Question

我正在尝试编写一个可以从python脚本调用的cython函数，该脚本使用c gsl库来计算spearman相关性和使用t分布的相应p值。我失败的.pyx文件如下：

import numpy as np
import numpy as np

def spearmanr(cdef double v1, cdef double v2, cdef int N):

     cdef extern from "gsl/gsl_statistics_double.h":
         double gsl_stats_spearman(double data1[],size_t stride1,double data2[],size_t stride2, size_t n)

     cdef int strides = 1
     cdef int n = N

     cdef double r = gsl_stats_spearmanr(v1,strides,v2,strides,n)

     cdef double tstat=r*((n-2)/(1-r**2))**0.5  

     cdef extern from "gsl/gsl_ranhist.h":
         double gsl_cdf_tdist_Q(double x, double nu)

     cdef double nu = N  %% Do I need to Type Cast?
     cdef double pval=gsl_cdf_tdist_Q(stat,nu)

     return r,pal

当我尝试编译时，我收到以下错误：

running build_ext
cythoning spear_coxen.pyx to spear_coxen.c

Error compiling Cython file:
------------------------------------------------------------
...
import numpy as np
cimport numpy as np

def spermanr(cdef double v1, cdef double  v2, cdef int N):
        ^
------------------------------------------------------------

spear_coxen.pyx:4:13: Expected an identifier, found 'cdef'

Error compiling Cython file:
------------------------------------------------------------
...
import numpy as np
cimport numpy as np

def spermanr(cdef double v1, cdef double  v2, cdef int N):
                    ^
------------------------------------------------------------

spear_coxen.pyx:4:25: Expected ')', found 'v1'
building 'spear_r' extension
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall   -Wstrict-prototypes -fPIC -I/usr/local/Anaconda2-2.5.0/envs/python27/include/python2.7 -c spear_coxen.c -o build/temp.linux-x86_64-2.7/spear_coxen.o
spear_coxen.c:1:2: error: #error Do not use this file, it is the result    of a failed Cython compilation.
error: command 'gcc' failed with exit status 1

我真的不确定这是否是正确的语法，因为我无法找到，因为搜索没有产生任何东西，只有琐碎的例子。如果有人能提供帮助，我们将不胜感激。谢谢

Answer 1

您不需要在函数参数中添加cdef。即。

def spearmanr(cdef double v1, cdef double v2, cdef int N):

应该是：

cpdef spearmanr(double v1, double v2, int N):

将GSL声明移到该函数声明之上，而不是在其中。然后它可以访问你声明的函数，例如

cdef extern from "gsl/gsl_statistics_double.h":

    double gsl_stats_spearman(double data1[],size_t stride1,double data2[],size_t stride2, size_t n)

对其他extern执行相同操作。

此外，您的声明看起来不正确（我不是在查看GSL文档），但double data1[]如果您认为这是一个数组，它应该是double[:,:] data1或向量double[:] data1 NumPy记忆视图。如果在data1和data2变量声明后这样做，那么它是否无法编译......

如何在cython

1 个答案: