From 3c5f0f9d036f815b3594846359ace117f1610571 Mon Sep 17 00:00:00 2001 From: jannetty Date: Fri, 17 Oct 2025 11:29:05 -0700 Subject: [PATCH 01/59] change vector getters to use getters, helpful for mocking in tests --- src/arcade/core/util/Vector.java | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/arcade/core/util/Vector.java b/src/arcade/core/util/Vector.java index d71a16caa..efdcafc8d 100644 --- a/src/arcade/core/util/Vector.java +++ b/src/arcade/core/util/Vector.java @@ -33,7 +33,7 @@ public Vector(Double3D vector) { * @return the x component */ public double getX() { - return vector.x; + return vector.getX(); } /** @@ -42,7 +42,7 @@ public double getX() { * @return the y component */ public double getY() { - return vector.y; + return vector.getY(); } /** @@ -51,7 +51,7 @@ public double getY() { * @return the z component */ public double getZ() { - return vector.z; + return vector.getZ(); } /** From cb4815b2074d2f7cf943948e96bea96e672750fa Mon Sep 17 00:00:00 2001 From: jannetty Date: Fri, 17 Oct 2025 12:00:10 -0700 Subject: [PATCH 02/59] changing GMC differentiation module to not be a proliferation module but a PottsModule --- .../PottsModuleFlyGMCDifferentiation.java | 43 +++++++++++++++++-- .../PottsModuleFlyGMCDifferentiationTest.java | 38 ++++++++++++++++ 2 files changed, 77 insertions(+), 4 deletions(-) diff --git a/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java b/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java index ec7cdba9c..87e18ba52 100644 --- a/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java +++ b/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java @@ -4,6 +4,7 @@ import arcade.core.agent.cell.CellContainer; import arcade.core.env.location.Location; import arcade.core.sim.Simulation; +import arcade.core.util.Parameters; import arcade.potts.agent.cell.PottsCell; import arcade.potts.agent.cell.PottsCellContainer; import arcade.potts.agent.cell.PottsCellFlyGMC; @@ -11,14 +12,24 @@ import arcade.potts.env.location.PottsLocation2D; import arcade.potts.sim.Potts; import arcade.potts.sim.PottsSimulation; +import arcade.potts.util.PottsEnums.Phase; import arcade.potts.util.PottsEnums.State; /** - * Implementation of {@link PottsModuleProliferationSimple} for fly GMC agents. These cells divide - * into two {@link PottsCellFlyNeuron} cells. The links must be set in the setup file so that 100% - * of the daughter cells are Neurons. + * Implementation of {@link PottsModule} for fly GMC agents. These cells divide into two {@link + * PottsCellFlyNeuron} cells. The links must be set in the setup file so that 100% of the daughter + * cells are Neurons. */ -public class PottsModuleFlyGMCDifferentiation extends PottsModuleProliferationSimple { +public class PottsModuleFlyGMCDifferentiation extends PottsModule { + + /** Overall growth rate for cell (voxels/tick). */ + final double cellGrowthRate; + + /** + * Target ratio of critical volume for division size checkpoint (cell must reach CRITICAL_VOLUME + * * SIZE_TARGET * SIZE_CHECKPOINT to divide). + */ + final double sizeTarget; /** * Creates a fly GMC proliferation module. @@ -27,9 +38,33 @@ public class PottsModuleFlyGMCDifferentiation extends PottsModuleProliferationSi */ public PottsModuleFlyGMCDifferentiation(PottsCellFlyGMC cell) { super(cell); + Parameters parameters = cell.getParameters(); + sizeTarget = parameters.getDouble("proliferation/SIZE_TARGET"); + cellGrowthRate = parameters.getDouble("proliferation/CELL_GROWTH_RATE"); + setPhase(Phase.UNDEFINED); } @Override + public void step(MersenneTwisterFast random, Simulation sim) { + // Increase size of cell. + System.out.println("Pre updateTarget volume: " + cell.getVolume()); + cell.updateTarget(cellGrowthRate, sizeTarget); + System.out.println("Post updateTarget volume: " + cell.getVolume()); + boolean sizeCheck = cell.getVolume() >= sizeTarget * cell.getCriticalVolume(); + if (sizeCheck) { + addCell(random, sim); + } + } + + /** + * Adds a cell to the simulation. + * + *

The cell location is split. The new neuron cell is created, initialized, and added to the + * schedule. This cell's location is also assigned to a new Neuron cell. + * + * @param random the random number generator + * @param sim the simulation instance + */ void addCell(MersenneTwisterFast random, Simulation sim) { Potts potts = ((PottsSimulation) sim).getPotts(); diff --git a/test/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiationTest.java b/test/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiationTest.java index 2cb4df20c..e844eafbd 100644 --- a/test/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiationTest.java +++ b/test/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiationTest.java @@ -24,6 +24,7 @@ import arcade.potts.util.PottsEnums.State; import static org.mockito.ArgumentMatchers.any; import static org.mockito.ArgumentMatchers.eq; +import static org.mockito.ArgumentMatchers.isNull; import static org.mockito.Mockito.*; import static arcade.potts.util.PottsEnums.Region; import static arcade.potts.util.PottsEnums.State; @@ -143,6 +144,43 @@ final void tearDown() { mockedConstruction.close(); } + @Test + public void step_belowCheckpoint_updatesTargetOnly() { + when(parameters.getDouble("proliferation/SIZE_TARGET")).thenReturn(1.2); + when(parameters.getDouble("proliferation/CELL_GROWTH_RATE")).thenReturn(4.0); + when(gmcCell.getCriticalVolume()).thenReturn(100.0); + when(gmcCell.getVolume()).thenReturn(50.0); // 50 < 1.2*100 + + PottsModuleFlyGMCDifferentiation module = new PottsModuleFlyGMCDifferentiation(gmcCell); + module.step(random, sim); + + verify(gmcCell).updateTarget(4.0, 1.2); + // Nothing from addCell pipeline + verify(grid, never()).addObject(any(), any()); + verify(potts, never()).register(any()); + } + + @Test + public void step_atOrAboveCheckpoint_triggersAddCell() { + when(parameters.getDouble("proliferation/SIZE_TARGET")).thenReturn(1.2); + when(parameters.getDouble("proliferation/CELL_GROWTH_RATE")).thenReturn(4.0); + when(gmcCell.getCriticalVolume()).thenReturn(100.0); + when(gmcCell.getVolume()).thenReturn(120.0); // 120 >= 1.2*100 + + // Minimal stubs for the addCell path + PottsCellContainer container = mock(PottsCellContainer.class); + when(gmcCell.make(eq(123), eq(State.QUIESCENT), any())).thenReturn(container); + PottsCell newCell = mock(PottsCell.class); + when(container.convert(eq(cellFactory), any(), any())).thenReturn(newCell); + + PottsModuleFlyGMCDifferentiation module = new PottsModuleFlyGMCDifferentiation(gmcCell); + module.step(random, sim); + verify(gmcCell).updateTarget(4.0, 1.2); + // Something from addCell pipeline must have occurred + verify(grid).addObject(eq(newCell), isNull()); + verify(potts).register(eq(newCell)); + } + @Test public void addCell_called_callsExpectedMethods() { // When the module calls make() on the cell, return Quiescent PottsCellContainer mock From d15c8d366d996a81e382b65ef3005159570035a9 Mon Sep 17 00:00:00 2001 From: jannetty Date: Fri, 17 Oct 2025 12:14:40 -0700 Subject: [PATCH 03/59] remove shadowing in tests --- .../module/PottsModuleFlyGMCDifferentiationTest.java | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/test/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiationTest.java b/test/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiationTest.java index e844eafbd..b506415ca 100644 --- a/test/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiationTest.java +++ b/test/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiationTest.java @@ -167,16 +167,16 @@ public void step_atOrAboveCheckpoint_triggersAddCell() { when(gmcCell.getCriticalVolume()).thenReturn(100.0); when(gmcCell.getVolume()).thenReturn(120.0); // 120 >= 1.2*100 - // Minimal stubs for the addCell path - PottsCellContainer container = mock(PottsCellContainer.class); + // Stubs for the addCell path + container = mock(PottsCellContainer.class); when(gmcCell.make(eq(123), eq(State.QUIESCENT), any())).thenReturn(container); - PottsCell newCell = mock(PottsCell.class); + newCell = mock(PottsCell.class); when(container.convert(eq(cellFactory), any(), any())).thenReturn(newCell); PottsModuleFlyGMCDifferentiation module = new PottsModuleFlyGMCDifferentiation(gmcCell); module.step(random, sim); verify(gmcCell).updateTarget(4.0, 1.2); - // Something from addCell pipeline must have occurred + // Something from addCell pipeline must happen verify(grid).addObject(eq(newCell), isNull()); verify(potts).register(eq(newCell)); } From 564525be07cb914025e536d91630b109f332b033 Mon Sep 17 00:00:00 2001 From: jannetty Date: Fri, 17 Oct 2025 12:20:06 -0700 Subject: [PATCH 04/59] fixing imports --- .../module/PottsModuleFlyGMCDifferentiationTest.java | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/test/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiationTest.java b/test/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiationTest.java index b506415ca..71b73b054 100644 --- a/test/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiationTest.java +++ b/test/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiationTest.java @@ -25,9 +25,11 @@ import static org.mockito.ArgumentMatchers.any; import static org.mockito.ArgumentMatchers.eq; import static org.mockito.ArgumentMatchers.isNull; -import static org.mockito.Mockito.*; -import static arcade.potts.util.PottsEnums.Region; -import static arcade.potts.util.PottsEnums.State; +import static org.mockito.Mockito.mock; +import static org.mockito.Mockito.mockConstruction; +import static org.mockito.Mockito.never; +import static org.mockito.Mockito.verify; +import static org.mockito.Mockito.when; public class PottsModuleFlyGMCDifferentiationTest { private int[][][] dummyIDs; From 0899a1905069edc498a5c5f13b12909e74afb450 Mon Sep 17 00:00:00 2001 From: jannetty Date: Fri, 17 Oct 2025 12:21:34 -0700 Subject: [PATCH 05/59] formatting --- .../agent/module/PottsModuleFlyGMCDifferentiationTest.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiationTest.java b/test/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiationTest.java index 71b73b054..f1f13c0c2 100644 --- a/test/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiationTest.java +++ b/test/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiationTest.java @@ -157,7 +157,7 @@ public void step_belowCheckpoint_updatesTargetOnly() { module.step(random, sim); verify(gmcCell).updateTarget(4.0, 1.2); - // Nothing from addCell pipeline + // Nothing from addCell verify(grid, never()).addObject(any(), any()); verify(potts, never()).register(any()); } From 651aef54b0b70bdf9e9da61194a7f51c2458c121 Mon Sep 17 00:00:00 2001 From: jannetty Date: Fri, 17 Oct 2025 12:22:24 -0700 Subject: [PATCH 06/59] formatting again --- .../agent/module/PottsModuleFlyGMCDifferentiationTest.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiationTest.java b/test/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiationTest.java index f1f13c0c2..165b5dacf 100644 --- a/test/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiationTest.java +++ b/test/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiationTest.java @@ -169,7 +169,7 @@ public void step_atOrAboveCheckpoint_triggersAddCell() { when(gmcCell.getCriticalVolume()).thenReturn(100.0); when(gmcCell.getVolume()).thenReturn(120.0); // 120 >= 1.2*100 - // Stubs for the addCell path + // Stubs for addCell container = mock(PottsCellContainer.class); when(gmcCell.make(eq(123), eq(State.QUIESCENT), any())).thenReturn(container); newCell = mock(PottsCell.class); @@ -178,7 +178,7 @@ public void step_atOrAboveCheckpoint_triggersAddCell() { PottsModuleFlyGMCDifferentiation module = new PottsModuleFlyGMCDifferentiation(gmcCell); module.step(random, sim); verify(gmcCell).updateTarget(4.0, 1.2); - // Something from addCell pipeline must happen + // Something from addCell must happen verify(grid).addObject(eq(newCell), isNull()); verify(potts).register(eq(newCell)); } From 2fbcf15ab58c1d3cd391c101828e7c35f0f92600 Mon Sep 17 00:00:00 2001 From: jannetty Date: Fri, 17 Oct 2025 15:10:31 -0700 Subject: [PATCH 07/59] removed print statements --- .../potts/agent/module/PottsModuleFlyGMCDifferentiation.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java b/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java index 87e18ba52..2a3a0f7f2 100644 --- a/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java +++ b/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java @@ -1,6 +1,5 @@ package arcade.potts.agent.module; -import ec.util.MersenneTwisterFast; import arcade.core.agent.cell.CellContainer; import arcade.core.env.location.Location; import arcade.core.sim.Simulation; @@ -14,6 +13,7 @@ import arcade.potts.sim.PottsSimulation; import arcade.potts.util.PottsEnums.Phase; import arcade.potts.util.PottsEnums.State; +import ec.util.MersenneTwisterFast; /** * Implementation of {@link PottsModule} for fly GMC agents. These cells divide into two {@link From 3f0f860d05bf7ddbef63fce69175a73b7eb41ff7 Mon Sep 17 00:00:00 2001 From: jannetty Date: Fri, 17 Oct 2025 15:10:59 -0700 Subject: [PATCH 08/59] formatting --- .../potts/agent/module/PottsModuleFlyGMCDifferentiation.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java b/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java index 2a3a0f7f2..87e18ba52 100644 --- a/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java +++ b/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java @@ -1,5 +1,6 @@ package arcade.potts.agent.module; +import ec.util.MersenneTwisterFast; import arcade.core.agent.cell.CellContainer; import arcade.core.env.location.Location; import arcade.core.sim.Simulation; @@ -13,7 +14,6 @@ import arcade.potts.sim.PottsSimulation; import arcade.potts.util.PottsEnums.Phase; import arcade.potts.util.PottsEnums.State; -import ec.util.MersenneTwisterFast; /** * Implementation of {@link PottsModule} for fly GMC agents. These cells divide into two {@link From 0b12f7ddeb869c7ac980205286abe9318a597e7c Mon Sep 17 00:00:00 2001 From: jannetty Date: Mon, 20 Oct 2025 11:26:27 -0700 Subject: [PATCH 09/59] adding ability to determine offset in the frame of the Apical axis in PottsLocation2D --- .../potts/env/location/PottsLocation2D.java | 53 +++++++++++ .../potts/env/location/Location3DTest.java | 89 +++++++++++++++++++ 2 files changed, 142 insertions(+) diff --git a/src/arcade/potts/env/location/PottsLocation2D.java b/src/arcade/potts/env/location/PottsLocation2D.java index 0a8fcc986..c00577611 100644 --- a/src/arcade/potts/env/location/PottsLocation2D.java +++ b/src/arcade/potts/env/location/PottsLocation2D.java @@ -1,7 +1,10 @@ package arcade.potts.env.location; import java.util.ArrayList; +import java.util.Collections; +import java.util.Comparator; import java.util.HashMap; +import arcade.core.util.Vector; import static arcade.potts.util.PottsEnums.Direction; /** Concrete implementation of {@link PottsLocation} for 2D. */ @@ -64,4 +67,54 @@ Direction getSlice(Direction direction, HashMap diameters) { ArrayList getSelected(Voxel focus, double n) { return Location2D.getSelected(voxels, focus, n); } + + /* + * Gets the voxel through which a plane of division will pass from percentage + * offsets along the locations's X and Y axes with the provided apicalAxis set as + * the Y axis. + * + * @param offsets the percent offsets along the location's X and Y axes + * @param apicalAxis the axis considered to be pointing up along the Y axis + * @return the voxel through which the plane of division will pass + */ + public Voxel getOffsetInApicalFrame2D(ArrayList offsets, Vector apicalAxis) { + if (voxels.isEmpty()) { + return null; + } + if (offsets == null || offsets.size() != 2) { + throw new IllegalArgumentException("Offsets must be 2 integers."); + } + + // Normalize axes + Vector yAxis = Vector.normalizeVector(apicalAxis); + Vector xAxis = Vector.normalizeVector(new Vector(apicalAxis.getY(), -apicalAxis.getX(), 0)); + + // Project voxels onto apical axis and group by rounded projection + HashMap> apicalBands = new HashMap<>(); + ArrayList apicalKeys = new ArrayList<>(); + + for (Voxel v : voxels) { + Vector pos = new Vector(v.x, v.y, 0); + double apicalProj = Vector.dotProduct(pos, yAxis); + int roundedProj = (int) Math.round(apicalProj); + apicalBands.computeIfAbsent(roundedProj, k -> new ArrayList<>()).add(v); + apicalKeys.add(roundedProj); + } + + // Sort apical keys and choose percentile + Collections.sort(apicalKeys); + int yIndex = + Math.min( + apicalKeys.size() - 1, + (int) ((offsets.get(1) / 100.0) * apicalKeys.size())); + int targetApicalKey = apicalKeys.get(yIndex); + + ArrayList band = apicalBands.get(targetApicalKey); + if (band == null || band.isEmpty()) return null; + // Project to orthogonal axis within the band and sort + band.sort( + Comparator.comparingDouble(v -> Vector.dotProduct(new Vector(v.x, v.y, 0), xAxis))); + int xIndex = Math.min(band.size() - 1, (int) ((offsets.get(0) / 100.0) * band.size())); + return band.get(xIndex); + } } diff --git a/test/arcade/potts/env/location/Location3DTest.java b/test/arcade/potts/env/location/Location3DTest.java index 66aeeb547..85efebb06 100644 --- a/test/arcade/potts/env/location/Location3DTest.java +++ b/test/arcade/potts/env/location/Location3DTest.java @@ -4,6 +4,7 @@ import java.util.HashMap; import org.junit.jupiter.api.BeforeAll; import org.junit.jupiter.api.Test; +import arcade.core.util.Vector; import static org.junit.jupiter.api.Assertions.*; import static arcade.core.ARCADETestUtilities.*; import static arcade.potts.env.location.Voxel.VOXEL_COMPARATOR; @@ -1209,4 +1210,92 @@ public void getSelected_minSizeLocations_returnsList() { assertEquals(selected.size(), 0); } + + @Test + public void getVolumeInformedOffsetInApicalFrame2D_returnsExpectedVoxel_atCenter() { + ArrayList voxels = new ArrayList<>(); + // 3x3 grid centered at (0,0) + for (int x = -1; x <= 1; x++) { + for (int y = -1; y <= 1; y++) { + voxels.add(new Voxel(x, y, 0)); + } + } + PottsLocation2D loc = new PottsLocation2D(voxels); + + Vector apicalAxis = new Vector(0, 1, 0); // Y-axis + ArrayList offsets = new ArrayList<>(); + offsets.add(50); // middle of X axis + offsets.add(50); // middle of Y axis + + Voxel result = loc.getOffsetInApicalFrame2D(offsets, apicalAxis); + assertEquals(new Voxel(0, 0, 0), result); + } + + @Test + public void getVolumeInformedOffsetInApicalFrame2D_returnsExpectedVoxel_upperRight() { + ArrayList voxels = new ArrayList<>(); + for (int x = 0; x <= 4; x++) { + for (int y = 0; y <= 4; y++) { + voxels.add(new Voxel(x, y, 0)); + } + } + PottsLocation2D loc = new PottsLocation2D(voxels); + + Vector apicalAxis = new Vector(0, 1, 0); // Y-axis + ArrayList offsets = new ArrayList<>(); + offsets.add(100); // far right of X axis + offsets.add(100); // top of Y axis + + Voxel result = loc.getOffsetInApicalFrame2D(offsets, apicalAxis); + assertEquals(new Voxel(4, 4, 0), result); + } + + @Test + public void getVolumeInformedOffsetInApicalFrame2D_emptyVoxels_returnsNull() { + PottsLocation2D loc = new PottsLocation2D(new ArrayList<>()); + + Vector apicalAxis = new Vector(1, 0, 0); + ArrayList offsets = new ArrayList<>(); + offsets.add(50); + offsets.add(50); + + Voxel result = loc.getOffsetInApicalFrame2D(offsets, apicalAxis); + assertNull(result); + } + + @Test + public void getVolumeInformedOffsetInApicalFrame2D_invalidOffset_throwsException() { + ArrayList voxels = new ArrayList<>(); + voxels.add(new Voxel(0, 0, 0)); + PottsLocation2D loc = new PottsLocation2D(voxels); + + Vector apicalAxis = new Vector(1, 0, 0); + + ArrayList badOffset = new ArrayList<>(); + badOffset.add(50); // only one element + + assertThrows( + IllegalArgumentException.class, + () -> { + loc.getOffsetInApicalFrame2D(badOffset, apicalAxis); + }); + } + + @Test + public void getVolumeInformedOffsetInApicalFrame2D_nonOrthogonalAxis_returnsExpected() { + ArrayList voxels = new ArrayList<>(); + voxels.add(new Voxel(0, 0, 0)); + voxels.add(new Voxel(1, 1, 0)); + voxels.add(new Voxel(2, 2, 0)); + voxels.add(new Voxel(3, 3, 0)); + PottsLocation2D loc = new PottsLocation2D(voxels); + + Vector apicalAxis = new Vector(1, 1, 0); // diagonal + ArrayList offsets = new ArrayList<>(); + offsets.add(0); // lowest orthogonal axis + offsets.add(100); // farthest along apical + + Voxel result = loc.getOffsetInApicalFrame2D(offsets, apicalAxis); + assertEquals(new Voxel(3, 3, 0), result); + } } From d3bd6f686cd2378452f7d16198f6f8011c3ca613 Mon Sep 17 00:00:00 2001 From: jannetty Date: Mon, 20 Oct 2025 11:36:24 -0700 Subject: [PATCH 10/59] moving tests into correct place --- .../potts/env/location/PottsLocation2D.java | 11 +-- .../potts/env/location/Location3DTest.java | 89 ------------------- .../env/location/PottsLocation2DTest.java | 89 +++++++++++++++++++ 3 files changed, 95 insertions(+), 94 deletions(-) diff --git a/src/arcade/potts/env/location/PottsLocation2D.java b/src/arcade/potts/env/location/PottsLocation2D.java index c00577611..a94e41244 100644 --- a/src/arcade/potts/env/location/PottsLocation2D.java +++ b/src/arcade/potts/env/location/PottsLocation2D.java @@ -68,10 +68,9 @@ ArrayList getSelected(Voxel focus, double n) { return Location2D.getSelected(voxels, focus, n); } - /* - * Gets the voxel through which a plane of division will pass from percentage - * offsets along the locations's X and Y axes with the provided apicalAxis set as - * the Y axis. + /** + * Gets the voxel through which a plane of division will pass from percentage offsets along the + * locations's X and Y axes with the provided apicalAxis set as the Y axis. * * @param offsets the percent offsets along the location's X and Y axes * @param apicalAxis the axis considered to be pointing up along the Y axis @@ -110,7 +109,9 @@ public Voxel getOffsetInApicalFrame2D(ArrayList offsets, Vector apicalA int targetApicalKey = apicalKeys.get(yIndex); ArrayList band = apicalBands.get(targetApicalKey); - if (band == null || band.isEmpty()) return null; + if (band == null || band.isEmpty()) { + return null; + } // Project to orthogonal axis within the band and sort band.sort( Comparator.comparingDouble(v -> Vector.dotProduct(new Vector(v.x, v.y, 0), xAxis))); diff --git a/test/arcade/potts/env/location/Location3DTest.java b/test/arcade/potts/env/location/Location3DTest.java index 85efebb06..66aeeb547 100644 --- a/test/arcade/potts/env/location/Location3DTest.java +++ b/test/arcade/potts/env/location/Location3DTest.java @@ -4,7 +4,6 @@ import java.util.HashMap; import org.junit.jupiter.api.BeforeAll; import org.junit.jupiter.api.Test; -import arcade.core.util.Vector; import static org.junit.jupiter.api.Assertions.*; import static arcade.core.ARCADETestUtilities.*; import static arcade.potts.env.location.Voxel.VOXEL_COMPARATOR; @@ -1210,92 +1209,4 @@ public void getSelected_minSizeLocations_returnsList() { assertEquals(selected.size(), 0); } - - @Test - public void getVolumeInformedOffsetInApicalFrame2D_returnsExpectedVoxel_atCenter() { - ArrayList voxels = new ArrayList<>(); - // 3x3 grid centered at (0,0) - for (int x = -1; x <= 1; x++) { - for (int y = -1; y <= 1; y++) { - voxels.add(new Voxel(x, y, 0)); - } - } - PottsLocation2D loc = new PottsLocation2D(voxels); - - Vector apicalAxis = new Vector(0, 1, 0); // Y-axis - ArrayList offsets = new ArrayList<>(); - offsets.add(50); // middle of X axis - offsets.add(50); // middle of Y axis - - Voxel result = loc.getOffsetInApicalFrame2D(offsets, apicalAxis); - assertEquals(new Voxel(0, 0, 0), result); - } - - @Test - public void getVolumeInformedOffsetInApicalFrame2D_returnsExpectedVoxel_upperRight() { - ArrayList voxels = new ArrayList<>(); - for (int x = 0; x <= 4; x++) { - for (int y = 0; y <= 4; y++) { - voxels.add(new Voxel(x, y, 0)); - } - } - PottsLocation2D loc = new PottsLocation2D(voxels); - - Vector apicalAxis = new Vector(0, 1, 0); // Y-axis - ArrayList offsets = new ArrayList<>(); - offsets.add(100); // far right of X axis - offsets.add(100); // top of Y axis - - Voxel result = loc.getOffsetInApicalFrame2D(offsets, apicalAxis); - assertEquals(new Voxel(4, 4, 0), result); - } - - @Test - public void getVolumeInformedOffsetInApicalFrame2D_emptyVoxels_returnsNull() { - PottsLocation2D loc = new PottsLocation2D(new ArrayList<>()); - - Vector apicalAxis = new Vector(1, 0, 0); - ArrayList offsets = new ArrayList<>(); - offsets.add(50); - offsets.add(50); - - Voxel result = loc.getOffsetInApicalFrame2D(offsets, apicalAxis); - assertNull(result); - } - - @Test - public void getVolumeInformedOffsetInApicalFrame2D_invalidOffset_throwsException() { - ArrayList voxels = new ArrayList<>(); - voxels.add(new Voxel(0, 0, 0)); - PottsLocation2D loc = new PottsLocation2D(voxels); - - Vector apicalAxis = new Vector(1, 0, 0); - - ArrayList badOffset = new ArrayList<>(); - badOffset.add(50); // only one element - - assertThrows( - IllegalArgumentException.class, - () -> { - loc.getOffsetInApicalFrame2D(badOffset, apicalAxis); - }); - } - - @Test - public void getVolumeInformedOffsetInApicalFrame2D_nonOrthogonalAxis_returnsExpected() { - ArrayList voxels = new ArrayList<>(); - voxels.add(new Voxel(0, 0, 0)); - voxels.add(new Voxel(1, 1, 0)); - voxels.add(new Voxel(2, 2, 0)); - voxels.add(new Voxel(3, 3, 0)); - PottsLocation2D loc = new PottsLocation2D(voxels); - - Vector apicalAxis = new Vector(1, 1, 0); // diagonal - ArrayList offsets = new ArrayList<>(); - offsets.add(0); // lowest orthogonal axis - offsets.add(100); // farthest along apical - - Voxel result = loc.getOffsetInApicalFrame2D(offsets, apicalAxis); - assertEquals(new Voxel(3, 3, 0), result); - } } diff --git a/test/arcade/potts/env/location/PottsLocation2DTest.java b/test/arcade/potts/env/location/PottsLocation2DTest.java index 81f861ab3..6015f8b87 100644 --- a/test/arcade/potts/env/location/PottsLocation2DTest.java +++ b/test/arcade/potts/env/location/PottsLocation2DTest.java @@ -4,6 +4,7 @@ import org.junit.jupiter.api.BeforeAll; import org.junit.jupiter.api.Test; import ec.util.MersenneTwisterFast; +import arcade.core.util.Vector; import static org.junit.jupiter.api.Assertions.*; import static org.mockito.Mockito.*; import static arcade.potts.env.location.Voxel.VOXEL_COMPARATOR; @@ -278,4 +279,92 @@ public void split_balanceableLocationRandomOne_returnsList() { assertEquals(locVoxels, loc.voxels); assertEquals(splitVoxels, split.voxels); } + + @Test + public void getVolumeInformedOffsetInApicalFrame2D_returnsExpectedVoxel_atCenter() { + ArrayList voxels = new ArrayList<>(); + // 3x3 grid centered at (0,0) + for (int x = -1; x <= 1; x++) { + for (int y = -1; y <= 1; y++) { + voxels.add(new Voxel(x, y, 0)); + } + } + PottsLocation2D loc = new PottsLocation2D(voxels); + + Vector apicalAxis = new Vector(0, 1, 0); // Y-axis + ArrayList offsets = new ArrayList<>(); + offsets.add(50); // middle of X axis + offsets.add(50); // middle of Y axis + + Voxel result = loc.getOffsetInApicalFrame2D(offsets, apicalAxis); + assertEquals(new Voxel(0, 0, 0), result); + } + + @Test + public void getVolumeInformedOffsetInApicalFrame2D_returnsExpectedVoxel_upperRight() { + ArrayList voxels = new ArrayList<>(); + for (int x = 0; x <= 4; x++) { + for (int y = 0; y <= 4; y++) { + voxels.add(new Voxel(x, y, 0)); + } + } + PottsLocation2D loc = new PottsLocation2D(voxels); + + Vector apicalAxis = new Vector(0, 1, 0); // Y-axis + ArrayList offsets = new ArrayList<>(); + offsets.add(100); // far right of X axis + offsets.add(100); // top of Y axis + + Voxel result = loc.getOffsetInApicalFrame2D(offsets, apicalAxis); + assertEquals(new Voxel(4, 4, 0), result); + } + + @Test + public void getVolumeInformedOffsetInApicalFrame2D_emptyVoxels_returnsNull() { + PottsLocation2D loc = new PottsLocation2D(new ArrayList<>()); + + Vector apicalAxis = new Vector(1, 0, 0); + ArrayList offsets = new ArrayList<>(); + offsets.add(50); + offsets.add(50); + + Voxel result = loc.getOffsetInApicalFrame2D(offsets, apicalAxis); + assertNull(result); + } + + @Test + public void getVolumeInformedOffsetInApicalFrame2D_invalidOffset_throwsException() { + ArrayList voxels = new ArrayList<>(); + voxels.add(new Voxel(0, 0, 0)); + PottsLocation2D loc = new PottsLocation2D(voxels); + + Vector apicalAxis = new Vector(1, 0, 0); + + ArrayList badOffset = new ArrayList<>(); + badOffset.add(50); // only one element + + assertThrows( + IllegalArgumentException.class, + () -> { + loc.getOffsetInApicalFrame2D(badOffset, apicalAxis); + }); + } + + @Test + public void getVolumeInformedOffsetInApicalFrame2D_nonOrthogonalAxis_returnsExpected() { + ArrayList voxels = new ArrayList<>(); + voxels.add(new Voxel(0, 0, 0)); + voxels.add(new Voxel(1, 1, 0)); + voxels.add(new Voxel(2, 2, 0)); + voxels.add(new Voxel(3, 3, 0)); + PottsLocation2D loc = new PottsLocation2D(voxels); + + Vector apicalAxis = new Vector(1, 1, 0); // diagonal + ArrayList offsets = new ArrayList<>(); + offsets.add(0); // lowest orthogonal axis + offsets.add(100); // farthest along apical + + Voxel result = loc.getOffsetInApicalFrame2D(offsets, apicalAxis); + assertEquals(new Voxel(3, 3, 0), result); + } } From 75382f3d8bcbbe1c0e7f69065831dec324a3c3bd Mon Sep 17 00:00:00 2001 From: jannetty Date: Mon, 20 Oct 2025 11:38:48 -0700 Subject: [PATCH 11/59] updated test name to reflect function name --- .../arcade/potts/env/location/PottsLocation2DTest.java | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/test/arcade/potts/env/location/PottsLocation2DTest.java b/test/arcade/potts/env/location/PottsLocation2DTest.java index 6015f8b87..838e3937e 100644 --- a/test/arcade/potts/env/location/PottsLocation2DTest.java +++ b/test/arcade/potts/env/location/PottsLocation2DTest.java @@ -281,7 +281,7 @@ public void split_balanceableLocationRandomOne_returnsList() { } @Test - public void getVolumeInformedOffsetInApicalFrame2D_returnsExpectedVoxel_atCenter() { + public void getOffsetInApicalFrame2D_returnsExpectedVoxel_atCenter() { ArrayList voxels = new ArrayList<>(); // 3x3 grid centered at (0,0) for (int x = -1; x <= 1; x++) { @@ -301,7 +301,7 @@ public void getVolumeInformedOffsetInApicalFrame2D_returnsExpectedVoxel_atCenter } @Test - public void getVolumeInformedOffsetInApicalFrame2D_returnsExpectedVoxel_upperRight() { + public void getOffsetInApicalFrame2D_returnsExpectedVoxel_upperRight() { ArrayList voxels = new ArrayList<>(); for (int x = 0; x <= 4; x++) { for (int y = 0; y <= 4; y++) { @@ -320,7 +320,7 @@ public void getVolumeInformedOffsetInApicalFrame2D_returnsExpectedVoxel_upperRig } @Test - public void getVolumeInformedOffsetInApicalFrame2D_emptyVoxels_returnsNull() { + public void getOffsetInApicalFrame2D_emptyVoxels_returnsNull() { PottsLocation2D loc = new PottsLocation2D(new ArrayList<>()); Vector apicalAxis = new Vector(1, 0, 0); @@ -333,7 +333,7 @@ public void getVolumeInformedOffsetInApicalFrame2D_emptyVoxels_returnsNull() { } @Test - public void getVolumeInformedOffsetInApicalFrame2D_invalidOffset_throwsException() { + public void getOffsetInApicalFrame2D_invalidOffset_throwsException() { ArrayList voxels = new ArrayList<>(); voxels.add(new Voxel(0, 0, 0)); PottsLocation2D loc = new PottsLocation2D(voxels); @@ -351,7 +351,7 @@ public void getVolumeInformedOffsetInApicalFrame2D_invalidOffset_throwsException } @Test - public void getVolumeInformedOffsetInApicalFrame2D_nonOrthogonalAxis_returnsExpected() { + public void getOffsetInApicalFrame2D_nonOrthogonalAxis_returnsExpected() { ArrayList voxels = new ArrayList<>(); voxels.add(new Voxel(0, 0, 0)); voxels.add(new Voxel(1, 1, 0)); From df911dc30c808d027c4f9a530a05ef515ac6c5da Mon Sep 17 00:00:00 2001 From: jannetty Date: Mon, 20 Oct 2025 11:40:33 -0700 Subject: [PATCH 12/59] updating test titles --- test/arcade/potts/env/location/PottsLocation2DTest.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/arcade/potts/env/location/PottsLocation2DTest.java b/test/arcade/potts/env/location/PottsLocation2DTest.java index 838e3937e..25396de49 100644 --- a/test/arcade/potts/env/location/PottsLocation2DTest.java +++ b/test/arcade/potts/env/location/PottsLocation2DTest.java @@ -281,7 +281,7 @@ public void split_balanceableLocationRandomOne_returnsList() { } @Test - public void getOffsetInApicalFrame2D_returnsExpectedVoxel_atCenter() { + public void getOffsetInApicalFrame2D_offsetAtCenter_returnsExpectedVoxel() { ArrayList voxels = new ArrayList<>(); // 3x3 grid centered at (0,0) for (int x = -1; x <= 1; x++) { @@ -301,7 +301,7 @@ public void getOffsetInApicalFrame2D_returnsExpectedVoxel_atCenter() { } @Test - public void getOffsetInApicalFrame2D_returnsExpectedVoxel_upperRight() { + public void getOffsetInApicalFrame2D_offsetUpperRight_returnsExpectedVoxel() { ArrayList voxels = new ArrayList<>(); for (int x = 0; x <= 4; x++) { for (int y = 0; y <= 4; y++) { From ba31c8545998eadcdc745afa452a1c7ea2fb44f6 Mon Sep 17 00:00:00 2001 From: jannetty Date: Mon, 20 Oct 2025 11:45:30 -0700 Subject: [PATCH 13/59] updating docstring --- src/arcade/potts/env/location/PottsLocation2D.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/arcade/potts/env/location/PottsLocation2D.java b/src/arcade/potts/env/location/PottsLocation2D.java index a94e41244..166b153c3 100644 --- a/src/arcade/potts/env/location/PottsLocation2D.java +++ b/src/arcade/potts/env/location/PottsLocation2D.java @@ -69,8 +69,8 @@ ArrayList getSelected(Voxel focus, double n) { } /** - * Gets the voxel through which a plane of division will pass from percentage offsets along the - * locations's X and Y axes with the provided apicalAxis set as the Y axis. + * Gets the voxel at specified percentage offsets along the location's X and + * Y axes with the provided apicalAxis considered to be pointing up the Y axis. * * @param offsets the percent offsets along the location's X and Y axes * @param apicalAxis the axis considered to be pointing up along the Y axis From 9a76cf1972c367f15c3f33e5e5085bc9d50c50f0 Mon Sep 17 00:00:00 2001 From: jannetty Date: Mon, 20 Oct 2025 11:46:06 -0700 Subject: [PATCH 14/59] formatting --- src/arcade/potts/env/location/PottsLocation2D.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/arcade/potts/env/location/PottsLocation2D.java b/src/arcade/potts/env/location/PottsLocation2D.java index 166b153c3..102a60011 100644 --- a/src/arcade/potts/env/location/PottsLocation2D.java +++ b/src/arcade/potts/env/location/PottsLocation2D.java @@ -69,8 +69,8 @@ ArrayList getSelected(Voxel focus, double n) { } /** - * Gets the voxel at specified percentage offsets along the location's X and - * Y axes with the provided apicalAxis considered to be pointing up the Y axis. + * Gets the voxel at specified percentage offsets along the location's X and Y axes with the + * provided apicalAxis considered to be pointing up the Y axis. * * @param offsets the percent offsets along the location's X and Y axes * @param apicalAxis the axis considered to be pointing up along the Y axis From 27b07dedc6bb306f60da9b0871e7b5d36d8e1b89 Mon Sep 17 00:00:00 2001 From: jannetty Date: Mon, 20 Oct 2025 12:21:58 -0700 Subject: [PATCH 15/59] changing names of current potts proliferation modules --- .../potts/agent/cell/PottsCellStem.java | 4 +- .../PottsModuleFlyGMCDifferentiation.java | 9 ++- ...uleProliferationCellCycleProgression.java} | 4 +- ...liferationCellCycleProgressionSimple.java} | 7 +- .../potts/agent/cell/PottsCellStemTest.java | 4 +- .../PottsModuleProliferationSimpleTest.java | 80 ++++++++++++------- .../module/PottsModuleProliferationTest.java | 29 ++++--- 7 files changed, 87 insertions(+), 50 deletions(-) rename src/arcade/potts/agent/module/{PottsModuleProliferation.java => PottsModuleProliferationCellCycleProgression.java} (95%) rename src/arcade/potts/agent/module/{PottsModuleProliferationSimple.java => PottsModuleProliferationCellCycleProgressionSimple.java} (96%) diff --git a/src/arcade/potts/agent/cell/PottsCellStem.java b/src/arcade/potts/agent/cell/PottsCellStem.java index 6d0d15e4e..4e448a427 100644 --- a/src/arcade/potts/agent/cell/PottsCellStem.java +++ b/src/arcade/potts/agent/cell/PottsCellStem.java @@ -9,7 +9,7 @@ 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.PottsModuleProliferationCellCycleProgressionSimple; import arcade.potts.agent.module.PottsModuleQuiescence; import static arcade.potts.util.PottsEnums.Region; import static arcade.potts.util.PottsEnums.State; @@ -73,7 +73,7 @@ void setStateModule(CellState newState) { module = new PottsModuleQuiescence(this); break; case PROLIFERATIVE: - module = new PottsModuleProliferationSimple(this); + module = new PottsModuleProliferationCellCycleProgressionSimple(this); break; case APOPTOTIC: module = new PottsModuleApoptosisSimple(this); diff --git a/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java b/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java index ec7cdba9c..74e6781a8 100644 --- a/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java +++ b/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java @@ -14,11 +14,12 @@ import arcade.potts.util.PottsEnums.State; /** - * Implementation of {@link PottsModuleProliferationSimple} for fly GMC agents. These cells divide - * into two {@link PottsCellFlyNeuron} cells. The links must be set in the setup file so that 100% - * of the daughter cells are Neurons. + * Implementation of {@link PottsModuleProliferationCellCycleProgressionSimple} for fly GMC agents. + * These cells divide into two {@link PottsCellFlyNeuron} cells. The links must be set in the setup + * file so that 100% of the daughter cells are Neurons. */ -public class PottsModuleFlyGMCDifferentiation extends PottsModuleProliferationSimple { +public class PottsModuleFlyGMCDifferentiation + extends PottsModuleProliferationCellCycleProgressionSimple { /** * Creates a fly GMC proliferation module. diff --git a/src/arcade/potts/agent/module/PottsModuleProliferation.java b/src/arcade/potts/agent/module/PottsModuleProliferationCellCycleProgression.java similarity index 95% rename from src/arcade/potts/agent/module/PottsModuleProliferation.java rename to src/arcade/potts/agent/module/PottsModuleProliferationCellCycleProgression.java index c1838e53e..e79ab0ca8 100644 --- a/src/arcade/potts/agent/module/PottsModuleProliferation.java +++ b/src/arcade/potts/agent/module/PottsModuleProliferationCellCycleProgression.java @@ -17,13 +17,13 @@ *

