From f18ae8b8b77c7a8e86ff6fb8d0bbd9a8e32e4fa4 Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Mon, 13 Aug 2018 18:22:12 +0200 Subject: [PATCH 1/2] Fix(python) Replace logX(.) by log(X,.) in observables during model import (Fixes #382) --- python/amici/sbml_import.py | 1 + 1 file changed, 1 insertion(+) diff --git a/python/amici/sbml_import.py b/python/amici/sbml_import.py index 46a9458f24..22db7cec70 100644 --- a/python/amici/sbml_import.py +++ b/python/amici/sbml_import.py @@ -784,6 +784,7 @@ def computeModelEquationsObjectiveFunction(self, observables={}, sigmas={}): # add user-provided observables or make all species observable if(observables): + 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) From ad205d77fd19d65e1e549111aa973fff53e7538b Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Mon, 13 Aug 2018 18:25:18 +0200 Subject: [PATCH 2/2] Fix(python) Replace logX(.) by log(X,.) in observables during model import (Fixes #382) --- python/amici/sbml_import.py | 1 + 1 file changed, 1 insertion(+) diff --git a/python/amici/sbml_import.py b/python/amici/sbml_import.py index 22db7cec70..64c7f5138b 100644 --- a/python/amici/sbml_import.py +++ b/python/amici/sbml_import.py @@ -784,6 +784,7 @@ 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()