cpp/utils/io.cpp

//
// Created by dominik on 8/14/24.
//
#include "io.h"

#include <sstream>
#include <fstream>
#include <iostream>
#include <algorithm>
#include <complex>
#include <vector>
#include <iomanip>
#include <unordered_map>
#include <map>
#include <string>
#include <filesystem>



Arguments parse_args(const int argc, char* argv[]) {
    if (argc < 3) {
        throw std::runtime_error("Not enough arguments: missing parameter file");
    }

    Arguments args;

    const std::vector<std::string> input_args(argv + 1, argv + argc);

    for (auto it = input_args.begin();  it != input_args.end(); ++it) {
        std::cout << *it << std::endl;
        if (it->at(0) == '-') {

            if (*it == "--spectrum") {
                args.spectrum = true;
                std::cout << "spectrum: " << args.spectrum << std::endl;
                continue;
            }

            if (*it == "--ste") {
                args.ste = true;
                std::cout << "ste: " << args.ste << std::endl;
                continue;
            }

            std::string stripped_arg;
            if (it->size() > 2 && it->at(0) == '-' && it->at(1) == '-') {
                stripped_arg = it->substr(2, it->size());
            } else if (it->size() > 1 && it->at(0) == '-') {
                stripped_arg = it->substr(1, it->size());
            }
            std::transform(stripped_arg.begin(), stripped_arg.end(), stripped_arg.begin(), [](unsigned char c) { return std::tolower(c); });
            const auto stripped_value = std::stod(*(++it), nullptr);
            args.optional[stripped_arg] = stripped_value;
            continue;
        }

        if (args.parameter_file.empty()) {
            std::cout << *it << " is parameter_file" << std::endl;
            args.parameter_file = *it;
            continue;
        }

        if (args.motion_type.empty()) {
            std::cout << *it << " is motion model" << std::endl;
            args.motion_type = *it;
            continue;
        }

        throw std::invalid_argument("too many positional arguments");
    }

    if (args.parameter_file.empty()) {
        throw std::invalid_argument("Missing parameter file");
    }

    if (args.motion_type.empty()) {
        throw std::invalid_argument("Missing motion model");
    }
    return args;
}


std::unordered_map<std::string, double> read_parameter(const std::filesystem::path& infile) {
    if (!std::filesystem::exists(infile)) {
        std::cerr << "File " << infile << " does not exist" << std::endl;
        exit(1);
    }

    std::ifstream instream(infile);

    std::unordered_map<std::string, double> parameter;

    std::string line;
    std::string delim = "=";
    std::string key;
    std::string value;
    size_t delim_pos;

    while (std::getline(instream, line)) {
        // skip comment lines starting with #, and empty lines
        if (line[0] == '#' || line.length() == 1) continue;

        // strip spaces from line to have always key=value
        line.erase(std::remove(line.begin(), line.end(), ' '), line.end());

        // split at '=' character and add to map
        delim_pos = line.find('=');
        key = line.substr(0, delim_pos);
        value = line.substr(delim_pos+1);
        parameter[key] = std::stod(value);
    }

    // print result
    std::cout << "Found parameter\n";
    for (const auto& [key, value]: parameter) {
        std::cout << "  " << key << ": " << std::to_string(value) << "\n";
    }
    std::cout << std::endl;

    return parameter;
}


void fid_write_out(const std::string& filename, const std::vector<double>& x, const std::vector<double>& y, const double tau, const double t_evo) {
    auto size = x.size();

    std::ostringstream sfile;
    sfile << filename << "_";
    sfile << std::setprecision(6) << std::scientific;
    sfile << "tau=" << tau << "_tevo=" << t_evo << ".dat";
    {
        std::string outfile = sfile.str();
        std::ofstream fid_file(outfile, std::ios::out);
        for (unsigned int i = 0; i < size; i++) {
            fid_file << x[i] << "\t" << y[i] << "\n";
        }
    }
}

void fid_write_out(const std::string& filename, const std::vector<double>& x, const std::map<double, std::vector<double>>& y, const double tau) {
    auto size = x.size();

    std::ostringstream sfile;
    sfile << filename << "_";
    sfile << std::setprecision(6) << std::scientific;
    sfile << "tau=" << tau << ".dat";
    {
        std::string outfile = sfile.str();
        std::ofstream fid_file(outfile, std::ios::out);
        fid_file << "#";
        for (const auto& [t_echo_j, _] : y) {
            fid_file << t_echo_j << "\t";
        }
        fid_file << std::endl;

        for (unsigned int i = 0; i < size; i++) {
            fid_file << x[i];
            for (const auto& [_, fid_j] : y) {
                fid_file << "\t" << fid_j[i];
            }
            fid_file << "\n";
        }
    }
}