Load and store Optimizations as YAML.

refs #31
- Introduces custom BeanSerializer using SnakeYAML
- Removed previous json package
- Introduces eva2.yaml package
- Hidden properties are not saved
- Reintroduces output in text window

.gitignore

@@ -1,6 +1,7 @@
 /build/
 out/
 *.ser
+*.yml
 .settings/
 .project
 .classpath

src/eva2/json/package-info.java

@@ -1,4 +0,0 @@
-/**
- * JSON package for serializing and deserializing optimization configurations.
- */
-package eva2.json;

src/eva2/optimization/modules/AbstractOptimizationParameters.java

@@ -3,18 +3,18 @@ package eva2.optimization.modules;
 import eva2.gui.BeanInspector;
 import eva2.optimization.go.InterfaceNotifyOnInformers;
 import eva2.optimization.go.InterfaceOptimizationParameters;
-import eva2.optimization.population.InterfacePopulationChangedEventListener;
 import eva2.optimization.operator.postprocess.InterfacePostProcessParams;
 import eva2.optimization.operator.postprocess.PostProcessParams;
 import eva2.optimization.operator.terminators.InterfaceTerminator;
+import eva2.optimization.population.InterfacePopulationChangedEventListener;
+import eva2.optimization.strategies.InterfaceOptimizer;
 import eva2.problems.InterfaceAdditionalPopulationInformer;
 import eva2.problems.InterfaceOptimizationProblem;
-import eva2.optimization.strategies.InterfaceOptimizer;
-import eva2.tools.Serializer;
 import eva2.util.annotation.Parameter;
+import eva2.yaml.BeanSerializer;
 
-import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
+import java.io.IOException;
 import java.io.Serializable;
 import java.util.LinkedList;
 import java.util.List;
@@ -121,15 +121,17 @@ public abstract class AbstractOptimizationParameters implements InterfaceOptimiz
     public void saveInstance(String fileName) {
         try {
             FileOutputStream fileStream = new FileOutputStream(fileName);
-            Serializer.storeObject(fileStream, this);
+            String yaml = BeanSerializer.serializeObject(this);
-        } catch (FileNotFoundException ex) {
+            fileStream.write(yaml.getBytes());
+            fileStream.close();
+        } catch (IOException ex) {
             LOGGER.log(Level.WARNING, "Could not store instance object.", ex);
         }
     }
 
     @Override
     public void saveInstance() {
-        String fileName = this.getClass().getSimpleName() + ".ser";
+        String fileName = this.getClass().getSimpleName() + ".yml";
         saveInstance(fileName);
     }
 

src/eva2/optimization/modules/OptimizationParameters.java

@@ -4,12 +4,11 @@ import eva2.optimization.go.InterfaceOptimizationParameters;
 import eva2.optimization.operator.terminators.EvaluationTerminator;
 import eva2.optimization.operator.terminators.InterfaceTerminator;
 import eva2.optimization.strategies.DifferentialEvolution;
+import eva2.optimization.strategies.InterfaceOptimizer;
 import eva2.problems.F1Problem;
 import eva2.problems.InterfaceOptimizationProblem;
-import eva2.optimization.strategies.GeneticAlgorithm;
-import eva2.optimization.strategies.InterfaceOptimizer;
-import eva2.tools.Serializer;
 import eva2.util.annotation.Description;
+import org.yaml.snakeyaml.Yaml;
 
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
@@ -35,21 +34,21 @@ public class OptimizationParameters extends AbstractOptimizationParameters imple
      * @return
      */
     public static OptimizationParameters getInstance() {
-        return getInstance("OptimizationParameters.ser", true);
+        return getInstance("OptimizationParameters.yml", true);
     }
 
     /**
      * Create an instance from a given serialized parameter file.
      *
-     * @param serParamFile Serialized Parameter File
+     * @param yamlFile Serialized Parameter File
      * @param casually     if true, standard parameters are used quietly if the params cannot be loaded
      * @return a OptimizationParameters instance
      */
-    public static OptimizationParameters getInstance(String serParamFile, final boolean casually) {
+    public static OptimizationParameters getInstance(String yamlFile, final boolean casually) {
         OptimizationParameters instance = null;
         try {
-            FileInputStream fileStream = new FileInputStream(serParamFile);
+            FileInputStream fileStream = new FileInputStream(yamlFile);
-            instance = (OptimizationParameters) Serializer.loadObject(fileStream, casually);
+            instance = (OptimizationParameters) new Yaml().load(fileStream);
         } catch (FileNotFoundException ex) {
             LOGGER.log(Level.WARNING, "Could not load instance object.", ex);
         }

