Allison/debugging

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

@@ -141,6 +141,7 @@ public void step(SimState simstate) {
             }
 
             maxConfluency = population.getInt("MAX_DENSITY");
+            maxConfluency = (maxConfluency >= 0 ? maxConfluency : Integer.MAX_VALUE);
 
             int pop = population.getInt("CODE");
 
@@ -360,9 +361,7 @@ protected boolean checkLocationSpace(Location loc, PatchGrid grid) {
             for (Object cellObj : bag) {
                 PatchCell cell = (PatchCell) cellObj;
                 if (cell instanceof PatchCellCART) {
-                    totalVol =
-                            PatchCell.calculateTotalVolume(bag)
-                                    + parameters.getDouble("T_CELL_VOL_AVG");
+                    totalVol = PatchCell.calculateTotalVolume(bag) + cell.getVolume();
                     currentHeight = totalVol / locArea;
                 }
                 if (cell instanceof PatchCellTissue) {

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

@@ -56,16 +56,16 @@
     protected boolean activated;
 
     /** number of current PDL-1 receptors on CART cell. */
-    protected int selfReceptors;
+    public int selfReceptors;
 
     /** initial number of PDL-1 receptors on CART cell. */
     protected int selfReceptorsStart;
 
     /** number of bound CAR antigens. */
-    protected int boundCARAntigensCount;
+    public int boundCARAntigensCount;
 
     /** number of bound PDL-1 antigens. */
-    protected int boundSelfAntigensCount;
+    public int boundSelfAntigensCount;
 
     /** number of neighbors that T cell is able to search through. */
     protected final double searchAbility;
@@ -160,8 +160,8 @@
         // initialized non-loaded parameters
         boundCARAntigensCount = 0;
         boundSelfAntigensCount = 0;
-        lastActiveTicker = 0;
-        activated = true;
+        // lastActiveTicker = 0;
+        activated = false;
         boundTarget = null;
 
         // Set loaded parameters.
@@ -259,6 +259,15 @@
         return this.activated;
     }
 
+    /**
+     * Sets the cell activation status.
+     *
+     * @param activated the activation status to set
+     */
+    public void setActivationStatus(boolean activated) {
+        this.activated = activated;
+    }
+
     /**
      * Adds only tissue cells to the provided bag.
      *

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

@@ -153,7 +153,10 @@ public PatchCellContainer createCellForPopulation(int id, int pop) {
         MiniBox population = popToParameters.get(pop);
         Parameters parameters = new Parameters(population, null, random);
 
-        double compression = parameters.getDouble("COMPRESSION_TOLERANCE");
+        double compression =
+                parameters.getDouble("COMPRESSION_TOLERANCE") >= 0
+                        ? parameters.getDouble("COMPRESSION_TOLERANCE")
+                        : Double.MAX_VALUE;
 
         double volume = parameters.getDouble("CELL_VOLUME");
         double height = parameters.getDouble("CELL_HEIGHT");

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

@@ -8,6 +8,7 @@
 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.env.grid.PatchGrid;
 import static arcade.patch.util.PatchEnums.State;
 
@@ -47,17 +48,20 @@ public PatchModuleApoptosis(PatchCell cell) {
     @Override
     public void step(MersenneTwisterFast random, Simulation sim) {
         if (ticker > deathDuration) {
-            // Induce one neighboring quiescent cell to proliferate.
-            ArrayList<Location> neighborhood = location.getNeighbors();
-            neighborhood.add(location);
-            Bag bag = ((PatchGrid) sim.getGrid()).getObjectsAtLocations(neighborhood);
+            // CART cells do not induce neighboring tissue cells to proliferate.
+            if (!(cell instanceof PatchCellCART)) {
+                // Induce one neighboring quiescent cell to proliferate.
+                ArrayList<Location> neighborhood = location.getNeighbors();
+                neighborhood.add(location);
+                Bag bag = ((PatchGrid) sim.getGrid()).getObjectsAtLocations(neighborhood);
 
