Feature/add pdelike nbgrowth

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

@@ -1,5 +1,6 @@
 package arcade.potts.agent.cell;
 
+import java.security.InvalidParameterException;
 import java.util.ArrayList;
 import java.util.EnumMap;
 import java.util.HashMap;
@@ -213,8 +214,13 @@ void parseValues(Series series) {
             if (linkKeys.size() > 0) {
                 links = new GrabBag();
                 for (String linkKey : linkKeys) {
-                    int popLink = series.populations.get(linkKey).getInt("CODE");
-                    links.add(popLink, linksBox.getDouble(linkKey));
+                    try {
+                        int popLink = series.populations.get(linkKey).getInt("CODE");
+                        links.add(popLink, linksBox.getDouble(linkKey));
+                    } catch (Exception e) {
+                        throw new InvalidParameterException(
+                                "A population link is set that references a population that does not exist.");
+                    }
                 }
             }
 

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

@@ -20,13 +20,16 @@
  */
 public class PottsModuleFlyGMCDifferentiation extends PottsModuleProliferationVolumeBasedDivision {
 
+    Boolean pdeLike;
+
     /**
      * Creates a fly GMC proliferation module.
      *
      * @param cell the cell to which this module is attached
      */
     public PottsModuleFlyGMCDifferentiation(PottsCellFlyGMC cell) {
         super(cell);
+        pdeLike = (cell.getParameters().getInt("proliferation/PDELIKE") != 0);
     }
 
     /**
@@ -93,10 +96,40 @@ void addCell(MersenneTwisterFast random, Simulation sim) {
     }
 
     public void updateGrowthRate(Simulation sim) {
-        if (dynamicGrowthRateVolume == false) {
+        if (!dynamicGrowthRateVolume) {
             cellGrowthRate = cellGrowthRateBase;
-        } else if (dynamicGrowthRateVolume == true) {
-            updateVolumeBasedGrowthRate();
+        } else {
+            if (!pdeLike) {
+                updateCellVolumeBasedGrowthRate(
+                        cell.getLocation().getVolume(), cell.getCriticalVolume());
+            } else {
+                // PDE-like: use population-wide averages for GMCs (same pop as this cell)
+                sim.util.Bag objs = sim.getGrid().getAllObjects();
+
+                double volSum = 0.0;
+                double critSum = 0.0;
+                int count = 0;
+
+                for (int i = 0; i < objs.numObjs; i++) {
+                    Object o = objs.objs[i];
+                    if (!(o instanceof arcade.potts.agent.cell.PottsCell)) continue;
+
+                    arcade.potts.agent.cell.PottsCell c = (arcade.potts.agent.cell.PottsCell) o;
+                    if (c.getPop() != cell.getPop()) continue; // keep to same population
+
+                    if (o instanceof arcade.potts.agent.cell.PottsCellFlyGMC) {
+                        arcade.potts.agent.cell.PottsCellFlyGMC gmc =
+                                (arcade.potts.agent.cell.PottsCellFlyGMC) o;
+                        volSum += gmc.getLocation().getVolume();
+                        critSum += gmc.getCriticalVolume();
+                        count++;
+                    }
+                }
+                double avgVolume = volSum / count;
+                double avgCritVol = critSum / count;
+                updateCellVolumeBasedGrowthRate(avgVolume, avgCritVol);
+                System.out.println("GMC " + cell.getID() + "growth rate = " + cellGrowthRate);
+            }
         }
     }
 }

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

@@ -3,6 +3,7 @@
 import java.security.InvalidParameterException;
 import java.util.ArrayList;
 import java.util.HashSet;
+import sim.util.Bag;
 import sim.util.Double3D;
 import ec.util.MersenneTwisterFast;
 import arcade.core.env.location.Location;
@@ -59,7 +60,7 @@ public class PottsModuleFlyStemProliferation extends PottsModuleProliferationVol
     final boolean volumeBasedCriticalVolume;
 
