2OP4u 2OP4u - 28 days ago 14
Java Question

Tiny GP output in text file

I've recently stumbled upon Tiny GP (A Genetic Programming program), and I found it pretty useful, so I decided to change all

System.out.println()
in the program to a write to text file method.

Problem: In the text file, for some reason, only says "PROBLEM SOLVED", instead of printing out generations and other things that it is supposed to (see code).

Tiny GP modified class file:

package main;

/*
* Program: tiny_gp.java
*
* Author: Riccardo Poli (email: rpoli@essex.ac.uk)
*
* Modified by Preston Tang
*/
import java.util.*;
import java.io.*;
import java.text.DecimalFormat;

public class tiny_gp {

String Name;
double[] fitness;
char[][] pop;
static Random rd = new Random();
static final int ADD = 110,
SUB = 111,
MUL = 112,
DIV = 113,
FSET_START = ADD,
FSET_END = DIV;
static double[] x = new double[FSET_START];
static double minrandom, maxrandom;
static char[] program;
static int PC;
static int varnumber, fitnesscases, randomnumber;
static double fbestpop = 0.0, favgpop = 0.0;
static long seed;
static double avg_len;
static final int MAX_LEN = 10000,
POPSIZE = 100000,
DEPTH = 5,
GENERATIONS = 100,
TSIZE = 2;
public static final double PMUT_PER_NODE = 0.05,
CROSSOVER_PROB = 0.9;
public static double[][] targets;

public double run() {
/* Interpreter */

char primitive = program[PC++];
if (primitive < FSET_START) {
return (x[primitive]);
}
switch (primitive) {
case ADD:
return (run() + run());
case SUB:
return (run() - run());
case MUL:
return (run() * run());
case DIV: {
double num = run(), den = run();
if (Math.abs(den) <= 0.001) {
return (num);
} else {
return (num / den);
}
}
}
return (0.0); // should never get here
}

public int traverse(char[] buffer, int buffercount) {
if (buffer[buffercount] < FSET_START) {
return (++buffercount);
}

switch (buffer[buffercount]) {
case ADD:
case SUB:
case MUL:
case DIV:
return (traverse(buffer, traverse(buffer, ++buffercount)));
}
return (0); // should never get here
}

public void setup_fitness(String fname) {
try {
int i, j;
String line;

BufferedReader in
= new BufferedReader(
new FileReader(fname));
line = in.readLine();
StringTokenizer tokens = new StringTokenizer(line);
varnumber = Integer.parseInt(tokens.nextToken().trim());
randomnumber = Integer.parseInt(tokens.nextToken().trim());
minrandom = Double.parseDouble(tokens.nextToken().trim());
maxrandom = Double.parseDouble(tokens.nextToken().trim());
fitnesscases = Integer.parseInt(tokens.nextToken().trim());
targets = new double[fitnesscases][varnumber + 1];
if (varnumber + randomnumber >= FSET_START) {
Write("too many variables and constants");
//System.out.println("too many variables and constants");
}

for (i = 0; i < fitnesscases; i++) {
line = in.readLine();
tokens = new StringTokenizer(line);
for (j = 0; j <= varnumber; j++) {
targets[i][j] = Double.parseDouble(tokens.nextToken().trim());
}
}
in.close();
} catch (FileNotFoundException e) {
Write("ERROR: Please provide a data file");
//System.out.println("ERROR: Please provide a data file");
System.exit(0);
} catch (Exception e) {
Write("ERROR: Incorrect data format");
//System.out.println("ERROR: Incorrect data format");
System.exit(0);
}
}

public double fitness_function(char[] Prog) {
int i = 0, len;
double result, fit = 0.0;

len = traverse(Prog, 0);
for (i = 0; i < fitnesscases; i++) {
for (int j = 0; j < varnumber; j++) {
x[j] = targets[i][j];
}
program = Prog;
PC = 0;
result = run();
fit += Math.abs(result - targets[i][varnumber]);
}
return (-fit);
}

public int grow(char[] buffer, int pos, int max, int depth) {
char prim = (char) rd.nextInt(2);
int one_child;

if (pos >= max) {
return (-1);
}

if (pos == 0) {
prim = 1;
}

if (prim == 0 || depth == 0) {
prim = (char) rd.nextInt(varnumber + randomnumber);
buffer[pos] = prim;
return (pos + 1);
} else {
prim = (char) (rd.nextInt(FSET_END - FSET_START + 1) + FSET_START);
switch (prim) {
case ADD:
case SUB:
case MUL:
case DIV:
buffer[pos] = prim;
one_child = grow(buffer, pos + 1, max, depth - 1);
if (one_child < 0) {
return (-1);
}
return (grow(buffer, one_child, max, depth - 1));
}
}
return (0); // should never get here
}

