forked from scikit-learn/scikit-learn
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy path_hierarchical.cpp
21636 lines (20137 loc) · 841 KB
/
_hierarchical.cpp
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
/* Generated by Cython 0.19.1 on Mon Feb 17 15:12:38 2014 */
#define PY_SSIZE_T_CLEAN
#ifndef CYTHON_USE_PYLONG_INTERNALS
#ifdef PYLONG_BITS_IN_DIGIT
#define CYTHON_USE_PYLONG_INTERNALS 0
#else
#include "pyconfig.h"
#ifdef PYLONG_BITS_IN_DIGIT
#define CYTHON_USE_PYLONG_INTERNALS 1
#else
#define CYTHON_USE_PYLONG_INTERNALS 0
#endif
#endif
#endif
#include "Python.h"
#ifndef Py_PYTHON_H
#error Python headers needed to compile C extensions, please install development version of Python.
#elif PY_VERSION_HEX < 0x02040000
#error Cython requires Python 2.4+.
#else
#include <stddef.h> /* For offsetof */
#ifndef offsetof
#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
#endif
#if !defined(WIN32) && !defined(MS_WINDOWS)
#ifndef __stdcall
#define __stdcall
#endif
#ifndef __cdecl
#define __cdecl
#endif
#ifndef __fastcall
#define __fastcall
#endif
#endif
#ifndef DL_IMPORT
#define DL_IMPORT(t) t
#endif
#ifndef DL_EXPORT
#define DL_EXPORT(t) t
#endif
#ifndef PY_LONG_LONG
#define PY_LONG_LONG LONG_LONG
#endif
#ifndef Py_HUGE_VAL
#define Py_HUGE_VAL HUGE_VAL
#endif
#ifdef PYPY_VERSION
#define CYTHON_COMPILING_IN_PYPY 1
#define CYTHON_COMPILING_IN_CPYTHON 0
#else
#define CYTHON_COMPILING_IN_PYPY 0
#define CYTHON_COMPILING_IN_CPYTHON 1
#endif
#if PY_VERSION_HEX < 0x02050000
typedef int Py_ssize_t;
#define PY_SSIZE_T_MAX INT_MAX
#define PY_SSIZE_T_MIN INT_MIN
#define PY_FORMAT_SIZE_T ""
#define CYTHON_FORMAT_SSIZE_T ""
#define PyInt_FromSsize_t(z) PyInt_FromLong(z)
#define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o)
#define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \
(PyErr_Format(PyExc_TypeError, \
"expected index value, got %.200s", Py_TYPE(o)->tp_name), \
(PyObject*)0))
#define __Pyx_PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && \
!PyComplex_Check(o))
#define PyIndex_Check __Pyx_PyIndex_Check
#define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message)
#define __PYX_BUILD_PY_SSIZE_T "i"
#else
#define __PYX_BUILD_PY_SSIZE_T "n"
#define CYTHON_FORMAT_SSIZE_T "z"
#define __Pyx_PyIndex_Check PyIndex_Check
#endif
#if PY_VERSION_HEX < 0x02060000
#define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt)
#define Py_TYPE(ob) (((PyObject*)(ob))->ob_type)
#define Py_SIZE(ob) (((PyVarObject*)(ob))->ob_size)
#define PyVarObject_HEAD_INIT(type, size) \
PyObject_HEAD_INIT(type) size,
#define PyType_Modified(t)
typedef struct {
void *buf;
PyObject *obj;
Py_ssize_t len;
Py_ssize_t itemsize;
int readonly;
int ndim;
char *format;
Py_ssize_t *shape;
Py_ssize_t *strides;
Py_ssize_t *suboffsets;
void *internal;
} Py_buffer;
#define PyBUF_SIMPLE 0
#define PyBUF_WRITABLE 0x0001
#define PyBUF_FORMAT 0x0004
#define PyBUF_ND 0x0008
#define PyBUF_STRIDES (0x0010 | PyBUF_ND)
#define PyBUF_C_CONTIGUOUS (0x0020 | PyBUF_STRIDES)
#define PyBUF_F_CONTIGUOUS (0x0040 | PyBUF_STRIDES)
#define PyBUF_ANY_CONTIGUOUS (0x0080 | PyBUF_STRIDES)
#define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES)
#define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE)
#define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE)
typedef int (*getbufferproc)(PyObject *, Py_buffer *, int);
typedef void (*releasebufferproc)(PyObject *, Py_buffer *);
#endif
#if PY_MAJOR_VERSION < 3
#define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
#define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
PyCode_New(a, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
#else
#define __Pyx_BUILTIN_MODULE_NAME "builtins"
#define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
#endif
#if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6
#define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict")
#endif
#if PY_MAJOR_VERSION >= 3
