents[node] # <<<<<<<<<<<<<<
* while parent != node:
* node = parent
*/
__pyx_t_5 = __pyx_v_node;
- __pyx_v_parent = (*__Pyx_BufPtrStrided1d(__pyx_t_7sklearn_7cluster_13_hierarchical_INT *, __pyx_pybuffernd_parents.rcbuffer->pybuffer.buf, __pyx_t_5, __pyx_pybuffernd_parents.diminfo[0].strides));
+ __pyx_v_parent = (*__Pyx_BufPtrStrided1d(__pyx_t_7sklearn_7cluster_13_hierarchical_INTP *, __pyx_pybuffernd_parents.rcbuffer->pybuffer.buf, __pyx_t_5, __pyx_pybuffernd_parents.diminfo[0].strides));
- /* "sklearn/cluster/_hierarchical.pyx":131
+ /* "sklearn/cluster/_hierarchical.pyx":138
* for node in nodes:
* parent = parents[node]
* while parent != node: # <<<<<<<<<<<<<<
@@ -2351,10 +2474,10 @@ static PyObject *__pyx_pf_7sklearn_7cluster_13_hierarchical_6_get_parents(CYTHON
* parent = parents[node]
*/
while (1) {
- __pyx_t_6 = (__pyx_v_parent != __pyx_v_node);
+ __pyx_t_6 = ((__pyx_v_parent != __pyx_v_node) != 0);
if (!__pyx_t_6) break;
- /* "sklearn/cluster/_hierarchical.pyx":132
+ /* "sklearn/cluster/_hierarchical.pyx":139
* parent = parents[node]
* while parent != node:
* node = parent # <<<<<<<<<<<<<<
@@ -2363,7 +2486,7 @@ static PyObject *__pyx_pf_7sklearn_7cluster_13_hierarchical_6_get_parents(CYTHON
*/
__pyx_v_node = __pyx_v_parent;
- /* "sklearn/cluster/_hierarchical.pyx":133
+ /* "sklearn/cluster/_hierarchical.pyx":140
* while parent != node:
* node = parent
* parent = parents[node] # <<<<<<<<<<<<<<
@@ -2371,10 +2494,10 @@ static PyObject *__pyx_pf_7sklearn_7cluster_13_hierarchical_6_get_parents(CYTHON
* not_visited[node] = 0
*/
__pyx_t_7 = __pyx_v_node;
- __pyx_v_parent = (*__Pyx_BufPtrStrided1d(__pyx_t_7sklearn_7cluster_13_hierarchical_INT *, __pyx_pybuffernd_parents.rcbuffer->pybuffer.buf, __pyx_t_7, __pyx_pybuffernd_parents.diminfo[0].strides));
+ __pyx_v_parent = (*__Pyx_BufPtrStrided1d(__pyx_t_7sklearn_7cluster_13_hierarchical_INTP *, __pyx_pybuffernd_parents.rcbuffer->pybuffer.buf, __pyx_t_7, __pyx_pybuffernd_parents.diminfo[0].strides));
}
- /* "sklearn/cluster/_hierarchical.pyx":134
+ /* "sklearn/cluster/_hierarchical.pyx":141
* node = parent
* parent = parents[node]
* if not_visited[node]: # <<<<<<<<<<<<<<
@@ -2382,38 +2505,38 @@ static PyObject *__pyx_pf_7sklearn_7cluster_13_hierarchical_6_get_parents(CYTHON
* heads.append(node)
*/
__pyx_t_8 = __pyx_v_node;
- __pyx_t_9 = (*__Pyx_BufPtrStrided1d(__pyx_t_7sklearn_7cluster_13_hierarchical_INT8 *, __pyx_pybuffernd_not_visited.rcbuffer->pybuffer.buf, __pyx_t_8, __pyx_pybuffernd_not_visited.diminfo[0].strides));
- if (__pyx_t_9) {
+ __pyx_t_6 = ((*__Pyx_BufPtrCContig1d(__pyx_t_7sklearn_7cluster_13_hierarchical_INT8 *, __pyx_pybuffernd_not_visited.rcbuffer->pybuffer.buf, __pyx_t_8, __pyx_pybuffernd_not_visited.diminfo[0].strides)) != 0);
+ if (__pyx_t_6) {
- /* "sklearn/cluster/_hierarchical.pyx":135
+ /* "sklearn/cluster/_hierarchical.pyx":142
* parent = parents[node]
* if not_visited[node]:
* not_visited[node] = 0 # <<<<<<<<<<<<<<
* heads.append(node)
* return heads
*/
- __pyx_t_10 = __pyx_v_node;
- *__Pyx_BufPtrStrided1d(__pyx_t_7sklearn_7cluster_13_hierarchical_INT8 *, __pyx_pybuffernd_not_visited.rcbuffer->pybuffer.buf, __pyx_t_10, __pyx_pybuffernd_not_visited.diminfo[0].strides) = 0;
+ __pyx_t_9 = __pyx_v_node;
+ *__Pyx_BufPtrCContig1d(__pyx_t_7sklearn_7cluster_13_hierarchical_INT8 *, __pyx_pybuffernd_not_visited.rcbuffer->pybuffer.buf, __pyx_t_9, __pyx_pybuffernd_not_visited.diminfo[0].strides) = 0;
- /* "sklearn/cluster/_hierarchical.pyx":136
+ /* "sklearn/cluster/_hierarchical.pyx":143
* if not_visited[node]:
* not_visited[node] = 0
* heads.append(node) # <<<<<<<<<<<<<<
* return heads
*/
- __pyx_t_4 = PyLong_FromUnsignedLong(__pyx_v_node); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyInt_to_py_Py_intptr_t(__pyx_v_node); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 143; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_11 = __Pyx_PyObject_Append(__pyx_v_heads, __pyx_t_4); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_11);
+ __pyx_t_10 = __Pyx_PyObject_Append(__pyx_v_heads, __pyx_t_4); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 143; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
goto __pyx_L7;
}
__pyx_L7:;
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "sklearn/cluster/_hierarchical.pyx":137
+ /* "sklearn/cluster/_hierarchical.pyx":144
* not_visited[node] = 0
* heads.append(node)
* return heads # <<<<<<<<<<<<<<
@@ -2428,7 +2551,7 @@ static PyObject *__pyx_pf_7sklearn_7cluster_13_hierarchical_6_get_parents(CYTHON
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_4);
- __Pyx_XDECREF(__pyx_t_11);
+ __Pyx_XDECREF(__pyx_t_10);
{ PyObject *__pyx_type, *__pyx_value, *__pyx_tb;
__Pyx_ErrFetch(&__pyx_type, &__pyx_value, &__pyx_tb);
__Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_not_visited.rcbuffer->pybuffer);
@@ -2462,7 +2585,7 @@ static CYTHON_UNUSED int __pyx_pw_5numpy_7ndarray_1__getbuffer__(PyObject *__pyx
* # -- the details of this may change.
* def __getbuffer__(ndarray self, Py_buffer* info, int flags): # <<<<<<<<<<<<<<
* # This implementation of getbuffer is geared towards Cython
- * # requirements, and does not yet fulfill the PEP.
+ * # requirements, and does not yet fullfill the PEP.
*/
static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags) {
@@ -2503,7 +2626,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*
* cdef int copy_shape, i, ndim
*/
- __pyx_t_1 = (__pyx_v_info == NULL);
+ __pyx_t_1 = ((__pyx_v_info == NULL) != 0);
if (__pyx_t_1) {
__pyx_r = 0;
goto __pyx_L0;
@@ -2545,7 +2668,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
* copy_shape = 1
* else:
*/
- __pyx_t_1 = ((sizeof(npy_intp)) != (sizeof(Py_ssize_t)));
+ __pyx_t_1 = (((sizeof(npy_intp)) != (sizeof(Py_ssize_t))) != 0);
if (__pyx_t_1) {
/* "numpy.pxd":209
@@ -2578,7 +2701,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
* and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)):
* raise ValueError(u"ndarray is not C contiguous")
*/
- __pyx_t_1 = ((__pyx_v_flags & PyBUF_C_CONTIGUOUS) == PyBUF_C_CONTIGUOUS);
+ __pyx_t_1 = (((__pyx_v_flags & PyBUF_C_CONTIGUOUS) == PyBUF_C_CONTIGUOUS) != 0);
if (__pyx_t_1) {
/* "numpy.pxd":214
@@ -2588,7 +2711,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
* raise ValueError(u"ndarray is not C contiguous")
*
*/
- __pyx_t_2 = (!PyArray_CHKFLAGS(__pyx_v_self, NPY_C_CONTIGUOUS));
+ __pyx_t_2 = ((!(PyArray_CHKFLAGS(__pyx_v_self, NPY_C_CONTIGUOUS) != 0)) != 0);
__pyx_t_3 = __pyx_t_2;
} else {
__pyx_t_3 = __pyx_t_1;
@@ -2618,7 +2741,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
* and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)):
* raise ValueError(u"ndarray is not Fortran contiguous")
*/
- __pyx_t_3 = ((__pyx_v_flags & PyBUF_F_CONTIGUOUS) == PyBUF_F_CONTIGUOUS);
+ __pyx_t_3 = (((__pyx_v_flags & PyBUF_F_CONTIGUOUS) == PyBUF_F_CONTIGUOUS) != 0);
if (__pyx_t_3) {
/* "numpy.pxd":218
@@ -2628,7 +2751,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
* raise ValueError(u"ndarray is not Fortran contiguous")
*
*/
- __pyx_t_1 = (!PyArray_CHKFLAGS(__pyx_v_self, NPY_F_CONTIGUOUS));
+ __pyx_t_1 = ((!(PyArray_CHKFLAGS(__pyx_v_self, NPY_F_CONTIGUOUS) != 0)) != 0);
__pyx_t_2 = __pyx_t_1;
} else {
__pyx_t_2 = __pyx_t_3;
@@ -2676,7 +2799,8 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
* # Allocate new buffer for strides and shape info.
* # This is allocated as one block, strides first.
*/
- if (__pyx_v_copy_shape) {
+ __pyx_t_2 = (__pyx_v_copy_shape != 0);
+ if (__pyx_t_2) {
/* "numpy.pxd":226
* # Allocate new buffer for strides and shape info.
