Feature/add flystemcells daughterstem

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

@@ -22,6 +22,9 @@
 import arcade.potts.env.location.Voxel;
 import arcade.potts.sim.Potts;
 import arcade.potts.sim.PottsSimulation;
+import arcade.potts.util.PottsEnums.Direction;
+import arcade.potts.util.PottsEnums.Phase;
+import arcade.potts.util.PottsEnums.State;
 import static arcade.potts.util.PottsEnums.Direction;
 import static arcade.potts.util.PottsEnums.Phase;
 import static arcade.potts.util.PottsEnums.State;
@@ -81,8 +84,15 @@ public class PottsModuleFlyStemProliferation extends PottsModuleProliferationVol
      */
     final double nbContactHillN;
 
+    /*
+     * Boolean flag for whether the daughter cell's differentiation is determined deterministically.
+     */
+    final boolean hasDeterministicDifferentiation;
+
     final double initialSize;
 
+    public static final double EPSILON = 1e-8;
+
     /**
      * Creates a proliferation {@code Module} for the given {@link PottsCellFlyStem}.
      *
@@ -127,13 +137,20 @@ public PottsModuleFlyStemProliferation(PottsCellFlyStem cell) {
         nbContactHalfMax = parameters.getDouble("proliferation/NB_CONTACT_HALF_MAX");
         nbContactHillN = parameters.getDouble("proliferation/NB_CONTACT_HILL_N");
 
+        String hasDeterministicDifferentiationString =
+                parameters.getString("proliferation/HAS_DETERMINISTIC_DIFFERENTIATION");
+        if (!hasDeterministicDifferentiationString.equals("TRUE")
+                && !hasDeterministicDifferentiationString.equals("FALSE")) {
+            throw new InvalidParameterException(
+                    "hasDeterministicDifferentiation must be either TRUE or FALSE");
+        }
+        hasDeterministicDifferentiation = hasDeterministicDifferentiationString.equals("TRUE");
+
         initialSize = cell.getVolume();
 
         setPhase(Phase.UNDEFINED);
     }
 
-    public static final double EPSILON = 1e-8;
-
     @Override
     public void addCell(MersenneTwisterFast random, Simulation sim) {
         Potts potts = ((PottsSimulation) sim).getPotts();
@@ -143,7 +160,7 @@ public void addCell(MersenneTwisterFast random, Simulation sim) {
         PottsLocation2D parentLoc = (PottsLocation2D) cell.getLocation();
         PottsLocation daughterLoc = (PottsLocation) parentLoc.split(random, divisionPlane);
 
-        boolean isDaughterStem = daughterStem(parentLoc, daughterLoc);
+        boolean isDaughterStem = daughterStem(parentLoc, daughterLoc, divisionPlane);
 
         if (isDaughterStem) {
             makeDaughterStemCell(daughterLoc, sim, potts, random);
@@ -301,6 +318,15 @@ public Plane getMUDDivisionPlane(PottsCellFlyStem cell) {
                         Direction.XY_PLANE.vector,
                         StemType.MUDMUT.splitDirectionRotation);
         Voxel splitVoxel = getCellSplitVoxel(StemType.MUDMUT, cell, defaultNormal);
+        System.out.println(
+                "in getMUDDivisionPlane, default Normal = ("
+                        + defaultNormal.getX()
+                        + ", "
+                        + +defaultNormal.getY()
+                        + ", "
+                        + +defaultNormal.getZ()
+                        + ", "
+                        + ")");
         return new Plane(new Double3D(splitVoxel.x, splitVoxel.y, splitVoxel.z), defaultNormal);
     }
 
@@ -328,7 +354,7 @@ public static Voxel getCellSplitVoxel(
      * @param loc2 the other cell location post division
      * @return whether or not the daughter cell should be a stem cell
      */
-    public boolean daughterStem(PottsLocation loc1, PottsLocation loc2) {
+    private boolean daughterStemRuleBasedDifferentiation(PottsLocation loc1, PottsLocation loc2) {
         if (((PottsCellFlyStem) cell).getStemType() == StemType.WT) {
             return false;
         } else if (((PottsCellFlyStem) cell).getStemType() == StemType.MUDMUT) {
@@ -351,6 +377,48 @@ public boolean daughterStem(PottsLocation loc1, PottsLocation loc2) {
                 "Invalid differentiation ruleset: " + differentiationRuleset);
     }
 
+    /*
+     * Determines whether the daughter cell should be a neuroblast or a GMC according to the orientation.
+     * This is deterministic.
+     *
+     * @param divisionPlane
+     * @return {@code true} if the daughter should be a stem cell. {@code false} if the daughter should be a GMC.
+     */
+    private boolean daughterStemDeterministic(Plane divisionPlane) {
+
+        Vector normalVector = divisionPlane.getUnitNormalVector();
+
+        Vector apicalAxis = ((PottsCellFlyStem) cell).getApicalAxis();
+        Vector expectedMUDNormalVector =
+                Vector.rotateVectorAroundAxis(
+                        apicalAxis,
+                        Direction.XY_PLANE.vector,
+                        StemType.MUDMUT.splitDirectionRotation);
+        // If TRUE, the daughter should be stem. Otherwise, should be GMC
+        return Math.abs(normalVector.getX() - expectedMUDNormalVector.getX()) <= EPSILON
+                && Math.abs(normalVector.getY() - expectedMUDNormalVector.getY()) <= EPSILON
+                && Math.abs(normalVector.getZ() - expectedMUDNormalVector.getZ()) <= EPSILON;
+    }
+
+    /**
+     * Determines whether a daughter cell should remain a stem cell or differentiate into a GMC.
+     *
+     * <p>This method serves as a wrapper that delegates to either a deterministic or rule-based
+     * differentiation mechanism depending on the value of {@code hasDeterministicDifferentiation}.
+     *
+     * @param parentsLoc the location of the parent cell before division
+     * @param daughterLoc the location of the daughter cell after division
+     * @param divisionPlane the plane of division for the daughter cell
+     * @return {@code true} if the daughter should remain a stem cell; {@code false} if it should be
+     *     a GMC
+     */
+    public boolean daughterStem(
+            PottsLocation2D parentsLoc, PottsLocation daughterLoc, Plane divisionPlane) {
+        return hasDeterministicDifferentiation
+                ? daughterStemDeterministic(divisionPlane)
+                : daughterStemRuleBasedDifferentiation(parentsLoc, daughterLoc);
+    }
+
     /**
      * Determines if the distance between two centroids, projected along the apical axis, is less
      * than or equal to the given range.

src/arcade/potts/parameter.potts.xml

@@ -80,6 +80,7 @@
     <!-- ── NB and GMC critical volume options ────────────────────────── -->
     <population.module module="proliferation" id="VOLUME_BASED_CRITICAL_VOLUME" value="0" description="1 → critical volume scales with daughter volume; 0 → use max (type-based) value" />
     <population.module module="proliferation" id="VOLUME_BASED_CRITICAL_VOLUME_MULTIPLIER" value="2" description="if enabled, GMC critical volume = daughter_volume × multiplier" />
+    <population.module module="proliferation" id="HAS_DETERMINISTIC_DIFFERENTIATION" value="TRUE" description="if TRUE, differentiation is determined deterministically" />
 
     <!-- apoptosis module parameters -->
     <population.module module="apoptosis" id="RATE_EARLY" value="4" units="steps/hour" conversion="DT" description="rate of events in early apoptosis phase" />