#define Py_TPFLAGS_CHECKTYPES 0
#define Py_TPFLAGS_HAVE_INDEX 0
#endif
#if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3)
#define Py_TPFLAGS_HAVE_NEWBUFFER 0
#endif
#if PY_VERSION_HEX < 0x02060000
#define Py_TPFLAGS_HAVE_VERSION_TAG 0
#endif
#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
#define CYTHON_PEP393_ENABLED 1
#define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \
0 : _PyUnicode_Ready((PyObject *)(op)))
#define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
#define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
#define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i)
#else
#define CYTHON_PEP393_ENABLED 0
#define __Pyx_PyUnicode_READY(op) (0)
#define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
#define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
#define __Pyx_PyUnicode_READ(k, d, i) ((k=k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
#endif
#if PY_MAJOR_VERSION >= 3
#define PyBaseString_Type PyUnicode_Type
#define PyStringObject PyUnicodeObject
#define PyString_Type PyUnicode_Type
#define PyString_Check PyUnicode_Check
#define PyString_CheckExact PyUnicode_CheckExact
#endif
#if PY_VERSION_HEX < 0x02060000
#define PyBytesObject PyStringObject
#define PyBytes_Type PyString_Type
#define PyBytes_Check PyString_Check
#define PyBytes_CheckExact PyString_CheckExact
#define PyBytes_FromString PyString_FromString
#define PyBytes_FromStringAndSize PyString_FromStringAndSize
#define PyBytes_FromFormat PyString_FromFormat
#define PyBytes_DecodeEscape PyString_DecodeEscape
#define PyBytes_AsString PyString_AsString
#define PyBytes_AsStringAndSize PyString_AsStringAndSize
#define PyBytes_Size PyString_Size
#define PyBytes_AS_STRING PyString_AS_STRING
#define PyBytes_GET_SIZE PyString_GET_SIZE
#define PyBytes_Repr PyString_Repr
#define PyBytes_Concat PyString_Concat
#define PyBytes_ConcatAndDel PyString_ConcatAndDel
#endif
#if PY_MAJOR_VERSION >= 3
#define __Pyx_PyBaseString_Check(obj) PyUnicode_Check(obj)
#define __Pyx_PyBaseString_CheckExact(obj) PyUnicode_CheckExact(obj)
#else
#define __Pyx_PyBaseString_Check(obj) (PyString_CheckExact(obj) || PyUnicode_CheckExact(obj) || \
PyString_Check(obj) || PyUnicode_Check(obj))
#define __Pyx_PyBaseString_CheckExact(obj) (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)
#endif
#ifndef PySet_CheckExact
#define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
#endif
#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type)
#if PY_MAJOR_VERSION >= 3
#define PyIntObject PyLongObject
#define PyInt_Type PyLong_Type
#define PyInt_Check(op) PyLong_Check(op)
#define PyInt_CheckExact(op) PyLong_CheckExact(op)
#define PyInt_FromString PyLong_FromString
#define PyInt_FromUnicode PyLong_FromUnicode
#define PyInt_FromLong PyLong_FromLong
#define PyInt_FromSize_t PyLong_FromSize_t
#define PyInt_FromSsize_t PyLong_FromSsize_t
#define PyInt_AsLong PyLong_AsLong
#define PyInt_AS_LONG PyLong_AS_LONG
#define PyInt_AsSsize_t PyLong_AsSsize_t
#define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask
#define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask
#endif
#if PY_MAJOR_VERSION >= 3
#define PyBoolObject PyLongObject
#endif
#if PY_VERSION_HEX < 0x03020000
typedef long Py_hash_t;
#define __Pyx_PyInt_FromHash_t PyInt_FromLong
#define __Pyx_PyInt_AsHash_t PyInt_AsLong
#else
#define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t
#define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t
#endif
#if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300)
#define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b)
#define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value)
#define __Pyx_PySequence_DelSlice(obj, a, b) PySequence_DelSlice(obj, a, b)
#else
#define __Pyx_PySequence_GetSlice(obj, a, b) (unlikely(!(obj)) ? \
(PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), (PyObject*)0) : \
