- replace NaN values in condition columns with their model value

Author: fbergmann

copasi_petab_importer/convert_petab.py

@@ -600,8 +600,26 @@ def create_mapping(self, experiments, petab):
                         continue
                 obj_map.setRole(num_cols + i, role)
 
-    def generate_copasi_data(self, petab):
+    def update_conditions(self, petab):
+        # go through all columns of the condition table
+        # and replace potential NaN entries with the value from the model
+        # ignore the first column (conditionId)
+        for col in petab.condition_data.columns[1:]:
+            if petab.condition_data[col].isna().any():
+                for i in range(petab.condition_data.shape[0]):
+                    if np.isnan(petab.condition_data.loc[i, col]):
+                        obj = dm.findObjectByDisplayName(str('Values[' + col + ']'))
+                        if obj is None:
+                            obj = dm.findObjectByDisplayName(col)
+                        if obj is not None:
+                            if isinstance(obj, COPASI.CMetab):
+                                value = obj.getInitialConcentration()
+                            else:
+                                value = obj.getInitialValue()
+                            petab.condition_data.loc[i, col] = value
 
+    def generate_copasi_data(self, petab):
+        self.update_conditions(petab)
         self.experiments = self.get_experiments(petab)
         self.write_experiments(self.experiments, petab)
         self.create_mapping(self.experiments, petab)

test/test_importer.py

@@ -16,6 +16,7 @@
 except ImportError:
     petab_tests_available = False
 
+
 class TestConverter(unittest.TestCase):
     def test_copasi_version(self):
         self.assertGreater(int(COPASI.CVersion.VERSION.getVersionDevel()),  214,
@@ -45,6 +46,7 @@ def test_import_bruno(self):
         converter.convert()
 
         self.assertTrue(os.path.exists(converter.experimental_data_file))
+
     @unittest.skipIf(not os.path.exists(_BENCHMARK_DIR), 'benchmarks not available')
     def test_import_bachmann(self):
         petab_dir = os.path.join(_BENCHMARK_DIR, 'Bachmann_MSB2011')
@@ -58,6 +60,7 @@ def test_import_bachmann(self):
         converter.convert()
 
         self.assertTrue(os.path.exists(converter.experimental_data_file))
+
     @unittest.skipUnless(petab_tests_available, 'petabtests need to be installed to run this')
     def test_petabtest_import(self):
         cases = [c for c in glob.glob(str(petabtests.CASES_DIR) + '/*/*.yaml') if '0' in c and 'solution' not in c]