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Complete Yaml output for CLI mode.

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Cleanup of AbstractStatistics
This commit is contained in:
Fabian Becker 2014-11-14 11:32:05 +01:00
parent 2e1f862718
commit 553002c834
2 changed files with 59 additions and 65 deletions
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57
src/eva2/cli/Main.java
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@ -13,15 +13,13 @@ import eva2.optimization.statistics.InterfaceTextListener;
import eva2.optimization.strategies.InterfaceOptimizer; import eva2.optimization.strategies.InterfaceOptimizer;
import eva2.problems.InterfaceAdditionalPopulationInformer; import eva2.problems.InterfaceAdditionalPopulationInformer;
import eva2.problems.InterfaceOptimizationProblem; import eva2.problems.InterfaceOptimizationProblem;
import org.yaml.snakeyaml.DumperOptions;
import org.yaml.snakeyaml.Yaml;
import java.io.BufferedWriter;
import java.io.FileWriter;
import java.io.IOException;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.LinkedHashMap; import java.util.LinkedHashMap;
import java.util.List; import java.util.List;
import java.util.Map; import java.util.Map;
import java.util.logging.Logger;
/** /**
* *
@ -38,35 +36,38 @@ public class Main {
LinkedHashMap<String, Object> optimizationLog = new LinkedHashMap<>(); LinkedHashMap<String, Object> optimizationLog = new LinkedHashMap<>();
// Meta parameters // Meta parameters
optimizationLog.put("population_size", parameters.getOptimizer().getPopulation().getTargetSize()); optimizationLog.put("populationSize", parameters.getOptimizer().getPopulation().getTargetSize());
optimizationLog.put("number_of_runs", statisticsParameters.getMultiRuns()); optimizationLog.put("numberOfRuns", statisticsParameters.getMultiRuns());
optimizationLog.put("seed", parameters.getRandomSeed()); optimizationLog.put("seed", parameters.getRandomSeed());
// Container for individual runs YamlStatistics yamlStatistics = new YamlStatistics(statisticsParameters);
List<LinkedHashMap<String, Object>> runs = new ArrayList<>();
optimizationLog.put("runs", runs);
FileWriter fw; /**
BufferedWriter bw = null; * Runs optimization
try { */
fw = new FileWriter("derp.yml"); Processor optimizationProcessor = new Processor(yamlStatistics, parameters);
bw = new BufferedWriter(fw);
} catch (IOException ex) {
System.out.println(ex.getMessage());
System.exit(0);
}
Processor optimizationProcessor = new Processor(new YamlStatistics(statisticsParameters), parameters);
optimizationProcessor.setSaveParams(false); optimizationProcessor.setSaveParams(false);
optimizationProcessor.startOptimization(); optimizationProcessor.startOptimization();
optimizationProcessor.runOptimizationOnce(); optimizationProcessor.runOptimizationOnce();
/**
* Get run statistics
*/
optimizationLog.put("runs", yamlStatistics.getRuns());
/**
* Yaml configuration
*/
DumperOptions options = new DumperOptions();
options.setExplicitStart(true);
options.setExplicitEnd(true);
Yaml yaml = new Yaml();
System.out.println(yaml.dump(optimizationLog));
} }
} }
final class YamlStatistics implements InterfaceStatistics { final class YamlStatistics implements InterfaceStatistics {
private static final Logger LOGGER = Logger.getLogger(YamlStatistics.class.getName());
private InterfaceStatisticsParameters statisticsParameters; private InterfaceStatisticsParameters statisticsParameters;
private List<LinkedHashMap<String, Object>> runs; private List<LinkedHashMap<String, Object>> runs;
private LinkedHashMap<String, Object> currentRun; private LinkedHashMap<String, Object> currentRun;
@ -127,10 +128,10 @@ final class YamlStatistics implements InterfaceStatistics {
@Override @Override
public void createNextGenerationPerformed(PopulationInterface pop, InterfaceOptimizer opt, List<InterfaceAdditionalPopulationInformer> informerList) { public void createNextGenerationPerformed(PopulationInterface pop, InterfaceOptimizer opt, List<InterfaceAdditionalPopulationInformer> informerList) {
LinkedHashMap<String, Object> generation = new LinkedHashMap<>(); LinkedHashMap<String, Object> generation = new LinkedHashMap<>();
generation.put("bestFitness", pop.getBestFitness());