@@ -2774,7 +2898,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*
* cdef int t
*/
- __pyx_v_info->readonly = (!PyArray_ISWRITEABLE(__pyx_v_self));
+ __pyx_v_info->readonly = (!(PyArray_ISWRITEABLE(__pyx_v_self) != 0));
/* "numpy.pxd":239
*
@@ -2813,9 +2937,9 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
* # do not call releasebuffer
* info.obj = None
*/
- __pyx_t_2 = (!__pyx_v_hasfields);
+ __pyx_t_2 = ((!(__pyx_v_hasfields != 0)) != 0);
if (__pyx_t_2) {
- __pyx_t_3 = (!__pyx_v_copy_shape);
+ __pyx_t_3 = ((!(__pyx_v_copy_shape != 0)) != 0);
__pyx_t_1 = __pyx_t_3;
} else {
__pyx_t_1 = __pyx_t_2;
@@ -2860,7 +2984,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
* t = descr.type_num
* if ((descr.byteorder == c'>' and little_endian) or
*/
- __pyx_t_1 = (!__pyx_v_hasfields);
+ __pyx_t_1 = ((!(__pyx_v_hasfields != 0)) != 0);
if (__pyx_t_1) {
/* "numpy.pxd":254
@@ -2880,9 +3004,9 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
* (descr.byteorder == c'<' and not little_endian)):
* raise ValueError(u"Non-native byte order not supported")
*/
- __pyx_t_1 = (__pyx_v_descr->byteorder == '>');
+ __pyx_t_1 = ((__pyx_v_descr->byteorder == '>') != 0);
if (__pyx_t_1) {
- __pyx_t_2 = __pyx_v_little_endian;
+ __pyx_t_2 = (__pyx_v_little_endian != 0);
} else {
__pyx_t_2 = __pyx_t_1;
}
@@ -2895,9 +3019,9 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
* raise ValueError(u"Non-native byte order not supported")
* if t == NPY_BYTE: f = "b"
*/
- __pyx_t_1 = (__pyx_v_descr->byteorder == '<');
+ __pyx_t_1 = ((__pyx_v_descr->byteorder == '<') != 0);
if (__pyx_t_1) {
- __pyx_t_3 = (!__pyx_v_little_endian);
+ __pyx_t_3 = ((!(__pyx_v_little_endian != 0)) != 0);
__pyx_t_7 = __pyx_t_3;
} else {
__pyx_t_7 = __pyx_t_1;
@@ -2924,227 +3048,202 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
}
__pyx_L12:;
- /* "numpy.pxd":258
+ /* "numpy.pxd":274
+ * elif t == NPY_CDOUBLE: f = "Zd"
+ * elif t == NPY_CLONGDOUBLE: f = "Zg"
+ * elif t == NPY_OBJECT: f = "O" # <<<<<<<<<<<<<<
+ * else:
+ * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t)
+ */
+ switch (__pyx_v_t) {
+
+ /* "numpy.pxd":258
* (descr.byteorder == c'<' and not little_endian)):
* raise ValueError(u"Non-native byte order not supported")
* if t == NPY_BYTE: f = "b" # <<<<<<<<<<<<<<
* elif t == NPY_UBYTE: f = "B"
* elif t == NPY_SHORT: f = "h"
*/
- __pyx_t_1 = (__pyx_v_t == NPY_BYTE);
- if (__pyx_t_1) {
+ case NPY_BYTE:
__pyx_v_f = __pyx_k__b;
- goto __pyx_L13;
- }
+ break;
- /* "numpy.pxd":259
+ /* "numpy.pxd":259
* raise ValueError(u"Non-native byte order not supported")
* if t == NPY_BYTE: f = "b"
* elif t == NPY_UBYTE: f = "B" # <<<<<<<<<<<<<<
* elif t == NPY_SHORT: f = "h"
* elif t == NPY_USHORT: f = "H"
*/
- __pyx_t_1 = (__pyx_v_t == NPY_UBYTE);
- if (__pyx_t_1) {
+ case NPY_UBYTE:
__pyx_v_f = __pyx_k__B;
- goto __pyx_L13;
- }
+ break;
- /* "numpy.pxd":260
+ /* "numpy.pxd":260
* if t == NPY_BYTE: f = "b"
* elif t == NPY_UBYTE: f = "B"
* elif t == NPY_SHORT: f = "h" # <<<<<<<<<<<<<<
* elif t == NPY_USHORT: f = "H"
* elif t == NPY_INT: f = "i"
*/
- __pyx_t_1 = (__pyx_v_t == NPY_SHORT);
- if (__pyx_t_1) {
+ case NPY_SHORT:
__pyx_v_f = __pyx_k__h;
- goto __pyx_L13;
- }
+ break;
- /* "numpy.pxd":261
+ /* "numpy.pxd":261
* elif t == NPY_UBYTE: f = "B"
* elif t == NPY_SHORT: f = "h"
* elif t == NPY_USHORT: f = "H" # <<<<<<<<<<<<<<
* elif t == NPY_INT: f = "i"
* elif t == NPY_UINT: f = "I"
*/
- __pyx_t_1 = (__pyx_v_t == NPY_USHORT);
- if (__pyx_t_1) {
+ case NPY_USHORT:
__pyx_v_f = __pyx_k__H;
- goto __pyx_L13;
- }
+ break;
- /* "numpy.pxd":262
+ /* "numpy.pxd":262
* elif t == NPY_SHORT: f = "h"
* elif t == NPY_USHORT: f = "H"
* elif t == NPY_INT: f = "i" # <<<<<<<<<<<<<<
* elif t == NPY_UINT: f = "I"
* elif t == NPY_LONG: f = "l"
*/
- __pyx_t_1 = (__pyx_v_t == NPY_INT);
- if (__pyx_t_1) {
+ case NPY_INT:
__pyx_v_f = __pyx_k__i;
- goto __pyx_L13;
- }
+ break;
- /* "numpy.pxd":263
+ /* "numpy.pxd":263
* elif t == NPY_USHORT: f = "H"
* elif t == NPY_INT: f = "i"
* elif t == NPY_UINT: f = "I" # <<<<<<<<<<<<<<
* elif t == NPY_LONG: f = "l"
* elif t == NPY_ULONG: f = "L"
*/
- __pyx_t_1 = (__pyx_v_t == NPY_UINT);
- if (__pyx_t_1) {
+ case NPY_UINT:
__pyx_v_f = __pyx_k__I;
- goto __pyx_L13;
- }
+ break;
- /* "numpy.pxd":264
+ /* "numpy.pxd":264
* elif t == NPY_INT: f = "i"
* elif t == NPY_UINT: f = "I"
* elif t == NPY_LONG: f = "l" # <<<<<<<<<<<<<<
* elif t == NPY_ULONG: f = "L"
* elif t == NPY_LONGLONG: f = "q"
*/
- __pyx_t_1 = (__pyx_v_t == NPY_LONG);
- if (__pyx_t_1) {
+ case NPY_LONG:
__pyx_v_f = __pyx_k__l;
- goto __pyx_L13;
- }
+ break;
- /* "numpy.pxd":265
+ /* "numpy.pxd":265
* elif t == NPY_UINT: f = "I"
* elif t == NPY_LONG: f = "l"
* elif t == NPY_ULONG: f = "L" # <<<<<<<<<<<<<<
* elif t == NPY_LONGLONG: f = "q"
* elif t == NPY_ULONGLONG: f = "Q"
*/
- __pyx_t_1 = (__pyx_v_t == NPY_ULONG);
- if (__pyx_t_1) {
+ case NPY_ULONG:
__pyx_v_f = __pyx_k__L;
- goto __pyx_L13;
- }
+ break;
- /* "numpy.pxd":266
+ /* "numpy.pxd":266
* elif t == NPY_LONG: f = "l"
* elif t == NPY_ULONG: f = "L"
* elif t == NPY_LONGLONG: f = "q" # <<<<<<<<<<<<<<
* elif t == NPY_ULONGLONG: f = "Q"
* elif t == NPY_FLOAT: f = "f"
*/
- __pyx_t_1 = (__pyx_v_t == NPY_LONGLONG);
- if (__pyx_t_1) {
+ case NPY_LONGLONG:
__pyx_v_f = __pyx_k__q;
- goto __pyx_L13;
- }
+ break;
- /* "numpy.pxd":267
+ /* "numpy.pxd":267
* elif t == NPY_ULONG: f = "L"
* elif t == NPY_LONGLONG: f = "q"
* elif t == NPY_ULONGLONG: f = "Q" # <<<<<<<<<<<<<<
* elif t == NPY_FLOAT: f = "f"
* elif t == NPY_DOUBLE: f = "d"
*/
- __pyx_t_1 = (__pyx_v_t == NPY_ULONGLONG);
- if (__pyx_t_1) {
+ case NPY_ULONGLONG:
__pyx_v_f = __pyx_k__Q;
- goto __pyx_L13;
- }
+ break;
- /* "numpy.pxd":268
+ /* "numpy.pxd":268
* elif t == NPY_LONGLONG: f = "q"
* elif t == NPY_ULONGLONG: f = "Q"
* elif t == NPY_FLOAT: f = "f" # <<<<<<<<<<<<<<
* elif t == NPY_DOUBLE: f = "d"
* elif t == NPY_LONGDOUBLE: f = "g"
*/
- __pyx_t_1 = (__pyx_v_t == NPY_FLOAT);
- if (__pyx_t_1) {
+ case NPY_FLOAT:
__pyx_v_f = __pyx_k__f;
- goto __pyx_L13;
- }
+ break;
- /* "numpy.pxd":269
+ /* "numpy.pxd":269
* elif t == NPY_ULONGLONG: f = "Q"
* elif t == NPY_FLOAT: f = "f"
* elif t == NPY_DOUBLE: f = "d" # <<<<<<<<<<<<<<
* elif t == NPY_LONGDOUBLE: f = "g"
* elif t == NPY_CFLOAT: f = "Zf"
*/
- __pyx_t_1 = (__pyx_v_t == NPY_DOUBLE);
- if (__pyx_t_1) {
+ case NPY_DOUBLE:
__pyx_v_f = __pyx_k__d;
- goto __pyx_L13;
- }
+ break;
- /* "numpy.pxd":270
+ /* "numpy.pxd":270
* elif t == NPY_FLOAT: f = "f"
* elif t == NPY_DOUBLE: f = "d"
* elif t == NPY_LONGDOUBLE: f = "g" # <<<<<<<<<<<<<<
* elif t == NPY_CFLOAT: f = "Zf"
* elif t == NPY_CDOUBLE: f = "Zd"
*/
- __pyx_t_1 = (__pyx_v_t == NPY_LONGDOUBLE);
- if (__pyx_t_1) {
+ case NPY_LONGDOUBLE:
__pyx_v_f = __pyx_k__g;
- goto __pyx_L13;
- }
+ break;
- /* "numpy.pxd":271
+ /* "numpy.pxd":271
* elif t == NPY_DOUBLE: f = "d"
* elif t == NPY_LONGDOUBLE: f = "g"
* elif t == NPY_CFLOAT: f = "Zf" # <<<<<<<<<<<<<<
* elif t == NPY_CDOUBLE: f = "Zd"
* elif t == NPY_CLONGDOUBLE: f = "Zg"
*/
- __pyx_t_1 = (__pyx_v_t == NPY_CFLOAT);
- if (__pyx_t_1) {
+ case NPY_CFLOAT:
__pyx_v_f = __pyx_k__Zf;
- goto __pyx_L13;
- }
+ break;
- /* "numpy.pxd":272
+ /* "numpy.pxd":272
* elif t == NPY_LONGDOUBLE: f = "g"
* elif t == NPY_CFLOAT: f = "Zf"
* elif t == NPY_CDOUBLE: f = "Zd" # <<<<<<<<<<<<<<
* elif t == NPY_CLONGDOUBLE: f = "Zg"
* elif t == NPY_OBJECT: f = "O"
*/
- __pyx_t_1 = (__pyx_v_t == NPY_CDOUBLE);
- if (__pyx_t_1) {
+ case NPY_CDOUBLE:
__pyx_v_f = __pyx_k__Zd;
- goto __pyx_L13;
- }
+ break;
- /* "numpy.pxd":273
+ /* "numpy.pxd":273
* elif t == NPY_CFLOAT: f = "Zf"
* elif t == NPY_CDOUBLE: f = "Zd"
* elif t == NPY_CLONGDOUBLE: f = "Zg" # <<<<<<<<<<<<<<
* elif t == NPY_OBJECT: f = "O"
* else:
*/
- __pyx_t_1 = (__pyx_v_t == NPY_CLONGDOUBLE);
- if (__pyx_t_1) {
+ case NPY_CLONGDOUBLE:
__pyx_v_f = __pyx_k__Zg;
- goto __pyx_L13;
- }
+ break;
- /* "numpy.pxd":274
+ /* "numpy.pxd":274
* elif t == NPY_CDOUBLE: f = "Zd"
* elif t == NPY_CLONGDOUBLE: f = "Zg"
* elif t == NPY_OBJECT: f = "O" # <<<<<<<<<<<<<<
* else:
* raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t)
*/
- __pyx_t_1 = (__pyx_v_t == NPY_OBJECT);
- if (__pyx_t_1) {
+ case NPY_OBJECT:
__pyx_v_f = __pyx_k__O;
- goto __pyx_L13;
- }
- /*else*/ {
+ break;
+ default:
/* "numpy.pxd":276
* elif t == NPY_OBJECT: f = "O"
@@ -3169,8 +3268,8 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__Pyx_Raise(__pyx_t_8, 0, 0, 0);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
{__pyx_filename = __pyx_f[1]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ break;
}
- __pyx_L13:;
/* "numpy.pxd":277
* else:
@@ -3294,7 +3393,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s
* stdlib.free(info.format)
* if sizeof(npy_intp) != sizeof(Py_ssize_t):
*/
- __pyx_t_1 = PyArray_HASFIELDS(__pyx_v_self);
+ __pyx_t_1 = (PyArray_HASFIELDS(__pyx_v_self) != 0);
if (__pyx_t_1) {
/* "numpy.pxd":290
@@ -3316,7 +3415,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s
* stdlib.free(info.strides)
* # info.shape was stored after info.strides in the same block
*/
- __pyx_t_1 = ((sizeof(npy_intp)) != (sizeof(Py_ssize_t)));
+ __pyx_t_1 = (((sizeof(npy_intp)) != (sizeof(Py_ssize_t))) != 0);
if (__pyx_t_1) {
/* "numpy.pxd":292
@@ -3665,7 +3764,9 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
__Pyx_INCREF(__pyx_t_4);
#else
__pyx_t_3 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__pyx_t_4 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
#endif
} else if (1) {
__Pyx_RaiseNoneNotIterableError(); {__pyx_filename = __pyx_f[1]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -3745,9 +3846,9 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
* (child.byteorder == c'<' and not little_endian)):
* raise ValueError(u"Non-native byte order not supported")
*/
- __pyx_t_7 = (__pyx_v_child->byteorder == '>');
+ __pyx_t_7 = ((__pyx_v_child->byteorder == '>') != 0);
if (__pyx_t_7) {
- __pyx_t_8 = __pyx_v_little_endian;
+ __pyx_t_8 = (__pyx_v_little_endian != 0);
} else {
__pyx_t_8 = __pyx_t_7;
}
@@ -3760,9 +3861,9 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
* raise ValueError(u"Non-native byte order not supported")
* # One could encode it in the format string and have Cython
*/
- __pyx_t_7 = (__pyx_v_child->byteorder == '<');
+ __pyx_t_7 = ((__pyx_v_child->byteorder == '<') != 0);
if (__pyx_t_7) {
- __pyx_t_9 = (!__pyx_v_little_endian);
+ __pyx_t_9 = ((!(__pyx_v_little_endian != 0)) != 0);
__pyx_t_10 = __pyx_t_9;
} else {
__pyx_t_10 = __pyx_t_7;
@@ -3851,7 +3952,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
* t = child.type_num
* if end - f < 5:
*/
- __pyx_t_7 = (!PyDataType_HASFIELDS(__pyx_v_child));
+ __pyx_t_7 = ((!(PyDataType_HASFIELDS(__pyx_v_child) != 0)) != 0);
if (__pyx_t_7) {
/* "numpy.pxd":821
@@ -3874,7 +3975,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
* raise RuntimeError(u"Format string allocated too short.")