     /** Boolean flag indicating whether growth rate should be regulated by NB-NB contact. */
-    final boolean dynamicGrowthRateNBContact;
+    final boolean dynamicGrowthRateNBSelfRepression;
 
     final double volumeBasedCriticalVolumeMultiplier;
 
@@ -83,6 +84,12 @@ public class PottsModuleFlyStemProliferation extends PottsModuleProliferationVol
 
     final double initialSize;
 
+    /**
+     * Boolean determining whether growth and division rates are universal across all NBs. If true
+     * model behaviors is PDE-like, if false it is ABM-like.
+     */
+    final Boolean pdeLike;
+
     /**
      * Creates a proliferation {@code Module} for the given {@link PottsCellFlyStem}.
      *
@@ -113,10 +120,10 @@ public PottsModuleFlyStemProliferation(PottsCellFlyStem cell) {
         volumeBasedCriticalVolume =
                 (parameters.getInt("proliferation/VOLUME_BASED_CRITICAL_VOLUME") != 0);
 
-        dynamicGrowthRateNBContact =
-                (parameters.getInt("proliferation/DYNAMIC_GROWTH_RATE_NB_CONTACT") != 0);
+        dynamicGrowthRateNBSelfRepression =
+                (parameters.getInt("proliferation/DYNAMIC_GROWTH_RATE_NB_SELF_REPRESSION") != 0);
 
-        if (dynamicGrowthRateVolume && dynamicGrowthRateNBContact) {
+        if (dynamicGrowthRateVolume && dynamicGrowthRateNBSelfRepression) {
             throw new InvalidParameterException(
                     "Dynamic growth rate can be either volume-based or NB-contact-based, not both.");
         }
@@ -129,6 +136,8 @@ public PottsModuleFlyStemProliferation(PottsCellFlyStem cell) {
 
         initialSize = cell.getVolume();
 
+        pdeLike = (parameters.getInt("proliferation/PDELIKE") != 0);
+
         setPhase(Phase.UNDEFINED);
     }
 
@@ -165,24 +174,42 @@ public void addCell(MersenneTwisterFast random, Simulation sim) {
      */
     public void updateGrowthRate(Simulation sim) {
         if (dynamicGrowthRateVolume == true) {
-            updateVolumeBasedGrowthRate();
-        } else if (dynamicGrowthRateNBContact == true) {
-            updateNBContactGrowthRate(sim);
+            updateVolumeBasedGrowthRate(sim);
+        } else if (dynamicGrowthRateNBSelfRepression == true) {
+            updateGrowthRateBasedOnOtherNBs(sim);
         } else {
             cellGrowthRate = cellGrowthRateBase;
         }
     }
 
+    public void updateVolumeBasedGrowthRate(Simulation sim) {
+        if (pdeLike == false) {
+            updateCellVolumeBasedGrowthRate(
+                    cell.getLocation().getVolume(), cell.getCriticalVolume());
+        } else {
+            HashSet<PottsCellFlyStem> nbsInSimulation = getNBsInSimulation(sim);
+            double volSum = 0.0;
+            double critVolSum = 0.0;
+            for (PottsCellFlyStem nb : nbsInSimulation) {
+                volSum += nb.getLocation().getVolume();
+                critVolSum += nb.getCriticalVolume();
+            }
+            double avgVolume = volSum / nbsInSimulation.size();
+            double avgCritVol = critVolSum / nbsInSimulation.size();
+            updateCellVolumeBasedGrowthRate(avgVolume, avgCritVol);
+        }
+    }
+
     /**
-     * Gets the number of neighbors of this cell that are unique neuroblasts.
+     * Gets the neighbors of this cell that are unique neuroblasts.
      *
      * @param sim the simulation
      * @return the number of unique neuroblast neighbors
      */
-    protected Integer getNumNBNeighbors(Simulation sim) {
+    protected HashSet<PottsCellFlyStem> getNBNeighbors(Simulation sim) {
         Potts potts = ((PottsSimulation) sim).getPotts();
         ArrayList<Voxel> voxels = ((PottsLocation) cell.getLocation()).getVoxels();
-        HashSet<PottsCell> stemNeighbors = new HashSet<PottsCell>();
+        HashSet<PottsCellFlyStem> stemNeighbors = new HashSet<PottsCellFlyStem>();
 