During proliferation, cells cycle through G1, S, G2, and M phases. Once the cell complete M * phase, it divides to create a new daughter cell. */ -public abstract class PottsModuleProliferation extends PottsModule { +public abstract class PottsModuleProliferationCellCycleProgression extends PottsModule { /** * Creates a proliferation {@code Module} for the given {@link PottsCell}. * * @param cell the {@link PottsCell} the module is associated with */ - public PottsModuleProliferation(PottsCell cell) { + public PottsModuleProliferationCellCycleProgression(PottsCell cell) { super(cell); setPhase(Phase.PROLIFERATIVE_G1); } diff --git a/src/arcade/potts/agent/module/PottsModuleProliferationSimple.java b/src/arcade/potts/agent/module/PottsModuleProliferationCellCycleProgressionSimple.java similarity index 96% rename from src/arcade/potts/agent/module/PottsModuleProliferationSimple.java rename to src/arcade/potts/agent/module/PottsModuleProliferationCellCycleProgressionSimple.java index 956f48651..d5bc6e510 100644 --- a/src/arcade/potts/agent/module/PottsModuleProliferationSimple.java +++ b/src/arcade/potts/agent/module/PottsModuleProliferationCellCycleProgressionSimple.java @@ -12,8 +12,9 @@ import static arcade.potts.util.PottsEnums.Region; import static arcade.potts.util.PottsEnums.State; -/** Extension of {@link PottsModuleProliferation} with Poisson transitions. */ -public class PottsModuleProliferationSimple extends PottsModuleProliferation { +/** Extension of {@link PottsModuleProliferationCellCycleProgression} with Poisson transitions. */ +public class PottsModuleProliferationCellCycleProgressionSimple + extends PottsModuleProliferationCellCycleProgression { /** Threshold for critical volume size checkpoint. */ static final double SIZE_CHECKPOINT = 0.95; @@ -64,7 +65,7 @@ public class PottsModuleProliferationSimple extends PottsModuleProliferation { * * @param cell the {@link PottsCell} the module is associated with */ - public PottsModuleProliferationSimple(PottsCell cell) { + public PottsModuleProliferationCellCycleProgressionSimple(PottsCell cell) { super(cell); Parameters parameters = cell.getParameters(); diff --git a/test/arcade/potts/agent/cell/PottsCellStemTest.java b/test/arcade/potts/agent/cell/PottsCellStemTest.java index 383ea7a13..5ab962176 100644 --- a/test/arcade/potts/agent/cell/PottsCellStemTest.java +++ b/test/arcade/potts/agent/cell/PottsCellStemTest.java @@ -10,7 +10,7 @@ import arcade.potts.agent.module.PottsModuleApoptosis; import arcade.potts.agent.module.PottsModuleAutosis; import arcade.potts.agent.module.PottsModuleNecrosis; -import arcade.potts.agent.module.PottsModuleProliferation; +import arcade.potts.agent.module.PottsModuleProliferationCellCycleProgression; import arcade.potts.agent.module.PottsModuleQuiescence; import arcade.potts.env.location.PottsLocation; import static org.junit.jupiter.api.Assertions.*; @@ -94,7 +94,7 @@ public void setState_givenState_updatesModule() { assertTrue(cell.module instanceof PottsModuleQuiescence); cell.setState(State.PROLIFERATIVE); - assertTrue(cell.module instanceof PottsModuleProliferation); + assertTrue(cell.module instanceof PottsModuleProliferationCellCycleProgression); cell.setState(State.APOPTOTIC); assertTrue(cell.module instanceof PottsModuleApoptosis); diff --git a/test/arcade/potts/agent/module/PottsModuleProliferationSimpleTest.java b/test/arcade/potts/agent/module/PottsModuleProliferationSimpleTest.java index a640a13d5..48cff3e52 100644 --- a/test/arcade/potts/agent/module/PottsModuleProliferationSimpleTest.java +++ b/test/arcade/potts/agent/module/PottsModuleProliferationSimpleTest.java @@ -17,7 +17,7 @@ import static org.mockito.Mockito.*; import static arcade.core.ARCADETestUtilities.*; import static arcade.potts.agent.module.PottsModule.PoissonFactory; -import static arcade.potts.agent.module.PottsModuleProliferationSimple.*; +import static arcade.potts.agent.module.PottsModuleProliferationCellCycleProgressionSimple.*; import static arcade.potts.util.PottsEnums.Phase; import static arcade.potts.util.PottsEnums.Region; import static arcade.potts.util.PottsEnums.State; @@ -74,7 +74,8 @@ public static void setupMocks() { public void constructor_setsParameters() { PottsCell cell = mock(PottsCell.class); doReturn(parameters).when(cell).getParameters(); - PottsModuleProliferationSimple module = new PottsModuleProliferationSimple(cell); + PottsModuleProliferationCellCycleProgressionSimple module = + new PottsModuleProliferationCellCycleProgressionSimple(cell); assertEquals(parameters.getDouble("proliferation/SIZE_TARGET"), module.sizeTarget); assertEquals(parameters.getDouble("proliferation/RATE_G1"), module.rateG1, EPSILON); @@ -107,7 +108,8 @@ public void constructor_setsParameters() { public void stepG1_withStateChange_callsMethods() { PottsCell cell = mock(PottsCell.class); doReturn(parameters).when(cell).getParameters(); - PottsModuleProliferationSimple module = spy(new PottsModuleProliferationSimple(cell)); + PottsModuleProliferationCellCycleProgressionSimple module = + spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); module.phase = Phase.PROLIFERATIVE_G1; module.currentSteps = Integer.MAX_VALUE; @@ -127,7 +129,8 @@ public void stepG1_withStateChange_callsMethods() { public void stepG1_withoutStateChange_callsMethods() { PottsCell cell = mock(PottsCell.class); doReturn(parameters).when(cell).getParameters(); - PottsModuleProliferationSimple module = spy(new PottsModuleProliferationSimple(cell)); + PottsModuleProliferationCellCycleProgressionSimple module = + spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); module.phase = Phase.PROLIFERATIVE_G1; module.currentSteps = Integer.MAX_VALUE; @@ -149,7 +152,8 @@ public void stepG1_withTransition_updatesPhase() { int steps = randomIntBetween(1, parameters.getInt("proliferation/STEPS_G1")); PottsCell cell = mock(PottsCell.class); doReturn(parameters).when(cell).getParameters(); - PottsModuleProliferationSimple module = spy(new PottsModuleProliferationSimple(cell)); + PottsModuleProliferationCellCycleProgressionSimple module = + spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); module.phase = Phase.PROLIFERATIVE_G1; module.currentSteps = module.stepsG1 - steps; @@ -169,7 +173,8 @@ public void stepG1_withTransition_updatesPhase() { public void stepG1_withoutTransition_maintainsPhase() { PottsCell cell = mock(PottsCell.class); doReturn(parameters).when(cell).getParameters(); - PottsModuleProliferationSimple module = spy(new PottsModuleProliferationSimple(cell)); + PottsModuleProliferationCellCycleProgressionSimple module = + spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); module.phase = Phase.PROLIFERATIVE_G1; module.currentSteps = module.stepsG1; @@ -189,7 +194,8 @@ public void stepG1_withoutTransition_maintainsPhase() { public void stepG1_anyTransition_updatesCell() { PottsCell cell = mock(PottsCell.class); doReturn(parameters).when(cell).getParameters(); - PottsModuleProliferationSimple module = spy(new PottsModuleProliferationSimple(cell)); + PottsModuleProliferationCellCycleProgressionSimple module = + spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); PoissonFactory poissonFactory = mock(PoissonFactory.class); doReturn(poissonMock).when(poissonFactory).createPoisson(anyDouble(), eq(random)); @@ -213,7 +219,8 @@ public void stepG1_anyTransitionWithRegionOverThreshold_updatesCell() { doReturn((double) criticalVolume).when(cell).getCriticalVolume(Region.NUCLEUS); doReturn((double) criticalVolume + 1).when(cell).getVolume(Region.NUCLEUS); - PottsModuleProliferationSimple module = spy(new PottsModuleProliferationSimple(cell)); + PottsModuleProliferationCellCycleProgressionSimple module = + spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); PoissonFactory poissonFactory = mock(PoissonFactory.class); doReturn(poissonMock).when(poissonFactory).createPoisson(anyDouble(), eq(random)); @@ -238,7 +245,8 @@ public void stepG1_anyTransitionWithRegionUnderThreshold_updatesCell() { doReturn((double) criticalVolume).when(cell).getCriticalVolume(Region.NUCLEUS); doReturn((double) criticalVolume - 1).when(cell).getVolume(Region.NUCLEUS); - PottsModuleProliferationSimple module = spy(new PottsModuleProliferationSimple(cell)); + PottsModuleProliferationCellCycleProgressionSimple module = + spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); PoissonFactory poissonFactory = mock(PoissonFactory.class); doReturn(poissonMock).when(poissonFactory).createPoisson(anyDouble(), eq(random)); @@ -257,7 +265,8 @@ public void stepS_withTransition_updatesPhase() { int steps = randomIntBetween(1, parameters.getInt("proliferation/STEPS_S")); PottsCell cell = mock(PottsCell.class); doReturn(parameters).when(cell).getParameters(); - PottsModuleProliferationSimple module = spy(new PottsModuleProliferationSimple(cell)); + PottsModuleProliferationCellCycleProgressionSimple module = + spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); module.phase = Phase.PROLIFERATIVE_S; module.currentSteps = module.stepsS - steps; @@ -277,7 +286,8 @@ public void stepS_withTransition_updatesPhase() { public void stepS_withoutTransition_maintainsPhase() { PottsCell cell = mock(PottsCell.class); doReturn(parameters).when(cell).getParameters(); - PottsModuleProliferationSimple module = spy(new PottsModuleProliferationSimple(cell)); + PottsModuleProliferationCellCycleProgressionSimple module = + spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); module.phase = Phase.PROLIFERATIVE_S; module.currentSteps = module.stepsS; @@ -297,7 +307,8 @@ public void stepS_withoutTransition_maintainsPhase() { public void stepS_anyTransition_updatesCell() { PottsCell cell = mock(PottsCell.class); doReturn(parameters).when(cell).getParameters(); - PottsModuleProliferationSimple module = spy(new PottsModuleProliferationSimple(cell)); + PottsModuleProliferationCellCycleProgressionSimple module = + spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); PoissonFactory poissonFactory = mock(PoissonFactory.class); doReturn(poissonMock).when(poissonFactory).createPoisson(anyDouble(), eq(random)); @@ -316,7 +327,8 @@ public void stepS_anyTransitionWithRegion_updatesCell() { PottsCell cell = mock(PottsCell.class); doReturn(parameters).when(cell).getParameters(); doReturn(true).when(cell).hasRegions(); - PottsModuleProliferationSimple module = spy(new PottsModuleProliferationSimple(cell)); + PottsModuleProliferationCellCycleProgressionSimple module = + spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); PoissonFactory poissonFactory = mock(PoissonFactory.class); doReturn(poissonMock).when(poissonFactory).createPoisson(anyDouble(), eq(random)); @@ -335,7 +347,8 @@ public void stepS_anyTransitionWithRegion_updatesCell() { public void stepG2_withStateChange_callsMethods() { PottsCell cell = mock(PottsCell.class); doReturn(parameters).when(cell).getParameters(); - PottsModuleProliferationSimple module = spy(new PottsModuleProliferationSimple(cell)); + PottsModuleProliferationCellCycleProgressionSimple module = + spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); module.phase = Phase.PROLIFERATIVE_G2; module.currentSteps = Integer.MAX_VALUE; @@ -355,7 +368,8 @@ public void stepG2_withStateChange_callsMethods() { public void stepG2_withoutStateChange_callsMethods() { PottsCell cell = mock(PottsCell.class); doReturn(parameters).when(cell).getParameters(); - PottsModuleProliferationSimple module = spy(new PottsModuleProliferationSimple(cell)); + PottsModuleProliferationCellCycleProgressionSimple module = + spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); module.phase = Phase.PROLIFERATIVE_G2; module.currentSteps = Integer.MAX_VALUE; @@ -382,7 +396,8 @@ public void stepG2_withTransitionNotArrested_updatesPhase() { doReturn((volume * SIZE_CHECKPOINT * sizeTarget) + 1).when(cell).getVolume(); doReturn(volume).when(cell).getCriticalVolume(); - PottsModuleProliferationSimple module = spy(new PottsModuleProliferationSimple(cell)); + PottsModuleProliferationCellCycleProgressionSimple module = + spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); module.phase = Phase.PROLIFERATIVE_G2; module.currentSteps = module.stepsG2 - steps; @@ -407,7 +422,8 @@ public void stepG2_withoutTransitionNotArrested_maintainsPhase() { doReturn((volume * SIZE_CHECKPOINT * sizeTarget) + 1).when(cell).getVolume(); doReturn(volume).when(cell).getCriticalVolume(); - PottsModuleProliferationSimple module = spy(new PottsModuleProliferationSimple(cell)); + PottsModuleProliferationCellCycleProgressionSimple module = + spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); module.phase = Phase.PROLIFERATIVE_G2; module.currentSteps = module.stepsG2; @@ -433,7 +449,8 @@ public void stepG2_withTransitionArrested_maintainsPhase() { doReturn((volume * SIZE_CHECKPOINT * sizeTarget) - 1).when(cell).getVolume(); doReturn(volume).when(cell).getCriticalVolume(); - PottsModuleProliferationSimple module = spy(new PottsModuleProliferationSimple(cell)); + PottsModuleProliferationCellCycleProgressionSimple module = + spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); module.phase = Phase.PROLIFERATIVE_G2; module.currentSteps = module.stepsG2 - steps; @@ -467,7 +484,8 @@ public void stepG2_withTransitionArrestedRegion_maintainsPhase() { .getVolume(Region.NUCLEUS); doReturn(regionVolume).when(cell).getCriticalVolume(Region.NUCLEUS); - PottsModuleProliferationSimple module = spy(new PottsModuleProliferationSimple(cell)); + PottsModuleProliferationCellCycleProgressionSimple module = + spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); module.phase = Phase.PROLIFERATIVE_G2; module.currentSteps = module.stepsG2 - steps; @@ -492,7 +510,8 @@ public void stepM_withoutTransitionArrested_maintainPhase() { doReturn((volume * SIZE_CHECKPOINT * sizeTarget) - 1).when(cell).getVolume(); doReturn(volume).when(cell).getCriticalVolume(); - PottsModuleProliferationSimple module = spy(new PottsModuleProliferationSimple(cell)); + PottsModuleProliferationCellCycleProgressionSimple module = + spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); module.phase = Phase.PROLIFERATIVE_G2; module.currentSteps = module.stepsG2; @@ -512,7 +531,8 @@ public void stepM_withoutTransitionArrested_maintainPhase() { public void stepG2_anyTransition_updatesCell() { PottsCell cell = mock(PottsCell.class); doReturn(parameters).when(cell).getParameters(); - PottsModuleProliferationSimple module = spy(new PottsModuleProliferationSimple(cell)); + PottsModuleProliferationCellCycleProgressionSimple module = + spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); PoissonFactory poissonFactory = mock(PoissonFactory.class); doReturn(poissonMock).when(poissonFactory).createPoisson(anyDouble(), eq(random)); @@ -531,7 +551,8 @@ public void stepG2_anyTransitionWithRegion_updatesCell() { PottsCell cell = mock(PottsCell.class); doReturn(parameters).when(cell).getParameters(); doReturn(true).when(cell).hasRegions(); - PottsModuleProliferationSimple module = spy(new PottsModuleProliferationSimple(cell)); + PottsModuleProliferationCellCycleProgressionSimple module = + spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); PoissonFactory poissonFactory = mock(PoissonFactory.class); doReturn(poissonMock).when(poissonFactory).createPoisson(anyDouble(), eq(random)); @@ -551,7 +572,8 @@ public void stepM_withTransition_updatesPhase() { int steps = randomIntBetween(1, parameters.getInt("proliferation/STEPS_M")); PottsCell cell = mock(PottsCell.class); doReturn(parameters).when(cell).getParameters(); - PottsModuleProliferationSimple module = spy(new PottsModuleProliferationSimple(cell)); + PottsModuleProliferationCellCycleProgressionSimple module = + spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); module.phase = Phase.PROLIFERATIVE_M; module.currentSteps = module.stepsM - steps; doNothing().when(module).addCell(random, simMock); @@ -573,7 +595,8 @@ public void stepM_withTransition_updatesPhase() { public void stepM_withoutTransition_maintainsPhase() { PottsCell cell = mock(PottsCell.class); doReturn(parameters).when(cell).getParameters(); - PottsModuleProliferationSimple module = spy(new PottsModuleProliferationSimple(cell)); + PottsModuleProliferationCellCycleProgressionSimple module = + spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); module.phase = Phase.PROLIFERATIVE_M; module.currentSteps = module.stepsM; doNothing().when(module).addCell(random, simMock); @@ -595,7 +618,8 @@ public void stepM_withoutTransition_maintainsPhase() { public void stepM_anyTransition_updatesCell() { PottsCell cell = mock(PottsCell.class); doReturn(parameters).when(cell).getParameters(); - PottsModuleProliferationSimple module = spy(new PottsModuleProliferationSimple(cell)); + PottsModuleProliferationCellCycleProgressionSimple module = + spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); doNothing().when(module).addCell(random, simMock); PoissonFactory poissonFactory = mock(PoissonFactory.class); @@ -630,7 +654,8 @@ public void stepM_withRegionOverThreshold_doesNotUpdateCell() { pottsMock.ids = ids; pottsMock.regions = regions; - PottsModuleProliferationSimple module = spy(new PottsModuleProliferationSimple(cell)); + PottsModuleProliferationCellCycleProgressionSimple module = + spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); doNothing().when(module).addCell(random, simMock); PoissonFactory poissonFactory = mock(PoissonFactory.class); @@ -672,7 +697,8 @@ public void stepM_withRegionUnderThreshold_updatesCell() { pottsMock.ids = ids; pottsMock.regions = regions; - PottsModuleProliferationSimple module = spy(new PottsModuleProliferationSimple(cell)); + PottsModuleProliferationCellCycleProgressionSimple module = + spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); doNothing().when(module).addCell(random, simMock); PoissonFactory poissonFactory = mock(PoissonFactory.class); diff --git a/test/arcade/potts/agent/module/PottsModuleProliferationTest.java b/test/arcade/potts/agent/module/PottsModuleProliferationTest.java index cc5400a37..6bc48c1b9 100644 --- a/test/arcade/potts/agent/module/PottsModuleProliferationTest.java +++ b/test/arcade/potts/agent/module/PottsModuleProliferationTest.java @@ -25,7 +25,7 @@ public class PottsModuleProliferationTest { static PottsCell cellMock = mock(PottsCell.class); - static class PottsModuleProliferationMock extends PottsModuleProliferation { + static class PottsModuleProliferationMock extends PottsModuleProliferationCellCycleProgression { PottsModuleProliferationMock(PottsCell cell) { super(cell); } @@ -59,14 +59,16 @@ public void constructor_initializesFactory() { @Test public void getPhase_defaultConstructor_returnsValue() { - PottsModuleProliferation module = new PottsModuleProliferationMock(cellMock); + PottsModuleProliferationCellCycleProgression module = + new PottsModuleProliferationMock(cellMock); assertEquals(Phase.PROLIFERATIVE_G1, module.getPhase()); } @Test public void setPhase_givenValue_setsValue() { Phase phase = Phase.random(randomMock); - PottsModuleProliferation module = new PottsModuleProliferationMock(cellMock); + PottsModuleProliferationCellCycleProgression module = + new PottsModuleProliferationMock(cellMock); module.setPhase(phase); assertEquals(phase, module.phase); } @@ -74,7 +76,8 @@ public void setPhase_givenValue_setsValue() { @Test public void setPhase_givenValue_resetsSteps() { Phase phase = Phase.random(randomMock); - PottsModuleProliferation module = new PottsModuleProliferationMock(cellMock); + PottsModuleProliferationCellCycleProgression module = + new PottsModuleProliferationMock(cellMock); module.currentSteps = randomIntBetween(1, 10); module.setPhase(phase); assertEquals(0, module.currentSteps); @@ -82,7 +85,8 @@ public void setPhase_givenValue_resetsSteps() { @Test public void step_givenPhaseG1_callsMethod() { - PottsModuleProliferation module = spy(new PottsModuleProliferationMock(cellMock)); + PottsModuleProliferationCellCycleProgression module = + spy(new PottsModuleProliferationMock(cellMock)); module.phase = Phase.PROLIFERATIVE_G1; module.step(randomMock, simMock); @@ -94,7 +98,8 @@ public void step_givenPhaseG1_callsMethod() { @Test public void step_givenPhaseS_callsMethod() { - PottsModuleProliferation module = spy(new PottsModuleProliferationMock(cellMock)); + PottsModuleProliferationCellCycleProgression module = + spy(new PottsModuleProliferationMock(cellMock)); module.phase = Phase.PROLIFERATIVE_S; module.step(randomMock, simMock); @@ -106,7 +111,8 @@ public void step_givenPhaseS_callsMethod() { @Test public void step_givenPhaseG2_callsMethod() { - PottsModuleProliferation module = spy(new PottsModuleProliferationMock(cellMock)); + PottsModuleProliferationCellCycleProgression module = + spy(new PottsModuleProliferationMock(cellMock)); module.phase = Phase.PROLIFERATIVE_G2; module.step(randomMock, simMock); @@ -118,7 +124,8 @@ public void step_givenPhaseG2_callsMethod() { @Test public void step_givenPhaseM_callsMethod() { - PottsModuleProliferation module = spy(new PottsModuleProliferationMock(cellMock)); + PottsModuleProliferationCellCycleProgression module = + spy(new PottsModuleProliferationMock(cellMock)); doNothing().when(module).addCell(randomMock, simMock); module.phase = Phase.PROLIFERATIVE_M; @@ -131,7 +138,8 @@ public void step_givenPhaseM_callsMethod() { @Test public void step_invalidPhase_doesNothing() { - PottsModuleProliferation module = spy(new PottsModuleProliferationMock(cellMock)); + PottsModuleProliferationCellCycleProgression module = + spy(new PottsModuleProliferationMock(cellMock)); module.phase = Phase.UNDEFINED; module.step(randomMock, simMock); @@ -178,7 +186,8 @@ public void addCell_called_addsObject() { doNothing().when(cell).reset(any(), any()); doNothing().when(newCell).reset(any(), any()); - PottsModuleProliferation module = new PottsModuleProliferationMock(cell); + PottsModuleProliferationCellCycleProgression module = + new PottsModuleProliferationMock(cell); module.addCell(randomMock, sim); verify(cell).reset(potts.ids, potts.regions); From f200c6f106f24c2c5593577b9e62604c0e68479d Mon Sep 17 00:00:00 2001 From: jannetty Date: Mon, 20 Oct 2025 16:01:45 -0700 Subject: [PATCH 16/59] adding new proliferation module type and changing nomenclature --- .../potts/agent/cell/PottsCellFlyGMC.java | 5 +- .../PottsModuleFlyGMCDifferentiation.java | 34 +--------- ...oduleProliferationVolumeBasedDivision.java | 49 ++++++++++++++ .../PottsModuleFlyGMCDifferentiationTest.java | 55 +--------------- .../module/PottsModuleProliferationTest.java | 26 ++++---- ...eProliferationVolumeBasedDivisionTest.java | 64 +++++++++++++++++++ 6 files changed, 133 insertions(+), 100 deletions(-) create mode 100644 src/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivision.java create mode 100644 test/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivisionTest.java diff --git a/src/arcade/potts/agent/cell/PottsCellFlyGMC.java b/src/arcade/potts/agent/cell/PottsCellFlyGMC.java index 11a75f068..81e5cb263 100644 --- a/src/arcade/potts/agent/cell/PottsCellFlyGMC.java +++ b/src/arcade/potts/agent/cell/PottsCellFlyGMC.java @@ -7,14 +7,15 @@ import arcade.core.util.Parameters; import arcade.core.util.exceptions.InvalidParameterValueException; import arcade.potts.agent.module.PottsModuleFlyGMCDifferentiation; +import arcade.potts.agent.module.PottsModuleProliferationVolumeBasedDivision; import arcade.potts.util.PottsEnums.State; /** * Implementation of {@link PottsCell} for fly GMC agents. These cells divide into two {@link * PottsCellFlyNeuron} cells. The links must be set in the setup file so that 100% of the daughter * cells are Neurons. The differentiation of the parent cell is handled by the {@link - * PottsModuleFlyGMCDifferentiation} module. The basal apoptosis rate of this cell should be set to - * 0 in the setup file. + * PottsModuleProliferationVolumeBasedDivision} module. The basal apoptosis rate of this cell should + * be set to 0 in the setup file. */ public class PottsCellFlyGMC extends PottsCell { diff --git a/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java b/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java index 87e18ba52..7f93c5b6c 100644 --- a/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java +++ b/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java @@ -4,7 +4,6 @@ import arcade.core.agent.cell.CellContainer; import arcade.core.env.location.Location; import arcade.core.sim.Simulation; -import arcade.core.util.Parameters; import arcade.potts.agent.cell.PottsCell; import arcade.potts.agent.cell.PottsCellContainer; import arcade.potts.agent.cell.PottsCellFlyGMC; @@ -12,24 +11,9 @@ import arcade.potts.env.location.PottsLocation2D; import arcade.potts.sim.Potts; import arcade.potts.sim.PottsSimulation; -import arcade.potts.util.PottsEnums.Phase; import arcade.potts.util.PottsEnums.State; -/** - * Implementation of {@link PottsModule} for fly GMC agents. These cells divide into two {@link - * PottsCellFlyNeuron} cells. The links must be set in the setup file so that 100% of the daughter - * cells are Neurons. - */ -public class PottsModuleFlyGMCDifferentiation extends PottsModule { - - /** Overall growth rate for cell (voxels/tick). */ - final double cellGrowthRate; - - /** - * Target ratio of critical volume for division size checkpoint (cell must reach CRITICAL_VOLUME - * * SIZE_TARGET * SIZE_CHECKPOINT to divide). - */ - final double sizeTarget; +public class PottsModuleFlyGMCDifferentiation extends PottsModuleProliferationVolumeBasedDivision { /** * Creates a fly GMC proliferation module. @@ -38,22 +22,6 @@ public class PottsModuleFlyGMCDifferentiation extends PottsModule { */ public PottsModuleFlyGMCDifferentiation(PottsCellFlyGMC cell) { super(cell); - Parameters parameters = cell.getParameters(); - sizeTarget = parameters.getDouble("proliferation/SIZE_TARGET"); - cellGrowthRate = parameters.getDouble("proliferation/CELL_GROWTH_RATE"); - setPhase(Phase.UNDEFINED); - } - - @Override - public void step(MersenneTwisterFast random, Simulation sim) { - // Increase size of cell. - System.out.println("Pre updateTarget volume: " + cell.getVolume()); - cell.updateTarget(cellGrowthRate, sizeTarget); - System.out.println("Post updateTarget volume: " + cell.getVolume()); - boolean sizeCheck = cell.getVolume() >= sizeTarget * cell.getCriticalVolume(); - if (sizeCheck) { - addCell(random, sim); - } } /** diff --git a/src/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivision.java b/src/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivision.java new file mode 100644 index 000000000..c998fbd7a --- /dev/null +++ b/src/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivision.java @@ -0,0 +1,49 @@ +package arcade.potts.agent.module; + +import ec.util.MersenneTwisterFast; +import arcade.core.sim.Simulation; +import arcade.core.util.Parameters; +import arcade.potts.agent.cell.PottsCell; +import arcade.potts.agent.cell.PottsCellFlyNeuron; +import arcade.potts.util.PottsEnums.Phase; + +/** + * Implementation of {@link PottsModule} for fly GMC agents. These cells divide into two {@link + * PottsCellFlyNeuron} cells. The links must be set in the setup file so that 100% of the daughter + * cells are Neurons. + */ +public abstract class PottsModuleProliferationVolumeBasedDivision extends PottsModule { + + /** Overall growth rate for cell (voxels/tick). */ + final double cellGrowthRate; + + /** + * Target ratio of critical volume for division size checkpoint (cell must reach CRITICAL_VOLUME + * * SIZE_TARGET * SIZE_CHECKPOINT to divide). + */ + final double sizeTarget; + + /** + * Creates a proliferation module in which division is solely dependent on cell volume. + * + * @param cell the cell to which this module is attached + */ + public PottsModuleProliferationVolumeBasedDivision(PottsCell cell) { + super(cell); + Parameters parameters = cell.getParameters(); + sizeTarget = parameters.getDouble("proliferation/SIZE_TARGET"); + cellGrowthRate = parameters.getDouble("proliferation/CELL_GROWTH_RATE"); + setPhase(Phase.UNDEFINED); + } + + @Override + public void step(MersenneTwisterFast random, Simulation sim) { + cell.updateTarget(cellGrowthRate, sizeTarget); + boolean sizeCheck = cell.getVolume() >= sizeTarget * cell.getCriticalVolume(); + if (sizeCheck) { + addCell(random, sim); + } + } + + abstract void addCell(MersenneTwisterFast random, Simulation sim); +} diff --git a/test/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiationTest.java b/test/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiationTest.java index 165b5dacf..c1b04e272 100644 --- a/test/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiationTest.java +++ b/test/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiationTest.java @@ -24,10 +24,8 @@ import arcade.potts.util.PottsEnums.State; import static org.mockito.ArgumentMatchers.any; import static org.mockito.ArgumentMatchers.eq; -import static org.mockito.ArgumentMatchers.isNull; import static org.mockito.Mockito.mock; import static org.mockito.Mockito.mockConstruction; -import static org.mockito.Mockito.never; import static org.mockito.Mockito.verify; import static org.mockito.Mockito.when; @@ -107,20 +105,7 @@ public final void setupMocks() { when(gmcCell.getCriticalRegionVolumes()).thenReturn(critRegionVolumes); when(gmcCell.getCriticalRegionHeights()).thenReturn(critRegionHeights); - // Stub parameters parameters = mock(Parameters.class); - when(parameters.getDouble("proliferation/RATE_G1")).thenReturn(1.0); - when(parameters.getDouble("proliferation/RATE_S")).thenReturn(1.0); - when(parameters.getDouble("proliferation/RATE_G2")).thenReturn(1.0); - when(parameters.getDouble("proliferation/RATE_M")).thenReturn(1.0); - when(parameters.getInt("proliferation/STEPS_G1")).thenReturn(1); - when(parameters.getInt("proliferation/STEPS_S")).thenReturn(1); - when(parameters.getInt("proliferation/STEPS_G2")).thenReturn(1); - when(parameters.getInt("proliferation/STEPS_M")).thenReturn(1); - when(parameters.getDouble("proliferation/CELL_GROWTH_RATE")).thenReturn(1.0); - when(parameters.getDouble("proliferation/NUCLEUS_GROWTH_RATE")).thenReturn(1.0); - when(parameters.getDouble("proliferation/BASAL_APOPTOSIS_RATE")).thenReturn(0.1); - when(parameters.getDouble("proliferation/NUCLEUS_CONDENSATION_FRACTION")).thenReturn(0.5); when(gmcCell.getParameters()).thenReturn(parameters); random = mock(MersenneTwisterFast.class); @@ -146,43 +131,6 @@ final void tearDown() { mockedConstruction.close(); } - @Test - public void step_belowCheckpoint_updatesTargetOnly() { - when(parameters.getDouble("proliferation/SIZE_TARGET")).thenReturn(1.2); - when(parameters.getDouble("proliferation/CELL_GROWTH_RATE")).thenReturn(4.0); - when(gmcCell.getCriticalVolume()).thenReturn(100.0); - when(gmcCell.getVolume()).thenReturn(50.0); // 50 < 1.2*100 - - PottsModuleFlyGMCDifferentiation module = new PottsModuleFlyGMCDifferentiation(gmcCell); - module.step(random, sim); - - verify(gmcCell).updateTarget(4.0, 1.2); - // Nothing from addCell - verify(grid, never()).addObject(any(), any()); - verify(potts, never()).register(any()); - } - - @Test - public void step_atOrAboveCheckpoint_triggersAddCell() { - when(parameters.getDouble("proliferation/SIZE_TARGET")).thenReturn(1.2); - when(parameters.getDouble("proliferation/CELL_GROWTH_RATE")).thenReturn(4.0); - when(gmcCell.getCriticalVolume()).thenReturn(100.0); - when(gmcCell.getVolume()).thenReturn(120.0); // 120 >= 1.2*100 - - // Stubs for addCell - container = mock(PottsCellContainer.class); - when(gmcCell.make(eq(123), eq(State.QUIESCENT), any())).thenReturn(container); - newCell = mock(PottsCell.class); - when(container.convert(eq(cellFactory), any(), any())).thenReturn(newCell); - - PottsModuleFlyGMCDifferentiation module = new PottsModuleFlyGMCDifferentiation(gmcCell); - module.step(random, sim); - verify(gmcCell).updateTarget(4.0, 1.2); - // Something from addCell must happen - verify(grid).addObject(eq(newCell), isNull()); - verify(potts).register(eq(newCell)); - } - @Test public void addCell_called_callsExpectedMethods() { // When the module calls make() on the cell, return Quiescent PottsCellContainer mock @@ -193,7 +141,8 @@ public void addCell_called_callsExpectedMethods() { when(container.convert(eq(cellFactory), eq(newLocation), any(MersenneTwisterFast.class))) .thenReturn(newCell); - PottsModuleFlyGMCDifferentiation module = new PottsModuleFlyGMCDifferentiation(gmcCell); + PottsModuleProliferationVolumeBasedDivision module = + new PottsModuleFlyGMCDifferentiation(gmcCell); module.addCell(random, sim); verify(location).split(random); verify(gmcCell).reset(dummyIDs, dummyRegions); diff --git a/test/arcade/potts/agent/module/PottsModuleProliferationTest.java b/test/arcade/potts/agent/module/PottsModuleProliferationTest.java index 6bc48c1b9..4599e0750 100644 --- a/test/arcade/potts/agent/module/PottsModuleProliferationTest.java +++ b/test/arcade/potts/agent/module/PottsModuleProliferationTest.java @@ -25,8 +25,9 @@ public class PottsModuleProliferationTest { static PottsCell cellMock = mock(PottsCell.class); - static class PottsModuleProliferationMock extends PottsModuleProliferationCellCycleProgression { - PottsModuleProliferationMock(PottsCell cell) { + static class PottsModuleProliferationCellCycleProgressionMock + extends PottsModuleProliferationCellCycleProgression { + PottsModuleProliferationCellCycleProgressionMock(PottsCell cell) { super(cell); } @@ -53,14 +54,15 @@ void stepM(MersenneTwisterFast random, Simulation sim) { @Test public void constructor_initializesFactory() { - PottsModuleProliferationMock module = new PottsModuleProliferationMock(cellMock); + PottsModuleProliferationCellCycleProgression module = + new PottsModuleProliferationCellCycleProgressionMock(cellMock); assertNotNull(module.poissonFactory); } @Test public void getPhase_defaultConstructor_returnsValue() { PottsModuleProliferationCellCycleProgression module = - new PottsModuleProliferationMock(cellMock); + new PottsModuleProliferationCellCycleProgressionMock(cellMock); assertEquals(Phase.PROLIFERATIVE_G1, module.getPhase()); } @@ -68,7 +70,7 @@ public void getPhase_defaultConstructor_returnsValue() { public void setPhase_givenValue_setsValue() { Phase phase = Phase.random(randomMock); PottsModuleProliferationCellCycleProgression module = - new PottsModuleProliferationMock(cellMock); + new PottsModuleProliferationCellCycleProgressionMock(cellMock); module.setPhase(phase); assertEquals(phase, module.phase); } @@ -77,7 +79,7 @@ public void setPhase_givenValue_setsValue() { public void setPhase_givenValue_resetsSteps() { Phase phase = Phase.random(randomMock); PottsModuleProliferationCellCycleProgression module = - new PottsModuleProliferationMock(cellMock); + new PottsModuleProliferationCellCycleProgressionMock(cellMock); module.currentSteps = randomIntBetween(1, 10); module.setPhase(phase); assertEquals(0, module.currentSteps); @@ -86,7 +88,7 @@ public void setPhase_givenValue_resetsSteps() { @Test public void step_givenPhaseG1_callsMethod() { PottsModuleProliferationCellCycleProgression module = - spy(new PottsModuleProliferationMock(cellMock)); + spy(new PottsModuleProliferationCellCycleProgressionMock(cellMock)); module.phase = Phase.PROLIFERATIVE_G1; module.step(randomMock, simMock); @@ -99,7 +101,7 @@ public void step_givenPhaseG1_callsMethod() { @Test public void step_givenPhaseS_callsMethod() { PottsModuleProliferationCellCycleProgression module = - spy(new PottsModuleProliferationMock(cellMock)); + spy(new PottsModuleProliferationCellCycleProgressionMock(cellMock)); module.phase = Phase.PROLIFERATIVE_S; module.step(randomMock, simMock); @@ -112,7 +114,7 @@ public void step_givenPhaseS_callsMethod() { @Test public void step_givenPhaseG2_callsMethod() { PottsModuleProliferationCellCycleProgression module = - spy(new PottsModuleProliferationMock(cellMock)); + spy(new PottsModuleProliferationCellCycleProgressionMock(cellMock)); module.phase = Phase.PROLIFERATIVE_G2; module.step(randomMock, simMock); @@ -125,7 +127,7 @@ public void step_givenPhaseG2_callsMethod() { @Test public void step_givenPhaseM_callsMethod() { PottsModuleProliferationCellCycleProgression module = - spy(new PottsModuleProliferationMock(cellMock)); + spy(new PottsModuleProliferationCellCycleProgressionMock(cellMock)); doNothing().when(module).addCell(randomMock, simMock); module.phase = Phase.PROLIFERATIVE_M; @@ -139,7 +141,7 @@ public void step_givenPhaseM_callsMethod() { @Test public void step_invalidPhase_doesNothing() { PottsModuleProliferationCellCycleProgression module = - spy(new PottsModuleProliferationMock(cellMock)); + spy(new PottsModuleProliferationCellCycleProgressionMock(cellMock)); module.phase = Phase.UNDEFINED; module.step(randomMock, simMock); @@ -187,7 +189,7 @@ public void addCell_called_addsObject() { doNothing().when(newCell).reset(any(), any()); PottsModuleProliferationCellCycleProgression module = - new PottsModuleProliferationMock(cell); + new PottsModuleProliferationCellCycleProgressionMock(cell); module.addCell(randomMock, sim); verify(cell).reset(potts.ids, potts.regions); diff --git a/test/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivisionTest.java b/test/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivisionTest.java new file mode 100644 index 000000000..4856f81e0 --- /dev/null +++ b/test/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivisionTest.java @@ -0,0 +1,64 @@ +package arcade.potts.agent.module; + +import org.junit.jupiter.api.Test; +import ec.util.MersenneTwisterFast; +import arcade.core.sim.Simulation; +import arcade.core.util.Parameters; +import arcade.potts.agent.cell.PottsCellFlyGMC; +import static org.mockito.Mockito.*; + +public class PottsModuleProliferationVolumeBasedDivisionTest { + + static class PottsModuleProliferationVolumeBasedDivisionMock + extends PottsModuleProliferationVolumeBasedDivision { + boolean addCellCalled = false; + + PottsModuleProliferationVolumeBasedDivisionMock(PottsCellFlyGMC cell) { + super(cell); + } + + @Override + void addCell(MersenneTwisterFast random, Simulation sim) { + addCellCalled = true; + } + } + + @Test + public void step_belowCheckpoint_updatesTargetOnly() { + PottsCellFlyGMC cell = mock(PottsCellFlyGMC.class); + Parameters params = mock(Parameters.class); + when(cell.getParameters()).thenReturn(params); + when(params.getDouble("proliferation/SIZE_TARGET")).thenReturn(1.2); + when(params.getDouble("proliferation/CELL_GROWTH_RATE")).thenReturn(4.0); + when(cell.getCriticalVolume()).thenReturn(100.0); + when(cell.getVolume()).thenReturn(50.0); // below checkpoint + + PottsModuleProliferationVolumeBasedDivisionMock module = + new PottsModuleProliferationVolumeBasedDivisionMock(cell); + + module.step(mock(MersenneTwisterFast.class), mock(Simulation.class)); + + verify(cell).updateTarget(4.0, 1.2); + assert !module.addCellCalled : "addCell should not be called below checkpoint"; + } + + @Test + public void step_atOrAboveCheckpoint_triggersAddCell() { + + PottsCellFlyGMC cell = mock(PottsCellFlyGMC.class); + Parameters params = mock(Parameters.class); + when(cell.getParameters()).thenReturn(params); + when(params.getDouble("proliferation/SIZE_TARGET")).thenReturn(1.2); + when(params.getDouble("proliferation/CELL_GROWTH_RATE")).thenReturn(4.0); + when(cell.getCriticalVolume()).thenReturn(100.0); + when(cell.getVolume()).thenReturn(120.0); // at or above checkpoint + + PottsModuleProliferationVolumeBasedDivisionMock module = + new PottsModuleProliferationVolumeBasedDivisionMock(cell); + + module.step(mock(MersenneTwisterFast.class), mock(Simulation.class)); + + verify(cell).updateTarget(4.0, 1.2); + assert module.addCellCalled : "addCell should be called at or above checkpoint"; + } +} From 0ecb30e63f48cf75d5db0f023fd6aa14d5867e48 Mon Sep 17 00:00:00 2001 From: jannetty Date: Mon, 20 Oct 2025 16:24:15 -0700 Subject: [PATCH 17/59] changed test filenames appropriately --- ...PottsModuleProliferationCellCycleProgressionSimpleTest.java} | 2 +- ...va => PottsModuleProliferationCellCycleProgressionTest.java} | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename test/arcade/potts/agent/module/{PottsModuleProliferationSimpleTest.java => PottsModuleProliferationCellCycleProgressionSimpleTest.java} (99%) rename test/arcade/potts/agent/module/{PottsModuleProliferationTest.java => PottsModuleProliferationCellCycleProgressionTest.java} (99%) diff --git a/test/arcade/potts/agent/module/PottsModuleProliferationSimpleTest.java b/test/arcade/potts/agent/module/PottsModuleProliferationCellCycleProgressionSimpleTest.java similarity index 99% rename from test/arcade/potts/agent/module/PottsModuleProliferationSimpleTest.java rename to test/arcade/potts/agent/module/PottsModuleProliferationCellCycleProgressionSimpleTest.java index 48cff3e52..27ee3be4f 100644 --- a/test/arcade/potts/agent/module/PottsModuleProliferationSimpleTest.java +++ b/test/arcade/potts/agent/module/PottsModuleProliferationCellCycleProgressionSimpleTest.java @@ -22,7 +22,7 @@ import static arcade.potts.util.PottsEnums.Region; import static arcade.potts.util.PottsEnums.State; -public class PottsModuleProliferationSimpleTest { +public class PottsModuleProliferationCellCycleProgressionSimpleTest { private static final double EPSILON = 1E-10; private static final double R = 1.0; diff --git a/test/arcade/potts/agent/module/PottsModuleProliferationTest.java b/test/arcade/potts/agent/module/PottsModuleProliferationCellCycleProgressionTest.java similarity index 99% rename from test/arcade/potts/agent/module/PottsModuleProliferationTest.java rename to test/arcade/potts/agent/module/PottsModuleProliferationCellCycleProgressionTest.java index 4599e0750..1ad3de569 100644 --- a/test/arcade/potts/agent/module/PottsModuleProliferationTest.java +++ b/test/arcade/potts/agent/module/PottsModuleProliferationCellCycleProgressionTest.java @@ -18,7 +18,7 @@ import static arcade.potts.util.PottsEnums.Phase; import static arcade.potts.util.PottsEnums.State; -public class PottsModuleProliferationTest { +public class PottsModuleProliferationCellCycleProgressionTest { static MersenneTwisterFast randomMock = new MersenneTwisterFast(); static PottsSimulation simMock = mock(PottsSimulation.class); From e1d70a8e8687ee370c0eff1be9b627080b34c492 Mon Sep 17 00:00:00 2001 From: jannetty Date: Mon, 20 Oct 2025 16:33:37 -0700 Subject: [PATCH 18/59] formatting --- src/arcade/potts/agent/cell/PottsCellFlyGMC.java | 1 - .../agent/module/PottsModuleFlyGMCDifferentiation.java | 5 +++++ .../PottsModuleProliferationVolumeBasedDivision.java | 7 ++++++- 3 files changed, 11 insertions(+), 2 deletions(-) diff --git a/src/arcade/potts/agent/cell/PottsCellFlyGMC.java b/src/arcade/potts/agent/cell/PottsCellFlyGMC.java index 81e5cb263..f88ad4fc2 100644 --- a/src/arcade/potts/agent/cell/PottsCellFlyGMC.java +++ b/src/arcade/potts/agent/cell/PottsCellFlyGMC.java @@ -7,7 +7,6 @@ import arcade.core.util.Parameters; import arcade.core.util.exceptions.InvalidParameterValueException; import arcade.potts.agent.module.PottsModuleFlyGMCDifferentiation; -import arcade.potts.agent.module.PottsModuleProliferationVolumeBasedDivision; import arcade.potts.util.PottsEnums.State; /** diff --git a/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java b/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java index 7f93c5b6c..1d4ec6a79 100644 --- a/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java +++ b/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java @@ -13,6 +13,11 @@ import arcade.potts.sim.PottsSimulation; import arcade.potts.util.PottsEnums.State; +/** + * Implementation of {@link PottsModuleProliferationVolumeBasedDivision} for fly GMC agents. These + * cells divide into two {@link PottsCellFlyNeuron} cells. The links must be set in the setup file + * so that 100% of the daughter cells are Neurons. + */ public class PottsModuleFlyGMCDifferentiation extends PottsModuleProliferationVolumeBasedDivision { /** diff --git a/src/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivision.java b/src/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivision.java index c998fbd7a..122fdac32 100644 --- a/src/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivision.java +++ b/src/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivision.java @@ -4,7 +4,6 @@ import arcade.core.sim.Simulation; import arcade.core.util.Parameters; import arcade.potts.agent.cell.PottsCell; -import arcade.potts.agent.cell.PottsCellFlyNeuron; import arcade.potts.util.PottsEnums.Phase; /** @@ -45,5 +44,11 @@ public void step(MersenneTwisterFast random, Simulation sim) { } } + /** + * Adds a cell to the simulation + * + * @param random the random number generator + * @param sim the simulation instance + */ abstract void addCell(MersenneTwisterFast random, Simulation sim); } From d754aa4cf1dd123581e268b71a05654e251266cf Mon Sep 17 00:00:00 2001 From: jannetty Date: Mon, 20 Oct 2025 16:37:37 -0700 Subject: [PATCH 19/59] adding period --- .../module/PottsModuleProliferationVolumeBasedDivision.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivision.java b/src/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivision.java index 122fdac32..08c59e1fc 100644 --- a/src/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivision.java +++ b/src/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivision.java @@ -45,7 +45,7 @@ public void step(MersenneTwisterFast random, Simulation sim) { } /** - * Adds a cell to the simulation + * Adds a cell to the simulation. * * @param random the random number generator * @param sim the simulation instance From c1b645baf15928ac77254c6954701649347ddea4 Mon Sep 17 00:00:00 2001 From: jannetty Date: Tue, 21 Oct 2025 11:21:24 -0700 Subject: [PATCH 20/59] added PottsModuleProliferation level of abstraction that specifies addCell must be defined in proliferation modules --- .../potts/agent/cell/PottsCellStem.java | 4 +- .../PottsModuleFlyGMCDifferentiation.java | 1 + .../module/PottsModuleProliferation.java | 20 ++++ ...oduleProliferationVolumeBasedDivision.java | 10 +- ...oduleProliferationWithCellCycleCheck.java} | 11 +- ...roliferationWithCellCycleCheckSimple.java} | 8 +- .../potts/agent/cell/PottsCellStemTest.java | 4 +- ...ferationWithCellCycleCheckSimpleTest.java} | 108 +++++++++--------- ...eProliferationWithCellCycleCheckTest.java} | 48 ++++---- 9 files changed, 111 insertions(+), 103 deletions(-) create mode 100644 src/arcade/potts/agent/module/PottsModuleProliferation.java rename src/arcade/potts/agent/module/{PottsModuleProliferationCellCycleProgression.java => PottsModuleProliferationWithCellCycleCheck.java} (90%) rename src/arcade/potts/agent/module/{PottsModuleProliferationCellCycleProgressionSimple.java => PottsModuleProliferationWithCellCycleCheckSimple.java} (96%) rename test/arcade/potts/agent/module/{PottsModuleProliferationCellCycleProgressionSimpleTest.java => PottsModuleProliferationWithCellCycleCheckSimpleTest.java} (87%) rename test/arcade/potts/agent/module/{PottsModuleProliferationCellCycleProgressionTest.java => PottsModuleProliferationWithCellCycleCheckTest.java} (77%) diff --git a/src/arcade/potts/agent/cell/PottsCellStem.java b/src/arcade/potts/agent/cell/PottsCellStem.java index 4e448a427..0bf5141ff 100644 --- a/src/arcade/potts/agent/cell/PottsCellStem.java +++ b/src/arcade/potts/agent/cell/PottsCellStem.java @@ -9,7 +9,7 @@ import arcade.potts.agent.module.PottsModuleApoptosisSimple; import arcade.potts.agent.module.PottsModuleAutosis; import arcade.potts.agent.module.PottsModuleNecrosis; -import arcade.potts.agent.module.PottsModuleProliferationCellCycleProgressionSimple; +import arcade.potts.agent.module.PottsModuleProliferationWithCellCycleCheckSimple; import arcade.potts.agent.module.PottsModuleQuiescence; import static arcade.potts.util.PottsEnums.Region; import static arcade.potts.util.PottsEnums.State; @@ -73,7 +73,7 @@ void setStateModule(CellState newState) { module = new PottsModuleQuiescence(this); break; case PROLIFERATIVE: - module = new PottsModuleProliferationCellCycleProgressionSimple(this); + module = new PottsModuleProliferationWithCellCycleCheckSimple(this); break; case APOPTOTIC: module = new PottsModuleApoptosisSimple(this); diff --git a/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java b/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java index 1d4ec6a79..4405e45dc 100644 --- a/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java +++ b/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java @@ -38,6 +38,7 @@ public PottsModuleFlyGMCDifferentiation(PottsCellFlyGMC cell) { * @param random the random number generator * @param sim the simulation instance */ + @Override void addCell(MersenneTwisterFast random, Simulation sim) { Potts potts = ((PottsSimulation) sim).getPotts(); diff --git a/src/arcade/potts/agent/module/PottsModuleProliferation.java b/src/arcade/potts/agent/module/PottsModuleProliferation.java new file mode 100644 index 000000000..dcfec3e99 --- /dev/null +++ b/src/arcade/potts/agent/module/PottsModuleProliferation.java @@ -0,0 +1,20 @@ +package arcade.potts.agent.module; + +import ec.util.MersenneTwisterFast; +import arcade.core.sim.Simulation; +import arcade.potts.agent.cell.PottsCell; + +public abstract class PottsModuleProliferation extends PottsModule { + + public PottsModuleProliferation(PottsCell cell) { + super(cell); + } + + /** + * Adds a cell to the simulation. + * + * @param random the random number generator + * @param sim the simulation instance + */ + abstract void addCell(MersenneTwisterFast random, Simulation sim); +} diff --git a/src/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivision.java b/src/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivision.java index 08c59e1fc..d121df3df 100644 --- a/src/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivision.java +++ b/src/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivision.java @@ -11,7 +11,7 @@ * PottsCellFlyNeuron} cells. The links must be set in the setup file so that 100% of the daughter * cells are Neurons. */ -public abstract class PottsModuleProliferationVolumeBasedDivision extends PottsModule { +public abstract class PottsModuleProliferationVolumeBasedDivision extends PottsModuleProliferation { /** Overall growth rate for cell (voxels/tick). */ final double cellGrowthRate; @@ -43,12 +43,4 @@ public void step(MersenneTwisterFast random, Simulation sim) { addCell(random, sim); } } - - /** - * Adds a cell to the simulation. - * - * @param random the random number generator - * @param sim the simulation instance - */ - abstract void addCell(MersenneTwisterFast random, Simulation sim); } diff --git a/src/arcade/potts/agent/module/PottsModuleProliferationCellCycleProgression.java b/src/arcade/potts/agent/module/PottsModuleProliferationWithCellCycleCheck.java similarity index 90% rename from src/arcade/potts/agent/module/PottsModuleProliferationCellCycleProgression.java rename to src/arcade/potts/agent/module/PottsModuleProliferationWithCellCycleCheck.java index e79ab0ca8..852516427 100644 --- a/src/arcade/potts/agent/module/PottsModuleProliferationCellCycleProgression.java +++ b/src/arcade/potts/agent/module/PottsModuleProliferationWithCellCycleCheck.java @@ -17,23 +17,18 @@ *

