generateSynthetic.cpp

#include "syntheticExample.hpp"

#include <csv.h>
#include <cxxopts.hpp>

#include <fstream>
#include <sstream>

using namespace JointDeconv;

int main(int argc, char* argv[])
{
  //////////////////////
  // Argument parsing //
  //////////////////////

  const auto to_string = [](const auto& any) {
    std::stringstream converter;
    converter << any;
    return std::string(converter.str());
  };

  std::string command_line;
  for (int i = 0; i < argc; i++)
  {
    command_line += argv[i];
    command_line += ' ';
  }

  cxxopts::Options options(argv[0], "Generates some synthetic data");

  // Default parameter values
  //
  int c = +1;
  double noiseSTD = 0.2;
  int randomGenerator_seed = 0;
  int what = 0;

  options.add_options()
      //
      ("c,concavity",
       "Baseline concavity, an integer in {-1,0,+1}",
       cxxopts::value<int>(c),
       to_string(c))
      //
      ("n,noise",
       "Noise standard deviation (>0)",
       cxxopts::value<double>(noiseSTD),
       to_string(noiseSTD))
      //
      ("s,seed",
       "Random number generator seed",
       cxxopts::value<int>(randomGenerator_seed),
       to_string(randomGenerator_seed))
      //
      ("what",
       "0-data, 1-ground truth, 2-peak list",
       cxxopts::value<int>(what),
       to_string(what))
      //
      ("help", "Print help");

  // CAVEAT: after options.parse(argc, argv); argc is set=1
  // -> we have to check its value before
  //
  options.parse(argc, argv);

  if (options.count("help"))
  {
    std::cout << options.help() << std::endl;
    exit(0);
  }

  if ((c != -1) && (c != 0) && (c != +1))
  {
    std::cerr << "\nError: c value " << c << " is not in {-1,0,+1}"
              << std::endl;
    return EXIT_FAILURE;
  }

  if (noiseSTD < 0)
  {
    std::cout << "#Error: noiseSTD= " << noiseSTD
              << " is not a nonnegative number" << std::endl;
    return EXIT_FAILURE;
  }

  if ((what != 0) && (what != 1) && (what != 2))
  {
    std::cerr << "\nError: x value " << what << " is not in {0,1,2}"
              << std::endl;
    return EXIT_FAILURE;
  }

  const auto data = create_syntheticExample(c, noiseSTD, randomGenerator_seed);
  const auto n = data.y.size();

  if (what == 0)
  {
    std::cout << "# x, y (" << command_line << ")" << std::endl;

    for (Index_t i = 0; i < n; i++)
    {
      std::cout << i << "," << data.y[i] << std::endl;
    }
  }
  else if (what == 1)
  {
    std::cout << "# x, y, peak, baseline, noise (" << command_line << ")"
              << std::endl;
    for (Index_t i = 0; i < n; i++)
    {
      std::cout << i << ", " << data.y[i] << ", " << data.y_peak[i] << ", "
                << data.y_baseline[i] << ", " << data.y_noise[i] << std::endl;
    }
  }
  else
  {
    std::cout << "# h, μ, σ (" << command_line << ")" << std::endl;
    for (Index_t i = 0; i < data.peaks.I_size(); i++)
    {
      std::cout << data.peaks(i, 0) << ", " << data.peaks(i, 1) << ", "
                << data.peaks(i, 2) << std::endl;
    }
  }
  return EXIT_SUCCESS;
}