Adding new abstract potts proliferation module that does not progress through cell cycle

src/arcade/core/util/Vector.java

@@ -33,7 +33,7 @@ public Vector(Double3D vector) {
      * @return the x component
      */
     public double getX() {
-        return vector.x;
+        return vector.getX();
     }
 
     /**
@@ -42,7 +42,7 @@ public double getX() {
      * @return the y component
      */
     public double getY() {
-        return vector.y;
+        return vector.getY();
     }
 
     /**
@@ -51,7 +51,7 @@ public double getY() {
      * @return the z component
      */
     public double getZ() {
-        return vector.z;
+        return vector.getZ();
     }
 
     /**

src/arcade/potts/agent/cell/PottsCellFlyGMC.java

@@ -13,8 +13,8 @@
  * Implementation of {@link PottsCell} for fly GMC agents. These cells divide into two {@link
  * PottsCellFlyNeuron} cells. The links must be set in the setup file so that 100% of the daughter
  * cells are Neurons. The differentiation of the parent cell is handled by the {@link
- * PottsModuleFlyGMCDifferentiation} module. The basal apoptosis rate of this cell should be set to
- * 0 in the setup file.
+ * PottsModuleProliferationVolumeBasedDivision} module. The basal apoptosis rate of this cell should
+ * be set to 0 in the setup file.
  */
 public class PottsCellFlyGMC extends PottsCell {
 

src/arcade/potts/agent/cell/PottsCellStem.java

@@ -9,7 +9,7 @@
 import arcade.potts.agent.module.PottsModuleApoptosisSimple;
 import arcade.potts.agent.module.PottsModuleAutosis;
 import arcade.potts.agent.module.PottsModuleNecrosis;
-import arcade.potts.agent.module.PottsModuleProliferationSimple;
+import arcade.potts.agent.module.PottsModuleProliferationCellCycleProgressionSimple;
 import arcade.potts.agent.module.PottsModuleQuiescence;
 import static arcade.potts.util.PottsEnums.Region;
 import static arcade.potts.util.PottsEnums.State;
@@ -73,7 +73,7 @@ void setStateModule(CellState newState) {
                 module = new PottsModuleQuiescence(this);
                 break;
             case PROLIFERATIVE:
-                module = new PottsModuleProliferationSimple(this);
+                module = new PottsModuleProliferationCellCycleProgressionSimple(this);
                 break;
             case APOPTOTIC:
                 module = new PottsModuleApoptosisSimple(this);

src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java

@@ -14,11 +14,11 @@
 import arcade.potts.util.PottsEnums.State;
 
 /**
- * Implementation of {@link PottsModuleProliferationSimple} for fly GMC agents. These cells divide
- * into two {@link PottsCellFlyNeuron} cells. The links must be set in the setup file so that 100%
- * of the daughter cells are Neurons.
+ * Implementation of {@link PottsModuleProliferationVolumeBasedDivision} for fly GMC agents. These
+ * cells divide into two {@link PottsCellFlyNeuron} cells. The links must be set in the setup file
+ * so that 100% of the daughter cells are Neurons.
  */
-public class PottsModuleFlyGMCDifferentiation extends PottsModuleProliferationSimple {
+public class PottsModuleFlyGMCDifferentiation extends PottsModuleProliferationVolumeBasedDivision {
 
     /**
      * Creates a fly GMC proliferation module.
@@ -29,7 +29,15 @@ public PottsModuleFlyGMCDifferentiation(PottsCellFlyGMC cell) {
         super(cell);
     }
 
-    @Override
+    /**
+     * Adds a cell to the simulation.
+     *
+     * <p>The cell location is split. The new neuron cell is created, initialized, and added to the
+     * schedule. This cell's location is also assigned to a new Neuron cell.
+     *
+     * @param random the random number generator
+     * @param sim the simulation instance
+     */
     void addCell(MersenneTwisterFast random, Simulation sim) {
         Potts potts = ((PottsSimulation) sim).getPotts();
 

src/arcade/potts/agent/module/PottsModuleProliferation.java → src/arcade/potts/agent/module/PottsModuleProliferationCellCycleProgression.java