(likely((obj)->ob_type->tp_as_mapping) ? (PySequence_GetSlice(obj, a, b)) : \
(PyErr_Format(PyExc_TypeError, "'%.200s' object is unsliceable", (obj)->ob_type->tp_name), (PyObject*)0)))
#define __Pyx_PySequence_SetSlice(obj, a, b, value) (unlikely(!(obj)) ? \
(PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
(likely((obj)->ob_type->tp_as_mapping) ? (PySequence_SetSlice(obj, a, b, value)) : \
(PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice assignment", (obj)->ob_type->tp_name), -1)))
#define __Pyx_PySequence_DelSlice(obj, a, b) (unlikely(!(obj)) ? \
(PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
(likely((obj)->ob_type->tp_as_mapping) ? (PySequence_DelSlice(obj, a, b)) : \
(PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice deletion", (obj)->ob_type->tp_name), -1)))
#endif
#if PY_MAJOR_VERSION >= 3
#define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func))
#endif
#if PY_VERSION_HEX < 0x02050000
#define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),((char *)(n)))
#define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),((char *)(n)),(a))
#define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),((char *)(n)))
#else
#define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),(n))
#define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),(n),(a))
#define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),(n))
#endif
#if PY_VERSION_HEX < 0x02050000
#define __Pyx_NAMESTR(n) ((char *)(n))
#define __Pyx_DOCSTR(n) ((char *)(n))
#else
#define __Pyx_NAMESTR(n) (n)
#define __Pyx_DOCSTR(n) (n)
#endif
#ifndef CYTHON_INLINE
#if defined(__GNUC__)
#define CYTHON_INLINE __inline__
#elif defined(_MSC_VER)
#define CYTHON_INLINE __inline
#elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
#define CYTHON_INLINE inline
#else
#define CYTHON_INLINE
#endif
#endif
#ifndef CYTHON_RESTRICT
#if defined(__GNUC__)
#define CYTHON_RESTRICT __restrict__
#elif defined(_MSC_VER)
#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
#define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y)
#define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y)
#else
#define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y)
#define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y)
#endif
#ifndef __PYX_EXTERN_C
#ifdef __cplusplus
#define __PYX_EXTERN_C extern "C"
#else
#define __PYX_EXTERN_C extern
#endif
#endif
#if defined(WIN32) || defined(MS_WINDOWS)
#define _USE_MATH_DEFINES
#endif
#include <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"
#include "numpy/ufuncobject.h"
#include <utility>
#include "ios"
#include "new"
#include "stdexcept"
#include "typeinfo"
#include <map>
#include "pythread.h"
#include "pystate.h"
#ifdef _OPENMP
#include <omp.h>
#endif /* _OPENMP */
#ifdef PYREX_WITHOUT_ASSERTIONS
#define CYTHON_WITHOUT_ASSERTIONS
#endif
#ifndef CYTHON_UNUSED
# if defined(__GNUC__)
# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
# define CYTHON_UNUSED __attribute__ ((__unused__))
# else
# define CYTHON_UNUSED
# endif
# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER))
# define CYTHON_UNUSED __attribute__ ((__unused__))
# else
# define CYTHON_UNUSED
# endif
#endif
typedef struct {PyObject **p; char *s; const Py_ssize_t n; const char* encoding;
const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; /*proto*/
#define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0
#define __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT 0
#define __PYX_DEFAULT_STRING_ENCODING ""
#define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString
#define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
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 */
#if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))
#define likely(x) __builtin_expect(!!(x), 1)
#define unlikely(x) __builtin_expect(!!(x), 0)
#else /* __GNUC__ > 2 ... */
#define likely(x) (x)
#define unlikely(x) (x)
#endif /* __GNUC__ > 2 ... */