         for (Voxel v : voxels) {
             HashSet<Integer> uniqueIDs = potts.getUniqueIDs(v.x, v.y, v.z);
@@ -193,50 +220,32 @@ protected Integer getNumNBNeighbors(Simulation sim) {
                 }
                 if (cell.getPop() == neighbor.getPop()) {
                     if (neighbor.getID() != cell.getID()) {
-                        stemNeighbors.add((PottsCell) sim.getGrid().getObjectAt(id));
+                        stemNeighbors.add((PottsCellFlyStem) sim.getGrid().getObjectAt(id));
                     }
                 }
             }
         }
-        return stemNeighbors.size();
+        return stemNeighbors;
     }
 
-    /**
-     * Updates the cell's growth rate based on the number of neighboring neuroblasts.
-     *
-     * <p>This method applies a Hill-type repression function to scale the cell's base growth rate
-     * according to local neuroblast density. Specifically, it counts the number of neighboring
-     * neuroblasts (using {@link #getNumNBNeighbors(Simulation)}) and applies:
-     *
-     * <pre>
-     *   hillRepression = K^n / (K^n + Np^n)
-     *   cellGrowthRate = cellGrowthRateBase * hillRepression
-     * </pre>
-     *
-     * where:
-     *
-     * <ul>
-     *   <li><code>Np</code> is the number of neighboring neuroblasts
-     *   <li><code>K</code> is the half-max parameter for repression
-     *       (proliferation/NB_CONTACT_HALF_MAX)
-     *   <li><code>n</code> is the Hill coefficient controlling steepness
-     *       (proliferation/NB_CONTACT_HILL_N)
-     *   <li><code>cellGrowthRateBase</code> is the base growth rate in the absence of neighbors
-     * </ul>
-     *
-     * <p>This formulation ensures that when Np = 0, the cell grows at the base rate, and as the
-     * number of neighbors increases, growth is repressed toward zero.
-     *
-     * @param sim the simulation
-     */
-    protected void updateNBContactGrowthRate(Simulation sim) {
-        int NpRaw = getNumNBNeighbors(sim);
-        double Np = Math.max(0.0, (double) NpRaw);
+    protected void updateGrowthRateBasedOnOtherNBs(Simulation sim) {
+        int npRaw;
+        if (pdeLike) {
+            npRaw = getNBsInSimulation(sim).size();
+        } else {
+            npRaw = getNBNeighbors(sim).size();
+        }
+        double np = Math.max(0.0, (double) npRaw);
 
         double Kn = Math.pow(nbContactHalfMax, nbContactHillN);
-        double Npn = Math.pow(Np, nbContactHillN);
+        double Npn = Math.pow(np, nbContactHillN);
 
-        double hillRepression = Kn / (Kn + Npn);
+        double hillRepression;
+        if (Kn == 0.0) {
+            hillRepression = (np == 0.0) ? 1.0 : 0.0;
+        } else {
+            hillRepression = Kn / (Kn + Npn);
+        }
 
         cellGrowthRate = cellGrowthRateBase * hillRepression;
     }
@@ -578,4 +587,18 @@ public static PottsLocation getBasalLocation(
 
         return (proj1 < proj2) ? loc2 : loc1; // higher projection = more basal
     }
+
+    public HashSet<PottsCellFlyStem> getNBsInSimulation(Simulation sim) {
+        HashSet<PottsCellFlyStem> nbsInSimulation = new HashSet<>();
+        Bag simObjects = sim.getGrid().getAllObjects();
+        for (int i = 0; i < simObjects.numObjs; i++) {
+            Object o = simObjects.objs[i];
+            if (!(o instanceof PottsCell)) continue; // skip non-cell objects
+            PottsCell cellInSim = (PottsCell) o;
+            if (cell.getPop() == cellInSim.getPop() && o instanceof PottsCellFlyStem) {
+                nbsInSimulation.add((PottsCellFlyStem) o);
+            }
+        }
+        return nbsInSimulation;
+    }
 }

