Make PottsCell Abstract Class (#13)

* Broke setState into two functions so in future setStateModule can be implemented differently by different cell types * added divisions setter for use in future subclass make functions * added getCriticalRegionVolumes and Heights for use in future subclass cell constructors * changed parameter name to overcome HiddenFieldCheck error * added Javadoc comments on new getters and setters * changed parameter name in setStateModule to overcome hidden field error. Formatting fix. * added getter and setter tests. formatting fix * formatting fix * deleted getters/setters. Made necessary fields not public. Deleted associated tests * deleted unnecessary imports and formatting fix * made fields that alread had getters public so no elements of PottsCell constructor need to be accessed via getters * typo fix * deleted unnecessary import and formatting fix * made PottsCell abstract class. Made default cell type PottsCellStem. Changed PottsCell tests to be PottsCellStem tests. Changed PottsCellContainer to default to making PottsCellStem cells * fixed merge issues * Moved assignment of potts cell class when none specified to PottsSeries. Deleted abstract make in PottsCell. Casted to PottsCell in PottsModule * updated parameters mock to return stem when parameters.get(CLASS) is called * Moved PottsCell make, state, and module tests into PottsCellStemTest. Made mock implementation of PottsCell for PottsCellTest * added content to PottsSeriesTest to make sure class is set to stem as default and to a given string if a given string is provided * Finished adjusting PottsSeriesTest to test for default cell class being set * formatting fixes * Addressing Jessica's comments * formattig fixes * removing code comments * added ability to assign one real state to PottsCellMock for testing purposes * formatting fix * added mocks for PottsModule getPhase return in PottsCellTest tests * formatting * Fix minor formatting and move remaining make test to PottsCellStem --------- Co-authored-by: jessicasyu <[email protected]>
bagherilab · Jul 30, 2024 · 1c6b1bb · 1c6b1bb
1 parent f15f446
commit 1c6b1bb
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Showing 9 changed files with 395 additions and 187 deletions.
diff --git a/src/arcade/potts/agent/cell/PottsCell.java b/src/arcade/potts/agent/cell/PottsCell.java
@@ -4,7 +4,6 @@
 import sim.engine.Schedule;
 import sim.engine.SimState;
 import sim.engine.Stoppable;
-import ec.util.MersenneTwisterFast;
 import arcade.core.agent.cell.Cell;
 import arcade.core.agent.cell.CellContainer;
 import arcade.core.agent.cell.CellState;
@@ -15,15 +14,9 @@
 import arcade.core.sim.Simulation;
 import arcade.core.util.MiniBox;
 import arcade.potts.agent.module.PottsModule;
-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.PottsModuleQuiescence;
 import arcade.potts.env.location.PottsLocation;
 import static arcade.potts.util.PottsEnums.Ordering;
 import static arcade.potts.util.PottsEnums.Region;
-import static arcade.potts.util.PottsEnums.State;
 
 /**
  * Implementation of {@link Cell} for potts models.
@@ -46,7 +39,7 @@
  * by the specific Hamiltonian class instance.
  */
 
-public final class PottsCell implements Cell {
+public abstract class PottsCell implements Cell {
     /** Stopper used to stop this agent from being stepped in the schedule. */
     Stoppable stopper;
 
@@ -303,15 +296,6 @@ public double getCriticalHeight(Region region) {
     @Override
     public void stop() { stopper.stop(); }
 