#else /* __GNUC__ */
#define likely(x) (x)
#define unlikely(x) (x)
#endif /* __GNUC__ */
static PyObject *__pyx_m;
static PyObject *__pyx_d;
static PyObject *__pyx_b;
static PyObject *__pyx_empty_tuple;
static PyObject *__pyx_empty_bytes;
static int __pyx_lineno;
static int __pyx_clineno = 0;
static const char * __pyx_cfilenm= __FILE__;
static const char *__pyx_filename;
#if !defined(CYTHON_CCOMPLEX)
#if defined(__cplusplus)
#define CYTHON_CCOMPLEX 1
#elif defined(_Complex_I)
#define CYTHON_CCOMPLEX 1
#else
#define CYTHON_CCOMPLEX 0
#endif
#endif
#if CYTHON_CCOMPLEX
#ifdef __cplusplus
#include <complex>
#else
#include <complex.h>
#endif
#endif
#if CYTHON_CCOMPLEX && !defined(__cplusplus) && defined(__sun__) && defined(__GNUC__)
#undef _Complex_I
#define _Complex_I 1.0fj
#endif
static const char *__pyx_f[] = {
"_hierarchical.pyx",
"numpy.pxd",
"stringsource",
"type.pxd",
"fast_dict.pxd",
};
#define IS_UNSIGNED(type) (((type) -1) > 0)
struct __Pyx_StructField_;
#define __PYX_BUF_FLAGS_PACKED_STRUCT (1 << 0)
typedef struct {
const char* name; /* for error messages only */
struct __Pyx_StructField_* fields;
size_t size; /* sizeof(type) */
size_t arraysize[8]; /* length of array in each dimension */
int ndim;
char typegroup; /* _R_eal, _C_omplex, Signed _I_nt, _U_nsigned int, _S_truct, _P_ointer, _O_bject, c_H_ar */
char is_unsigned;
int flags;
} __Pyx_TypeInfo;
typedef struct __Pyx_StructField_ {
__Pyx_TypeInfo* type;
const char* name;
size_t offset;
} __Pyx_StructField;
typedef struct {
__Pyx_StructField* field;
size_t parent_offset;
} __Pyx_BufFmt_StackElem;
typedef struct {
__Pyx_StructField root;
__Pyx_BufFmt_StackElem* head;
size_t fmt_offset;
size_t new_count, enc_count;
size_t struct_alignment;
int is_complex;
char enc_type;
char new_packmode;
char enc_packmode;
char is_valid_array;
} __Pyx_BufFmt_Context;
struct __pyx_memoryview_obj;
typedef struct {
struct __pyx_memoryview_obj *memview;
char *data;
Py_ssize_t shape[8];
Py_ssize_t strides[8];
Py_ssize_t suboffsets[8];
} __Pyx_memviewslice;
#include <pythread.h>
#ifndef CYTHON_ATOMICS
#define CYTHON_ATOMICS 1
#endif
#define __pyx_atomic_int_type int
#if CYTHON_ATOMICS && __GNUC__ >= 4 && (__GNUC_MINOR__ > 1 || \
(__GNUC_MINOR__ == 1 && __GNUC_PATCHLEVEL >= 2)) && \
!defined(__i386__)
#define __pyx_atomic_incr_aligned(value, lock) __sync_fetch_and_add(value, 1)
#define __pyx_atomic_decr_aligned(value, lock) __sync_fetch_and_sub(value, 1)
#ifdef __PYX_DEBUG_ATOMICS
#warning "Using GNU atomics"
#endif
#elif CYTHON_ATOMICS && MSC_VER
#include <Windows.h>
#define __pyx_atomic_int_type LONG
#define __pyx_atomic_incr_aligned(value, lock) InterlockedIncrement(value)
#define __pyx_atomic_decr_aligned(value, lock) InterlockedDecrement(value)
#ifdef __PYX_DEBUG_ATOMICS
#warning "Using MSVC atomics"
#endif
#elif CYTHON_ATOMICS && (defined(__ICC) || defined(__INTEL_COMPILER)) && 0
#define __pyx_atomic_incr_aligned(value, lock) _InterlockedIncrement(value)
#define __pyx_atomic_decr_aligned(value, lock) _InterlockedDecrement(value)
#ifdef __PYX_DEBUG_ATOMICS
#warning "Using Intel atomics"
#endif
#else
#undef CYTHON_ATOMICS
#define CYTHON_ATOMICS 0
#ifdef __PYX_DEBUG_ATOMICS
#warning "Not using atomics"
#endif
#endif
typedef volatile __pyx_atomic_int_type __pyx_atomic_int;
#if CYTHON_ATOMICS
#define __pyx_add_acquisition_count(memview) \
__pyx_atomic_incr_aligned(__pyx_get_slice_count_pointer(memview), memview->lock)
#define __pyx_sub_acquisition_count(memview) \
__pyx_atomic_decr_aligned(__pyx_get_slice_count_pointer(memview), memview->lock)
#else
#define __pyx_add_acquisition_count(memview) \
__pyx_add_acquisition_count_locked(__pyx_get_slice_count_pointer(memview), memview->lock)
#define __pyx_sub_acquisition_count(memview) \
__pyx_sub_acquisition_count_locked(__pyx_get_slice_count_pointer(memview), memview->lock)
#endif
/* "numpy.pxd":723
* # in Cython to enable them only on the right systems.
