Another JEInterface update

resources/MatlabInterface/@JEInterface/evaluateJE.m

@@ -1,11 +0,0 @@
-function v = evaluate(int)
-% Interface function for JavaEvA 2.
-% Will be called by the MatlabProblem to obtain the target function value
-% for a sample individual.
-
-x = int.mp.getCurrentDoubleArray;
-if (isempty(int.args))
-    int.mp.setResult(feval(int.f, x));
-else
-    int.mp.setResult(feval(int.f, x, int.args));
-end

resources/MatlabInterface/@JEInterface/isFinished.m

@@ -1,4 +1,5 @@
 function b = isFinished(int)
+% Deprecated: optimization now runs synchronously. 
 % Returns 1 if the optimization was finished, else 0
 
 b = int.finished;

resources/MatlabInterface/@JEInterface/runEvalLoopJE.m

@@ -9,6 +9,7 @@ function int=runEvalLoopJE(int, optOrPostProc, optType, outputFilePrefix, steps,
 % when optimizing. nBest may be -1 to show all.
 
 global stopOptimization
+global JEMediator
 
 if ~isempty(int.mediator)
     int.mediator.quit
@@ -18,6 +19,7 @@ end
 % set up a mediator and inform JE
 int.mediator = javaeva.server.go.problems.MatlabEvalMediator;
 int.mp.setMediator(int.mediator);
+JEMediator=int.mediator;
 
 % start the JE thread
 if (optOrPostProc == 1)
@@ -34,7 +36,7 @@ end
 % stopOptimization is empty. if it is then it is not the toolbox calling
 % and we create an own button to stop it.
 if isempty(stopOptimization),
-    % create a cancel button box (only in the case that
+    % create a cancel button box (case without SBtoolbox)
     h=figure('Position',[100 600 250 80], 'MenuBar', 'none', 'Name', 'JavaEvA optimization running...', 'NumberTitle','off');
     uicontrol(h,'Style', 'pushbutton', 'String', 'Cancel', 'Position', [25 25 60 30], 'Callback', 'global stopOptimization; stopOptimization=1;');
     uicontrol(h,'Style', 'text', 'String', stopText, 'Position', [100 25 120 30]);
@@ -51,6 +53,7 @@ end
 stopOnce=1;
 
 % repeat the mediator thread and eval call until finished
+try
     while (~int.mediator.isFinished())
         int.mediator.run;
         if (~int.mediator.isFinished())
@@ -69,6 +72,16 @@ while (~int.mediator.isFinished())
             end
         end
     end
+    clear global JEMediator;
+catch
+    disp('Error in evaluate!');
+    %int.mediator.quit; % just in case
+    %int.mediator='';
+    if (nontoolboxopt == 1)
+        if (ishandle(h)) , close(h); end
+        clear global stopOptimization
+    end
+end
 
 % write back results
 int=setResultJE(int, int.mediator.getSolution());
@@ -81,6 +94,6 @@ int.mediator='';
 % and not from the toolboxes parameter estimation function (which has an
 % own stop button). we decide this by checking nontoolboxopt
 if nontoolboxopt == 1,
-    close(h);
+    if (ishandle(h)) , close(h); end
     clear global stopOptimization
 end

resources/MatlabInterface/@JEInterface/stopOptimize.m

@@ -1,9 +1,22 @@
-function int = stopOptimize(int)
+function int = stopOptimize(int, varargin)
-% Stop a running optimization
+% Stop a running optimization. 
+%   stopOptimize(JI [,'kill'])
+%       If 'kill' is given as second argument, the mediator thread is
+%       stopped, relevant if optimization was stopped using CTRL-C and the
+%       mediator is a running zombie.
+
+global JEMediator
     
 %disp('in Stop!');
 int.mp.stopOptimize;
-%if (~isempty(int.mediator))
+
-%    int.mediator.quit; % just in case
+if (nargin > 1) && (ischar(varargin{1}) && (strcmp(varargin{1},'kill')==1))
-%    int.mediator='';
+    if (~isempty(JEMediator))
-%end
+        disp('killing mediator...');
+        JEMediator.quit; % just in case
+        JEMediator='';
+        clear global JEMediator;
+    else 
+        disp('no mediator to kill');
+    end
+end

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

@@ -1,5 +1,7 @@
 package javaeva.server.go.problems;
 
+import javaeva.gui.BeanInspector;
+
 /**
  * This implements a thread acting as a mediator between JavaEvA and Matlab. Thanks to the idea 
  * of Henning Schmidt!
@@ -26,7 +28,7 @@ public class MatlabEvalMediator implements Runnable {
 	volatile boolean fin = false;
 	volatile double[] question = null;
 	volatile double[] answer = null;
-	volatile boolean quit = false;
+	boolean quit = false;
 	volatile double[] optSolution = null;
 	volatile double[][] optSolSet = null;
 //	MatlabProblem mp = null;
@@ -44,17 +46,16 @@ public class MatlabEvalMediator implements Runnable {
 		question = x;
 		requesting = true;
 //		int k=0;
-//		mp.log("Requesting eval for " + BeanInspector.toString(x) + ", req state is " + requesting + "\n"); 
+//		System.out.println("Requesting eval for " + BeanInspector.toString(x) + ", req state is " + requesting + "\n"); 
 		while (requesting && !quit) {
 			// 	wait for matlab to answer the question
 			if (sleepTime > 0) try { Thread.sleep(sleepTime); } catch(Exception e) {};
-//			k++;
+//			if ((k%100)==0) {
-//			if (k>100) {
 //				System.out.println("waiting for matlab to answer...");
-//				k=0;
 //			}
+//			k++;
 		}
-//		mp.log("Requesting done \n");
+//		System.out.println("Requesting done \n");
 		// matlab is finished, answer is here
 		return getAnswer(); // return to JE with answer
 	}
@@ -67,13 +68,12 @@ public class MatlabEvalMediator implements Runnable {
 		while (!requesting && !isFinished() && !quit) {
 			// wait for JE to pose a question or finish all
 			if (sleepTime > 0) try { Thread.sleep(sleepTime); } catch(Exception e) {};
-//			k++;
+//			if ((k%100)==0) {
-//			if (k>100) {
 //				System.out.println("waiting for JE to ask...");
-//				k=0;
 //			}
+//			k++;
 		}
-//		mp.log("-- Request arrived in MP thread\n");
+//		System.out.println("-- Request arrived in MP thread\n");
 		// requesting is true, now finish and let Matlab work
 	}
 
@@ -81,6 +81,7 @@ public class MatlabEvalMediator implements Runnable {
 	 * Cancel waiting in any case.
 	 */
 	public void quit() {
+//		System.out.println("IN QUIT!");
 		quit = true;
 	}