How can I import .csv file data into gsl_vectors in C++?

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I have a .csv file that looks like:

X,Y,Z
0,0,0
0,0,0
-0.00624347,-0.0182673,1.00063
-0.00845628,-0.0374925,1.00058
-0.00494793,-0.0295639,0.927447
-0.00285682,-0.0926582,0.885783
-0.00832563,-0.02957,0.697834

And I want to put it into three gsl_vectors (from GSL: https://www.gnu.org/software/gsl/doc/html/vectors.html) corresponding to the column X, column Y and column Z respectively. The reason why I want to do this is because I later want to use the functions that are implemented in the GNU Scientific Library on this data. I want to emphasize that these functions can only work on gsl_vectors and not on std:vectors.

My approaches:

  1. Put the data from the .csv into std:vectors, and then transform those vectors into gsl_vectors. That did not work.

  2. Put the data from the .csv file into gsl_vectors directly:

    #include <iostream>
#include <fstream>
#include <istream>
#include <string>
#include <sstream>
#include <algorithm>
#include <gsl/gsl_linalg.h>
#include <gsl/gsl_vector.h>

struct acceleration {
    gsl_vector AccX;
    gsl_vector AccY;
    gsl_vector AccZ;
};

// Function prototypes
acceleration read_csv(acceleration& A);
// End function prototypes

int main(void)
{
    // ==================READ THE CSV=========================
    acceleration data;
    data = read_csv(data);
    printf("/n");
    gsl_vector_fprintf(stdout, &data.AccX, "%lf");

    return 0;
}

acceleration read_csv(acceleration& SA)
{
    std::string buffer; /* Declare a buffer for the data that will be read */
    std::string bacx, bacy, bacz;
    std::ifstream inputfile;
    inputfile.open("buffer.csv"); /* Open file for reading */
    if (!inputfile.is_open())
    {
        std::cout << "Error opening file" << std::endl;
    }

    std::stringstream aux(buffer);
    getline(aux, bacx, ',');
    getline(aux, bacy, ',');
    getline(aux, bacz, ',');
    size_t i{ 0 };

    while (getline(inputfile, buffer))
    {
        std::stringstream aux(buffer);

        getline(aux, bacx, ',');
        if (bacx.compare("AX") != 0)
            gsl_vector_set(&SA.AccX, i, stod(bacx));

        getline(aux, bacy, ',');
        if (bacy.compare("AY") != 0)
            gsl_vector_set(&SA.AccY, i, stod(bacy));

        getline(aux, bacz, ',');
        if (bacz.compare("AZ") != 0)
            gsl_vector_set(&SA.AccZ, i, stod(bacz));
        i++;
    }
    inputfile.close();
    return (SA);

}

    This gives no output on the Console and if I debug it, the function gsl_vector_set throws an exception:

    Exception thrown at 0x7A5EED1A (gsld.dll) in progr.exe: 0xC0000005: Access violation writing location 0x3333332

    At gsl_set_vector's line: v->data[i * v->stride] = x;

  3. Put the .csv data into a gsl_block and then slice it into gsl_vectors. Here I get an exception when trying to put the data into the block. Then, for slicing the block into vectors, I assume I'll have to use the gsl_vector_alloc_from_block() function, yet I did not find any example on how to use this function. I do need to see how others use functions generally because I'm new to C++. Here is what I have until now for this idea:

    #include <iostream>
#include <fstream>
#include <gsl/gsl_linalg.h>
#include <gsl/gsl_vector.h>

// Function prototypes
gsl_block read_csv(void);
// End function prototypes

int main(void)
{
    // ================== READ THE CSV INTO A BLOCK =========================
    gsl_block data;
    data = read_csv();
    // ================= NOW SLICE THE BLOCK: HOW? ==========================
    // Use gsl_vector_alloc_from_block(), but how?
    return 0;
}

// Function declarations
gsl_block read_csv(void)
{
    FILE* inputfile;
    fopen_s(&inputfile, "buffer.csv", "r"); /* Open file for reading */
    if (inputfile == NULL)
        std::cout << "file does not exist \n";
    fseek(inputfile, 0L, SEEK_END); // Go until the end
    int file_size = ftell(inputfile); // In order to tell the size of the file
    gsl_block* b = gsl_block_alloc(file_size);
    if(inputfile)
        gsl_block_fscanf(inputfile, b);

    fclose(inputfile);

    return *b;

}
// End function declarations

    If I run this I get:

    Debug Error! abort() has been called

    And on the Console it is shown:

    gsl: C:\DEV\vcpkg\buildtrees\gsl\src\gsl-2-fb511965d5.clean\block\fprintf_source.c:90: ERROR: fscanf failed Default GSL error handler invoked.

    If I debug this, the gsl_error function throws an exception:

    progr.exe has triggered a breakpoint.

    At abort ();

To sum up, I actually want to read the .csv file into gsl_vectors. If my approaches are not OK, it is understandable.

gsl vector csv c++
1 Answers

You can read the CSV file into gsl vectors the following way:

#include <stdio.h>
#include <string>
#include <iostream>
#include <fstream>
#include <sstream>
#include <gsl/gsl_vector.h>

int main ()
{
  int i = 0, rows = 7;

  // Allocate vectors
  gsl_vector *X = gsl_vector_alloc (rows);
  gsl_vector *Y = gsl_vector_alloc (rows);
  gsl_vector *Z = gsl_vector_alloc (rows);

  // Open the file
  std::ifstream openfile("data.csv");
  openfile.ignore(10000, '\n'); // Ignore the header
  std::string line;

  while (getline(openfile, line, '\n'))
  {
    std::string a, b, c;
    std::stringstream iss(line);
    getline(getline(getline (iss, a, ','), b, ','), c, ',');
    // std::cout << a << ' ' << b << ' ' << c << std::endl;

    // Set vectors
    gsl_vector_set (X, i, std::stod(a));
    gsl_vector_set (Y, i, std::stod(b));
    gsl_vector_set (Z, i, std::stod(c));

    i += 1;
  }

  // Close the file
  openfile.close();

  for(i = 0; i < rows; ++i)
  {
      // Get vectors
      std::cout << gsl_vector_get (X, i) << "\t";
      std::cout << gsl_vector_get (Y, i) << "\t";
      std::cout << gsl_vector_get (Z, i) << "\n";
  }

  // Do some processing with the vectors

  // Free allocated memory at the end
  gsl_vector_free (X);
  gsl_vector_free (Y);
  gsl_vector_free (Z);

  return 0;
}

Firstly, I open the data.csv using ifstream and read each line into three variables (splitting them through a comma). Secondly, I cast them into double and store them in the gsl vectors. Lastly, I print them for verification.

user_89933410
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