/*
* Encog(tm) Core v3.4 - Java Version
* http://www.heatonresearch.com/encog/
* https://github.com/encog/encog-java-core
* Copyright 2008-2016 Heaton Research, Inc.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
* For more information on Heaton Research copyrights, licenses
* and trademarks visit:
* http://www.heatonresearch.com/copyright
*/
package org.encog.ml.prg;
import java.io.InputStream;
import java.io.OutputStream;
import java.util.List;
import java.util.Map;
import org.encog.EncogError;
import org.encog.ml.ea.genome.Genome;
import org.encog.ml.ea.species.BasicSpecies;
import org.encog.ml.ea.species.Species;
import org.encog.ml.prg.expvalue.ValueType;
import org.encog.ml.prg.extension.ProgramExtensionTemplate;
import org.encog.ml.prg.train.PrgPopulation;
import org.encog.persist.EncogFileSection;
import org.encog.persist.EncogPersistor;
import org.encog.persist.EncogReadHelper;
import org.encog.persist.EncogWriteHelper;
import org.encog.util.csv.CSVFormat;
/**
* Persist the Encog population.
*/
public class PersistPrgPopulation implements EncogPersistor {
/**
* {@inheritDoc}
*/
@Override
public int getFileVersion() {
return 1;
}
/**
* {@inheritDoc}
*/
@Override
public String getPersistClassString() {
return "PrgPopulation";
}
/**
* Get the type string for the specified variable mapping.
*
* @param mapping
* The mapping.
* @return The value.
*/
private String getType(final VariableMapping mapping) {
switch (mapping.getVariableType()) {
case floatingType:
return "f";
case stringType:
return "s";
case booleanType:
return "b";
case intType:
return "i";
case enumType:
return "e";
}
throw new EncogError("Unknown type: "
+ mapping.getVariableType().toString());
}
/**
* {@inheritDoc}
*/
@Override
public Object read(final InputStream is) {
final EncogProgramContext context = new EncogProgramContext();
final PrgPopulation result = new PrgPopulation(context, 0);
final EncogReadHelper in = new EncogReadHelper(is);
EncogFileSection section;
int count = 0;
Species lastSpecies = null;
while ((section = in.readNextSection()) != null) {
if (section.getSectionName().equals("BASIC")
&& section.getSubSectionName().equals("PARAMS")) {
final Map<String, String> params = section.parseParams();
result.getProperties().putAll(params);
} else if (section.getSectionName().equals("BASIC")
&& section.getSubSectionName().equals("EPL-POPULATION")) {
for (final String line : section.getLines()) {
final List<String> cols = EncogFileSection
.splitColumns(line);
if (cols.get(0).equalsIgnoreCase("s")) {
lastSpecies = new BasicSpecies();
lastSpecies.setAge(Integer.parseInt(cols.get(1)));
lastSpecies.setBestScore(CSVFormat.EG_FORMAT.parse(cols
.get(2)));
lastSpecies.setPopulation(result);
lastSpecies.setGensNoImprovement(Integer.parseInt(cols
.get(3)));
result.getSpecies().add(lastSpecies);
} else if (cols.get(0).equalsIgnoreCase("p")) {
double score = 0;
double adjustedScore = 0;
if (cols.get(1).equalsIgnoreCase("nan")
|| cols.get(2).equalsIgnoreCase("nan")) {
score = Double.NaN;
adjustedScore = Double.NaN;
} else {
score = CSVFormat.EG_FORMAT.parse(cols.get(1));
adjustedScore = CSVFormat.EG_FORMAT.parse(cols
.get(2));
}
final String code = cols.get(3);
final EncogProgram prg = new EncogProgram(context);
prg.compileEPL(code);
prg.setScore(score);
prg.setSpecies(lastSpecies);
prg.setAdjustedScore(adjustedScore);
if (lastSpecies == null) {
throw new EncogError(
"Have not defined a species yet");
} else {
lastSpecies.add(prg);
}
count++;
}
}
} else if (section.getSectionName().equals("BASIC")
&& section.getSubSectionName().equals("EPL-OPCODES")) {