During proliferation, cells cycle through G1, S, G2, and M phases. Once the cell complete M * phase, it divides to create a new daughter cell. */ -public abstract class PottsModuleProliferationCellCycleProgression extends PottsModule { +public abstract class PottsModuleProliferationWithCellCycleCheck extends PottsModuleProliferation { /** * Creates a proliferation {@code Module} for the given {@link PottsCell}. * * @param cell the {@link PottsCell} the module is associated with */ - public PottsModuleProliferationCellCycleProgression(PottsCell cell) { + public PottsModuleProliferationWithCellCycleCheck(PottsCell cell) { super(cell); setPhase(Phase.PROLIFERATIVE_G1); } - /** - * Calls the step method for the current simple phase. - * - * @param random the random number generator - * @param sim the simulation instance - */ + @Override public void step(MersenneTwisterFast random, Simulation sim) { switch (phase) { case PROLIFERATIVE_G1: diff --git a/src/arcade/potts/agent/module/PottsModuleProliferationCellCycleProgressionSimple.java b/src/arcade/potts/agent/module/PottsModuleProliferationWithCellCycleCheckSimple.java similarity index 96% rename from src/arcade/potts/agent/module/PottsModuleProliferationCellCycleProgressionSimple.java rename to src/arcade/potts/agent/module/PottsModuleProliferationWithCellCycleCheckSimple.java index d5bc6e510..4b22c864a 100644 --- a/src/arcade/potts/agent/module/PottsModuleProliferationCellCycleProgressionSimple.java +++ b/src/arcade/potts/agent/module/PottsModuleProliferationWithCellCycleCheckSimple.java @@ -12,9 +12,9 @@ import static arcade.potts.util.PottsEnums.Region; import static arcade.potts.util.PottsEnums.State; -/** Extension of {@link PottsModuleProliferationCellCycleProgression} with Poisson transitions. */ -public class PottsModuleProliferationCellCycleProgressionSimple - extends PottsModuleProliferationCellCycleProgression { +/** Extension of {@link PottsModuleProliferationWithCellCycleCheck} with Poisson transitions. */ +public class PottsModuleProliferationWithCellCycleCheckSimple + extends PottsModuleProliferationWithCellCycleCheck { /** Threshold for critical volume size checkpoint. */ static final double SIZE_CHECKPOINT = 0.95; @@ -65,7 +65,7 @@ public class PottsModuleProliferationCellCycleProgressionSimple * * @param cell the {@link PottsCell} the module is associated with */ - public PottsModuleProliferationCellCycleProgressionSimple(PottsCell cell) { + public PottsModuleProliferationWithCellCycleCheckSimple(PottsCell cell) { super(cell); Parameters parameters = cell.getParameters(); diff --git a/test/arcade/potts/agent/cell/PottsCellStemTest.java b/test/arcade/potts/agent/cell/PottsCellStemTest.java index 5ab962176..9d876199a 100644 --- a/test/arcade/potts/agent/cell/PottsCellStemTest.java +++ b/test/arcade/potts/agent/cell/PottsCellStemTest.java @@ -10,7 +10,7 @@ import arcade.potts.agent.module.PottsModuleApoptosis; import arcade.potts.agent.module.PottsModuleAutosis; import arcade.potts.agent.module.PottsModuleNecrosis; -import arcade.potts.agent.module.PottsModuleProliferationCellCycleProgression; +import arcade.potts.agent.module.PottsModuleProliferationWithCellCycleCheck; import arcade.potts.agent.module.PottsModuleQuiescence; import arcade.potts.env.location.PottsLocation; import static org.junit.jupiter.api.Assertions.*; @@ -94,7 +94,7 @@ public void setState_givenState_updatesModule() { assertTrue(cell.module instanceof PottsModuleQuiescence); cell.setState(State.PROLIFERATIVE); - assertTrue(cell.module instanceof PottsModuleProliferationCellCycleProgression); + assertTrue(cell.module instanceof PottsModuleProliferationWithCellCycleCheck); cell.setState(State.APOPTOTIC); assertTrue(cell.module instanceof PottsModuleApoptosis); diff --git a/test/arcade/potts/agent/module/PottsModuleProliferationCellCycleProgressionSimpleTest.java b/test/arcade/potts/agent/module/PottsModuleProliferationWithCellCycleCheckSimpleTest.java similarity index 87% rename from test/arcade/potts/agent/module/PottsModuleProliferationCellCycleProgressionSimpleTest.java rename to test/arcade/potts/agent/module/PottsModuleProliferationWithCellCycleCheckSimpleTest.java index 27ee3be4f..aa167211b 100644 --- a/test/arcade/potts/agent/module/PottsModuleProliferationCellCycleProgressionSimpleTest.java +++ b/test/arcade/potts/agent/module/PottsModuleProliferationWithCellCycleCheckSimpleTest.java @@ -17,12 +17,12 @@ import static org.mockito.Mockito.*; import static arcade.core.ARCADETestUtilities.*; import static arcade.potts.agent.module.PottsModule.PoissonFactory; -import static arcade.potts.agent.module.PottsModuleProliferationCellCycleProgressionSimple.*; +import static arcade.potts.agent.module.PottsModuleProliferationWithCellCycleCheckSimple.*; import static arcade.potts.util.PottsEnums.Phase; import static arcade.potts.util.PottsEnums.Region; import static arcade.potts.util.PottsEnums.State; -public class PottsModuleProliferationCellCycleProgressionSimpleTest { +public class PottsModuleProliferationWithCellCycleCheckSimpleTest { private static final double EPSILON = 1E-10; private static final double R = 1.0; @@ -74,8 +74,8 @@ public static void setupMocks() { public void constructor_setsParameters() { PottsCell cell = mock(PottsCell.class); doReturn(parameters).when(cell).getParameters(); - PottsModuleProliferationCellCycleProgressionSimple module = - new PottsModuleProliferationCellCycleProgressionSimple(cell); + PottsModuleProliferationWithCellCycleCheckSimple module = + new PottsModuleProliferationWithCellCycleCheckSimple(cell); assertEquals(parameters.getDouble("proliferation/SIZE_TARGET"), module.sizeTarget); assertEquals(parameters.getDouble("proliferation/RATE_G1"), module.rateG1, EPSILON); @@ -108,8 +108,8 @@ public void constructor_setsParameters() { public void stepG1_withStateChange_callsMethods() { PottsCell cell = mock(PottsCell.class); doReturn(parameters).when(cell).getParameters(); - PottsModuleProliferationCellCycleProgressionSimple module = - spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); + PottsModuleProliferationWithCellCycleCheckSimple module = + spy(new PottsModuleProliferationWithCellCycleCheckSimple(cell)); module.phase = Phase.PROLIFERATIVE_G1; module.currentSteps = Integer.MAX_VALUE; @@ -129,8 +129,8 @@ public void stepG1_withStateChange_callsMethods() { public void stepG1_withoutStateChange_callsMethods() { PottsCell cell = mock(PottsCell.class); doReturn(parameters).when(cell).getParameters(); - PottsModuleProliferationCellCycleProgressionSimple module = - spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); + PottsModuleProliferationWithCellCycleCheckSimple module = + spy(new PottsModuleProliferationWithCellCycleCheckSimple(cell)); module.phase = Phase.PROLIFERATIVE_G1; module.currentSteps = Integer.MAX_VALUE; @@ -152,8 +152,8 @@ public void stepG1_withTransition_updatesPhase() { int steps = randomIntBetween(1, parameters.getInt("proliferation/STEPS_G1")); PottsCell cell = mock(PottsCell.class); doReturn(parameters).when(cell).getParameters(); - PottsModuleProliferationCellCycleProgressionSimple module = - spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); + PottsModuleProliferationWithCellCycleCheckSimple module = + spy(new PottsModuleProliferationWithCellCycleCheckSimple(cell)); module.phase = Phase.PROLIFERATIVE_G1; module.currentSteps = module.stepsG1 - steps; @@ -173,8 +173,8 @@ public void stepG1_withTransition_updatesPhase() { public void stepG1_withoutTransition_maintainsPhase() { PottsCell cell = mock(PottsCell.class); doReturn(parameters).when(cell).getParameters(); - PottsModuleProliferationCellCycleProgressionSimple module = - spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); + PottsModuleProliferationWithCellCycleCheckSimple module = + spy(new PottsModuleProliferationWithCellCycleCheckSimple(cell)); module.phase = Phase.PROLIFERATIVE_G1; module.currentSteps = module.stepsG1; @@ -194,8 +194,8 @@ public void stepG1_withoutTransition_maintainsPhase() { public void stepG1_anyTransition_updatesCell() { PottsCell cell = mock(PottsCell.class); doReturn(parameters).when(cell).getParameters(); - PottsModuleProliferationCellCycleProgressionSimple module = - spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); + PottsModuleProliferationWithCellCycleCheckSimple module = + spy(new PottsModuleProliferationWithCellCycleCheckSimple(cell)); PoissonFactory poissonFactory = mock(PoissonFactory.class); doReturn(poissonMock).when(poissonFactory).createPoisson(anyDouble(), eq(random)); @@ -219,8 +219,8 @@ public void stepG1_anyTransitionWithRegionOverThreshold_updatesCell() { doReturn((double) criticalVolume).when(cell).getCriticalVolume(Region.NUCLEUS); doReturn((double) criticalVolume + 1).when(cell).getVolume(Region.NUCLEUS); - PottsModuleProliferationCellCycleProgressionSimple module = - spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); + PottsModuleProliferationWithCellCycleCheckSimple module = + spy(new PottsModuleProliferationWithCellCycleCheckSimple(cell)); PoissonFactory poissonFactory = mock(PoissonFactory.class); doReturn(poissonMock).when(poissonFactory).createPoisson(anyDouble(), eq(random)); @@ -245,8 +245,8 @@ public void stepG1_anyTransitionWithRegionUnderThreshold_updatesCell() { doReturn((double) criticalVolume).when(cell).getCriticalVolume(Region.NUCLEUS); doReturn((double) criticalVolume - 1).when(cell).getVolume(Region.NUCLEUS); - PottsModuleProliferationCellCycleProgressionSimple module = - spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); + PottsModuleProliferationWithCellCycleCheckSimple module = + spy(new PottsModuleProliferationWithCellCycleCheckSimple(cell)); PoissonFactory poissonFactory = mock(PoissonFactory.class); doReturn(poissonMock).when(poissonFactory).createPoisson(anyDouble(), eq(random)); @@ -265,8 +265,8 @@ public void stepS_withTransition_updatesPhase() { int steps = randomIntBetween(1, parameters.getInt("proliferation/STEPS_S")); PottsCell cell = mock(PottsCell.class); doReturn(parameters).when(cell).getParameters(); - PottsModuleProliferationCellCycleProgressionSimple module = - spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); + PottsModuleProliferationWithCellCycleCheckSimple module = + spy(new PottsModuleProliferationWithCellCycleCheckSimple(cell)); module.phase = Phase.PROLIFERATIVE_S; module.currentSteps = module.stepsS - steps; @@ -286,8 +286,8 @@ public void stepS_withTransition_updatesPhase() { public void stepS_withoutTransition_maintainsPhase() { PottsCell cell = mock(PottsCell.class); doReturn(parameters).when(cell).getParameters(); - PottsModuleProliferationCellCycleProgressionSimple module = - spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); + PottsModuleProliferationWithCellCycleCheckSimple module = + spy(new PottsModuleProliferationWithCellCycleCheckSimple(cell)); module.phase = Phase.PROLIFERATIVE_S; module.currentSteps = module.stepsS; @@ -307,8 +307,8 @@ public void stepS_withoutTransition_maintainsPhase() { public void stepS_anyTransition_updatesCell() { PottsCell cell = mock(PottsCell.class); doReturn(parameters).when(cell).getParameters(); - PottsModuleProliferationCellCycleProgressionSimple module = - spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); + PottsModuleProliferationWithCellCycleCheckSimple module = + spy(new PottsModuleProliferationWithCellCycleCheckSimple(cell)); PoissonFactory poissonFactory = mock(PoissonFactory.class); doReturn(poissonMock).when(poissonFactory).createPoisson(anyDouble(), eq(random)); @@ -327,8 +327,8 @@ public void stepS_anyTransitionWithRegion_updatesCell() { PottsCell cell = mock(PottsCell.class); doReturn(parameters).when(cell).getParameters(); doReturn(true).when(cell).hasRegions(); - PottsModuleProliferationCellCycleProgressionSimple module = - spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); + PottsModuleProliferationWithCellCycleCheckSimple module = + spy(new PottsModuleProliferationWithCellCycleCheckSimple(cell)); PoissonFactory poissonFactory = mock(PoissonFactory.class); doReturn(poissonMock).when(poissonFactory).createPoisson(anyDouble(), eq(random)); @@ -347,8 +347,8 @@ public void stepS_anyTransitionWithRegion_updatesCell() { public void stepG2_withStateChange_callsMethods() { PottsCell cell = mock(PottsCell.class); doReturn(parameters).when(cell).getParameters(); - PottsModuleProliferationCellCycleProgressionSimple module = - spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); + PottsModuleProliferationWithCellCycleCheckSimple module = + spy(new PottsModuleProliferationWithCellCycleCheckSimple(cell)); module.phase = Phase.PROLIFERATIVE_G2; module.currentSteps = Integer.MAX_VALUE; @@ -368,8 +368,8 @@ public void stepG2_withStateChange_callsMethods() { public void stepG2_withoutStateChange_callsMethods() { PottsCell cell = mock(PottsCell.class); doReturn(parameters).when(cell).getParameters(); - PottsModuleProliferationCellCycleProgressionSimple module = - spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); + PottsModuleProliferationWithCellCycleCheckSimple module = + spy(new PottsModuleProliferationWithCellCycleCheckSimple(cell)); module.phase = Phase.PROLIFERATIVE_G2; module.currentSteps = Integer.MAX_VALUE; @@ -396,8 +396,8 @@ public void stepG2_withTransitionNotArrested_updatesPhase() { doReturn((volume * SIZE_CHECKPOINT * sizeTarget) + 1).when(cell).getVolume(); doReturn(volume).when(cell).getCriticalVolume(); - PottsModuleProliferationCellCycleProgressionSimple module = - spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); + PottsModuleProliferationWithCellCycleCheckSimple module = + spy(new PottsModuleProliferationWithCellCycleCheckSimple(cell)); module.phase = Phase.PROLIFERATIVE_G2; module.currentSteps = module.stepsG2 - steps; @@ -422,8 +422,8 @@ public void stepG2_withoutTransitionNotArrested_maintainsPhase() { doReturn((volume * SIZE_CHECKPOINT * sizeTarget) + 1).when(cell).getVolume(); doReturn(volume).when(cell).getCriticalVolume(); - PottsModuleProliferationCellCycleProgressionSimple module = - spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); + PottsModuleProliferationWithCellCycleCheckSimple module = + spy(new PottsModuleProliferationWithCellCycleCheckSimple(cell)); module.phase = Phase.PROLIFERATIVE_G2; module.currentSteps = module.stepsG2; @@ -449,8 +449,8 @@ public void stepG2_withTransitionArrested_maintainsPhase() { doReturn((volume * SIZE_CHECKPOINT * sizeTarget) - 1).when(cell).getVolume(); doReturn(volume).when(cell).getCriticalVolume(); - PottsModuleProliferationCellCycleProgressionSimple module = - spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); + PottsModuleProliferationWithCellCycleCheckSimple module = + spy(new PottsModuleProliferationWithCellCycleCheckSimple(cell)); module.phase = Phase.PROLIFERATIVE_G2; module.currentSteps = module.stepsG2 - steps; @@ -484,8 +484,8 @@ public void stepG2_withTransitionArrestedRegion_maintainsPhase() { .getVolume(Region.NUCLEUS); doReturn(regionVolume).when(cell).getCriticalVolume(Region.NUCLEUS); - PottsModuleProliferationCellCycleProgressionSimple module = - spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); + PottsModuleProliferationWithCellCycleCheckSimple module = + spy(new PottsModuleProliferationWithCellCycleCheckSimple(cell)); module.phase = Phase.PROLIFERATIVE_G2; module.currentSteps = module.stepsG2 - steps; @@ -510,8 +510,8 @@ public void stepM_withoutTransitionArrested_maintainPhase() { doReturn((volume * SIZE_CHECKPOINT * sizeTarget) - 1).when(cell).getVolume(); doReturn(volume).when(cell).getCriticalVolume(); - PottsModuleProliferationCellCycleProgressionSimple module = - spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); + PottsModuleProliferationWithCellCycleCheckSimple module = + spy(new PottsModuleProliferationWithCellCycleCheckSimple(cell)); module.phase = Phase.PROLIFERATIVE_G2; module.currentSteps = module.stepsG2; @@ -531,8 +531,8 @@ public void stepM_withoutTransitionArrested_maintainPhase() { public void stepG2_anyTransition_updatesCell() { PottsCell cell = mock(PottsCell.class); doReturn(parameters).when(cell).getParameters(); - PottsModuleProliferationCellCycleProgressionSimple module = - spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); + PottsModuleProliferationWithCellCycleCheckSimple module = + spy(new PottsModuleProliferationWithCellCycleCheckSimple(cell)); PoissonFactory poissonFactory = mock(PoissonFactory.class); doReturn(poissonMock).when(poissonFactory).createPoisson(anyDouble(), eq(random)); @@ -551,8 +551,8 @@ public void stepG2_anyTransitionWithRegion_updatesCell() { PottsCell cell = mock(PottsCell.class); doReturn(parameters).when(cell).getParameters(); doReturn(true).when(cell).hasRegions(); - PottsModuleProliferationCellCycleProgressionSimple module = - spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); + PottsModuleProliferationWithCellCycleCheckSimple module = + spy(new PottsModuleProliferationWithCellCycleCheckSimple(cell)); PoissonFactory poissonFactory = mock(PoissonFactory.class); doReturn(poissonMock).when(poissonFactory).createPoisson(anyDouble(), eq(random)); @@ -572,8 +572,8 @@ public void stepM_withTransition_updatesPhase() { int steps = randomIntBetween(1, parameters.getInt("proliferation/STEPS_M")); PottsCell cell = mock(PottsCell.class); doReturn(parameters).when(cell).getParameters(); - PottsModuleProliferationCellCycleProgressionSimple module = - spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); + PottsModuleProliferationWithCellCycleCheckSimple module = + spy(new PottsModuleProliferationWithCellCycleCheckSimple(cell)); module.phase = Phase.PROLIFERATIVE_M; module.currentSteps = module.stepsM - steps; doNothing().when(module).addCell(random, simMock); @@ -595,8 +595,8 @@ public void stepM_withTransition_updatesPhase() { public void stepM_withoutTransition_maintainsPhase() { PottsCell cell = mock(PottsCell.class); doReturn(parameters).when(cell).getParameters(); - PottsModuleProliferationCellCycleProgressionSimple module = - spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); + PottsModuleProliferationWithCellCycleCheckSimple module = + spy(new PottsModuleProliferationWithCellCycleCheckSimple(cell)); module.phase = Phase.PROLIFERATIVE_M; module.currentSteps = module.stepsM; doNothing().when(module).addCell(random, simMock); @@ -618,8 +618,8 @@ public void stepM_withoutTransition_maintainsPhase() { public void stepM_anyTransition_updatesCell() { PottsCell cell = mock(PottsCell.class); doReturn(parameters).when(cell).getParameters(); - PottsModuleProliferationCellCycleProgressionSimple module = - spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); + PottsModuleProliferationWithCellCycleCheckSimple module = + spy(new PottsModuleProliferationWithCellCycleCheckSimple(cell)); doNothing().when(module).addCell(random, simMock); PoissonFactory poissonFactory = mock(PoissonFactory.class); @@ -654,8 +654,8 @@ public void stepM_withRegionOverThreshold_doesNotUpdateCell() { pottsMock.ids = ids; pottsMock.regions = regions; - PottsModuleProliferationCellCycleProgressionSimple module = - spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); + PottsModuleProliferationWithCellCycleCheckSimple module = + spy(new PottsModuleProliferationWithCellCycleCheckSimple(cell)); doNothing().when(module).addCell(random, simMock); PoissonFactory poissonFactory = mock(PoissonFactory.class); @@ -697,8 +697,8 @@ public void stepM_withRegionUnderThreshold_updatesCell() { pottsMock.ids = ids; pottsMock.regions = regions; - PottsModuleProliferationCellCycleProgressionSimple module = - spy(new PottsModuleProliferationCellCycleProgressionSimple(cell)); + PottsModuleProliferationWithCellCycleCheckSimple module = + spy(new PottsModuleProliferationWithCellCycleCheckSimple(cell)); doNothing().when(module).addCell(random, simMock); PoissonFactory poissonFactory = mock(PoissonFactory.class); diff --git a/test/arcade/potts/agent/module/PottsModuleProliferationCellCycleProgressionTest.java b/test/arcade/potts/agent/module/PottsModuleProliferationWithCellCycleCheckTest.java similarity index 77% rename from test/arcade/potts/agent/module/PottsModuleProliferationCellCycleProgressionTest.java rename to test/arcade/potts/agent/module/PottsModuleProliferationWithCellCycleCheckTest.java index 1ad3de569..35838a038 100644 --- a/test/arcade/potts/agent/module/PottsModuleProliferationCellCycleProgressionTest.java +++ b/test/arcade/potts/agent/module/PottsModuleProliferationWithCellCycleCheckTest.java @@ -18,16 +18,16 @@ import static arcade.potts.util.PottsEnums.Phase; import static arcade.potts.util.PottsEnums.State; -public class PottsModuleProliferationCellCycleProgressionTest { +public class PottsModuleProliferationWithCellCycleCheckTest { static MersenneTwisterFast randomMock = new MersenneTwisterFast(); static PottsSimulation simMock = mock(PottsSimulation.class); static PottsCell cellMock = mock(PottsCell.class); - static class PottsModuleProliferationCellCycleProgressionMock - extends PottsModuleProliferationCellCycleProgression { - PottsModuleProliferationCellCycleProgressionMock(PottsCell cell) { + static class PottsModuleProliferationwithCellCycleCheckMock + extends PottsModuleProliferationWithCellCycleCheck { + PottsModuleProliferationwithCellCycleCheckMock(PottsCell cell) { super(cell); } @@ -54,23 +54,23 @@ void stepM(MersenneTwisterFast random, Simulation sim) { @Test public void constructor_initializesFactory() { - PottsModuleProliferationCellCycleProgression module = - new PottsModuleProliferationCellCycleProgressionMock(cellMock); + PottsModuleProliferationWithCellCycleCheck module = + new PottsModuleProliferationwithCellCycleCheckMock(cellMock); assertNotNull(module.poissonFactory); } @Test public void getPhase_defaultConstructor_returnsValue() { - PottsModuleProliferationCellCycleProgression module = - new PottsModuleProliferationCellCycleProgressionMock(cellMock); + PottsModuleProliferationWithCellCycleCheck module = + new PottsModuleProliferationwithCellCycleCheckMock(cellMock); assertEquals(Phase.PROLIFERATIVE_G1, module.getPhase()); } @Test public void setPhase_givenValue_setsValue() { Phase phase = Phase.random(randomMock); - PottsModuleProliferationCellCycleProgression module = - new PottsModuleProliferationCellCycleProgressionMock(cellMock); + PottsModuleProliferationWithCellCycleCheck module = + new PottsModuleProliferationwithCellCycleCheckMock(cellMock); module.setPhase(phase); assertEquals(phase, module.phase); } @@ -78,8 +78,8 @@ public void setPhase_givenValue_setsValue() { @Test public void setPhase_givenValue_resetsSteps() { Phase phase = Phase.random(randomMock); - PottsModuleProliferationCellCycleProgression module = - new PottsModuleProliferationCellCycleProgressionMock(cellMock); + PottsModuleProliferationWithCellCycleCheck module = + new PottsModuleProliferationwithCellCycleCheckMock(cellMock); module.currentSteps = randomIntBetween(1, 10); module.setPhase(phase); assertEquals(0, module.currentSteps); @@ -87,8 +87,8 @@ public void setPhase_givenValue_resetsSteps() { @Test public void step_givenPhaseG1_callsMethod() { - PottsModuleProliferationCellCycleProgression module = - spy(new PottsModuleProliferationCellCycleProgressionMock(cellMock)); + PottsModuleProliferationWithCellCycleCheck module = + spy(new PottsModuleProliferationwithCellCycleCheckMock(cellMock)); module.phase = Phase.PROLIFERATIVE_G1; module.step(randomMock, simMock); @@ -100,8 +100,8 @@ public void step_givenPhaseG1_callsMethod() { @Test public void step_givenPhaseS_callsMethod() { - PottsModuleProliferationCellCycleProgression module = - spy(new PottsModuleProliferationCellCycleProgressionMock(cellMock)); + PottsModuleProliferationWithCellCycleCheck module = + spy(new PottsModuleProliferationwithCellCycleCheckMock(cellMock)); module.phase = Phase.PROLIFERATIVE_S; module.step(randomMock, simMock); @@ -113,8 +113,8 @@ public void step_givenPhaseS_callsMethod() { @Test public void step_givenPhaseG2_callsMethod() { - PottsModuleProliferationCellCycleProgression module = - spy(new PottsModuleProliferationCellCycleProgressionMock(cellMock)); + PottsModuleProliferationWithCellCycleCheck module = + spy(new PottsModuleProliferationwithCellCycleCheckMock(cellMock)); module.phase = Phase.PROLIFERATIVE_G2; module.step(randomMock, simMock); @@ -126,8 +126,8 @@ public void step_givenPhaseG2_callsMethod() { @Test public void step_givenPhaseM_callsMethod() { - PottsModuleProliferationCellCycleProgression module = - spy(new PottsModuleProliferationCellCycleProgressionMock(cellMock)); + PottsModuleProliferationWithCellCycleCheck module = + spy(new PottsModuleProliferationwithCellCycleCheckMock(cellMock)); doNothing().when(module).addCell(randomMock, simMock); module.phase = Phase.PROLIFERATIVE_M; @@ -140,8 +140,8 @@ public void step_givenPhaseM_callsMethod() { @Test public void step_invalidPhase_doesNothing() { - PottsModuleProliferationCellCycleProgression module = - spy(new PottsModuleProliferationCellCycleProgressionMock(cellMock)); + PottsModuleProliferationWithCellCycleCheck module = + spy(new PottsModuleProliferationwithCellCycleCheckMock(cellMock)); module.phase = Phase.UNDEFINED; module.step(randomMock, simMock); @@ -188,8 +188,8 @@ public void addCell_called_addsObject() { doNothing().when(cell).reset(any(), any()); doNothing().when(newCell).reset(any(), any()); - PottsModuleProliferationCellCycleProgression module = - new PottsModuleProliferationCellCycleProgressionMock(cell); + PottsModuleProliferationWithCellCycleCheck module = + new PottsModuleProliferationwithCellCycleCheckMock(cell); module.addCell(randomMock, sim); verify(cell).reset(potts.ids, potts.regions); From 6695b290f7f48544f35b5378c8921a23ad26b087 Mon Sep 17 00:00:00 2001 From: jannetty Date: Tue, 21 Oct 2025 11:34:48 -0700 Subject: [PATCH 21/59] adding missing javadocs --- src/arcade/potts/agent/module/PottsModuleProliferation.java | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/src/arcade/potts/agent/module/PottsModuleProliferation.java b/src/arcade/potts/agent/module/PottsModuleProliferation.java index dcfec3e99..cda674b14 100644 --- a/src/arcade/potts/agent/module/PottsModuleProliferation.java +++ b/src/arcade/potts/agent/module/PottsModuleProliferation.java @@ -4,8 +4,14 @@ import arcade.core.sim.Simulation; import arcade.potts.agent.cell.PottsCell; +/** Abstract extention of {@link PottsModule} for proliferation modules. */ public abstract class PottsModuleProliferation extends PottsModule { + /** + * Creates a proliferation module. + * + * @param cell the cell to which this module is attached + */ public PottsModuleProliferation(PottsCell cell) { super(cell); } From 232d1aec421bb4d0a6a297b5351c084854d9ff5b Mon Sep 17 00:00:00 2001 From: jannetty Date: Tue, 21 Oct 2025 13:13:39 -0700 Subject: [PATCH 22/59] wip-adding-flystemcellfiles --- .../potts/agent/cell/PottsCellContainer.java | 4 + .../potts/agent/cell/PottsCellFlyStem.java | 163 ++++++++++ .../PottsModuleFlyStemProliferation.java | 301 ++++++++++++++++++ 3 files changed, 468 insertions(+) create mode 100644 src/arcade/potts/agent/cell/PottsCellFlyStem.java create mode 100644 src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java diff --git a/src/arcade/potts/agent/cell/PottsCellContainer.java b/src/arcade/potts/agent/cell/PottsCellContainer.java index 6bc855314..10e3f170b 100644 --- a/src/arcade/potts/agent/cell/PottsCellContainer.java +++ b/src/arcade/potts/agent/cell/PottsCellContainer.java @@ -176,6 +176,10 @@ public Cell convert( return new PottsCellFlyNeuron(this, location, parameters, links); case "fly-gmc": return new PottsCellFlyGMC(this, location, parameters, links); + case "fly-stem-wt": + return new PottsCellFlyStem(this, location, parameters, links); + case "fly-stem-mudmut": + return new PottsCellFlyStem(this, location, parameters, links); default: case "stem": return new PottsCellStem(this, location, parameters, links); diff --git a/src/arcade/potts/agent/cell/PottsCellFlyStem.java b/src/arcade/potts/agent/cell/PottsCellFlyStem.java new file mode 100644 index 000000000..44aa96ba2 --- /dev/null +++ b/src/arcade/potts/agent/cell/PottsCellFlyStem.java @@ -0,0 +1,163 @@ +package arcade.potts.agent.cell; + +import ec.util.MersenneTwisterFast; +import arcade.core.agent.cell.CellState; +import arcade.core.env.location.Location; +import arcade.core.util.GrabBag; +import arcade.core.util.Parameters; +import arcade.core.util.Vector; +import arcade.potts.agent.module.PottsModule; +import arcade.potts.agent.module.PottsModuleFlyStemProliferation; +import arcade.potts.util.PottsEnums.Phase; +import static arcade.potts.util.PottsEnums.State; + +public class PottsCellFlyStem extends PottsCell { + /** Enum outlining parameters for each cell type. */ + public enum StemType { + /** Wild type stem cell. */ + WT(50, 75, 0, 0.25), + + /** mud Mutant stem cell. */ + MUDMUT(50, 50, -90, 0.5); + + /** Percentage x offset from cell edge where division will occur. */ + public final int splitOffsetPercentX; + + /** Percentage y offset from cell edge where division will occur. */ + public final int splitOffsetPercentY; + + /** Default direction of division is rotated this much off the apical vector. */ + public final double splitDirectionRotation; + + /** + * The proportion of the stem cell's critical volume that will be the daughter cell's + * critical volume. + */ + public final double daughterCellCriticalVolumeProportion; + + /** + * Constructor for StemType. + * + * @param splitOffsetPercentX percentage x offset from cell edge where division will occur + * @param splitOffsetPercentY percentage y offset from cell edge where division will occur + * @param splitDirectionRotation the plane of division's rotation off the apical vector + * @param daughterCellCriticalVolumeProportion proportion of the stem cell's critical volume + * that will be the daughter cell's critical volume + */ + StemType( + int splitOffsetPercentX, + int splitOffsetPercentY, + double splitDirectionRotation, + double daughterCellCriticalVolumeProportion) { + this.splitOffsetPercentX = splitOffsetPercentX; + this.splitOffsetPercentY = splitOffsetPercentY; + this.splitDirectionRotation = splitDirectionRotation; + this.daughterCellCriticalVolumeProportion = daughterCellCriticalVolumeProportion; + } + } + + /** The type of stem cell. */ + public final StemType stemType; + + private Vector apicalAxis; + + /** + * Constructor for PottsCellFlyStem. + * + * @param container the container for the cell + * @param location the location of the cell + * @param parameters the parameters for the cell + * @param links the links for the cell + * @throws IllegalArgumentException if the stem type is not recognized + */ + public PottsCellFlyStem( + PottsCellContainer container, Location location, Parameters parameters, GrabBag links) { + super(container, location, parameters, links); + + if (module != null) { + ((PottsModule) module).setPhase(Phase.UNDEFINED); + } + + String stemTypeString = parameters.getString("CLASS"); + switch (stemTypeString) { + case "fly-stem-wt": + stemType = StemType.WT; + break; + case "fly-stem-mudmut": + stemType = StemType.MUDMUT; + break; + default: + throw new IllegalArgumentException("Unknown StemType: " + stemTypeString); + } + } + + public void setApicalAxis(Vector apicalAxis) { + this.apicalAxis = apicalAxis; + } + + /** + * Gets the apical axis of the cell. If no apical axis is set, it returns a vector along the y + * axis as a default vector + * + * @return the apical axis of the cell + */ + public Vector getApicalAxis() { + if (apicalAxis != null) { + return apicalAxis; + } else { + return new Vector(0, 1, 0); + } + } + + @Override + public PottsCellContainer make(int newID, CellState newState, MersenneTwisterFast random) { + throw new UnsupportedOperationException( + "make(int, CellState, MersenneTwisterFast) not supported. Please use make(int, CellState, MersenneTwisterFast, int, double) instead."); + } + + public PottsCellContainer make( + int newID, + CellState newState, + MersenneTwisterFast random, + int newPop, + double daughterCellCriticalVolume) { + + divisions++; + + return new PottsCellContainer( + newID, + id, + newPop, + age, + divisions, + newState, + Phase.UNDEFINED, + 0, + null, + daughterCellCriticalVolume, + criticalHeight, + criticalRegionVolumes, + criticalRegionHeights); + } + + @Override + void setStateModule(CellState newState) { + switch ((State) newState) { + case PROLIFERATIVE: + module = new PottsModuleFlyStemProliferation(this); + break; + default: + module = null; + break; + } + } + + /** + * Gets the stem type of the cell. + * + * @return the stem type of the cell + */ + public final StemType getStemType() { + return stemType; + } +} diff --git a/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java b/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java new file mode 100644 index 000000000..53bec2ce3 --- /dev/null +++ b/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java @@ -0,0 +1,301 @@ +package arcade.potts.agent.module; + +import java.util.ArrayList; +import sim.util.Double3D; +import ec.util.MersenneTwisterFast; +import arcade.core.sim.Simulation; +import arcade.core.util.Parameters; +import arcade.core.util.Plane; +import arcade.core.util.Vector; +import arcade.core.util.distributions.Distribution; +import arcade.core.util.distributions.NormalDistribution; +import arcade.potts.agent.cell.PottsCellContainer; +import arcade.potts.agent.cell.PottsCellFlyStem; +import arcade.potts.agent.cell.PottsCellFlyStem.StemType; +import arcade.potts.env.location.PottsLocation; +import arcade.potts.env.location.PottsLocation2D; +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 static arcade.potts.util.PottsEnums.Direction; +import static arcade.potts.util.PottsEnums.Phase; + +public class PottsModuleFlyStemProliferation extends PottsModuleProliferationVolumeBasedDivision { + + /** Threshold for critical volume size checkpoint. */ + static final double SIZE_CHECKPOINT = 0.95; + + /** + * Target ratio of critical volume for division size checkpoint (cell must reach CRITICAL_VOLUME + * * SIZE_TARGET * SIZE_CHECKPOINT to divide). + */ + double sizeTarget; + + /** Base growth rate for stem cells. */ + final double cellGrowthRateBase; + + /** Current growth rate for stem cells. */ + double cellGrowthRate; + + /** Basal rate of apoptosis (ticks^-1). */ + final double basalApoptosisRate; + + /** Distribution that determines rotational offset of cell's division plane. */ + final NormalDistribution splitDirectionDistribution; + + /** Ruleset for determining which daughter cell is the GMC. Can be `volume` or `location`. */ + final String differentiationRuleset; + + final String apicalAxisRuleset; + + final Distribution apicalAxisRotationDistribution; + + final boolean dynamicGrowthRateVolume; + + final boolean volumeBasedCriticalVolume; + + final double volumeBasedCriticalVolumeMultiplier; + + final double growthRateVolumeSensitivity; + + /** + * Range of values considered equal when determining daughter cell identity. ex. if ruleset is + * location, range determines the distance between centroid y values that is considered equal. + */ + final double range; + + /** + * Creates a proliferation {@code Module} for the given {@link PottsCellFlyStem}. + * + * @param cell the {@link PottsCellFlyStem} the module is associated with + */ + public PottsModuleFlyStemProliferation(PottsCellFlyStem cell) { + super(cell); + + if (cell.hasRegions()) { + throw new UnsupportedOperationException( + "Regions are not yet implemented for fly cells"); + } + + Parameters parameters = cell.getParameters(); + + sizeTarget = parameters.getDouble("proliferation/SIZE_TARGET"); + cellGrowthRateBase = parameters.getDouble("proliferation/CELL_GROWTH_RATE"); + basalApoptosisRate = parameters.getDouble("proliferation/BASAL_APOPTOSIS_RATE"); + splitDirectionDistribution = + (NormalDistribution) + parameters.getDistribution("proliferation/DIV_ROTATION_DISTRIBUTION"); + differentiationRuleset = parameters.getString("proliferation/DIFFERENTIATION_RULESET"); + range = parameters.getDouble("proliferation/DIFFERENTIATION_RULESET_EQUALITY_RANGE"); + apicalAxisRuleset = parameters.getString("proliferation/APICAL_AXIS_RULESET"); + apicalAxisRotationDistribution = + (Distribution) + parameters.getDistribution( + "proliferation/APICAL_AXIS_ROTATION_DISTRIBUTION"); + + dynamicGrowthRateVolume = + (parameters.getInt("proliferation/DYNAMIC_GROWTH_RATE_VOLUME") != 0); + updateGrowthRate(); + + volumeBasedCriticalVolume = + (parameters.getInt("proliferation/VOLUME_BASED_CRITICAL_VOLUME") != 0); + + volumeBasedCriticalVolumeMultiplier = + (parameters.getDouble("proliferation/VOLUME_BASED_CRITICAL_VOLUME_MULTIPLIER")); + growthRateVolumeSensitivity = + parameters.getDouble("proliferation/GROWTH_RATE_VOLUME_SENSITIVITY"); + + setPhase(Phase.UNDEFINED); + } + + public static final double EPSILON = 1e-8; + + @Override + public void addCell(MersenneTwisterFast random, Simulation sim) { + Potts potts = ((PottsSimulation) sim).getPotts(); + PottsCellFlyStem flyStemCell = (PottsCellFlyStem) cell; + + Plane divisionPlane = chooseDivisionPlane(flyStemCell); + PottsLocation2D parentLoc = (PottsLocation2D) cell.getLocation(); + PottsLocation daughterLoc = (PottsLocation) parentLoc.split(random, divisionPlane); + + boolean isDaughterStem = daughterStem(parentLoc, daughterLoc); + + if (isDaughterStem) { + makeDaughterStemCell(daughterLoc, sim, potts, random); + } else { + makeDaughterGMC( + parentLoc, + daughterLoc, + sim, + potts, + random, + divisionPlane.getUnitNormalVector()); + } + } + + /** + * Updates the cell growth rate based on the current parameter settings. + * + *

