Updating the JEInterface Matlab code

resources/MatlabInterface/@JEInterface/JEInterface.m

@@ -3,19 +3,18 @@ function int = JEInterface(fhandle, range, varargin)
 %       JEInterface(interfaceName, fhandle, range)
 %       JEInterface(interfaceName, fhandle, range, defaultargs)
 %       JEInterface(interfaceName, fhandle, range, defaultargs, options...)
-
+%
-
+% Arguments: 
-% arguments: 
 %   fhandle: a function handle defining the optimization target.
 %   range: a 2 x dim array defining the solution subspace with lower and
-%      upper bounds - or a scalar defining the bitwidth for binary
+%      upper bounds; or a scalar defining the bitwidth for binary
 %      problems.
 %   defaultArgs: (optional) additional constant argument to the target
 %       function, empty by default.
 %   options: (optional) options as name-value pairs defining optimization parameters,
 %       especially tolerance and maximum function calls.
 %       Check makeOoptions for default settings.
-
+%
 % Further options may be specified using setOptions with a JE options struct.
 % Main options are:
 %   TolX: convergence criterion in the solution space
@@ -85,13 +84,13 @@ if (nargin>2)
         if (rem(nargin,2)==0)
             error('Invalid number of arguments!');
         end
-        disp('Reading options...');
+        disp('Reading options:');
         for i=2:2:nargin-2
             int=setOpt(int, varargin{i}, varargin{i+1});
         end
     end
 end  
-
+display(getOptions(int));
 % finally create the java object
 int.mp = eva2.server.go.problems.MatlabProblem(int.dim, int.range);
 disp('Java object created');

resources/MatlabInterface/@JEInterface/makeOptions.m

@@ -1,18 +1,31 @@
 function opts = makeOptions(int, varargin)
 % Create a JEInterface options set from scratch. Possible fields are:
 %'Display';
-%'MaxFunEvals';'MaxIter';'TolFun';'TolFunEvals';TolX';'TolXEvals', where
+%'MaxFunEvals';'MaxIter';'TolFun';'TolFunEvals';TolX';'TolXEvals', which,
-% all but 'TolFunEvals', 'TolXEvals' are used similar to the optimset. 
+% except for 'TolFunEvals' and 'TolXEvals', are used similar to the optimset. 
 % The latter two are interpreted as the numbers of evaluations required
 % to assume convergence. Default values are TolXEvals=TolFunEvals=200,
 % TolX=TolFun=1e-4, MaxFunEvals uses a default from EvA2.
+% Further options are 'CreateStopBox' and 'NiceSleepTime' which are
+% JE-specific. The 'CreateStopBox' option toggles the GUI box with stop
+% button provided for graceful interruption of an optimization run.
+% In cases without X-forwarding, a deactivation by setting it to 0 may be required,
+% but note that killing optimization may break the threading mechanism. Try stopOptimize with
+% the 'kill' option.
+%
+% 'NiceSleepTime' allows setting a sleep time (in ms) for the concurrent
+% threading. Technically, either the Matlab
+% or the Java thread is always waiting for the other one, which may require 
+% full CPU if no sleep time is employed. However, for quick function evaluations,
+% even minor sleep times substantially reduce allover efficiency, so we advice
+% to set small sleep times (e.g. 5 ms) only if a single function evaluation 
+% takes considerably longer and leave the sleep time at zero otherwise.
+%
 % Notice that this method creates a parameter set but does not assign it
 % to the interface instance. Use setOptions to do that.
 
 allfields = {'Display'; 'MaxFunEvals';'MaxIter';'TolFun';'TolFunEvals';...
-    'TolX';'TolXEvals'};
+    'TolX'; 'TolXEvals'; 'CreateStopBox'; 'NiceSleepTime'};
-
-specialfields={'TolFunEvals', 'TolXEvals'};
 
 nvararg=nargin-1;
 if rem(nvararg,2)==1
@@ -36,6 +49,8 @@ opts.('TolX') = 1e-4;
 opts.('TolXEvals') = 200;
 opts.('TolFun') = 1e-4;
 opts.('TolFunEvals') = 200;
+opts.('CreateStopBox')=1;
+opts.('NiceSleepTime')=0;
 
 for i=1:nvararg/2
     name=varargin{2*i-1};
@@ -48,18 +63,27 @@ for i=1:nvararg/2
         if isempty(optIndex)
             error('Unknown option %s !', name);
         else
-            if ~isempty(strmatch(name, specialfields,'exact'))
+            switch name
-                % test for integer
+                case {'TolFunEvals', 'TolXEvals'} % for special fields, integers > 1 are allowed
-                if (~isscalar(value) || ~isnumeric(value) || round(value)<1)
+                    if ~isscalar(value) || ~isnumeric(value) || round(value)<1
-                    error('invalid value type for %s, expecting numeric scalar > 1!', name);
+                        error('Invalid value type for %s, expecting positive numeric scalar!', name);
-                end
+                    end;
-                value=round(value);
+                    value=round(value);
-            else
+                case 'CreateStopBox'
-                % test using optimset
+                    if ~isscalar(value) || ~isnumeric(value) || round(value)<0 || round(value)>1
-                optimset(stdSet, name, value);
+                        error('Invalid value type for %s, expecting 0 or 1!', name);
+                    end;
+                    value=round(value);
+                case 'NiceSleepTime'
+                    if ~isscalar(value) || ~isnumeric(value) || round(value)<0 ;
+                        error('Invalid value type for %s, expecting numeric scalar >= 0!', name);
+                    end;
+                    value=round(value);
+                otherwise                % test using optimset
+                    optimset(stdSet, name, value);
             end
             % assign to struct
             opts.(allfields{optIndex,:}) = value;
         end
     end
-end
+end

resources/MatlabInterface/@JEInterface/runEvalLoopJE.m

@@ -19,11 +19,15 @@ if ~isempty(int.mediator)
     int.mediator.quit
     int.mediator='';
 end
+% disp(sprintf('creating mediator'));
 
