/*
 * Copyright (C) 2010
 *
 * 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 2
 * 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, write to the Free Software
 * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 */

package rules;

import static org.nuiton.i18n.I18n._;
import org.nuiton.j2r.REngine;
import org.nuiton.j2r.RException;
import org.nuiton.j2r.RProxy;
import org.nuiton.j2r.types.RDataFrame;
import org.nuiton.topia.*;// pour pouvoir utiliser la methode StringUtil.toDouble()
import org.nuiton.util.*;// pour pouvoir utiliser la methode StringUtil.toDouble()
import scripts.ResultName;
import scripts.SiMatrix;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import fr.ifremer.isisfish.types.Date;
import fr.ifremer.isisfish.types.Month;
import scripts.ResultName;
import java.io.Writer;
import fr.ifremer.isisfish.export.Export;
import java.io.File;
import java.util.Arrays;
import java.util.ArrayList;
import java.util.List;
import org.nuiton.util.FileUtil;
import org.nuiton.math.matrix.*;
import fr.ifremer.isisfish.entities.Population;
import fr.ifremer.isisfish.util.Doc;
import fr.ifremer.isisfish.simulator.SimulationContext;
import fr.ifremer.isisfish.types.Date;
import fr.ifremer.isisfish.entities.*;
import fr.ifremer.isisfish.rule.AbstractRule;
import fr.ifremer.isisfish.datastore.SimulationStorage;
import fr.ifremer.isisfish.datastore.ResultStorage;
import org.nuiton.math.matrix.MatrixIterator;
import org.nuiton.topia.TopiaContext;
import fr.ifremer.isisfish.simulator.SimulationControl;
import fr.ifremer.isisfish.simulator.SimulationProperties;



/**
 * XSA.java
 *
 * Created: 11 mars 2010
 *
 * @author ben <user.name@vcs.hostName>
 * @version $Revision: 1545 $
 * Last update: $Date: 12 juillet 2011 $
 * by : $Author: Paul et Youen $
 */
public class XSA extends AbstractRule {

	/** to use log facility, just put in your code: log.info("..."); */
	private static Log log = LogFactory.getLog(XSA.class);
	
	//String param_pathInputs = "F:/D/Projets/deepfishman/Blue ling/";
	//String param_InputsStockObject = "F:/D/Projets/deepfishman/Blue ling/bli567ind.txt";
	//String param_InputsFleetObject = "F:/D/Projets/deepfishman/Blue ling/bli567fl.txt";
	String param_InputsStockObject = "F:/D/Projets/deepfishman/Blue ling/bli567ind.txt";
	String param_InputsFleetObject = "F:/D/Projets/deepfishman/Blue ling/bli567fl.txt";
	String param_pathOutputs = "F:/D/Projets/deepfishman/Blue ling/";
	public Population param_pop = null;
	public Strategy param_StrategyTunning = null;
	public String param_GroupRange = "7;20";
	protected TopiaContext db = null;

	private MatrixND catchYear0;
	private MatrixND effortS1Met0;
	private MatrixND catchS1Met0;
	public MatrixND matrixCpue;
	public  MatrixND matrixNageExport;
	public  MatrixND matrixFageExport;
	public static double ssbExport, fbarExport;

	RDataFrame FauxAges;
	RDataFrame NauxAges;
	// Configuration

	@Doc("Mois de l'evaluation")
	public Month param_month = Month.JANUARY;
    
	// Matrices necessaires
	public String [] necessaryResult = {
		ResultName.MATRIX_ABUNDANCE,
		ResultName.MATRIX_BIOMASS,
		ResultName.MATRIX_CATCH_PER_STRATEGY_MET_PER_ZONE_POP,
		ResultName.MATRIX_DISCARDS_PER_STR_MET_PER_ZONE_POP,
		ResultName.MATRIX_DISCARDS_WEIGHT_PER_STR_MET_PER_ZONE_POP 
    };

    public String[] getNecessaryResult() {
		return this.necessaryResult;
	}

	public String getDescription() throws Exception {
		return _("Fait une XSA");
	}


    public void init(SimulationContext context) throws Exception {

		Date date = new Date(0);
		
