- when adding fit parameters, ensure that they are for initial refere…

…nces, not transient ones

basico/model_info.py

@@ -4469,12 +4469,15 @@ def _get_named_value(obj, name):
     return value
 
 
-def _get_object(name_or_reference, **kwargs):
+def _get_object(name_or_reference, initial=False, **kwargs):
     """Returns the reference object for the given name
 
     :param name_or_reference: display name of model element
     :type name_or_reference: str or COPASI.CDataObject
 
+    :param initial: if True, an initial reference will be returned, rather than a transient one
+    :type initial: bool
+
     :param kwargs: optional parameters
 
         - | `model`: to specify the data model to be used (if not specified
@@ -4491,17 +4494,45 @@ def _get_object(name_or_reference, **kwargs):
         obj = model.findObjectByDisplayName(name_or_reference)
         if obj is None:
             return None
-        if obj.getObjectType() != 'Reference':
-            obj = obj.getValueReference()
+        if obj.getObjectType() == 'Metabolite':
+            if initial:
+                obj = obj.getInitialConcentrationReference()
+            else:
+                obj = obj.getConcentrationReference()
+        elif obj.getObjectType() != 'Reference':
+            if initial and not isinstance(obj, COPASI.CCopasiParameter):
+                obj = obj.getInitialValueReference()
+            else:
+                obj = obj.getValueReference()
+
+        # ensure reference is initial or transient as required
+        if initial:
+            obj_name = obj.getObjectName()
+            if obj_name == 'Concentration':
+                obj = obj.getObjectParent().getInitialConcentrationReference()
+            if obj_name in ['Value', 'Volume', 'ParticleNumber']:
+                parent = obj.getObjectParent()
+                if not isinstance(parent, COPASI.CCopasiParameter):
+                    obj = parent.getInitialValueReference()
+        else:
+            obj_name = obj.getObjectName()
+            if obj_name == 'InitialConcentration':
+                obj = obj.getObjectParent().getConcentrationReference()
+            if obj_name in ['InitialValue', 'InitialVolume', 'InitialParticleNumber']:
+                parent = obj.getObjectParent()
+                obj = parent.getValueReference()
     return obj
 
 
-def get_value(name_or_reference, **kwargs):
+def get_value(name_or_reference, initial=False, **kwargs):
     """Gets the value of the named element or nones
 
     :param name_or_reference: display name of model element
     :type name_or_reference: str or COPASI.CDataObject
 
+    :param initial: if True, an initial value will be returned, rather than a transient one
+    :type initial: bool
+
     :param kwargs: optional parameters
 
         - | `model`: to specify the data model to be used (if not specified
@@ -4512,20 +4543,23 @@ def get_value(name_or_reference, **kwargs):
     """
     model = model_io.get_model_from_dict_or_default(kwargs)
 
-    obj = _get_object(name_or_reference, model=model)
+    obj = _get_object(name_or_reference, initial=initial, model=model)
 
     if obj is None:
         return None
 
     return _get_value_from_reference(obj)
 
 
-def get_cn(name_or_reference, **kwargs):
+def get_cn(name_or_reference, initial=False, **kwargs):
     """Gets the cn of the named element or none
 
     :param name_or_reference: display name of model element
     :type name_or_reference: str or COPASI.CDataObject
 
+    :param initial: if True, an initial reference cn will be returned, rather than a transient one
+    :type initial: bool
+
     :param kwargs: optional parameters
 
         - | `model`: to specify the data model to be used (if not specified
@@ -4536,7 +4570,7 @@ def get_cn(name_or_reference, **kwargs):
     """
     model = model_io.get_model_from_dict_or_default(kwargs)
 
-    obj = _get_object(name_or_reference, model=model)
+    obj = _get_object(name_or_reference, initial=initial, model=model)
 
     if obj is None:
         return None

basico/task_parameterestimation.py

@@ -686,14 +686,12 @@ def set_fit_parameters(fit_parameters, model=None):
         if 'cn' in item:
             cn = COPASI.CCommonName(item.cn)
 
-        if 'name' in item:
+        elif 'name' in item:
             name = item['name']
             if not cn:
-                obj = model.findObjectByDisplayName(name)
+                obj = basico.model_info._get_object(name, initial=True, model=model)
                 if obj:
                     cn = obj.getCN()
-                    if _get_role_for_reference(obj.getObjectName()) == COPASI.CExperiment.ignore:
-                        cn = obj.getValueReference().getCN()
 
         if not cn:
             logging.warning('object {0} not found'.format(name))