Merge pull request #400 from ICB-DCM/fix_382

Fix(python) Replace logX(.) by log(X,.) in observables during model i…
AMICI-dev · Aug 13, 2018 · 62a8dc3 · 62a8dc3
2 parents 7153063 + ad205d7
commit 62a8dc3
Showing 1 changed file with 2 additions and 0 deletions.
diff --git a/python/amici/sbml_import.py b/python/amici/sbml_import.py
@@ -784,6 +784,8 @@ def computeModelEquationsObjectiveFunction(self, observables={}, sigmas={}):
 
         # add user-provided observables or make all species observable
         if(observables):
+            # Replace logX(.) by log(X,.) since symengine cannot parse the former
+            observables = { key: re.sub(r'(^|\W)log(\d+)\(', r'\1log(\2, ', formula) for key, formula in observables.items() }
             self.observables = sp.DenseMatrix([observables[observable]['formula'] for observable in observables])
             observableNames = [observables[observable]['name'] if 'name' in observables[observable].keys()
                                else 'y' + str(index)