*
*/
- __pyx_t_7 = ((__pyx_v_end - __pyx_v_f) < 5);
+ __pyx_t_7 = (((__pyx_v_end - __pyx_v_f) < 5) != 0);
if (__pyx_t_7) {
/* "numpy.pxd":823
@@ -4296,6 +4397,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a
PyObject *__pyx_v_baseptr;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
+ int __pyx_t_2;
__Pyx_RefNannySetupContext("set_array_base", 0);
/* "numpy.pxd":967
@@ -4306,7 +4408,8 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a
* else:
*/
__pyx_t_1 = (__pyx_v_base == Py_None);
- if (__pyx_t_1) {
+ __pyx_t_2 = (__pyx_t_1 != 0);
+ if (__pyx_t_2) {
/* "numpy.pxd":968
* cdef PyObject* baseptr
@@ -4382,7 +4485,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py
* return None
* else:
*/
- __pyx_t_1 = (__pyx_v_arr->base == NULL);
+ __pyx_t_1 = ((__pyx_v_arr->base == NULL) != 0);
if (__pyx_t_1) {
/* "numpy.pxd":977
@@ -4425,7 +4528,11 @@ static PyMethodDef __pyx_methods[] = {
#if PY_MAJOR_VERSION >= 3
static struct PyModuleDef __pyx_moduledef = {
+ #if PY_VERSION_HEX < 0x03020000
+ { PyObject_HEAD_INIT(NULL) NULL, 0, NULL },
+ #else
PyModuleDef_HEAD_INIT,
+ #endif
__Pyx_NAMESTR("_hierarchical"),
0, /* m_doc */
-1, /* m_size */
@@ -4448,10 +4555,14 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_kp_u_9, __pyx_k_9, sizeof(__pyx_k_9), 0, 1, 0, 0},
{&__pyx_n_s__RuntimeError, __pyx_k__RuntimeError, sizeof(__pyx_k__RuntimeError), 0, 0, 1, 1},
{&__pyx_n_s__ValueError, __pyx_k__ValueError, sizeof(__pyx_k__ValueError), 0, 0, 1, 1},
+ {&__pyx_n_s____import__, __pyx_k____import__, sizeof(__pyx_k____import__), 0, 0, 1, 1},
{&__pyx_n_s____main__, __pyx_k____main__, sizeof(__pyx_k____main__), 0, 0, 1, 1},
+ {&__pyx_n_s____pyx_getbuffer, __pyx_k____pyx_getbuffer, sizeof(__pyx_k____pyx_getbuffer), 0, 0, 1, 1},
+ {&__pyx_n_s____pyx_releasebuffer, __pyx_k____pyx_releasebuffer, sizeof(__pyx_k____pyx_releasebuffer), 0, 0, 1, 1},
{&__pyx_n_s____test__, __pyx_k____test__, sizeof(__pyx_k____test__), 0, 0, 1, 1},
{&__pyx_n_s___get_parents, __pyx_k___get_parents, sizeof(__pyx_k___get_parents), 0, 0, 1, 1},
{&__pyx_n_s___hc_get_descendent, __pyx_k___hc_get_descendent, sizeof(__pyx_k___hc_get_descendent), 0, 0, 1, 1},
+ {&__pyx_n_s__append, __pyx_k__append, sizeof(__pyx_k__append), 0, 0, 1, 1},
{&__pyx_n_s__children, __pyx_k__children, sizeof(__pyx_k__children), 0, 0, 1, 1},
{&__pyx_n_s__col, __pyx_k__col, sizeof(__pyx_k__col), 0, 0, 1, 1},
{&__pyx_n_s__compute_ward_dist, __pyx_k__compute_ward_dist, sizeof(__pyx_k__compute_ward_dist), 0, 0, 1, 1},
@@ -4480,6 +4591,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s__pa, __pyx_k__pa, sizeof(__pyx_k__pa), 0, 0, 1, 1},
{&__pyx_n_s__parent, __pyx_k__parent, sizeof(__pyx_k__parent), 0, 0, 1, 1},
{&__pyx_n_s__parents, __pyx_k__parents, sizeof(__pyx_k__parents), 0, 0, 1, 1},
+ {&__pyx_n_s__pop, __pyx_k__pop, sizeof(__pyx_k__pop), 0, 0, 1, 1},
{&__pyx_n_s__range, __pyx_k__range, sizeof(__pyx_k__range), 0, 0, 1, 1},
{&__pyx_n_s__res, __pyx_k__res, sizeof(__pyx_k__res), 0, 0, 1, 1},
{&__pyx_n_s__row, __pyx_k__row, sizeof(__pyx_k__row), 0, 0, 1, 1},
@@ -4488,9 +4600,9 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{0, 0, 0, 0, 0, 0, 0}
};
static int __Pyx_InitCachedBuiltins(void) {
- __pyx_builtin_range = __Pyx_GetName(__pyx_b, __pyx_n_s__range); if (!__pyx_builtin_range) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 23; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_ValueError = __Pyx_GetName(__pyx_b, __pyx_n_s__ValueError); if (!__pyx_builtin_ValueError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_RuntimeError = __Pyx_GetName(__pyx_b, __pyx_n_s__RuntimeError); if (!__pyx_builtin_RuntimeError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_range = __Pyx_GetBuiltinName(__pyx_n_s__range); if (!__pyx_builtin_range) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_ValueError = __Pyx_GetBuiltinName(__pyx_n_s__ValueError); if (!__pyx_builtin_ValueError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_RuntimeError = __Pyx_GetBuiltinName(__pyx_n_s__RuntimeError); if (!__pyx_builtin_RuntimeError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
return 0;
__pyx_L1_error:;
return -1;
@@ -4507,11 +4619,8 @@ static int __Pyx_InitCachedConstants(void) {
*
* if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS)
*/
- __pyx_k_tuple_3 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_3 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_u_2)); if (unlikely(!__pyx_k_tuple_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_3);
- __Pyx_INCREF(((PyObject *)__pyx_kp_u_2));
- PyTuple_SET_ITEM(__pyx_k_tuple_3, 0, ((PyObject *)__pyx_kp_u_2));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_u_2));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_3));
/* "numpy.pxd":219
@@ -4521,11 +4630,8 @@ static int __Pyx_InitCachedConstants(void) {
*
* info.buf = PyArray_DATA(self)
*/
- __pyx_k_tuple_5 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_5 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_u_4)); if (unlikely(!__pyx_k_tuple_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_5);
- __Pyx_INCREF(((PyObject *)__pyx_kp_u_4));
- PyTuple_SET_ITEM(__pyx_k_tuple_5, 0, ((PyObject *)__pyx_kp_u_4));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_u_4));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_5));
/* "numpy.pxd":257
@@ -4535,11 +4641,8 @@ static int __Pyx_InitCachedConstants(void) {
* if t == NPY_BYTE: f = "b"
* elif t == NPY_UBYTE: f = "B"
*/
- __pyx_k_tuple_7 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_7)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_7 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_u_6)); if (unlikely(!__pyx_k_tuple_7)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_7);
- __Pyx_INCREF(((PyObject *)__pyx_kp_u_6));
- PyTuple_SET_ITEM(__pyx_k_tuple_7, 0, ((PyObject *)__pyx_kp_u_6));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_u_6));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_7));
/* "numpy.pxd":799
@@ -4549,11 +4652,8 @@ static int __Pyx_InitCachedConstants(void) {
*
* if ((child.byteorder == c'>' and little_endian) or
*/
- __pyx_k_tuple_10 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_10)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_10 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_u_9)); if (unlikely(!__pyx_k_tuple_10)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_10);
- __Pyx_INCREF(((PyObject *)__pyx_kp_u_9));
- PyTuple_SET_ITEM(__pyx_k_tuple_10, 0, ((PyObject *)__pyx_kp_u_9));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_u_9));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_10));
/* "numpy.pxd":803
@@ -4563,11 +4663,8 @@ static int __Pyx_InitCachedConstants(void) {
* # One could encode it in the format string and have Cython
* # complain instead, BUT: < and > in format strings also imply
*/
- __pyx_k_tuple_11 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_11)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_11 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_u_6)); if (unlikely(!__pyx_k_tuple_11)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_11);
- __Pyx_INCREF(((PyObject *)__pyx_kp_u_6));
- PyTuple_SET_ITEM(__pyx_k_tuple_11, 0, ((PyObject *)__pyx_kp_u_6));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_u_6));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_11));
/* "numpy.pxd":823
@@ -4577,156 +4674,57 @@ static int __Pyx_InitCachedConstants(void) {
*
* # Until ticket #99 is fixed, use integers to avoid warnings
*/
- __pyx_k_tuple_13 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_13)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_13 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_u_12)); if (unlikely(!__pyx_k_tuple_13)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_13);
- __Pyx_INCREF(((PyObject *)__pyx_kp_u_12));
- PyTuple_SET_ITEM(__pyx_k_tuple_13, 0, ((PyObject *)__pyx_kp_u_12));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_u_12));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_13));
- /* "sklearn/cluster/_hierarchical.pyx":14
+ /* "sklearn/cluster/_hierarchical.pyx":17
* @cython.wraparound(False)
* @cython.cdivision(True)
- * def compute_ward_dist(np.ndarray[DOUBLE, ndim=1] m_1,\ # <<<<<<<<<<<<<<
- * np.ndarray[DOUBLE, ndim=2] m_2,\
- * np.ndarray[INT, ndim=1] coord_row,
+ * def compute_ward_dist(np.ndarray[DOUBLE, ndim=1, mode='c'] m_1, # <<<<<<<<<<<<<<
+ * np.ndarray[DOUBLE, ndim=2, mode='c'] m_2,
+ * np.ndarray[INTP, ndim=1, mode='c'] coord_row,
*/
- __pyx_k_tuple_14 = PyTuple_New(13); if (unlikely(!__pyx_k_tuple_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 14; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_14 = PyTuple_Pack(13, ((PyObject *)__pyx_n_s__m_1), ((PyObject *)__pyx_n_s__m_2), ((PyObject *)__pyx_n_s__coord_row), ((PyObject *)__pyx_n_s__coord_col), ((PyObject *)__pyx_n_s__res), ((PyObject *)__pyx_n_s__size_max), ((PyObject *)__pyx_n_s__n_features), ((PyObject *)__pyx_n_s__i), ((PyObject *)__pyx_n_s__j), ((PyObject *)__pyx_n_s__row), ((PyObject *)__pyx_n_s__col), ((PyObject *)__pyx_n_s__pa), ((PyObject *)__pyx_n_s__n)); if (unlikely(!__pyx_k_tuple_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 17; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_14);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__m_1));