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

@@ -69,22 +69,8 @@ public void step(MersenneTwisterFast random, Simulation sim) {
      */
     public abstract void updateGrowthRate(Simulation sim);
 
-    /**
-     * Updates the cell growth rate based on the volume of the cell.
-     *
-     * <p>The growth rate is scaled according to a power-law relationship between the current cell
-     * volume and its critical volume. As the cell volume increases relative to the critical volume,
-     * the growth rate accelerates proportionally:
-     *
-     * <pre>
-     *   growthRate = baseGrowthRate * (volume / criticalVolume) ^ sensitivity
-     * </pre>
-     *
-     * This allows larger cells to grow faster, capturing volume-dependent growth dynamics.
-     */
-    public void updateVolumeBasedGrowthRate() {
-        double volume = cell.getLocation().getVolume();
-        double Ka = cell.getCriticalVolume();
+    public void updateCellVolumeBasedGrowthRate(double volume, double cellCriticalVolume) {
+        double Ka = cellCriticalVolume;
         cellGrowthRate = cellGrowthRateBase * Math.pow((volume / Ka), growthRateVolumeSensitivity);
     }
 }

src/arcade/potts/parameter.potts.xml

@@ -63,11 +63,15 @@
     <population.module module="proliferation" id="BASAL_APOPTOSIS_RATE" value="0.00127128" units="hours^-1" conversion="DT" description="basal rate of apoptosis" />
     <population.module module="proliferation" id="NUCLEUS_GROWTH_RATE" value="30" units="um^3/hour" conversion="DS^-3.DT" description="basal rate of nucleus growth" />
     <population.module module="proliferation" id="NUCLEUS_CONDENSATION_FRACTION" value="0.5" description="fraction of nuclear volume when condensed" />
+
+    <!-- ── Fly cell proliferation module parameters ───────────────────── -->
+    <!-- ── Dictating whether NB behavior should be the same across all NBs ──────── -->
+    <population.module module="proliferation" id="PDELIKE" value="0" description="1 → all cells of a given type have same growth and division dynamics based on average metrics across the population; 0 → Cell growth and division is determined on a cell-by-cell basis, cells can differ from other cells of the same type" />
     <!-- ── Growth rate sensitivity to cell volume dynamics ───────────────────── -->
     <population.module module="proliferation" id="DYNAMIC_GROWTH_RATE_VOLUME" value="0" description="1 → enable volume-sensitive growth rate; 0 → disabled" />
     <population.module module="proliferation" id="GROWTH_RATE_VOLUME_SENSITIVITY" value="1.0" description="exponent in (volume/criticalVolume)^sensitivity when volume rule is enabled" />
-    <!-- ── NB Growth rate sensitivity to neighboring NBs ─────────────────────── -->
-    <population.module module="proliferation" id="DYNAMIC_GROWTH_RATE_NB_CONTACT" value="0" description="1 → enable NB-contact repression; 0 → disabled (mutually exclusive with volume rule)" />
+    <!-- ── NB Growth rate sensitivity to neighboring NBs, only valid if growth and division is not universal ────── -->
+    <population.module module="proliferation" id="DYNAMIC_GROWTH_RATE_NB_SELF_REPRESSION" value="0" description="1 → enable NB-NB repression; 0 → disabled (mutually exclusive with volume rule)" />
     <population.module module="proliferation" id="NB_CONTACT_HALF_MAX" value="1.0" units="neighbors" description="K: NB neighbor count giving 50% repression" />
     <population.module module="proliferation" id="NB_CONTACT_HILL_N" value="2.0" description="Hill exponent controlling repression steepness" />
     <!-- ── NB division rules ───────────────────────────── -->