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Minor adaptations.

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This commit is contained in:
Marcel Kronfeld
2008-04-11 11:39:24 +00:00
parent 50511b0ed5
commit 7633618f59
18 changed files with 180 additions and 84 deletions
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12
resources/MatlabInterface/@JEInterface/JEInterface.m
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@@ -12,6 +12,18 @@ function int = JEInterface(interfaceName, fhandle, range, varargin)
% JavaEvA default values.
% defaultArgs: (optional) additional constant argument to the target
% function, empty by default.
% Recognized options are:
% TolX: convergence criterion in the solution space
% TolFun: convergence criterion in the target space
% MaxFunEvals: maximum number of function evaluations
% Display: 'off'/'final'/'notify'/'iter', where 'notify' corresponds to
% displaying every k-th iteration, which k=10 as default.
% The termination criterion of a run is a combination of the TolX, TolFun and
% MaxFunEvals criteria. The run terminates if MaxFunEvals has been reached
% or the best solution changes both in domain and codomain less than TolX
% and TolFun for a certain time, e.g. 100 evaluations.
% To ignore a criterion, set it to 0. E.g. to perform 10^5 evaluations in
% any case, set TolX=TolFun=0 and MaxFunEvals=10^5.
int.args = [];
int.opts = optimset('MaxFunEvals', javaeva.OptimizerFactory.getDefaultFitCalls, 'TolX', 1e-4, 'TolFun', 1e-4);

34
resources/MatlabInterface/@JEInterface/optimize.m
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@@ -1,18 +1,18 @@
function retInt = optimize(int, optType, varargin)
% Start a JavaEvA optimization run.
% optimize(interface, optType, [, outputFilePrefix ] )
% where
% where
% interface: instance of JEInterface
% optType: integer indicating the type of the optimization strategy
% to use.
% resultFilePrefix: (optional) char prefix for an optional verbose
% output file
if (int.finished == 0)
if (int.finished == 0)
error('please wait for the current run to finish');
end
if ((nargin == 2) || (nargin == 3))
if (nargin == 3)
if (nargin == 3)
outputFilePrefix = varargin{1};
else
outputFilePrefix = 'none';
@@ -27,9 +27,9 @@ if ((nargin == 2) || (nargin == 3))
xTol = int.opts.TolX;
maxEvals = int.opts.MaxFunEvals;
fTol = int.opts.TolFun;
import javaeva.server.go.operators.terminators.PhenotypeConvergenceTerminator;
import javaeva.server.go.operators.terminators.FitnessConvergenceTerminator;
import javaeva.server.go.operators.terminators.FitnessConvergenceTerminator;
import javaeva.server.go.operators.terminators.CombinedTerminator;
import javaeva.server.go.operators.terminators.EvaluationTerminator;
import javaeva.OptimizerFactory;
@@ -39,6 +39,7 @@ if ((nargin == 2) || (nargin == 3))
% values of 1e-4 in . Thats what we do as well
if (isempty(int.opts.TolX)) ; xTol = 1e-4; end
if (isempty(int.opts.TolFun)) ; fTol = 1e-4; end
% construct Terminators
if ((xTol > 0) && (fTol > 0))
% both criteria are given, use combination
@@ -48,12 +49,12 @@ if ((nargin == 2) || (nargin == 3))
else if (fTol > 0 ) % only fitness covnergence
convTerm = FitnessConvergenceTerminator(fTol, 100, 1, 1);
else
convTerm = 'undef'; % signal that there is no terminator yet
convTerm = 'undef'; % signal that there is no terminator yet
end
end
end
if (ischar(convTerm)) % if no convergence terminator is defined so far, use fitness calls
if (ischar(convTerm)) % if no convergence terminator is defined so far, use fitness calls
if (isempty(maxEvals))
error('Error: no termination criterion defined! Please check options.');
% int.opts.MaxFunEvals = OptimizerFactory.getDefaultFitCalls;
@@ -61,9 +62,9 @@ if ((nargin == 2) || (nargin == 3))
end
convTerm = EvaluationTerminator(maxEvals);
javaeva.OptimizerFactory.setTerminator(convTerm);
else % there is a convergence terminator
else % there is a convergence terminator
javaeva.OptimizerFactory.setTerminator(convTerm); % so set it
if (~isempty(maxEvals))
if (~isempty(maxEvals) && (maxEvals > 0))
% if TolX/TolFun plus MaxFunEvals is defined additionally, combine an
% EvaluationTerminator in disjunction, as Matlab does.
javaeva.OptimizerFactory.addTerminator(EvaluationTerminator(maxEvals), 0);
@@ -73,14 +74,21 @@ if ((nargin == 2) || (nargin == 3))
% set display
if (strcmp(int.opts.Display,'off') || isempty(int.opts.Display))
int.mp.setStatsOutput(0);
elseif (strcmp(int.opts.Display, 'iter'))
elseif (strcmp(int.opts.Display, 'final'))
int.mp.setStatsOutput(1);
elseif (strcmp(int.opts.Display, 'notify'))
% 'notify' is not the perfect notion for "show every k-th
% iteration", but optimset wont allow changing names.
int.mp.setStatsOutput(2);
elseif (strcmp(int.opts.Display, 'iter'))
% this should rather be 2 in JE slang, but in matlab slang its more like 3
int.mp.setStatsOutput(3);
else
error('invalid Display option, only off/iter are recognized');
error('invalid Display option, only off/final/notify/iter are recognized');
end
int=runEvalLoopJE(int, 1, optType, outputFilePrefix, -1, -1, -1);
else
error('Wrong number of arguments!')
end