		REngine engine = new RProxy();
            
		engine.voidEval("library(FLXSA)");
		String pathObject = "stock<-readFLStock(\"" +  param_InputsStockObject + "\")" ;

log.info("param_GroupRange ="+ param_GroupRange);
log.info("pathObject =" + pathObject);
		engine.voidEval(pathObject);
		
		String pathFleet = "indices<-readFLIndices(\"" +  param_InputsFleetObject + "\")";
		
log.info("pathObject =" + pathFleet);		

		engine.voidEval(pathFleet);

   		  //engine.voidEval("stock<-readFLStock(\"F:/D/Projets/deepfishman/Blue ling/bli567ind.txt\")");
   		  //
		  //engine.voidEval("indices<-readFLIndices(\"F:/D/Projets/deepfishman/Blue ling/bli567fl.txt\")");

		
		// Parametres XSA		  
		engine.voidEval("tol<-1.e-09");
		engine.voidEval("maxit<-1000");
		engine.voidEval("min.nse<-0.3");
		engine.voidEval("fse<-2.0");
		engine.voidEval("rage<-9");
		engine.voidEval("qage<-17");
		engine.voidEval("shk.n<-TRUE");
		engine.voidEval("shk.f<-TRUE");
		engine.voidEval("shk.yrs<-5");
		engine.voidEval("shk.ages<-5");
		engine.voidEval("window<-100");
		engine.voidEval("tsrange<-20");
		engine.voidEval("tspower<-3");
		// stocke dans FLXSA les parametres
		engine.voidEval("xsa.control<-FLXSA.control(tol=tol,maxit=maxit,min.nse=min.nse,fse=fse,rage=rage,qage=qage,shk.n=shk.n,shk.f=shk.f,shk.yrs=shk.yrs,shk.ages=shk.ages,window=window,tsrange=tsrange,tspower=tspower,vpa=FALSE)");
		engine.voidEval("stock@catch.n <- stock@landings.n"); // recupere les capt aux ages de l annee precedente	


		
		String saveOutputs = "save.image(file=\"" + param_pathOutputs + "xsaRes.RData\")";
		engine.voidEval(saveOutputs); // sauver l'objet pour pouvoir le rouvrir ensuite pour utilisation
  		  //engine.voidEval("save.image(file=\"F:/D/Projets/deepfishman/Blue ling/xsaRes.RData\")"); // sauver l'objet pour pouvoir le rouvrir ensuite pour utilisation
    		  
    }


	/**
	* La condition qui doit etre vrai pour faire les actions
	* @param simulation La simulation pour lequel on utilise cette regle
	* @return vrai si on souhaite que les actions soit faites
	*/

	public boolean condition(SimulationContext context, Date date, Metier metier) throws Exception {
		Month currentMonth = date.getMonth();
		if (currentMonth.equals(param_month) && (date.getYear() > 0)) { 
			return true;
		}
		else return false;        
    }

	// Booleen permettant que ne boucler que sur un seul metier dans la preaction :
	boolean first = true;

	/**
	* @param simulation La simulation pour lequel on utilise cette regle
	*/
	public void preAction(SimulationContext context, Date date, Metier metier) throws Exception {

		if (first){
		
		
			ResultStorage resultmanager = context.getSimulationStorage().getResultStorage();
			for (Date dat = date.previousYear(); dat.before(date); dat = dat.next()) {
				MatrixND CatchPop = resultmanager.getMatrix(dat,param_pop,ResultName.MATRIX_CATCH_PER_STRATEGY_MET_PER_ZONE_POP);
				// reccupere les catches at age de l annee passee
				MatrixND Prov2 = CatchPop.sumOverDim(0);// sumOver str
				Prov2=Prov2.sumOverDim(1);// sum over metier
				Prov2=Prov2.sumOverDim(3); // sum over zones
				Prov2=Prov2.reduce();
				if(dat.equals( date.previousYear())){
log.info("test our voir comme ca");
					catchYear0 = Prov2;
				}else{
log.info("test our voir comme ca 2");
log.info("Prov2= " + Prov2);
log.info("catchYear0= " + catchYear0);
					catchYear0.add(Prov2);
				}
				