public int print_indiv(char[] buffer, int buffercounter) {
int a1 = 0, a2;
if (buffer[buffercounter] < FSET_START) {
if (buffer[buffercounter] < varnumber) {
Write("X" + (buffer[buffercounter] + 1) + " ");
//System.out.print("X" + (buffer[buffercounter] + 1) + " ");
} else {
WriteDouble(x[buffer[buffercounter]]);
//System.out.print(x[buffer[buffercounter]]);
}
return (++buffercounter);
}
switch (buffer[buffercounter]) {
case ADD:
Write("(");
//System.out.print("(");
a1 = print_indiv(buffer, ++buffercounter);
Write(" + ");
//System.out.print(" + ");
break;
case SUB:
Write("(");
//System.out.print("(");
a1 = print_indiv(buffer, ++buffercounter);
Write(" - ");
//System.out.print(" - ");
break;
case MUL:
Write("(");
//System.out.print("(");
a1 = print_indiv(buffer, ++buffercounter);
Write(" * ");
//System.out.print(" * ");
break;
case DIV:
Write("(");
//System.out.print("(");
a1 = print_indiv(buffer, ++buffercounter);
Write(" / ");
//System.out.print(" / ");
break;
}
a2 = print_indiv(buffer, a1);
Write(")");
//System.out.print(")");
return (a2);
}

public static char[] buffer = new char[MAX_LEN];

public char[] create_random_indiv(int depth) {
char[] ind;
int len;

len = grow(buffer, 0, MAX_LEN, depth);

while (len < 0) {
len = grow(buffer, 0, MAX_LEN, depth);
}

ind = new char[len];

System.arraycopy(buffer, 0, ind, 0, len);
return (ind);
}

public char[][] create_random_pop(int n, int depth, double[] fitness) {
char[][] pop = new char[n][];
int i;

for (i = 0; i < n; i++) {
pop[i] = create_random_indiv(depth);
fitness[i] = fitness_function(pop[i]);
}
return (pop);
}

public void stats(double[] fitness, char[][] pop, int gen) {
int i, best = rd.nextInt(POPSIZE);
int node_count = 0;
fbestpop = fitness[best];
favgpop = 0.0;

for (i = 0; i < POPSIZE; i++) {
node_count += traverse(pop[i], 0);
favgpop += fitness[i];
if (fitness[i] > fbestpop) {
best = i;
fbestpop = fitness[i];
}
}
avg_len = (double) node_count / POPSIZE;
favgpop /= POPSIZE;
Write("Generation=" + gen + " Avg Fitness=" + (-favgpop)
+ " Best Fitness=" + (-fbestpop) + " Avg Size=" + avg_len
+ "\nBest Individual: ");
//System.out.print("Generation=" + gen + " Avg Fitness=" + (-favgpop)
// + " Best Fitness=" + (-fbestpop) + " Avg Size=" + avg_len
// + "\nBest Individual: ");
print_indiv(pop[best], 0);
Write("\n");
//System.out.print("\n");
//System.out.flush();
}

public int tournament(double[] fitness, int tsize) {
int best = rd.nextInt(POPSIZE), i, competitor;
double fbest = -1.0e34;

for (i = 0; i < tsize; i++) {
competitor = rd.nextInt(POPSIZE);
if (fitness[competitor] > fbest) {
fbest = fitness[competitor];
best = competitor;
}
}
return (best);
}

public int negative_tournament(double[] fitness, int tsize) {
int worst = rd.nextInt(POPSIZE), i, competitor;
double fworst = 1e34;

for (i = 0; i < tsize; i++) {
competitor = rd.nextInt(POPSIZE);
if (fitness[competitor] < fworst) {
fworst = fitness[competitor];
worst = competitor;
}
}
return (worst);
}

public char[] crossover(char[] parent1, char[] parent2) {
int xo1start, xo1end, xo2start, xo2end;
char[] offspring;
int len1 = traverse(parent1, 0);
int len2 = traverse(parent2, 0);
int lenoff;

xo1start = rd.nextInt(len1);
xo1end = traverse(parent1, xo1start);

xo2start = rd.nextInt(len2);
xo2end = traverse(parent2, xo2start);

lenoff = xo1start + (xo2end - xo2start) + (len1 - xo1end);

offspring = new char[lenoff];

System.arraycopy(parent1, 0, offspring, 0, xo1start);
System.arraycopy(parent2, xo2start, offspring, xo1start,
(xo2end - xo2start));
System.arraycopy(parent1, xo1end, offspring,
xo1start + (xo2end - xo2start),
(len1 - xo1end));

return (offspring);
}

public char[] mutation(char[] parent, double pmut) {
int len = traverse(parent, 0), i;
int mutsite;
char[] parentcopy = new char[len];

