将文件句柄传递给cython函数

Question

我想用cython编译一个python函数,用于读取跳过一些记录的二进制文件(不读取整个文件然后切片,因为我的内存不足).我可以想出这样的事情:

    def FromFileSkip(fid, count=1, skip=0):            
        if skip>=0:
            data = numpy.zeros(count)
            k = 0
            while k<count:
                try:
                    data[k] = numpy.fromfile(fid, count=1, dtype=dtype)
                    fid.seek(skip, 1)
                    k +=1
                except ValueError:
                    data = data[:k]
                    break
            return data

然后我可以使用这样的功能:

 f = open(filename)
 data = FromFileSkip(f,...

但是,为了用cython编译函数"FromFileSkip",我想定义函数中涉及的所有类型,所以"fid"也是文件处理程序.如何在cython中定义其类型,因为它不是"标准"类型,例如整数.谢谢.

Answer 1

定义类型fid将无济于事,因为调用python函数仍然很昂贵.尝试用"-a"标志编译你的例子,看看我的意思.但是,您可以使用低级C函数进行文件处理,以避免循环中的python开销.为了举例,我假设数据从文件的开头开始,其类型是double

from libc.stdio cimport *                                                                

cdef extern from "stdio.h":
    FILE *fdopen(int, const char *)

import numpy as np
cimport numpy as np

DTYPE = np.double # or whatever your type is
ctypedef np.double_t DTYPE_t # or whatever your type is

def FromFileSkip(fid, int count=1, int skip=0):
    cdef int k
    cdef FILE* cfile
    cdef np.ndarray[DTYPE_t, ndim=1] data
    cdef DTYPE_t* data_ptr

    cfile = fdopen(fid.fileno(), 'rb') # attach the stream
    data = np.zeros(count).astype(DTYPE)
    data_ptr = <DTYPE_t*>data.data

    # maybe skip some header bytes here
    # ...

    for k in range(count):
        if fread(<void*>(data_ptr + k), sizeof(DTYPE_t), 1, cfile) < 0:
            break
        if fseek(cfile, skip, SEEK_CUR):
            break

    return data

请注意,输出cython -a example.pyx显示循环内没有python开销.