				// reccupere les catches at age de la flottille tunning
				MatrixND Prov3 = CatchPop.getSubMatrix(0,param_StrategyTunning);
				Prov3=Prov3.sumOverDim(3).reduce(); // sum over zones 
				if(dat.equals( date.previousYear())){
					catchS1Met0 = Prov3;
				}else{
					catchS1Met0.add(Prov3);
				}
				// reccupere effort de la flottille tunning 
				MatrixND Effort = resultmanager.getMatrix(dat,ResultName.MATRIX_EFFORT_NOMINAL_PER_STRATEGY_MET);
log.info("Effort = " +Effort);
log.info("param_StrategyTunning = " +param_StrategyTunning.getName());

				if(dat.equals( date.previousYear())){
					effortS1Met0 = Effort.copy().getSubMatrix(0,param_StrategyTunning).reduce();
				}else{
					effortS1Met0.add(Effort.copy().getSubMatrix(0,param_StrategyTunning).reduce());
				}
					
				
			}
				
			// compute CPUE
			MatrixND matrixCpue = catchS1Met0;
			int dummyMet = 0;
log.info("effortS1Met0 = " + effortS1Met0);
			for(MatrixIterator i = effortS1Met0.iterator(); i.hasNext();){
			i.next();
				if(i.getValue() > 0){
					dummyMet++;
				}
			}
			log.info("dum met"+dummyMet);
			for(MatrixIterator i = matrixCpue.iterator(); i.hasNext();){
				i.next();
				log.info("i"+i.getValue());
				Metier met = (Metier)i.getSemanticsCoordinates()[0];
				log.info("met"+met.getName());
				if(effortS1Met0.getValue(met) > 0){
					log.info("val met"+effortS1Met0.getValue(met));
					i.setValue(i.getValue()/effortS1Met0.getValue(met));
					log.info("i"+i.getValue());
				}
			}
			log.info("cpue"+matrixCpue);
			matrixCpue=matrixCpue.sumOverDim(0).reduce();
			log.info("cpue2"+matrixCpue);
			double div = 1/(double)dummyMet;
			log.info("div"+div);
			if(dummyMet > 0) matrixCpue = matrixCpue.divs(div);
			log.info("cpue3"+matrixCpue);
			
		
	
					// Si on est au mois de Janvier, avant le pas de temps: 
					// Recuperer les captures aux ages etc du pas de temps precedent
					// realiser la xsa
					//log.info("Avant engine");
					REngine engine = new RProxy();
					//log.info("Avant import");
					
					String loadCommand = "load(file=\"" + param_pathOutputs + "xsaRes.RData\")";
					engine.voidEval(loadCommand);
					//engine.voidEval("load(file=\"F:/D/Projets/deepfishman/Blue ling/xsaRes.RData\")");
					
					// etendre l'objet FLR
					// Objet Stock
					engine.voidEval("stock<-window(stock,end=range(stock)[5]+1)"); // On agrandit la fenetre temporelle du stock de 1 YV
					
					log.info("catchYear0" + catchYear0);
					
					String [] stringGroupRange = param_GroupRange.split(";");
					double [] dgroupRange = StringUtil.toArrayDouble(stringGroupRange[0], stringGroupRange[1]);
					int[] groupRange = new int[] {(int)dgroupRange[0],(int)dgroupRange[1]};
					MatrixND caaAexprter = catchYear0.getSubMatrix(0,groupRange[0],groupRange[1]-groupRange[0]+1);
					log.info("caaAexporter" + caaAexprter);
					//
					// create vector of catch values for R
					String essaimatrix = "test <- c(";
						for(MatrixIterator i = caaAexprter.iterator();i.hasNext();){
						i.next();
						PopulationGroup grp = (PopulationGroup)i.getSemanticsCoordinates()[0];
						if (grp.getId() < groupRange[1]) {
                            essaimatrix += i.getValue() + ",";
                        } else {
                            essaimatrix += i.getValue();
                        }
						}
						essaimatrix = essaimatrix + ")";
                    engine.voidEval(essaimatrix);
                    //log.info("essaimatrix=" + essaimatrix);
					//engine.voidEval("save.image(file=\"F:/D/Projets/deepfishman/Blue ling/xsaRes.RData\")");
						
