PEtab parameter mapping: minor speedup

Avoid repeated lookups. Saves just a few seconds for Froehlich_CellSystems2018, but better than nothing...
dweindl · Jan 30, 2025 · d0ce54b · d0ce54b
1 parent 923b8f4
commit d0ce54b
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Showing 2 changed files with 12 additions and 8 deletions.
diff --git a/python/sdist/amici/petab/conditions.py b/python/sdist/amici/petab/conditions.py
@@ -134,16 +134,21 @@ def _get_par(model_par, value, mapping):
                 # condition table overrides must have been handled already,
                 # e.g. by the PEtab parameter mapping, but parameters from
                 # InitialAssignments may still be present.
-                if mapping[value] == model_par:
+                if (mapped_value := mapping[value]) == model_par:
                     # prevent infinite recursion
                     raise
-                return _get_par(value, mapping[value], mapping)
-        if model_par in problem_parameters:
+                return _get_par(value, mapped_value, mapping)
+
+        try:
             # user-provided
             return problem_parameters[model_par]
+        except KeyError:
+            pass
+
         # prevent nan-propagation in derivative
         if np.isnan(value):
             return 0.0
+
         # constant value
         return value
 

diff --git a/python/sdist/amici/petab/util.py b/python/sdist/amici/petab/util.py
@@ -26,14 +26,15 @@ def get_states_in_condition_table(
     if petab_problem.model.type_id not in (MODEL_TYPE_SBML, MODEL_TYPE_PYSB):
         raise NotImplementedError()
 
-    species_check_funs = {
+    species_check_fun = {
         MODEL_TYPE_SBML: lambda x: _element_is_sbml_state(
             petab_problem.sbml_model, x
         ),
         MODEL_TYPE_PYSB: lambda x: _element_is_pysb_pattern(
             petab_problem.model.model, x
         ),
-    }
+    }[petab_problem.model.type_id]
+
     states = {
         resolve_mapping(petab_problem.mapping_df, col): (None, None)
         if condition is None
@@ -48,9 +49,7 @@ def get_states_in_condition_table(
             else None,
         )
         for col in petab_problem.condition_df.columns
-        if species_check_funs[petab_problem.model.type_id](
-            resolve_mapping(petab_problem.mapping_df, col)
-        )
+        if species_check_fun(resolve_mapping(petab_problem.mapping_df, col))
     }
 
     if petab_problem.model.type_id == MODEL_TYPE_PYSB: