Adding and logging cell cycles

src/arcade/patch/agent/action/PatchActionConvert.java

@@ -87,7 +87,8 @@ public void step(SimState simstate) {
                         oldCell.getVolume(),
                         oldCell.getHeight(),
                         oldCell.getCriticalVolume(),
-                        oldCell.getCriticalHeight());
+                        oldCell.getCriticalHeight(),
+                        oldCell.getCycles());
         PatchCell newCell =
                 (PatchCell) cellContainer.convert(sim.cellFactory, location, sim.random);
         grid.addObject(newCell, location);

src/arcade/patch/agent/cell/PatchCell.java

@@ -123,12 +123,12 @@ public abstract class PatchCell implements Cell {
     /** Cell parameters. */
     final Parameters parameters;
 
+    /** List of cell cycle lengths (in minutes). */
+    public final Bag cycles = new Bag();
+
     /** Cell population links. */
     final GrabBag links;
 
-    /** List of cell cycle lengths (in minutes). */
-    private final Bag cycles = new Bag();
-
     /** If cell is stopped in the simulation. */
     private boolean isStopped;
 
@@ -410,7 +410,8 @@ public CellContainer convert() {
                 volume,
                 height,
                 criticalVolume,
-                criticalHeight);
+                criticalHeight,
+                cycles);
     }
 
     /**

src/arcade/patch/agent/cell/PatchCellCARTCD4.java

@@ -52,7 +52,8 @@ public PatchCellContainer make(int newID, CellState newState, MersenneTwisterFas
                 volume,
                 height,
                 criticalVolume,
-                criticalHeight);
+                criticalHeight,
+                cycles);
     }
 
     @Override

src/arcade/patch/agent/cell/PatchCellCARTCD8.java

@@ -52,7 +52,8 @@ public PatchCellContainer make(int newID, CellState newState, MersenneTwisterFas
                 volume,
                 height,
                 criticalVolume,
-                criticalHeight);
+                criticalHeight,
+                cycles);
     }
 
     @Override

src/arcade/patch/agent/cell/PatchCellCancer.java

@@ -71,7 +71,8 @@ public PatchCellContainer make(int newID, CellState newState, MersenneTwisterFas
                 volume,
                 height,
                 criticalVolume,
-                criticalHeight);
+                criticalHeight,
+                cycles);
     }
 
     /**

src/arcade/patch/agent/cell/PatchCellCancerStem.java

@@ -65,6 +65,7 @@ public PatchCellContainer make(int newID, CellState newState, MersenneTwisterFas
                 volume,
                 height,
                 criticalVolume,
-                criticalHeight);
+                criticalHeight,
+                cycles);
     }
 }

src/arcade/patch/agent/cell/PatchCellContainer.java

@@ -1,5 +1,6 @@
 package arcade.patch.agent.cell;
 
+import sim.util.Bag;
 import ec.util.MersenneTwisterFast;
 import arcade.core.agent.cell.Cell;
 import arcade.core.agent.cell.CellContainer;
@@ -47,6 +48,9 @@ public final class PatchCellContainer implements CellContainer {
     /** Critical cell height [um]. */
     public final double criticalHeight;
 
+    /** Cell cycles. */
+    public final Bag cycles;
+
     /**
      * Creates a {@code PatchCellContainer} instance.
      *
@@ -60,6 +64,7 @@ public final class PatchCellContainer implements CellContainer {
      * @param height the cell height
      * @param criticalVolume the critical volume
      * @param criticalHeight the critical height
+     * @param cycles the cell cycles
      */
     public PatchCellContainer(
             int id,
@@ -71,7 +76,8 @@ public PatchCellContainer(
             double volume,
             double height,
             double criticalVolume,
-            double criticalHeight) {
+            double criticalHeight,
+            Bag cycles) {
         this.id = id;
         this.parent = parent;
         this.pop = pop;
@@ -82,6 +88,7 @@ public PatchCellContainer(
         this.height = height;
         this.criticalVolume = criticalVolume;
         this.criticalHeight = criticalHeight;
+        this.cycles = cycles;
     }
 
     @Override

src/arcade/patch/agent/cell/PatchCellFactory.java

@@ -6,6 +6,7 @@
 import java.util.HashSet;
 import java.util.Set;
 import java.util.logging.Logger;
+import sim.util.Bag;
 import ec.util.MersenneTwisterFast;
 import arcade.core.agent.cell.*;
 import arcade.core.sim.Series;
@@ -158,9 +159,19 @@ public PatchCellContainer createCellForPopulation(int id, int pop) {
         double volume = parameters.getDouble("CELL_VOLUME");
         double height = parameters.getDouble("CELL_HEIGHT");
         int age = parameters.getInt("CELL_AGE");
-
+        Bag cycles = new Bag();
         return new PatchCellContainer(
-                id, 0, pop, age, 0, State.UNDEFINED, volume, height, volume, height + compression);
+                id,
+                0,
+                pop,
+                age,
+                0,
+                State.UNDEFINED,
+                volume,
+                height,
+                volume,
+                height + compression,
+                cycles);
     }
 