					//engine.voidEval("test<-as.vector(" + caaAexprter + ")");
					engine.voidEval("stock@catch.n[,dim(stock@catch.n)[2],,,] <-test/1000" ); // recupere les capt aux ages de l annee precedente
					engine.voidEval("stock@catch.wt[,dim(stock@catch.n)[2],,,]<-as.vector(rowMeans(stock@catch.wt[,c((dim(stock@catch.wt)[2] - 1):(dim(stock@catch.wt)[2] - 3)),,,]))"); // calcule la moyenne des poids aux ages sur les 3 dernieres annees
					engine.voidEval("stock@landings.n[,dim(stock@landings.n)[2],,,]<-stock@catch.n[,dim(stock@catch.n)[2],,,] "); // pas de rejets les capt==debarquements
					engine.voidEval("stock@landings.wt[,dim(stock@landings.wt)[2],,,]<-as.vector(rowMeans(stock@landings.wt[,c((dim(stock@landings.wt)[2] - 1):(dim(stock@landings.wt)[2] - 3)),,,]))"); // calcule la moyenne des poids aux ages sur les 3 dernieres annees
					engine.voidEval("stock@stock.wt[,dim(stock@stock.wt)[2],,,]<-as.vector(rowMeans(stock@stock.wt[,c((dim(stock@stock.wt)[2] - 1):(dim(stock@stock.wt)[2] - 3)),,,]))"); // calcule la moyenne des poids aux ages sur les 3 dernieres annees
					engine.voidEval("stock@m[,dim(stock@m)[2],,,]<-stock@m[,dim(stock@m)[2] - 1,,,] "); // copie la M de l'anne precedente
					engine.voidEval("stock@mat[,dim(stock@mat)[2],,,]<-stock@mat[,dim(stock@mat)[2] - 1,,,] "); // copie la Maturite de l'anne precedente
					engine.voidEval("stock@harvest.spwn[,dim(stock@harvest.spwn)[2],,,]<-stock@harvest.spwn[,dim(stock@harvest.spwn)[2] - 1,,,] "); // 
					engine.voidEval("stock@m.spwn[,dim(stock@m.spwn)[2],,,]<-stock@m.spwn[,dim(stock@m.spwn)[2] - 1,,,] "); // 
		
					// Objet fleet
					engine.voidEval("indices<-window(indices,end=range(indices)[4]+1)"); // On agrandit la fenetre temporelle de fleet de 1 YV

log.info("matrixCpue =" +matrixCpue);

					MatrixND iaAexprter = matrixCpue.getSubMatrix(0,groupRange[0],groupRange[1]-groupRange[0]+1) ;
					
log.info("iaAexprter =" +iaAexprter);					
					// create vector of cpue values for R
					String essaimatrix2 = "test <- c(";
						for(MatrixIterator i = iaAexprter.iterator();i.hasNext();){
						i.next();
						PopulationGroup grp = (PopulationGroup)i.getSemanticsCoordinates()[0];
						if (grp.getId() < groupRange[1]) {
                            essaimatrix2 += i.getValue() + ",";
                        } else {
                            essaimatrix2 += i.getValue();
                        }
						}
						essaimatrix2 = essaimatrix2 + ")";
						
                    engine.voidEval(essaimatrix2);
					
					engine.voidEval("indices@.Data[[1]]@catch.n[,dim(indices@.Data[[1]]@catch.n)[2],,,]<-test/1000");// recupere les indices aux ages de l annee precedente
					engine.voidEval("indices@.Data[[1]]@effort[,dim(indices@.Data[[1]]@effort)[2],,,]<-1");// recupere les indices aux ages de l annee precedente
					 log.info("Avant XSA"); 
					// Faire la xsa
					engine.voidEval("xsa<-FLXSA(stock,indices,xsa.control)");
					log.info("Apres XSA");
					String save2 = "save.image(file=\"" + param_pathOutputs + "xsaRes.RData\")";
					engine.voidEval(save2);
					
