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package jcgp.backend.parsers;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.PrintWriter;
import java.util.Scanner;
import jcgp.backend.population.Chromosome;
import jcgp.backend.population.Connection;
import jcgp.backend.population.Input;
import jcgp.backend.population.Node;
import jcgp.backend.resources.Resources;
/**
* This class contains a method for parsing .chr files and another
* for writing .chr files from given chromosomes.
*
* @author Eduardo Pedroni
*
*/
public abstract class ChromosomeParser {
/**
* Use this method to parse .chr files into a given chromosome.
* <br><br>
* This is not fully defensive as it doesn't check for number of inputs,
* doesn't compare rows and columns individually and doesn't account for levels back. It
* is not viable to implement these defensive measures with the chromosome format used
* by CGP.
*
* @param file the .chr file to parse from.
* @param chromosome the chromosome to configure.
* @param resources the experiment resources.
*/
public static void parse(File file, Chromosome chromosome, Resources resources) {
/*
* Count the nodes to make sure the size of the .chr file matches the experiment parameters.
*
* We do this by using the scanner to get the node and output portions of the file as they
* are separated by 3 tab characters. Every number is replaced by a single known character,
* and the length of the string with the new characters is compared with that of a string
* where the new known character has been removed, yielding the total number of values.
*
* TODO this is NOT ideal and should be refactored
*
*/
FileReader fr;
try {
fr = new FileReader(file);
} catch (FileNotFoundException e) {
resources.println("[Parser] Error: could not find " + file.getAbsolutePath());
return;
}
Scanner in = new Scanner(fr);
in.useDelimiter("\\t\\t\\t");
String geneString = in.next().replaceAll("[0-9]+", "g");
String outString = in.next().replaceAll("[0-9]+", "o");
int geneCount = geneString.length() - geneString.replace("g", "").length();
int outCount = outString.length() - outString.replace("o", "").length();
in.close();
// if the acquired values match the current parameters, apply them to the chromosome
if ((geneCount == resources.nodes() * (resources.arity() + 1))
&& outCount == resources.outputs()) {
// prepare a new scanner
try {
fr = new FileReader(file);
} catch (FileNotFoundException e) {
resources.println("[Parser] Error: could not find " + file.getAbsolutePath());
return;
}
in = new Scanner(fr);
resources.println("[Parser] Parsing file: " + file.getAbsolutePath() + "...");
int gene;
Connection newConnection;
Node changingNode;
// for all nodes, columns first
for (int c = 0; c < resources.columns(); c++) {
for (int r = 0; r < resources.rows(); r++) {
// store the changing node
changingNode = chromosome.getNode(r, c);
// for every connection
for (int i = 0; i < resources.arity(); i++) {
// get connection number from the .chr file
gene = in.nextInt();
if (gene < resources.inputs()) {
// connection was an input
newConnection = chromosome.getInput(gene);
} else {
// connection was another node, calculate which from its number
newConnection = chromosome.getNode((gene - resources.inputs()) % resources.rows(),
(gene - resources.inputs()) / resources.rows());
}
changingNode.setConnection(i, newConnection);
}
// set the function, straight indexing should work - this is not entirely
// safe, but it is not viable to check for functionset compatibility
changingNode.setFunction(resources.getFunction(in.nextInt()));
}
}
// outputs
for (int o = 0; o < resources.outputs(); o ++) {
gene = in.nextInt();
if (gene < resources.inputs()) {
// connection was an input
newConnection = chromosome.getInput(gene);
} else {
// connection was another node, calculate which from its number
newConnection = chromosome.getNode((gene - resources.inputs()) % resources.rows(),
(gene - resources.inputs()) / resources.rows());
}
chromosome.getOutput(o).setSource(newConnection);
}
in.close();
resources.println("[Parser] File parsed successfully");
} else {
resources.println("[Parser] Error: the number of genes of the chromosome in " + file.getName() + " does not match that of the experiment");
}
}
/**
* Writes a chromosome into the specified .chr file.
* <br><br>
* The file is written in the standard .chr format and can
* be read by the original CGP implementation.
*
* @param file the file to write to.
* @param chromosome the chromosome to save.
* @param resources a reference to the experiment's resources.
*/
public static void save(File file, Chromosome chromosome, Resources resources) {
PrintWriter writer;
try {
writer = new PrintWriter(file);
} catch (FileNotFoundException e) {
resources.println("[Parser] Error: could not find " + file.getAbsolutePath());
return;
}
resources.println("[Parser] Saving to " + file.getAbsolutePath() + "...");
// for all nodes, columns first
for (int c = 0; c < resources.columns(); c++) {
for (int r = 0; r < resources.rows(); r++) {
for (int i = 0; i < resources.arity(); i++) {
// print the connections, separated by spaces
Connection conn = chromosome.getNode(r, c).getConnection(i);
if (conn instanceof Input) {
writer.print(" " + ((Input) conn).getIndex());
} else if (conn instanceof Node) {
writer.print(" " + (((((Node) conn).getColumn() + 1) * resources.inputs()) + ((Node) conn).getRow()));
} else {
resources.println("[Parser] Error: could not handle " + conn.getClass() + " as a subclass of Connection");
}
}
// print the function numbers
writer.print(" " + resources.getFunctionIndex(chromosome.getNode(r, c).getFunction()));
// node is done, print tab
writer.print("\t");
}
}
// nodes are done, print two tabs to separate from output
writer.print("\t\t");
for (int o = 0; o < resources.outputs(); o ++) {
Connection source = chromosome.getOutput(o).getSource();
if (source instanceof Input) {
writer.print(" " + ((Input) source).getIndex());
} else if (source instanceof Node) {
writer.print(" " + (((((Node) source).getColumn() + 1) * resources.inputs()) + ((Node) source).getRow()));
} else {
resources.println("[Parser] Error: could not handle " + source.getClass() + " as a subclass of Connection");
}
}
writer.close();
resources.println("[Parser] Chromosome saved successfully");
}
/**
* Writes a chromosome to the console in .chr format. Note
* that, if using a GUI console, that console must be flushed for the
* output to appear.
*
* @param chromosome the chromosome to save.
* @param resources a reference to the experiment's resources.
*/
public static void print(Chromosome chromosome, Resources resources) {
// for all nodes, columns first
for (int c = 0; c < resources.columns(); c++) {
for (int r = 0; r < resources.rows(); r++) {
for (int i = 0; i < resources.arity(); i++) {
// print the connections, separated by spaces
Connection conn = chromosome.getNode(r, c).getConnection(i);
if (conn instanceof Input) {
resources.print(" " + ((Input) conn).getIndex());
} else if (conn instanceof Node) {
resources.print(" " + (((((Node) conn).getColumn() + 1) * resources.inputs()) + ((Node) conn).getRow()));
} else {
resources.println("[Parser] Error: could not handle " + conn.getClass() + " as a subclass of Connection");
}
}
// print the function numbers
resources.print(" " + resources.getFunctionIndex(chromosome.getNode(r, c).getFunction()));
// node is done, print tab
resources.print("\t");
}
}
// nodes are done, print two tabs to separate from output
resources.print("\t\t");
for (int o = 0; o < resources.outputs(); o ++) {
Connection source = chromosome.getOutput(o).getSource();
if (source instanceof Input) {
resources.print(" " + ((Input) source).getIndex());
} else if (source instanceof Node) {
resources.print(" " + (((((Node) source).getColumn() + 1) * resources.inputs()) + ((Node) source).getRow()));
} else {
resources.println("[Parser] Error: could not handle " + source.getClass() + " as a subclass of Connection");
}
}
resources.println("");
}
}
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