 % set up a mediator and inform JE
-int.mediator = eva2.server.go.problems.MatlabEvalMediator;
+int.mediator = eva2.server.go.problems.MatlabEvalMediator(int.opts.NiceSleepTime);
 int.mp.setMediator(int.mediator);
 JEMediator=int.mediator;
+createStopBox=int.opts.CreateStopBox;
+
+% disp(sprintf('mediator created, calling optimize'));
 
 % start the JE thread
 if (optOrPostProc == 1)
@@ -33,6 +37,7 @@ else % post processing
     stopText='Stop EvA2 post processing';
     int.mp.requestPostProcessing(steps, sigmaClust, nBest);
 end
+% disp(sprintf('calling optimize done'));
 
 % handle the case when the optimization has been called from a users script
 % and not from the toolboxes parameter estimation function (which has an
@@ -47,10 +52,15 @@ if isempty(stopOptimization),
     disp(sprintf('Starting optimization at %s', timeStr));
     % create a cancel button box (case without SBtoolbox)
     stopText=sprintf('%s (%s)', stopText, timeStr);
-    boxHandle=figure('Position',[100 600 250 80], 'MenuBar', 'none', 'Name', 'EvA2 optimization...', 'NumberTitle','off');
+    if (createStopBox == 1)
-    uicontrol(boxHandle,'Style', 'pushbutton', 'String', 'Cancel', 'Position', [25 25 60 30], 'Callback', 'global stopOptimization; stopOptimization=1;');
+        boxHandle=figure('Position',[100 600 250 80], 'MenuBar', 'none', 'Name', 'EvA2 optimization...', 'NumberTitle','off');
-    uicontrol(boxHandle,'Style', 'text', 'String', stopText, 'Position', [100 15 130 50]);
+        uicontrol(boxHandle,'Style', 'pushbutton', 'String', 'Cancel', 'Position', [25 25 60 30], 'Callback', 'global stopOptimization; stopOptimization=1;');
-    drawnow;
+        uicontrol(boxHandle,'Style', 'text', 'String', stopText, 'Position', [100 15 130 50]);
+        drawnow;
+%    else
+%        disp(stopText);
+    end
+   
     % set flag for non toolbox optimization
     nontoolboxopt = 1;
 else
@@ -60,13 +70,19 @@ else
 end
 
 stopOnce=1;
-
+cnt=1;
+% disp(sprintf('before eval loop... %d',cnt));
 % repeat the mediator thread and eval call until finished
 try
     while (~int.mediator.isFinished())
-        int.mediator.run;
+% 		disp(sprintf('running mediator id %d',cnt));
+        int.mediator.run(cnt);
+% 		disp(sprintf('after running mediator id %d',cnt));
+	cnt=cnt+1;
         if (~int.mediator.isFinished())
+		%disp('getting question');
             x = int.mediator.getQuestion();
+		%disp('question asked');
             if (isempty(int.range))
                 %size(x)
                 x=convertUnsignedJE(int, x);
@@ -80,6 +96,7 @@ try
                 else
                     res = feval(int.f, x, int.args);
                 end
+% 		disp(sprintf('res is %d',res));
                 %res
             catch ME
                 disp('function evaluation failed:');
@@ -87,6 +104,7 @@ try
                 stopOptimization=1;
             end
             int.mediator.setAnswer(res);
+		%disp('answer provided');
             drawnow;
             if ((stopOptimization==1) && (stopOnce==1))
                 disp('User interrupt requested ...');
@@ -108,7 +126,7 @@ catch ME
     %    clear global stopOptimization
     %end
 end
-
+% disp('writing back results');
 % write back results
 int=setResultJE(int, int.mediator.getSolution());
 int=setResultArrayJE(int, int.mediator.getSolutionSet());
@@ -120,6 +138,9 @@ 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,
-    if (ishandle(boxHandle)) , close(boxHandle); end
+    if createStopBox==1
+        if (ishandle(boxHandle)) , close(boxHandle); end
+    end
     clear global stopOptimization
 end
+% disp('runEvalLoop done');

resources/MatlabInterface/@JEInterface/setVerbose.m

@@ -14,8 +14,11 @@ end
 if (nargin > 2)
     if ischar(varargin{1})
         fname=varargin{1};
-        disp('Writing debug output to ');
+	if (bOn==1)
-        disp(fname);
+	    disp(['Writing debug output to ' fname]);
+	else
+	    disp('Debug output deactivated');
+        end
     else
         disp('Invalid third argument, expected char. Using default output file name');
     end