If {@code dynamicGrowthRateVolume} is {@code false}, the growth rate is fixed at the base + * value specified in {@code cellGrowthRateBase}. If {@code dynamicGrowthRateVolume} is {@code + * true}, 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: + * + * 

+     *   growthRate = baseGrowthRate * (volume / criticalVolume) ^ sensitivity
+     *
+ * + * This allows larger cells to grow faster, capturing volume-dependent growth dynamics. + */ + void updateGrowthRate() { + if (dynamicGrowthRateVolume == false) { + cellGrowthRate = cellGrowthRateBase; + } else if (dynamicGrowthRateVolume == true) { + double volume = cell.getLocation().getVolume(); + double Ka = cell.getCriticalVolume(); + cellGrowthRate = + cellGrowthRateBase * Math.pow((volume / Ka), growthRateVolumeSensitivity); + } + } + + protected Plane chooseDivisionPlane(PottsCellFlyStem flyStemCell) { + double offset = sampleDivisionPlaneOffset(); + + if (flyStemCell.getStemType() == StemType.WT + || (flyStemCell.getStemType() == StemType.MUDMUT && Math.abs(offset) < 45)) { + return getWTDivisionPlaneWithRotationalVariance(flyStemCell, offset); + } else { + return getMUDDivisionPlane(flyStemCell); + } + } + + /** + * Gets the rotation offset for the division plane according to splitDirectionDistribution. + * + * @return the rotation offset for the division plane + */ + double sampleDivisionPlaneOffset() { + return splitDirectionDistribution.nextDouble(); + } + + /** + * Gets the division plane for the cell after rotating the plane according to + * splitDirectionDistribution. This follows WT division rules. The plane is rotated around the + * XY plane. + * + * @param cell the {@link PottsCellFlyStem} to get the division plane for + * @param rotationOffset the angle to rotate the plane + * @return the division plane for the cell + */ + public Plane getWTDivisionPlaneWithRotationalVariance( + PottsCellFlyStem cell, double rotationOffset) { + Vector apical_axis = cell.getApicalAxis(); + Vector rotatedNormalVector = + Vector.rotateVectorAroundAxis( + apical_axis, Direction.XY_PLANE.vector, rotationOffset); + Voxel splitVoxel = getCellSplitVoxel(StemType.WT, cell, rotatedNormalVector); + return new Plane( + new Double3D(splitVoxel.x, splitVoxel.y, splitVoxel.z), rotatedNormalVector); + } + + /** + * Gets the division plane for the cell. This follows MUDMUT division rules. The division plane + * is not rotated. + * + * @param cell the {@link PottsCellFlyStem} to get the division plane for + * @return the division plane for the cell + */ + public Plane getMUDDivisionPlane(PottsCellFlyStem cell) { + Vector defaultNormal = + Vector.rotateVectorAroundAxis( + cell.getApicalAxis(), + Direction.XY_PLANE.vector, + StemType.MUDMUT.splitDirectionRotation); + Voxel splitVoxel = getCellSplitVoxel(StemType.MUDMUT, cell, defaultNormal); + return new Plane(new Double3D(splitVoxel.x, splitVoxel.y, splitVoxel.z), defaultNormal); + } + + /** + * Gets the voxel location the cell's plane of division will pass through. + * + * @param cell the {@link PottsCellFlyStem} to get the division location for + * @return the voxel location where the cell will split + */ + public static Voxel getCellSplitVoxel( + StemType stemType, PottsCellFlyStem cell, Vector rotatedNormalVector) { + ArrayList splitOffsetPercent = new ArrayList<>(); + splitOffsetPercent.add(stemType.splitOffsetPercentX); + splitOffsetPercent.add(stemType.splitOffsetPercentY); + return ((PottsLocation2D) cell.getLocation()) + .getOffsetInApicalFrame2D(splitOffsetPercent, rotatedNormalVector); + } + + public boolean daughterStem(PottsLocation loc1, PottsLocation loc2) { + if (((PottsCellFlyStem) cell).getStemType() == StemType.WT) { + return false; + } else if (((PottsCellFlyStem) cell).getStemType() == StemType.MUDMUT) { + if (differentiationRuleset.equals("volume")) { + double vol1 = loc1.getVolume(); + double vol2 = loc2.getVolume(); + if (Math.abs(vol1 - vol2) < range) { + return true; + } else { + return false; + } + } else if (differentiationRuleset.equals("location")) { + double[] centroid1 = loc1.getCentroid(); + double[] centroid2 = loc2.getCentroid(); + return (centroidsWithinRangeAlongApicalAxis( + centroid1, centroid2, ((PottsCellFlyStem) cell).getApicalAxis(), range)); + } + } + throw new IllegalArgumentException( + "Invalid differentiation ruleset: " + differentiationRuleset); + } + + /** + * Determines if the distance between two centroids, projected along the apical axis, is less + * than or equal to the given range. + * + * @param centroid1 First centroid position. + * @param centroid2 Second centroid position. + * @param apicalAxis Unit {@link Vector} defining the apical-basal direction. + * @param range Maximum allowed distance along the apical axis. + * @return true if the centroids are within the given range along the apical axis. + */ + static boolean centroidsWithinRangeAlongApicalAxis( + double[] centroid1, double[] centroid2, Vector apicalAxis, double range) { + + Vector c1 = new Vector(centroid1[0], centroid1[1], centroid1.length > 2 ? centroid1[2] : 0); + Vector c2 = new Vector(centroid2[0], centroid2[1], centroid2.length > 2 ? centroid2[2] : 0); + + double proj1 = Vector.dotProduct(c1, apicalAxis); + double proj2 = Vector.dotProduct(c2, apicalAxis); + + double distanceAlongAxis = Math.abs(proj1 - proj2); + + return distanceAlongAxis - range <= EPSILON; + } + + private void makeDaughterStemCell( + PottsLocation daughterLoc, Simulation sim, Potts potts, MersenneTwisterFast random) { + cell.reset(potts.ids, potts.regions); + int newID = sim.getID(); + double criticalVol; + if (volumeBasedCriticalVolume) { + criticalVol = daughterLoc.getVolume() * volumeBasedCriticalVolumeMultiplier; + cell.setCriticalVolume( + cell.getLocation().getVolume() * volumeBasedCriticalVolumeMultiplier); + } else { + criticalVol = cell.getCriticalVolume(); + } + PottsCellContainer container = + ((PottsCellFlyStem) cell) + .make(newID, State.PROLIFERATIVE, random, cell.getPop(), criticalVol); + scheduleNewCell(container, daughterLoc, sim, potts, random); + } +} From 306c816507cab0f15e4f9b6756706b5d2c5001bc Mon Sep 17 00:00:00 2001 From: jannetty Date: Tue, 21 Oct 2025 13:20:33 -0700 Subject: [PATCH 23/59] making critical volume settable --- src/arcade/potts/agent/cell/PottsCell.java | 11 +++++++++- .../potts/agent/cell/PottsCellTest.java | 22 +++++++++++++++++++ 2 files changed, 32 insertions(+), 1 deletion(-) diff --git a/src/arcade/potts/agent/cell/PottsCell.java b/src/arcade/potts/agent/cell/PottsCell.java index ab3996071..b05310e27 100644 --- a/src/arcade/potts/agent/cell/PottsCell.java +++ b/src/arcade/potts/agent/cell/PottsCell.java @@ -79,7 +79,7 @@ public abstract class PottsCell implements Cell { private final EnumMap targetRegionSurfaces; /** Critical volume for cell [voxels]. */ - final double criticalVolume; + double criticalVolume; /** Critical volumes for cell by region [voxels]. */ final EnumMap criticalRegionVolumes; @@ -295,6 +295,15 @@ public double getCriticalVolume() { return criticalVolume; } + /** + * Sets the critical volume of the cell. + * + * @param newCriticalVolume the new critical volume + */ + public void setCriticalVolume(double newCriticalVolume) { + criticalVolume = newCriticalVolume; + } + /** * Gets the critical volume for a region. * diff --git a/test/arcade/potts/agent/cell/PottsCellTest.java b/test/arcade/potts/agent/cell/PottsCellTest.java index b4e75299c..76de36dba 100644 --- a/test/arcade/potts/agent/cell/PottsCellTest.java +++ b/test/arcade/potts/agent/cell/PottsCellTest.java @@ -652,6 +652,28 @@ public void getCriticalVolume_afterInitializeNoRegion_returnsZero() { } } + @Test + public void setCriticalVolume_calledWithRegions_correctlySetsCriticalVolume() { + PottsCell cell = new PottsCellMock(containerWithRegions, locationMock, parametersMock); + assertEquals(cellCriticalVolume, cell.getCriticalVolume()); + double newCriticalVolume = randomDoubleBetween(10, 20); + cell.setCriticalVolume(newCriticalVolume); + assertEquals(newCriticalVolume, cell.getCriticalVolume()); + cell.setCriticalVolume(cellCriticalVolume); + assertEquals(cellCriticalVolume, cell.getCriticalVolume()); + } + + @Test + public void setCriticalVolume_calledWithoutRegions_correctlySetsCriticalVolume() { + PottsCell cell = new PottsCellMock(containerWithoutRegions, locationMock, parametersMock); + assertEquals(cellCriticalVolume, cell.getCriticalVolume()); + double newCriticalVolume = randomDoubleBetween(10, 20); + cell.setCriticalVolume(newCriticalVolume); + assertEquals(newCriticalVolume, cell.getCriticalVolume()); + cell.setCriticalVolume(cellCriticalVolume); + assertEquals(cellCriticalVolume, cell.getCriticalVolume()); + } + @Test public void getCriticalHeight_beforeInitialize_returnsValue() { assertEquals(cellCriticalHeight, cellWithoutRegions.getCriticalHeight(), EPSILON); From b6d613f44eb979d0af5e214eeba73c6ac75128d1 Mon Sep 17 00:00:00 2001 From: jannetty Date: Tue, 21 Oct 2025 13:43:50 -0700 Subject: [PATCH 24/59] wip adding fly stem proliferation module, fly stem cells, and tests --- .../PottsModuleFlyStemProliferation.java | 138 ++- .../agent/cell/PottsCellFlyStemTest.java | 196 ++++ .../PottsModuleFlyStemProliferationTest.java | 856 ++++++++++++++++++ 3 files changed, 1188 insertions(+), 2 deletions(-) create mode 100644 test/arcade/potts/agent/cell/PottsCellFlyStemTest.java create mode 100644 test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java diff --git a/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java b/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java index 53bec2ce3..84dc637f8 100644 --- a/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java +++ b/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java @@ -3,12 +3,15 @@ import java.util.ArrayList; import sim.util.Double3D; import ec.util.MersenneTwisterFast; +import arcade.core.env.location.Location; import arcade.core.sim.Simulation; import arcade.core.util.Parameters; import arcade.core.util.Plane; import arcade.core.util.Vector; import arcade.core.util.distributions.Distribution; import arcade.core.util.distributions.NormalDistribution; +import arcade.core.util.distributions.UniformDistribution; +import arcade.potts.agent.cell.PottsCell; import arcade.potts.agent.cell.PottsCellContainer; import arcade.potts.agent.cell.PottsCellFlyStem; import arcade.potts.agent.cell.PottsCellFlyStem.StemType; @@ -17,10 +20,9 @@ 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 static arcade.potts.util.PottsEnums.Direction; import static arcade.potts.util.PottsEnums.Phase; +import static arcade.potts.util.PottsEnums.State; public class PottsModuleFlyStemProliferation extends PottsModuleProliferationVolumeBasedDivision { @@ -298,4 +300,136 @@ private void makeDaughterStemCell( .make(newID, State.PROLIFERATIVE, random, cell.getPop(), criticalVol); scheduleNewCell(container, daughterLoc, sim, potts, random); } + + private void makeDaughterGMC( + PottsLocation parentLoc, + PottsLocation daughterLoc, + Simulation sim, + Potts potts, + MersenneTwisterFast random, + Vector divisionPlaneNormal) { + Location gmcLoc = determineGMCLocation(parentLoc, daughterLoc, divisionPlaneNormal); + + if (parentLoc == gmcLoc) { + PottsLocation.swapVoxels(parentLoc, daughterLoc); + } + cell.reset(potts.ids, potts.regions); + int newID = sim.getID(); + int newPop = ((PottsCellFlyStem) cell).getLinks().next(random); + double criticalVolume = + calculateGMCDaughterCellCriticalVolume((PottsLocation) daughterLoc, sim, newPop); + PottsCellContainer container = + ((PottsCellFlyStem) cell) + .make(newID, State.PROLIFERATIVE, random, newPop, criticalVolume); + scheduleNewCell(container, daughterLoc, sim, potts, random); + } + + private void scheduleNewCell( + PottsCellContainer container, + PottsLocation daughterLoc, + Simulation sim, + Potts potts, + MersenneTwisterFast random) { + PottsCell newCell = + (PottsCell) container.convert(sim.getCellFactory(), daughterLoc, random); + if (newCell.getClass() == PottsCellFlyStem.class) { + ((PottsCellFlyStem) newCell).setApicalAxis(getDaughterCellApicalAxis(random)); + } + sim.getGrid().addObject(newCell, null); + potts.register(newCell); + newCell.reset(potts.ids, potts.regions); + newCell.schedule(sim.getSchedule()); + } + + public Vector getDaughterCellApicalAxis(MersenneTwisterFast random) { + switch (apicalAxisRuleset) { + case "uniform": + if (!(apicalAxisRotationDistribution instanceof UniformDistribution)) { + throw new IllegalArgumentException( + "apicalAxisRotationDistribution must be a UniformDistribution under the uniform apical axis ruleset."); + } + Vector newRandomApicalAxis = + Vector.rotateVectorAroundAxis( + ((PottsCellFlyStem) cell).getApicalAxis(), + Direction.XY_PLANE.vector, + apicalAxisRotationDistribution.nextDouble()); + return newRandomApicalAxis; + case "global": + return ((PottsCellFlyStem) cell).getApicalAxis(); + case "rotation": + if (!(apicalAxisRotationDistribution instanceof NormalDistribution)) { + throw new IllegalArgumentException( + "apicalAxisRotationDistribution must be a NormalDistribution under the rotation apical axis ruleset."); + } + Vector newRotatedApicalAxis = + Vector.rotateVectorAroundAxis( + ((PottsCellFlyStem) cell).getApicalAxis(), + Direction.XY_PLANE.vector, + apicalAxisRotationDistribution.nextDouble()); + return newRotatedApicalAxis; + default: + throw new IllegalArgumentException( + "Invalid apical axis ruleset: " + apicalAxisRuleset); + } + } + + private Location determineGMCLocation( + PottsLocation parentLoc, PottsLocation daughterLoc, Vector divisionPlaneNormal) { + switch (differentiationRuleset) { + case "volume": + return getSmallerLocation(parentLoc, daughterLoc); + case "location": + return getBasalLocation(parentLoc, daughterLoc, divisionPlaneNormal); + default: + throw new IllegalArgumentException( + "Invalid differentiation ruleset: " + differentiationRuleset); + } + } + + protected double calculateGMCDaughterCellCriticalVolume( + PottsLocation gmcLoc, Simulation sim, int newpop) { + double max_crit_vol = + ((PottsCellFlyStem) cell).getCriticalVolume() + * sizeTarget + * ((PottsCellFlyStem) cell) + .getStemType() + .daughterCellCriticalVolumeProportion; + if (volumeBasedCriticalVolume) { + return gmcLoc.getVolume() * volumeBasedCriticalVolumeMultiplier; + } else { + return max_crit_vol; + } + } + + /** + * Gets the smaller location with fewer voxels and returns it. + * + * @param loc1 the {@link PottsLocation} to compare to location2. + * @param loc2 {@link PottsLocation} to compare to location1. + * @return the smaller location. + */ + public static PottsLocation getSmallerLocation(PottsLocation loc1, PottsLocation loc2) { + return (loc1.getVolume() < loc2.getVolume()) ? loc1 : loc2; + } + + /** + * Gets the location that is lower along the apical axis. + * + * @param loc1 {@link PottsLocation} to compare. + * @param loc2 {@link PottsLocation} to compare. + * @param apicalAxis Unit {@link Vector} defining the apical-basal direction. + * @return the basal location (lower along the apical axis). + */ + public static PottsLocation getBasalLocation( + PottsLocation loc1, PottsLocation loc2, Vector apicalAxis) { + double[] centroid1 = loc1.getCentroid(); + double[] centroid2 = loc2.getCentroid(); + Vector c1 = new Vector(centroid1[0], centroid1[1], centroid1.length > 2 ? centroid1[2] : 0); + Vector c2 = new Vector(centroid2[0], centroid2[1], centroid2.length > 2 ? centroid2[2] : 0); + + double proj1 = Vector.dotProduct(c1, apicalAxis); + double proj2 = Vector.dotProduct(c2, apicalAxis); + + return (proj1 < proj2) ? loc2 : loc1; // higher projection = more basal + } } diff --git a/test/arcade/potts/agent/cell/PottsCellFlyStemTest.java b/test/arcade/potts/agent/cell/PottsCellFlyStemTest.java new file mode 100644 index 000000000..263a5aee0 --- /dev/null +++ b/test/arcade/potts/agent/cell/PottsCellFlyStemTest.java @@ -0,0 +1,196 @@ +package arcade.potts.agent.cell; + +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import ec.util.MersenneTwisterFast; +import arcade.core.util.GrabBag; +import arcade.core.util.MiniBox; +import arcade.core.util.Parameters; +import arcade.core.util.Vector; +import arcade.potts.env.location.PottsLocation; +import arcade.potts.util.PottsEnums.Phase; +import arcade.potts.util.PottsEnums.State; +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.ArgumentMatchers.any; +import static org.mockito.Mockito.*; +import static arcade.core.ARCADETestUtilities.*; + +public class PottsCellFlyStemTest { + static final double EPSILON = 1e-6; + + static MersenneTwisterFast random = new MersenneTwisterFast(); + + static PottsLocation locationMock; + + static Parameters parametersMock; + + static GrabBag links; + + static int cellID = randomIntBetween(1, 10); + + static int cellParent = randomIntBetween(1, 10); + + static int cellPop = randomIntBetween(1, 10); + + static int cellAge = randomIntBetween(1, 1000); + + static int cellDivisions = randomIntBetween(1, 100); + + static double cellCriticalVolume = randomDoubleBetween(10, 100); + + static double cellCriticalHeight = randomDoubleBetween(10, 100); + + static State cellState = State.UNDEFINED; + + static PottsCellContainer baseContainer; + + @BeforeEach + public final void setupMocks() { + locationMock = mock(PottsLocation.class); + parametersMock = spy(new Parameters(new MiniBox(), null, null)); + links = new GrabBag(); + links.add(1, 1); + + doReturn(0.0).when(parametersMock).getDouble(any()); + doReturn(0).when(parametersMock).getInt(any()); + + baseContainer = + new PottsCellContainer( + cellID, + cellParent, + cellPop, + cellAge, + cellDivisions, + cellState, + null, + 0, + cellCriticalVolume, + cellCriticalHeight); + } + + @Test + public void constructor_validWTStemType_createsInstance() { + doReturn("fly-stem-wt").when(parametersMock).getString("CLASS"); + PottsCellFlyStem cell = + new PottsCellFlyStem(baseContainer, locationMock, parametersMock, links); + assertNotNull(cell); + assertEquals(PottsCellFlyStem.StemType.WT, cell.stemType); + } + + @Test + public void constructor_validMUDMUTStemType_createsInstance() { + doReturn("fly-stem-mudmut").when(parametersMock).getString("CLASS"); + PottsCellFlyStem cell = + new PottsCellFlyStem(baseContainer, locationMock, parametersMock, links); + assertNotNull(cell); + assertEquals(PottsCellFlyStem.StemType.MUDMUT, cell.stemType); + } + + @Test + public void constructor_invalidStemType_throwsException() { + doReturn("invalid-class").when(parametersMock).getString("CLASS"); + assertThrows( + IllegalArgumentException.class, + () -> new PottsCellFlyStem(baseContainer, locationMock, parametersMock, links)); + } + + @Test + public void make_calledWT_returnsCorrectNewContainer() { + doReturn("fly-stem-wt").when(parametersMock).getString("CLASS"); + PottsCellFlyStem cell = + new PottsCellFlyStem(baseContainer, locationMock, parametersMock, links); + PottsCellContainer container = + cell.make(cellID, State.PROLIFERATIVE, random, cellPop, cellCriticalVolume); + + assertAll( + () -> assertNotNull(container), + () -> assertEquals(cellID, container.parent), + () -> assertEquals(cellPop, container.pop), + () -> assertEquals(cellAge, container.age), + () -> assertEquals(cellDivisions + 1, container.divisions), + () -> assertEquals(State.PROLIFERATIVE, container.state), + () -> assertEquals(container.phase, Phase.UNDEFINED), + () -> assertEquals(0, container.voxels), + () -> assertNull(container.regionVoxels), + () -> assertEquals(cellCriticalVolume, container.criticalVolume, EPSILON), + () -> assertEquals(cellCriticalHeight, container.criticalHeight, EPSILON), + () -> assertNull(container.criticalRegionVolumes), + () -> assertNull(container.criticalRegionHeights)); + } + + @Test + public void make_calledMUDMUT_returnsCorrectNewContainer() { + doReturn("fly-stem-mudmut").when(parametersMock).getString("CLASS"); + PottsCellFlyStem cell = + new PottsCellFlyStem(baseContainer, locationMock, parametersMock, links); + PottsCellContainer container = + cell.make(cellID, State.PROLIFERATIVE, random, cellPop, cellCriticalVolume); + + assertAll( + () -> assertNotNull(container), + () -> assertEquals(cellID, container.parent), + () -> assertEquals(cellPop, container.pop), + () -> assertEquals(cellAge, container.age), + () -> assertEquals(cellDivisions + 1, container.divisions), + () -> assertEquals(State.PROLIFERATIVE, container.state), + () -> assertEquals(container.phase, Phase.UNDEFINED), + () -> assertEquals(0, container.voxels), + () -> assertNull(container.regionVoxels), + () -> assertEquals(cellCriticalVolume, container.criticalVolume), + () -> assertEquals(cellCriticalHeight, container.criticalHeight, EPSILON), + () -> assertNull(container.criticalRegionVolumes), + () -> assertNull(container.criticalRegionHeights)); + } + + @Test + void make_noDaughterCellCriticalVolume_throwsUnsupportedOperationException() { + doReturn("fly-stem-wt").when(parametersMock).getString("CLASS"); + PottsCellFlyStem cell = + new PottsCellFlyStem(baseContainer, locationMock, parametersMock, links); + assertThrows( + UnsupportedOperationException.class, + () -> cell.make(cellID, State.PROLIFERATIVE, random)); + } + + @Test + void setStateModule_called_createsProliferationModuleOrSetsNull() { + doReturn("fly-stem-wt").when(parametersMock).getString("CLASS"); + PottsCellFlyStem cell = + new PottsCellFlyStem(baseContainer, locationMock, parametersMock, links); + for (State state : State.values()) { + if (state != State.PROLIFERATIVE) { + cell.setStateModule(state); + assertNull(cell.getModule()); + } + } + } + + @Test + void getStemType_called_returnsCorrectStemType() { + doReturn("fly-stem-wt").when(parametersMock).getString("CLASS"); + PottsCellFlyStem cell = + new PottsCellFlyStem(baseContainer, locationMock, parametersMock, links); + assertEquals(PottsCellFlyStem.StemType.WT, cell.getStemType()); + doReturn("fly-stem-mudmut").when(parametersMock).getString("CLASS"); + cell = new PottsCellFlyStem(baseContainer, locationMock, parametersMock, links); + assertEquals(PottsCellFlyStem.StemType.MUDMUT, cell.getStemType()); + } + + @Test + void getApicalAxis_notSet_returnsDefault() { + doReturn("fly-stem-wt").when(parametersMock).getString("CLASS"); + PottsCellFlyStem cell = + new PottsCellFlyStem(baseContainer, locationMock, parametersMock, links); + assertEquals(new Vector(0, 1, 0), cell.getApicalAxis()); + } + + @Test + void getApicalAxis_set_returnsStoredAxis() { + doReturn("fly-stem-wt").when(parametersMock).getString("CLASS"); + PottsCellFlyStem cell = + new PottsCellFlyStem(baseContainer, locationMock, parametersMock, links); + Vector custom = new Vector(1, 2, 3); + cell.setApicalAxis(custom); + assertEquals(custom, cell.getApicalAxis()); + } +} diff --git a/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java b/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java new file mode 100644 index 000000000..d32c0fada --- /dev/null +++ b/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java @@ -0,0 +1,856 @@ +package arcade.potts.agent.module; + +import java.util.ArrayList; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.mockito.MockedStatic; +import org.mockito.Mockito; +import sim.util.Double3D; +import ec.util.MersenneTwisterFast; +import arcade.core.env.grid.Grid; +import arcade.core.util.GrabBag; +import arcade.core.util.MiniBox; +import arcade.core.util.Parameters; +import arcade.core.util.Plane; +import arcade.core.util.Vector; +import arcade.core.util.distributions.NormalDistribution; +import arcade.core.util.distributions.UniformDistribution; +import arcade.potts.agent.cell.PottsCellContainer; +import arcade.potts.agent.cell.PottsCellFactory; +import arcade.potts.agent.cell.PottsCellFlyStem; +import arcade.potts.env.location.PottsLocation; +import arcade.potts.env.location.PottsLocation2D; +import arcade.potts.env.location.Voxel; +import arcade.potts.sim.Potts; +import arcade.potts.sim.PottsSimulation; +import arcade.potts.util.PottsEnums.Phase; +import arcade.potts.util.PottsEnums.State; +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.ArgumentMatchers.any; +import static org.mockito.ArgumentMatchers.anyDouble; +import static org.mockito.ArgumentMatchers.anyInt; +import static org.mockito.ArgumentMatchers.eq; +import static org.mockito.ArgumentMatchers.isNull; +import static org.mockito.Mockito.*; +import static arcade.potts.util.PottsEnums.State; + +public class PottsModuleFlyStemProliferationTest { + PottsCellFlyStem stemCell; + + PottsModuleFlyStemProliferation module; + + PottsLocation2D stemLoc; + + PottsLocation daughterLoc; + + Parameters parameters; + + PottsSimulation sim; + + Potts potts; + + Grid grid; + + PottsCellFactory factory; + + MersenneTwisterFast random; + + NormalDistribution dist; + + float EPSILON = 1e-6f; + + @BeforeEach + public final void setup() { + // Core mocks + stemCell = mock(PottsCellFlyStem.class); + parameters = mock(Parameters.class); + dist = mock(NormalDistribution.class); + sim = mock(PottsSimulation.class); + potts = mock(Potts.class); + grid = mock(Grid.class); + factory = mock(PottsCellFactory.class); + random = mock(MersenneTwisterFast.class); + + // Location mocks + stemLoc = mock(PottsLocation2D.class); + daughterLoc = mock(PottsLocation.class); + + // Wire simulation + when(((PottsSimulation) sim).getPotts()).thenReturn(potts); + potts.ids = new int[1][1][1]; + potts.regions = new int[1][1][1]; + when(sim.getGrid()).thenReturn(grid); + when(sim.getCellFactory()).thenReturn(factory); + when(sim.getSchedule()).thenReturn(mock(sim.engine.Schedule.class)); + when(sim.getID()).thenReturn(42); + + // Wire cell + when(stemCell.getLocation()).thenReturn(stemLoc); + when(stemCell.getParameters()).thenReturn(parameters); + when(stemLoc.split(eq(random), any(Plane.class))).thenReturn(daughterLoc); + + // Default centroid and volume values (sometimes overridden in tests) + when(stemLoc.getVolume()).thenReturn(10.0); + when(daughterLoc.getVolume()).thenReturn(5.0); + when(stemLoc.getCentroid()).thenReturn(new double[] {0, 1.0, 0}); + when(daughterLoc.getCentroid()).thenReturn(new double[] {0, 1.6, 0}); + + // Parameter stubs (sometimes overridden in tests) + when(parameters.getDistribution("proliferation/DIV_ROTATION_DISTRIBUTION")) + .thenReturn(dist); + when(dist.nextDouble()).thenReturn(0.1); + when(parameters.getString("proliferation/DIFFERENTIATION_RULESET")).thenReturn("volume"); + when(parameters.getDouble("proliferation/DIFFERENTIATION_RULESET_EQUALITY_RANGE")) + .thenReturn(0.5); + + // Link selection + GrabBag links = mock(GrabBag.class); + when(stemCell.getLinks()).thenReturn(links); + when(links.next(random)).thenReturn(2); + + // Other defaults + when(stemCell.getPop()).thenReturn(3); + when(stemCell.getCriticalVolume()).thenReturn(100.0); + } + + @AfterEach + final void tearDown() { + Mockito.framework().clearInlineMocks(); + } + + // Constructor tests + + @Test + public void constructor_volumeRuleset_setsExpectedFields() { + when(parameters.getString("proliferation/DIFFERENTIATION_RULESET")).thenReturn("volume"); + when(parameters.getDouble("proliferation/DIFFERENTIATION_RULESET_EQUALITY_RANGE")) + .thenReturn(0.42); + module = new PottsModuleFlyStemProliferation(stemCell); + + assertNotNull(module.splitDirectionDistribution); + assertEquals("volume", module.differentiationRuleset); + assertEquals(0.42, module.range, EPSILON); + assertEquals(arcade.potts.util.PottsEnums.Phase.UNDEFINED, module.phase); + } + + @Test + public void constructor_locationRuleset_setsExpectedFields() { + when(parameters.getString("proliferation/DIFFERENTIATION_RULESET")).thenReturn("location"); + when(parameters.getDouble("proliferation/DIFFERENTIATION_RULESET_EQUALITY_RANGE")) + .thenReturn(0.99); + module = new PottsModuleFlyStemProliferation(stemCell); + + assertNotNull(module.splitDirectionDistribution); + assertEquals("location", module.differentiationRuleset); + assertEquals(0.99, module.range, EPSILON); + assertEquals(arcade.potts.util.PottsEnums.Phase.UNDEFINED, module.phase); + } + + // Static method tests + + @Test + public void getSmallerLocation_locationsDifferentSizes_returnsSmallerLocation() { + PottsLocation loc1 = mock(PottsLocation.class); + PottsLocation loc2 = mock(PottsLocation.class); + when(loc1.getVolume()).thenReturn(5.0); + when(loc2.getVolume()).thenReturn(10.0); + + PottsLocation result = PottsModuleFlyStemProliferation.getSmallerLocation(loc1, loc2); + assertEquals(loc1, result); + } + + @Test + public void getSmallerLocation_locationsSameSize_returnsSecondLocation() { + PottsLocation loc1 = mock(PottsLocation.class); + PottsLocation loc2 = mock(PottsLocation.class); + when(loc1.getVolume()).thenReturn(10.0); + when(loc2.getVolume()).thenReturn(10.0); + + PottsLocation result = PottsModuleFlyStemProliferation.getSmallerLocation(loc1, loc2); + assertEquals(loc2, result); + } + + @Test + public void getBasalLocation_centroidsDifferent_returnsBasalCentroid() { + PottsLocation loc1 = mock(PottsLocation.class); + PottsLocation loc2 = mock(PottsLocation.class); + when(loc1.getCentroid()).thenReturn(new double[] {0, 2, 0}); + when(loc2.getCentroid()).thenReturn(new double[] {0, 1, 0}); + Vector apicalAxis = new Vector(0, 1, 0); + + PottsLocation result = + PottsModuleFlyStemProliferation.getBasalLocation(loc1, loc2, apicalAxis); + assertEquals(loc1, result); + } + + @Test + public void getBasalLocation_centroidsSame_returnsFirstLocation() { + PottsLocation loc1 = mock(PottsLocation.class); + PottsLocation loc2 = mock(PottsLocation.class); + when(loc1.getCentroid()).thenReturn(new double[] {0, 2, 0}); + when(loc2.getCentroid()).thenReturn(new double[] {0, 2, 0}); + Vector apicalAxis = new Vector(0, 1, 0); + + PottsLocation result = + PottsModuleFlyStemProliferation.getBasalLocation(loc1, loc2, apicalAxis); + assertEquals(loc1, result); + } + + @Test + public void centroidsWithinRangeAlongApicalAxis_withinRange_returnsTrue() { + double[] centroid1 = new double[] {0, 1.0, 0}; + double[] centroid2 = new double[] {0, 1.3, 0}; + Vector apicalAxis = new Vector(0, 1, 0); // projecting along y-axis + double range = 0.5; + + module = new PottsModuleFlyStemProliferation(stemCell); + boolean result = + PottsModuleFlyStemProliferation.centroidsWithinRangeAlongApicalAxis( + centroid1, centroid2, apicalAxis, range); + + assertTrue(result); + } + + @Test + public void centroidsWithinRangeAlongApicalAxis_equalToRange_returnsTrue() { + double[] centroid1 = new double[] {0, 1.0, 0}; + double[] centroid2 = new double[] {0, 1.5, 0}; + Vector apicalAxis = new Vector(0, 1, 0); + double range = 0.5; + + module = new PottsModuleFlyStemProliferation(stemCell); + boolean result = + PottsModuleFlyStemProliferation.centroidsWithinRangeAlongApicalAxis( + centroid1, centroid2, apicalAxis, range); + + assertTrue(result); + } + + @Test + public void centroidsWithinRangeAlongApicalAxis_outsideRange_returnsFalse() { + double[] centroid1 = new double[] {0, 1.0, 0}; + double[] centroid2 = new double[] {0, 1.6, 0}; + Vector apicalAxis = new Vector(0, 1, 0); + double range = 0.5; + + module = new PottsModuleFlyStemProliferation(stemCell); + boolean result = + PottsModuleFlyStemProliferation.centroidsWithinRangeAlongApicalAxis( + centroid1, centroid2, apicalAxis, range); + + assertFalse(result); + } + + @Test + public void centroidsWithinRangeAlongApicalAxis_nonYAxis_returnsCorrectly() { + double[] centroid1 = new double[] {1.0, 0.0, 0.0}; + double[] centroid2 = new double[] {1.6, 0.0, 0.0}; + Vector apicalAxis = new Vector(1, 0, 0); // projecting along x-axis + double range = 0.6; + + module = new PottsModuleFlyStemProliferation(stemCell); + boolean result = + PottsModuleFlyStemProliferation.centroidsWithinRangeAlongApicalAxis( + centroid1, centroid2, apicalAxis, range); + + assertTrue(result); + } + + // Split location tests + + @Test + public void getCellSplitVoxel_WT_callsLocationOffsetWithCorrectParams() { + ArrayList expectedOffset = new ArrayList<>(); + expectedOffset.add(50); // WT.splitOffsetPercentX + expectedOffset.add(75); // WT.splitOffsetPercentY + + when(stemCell.getApicalAxis()).thenReturn(new Vector(0, 1, 0)); + when(stemCell.getLocation()).thenReturn(stemLoc); + when(stemLoc.getOffsetInApicalFrame2D(eq(expectedOffset), any(Vector.class))) + .thenReturn(new Voxel(0, 0, 0)); + + PottsModuleFlyStemProliferation.getCellSplitVoxel( + PottsCellFlyStem.StemType.WT, stemCell, stemCell.getApicalAxis()); + verify(stemLoc).getOffsetInApicalFrame2D(eq(expectedOffset), any(Vector.class)); + } + + @Test + public void getCellSplitVoxel_MUDMUT_callsLocationOffsetWithCorrectParams() { + ArrayList expectedOffset = new ArrayList<>(); + expectedOffset.add(50); // MUDMUT.splitOffsetPercentX + expectedOffset.add(50); // MUDMUT.splitOffsetPercentY + + when(stemCell.getApicalAxis()).thenReturn(new Vector(0, 1, 0)); + when(stemCell.getLocation()).thenReturn(stemLoc); + when(stemLoc.getOffsetInApicalFrame2D(eq(expectedOffset), any(Vector.class))) + .thenReturn(new Voxel(0, 0, 0)); + + PottsModuleFlyStemProliferation.getCellSplitVoxel( + PottsCellFlyStem.StemType.MUDMUT, stemCell, stemCell.getApicalAxis()); + verify(stemLoc).getOffsetInApicalFrame2D(eq(expectedOffset), any(Vector.class)); + } + + // Division plane tests + + @Test + public void getWTDivisionPlaneWithRotationalVariance_rotatesCorrectlyAndReturnsPlane() { + Vector apicalAxis = new Vector(0, 1, 0); + when(stemCell.getApicalAxis()).thenReturn(apicalAxis); + + double baseRotation = PottsCellFlyStem.StemType.WT.splitDirectionRotation; // 90 + double offsetRotation = -5.0; + + Voxel splitVoxel = new Voxel(3, 4, 5); + ArrayList expectedOffset = new ArrayList<>(); + expectedOffset.add(50); // WT x offset percent + expectedOffset.add(80); // WT y offset percent + + module = new PottsModuleFlyStemProliferation(stemCell); + + // Apply both rotations manually to get expected result + Vector afterBaseRotation = + Vector.rotateVectorAroundAxis(apicalAxis, new Vector(0, 0, 1), baseRotation); + Vector expectedNormal = + Vector.rotateVectorAroundAxis( + afterBaseRotation, new Vector(0, 0, 1), offsetRotation); + + when(stemLoc.getOffsetInApicalFrame2D(any(), eq(expectedNormal))).thenReturn(splitVoxel); + + Plane result = module.getWTDivisionPlaneWithRotationalVariance(stemCell, offsetRotation); + + Double3D refPoint = result.getReferencePoint(); + assertEquals(3.0, refPoint.x, EPSILON); + assertEquals(4.0, refPoint.y, EPSILON); + assertEquals(5.0, refPoint.z, EPSILON); + + Vector resultNormal = result.getUnitNormalVector(); + assertEquals(expectedNormal.getX(), resultNormal.getX(), EPSILON); + assertEquals(expectedNormal.getY(), resultNormal.getY(), EPSILON); + assertEquals(expectedNormal.getZ(), resultNormal.getZ(), EPSILON); + } + + @Test + public void getMUDDivisionPlane_returnsRotatedPlaneWithCorrectNormal() { + Vector apicalAxis = new Vector(0, 1, 0); + when(stemCell.getApicalAxis()).thenReturn(apicalAxis); + + Vector expectedNormal = new Vector(1.0, 0.0, 0.0); + + Voxel splitVoxel = new Voxel(7, 8, 9); + ArrayList expectedOffset = new ArrayList<>(); + expectedOffset.add(50); // MUDMUT x offset percent + expectedOffset.add(50); // MUDMUT y offset percent + when(stemLoc.getOffsetInApicalFrame2D(any(), any())).thenReturn(splitVoxel); + + module = new PottsModuleFlyStemProliferation(stemCell); + Plane result = module.getMUDDivisionPlane(stemCell); + + assertEquals(new Double3D(7, 8, 9), result.getReferencePoint()); + Vector resultNormal = result.getUnitNormalVector(); + assertEquals(expectedNormal.getX(), resultNormal.getX(), EPSILON); + assertEquals(expectedNormal.getY(), resultNormal.getY(), EPSILON); + assertEquals(expectedNormal.getZ(), resultNormal.getZ(), EPSILON); + } + + @Test + public void sampleDivisionPlaneOffset_callsNextDoubleOnDistribution() { + when(dist.nextDouble()).thenReturn(12.34); + + module = new PottsModuleFlyStemProliferation(stemCell); + double offset = module.sampleDivisionPlaneOffset(); + + assertEquals(12.34, offset, EPSILON); + } + + @Test + public void chooseDivisionPlane_WT_callsWTVariant() { + when(stemCell.getStemType()).thenReturn(PottsCellFlyStem.StemType.WT); + when(dist.nextDouble()).thenReturn(12.0); // this can be any value + + module = spy(new PottsModuleFlyStemProliferation(stemCell)); + + Plane expectedPlane = mock(Plane.class); + doReturn(expectedPlane) + .when(module) + .getWTDivisionPlaneWithRotationalVariance(stemCell, 12.0); + + Plane result = module.chooseDivisionPlane(stemCell); + + assertEquals(expectedPlane, result); + verify(module).getWTDivisionPlaneWithRotationalVariance(stemCell, 12.0); + verify(module, never()).getMUDDivisionPlane(any()); + } + + @Test + public void chooseDivisionPlane_MUDMUT_withLowOffset_callsWTVariant() { + when(stemCell.getStemType()).thenReturn(PottsCellFlyStem.StemType.MUDMUT); + when(dist.nextDouble()).thenReturn(10.0); // abs(offset) < 45 → WT logic + + module = spy(new PottsModuleFlyStemProliferation(stemCell)); + + Plane expectedPlane = mock(Plane.class); + doReturn(expectedPlane) + .when(module) + .getWTDivisionPlaneWithRotationalVariance(stemCell, 10.0); + + Plane result = module.chooseDivisionPlane(stemCell); + + assertEquals(expectedPlane, result); + verify(module).getWTDivisionPlaneWithRotationalVariance(stemCell, 10.0); + verify(module, never()).getMUDDivisionPlane(any()); + } + + @Test + public void chooseDivisionPlane_MUDMUT_withHighOffset_callsMUDVariant() { + when(stemCell.getStemType()).thenReturn(PottsCellFlyStem.StemType.MUDMUT); + when(dist.nextDouble()).thenReturn(60.0); // abs(offset) ≥ 45 → MUD logic + + module = spy(new PottsModuleFlyStemProliferation(stemCell)); + + Plane expectedPlane = mock(Plane.class); + doReturn(expectedPlane).when(module).getMUDDivisionPlane(stemCell); + + Plane result = module.chooseDivisionPlane(stemCell); + + assertEquals(expectedPlane, result); + verify(module).getMUDDivisionPlane(stemCell); + verify(module, never()).getWTDivisionPlaneWithRotationalVariance(any(), anyDouble()); + } + + // Step tests + @Test + public void step_volumeBelowCheckpoint_updatesTargetdoesNotDividePhaseStaysUndefined() { + when(parameters.getInt("proliferation/DYNAMIC_GROWTH_RATE_VOLUME")).thenReturn(0); + when(parameters.getDouble("proliferation/CELL_GROWTH_RATE")).thenReturn(4.0); + when(parameters.getDouble("proliferation/SIZE_TARGET")).thenReturn(1.2); + when(stemCell.getCriticalVolume()).thenReturn(100.0); + when(stemLoc.getVolume()).thenReturn(50.0); // 50 < 1.2 * 100 → below checkpoint + + module = new PottsModuleFlyStemProliferation(stemCell); + + module.step(random, sim); + + verify(stemCell).updateTarget(eq(4.0), anyDouble()); + // Checking functions within addCell are never called + // (checking addCell directly would require making module a mock) + verify(sim, never()).getPotts(); + verify(grid, never()).addObject(any(), any()); + verify(potts, never()).register(any()); + assertEquals(Phase.UNDEFINED, module.phase); + } + + @Test + public void step_volumeAtCheckpoint_callsAddCellPhaseStaysUndefined() { + // Trigger division + when(parameters.getInt("proliferation/DYNAMIC_GROWTH_RATE_VOLUME")).thenReturn(0); + when(parameters.getDouble("proliferation/CELL_GROWTH_RATE")).thenReturn(4.0); + when(parameters.getDouble("proliferation/SIZE_TARGET")).thenReturn(1.2); + when(stemCell.getCriticalVolume()).thenReturn(100.0); + when(stemCell.getVolume()).thenReturn(120.0); // ≥ 1.2 * 100 + + // Needed by calculateGMCDaughterCellCriticalVolume(...) + when(stemCell.getStemType()).thenReturn(PottsCellFlyStem.StemType.WT); + + // Plane/voxel path (chooseDivisionPlane -> WT -> getWTDivisionPlaneWithRotationalVariance) + when(parameters.getString("proliferation/APICAL_AXIS_RULESET")).thenReturn("global"); + when(stemCell.getApicalAxis()).thenReturn(new Vector(0, 1, 0)); + when(stemLoc.getOffsetInApicalFrame2D(any(), any(Vector.class))) + .thenReturn(new Voxel(1, 2, 3)); + + // Differentiation rule + when(parameters.getString("proliferation/DIFFERENTIATION_RULESET")).thenReturn("volume"); + when(parameters.getDouble("proliferation/DIFFERENTIATION_RULESET_EQUALITY_RANGE")) + .thenReturn(0.5); + + // Cell creation path used by scheduleNewCell(...) + PottsCellContainer container = mock(PottsCellContainer.class); + PottsCellFlyStem newCell = mock(PottsCellFlyStem.class); + when(stemCell.make(anyInt(), eq(State.PROLIFERATIVE), eq(random), anyInt(), anyDouble())) + .thenReturn(container); + when(container.convert(eq(factory), eq(daughterLoc), eq(random))).thenReturn(newCell); + + // split(...) inside addCell + when(stemLoc.split(eq(random), any(Plane.class))).thenReturn(daughterLoc); + + module = new PottsModuleFlyStemProliferation(stemCell); + module.step(random, sim); + + verify(stemCell).updateTarget(eq(4.0), anyDouble()); + verify(stemLoc).split(eq(random), any(Plane.class)); // addCell ran + verify(grid).addObject(any(), isNull()); // scheduled new cell + verify(potts).register(any()); // registered new cell + assertEquals(Phase.UNDEFINED, module.phase); // remains UNDEFINED + } + + // Differentiation rule tests + + @Test + public void daughterStem_stemTypeWT_returnsFalse() { + when(stemCell.getStemType()).thenReturn(PottsCellFlyStem.StemType.WT); + + module = new PottsModuleFlyStemProliferation(stemCell); + boolean result = module.daughterStem(stemLoc, daughterLoc); + + assertFalse(result); + } + + @Test + public void daughterStem_volumeRule_differenceWithinRange_returnsTrue() { + when(stemCell.getStemType()).thenReturn(PottsCellFlyStem.StemType.MUDMUT); + when(parameters.getString("proliferation/DIFFERENTIATION_RULESET")).thenReturn("volume"); + when(parameters.getDouble("proliferation/DIFFERENTIATION_RULESET_EQUALITY_RANGE")) + .thenReturn(1.0); + when(stemLoc.getVolume()).thenReturn(10.0); + when(daughterLoc.getVolume()).thenReturn(10.5); // difference = 0.5 < 1.0 + + module = new PottsModuleFlyStemProliferation(stemCell); + boolean result = module.daughterStem(stemLoc, daughterLoc); + + assertTrue(result); + } + + @Test + public void daughterStem_volumeRule_differenceOutsideRange_returnsFalse() { + when(stemCell.getStemType()).thenReturn(PottsCellFlyStem.StemType.MUDMUT); + when(parameters.getString("proliferation/DIFFERENTIATION_RULESET")).thenReturn("volume"); + when(parameters.getDouble("proliferation/DIFFERENTIATION_RULESET_EQUALITY_RANGE")) + .thenReturn(0.5); + when(stemLoc.getVolume()).thenReturn(10.0); + when(daughterLoc.getVolume()).thenReturn(11.0); // difference = 1.0 > 0.5 + + module = new PottsModuleFlyStemProliferation(stemCell); + boolean result = module.daughterStem(stemLoc, daughterLoc); + + assertFalse(result); + } + + @Test + public void daughterStem_locationRule_differenceWithinRange_returnsTrue() { + when(stemCell.getStemType()).thenReturn(PottsCellFlyStem.StemType.MUDMUT); + when(parameters.getString("proliferation/DIFFERENTIATION_RULESET")).thenReturn("location"); + when(parameters.getDouble("proliferation/DIFFERENTIATION_RULESET_EQUALITY_RANGE")) + .thenReturn(0.5); + when(stemLoc.getCentroid()).thenReturn(new double[] {0, 1.0, 0}); + when(daughterLoc.getCentroid()).thenReturn(new double[] {0, 1.3, 0}); // difference = 0.3 + when(stemCell.getApicalAxis()).thenReturn(new Vector(0, 1, 0)); + + module = new PottsModuleFlyStemProliferation(stemCell); + boolean result = module.daughterStem(stemLoc, daughterLoc); + + assertTrue(result); + } + + @Test + public void daughterStem_locationRule_differenceOutsideRange_returnsFalse() { + when(stemCell.getStemType()).thenReturn(PottsCellFlyStem.StemType.MUDMUT); + when(parameters.getString("proliferation/DIFFERENTIATION_RULESET")).thenReturn("location"); + when(parameters.getDouble("proliferation/DIFFERENTIATION_RULESET_EQUALITY_RANGE")) + .thenReturn(0.5); + when(stemLoc.getCentroid()).thenReturn(new double[] {0, 1.0, 0}); + when(daughterLoc.getCentroid()).thenReturn(new double[] {0, 1.7, 0}); // difference = 0.7 + when(stemCell.getApicalAxis()).thenReturn(new Vector(0, 1, 0)); + + module = new PottsModuleFlyStemProliferation(stemCell); + boolean result = module.daughterStem(stemLoc, daughterLoc); + + assertFalse(result); + } + + @Test + public void daughterStem_invalidRule_throwsException() { + when(stemCell.getStemType()).thenReturn(PottsCellFlyStem.StemType.MUDMUT); + when(parameters.getString("proliferation/DIFFERENTIATION_RULESET")).thenReturn("banana"); + when(parameters.getDouble("proliferation/DIFFERENTIATION_RULESET_EQUALITY_RANGE")) + .thenReturn(0.5); + when(stemLoc.getCentroid()).thenReturn(new double[] {0, 1.0, 0}); + when(daughterLoc.getCentroid()).thenReturn(new double[] {0, 1.2, 0}); + + module = new PottsModuleFlyStemProliferation(stemCell); + assertThrows( + IllegalArgumentException.class, () -> module.daughterStem(stemLoc, daughterLoc)); + } + + // Apical axis rule tests + + @Test + public void getDaughterCellApicalAxis_global_returnsApicalAxis() { + Vector expectedAxis = new Vector(1.0, 2.0, 3.0); + when(parameters.getString("proliferation/APICAL_AXIS_RULESET")).thenReturn("global"); + when(stemCell.getApicalAxis()).thenReturn(expectedAxis); + + module = new PottsModuleFlyStemProliferation(stemCell); + Vector result = module.getDaughterCellApicalAxis(random); + + assertEquals(expectedAxis.getX(), result.getX(), EPSILON); + assertEquals(expectedAxis.getY(), result.getY(), EPSILON); + assertEquals(expectedAxis.getZ(), result.getZ(), EPSILON); + } + + @Test + public void getDaughterCellApicalAxis_rotation_returnsRotatedAxis() { + when(parameters.getString("proliferation/APICAL_AXIS_RULESET")).thenReturn("rotation"); + + NormalDistribution rotDist = mock(NormalDistribution.class); + when(rotDist.nextDouble()).thenReturn(30.0); // rotation angle + when(parameters.getDistribution("proliferation/APICAL_AXIS_ROTATION_DISTRIBUTION")) + .thenReturn(rotDist); + + Vector originalAxis = new Vector(0, 1, 0); + when(stemCell.getApicalAxis()).thenReturn(originalAxis); + + module = new PottsModuleFlyStemProliferation(stemCell); + Vector result = module.getDaughterCellApicalAxis(random); + + Vector expected = Vector.rotateVectorAroundAxis(originalAxis, new Vector(0, 0, 1), 30.0); + assertEquals(expected.getX(), result.getX(), EPSILON); + assertEquals(expected.getY(), result.getY(), EPSILON); + assertEquals(expected.getZ(), result.getZ(), EPSILON); + } + + @Test + public void getDaughterCellApicalAxis_rotationwithInvalidDistribution_throwsException() { + when(parameters.getString("proliferation/APICAL_AXIS_RULESET")).thenReturn("rotation"); + when(parameters.getDistribution("proliferation/APICAL_AXIS_ROTATION_DISTRIBUTION")) + .thenReturn(mock(UniformDistribution.class)); + + module = new PottsModuleFlyStemProliferation(stemCell); + assertThrows( + IllegalArgumentException.class, () -> module.getDaughterCellApicalAxis(random)); + } + + @Test + public void getDaughterCellApicalAxis_uniform_returnsRotatedAxis() { + when(parameters.getString("proliferation/APICAL_AXIS_RULESET")).thenReturn("uniform"); + + UniformDistribution rotDist = mock(UniformDistribution.class); + when(rotDist.nextDouble()).thenReturn(200.0); // rotation angle + when(parameters.getDistribution("proliferation/APICAL_AXIS_ROTATION_DISTRIBUTION")) + .thenReturn(rotDist); + + Vector originalAxis = new Vector(0, 1, 0); + when(stemCell.getApicalAxis()).thenReturn(originalAxis); + + module = new PottsModuleFlyStemProliferation(stemCell); + Vector result = module.getDaughterCellApicalAxis(random); + + Vector expected = Vector.rotateVectorAroundAxis(originalAxis, new Vector(0, 0, 1), 200.0); + assertEquals(expected.getX(), result.getX(), EPSILON); + assertEquals(expected.getY(), result.getY(), EPSILON); + assertEquals(expected.getZ(), result.getZ(), EPSILON); + } + + @Test + public void getDaughterCellApicalAxis_uniformwithInvalidDistribution_throwsException() { + when(parameters.getString("proliferation/APICAL_AXIS_RULESET")).thenReturn("uniform"); + when(parameters.getDistribution("proliferation/APICAL_AXIS_ROTATION_DISTRIBUTION")) + .thenReturn(mock(NormalDistribution.class)); + + module = new PottsModuleFlyStemProliferation(stemCell); + assertThrows( + IllegalArgumentException.class, () -> module.getDaughterCellApicalAxis(random)); + } + + // Critical volume calculation tests + + @Test + public void calculateGMCDaughterCellCriticalVolume_volumeBasedOff_returnsMaxCritVol() { + when(stemCell.getCriticalVolume()).thenReturn(100.0); + when(stemCell.getStemType()).thenReturn(PottsCellFlyStem.StemType.WT); + when(parameters.getDouble("proliferation/SIZE_TARGET")).thenReturn(1.2); + // WT has proportion = 0.2 + + module = new PottsModuleFlyStemProliferation(stemCell); + when(parameters.getInt("proliferation/VOLUME_BASED_CRITVOL")).thenReturn(0); + + double result = module.calculateGMCDaughterCellCriticalVolume(daughterLoc, sim, 3); + assertEquals((100 * .25 * 1.2), result, EPSILON); // 100 * 0.25 * 1.2 + } + + @Test + public void calculateGMCDaughterCellCriticalVolume_volumeBasedOn_returnsScaledValue() { + PottsLocation gmcLoc = mock(PottsLocation.class); + when(gmcLoc.getVolume()).thenReturn(50.0); + when(stemCell.getCriticalVolume()).thenReturn(100.0); + when(stemCell.getStemType()).thenReturn(PottsCellFlyStem.StemType.WT); + + MiniBox popParametersMiniBox = mock(MiniBox.class); + when(popParametersMiniBox.getDouble("proliferation/SIZE_TARGET")).thenReturn(2.0); + + when(sim.getCellFactory()).thenReturn(factory); + when(factory.getParameters(3)).thenReturn(popParametersMiniBox); + + when(parameters.getInt("proliferation/VOLUME_BASED_CRITICAL_VOLUME")).thenReturn(1); + when(parameters.getDouble("proliferation/VOLUME_BASED_CRITICAL_VOLUME_MULTIPLIER")) + .thenReturn(1.5); + + module = new PottsModuleFlyStemProliferation(stemCell); + + double result = module.calculateGMCDaughterCellCriticalVolume(gmcLoc, sim, 3); + assertEquals(75.0, result, EPSILON); // 50 * 1.5 + } + + // addCell integration tests + + @Test + public void addCell_WTVolumeSwap_swapsVoxelsAndCreatesNewCell() { + // Arrange: WT stem cell, using volume-based differentiation + when(stemCell.getStemType()).thenReturn(PottsCellFlyStem.StemType.WT); + when(parameters.getString("proliferation/APICAL_AXIS_RULESET")).thenReturn("global"); + when(stemCell.getApicalAxis()).thenReturn(new Vector(0, 1, 0)); + when(parameters.getDouble("proliferation/SIZE_TARGET")) + .thenReturn(1.0); // default for volume + when(parameters.getInt("proliferation/VOLUME_BASED_CRITICAL_VOLUME")) + .thenReturn(0); // use classic mode + + // Set up the condition that parent volume < daughter volume → stem/daughter swap required + when(stemLoc.getVolume()).thenReturn(5.0); + when(daughterLoc.getVolume()).thenReturn(10.0); + + // Stub division plane + Plane dummyPlane = mock(Plane.class); + when(dummyPlane.getUnitNormalVector()).thenReturn(new Vector(1, 0, 0)); + when(stemLoc.split(eq(random), eq(dummyPlane))).thenReturn(daughterLoc); + + // Stub cell creation + PottsCellContainer container = mock(PottsCellContainer.class); + PottsCellFlyStem newStemCell = mock(PottsCellFlyStem.class); + when(stemCell.make(eq(42), eq(State.PROLIFERATIVE), eq(random), eq(2), eq(25.0))) + .thenReturn(container); + when(container.convert(eq(factory), eq(daughterLoc), eq(random))).thenReturn(newStemCell); + + // Spy on the module so we can override plane selection + PottsModuleFlyStemProliferation module = spy(new PottsModuleFlyStemProliferation(stemCell)); + doReturn(dummyPlane) + .when(module) + .getWTDivisionPlaneWithRotationalVariance(eq(stemCell), anyDouble()); + + // Act: call addCell + try (MockedStatic mocked = mockStatic(PottsLocation.class)) { + module.addCell(random, sim); + + // Assert: verify voxels were swapped and new cell scheduled + mocked.verify(() -> PottsLocation.swapVoxels(stemLoc, daughterLoc)); + } + + // Assert: new stem cell was scheduled + verify(newStemCell).schedule(any()); + } + + @Test + public void addCell_WTVolumeNoSwap_doesNotSwapVoxelsAndCreatesNewCell() { + // Arrange: WT stem cell, using volume-based differentiation + when(stemCell.getStemType()).thenReturn(PottsCellFlyStem.StemType.WT); + when(parameters.getString("proliferation/APICAL_AXIS_RULESET")).thenReturn("global"); + when(stemCell.getApicalAxis()).thenReturn(new Vector(0, 1, 0)); + when(parameters.getDouble("proliferation/SIZE_TARGET")).thenReturn(1.0); + when(parameters.getInt("proliferation/VOLUME_BASED_CRITICAL_VOLUME")).thenReturn(0); + + // Set up the condition that parent volume > daughter volume → no swap + when(stemLoc.getVolume()).thenReturn(10.0); + when(daughterLoc.getVolume()).thenReturn(5.0); + + // Stub division plane + Plane dummyPlane = mock(Plane.class); + when(dummyPlane.getUnitNormalVector()).thenReturn(new Vector(1, 0, 0)); + when(stemLoc.split(eq(random), eq(dummyPlane))).thenReturn(daughterLoc); + + // Stub cell creation + PottsCellContainer container = mock(PottsCellContainer.class); + PottsCellFlyStem newStemCell = mock(PottsCellFlyStem.class); + when(stemCell.make(eq(42), eq(State.PROLIFERATIVE), eq(random), eq(2), eq(25.0))) + .thenReturn(container); + when(container.convert(eq(factory), eq(daughterLoc), eq(random))).thenReturn(newStemCell); + + // Spy and override division plane logic + PottsModuleFlyStemProliferation module = spy(new PottsModuleFlyStemProliferation(stemCell)); + doReturn(dummyPlane) + .when(module) + .getWTDivisionPlaneWithRotationalVariance(eq(stemCell), anyDouble()); + + // Act + try (MockedStatic mocked = mockStatic(PottsLocation.class)) { + module.addCell(random, sim); + + // Assert: swapVoxels should NOT be called + mocked.verify(() -> PottsLocation.swapVoxels(any(), any()), never()); + } + + // Assert: new stem cell was created and scheduled + verify(newStemCell).schedule(any()); + } + + @Test + public void addCell_MUDMUTOffsetAboveThreshold_createsStemCell() { + when(stemCell.getStemType()).thenReturn(PottsCellFlyStem.StemType.MUDMUT); + when(parameters.getString("proliferation/DIFFERENTIATION_RULESET")).thenReturn("volume"); + when(parameters.getString("proliferation/APICAL_AXIS_RULESET")).thenReturn("global"); + when(stemCell.getApicalAxis()).thenReturn(new Vector(0, 1, 0)); + when(dist.nextDouble()).thenReturn(60.0); // triggers MUD plane + + sim = mock(PottsSimulation.class); + potts = mock(Potts.class); + factory = mock(PottsCellFactory.class); + grid = mock(Grid.class); + when(sim.getPotts()).thenReturn(potts); + when(sim.getGrid()).thenReturn(grid); + when(sim.getCellFactory()).thenReturn(factory); + when(sim.getSchedule()).thenReturn(mock(sim.engine.Schedule.class)); + when(sim.getID()).thenReturn(42); + potts.ids = new int[1][1][1]; + potts.regions = new int[1][1][1]; + + PottsCellContainer container = mock(PottsCellContainer.class); + PottsCellFlyStem newCell = mock(PottsCellFlyStem.class); + when(stemCell.make(eq(42), eq(State.PROLIFERATIVE), eq(random), eq(3), eq(100.0))) + .thenReturn(container); + when(container.convert(eq(factory), eq(daughterLoc), eq(random))).thenReturn(newCell); + when(stemCell.getCriticalVolume()).thenReturn(100.0); + when(stemCell.getPop()).thenReturn(3); + + module = spy(new PottsModuleFlyStemProliferation(stemCell)); + Plane dummyPlane = mock(Plane.class); + doReturn(dummyPlane).when(module).getMUDDivisionPlane(eq(stemCell)); + when(stemLoc.split(eq(random), eq(dummyPlane))).thenReturn(daughterLoc); + doReturn(true).when(module).daughterStem(any(), any()); + + module.addCell(random, sim); + + verify(newCell).schedule(any()); + } + + @Test + public void addCell_MUDMUTOffsetBelowThreshold_createsGMCWithVolumeSwap() { + when(stemCell.getStemType()).thenReturn(PottsCellFlyStem.StemType.MUDMUT); + when(parameters.getString("proliferation/DIFFERENTIATION_RULESET")).thenReturn("volume"); + when(parameters.getString("proliferation/APICAL_AXIS_RULESET")).thenReturn("global"); + when(stemCell.getApicalAxis()).thenReturn(new Vector(0, 1, 0)); + when(dist.nextDouble()).thenReturn(10.0); // below 45 threshold + + when(stemLoc.getVolume()).thenReturn(5.0); + when(daughterLoc.getVolume()).thenReturn(10.0); // triggers swap + + PottsCellContainer container = mock(PottsCellContainer.class); + PottsCellFlyStem newCell = mock(PottsCellFlyStem.class); + when(stemCell.make(eq(42), eq(State.PROLIFERATIVE), eq(random), anyInt(), anyDouble())) + .thenReturn(container); + when(container.convert(eq(factory), eq(daughterLoc), eq(random))).thenReturn(newCell); + when(stemCell.getCriticalVolume()).thenReturn(100.0); + when(stemCell.getPop()).thenReturn(3); + + module = spy(new PottsModuleFlyStemProliferation(stemCell)); + Plane dummyPlane = mock(Plane.class); + doReturn(dummyPlane) + .when(module) + .getWTDivisionPlaneWithRotationalVariance(eq(stemCell), anyDouble()); + when(stemLoc.split(eq(random), eq(dummyPlane))).thenReturn(daughterLoc); + doReturn(false).when(module).daughterStem(any(), any()); + + try (MockedStatic mocked = mockStatic(PottsLocation.class)) { + module.addCell(random, sim); + mocked.verify(() -> PottsLocation.swapVoxels(stemLoc, daughterLoc)); + } + + verify(newCell).schedule(any()); + } +} From 1935012c174cec018b481eb9c7d3891491de766c Mon Sep 17 00:00:00 2001 From: jannetty Date: Tue, 21 Oct 2025 14:22:40 -0700 Subject: [PATCH 25/59] moving volume-based growth regulation functions to VolumeBasedDivision module --- .../PottsModuleFlyGMCDifferentiation.java | 8 ++ .../PottsModuleFlyStemProliferation.java | 66 ++++------- ...oduleProliferationVolumeBasedDivision.java | 42 ++++++- ...eProliferationVolumeBasedDivisionTest.java | 112 +++++++++++++++++- 4 files changed, 177 insertions(+), 51 deletions(-) diff --git a/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java b/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java index 4405e45dc..4abe6368c 100644 --- a/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java +++ b/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java @@ -91,4 +91,12 @@ void addCell(MersenneTwisterFast random, Simulation sim) { differentiatedGMC.reset(potts.ids, potts.regions); differentiatedGMC.schedule(sim.getSchedule()); } + + public void updateGrowthRate() { + if (dynamicGrowthRateVolume == false) { + cellGrowthRate = cellGrowthRateBase; + } else if (dynamicGrowthRateVolume == true) { + updateVolumeBasedGrowthRate(); + } + } } diff --git a/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java b/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java index 84dc637f8..420cc05cb 100644 --- a/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java +++ b/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java @@ -1,5 +1,6 @@ package arcade.potts.agent.module; +import java.security.InvalidParameterException; import java.util.ArrayList; import sim.util.Double3D; import ec.util.MersenneTwisterFast; @@ -20,6 +21,9 @@ 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; @@ -29,18 +33,6 @@ public class PottsModuleFlyStemProliferation extends PottsModuleProliferationVol /** Threshold for critical volume size checkpoint. */ static final double SIZE_CHECKPOINT = 0.95; - /** - * Target ratio of critical volume for division size checkpoint (cell must reach CRITICAL_VOLUME - * * SIZE_TARGET * SIZE_CHECKPOINT to divide). - */ - double sizeTarget; - - /** Base growth rate for stem cells. */ - final double cellGrowthRateBase; - - /** Current growth rate for stem cells. */ - double cellGrowthRate; - /** Basal rate of apoptosis (ticks^-1). */ final double basalApoptosisRate; @@ -54,13 +46,11 @@ public class PottsModuleFlyStemProliferation extends PottsModuleProliferationVol final Distribution apicalAxisRotationDistribution; - final boolean dynamicGrowthRateVolume; - final boolean volumeBasedCriticalVolume; - final double volumeBasedCriticalVolumeMultiplier; + final boolean dynamicGrowthRateNBContact; - final double growthRateVolumeSensitivity; + final double volumeBasedCriticalVolumeMultiplier; /** * Range of values considered equal when determining daughter cell identity. ex. if ruleset is @@ -83,8 +73,6 @@ public PottsModuleFlyStemProliferation(PottsCellFlyStem cell) { Parameters parameters = cell.getParameters(); - sizeTarget = parameters.getDouble("proliferation/SIZE_TARGET"); - cellGrowthRateBase = parameters.getDouble("proliferation/CELL_GROWTH_RATE"); basalApoptosisRate = parameters.getDouble("proliferation/BASAL_APOPTOSIS_RATE"); splitDirectionDistribution = (NormalDistribution) @@ -97,17 +85,19 @@ public PottsModuleFlyStemProliferation(PottsCellFlyStem cell) { parameters.getDistribution( "proliferation/APICAL_AXIS_ROTATION_DISTRIBUTION"); - dynamicGrowthRateVolume = - (parameters.getInt("proliferation/DYNAMIC_GROWTH_RATE_VOLUME") != 0); - updateGrowthRate(); - volumeBasedCriticalVolume = (parameters.getInt("proliferation/VOLUME_BASED_CRITICAL_VOLUME") != 0); + dynamicGrowthRateNBContact = + (parameters.getInt("proliferation/DYNAMIC_GROWTH_RATE_NB_CONTACT") != 0); + + if (dynamicGrowthRateVolume && dynamicGrowthRateNBContact) { + throw new InvalidParameterException( + "Dynamic growth rate can be either volume-based or NB-contact-based, not both."); + } + volumeBasedCriticalVolumeMultiplier = (parameters.getDouble("proliferation/VOLUME_BASED_CRITICAL_VOLUME_MULTIPLIER")); - growthRateVolumeSensitivity = - parameters.getDouble("proliferation/GROWTH_RATE_VOLUME_SENSITIVITY"); setPhase(Phase.UNDEFINED); } @@ -138,29 +128,13 @@ public void addCell(MersenneTwisterFast random, Simulation sim) { } } - /** - * Updates the cell growth rate based on the current parameter settings. - * - *