*
* ctypedef npy_int8 int8_t # <<<<<<<<<<<<<<
* ctypedef npy_int16 int16_t
* ctypedef npy_int32 int32_t
*/
typedef npy_int8 __pyx_t_5numpy_int8_t;
/* "numpy.pxd":724
*
* ctypedef npy_int8 int8_t
* ctypedef npy_int16 int16_t # <<<<<<<<<<<<<<
* ctypedef npy_int32 int32_t
* ctypedef npy_int64 int64_t
*/
typedef npy_int16 __pyx_t_5numpy_int16_t;
/* "numpy.pxd":725
* ctypedef npy_int8 int8_t
* ctypedef npy_int16 int16_t
* ctypedef npy_int32 int32_t # <<<<<<<<<<<<<<
* ctypedef npy_int64 int64_t
* #ctypedef npy_int96 int96_t
*/
typedef npy_int32 __pyx_t_5numpy_int32_t;
/* "numpy.pxd":726
* ctypedef npy_int16 int16_t
* ctypedef npy_int32 int32_t
* ctypedef npy_int64 int64_t # <<<<<<<<<<<<<<
* #ctypedef npy_int96 int96_t
* #ctypedef npy_int128 int128_t
*/
typedef npy_int64 __pyx_t_5numpy_int64_t;
/* "numpy.pxd":730
* #ctypedef npy_int128 int128_t
*
* ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<<
* ctypedef npy_uint16 uint16_t
* ctypedef npy_uint32 uint32_t
*/
typedef npy_uint8 __pyx_t_5numpy_uint8_t;
/* "numpy.pxd":731
*
* ctypedef npy_uint8 uint8_t
* ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<<
* ctypedef npy_uint32 uint32_t
* ctypedef npy_uint64 uint64_t
*/
typedef npy_uint16 __pyx_t_5numpy_uint16_t;
/* "numpy.pxd":732
* ctypedef npy_uint8 uint8_t
* ctypedef npy_uint16 uint16_t
* ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<<
* ctypedef npy_uint64 uint64_t
* #ctypedef npy_uint96 uint96_t
*/
typedef npy_uint32 __pyx_t_5numpy_uint32_t;
/* "numpy.pxd":733
* ctypedef npy_uint16 uint16_t
* ctypedef npy_uint32 uint32_t
* ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<<
* #ctypedef npy_uint96 uint96_t
* #ctypedef npy_uint128 uint128_t
*/
typedef npy_uint64 __pyx_t_5numpy_uint64_t;
/* "numpy.pxd":737
* #ctypedef npy_uint128 uint128_t
*
* ctypedef npy_float32 float32_t # <<<<<<<<<<<<<<
* ctypedef npy_float64 float64_t
* #ctypedef npy_float80 float80_t
*/
typedef npy_float32 __pyx_t_5numpy_float32_t;
/* "numpy.pxd":738
*
* ctypedef npy_float32 float32_t
* ctypedef npy_float64 float64_t # <<<<<<<<<<<<<<
* #ctypedef npy_float80 float80_t
* #ctypedef npy_float128 float128_t
*/
typedef npy_float64 __pyx_t_5numpy_float64_t;
/* "numpy.pxd":747
* # The int types are mapped a bit surprising --
* # numpy.int corresponds to 'l' and numpy.long to 'q'
* ctypedef npy_long int_t # <<<<<<<<<<<<<<
* ctypedef npy_longlong long_t
* ctypedef npy_longlong longlong_t
*/
typedef npy_long __pyx_t_5numpy_int_t;
/* "numpy.pxd":748
* # numpy.int corresponds to 'l' and numpy.long to 'q'
* ctypedef npy_long int_t
* ctypedef npy_longlong long_t # <<<<<<<<<<<<<<
* ctypedef npy_longlong longlong_t
*
*/
typedef npy_longlong __pyx_t_5numpy_long_t;
/* "numpy.pxd":749
* ctypedef npy_long int_t
* ctypedef npy_longlong long_t
* ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<<
*
* ctypedef npy_ulong uint_t
*/
typedef npy_longlong __pyx_t_5numpy_longlong_t;
/* "numpy.pxd":751
* ctypedef npy_longlong longlong_t
*
* ctypedef npy_ulong uint_t # <<<<<<<<<<<<<<
* ctypedef npy_ulonglong ulong_t
* ctypedef npy_ulonglong ulonglong_t
*/
