Segmentation error in mex file

Here is the mex code I wrote to read in a tab-delimited file. The mex file got created but it causes my MATLAB to end abruptly and give the following error. Can anyone help me where I am going wrong? Please let me know if any further information is required. I have attached the error report though I do not know if it can help

Abnormal termination: Segmentation violation

#include "mex.h"
#include "matrix.h"
#include <stdio.h>
#include<string.h>
#include<stdlib.h>  

void mexFunction(int nlhs,mxArray *plhs[],int nrhs,const mxArray *prhs[])
{   

      FILE *ptr_file;
      const char **field_names;       /* pointers to field names */
      char *buf[1024];
      char *temp[20];
      int count;
      int i, j, k, l;
      int date_field, mva_field, qc_load_field, air_field, qc_air_field, oil_field, qc_oil_field, wind_a_field, qc_wind_a_field, wind_b_field, qc_wind_b_field, wind_c_field, qc_wind_c_field, tamb1_field, qc_tamb1_field;
      char *NAME;
      NAME=mxArrayToString(prhs[0]);
      count = 0;
  //open file to count elements   
      ptr_file =fopen(NAME,"r");
      if (ptr_file != NULL)
      {
  //skip first 3 lines    
      fgets(buf, sizeof(buf), ptr_file);
      fgets(buf, sizeof(buf), ptr_file);
      fgets(buf, sizeof(buf), ptr_file);
  //start counting no. of elements    
      while(fgets(buf, sizeof(buf), ptr_file) != NULL)
          count++;
      fclose(ptr_file);
      }
          field_names[0] = "date";
      field_names[1] = "mva";
      field_names[2] = "qc_load";
      field_names[3] = "air";
      field_names[4] = "qc_air";
      field_names[5] = "oil";
      field_names[6] = "qc_oil";
      field_names[7] = "wind_a";
      field_names[8] = "qc_wind_a";
      field_names[9] = "wind_b";
      field_names[10] = "qc_wind_b";
      field_names[11] = "wind_c";
      field_names[12] = "qc_wind_c"; 
      field_names[13] = "tamb1";
      field_names[14] = "qc_tamb1"; 

      plhs[0] = mxCreateStructMatrix(count, 1, 15, field_names);
      plhs[1] = mxCreateDoubleMatrix(1,1,mxREAL);
      date_field = mxGetFieldNumber(plhs[0],"date");
      mva_field = mxGetFieldNumber(plhs[0],"mva");
      qc_load_field = mxGetFieldNumber(plhs[0],"qc_load");
      air_field = mxGetFieldNumber(plhs[0],"air");
      qc_air_field = mxGetFieldNumber(plhs[0],"qc_air");
      oil_field = mxGetFieldNumber(plhs[0],"oil");
      qc_oil_field = mxGetFieldNumber(plhs[0],"qc_oil");
      wind_a_field = mxGetFieldNumber(plhs[0],"wind_a");
      qc_wind_a_field = mxGetFieldNumber(plhs[0],"qc_wind_a");
      wind_b_field = mxGetFieldNumber(plhs[0],"wind_b");
      qc_wind_b_field = mxGetFieldNumber(plhs[0],"qc_wind_b");
      wind_c_field = mxGetFieldNumber(plhs[0],"wind_c");
      qc_wind_c_field = mxGetFieldNumber(plhs[0],"qc_wind_c");
      tamb1_field = mxGetFieldNumber(plhs[0],"tamb1");
      qc_tamb1_field = mxGetFieldNumber(plhs[0],"qc_tamb1");

//open file again for storing elements columnwise
    ptr_file =fopen(NAME,"r");
    if (ptr_file != NULL)
    {
//skip first 3 lines    
    fgets(buf, sizeof(buf), ptr_file);
    fgets(buf, sizeof(buf), ptr_file);
    fgets(buf, sizeof(buf), ptr_file);  
//start collecting data 
    for(i=0;i<count;i++){   //increment line
        //get line
        fgets(buf, sizeof(buf), ptr_file);
        j=0;
        k=0;
        //extract first word
        while(buf[j] != '\t'){
            temp[k] = buf[j];
            j++;
            k++;
        }
        temp[k] = '\0';
        j++;
        mxSetFieldByNumber(plhs[0],i,date_field,mxCreateString(temp));
//      strcpy(elem[i].date, temp);

          //extract second word
          k=0;
          while(buf[j] != '\t'){
              temp[k] = buf[j];
              j++;
              k++;
          }
          temp[k] = '\0';
          j++;
  //      elem[i].mva = atof(temp);
          *mxGetPr(plhs[1]) = atof(temp);
          mxSetFieldByNumber(plhs[0],i,mva_field,plhs[1]);    

          //extract third word
          k=0;
          while(buf[j] != '\t'){
              temp[k] = buf[j];
              j++;
              k++;
          }
          temp[k] = '\0';
          j++;
  //      strcpy(elem[i].qc_load, temp);  
          mxSetFieldByNumber(plhs[0],i,qc_load_field,mxCreateString(temp));
  // similarly for other fields of the structure. 
      fclose(ptr_file);
      }
  }

Answer 1

[James Tursa]

I don't see anywhere where you allocate field_names:

const char **field_names;       /* pointers to field names */
    :
field_names[0] = "date";

That, in and of itself, will bomb your code and MATLAB.