-    @Override
-    public PottsCell make(int newID, CellState newState, Location newLocation,
-                          MersenneTwisterFast random) {
-        divisions++;
-        return new PottsCell(newID, id, pop, newState, age, divisions, newLocation,
-                            hasRegions, parameters, criticalVolume, criticalHeight,
-                            criticalRegionVolumes, criticalRegionHeights);
-    }
-
     @Override
     public void setState(CellState newState) {
         this.state = newState;
@@ -323,29 +307,7 @@ public void setState(CellState newState) {
      *
      * @param newState  the cell state
      */
-    public void setStateModule(CellState newState) {
-        switch ((State) newState) {
-            case QUIESCENT:
-                module = new PottsModuleQuiescence(this);
-                break;
-            case PROLIFERATIVE:
-                module = new PottsModuleProliferationSimple(this);
-                break;
-            case APOPTOTIC:
-                module = new PottsModuleApoptosisSimple(this);
-                break;
-            case NECROTIC:
-                module = new PottsModuleNecrosis(this);
-                break;
-            case AUTOTIC:
-                module = new PottsModuleAutosis(this);
-                break;
-            default:
-                // State must be one of the above cases.
-                module = null;
-                break;
-        }
-    }
+    abstract void setStateModule(CellState newState);
 
     @Override
     public void schedule(Schedule schedule) {

diff --git a/src/arcade/potts/agent/cell/PottsCellContainer.java b/src/arcade/potts/agent/cell/PottsCellContainer.java
@@ -141,15 +141,18 @@ private Cell convert(PottsCellFactory factory, Location location) {
 
         // Make cell.
         PottsCell cell;
-
-        if (factory.popToRegions.get(pop)) {
-            cell = new PottsCell(id, parent, pop, state, age, divisions,
-                    location, true, parameters, criticalVolume, criticalHeight,
-                    criticalRegionVolumes, criticalRegionHeights);
-        } else {
-            cell = new PottsCell(id, parent, pop, state, age, divisions,
-                    location, false, parameters, criticalVolume, criticalHeight,
-                    null, null);
+        switch (parameters.get("CLASS")) {
+            default:
+            case "stem":
+                if (factory.popToRegions.get(pop)) {
+                    cell = new PottsCellStem(id, parent, pop, state, age, divisions,
+                            location, true, parameters, criticalVolume, criticalHeight,
+                            criticalRegionVolumes, criticalRegionHeights);
+                } else {
+                    cell = new PottsCellStem(id, parent, pop, state, age, divisions,
+                            location, false, parameters, criticalVolume, criticalHeight,
+                            null, null);
+                }
         }
 
         // Update cell module.

diff --git a/src/arcade/potts/agent/cell/PottsCellStem.java b/src/arcade/potts/agent/cell/PottsCellStem.java
@@ -0,0 +1,82 @@
+package arcade.potts.agent.cell;
+
+import java.util.EnumMap;
+import ec.util.MersenneTwisterFast;
+import arcade.core.agent.cell.CellState;
+import arcade.core.env.location.Location;
+import arcade.core.util.MiniBox;
+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.PottsModuleQuiescence;
+import static arcade.potts.util.PottsEnums.Region;
+import static arcade.potts.util.PottsEnums.State;
+
+/**
+ * Extension of {@link PottsCell} for stem cells.
+ * <p>
+ * This is the default cell type for Potts models.
+ */
+public final class PottsCellStem extends PottsCell {
+
+    /**
+     * Creates a {@code PottsCellStem} agent.
+     *
+     * @param id  the cell ID
+     * @param parent  the parent ID
+     * @param pop  the cell population index
+     * @param state  the cell state
+     * @param age  the cell age
+     * @param divisions  the number of cell divisions
+     * @param location  the {@link Location} of the cell
+     * @param hasRegions  {@code true} if cell has regions, {@code false} otherwise
+     * @param parameters  the dictionary of parameters
+     * @param criticalVolume  the critical cell volume
+     * @param criticalHeight  the critical cell height
+     * @param criticalRegionVolumes  the map of critical volumes for regions
+     * @param criticalRegionHeights  the map of critical heights for regions
+     */
+    public PottsCellStem(int id, int parent, int pop, CellState state, int age, int divisions,
+                         Location location, boolean hasRegions, MiniBox parameters,
+                         double criticalVolume, double criticalHeight,
+                         EnumMap<Region, Double> criticalRegionVolumes,
+                         EnumMap<Region, Double> criticalRegionHeights) {
+        super(id, parent, pop, state, age, divisions, location, hasRegions, parameters,
+                criticalVolume, criticalHeight, criticalRegionVolumes, criticalRegionHeights);
+    }
+
+    @Override
+    public PottsCell make(int newID, CellState newState, Location newLocation,
+                          MersenneTwisterFast random) {
+        divisions++;
+        return new PottsCellStem(newID, id, pop, newState, age, divisions, newLocation,
+                hasRegions, parameters, criticalVolume, criticalHeight,
+                criticalRegionVolumes, criticalRegionHeights);
+    }
+
+    @Override
+    void setStateModule(CellState newState) {
+        switch ((State) newState) {
+            case QUIESCENT:
+                module = new PottsModuleQuiescence(this);
+                break;
+            case PROLIFERATIVE:
+                module = new PottsModuleProliferationSimple(this);
+                break;
+            case APOPTOTIC:
+                module = new PottsModuleApoptosisSimple(this);
+                break;
+            case NECROTIC:
+                module = new PottsModuleNecrosis(this);
+                break;
+            case AUTOTIC:
+                module = new PottsModuleAutosis(this);
+                break;
+            default:
+                // State must be one of the above cases.
+                module = null;
+                break;
+        }
+    }
+}
diff --git a/src/arcade/potts/agent/module/PottsModuleProliferation.java b/src/arcade/potts/agent/module/PottsModuleProliferation.java
@@ -103,7 +103,7 @@ void addCell(MersenneTwisterFast random, Simulation sim) {
 