32
resources/MatlabInterface/@JEInterface/runEvalLoopJE.m
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@@ -2,6 +2,10 @@ function int=runEvalLoopJE(int, optOrPostProc, optType, outputFilePrefix, steps,
% Internal method starting a JavaEvA optimization loop.
% Calling this directly may interfere with optimization.
% This function handles the communciation between JE and Matlab, main
% optimization configuration is done in the
% optimize/optimizeWith/postProcess functions from which this one should be
% called.
% optOrPostProc: 1 for optimize, 2 for postProcess
% optType, outputFilePrefix are parameters for optimize, dont care when
% postprocessing.
@@ -35,17 +39,19 @@ end
% own stop button). we decide this by checking if the global variable
% 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 (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]);
drawnow;
% set it to 0 now
if isempty(stopOptimization),
% set switch to 0 now
stopOptimization = 0;
% create a cancel button box (case without SBtoolbox)
boxHandle=figure('Position',[100 600 250 80], 'MenuBar', 'none', 'Name', 'JavaEvA optimization running...', 'NumberTitle','off');
uicontrol(boxHandle,'Style', 'pushbutton', 'String', 'Cancel', 'Position', [25 25 60 30], 'Callback', 'global stopOptimization; stopOptimization=1;');
uicontrol(boxHandle,'Style', 'text', 'String', stopText, 'Position', [100 25 120 30]);
drawnow;
% set flag for non toolbox optimization
nontoolboxopt = 1;
else
% disp('seems like the toolbox is going on');
% its an estimation using the toolbox' parameter estimation thing
nontoolboxopt = 0;
end
@@ -77,10 +83,12 @@ 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
% why should this be done more than once in the end?
%if (nontoolboxopt == 1)
% if (ishandle(int.boxHandle)) , close(int.boxHandle); int.boxHandle=''; end
% clear global stopOptimization
%end
end
% write back results
@@ -94,6 +102,6 @@ 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,
if (ishandle(h)) , close(h); end
if (ishandle(boxHandle)) , close(boxHandle); end
clear global stopOptimization
end

1
resources/MatlabInterface/@JEInterface/stopOptimize.m
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@@ -16,6 +16,7 @@ if (nargin > 1) && (ischar(varargin{1}) && (strcmp(varargin{1},'kill')==1))
JEMediator.quit; % just in case
JEMediator='';
clear global JEMediator;
clear global stopOptimization;
else
disp('no mediator to kill');
end