-            bag.shuffle(random);
-            for (Object obj : bag) {
-                Cell neighbor = (Cell) obj;
-                if (neighbor.getState() == State.QUIESCENT) {
-                    neighbor.setState(State.PROLIFERATIVE);
-                    break;
+                bag.shuffle(random);
+                for (Object obj : bag) {
+                    Cell neighbor = (Cell) obj;
+                    if (neighbor.getState() == State.QUIESCENT) {
+                        neighbor.setState(State.PROLIFERATIVE);
+                        break;
+                    }
                 }
             }
 

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

@@ -59,7 +59,7 @@
         duration = 0;
         // Load parameters.
         Parameters parameters = cell.getParameters();
-        synthesisDuration = parameters.getInt("proliferation/SYNTHESIS_DURATION");
+        synthesisDuration = parameters.getInt("SYNTHESIS_DURATION");
     }
 
     @Override
@@ -106,6 +106,18 @@
                                             newLocation,
                                             random,
                                             newParameters);
+
+                    if (cell instanceof PatchCellCART) {
+                        ((PatchCellCART) newCell)
+                                .setActivationStatus(((PatchCellCART) cell).getActivationStatus());
+                        ((PatchCellCART) newCell).boundSelfAntigensCount =
+                                ((PatchCellCART) cell).boundSelfAntigensCount;
+                        ((PatchCellCART) newCell).selfReceptors =
+                                ((PatchCellCART) cell).selfReceptors;
+                        ((PatchCellCART) newCell).boundCARAntigensCount =
+                                ((PatchCellCART) cell).boundCARAntigensCount;
+                    }
+
                     sim.getGrid().addObject(newCell, newLocation);
                     newCell.schedule(sim.getSchedule());
 
@@ -125,7 +137,7 @@
                         PatchProcess process = (PatchProcess) newCell.getProcess(domain);
                         process.update(cell.getProcess(domain));
                     }
                     // TODO: Update environment generator sites.
                 } else {
                     ticker++;
                 }

src/arcade/patch/parameter.patch.xml

@@ -25,6 +25,8 @@
     <population id="MAX_DENSITY" value="-1" description="maximum amount of cells in location, -1 means no limit" />
     <population id="ACCURACY" value="0.8" description="accuracy to select highest glucose concentration in future location" />
     <population id="AFFINITY" value="0.5" description="movement toward center affinity when selecting future location" />
+    <population id="SYNTHESIS_DURATION" value="637" units="min" description="time required for DNA synthesis" />
+
 
     <!-- CAR T specific parameters -->
     <population id="ANERGIC_FRACTION" value="0.5" description="fraction of anergic cells that become apoptotic" />
@@ -44,8 +46,6 @@
     <population id="CONTACT_FRAC" value="0.2" description="fraction of cell surface contacting a bound cell during a binding event" />
     <population id="BOUND_TIME" value="360" description="6 hours" />
 
-    <!-- proliferation module parameters -->
-    <population.module module="proliferation" id="SYNTHESIS_DURATION" value="637" units="min" description="time required for DNA synthesis" />
 
     <!-- migration module parameters -->
     <population.module module="migration" id="MIGRATION_RATE" value="0.24" unit="um/min" description="cell migration rate" />

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

@@ -251,7 +251,7 @@ public void setState_proliferation_createsCell() {
         Schedule scheduleMock = mock(Schedule.class);
         doReturn(0.0).when(parametersMock).getDouble(any(String.class));
         doReturn(0).when(parametersMock).getInt(any(String.class));
-        doReturn(1).when(parametersMock).getInt("proliferation/SYNTHESIS_DURATION");
+        doReturn(1).when(parametersMock).getInt("SYNTHESIS_DURATION");
         doReturn(cellID + 1).when(simMock).getID();
         doReturn(scheduleMock).when(simMock).getSchedule();
         doReturn(null).when(scheduleMock).scheduleRepeating(anyInt(), anyInt(), any());