src/eva2/optimization/modules/Processor.java

@@ -4,7 +4,6 @@ import eva2.gui.BeanInspector;
 import eva2.optimization.OptimizationStateListener;
 import eva2.optimization.go.InterfaceNotifyOnInformers;
 import eva2.optimization.go.InterfaceOptimizationParameters;
-import eva2.optimization.population.InterfacePopulationChangedEventListener;
 import eva2.optimization.operator.paramcontrol.ConstantParameters;
 import eva2.optimization.operator.paramcontrol.InterfaceParameterControl;
 import eva2.optimization.operator.postprocess.PostProcess;
@@ -12,13 +11,14 @@ import eva2.optimization.operator.postprocess.PostProcessParams;
 import eva2.optimization.operator.terminators.EvaluationTerminator;
 import eva2.optimization.operator.terminators.GenerationTerminator;
 import eva2.optimization.operator.terminators.InterfaceTerminator;
+import eva2.optimization.population.InterfacePopulationChangedEventListener;
 import eva2.optimization.population.Population;
-import eva2.problems.AbstractOptimizationProblem;
-import eva2.problems.InterfaceAdditionalPopulationInformer;
 import eva2.optimization.statistics.InterfaceStatistics;
 import eva2.optimization.statistics.InterfaceTextListener;
 import eva2.optimization.statistics.StatisticsWithGUI;
 import eva2.optimization.strategies.InterfaceOptimizer;
+import eva2.problems.AbstractOptimizationProblem;
+import eva2.problems.InterfaceAdditionalPopulationInformer;
 import eva2.problems.InterfaceOptimizationProblem;
 import eva2.tools.EVAERROR;
 import eva2.tools.StringTools;
@@ -48,7 +48,7 @@ public class Processor extends Thread implements InterfaceProcessor, InterfacePo
     private InterfaceStatistics statistics;
     private InterfaceOptimizationParameters optimizationParameters;
     private boolean createInitialPopulations = true;
-    private boolean saveParams = false;
+    private boolean saveParams = true;
     private OptimizationStateListener optimizationStateListener;
     private boolean wasRestarted = false;
     private int runCounter = 0;
@@ -167,7 +167,6 @@ public class Processor extends Thread implements InterfaceProcessor, InterfacePo
             EVAERROR.clearMsgCache();
             while (isOptimizationRunning()) {
                 setPriority(3);
-                // ToDo: Do we need this really?
                 if (saveParams) {
                     try {
                         optimizationParameters.saveInstance();

src/eva2/optimization/statistics/AbstractStatistics.java

@@ -12,6 +12,7 @@ import eva2.tools.StringSelection;
 import eva2.tools.StringTools;
 import eva2.tools.ToolBox;
 import eva2.tools.math.Mathematics;
+import eva2.yaml.BeanSerializer;
 
 import java.io.File;
 import java.io.FileOutputStream;
@@ -195,7 +196,7 @@ public abstract class AbstractStatistics implements InterfaceTextListener, Inter
      *
      * @param infoString
      */
-    protected void initOutput(String infoString) {
+    protected void initializeOutput(String infoString) {
         String startDate = getDateString();
         // open the result file:
         if (doFileOutput()  // not "text-window only"
@@ -271,15 +272,11 @@ public abstract class AbstractStatistics implements InterfaceTextListener, Inter
             if (saveParams) {
                 statisticsParameter.saveInstance();
             }
-            initOutput(infoString);
+            initializeOutput(infoString);
             bestIndyAllRuns = null;
             bestFeasibleAllRuns = null;
-//			meanBestOfRunFitness = null;
-//			meanBestFeasibleFit = null;
             runBestFeasibleList = new ArrayList<>();
             runBestFitList = new ArrayList<>();
-//			if (refineMultiRuns) meanCollection = new ArrayList<double[][]>();
-//			else meanCollection = null;
             if (refineMultiRuns) {
                 sumDataCollection = new ArrayList<>();
             } else {
@@ -289,7 +286,6 @@ public abstract class AbstractStatistics implements InterfaceTextListener, Inter
             finalObjectData = null;
 
             statDataSumOverAll = null;
-//			lastAdditionalInfoSums = null;
             feasibleFoundAfterSum = -1;
             numOfRunsFeasibleFound = 0;
 