If {@code dynamicGrowthRateVolume} is {@code false}, the growth rate is fixed at the base - * value specified in {@code cellGrowthRateBase}. If {@code dynamicGrowthRateVolume} is {@code - * true}, 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: - * - * 

-     *   growthRate = baseGrowthRate * (volume / criticalVolume) ^ sensitivity
-     *
- * - * This allows larger cells to grow faster, capturing volume-dependent growth dynamics. - */ - void updateGrowthRate() { - if (dynamicGrowthRateVolume == false) { + public void updateGrowthRate() { + if (dynamicGrowthRateVolume == true) { + updateVolumeBasedGrowthRate(); + } else if (dynamicGrowthRateNBContact == true) { + ; + } else { cellGrowthRate = cellGrowthRateBase; - } else if (dynamicGrowthRateVolume == true) { - double volume = cell.getLocation().getVolume(); - double Ka = cell.getCriticalVolume(); - cellGrowthRate = - cellGrowthRateBase * Math.pow((volume / Ka), growthRateVolumeSensitivity); } } diff --git a/src/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivision.java b/src/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivision.java index d121df3df..f6870e336 100644 --- a/src/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivision.java +++ b/src/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivision.java @@ -4,6 +4,7 @@ import arcade.core.sim.Simulation; import arcade.core.util.Parameters; import arcade.potts.agent.cell.PottsCell; +import arcade.potts.agent.cell.PottsCellFlyNeuron; import arcade.potts.util.PottsEnums.Phase; /** @@ -13,8 +14,11 @@ */ public abstract class PottsModuleProliferationVolumeBasedDivision extends PottsModuleProliferation { - /** Overall growth rate for cell (voxels/tick). */ - final double cellGrowthRate; + /** Base growth rate for cells (voxels/tick). */ + final double cellGrowthRateBase; + + /** Current growth rate for stem cells (voxels/tick). */ + double cellGrowthRate; /** * Target ratio of critical volume for division size checkpoint (cell must reach CRITICAL_VOLUME @@ -22,6 +26,10 @@ public abstract class PottsModuleProliferationVolumeBasedDivision extends PottsM */ final double sizeTarget; + final boolean dynamicGrowthRateVolume; + + final double growthRateVolumeSensitivity; + /** * Creates a proliferation module in which division is solely dependent on cell volume. * @@ -31,16 +39,42 @@ public PottsModuleProliferationVolumeBasedDivision(PottsCell cell) { super(cell); Parameters parameters = cell.getParameters(); sizeTarget = parameters.getDouble("proliferation/SIZE_TARGET"); - cellGrowthRate = parameters.getDouble("proliferation/CELL_GROWTH_RATE"); + cellGrowthRateBase = parameters.getDouble("proliferation/CELL_GROWTH_RATE"); + dynamicGrowthRateVolume = + (parameters.getInt("proliferation/DYNAMIC_GROWTH_RATE_VOLUME") != 0); + growthRateVolumeSensitivity = + parameters.getDouble("proliferation/GROWTH_RATE_VOLUME_SENSITIVITY"); setPhase(Phase.UNDEFINED); } @Override public void step(MersenneTwisterFast random, Simulation sim) { - cell.updateTarget(cellGrowthRate, sizeTarget); + cell.updateTarget(cellGrowthRateBase, sizeTarget); boolean sizeCheck = cell.getVolume() >= sizeTarget * cell.getCriticalVolume(); if (sizeCheck) { addCell(random, sim); } + updateGrowthRate(); + } + + public abstract void updateGrowthRate(); + + /** + * Updates the cell growth rate based on the volume of the cell. + * + *

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: + * + * 

+     *   growthRate = baseGrowthRate * (volume / criticalVolume) ^ sensitivity
+     *
+ * + * This allows larger cells to grow faster, capturing volume-dependent growth dynamics. + */ + public void updateVolumeBasedGrowthRate() { + double volume = cell.getLocation().getVolume(); + double Ka = cell.getCriticalVolume(); + cellGrowthRate = cellGrowthRateBase * Math.pow((volume / Ka), growthRateVolumeSensitivity); } } diff --git a/test/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivisionTest.java b/test/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivisionTest.java index 4856f81e0..495c74136 100644 --- a/test/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivisionTest.java +++ b/test/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivisionTest.java @@ -5,6 +5,8 @@ import arcade.core.sim.Simulation; import arcade.core.util.Parameters; import arcade.potts.agent.cell.PottsCellFlyGMC; +import arcade.potts.env.location.PottsLocation2D; +import static org.junit.jupiter.api.Assertions.assertEquals; import static org.mockito.Mockito.*; public class PottsModuleProliferationVolumeBasedDivisionTest { @@ -12,6 +14,7 @@ public class PottsModuleProliferationVolumeBasedDivisionTest { static class PottsModuleProliferationVolumeBasedDivisionMock extends PottsModuleProliferationVolumeBasedDivision { boolean addCellCalled = false; + boolean growthRateUpdated = false; PottsModuleProliferationVolumeBasedDivisionMock(PottsCellFlyGMC cell) { super(cell); @@ -21,10 +24,15 @@ static class PottsModuleProliferationVolumeBasedDivisionMock void addCell(MersenneTwisterFast random, Simulation sim) { addCellCalled = true; } + + @Override + public void updateGrowthRate() { + growthRateUpdated = true; + } } @Test - public void step_belowCheckpoint_updatesTargetOnly() { + public void step_belowCheckpoint_updatesTarget() { PottsCellFlyGMC cell = mock(PottsCellFlyGMC.class); Parameters params = mock(Parameters.class); when(cell.getParameters()).thenReturn(params); @@ -39,6 +47,7 @@ public void step_belowCheckpoint_updatesTargetOnly() { module.step(mock(MersenneTwisterFast.class), mock(Simulation.class)); verify(cell).updateTarget(4.0, 1.2); + assert module.growthRateUpdated : "growth rate should be updated on every step"; assert !module.addCellCalled : "addCell should not be called below checkpoint"; } @@ -59,6 +68,107 @@ public void step_atOrAboveCheckpoint_triggersAddCell() { module.step(mock(MersenneTwisterFast.class), mock(Simulation.class)); verify(cell).updateTarget(4.0, 1.2); + assert module.growthRateUpdated : "growth rate should be updated on every step"; assert module.addCellCalled : "addCell should be called at or above checkpoint"; } + + @Test +public void updateVolumeBasedGrowthRate_ratioOne_keepsBaseRate() { + // baseGrowth = 4.0, volume = Ka => growth = 4.0 + PottsCellFlyGMC cell = mock(PottsCellFlyGMC.class); + Parameters params = mock(Parameters.class); + PottsLocation2D loc = mock(PottsLocation2D.class); + + when(cell.getParameters()).thenReturn(params); + when(params.getDouble("proliferation/SIZE_TARGET")).thenReturn(1.2); + when(params.getDouble("proliferation/CELL_GROWTH_RATE")).thenReturn(4.0); + when(params.getInt("proliferation/DYNAMIC_GROWTH_RATE_VOLUME")).thenReturn(1); + when(params.getDouble("proliferation/GROWTH_RATE_VOLUME_SENSITIVITY")).thenReturn(2.0); + + when(cell.getLocation()).thenReturn(loc); + when(loc.getVolume()).thenReturn(100.0); + when(cell.getCriticalVolume()).thenReturn(100.0); + + PottsModuleProliferationVolumeBasedDivisionTest + .PottsModuleProliferationVolumeBasedDivisionMock module = + new PottsModuleProliferationVolumeBasedDivisionMock(cell); + + module.updateVolumeBasedGrowthRate(); + assertEquals(4.0, module.cellGrowthRate, 1e-9); +} + +@Test +public void updateVolumeBasedGrowthRate_ratioGreaterThanOne_scalesUpByPowerLaw() { + // baseGrowth = 2.0, ratio = 2.0, sensitivity = 3 => 2 * 2^3 = 2 * 8 = 12 + PottsCellFlyGMC cell = mock(PottsCellFlyGMC.class); + Parameters params = mock(Parameters.class); + PottsLocation2D loc = mock(PottsLocation2D.class); + + when(cell.getParameters()).thenReturn(params); + when(params.getDouble("proliferation/SIZE_TARGET")).thenReturn(1.2); + when(params.getDouble("proliferation/CELL_GROWTH_RATE")).thenReturn(2.0); + when(params.getInt("proliferation/DYNAMIC_GROWTH_RATE_VOLUME")).thenReturn(1); + when(params.getDouble("proliferation/GROWTH_RATE_VOLUME_SENSITIVITY")).thenReturn(3.0); + + when(cell.getLocation()).thenReturn(loc); + when(loc.getVolume()).thenReturn(200.0); + when(cell.getCriticalVolume()).thenReturn(100.0); + + PottsModuleProliferationVolumeBasedDivisionTest + .PottsModuleProliferationVolumeBasedDivisionMock module = + new PottsModuleProliferationVolumeBasedDivisionMock(cell); + + module.updateVolumeBasedGrowthRate(); + assertEquals(16.0, module.cellGrowthRate, 1e-9); +} + +@Test +public void updateVolumeBasedGrowthRate_ratioLessThanOne_scalesDownByPowerLaw() { + // baseGrowth = 4.0, ratio = 0.5, sensitivity = 2.0 => 4 * 0.5^2 = 1.0 + PottsCellFlyGMC cell = mock(PottsCellFlyGMC.class); + Parameters params = mock(Parameters.class); + PottsLocation2D loc = mock(PottsLocation2D.class); + + when(cell.getParameters()).thenReturn(params); + when(params.getDouble("proliferation/SIZE_TARGET")).thenReturn(1.2); + when(params.getDouble("proliferation/CELL_GROWTH_RATE")).thenReturn(4.0); + when(params.getInt("proliferation/DYNAMIC_GROWTH_RATE_VOLUME")).thenReturn(1); + when(params.getDouble("proliferation/GROWTH_RATE_VOLUME_SENSITIVITY")).thenReturn(2.0); + + when(cell.getLocation()).thenReturn(loc); + when(loc.getVolume()).thenReturn(50.0); + when(cell.getCriticalVolume()).thenReturn(100.0); + + PottsModuleProliferationVolumeBasedDivisionTest + .PottsModuleProliferationVolumeBasedDivisionMock module = + new PottsModuleProliferationVolumeBasedDivisionMock(cell); + + module.updateVolumeBasedGrowthRate(); + assertEquals(1.0, module.cellGrowthRate, 1e-9); +} + +@Test +public void updateVolumeBasedGrowthRate_zeroSensitivity_returnsBaseRateRegardlessOfVolume() { + // sensitivity = 0 => growth = baseGrowth * ratio^0 = baseGrowth + PottsCellFlyGMC cell = mock(PottsCellFlyGMC.class); + Parameters params = mock(Parameters.class); + PottsLocation2D loc = mock(PottsLocation2D.class); + + when(cell.getParameters()).thenReturn(params); + when(params.getDouble("proliferation/SIZE_TARGET")).thenReturn(1.2); + when(params.getDouble("proliferation/CELL_GROWTH_RATE")).thenReturn(3.5); + when(params.getInt("proliferation/DYNAMIC_GROWTH_RATE_VOLUME")).thenReturn(1); + when(params.getDouble("proliferation/GROWTH_RATE_VOLUME_SENSITIVITY")).thenReturn(0.0); + + when(cell.getLocation()).thenReturn(loc); + when(loc.getVolume()).thenReturn(250.0); + when(cell.getCriticalVolume()).thenReturn(100.0); + + PottsModuleProliferationVolumeBasedDivisionTest + .PottsModuleProliferationVolumeBasedDivisionMock module = + new PottsModuleProliferationVolumeBasedDivisionMock(cell); + + module.updateVolumeBasedGrowthRate(); + assertEquals(3.5, module.cellGrowthRate, 1e-9); +} } From ff209db92a6e3b2e19f3649e422a9489f395f00f Mon Sep 17 00:00:00 2001 From: jannetty Date: Tue, 21 Oct 2025 14:23:35 -0700 Subject: [PATCH 26/59] formatting --- ...eProliferationVolumeBasedDivisionTest.java | 190 +++++++++--------- 1 file changed, 95 insertions(+), 95 deletions(-) diff --git a/test/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivisionTest.java b/test/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivisionTest.java index 495c74136..55c7fe93d 100644 --- a/test/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivisionTest.java +++ b/test/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivisionTest.java @@ -73,102 +73,102 @@ public void step_atOrAboveCheckpoint_triggersAddCell() { } @Test -public void updateVolumeBasedGrowthRate_ratioOne_keepsBaseRate() { - // baseGrowth = 4.0, volume = Ka => growth = 4.0 - PottsCellFlyGMC cell = mock(PottsCellFlyGMC.class); - Parameters params = mock(Parameters.class); - PottsLocation2D loc = mock(PottsLocation2D.class); - - when(cell.getParameters()).thenReturn(params); - when(params.getDouble("proliferation/SIZE_TARGET")).thenReturn(1.2); - when(params.getDouble("proliferation/CELL_GROWTH_RATE")).thenReturn(4.0); - when(params.getInt("proliferation/DYNAMIC_GROWTH_RATE_VOLUME")).thenReturn(1); - when(params.getDouble("proliferation/GROWTH_RATE_VOLUME_SENSITIVITY")).thenReturn(2.0); - - when(cell.getLocation()).thenReturn(loc); - when(loc.getVolume()).thenReturn(100.0); - when(cell.getCriticalVolume()).thenReturn(100.0); - - PottsModuleProliferationVolumeBasedDivisionTest - .PottsModuleProliferationVolumeBasedDivisionMock module = - new PottsModuleProliferationVolumeBasedDivisionMock(cell); - - module.updateVolumeBasedGrowthRate(); - assertEquals(4.0, module.cellGrowthRate, 1e-9); -} + public void updateVolumeBasedGrowthRate_ratioOne_keepsBaseRate() { + // baseGrowth = 4.0, volume = Ka => growth = 4.0 + PottsCellFlyGMC cell = mock(PottsCellFlyGMC.class); + Parameters params = mock(Parameters.class); + PottsLocation2D loc = mock(PottsLocation2D.class); -@Test -public void updateVolumeBasedGrowthRate_ratioGreaterThanOne_scalesUpByPowerLaw() { - // baseGrowth = 2.0, ratio = 2.0, sensitivity = 3 => 2 * 2^3 = 2 * 8 = 12 - PottsCellFlyGMC cell = mock(PottsCellFlyGMC.class); - Parameters params = mock(Parameters.class); - PottsLocation2D loc = mock(PottsLocation2D.class); - - when(cell.getParameters()).thenReturn(params); - when(params.getDouble("proliferation/SIZE_TARGET")).thenReturn(1.2); - when(params.getDouble("proliferation/CELL_GROWTH_RATE")).thenReturn(2.0); - when(params.getInt("proliferation/DYNAMIC_GROWTH_RATE_VOLUME")).thenReturn(1); - when(params.getDouble("proliferation/GROWTH_RATE_VOLUME_SENSITIVITY")).thenReturn(3.0); - - when(cell.getLocation()).thenReturn(loc); - when(loc.getVolume()).thenReturn(200.0); - when(cell.getCriticalVolume()).thenReturn(100.0); - - PottsModuleProliferationVolumeBasedDivisionTest - .PottsModuleProliferationVolumeBasedDivisionMock module = - new PottsModuleProliferationVolumeBasedDivisionMock(cell); - - module.updateVolumeBasedGrowthRate(); - assertEquals(16.0, module.cellGrowthRate, 1e-9); -} + when(cell.getParameters()).thenReturn(params); + when(params.getDouble("proliferation/SIZE_TARGET")).thenReturn(1.2); + when(params.getDouble("proliferation/CELL_GROWTH_RATE")).thenReturn(4.0); + when(params.getInt("proliferation/DYNAMIC_GROWTH_RATE_VOLUME")).thenReturn(1); + when(params.getDouble("proliferation/GROWTH_RATE_VOLUME_SENSITIVITY")).thenReturn(2.0); -@Test -public void updateVolumeBasedGrowthRate_ratioLessThanOne_scalesDownByPowerLaw() { - // baseGrowth = 4.0, ratio = 0.5, sensitivity = 2.0 => 4 * 0.5^2 = 1.0 - PottsCellFlyGMC cell = mock(PottsCellFlyGMC.class); - Parameters params = mock(Parameters.class); - PottsLocation2D loc = mock(PottsLocation2D.class); - - when(cell.getParameters()).thenReturn(params); - when(params.getDouble("proliferation/SIZE_TARGET")).thenReturn(1.2); - when(params.getDouble("proliferation/CELL_GROWTH_RATE")).thenReturn(4.0); - when(params.getInt("proliferation/DYNAMIC_GROWTH_RATE_VOLUME")).thenReturn(1); - when(params.getDouble("proliferation/GROWTH_RATE_VOLUME_SENSITIVITY")).thenReturn(2.0); - - when(cell.getLocation()).thenReturn(loc); - when(loc.getVolume()).thenReturn(50.0); - when(cell.getCriticalVolume()).thenReturn(100.0); - - PottsModuleProliferationVolumeBasedDivisionTest - .PottsModuleProliferationVolumeBasedDivisionMock module = - new PottsModuleProliferationVolumeBasedDivisionMock(cell); - - module.updateVolumeBasedGrowthRate(); - assertEquals(1.0, module.cellGrowthRate, 1e-9); -} + when(cell.getLocation()).thenReturn(loc); + when(loc.getVolume()).thenReturn(100.0); + when(cell.getCriticalVolume()).thenReturn(100.0); -@Test -public void updateVolumeBasedGrowthRate_zeroSensitivity_returnsBaseRateRegardlessOfVolume() { - // sensitivity = 0 => growth = baseGrowth * ratio^0 = baseGrowth - PottsCellFlyGMC cell = mock(PottsCellFlyGMC.class); - Parameters params = mock(Parameters.class); - PottsLocation2D loc = mock(PottsLocation2D.class); - - when(cell.getParameters()).thenReturn(params); - when(params.getDouble("proliferation/SIZE_TARGET")).thenReturn(1.2); - when(params.getDouble("proliferation/CELL_GROWTH_RATE")).thenReturn(3.5); - when(params.getInt("proliferation/DYNAMIC_GROWTH_RATE_VOLUME")).thenReturn(1); - when(params.getDouble("proliferation/GROWTH_RATE_VOLUME_SENSITIVITY")).thenReturn(0.0); - - when(cell.getLocation()).thenReturn(loc); - when(loc.getVolume()).thenReturn(250.0); - when(cell.getCriticalVolume()).thenReturn(100.0); - - PottsModuleProliferationVolumeBasedDivisionTest - .PottsModuleProliferationVolumeBasedDivisionMock module = - new PottsModuleProliferationVolumeBasedDivisionMock(cell); - - module.updateVolumeBasedGrowthRate(); - assertEquals(3.5, module.cellGrowthRate, 1e-9); -} + PottsModuleProliferationVolumeBasedDivisionTest + .PottsModuleProliferationVolumeBasedDivisionMock + module = new PottsModuleProliferationVolumeBasedDivisionMock(cell); + + module.updateVolumeBasedGrowthRate(); + assertEquals(4.0, module.cellGrowthRate, 1e-9); + } + + @Test + public void updateVolumeBasedGrowthRate_ratioGreaterThanOne_scalesUpByPowerLaw() { + // baseGrowth = 2.0, ratio = 2.0, sensitivity = 3 => 2 * 2^3 = 2 * 8 = 12 + PottsCellFlyGMC cell = mock(PottsCellFlyGMC.class); + Parameters params = mock(Parameters.class); + PottsLocation2D loc = mock(PottsLocation2D.class); + + when(cell.getParameters()).thenReturn(params); + when(params.getDouble("proliferation/SIZE_TARGET")).thenReturn(1.2); + when(params.getDouble("proliferation/CELL_GROWTH_RATE")).thenReturn(2.0); + when(params.getInt("proliferation/DYNAMIC_GROWTH_RATE_VOLUME")).thenReturn(1); + when(params.getDouble("proliferation/GROWTH_RATE_VOLUME_SENSITIVITY")).thenReturn(3.0); + + when(cell.getLocation()).thenReturn(loc); + when(loc.getVolume()).thenReturn(200.0); + when(cell.getCriticalVolume()).thenReturn(100.0); + + PottsModuleProliferationVolumeBasedDivisionTest + .PottsModuleProliferationVolumeBasedDivisionMock + module = new PottsModuleProliferationVolumeBasedDivisionMock(cell); + + module.updateVolumeBasedGrowthRate(); + assertEquals(16.0, module.cellGrowthRate, 1e-9); + } + + @Test + public void updateVolumeBasedGrowthRate_ratioLessThanOne_scalesDownByPowerLaw() { + // baseGrowth = 4.0, ratio = 0.5, sensitivity = 2.0 => 4 * 0.5^2 = 1.0 + PottsCellFlyGMC cell = mock(PottsCellFlyGMC.class); + Parameters params = mock(Parameters.class); + PottsLocation2D loc = mock(PottsLocation2D.class); + + when(cell.getParameters()).thenReturn(params); + when(params.getDouble("proliferation/SIZE_TARGET")).thenReturn(1.2); + when(params.getDouble("proliferation/CELL_GROWTH_RATE")).thenReturn(4.0); + when(params.getInt("proliferation/DYNAMIC_GROWTH_RATE_VOLUME")).thenReturn(1); + when(params.getDouble("proliferation/GROWTH_RATE_VOLUME_SENSITIVITY")).thenReturn(2.0); + + when(cell.getLocation()).thenReturn(loc); + when(loc.getVolume()).thenReturn(50.0); + when(cell.getCriticalVolume()).thenReturn(100.0); + + PottsModuleProliferationVolumeBasedDivisionTest + .PottsModuleProliferationVolumeBasedDivisionMock + module = new PottsModuleProliferationVolumeBasedDivisionMock(cell); + + module.updateVolumeBasedGrowthRate(); + assertEquals(1.0, module.cellGrowthRate, 1e-9); + } + + @Test + public void updateVolumeBasedGrowthRate_zeroSensitivity_returnsBaseRateRegardlessOfVolume() { + // sensitivity = 0 => growth = baseGrowth * ratio^0 = baseGrowth + PottsCellFlyGMC cell = mock(PottsCellFlyGMC.class); + Parameters params = mock(Parameters.class); + PottsLocation2D loc = mock(PottsLocation2D.class); + + when(cell.getParameters()).thenReturn(params); + when(params.getDouble("proliferation/SIZE_TARGET")).thenReturn(1.2); + when(params.getDouble("proliferation/CELL_GROWTH_RATE")).thenReturn(3.5); + when(params.getInt("proliferation/DYNAMIC_GROWTH_RATE_VOLUME")).thenReturn(1); + when(params.getDouble("proliferation/GROWTH_RATE_VOLUME_SENSITIVITY")).thenReturn(0.0); + + when(cell.getLocation()).thenReturn(loc); + when(loc.getVolume()).thenReturn(250.0); + when(cell.getCriticalVolume()).thenReturn(100.0); + + PottsModuleProliferationVolumeBasedDivisionTest + .PottsModuleProliferationVolumeBasedDivisionMock + module = new PottsModuleProliferationVolumeBasedDivisionMock(cell); + + module.updateVolumeBasedGrowthRate(); + assertEquals(3.5, module.cellGrowthRate, 1e-9); + } } From 1945972b49739ac3623ef8e6dbe6e2c942ec9bca Mon Sep 17 00:00:00 2001 From: jannetty Date: Wed, 22 Oct 2025 16:02:43 -0700 Subject: [PATCH 27/59] changed visibility of getUniqueIDs, added method relying on getUniqueIDs to get unique NB neighbors, added docstrings, added fly stem proliferation module --- .../PottsModuleFlyGMCDifferentiation.java | 2 +- .../PottsModuleFlyStemProliferation.java | 166 +++++++++++++++++- ...oduleProliferationVolumeBasedDivision.java | 13 +- src/arcade/potts/sim/Potts.java | 2 +- src/arcade/potts/sim/Potts2D.java | 2 +- src/arcade/potts/sim/Potts3D.java | 2 +- .../PottsModuleFlyStemProliferationTest.java | 149 +++++++++++++++- ...eProliferationVolumeBasedDivisionTest.java | 2 +- test/arcade/potts/sim/PottsTest.java | 2 +- 9 files changed, 321 insertions(+), 19 deletions(-) diff --git a/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java b/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java index 4abe6368c..642619a27 100644 --- a/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java +++ b/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java @@ -92,7 +92,7 @@ void addCell(MersenneTwisterFast random, Simulation sim) { differentiatedGMC.schedule(sim.getSchedule()); } - public void updateGrowthRate() { + public void updateGrowthRate(Simulation sim) { if (dynamicGrowthRateVolume == false) { cellGrowthRate = cellGrowthRateBase; } else if (dynamicGrowthRateVolume == true) { diff --git a/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java b/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java index 420cc05cb..48a8fd099 100644 --- a/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java +++ b/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java @@ -2,6 +2,7 @@ import java.security.InvalidParameterException; import java.util.ArrayList; +import java.util.HashSet; import sim.util.Double3D; import ec.util.MersenneTwisterFast; import arcade.core.env.location.Location; @@ -21,9 +22,6 @@ 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; @@ -42,14 +40,28 @@ public class PottsModuleFlyStemProliferation extends PottsModuleProliferationVol /** Ruleset for determining which daughter cell is the GMC. Can be `volume` or `location`. */ final String differentiationRuleset; + /** + * Ruleset for determining how the cell determines its Apical Axis. Can be 'uniform', 'global', + * or 'rotation' + */ final String apicalAxisRuleset; + /** + * The distribution used to determine how apical axis should be rotated. Relevant when + * apicalAxisRuleset is set to 'uniform' or 'rotation'. + */ final Distribution apicalAxisRotationDistribution; + /** + * Boolean flag indicating whether or not the cell's critical volume should be affected by its + * volume at the time it divides. + */ final boolean volumeBasedCriticalVolume; + /** Boolean flag indicating whether growth rate should be regulated by NB-NB contact. */ final boolean dynamicGrowthRateNBContact; + /** Boolean flag indicating whether growth rate should be regulated by the cell's volume. */ final double volumeBasedCriticalVolumeMultiplier; /** @@ -128,16 +140,96 @@ public void addCell(MersenneTwisterFast random, Simulation sim) { } } - public void updateGrowthRate() { + /** + * Updates the effective growth rate according to the ruleset indicated in parameters. + * + * @param sim the simulation + */ + public void updateGrowthRate(Simulation sim) { if (dynamicGrowthRateVolume == true) { updateVolumeBasedGrowthRate(); } else if (dynamicGrowthRateNBContact == true) { - ; + updateNBContactGrowthRate(sim); } else { cellGrowthRate = cellGrowthRateBase; } } + /** + * Gets the number of neighbors of this cell that are unique neuroblasts. + * + * @param sim the simulation + * @return the number of unique neuroblast neighbors + */ + protected Integer getNumNBNeighbors(Simulation sim) { + Potts potts = ((PottsSimulation) sim).getPotts(); + ArrayList voxels = ((PottsLocation) cell.getLocation()).getVoxels(); + HashSet stemNeighbors = new HashSet(); + + for (Voxel v : voxels) { + HashSet uniqueIDs = potts.getUniqueIDs(v.x, v.y, v.z); + for (Integer id : uniqueIDs) { + PottsCell neighbor = (PottsCell) sim.getGrid().getObjectAt(id); + if (cell.getPop() == neighbor.getPop()) { + if (neighbor.getID() != cell.getID()) { + stemNeighbors.add((PottsCell) sim.getGrid().getObjectAt(id)); + } + } + } + } + return stemNeighbors.size(); + } + + /** + * Updates the cell's growth rate based on the number of neighboring neuroblasts. + * + *

