Error with gsl_matrix_fscanf(file,matrix) - c

Question

So right now I am simply trying to take a dummy data file,
1.30640 1
0.91751 1
0.49312 1
0.49312 0
1.79859 1
1.86360 1
0.12313 1
0.12313 0
-0.19091 1
1.82377 1
0.63205 1
0.63205 0
1.23357 1
0.62110 1
0.80438 1
and at the moment store it as a gal_matrix for manipulations later. Below is code which simply at the moment, given a data file name finds out how long it is (i.e. number of rows), initializes a gsl_matrix struct and then try to scan the text file into that matrix, called chain.
#include <stdio.h> // Needed for printf() and feof()
#include <math.h> // Needed for pow().
#include <stdlib.h> // Needed for exit() and atof()
#include <string.h> // Needed for strcmp()
#include <gsl/gsl_matrix.h> // Needed for matrix manipulations
/*------------ Defines -----------------------------------------------------------------*/
#define MAX_SIZE 10000000 // Maximum size of the time series array
#define NUM_LAG 1000 // Number of lags to calculate for
/*
*----------------------------------------------------------------------------------------
* Main program
*----------------------------------------------------------------------------------------
*/
int main(int argc, char* argv[]) {
//--------Initialization--------------------------------------------------------------
double ac_value; // computed autocorrelation value
int i,j; // Loop counter
long int N;
double mean, variance;
gsl_matrix * chains;
char filename[100];
FILE* in_file; // input file
FILE* out_file; // output file
int no_params; // number of parameters to calculate autocorrelation for
int first_column; // Which column first corresponds to a chain
int ch; // to determine number of samples in file
printf("-------------------------------------------------------------------------\n");
//--------Check that there are the correct number of arguments passed-----------------
if(argc != 4) {
printf("usage: ./auto_corr chainfile no_params first_column \n");
exit(1); // 0 means success typically, non-zero indicates an error
}
//--------Extract arguments-----------------------------------------------------------
sprintf(filename,"%s",argv[1]); // convert input file to string
in_file = fopen(filename,"rb"); // open input file for reading
no_params = atoi(argv[2]);
first_column = atoi(argv[3]);
//--------What is the number of samples in chain file?--------------------------------
N = 0; // Initialize count
while(!feof(in_file)) {
ch = fgetc(in_file);
if(ch == '\n'){
N++;
}
}
printf("Number of samples: %li\n", N); // print number of samples
if (N > MAX_SIZE) { // throw error if there are too many samples
printf("ERROR - Too many samples! MAX_SIZE = %i", MAX_SIZE);
exit(2);
}
//--------Generate a gsl matrix from the chains---------------------------------------
printf("%i\n", no_params);
chains = gsl_matrix_alloc(N, no_params); // allocate memory for gsl_matrix(rows, cols)
// print the matrix (for testing)
printf("Chain matrix \n");
for (int m=0;m<N;m++) { //rows
for (int n=0; n<no_params;n++) { // columns
printf("%f ",gsl_matrix_get(chains,m,n));
}
printf("\n");
}
// gsl_matrix_fprintf(stdout,chains,"%f"); // easy way to print, no formatting though
gsl_matrix_fscanf(in_file, chains); // read in chains to the gsl_matrix
fclose(in_file);
The error is occurring in the gsl_matrix_fscanf line, and the output I am seeing is
$ ./auto_corr auto_corr_test_data.dat 2 0
-------------------------------------------------------------------------
Number of samples: 15
2
Chain matrix
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
gsl: ./fprintf_source.c:165: ERROR: fscanf failed
Default GSL error handler invoked.
Abort trap: 6

Answer 1

I forgot to rewind the input file after I determined the number of rows.