Matlab interface now uses true binary data type for binary problems

resources/MatlabInterface/@JEInterface/convertUnsignedJE.m

@@ -2,13 +2,24 @@ function [ z ] = convertUnsignedJE( int, x )
 %CONVERTUNSIGNEDJE Convert signed 32-bit integer to unsigned.
 %   Detailed explanation goes here
 
-z=zeros(size(x,1),size(x,2), 'uint32');
+if strcmp(class(x),'java.util.BitSet')
-for j=1 : size(x,1)
+    z=num2str(10^(int.dim-1));
-    for i=1 : size(x,2) 
+    for i=1:int.dim
-        if (x(j,i) < 0) 
+        if (x.get(i-1))  % Java indices start at zero!
-            z(j,i) = 1+bitxor(uint32(-x(j,i)), int.hexMask);
+            z(i)='1';
         else
-            z(j,i) = x(j,i);
+            z(i)='0';
+        end
+    end
+else
+    z=zeros(size(x,1),size(x,2), 'int32');
+    for j=1 : size(x,1)
+        for i=1 : size(x,2)
+            if (x(j,i) < 0)
+                z(j,i) = 1+bitxor(uint32(-x(j,i)), int.hexMask);
+            else
+                z(j,i) = x(j,i);
+            end
         end
     end
 end

resources/MatlabInterface/@JEInterface/runEvalLoopJE.m

@@ -78,7 +78,7 @@ try
  		% disp(sprintf('running mediator id %d',cnt));
         int.mediator.run(cnt);
  		% disp(sprintf('after running mediator id %d',cnt));
-	cnt=cnt+1;
+        cnt=cnt+1;
         if (~int.mediator.isFinished())
 		% disp('getting question');
             x = int.mediator.getQuestion();

resources/MatlabInterface/@JEInterface/testEvalFunc.m

@@ -6,11 +6,13 @@ if (isempty(int.range))
     % binary problem
     s=sprintf('Binary problem of bitwidth %d', int.dim);
     disp(s);
-    numInts=ceil(int.dim/wordwidth);
+    %numInts=ceil(int.dim/wordwidth);
     % generate trial vector
-    x=ceil(rand(1,numInts).*(2^wordwidth));
+    %x=ceil(rand(1,numInts).*(2^wordwidth));
-    overheadBits=numInts*wordwidth-int.dim;
+    %overheadBits=numInts*wordwidth-int.dim;
-    x(numInts)=bitshift(x(numInts),-overheadBits); % shift right by overhead
+    %x(numInts)=bitshift(x(numInts),-overheadBits); % shift right by overhead
+    bs=eva2.tools.math.RNG.randomBitSet(0.5, int.dim);
+    x=convertUnsignedJE(int, bs);
 else
     % double problem
     x=rand(1, int.dim);
@@ -35,9 +37,10 @@ try
         res = feval(int.f, x, int.args);
     end
 catch ME
-    disp('Function evaluation failed:');
+    disp('JEInterface: Test function evaluation failed:');
     disp(ME.message);
-    error(['Test failed! ' ME.message]);
+    rethrow(ME);
+    %error(['Test failed! ' ME.message]);
 end
             
 disp('Function returned: ');

src/eva2/server/go/problems/MatlabEvalMediator.java

@@ -1,5 +1,7 @@
 package eva2.server.go.problems;
 
+import java.util.BitSet;
+
 import eva2.gui.BeanInspector;
 
 /**
@@ -240,7 +242,7 @@ public class MatlabEvalMediator {
 		optSolSet = solSet;
 	}
 	
-	void setSolutionSet(int[][] solSet) {
+	void setSolutionSet(BitSet[] solSet) {
 //		System.err.println("setting SolSet " + ((solSet != null) ? solSet.length : 0));
 		optSolSet = solSet;
 	}

src/eva2/server/go/problems/MatlabProblem.java

@@ -5,15 +5,17 @@ import java.io.FileOutputStream;
 import java.io.PrintStream;
 import java.io.Serializable;
 import java.util.Arrays;
+import java.util.BitSet;
 
 import eva2.OptimizerFactory;
 import eva2.OptimizerRunnable;
 import eva2.gui.BeanInspector;
+import eva2.server.go.PopulationInterface;
 import eva2.server.go.individuals.AbstractEAIndividual;
 import eva2.server.go.individuals.ESIndividualDoubleData;
-import eva2.server.go.individuals.GAIndividualIntegerData;
+import eva2.server.go.individuals.GAIndividualBinaryData;
+import eva2.server.go.individuals.InterfaceDataTypeBinary;
 import eva2.server.go.individuals.InterfaceDataTypeDouble;
-import eva2.server.go.individuals.InterfaceDataTypeInteger;
 import eva2.server.go.operators.postprocess.InterfacePostProcessParams;
 import eva2.server.go.operators.postprocess.PostProcess;
 import eva2.server.go.operators.postprocess.PostProcessParams;
@@ -25,6 +27,7 @@ import eva2.server.go.operators.terminators.PopulationMeasureTerminator.Stagnati
 import eva2.server.go.populations.Population;
 import eva2.server.go.strategies.InterfaceOptimizer;
 import eva2.server.stat.InterfaceTextListener;
+import eva2.tools.ToolBox;
 
