Mutate Patch Action

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

@@ -0,0 +1,132 @@
+package arcade.patch.agent.action;
+
+import java.util.ArrayList;
+import sim.engine.Schedule;
+import sim.engine.SimState;
+import sim.util.Bag;
+import arcade.core.agent.action.Action;
+import arcade.core.env.location.Location;
+import arcade.core.sim.Series;
+import arcade.core.sim.Simulation;
+import arcade.core.util.MiniBox;
+import arcade.patch.agent.cell.PatchCell;
+import arcade.patch.agent.cell.PatchCellContainer;
+import arcade.patch.env.grid.PatchGrid;
+import arcade.patch.env.location.Coordinate;
+import arcade.patch.sim.PatchSeries;
+import arcade.patch.sim.PatchSimulation;
+import static arcade.patch.util.PatchEnums.Ordering;
+
+/**
+ * Implementation of {@link Action} for converting cells to a different class.
+ *
+ * <p>The action is stepped once after {@code TIME_DELAY}. The action will convert all the healthy
+ * tissue cells within the given radius into cancer cells.
+ */
+public class PatchActionMutate implements Action {
+    /** Time delay before calling the action [min]. */
+    private final int timeDelay;
+
+    /** Grid radius where cells are mutated. */
+    private final int mutateRadius;
+
+    /** Population code for cancer. */
+    private int cancerPop;
+
+    /** Population code for healthy cells. */
+    private int healthyPop;
+
+    /** Grid depth that cells are mutated. */
+    private final int mutateDepth;
+
+    /**
+     * Creates a {@link Action} for converting healthy cell agents into cancer cell agents.
+     *
+     * <p>Loaded parameters include:
+     *
+     * <ul>
+     *   <li>{@code TIME_DELAY} = time delay before calling the action
+     *   <li>{@code MUTATE_RADIUS} = grid radius where cells are mutated
+     *   <li>{@code MUTATE_DEPTH} = grid depth that cells are mutated
+     * </ul>
+     *
+     * @param series the simulation series
+     * @param parameters the component parameters dictionary
+     */
+    public PatchActionMutate(Series series, MiniBox parameters) {
+        // Set loaded parameters.
+        timeDelay = parameters.getInt("TIME_DELAY");
+        mutateRadius = parameters.getInt("MUTATE_RADIUS");
+        mutateDepth = ((PatchSeries) series).depth;
+        healthyPop = -1;
+        cancerPop = -1;
+        // Grab popuation codes for healthy and cancer cells.
+        for (String popName : series.populations.keySet()) {
+            if (series.populations.get(popName).get("CLASS").contains("tissue")) {
+                healthyPop = series.populations.get(popName).getInt("CODE");
+            } else if (series.populations.get(popName).get("CLASS").contains("cancer_stem")
+                    || series.populations.get(popName).get("CLASS").contains("cancer")) {
+                cancerPop = series.populations.get(popName).getInt("CODE");
+            }
+        }
+        if (healthyPop == -1 || cancerPop == -1) {
+            throw new IllegalArgumentException(
+                    "Please initialize both healthy and cancer populations in input file.");
+        }
+    }
+
+    @Override
+    public void schedule(Schedule schedule) {
+        schedule.scheduleOnce(timeDelay, Ordering.ACTIONS.ordinal(), this);
+    }
+
+    @Override
+    public void register(Simulation sim, String population) {}
+
+    @Override
+    public void step(SimState simstate) {
+        PatchSimulation sim = (PatchSimulation) simstate;
+        PatchGrid grid = (PatchGrid) sim.getGrid();
+
+        // Get cells at center of simulation.
+        ArrayList<Coordinate> coordinates =
+                sim.locationFactory.getCoordinates(mutateRadius, mutateDepth);
+        for (Coordinate coordinate : coordinates) {
+            Bag bag = (Bag) grid.getObjectAt(coordinate.hashCode());
+
+            if (bag == null) {
+                continue;
+            }
+
+            for (int i = 0; i < bag.numObjs; i++) {
+                // Select old cell and remove from simulation.
+                PatchCell oldCell = (PatchCell) bag.get(i);
+                // Only remove and mutate if cell is healthy.
+                if (oldCell.getPop() == healthyPop) {
+                    Location location = oldCell.getLocation();
+                    grid.removeObject(oldCell, oldCell.getLocation());
+                    oldCell.stop();
+
+                    // Create new cancer cell and add to simulation.
+                    PatchCellContainer cellContainer =
+                            new PatchCellContainer(
+                                    oldCell.getID(),
+                                    oldCell.getParent(),
+                                    cancerPop,
+                                    oldCell.getAge(),
+                                    oldCell.getDivisions(),
+                                    oldCell.getState(),
+                                    oldCell.getVolume(),
+                                    oldCell.getHeight(),
+                                    oldCell.getCriticalVolume(),
+                                    oldCell.getCriticalHeight());
+                    PatchCell newCell =
+                            (PatchCell)
+                                    cellContainer.convert(sim.cellFactory, location, sim.random);
+                    grid.addObject(newCell, location);
+                    newCell.schedule(sim.getSchedule());
+                }
+            }
+        }
+    }
+}

src/arcade/patch/parameter.patch.xml

@@ -125,6 +125,10 @@
     <!-- convert action parameters -->
     <action class="convert" id="TIME_DELAY" value="0" units="min" description="time delay before calling the action" />
 
+    <!-- mutate action parameters -->
+    <action class="mutate" id="TIME_DELAY" value="0" units="min" description="time delay before calling the action" />
+    <action class="mutate" id="MUTATE_RADIUS" value="1" description="grid radius where cells are mutated" />
+
     <!-- COMPONENTS ======================================================== -->
 
     <!-- source sites component parameters -->

src/arcade/patch/sim/PatchSimulationHex.java

@@ -6,6 +6,7 @@
 import arcade.core.util.MiniBox;
 import arcade.patch.agent.action.PatchActionConvert;
 import arcade.patch.agent.action.PatchActionInsert;
+import arcade.patch.agent.action.PatchActionMutate;
 import arcade.patch.agent.action.PatchActionRemove;
 import arcade.patch.agent.cell.PatchCellFactory;
 import arcade.patch.env.component.PatchComponentCycle;
@@ -58,6 +59,8 @@ public Action makeAction(String actionClass, MiniBox parameters) {
                 return new PatchActionRemove(series, parameters);
             case "convert":
                 return new PatchActionConvert(series, parameters);
+            case "mutate":
+                return new PatchActionMutate(series, parameters);
             default:
                 return null;
         }

src/arcade/patch/sim/PatchSimulationRect.java

@@ -6,6 +6,7 @@
 import arcade.core.util.MiniBox;
 import arcade.patch.agent.action.PatchActionConvert;
 import arcade.patch.agent.action.PatchActionInsert;
+import arcade.patch.agent.action.PatchActionMutate;
 import arcade.patch.agent.action.PatchActionRemove;
 import arcade.patch.agent.cell.PatchCellFactory;
 import arcade.patch.env.component.PatchComponentCycle;
@@ -58,6 +59,8 @@ public Action makeAction(String actionClass, MiniBox parameters) {
                 return new PatchActionRemove(series, parameters);
             case "convert":
                 return new PatchActionConvert(series, parameters);
+            case "mutate":
+                return new PatchActionMutate(series, parameters);
             default:
                 return null;
         }