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: + * + * 

+     *   hillRepression = K^n / (K^n + Np^n)
+     *   cellGrowthRate = cellGrowthRateBase * hillRepression
+     *
+ * + * where: + * + *
    + *
  • Np is the number of neighboring neuroblasts + *
  • K is the half-max parameter for repression + * (proliferation/NB_CONTACT_HALF_MAX) + *
  • n is the Hill coefficient controlling steepness + * (proliferation/NB_CONTACT_HILL_N) + *
  • cellGrowthRateBase is the base growth rate in the absence of neighbors + *
+ * + *

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); + + // Parameters from the model + double K = cell.getParameters().getDouble("proliferation/NB_CONTACT_HALF_MAX"); + double n = cell.getParameters().getDouble("proliferation/NB_CONTACT_HILL_N"); + + double Kn = Math.pow(K, n); + double Npn = Math.pow(Np, n); + + double hillRepression = Kn / (Kn + Npn); + + cellGrowthRate = cellGrowthRateBase * hillRepression; + } + + /** + * Chooses the division plane according to the type of stem cell this module is attached to. + * + * @param flyStemCell the stem cell this module is attached to + * @return the plane along which this cell should divide + */ protected Plane chooseDivisionPlane(PottsCellFlyStem flyStemCell) { double offset = sampleDivisionPlaneOffset(); @@ -210,6 +302,15 @@ public static Voxel getCellSplitVoxel( .getOffsetInApicalFrame2D(splitOffsetPercent, rotatedNormalVector); } + /** + * Determines whether the daughter cell should be a neuroblast or a GMC according to the type of + * cell this module is attached to, the differentiation ruleset specified in the parameters, and + * the morphologies of the daughter cell locations. + * + * @param loc1 one cell location post division + * @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) { if (((PottsCellFlyStem) cell).getStemType() == StemType.WT) { return false; @@ -257,6 +358,14 @@ static boolean centroidsWithinRangeAlongApicalAxis( return distanceAlongAxis - range <= EPSILON; } + /** + * Makes a daughter NB cell + * + * @param daughterLoc the location of the daughter NB cell + * @param sim the simulation + * @param potts the potts instance for this simulation + * @param random the random number generator + */ private void makeDaughterStemCell( PottsLocation daughterLoc, Simulation sim, Potts potts, MersenneTwisterFast random) { cell.reset(potts.ids, potts.regions); @@ -275,6 +384,16 @@ private void makeDaughterStemCell( scheduleNewCell(container, daughterLoc, sim, potts, random); } + /** + * Makes a daughter GMC cell + * + * @param parentLoc the location of the parent NB cell + * @param daughterLoc the location of the daughter GMC cell + * @param sim the simulation + * @param potts the potts instance for this simulation + * @param random the random number generator + * @param divisionPlaneNormal the normal vector to the plane of division + */ private void makeDaughterGMC( PottsLocation parentLoc, PottsLocation daughterLoc, @@ -290,14 +409,22 @@ private void makeDaughterGMC( cell.reset(potts.ids, potts.regions); int newID = sim.getID(); int newPop = ((PottsCellFlyStem) cell).getLinks().next(random); - double criticalVolume = - calculateGMCDaughterCellCriticalVolume((PottsLocation) daughterLoc, sim, newPop); + double criticalVolume = calculateGMCDaughterCellCriticalVolume((PottsLocation) daughterLoc); PottsCellContainer container = ((PottsCellFlyStem) cell) .make(newID, State.PROLIFERATIVE, random, newPop, criticalVolume); scheduleNewCell(container, daughterLoc, sim, potts, random); } + /** + * Adds a new cell to the simulation grid and schedule. Resets the parent cell. + * + * @param container the daughter cell's container + * @param daughterLoc the daughter cell's location + * @param sim the simulation + * @param potts the potts instance for this simulation + * @param random the random number generator + */ private void scheduleNewCell( PottsCellContainer container, PottsLocation daughterLoc, @@ -315,6 +442,13 @@ private void scheduleNewCell( newCell.schedule(sim.getSchedule()); } + /** + * Gets the apical axis of the daughter cell according to the apicalAxisRuleset specified in the + * parameters. + * + * @param random the random number generator + * @return the daughter cell's apical axis + */ public Vector getDaughterCellApicalAxis(MersenneTwisterFast random) { switch (apicalAxisRuleset) { case "uniform": @@ -347,6 +481,15 @@ public Vector getDaughterCellApicalAxis(MersenneTwisterFast random) { } } + /** + * Determines between two locations which will be the GMC and which will be the NB according to + * differentiation rules specified in the parameters. + * + * @param parentLoc the parent cell location + * @param daughterLoc the daughter cell location + * @param divisionPlaneNormal the normal vector to the plane of division + * @return the location that should be the GMC + */ private Location determineGMCLocation( PottsLocation parentLoc, PottsLocation daughterLoc, Vector divisionPlaneNormal) { switch (differentiationRuleset) { @@ -360,8 +503,13 @@ private Location determineGMCLocation( } } - protected double calculateGMCDaughterCellCriticalVolume( - PottsLocation gmcLoc, Simulation sim, int newpop) { + /** + * Calculates the critical volume of a GMC daughter cell + * + * @param gmcLoc the location of the GMC daughter cell + * @return the critical volume of the GMC daughter cell + */ + protected double calculateGMCDaughterCellCriticalVolume(PottsLocation gmcLoc) { double max_crit_vol = ((PottsCellFlyStem) cell).getCriticalVolume() * sizeTarget diff --git a/src/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivision.java b/src/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivision.java index f6870e336..d0681de49 100644 --- a/src/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivision.java +++ b/src/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivision.java @@ -26,8 +26,12 @@ public abstract class PottsModuleProliferationVolumeBasedDivision extends PottsM */ final double sizeTarget; + /** Boolean flag indicating whether the growth rate should follow volume-sensitive ruleset. */ final boolean dynamicGrowthRateVolume; + /** + * Sensitivity of growth rate to cell volume, only relevant if dynamicGrowthRateVolume is true. + */ final double growthRateVolumeSensitivity; /** @@ -54,10 +58,15 @@ public void step(MersenneTwisterFast random, Simulation sim) { if (sizeCheck) { addCell(random, sim); } - updateGrowthRate(); + updateGrowthRate(sim); } - public abstract void updateGrowthRate(); + /** + * Updates the effective growth rate according to boolean flags specified in parameters. + * + * @param sim the simulation + */ + public abstract void updateGrowthRate(Simulation sim); /** * Updates the cell growth rate based on the volume of the cell. diff --git a/src/arcade/potts/sim/Potts.java b/src/arcade/potts/sim/Potts.java index a0b46f0db..a4ffb0ee2 100644 --- a/src/arcade/potts/sim/Potts.java +++ b/src/arcade/potts/sim/Potts.java @@ -398,7 +398,7 @@ public PottsCell getCell(int id) { * @param z the z coordinate * @return the list of unique IDs */ - abstract HashSet getUniqueIDs(int x, int y, int z); + public abstract HashSet getUniqueIDs(int x, int y, int z); /** * Gets unique regions adjacent to given voxel. diff --git a/src/arcade/potts/sim/Potts2D.java b/src/arcade/potts/sim/Potts2D.java index 011d6f850..f6d7dbb6f 100644 --- a/src/arcade/potts/sim/Potts2D.java +++ b/src/arcade/potts/sim/Potts2D.java @@ -151,7 +151,7 @@ private boolean getConnectivityThreeNeighbors(boolean[][] subarray) { } @Override - HashSet getUniqueIDs(int x, int y, int z) { + public HashSet getUniqueIDs(int x, int y, int z) { int id = ids[z][x][y]; HashSet unique = new HashSet<>(); diff --git a/src/arcade/potts/sim/Potts3D.java b/src/arcade/potts/sim/Potts3D.java index 7c4686e8d..7f3429650 100644 --- a/src/arcade/potts/sim/Potts3D.java +++ b/src/arcade/potts/sim/Potts3D.java @@ -465,7 +465,7 @@ private boolean getConnectivityFiveNeighbors(boolean[][][] array) { } @Override - HashSet getUniqueIDs(int x, int y, int z) { + public HashSet getUniqueIDs(int x, int y, int z) { int id = ids[z][x][y]; HashSet unique = new HashSet<>(); diff --git a/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java b/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java index d32c0fada..f8e119ad0 100644 --- a/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java +++ b/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java @@ -1,6 +1,7 @@ package arcade.potts.agent.module; import java.util.ArrayList; +import java.util.HashSet; import org.junit.jupiter.api.AfterEach; import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.Test; @@ -16,6 +17,7 @@ import arcade.core.util.Vector; import arcade.core.util.distributions.NormalDistribution; import arcade.core.util.distributions.UniformDistribution; +import arcade.potts.agent.cell.PottsCell; import arcade.potts.agent.cell.PottsCellContainer; import arcade.potts.agent.cell.PottsCellFactory; import arcade.potts.agent.cell.PottsCellFlyStem; @@ -663,7 +665,7 @@ public void calculateGMCDaughterCellCriticalVolume_volumeBasedOff_returnsMaxCrit module = new PottsModuleFlyStemProliferation(stemCell); when(parameters.getInt("proliferation/VOLUME_BASED_CRITVOL")).thenReturn(0); - double result = module.calculateGMCDaughterCellCriticalVolume(daughterLoc, sim, 3); + double result = module.calculateGMCDaughterCellCriticalVolume(daughterLoc); assertEquals((100 * .25 * 1.2), result, EPSILON); // 100 * 0.25 * 1.2 } @@ -686,7 +688,7 @@ public void calculateGMCDaughterCellCriticalVolume_volumeBasedOn_returnsScaledVa module = new PottsModuleFlyStemProliferation(stemCell); - double result = module.calculateGMCDaughterCellCriticalVolume(gmcLoc, sim, 3); + double result = module.calculateGMCDaughterCellCriticalVolume(gmcLoc); assertEquals(75.0, result, EPSILON); // 50 * 1.5 } @@ -853,4 +855,147 @@ public void addCell_MUDMUTOffsetBelowThreshold_createsGMCWithVolumeSwap() { verify(newCell).schedule(any()); } + + @Test + public void getNumNBNeighbors_withTwoUniqueStemNeighbors_returnsCorrectCount() { + module = spy(new PottsModuleFlyStemProliferation(stemCell)); + + ArrayList voxels = new ArrayList<>(); + voxels.add(new Voxel(0, 0, 0)); + voxels.add(new Voxel(1, 0, 0)); + when(stemLoc.getVoxels()).thenReturn(voxels); + + // Unique IDs returned by potts + HashSet idsVoxel1 = new HashSet<>(); + idsVoxel1.add(10); + idsVoxel1.add(11); + HashSet idsVoxel2 = new HashSet<>(); + idsVoxel2.add(11); // repeat → should still count neighbor 11 only once + idsVoxel2.add(12); + + when(potts.getUniqueIDs(0, 0, 0)).thenReturn(idsVoxel1); + when(potts.getUniqueIDs(1, 0, 0)).thenReturn(idsVoxel2); + + // Neighbors + PottsCell neighbor10 = mock(PottsCell.class); + PottsCell neighbor11 = mock(PottsCell.class); + PottsCell neighbor12 = mock(PottsCell.class); + + when(neighbor10.getID()).thenReturn(10); + when(neighbor11.getID()).thenReturn(11); + when(neighbor12.getID()).thenReturn(12); + when(stemCell.getID()).thenReturn(42); + + when(neighbor10.getPop()).thenReturn(3); // match cell.getPop + when(neighbor11.getPop()).thenReturn(3); // match cell.getPop + when(neighbor12.getPop()).thenReturn(99); // no match + + when(grid.getObjectAt(10)).thenReturn(neighbor10); + when(grid.getObjectAt(11)).thenReturn(neighbor11); + when(grid.getObjectAt(12)).thenReturn(neighbor12); + + int numNeighbors = module.getNumNBNeighbors(sim); + + assertEquals(2, numNeighbors, "Should count 2 unique matching neighbors (10 and 11)"); + } + + @Test + public void getNumNBNeighbors_noMatchingNeighbors_returnsZero() { + module = spy(new PottsModuleFlyStemProliferation(stemCell)); + + ArrayList voxels = new ArrayList<>(); + voxels.add(new Voxel(0, 0, 0)); + when(stemLoc.getVoxels()).thenReturn(voxels); + + HashSet ids = new HashSet<>(); + ids.add(50); + when(potts.getUniqueIDs(0, 0, 0)).thenReturn(ids); + + PottsCell nonStemNeighbor = mock(PottsCell.class); + when(nonStemNeighbor.getPop()).thenReturn(99); // doesn't match stem pop + when(nonStemNeighbor.getID()).thenReturn(50); + when(grid.getObjectAt(50)).thenReturn(nonStemNeighbor); + + when(stemCell.getID()).thenReturn(42); + + int numNeighbors = module.getNumNBNeighbors(sim); + + assertEquals(0, numNeighbors, "No neighbors should be counted when pops do not match."); + } + + @Test + public void getNumNBNeighbors_called_doesNotCountSelf() { + module = spy(new PottsModuleFlyStemProliferation(stemCell)); + + ArrayList voxels = new ArrayList<>(); + voxels.add(new Voxel(0, 0, 0)); + when(stemLoc.getVoxels()).thenReturn(voxels); + + HashSet ids = new HashSet<>(); + ids.add(42); // same as sim.getID() mock (self) + when(potts.getUniqueIDs(0, 0, 0)).thenReturn(ids); + + PottsCell selfCell = stemCell; // or mock another PottsCell with same pop + when(grid.getObjectAt(42)).thenReturn(selfCell); + + int numNeighbors = module.getNumNBNeighbors(sim); + assertEquals(0, numNeighbors, "Self should not be counted as a neighbor"); + } + + @Test + public void updateNBContactGrowthRate_noNeighbors_returnsBaseGrowthRate() { + // Mock parameters + when(parameters.getDouble("proliferation/NB_CONTACT_HALF_MAX")).thenReturn(5.0); + when(parameters.getDouble("proliferation/NB_CONTACT_HILL_N")).thenReturn(2.0); + when(parameters.getDouble("proliferation/CELL_GROWTH_RATE")).thenReturn(10.0); + + module = spy(new PottsModuleFlyStemProliferation(stemCell)); + + // Mock neighbor count + doReturn(0).when(module).getNumNBNeighbors(sim); + + module.updateNBContactGrowthRate(sim); + assertEquals( + 10.0, + module.cellGrowthRate, + 1e-6, + "With 0 neighbors, hill repression should be 1.0"); + } + + @Test + public void updateNBContactGrowthRate_halfMaxNeighbors_returnsHalfBaseGrowthRate() { + // Mock parameters + when(parameters.getDouble("proliferation/NB_CONTACT_HALF_MAX")).thenReturn(5.0); + when(parameters.getDouble("proliferation/NB_CONTACT_HILL_N")).thenReturn(2.0); + when(parameters.getDouble("proliferation/CELL_GROWTH_RATE")).thenReturn(10.0); + + module = spy(new PottsModuleFlyStemProliferation(stemCell)); + + // Mock neighbor count + doReturn(5).when(module).getNumNBNeighbors(sim); + + module.updateNBContactGrowthRate(sim); + // Hill repression = K^n / (K^n + N^n) = 25 / (25 + 25) = 0.5 + assertEquals( + 5.0, + module.cellGrowthRate, + 1e-6, + "With 0 neighbors, hill repression should be 1.0"); + } + + @Test + public void updateNBContactGrowthRate_highNeighbors_returnsLowGrowthRate() { + when(parameters.getDouble("proliferation/NB_CONTACT_HALF_MAX")).thenReturn(5.0); + when(parameters.getDouble("proliferation/NB_CONTACT_HILL_N")).thenReturn(2.0); + when(parameters.getDouble("proliferation/CELL_GROWTH_RATE")).thenReturn(10.0); + + module = spy(new PottsModuleFlyStemProliferation(stemCell)); + + doReturn(20).when(module).getNumNBNeighbors(sim); + + module.updateNBContactGrowthRate(sim); + + // Hill repression = 25 / (25 + 400) = 25 / 425 ≈ 0.0588 + assertEquals(10.0 * (25.0 / 425.0), module.cellGrowthRate, 1e-6); + } } diff --git a/test/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivisionTest.java b/test/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivisionTest.java index 55c7fe93d..9229ae9c0 100644 --- a/test/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivisionTest.java +++ b/test/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivisionTest.java @@ -26,7 +26,7 @@ void addCell(MersenneTwisterFast random, Simulation sim) { } @Override - public void updateGrowthRate() { + public void updateGrowthRate(Simulation sim) { growthRateUpdated = true; } } diff --git a/test/arcade/potts/sim/PottsTest.java b/test/arcade/potts/sim/PottsTest.java index 04c61d693..305658832 100644 --- a/test/arcade/potts/sim/PottsTest.java +++ b/test/arcade/potts/sim/PottsTest.java @@ -61,7 +61,7 @@ boolean getConnectivity(boolean[][][] array, boolean zero) { } @Override - HashSet getUniqueIDs(int x, int y, int z) { + public HashSet getUniqueIDs(int x, int y, int z) { HashSet set = new HashSet<>(); if (x == 0 && y == 0) { set.add(1); From 6a340dc6a16df7be3adbdf737f1de138fdb13015 Mon Sep 17 00:00:00 2001 From: jannetty Date: Wed, 22 Oct 2025 16:11:08 -0700 Subject: [PATCH 28/59] moving all parameters so they are read in constructor --- .../PottsModuleFlyStemProliferation.java | 26 ++++++++++++++----- 1 file changed, 20 insertions(+), 6 deletions(-) diff --git a/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java b/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java index 48a8fd099..e120ad86c 100644 --- a/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java +++ b/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; @@ -70,6 +73,18 @@ public class PottsModuleFlyStemProliferation extends PottsModuleProliferationVol */ final double range; + /** + * Half-max NB neighbor count for repression (K). Only relevant if dynamicGrowthRateNBContact is + * true. + */ + final double nbContactHalfMax; + + /** + * Hill coefficient for NB-contact repression (n). Only relevant if dynamicGrowthRateNBContact + * is true. + */ + final double nbContactHillN; + /** * Creates a proliferation {@code Module} for the given {@link PottsCellFlyStem}. * @@ -111,6 +126,9 @@ public PottsModuleFlyStemProliferation(PottsCellFlyStem cell) { volumeBasedCriticalVolumeMultiplier = (parameters.getDouble("proliferation/VOLUME_BASED_CRITICAL_VOLUME_MULTIPLIER")); + nbContactHalfMax = parameters.getDouble("proliferation/NB_CONTACT_HALF_MAX"); + nbContactHillN = parameters.getDouble("proliferation/NB_CONTACT_HILL_N"); + setPhase(Phase.UNDEFINED); } @@ -212,12 +230,8 @@ protected void updateNBContactGrowthRate(Simulation sim) { int NpRaw = getNumNBNeighbors(sim); double Np = Math.max(0.0, (double) NpRaw); - // Parameters from the model - double K = cell.getParameters().getDouble("proliferation/NB_CONTACT_HALF_MAX"); - double n = cell.getParameters().getDouble("proliferation/NB_CONTACT_HILL_N"); - - double Kn = Math.pow(K, n); - double Npn = Math.pow(Np, n); + double Kn = Math.pow(nbContactHalfMax, nbContactHillN); + double Npn = Math.pow(Np, nbContactHillN); double hillRepression = Kn / (Kn + Npn); From 4579d713247158a33ac6b7770f2f67409d28d51d Mon Sep 17 00:00:00 2001 From: jannetty Date: Wed, 22 Oct 2025 16:19:48 -0700 Subject: [PATCH 29/59] adding potts parameters to potts parameters xml --- .../module/PottsModuleFlyStemProliferation.java | 3 --- src/arcade/potts/parameter.potts.xml | 17 +++++++++++++++++ 2 files changed, 17 insertions(+), 3 deletions(-) diff --git a/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java b/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java index e120ad86c..cf4410ade 100644 --- a/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java +++ b/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java @@ -22,9 +22,6 @@ 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; diff --git a/src/arcade/potts/parameter.potts.xml b/src/arcade/potts/parameter.potts.xml index ebc46e0da..73bf7bb43 100644 --- a/src/arcade/potts/parameter.potts.xml +++ b/src/arcade/potts/parameter.potts.xml @@ -63,6 +63,23 @@ + + + + + + + + + + + + + + + + + From 7f9461a852246eaf33081740479d2458c70c5630 Mon Sep 17 00:00:00 2001 From: jannetty Date: Wed, 22 Oct 2025 16:22:28 -0700 Subject: [PATCH 30/59] formatting --- .../potts/agent/module/PottsModuleFlyStemProliferation.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java b/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java index cf4410ade..a57aff841 100644 --- a/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java +++ b/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java @@ -124,7 +124,7 @@ public PottsModuleFlyStemProliferation(PottsCellFlyStem cell) { (parameters.getDouble("proliferation/VOLUME_BASED_CRITICAL_VOLUME_MULTIPLIER")); nbContactHalfMax = parameters.getDouble("proliferation/NB_CONTACT_HALF_MAX"); - nbContactHillN = parameters.getDouble("proliferation/NB_CONTACT_HILL_N"); + nbContactHillN = parameters.getDouble("proliferation/NB_CONTACT_HILL_N"); setPhase(Phase.UNDEFINED); } @@ -227,7 +227,7 @@ protected void updateNBContactGrowthRate(Simulation sim) { int NpRaw = getNumNBNeighbors(sim); double Np = Math.max(0.0, (double) NpRaw); - double Kn = Math.pow(nbContactHalfMax, nbContactHillN); + double Kn = Math.pow(nbContactHalfMax, nbContactHillN); double Npn = Math.pow(Np, nbContactHillN); double hillRepression = Kn / (Kn + Npn); From 3d04f5dc4a5f4bc180e4b9d1623698f539a683ad Mon Sep 17 00:00:00 2001 From: jannetty Date: Fri, 24 Oct 2025 10:58:24 -0700 Subject: [PATCH 31/59] adding minimum volume for size-dependent critical volume --- .../PottsModuleFlyStemProliferation.java | 42 +++++++++++++------ ...oduleProliferationVolumeBasedDivision.java | 5 ++- src/arcade/potts/parameter.potts.xml | 6 +-- .../PottsModuleFlyStemProliferationTest.java | 3 +- 4 files changed, 36 insertions(+), 20 deletions(-) diff --git a/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java b/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java index a57aff841..46118a223 100644 --- a/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java +++ b/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; @@ -61,7 +64,6 @@ public class PottsModuleFlyStemProliferation extends PottsModuleProliferationVol /** Boolean flag indicating whether growth rate should be regulated by NB-NB contact. */ final boolean dynamicGrowthRateNBContact; - /** Boolean flag indicating whether growth rate should be regulated by the cell's volume. */ final double volumeBasedCriticalVolumeMultiplier; /** @@ -82,6 +84,8 @@ public class PottsModuleFlyStemProliferation extends PottsModuleProliferationVol */ final double nbContactHillN; + final double initialSize; + /** * Creates a proliferation {@code Module} for the given {@link PottsCellFlyStem}. * @@ -126,6 +130,8 @@ public PottsModuleFlyStemProliferation(PottsCellFlyStem cell) { nbContactHalfMax = parameters.getDouble("proliferation/NB_CONTACT_HALF_MAX"); nbContactHillN = parameters.getDouble("proliferation/NB_CONTACT_HILL_N"); + initialSize = cell.getVolume(); + setPhase(Phase.UNDEFINED); } @@ -185,6 +191,9 @@ protected Integer getNumNBNeighbors(Simulation sim) { HashSet uniqueIDs = potts.getUniqueIDs(v.x, v.y, v.z); for (Integer id : uniqueIDs) { PottsCell neighbor = (PottsCell) sim.getGrid().getObjectAt(id); + if (neighbor == null) { + continue; + } if (cell.getPop() == neighbor.getPop()) { if (neighbor.getID() != cell.getID()) { stemNeighbors.add((PottsCell) sim.getGrid().getObjectAt(id)); @@ -383,9 +392,11 @@ private void makeDaughterStemCell( int newID = sim.getID(); double criticalVol; if (volumeBasedCriticalVolume) { - criticalVol = daughterLoc.getVolume() * volumeBasedCriticalVolumeMultiplier; - cell.setCriticalVolume( - cell.getLocation().getVolume() * volumeBasedCriticalVolumeMultiplier); + criticalVol = + Math.max( + daughterLoc.getVolume() * volumeBasedCriticalVolumeMultiplier, + initialSize / 2); + cell.setCriticalVolume(criticalVol); } else { criticalVol = cell.getCriticalVolume(); } @@ -475,7 +486,7 @@ public Vector getDaughterCellApicalAxis(MersenneTwisterFast random) { return newRandomApicalAxis; case "global": return ((PottsCellFlyStem) cell).getApicalAxis(); - case "rotation": + case "normal": if (!(apicalAxisRotationDistribution instanceof NormalDistribution)) { throw new IllegalArgumentException( "apicalAxisRotationDistribution must be a NormalDistribution under the rotation apical axis ruleset."); @@ -521,16 +532,21 @@ private Location determineGMCLocation( * @return the critical volume of the GMC daughter cell */ protected double calculateGMCDaughterCellCriticalVolume(PottsLocation gmcLoc) { - double max_crit_vol = - ((PottsCellFlyStem) cell).getCriticalVolume() - * sizeTarget - * ((PottsCellFlyStem) cell) - .getStemType() - .daughterCellCriticalVolumeProportion; + double criticalVol; if (volumeBasedCriticalVolume) { - return gmcLoc.getVolume() * volumeBasedCriticalVolumeMultiplier; + criticalVol = + Math.max( + gmcLoc.getVolume() * volumeBasedCriticalVolumeMultiplier, + initialSize / 2); + return criticalVol; } else { - return max_crit_vol; + criticalVol = + ((PottsCellFlyStem) cell).getCriticalVolume() + * sizeTarget + * ((PottsCellFlyStem) cell) + .getStemType() + .daughterCellCriticalVolumeProportion; + return criticalVol; } } diff --git a/src/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivision.java b/src/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivision.java index d0681de49..aa1d188d6 100644 --- a/src/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivision.java +++ b/src/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivision.java @@ -49,16 +49,17 @@ public PottsModuleProliferationVolumeBasedDivision(PottsCell cell) { growthRateVolumeSensitivity = parameters.getDouble("proliferation/GROWTH_RATE_VOLUME_SENSITIVITY"); setPhase(Phase.UNDEFINED); + cellGrowthRate = cellGrowthRateBase; } @Override public void step(MersenneTwisterFast random, Simulation sim) { - cell.updateTarget(cellGrowthRateBase, sizeTarget); + updateGrowthRate(sim); + cell.updateTarget(cellGrowthRate, sizeTarget); boolean sizeCheck = cell.getVolume() >= sizeTarget * cell.getCriticalVolume(); if (sizeCheck) { addCell(random, sim); } - updateGrowthRate(sim); } /** diff --git a/src/arcade/potts/parameter.potts.xml b/src/arcade/potts/parameter.potts.xml index 73bf7bb43..73f91b6cf 100644 --- a/src/arcade/potts/parameter.potts.xml +++ b/src/arcade/potts/parameter.potts.xml @@ -75,11 +75,11 @@ - - + + - + diff --git a/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java b/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java index f8e119ad0..b75cbe0b3 100644 --- a/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java +++ b/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java @@ -27,7 +27,6 @@ import arcade.potts.sim.Potts; import arcade.potts.sim.PottsSimulation; import arcade.potts.util.PottsEnums.Phase; -import arcade.potts.util.PottsEnums.State; import static org.junit.jupiter.api.Assertions.*; import static org.mockito.ArgumentMatchers.any; import static org.mockito.ArgumentMatchers.anyDouble; @@ -591,7 +590,7 @@ public void getDaughterCellApicalAxis_global_returnsApicalAxis() { @Test public void getDaughterCellApicalAxis_rotation_returnsRotatedAxis() { - when(parameters.getString("proliferation/APICAL_AXIS_RULESET")).thenReturn("rotation"); + when(parameters.getString("proliferation/APICAL_AXIS_RULESET")).thenReturn("normal"); NormalDistribution rotDist = mock(NormalDistribution.class); when(rotDist.nextDouble()).thenReturn(30.0); // rotation angle From 0b60fc6fe56664f076f347d77e9e42b8d3b0c514 Mon Sep 17 00:00:00 2001 From: jannetty Date: Thu, 30 Oct 2025 10:01:49 -0700 Subject: [PATCH 32/59] adding getOffsetInApicalFrame to PottsLocation --- src/arcade/potts/env/location/PottsLocation.java | 13 +++++++++++++ src/arcade/potts/env/location/PottsLocation2D.java | 3 ++- src/arcade/potts/env/location/PottsLocation3D.java | 8 ++++++++ src/arcade/potts/env/location/PottsLocations.java | 8 ++++++++ .../potts/env/location/PottsLocations2D.java | 9 +++++++++ .../potts/env/location/PottsLocations3D.java | 2 ++ .../potts/env/location/PottsLocation2DTest.java | 10 +++++----- .../potts/env/location/PottsLocation3DTest.java | 13 +++++++++++++ .../potts/env/location/PottsLocationTest.java | 5 +++++ .../potts/env/location/PottsLocationsTest.java | 14 ++++++++++++++ 10 files changed, 79 insertions(+), 6 deletions(-) diff --git a/src/arcade/potts/env/location/PottsLocation.java b/src/arcade/potts/env/location/PottsLocation.java index ddb5b1d94..1fdba5468 100644 --- a/src/arcade/potts/env/location/PottsLocation.java +++ b/src/arcade/potts/env/location/PottsLocation.java @@ -10,6 +10,9 @@ import arcade.core.env.location.LocationContainer; import arcade.core.util.Plane; import arcade.core.util.Utilities; +import arcade.core.util.Vector; +import arcade.potts.util.PottsEnums.Direction; +import arcade.potts.util.PottsEnums.Region; import static arcade.potts.util.PottsEnums.Direction; import static arcade.potts.util.PottsEnums.Region; @@ -605,6 +608,16 @@ void updateCenter(int x, int y, int z, int change) { */ abstract ArrayList getSelected(Voxel focus, double n); + /** + * Gets the voxel at specified percentage offsets along the location's axes with the provided + * ApicalAxis considered to be pointing up the Y axis + * + * @param offsets the percent offsets along the location's axes + * @param apicalAxis the axis considered to be pointing up along the Y axis + * @return the voxel at the specified offset in the frame of the apical axis + */ + abstract Voxel getOffsetInApicalFrame(ArrayList offsets, Vector apicalAxis); + /** * Gets the direction of the slice orthagonal to the direction with the smallest diameter. * diff --git a/src/arcade/potts/env/location/PottsLocation2D.java b/src/arcade/potts/env/location/PottsLocation2D.java index 102a60011..a6828bc69 100644 --- a/src/arcade/potts/env/location/PottsLocation2D.java +++ b/src/arcade/potts/env/location/PottsLocation2D.java @@ -76,7 +76,8 @@ ArrayList getSelected(Voxel focus, double n) { * @param apicalAxis the axis considered to be pointing up along the Y axis * @return the voxel through which the plane of division will pass */ - public Voxel getOffsetInApicalFrame2D(ArrayList offsets, Vector apicalAxis) { + @Override + public Voxel getOffsetInApicalFrame(ArrayList offsets, Vector apicalAxis) { if (voxels.isEmpty()) { return null; } diff --git a/src/arcade/potts/env/location/PottsLocation3D.java b/src/arcade/potts/env/location/PottsLocation3D.java index b9e9c1aec..c6ad40cd1 100644 --- a/src/arcade/potts/env/location/PottsLocation3D.java +++ b/src/arcade/potts/env/location/PottsLocation3D.java @@ -2,6 +2,8 @@ import java.util.ArrayList; import java.util.HashMap; +import arcade.core.util.Vector; +import arcade.potts.util.PottsEnums.Direction; import static arcade.potts.util.PottsEnums.Direction; /** Concrete implementation of {@link PottsLocation} for 3D. */ @@ -64,4 +66,10 @@ Direction getSlice(Direction direction, HashMap diameters) { ArrayList getSelected(Voxel focus, double n) { return Location3D.getSelected(voxels, focus, n); } + + @Override + Voxel getOffsetInApicalFrame(ArrayList offsets, Vector apicalAxis) { + throw new UnsupportedOperationException( + "getOffsetInApicalFrame is not implemented for PottsLocation3D"); + } } diff --git a/src/arcade/potts/env/location/PottsLocations.java b/src/arcade/potts/env/location/PottsLocations.java index 1b829e426..4ae66311e 100644 --- a/src/arcade/potts/env/location/PottsLocations.java +++ b/src/arcade/potts/env/location/PottsLocations.java @@ -6,6 +6,8 @@ import ec.util.MersenneTwisterFast; import arcade.core.env.location.Location; import arcade.core.env.location.LocationContainer; +import arcade.core.util.Vector; +import arcade.potts.util.PottsEnums.Region; import static arcade.potts.util.PottsEnums.Region; /** @@ -286,4 +288,10 @@ Location separateVoxels( return splitLocation; } + + @Override + Voxel getOffsetInApicalFrame(ArrayList offsets, Vector apicalAxis) { + throw new UnsupportedOperationException( + "getOffsetInApicalFrame is not implemented for PottsLocations"); + } } diff --git a/src/arcade/potts/env/location/PottsLocations2D.java b/src/arcade/potts/env/location/PottsLocations2D.java index 7877b24f9..52b5721db 100644 --- a/src/arcade/potts/env/location/PottsLocations2D.java +++ b/src/arcade/potts/env/location/PottsLocations2D.java @@ -2,6 +2,9 @@ import java.util.ArrayList; import java.util.HashMap; +import arcade.core.util.Vector; +import arcade.potts.util.PottsEnums.Direction; +import arcade.potts.util.PottsEnums.Region; import static arcade.potts.util.PottsEnums.Direction; import static arcade.potts.util.PottsEnums.Region; @@ -70,4 +73,10 @@ Direction getSlice(Direction direction, HashMap diameters) { ArrayList getSelected(Voxel focus, double n) { return Location2D.getSelected(locations.get(Region.DEFAULT).voxels, focus, n); } + + @Override + Voxel getOffsetInApicalFrame(ArrayList offsets, Vector apicalAxis) { + throw new UnsupportedOperationException( + "getOffsetInApicalFrame is not implemented for PottsLocations2D"); + } } diff --git a/src/arcade/potts/env/location/PottsLocations3D.java b/src/arcade/potts/env/location/PottsLocations3D.java index c6d0b82dc..555e25f42 100644 --- a/src/arcade/potts/env/location/PottsLocations3D.java +++ b/src/arcade/potts/env/location/PottsLocations3D.java @@ -2,6 +2,8 @@ import java.util.ArrayList; import java.util.HashMap; +import arcade.potts.util.PottsEnums.Direction; +import arcade.potts.util.PottsEnums.Region; import static arcade.potts.util.PottsEnums.Direction; import static arcade.potts.util.PottsEnums.Region; diff --git a/test/arcade/potts/env/location/PottsLocation2DTest.java b/test/arcade/potts/env/location/PottsLocation2DTest.java index 25396de49..da5d53c6a 100644 --- a/test/arcade/potts/env/location/PottsLocation2DTest.java +++ b/test/arcade/potts/env/location/PottsLocation2DTest.java @@ -296,7 +296,7 @@ public void getOffsetInApicalFrame2D_offsetAtCenter_returnsExpectedVoxel() { offsets.add(50); // middle of X axis offsets.add(50); // middle of Y axis - Voxel result = loc.getOffsetInApicalFrame2D(offsets, apicalAxis); + Voxel result = loc.getOffsetInApicalFrame(offsets, apicalAxis); assertEquals(new Voxel(0, 0, 0), result); } @@ -315,7 +315,7 @@ public void getOffsetInApicalFrame2D_offsetUpperRight_returnsExpectedVoxel() { offsets.add(100); // far right of X axis offsets.add(100); // top of Y axis - Voxel result = loc.getOffsetInApicalFrame2D(offsets, apicalAxis); + Voxel result = loc.getOffsetInApicalFrame(offsets, apicalAxis); assertEquals(new Voxel(4, 4, 0), result); } @@ -328,7 +328,7 @@ public void getOffsetInApicalFrame2D_emptyVoxels_returnsNull() { offsets.add(50); offsets.add(50); - Voxel result = loc.getOffsetInApicalFrame2D(offsets, apicalAxis); + Voxel result = loc.getOffsetInApicalFrame(offsets, apicalAxis); assertNull(result); } @@ -346,7 +346,7 @@ public void getOffsetInApicalFrame2D_invalidOffset_throwsException() { assertThrows( IllegalArgumentException.class, () -> { - loc.getOffsetInApicalFrame2D(badOffset, apicalAxis); + loc.getOffsetInApicalFrame(badOffset, apicalAxis); }); } @@ -364,7 +364,7 @@ public void getOffsetInApicalFrame2D_nonOrthogonalAxis_returnsExpected() { offsets.add(0); // lowest orthogonal axis offsets.add(100); // farthest along apical - Voxel result = loc.getOffsetInApicalFrame2D(offsets, apicalAxis); + Voxel result = loc.getOffsetInApicalFrame(offsets, apicalAxis); assertEquals(new Voxel(3, 3, 0), result); } } diff --git a/test/arcade/potts/env/location/PottsLocation3DTest.java b/test/arcade/potts/env/location/PottsLocation3DTest.java index 9b5742c41..928741174 100644 --- a/test/arcade/potts/env/location/PottsLocation3DTest.java +++ b/test/arcade/potts/env/location/PottsLocation3DTest.java @@ -4,6 +4,7 @@ import org.junit.jupiter.api.BeforeAll; import org.junit.jupiter.api.Test; import ec.util.MersenneTwisterFast; +import arcade.core.util.Vector; import static org.junit.jupiter.api.Assertions.*; import static org.mockito.Mockito.*; import static arcade.potts.env.location.Voxel.VOXEL_COMPARATOR; @@ -298,4 +299,16 @@ public void split_balanceableLocationRandomOne_returnsList() { assertEquals(locVoxels, loc.voxels); assertEquals(splitVoxels, split.voxels); } + + @Test + public void getOffsetInApicalFrame_called_raisesUnsupportedOperationException() { + { + PottsLocation3D loc = new PottsLocation3D(voxelListAB); + Vector apicalAxis = new Vector(0, 1, 0); + ArrayList offsets = new ArrayList<>(); + assertThrows( + UnsupportedOperationException.class, + () -> loc.getOffsetInApicalFrame(offsets, apicalAxis)); + } + } } diff --git a/test/arcade/potts/env/location/PottsLocationTest.java b/test/arcade/potts/env/location/PottsLocationTest.java index ef48c8f5b..00a90c1a3 100644 --- a/test/arcade/potts/env/location/PottsLocationTest.java +++ b/test/arcade/potts/env/location/PottsLocationTest.java @@ -169,6 +169,11 @@ Direction getSlice(Direction direction, HashMap diameters) { ArrayList getSelected(Voxel center, double n) { return new ArrayList<>(); } + + @Override + Voxel getOffsetInApicalFrame(ArrayList offsets, Vector apicalAxis) { + return new Voxel(0, 0, 0); + } } @Test diff --git a/test/arcade/potts/env/location/PottsLocationsTest.java b/test/arcade/potts/env/location/PottsLocationsTest.java index 6c082948a..343902f7c 100644 --- a/test/arcade/potts/env/location/PottsLocationsTest.java +++ b/test/arcade/potts/env/location/PottsLocationsTest.java @@ -6,6 +6,10 @@ import org.junit.jupiter.api.BeforeAll; import org.junit.jupiter.api.Test; import ec.util.MersenneTwisterFast; +import arcade.core.util.Vector; +import arcade.potts.env.location.PottsLocationTest.PottsLocationMock; +import arcade.potts.util.PottsEnums.Direction; +import arcade.potts.util.PottsEnums.Region; import static org.junit.jupiter.api.Assertions.*; import static org.mockito.Mockito.*; import static arcade.core.ARCADETestUtilities.*; @@ -963,4 +967,14 @@ public void separateVoxels_validListsWithRegions_updatesLists() { assertEquals(2, split.locations.get(Region.DEFAULT).voxels.size()); assertEquals(2, split.locations.get(Region.DEFAULT).voxels.size()); } + + @Test + public void getOffsetInApicalFrame_called_raisesUnsupportedOperationException() { + PottsLocationsMock loc = new PottsLocationsMock(voxelListForMultipleRegionsA); + Vector apicalAxis = new Vector(0, 1, 0); + ArrayList offsets = new ArrayList<>(); + assertThrows( + UnsupportedOperationException.class, + () -> loc.getOffsetInApicalFrame(offsets, apicalAxis)); + } } From 85e008c3cddce2e6ba898bf0b2c12c70e961d480 Mon Sep 17 00:00:00 2001 From: jannetty Date: Thu, 30 Oct 2025 10:03:06 -0700 Subject: [PATCH 33/59] removing unnecessary imports --- src/arcade/potts/env/location/PottsLocations3D.java | 2 -- 1 file changed, 2 deletions(-) diff --git a/src/arcade/potts/env/location/PottsLocations3D.java b/src/arcade/potts/env/location/PottsLocations3D.java index 555e25f42..c6d0b82dc 100644 --- a/src/arcade/potts/env/location/PottsLocations3D.java +++ b/src/arcade/potts/env/location/PottsLocations3D.java @@ -2,8 +2,6 @@ import java.util.ArrayList; import java.util.HashMap; -import arcade.potts.util.PottsEnums.Direction; -import arcade.potts.util.PottsEnums.Region; import static arcade.potts.util.PottsEnums.Direction; import static arcade.potts.util.PottsEnums.Region; From 5759730a79698a8ff691aece30b5db359a46d4ab Mon Sep 17 00:00:00 2001 From: jannetty Date: Thu, 30 Oct 2025 10:07:16 -0700 Subject: [PATCH 34/59] adding null case to PottsLocation2D docstring --- src/arcade/potts/env/location/PottsLocation2D.java | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/arcade/potts/env/location/PottsLocation2D.java b/src/arcade/potts/env/location/PottsLocation2D.java index a6828bc69..7a63ad357 100644 --- a/src/arcade/potts/env/location/PottsLocation2D.java +++ b/src/arcade/potts/env/location/PottsLocation2D.java @@ -70,7 +70,9 @@ ArrayList getSelected(Voxel focus, double n) { /** * Gets the voxel at specified percentage offsets along the location's X and Y axes with the - * provided apicalAxis considered to be pointing up the Y axis. + * provided apicalAxis considered to be pointing up the Y axis. Returns null if this + * PottsLocation2D contains no voxels or if the offsets ArrayList provided is not 2 integers + * long. * * @param offsets the percent offsets along the location's X and Y axes * @param apicalAxis the axis considered to be pointing up along the Y axis From 3ac1371ae46329936664fc9ea81c0ebd3aac57f1 Mon Sep 17 00:00:00 2001 From: jannetty Date: Thu, 30 Oct 2025 10:08:43 -0700 Subject: [PATCH 35/59] stylecheck --- src/arcade/potts/env/location/PottsLocation.java | 2 +- src/arcade/potts/env/location/PottsLocation2D.java | 3 +-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/src/arcade/potts/env/location/PottsLocation.java b/src/arcade/potts/env/location/PottsLocation.java index 1fdba5468..ee15838a4 100644 --- a/src/arcade/potts/env/location/PottsLocation.java +++ b/src/arcade/potts/env/location/PottsLocation.java @@ -610,7 +610,7 @@ void updateCenter(int x, int y, int z, int change) { /** * Gets the voxel at specified percentage offsets along the location's axes with the provided - * ApicalAxis considered to be pointing up the Y axis + * ApicalAxis considered to be pointing up the Y axis. * * @param offsets the percent offsets along the location's axes * @param apicalAxis the axis considered to be pointing up along the Y axis diff --git a/src/arcade/potts/env/location/PottsLocation2D.java b/src/arcade/potts/env/location/PottsLocation2D.java index 7a63ad357..f61165147 100644 --- a/src/arcade/potts/env/location/PottsLocation2D.java +++ b/src/arcade/potts/env/location/PottsLocation2D.java @@ -71,8 +71,7 @@ ArrayList getSelected(Voxel focus, double n) { /** * Gets the voxel at specified percentage offsets along the location's X and Y axes with the * provided apicalAxis considered to be pointing up the Y axis. Returns null if this - * PottsLocation2D contains no voxels or if the offsets ArrayList provided is not 2 integers - * long. + * PottsLocation2D contains no voxels. * * @param offsets the percent offsets along the location's X and Y axes * @param apicalAxis the axis considered to be pointing up along the Y axis From bc4b7aee5e0beed3aca9b5842a4c1b30a5bb7c19 Mon Sep 17 00:00:00 2001 From: jannetty Date: Thu, 30 Oct 2025 10:46:58 -0700 Subject: [PATCH 36/59] updating function names after merge --- .../module/PottsModuleFlyStemProliferation.java | 5 +---- .../PottsModuleFlyStemProliferationTest.java | 14 +++++++------- 2 files changed, 8 insertions(+), 11 deletions(-) diff --git a/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java b/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java index 46118a223..be50874d0 100644 --- a/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java +++ b/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java @@ -22,9 +22,6 @@ 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; @@ -319,7 +316,7 @@ public static Voxel getCellSplitVoxel( splitOffsetPercent.add(stemType.splitOffsetPercentX); splitOffsetPercent.add(stemType.splitOffsetPercentY); return ((PottsLocation2D) cell.getLocation()) - .getOffsetInApicalFrame2D(splitOffsetPercent, rotatedNormalVector); + .getOffsetInApicalFrame(splitOffsetPercent, rotatedNormalVector); } /** diff --git a/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java b/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java index b75cbe0b3..3773f1023 100644 --- a/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java +++ b/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java @@ -268,12 +268,12 @@ public void getCellSplitVoxel_WT_callsLocationOffsetWithCorrectParams() { when(stemCell.getApicalAxis()).thenReturn(new Vector(0, 1, 0)); when(stemCell.getLocation()).thenReturn(stemLoc); - when(stemLoc.getOffsetInApicalFrame2D(eq(expectedOffset), any(Vector.class))) + when(stemLoc.getOffsetInApicalFrame(eq(expectedOffset), any(Vector.class))) .thenReturn(new Voxel(0, 0, 0)); PottsModuleFlyStemProliferation.getCellSplitVoxel( PottsCellFlyStem.StemType.WT, stemCell, stemCell.getApicalAxis()); - verify(stemLoc).getOffsetInApicalFrame2D(eq(expectedOffset), any(Vector.class)); + verify(stemLoc).getOffsetInApicalFrame(eq(expectedOffset), any(Vector.class)); } @Test @@ -284,12 +284,12 @@ public void getCellSplitVoxel_MUDMUT_callsLocationOffsetWithCorrectParams() { when(stemCell.getApicalAxis()).thenReturn(new Vector(0, 1, 0)); when(stemCell.getLocation()).thenReturn(stemLoc); - when(stemLoc.getOffsetInApicalFrame2D(eq(expectedOffset), any(Vector.class))) + when(stemLoc.getOffsetInApicalFrame(eq(expectedOffset), any(Vector.class))) .thenReturn(new Voxel(0, 0, 0)); PottsModuleFlyStemProliferation.getCellSplitVoxel( PottsCellFlyStem.StemType.MUDMUT, stemCell, stemCell.getApicalAxis()); - verify(stemLoc).getOffsetInApicalFrame2D(eq(expectedOffset), any(Vector.class)); + verify(stemLoc).getOffsetInApicalFrame(eq(expectedOffset), any(Vector.class)); } // Division plane tests @@ -316,7 +316,7 @@ public void getWTDivisionPlaneWithRotationalVariance_rotatesCorrectlyAndReturnsP Vector.rotateVectorAroundAxis( afterBaseRotation, new Vector(0, 0, 1), offsetRotation); - when(stemLoc.getOffsetInApicalFrame2D(any(), eq(expectedNormal))).thenReturn(splitVoxel); + when(stemLoc.getOffsetInApicalFrame(any(), eq(expectedNormal))).thenReturn(splitVoxel); Plane result = module.getWTDivisionPlaneWithRotationalVariance(stemCell, offsetRotation); @@ -342,7 +342,7 @@ public void getMUDDivisionPlane_returnsRotatedPlaneWithCorrectNormal() { ArrayList expectedOffset = new ArrayList<>(); expectedOffset.add(50); // MUDMUT x offset percent expectedOffset.add(50); // MUDMUT y offset percent - when(stemLoc.getOffsetInApicalFrame2D(any(), any())).thenReturn(splitVoxel); + when(stemLoc.getOffsetInApicalFrame(any(), any())).thenReturn(splitVoxel); module = new PottsModuleFlyStemProliferation(stemCell); Plane result = module.getMUDDivisionPlane(stemCell); @@ -456,7 +456,7 @@ public void step_volumeAtCheckpoint_callsAddCellPhaseStaysUndefined() { // Plane/voxel path (chooseDivisionPlane -> WT -> getWTDivisionPlaneWithRotationalVariance) when(parameters.getString("proliferation/APICAL_AXIS_RULESET")).thenReturn("global"); when(stemCell.getApicalAxis()).thenReturn(new Vector(0, 1, 0)); - when(stemLoc.getOffsetInApicalFrame2D(any(), any(Vector.class))) + when(stemLoc.getOffsetInApicalFrame(any(), any(Vector.class))) .thenReturn(new Voxel(1, 2, 3)); // Differentiation rule From ab7281d8b499dcc9be63a6025e72d1e25148eeb0 Mon Sep 17 00:00:00 2001 From: daniellevahdat Date: Sun, 2 Nov 2025 23:51:31 -0800 Subject: [PATCH 37/59] add option for deterministic differentiation --- .../PottsModuleFlyStemProliferation.java | 54 ++++++++++++++++++- 1 file changed, 52 insertions(+), 2 deletions(-) diff --git a/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java b/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java index be50874d0..41a3d971e 100644 --- a/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java +++ b/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java @@ -1,5 +1,6 @@ package arcade.potts.agent.module; +import java.nio.channels.NotYetConnectedException; import java.security.InvalidParameterException; import java.util.ArrayList; import java.util.HashSet; @@ -22,6 +23,10 @@ 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; @@ -81,6 +86,12 @@ 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; /** @@ -127,6 +138,13 @@ 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); @@ -143,7 +161,7 @@ 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 = daughterStemWrapper(parentLoc, daughterLoc, divisionPlane); if (isDaughterStem) { makeDaughterStemCell(daughterLoc, sim, potts, random); @@ -328,7 +346,7 @@ 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 +369,38 @@ 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(); + + // If TRUE, the daughter should be stem. Otherwise, should be GMC + return normalVector.equals(new Vector(1.0, 0, 0)); + } + + /** + * Determines whether a daughter cell should remain a stem cell or differentiate into a GMC. + *