					//engine.voidEval("save.image(file=\"F:/D/Projets/deepfishman/Blue ling/xsaRes.RData\")");
					
					// retourner ssb et f de la derniere annee
					engine.voidEval("range(stock)[3]<-range(xsa)[3]");
					engine.voidEval("stock<-stock+xsa");
					Double ssb = ((Double) engine.eval("ssb<-as.numeric(as.data.frame(ssb(stock)[1,ncol(ssb(stock))]))[7]")).doubleValue();
					Double fbar = ((Double) engine.eval("fbar<-as.numeric(as.data.frame(fbar(stock)[1,ncol(fbar(stock))]))[7]")).doubleValue();
					
				
					FauxAges = (RDataFrame) engine.eval("FauxAges <- as.data.frame(as.data.frame(harvest(stock)[,ncol(harvest(stock))])$data)");
					NauxAges = (RDataFrame) engine.eval("NauxAges<- as.data.frame(as.data.frame(stock.n(stock)[,ncol(stock.n(stock))])$data)");
					//MatrixND FauxAges = ((MatrixND) engine.eval("FauxAges <- as.data.frame(harvest(xsa.stock)[,ncol(harvest(xsa.stock))])$data")).doubleValue();
					//MatrixND NauxAges = ((MatrixND) engine.eval("NauxAges <- as.data.frame(stock.n(xsa.stock)[,ncol(stock.n(xsa.stock))])$data")).doubleValue();
					ssbExport = ssb;
					fbarExport = fbar;

					//log.info("agegroups = " + agegroups);
					
					// export XSA results to use in another rule
					List<PopulationGroup> agegroupsall = param_pop.getPopulationGroup();
					matrixNageExport = MatrixFactory.getInstance().create(
						"matrixNageExport",
						new List[]{agegroupsall},
						new String[]{"AgeGroupsAll"});
					matrixFageExport = MatrixFactory.getInstance().create(
						"matrixFageExport",
						new List[]{agegroupsall},
						new String[]{"AgeGroupsAll"});
						
					for (MatrixIterator iage = matrixNageExport.iterator(); iage.hasNext();){
						iage.next();
						PopulationGroup age = (PopulationGroup)iage.getSemanticsCoordinates()[0];
						if (age.getId() < groupRange[0]){
							iage.setValue(0.0);	
						} // end of iage if-test;
						else{
						//log.info("NauxAges.get(iage-7,1) = " + NauxAges.get(iage,1) + "iage= " + iage);
						//log.info("age = " + iage);
						//log.info("NauxAges = " + NauxAges.get(0,iage-7));
							iage.setValue((Double)  NauxAges.get(0,age.getId()-groupRange[0]));
						} // end of iage else-test;
					} // end of age for loop;
					for (MatrixIterator iage = matrixFageExport.iterator(); iage.hasNext();){
						iage.next();
						PopulationGroup age = (PopulationGroup)iage.getSemanticsCoordinates()[0];
						if (age.getId() < groupRange[0]){
							iage.setValue(0.0);	
						} // end of iage if-test;
						else{
						//log.info("NauxAges.get(iage-7,1) = " + NauxAges.get(iage,1) + "iage= " + iage);
						//log.info("age = " + iage);
						//log.info("NauxAges = " + NauxAges.get(0,iage-7));
							iage.setValue((Double)  FauxAges.get(0,age.getId()-groupRange[0]));
						} // end of iage else-test;
					} // end of age for loop;

					engine.voidEval(save2);
					//engine.voidEval("save.image(file=\"F:/D/Projets/deepfishman/Blue ling/xsaRes.RData\")");
					
				
			
			first = false;
		} // end of (first) if-test;

	}

	/**
	* @param simulation La simulation pour lequel on utilise cette regle
	*/
    public void postAction(SimulationContext context, Date date, Metier metier) throws Exception {
		first = true;
	}

}