 /**
  * Interface problem class for Matlab(TM). Towards EvA2 this behaves like any other double valued 
@@ -105,13 +108,18 @@ public class MatlabProblem extends AbstractOptimizationProblem implements Interf
 				((InterfaceDataTypeDouble)this.m_Template).SetDoubleRange(range);
 			}
 		} else {
-			if (m_Template == null) m_Template         = new GAIndividualIntegerData();
+			///// binary alternative
+			if (m_Template == null) m_Template         = new GAIndividualBinaryData(getProblemDimension());
+
+			///// Integer alternative
+			/*if (m_Template == null) m_Template         = new GAIndividualIntegerData();
 			int intLen = 1+((getProblemDimension()-1)/32);
 			int lastIntCodingBits = getProblemDimension()-((intLen-1)*32);
 			if (lastIntCodingBits > 32) System.err.println("ERROR in MatlabProblem:initTemplate");
 			((GAIndividualIntegerData)m_Template).setIntegerDataLength(intLen);
 			((GAIndividualIntegerData)m_Template).SetIntRange(Integer.MIN_VALUE, Integer.MAX_VALUE);
 			if (lastIntCodingBits < 32) ((GAIndividualIntegerData)m_Template).SetIntRange(intLen-1, 0, (int)Math.pow(2, lastIntCodingBits)-1);
+			*/ 			/////
 //			System.err.println("integer length is "+((GAIndividualIntegerData)m_Template).getIntegerData().length);
 //			System.err.println("Range is " + BeanInspector.toString(((GAIndividualIntegerData)m_Template).getIntRange()));
 //			m_Template         = new GAIndividualBinaryData();
@@ -266,6 +274,17 @@ public class MatlabProblem extends AbstractOptimizationProblem implements Interf
 		optimize(optType, outputFilePrefix, null, null);
 	}
 
+	/**
+	 * Start an optimization using the MatlabProblem. The optType references the standard
+	 * optimizer as in OptimizerFactory. An output file prefix is optional. In two arrays,
+	 * name-value mappings can be given as additional parameters to the optimizer.
+	 * 
+	 * @see OptimizerFactory.getOptRunnable
+	 * @param optType
+	 * @param outputFilePrefix
+	 * @param specParams
+	 * @param specValues
+	 */
 	public void optimize(final int optType, String outputFilePrefix, Object[] specParams, Object[] specValues) {
 		if (allowSingleRunnable && (runnable != null) && (!runnable.isFinished())) {
 			System.err.println("Please wait for the current optimization to finish");
@@ -399,21 +418,21 @@ public class MatlabProblem extends AbstractOptimizationProblem implements Interf
 				}
 				handler.setSolutionSet(solSet);
 			} else {
-				int[][] solSet = new int[pop.size()][];
+				BitSet[] solSet = new BitSet[pop.size()];
 				for (int i=0; i<pop.size(); i++) {
-					solSet[i]=((InterfaceDataTypeInteger)pop.getEAIndividual(i)).getIntegerData();
+					solSet[i]=((InterfaceDataTypeBinary)pop.getEAIndividual(i)).getBinaryData();
 				}
 				handler.setSolutionSet(solSet);
 			}
 		} else {
 			if (isDouble) handler.setSolutionSet((double[][])null);
-			else handler.setSolutionSet((int[][])null);
+			else handler.setSolutionSet((BitSet[])null);
 		}
 	}
 
 	void exportResultToMatlab(OptimizerRunnable runnable) {
 		if (isDouble) handler.setSolution(runnable.getDoubleSolution());
-		else handler.setSolution(runnable.getIntegerSolution());
+		else handler.setSolution(runnable.getBinarySolution());
 	}
 
 //	void exportResultToMatlab(double[] result) {
@@ -504,4 +523,18 @@ public class MatlabProblem extends AbstractOptimizationProblem implements Interf
 		log("retrieving initial range..., first entry: " + ((initialRange==null) ? "null" : BeanInspector.toString(initialRange[0])));
 		return initialRange;
 	}
+
+	@Override
+	public String[] getAdditionalDataHeader() {
+		return ToolBox.appendArrays(super.getAdditionalDataHeader(), "matlabSol");
+	}
+	@Override
+	public String[] getAdditionalDataInfo() {
+		return ToolBox.appendArrays(super.getAdditionalDataInfo(), "Additional solution representation");
+	}
+	@Override
+	public Object[] getAdditionalDataValue(PopulationInterface pop) {
+		String addStr=((AbstractEAIndividual)pop.getBestIndividual()).getStringRepresentation();
+		return ToolBox.appendArrays(super.getAdditionalDataValue(pop), addStr);
+	}
 }