Numpy->用Cython转换：编译错误：无法将“npy_intp *”到Python对象

Question

我有下面的代码将被propperly转换为用Cython：

from numpy import * 

## returns winning players or [] if undecided. 
def score(board): 
    scores = [] 
    checked = zeros(board.shape) 
    for i in xrange(len(board)): 
     for j in xrange(len(board)): 
      if checked[i,j] == 0 and board[i,j] !=0: 
       ... do stuf 

我在尝试转换到用Cython：

import numpy as np 
cimport numpy as np 

@cython.boundscheck(False) 
@cython.wraparound(False) 
@cython.nonecheck(False) 

## returns winning players or [] if undecided. 
def score(np.ndarray[int, ndim=2] board): 
    scores = [] 
    cdef np.ndarray[int, ndim = 2 ] checked 
    checked = np.zeros(board.shape) 
    for i in xrange(len(board)): 
     for j in xrange(len(board)): 
      if checked[i,j] == 0 and board[i,j] !=0: 
       ... do stuf 

但是当我编译：

$ python setup.py build_ext --inplace 
running build_ext 
cythoning newgox.pyx to newgox.c 


## returns winning players or [] if undecided. 
def score(np.ndarray[int, ndim=2] board): 
    scores = [] 
    cdef np.ndarray[int, ndim = 2 ] checked 
    checked = np.zeros(board.shape) 
        ^
------------------------------------------------------------ 

newgox.pyx:58:28: Cannot convert 'npy_intp *' to Python object 
building 'newgox' extension 

而且，我不知道这是LIS工作的正确方法在用Cython TS：

scores = [] 
if some_stuff_is_true: 
    scores.append(some_integer) 

编辑：

谢谢，现在的代码编译，但是当我运行它，我得到的错误：

File "newgox.pyx", line 63, in newgox.score (newgox.c:1710) 
    def score(np.ndarray[np.int, ndim=2] board): 
ValueError: Buffer dtype mismatch, expected 'int object' but got 'long' 

我绑这两个选项：

ctypedef np.int_t DTYPE_t 
DTYPE = np.int 

然后继续：

board = zeros((5,5), dtype = DTYPE) 
def score(np.ndarray[DTYPE, ndim=2] board): 

或只是在双方的声明：

... np.int ... 

这导致了同样的错误，但签名：

ValueError: Buffer dtype mismatch, expected 'int' but got 'long' 

---

感谢bellamyj，但您建议的代码不能编译，

$ python setup.py build_ext --inplace 
running build_ext 
cythoning newgox.pyx to newgox.c 
building 'newgox' extension 
gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -O2 -DNDEBUG -g -O3 -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c newgox.c -o build/temp.macosx-10.6-intel-2.7/newgox.o 

newgox.c:238:31: error: numpy/arrayobject.h: No such file or directory 
newgox.c:239:31: error: numpy/ufuncobject.h: No such file or directory 
newgox.c:356: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘__pyx_t_5numpy_int8_t’ 
newgox.c:365: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘__pyx_t_5numpy_int16_t’ 
newgox.c:374: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘__pyx_t_5numpy_int32_t’ 

而且它继续t列举所有其他类型。

然后告诉我：

newgox.c:978: error: expected ‘)’ before ‘*’ token 
newgox.c:979: error: expected ‘)’ before ‘*’ token 
newgox.c:980: error: expected ‘)’ before ‘*’ token 
newgox.c:983: error: expected declaration specifiers or ‘...’ before ‘PyArrayObject’ 
newgox.c:984: error: expected declaration specifiers or ‘...’ before ‘PyArrayObject’ 
newgox.c:985: error: expected ‘)’ before ‘*’ token 
newgox.c:987: error: ‘__pyx_t_5numpy_int32_t’ undeclared here (not in a function) 
newgox.c: In function ‘__pyx_pf_6newgox_7score’: 
newgox.c:1638: error: ‘PyArrayObject’ undeclared (first use in this function) 
newgox.c:1638: error: (Each undeclared identifier is reported only once 
newgox.c:1638: error: for each function it appears in.) 
newgox.c:1638: error: ‘__pyx_v_checked’ undeclared (first use in this function) 
newgox.c:1659: error: ‘__pyx_t_5’ undeclared (first use in this function) 
newgox.c:1721: error: expected expression before ‘)’ token 
newgox.c:1723: error: expected expression before ‘)’ token 
newgox.c:1747: error: expected expression before ‘)’ token 
newgox.c:1766: error: expected expression before ‘)’ token 
newgox.c:1813: error: expected expression before ‘)’ token 
newgox.c:1846: error: expected expression before ‘)’ token 
newgox.c:1846: error: too many arguments to function ‘__pyx_f_6newgox_check_life’ 
newgox.c:2009: error: expected expression before ‘)’ token 
newgox.c:2009: warning: assignment makes pointer from integer without a cast 
newgox.c:2012: error: expected expression before ‘)’ token 
newgox.c:2032: error: expected expression before ‘)’ token 
newgox.c: At top level: 
newgox.c:2088: error: expected declaration specifiers or ‘...’ before ‘PyArrayObject’ 
newgox.c: In function ‘__pyx_f_6newgox_check_life’: 
newgox.c:2124: error: ‘__pyx_v_board’ undeclared (first use in this function) 
newgox.c:2160: error: ‘PyArrayObject’ undeclared (first use in this function) 
newgox.c:2160: error: expected expression before ‘)’ token 
newgox.c:2160: error: too many arguments to function ‘__pyx_f_6newgox_liberty’ 
newgox.c:2420: error: too many arguments to function ‘__pyx_f_6newgox_check_life’ 
newgox.c: At top level: 
newgox.c:2583: error: expected declaration specifiers or ‘...’ before ‘PyArrayObject’ 
newgox.c: In function ‘__pyx_f_6newgox_liberty’: 
newgox.c:2610: error: ‘__pyx_v_board’ undeclared (first use in this function) 
newgox.c: At top level: 
newgox.c:2859: error: expected ‘)’ before ‘*’ token 
newgox.c: In function ‘__pyx_pf_5numpy_7ndarray___getbuffer__’: 
newgox.c:2999: error: ‘PyArray_Descr’ undeclared (first use in this function) 
newgox.c:2999: error: ‘__pyx_v_descr’ undeclared (first use in this function) 
newgox.c:3062: error: ‘PyArrayObject’ undeclared (first use in this function) 
newgox.c:3062: error: expected expression before ‘)’ token 
newgox.c:3071: error: ‘npy_intp’ undeclared (first use in this function) 
newgox.c:3114: error: expected expression before ‘)’ token 
newgox.c:3114: error: ‘NPY_C_CONTIGUOUS’ undeclared (first use in this function) 
newgox.c:3154: error: expected expression before ‘)’ token 
newgox.c:3154: error: ‘NPY_F_CONTIGUOUS’ undeclared (first use in this function) 
newgox.c:3184: error: expected expression before ‘)’ token 
newgox.c:3184: warning: assignment makes pointer from integer without a cast 
newgox.c:3240: error: expected expression before ‘)’ token 
newgox.c:3240: error: subscripted value is neither array nor pointer 
newgox.c:3249: error: expected expression before ‘)’ token 
newgox.c:3249: error: subscripted value is neither array nor pointer 
newgox.c:3262: error: expected expression before ‘)’ token 
newgox.c:3271: error: expected expression before ‘)’ token 
newgox.c:3291: error: expected expression before ‘)’ token 

