import java.util.ArrayList;
import java.util.List;

import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;

import scripts.SiMatrix;
import fr.ifremer.isisfish.datastore.RegionStorage;
import fr.ifremer.isisfish.entities.EffortDescription;
import fr.ifremer.isisfish.entities.EffortDescriptionDAO;
import fr.ifremer.isisfish.datastore.SimulationStorage;
import fr.ifremer.isisfish.entities.FisheryRegion;
import fr.ifremer.isisfish.entities.Gear;
import fr.ifremer.isisfish.entities.Metier;
import fr.ifremer.isisfish.entities.MetierDAO;
import fr.ifremer.isisfish.entities.Population;
import fr.ifremer.isisfish.entities.PopulationGroup;
import fr.ifremer.isisfish.entities.Species;
import fr.ifremer.isisfish.entities.MetierSeasonInfo;
import fr.ifremer.isisfish.entities.MetierSeasonInfoDAO;
import fr.ifremer.isisfish.entities.SetOfVessels;
import fr.ifremer.isisfish.entities.Strategy;
import fr.ifremer.isisfish.entities.StrategyMonthInfo;
import fr.ifremer.isisfish.entities.Zone;
import fr.ifremer.isisfish.rule.AbstractRule;
import fr.ifremer.isisfish.simulator.SimulationContext;
import fr.ifremer.isisfish.types.TimeStep;
import fr.ifremer.isisfish.types.Month;
import fr.ifremer.isisfish.util.Doc;
import org.nuiton.math.matrix.*;
import java.io.File;
import java.io.FileReader;
import org.nuiton.math.matrix.MatrixND;
import org.nuiton.math.matrix.*;
import org.nuiton.util.*;
import org.nuiton.topia.*;
import fr.ifremer.isisfish.*;
import fr.ifremer.isisfish.types.*;
import fr.ifremer.isisfish.entities.*;


String simu = context.getSimulationControl().getId(); 

System.out.println("nom de la simu en cours : " + simu);

String[] decoupe = simu.split("_") ;

String ind = decoupe[1];

String path = "Q:/ISIS-Fish/calibrISIS_1pop/RUN/" + ind + "/q.csv";

File Accessibility = new File(path);

matAccessibility = MatrixFactory.getInstance().create(Accessibility);

System.out.println("matrice importee" + matAccessibility);

for (Population pop : context.getSimulationStorage().getParameter().getPopulations()) {
  
  pop = (Population) context.getDB().findByTopiaId(pop.getTopiaId()); // recupere population ciblee
  
  MatrixND c = pop.getCapturability();
  System.out.println("ancienne matrice" + pop + c);
  for (MatrixIterator i = c.iterator(); i.hasNext();){
    i.next() ;
    Object [] sem = i.getSemanticsCoordinates();
    PopulationGroup group = (PopulationGroup)sem[0];
    double q = (double)matAccessibility.getValue(group.getId());
    i.setValue(q);
  }
  System.out.println("Nouvelle matrice" + pop + c);
}