@@ -305,14 +301,14 @@ public abstract class AbstractStatistics implements InterfaceTextListener, Inter
         if (printRunIntroVerbosity()) {
             printToTextListener("\n****** Multirun " + runNumber);
         }
-        /*
-        ToDo: Figure out if we need this. Right now it is just spamming the text output
         if (params != null) {
             if (printRunIntroVerbosity()) {
-                printToTextListener("\nOptimization parameters: ");
+                printToTextListener("\nOptimization parameters: \n");
-                printToTextListener(BeanInspector.niceToString(params));
+                printToTextListener(BeanSerializer.serializeObject(params));
             }
         }
+        /*
+        ToDo: Figure out if we need this. Right now it is just spamming the text output
         if (printRunIntroVerbosity()) {
             printToTextListener("\nStatistics parameters: ");
             printToTextListener(BeanInspector.niceToString(getStatisticsParameter()) + '\n');

src/eva2/optimization/statistics/StatisticsParameters.java

@@ -9,6 +9,7 @@ import eva2.tools.SelectedTag;
 import eva2.tools.Serializer;
 import eva2.tools.StringSelection;
 import eva2.util.annotation.Description;
+import eva2.util.annotation.Parameter;
 
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
@@ -31,7 +32,6 @@ import java.util.logging.Logger;
  */
 @Description(value = "Configure statistics and output of the optimization run. Changes to the data selection state will not take effect during a run.")
 public class StatisticsParameters implements InterfaceStatisticsParameters, InterfaceNotifyOnInformers, Serializable {
-    private static final long serialVersionUID = -8681061379203108390L;
     private static final Logger LOGGER = Logger.getLogger(StatisticsParameters.class.getName());
     public final static int VERBOSITY_NONE = 0;
     public final static int VERBOSITY_FINAL = 1;
@@ -169,13 +169,6 @@ public class StatisticsParameters implements InterfaceStatisticsParameters, Inte
         return "Number of independent optimization runs to evaluate.";
     }
 
-    /**
-     *
-     */
-    public String infoStringTipText() {
-        return "Infostring displayed on fitness graph by pressing the right mouse button.";
-    }
-
     /**
      * Use averaged graph for multi-run plots or not
      */
@@ -232,14 +225,11 @@ public class StatisticsParameters implements InterfaceStatisticsParameters, Inte
         return outputTo.getSelectedTagID() > 0;
     }
 
-    public String convergenceRateThresholdTipText() {
-        return "Provided the optimal fitness is at zero, give the threshold below which it is considered as 'reached'";
-    }
-
     /**
      * @param x
      */
     @Override
+    @Parameter(description = "Provided the optimal fitness is at zero, give the threshold below which it is considered as 'reached'")
     public void setConvergenceRateThreshold(double x) {
         convergenceRateThreshold = x;
     }
@@ -258,14 +248,11 @@ public class StatisticsParameters implements InterfaceStatisticsParameters, Inte
     }
 
     @Override
+    @Parameter(description = "Output all available data fields or only the selected entries as value.")
     public void setOutputAllFieldsAsText(boolean bShowFullText) {
         showAdditionalProblemInfo = bShowFullText;
     }
 
-    public String outputAllFieldsAsTextTipText() {
-        return "Output all available data fields or only the selected entries as value.";
-    }
-
     public void hideHideable() {
         setOutputVerbosity(getOutputVerbosity());
     }
@@ -296,14 +283,11 @@ public class StatisticsParameters implements InterfaceStatisticsParameters, Inte
     }
 
     @Override
+    @Parameter(description = "Set the interval of data output for intermediate verbosity (in generations).")
     public void setOutputVerbosityK(int k) {
         verbosityK = k;
     }
 
-    public String outputVerbosityKTipText() {
-        return "Set the interval of data output for intermediate verbosity (in generations).";
-    }
-
     @Override
     public SelectedTag getOutputTo() {
         return outputTo;
@@ -314,13 +298,11 @@ public class StatisticsParameters implements InterfaceStatisticsParameters, Inte
         outputTo = tag;
     }
 