     /**

src/arcade/patch/agent/cell/PatchCellRandom.java

@@ -56,7 +56,8 @@ public PatchCellContainer make(int newID, CellState newState, MersenneTwisterFas
                 volume,
                 height,
                 criticalVolume,
-                criticalHeight);
+                criticalHeight,
+                cycles);
     }
 
     @Override

src/arcade/patch/agent/cell/PatchCellTissue.java

@@ -82,7 +82,8 @@ public PatchCellContainer make(int newID, CellState newState, MersenneTwisterFas
                 volume,
                 height,
                 criticalVolume,
-                criticalHeight);
+                criticalHeight,
+                cycles);
     }
 
     @Override

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

@@ -10,6 +10,7 @@
 import com.google.gson.JsonElement;
 import com.google.gson.JsonObject;
 import com.google.gson.JsonParseException;
+import sim.util.Bag;
 import arcade.core.agent.cell.CellContainer;
 import arcade.core.env.location.LocationContainer;
 import arcade.core.sim.output.OutputDeserializer;
@@ -67,7 +68,10 @@ public PatchCellContainer deserialize(
             int divisions = jsonObject.get("divisions").getAsInt();
             double volume = jsonObject.get("volume").getAsDouble();
             double height = jsonObject.get("height").getAsDouble();
-
+            Bag cycles = new Bag();
+            for (JsonElement cycle : jsonObject.get("cycles").getAsJsonArray()) {
+                cycles.add(cycle.getAsDouble());
+            }
             State state = State.valueOf(jsonObject.get("state").getAsString());
 
             JsonArray criticals = jsonObject.get("criticals").getAsJsonArray();
@@ -84,7 +88,8 @@ public PatchCellContainer deserialize(
                     volume,
                     height,
                     criticalVolume,
-                    criticalHeight);
+                    criticalHeight,
+                    cycles);
         }
     }
 

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

@@ -10,6 +10,7 @@
 import com.google.gson.JsonObject;
 import com.google.gson.JsonSerializationContext;
 import com.google.gson.JsonSerializer;
+import sim.util.Bag;
 import arcade.core.agent.cell.CellContainer;
 import arcade.core.env.location.Location;
 import arcade.core.env.location.LocationContainer;
@@ -155,8 +156,13 @@
             criticals.add((int) (100 * src.criticalHeight) / 100.0);
             json.add("criticals", criticals);
 
             // TODO: add cycles
-
+            Bag cycles = src.cycles;
+            JsonArray jsonCycles = new JsonArray();
+            for (Object cycle : cycles) {
+                jsonCycles.add(cycle.toString());
+            }
+            json.add("cycles", jsonCycles);
             return json;
         }
     }

test/arcade/patch/agent/cell/PatchCellCARTCD4Test.java

@@ -5,6 +5,7 @@
 import org.junit.jupiter.api.Test;
 import sim.engine.Schedule;
 import sim.engine.Steppable;
+import sim.util.Bag;
 import ec.util.MersenneTwisterFast;
 import arcade.core.sim.Simulation;
 import arcade.core.util.MiniBox;
@@ -51,7 +52,7 @@ public final void setUp() {
         double criticalVolume = randomDoubleBetween(100, 200);
         double criticalHeight = randomDoubleBetween(4, 10);
         State state = State.UNDEFINED;
-
+        Bag cycles = new Bag();
         container =
                 new PatchCellContainer(
                         id,
@@ -63,7 +64,8 @@ public final void setUp() {
                         volume,
                         height,
                         criticalVolume,
-                        criticalHeight);
+                        criticalHeight,
+                        cycles);
 
         doReturn(1.0).when(parametersMock).getDouble(any(String.class));
         doReturn(1).when(parametersMock).getInt(any(String.class));

test/arcade/patch/agent/cell/PatchCellCARTCD8Test.java

@@ -5,6 +5,7 @@
 import org.junit.jupiter.api.Test;
 import sim.engine.Schedule;
 import sim.engine.Steppable;
+import sim.util.Bag;
 import ec.util.MersenneTwisterFast;
 import arcade.core.sim.Simulation;
 import arcade.core.util.MiniBox;
@@ -51,7 +52,7 @@ public final void setUp() throws NoSuchFieldException, IllegalAccessException {
         double criticalVolume = randomDoubleBetween(100, 200);
         double criticalHeight = randomDoubleBetween(4, 10);
         State state = State.UNDEFINED;
-
+        Bag cycles = new Bag();
         container =
                 new PatchCellContainer(
                         id,
@@ -63,7 +64,8 @@ public final void setUp() throws NoSuchFieldException, IllegalAccessException {
                         volume,
                         height,
                         criticalVolume,
-                        criticalHeight);
+                        criticalHeight,
+                        cycles);
 
         doReturn(0.0).when(parameters).getDouble(any(String.class));
         doReturn(0).when(parameters).getInt(any(String.class));

test/arcade/patch/agent/cell/PatchCellCARTTest.java

@@ -44,6 +44,8 @@ public class PatchCellCARTTest {
 
     private static Bag bag;
 