@@ -17,13 +17,13 @@
  * <p>During proliferation, cells cycle through G1, S, G2, and M phases. Once the cell complete M
  * phase, it divides to create a new daughter cell.
  */
-public abstract class PottsModuleProliferation extends PottsModule {
+public abstract class PottsModuleProliferationCellCycleProgression extends PottsModule {
     /**
      * Creates a proliferation {@code Module} for the given {@link PottsCell}.
      *
      * @param cell the {@link PottsCell} the module is associated with
      */
-    public PottsModuleProliferation(PottsCell cell) {
+    public PottsModuleProliferationCellCycleProgression(PottsCell cell) {
         super(cell);
         setPhase(Phase.PROLIFERATIVE_G1);
     }

src/arcade/potts/agent/module/PottsModuleProliferationSimple.java → src/arcade/potts/agent/module/PottsModuleProliferationCellCycleProgressionSimple.java

@@ -12,8 +12,9 @@
 import static arcade.potts.util.PottsEnums.Region;
 import static arcade.potts.util.PottsEnums.State;
 
-/** Extension of {@link PottsModuleProliferation} with Poisson transitions. */
-public class PottsModuleProliferationSimple extends PottsModuleProliferation {
+/** Extension of {@link PottsModuleProliferationCellCycleProgression} with Poisson transitions. */
+public class PottsModuleProliferationCellCycleProgressionSimple
+        extends PottsModuleProliferationCellCycleProgression {
     /** Threshold for critical volume size checkpoint. */
     static final double SIZE_CHECKPOINT = 0.95;
 
@@ -64,7 +65,7 @@ public class PottsModuleProliferationSimple extends PottsModuleProliferation {
      *
      * @param cell the {@link PottsCell} the module is associated with
      */
-    public PottsModuleProliferationSimple(PottsCell cell) {
+    public PottsModuleProliferationCellCycleProgressionSimple(PottsCell cell) {
         super(cell);
 
         Parameters parameters = cell.getParameters();

src/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivision.java

@@ -0,0 +1,54 @@
+package arcade.potts.agent.module;
+
+import ec.util.MersenneTwisterFast;
+import arcade.core.sim.Simulation;
+import arcade.core.util.Parameters;
+import arcade.potts.agent.cell.PottsCell;
+import arcade.potts.util.PottsEnums.Phase;
+
+/**
+ * Implementation of {@link PottsModule} for fly GMC agents. These cells divide into two {@link
+ * PottsCellFlyNeuron} cells. The links must be set in the setup file so that 100% of the daughter
+ * cells are Neurons.
+ */
+public abstract class PottsModuleProliferationVolumeBasedDivision extends PottsModule {
+
+    /** Overall growth rate for cell (voxels/tick). */
+    final double cellGrowthRate;
+
+    /**
+     * Target ratio of critical volume for division size checkpoint (cell must reach CRITICAL_VOLUME
+     * * SIZE_TARGET * SIZE_CHECKPOINT to divide).
+     */
+    final double sizeTarget;
+
+    /**
+     * Creates a proliferation module in which division is solely dependent on cell volume.
+     *
+     * @param cell the cell to which this module is attached
+     */
+    public PottsModuleProliferationVolumeBasedDivision(PottsCell cell) {
+        super(cell);
+        Parameters parameters = cell.getParameters();
+        sizeTarget = parameters.getDouble("proliferation/SIZE_TARGET");
+        cellGrowthRate = parameters.getDouble("proliferation/CELL_GROWTH_RATE");
+        setPhase(Phase.UNDEFINED);
+    }
+
+    @Override
+    public void step(MersenneTwisterFast random, Simulation sim) {
+        cell.updateTarget(cellGrowthRate, sizeTarget);
+        boolean sizeCheck = cell.getVolume() >= sizeTarget * cell.getCriticalVolume();
+        if (sizeCheck) {
+            addCell(random, sim);
+        }
+    }
+
+    /**
+     * Adds a cell to the simulation.
+     *
+     * @param random the random number generator
+     * @param sim the simulation instance
+     */
+    abstract void addCell(MersenneTwisterFast random, Simulation sim);
+}

