/*    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) 2015  INRIA Saclay (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/>.
  */


#include <gudhi/reader_utils.h>
#include <gudhi/Bitmap_cubical_complex.h>
#include <gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h>
#include <gudhi/Persistent_cohomology.h>

using namespace Gudhi;
using namespace Gudhi::Cubical_complex;
using namespace Gudhi::persistent_cohomology;

//standard stuff
#include <iostream>
#include <sstream>
#include <vector>

using namespace std;

int main( int argc , char** argv )
{
    clock_t beginOfProgram = clock();

    cout << "This program computes persistent homology, by using Bitmap_cubical_complex_periodic_boundary_conditions class, of cubical complexes provided in text files in Perseus style (the only numbered in \
the first line is a dimension D of a bitmap. In the lines I between 2 and D+1 there are numbers of top dimensional cells in the direction I. Let N denote product \
of the numbers in the lines between 2 and D. In the lines D+2 to D+2+N there are filtrations of top dimensional cells. We assume that the cells are in the \
lexicographical order. See CubicalOneSphere.txt or CubicalTwoSphere.txt for example." << endl;

    int p = 2;
    double min_persistence = 0;

    if ( argc != 2 )
    {
        cout << "Wrong number of parameters. Please provide the name of a file with a Perseus style bitmap at the input. The program will now terminate.\n";
        return 1;
    }

    Bitmap_cubical_complex< Bitmap_cubical_complex_periodic_boundary_conditions_base<float> > b( argv[1] );

    cerr << "Here \n";

    clock_t endCreateBitmap = clock();
    double elapsed_secsCreateBitmap = double(endCreateBitmap - beginOfProgram) / CLOCKS_PER_SEC;
    cerr << "Time of creation of bitmap : " << elapsed_secsCreateBitmap << endl;
    


    // Compute the persistence diagram of the complex
    persistent_cohomology::Persistent_cohomology< Bitmap_cubical_complex< Bitmap_cubical_complex_periodic_boundary_conditions_base<float> >, Field_Zp > pcoh(b,true);
    pcoh.init_coefficients( p ); //initilizes the coefficient field for homology
    pcoh.compute_persistent_cohomology( min_persistence );


    stringstream ss;
    ss << argv[1] << "_persistence";
    std::ofstream out((char*)ss.str().c_str());
    pcoh.output_diagram(out);
    out.close();

    clock_t endOfProgram = clock();
    double elapsed_secsOfProgram = double(endOfProgram - beginOfProgram) / CLOCKS_PER_SEC;
    cerr << "Overall execution time : " << elapsed_secsOfProgram << endl;
    return 0;
}