- PyTuple_SET_ITEM(__pyx_k_tuple_14, 0, ((PyObject *)__pyx_n_s__m_1));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__m_1));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__m_2));
- PyTuple_SET_ITEM(__pyx_k_tuple_14, 1, ((PyObject *)__pyx_n_s__m_2));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__m_2));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__coord_row));
- PyTuple_SET_ITEM(__pyx_k_tuple_14, 2, ((PyObject *)__pyx_n_s__coord_row));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__coord_row));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__coord_col));
- PyTuple_SET_ITEM(__pyx_k_tuple_14, 3, ((PyObject *)__pyx_n_s__coord_col));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__coord_col));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__res));
- PyTuple_SET_ITEM(__pyx_k_tuple_14, 4, ((PyObject *)__pyx_n_s__res));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__res));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__size_max));
- PyTuple_SET_ITEM(__pyx_k_tuple_14, 5, ((PyObject *)__pyx_n_s__size_max));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__size_max));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__n_features));
- PyTuple_SET_ITEM(__pyx_k_tuple_14, 6, ((PyObject *)__pyx_n_s__n_features));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__n_features));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__i));
- PyTuple_SET_ITEM(__pyx_k_tuple_14, 7, ((PyObject *)__pyx_n_s__i));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__i));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__j));
- PyTuple_SET_ITEM(__pyx_k_tuple_14, 8, ((PyObject *)__pyx_n_s__j));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__j));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__row));
- PyTuple_SET_ITEM(__pyx_k_tuple_14, 9, ((PyObject *)__pyx_n_s__row));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__row));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__col));
- PyTuple_SET_ITEM(__pyx_k_tuple_14, 10, ((PyObject *)__pyx_n_s__col));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__col));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__pa));
- PyTuple_SET_ITEM(__pyx_k_tuple_14, 11, ((PyObject *)__pyx_n_s__pa));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__pa));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__n));
- PyTuple_SET_ITEM(__pyx_k_tuple_14, 12, ((PyObject *)__pyx_n_s__n));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__n));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_14));
- __pyx_k_codeobj_15 = (PyObject*)__Pyx_PyCode_New(5, 0, 13, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_14, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_16, __pyx_n_s__compute_ward_dist, 14, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 14; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_codeobj_15 = (PyObject*)__Pyx_PyCode_New(5, 0, 13, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_14, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_16, __pyx_n_s__compute_ward_dist, 17, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 17; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "sklearn/cluster/_hierarchical.pyx":34
+ /* "sklearn/cluster/_hierarchical.pyx":38
*
*
- * def _hc_get_descendent(int node, children, int n_leaves): # <<<<<<<<<<<<<<
+ * def _hc_get_descendent(INTP node, children, INTP n_leaves): # <<<<<<<<<<<<<<
* """
* Function returning all the descendent leaves of a set of nodes in the tree.
*/
- __pyx_k_tuple_18 = PyTuple_New(7); if (unlikely(!__pyx_k_tuple_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_18 = PyTuple_Pack(7, ((PyObject *)__pyx_n_s__node), ((PyObject *)__pyx_n_s__children), ((PyObject *)__pyx_n_s__n_leaves), ((PyObject *)__pyx_n_s__ind), ((PyObject *)__pyx_n_s__descendent), ((PyObject *)__pyx_n_s__i), ((PyObject *)__pyx_n_s__n_indices)); if (unlikely(!__pyx_k_tuple_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_18);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__node));
- PyTuple_SET_ITEM(__pyx_k_tuple_18, 0, ((PyObject *)__pyx_n_s__node));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__node));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__children));
- PyTuple_SET_ITEM(__pyx_k_tuple_18, 1, ((PyObject *)__pyx_n_s__children));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__children));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__n_leaves));
- PyTuple_SET_ITEM(__pyx_k_tuple_18, 2, ((PyObject *)__pyx_n_s__n_leaves));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__n_leaves));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__ind));
- PyTuple_SET_ITEM(__pyx_k_tuple_18, 3, ((PyObject *)__pyx_n_s__ind));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ind));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__descendent));
- PyTuple_SET_ITEM(__pyx_k_tuple_18, 4, ((PyObject *)__pyx_n_s__descendent));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__descendent));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__n_indices));
- PyTuple_SET_ITEM(__pyx_k_tuple_18, 5, ((PyObject *)__pyx_n_s__n_indices));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__n_indices));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__i));
- PyTuple_SET_ITEM(__pyx_k_tuple_18, 6, ((PyObject *)__pyx_n_s__i));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__i));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_18));
- __pyx_k_codeobj_19 = (PyObject*)__Pyx_PyCode_New(3, 0, 7, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_18, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_16, __pyx_n_s___hc_get_descendent, 34, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_codeobj_19 = (PyObject*)__Pyx_PyCode_New(3, 0, 7, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_18, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_16, __pyx_n_s___hc_get_descendent, 38, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "sklearn/cluster/_hierarchical.pyx":76
+ /* "sklearn/cluster/_hierarchical.pyx":82
* @cython.boundscheck(False)
* @cython.wraparound(False)
- * def hc_get_heads(np.ndarray[INT, ndim=1] parents, copy=True): # <<<<<<<<<<<<<<
- * """ Return the heads of the forest, as defined by parents
+ * def hc_get_heads(np.ndarray[INTP, ndim=1] parents, copy=True): # <<<<<<<<<<<<<<
+ * """Returns the heads of the forest, as defined by parents.
*
*/
- __pyx_k_tuple_20 = PyTuple_New(6); if (unlikely(!__pyx_k_tuple_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_20 = PyTuple_Pack(6, ((PyObject *)__pyx_n_s__parents), ((PyObject *)__pyx_n_s__copy), ((PyObject *)__pyx_n_s__parent), ((PyObject *)__pyx_n_s__node0), ((PyObject *)__pyx_n_s__node), ((PyObject *)__pyx_n_s__size)); if (unlikely(!__pyx_k_tuple_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_20);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__parents));
- PyTuple_SET_ITEM(__pyx_k_tuple_20, 0, ((PyObject *)__pyx_n_s__parents));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__parents));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__copy));
- PyTuple_SET_ITEM(__pyx_k_tuple_20, 1, ((PyObject *)__pyx_n_s__copy));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__copy));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__parent));
- PyTuple_SET_ITEM(__pyx_k_tuple_20, 2, ((PyObject *)__pyx_n_s__parent));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__parent));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__node0));
- PyTuple_SET_ITEM(__pyx_k_tuple_20, 3, ((PyObject *)__pyx_n_s__node0));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__node0));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__node));
- PyTuple_SET_ITEM(__pyx_k_tuple_20, 4, ((PyObject *)__pyx_n_s__node));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__node));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__size));
- PyTuple_SET_ITEM(__pyx_k_tuple_20, 5, ((PyObject *)__pyx_n_s__size));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__size));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_20));
- __pyx_k_codeobj_21 = (PyObject*)__Pyx_PyCode_New(2, 0, 6, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_20, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_16, __pyx_n_s__hc_get_heads, 76, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_codeobj_21 = (PyObject*)__Pyx_PyCode_New(2, 0, 6, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_20, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_16, __pyx_n_s__hc_get_heads, 82, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "sklearn/cluster/_hierarchical.pyx":110
+ /* "sklearn/cluster/_hierarchical.pyx":116
* @cython.boundscheck(False)
* @cython.wraparound(False)
- * def _get_parents(nodes, heads, np.ndarray[INT, ndim=1] parents, # <<<<<<<<<<<<<<
- * np.ndarray[INT8, ndim=1] not_visited):
- * """ Return the heads of the given nodes, as defined by parents
+ * def _get_parents(nodes, heads, np.ndarray[INTP, ndim=1] parents, # <<<<<<<<<<<<<<
+ * np.ndarray[INT8, ndim=1, mode='c'] not_visited):
+ * """Returns the heads of the given nodes, as defined by parents.