generation.put("meanFitness", pop.getMeanFitness());
generation.put("functionCalls", pop.getFunctionCalls());
generation.put("generation", currentGeneration); generation.put("generation", currentGeneration);
generation.put("bestFitness", pop.getBestFitness().clone());
generation.put("meanFitness", pop.getMeanFitness().clone());
generation.put("functionCalls", pop.getFunctionCalls());
this.currentGenerations.add(generation); this.currentGenerations.add(generation);
this.currentGeneration++; this.currentGeneration++;
} }
@ -159,4 +160,8 @@ final class YamlStatistics implements InterfaceStatistics {
public void postProcessingPerformed(Population resultPop) { public void postProcessingPerformed(Population resultPop) {
} }
public List<LinkedHashMap<String, Object>> getRuns() {
return this.runs;
}
} }

67
src/eva2/optimization/statistics/AbstractStatistics.java
View File

@ -21,6 +21,8 @@ import java.io.PrintWriter;
import java.text.SimpleDateFormat; import java.text.SimpleDateFormat;
import java.util.*; import java.util.*;
import java.util.concurrent.CopyOnWriteArraySet; import java.util.concurrent.CopyOnWriteArraySet;
import java.util.logging.Level;
import java.util.logging.Logger;
/** /**
* An abstract class handling statistics. Most important stuff happens in startOptimizationPerformed, stopOptimizationPerformed * An abstract class handling statistics. Most important stuff happens in startOptimizationPerformed, stopOptimizationPerformed
@ -43,6 +45,7 @@ import java.util.concurrent.CopyOnWriteArraySet;
* Listeners implementing InterfaceStatisticsListener receive the raw data per iteration. * Listeners implementing InterfaceStatisticsListener receive the raw data per iteration.
*/ */
public abstract class AbstractStatistics implements InterfaceTextListener, InterfaceStatistics { public abstract class AbstractStatistics implements InterfaceTextListener, InterfaceStatistics {
private static final Logger LOGGER = Logger.getLogger(AbstractStatistics.class.getName());
private transient PrintWriter resultOut; private transient PrintWriter resultOut;
protected InterfaceStatisticsParameters statisticsParameter; protected InterfaceStatisticsParameters statisticsParameter;
@ -181,14 +184,13 @@ public abstract class AbstractStatistics implements InterfaceTextListener, Inter
/** /**
* Collect start date and time of the run and if indicated, open a file output stream. * Collect start date and time of the run and if indicated, open a file output stream.
* *
* @param infoString * @param infoString Info string for the optimization run
*/ */
protected void initializeOutput(String infoString) { protected void initializeOutput(String infoString) {
String startDate = getDateString(); String startDate = getDateString();
// open the result file: // open the result file:
if (doFileOutput() // not "text-window only" if (doFileOutput() // not "text-window only"
&& (statisticsParameter.getOutputVerbosity() != InterfaceStatisticsParameters.OutputVerbosity.NONE)) { // verbosity accordingly high && (statisticsParameter.getOutputVerbosity() != InterfaceStatisticsParameters.OutputVerbosity.NONE)) { // verbosity accordingly high
//!resFName.equalsIgnoreCase("none") && !resFName.equals("")) {
String fnameBase = makeOutputFileName(statisticsParameter.getResultFilePrefix(), infoString, startDate); String fnameBase = makeOutputFileName(statisticsParameter.getResultFilePrefix(), infoString, startDate);
int cnt = 0; int cnt = 0;
String fname = fnameBase; String fname = fnameBase;
@ -199,10 +201,8 @@ public abstract class AbstractStatistics implements InterfaceTextListener, Inter
try { try {
resultOut = new PrintWriter(new FileOutputStream(fname)); resultOut = new PrintWriter(new FileOutputStream(fname));
} catch (Exception e) { } catch (Exception e) {
e.printStackTrace(); LOGGER.log(Level.WARNING, "Error while opening log file", e);
System.out.println("Error: " + e);
} }
resultOut.println("StartDate:" + startDate);
} else { } else {
resultOut = null; resultOut = null;
} }
@ -211,10 +211,10 @@ public abstract class AbstractStatistics implements InterfaceTextListener, Inter
/** /**
* Return a simple String describing the current date and time. * Return a simple String describing the current date and time.