+    @Parameter(description = "Set the output destination; to deactivate output, set verbosity to none.")
     public void setOutputTo(int i) {
         outputTo.setSelectedTag(i);
     }
 
-    public String outputToTipText() {
-        return "Set the output destination; to deactivate output, set verbosity to none.";
-    }
 
     @Override
     public StringSelection getFieldSelection() {
@@ -328,13 +310,11 @@ public class StatisticsParameters implements InterfaceStatisticsParameters, Inte
     }
 
     @Override
+    @Parameter(description = "Select the data fields to be collected and plotted. Note that only simple types can be plotted to the GUI.")
     public void setFieldSelection(StringSelection v) {
         graphSel = v;
     }
 
-    public String fieldSelectionTipText() {
-        return "Select the data fields to be collected and plotted. Note that only simple types can be plotted to the GUI.";
-    }
 
     /**
      * May be called to dynamically alter the set of graphs that can be

src/eva2/optimization/tools/FileTools.java

@@ -110,7 +110,6 @@ public class FileTools {
      * a PrintWriter while other objects are written using an ObjectOutputStream.
      *
      * @param parentComponent the parent component
-     * @param fc              a filechooser or null to create a new one
      * @param object          The object to save.
      */
     public static boolean saveObjectWithFileChooser(Component parentComponent, Object object) {
@@ -208,10 +207,10 @@ public class FileTools {
         String predefName = null;
         try {
             predefName = (String) BeanInspector.callIfAvailable(object, "getName", null);
-            predefName = StringTools.simplifySymbols(predefName) + ".ser";
+            predefName = StringTools.simplifySymbols(predefName) + ".yml";
         } catch (Exception e) {
             predefName = object.getClass().getName();
-            predefName = StringTools.simplifySymbols(predefName) + ".ser";
+            predefName = StringTools.simplifySymbols(predefName) + ".yml";
         }
 
         if (!folder.exists()) {

src/eva2/yaml/BeanSerializer.java

@@ -0,0 +1,61 @@
+package eva2.yaml;
+
+import eva2.util.annotation.Hidden;
+import org.yaml.snakeyaml.DumperOptions;
+import org.yaml.snakeyaml.Yaml;
+import org.yaml.snakeyaml.introspector.Property;
+import org.yaml.snakeyaml.representer.Representer;
+
+import java.beans.BeanInfo;
+import java.beans.IntrospectionException;
+import java.beans.Introspector;
+import java.beans.PropertyDescriptor;
+import java.lang.reflect.Method;
+import java.util.ArrayList;
+import java.util.Set;
+import java.util.TreeSet;
+
+/**
+ * Created by becker on 02.11.2014.
+ */
+public class BeanSerializer {
+
+    public static String serializeObject(Object obj) {
+        DumperOptions options = new DumperOptions();
+        options.setAllowReadOnlyProperties(false);
+        options.setIndent(4);
+        Yaml yaml = new Yaml(new OptimizationRepresenter(), options);
+        return yaml.dump(obj);
+    }
+
+
+}
+
+class OptimizationRepresenter extends Representer {
+    @Override
+    protected Set<Property> getProperties(Class<?> type)
+            throws IntrospectionException {
+
+        Set<Property> set = super.getProperties(type);
+        Set<Property> filtered = new TreeSet<>();
+        BeanInfo info = Introspector.getBeanInfo(type, Object.class);
+        PropertyDescriptor[] properties = info.getPropertyDescriptors();
+        ArrayList<String> hiddenProperties = new ArrayList<>();
+
+        // We don't want to save Hidden properties
+        for (PropertyDescriptor p : properties) {
+            Method setter = p.getWriteMethod();
+            if (setter != null && setter.isAnnotationPresent(Hidden.class) || p.isHidden()) {
+                hiddenProperties.add(p.getName());
+            }
+        }
+
+        for (Property prop : set) {
+            String name = prop.getName();
+            if (!hiddenProperties.contains(name)) {
+                filtered.add(prop);
+            }
+        }
+        return filtered;
+    }
+}

src/eva2/yaml/OptimizationRun.java

@@ -1,4 +1,4 @@
-package eva2.json;
+package eva2.yaml;
 
 import java.util.ArrayList;
 import java.util.List;

src/eva2/yaml/package-info.java

@@ -0,0 +1,4 @@
+/**
+ * YAML package for serializing and deserializing optimization configurations.
+ */
+package eva2.yaml;