add Priors to PEtab Import & Export

Author: timo-rachel

arFramework3/Advanced/arLoadParsPEtab.m

@@ -43,14 +43,21 @@ function arLoadParsPEtab(filename)
     end
 end
 
+% Remap PEtab prior types to d2d prior types
+T.initializationPriorType = cellstr(T.initializationPriorType);  % Convert char array to cell array of strings
+petab_to_d2d = containers.Map({'parameterScaleUniform', 'normal', 'uniform', 'laplace'}, {0, 1, 2, 3});
+T.initializationPriorType = cellfun(@(x) petab_to_d2d(x), T.initializationPriorType);
+
 % this is currently under development on the PEtab side.
-if isfield(T,'priorType')
+if isfield(T,'initializationPriorType')
 for i=1:length(BothPars)
-    if ischar(T.priorType(ib(i)))
-        if isnumeric(T.priorParameters)
-            arSetPrior(ia(i),T.priorType(ib(i)),T.priorParameters(ib(i),1),T.priorParameters(ib(i),2))
+    if ~isempty(T.initializationPriorType(ib(i)))
+        if T.initializationPriorType(ib(i)) ~= 0
+            PriorParameters = str2num(T.initializationPriorParameters(ib(i),:));
+            arSetPrior(ia(i),T.initializationPriorType(ib(i),:), ...
+                PriorParameters(1), PriorParameters(2))
         else
-            arSetPrior(ia(i),T.priorType(ib(i)))
+            arSetPrior(ia(i),T.initializationPriorType(ib(i),:))
         end
     end
 end

arFramework3/ImportExport/arExportPEtab.m

@@ -304,11 +304,32 @@ function writeParameterTable(IDs)
 lowerBound(ar.qLog10 == 1) = 10.^ar.lb(ar.qLog10 == 1);
 upperBound(ar.qLog10 == 1) = 10.^ar.ub(ar.qLog10 == 1);
 
+% priors
+% map d2d prior definations 0-3 to corresponding PEtab prior definations
+priorTypes = {'parameterScaleUniform', 'normal', 'uniform', 'laplace'};
+initializationPriorType = priorTypes(ar.type + 1);
+% initializationPriorParameters
+initializationPriorParameters = cell(size(ar.type));
+for i = 1:length(ar.type)
+    switch ar.type(i)
+        case 0  % No prior
+            initializationPriorParameters{i} = '';
+        case 1  % Normal
+            initializationPriorParameters{i} = sprintf('%f, %f', ar.mean(i), ar.std(i));
+        case 2  % Uniform
+            initializationPriorParameters{i} = sprintf('%f, %f', ar.lb(i), ar.ub(i));
+        case 3  % Laplace
+            initializationPriorParameters{i} = sprintf('%f, %f', ar.mean(i), ar.std(i));
+    end
+end
+
 % build table and write to disk
 variableNames = {'parameterId', 'parameterName', 'parameterScale', ...
-    'lowerBound', 'upperBound', 'nominalValue', 'estimate',};
+    'lowerBound', 'upperBound', 'nominalValue', 'estimate', ...
+    'initializationPriorType', 'initializationPriorParameters'};
 parT = table(parameterId(:), parameterName(:), parameterScale(:), ...
     lowerBound(:), upperBound(:), nominalValue(:), estimate(:), ...
+    initializationPriorType(:), initializationPriorParameters(:),...
     'VariableNames', variableNames);
 writetable(parT, ['PEtab' filesep IDs.name '_parameters.tsv'],...
     'Delimiter', '\t', 'FileType', 'text')

arFramework3/ImportExport/arImportPEtab.m

@@ -116,17 +116,6 @@ function arImportPEtab(name, doPreEq)
 arFindInputs(); % might overwrite parameters due to ar.pExtern, but input times might be in parameters table.
 arLoadParsPEtab(PEparas);
 
-if exist('Tms','var')
-    [BothPars,ia] = intersect(ar.pLabel,Tms_fn);
-    for i=1:length(BothPars)
-        if strcmp(Tms.(BothPars{i})(ms),'-')       % if Tms.(BothPars{i})(ms) == 0
-            arSetPars(BothPars(i), ar.p(ia), 0);
-            %else
-            %    arSetPars(BothPars(i), ar.p(ia)*Tms.(BothPars{i})(ms));
-        end
-    end
-end
-
 %% pre-equilibration
 if doPreEq
     tstart = -1e7;

arFramework3/arSetPrior.m

@@ -53,7 +53,9 @@ function arSetPrior( par, type, mean, std )
 
     for a = 1 : length( par )
         ar.type(par(a)) = type;
-        ar.mean(par(a)) = mean;
-        ar.std(par(a)) = std;
+        if ar.type(par(a)) ~= 0
+            ar.mean(par(a)) = mean;
+            ar.std(par(a)) = std;
+        end
     end
 end