Add event logging

src/arcade/patch/PatchARCADE.java

@@ -34,6 +34,7 @@ public OutputSaver getSaver(Series series) {
         PatchOutputSaver saver = new PatchOutputSaver(series);
         saver.saveGraph = settings.contains("SAVE_GRAPH");
         saver.saveLattice = settings.contains("SAVE_LAYERS");
+        saver.saveEvents = settings.contains("SAVE_EVENTS");
         return saver;
     }
 }

src/arcade/patch/agent/module/PatchModuleCytotoxicity.java

@@ -1,12 +1,16 @@
 package arcade.patch.agent.module;
 
+import java.util.HashMap;
+import java.util.Map;
 import ec.util.MersenneTwisterFast;
 import arcade.core.sim.Simulation;
 import arcade.core.util.Parameters;
 import arcade.patch.agent.cell.PatchCell;
 import arcade.patch.agent.cell.PatchCellCART;
 import arcade.patch.agent.cell.PatchCellTissue;
 import arcade.patch.agent.process.PatchProcessInflammation;
+import arcade.patch.env.location.PatchLocation;
+import arcade.patch.sim.PatchSimulation;
 import static arcade.patch.util.PatchEnums.Domain;
 import static arcade.patch.util.PatchEnums.State;
 
@@ -68,6 +72,18 @@ public void step(MersenneTwisterFast random, Simulation sim) {
                 tissueCell.setState(State.APOPTOTIC);
                 granzyme--;
                 inflammation.setInternal("granzyme", granzyme);
+
+                // Log cytotoxicity event
+                PatchSimulation patchSim = (PatchSimulation) sim;
+                Map<String, Object> eventData = new HashMap<>();
+                eventData.put("t-cell-id", cell.getID());
+                eventData.put("tissue-cell-id", target.getID());
+                eventData.put("tissue-cell-type", target.getPop());
+                eventData.put("type", "lysis");
+                eventData.put("timestamp", (int) ((PatchSimulation) sim).getSchedule().getTime());
+                eventData.put(
+                        "tissue-location", ((PatchLocation) target.getLocation()).getCoordinate());
+                patchSim.logEvent(eventData);
             }
         }
 

src/arcade/patch/command.patch.xml

@@ -1,4 +1,5 @@
 <commands>
     <switch id="SAVE_GRAPH" short="g" long="graph" help="Save the GRAPH output files" />
     <switch id="SAVE_LAYERS" short="l" long="layers" help="Save the LAYERS output files" />
+    <switch id="SAVE_EVENTS" short="e" long="events" help="Save the EVENTS output files" />
 </commands>

src/arcade/patch/sim/PatchSimulation.java

@@ -4,6 +4,8 @@
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
 import java.util.Set;
 import com.google.gson.reflect.TypeToken;
 import sim.engine.Schedule;
@@ -55,6 +57,9 @@ public abstract class PatchSimulation extends SimState implements Simulation {
     /** Cell ID tracker. */
     int id;
 
+    /** List to store events throughout the simulation. */
+    private final List<Map<String, Object>> events;
+
     /** Location factory instance for the simulation. */
     public final PatchLocationFactory locationFactory;
 
@@ -81,6 +86,7 @@ public PatchSimulation(long seed, Series series) {
         this.locationFactory = makeLocationFactory();
         this.cellFactory = makeCellFactory();
         this.latticeFactory = makeLatticeFactory();
+        this.events = new ArrayList<>();
     }
 
     @Override
@@ -214,6 +220,24 @@ public Set<Location> getAllLocations() {
         return locations;
     }
 
+    /**
+     * Log an event to the simulation's event list.
+     *
+     * @param event logging information corresponding to the event
+     */
+    public void logEvent(Map<String, Object> event) {
+        events.add(event);
+    }
+
+    /**
+     * Get the list of events logged during the simulation.
+     *
+     * @return the list of events
+     */
+    public List<Map<String, Object>> getEvents() {
+        return new ArrayList<>(events);
+    }
+
     /**
      * Called at the start of the simulation to set up agents and environment and schedule actions
      * and components as needed.

