Updates transient function

arFramework3/Examples/ToyModels/TransientFunction/TransientFunction_library/WriteTextSummary.m

@@ -0,0 +1,82 @@
+% WriteTextSummary(fit, folder)
+% 
+%   fit     a fit or cell array of fits as generated by
+%   arConditon2NewDataStruct*.m
+% 
+%   folder  [WriteTextSummary]
+% 
+% This function write matlab code for simulating the dynamics based on
+% fitted transient functions in the specified folder.
+% 
+%   Example:
+% arLoad
+% fits = arApproximateTimeCoursesByTransientFunction2;
+% WriteTextSummary(fits)
+% t = linspace(0,100,101);
+% plot(t,feval(fits{1}.label,t));
+
+function WriteTextSummary(fit,folder)
+if ~exist('folder','var') || isempty(folder)
+    folder = 'WriteTextSummary';
+end
+if ~isdir(folder)
+    mkdir(folder);
+end
+
+if iscell(fit)
+    for i=1:length(fit)
+        if isfield(fit{i},'pLabel') % otherwise fitting failed
+            WriteTextSummary(fit{i});
+        else
+            fprintf('WriteTextSummary.m: It seems that fit{%i} fitting was failed.\n',i)
+        end
+    end
+
+else
+    if isfield(fit,'label')
+        name = sprintf('%s',fit.label);
+    else
+        name = sprintf('Model%i_%s_condition%i',fit.m, fit.x, fit.c);
+    end
+    name = strrep(name,' ','_');
+    filename = [folder,filesep,name,'.m'];
+    fid = fopen(filename,'w');
+
+    fprintf(fid,'%s This function can be used to approximate model%i, condition%i, dynamic variable %s\n\n','%',fit.m, fit.c, fit.x);
+    fprintf(fid,'function [out, outSD] = %s(t)\n',name);
+    for i=1:length(fit.data.p)
+        if strcmp('init____dummy___',fit.data.p{i})~=1  % omit this D2D dummy parameter
+            if strcmp(fit.data.p{i},fit.data.fp{i})~=1
+                fprintf(fid,'%s = %s;\n',fit.data.p{i},fit.data.fp{i});
+            else
+                ind = strmatch(fit.data.p{i},fit.pLabel,'exact');
+                fprintf(fid,'%s = %f;\n',fit.data.p{i},fit.p(ind));
+            end
+        end
+    end
+    fprintf(fid,'\n');
+    for i=1:length(fit.data.fu)
+        fprintf(fid,'%s = %s;\n',fit.u{i},Replacements(fit.data.fu{i}));
+    end
+    fprintf(fid,'\n');
+    for i=1:length(fit.data.fy)
+        fprintf(fid,'out = %s;\n',Replacements(fit.data.fy{i}));
+    end
+    fprintf(fid,'\n');
+    fprintf(fid,'outSD = NaN(size(out));\n');
+    fprintf(fid,'outSD(:) = %f;\n',fit.approxErr);
+    fprintf(fid,'\n');
+
+
+
+
+
+    fclose(fid);
+end
+
+
+function out = Replacements(in)
+out = strrep(in,'*','.*');
+out = strrep(out,'/','./');
+out = strrep(out,'^','.^');
+

arFramework3/Examples/ToyModels/TransientFunction/TransientFunction_library/arApproximateTimeCoursesByTransientFunction2.m

@@ -100,7 +100,7 @@
 % load tmp fits % if specific fits should only be fitted
 %%
 for d=1:length(fits)    
-%     try
+    try
         arInit;
         arLoadModel('TransientFunction_ForConditionFit2');
 %         fits{d}.data.fp{4} = '(100)'  % for bachmann and conditions with too short tExp
@@ -156,17 +156,22 @@
             plotFitTransient(fits(d),plotfolder);
         end
 
-%     catch ERR
-%         pcatch{end+1} = struct('p',ar.p,'lb',ar.lb,'ub',ar.ub);
-%         save error ok pcatch
-%     end
+    catch ERR
+        pcatch{end+1} = struct('p',ar.p,'lb',ar.lb,'ub',ar.ub);
+        save error ok pcatch
+    end
 end
+save arApproximateTimeCoursesByTransientFunction2
 arPlot
 
 
 %% calculate the approximation error from the fitted SD
 for i=1:length(fits)
-    fits{i}.approxErr = 10.^fits{i}.p(4)./range(fits{i}.data.yExp);
+    if(isfield(fits{i},''))
+        fits{i}.approxErr = 10.^fits{i}.p(4)./range(fits{i}.data.yExp);
+    else
+        fits{i}.approxErr = NaN*range(fits{i}.data.yExp);
+    end
 end
 
 

arFramework3/Examples/ToyModels/TransientFunction/TransientFunction_library/arSetParsTransient.m

@@ -0,0 +1,42 @@
+% This function calls arSetPars but also translates info (e.g. bounds) into
+% ar.fit_transient
+function arSetParsTransient(pLabel, varargin)
+global ar
+if length(varargin)>0
+    p = varargin{1};
+else
+    p = [];
+end
+if length(varargin)>1
+    qFit = varargin{2};
+else
+    qFit = [];
+end
+if length(varargin)>2
+    qLog10 = varargin{3};
+else
+    qLog10 = [];
+end
+if length(varargin)>3
+    lb = varargin{4};
+else
+    lb = [];
+end
+if length(varargin)>4
+    ub = varargin{5};
+else
+    ub = [];
+end
+
+% translate bounds to fit_transient.bounds
+if(isfield(ar,'fit_transient'))
+    ind = strmatch(pLabel,ar.fit_transient.bounds.pLabel,'exact');
+    if ~isemtpy(lb)
+        ar.fit_transient.bounds.lb(ind) = lb;
+    end
+    if ~isemtpy(ub)
+        ar.fit_transient.bounds.ub(ind) = ub;
+    end
+end
+% arSetPars(pLabel, [p], [qFit], [qLog10], [lb], [ub], [type], [meanp], [stdp])
+arSetPars(pLabel_or_ar, varargin{:})