Reading and writing an array in a file using C functions in cython

Question

I am instantiating a class in cython. I want to declare one of the instance which is an array of float values once by computing it with a given function and save it in a binary file using c functions. For the further call of my class if the input file does already exist, the instance would be declared by reading the array from the file otherwise it would compute it again.

import numpy as np
cimport numpy as np
cimport cython

from libc.stdio cimport FILE, fopen, fwrite, fscanf, fclose, fseek, SEEK_END, ftell, stdout, stderr
cdef extern from "math.h":
    double exp(double) nogil
    double log(double) nogil

cdef class Hit(object):
    cdef public double[::1] zs, Da
    cdef char* path

    def __cinit__(self, zs=None, path=None):
        if path is None:
           raise ValueError("Could not find a path to the file which contains the table of distances")
        else:
           self.path=path
        if zs is None:
           raise ValueError("You must give an array which contains the steps!")
        self.zs=zs
        cdef Py_ssize_t i, N
        N=len(self.zs)
        cdef FILE *ptr_fr
        cdef FILE *ptr_fw
        cdef double[::1] ptr_d = np.empty((N,))
        ptr_fr = fopen(self.path, "rb")
        ptr_fw = fopen(self.path, "wb")
        if (ptr_fr==NULL):
           print "I/O Error: cannot open file {}".format( self.path)  
           for i from N > i >= 0:
               ptr_d[i]=log(self.zs[i]+1.) /(1- self.zs[i])**0.5    
           if (ptr_fw == NULL):
               print "Unable to open file!\n"
           else:
               print "Opened file successfully for writing.\n"
               fwrite(<void*>&ptr_d[0], sizeof(double), N, ptr_fw)
               fclose(ptr_fw)
               self.Da = ptr_d

        else: 
           for i from N > i >= 0:
               fscanf(ptr_fr,"%f", &ptr_d[i])

           fclose(ptr_fr)
           self.Da = ptr_d

When I run my code for the second time the values that returns from reading a file to a pointer is correct, however I think the way I allocated the pointer to a memoryview has a problem since all the values in self.Da instance are zeros. Any suggestion ?!!

Answer 1

The answer to my own question is:

import numpy as np
cimport numpy as np
cimport cython
from libc.stdio cimport FILE, fopen, fwrite, fscanf, fclose, fprintf, fseek, ftell, SEEK_END, rewind, fread
from numpy cimport float64_t
from libc.stdlib cimport malloc, free
cdef extern from "math.h":
    double exp(double) nogil
    double log(double) nogil

cdef class Hit(object):
    cdef public double[::1] zs,  Da
    cdef char* path

    @cython.boundscheck(False)
    @cython.cdivision(True)
    @cython.wraparound(False)
    @cython.nonecheck(False)
    def __cinit__(self, path=None, zs=None):
        if path is None:
           raise ValueError("Could not find a path to the file which contains the table of distances")
        else:
           self.path=path

        if zs is None:
           raise ValueError("You must give an array which contains the steps!")
        self.zs=zs

        cdef Py_ssize_t i, N, lSize
        N=len(np.ascontiguousarray(self.zs))
        print "Input file should have ",N
        cdef FILE *ptr_fr
        cdef FILE *ptr_fw
        cdef size_t result
        cdef double *ptr_d= <double *>malloc(N * sizeof(double))
        ptr_fr = fopen(self.path, "rb")        
        if (ptr_fr==NULL):
           print "I/O Error: cannot open file {}".format( self.path) 
           for i from N > i >= 0:
               ptr_d[i]=log(self.zs[i])
               print ptr_d[i]
           ptr_fw = fopen(self.path, "wb")
           if (ptr_fw == NULL):
               print "Unable to open file!\n"

           else:

               print "Opened file successfully for writing.\n"
               fwrite(ptr_d, sizeof(double), N, ptr_fw)
               fclose(ptr_fw)
               self.Da = np.asarray(<double[:N]>ptr_d)
        else: 
           fseek (ptr_fr , 0 , SEEK_END)
           lSize = ftell (ptr_fr)
           print lSize
           rewind (ptr_fr)
           result=fread(ptr_d,sizeof(double),lSize ,ptr_fr )
           for i from N > i >= 0:
               print ptr_d[i]
           fclose(ptr_fr)
           self.Da = np.asarray(<double[:N]>ptr_d)
        print np.ascontiguousarray(self.Da)

        free(ptr_d)

Answer 2

You should change your line:

ptr_fw = fopen(self.path, "wb")

For

ptr_fw = fopen(self.path, "ab")

See http://www.cplusplus.com/reference/cstdio/fopen/

[w option] write: Create an empty file for output operations. If a file with the same name already exists, its contents are discarded and the file is treated as a new empty file.

While

[a option] append: Open file for output at the end of a file. Output operations always write data at the end of the file, expanding it. Repositioning operations (fseek, fsetpos, rewind) are ignored. The file is created if it does not exist.

The brackets are mine. You were deleting the content in path once you opened it. So the next time, you opened an empty file.

UPDATE: (I did both of these changes on your first implementation)

Plus, change your

fwrite(<void*>&ptr_d[0], sizeof(double), N, ptr_fw)

for:

       for i in range(N):
           fprintf(ptr_fw, "%lf\n", ptr_d[N-i-1])

You were reading formated but writting unformatted (remember to cimport fprintf from stdio, and the change above is also important).