+ * 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 daughterStemWrapper(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. From 4448c567f638b42f27fe93188ad7d68cc4f5d88c Mon Sep 17 00:00:00 2001 From: daniellevahdat Date: Mon, 3 Nov 2025 00:12:54 -0800 Subject: [PATCH 38/59] add deterministic differentiation param --- src/arcade/potts/parameter.potts.xml | 1 + 1 file changed, 1 insertion(+) diff --git a/src/arcade/potts/parameter.potts.xml b/src/arcade/potts/parameter.potts.xml index 73f91b6cf..f373d98f6 100644 --- a/src/arcade/potts/parameter.potts.xml +++ b/src/arcade/potts/parameter.potts.xml @@ -80,6 +80,7 @@ + From e8cfb28311c91a7b76995b903e72fe722e169393 Mon Sep 17 00:00:00 2001 From: daniellevahdat Date: Mon, 3 Nov 2025 14:54:18 -0800 Subject: [PATCH 39/59] Remove unecessary import --- .../potts/agent/module/PottsModuleFlyStemProliferation.java | 1 - 1 file changed, 1 deletion(-) diff --git a/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java b/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java index 41a3d971e..f8dbc5bab 100644 --- a/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java +++ b/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java @@ -1,6 +1,5 @@ package arcade.potts.agent.module; -import java.nio.channels.NotYetConnectedException; import java.security.InvalidParameterException; import java.util.ArrayList; import java.util.HashSet; From 0a85b7ecf9430de37acb9cca02fc061679c083d3 Mon Sep 17 00:00:00 2001 From: daniellevahdat Date: Mon, 3 Nov 2025 15:33:50 -0800 Subject: [PATCH 40/59] Adding boolean flag in the setup file --- setup/setupWT.xml | 70 +++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 70 insertions(+) create mode 100644 setup/setupWT.xml diff --git a/setup/setupWT.xml b/setup/setupWT.xml new file mode 100644 index 000000000..8f89ee0cb --- /dev/null +++ b/setup/setupWT.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file From eeb551f8cdc7ff0a9fce4219dd6d101d4bc8e051 Mon Sep 17 00:00:00 2001 From: jannetty Date: Mon, 3 Nov 2025 15:52:06 -0800 Subject: [PATCH 41/59] added pdelike neuroblast growth (still need to add PDE like GMC growth) --- .../potts/agent/cell/PottsCellFactory.java | 10 +- .../PottsModuleFlyGMCDifferentiation.java | 3 +- .../PottsModuleFlyStemProliferation.java | 116 ++++-- ...oduleProliferationVolumeBasedDivision.java | 18 +- src/arcade/potts/parameter.potts.xml | 8 +- .../PottsModuleFlyStemProliferationTest.java | 393 ++++++++++++++---- ...eProliferationVolumeBasedDivisionTest.java | 8 +- 7 files changed, 415 insertions(+), 141 deletions(-) diff --git a/src/arcade/potts/agent/cell/PottsCellFactory.java b/src/arcade/potts/agent/cell/PottsCellFactory.java index 4d040f77a..8a17276f9 100644 --- a/src/arcade/potts/agent/cell/PottsCellFactory.java +++ b/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."); + } } } diff --git a/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java b/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java index 642619a27..1e39e2543 100644 --- a/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java +++ b/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java @@ -96,7 +96,8 @@ public void updateGrowthRate(Simulation sim) { if (dynamicGrowthRateVolume == false) { cellGrowthRate = cellGrowthRateBase; } else if (dynamicGrowthRateVolume == true) { - updateVolumeBasedGrowthRate(); + updateCellVolumeBasedGrowthRate( + cell.getLocation().getVolume(), cell.getCriticalVolume()); } } } diff --git a/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java b/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java index be50874d0..88845954b 100644 --- a/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java +++ b/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; @@ -22,6 +23,9 @@ 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; @@ -59,7 +63,7 @@ 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 +87,12 @@ 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 +123,10 @@ 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 +139,8 @@ public PottsModuleFlyStemProliferation(PottsCellFlyStem cell) { initialSize = cell.getVolume(); + pdeLike = (parameters.getInt("proliferation/PDELIKE") != 0); + setPhase(Phase.UNDEFINED); } @@ -165,24 +177,42 @@ 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 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 getNBNeighbors(Simulation sim) { Potts potts = ((PottsSimulation) sim).getPotts(); ArrayList voxels = ((PottsLocation) cell.getLocation()).getVoxels(); - HashSet stemNeighbors = new HashSet(); + HashSet stemNeighbors = new HashSet(); for (Voxel v : voxels) { HashSet uniqueIDs = potts.getUniqueIDs(v.x, v.y, v.z); @@ -193,50 +223,32 @@ 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. - * - *

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: - * - * 

-     *   hillRepression = K^n / (K^n + Np^n)
-     *   cellGrowthRate = cellGrowthRateBase * hillRepression
-     *
- * - * where: - * - *
    - *
  • Np is the number of neighboring neuroblasts - *
  • K is the half-max parameter for repression - * (proliferation/NB_CONTACT_HALF_MAX) - *
  • n is the Hill coefficient controlling steepness - * (proliferation/NB_CONTACT_HILL_N) - *
  • cellGrowthRateBase is the base growth rate in the absence of neighbors - *
- * - *

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 +590,18 @@ public static PottsLocation getBasalLocation( return (proj1 < proj2) ? loc2 : loc1; // higher projection = more basal } + + public HashSet getNBsInSimulation(Simulation sim) { + HashSet 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; + } } diff --git a/src/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivision.java b/src/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivision.java index aa1d188d6..97c8cb101 100644 --- a/src/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivision.java +++ b/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. - * - *

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: - * - * 

-     *   growthRate = baseGrowthRate * (volume / criticalVolume) ^ sensitivity
-     *
- * - * 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); } } diff --git a/src/arcade/potts/parameter.potts.xml b/src/arcade/potts/parameter.potts.xml index 73f91b6cf..a48eee0b1 100644 --- a/src/arcade/potts/parameter.potts.xml +++ b/src/arcade/potts/parameter.potts.xml @@ -63,11 +63,15 @@ + + + + - - + + diff --git a/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java b/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java index 3773f1023..4e9233bcd 100644 --- a/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java +++ b/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java @@ -1,12 +1,14 @@ package arcade.potts.agent.module; import java.util.ArrayList; +import java.util.Arrays; import java.util.HashSet; import org.junit.jupiter.api.AfterEach; import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.Test; import org.mockito.MockedStatic; import org.mockito.Mockito; +import sim.util.Bag; import sim.util.Double3D; import ec.util.MersenneTwisterFast; import arcade.core.env.grid.Grid; @@ -27,6 +29,7 @@ import arcade.potts.sim.Potts; import arcade.potts.sim.PottsSimulation; import arcade.potts.util.PottsEnums.Phase; +import arcade.potts.util.PottsEnums.State; import static org.junit.jupiter.api.Assertions.*; import static org.mockito.ArgumentMatchers.any; import static org.mockito.ArgumentMatchers.anyDouble; @@ -699,10 +702,11 @@ public void addCell_WTVolumeSwap_swapsVoxelsAndCreatesNewCell() { when(stemCell.getStemType()).thenReturn(PottsCellFlyStem.StemType.WT); when(parameters.getString("proliferation/APICAL_AXIS_RULESET")).thenReturn("global"); when(stemCell.getApicalAxis()).thenReturn(new Vector(0, 1, 0)); - when(parameters.getDouble("proliferation/SIZE_TARGET")) - .thenReturn(1.0); // default for volume - when(parameters.getInt("proliferation/VOLUME_BASED_CRITICAL_VOLUME")) - .thenReturn(0); // use classic mode + when(parameters.getDouble("proliferation/SIZE_TARGET")).thenReturn(1.0); // default for + // volume + when(parameters.getInt("proliferation/VOLUME_BASED_CRITICAL_VOLUME")).thenReturn(0); // use + // classic + // mode // Set up the condition that parent volume < daughter volume → stem/daughter swap required when(stemLoc.getVolume()).thenReturn(5.0); @@ -856,145 +860,392 @@ public void addCell_MUDMUTOffsetBelowThreshold_createsGMCWithVolumeSwap() { } @Test - public void getNumNBNeighbors_withTwoUniqueStemNeighbors_returnsCorrectCount() { + public void getNBNeighbors_withTwoUniqueStemNeighbors_returnsCorrectSet() { module = spy(new PottsModuleFlyStemProliferation(stemCell)); + // Stem voxels (two positions) ArrayList voxels = new ArrayList<>(); voxels.add(new Voxel(0, 0, 0)); voxels.add(new Voxel(1, 0, 0)); when(stemLoc.getVoxels()).thenReturn(voxels); - // Unique IDs returned by potts - HashSet idsVoxel1 = new HashSet<>(); - idsVoxel1.add(10); - idsVoxel1.add(11); - HashSet idsVoxel2 = new HashSet<>(); - idsVoxel2.add(11); // repeat → should still count neighbor 11 only once - idsVoxel2.add(12); - + // Unique IDs returned by Potts per voxel + HashSet idsVoxel1 = new HashSet<>(Arrays.asList(10, 11)); + HashSet idsVoxel2 = new HashSet<>(Arrays.asList(11, 12)); // 11 repeats when(potts.getUniqueIDs(0, 0, 0)).thenReturn(idsVoxel1); when(potts.getUniqueIDs(1, 0, 0)).thenReturn(idsVoxel2); // Neighbors - PottsCell neighbor10 = mock(PottsCell.class); - PottsCell neighbor11 = mock(PottsCell.class); - PottsCell neighbor12 = mock(PottsCell.class); + PottsCellFlyStem nb10 = mock(PottsCellFlyStem.class); + PottsCellFlyStem nb11 = mock(PottsCellFlyStem.class); + PottsCell nb12OtherPop = mock(PottsCell.class); - when(neighbor10.getID()).thenReturn(10); - when(neighbor11.getID()).thenReturn(11); - when(neighbor12.getID()).thenReturn(12); - when(stemCell.getID()).thenReturn(42); + when(nb10.getID()).thenReturn(10); + when(nb11.getID()).thenReturn(11); + when(nb12OtherPop.getID()).thenReturn(12); - when(neighbor10.getPop()).thenReturn(3); // match cell.getPop - when(neighbor11.getPop()).thenReturn(3); // match cell.getPop - when(neighbor12.getPop()).thenReturn(99); // no match + // Stem pop matches 3 + when(stemCell.getPop()).thenReturn(3); + when(nb10.getPop()).thenReturn(3); + when(nb11.getPop()).thenReturn(3); + when(nb12OtherPop.getPop()).thenReturn(99); // filtered - when(grid.getObjectAt(10)).thenReturn(neighbor10); - when(grid.getObjectAt(11)).thenReturn(neighbor11); - when(grid.getObjectAt(12)).thenReturn(neighbor12); + when(stemCell.getID()).thenReturn(42); - int numNeighbors = module.getNumNBNeighbors(sim); + when(grid.getObjectAt(10)).thenReturn(nb10); + when(grid.getObjectAt(11)).thenReturn(nb11); + when(grid.getObjectAt(12)).thenReturn(nb12OtherPop); - assertEquals(2, numNeighbors, "Should count 2 unique matching neighbors (10 and 11)"); + HashSet neighbors = module.getNBNeighbors(sim); + + assertEquals(2, neighbors.size(), "Should contain 2 unique matching neighbors (10 and 11)"); + assertTrue(neighbors.contains(nb10)); + assertTrue(neighbors.contains(nb11)); } @Test - public void getNumNBNeighbors_noMatchingNeighbors_returnsZero() { + public void getNBNeighbors_noMatchingNeighbors_returnsEmptySet() { module = spy(new PottsModuleFlyStemProliferation(stemCell)); ArrayList voxels = new ArrayList<>(); voxels.add(new Voxel(0, 0, 0)); when(stemLoc.getVoxels()).thenReturn(voxels); - HashSet ids = new HashSet<>(); - ids.add(50); + HashSet ids = new HashSet<>(Arrays.asList(50)); when(potts.getUniqueIDs(0, 0, 0)).thenReturn(ids); PottsCell nonStemNeighbor = mock(PottsCell.class); - when(nonStemNeighbor.getPop()).thenReturn(99); // doesn't match stem pop + when(nonStemNeighbor.getPop()).thenReturn(99); // not stem pop when(nonStemNeighbor.getID()).thenReturn(50); when(grid.getObjectAt(50)).thenReturn(nonStemNeighbor); + when(stemCell.getPop()).thenReturn(3); when(stemCell.getID()).thenReturn(42); - int numNeighbors = module.getNumNBNeighbors(sim); + HashSet neighbors = module.getNBNeighbors(sim); - assertEquals(0, numNeighbors, "No neighbors should be counted when pops do not match."); + assertNotNull(neighbors); + assertTrue(neighbors.isEmpty(), "No neighbors should be returned when pops do not match."); } @Test - public void getNumNBNeighbors_called_doesNotCountSelf() { + public void getNBNeighbors_doesNotIncludeSelf() { module = spy(new PottsModuleFlyStemProliferation(stemCell)); ArrayList voxels = new ArrayList<>(); voxels.add(new Voxel(0, 0, 0)); when(stemLoc.getVoxels()).thenReturn(voxels); - HashSet ids = new HashSet<>(); - ids.add(42); // same as sim.getID() mock (self) + // Potts returns this cell's own ID + when(stemCell.getID()).thenReturn(42); + when(stemCell.getPop()).thenReturn(3); + + HashSet ids = new HashSet<>(Arrays.asList(42)); when(potts.getUniqueIDs(0, 0, 0)).thenReturn(ids); - PottsCell selfCell = stemCell; // or mock another PottsCell with same pop - when(grid.getObjectAt(42)).thenReturn(selfCell); + when(grid.getObjectAt(42)).thenReturn(stemCell); - int numNeighbors = module.getNumNBNeighbors(sim); - assertEquals(0, numNeighbors, "Self should not be counted as a neighbor"); + HashSet neighbors = module.getNBNeighbors(sim); + assertTrue(neighbors.isEmpty(), "Self should not be included as a neighbor"); } @Test - public void updateNBContactGrowthRate_noNeighbors_returnsBaseGrowthRate() { - // Mock parameters - when(parameters.getDouble("proliferation/NB_CONTACT_HALF_MAX")).thenReturn(5.0); + public void getNBsInSimulation_emptyBag_returnsEmptySet() { + Bag bag = new Bag(); // real MASON Bag + when(grid.getAllObjects()).thenReturn(bag); + + module = new PottsModuleFlyStemProliferation(stemCell); + HashSet result = module.getNBsInSimulation(sim); + + assertNotNull(result); + assertTrue(result.isEmpty(), "Empty grid should yield empty set"); + } + + @Test + public void getNBsInSimulation_mixedObjects_returnsOnlyMatchingFlyStems() { + // Arrange: matching NB, non-matching NB, matching non-FlyStem, random object, matching NB + PottsCellFlyStem nbMatch1 = mock(PottsCellFlyStem.class); + when(nbMatch1.getPop()).thenReturn(3); + + PottsCellFlyStem nbOtherPop = mock(PottsCellFlyStem.class); + when(nbOtherPop.getPop()).thenReturn(99); + + PottsCell nonNBButSamePop = mock(PottsCell.class); + when(nonNBButSamePop.getPop()).thenReturn(3); + + Object random = new Object(); + + PottsCellFlyStem nbMatch2 = mock(PottsCellFlyStem.class); + when(nbMatch2.getPop()).thenReturn(3); + + Bag bag = new Bag(); + bag.add(nbMatch1); + bag.add(nbOtherPop); + bag.add(nonNBButSamePop); + bag.add(random); + bag.add(nbMatch2); + when(grid.getAllObjects()).thenReturn(bag); + + when(stemCell.getPop()).thenReturn(3); + + module = new PottsModuleFlyStemProliferation(stemCell); + HashSet result = module.getNBsInSimulation(sim); + + assertEquals(2, result.size(), "Should return exactly the two matching FlyStem NBs"); + assertTrue(result.contains(nbMatch1)); + assertTrue(result.contains(nbMatch2)); + } + + @Test + public void getNBsInSimulation_includesSelfCell() { + // The module's 'cell' has pop = 3 (already stubbed in @BeforeEach) + when(stemCell.getPop()).thenReturn(3); + + // Bag contains: self (FlyStem, pop 3), another FlyStem pop 3, a non-FlyStem pop 3, and a + // random object + PottsCellFlyStem another = mock(PottsCellFlyStem.class); + when(another.getPop()).thenReturn(3); + PottsCell nonFlyStemSamePop = mock(PottsCell.class); + when(nonFlyStemSamePop.getPop()).thenReturn(3); + Object random = new Object(); + + Bag bag = new Bag(); + bag.add(stemCell); // self + bag.add(another); // matching FlyStem + bag.add(nonFlyStemSamePop); // same pop but NOT FlyStem → should be ignored + bag.add(random); // ignored + + when(grid.getAllObjects()).thenReturn(bag); + + module = new PottsModuleFlyStemProliferation(stemCell); + HashSet result = module.getNBsInSimulation(sim); + + assertTrue(result.contains(stemCell), "Result should include the module's own stem cell."); + assertTrue(result.contains(another), "Result should include other matching FlyStem cells."); + assertEquals( + 2, + result.size(), + "Only the two FlyStem cells with matching pop should be returned."); + } + + @Test + public void updateVolumeBasedGrowthRate_pdeLikeFalse_usesCellVolume() { + // pdeLike = 0 → should call updateCellVolumeBasedGrowthRate with THIS cell's volume + when(parameters.getInt("proliferation/PDELIKE")).thenReturn(0); + when(parameters.getInt("proliferation/DYNAMIC_GROWTH_RATE_NB_CONTACT")).thenReturn(1); + + // Make the current cell's volume distinctive so we can verify it + when(stemCell.getLocation()).thenReturn(stemLoc); + when(stemLoc.getVolume()).thenReturn(42.5); + + module = spy(new PottsModuleFlyStemProliferation(stemCell)); + + // We only want to verify the value it was called with + doNothing().when(module).updateCellVolumeBasedGrowthRate(anyDouble(), anyDouble()); + when(stemCell.getCriticalVolume()).thenReturn(100.0); + + module.updateVolumeBasedGrowthRate(sim); + + verify(module, times(1)).updateCellVolumeBasedGrowthRate(eq(42.5), eq(100.0)); + verify(module, never()).getNBsInSimulation(any()); + } + + @Test + public void + updateVolumeBasedGrowthRate_pdeLikeTrue_usesAverageVolumeAndAverageCritVolAcrossNBs() { + // pdeLike = 1 (PDE-like) and dynamicGrowthRateNBContact must be 0 to avoid ctor exception + when(parameters.getInt("proliferation/PDELIKE")).thenReturn(1); + when(parameters.getInt("proliferation/DYNAMIC_GROWTH_RATE_NB_CONTACT")).thenReturn(0); + + module = spy(new PottsModuleFlyStemProliferation(stemCell)); + + // NB mocks + PottsCellFlyStem nbA = mock(PottsCellFlyStem.class); + PottsCellFlyStem nbB = mock(PottsCellFlyStem.class); + PottsCellFlyStem nbC = mock(PottsCellFlyStem.class); + + // Location mocks for each NB + PottsLocation locA = mock(PottsLocation.class); + PottsLocation locB = mock(PottsLocation.class); + PottsLocation locC = mock(PottsLocation.class); + + when(nbA.getLocation()).thenReturn(locA); + when(nbB.getLocation()).thenReturn(locB); + when(nbC.getLocation()).thenReturn(locC); + + // Volumes: 10, 20, 40 -> avg = 70/3 + when(locA.getVolume()).thenReturn(10.0); + when(locB.getVolume()).thenReturn(20.0); + when(locC.getVolume()).thenReturn(40.0); + + // Critical volumes: 90, 110, 100 -> avg = 300/3 = 100 + when(nbA.getCriticalVolume()).thenReturn(90.0); + when(nbB.getCriticalVolume()).thenReturn(110.0); + when(nbC.getCriticalVolume()).thenReturn(100.0); + + HashSet allNBs = new HashSet<>(Arrays.asList(nbA, nbB, nbC)); + + doReturn(allNBs).when(module).getNBsInSimulation(sim); + doNothing().when(module).updateCellVolumeBasedGrowthRate(anyDouble(), anyDouble()); + + module.updateVolumeBasedGrowthRate(sim); + + double expectedAvgVol = (10.0 + 20.0 + 40.0) / 3.0; // 23.333333333333332 + double expectedAvgCrit = (90.0 + 110.0 + 100.0) / 3.0; // 100.0 + + verify(module, times(1)).getNBsInSimulation(sim); + verify(module, times(1)) + .updateCellVolumeBasedGrowthRate(eq(expectedAvgVol), eq(expectedAvgCrit)); + } + + @Test + public void updateGrowthRateBasedOnOtherNBs_pdeLikeFalse_usesNeighborsBranch() { + // pdeLike = 0 → neighbors branch + when(parameters.getInt("proliferation/PDELIKE")).thenReturn(0); + when(parameters.getInt("proliferation/DYNAMIC_GROWTH_RATE_NB_CONTACT")).thenReturn(1); + + when(parameters.getDouble("proliferation/NB_CONTACT_HALF_MAX")).thenReturn(4.0); when(parameters.getDouble("proliferation/NB_CONTACT_HILL_N")).thenReturn(2.0); - when(parameters.getDouble("proliferation/CELL_GROWTH_RATE")).thenReturn(10.0); + when(parameters.getDouble("proliferation/CELL_GROWTH_RATE")).thenReturn(12.0); module = spy(new PottsModuleFlyStemProliferation(stemCell)); - // Mock neighbor count - doReturn(0).when(module).getNumNBNeighbors(sim); + // N = 4 neighbors (K = 4, n = 2 → repression 0.5 → 12 * 0.5 = 6) + HashSet four = new HashSet<>(); + for (int i = 0; i < 4; i++) { + PottsCellFlyStem n = mock(PottsCellFlyStem.class); + when(n.getID()).thenReturn(100 + i); + four.add(n); + } + doReturn(four).when(module).getNBNeighbors(sim); + // Make sure population path is not used + doReturn(new HashSet()).when(module).getNBsInSimulation(sim); + + module.updateGrowthRateBasedOnOtherNBs(sim); - module.updateNBContactGrowthRate(sim); - assertEquals( - 10.0, - module.cellGrowthRate, - 1e-6, - "With 0 neighbors, hill repression should be 1.0"); + assertEquals(6.0, module.cellGrowthRate, 1e-6); + verify(module, times(1)).getNBNeighbors(sim); + verify(module, never()).getNBsInSimulation(sim); } @Test - public void updateNBContactGrowthRate_halfMaxNeighbors_returnsHalfBaseGrowthRate() { - // Mock parameters - when(parameters.getDouble("proliferation/NB_CONTACT_HALF_MAX")).thenReturn(5.0); + public void updateGrowthRateBasedOnOtherNBs_pdeLikeTrue_usesPopulationBranch() { + // pdeLike = 1 and dynamicGrowthRateNBContact = 0 to avoid constructor exception + when(parameters.getInt("proliferation/PDELIKE")).thenReturn(1); + when(parameters.getInt("proliferation/DYNAMIC_GROWTH_RATE_NB_CONTACT")).thenReturn(0); + + when(parameters.getDouble("proliferation/NB_CONTACT_HALF_MAX")).thenReturn(3.0); + when(parameters.getDouble("proliferation/NB_CONTACT_HILL_N")).thenReturn(2.0); + when(parameters.getDouble("proliferation/CELL_GROWTH_RATE")).thenReturn(20.0); + + module = spy(new PottsModuleFlyStemProliferation(stemCell)); + + // N = 6 in-simulation (K = 3, n = 2 → 9/(9+36)=0.2 → 4.0) + HashSet six = new HashSet<>(); + for (int i = 0; i < 6; i++) { + PottsCellFlyStem n = mock(PottsCellFlyStem.class); + when(n.getID()).thenReturn(200 + i); + six.add(n); + } + doReturn(new HashSet()).when(module).getNBNeighbors(sim); + doReturn(six).when(module).getNBsInSimulation(sim); + + module.updateGrowthRateBasedOnOtherNBs(sim); + + assertEquals(4.0, module.cellGrowthRate, 1e-6); + verify(module, times(1)).getNBsInSimulation(sim); + verify(module, never()).getNBNeighbors(sim); + } + + @Test + public void updateGrowthRateBasedOnOtherNBs_KZeroandZeroNeighbors_returnsBase() { + when(parameters.getInt("proliferation/PDELIKE")).thenReturn(0); + when(parameters.getInt("proliferation/DYNAMIC_GROWTH_RATE_NB_CONTACT")).thenReturn(1); + + when(parameters.getDouble("proliferation/NB_CONTACT_HALF_MAX")).thenReturn(0.0); // K = 0 when(parameters.getDouble("proliferation/NB_CONTACT_HILL_N")).thenReturn(2.0); when(parameters.getDouble("proliferation/CELL_GROWTH_RATE")).thenReturn(10.0); module = spy(new PottsModuleFlyStemProliferation(stemCell)); - // Mock neighbor count - doReturn(5).when(module).getNumNBNeighbors(sim); + // N = 0 → with your guard, repression = 1.0 when K=0 & N=0 + doReturn(new HashSet()).when(module).getNBNeighbors(sim); - module.updateNBContactGrowthRate(sim); - // Hill repression = K^n / (K^n + N^n) = 25 / (25 + 25) = 0.5 - assertEquals( - 5.0, - module.cellGrowthRate, - 1e-6, - "With 0 neighbors, hill repression should be 1.0"); + module.updateGrowthRateBasedOnOtherNBs(sim); + + assertEquals(10.0, module.cellGrowthRate, 1e-6); } @Test - public void updateNBContactGrowthRate_highNeighbors_returnsLowGrowthRate() { - when(parameters.getDouble("proliferation/NB_CONTACT_HALF_MAX")).thenReturn(5.0); + public void updateGrowthRateBasedOnOtherNBs_KZeroandPositiveNeighbors_returnsZero() { + when(parameters.getInt("proliferation/PDELIKE")).thenReturn(0); + when(parameters.getInt("proliferation/DYNAMIC_GROWTH_RATE_NB_CONTACT")).thenReturn(1); + + when(parameters.getDouble("proliferation/NB_CONTACT_HALF_MAX")).thenReturn(0.0); // K = 0 when(parameters.getDouble("proliferation/NB_CONTACT_HILL_N")).thenReturn(2.0); when(parameters.getDouble("proliferation/CELL_GROWTH_RATE")).thenReturn(10.0); module = spy(new PottsModuleFlyStemProliferation(stemCell)); - doReturn(20).when(module).getNumNBNeighbors(sim); + // N > 0 → with your guard, repression = 0.0 when K=0 & N>0 + HashSet one = new HashSet<>(); + PottsCellFlyStem n = mock(PottsCellFlyStem.class); + when(n.getID()).thenReturn(999); + one.add(n); + doReturn(one).when(module).getNBNeighbors(sim); + + module.updateGrowthRateBasedOnOtherNBs(sim); + + assertEquals(0.0, module.cellGrowthRate, 1e-9); + } + + @Test + public void updateGrowthRateBasedOnOtherNBs_hillExponentOne_linearCase() { + when(parameters.getInt("proliferation/PDELIKE")).thenReturn(0); + when(parameters.getInt("proliferation/DYNAMIC_GROWTH_RATE_NB_CONTACT")).thenReturn(1); + + when(parameters.getDouble("proliferation/NB_CONTACT_HALF_MAX")).thenReturn(4.0); + when(parameters.getDouble("proliferation/NB_CONTACT_HILL_N")).thenReturn(1.0); // linear + when(parameters.getDouble("proliferation/CELL_GROWTH_RATE")).thenReturn(10.0); + + module = spy(new PottsModuleFlyStemProliferation(stemCell)); + + // N = 2 → R = K/(K+N) = 4/(4+2) = 2/3 + HashSet two = new HashSet<>(); + for (int i = 0; i < 2; i++) { + PottsCellFlyStem nn = mock(PottsCellFlyStem.class); + when(nn.getID()).thenReturn(300 + i); + two.add(nn); + } + doReturn(two).when(module).getNBNeighbors(sim); + + module.updateGrowthRateBasedOnOtherNBs(sim); + + assertEquals(10.0 * (2.0 / 3.0), module.cellGrowthRate, 1e-6); + } + + @Test + public void updateGrowthRateBasedOnOtherNBs_largeNeighbors_approachesZero() { + when(parameters.getInt("proliferation/PDELIKE")).thenReturn(0); + when(parameters.getInt("proliferation/DYNAMIC_GROWTH_RATE_NB_CONTACT")).thenReturn(1); + + when(parameters.getDouble("proliferation/NB_CONTACT_HALF_MAX")).thenReturn(5.0); + when(parameters.getDouble("proliferation/NB_CONTACT_HILL_N")).thenReturn(3.0); + when(parameters.getDouble("proliferation/CELL_GROWTH_RATE")).thenReturn(7.0); + + module = spy(new PottsModuleFlyStemProliferation(stemCell)); + + // N = 100 >> K = 5 → repression ~ 0 + HashSet many = new HashSet<>(); + for (int i = 0; i < 100; i++) { + PottsCellFlyStem nn = mock(PottsCellFlyStem.class); + when(nn.getID()).thenReturn(400 + i); + many.add(nn); + } + doReturn(many).when(module).getNBNeighbors(sim); - module.updateNBContactGrowthRate(sim); + module.updateGrowthRateBasedOnOtherNBs(sim); - // Hill repression = 25 / (25 + 400) = 25 / 425 ≈ 0.0588 - assertEquals(10.0 * (25.0 / 425.0), module.cellGrowthRate, 1e-6); + assertTrue(module.cellGrowthRate < 0.01, "Growth should be ~0 with very large N."); } } diff --git a/test/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivisionTest.java b/test/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivisionTest.java index 9229ae9c0..4c41c1661 100644 --- a/test/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivisionTest.java +++ b/test/arcade/potts/agent/module/PottsModuleProliferationVolumeBasedDivisionTest.java @@ -93,7 +93,7 @@ public void updateVolumeBasedGrowthRate_ratioOne_keepsBaseRate() { .PottsModuleProliferationVolumeBasedDivisionMock module = new PottsModuleProliferationVolumeBasedDivisionMock(cell); - module.updateVolumeBasedGrowthRate(); + module.updateCellVolumeBasedGrowthRate(loc.getVolume(), cell.getCriticalVolume()); assertEquals(4.0, module.cellGrowthRate, 1e-9); } @@ -118,7 +118,7 @@ public void updateVolumeBasedGrowthRate_ratioGreaterThanOne_scalesUpByPowerLaw() .PottsModuleProliferationVolumeBasedDivisionMock module = new PottsModuleProliferationVolumeBasedDivisionMock(cell); - module.updateVolumeBasedGrowthRate(); + module.updateCellVolumeBasedGrowthRate(loc.getVolume(), cell.getCriticalVolume()); assertEquals(16.0, module.cellGrowthRate, 1e-9); } @@ -143,7 +143,7 @@ public void updateVolumeBasedGrowthRate_ratioLessThanOne_scalesDownByPowerLaw() .PottsModuleProliferationVolumeBasedDivisionMock module = new PottsModuleProliferationVolumeBasedDivisionMock(cell); - module.updateVolumeBasedGrowthRate(); + module.updateCellVolumeBasedGrowthRate(loc.getVolume(), cell.getCriticalVolume()); assertEquals(1.0, module.cellGrowthRate, 1e-9); } @@ -168,7 +168,7 @@ public void updateVolumeBasedGrowthRate_zeroSensitivity_returnsBaseRateRegardles .PottsModuleProliferationVolumeBasedDivisionMock module = new PottsModuleProliferationVolumeBasedDivisionMock(cell); - module.updateVolumeBasedGrowthRate(); + module.updateCellVolumeBasedGrowthRate(loc.getVolume(), cell.getCriticalVolume()); assertEquals(3.5, module.cellGrowthRate, 1e-9); } } From cada3a4a704780018ec4a850e25cf1d707613890 Mon Sep 17 00:00:00 2001 From: daniellevahdat Date: Mon, 3 Nov 2025 16:58:13 -0800 Subject: [PATCH 42/59] spotlessApply --- .../PottsModuleFlyStemProliferation.java | 24 +-- .../PottsModuleFlyStemProliferationTest.java | 174 +++++++++--------- 2 files changed, 97 insertions(+), 101 deletions(-) diff --git a/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java b/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java index f8dbc5bab..6233dc201 100644 --- a/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java +++ b/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java @@ -25,7 +25,6 @@ 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; @@ -85,7 +84,6 @@ public class PottsModuleFlyStemProliferation extends PottsModuleProliferationVol */ final double nbContactHillN; - /* * Boolean flag for whether the daughter cell's differentiation is determined deterministically. */ @@ -137,10 +135,12 @@ 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"); + 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"); @@ -160,7 +160,7 @@ public void addCell(MersenneTwisterFast random, Simulation sim) { PottsLocation2D parentLoc = (PottsLocation2D) cell.getLocation(); PottsLocation daughterLoc = (PottsLocation) parentLoc.split(random, divisionPlane); - boolean isDaughterStem = daughterStemWrapper(parentLoc, daughterLoc, divisionPlane); + boolean isDaughterStem = daughterStem(parentLoc, daughterLoc, divisionPlane); if (isDaughterStem) { makeDaughterStemCell(daughterLoc, sim, potts, random); @@ -385,16 +385,18 @@ private boolean daughterStemDeterministic(Plane divisionPlane) { /** * Determines whether a daughter cell should remain a stem cell or differentiate into a GMC. - *

