public void analyze() throws Exception {
HashMap<String, ArrayList<String>> outputDataPaths = new HashMap<String, ArrayList<String>>();
File outDir = new File(_outputPath);
File reportDir = new File(_reportPath);
if (!reportDir.exists()) reportDir.mkdirs();
FilenameFilter filter =
new FilenameFilter() {
public boolean accept(File arg0, String arg1) {
if (arg1.equals(".svn")) return false;
else return true;
}
};
// delete all in Statistics directory
for (String s : reportDir.list(filter)) new File(_reportPath + "/" + s).delete();
DataNode report = new DataNode("report");
// list all Output|s directories
for (String s : outDir.list(filter)) {
String config = _outputPath + "/" + s + "/config.xml";
if (new File(config).exists()) {
List<DataNode> runs =
processDirectorySet(
new File(_outputPath + "/" + s).listFiles(), _outputPath, _reportPath, s);
DataNode batch = new DataNode("batch");
for (DataNode dn : runs) batch.putDataNode(dn);
batch.putValue("id", s);
String[] date = s.split("-");
batch.putValue("date", date[0] + "-" + date[1]);
batch.putDataNode(XmlHelper.readXml(new File(config)));
report.putDataNode(batch);
}
}
XmlHelper.writeXml(report, _reportPath + "/report.xml");
TransformerFactory tFactory = TransformerFactory.newInstance();
Transformer transformer =
tFactory.newTransformer(
new javax.xml.transform.stream.StreamSource(
getClass().getResourceAsStream("report.xsl")));
transformer.transform(
new javax.xml.transform.stream.StreamSource(_reportPath + "/report.xml"),
new javax.xml.transform.stream.StreamResult(
new FileOutputStream(_reportPath + "/report.html")));
}
public void runFromConfigFile(String configPath) throws Exception {
ProblemConfig config = new ProblemConfig(XmlHelper.readXml(new File(configPath)));
String problemID = config.getDataNode("Problem").getValueStr("id");
String algorithmID = config.getDataNode("Algorithm").getValueStr("id");
// provider and factory
IProblemProvider provider = ProblemProvider.getProblemProviders().get(problemID);
IAlgorithmFactory factory = provider.getAlgorithmFactory(algorithmID);
// problem instance
ProblemInstanceInfo instance = provider.initProblemInstance(config);
// algorithm
IAlgorithmAdapter algorithm = factory.createAlgorithm(instance, config);
AlgorithmParams algNode = config.getAlgorithmParams();
Object[][] solutions =
provider.generateInitialSolutions(
algNode.getDataNode("Parameters").getValueInt("numSolutions"), instance);
System.out.printf("%s: %4s %s\n", "Problem", "", problemID);
System.out.printf("%s: %2s %s\n", "Algorithm", "", algorithmID);
System.out.printf("%s: %3s %s\n", "Instance", "", instance);
System.out.println("Running ...");
algorithm.solutionsFromPhenotype(solutions);
algorithm.setParameters(algNode);
algorithm.startSearching();
solutions = algorithm.solutionsToPhenotype();
// phenotype evaluator
IPhenotypeEvaluator evaluator = provider.initPhenotypeEvaluator();
double[] result = evaluator.evaluate(solutions[0], instance);
System.out.printf("%s: %5s %s\n", "Result", "", result[0]);
// System.out.println(": " + result[0]);
System.out.printf("%s: %3s ", "Solution", "");
for (int i = 0; i < solutions[0].length; i++) System.out.print(solutions[0][i] + " ");
System.out.println();
AlgorithmReport report = algorithm.getReport();
report.save("output/" + System.currentTimeMillis() + ".xml");
}
private List<DataNode> processDirectorySet(
File[] files, String destDirPath, String reportFileName, String hash) throws Exception {
HashMap<String, List<Double>> _fitnesses = new HashMap<String, List<Double>>();
for (File d : files) {
if (!d.isDirectory()) continue;
File problemXml = new File(d.getPath() + "/Problem.xml");
if (problemXml.exists()) {
DataNode data = XmlHelper.readXml(problemXml);
List<DataNode> solList = data.getDataNodes("Solution");
if (solList.size() > 0) {
double fitness = solList.get(solList.size() - 1).getValueDouble("fitness");
String instance = data.getValueStr("instance");
if (!_fitnesses.containsKey(instance)) _fitnesses.put(instance, new ArrayList<Double>());
_fitnesses.get(instance).add(fitness);
}
}
}
ArrayList<DataNode> runSet = new ArrayList<DataNode>();
for (String in : _fitnesses.keySet()) {
DataNode run = new DataNode("run");
run.putValue("instance", in);
Pattern p = Pattern.compile("^[a-zA-Z]+([0-9]+).*");
Matcher m = p.matcher(in);
if (m.find()) {
run.putValue("size", m.group(1));
}
run.putDataNode(new DataNode("stats"));
DataNode stats = run.getDataNode("stats");
double fitness = 0;
double fitness2 = 0;
double min = Integer.MAX_VALUE;
double max = Integer.MIN_VALUE;
int numSolutions = 0;
for (Double f : _fitnesses.get(in)) {
fitness += f;
fitness2 += f * f;
if (f < min) min = f;
if (f > max) max = f;
numSolutions++;
}
stats.putValue("minFitness", min);
stats.putValue("avgFitness", fitness / numSolutions);
stats.putValue(
"devFitness",
Math.sqrt(fitness2 / numSolutions - Math.pow(stats.getValueDouble("avgFitness"), 2)));
stats.putValue(
"cfvFitness", stats.getValueDouble("devFitness") / stats.getValueDouble("avgFitness"));
stats.putValue("maxFitness", max);
stats.putValue("numOfRuns", numSolutions);
runSet.add(run);
// XmlHelper.writeXml(run, destDirPath+"/"+reportFileName+".xml");
}
return runSet;
}
