Fix in export functions

SBML: init parameters were not assigned correctly PEtab: log trafo of observables was not correct
Data2Dynamics · Jul 1, 2024 · 4275344 · 4275344
1 parent 1b910bb
commit 4275344
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Showing 2 changed files with 8 additions and 4 deletions.
diff --git a/arFramework3/ImportExport/arExportPEtab.m b/arFramework3/ImportExport/arExportPEtab.m
@@ -95,7 +95,11 @@ function arExportPEtab(name, export_SBML)
     % reformat to match PEtab requirements
     finalCondTab = array2table(transpose(condT{:,:}));
     finalCondTab = [condT.Properties.VariableNames', finalCondTab];
-    finalCondTab.Properties.VariableNames = ['conditionID' finalCondTab{1,2:end}];
+    if all(qRemove)
+        finalCondTab.Properties.VariableNames = {'conditionID'};
+    else    
+        finalCondTab.Properties.VariableNames = ['conditionID' finalCondTab{1,2:end}];
+    end
     finalCondTab = finalCondTab(3:end, :);
 
     % export conditions table
@@ -202,7 +206,7 @@ function arExportPEtab(name, export_SBML)
         rowsToAdd = [table(repmat(IDs.obs{d}(iy), [length(time),1]), 'VariableNames', {'observableId'})];
 
         % convert measurements if necessary (log10, normalize)
-        if ar.model(m).data(d).logfitting(iy)
+        if ar.model(m).data(d).logplotting(iy)
             measurement = 10.^(ar.model(m).data(d).yExp(:, iy));
         else
             measurement = ar.model(m).data(d).yExp(:, iy);

diff --git a/arFramework3/ImportExport/arExportSBML_FullModel.m b/arFramework3/ImportExport/arExportSBML_FullModel.m
@@ -223,8 +223,8 @@ function arExportSBML_FullModel(m,name)
             elseif(sum(qp)==0 || is_set)
                 qp = ismember(ar.model(m).p, ar.model(m).px0{jx}); %R2013a compatible
                 if(sum(qp)==1)
-                    % pvalue = char(arSym(ar.model(m).fp{qp}));
-                    pvalue = char(arSym(ar.model(m).p{qp}));
+                    pvalue = char(arSym(ar.model(m).fp{qp}));
+                    % pvalue = char(arSym(ar.model(m).p{qp}));
                     %                     if(~isnan(str2num(pvalue))) %#ok
                     %                         pvalue = str2num(pvalue); %#ok
                     %                         M.species(jx).initialConcentration = pvalue;