+    static Bag cycles = new Bag();
+
     static class PatchCellMock extends PatchCellCART {
         PatchCellMock(PatchCellContainer container, Location location, Parameters parameters) {
             super(container, location, parameters, null);
@@ -61,7 +63,8 @@ public PatchCellContainer make(int newID, CellState newState, MersenneTwisterFas
                     volume,
                     height,
                     criticalVolume,
-                    criticalHeight);
+                    criticalHeight,
+                    cycles);
         }
 
         @Override
@@ -98,7 +101,8 @@ public final void setUp() throws NoSuchFieldException, IllegalAccessException {
                         volume,
                         height,
                         criticalVolume,
-                        criticalHeight);
+                        criticalHeight,
+                        cycles);
 
         when(parameters.getDouble("ENERGY_THRESHOLD")).thenReturn(1.0);
         when(parameters.getDouble("NECROTIC_FRACTION"))

test/arcade/patch/agent/cell/PatchCellCancerStemTest.java

@@ -3,6 +3,7 @@
 import java.util.ArrayList;
 import org.junit.jupiter.api.BeforeAll;
 import org.junit.jupiter.api.Test;
+import sim.util.Bag;
 import ec.util.MersenneTwisterFast;
 import arcade.core.util.GrabBag;
 import arcade.core.util.MiniBox;
@@ -60,6 +61,8 @@ public class PatchCellCancerStemTest {
 
     static State cellState = State.QUIESCENT;
 
+    static Bag cellCycles = new Bag();
+
     @BeforeAll
     public static void setupMocks() {
         simMock = mock(PatchSimulation.class);
@@ -99,7 +102,8 @@ public void step_calledWhenAgeGreaterThanApoptosisAge_doesNotSetApoptoticState()
                             cellVolume,
                             cellHeight,
                             cellCriticalVolume,
-                            cellCriticalHeight);
+                            cellCriticalHeight,
+                            cellCycles);
             PatchCell cell = spy(new PatchCellCancerStem(container, locationMock, parametersMock));
             cell.module = module;
             cell.processes.put(Domain.METABOLISM, metabolismMock);
@@ -149,7 +153,8 @@ public void make_called_createsContainer() {
                         volume,
                         height,
                         criticalVolume,
-                        criticalHeight);
+                        criticalHeight,
+                        cellCycles);
 
         PatchCellCancerStem cell =
                 new PatchCellCancerStem(cellContainer, locationMock, parametersMock, links);
@@ -198,7 +203,8 @@ public void make_calledWithLinks_createsContainer() {
                         volume,
                         height,
                         criticalVolume,
-                        criticalHeight);
+                        criticalHeight,
+                        cellCycles);
 
         PatchCellCancerStem cell =
                 new PatchCellCancerStem(cellContainer, locationMock, parametersMock, links);

test/arcade/patch/agent/cell/PatchCellCancerTest.java

@@ -2,6 +2,7 @@
 
 import org.junit.jupiter.api.BeforeAll;
 import org.junit.jupiter.api.Test;
+import sim.util.Bag;
 import ec.util.MersenneTwisterFast;
 import arcade.core.util.GrabBag;
 import arcade.core.util.MiniBox;
@@ -56,6 +57,8 @@ public class PatchCellCancerTest {
 
     static State cellState = State.QUIESCENT;
 
+    static Bag cellCycles = new Bag();
+
     @BeforeAll
     public static void setupMocks() {
         simMock = mock(PatchSimulation.class);
@@ -99,7 +102,8 @@ public void make_called_createsContainer() {
                         volume,
                         height,
                         criticalVolume,
-                        criticalHeight);
+                        criticalHeight,
+                        cellCycles);
 
         PatchCellCancer cell =
                 new PatchCellCancer(cellContainer, locationMock, parametersMock, links);
@@ -148,7 +152,8 @@ public void make_calledWithLinks_createsContainer() {
                         volume,
                         height,
                         criticalVolume,
-                        criticalHeight);
+                        criticalHeight,
+                        cellCycles);
 
         PatchCellCancer cell =
                 new PatchCellCancer(cellContainer, locationMock, parametersMock, links);