*/
- __pyx_k_tuple_22 = PyTuple_New(6); if (unlikely(!__pyx_k_tuple_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_22 = PyTuple_Pack(6, ((PyObject *)__pyx_n_s__nodes), ((PyObject *)__pyx_n_s__heads), ((PyObject *)__pyx_n_s__parents), ((PyObject *)__pyx_n_s__not_visited), ((PyObject *)__pyx_n_s__parent), ((PyObject *)__pyx_n_s__node)); if (unlikely(!__pyx_k_tuple_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 116; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_22);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__nodes));
- PyTuple_SET_ITEM(__pyx_k_tuple_22, 0, ((PyObject *)__pyx_n_s__nodes));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__nodes));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__heads));
- PyTuple_SET_ITEM(__pyx_k_tuple_22, 1, ((PyObject *)__pyx_n_s__heads));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__heads));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__parents));
- PyTuple_SET_ITEM(__pyx_k_tuple_22, 2, ((PyObject *)__pyx_n_s__parents));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__parents));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__not_visited));
- PyTuple_SET_ITEM(__pyx_k_tuple_22, 3, ((PyObject *)__pyx_n_s__not_visited));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__not_visited));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__parent));
- PyTuple_SET_ITEM(__pyx_k_tuple_22, 4, ((PyObject *)__pyx_n_s__parent));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__parent));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__node));
- PyTuple_SET_ITEM(__pyx_k_tuple_22, 5, ((PyObject *)__pyx_n_s__node));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__node));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_22));
- __pyx_k_codeobj_23 = (PyObject*)__Pyx_PyCode_New(4, 0, 6, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_22, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_16, __pyx_n_s___get_parents, 110, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_codeobj_23 = (PyObject*)__Pyx_PyCode_New(4, 0, 6, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_22, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_16, __pyx_n_s___get_parents, 116, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 116; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_RefNannyFinishContext();
return 0;
__pyx_L1_error:;
@@ -4751,6 +4749,9 @@ PyMODINIT_FUNC PyInit__hierarchical(void)
#endif
{
PyObject *__pyx_t_1 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_RefNannyDeclarations
#if CYTHON_REFNANNY
__Pyx_RefNanny = __Pyx_RefNannyImportAPI("refnanny");
@@ -4788,6 +4789,8 @@ PyMODINIT_FUNC PyInit__hierarchical(void)
__pyx_m = PyModule_Create(&__pyx_moduledef);
#endif
if (unlikely(!__pyx_m)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_d = PyModule_GetDict(__pyx_m); if (unlikely(!__pyx_d)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ Py_INCREF(__pyx_d);
#if PY_MAJOR_VERSION >= 3
{
PyObject *modules = PyImport_GetModuleDict(); if (unlikely(!modules)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -4803,6 +4806,9 @@ PyMODINIT_FUNC PyInit__hierarchical(void)
if (__Pyx_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
/*--- Initialize various global constants etc. ---*/
if (unlikely(__Pyx_InitGlobals() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #if PY_MAJOR_VERSION < 3 && (__PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT)
+ if (__Pyx_init_sys_getdefaultencoding_params() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
if (__pyx_module_is_main_sklearn__cluster___hierarchical) {
if (__Pyx_SetAttrString(__pyx_m, "__name__", __pyx_n_s____main__) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
}
@@ -4831,17 +4837,19 @@ PyMODINIT_FUNC PyInit__hierarchical(void)
/*--- Function import code ---*/
/*--- Execution code ---*/
- /* "sklearn/cluster/_hierarchical.pyx":1
+ /* "sklearn/cluster/_hierarchical.pyx":3
+ * # Author: Gael Varoquaux <gael.varoquaux@normalesup.org>
+ *
* import numpy as np # <<<<<<<<<<<<<<
* cimport numpy as np
* cimport cython
*/
- __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__numpy), 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__numpy), 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__np, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_d, __pyx_n_s__np, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "sklearn/cluster/_hierarchical.pyx":8
+ /* "sklearn/cluster/_hierarchical.pyx":11
* ctypedef np.int8_t INT8
*
* np.import_array() # <<<<<<<<<<<<<<
@@ -4850,67 +4858,67 @@ PyMODINIT_FUNC PyInit__hierarchical(void)
*/
import_array();
- /* "sklearn/cluster/_hierarchical.pyx":14
+ /* "sklearn/cluster/_hierarchical.pyx":17
* @cython.wraparound(False)
* @cython.cdivision(True)
- * def compute_ward_dist(np.ndarray[DOUBLE, ndim=1] m_1,\ # <<<<<<<<<<<<<<
- * np.ndarray[DOUBLE, ndim=2] m_2,\
- * np.ndarray[INT, ndim=1] coord_row,
+ * def compute_ward_dist(np.ndarray[DOUBLE, ndim=1, mode='c'] m_1, # <<<<<<<<<<<<<<
+ * np.ndarray[DOUBLE, ndim=2, mode='c'] m_2,
+ * np.ndarray[INTP, ndim=1, mode='c'] coord_row,
*/
- __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_7sklearn_7cluster_13_hierarchical_1compute_ward_dist, NULL, __pyx_n_s_17); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 14; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_7sklearn_7cluster_13_hierarchical_1compute_ward_dist, NULL, __pyx_n_s_17); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 17; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__compute_ward_dist, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 14; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_d, __pyx_n_s__compute_ward_dist, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 17; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "sklearn/cluster/_hierarchical.pyx":34
+ /* "sklearn/cluster/_hierarchical.pyx":38
*
*
- * def _hc_get_descendent(int node, children, int n_leaves): # <<<<<<<<<<<<<<
+ * def _hc_get_descendent(INTP node, children, INTP n_leaves): # <<<<<<<<<<<<<<
* """
* Function returning all the descendent leaves of a set of nodes in the tree.
*/
- __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_7sklearn_7cluster_13_hierarchical_3_hc_get_descendent, NULL, __pyx_n_s_17); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_7sklearn_7cluster_13_hierarchical_3_hc_get_descendent, NULL, __pyx_n_s_17); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s___hc_get_descendent, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_d, __pyx_n_s___hc_get_descendent, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "sklearn/cluster/_hierarchical.pyx":76
+ /* "sklearn/cluster/_hierarchical.pyx":82
* @cython.boundscheck(False)
* @cython.wraparound(False)
- * def hc_get_heads(np.ndarray[INT, ndim=1] parents, copy=True): # <<<<<<<<<<<<<<
- * """ Return the heads of the forest, as defined by parents
+ * def hc_get_heads(np.ndarray[INTP, ndim=1] parents, copy=True): # <<<<<<<<<<<<<<
+ * """Returns the heads of the forest, as defined by parents.
*
*/
- __pyx_t_1 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_k_1 = __pyx_t_1;
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
- __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_7sklearn_7cluster_13_hierarchical_5hc_get_heads, NULL, __pyx_n_s_17); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_7sklearn_7cluster_13_hierarchical_5hc_get_heads, NULL, __pyx_n_s_17); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__hc_get_heads, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_d, __pyx_n_s__hc_get_heads, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "sklearn/cluster/_hierarchical.pyx":110
+ /* "sklearn/cluster/_hierarchical.pyx":116
* @cython.boundscheck(False)
* @cython.wraparound(False)
- * def _get_parents(nodes, heads, np.ndarray[INT, ndim=1] parents, # <<<<<<<<<<<<<<
- * np.ndarray[INT8, ndim=1] not_visited):
- * """ Return the heads of the given nodes, as defined by parents
+ * def _get_parents(nodes, heads, np.ndarray[INTP, ndim=1] parents, # <<<<<<<<<<<<<<
+ * np.ndarray[INT8, ndim=1, mode='c'] not_visited):
+ * """Returns the heads of the given nodes, as defined by parents.
*/
- __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_7sklearn_7cluster_13_hierarchical_7_get_parents, NULL, __pyx_n_s_17); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_7sklearn_7cluster_13_hierarchical_7_get_parents, NULL, __pyx_n_s_17); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 116; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s___get_parents, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_d, __pyx_n_s___get_parents, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 116; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
/* "sklearn/cluster/_hierarchical.pyx":1
- * import numpy as np # <<<<<<<<<<<<<<
- * cimport numpy as np
- * cimport cython
+ * # Author: Gael Varoquaux <gael.varoquaux@normalesup.org> # <<<<<<<<<<<<<<
+ *
+ * import numpy as np
*/
__pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s____test__, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_d, __pyx_n_s____test__, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
/* "numpy.pxd":975
@@ -4955,17 +4963,15 @@ end:
}
#endif /* CYTHON_REFNANNY */
-static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name) {
- PyObject *result;
- result = PyObject_GetAttr(dict, name);
- if (!result) {
- if (dict != __pyx_b) {
- PyErr_Clear();
- result = PyObject_GetAttr(__pyx_b, name);
- }
- if (!result) {
- PyErr_SetObject(PyExc_NameError, name);
- }
+static PyObject *__Pyx_GetBuiltinName(PyObject *name) {
+ PyObject* result = __Pyx_PyObject_GetAttrStr(__pyx_b, name);
+ if (unlikely(!result)) {
+ PyErr_Format(PyExc_NameError,
+#if PY_MAJOR_VERSION >= 3
+ "name '%U' is not defined", name);
+#else
+ "name '%s' is not defined", PyString_AS_STRING(name));
+#endif
}
return result;
}
@@ -5703,6 +5709,117 @@ static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyOb
#endif
}
+static CYTHON_INLINE PyObject* __Pyx_PyObject_Pop(PyObject* L) {
+#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x02040000
+ if (likely(PyList_CheckExact(L))
+ && likely(PyList_GET_SIZE(L) > (((PyListObject*)L)->allocated >> 1))) {
+ Py_SIZE(L) -= 1;
+ return PyList_GET_ITEM(L, PyList_GET_SIZE(L));
+ }
+#if PY_VERSION_HEX >= 0x02050000
+ else if (Py_TYPE(L) == (&PySet_Type)) {
+ return PySet_Pop(L);
+ }
+#endif
+#endif
+ return __Pyx_PyObject_CallMethod0(L, __pyx_n_s__pop);
+}
+
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) {
+ PyObject *r;
+ if (!j) return NULL;
+ r = PyObject_GetItem(o, j);
+ Py_DECREF(j);
+ return r;
+}
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
+ int wraparound, int boundscheck) {
+#if CYTHON_COMPILING_IN_CPYTHON
+ if (wraparound & unlikely(i < 0)) i += PyList_GET_SIZE(o);
+ if ((!boundscheck) || likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
+ PyObject *r = PyList_GET_ITEM(o, i);
+ Py_INCREF(r);
+ return r;
+ }
+ return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+#else
+ return PySequence_GetItem(o, i);
+#endif
+}
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
+ int wraparound, int boundscheck) {
+#if CYTHON_COMPILING_IN_CPYTHON
+ if (wraparound & unlikely(i < 0)) i += PyTuple_GET_SIZE(o);
+ if ((!boundscheck) || likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
+ PyObject *r = PyTuple_GET_ITEM(o, i);
+ Py_INCREF(r);
+ return r;
+ }