* *
* @return * @return A string containing current date and time
*/ */
public static String getDateString() { public static String getDateString() {
SimpleDateFormat formatter = new SimpleDateFormat("E'_'yyyy.MM.dd'_at_'HH.mm.ss"); SimpleDateFormat formatter = new SimpleDateFormat("yyyy-MM-dd_HH.mm.ss");
return formatter.format(new Date()); return formatter.format(new Date());
} }
@ -223,14 +223,14 @@ public abstract class AbstractStatistics implements InterfaceTextListener, Inter
} }
private String makeOutputFileName(String prefix, String infoString, String startDate) { private String makeOutputFileName(String prefix, String infoString, String startDate) {
return (prefix + "_" + infoString).replace(' ', '_') + "_" + startDate + ".txt"; return (prefix + "_" + infoString).replace(' ', '_') + "_" + startDate + ".log";
} }
/** /**
* If set to true, before every run the parameters will be stored to a file at the start * If set to true, before every run the parameters will be stored to a file at the start
* of each run. Default is true. * of each run. Default is true.
* *
* @param doSave * @param doSave Whether to save a serialized version of the optimization parameters or not.
*/ */
public void setSaveParams(boolean doSave) { public void setSaveParams(boolean doSave) {
saveParams = doSave; saveParams = doSave;
@ -307,7 +307,7 @@ public abstract class AbstractStatistics implements InterfaceTextListener, Inter
@Override @Override
public void stopOptimizationPerformed(boolean normal, String stopMessage) { public void stopOptimizationPerformed(boolean normal, String stopMessage) {
if (lastSols == null) { if (lastSols == null) {
System.err.println("WARNING, possibly there was no call to createNextGenerationPerformed before calling stopOptimizationPerformed (AbstractStatistics)."); LOGGER.warning("WARNING, possibly there was no call to createNextGenerationPerformed before calling stopOptimizationPerformed (AbstractStatistics).");
} }
if (iterationCounter < sumDataCollection.size()) { if (iterationCounter < sumDataCollection.size()) {
@ -377,9 +377,6 @@ public abstract class AbstractStatistics implements InterfaceTextListener, Inter
if (!printRunStoppedVerbosity() && printFinalVerbosity()) { if (!printRunStoppedVerbosity() && printFinalVerbosity()) {
printToTextListener("."); printToTextListener(".");
} }
// if (currentBestFit!= null) {
// if (printRunStoppedVerbosity()) printToTextListener(" Best Fitness: " + BeanInspector.toString(currentBestFit) + "\n");
// }
fireDataListenersStartStop(optRunsPerformed, normal, false); fireDataListenersStartStop(optRunsPerformed, normal, false);
} }
@ -406,9 +403,6 @@ public abstract class AbstractStatistics implements InterfaceTextListener, Inter
private PopulationInterface makeStatsPop() { private PopulationInterface makeStatsPop() {
Population pop = new Population(1); Population pop = new Population(1);
// if (bestCurrentIndy!=null) pop.add(bestCurrentIndy);
// if (bestOfRunIndy!=null) pop.add(bestOfRunIndy);
// if (bestOfRunFeasibleIndy!=null) pop.add(bestOfRunFeasibleIndy);
if (bestIndyAllRuns != null) { if (bestIndyAllRuns != null) {
pop.add(bestIndyAllRuns); pop.add(bestIndyAllRuns);
} }
@ -434,19 +428,19 @@ public abstract class AbstractStatistics implements InterfaceTextListener, Inter
/** /**
* Calculate the mean fitness of final best individuals over the last series of multi-runs. * Calculate the mean fitness of final best individuals over the last series of multi-runs.