test/arcade/potts/agent/cell/PottsCellStemTest.java

@@ -10,7 +10,7 @@
 import arcade.potts.agent.module.PottsModuleApoptosis;
 import arcade.potts.agent.module.PottsModuleAutosis;
 import arcade.potts.agent.module.PottsModuleNecrosis;
-import arcade.potts.agent.module.PottsModuleProliferation;
+import arcade.potts.agent.module.PottsModuleProliferationCellCycleProgression;
 import arcade.potts.agent.module.PottsModuleQuiescence;
 import arcade.potts.env.location.PottsLocation;
 import static org.junit.jupiter.api.Assertions.*;
@@ -94,7 +94,7 @@ public void setState_givenState_updatesModule() {
         assertTrue(cell.module instanceof PottsModuleQuiescence);
 
         cell.setState(State.PROLIFERATIVE);
-        assertTrue(cell.module instanceof PottsModuleProliferation);
+        assertTrue(cell.module instanceof PottsModuleProliferationCellCycleProgression);
 
         cell.setState(State.APOPTOTIC);
         assertTrue(cell.module instanceof PottsModuleApoptosis);

test/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiationTest.java

@@ -24,9 +24,10 @@
 import arcade.potts.util.PottsEnums.State;
 import static org.mockito.ArgumentMatchers.any;
 import static org.mockito.ArgumentMatchers.eq;
-import static org.mockito.Mockito.*;
-import static arcade.potts.util.PottsEnums.Region;
-import static arcade.potts.util.PottsEnums.State;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.mockConstruction;
+import static org.mockito.Mockito.verify;
+import static org.mockito.Mockito.when;
 
 public class PottsModuleFlyGMCDifferentiationTest {
     private int[][][] dummyIDs;
@@ -104,20 +105,7 @@ public final void setupMocks() {
         when(gmcCell.getCriticalRegionVolumes()).thenReturn(critRegionVolumes);
         when(gmcCell.getCriticalRegionHeights()).thenReturn(critRegionHeights);
 
-        // Stub parameters
         parameters = mock(Parameters.class);
-        when(parameters.getDouble("proliferation/RATE_G1")).thenReturn(1.0);
-        when(parameters.getDouble("proliferation/RATE_S")).thenReturn(1.0);
-        when(parameters.getDouble("proliferation/RATE_G2")).thenReturn(1.0);
-        when(parameters.getDouble("proliferation/RATE_M")).thenReturn(1.0);
-        when(parameters.getInt("proliferation/STEPS_G1")).thenReturn(1);
-        when(parameters.getInt("proliferation/STEPS_S")).thenReturn(1);
-        when(parameters.getInt("proliferation/STEPS_G2")).thenReturn(1);
-        when(parameters.getInt("proliferation/STEPS_M")).thenReturn(1);
-        when(parameters.getDouble("proliferation/CELL_GROWTH_RATE")).thenReturn(1.0);
-        when(parameters.getDouble("proliferation/NUCLEUS_GROWTH_RATE")).thenReturn(1.0);
-        when(parameters.getDouble("proliferation/BASAL_APOPTOSIS_RATE")).thenReturn(0.1);
-        when(parameters.getDouble("proliferation/NUCLEUS_CONDENSATION_FRACTION")).thenReturn(0.5);
         when(gmcCell.getParameters()).thenReturn(parameters);
 
         random = mock(MersenneTwisterFast.class);
@@ -153,7 +141,8 @@ public void addCell_called_callsExpectedMethods() {
         when(container.convert(eq(cellFactory), eq(newLocation), any(MersenneTwisterFast.class)))
                 .thenReturn(newCell);
 
-        PottsModuleFlyGMCDifferentiation module = new PottsModuleFlyGMCDifferentiation(gmcCell);
+        PottsModuleProliferationVolumeBasedDivision module =
+                new PottsModuleFlyGMCDifferentiation(gmcCell);
         module.addCell(random, sim);
         verify(location).split(random);
         verify(gmcCell).reset(dummyIDs, dummyRegions);