for (final String line : section.getLines()) {
final List<String> cols = EncogFileSection
.splitColumns(line);
final String name = cols.get(0);
final int args = Integer.parseInt(cols.get(1));
result.getContext().getFunctions().addExtension(name, args);
}
} else if (section.getSectionName().equals("BASIC")
&& section.getSubSectionName().equals("EPL-SYMBOLIC")) {
boolean first = true;
for (final String line : section.getLines()) {
if (!first) {
final List<String> cols = EncogFileSection
.splitColumns(line);
final String name = cols.get(0);
final String t = cols.get(1);
ValueType vt = null;
if (t.equalsIgnoreCase("f")) {
vt = ValueType.floatingType;
} else if (t.equalsIgnoreCase("b")) {
vt = ValueType.booleanType;
} else if (t.equalsIgnoreCase("i")) {
vt = ValueType.intType;
} else if (t.equalsIgnoreCase("s")) {
vt = ValueType.stringType;
} else if (t.equalsIgnoreCase("e")) {
vt = ValueType.enumType;
}
final int enumType = Integer.parseInt(cols.get(2));
final int enumCount = Integer.parseInt(cols.get(3));
final VariableMapping mapping = new VariableMapping(
name, vt, enumType, enumCount);
if (mapping.getName().length() > 0) {
result.getContext().defineVariable(mapping);
} else {
result.getContext().setResult(mapping);
}
} else {
first = false;
}
}
}
}
result.setPopulationSize(count);
// set the best genome, should be the first genome in the first species
if (result.getSpecies().size() > 0) {
final Species species = result.getSpecies().get(0);
if (species.getMembers().size() > 0) {
result.setBestGenome(species.getMembers().get(0));
}
// set the leaders
for (final Species sp : result.getSpecies()) {
if (sp.getMembers().size() > 0) {
sp.setLeader(sp.getMembers().get(0));
}
}
}
return result;
}
/**
* {@inheritDoc}
*/
@Override
public void save(final OutputStream os, final Object obj) {
final EncogWriteHelper out = new EncogWriteHelper(os);
final PrgPopulation pop = (PrgPopulation) obj;
out.addSection("BASIC");
out.addSubSection("PARAMS");
out.addProperties(pop.getProperties());
out.addSubSection("EPL-OPCODES");
for (final ProgramExtensionTemplate temp : pop.getContext()
.getFunctions().getOpCodes()) {
out.addColumn(temp.getName());
out.addColumn(temp.getChildNodeCount());
out.writeLine();
}
out.addSubSection("EPL-SYMBOLIC");
out.addColumn("name");
out.addColumn("type");
out.addColumn("enum");
out.addColumn("enum_type");
out.addColumn("enum_count");
out.writeLine();
// write the first line, the result
out.addColumn("");
out.addColumn(getType(pop.getContext().getResult()));
out.addColumn(pop.getContext().getResult().getEnumType());
out.addColumn(pop.getContext().getResult().getEnumValueCount());
out.writeLine();
// write the next lines, the variables
for (final VariableMapping mapping : pop.getContext()
.getDefinedVariables()) {
out.addColumn(mapping.getName());
out.addColumn(getType(mapping));
out.addColumn(mapping.getEnumType());
out.addColumn(mapping.getEnumValueCount());
out.writeLine();
}
out.addSubSection("EPL-POPULATION");
for (final Species species : pop.getSpecies()) {
if (species.getMembers().size() > 0) {
out.addColumn("s");
out.addColumn(species.getAge());
out.addColumn(species.getBestScore());
out.addColumn(species.getGensNoImprovement());
out.writeLine();
for (final Genome genome : species.getMembers()) {
final EncogProgram prg = (EncogProgram) genome;
out.addColumn("p");
if (Double.isInfinite(prg.getScore())
|| Double.isNaN(prg.getScore())) {
out.addColumn("NaN");
out.addColumn("NaN");
} else {
out.addColumn(prg.getScore());
out.addColumn(prg.getAdjustedScore());
}
out.addColumn(prg.generateEPL());
out.writeLine();
}
}
}
out.flush();
}
}