+ return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+#else
+ return PySequence_GetItem(o, i);
+#endif
+}
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i,
+ int is_list, int wraparound, int boundscheck) {
+#if CYTHON_COMPILING_IN_CPYTHON
+ if (is_list || PyList_CheckExact(o)) {
+ Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
+ if ((!boundscheck) || (likely((n >= 0) & (n < PyList_GET_SIZE(o))))) {
+ PyObject *r = PyList_GET_ITEM(o, n);
+ Py_INCREF(r);
+ return r;
+ }
+ }
+ else if (PyTuple_CheckExact(o)) {
+ Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o);
+ if ((!boundscheck) || likely((n >= 0) & (n < PyTuple_GET_SIZE(o)))) {
+ PyObject *r = PyTuple_GET_ITEM(o, n);
+ Py_INCREF(r);
+ return r;
+ }
+ } else {
+ PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
+ if (likely(m && m->sq_item)) {
+ if (wraparound && unlikely(i < 0) && likely(m->sq_length)) {
+ Py_ssize_t l = m->sq_length(o);
+ if (likely(l >= 0)) {
+ i += l;
+ } else {
+ if (PyErr_ExceptionMatches(PyExc_OverflowError))
+ PyErr_Clear();
+ else
+ return NULL;
+ }
+ }
+ return m->sq_item(o, i);
+ }
+ }
+#else
+ if (is_list || PySequence_Check(o)) {
+ return PySequence_GetItem(o, i);
+ }
+#endif
+ return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+}
+
+static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name) {
+ PyObject *result;
+#if CYTHON_COMPILING_IN_CPYTHON
+ result = PyDict_GetItem(__pyx_d, name);
+ if (result) {
+ Py_INCREF(result);
+ } else {
+#else
+ result = PyObject_GetItem(__pyx_d, name);
+ if (!result) {
+ PyErr_Clear();
+#endif
+ result = __Pyx_GetBuiltinName(name);
+ }
+ return result;
+}
+
static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) {
if (unlikely(!type)) {
PyErr_Format(PyExc_SystemError, "Missing type object");
@@ -5720,6 +5837,16 @@ static void __Pyx_RaiseBufferFallbackError(void) {
"Buffer acquisition failed on assignment; and then reacquiring the old buffer failed too!");
}
+static CYTHON_INLINE PyObject* __Pyx_PyObject_Append(PyObject* L, PyObject* x) {
+ if (likely(PyList_CheckExact(L))) {
+ if (unlikely(__Pyx_PyList_Append(L, x) < 0)) return NULL;
+ Py_INCREF(Py_None);
+ return Py_None; /* this is just to have an accurate signature */
+ } else {
+ return __Pyx_PyObject_CallMethod1(L, __pyx_n_s__append, x);
+ }
+}
+
#if PY_MAJOR_VERSION < 3
static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
CYTHON_UNUSED PyObject *cause) {
@@ -5758,24 +5885,23 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
}
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);
+ if (PyInstance_Check(type)) {
+ type = (PyObject*) ((PyInstanceObject*)type)->in_class;
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;
- }
+ } else {
+ type = 0;
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception must be an old-style class or instance");
+ goto raise_error;
+ }
+ #else
+ type = (PyObject*) Py_TYPE(type);
+ Py_INCREF(type);
+ if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception class must be a subclass of BaseException");
+ goto raise_error;
+ }
#endif
}
__Pyx_ErrRestore(type, value, tb);
@@ -5813,8 +5939,7 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
else if (PyTuple_Check(value)) {
Py_INCREF(value);
args = value;
- }
- else
+ } else
args = PyTuple_Pack(1, value);
if (!args)
goto bad;
@@ -5835,18 +5960,22 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
"raise: exception class must be a subclass of BaseException");
goto bad;
}
+#if PY_VERSION_HEX >= 0x03030000
+ if (cause) {
+#else
if (cause && cause != Py_None) {
+#endif
PyObject *fixed_cause;
- if (PyExceptionClass_Check(cause)) {
+ if (cause == Py_None) {
+ fixed_cause = NULL;
+ } else if (PyExceptionClass_Check(cause)) {
fixed_cause = PyObject_CallObject(cause, NULL);
if (fixed_cause == NULL)
goto bad;
- }
- else if (PyExceptionInstance_Check(cause)) {
+ } else if (PyExceptionInstance_Check(cause)) {
fixed_cause = cause;
Py_INCREF(fixed_cause);
- }
- else {
+ } else {
PyErr_SetString(PyExc_TypeError,
"exception causes must derive from "
"BaseException");
@@ -5932,27 +6061,23 @@ static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
#if PY_MAJOR_VERSION < 3
static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) {
- CYTHON_UNUSED PyObject *getbuffer_cobj;
#if PY_VERSION_HEX >= 0x02060000
if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags);
#endif
if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) return __pyx_pw_5numpy_7ndarray_1__getbuffer__(obj, view, flags);
#if PY_VERSION_HEX < 0x02060000
- if (obj->ob_type->tp_dict &&
- (getbuffer_cobj = PyMapping_GetItemString(obj->ob_type->tp_dict,
- "__pyx_getbuffer"))) {
- getbufferproc func;
- #if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION == 3 && PY_MINOR_VERSION == 0)
- func = (getbufferproc) PyCapsule_GetPointer(getbuffer_cobj, "getbuffer(obj, view, flags)");
- #else
- func = (getbufferproc) PyCObject_AsVoidPtr(getbuffer_cobj);
- #endif
- Py_DECREF(getbuffer_cobj);
- if (!func)
- goto fail;
- return func(obj, view, flags);
- } else {
- PyErr_Clear();
+ if (obj->ob_type->tp_dict) {
+ PyObject *getbuffer_cobj = PyObject_GetItem(
+ obj->ob_type->tp_dict, __pyx_n_s____pyx_getbuffer);
+ if (getbuffer_cobj) {
+ getbufferproc func = (getbufferproc) PyCObject_AsVoidPtr(getbuffer_cobj);
+ Py_DECREF(getbuffer_cobj);
+ if (!func)
+ goto fail;
+ return func(obj, view, flags);
+ } else {
+ PyErr_Clear();
+ }
}
#endif
PyErr_Format(PyExc_TypeError, "'%100s' does not have the buffer interface", Py_TYPE(obj)->tp_name);
@@ -5963,7 +6088,6 @@ fail:
}
static void __Pyx_ReleaseBuffer(Py_buffer *view) {
PyObject *obj = view->obj;
- CYTHON_UNUSED PyObject *releasebuffer_cobj;
if (!obj) return;
#if PY_VERSION_HEX >= 0x02060000
if (PyObject_CheckBuffer(obj)) {
@@ -5973,22 +6097,19 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) {
#endif
if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) { __pyx_pw_5numpy_7ndarray_3__releasebuffer__(obj, view); return; }
#if PY_VERSION_HEX < 0x02060000
- if (obj->ob_type->tp_dict &&
- (releasebuffer_cobj = PyMapping_GetItemString(obj->ob_type->tp_dict,
- "__pyx_releasebuffer"))) {
- releasebufferproc func;
- #if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION == 3 && PY_MINOR_VERSION == 0)
- func = (releasebufferproc) PyCapsule_GetPointer(releasebuffer_cobj, "releasebuffer(obj, view)");
- #else
- func = (releasebufferproc) PyCObject_AsVoidPtr(releasebuffer_cobj);
- #endif
- Py_DECREF(releasebuffer_cobj);
- if (!func)
- goto fail;
- func(obj, view);
- return;
- } else {
- PyErr_Clear();
+ if (obj->ob_type->tp_dict) {
+ PyObject *releasebuffer_cobj = PyObject_GetItem(
+ obj->ob_type->tp_dict, __pyx_n_s____pyx_releasebuffer);
+ if (releasebuffer_cobj) {
+ releasebufferproc func = (releasebufferproc) PyCObject_AsVoidPtr(releasebuffer_cobj);
+ Py_DECREF(releasebuffer_cobj);
+ if (!func)
+ goto fail;
+ func(obj, view);
+ return;
+ } else {
+ PyErr_Clear();
+ }
}
#endif
goto nofail;
@@ -6003,16 +6124,18 @@ nofail:
#endif /* PY_MAJOR_VERSION < 3 */
- static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level) {
- PyObject *py_import = 0;
+ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
PyObject *empty_list = 0;
PyObject *module = 0;
PyObject *global_dict = 0;
PyObject *empty_dict = 0;
PyObject *list;
- py_import = __Pyx_GetAttrString(__pyx_b, "__import__");
+ #if PY_VERSION_HEX < 0x03030000
+ PyObject *py_import;
+ py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s____import__);
if (!py_import)
goto bad;
+ #endif
if (from_list)
list = from_list;
else {
@@ -6032,13 +6155,17 @@ nofail:
#if PY_MAJOR_VERSION >= 3
if (level == -1) {
if (strchr(__Pyx_MODULE_NAME, '.')) {
- /* try package relative import first */
+ #if PY_VERSION_HEX < 0x03030000
PyObject *py_level = PyInt_FromLong(1);
if (!py_level)
goto bad;
module = PyObject_CallFunctionObjArgs(py_import,
name, global_dict, empty_dict, list, py_level, NULL);
Py_DECREF(py_level);
+ #else
+ module = PyImport_ImportModuleLevelObject(
+ name, global_dict, empty_dict, list, 1);
+ #endif
if (!module) {
if (!PyErr_ExceptionMatches(PyExc_ImportError))
goto bad;
@@ -6049,12 +6176,17 @@ nofail:
}
#endif
if (!module) {
+ #if PY_VERSION_HEX < 0x03030000
PyObject *py_level = PyInt_FromLong(level);
if (!py_level)
goto bad;
module = PyObject_CallFunctionObjArgs(py_import,
name, global_dict, empty_dict, list, py_level, NULL);
Py_DECREF(py_level);
+ #else
+ module = PyImport_ImportModuleLevelObject(
+ name, global_dict, empty_dict, list, level);
+ #endif
}
}
#else
@@ -6066,12 +6198,96 @@ nofail:
name, global_dict, empty_dict, list, NULL);
#endif
bad:
- Py_XDECREF(empty_list);
+ #if PY_VERSION_HEX < 0x03030000
Py_XDECREF(py_import);
+ #endif
+ Py_XDECREF(empty_list);
Py_XDECREF(empty_dict);
return module;
}
+static CYTHON_INLINE Py_intptr_t __Pyx_PyInt_from_py_Py_intptr_t(PyObject* x) {
+ const Py_intptr_t neg_one = (Py_intptr_t)-1, const_zero = (Py_intptr_t)0;
+ const int is_unsigned = const_zero < neg_one;
+ if (sizeof(Py_intptr_t) == sizeof(char)) {
+ if (is_unsigned)
+ return (Py_intptr_t)__Pyx_PyInt_AsUnsignedChar(x);
+ else
+ return (Py_intptr_t)__Pyx_PyInt_AsSignedChar(x);
+ } else if (sizeof(Py_intptr_t) == sizeof(short)) {
+ if (is_unsigned)
+ return (Py_intptr_t)__Pyx_PyInt_AsUnsignedShort(x);
+ else
+ return (Py_intptr_t)__Pyx_PyInt_AsSignedShort(x);
+ } else if (sizeof(Py_intptr_t) == sizeof(int)) {
+ if (is_unsigned)
+ return (Py_intptr_t)__Pyx_PyInt_AsUnsignedInt(x);
+ else
+ return (Py_intptr_t)__Pyx_PyInt_AsSignedInt(x);
+ } else if (sizeof(Py_intptr_t) == sizeof(long)) {
+ if (is_unsigned)
+ return (Py_intptr_t)__Pyx_PyInt_AsUnsignedLong(x);
+ else
+ return (Py_intptr_t)__Pyx_PyInt_AsSignedLong(x);
+ } else if (sizeof(Py_intptr_t) == sizeof(PY_LONG_LONG)) {
+ if (is_unsigned)
+ return (Py_intptr_t)__Pyx_PyInt_AsUnsignedLongLong(x);
+ else
+ return (Py_intptr_t)__Pyx_PyInt_AsSignedLongLong(x);
+ } else {
+ #if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
+ PyErr_SetString(PyExc_RuntimeError,
+ "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
+ #else
+ Py_intptr_t val;
+ PyObject *v = __Pyx_PyNumber_Int(x);
+ #if PY_MAJOR_VERSION < 3
+ if (likely(v) && !PyLong_Check(v)) {
+ PyObject *tmp = v;
+ v = PyNumber_Long(tmp);
+ Py_DECREF(tmp);
+ }
+ #endif
+ if (likely(v)) {
+ int one = 1; int is_little = (int)*(unsigned char *)&one;
+ unsigned char *bytes = (unsigned char *)&val;
+ int ret = _PyLong_AsByteArray((PyLongObject *)v,
+ bytes, sizeof(val),
+ is_little, !is_unsigned);
+ Py_DECREF(v);
+ if (likely(!ret))
+ return val;
+ }
+ #endif
+ return (Py_intptr_t)-1;
+ }
+}
+
+static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_Py_intptr_t(Py_intptr_t val) {
+ const Py_intptr_t neg_one = (Py_intptr_t)-1, const_zero = (Py_intptr_t)0;
+ const int is_unsigned = const_zero < neg_one;
+ if ((sizeof(Py_intptr_t) == sizeof(char)) ||
+ (sizeof(Py_intptr_t) == sizeof(short))) {
+ return PyInt_FromLong((long)val);
+ } else if ((sizeof(Py_intptr_t) == sizeof(int)) ||
+ (sizeof(Py_intptr_t) == sizeof(long))) {
+ if (is_unsigned)
+ return PyLong_FromUnsignedLong((unsigned long)val);
+ else
+ return PyInt_FromLong((long)val);
+ } else if (sizeof(Py_intptr_t) == sizeof(PY_LONG_LONG)) {
+ if (is_unsigned)
+ return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val);
+ else
+ return PyLong_FromLongLong((PY_LONG_LONG)val);
+ } else {
+ int one = 1; int little = (int)*(unsigned char *)&one;
+ unsigned char *bytes = (unsigned char *)&val;
+ return _PyLong_FromByteArray(bytes, sizeof(Py_intptr_t),