src/arcade/patch/sim/output/PatchOutputSaver.java

@@ -1,5 +1,7 @@
 package arcade.patch.sim.output;
 
+import java.util.List;
+import java.util.Map;
 import com.google.gson.Gson;
 import arcade.core.env.component.Component;
 import arcade.core.sim.Series;
@@ -17,6 +19,9 @@ public final class PatchOutputSaver extends OutputSaver {
     /** {@code true} to save lattices, {@code false} otherwise. */
     public boolean saveLattice;
 
+    /** {@code true} to save events, {@code false} otherwise. */
+    public boolean saveEvents;
+
     /**
      * Creates an {@code PatchOutputSaver} for the series.
      *
@@ -61,6 +66,22 @@ public void saveLayers(int tick) {
         write(patch, format(json, FORMAT_ELEMENTS));
     }
 
+    /**
+     * Save the collection of events to a JSON.
+     *
+     * @param tick the simulation tick
+     */
+    public void saveEventsToFile(int tick) {
+        if (saveEvents) {
+            List<Map<String, Object>> events = ((PatchSimulation) sim).getEvents();
+            if (!events.isEmpty()) {
+                String json = gson.toJson(events);
+                String path = prefix + String.format("_%06d.EVENTS.json", tick);
+                write(path, format(json, FORMAT_ELEMENTS));
+            }
+        }
+    }
+
     @Override
     public void save(int tick) {
         super.save(tick);
@@ -70,5 +91,8 @@ public void save(int tick) {
         if (saveLattice) {
             saveLayers(tick);
         }
+        if (saveEvents) {
+            saveEventsToFile(tick);
+        }
     }
 }

test/arcade/patch/agent/module/PatchModuleCytotoxicityTest.java

@@ -3,11 +3,14 @@
 import java.lang.reflect.Field;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
+import sim.engine.Schedule;
 import ec.util.MersenneTwisterFast;
 import arcade.core.util.Parameters;
 import arcade.patch.agent.cell.PatchCellCART;
 import arcade.patch.agent.cell.PatchCellTissue;
 import arcade.patch.agent.process.PatchProcessInflammation;
+import arcade.patch.env.location.Coordinate;
+import arcade.patch.env.location.PatchLocation;
 import arcade.patch.sim.PatchSimulation;
 import arcade.patch.util.PatchEnums.State;
 import static org.mockito.Mockito.*;
@@ -24,13 +27,20 @@ public class PatchModuleCytotoxicityTest {
 
     private PatchSimulation sim;
 
+    private PatchLocation mockLocation;
+
+    private Schedule mockSchedule;
+
     private MersenneTwisterFast randomMock;
 
     @BeforeEach
     public final void setUp() {
         mockCell = mock(PatchCellCART.class);
         mockTarget = mock(PatchCellTissue.class);
         mockInflammation = mock(PatchProcessInflammation.class);
+        mockLocation = mock(PatchLocation.class);
+        mockSchedule = mock(Schedule.class);
+
         sim = mock(PatchSimulation.class);
         randomMock = mock(MersenneTwisterFast.class);
         Parameters parameters = mock(Parameters.class);
@@ -41,6 +51,14 @@ public final void setUp() {
         when(mockCell.getProcess(any())).thenReturn(mockInflammation);
         when(mockInflammation.getInternal("granzyme")).thenReturn(1.0);
         when(mockCell.getBoundTarget()).thenReturn(mockTarget);
+        when(mockCell.getID()).thenReturn(1);
+        when(mockTarget.getID()).thenReturn(1);
+        when(mockTarget.getPop()).thenReturn(1);
+        when(mockTarget.getLocation()).thenReturn(mockLocation);
+
+        when(mockLocation.getCoordinate()).thenReturn(mock(Coordinate.class));
+        when(sim.getSchedule()).thenReturn(mockSchedule);
+        when(mockSchedule.getTime()).thenReturn(0.0);
 
         action = new PatchModuleCytotoxicity(mockCell);
     }