* *
* @return * @return Mean fitness
*/ */
public double[] getMeanBestFit(boolean requireFeasible) { public double[] getMeanBestFitness(boolean requireFeasible) {
return calcMeanFit(requireFeasible ? runBestFeasibleList : runBestFitList); return calculateMeanFitness(requireFeasible ? runBestFeasibleList : runBestFitList);
} }
/** /**
* Calculate the median fitness of final best individuals over the last series of multi-runs. * Calculate the median fitness of final best individuals over the last series of multi-runs.
* *
* @return * @return Median fitness
*/ */
public double[] getMedianBestFit(boolean requireFeasible) { public double[] getMedianBestFitness(boolean requireFeasible) {
return calcMedianFit(requireFeasible ? runBestFeasibleList : runBestFitList); return calculateMedianFitness(requireFeasible ? runBestFeasibleList : runBestFitList);
} }
protected void finalizeOutput() { protected void finalizeOutput() {
@ -476,7 +470,6 @@ public abstract class AbstractStatistics implements InterfaceTextListener, Inter
printToTextListener(textFieldDelimiter + (lastSum[i] / optRunsPerformed)); printToTextListener(textFieldDelimiter + (lastSum[i] / optRunsPerformed));
} }
} }
// for (int i=0; i<lastAdditionalInfoSums.length; i++) if (lastAdditionalInfoSums[i]!=null) printToTextListener(" \t"+(lastAdditionalInfoSums[i]/optRunsPerformed));
printToTextListener("\n"); printToTextListener("\n");
} }
@ -490,25 +483,25 @@ public abstract class AbstractStatistics implements InterfaceTextListener, Inter
if (optRunsPerformed > 1) { if (optRunsPerformed > 1) {
if (runBestFitList.size() > 0) { if (runBestFitList.size() > 0) {
if (printFinalVerbosity()) { if (printFinalVerbosity()) {
double[] meanBestFit = getMeanBestFit(false); double[] meanBestFit = getMeanBestFitness(false);
printToTextListener(" MultiRun stats: Mean best fitness: " + BeanInspector.toString(meanBestFit) + "\n"); printToTextListener(" MultiRun stats: Mean best fitness: " + BeanInspector.toString(meanBestFit) + "\n");
if (meanBestFit.length == 1) { if (meanBestFit.length == 1) {
printToTextListener(" MultiRun stats: Variance/Std.Dev.: " + BeanInspector.toString(calcStdDevVar(runBestFitList, meanBestFit[0])) + "\n"); printToTextListener(" MultiRun stats: Variance/Std.Dev.: " + BeanInspector.toString(calcStdDevVar(runBestFitList, meanBestFit[0])) + "\n");
} }
printToTextListener(" MultiRun stats: Median best fitn.: " + BeanInspector.toString(getMedianBestFit(false)) + "\n"); printToTextListener(" MultiRun stats: Median best fitn.: " + BeanInspector.toString(getMedianBestFitness(false)) + "\n");
} }
} }
if (printFinalVerbosity() && (bestFeasibleAllRuns != null)) { if (printFinalVerbosity() && (bestFeasibleAllRuns != null)) {
printIndy("Overall best feasible", bestFeasibleAllRuns); printIndy("Overall best feasible", bestFeasibleAllRuns);
} }
if (runBestFeasibleList.size() > 0) { // always output feasible stats even if theyre equal if (runBestFeasibleList.size() > 0) { // always output feasible stats even if they're equal
if (printFinalVerbosity()) { if (printFinalVerbosity()) {
double[] meanBestFeasibleFit = getMeanBestFit(true); double[] meanBestFeasibleFit = getMeanBestFitness(true);
printToTextListener(" MultiRun stats: Mean best feasible fitness (" + numOfRunsFeasibleFound + " runs): " + BeanInspector.toString(meanBestFeasibleFit) + "\n"); printToTextListener(" MultiRun stats: Mean best feasible fitness (" + numOfRunsFeasibleFound + " runs): " + BeanInspector.toString(meanBestFeasibleFit) + "\n");
if (meanBestFeasibleFit.length == 1) { if (meanBestFeasibleFit.length == 1) {
printToTextListener(" MultiRun stats: Variance/Std.Dev.: " + BeanInspector.toString(calcStdDevVar(runBestFeasibleList, meanBestFeasibleFit[0])) + "\n"); printToTextListener(" MultiRun stats: Variance/Std.Dev.: " + BeanInspector.toString(calcStdDevVar(runBestFeasibleList, meanBestFeasibleFit[0])) + "\n");