+ little, !is_unsigned);
+ }
+}
+
#if CYTHON_CCOMPLEX
#ifdef __cplusplus
static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) {
@@ -6502,10 +6718,15 @@ static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) {
return (int)__Pyx_PyInt_AsLong(x);
}
+#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
+#if CYTHON_USE_PYLONG_INTERNALS
+#include "longintrepr.h"
+#endif
+#endif
static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) {
const unsigned long neg_one = (unsigned long)-1, const_zero = 0;
const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
+#if PY_MAJOR_VERSION < 3
if (likely(PyInt_Check(x))) {
long val = PyInt_AS_LONG(x);
if (is_unsigned && unlikely(val < 0)) {
@@ -6518,6 +6739,16 @@ static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) {
#endif
if (likely(PyLong_Check(x))) {
if (is_unsigned) {
+#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
+#if CYTHON_USE_PYLONG_INTERNALS
+ if (sizeof(digit) <= sizeof(unsigned long)) {
+ switch (Py_SIZE(x)) {
+ case 0: return 0;
+ case 1: return (unsigned long) ((PyLongObject*)x)->ob_digit[0];
+ }
+ }
+#endif
+#endif
if (unlikely(Py_SIZE(x) < 0)) {
PyErr_SetString(PyExc_OverflowError,
"can't convert negative value to unsigned long");
@@ -6525,6 +6756,17 @@ static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) {
}
return (unsigned long)PyLong_AsUnsignedLong(x);
} else {
+#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
+#if CYTHON_USE_PYLONG_INTERNALS
+ if (sizeof(digit) <= sizeof(unsigned long)) {
+ switch (Py_SIZE(x)) {
+ case 0: return 0;
+ case 1: return +(unsigned long) ((PyLongObject*)x)->ob_digit[0];
+ case -1: return -(unsigned long) ((PyLongObject*)x)->ob_digit[0];
+ }
+ }
+#endif
+#endif
return (unsigned long)PyLong_AsLong(x);
}
} else {
@@ -6537,10 +6779,15 @@ static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) {
}
}
+#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
+#if CYTHON_USE_PYLONG_INTERNALS
+#include "longintrepr.h"
+#endif
+#endif
static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) {
const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0;
const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
+#if PY_MAJOR_VERSION < 3
if (likely(PyInt_Check(x))) {
long val = PyInt_AS_LONG(x);
if (is_unsigned && unlikely(val < 0)) {
@@ -6553,6 +6800,16 @@ static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObje
#endif
if (likely(PyLong_Check(x))) {
if (is_unsigned) {
+#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
+#if CYTHON_USE_PYLONG_INTERNALS
+ if (sizeof(digit) <= sizeof(unsigned PY_LONG_LONG)) {
+ switch (Py_SIZE(x)) {
+ case 0: return 0;
+ case 1: return (unsigned PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0];
+ }
+ }
+#endif
+#endif
if (unlikely(Py_SIZE(x) < 0)) {
PyErr_SetString(PyExc_OverflowError,
"can't convert negative value to unsigned PY_LONG_LONG");
@@ -6560,6 +6817,17 @@ static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObje
}
return (unsigned PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
} else {
+#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
+#if CYTHON_USE_PYLONG_INTERNALS
+ if (sizeof(digit) <= sizeof(unsigned PY_LONG_LONG)) {
+ switch (Py_SIZE(x)) {
+ case 0: return 0;
+ case 1: return +(unsigned PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0];
+ case -1: return -(unsigned PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0];
+ }
+ }
+#endif
+#endif
return (unsigned PY_LONG_LONG)PyLong_AsLongLong(x);
}
} else {
@@ -6572,10 +6840,15 @@ static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObje
}
}
+#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
+#if CYTHON_USE_PYLONG_INTERNALS
+#include "longintrepr.h"
+#endif
+#endif
static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) {
const long neg_one = (long)-1, const_zero = 0;
const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
+#if PY_MAJOR_VERSION < 3
if (likely(PyInt_Check(x))) {
long val = PyInt_AS_LONG(x);
if (is_unsigned && unlikely(val < 0)) {
@@ -6588,6 +6861,16 @@ static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) {
#endif
if (likely(PyLong_Check(x))) {
if (is_unsigned) {
+#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
+#if CYTHON_USE_PYLONG_INTERNALS
+ if (sizeof(digit) <= sizeof(long)) {
+ switch (Py_SIZE(x)) {
+ case 0: return 0;
+ case 1: return (long) ((PyLongObject*)x)->ob_digit[0];
+ }
+ }
+#endif
+#endif
if (unlikely(Py_SIZE(x) < 0)) {
PyErr_SetString(PyExc_OverflowError,
"can't convert negative value to long");
@@ -6595,6 +6878,17 @@ static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) {
}
return (long)PyLong_AsUnsignedLong(x);
} else {
+#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
+#if CYTHON_USE_PYLONG_INTERNALS
+ if (sizeof(digit) <= sizeof(long)) {
+ switch (Py_SIZE(x)) {
+ case 0: return 0;
+ case 1: return +(long) ((PyLongObject*)x)->ob_digit[0];
+ case -1: return -(long) ((PyLongObject*)x)->ob_digit[0];
+ }
+ }
+#endif
+#endif
return (long)PyLong_AsLong(x);
}
} else {
@@ -6607,10 +6901,15 @@ static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) {
}
}
+#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
+#if CYTHON_USE_PYLONG_INTERNALS
+#include "longintrepr.h"
+#endif
+#endif
static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) {
const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0;
const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
+#if PY_MAJOR_VERSION < 3
if (likely(PyInt_Check(x))) {
long val = PyInt_AS_LONG(x);
if (is_unsigned && unlikely(val < 0)) {
@@ -6623,6 +6922,16 @@ static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) {
#endif
if (likely(PyLong_Check(x))) {
if (is_unsigned) {
+#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
+#if CYTHON_USE_PYLONG_INTERNALS
+ if (sizeof(digit) <= sizeof(PY_LONG_LONG)) {
+ switch (Py_SIZE(x)) {
+ case 0: return 0;
+ case 1: return (PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0];
+ }
+ }
+#endif
+#endif
if (unlikely(Py_SIZE(x) < 0)) {
PyErr_SetString(PyExc_OverflowError,
"can't convert negative value to PY_LONG_LONG");
@@ -6630,6 +6939,17 @@ static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) {
}
return (PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
} else {
+#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
+#if CYTHON_USE_PYLONG_INTERNALS
+ if (sizeof(digit) <= sizeof(PY_LONG_LONG)) {
+ switch (Py_SIZE(x)) {
+ case 0: return 0;
+ case 1: return +(PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0];
+ case -1: return -(PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0];
+ }
+ }
+#endif
+#endif
return (PY_LONG_LONG)PyLong_AsLongLong(x);
}
} else {
@@ -6642,10 +6962,15 @@ static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) {
}
}
+#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
+#if CYTHON_USE_PYLONG_INTERNALS
+#include "longintrepr.h"
+#endif
+#endif
static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) {
const signed long neg_one = (signed long)-1, const_zero = 0;
const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
+#if PY_MAJOR_VERSION < 3
if (likely(PyInt_Check(x))) {
long val = PyInt_AS_LONG(x);
if (is_unsigned && unlikely(val < 0)) {
@@ -6658,6 +6983,16 @@ static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) {
#endif
if (likely(PyLong_Check(x))) {
if (is_unsigned) {
+#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
+#if CYTHON_USE_PYLONG_INTERNALS
+ if (sizeof(digit) <= sizeof(signed long)) {
+ switch (Py_SIZE(x)) {
+ case 0: return 0;
+ case 1: return (signed long) ((PyLongObject*)x)->ob_digit[0];
+ }
+ }
+#endif
+#endif
if (unlikely(Py_SIZE(x) < 0)) {
PyErr_SetString(PyExc_OverflowError,
"can't convert negative value to signed long");
@@ -6665,6 +7000,17 @@ static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) {
}
return (signed long)PyLong_AsUnsignedLong(x);
} else {
+#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
+#if CYTHON_USE_PYLONG_INTERNALS
+ if (sizeof(digit) <= sizeof(signed long)) {
+ switch (Py_SIZE(x)) {
+ case 0: return 0;
+ case 1: return +(signed long) ((PyLongObject*)x)->ob_digit[0];
+ case -1: return -(signed long) ((PyLongObject*)x)->ob_digit[0];
+ }
+ }
+#endif
+#endif
return (signed long)PyLong_AsLong(x);
}
} else {
@@ -6677,10 +7023,15 @@ static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) {
}
}
+#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
+#if CYTHON_USE_PYLONG_INTERNALS
+#include "longintrepr.h"
+#endif
+#endif
static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) {
const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0;
const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
+#if PY_MAJOR_VERSION < 3
if (likely(PyInt_Check(x))) {
long val = PyInt_AS_LONG(x);
if (is_unsigned && unlikely(val < 0)) {
@@ -6693,6 +7044,16 @@ static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject*
#endif
if (likely(PyLong_Check(x))) {
if (is_unsigned) {
+#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
+#if CYTHON_USE_PYLONG_INTERNALS
+ if (sizeof(digit) <= sizeof(signed PY_LONG_LONG)) {
+ switch (Py_SIZE(x)) {
+ case 0: return 0;
+ case 1: return (signed PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0];
+ }
+ }
+#endif
+#endif
if (unlikely(Py_SIZE(x) < 0)) {
PyErr_SetString(PyExc_OverflowError,
"can't convert negative value to signed PY_LONG_LONG");
@@ -6700,6 +7061,17 @@ static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject*
}
return (signed PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
} else {
+#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
+#if CYTHON_USE_PYLONG_INTERNALS
+ if (sizeof(digit) <= sizeof(signed PY_LONG_LONG)) {
+ switch (Py_SIZE(x)) {
+ case 0: return 0;
+ case 1: return +(signed PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0];
+ case -1: return -(signed PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0];
+ }
+ }
+#endif
+#endif
return (signed PY_LONG_LONG)PyLong_AsLongLong(x);
}
} else {
@@ -6757,6 +7129,10 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class
PyObject *result = 0;
PyObject *py_name = 0;
char warning[200];
+ Py_ssize_t basicsize;
+#ifdef Py_LIMITED_API
+ PyObject *py_basicsize;
+#endif
py_module = __Pyx_ImportModule(module_name);
if (!py_module)
goto bad;
@@ -6776,7 +7152,19 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class
module_name, class_name);
goto bad;
}
- if (!strict && (size_t)((PyTypeObject *)result)->tp_basicsize > size) {
+#ifndef Py_LIMITED_API
+ basicsize = ((PyTypeObject *)result)->tp_basicsize;
+#else
+ py_basicsize = PyObject_GetAttrString(result, "__basicsize__");
+ if (!py_basicsize)
+ goto bad;
+ basicsize = PyLong_AsSsize_t(py_basicsize);
+ Py_DECREF(py_basicsize);
+ py_basicsize = 0;
+ if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred())
+ goto bad;
+#endif
+ if (!strict && (size_t)basicsize > size) {
PyOS_snprintf(warning, sizeof(warning),
"%s.%s size changed, may indicate binary incompatibility",
module_name, class_name);
@@ -6786,7 +7174,7 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class
if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad;
#endif
}
- else if ((size_t)((PyTypeObject *)result)->tp_basicsize != size) {
+ else if ((size_t)basicsize != size) {
PyErr_Format(PyExc_ValueError,
"%s.%s has the wrong size, try recompiling",
module_name, class_name);
@@ -6992,27 +7380,82 @@ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
return 0;
}
-
-/* Type Conversion Functions */
-