This line will bomb your code if the caller does not request 2 outputs:

plhs[1] = mxCreateDoubleMatrix(1,1,mxREAL);

This line will eventually bomb MATLAB because you can't re-use mxArray pointers (plhs[1]) this way when stuffing them into a cell array or struct array:

mxSetFieldByNumber(plhs[0],i,mva_field,plhs[1]);

You need to create a brand new mxArray for each of these iterative calls, and not re-use plhs[1] over and over. In fact, you should not use plhs[1] here at all ... use a different mxArray pointer. (There is another unofficial way involving bumping up the reference count, but I will not go into that here)

[abc]

@James, thank you for your reply. I initially had a different mxArray pointer instead of plhs[1]. However I was constantly getting an error saying that it was illegal use of mxArray. Was the error becuase I was reusing that mxArray pointer as well? Would I need to declare as many mxArray pointers as many times I use the mxCreateDoubleMatrix?

Once again thank you for your reply. It seems there are some basic rules that I was violating. I apologize if the mistakes appear too silly, I have not worked with mex files before

[James Tursa]

You only need one mxArray * variable, you just need to create the mxArray that it points to new each iteration. E.g.,

mxArray *mx;
    :
LOOP {
    mx = mxCreateWhatever(etc);
    mxSetFieldByNumber(etc,etc,etc,mx);
}

Note that I have only one pointer variable, mx, but at each iteration it points to a brand new created mxArray.

As for the error you were getting, I could only comment if I saw the code itself (but it sounds like you had a pointer indirection issue).

Finally, no need to apologize. We have all been there and some of this stuff is not well documented (or even documented at all).

[abc]

@James, Got it! The error was that it was not initialized at the very beginning of the code I feel. Also I then used mxCreateDoubleScalar instead of mxCreateDoubleMatrix and it is running now. There is only a minor modification I need now. The date I get is in chars and so are some other fields. What I want to do from this in MATLAB is to form these fields into vectors. It is fine for the integer fields but for the fields that contain characters, if I read them all in an array, I get all the characters in a string like'5/1/2000 0:00 5/1/2000 0:01' and so on. I am trying to use mxCreateCharMatrixFromStrings in my mex code but it is not running successfully. There is the error of too few arguments to call

Here is the modification I made for that. I know that the problem is in plhs[0], it cannot be accessed like this I feel. But how can I copy it to a different array of strings? mxGetFieldByNumber will get me only one element of that field at a time. Should I then use a for loop to get all elements into an array of strings and then use this function of mxCreateCharMatrixFromStrings?

mxArray *strtmp
strtmp=mxCreateCharMatrixFromStrings((mwSize)count, (const char **) (plhs[0].date));

Answer 2

[Bruno Pop-Stefanov]

My intuition tells me that you get this error when you try to access temp[20]. You allocate an array temp of only 20 char, but you never check that k is less than 20. It's enough to have 20 characters (or more) between two tabs to crash your program.

Allocate a bigger array for temp and add if statements to check that you never go out of bounds when writing into temp and buf.

[abc]

@Bruno, Thank you for your prompt response. I understand what you are saying. I will try making the change you suggested. But I had tested my C code before mexing it and it was running fine. Is it possible that I made a mistake in mexing the file? If it helps I can attach my C code?

#include <stdio.h>
#include<string.h>
#include<stdlib.h>
#define NAME "Cooley3_dynxfmr_20100501000000_20100930235930.txt"

int main(void)
//int mexFunction(int INPUT, char *NAME)
{
//Structure
typedef struct _col{
  char date[20];
  float mva;
  char qc_load[1];
  float air;
  char qc_air[1];
  float oil;
  char qc_oil[1];
  float wind_a;
  char qc_wind_a[1];
  float wind_b;
  char qc_wind_b[1];
  float wind_c;
  char qc_wind_c[1];
  float tamb1;
  char qc_tamb1[1];
} col;  
  
  char buf[1024];
  char temp[20];
  int count = 0;
  int i, j, k, l;
  
//open file to count elements  
  int ptr_file =fopen(NAME,"r");
  if (ptr_file != NULL)
  {
//skip first 3 lines  
  fgets(buf, sizeof(buf), ptr_file);
  fgets(buf, sizeof(buf), ptr_file);
  fgets(buf, sizeof(buf), ptr_file);
//start counting no. of elements  
  while(fgets(buf, sizeof(buf), ptr_file) != NULL)
    count++;
  fclose(ptr_file);
  }
  col *elem = malloc(count*sizeof(col));
//open file again for storing elements columnwise
  ptr_file =fopen(NAME,"r");
  if (ptr_file != NULL)
  {
//skip first 3 lines  
  fgets(buf, sizeof(buf), ptr_file);
  fgets(buf, sizeof(buf), ptr_file);
  fgets(buf, sizeof(buf), ptr_file);  
//start collecting data  
  for(i=0;i<count;i++){  //increment line
    //get line
    fgets(buf, sizeof(buf), ptr_file);
    j=0;
    k=0;
    //extract first word
    while(buf[j] != '\t'){
      temp[k] = buf[j];
      j++;
      k++;
    }
    temp[k] = '\0';
    j++;
    strcpy(elem[i].date, temp);
    
    //extract second word
    k=0;
//    strcpy(temp, "\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0");
    while(buf[j] != '\t'){
      temp[k] = buf[j];
      j++;
      k++;
    }
    temp[k] = '\0';
    j++;
    elem[i].mva = atof(temp);  
    
    //extract third word
    k=0;
//    strcpy(temp, "\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0");
    while(buf[j] != '\t'){
      temp[k] = buf[j];
      j++;
      k++;
    }
    temp[k] = '\0';
    j++;
    strcpy(elem[i].qc_load, temp);  
    
    //similarly for all other words
  }
  
  fclose(ptr_file);
  }
  
printf("%s\t%f\t%s\t%f\t%f\t%s\n", elem[count-1].date, elem[count-1].mva, elem[count-1].qc_load, elem[count-1].air, elem[count-1].wind_a, elem[count-1].qc_wind_c);  
free(elem);
return 0;
}