typedef npy_ulong __pyx_t_5numpy_uint_t;
/* "numpy.pxd":752
*
* ctypedef npy_ulong uint_t
* ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<<
* ctypedef npy_ulonglong ulonglong_t
*
*/
typedef npy_ulonglong __pyx_t_5numpy_ulong_t;
/* "numpy.pxd":753
* ctypedef npy_ulong uint_t
* ctypedef npy_ulonglong ulong_t
* ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<<
*
* ctypedef npy_intp intp_t
*/
typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t;
/* "numpy.pxd":755
* ctypedef npy_ulonglong ulonglong_t
*
* ctypedef npy_intp intp_t # <<<<<<<<<<<<<<
* ctypedef npy_uintp uintp_t
*
*/
typedef npy_intp __pyx_t_5numpy_intp_t;
/* "numpy.pxd":756
*
* ctypedef npy_intp intp_t
* ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<<
*
* ctypedef npy_double float_t
*/
typedef npy_uintp __pyx_t_5numpy_uintp_t;
/* "numpy.pxd":758
* ctypedef npy_uintp uintp_t
*
* ctypedef npy_double float_t # <<<<<<<<<<<<<<
* ctypedef npy_double double_t
* ctypedef npy_longdouble longdouble_t
*/
typedef npy_double __pyx_t_5numpy_float_t;
/* "numpy.pxd":759
*
* ctypedef npy_double float_t
* ctypedef npy_double double_t # <<<<<<<<<<<<<<
* ctypedef npy_longdouble longdouble_t
*
*/
typedef npy_double __pyx_t_5numpy_double_t;
/* "numpy.pxd":760
* ctypedef npy_double float_t
* ctypedef npy_double double_t
* ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<<
*
* ctypedef npy_cfloat cfloat_t
*/
typedef npy_longdouble __pyx_t_5numpy_longdouble_t;
/* "sklearn/utils/fast_dict.pxd":14
*
* DTYPE = np.float64
* ctypedef np.float64_t DTYPE_t # <<<<<<<<<<<<<<
*
* ITYPE = np.intp
*/
typedef __pyx_t_5numpy_float64_t __pyx_t_7sklearn_5utils_9fast_dict_DTYPE_t;
/* "sklearn/utils/fast_dict.pxd":17
*
* ITYPE = np.intp
* ctypedef np.intp_t ITYPE_t # <<<<<<<<<<<<<<
*
* ###############################################################################
*/
typedef __pyx_t_5numpy_intp_t __pyx_t_7sklearn_5utils_9fast_dict_ITYPE_t;
/* "sklearn/cluster/_hierarchical.pyx":7
* cimport cython
*
* ctypedef np.float64_t DOUBLE # <<<<<<<<<<<<<<
* 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":8
*
* ctypedef np.float64_t DOUBLE
* ctypedef np.npy_intp INTP # <<<<<<<<<<<<<<
* ctypedef np.int8_t INT8
*
*/
typedef npy_intp __pyx_t_7sklearn_7cluster_13_hierarchical_INTP;
/* "sklearn/cluster/_hierarchical.pyx":9
* ctypedef np.float64_t DOUBLE
* ctypedef np.npy_intp INTP
* ctypedef np.int8_t INT8 # <<<<<<<<<<<<<<
*
* # Numpy must be initialized. When using numpy from C or Cython you must
*/
typedef __pyx_t_5numpy_int8_t __pyx_t_7sklearn_7cluster_13_hierarchical_INT8;
/* "sklearn/cluster/_hierarchical.pyx":23
*
* DTYPE = np.float64
* ctypedef np.float64_t DTYPE_t # <<<<<<<<<<<<<<
*
* ITYPE = np.intp
*/
typedef __pyx_t_5numpy_float64_t __pyx_t_7sklearn_7cluster_13_hierarchical_DTYPE_t;
/* "sklearn/cluster/_hierarchical.pyx":26
*
* ITYPE = np.intp
* ctypedef np.intp_t ITYPE_t # <<<<<<<<<<<<<<
*
* # Reimplementation for MSVC support
*/
typedef __pyx_t_5numpy_intp_t __pyx_t_7sklearn_7cluster_13_hierarchical_ITYPE_t;
#if CYTHON_CCOMPLEX
#ifdef __cplusplus
typedef ::std::complex< float > __pyx_t_float_complex;