+static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(char* c_str) {
+ return __Pyx_PyUnicode_FromStringAndSize(c_str, strlen(c_str));
+}
+static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) {
+ Py_ssize_t ignore;
+ return __Pyx_PyObject_AsStringAndSize(o, &ignore);
+}
+static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) {
+#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
+ if (
+#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
+ __Pyx_sys_getdefaultencoding_not_ascii &&
+#endif
+ PyUnicode_Check(o)) {
+#if PY_VERSION_HEX < 0x03030000
+ char* defenc_c;
+ PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL);
+ if (!defenc) return NULL;
+ defenc_c = PyBytes_AS_STRING(defenc);
+#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
+ {
+ char* end = defenc_c + PyBytes_GET_SIZE(defenc);
+ char* c;
+ for (c = defenc_c; c < end; c++) {
+ if ((unsigned char) (*c) >= 128) {
+ PyUnicode_AsASCIIString(o);
+ return NULL;
+ }
+ }
+ }
+#endif /*__PYX_DEFAULT_STRING_ENCODING_IS_ASCII*/
+ *length = PyBytes_GET_SIZE(defenc);
+ return defenc_c;
+#else /* PY_VERSION_HEX < 0x03030000 */
+ if (PyUnicode_READY(o) == -1) return NULL;
+#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
+ if (PyUnicode_IS_ASCII(o)) {
+ *length = PyUnicode_GET_DATA_SIZE(o);
+ return PyUnicode_AsUTF8(o);
+ } else {
+ PyUnicode_AsASCIIString(o);
+ return NULL;
+ }
+#else /* __PYX_DEFAULT_STRING_ENCODING_IS_ASCII */
+ return PyUnicode_AsUTF8AndSize(o, length);
+#endif /* __PYX_DEFAULT_STRING_ENCODING_IS_ASCII */
+#endif /* PY_VERSION_HEX < 0x03030000 */
+ } else
+#endif /* __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT */
+ {
+ char* result;
+ int r = PyBytes_AsStringAndSize(o, &result, length);
+ if (r < 0) {
+ return NULL;
+ } else {
+ return result;
+ }
+ }
+}
static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
int is_true = x == Py_True;
if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
else return PyObject_IsTrue(x);
}
-
static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
PyNumberMethods *m;
const char *name = NULL;
PyObject *res = NULL;
-#if PY_VERSION_HEX < 0x03000000
+#if PY_MAJOR_VERSION < 3
if (PyInt_Check(x) || PyLong_Check(x))
#else
if (PyLong_Check(x))
#endif
return Py_INCREF(x), x;
m = Py_TYPE(x)->tp_as_number;
-#if PY_VERSION_HEX < 0x03000000
+#if PY_MAJOR_VERSION < 3
if (m && m->nb_int) {
name = "int";
res = PyNumber_Int(x);
@@ -7028,7 +7471,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
}
#endif
if (res) {
-#if PY_VERSION_HEX < 0x03000000
+#if PY_MAJOR_VERSION < 3
if (!PyInt_Check(res) && !PyLong_Check(res)) {
#else
if (!PyLong_Check(res)) {
@@ -7046,7 +7489,6 @@ static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
}
return res;
}
-
static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
Py_ssize_t ival;
PyObject* x = PyNumber_Index(b);
@@ -7055,7 +7497,6 @@ static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
Py_DECREF(x);
return ival;
}
-
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
#if PY_VERSION_HEX < 0x02050000
if (ival <= LONG_MAX)
@@ -7069,14 +7510,12 @@ static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
return PyInt_FromSize_t(ival);
#endif
}
-
static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) {
unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x);
- if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) {
- return (size_t)-1;
- } else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) {
- PyErr_SetString(PyExc_OverflowError,
- "value too large to convert to size_t");
+ if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) {
+ if ((val != (unsigned PY_LONG_LONG)-1) || !PyErr_Occurred())
+ PyErr_SetString(PyExc_OverflowError,
+ "value too large to convert to size_t");
return (size_t)-1;
}
return (size_t)val;
diff --git a/sklearn/cluster/_hierarchical.pyx b/sklearn/cluster/_hierarchical.pyx
index 881c126a64..c07b90c71d 100644
--- a/sklearn/cluster/_hierarchical.pyx
+++ b/sklearn/cluster/_hierarchical.pyx
@@ -1,8 +1,11 @@
+# Author: Gael Varoquaux <gael.varoquaux@normalesup.org>
+
import numpy as np
cimport numpy as np
cimport cython
+
ctypedef np.float64_t DOUBLE
-ctypedef np.int_t INT
+ctypedef np.npy_intp INTP
ctypedef np.int8_t INT8
np.import_array()
@@ -11,41 +14,42 @@ np.import_array()
@cython.boundscheck(False)
@cython.wraparound(False)
@cython.cdivision(True)
-def compute_ward_dist(np.ndarray[DOUBLE, ndim=1] m_1,\
- np.ndarray[DOUBLE, ndim=2] m_2,\
- np.ndarray[INT, ndim=1] coord_row,
- np.ndarray[INT, ndim=1] coord_col,\
- np.ndarray[DOUBLE, ndim=1] res):
- cdef int size_max = coord_row.shape[0]
- cdef int n_features = m_2.shape[1]
- cdef int i, j, row, col
+def compute_ward_dist(np.ndarray[DOUBLE, ndim=1, mode='c'] m_1,
+ np.ndarray[DOUBLE, ndim=2, mode='c'] m_2,
+ np.ndarray[INTP, ndim=1, mode='c'] coord_row,
+ np.ndarray[INTP, ndim=1, mode='c'] coord_col,
+ np.ndarray[DOUBLE, ndim=1, mode='c'] res):
+ cdef INTP size_max = coord_row.shape[0]
+ cdef INTP n_features = m_2.shape[1]
+ cdef INTP i, j, row, col
cdef DOUBLE pa, n
+
for i in range(size_max):
row = coord_row[i]
col = coord_col[i]
n = (m_1[row] * m_1[col]) / (m_1[row] + m_1[col])
pa = 0.
for j in range(n_features):
- pa += (m_2[row, j] / m_1[row] - m_2[col, j] / m_1[col])**2
+ pa += (m_2[row, j] / m_1[row] - m_2[col, j] / m_1[col]) ** 2
res[i] = pa * n
return res
-def _hc_get_descendent(int node, children, int n_leaves):
+def _hc_get_descendent(INTP node, children, INTP n_leaves):
"""
Function returning all the descendent leaves of a set of nodes in the tree.
Parameters
----------
- node : int
+ node : integer
The node for which we want the descendents.
- children : list of pairs. Length of n_nodes
+ children : list of pairs, length n_nodes
The children of each non-leaf node. Values less than `n_samples` refer
to leaves of the tree. A greater value `i` indicates a node with
children `children[i - n_samples]`.
- n_leaves : int
+ n_leaves : integer
Number of leaves.
Returns
@@ -56,11 +60,12 @@ def _hc_get_descendent(int node, children, int n_leaves):
if node < n_leaves:
return ind
descendent = []
+
# It is actually faster to do the accounting of the number of
# elements is the list ourselves: len is a lengthy operation on a
# chained list
- cdef int n_indices = 1
- cdef int i
+ cdef INTP i, n_indices = 1
+
while n_indices:
i = ind.pop()
if i < n_leaves:
@@ -74,29 +79,29 @@ def _hc_get_descendent(int node, children, int n_leaves):
@cython.boundscheck(False)
@cython.wraparound(False)
-def hc_get_heads(np.ndarray[INT, ndim=1] parents, copy=True):
- """ Return the heads of the forest, as defined by parents
-
+def hc_get_heads(np.ndarray[INTP, ndim=1] parents, copy=True):
+ """Returns the heads of the forest, as defined by parents.
+
Parameters
- ===========
- parents: array of integers
+ ----------
+ parents : array of integers
The parent structure defining the forest (ensemble of trees)
- copy: boolean
+ copy : boolean
If copy is False, the input 'parents' array is modified inplace
Returns
- =======
- heads: array of integers of same shape as parents
+ -------
+ heads : array of integers of same shape as parents
The indices in the 'parents' of the tree heads
"""
- cdef unsigned int parent, node0, node, size
+ cdef INTP parent, node0, node, size
if copy:
parents = np.copy(parents)
size = parents.size
- for node0 in range(size):
- # Start from the top of the tree and go down
- node0 = size - node0 - 1
+
+ # Start from the top of the tree and go down
+ for node0 in range(size - 1, -1, -1):
node = node0
parent = parents[node]
while parent != node:
@@ -108,25 +113,26 @@ def hc_get_heads(np.ndarray[INT, ndim=1] parents, copy=True):
@cython.boundscheck(False)
@cython.wraparound(False)
-def _get_parents(nodes, heads, np.ndarray[INT, ndim=1] parents,
- np.ndarray[INT8, ndim=1] not_visited):
- """ Return the heads of the given nodes, as defined by parents
-
- Modifies in-place 'heads' and 'not_visited'
+def _get_parents(nodes, heads, np.ndarray[INTP, ndim=1] parents,
+ np.ndarray[INT8, ndim=1, mode='c'] not_visited):
+ """Returns the heads of the given nodes, as defined by parents.
+
+ Modifies 'heads' and 'not_visited' in-place.
Parameters
- ===========
- nodes: list of integers
+ ----------
+ nodes : list of integers
The nodes to start from
- heads: list of integers
+ heads : list of integers
A list to hold the results (modified inplace)
- parents: array of integers
+ parents : array of integers
The parent structure defining the tree
- not_visited:
+ not_visited
The tree nodes to consider (modified inplace)
"""
- cdef unsigned int parent, node
+ cdef INTP parent, node
+
for node in nodes:
parent = parents[node]
while parent != node:
diff --git a/sklearn/cluster/hierarchical.py b/sklearn/cluster/hierarchical.py
index 3d4b9165dd..8e101f3f63 100644
--- a/sklearn/cluster/hierarchical.py
+++ b/sklearn/cluster/hierarchical.py
@@ -95,7 +95,7 @@ def ward_tree(X, connectivity=None, n_components=None, copy=True,
'structured Ward clustering (i.e. with '
'explicit connectivity.', stacklevel=2)
out = hierarchy.ward(X)
- children_ = out[:, :2].astype(np.int)
+ children_ = out[:, :2].astype(np.intp)
return children_, 1, n_samples, None
# Compute the number of nodes
@@ -140,27 +140,27 @@ def ward_tree(X, connectivity=None, n_components=None, copy=True,
coord_row.extend(len(row) * [ind, ])
coord_col.extend(row)
- coord_row = np.array(coord_row, dtype=np.int)
- coord_col = np.array(coord_col, dtype=np.int)
+ coord_row = np.array(coord_row, dtype=np.intp, order='C')
+ coord_col = np.array(coord_col, dtype=np.intp, order='C')
# build moments as a list
- moments_1 = np.zeros(n_nodes)
+ moments_1 = np.zeros(n_nodes, order='C')
moments_1[:n_samples] = 1
- moments_2 = np.zeros((n_nodes, n_features))
+ moments_2 = np.zeros((n_nodes, n_features), order='C')
moments_2[:n_samples] = X
- inertia = np.empty(len(coord_row), dtype=np.float)
+ inertia = np.empty(len(coord_row), dtype=np.float, order='C')
_hierarchical.compute_ward_dist(moments_1, moments_2, coord_row, coord_col,
inertia)
inertia = list(six.moves.zip(inertia, coord_row, coord_col))
heapify(inertia)
# prepare the main fields
- parent = np.arange(n_nodes, dtype=np.int)
+ parent = np.arange(n_nodes, dtype=np.intp)
heights = np.zeros(n_nodes)
used_node = np.ones(n_nodes, dtype=bool)
children = []
- not_visited = np.empty(n_nodes, dtype=np.int8)
+ not_visited = np.empty(n_nodes, dtype=np.int8, order='C')
# recursive merge loop
for k in range(n_samples, n_nodes):
@@ -186,11 +186,11 @@ def ward_tree(X, connectivity=None, n_components=None, copy=True,
# List comprehension is faster than a for loop
[A[l].append(k) for l in coord_col]
A.append(coord_col)
- coord_col = np.array(coord_col, dtype=np.int)
- coord_row = np.empty_like(coord_col)
+ coord_col = np.array(coord_col, dtype=np.intp, order='C')
+ coord_row = np.empty(coord_col.shape, dtype=np.intp, order='C')
coord_row.fill(k)
n_additions = len(coord_row)
- ini = np.empty(n_additions, dtype=np.float)
+ ini = np.empty(n_additions, dtype=np.float, order='C')
_hierarchical.compute_ward_dist(moments_1, moments_2,
coord_row, coord_col, ini)
@@ -268,7 +268,7 @@ def _hc_cut(n_clusters, children, n_leaves):
# Insert the 2 children and remove the largest node
heappush(nodes, -these_children[0])
heappushpop(nodes, -these_children[1])
- label = np.zeros(n_leaves, dtype=np.int)
+ label = np.zeros(n_leaves, dtype=np.intp)
for i, node in enumerate(nodes):
label[_hierarchical._hc_get_descendent(-node, children, n_leaves)] = i
return label
--
GitLab