而且更多一些。

声明，它说：

newgox.c:2160: error: too many arguments to function ‘__pyx_f_6newgox_liberty’ 
newgox.c:2420: error: too many arguments to function ‘__pyx_f_6newgox_check_life’ 

但/ 1 check_life从比分我的电话是：

life, newly_checked = check_life(i,j,board,[]) 

而且它收到这样的：

# helper functions of score/1 
cdef check_life(int i, int j, np.ndarray[int, ndim=2] board, checked): 
    ... 
    return life, checked 

最后，是什么数据类型的种类是你使用的“i4”？

Answer 1

我不认为元组解包在Cython中的工作就像它在Python中一样。您必须使用(board.shape[0], board.shape[1])指定checked的大小。您还需要指定数据类型checked。默认np.zeros返回float64。您需要将其更改为int32以与声明的类型兼容。

这是一个应该运行的修改版本。

def score(np.ndarray[int, ndim=2] board): 

    cdef np.ndarray[np.int32_t, ndim = 2] checked 
    checked = np.zeros((board.shape[0], board.shape[1]), dtype='i4') 

    for i in xrange(len(board)): 
     for j in xrange(len(board)): 
      if checked[i,j] == 0 and board[i,j] !=0: 
       ... do stuff 

要回答你的问题的第二部分 - 是的，你可以追加到列表中的Cython函数。不过，据我了解，这涉及Python函数调用，因此它不会比Python中的相同操作更快。

更新1：

我相信这些错误是因为编译器无法找到NumPy的头文件。更新你的setup.py以包含这些文件的路径。该路径应该由np.get_include()函数输出。

import numpy as np 
from distutils.core import setup 
from distutils.extension import Extension 
from Cython.Distutils import build_ext 

setup(
     cmdclass={'build_ext': build_ext}, 
     ext_modules = [ 
       Extension("new_gox", 
         ["new_gox.pyx"], 
         include_dirs=[np.get_include()]) 
        ] 
    ) 

dtype i4是一个32位整数。它相当于np.int32。

我不确定'太多争论'错误是怎么回事。如果您在Python中调用该函数，则需要将其声明为def或cpdef。使用cdef声明的函数只能从Cython调用。这在Cython文档中描述为here。

Answer 2

np.intp是相同（无效*）

这样定义其类型：

ctypedef np.npy_intp SIZE_t    # Type for indices and counters 

源：

NPY_INTP == The enumeration value for a signed integer type which is the same size as a (void *) pointer. This is the type used by all arrays of indices.

因此，例如在用Cython ...

头文件file.h中的结构：

struct Cudamat_Struct1 { 
    float * dataHost; 
    float * dataDevice; 
    int onDevice; 
    int onHost; 
    (void *) shape; 
    int size; 
    int isTrans; // 0 or 1 
    int ownsData; 

}; 

地用Cython file.pxd文件：

cdef extern from "file.h": 
    cdef cppclass c_Cudamat_Struct "Cudamat_Struct": 
     float *dataHost 
     float *dataDevice 
     bint onDevice 
     bint onHost 
     SIZE_t * shape 
     int size 
     bint isTrans 
     bint ownsData 

最后在用Cython功能：

cdef pycublas_thrust_2d(): 
    cdef c_Cudamat_Struct1* mat = new c_Cudamat_Struct1() 

    cdef int N = 10 

    cdef np.ndarray[ndim=2, dtype=F32t] arrHost = np.ones((1,10),dtype=F32) 

    cdef int size = 10 

    cdef F32t[:,:] arrHost_ = arrHost 

    cdef F32t * arrHostPtr = &arrHost[0,0] 

    mat.dataHost = arrHostPtr 
    mat.shape = arrHost.shape 
    mat.size = size