#else
typedef float _Complex __pyx_t_float_complex;
#endif
#else
typedef struct { float real, imag; } __pyx_t_float_complex;
#endif
#if CYTHON_CCOMPLEX
#ifdef __cplusplus
typedef ::std::complex< double > __pyx_t_double_complex;
#else
typedef double _Complex __pyx_t_double_complex;
#endif
#else
typedef struct { double real, imag; } __pyx_t_double_complex;
#endif
/*--- Type declarations ---*/
struct __pyx_MemviewEnum_obj;
struct __pyx_obj_7sklearn_7cluster_13_hierarchical_WeightedEdge;
struct __pyx_memoryview_obj;
struct __pyx_memoryviewslice_obj;
struct __pyx_array_obj;
struct __pyx_obj_7sklearn_5utils_9fast_dict_IntFloatDict;
/* "numpy.pxd":762
* ctypedef npy_longdouble longdouble_t
*
* ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<<
* ctypedef npy_cdouble cdouble_t
* ctypedef npy_clongdouble clongdouble_t
*/
typedef npy_cfloat __pyx_t_5numpy_cfloat_t;
/* "numpy.pxd":763
*
* ctypedef npy_cfloat cfloat_t
* ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<<
* ctypedef npy_clongdouble clongdouble_t
*
*/
typedef npy_cdouble __pyx_t_5numpy_cdouble_t;
/* "numpy.pxd":764
* ctypedef npy_cfloat cfloat_t
* ctypedef npy_cdouble cdouble_t
* ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<<
*
* ctypedef npy_cdouble complex_t
*/
typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t;
/* "numpy.pxd":766
* ctypedef npy_clongdouble clongdouble_t
*
* ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<<
*
* cdef inline object PyArray_MultiIterNew1(a):
*/
typedef npy_cdouble __pyx_t_5numpy_complex_t;
/* "View.MemoryView":275
*
* @cname('__pyx_MemviewEnum')
* cdef class Enum(object): # <<<<<<<<<<<<<<
* cdef object name
* def __init__(self, name):
*/
struct __pyx_MemviewEnum_obj {
PyObject_HEAD
PyObject *name;
};
/* "sklearn/cluster/_hierarchical.pyx":295
* # An edge object for fast comparisons
*
* cdef class WeightedEdge: # <<<<<<<<<<<<<<
* cdef public ITYPE_t a
* cdef public ITYPE_t b
*/
struct __pyx_obj_7sklearn_7cluster_13_hierarchical_WeightedEdge {
PyObject_HEAD
__pyx_t_7sklearn_7cluster_13_hierarchical_ITYPE_t a;
__pyx_t_7sklearn_7cluster_13_hierarchical_ITYPE_t b;
__pyx_t_7sklearn_7cluster_13_hierarchical_DTYPE_t weight;
};
/* "View.MemoryView":308
*
* @cname('__pyx_memoryview')
* cdef class memoryview(object): # <<<<<<<<<<<<<<
*
* cdef object obj
*/
struct __pyx_memoryview_obj {
PyObject_HEAD
struct __pyx_vtabstruct_memoryview *__pyx_vtab;
PyObject *obj;
PyObject *_size;
PyObject *_array_interface;
PyThread_type_lock lock;
__pyx_atomic_int acquisition_count[2];
__pyx_atomic_int *acquisition_count_aligned_p;
Py_buffer view;
int flags;
int dtype_is_object;
__Pyx_TypeInfo *typeinfo;
};
/* "View.MemoryView":927
*
* @cname('__pyx_memoryviewslice')
* cdef class _memoryviewslice(memoryview): # <<<<<<<<<<<<<<
* "Internal class for passing memoryview slices to Python"
*
*/
struct __pyx_memoryviewslice_obj {
struct __pyx_memoryview_obj __pyx_base;
__Pyx_memviewslice from_slice;
PyObject *from_object;
PyObject *(*to_object_func)(char *);
int (*to_dtype_func)(char *, PyObject *);
};
/* "View.MemoryView":96
*
* @cname("__pyx_array")