testfitness.java

an external program called from Adam s FitnessFunction class in order to evaluate the fitness of a

import org.jgap.*;
import java.io.*;


public class Testfitness extends FitnessFunction {
   
    private void doCommand(String command, String dir) throws Exception{
        String line;
        //System.out.println("command: "+command);
        Process p = Runtime.getRuntime().exec(command, null, new File(dir));
        BufferedReader input = new BufferedReader(new 
InputStreamReader(p.getInputStream()));
        while ((line = input.readLine()) != null) {
            //System.out.println("OUTPUT: "+line);
        }
        input.close();
        input = new BufferedReader(new 
InputStreamReader(p.getErrorStream()));
        while ((line = input.readLine()) != null) {
            //System.out.println("ERROR: "+line);
        }       
        p.destroy();
    }

    public Testfitness(){
        //dummy constructor
    }

    public double evaluate(IChromosome a_subject ){
        double fitness;
        String command;
        String line;
        BufferedReader input;
        BufferedWriter output;
        try{
            //bad bad hardcoding to get to the directories needed!
            String tmpDir = "/tmp/";
            String oriDir = 
"/biol/people/mres/asf500/vlab-4.0/oofs/ext/java";
            //get the local ip/name
            String hostName = InetAddress.getLocalHost().getHostName();
            //String hostIP = InetAddress.getLocalHost().getHostAddress();
           
            /* bruteforce batch since this doesnt work very well           
            //construct a temp dir
            command = "mkdir "+tmpDir+"asf500_"+hostName;
            doCommand(command, "/");
               
           
            //move all stuff to a temp dir to work in
            command = "cp -vr "+oriDir+"/* asf500_"+tmpDir;
            doCommand(command, "/");*/

            tmpDir += "asf500_"+hostName;
           
            //open the files to read/write from/to
            input = new BufferedReader(new 
FileReader(oriDir+"/fractal.l.template"));
            output = new BufferedWriter(new 
FileWriter(tmpDir+"/fractal.l"));
            //read in each line
            while((line=input.readLine())!=null){
                //replace special chars with gene values
                for(int i=0; i<8; i++){
                    line = line.replaceAll("!GENE:"+i+"!", 
a_subject.getGene(i).getAllele().toString());
                }
                //write it back out again
                output.write(line+"\n");
                //debug line
                //System.out.println(in+" > "+line);
            }
         
            command = "cpfg -P preproc -m fractal.map -e fractal.e -g 
fractal.l fractal.v fractal.a";
            doCommand(command, tmpDir);           
           
            //read the output file
            //and work out the fitness
            input = new BufferedReader(new FileReader(tmpDir+"/test.log"));
            int leafTotal = 0;
            int leafIn = 0;
            int leafOut = 0;
            //read in each line
            while((line=input.readLine())!=null){
                line = line.substring(1,line.length()-1);
                String [] positions = line.split(",");
                if (positions.length == 3){
                    //System.out.println(positions[0]+" "+positions[1]+" 
"+positions[2]);
                    float x = Float.parseFloat(positions[0]);
                    float y = Float.parseFloat(positions[1]);
                    float z = Float.parseFloat(positions[2]);
                    //System.out.println(x+" "+y+" "+z);
                    leafTotal++;
                    if (x > -2.0 && x < 2.0
                        && y > 0.0 && y < 4.0
                        && z > -2.0 && z < 2.0){
                        leafIn++;
                    }else{
                        leafOut++;
                    }
                }
            }
            input.close();
           
            

            //System.out.println("This solution has a fitness value of 
"+fitness+" ("+leafIn+"/"+leafOut+")");
            return fitness;
           
        } catch (Exception err) {
            err.printStackTrace();
        }

        //System.out.println("ERROR This solution has a fitness value of 
"+1.0+"()");
        return 1.0;
    }
}