System.arraycopy(parent, 0, parentcopy, 0, len);
for (i = 0; i < len; i++) {
if (rd.nextDouble() < pmut) {
mutsite = i;
if (parentcopy[mutsite] < FSET_START) {
parentcopy[mutsite] = (char) rd.nextInt(varnumber + randomnumber);
} else {
switch (parentcopy[mutsite]) {
case ADD:
case SUB:
case MUL:
case DIV:
parentcopy[mutsite]
= (char) (rd.nextInt(FSET_END - FSET_START + 1)
+ FSET_START);
}
}
}
}
return (parentcopy);
}

public void print_parms() {
Write("-- TINY GP (Java version) --\n");
//System.out.print("-- TINY GP (Java version) --\n");
Write("SEED=" + seed + "\nMAX_LEN=" + MAX_LEN
+ "\nPOPSIZE=" + POPSIZE + "\nDEPTH=" + DEPTH
+ "\nCROSSOVER_PROB=" + CROSSOVER_PROB
+ "\nPMUT_PER_NODE=" + PMUT_PER_NODE
+ "\nMIN_RANDOM=" + minrandom
+ "\nMAX_RANDOM=" + maxrandom
+ "\nGENERATIONS=" + GENERATIONS
+ "\nTSIZE=" + TSIZE
+ "\n----------------------------------\n");
// System.out.print("SEED=" + seed + "\nMAX_LEN=" + MAX_LEN
// + "\nPOPSIZE=" + POPSIZE + "\nDEPTH=" + DEPTH
// + "\nCROSSOVER_PROB=" + CROSSOVER_PROB
// + "\nPMUT_PER_NODE=" + PMUT_PER_NODE
// + "\nMIN_RANDOM=" + minrandom
// + "\nMAX_RANDOM=" + maxrandom
// + "\nGENERATIONS=" + GENERATIONS
// + "\nTSIZE=" + TSIZE
// + "\n----------------------------------\n");
}

public tiny_gp(String fname, long s) {
fitness = new double[POPSIZE];
seed = s;
if (seed >= 0) {
rd.setSeed(seed);
}
setup_fitness(fname);
for (int i = 0; i < FSET_START; i++) {
x[i] = (maxrandom - minrandom) * rd.nextDouble() + minrandom;
}
pop = create_random_pop(POPSIZE, DEPTH, fitness);
}

public void evolve() {
int gen = 0, indivs, offspring, parent1, parent2, parent;
double newfit;
char[] newind;
print_parms();
stats(fitness, pop, 0);
for (gen = 1; gen < GENERATIONS; gen++) {
if (fbestpop > -1e-5) {
Write("PROBLEM SOLVED\n");
//System.out.print("PROBLEM SOLVED\n");
System.exit(0);
}
for (indivs = 0; indivs < POPSIZE; indivs++) {
if (rd.nextDouble() < CROSSOVER_PROB) {
parent1 = tournament(fitness, TSIZE);
parent2 = tournament(fitness, TSIZE);
newind = crossover(pop[parent1], pop[parent2]);
} else {
parent = tournament(fitness, TSIZE);
newind = mutation(pop[parent], PMUT_PER_NODE);
}
newfit = fitness_function(newind);
offspring = negative_tournament(fitness, TSIZE);
pop[offspring] = newind;
fitness[offspring] = newfit;
}
stats(fitness, pop, gen);
}
Write("PROBLEM *NOT* SOLVED\n");
//System.out.print("PROBLEM *NOT* SOLVED\n");
System.exit(1);
}

public void Write(String context) {

FileWriter fileWriter;
try {
fileWriter = new FileWriter("GP.txt");
try (BufferedWriter bufferedWriter = new BufferedWriter(fileWriter)) {
bufferedWriter.write(context);
}

} catch (IOException ex) {

}
}

public void WriteDouble(double context) {

FileWriter fileWriter;
try {
fileWriter = new FileWriter("GP.txt");
try (BufferedWriter bufferedWriter = new BufferedWriter(fileWriter)) {
String ncontext = Double.toString(context);
bufferedWriter.write(ncontext);
}

} catch (IOException ex) {

}
}
};


The Functions Mapper file that uses the Tiny GP class file:

package function_mapper;

import javax.swing.JOptionPane;
import main.*;

public class Function_Mapper {

public static void main(String[] args) {
String fname = JOptionPane.showInputDialog(null, "File Name", "Input Dialog", JOptionPane.INFORMATION_MESSAGE);
long s = -1;

if (args.length == 2) {
s = Integer.valueOf(args[0]).intValue();
fname = args[1];
}
if (args.length == 1) {
fname = args[0];
}

tiny_gp gp = new tiny_gp(fname, s);
gp.evolve();
}

}


Much help appreciated, thanks!

Answer

The Write method overwrites the contents of the file on each invocation. There are two ways to fix this.

An easier one, is to append file, instead of overwriting it. It could be achieved by passing append argument to the FileWriter (I simplified code a little bit along the way).

// true on the next line means "append"
try (Writer writer = new FileWriter("GP.txt", true)) { 
    writer.write(Double.toString(context));
} catch (IOException ex) {
}

A harder, but much fore efficient one is to openwriter in the constructor, use it in Write method, and close in the specially introduced close method of the tiny_gp.

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