} }
printToTextListener(" MultiRun stats: Median best feasible fitn. (: " + numOfRunsFeasibleFound + " runs): " + BeanInspector.toString(getMedianBestFit(true)) + "\n"); printToTextListener(" MultiRun stats: Median best feasible fitn. (: " + numOfRunsFeasibleFound + " runs): " + BeanInspector.toString(getMedianBestFitness(true)) + "\n");
} }
} }
if (refineMultiRuns && (sumDataCollection != null)) { if (refineMultiRuns && (sumDataCollection != null)) {
@ -553,8 +546,7 @@ public abstract class AbstractStatistics implements InterfaceTextListener, Inter
private double[] calcStdDevVar(ArrayList<IndividualInterface> list, double meanFit) { private double[] calcStdDevVar(ArrayList<IndividualInterface> list, double meanFit) {
double tmp, sum = 0; double tmp, sum = 0;
for (Iterator<IndividualInterface> iter = list.iterator(); iter.hasNext(); ) { for (IndividualInterface indy : list) {
IndividualInterface indy = iter.next();
tmp = indy.getFitness()[0] - meanFit; tmp = indy.getFitness()[0] - meanFit;
sum += (tmp * tmp); sum += (tmp * tmp);
} }
@ -567,10 +559,10 @@ public abstract class AbstractStatistics implements InterfaceTextListener, Inter
/** /**
* Calculate the mean fitness of a list of individuals. * Calculate the mean fitness of a list of individuals.
* *
* @param list * @param list List of individuals
* @return * @return Mean fitness of individuals in list
*/ */
public static double[] calcMeanFit(List<IndividualInterface> list) { public static double[] calculateMeanFitness(List<IndividualInterface> list) {
double[] sumFit = list.get(0).getFitness().clone(); double[] sumFit = list.get(0).getFitness().clone();
for (int i = 1; i < list.size(); i++) { for (int i = 1; i < list.size(); i++) {
Mathematics.vvAdd(sumFit, list.get(i).getFitness(), sumFit); Mathematics.vvAdd(sumFit, list.get(i).getFitness(), sumFit);
@ -580,10 +572,10 @@ public abstract class AbstractStatistics implements InterfaceTextListener, Inter
return sumFit; return sumFit;
} }
public static double[] calcMedianFit(List<IndividualInterface> list) { public static double[] calculateMedianFitness(List<IndividualInterface> list) {
ArrayList<double[]> dblAList = new ArrayList<>(list.size()); ArrayList<double[]> dblAList = new ArrayList<>(list.size());
for (int i = 0; i < list.size(); i++) { for (IndividualInterface indy : list) {
dblAList.add(list.get(i).getFitness()); dblAList.add(indy.getFitness());
} }
return Mathematics.median(dblAList, false); return Mathematics.median(dblAList, false);
} }
@ -631,13 +623,11 @@ public abstract class AbstractStatistics implements InterfaceTextListener, Inter
} }
} }
////////////// InterfaceTextListener
@Override @Override
public void print(String str) { public void print(String str) {
printToTextListener(str); printToTextListener(str);
} }
////////////// InterfaceTextListener
@Override @Override
public void println(String str) { public void println(String str) {
printToTextListener(str); printToTextListener(str);
@ -793,7 +783,6 @@ public abstract class AbstractStatistics implements InterfaceTextListener, Inter
ret[0] = functionCalls; ret[0] = functionCalls;
for (int i = 1; i <= selEnumVals.length; i++) { for (int i = 1; i <= selEnumVals.length; i++) {
switch (selEnumVals[i - 1]) { // the field i+1 contains enum value i, because field 0 is reserved for the number of function calls switch (selEnumVals[i - 1]) { // the field i+1 contains enum value i, because field 0 is reserved for the number of function calls
// currentBest, currentWorst, runBest, currentBestFeasible, runBestFeasible, avgPopDistance, maxPopDistance;
case currentBest: case currentBest:
ret[i] = currentBestFit[defaultFitCriterion]; ret[i] = currentBestFit[defaultFitCriterion];
break; break;