Fix/use display names (#184)

* use display name when creating type mapping in AgentData

* fix physicell tests

* add test for using correct display name

Author: Blair Lyons

simulariumio/data_objects/agent_data.py

@@ -214,14 +214,14 @@ def get_type_ids_and_mapping(self) -> Tuple[np.ndarray, Dict[str, Any]]:
                     tid = last_tid
                     last_tid += 1
                     type_id_mapping[type_name] = tid
-                    type_name_mapping[str(tid)] = {"name": type_name}
                     if type_name not in self.display_data:
                         raise DataError(
                             f"Please provide DisplayData for agent type {type_name}"
                         )
-                    type_name_mapping[str(tid)]["geometry"] = dict(
-                        self.display_data[type_name]
-                    )
+                    type_name_mapping[str(tid)] = {
+                        "name": self.display_data[type_name].name,
+                        "geometry" : dict(self.display_data[type_name])
+                    }
                 type_ids[time_index][agent_index] = type_id_mapping[type_name]
         return type_ids, type_name_mapping
 

simulariumio/physicell/physicell_converter.py

@@ -223,7 +223,7 @@ def _get_trajectory_data(
                     last_id=last_id,
                     type_mapping=type_mapping,
                 )
-                if type_mapping[tid] not in input_data.display_data:
+                if type_mapping[tid] not in result.display_data:
                     result.display_data[type_mapping[tid]] = DisplayData(
                         name=type_mapping[tid],
                         display_type=DISPLAY_TYPE.SPHERE,
@@ -376,6 +376,7 @@ def _read(
                             phase_id
                         )
                     agent_data.display_data[type_name] = display_data
+                    agent_data.display_data[type_name].name = type_name
         input_data.meta_data.scale_factor = scale_factor
         input_data.meta_data._set_box_size()
         return TrajectoryData(

simulariumio/tests/converters/test_trajectory_converter.py

@@ -274,6 +274,15 @@ def test_camera_defaults(camera, expected_camera):
 
 
 # test type mapping
+test_display_name = "Test display name"
+default_agents_converter._data.agent_data.display_data["C"].name = test_display_name
+default_agents_data_display_name = JsonWriter.format_trajectory_data(
+    default_agents_converter._data
+)
+display_name_type_mapping = minimal_custom_type_mappings()
+display_name_type_mapping["0"]["name"] = test_display_name
+
+
 @pytest.mark.parametrize(
     "typeMapping, expected_typeMapping",
     [
@@ -306,6 +315,10 @@ def test_camera_defaults(camera, expected_camera):
                 },
             },
         ),
+        (
+            default_agents_data_display_name["trajectoryInfo"]["typeMapping"],
+            display_name_type_mapping,
+        ),
     ],
 )
 def test_type_mapping(typeMapping, expected_typeMapping):