         // Create and schedule new cell.
         int newID = sim.getID();
-        PottsCell newCell = cell.make(newID, State.PROLIFERATIVE, newLocation, random);
+        PottsCell newCell = (PottsCell) cell.make(newID, State.PROLIFERATIVE, newLocation, random);
         sim.getGrid().addObject(newCell, null);
         potts.register(newCell);
         newCell.reset(potts.ids, potts.regions);

diff --git a/src/arcade/potts/sim/PottsSeries.java b/src/arcade/potts/sim/PottsSeries.java
@@ -17,6 +17,9 @@ public final class PottsSeries extends Series {
     /** Separator character for targets. */
     public static final String TARGET_SEPARATOR = ":";
 
+    /** Default cell class. */
+    public static final String DEFAULT_CELL_CLASS = "stem";
+
     /** Map of potts settings. */
     public MiniBox potts;
 
@@ -184,6 +187,12 @@ protected void updatePopulations(ArrayList<Box> populationsBox, MiniBox populati
             String id = box.getValue("id");
             String populationClass = box.getValue("class");
 
+            if (populationClass == null) {
+                populationClass = DEFAULT_CELL_CLASS;
+            }
+
+            // TODO: Use logger to print message when default class is used.
+
             // Create new population and update code.
             MiniBox population = new MiniBox();
             population.put("CODE", code++);

diff --git a/test/arcade/potts/agent/cell/PottsCellContainerTest.java b/test/arcade/potts/agent/cell/PottsCellContainerTest.java
@@ -109,6 +109,7 @@ public void convert_noRegions_createsObject() {
         double criticalVolume = randomDoubleBetween(10, 100);
         double criticalHeight = randomDoubleBetween(10, 100);
         MiniBox parameters = mock(MiniBox.class);
+        when(parameters.get("CLASS")).thenReturn("");
 
         factory.popToParameters.put(cellPop, parameters);
         factory.popToRegions.put(cellPop, false);
@@ -147,6 +148,7 @@ public void convert_withRegions_createsObject() {
         double criticalVolume = randomDoubleBetween(10, 100);
         double criticalHeight = randomDoubleBetween(10, 100);
         MiniBox parameters = mock(MiniBox.class);
+        when(parameters.get("CLASS")).thenReturn("");
 
         EnumSet<Region> regionList = EnumSet.of(Region.NUCLEUS, Region.UNDEFINED);
         doReturn(regionList).when(location).getRegions();