/*    This file is part of the Gudhi Library. The Gudhi library
 *    (Geometric Understanding in Higher Dimensions) is a generic C++
 *    library for computational topology.
 *
 *    Author(s):       Pawel Dlotko
 *
 *    Copyright (C) 2016  INRIA (France)
 *
 *    This program is free software: you can redistribute it and/or modify
 *    it under the terms of the GNU General Public License as published by
 *    the Free Software Foundation, either version 3 of the License, or
 *    (at your option) any later version.
 *
 *    This program is distributed in the hope that it will be useful,
 *    but WITHOUT ANY WARRANTY; without even the implied warranty of
 *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *    GNU General Public License for more details.
 *
 *    You should have received a copy of the GNU General Public License
 *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */

#ifndef READ_PERSISTENCE_FROM_FILE_H_
#define READ_PERSISTENCE_FROM_FILE_H_

#include <iostream>
#include <fstream>
#include <sstream>
#include <vector>
#include <algorithm>

namespace Gudhi {
namespace Persistence_representations {

/**
 * Universal procedure to read files with persistence. It ignores the lines starting from # (treat them as comments).
 * It reads the fist line which is not a comment and assume that there are some numerical entries over there. The
 *program assume
 * that each other line in the file, which is not a comment, have the same number of numerical entries (2, 3 or 4).
 * If there are two numerical entries per line, then the function assume that they are birth/death coordinates.
 * If there are three numerical entries per line, then the function assume that they are: dimension and birth/death
 *coordinates.
 * If there are four numerical entries per line, then the function assume that they are: the characteristic of a filed
 *over which
 * persistence was computed, dimension and birth/death coordinates.
 * The 'inf' string can appear only as a last element of a line.
 * The procedure returns vector of persistence pairs.
**/
std::vector<std::pair<double, double> > read_persistence_intervals_in_one_dimension_from_file(
    std::string const& filename, int dimension = -1, double what_to_substitute_for_infinite_bar = -1) {
  bool dbg = false;
  std::ifstream in;
  in.open(filename);
  // checking if the file exist:
  if (!in.good()) {
    std::cerr << "The file : " << filename << " do not exist. The program will now terminate \n";
    throw "The file from which you are trying to read the persistence landscape do not exist. The program will now terminate \n";
  }

  std::string line;
  std::vector<std::pair<double, double> > barcode;

  int number_of_entries_per_line = -1;

  while (!in.eof()) {
    getline(in, line);
    if (dbg) std::cerr << "Reading line : " << line << std::endl;
    if (!(line.length() == 0 || line[0] == '#')) {
      // If we do not know how many entries per line we have, we check it in below.
      if (number_of_entries_per_line == -1) {
        number_of_entries_per_line = 0;
        std::string line_copy(line);
        if (line_copy.find("inf") != std::string::npos) {
          size_t np = line_copy.find("inf");
          // replace symbols 'inf' in line_copy with white spaces:
          line_copy[np] = ' ';
          line_copy[np + 1] = ' ';
          line_copy[np + 2] = ' ';
          number_of_entries_per_line = 1;
        }
        // check how many entries we have in the line.
        std::stringstream ss(line_copy);
        double number;
        std::vector<double> this_line;
        while (ss >> number) {
          this_line.push_back(number);
        }
        number_of_entries_per_line += (int)this_line.size();
        if (dbg) {
          std::cerr << "number_of_entries_per_line : " << number_of_entries_per_line
                    << ". This number was obtained by analyzing this line : " << line << std::endl;
        }
        if ((number_of_entries_per_line < 2) || (number_of_entries_per_line > 4)) {
          std::cerr << "The input file you have provided have wrong number of numerical entries per line. The program "
                       "will now terminate. \n";
          throw "The input file you have provided have wrong number of numerical entries per line. The program will now terminate. \n";
        }
      }
      // In case there is an 'inf' string in this line, we are dealing with this situation in below.
      if (line.find("inf") != std::string::npos) {
        if (dbg) {
          std::cerr << "This line: " << line << " contains infinite interval. \n";
        }
        // first we substitute inf by white spaces:
        size_t np = line.find("inf");
        line[np] = ' ';
        line[np + 1] = ' ';
        line[np + 2] = ' ';
        if (what_to_substitute_for_infinite_bar != -1) {
          double beginn, field, dim;
          std::stringstream lineSS(line);
          if (number_of_entries_per_line == 4) lineSS >> field;
          if (number_of_entries_per_line >= 3) {
            lineSS >> dim;
          } else {
            dim = dimension;
          }
          lineSS >> beginn;
          if (dim == dimension) {
            if (beginn > what_to_substitute_for_infinite_bar) {
              barcode.push_back(std::make_pair(what_to_substitute_for_infinite_bar, beginn));
            } else {
              barcode.push_back(std::make_pair(beginn, what_to_substitute_for_infinite_bar));
            }
            if (dbg) {
              std::cerr << "this is the line that is going to the output : " << beginn << " , "
                        << what_to_substitute_for_infinite_bar << std::endl;
            }
          }
        } else {
          // this is a line with infinity. Since the variable what_to_substitute_for_infinite_bar have not been set up,
          // it means that this line will be skipped.
          if (dbg) {
            std::cerr << "We will skip it \n";
          }
        }
        continue;
      } else {
        // Then, we read the content of the line. We know that it do not contain 'inf' substring.
        std::stringstream lineSS(line);
        double beginn, endd, field, dim;
        if (number_of_entries_per_line == 4) lineSS >> field;
        if (number_of_entries_per_line >= 3) {
          lineSS >> dim;
        } else {
          dim = dimension;
        }
        lineSS >> beginn;
        lineSS >> endd;
        if (beginn > endd) {
          std::swap(beginn, endd);
        }
        if (dim == dimension) {
          barcode.push_back(std::make_pair(beginn, endd));
          if (dbg) {
            std::cerr << "This is a line that is going to the output : " << beginn << " , " << endd << std::endl;
          }
        } else {
          if ((number_of_entries_per_line == 3) && (dimension == -1)) {
            barcode.push_back(std::make_pair(beginn, endd));
          }
        }
      }
    } else {
      if (dbg) {
        std::cerr << "This is a comment line \n";
      }
    }
  }
  in.close();
  if (dbg) std::cerr << "End of reading \n";

  return barcode;
}  // read_persistence_intervals_in_one_dimension_from_file

}  // namespace Persistence_representations
}  // namespace Gudhi

#endif  // READ_PERSISTENCE_FROM_FILE_H_