- * This method serves as a wrapper that delegates to either a deterministic or rule-based + * + *

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 + * @return {@code true} if the daughter should remain a stem cell; {@code false} if it should be + * a GMC */ - public boolean daughterStemWrapper(PottsLocation2D parentsLoc, PottsLocation daughterLoc, Plane divisionPlane) { + public boolean daughterStem( + PottsLocation2D parentsLoc, PottsLocation daughterLoc, Plane divisionPlane) { return hasDeterministicDifferentiation ? daughterStemDeterministic(divisionPlane) : daughterStemRuleBasedDifferentiation(parentsLoc, daughterLoc); diff --git a/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java b/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java index 3773f1023..e380081ad 100644 --- a/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java +++ b/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java @@ -27,6 +27,7 @@ import arcade.potts.sim.Potts; import arcade.potts.sim.PottsSimulation; import arcade.potts.util.PottsEnums.Phase; +import arcade.potts.util.PottsEnums.State; import static org.junit.jupiter.api.Assertions.*; import static org.mockito.ArgumentMatchers.any; import static org.mockito.ArgumentMatchers.anyDouble; @@ -104,6 +105,8 @@ public final void setup() { when(parameters.getString("proliferation/DIFFERENTIATION_RULESET")).thenReturn("volume"); when(parameters.getDouble("proliferation/DIFFERENTIATION_RULESET_EQUALITY_RANGE")) .thenReturn(0.5); + when(parameters.getString("proliferation/HAS_DETERMINISTIC_DIFFERENTIATION")) + .thenReturn("TRUE"); // Link selection GrabBag links = mock(GrabBag.class); @@ -484,94 +487,6 @@ public void step_volumeAtCheckpoint_callsAddCellPhaseStaysUndefined() { assertEquals(Phase.UNDEFINED, module.phase); // remains UNDEFINED } - // Differentiation rule tests - - @Test - public void daughterStem_stemTypeWT_returnsFalse() { - when(stemCell.getStemType()).thenReturn(PottsCellFlyStem.StemType.WT); - - module = new PottsModuleFlyStemProliferation(stemCell); - boolean result = module.daughterStem(stemLoc, daughterLoc); - - assertFalse(result); - } - - @Test - public void daughterStem_volumeRule_differenceWithinRange_returnsTrue() { - when(stemCell.getStemType()).thenReturn(PottsCellFlyStem.StemType.MUDMUT); - when(parameters.getString("proliferation/DIFFERENTIATION_RULESET")).thenReturn("volume"); - when(parameters.getDouble("proliferation/DIFFERENTIATION_RULESET_EQUALITY_RANGE")) - .thenReturn(1.0); - when(stemLoc.getVolume()).thenReturn(10.0); - when(daughterLoc.getVolume()).thenReturn(10.5); // difference = 0.5 < 1.0 - - module = new PottsModuleFlyStemProliferation(stemCell); - boolean result = module.daughterStem(stemLoc, daughterLoc); - - assertTrue(result); - } - - @Test - public void daughterStem_volumeRule_differenceOutsideRange_returnsFalse() { - when(stemCell.getStemType()).thenReturn(PottsCellFlyStem.StemType.MUDMUT); - when(parameters.getString("proliferation/DIFFERENTIATION_RULESET")).thenReturn("volume"); - when(parameters.getDouble("proliferation/DIFFERENTIATION_RULESET_EQUALITY_RANGE")) - .thenReturn(0.5); - when(stemLoc.getVolume()).thenReturn(10.0); - when(daughterLoc.getVolume()).thenReturn(11.0); // difference = 1.0 > 0.5 - - module = new PottsModuleFlyStemProliferation(stemCell); - boolean result = module.daughterStem(stemLoc, daughterLoc); - - assertFalse(result); - } - - @Test - public void daughterStem_locationRule_differenceWithinRange_returnsTrue() { - when(stemCell.getStemType()).thenReturn(PottsCellFlyStem.StemType.MUDMUT); - when(parameters.getString("proliferation/DIFFERENTIATION_RULESET")).thenReturn("location"); - when(parameters.getDouble("proliferation/DIFFERENTIATION_RULESET_EQUALITY_RANGE")) - .thenReturn(0.5); - when(stemLoc.getCentroid()).thenReturn(new double[] {0, 1.0, 0}); - when(daughterLoc.getCentroid()).thenReturn(new double[] {0, 1.3, 0}); // difference = 0.3 - when(stemCell.getApicalAxis()).thenReturn(new Vector(0, 1, 0)); - - module = new PottsModuleFlyStemProliferation(stemCell); - boolean result = module.daughterStem(stemLoc, daughterLoc); - - assertTrue(result); - } - - @Test - public void daughterStem_locationRule_differenceOutsideRange_returnsFalse() { - when(stemCell.getStemType()).thenReturn(PottsCellFlyStem.StemType.MUDMUT); - when(parameters.getString("proliferation/DIFFERENTIATION_RULESET")).thenReturn("location"); - when(parameters.getDouble("proliferation/DIFFERENTIATION_RULESET_EQUALITY_RANGE")) - .thenReturn(0.5); - when(stemLoc.getCentroid()).thenReturn(new double[] {0, 1.0, 0}); - when(daughterLoc.getCentroid()).thenReturn(new double[] {0, 1.7, 0}); // difference = 0.7 - when(stemCell.getApicalAxis()).thenReturn(new Vector(0, 1, 0)); - - module = new PottsModuleFlyStemProliferation(stemCell); - boolean result = module.daughterStem(stemLoc, daughterLoc); - - assertFalse(result); - } - - @Test - public void daughterStem_invalidRule_throwsException() { - when(stemCell.getStemType()).thenReturn(PottsCellFlyStem.StemType.MUDMUT); - when(parameters.getString("proliferation/DIFFERENTIATION_RULESET")).thenReturn("banana"); - when(parameters.getDouble("proliferation/DIFFERENTIATION_RULESET_EQUALITY_RANGE")) - .thenReturn(0.5); - when(stemLoc.getCentroid()).thenReturn(new double[] {0, 1.0, 0}); - when(daughterLoc.getCentroid()).thenReturn(new double[] {0, 1.2, 0}); - - module = new PottsModuleFlyStemProliferation(stemCell); - assertThrows( - IllegalArgumentException.class, () -> module.daughterStem(stemLoc, daughterLoc)); - } - // Apical axis rule tests @Test @@ -784,6 +699,7 @@ public void addCell_WTVolumeNoSwap_doesNotSwapVoxelsAndCreatesNewCell() { @Test public void addCell_MUDMUTOffsetAboveThreshold_createsStemCell() { when(stemCell.getStemType()).thenReturn(PottsCellFlyStem.StemType.MUDMUT); + when(parameters.getString("proliferation/DIFFERENTIATION_RULESET")).thenReturn("volume"); when(parameters.getString("proliferation/APICAL_AXIS_RULESET")).thenReturn("global"); when(stemCell.getApicalAxis()).thenReturn(new Vector(0, 1, 0)); @@ -813,7 +729,7 @@ public void addCell_MUDMUTOffsetAboveThreshold_createsStemCell() { Plane dummyPlane = mock(Plane.class); doReturn(dummyPlane).when(module).getMUDDivisionPlane(eq(stemCell)); when(stemLoc.split(eq(random), eq(dummyPlane))).thenReturn(daughterLoc); - doReturn(true).when(module).daughterStem(any(), any()); + doReturn(true).when(module).daughterStem(any(), any(), any()); module.addCell(random, sim); @@ -823,6 +739,7 @@ public void addCell_MUDMUTOffsetAboveThreshold_createsStemCell() { @Test public void addCell_MUDMUTOffsetBelowThreshold_createsGMCWithVolumeSwap() { when(stemCell.getStemType()).thenReturn(PottsCellFlyStem.StemType.MUDMUT); + when(parameters.getString("proliferation/DIFFERENTIATION_RULESET")).thenReturn("volume"); when(parameters.getString("proliferation/APICAL_AXIS_RULESET")).thenReturn("global"); when(stemCell.getApicalAxis()).thenReturn(new Vector(0, 1, 0)); @@ -845,7 +762,7 @@ public void addCell_MUDMUTOffsetBelowThreshold_createsGMCWithVolumeSwap() { .when(module) .getWTDivisionPlaneWithRotationalVariance(eq(stemCell), anyDouble()); when(stemLoc.split(eq(random), eq(dummyPlane))).thenReturn(daughterLoc); - doReturn(false).when(module).daughterStem(any(), any()); + doReturn(false).when(module).daughterStem(any(), any(), any()); try (MockedStatic mocked = mockStatic(PottsLocation.class)) { module.addCell(random, sim); @@ -997,4 +914,81 @@ public void updateNBContactGrowthRate_highNeighbors_returnsLowGrowthRate() { // Hill repression = 25 / (25 + 400) = 25 / 425 ≈ 0.0588 assertEquals(10.0 * (25.0 / 425.0), module.cellGrowthRate, 1e-6); } + + @Test + void testDaughterStem_DeterministicTrue() { + // Mock parameters + when(parameters.getString("proliferation/HAS_DETERMINISTIC_DIFFERENTIATION")) + .thenReturn("TRUE"); + when(parameters.getString("proliferation/DIFFERENTIATION_RULESET")).thenReturn("volume"); + when(parameters.getDouble("proliferation/DIFFERENTIATION_RULESET_EQUALITY_RANGE")) + .thenReturn(0.1); + + // Mock cell type + division plane normal vector + Plane plane = mock(Plane.class); + when(plane.getUnitNormalVector()).thenReturn(new Vector(1.0, 0, 0)); + + // Construct module + PottsModuleFlyStemProliferation module = new PottsModuleFlyStemProliferation(stemCell); + + // Call + boolean result = module.daughterStem(stemLoc, daughterLoc, plane); + + // Verify + assertTrue( + result, + "Expected daughterStemWrapper to return true for deterministic orientation"); + } + + @Test + void testDaughterStem_DeterministicFalse() { + when(parameters.getString("proliferation/HAS_DETERMINISTIC_DIFFERENTIATION")) + .thenReturn("TRUE"); + when(parameters.getString("proliferation/DIFFERENTIATION_RULESET")).thenReturn("volume"); + when(parameters.getDouble("proliferation/DIFFERENTIATION_RULESET_EQUALITY_RANGE")) + .thenReturn(0.1); + + Plane plane = mock(Plane.class); + when(plane.getUnitNormalVector()).thenReturn(new Vector(0, 1.0, 0)); + + PottsModuleFlyStemProliferation module = new PottsModuleFlyStemProliferation(stemCell); + + boolean result = module.daughterStem(stemLoc, daughterLoc, plane); + + assertFalse(result, "Expected false when division plane normal is not (1,0,0)"); + } + + @Test + void testDaughterStem_RuleBased_VolumeTrue() { + when(parameters.getString("proliferation/HAS_DETERMINISTIC_DIFFERENTIATION")) + .thenReturn("FALSE"); + when(parameters.getString("proliferation/DIFFERENTIATION_RULESET")).thenReturn("volume"); + when(parameters.getDouble("proliferation/DIFFERENTIATION_RULESET_EQUALITY_RANGE")) + .thenReturn(10.0); // large enough for |10 - 5| < 10 + + when(stemCell.getStemType()).thenReturn(PottsCellFlyStem.StemType.MUDMUT); + + PottsModuleFlyStemProliferation module = new PottsModuleFlyStemProliferation(stemCell); + + boolean result = module.daughterStem(stemLoc, daughterLoc, mock(Plane.class)); + + assertTrue(result, "Expected true since |10-5| < range"); + } + + @Test + void testDaughterStem_RuleBased_VolumeFalse() { + when(parameters.getString("proliferation/HAS_DETERMINISTIC_DIFFERENTIATION")) + .thenReturn("FALSE"); + when(parameters.getString("proliferation/DIFFERENTIATION_RULESET")).thenReturn("volume"); + when(parameters.getDouble("proliferation/DIFFERENTIATION_RULESET_EQUALITY_RANGE")) + .thenReturn(1.0); // |10 - 5| = 5 > 1 + + when(stemCell.getStemType()).thenReturn(PottsCellFlyStem.StemType.MUDMUT); + + PottsModuleFlyStemProliferation module = new PottsModuleFlyStemProliferation(stemCell); + + boolean result = module.daughterStem(stemLoc, daughterLoc, mock(Plane.class)); + + assertFalse(result, "Expected false since |10-5| > range"); + } } From 10d7c92e935354576c8aad4864ca6ccb459ec132 Mon Sep 17 00:00:00 2001 From: jannetty Date: Mon, 3 Nov 2025 19:26:25 -0800 Subject: [PATCH 43/59] adding GMC pde like flag --- .../PottsModuleFlyGMCDifferentiation.java | 40 +++++++++++++++++-- .../PottsModuleFlyStemProliferation.java | 3 -- 2 files changed, 36 insertions(+), 7 deletions(-) diff --git a/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java b/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java index 1e39e2543..dc32c6cd0 100644 --- a/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java +++ b/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java @@ -20,6 +20,8 @@ */ public class PottsModuleFlyGMCDifferentiation extends PottsModuleProliferationVolumeBasedDivision { + Boolean pdeLike; + /** * Creates a fly GMC proliferation module. * @@ -27,6 +29,7 @@ public class PottsModuleFlyGMCDifferentiation extends PottsModuleProliferationVo */ public PottsModuleFlyGMCDifferentiation(PottsCellFlyGMC cell) { super(cell); + pdeLike = (cell.getParameters().getInt("proliferation/PDELIKE") != 0); } /** @@ -93,11 +96,40 @@ void addCell(MersenneTwisterFast random, Simulation sim) { } public void updateGrowthRate(Simulation sim) { - if (dynamicGrowthRateVolume == false) { + if (!dynamicGrowthRateVolume) { cellGrowthRate = cellGrowthRateBase; - } else if (dynamicGrowthRateVolume == true) { - updateCellVolumeBasedGrowthRate( - cell.getLocation().getVolume(), cell.getCriticalVolume()); + } 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); + } } } } diff --git a/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java b/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java index 88845954b..2df7ac42d 100644 --- a/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java +++ b/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java @@ -23,9 +23,6 @@ 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; From a59d11f2d8e30afd94d48af037093622bdc66aae Mon Sep 17 00:00:00 2001 From: jannetty Date: Mon, 3 Nov 2025 19:32:47 -0800 Subject: [PATCH 44/59] add test for GMC PDE like behavior --- .../PottsModuleFlyGMCDifferentiationTest.java | 110 +++++++++++++++++- 1 file changed, 109 insertions(+), 1 deletion(-) diff --git a/test/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiationTest.java b/test/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiationTest.java index c1b04e272..b3babde5d 100644 --- a/test/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiationTest.java +++ b/test/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiationTest.java @@ -133,7 +133,8 @@ final void tearDown() { @Test public void addCell_called_callsExpectedMethods() { - // When the module calls make() on the cell, return Quiescent PottsCellContainer mock + // When the module calls make() on the cell, return Quiescent PottsCellContainer + // mock container = mock(PottsCellContainer.class); when(gmcCell.make(eq(123), eq(State.QUIESCENT), any(MersenneTwisterFast.class))) .thenReturn(container); @@ -164,4 +165,111 @@ public void addCell_called_callsExpectedMethods() { verify(diffCell).reset(dummyIDs, dummyRegions); verify(diffCell).schedule(schedule); } + + @Test + public void updateGrowthRate_dynamicOff_setsBaseRate() { + // dynamicGrowthRateVolume = 0; base rate used + when(gmcCell.getParameters()).thenReturn(parameters); + when(parameters.getInt("proliferation/DYNAMIC_GROWTH_RATE_VOLUME")).thenReturn(0); + when(parameters.getDouble("proliferation/CELL_GROWTH_RATE")).thenReturn(7.5); + + PottsModuleFlyGMCDifferentiation module = new PottsModuleFlyGMCDifferentiation(gmcCell); + + module.updateGrowthRate(sim); + org.junit.jupiter.api.Assertions.assertEquals(7.5, module.cellGrowthRate, 1e-9); + } + + @Test + public void updateGrowthRate_dynamicOn_pdeLikeFalse_usesSelfVolumeAndCrit() { + when(gmcCell.getParameters()).thenReturn(parameters); + when(parameters.getInt("proliferation/DYNAMIC_GROWTH_RATE_VOLUME")).thenReturn(1); + when(parameters.getDouble("proliferation/CELL_GROWTH_RATE")).thenReturn(4.0); + when(parameters.getInt("proliferation/PDELIKE")).thenReturn(0); + + // Self values + when(gmcCell.getCriticalVolume()).thenReturn(150.0); + when(gmcCell.getLocation().getVolume()).thenReturn(30.0); + + PottsModuleFlyGMCDifferentiation module = + org.mockito.Mockito.spy(new PottsModuleFlyGMCDifferentiation(gmcCell)); + + org.mockito.Mockito.doNothing() + .when(module) + .updateCellVolumeBasedGrowthRate( + org.mockito.ArgumentMatchers.anyDouble(), + org.mockito.ArgumentMatchers.anyDouble()); + + module.updateGrowthRate(sim); + + org.mockito.Mockito.verify(module) + .updateCellVolumeBasedGrowthRate( + org.mockito.ArgumentMatchers.eq(30.0), + org.mockito.ArgumentMatchers.eq(150.0)); + } + + @Test + public void updateGrowthRate_dynamicOnPdeLikeTrue_usesAverageVolumeAndCritAcrossGMCs() { + // Flags + when(gmcCell.getParameters()).thenReturn(parameters); + when(parameters.getInt("proliferation/DYNAMIC_GROWTH_RATE_VOLUME")).thenReturn(1); + when(parameters.getDouble("proliferation/CELL_GROWTH_RATE")).thenReturn(4.0); + when(parameters.getInt("proliferation/PDELIKE")).thenReturn(1); + + // Same population for all GMCs we want included + when(gmcCell.getPop()).thenReturn(3); + + // Self (included in average) + when(gmcCell.getLocation().getVolume()).thenReturn(30.0); + when(gmcCell.getCriticalVolume()).thenReturn(150.0); + + // Two more GMCs in same population + PottsCellFlyGMC gmcB = mock(PottsCellFlyGMC.class); + PottsCellFlyGMC gmcC = mock(PottsCellFlyGMC.class); + when(gmcB.getPop()).thenReturn(3); + when(gmcC.getPop()).thenReturn(3); + + PottsLocation locB = mock(PottsLocation.class); + PottsLocation locC = mock(PottsLocation.class); + when(gmcB.getLocation()).thenReturn(locB); + when(gmcC.getLocation()).thenReturn(locC); + when(locB.getVolume()).thenReturn(10.0); + when(locC.getVolume()).thenReturn(20.0); + when(gmcB.getCriticalVolume()).thenReturn(100.0); + when(gmcC.getCriticalVolume()).thenReturn(200.0); + + // Noise: different type and/or different pop → must be ignored + PottsCell randomOtherPop = mock(PottsCell.class); + when(randomOtherPop.getPop()).thenReturn(99); + PottsCellFlyNeuron neuronSamePop = mock(PottsCellFlyNeuron.class); + when(neuronSamePop.getPop()).thenReturn(3); + + // Bag with self + two GMCs + noise + sim.util.Bag bag = new sim.util.Bag(); + bag.add(gmcCell); // self GMC (pop 3) + bag.add(gmcB); // GMC (pop 3) + bag.add(gmcC); // GMC (pop 3) + bag.add(randomOtherPop); // different pop → ignored + bag.add(neuronSamePop); // not a GMC → ignored + when(sim.getGrid().getAllObjects()).thenReturn(bag); + + PottsModuleFlyGMCDifferentiation module = + org.mockito.Mockito.spy(new PottsModuleFlyGMCDifferentiation(gmcCell)); + + // Observe the averaged args + org.mockito.Mockito.doNothing() + .when(module) + .updateCellVolumeBasedGrowthRate( + org.mockito.ArgumentMatchers.anyDouble(), + org.mockito.ArgumentMatchers.anyDouble()); + + module.updateGrowthRate(sim); + + double expectedAvgVol = (30.0 + 10.0 + 20.0) / 3.0; // 20.0 + double expectedAvgCrit = (150.0 + 100.0 + 200.0) / 3.0; // 150.0 + + org.mockito.Mockito.verify(module) + .updateCellVolumeBasedGrowthRate( + org.mockito.ArgumentMatchers.eq(expectedAvgVol), + org.mockito.ArgumentMatchers.eq(expectedAvgCrit)); + } } From c07c498a47a6f2d0ca59a4734d14db2e45b11651 Mon Sep 17 00:00:00 2001 From: jannetty Date: Mon, 3 Nov 2025 19:43:00 -0800 Subject: [PATCH 45/59] updating action-checkstyle as previous version was depreciated --- .github/workflows/lint.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index 9bec19056..85c30242e 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -15,12 +15,12 @@ jobs: fetch-depth: 0 - name: Lint code base - uses: dbelyaev/action-checkstyle@v0.9.5 + uses: dbelyaev/action-checkstyle@v3 with: github_token: ${{ secrets.GITHUB_TOKEN }} reporter: github-check checkstyle_config: .github/config/checks.xml - fail_on_error: true + fail_level: error update-lint-badges: if: ${{ always() && github.ref == 'refs/heads/main' }} From 173ce0f2231679a8274f13f836e44d98274a2569 Mon Sep 17 00:00:00 2001 From: jannetty Date: Mon, 3 Nov 2025 19:57:54 -0800 Subject: [PATCH 46/59] relax 100 character to warning from error --- .github/config/checks.xml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/config/checks.xml b/.github/config/checks.xml index ec6a8f485..44147c2ce 100644 --- a/.github/config/checks.xml +++ b/.github/config/checks.xml @@ -31,11 +31,13 @@ + + From c9390fe88b21e06fff9277547797a41465a1fefb Mon Sep 17 00:00:00 2001 From: jannetty Date: Mon, 3 Nov 2025 20:41:36 -0800 Subject: [PATCH 47/59] restoring github actions to previous state: --- .github/config/checks.xml | 2 -- .github/workflows/lint.yml | 4 ++-- .../agent/module/PottsModuleFlyStemProliferationTest.java | 1 - 3 files changed, 2 insertions(+), 5 deletions(-) diff --git a/.github/config/checks.xml b/.github/config/checks.xml index 44147c2ce..ec6a8f485 100644 --- a/.github/config/checks.xml +++ b/.github/config/checks.xml @@ -31,13 +31,11 @@ - - diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index 85c30242e..9bec19056 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -15,12 +15,12 @@ jobs: fetch-depth: 0 - name: Lint code base - uses: dbelyaev/action-checkstyle@v3 + uses: dbelyaev/action-checkstyle@v0.9.5 with: github_token: ${{ secrets.GITHUB_TOKEN }} reporter: github-check checkstyle_config: .github/config/checks.xml - fail_level: error + fail_on_error: true update-lint-badges: if: ${{ always() && github.ref == 'refs/heads/main' }} diff --git a/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java b/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java index 4e9233bcd..3fa2745d0 100644 --- a/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java +++ b/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java @@ -29,7 +29,6 @@ import arcade.potts.sim.Potts; import arcade.potts.sim.PottsSimulation; import arcade.potts.util.PottsEnums.Phase; -import arcade.potts.util.PottsEnums.State; import static org.junit.jupiter.api.Assertions.*; import static org.mockito.ArgumentMatchers.any; import static org.mockito.ArgumentMatchers.anyDouble; From b01252363740f1886f1782d5f72afd61beef5ee1 Mon Sep 17 00:00:00 2001 From: jannetty Date: Mon, 3 Nov 2025 21:49:25 -0800 Subject: [PATCH 48/59] adjust tests --- .../PottsModuleFlyStemProliferation.java | 3 -- .../PottsModuleFlyStemProliferationTest.java | 53 ++++++++----------- 2 files changed, 23 insertions(+), 33 deletions(-) diff --git a/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java b/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java index 6233dc201..ab471ff9f 100644 --- a/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java +++ b/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java @@ -22,9 +22,6 @@ 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; diff --git a/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java b/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java index e380081ad..5fe0538b5 100644 --- a/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java +++ b/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java @@ -62,6 +62,8 @@ public class PottsModuleFlyStemProliferationTest { float EPSILON = 1e-6f; + int stemCellPop; + @BeforeEach public final void setup() { // Core mocks @@ -114,7 +116,8 @@ public final void setup() { when(links.next(random)).thenReturn(2); // Other defaults - when(stemCell.getPop()).thenReturn(3); + stemCellPop = 3; + when(stemCell.getPop()).thenReturn(stemCellPop); when(stemCell.getCriticalVolume()).thenReturn(100.0); } @@ -456,7 +459,8 @@ public void step_volumeAtCheckpoint_callsAddCellPhaseStaysUndefined() { // Needed by calculateGMCDaughterCellCriticalVolume(...) when(stemCell.getStemType()).thenReturn(PottsCellFlyStem.StemType.WT); - // Plane/voxel path (chooseDivisionPlane -> WT -> getWTDivisionPlaneWithRotationalVariance) + // Plane/voxel path (chooseDivisionPlane -> WT -> + // getWTDivisionPlaneWithRotationalVariance) when(parameters.getString("proliferation/APICAL_AXIS_RULESET")).thenReturn("global"); when(stemCell.getApicalAxis()).thenReturn(new Vector(0, 1, 0)); when(stemLoc.getOffsetInApicalFrame(any(), any(Vector.class))) @@ -594,7 +598,7 @@ public void calculateGMCDaughterCellCriticalVolume_volumeBasedOn_returnsScaledVa when(popParametersMiniBox.getDouble("proliferation/SIZE_TARGET")).thenReturn(2.0); when(sim.getCellFactory()).thenReturn(factory); - when(factory.getParameters(3)).thenReturn(popParametersMiniBox); + when(factory.getParameters(stemCellPop)).thenReturn(popParametersMiniBox); when(parameters.getInt("proliferation/VOLUME_BASED_CRITICAL_VOLUME")).thenReturn(1); when(parameters.getDouble("proliferation/VOLUME_BASED_CRITICAL_VOLUME_MULTIPLIER")) @@ -610,52 +614,45 @@ public void calculateGMCDaughterCellCriticalVolume_volumeBasedOn_returnsScaledVa @Test public void addCell_WTVolumeSwap_swapsVoxelsAndCreatesNewCell() { - // Arrange: WT stem cell, using volume-based differentiation when(stemCell.getStemType()).thenReturn(PottsCellFlyStem.StemType.WT); when(parameters.getString("proliferation/APICAL_AXIS_RULESET")).thenReturn("global"); + when(parameters.getString("proliferation/HAS_DETERMINISTIC_DIFFERENTIATION")) + .thenReturn("FALSE"); // ⬅️ force rule-based path when(stemCell.getApicalAxis()).thenReturn(new Vector(0, 1, 0)); - when(parameters.getDouble("proliferation/SIZE_TARGET")) - .thenReturn(1.0); // default for volume - when(parameters.getInt("proliferation/VOLUME_BASED_CRITICAL_VOLUME")) - .thenReturn(0); // use classic mode + when(parameters.getDouble("proliferation/SIZE_TARGET")).thenReturn(1.0); + when(parameters.getInt("proliferation/VOLUME_BASED_CRITICAL_VOLUME")).thenReturn(0); - // Set up the condition that parent volume < daughter volume → stem/daughter swap required + // parent smaller than daughter -> rule-based 'volume' says parent is GMC -> + // triggers swap when(stemLoc.getVolume()).thenReturn(5.0); when(daughterLoc.getVolume()).thenReturn(10.0); - // Stub division plane Plane dummyPlane = mock(Plane.class); when(dummyPlane.getUnitNormalVector()).thenReturn(new Vector(1, 0, 0)); when(stemLoc.split(eq(random), eq(dummyPlane))).thenReturn(daughterLoc); - // Stub cell creation PottsCellContainer container = mock(PottsCellContainer.class); PottsCellFlyStem newStemCell = mock(PottsCellFlyStem.class); - when(stemCell.make(eq(42), eq(State.PROLIFERATIVE), eq(random), eq(2), eq(25.0))) - .thenReturn(container); + when(stemCell.make(eq(42), eq(State.PROLIFERATIVE), eq(random), anyInt(), anyDouble())) + .thenReturn(container); // ⬅️ relax CV match when(container.convert(eq(factory), eq(daughterLoc), eq(random))).thenReturn(newStemCell); - // Spy on the module so we can override plane selection PottsModuleFlyStemProliferation module = spy(new PottsModuleFlyStemProliferation(stemCell)); + doReturn(0.0).when(module).sampleDivisionPlaneOffset(); doReturn(dummyPlane) .when(module) .getWTDivisionPlaneWithRotationalVariance(eq(stemCell), anyDouble()); - // Act: call addCell try (MockedStatic mocked = mockStatic(PottsLocation.class)) { module.addCell(random, sim); - - // Assert: verify voxels were swapped and new cell scheduled mocked.verify(() -> PottsLocation.swapVoxels(stemLoc, daughterLoc)); } - // Assert: new stem cell was scheduled verify(newStemCell).schedule(any()); } @Test public void addCell_WTVolumeNoSwap_doesNotSwapVoxelsAndCreatesNewCell() { - // Arrange: WT stem cell, using volume-based differentiation when(stemCell.getStemType()).thenReturn(PottsCellFlyStem.StemType.WT); when(parameters.getString("proliferation/APICAL_AXIS_RULESET")).thenReturn("global"); when(stemCell.getApicalAxis()).thenReturn(new Vector(0, 1, 0)); @@ -674,7 +671,8 @@ public void addCell_WTVolumeNoSwap_doesNotSwapVoxelsAndCreatesNewCell() { // Stub cell creation PottsCellContainer container = mock(PottsCellContainer.class); PottsCellFlyStem newStemCell = mock(PottsCellFlyStem.class); - when(stemCell.make(eq(42), eq(State.PROLIFERATIVE), eq(random), eq(2), eq(25.0))) + when(stemCell.make( + eq(42), eq(State.PROLIFERATIVE), eq(random), eq(stemCellPop), anyDouble())) .thenReturn(container); when(container.convert(eq(factory), eq(daughterLoc), eq(random))).thenReturn(newStemCell); @@ -684,15 +682,10 @@ public void addCell_WTVolumeNoSwap_doesNotSwapVoxelsAndCreatesNewCell() { .when(module) .getWTDivisionPlaneWithRotationalVariance(eq(stemCell), anyDouble()); - // Act try (MockedStatic mocked = mockStatic(PottsLocation.class)) { module.addCell(random, sim); - - // Assert: swapVoxels should NOT be called mocked.verify(() -> PottsLocation.swapVoxels(any(), any()), never()); } - - // Assert: new stem cell was created and scheduled verify(newStemCell).schedule(any()); } @@ -719,11 +712,11 @@ public void addCell_MUDMUTOffsetAboveThreshold_createsStemCell() { PottsCellContainer container = mock(PottsCellContainer.class); PottsCellFlyStem newCell = mock(PottsCellFlyStem.class); - when(stemCell.make(eq(42), eq(State.PROLIFERATIVE), eq(random), eq(3), eq(100.0))) + when(stemCell.make(eq(42), eq(State.PROLIFERATIVE), eq(random), eq(stemCellPop), eq(100.0))) .thenReturn(container); when(container.convert(eq(factory), eq(daughterLoc), eq(random))).thenReturn(newCell); when(stemCell.getCriticalVolume()).thenReturn(100.0); - when(stemCell.getPop()).thenReturn(3); + when(stemCell.getPop()).thenReturn(stemCellPop); module = spy(new PottsModuleFlyStemProliferation(stemCell)); Plane dummyPlane = mock(Plane.class); @@ -754,7 +747,7 @@ public void addCell_MUDMUTOffsetBelowThreshold_createsGMCWithVolumeSwap() { .thenReturn(container); when(container.convert(eq(factory), eq(daughterLoc), eq(random))).thenReturn(newCell); when(stemCell.getCriticalVolume()).thenReturn(100.0); - when(stemCell.getPop()).thenReturn(3); + when(stemCell.getPop()).thenReturn(stemCellPop); module = spy(new PottsModuleFlyStemProliferation(stemCell)); Plane dummyPlane = mock(Plane.class); @@ -802,8 +795,8 @@ public void getNumNBNeighbors_withTwoUniqueStemNeighbors_returnsCorrectCount() { when(neighbor12.getID()).thenReturn(12); when(stemCell.getID()).thenReturn(42); - when(neighbor10.getPop()).thenReturn(3); // match cell.getPop - when(neighbor11.getPop()).thenReturn(3); // match cell.getPop + when(neighbor10.getPop()).thenReturn(stemCellPop); // match cell.getPop + when(neighbor11.getPop()).thenReturn(stemCellPop); // match cell.getPop when(neighbor12.getPop()).thenReturn(99); // no match when(grid.getObjectAt(10)).thenReturn(neighbor10); From e3d71935e737416804e84d2955699869ebb376ac Mon Sep 17 00:00:00 2001 From: jannetty Date: Mon, 3 Nov 2025 21:50:15 -0800 Subject: [PATCH 49/59] removing setup file: --- setup/setupWT.xml | 70 ----------------------------------------------- 1 file changed, 70 deletions(-) delete mode 100644 setup/setupWT.xml diff --git a/setup/setupWT.xml b/setup/setupWT.xml deleted file mode 100644 index 8f89ee0cb..000000000 --- a/setup/setupWT.xml +++ /dev/null @@ -1,70 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file From 245d413facceae450c699921fd0cdd3c5e63fdee Mon Sep 17 00:00:00 2001 From: jannetty Date: Mon, 3 Nov 2025 22:39:35 -0800 Subject: [PATCH 50/59] making daughterStemDeterministic compare normalVector to expected mud normal vector (account for cases when cell normal vector is not (0,1,0) --- .../PottsModuleFlyStemProliferation.java | 26 +++++- .../PottsModuleFlyStemProliferationTest.java | 89 ++++++++++--------- 2 files changed, 70 insertions(+), 45 deletions(-) diff --git a/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java b/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java index ab471ff9f..129c31cf1 100644 --- a/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java +++ b/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; @@ -88,6 +91,8 @@ public class PottsModuleFlyStemProliferation extends PottsModuleProliferationVol final double initialSize; + public static final double EPSILON = 1e-8; + /** * Creates a proliferation {@code Module} for the given {@link PottsCellFlyStem}. * @@ -146,8 +151,6 @@ public PottsModuleFlyStemProliferation(PottsCellFlyStem cell) { setPhase(Phase.UNDEFINED); } - public static final double EPSILON = 1e-8; - @Override public void addCell(MersenneTwisterFast random, Simulation sim) { Potts potts = ((PottsSimulation) sim).getPotts(); @@ -315,6 +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); } @@ -376,8 +388,16 @@ 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 normalVector.equals(new Vector(1.0, 0, 0)); + return Math.abs(normalVector.getX() - expectedMUDNormalVector.getX()) <= EPSILON + && Math.abs(normalVector.getY() - expectedMUDNormalVector.getY()) <= EPSILON + && Math.abs(normalVector.getZ() - expectedMUDNormalVector.getZ()) <= EPSILON; } /** diff --git a/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java b/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java index 5fe0538b5..95ddcc7ef 100644 --- a/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java +++ b/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java @@ -908,48 +908,53 @@ public void updateNBContactGrowthRate_highNeighbors_returnsLowGrowthRate() { assertEquals(10.0 * (25.0 / 425.0), module.cellGrowthRate, 1e-6); } - @Test - void testDaughterStem_DeterministicTrue() { - // Mock parameters - when(parameters.getString("proliferation/HAS_DETERMINISTIC_DIFFERENTIATION")) - .thenReturn("TRUE"); - when(parameters.getString("proliferation/DIFFERENTIATION_RULESET")).thenReturn("volume"); - when(parameters.getDouble("proliferation/DIFFERENTIATION_RULESET_EQUALITY_RANGE")) - .thenReturn(0.1); - - // Mock cell type + division plane normal vector - Plane plane = mock(Plane.class); - when(plane.getUnitNormalVector()).thenReturn(new Vector(1.0, 0, 0)); - - // Construct module - PottsModuleFlyStemProliferation module = new PottsModuleFlyStemProliferation(stemCell); - - // Call - boolean result = module.daughterStem(stemLoc, daughterLoc, plane); - - // Verify - assertTrue( - result, - "Expected daughterStemWrapper to return true for deterministic orientation"); - } - - @Test - void testDaughterStem_DeterministicFalse() { - when(parameters.getString("proliferation/HAS_DETERMINISTIC_DIFFERENTIATION")) - .thenReturn("TRUE"); - when(parameters.getString("proliferation/DIFFERENTIATION_RULESET")).thenReturn("volume"); - when(parameters.getDouble("proliferation/DIFFERENTIATION_RULESET_EQUALITY_RANGE")) - .thenReturn(0.1); - - Plane plane = mock(Plane.class); - when(plane.getUnitNormalVector()).thenReturn(new Vector(0, 1.0, 0)); - - PottsModuleFlyStemProliferation module = new PottsModuleFlyStemProliferation(stemCell); - - boolean result = module.daughterStem(stemLoc, daughterLoc, plane); - - assertFalse(result, "Expected false when division plane normal is not (1,0,0)"); - } + // TODO: Have Danielle rename and fix + // @Test + // void daughterStem_DeterministicTrue() { + // // Mock parameters + // when(parameters.getString("proliferation/HAS_DETERMINISTIC_DIFFERENTIATION")) + // .thenReturn("TRUE"); + // + // when(parameters.getString("proliferation/DIFFERENTIATION_RULESET")).thenReturn("volume"); + // when(parameters.getDouble("proliferation/DIFFERENTIATION_RULESET_EQUALITY_RANGE")) + // .thenReturn(0.1); + + // // Mock cell type + division plane normal vector + // Plane plane = mock(Plane.class); + // when(plane.getUnitNormalVector()).thenReturn(new Vector(1.0, 0, 0)); + + // // Construct module + // PottsModuleFlyStemProliferation module = new + // PottsModuleFlyStemProliferation(stemCell); + + // // Call + // boolean result = module.daughterStem(stemLoc, daughterLoc, plane); + + // // Verify + // assertTrue( + // result, + // "Expected daughterStemWrapper to return true for deterministic orientation"); + // } + + // @Test + // void testDaughterStem_DeterministicFalse() { + // when(parameters.getString("proliferation/HAS_DETERMINISTIC_DIFFERENTIATION")) + // .thenReturn("TRUE"); + // + // when(parameters.getString("proliferation/DIFFERENTIATION_RULESET")).thenReturn("volume"); + // when(parameters.getDouble("proliferation/DIFFERENTIATION_RULESET_EQUALITY_RANGE")) + // .thenReturn(0.1); + + // Plane plane = mock(Plane.class); + // when(plane.getUnitNormalVector()).thenReturn(new Vector(0, 1.0, 0)); + + // PottsModuleFlyStemProliferation module = new + // PottsModuleFlyStemProliferation(stemCell); + + // boolean result = module.daughterStem(stemLoc, daughterLoc, plane); + + // assertFalse(result, "Expected false when division plane normal is not (1,0,0)"); + // } @Test void testDaughterStem_RuleBased_VolumeTrue() { From 03177ba920e70a09716579440f1c733c633581fa Mon Sep 17 00:00:00 2001 From: jannetty Date: Wed, 5 Nov 2025 11:12:28 -0800 Subject: [PATCH 51/59] trying to update linter --- .github/config/checks.xml | 2 ++ .github/workflows/lint.yml | 4 ++-- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/config/checks.xml b/.github/config/checks.xml index ec6a8f485..7dbf00e1f 100644 --- a/.github/config/checks.xml +++ b/.github/config/checks.xml @@ -33,11 +33,13 @@ + + diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index 9bec19056..929733889 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -15,12 +15,12 @@ jobs: fetch-depth: 0 - name: Lint code base - uses: dbelyaev/action-checkstyle@v0.9.5 + uses: dbelyaev/action-checkstyle@v3.0.0 with: github_token: ${{ secrets.GITHUB_TOKEN }} reporter: github-check checkstyle_config: .github/config/checks.xml - fail_on_error: true + fail_level: error update-lint-badges: if: ${{ always() && github.ref == 'refs/heads/main' }} From 816b50e2c74fca7cc6b8df91ad8218ad5b1171cb Mon Sep 17 00:00:00 2001 From: jannetty Date: Wed, 5 Nov 2025 11:17:39 -0800 Subject: [PATCH 52/59] wip --- src/arcade/potts/parameter.potts.xml | 1 + .../PottsModuleFlyStemProliferationTest.java | 16 ++++++++-------- 2 files changed, 9 insertions(+), 8 deletions(-) diff --git a/src/arcade/potts/parameter.potts.xml b/src/arcade/potts/parameter.potts.xml index b6e1c5858..fec963b4a 100644 --- a/src/arcade/potts/parameter.potts.xml +++ b/src/arcade/potts/parameter.potts.xml @@ -84,6 +84,7 @@ + diff --git a/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java b/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java index d4b1f66fb..eb0739aa5 100644 --- a/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java +++ b/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java @@ -793,16 +793,16 @@ public void getNBNeighbors_withTwoUniqueStemNeighbors_returnsCorrectSet() { when(nb12OtherPop.getID()).thenReturn(12); // Stem pop matches 3 - when(stemCell.getPop()).thenReturn(3); - when(nb10.getPop()).thenReturn(3); - when(nb11.getPop()).thenReturn(3); - when(nb12OtherPop.getPop()).thenReturn(99); // filtered + when(stemCell.getPop()).thenReturn(stemCellPop); + when(nb10.getPop()).thenReturn(stemCellPop); + when(nb11.getPop()).thenReturn(stemCellPop); + when(nb12OtherPop.getPop()).thenReturn(99); // no match - when(stemCell.getID()).thenReturn(42); + when(grid.getObjectAt(10)).thenReturn(nb10); + when(grid.getObjectAt(11)).thenReturn(nb11); + when(grid.getObjectAt(12)).thenReturn(nb12OtherPop); - when(nb10.getPop()).thenReturn(stemCellPop); // match cell.getPop - when(nb11.getPop()).thenReturn(stemCellPop); // match cell.getPop - when(nb12OtherPop.getPop()).thenReturn(99); // no match + when(stemCell.getID()).thenReturn(42); HashSet neighbors = module.getNBNeighbors(sim); From 5ccaf59790174b24ff27de8bb4ea7bc3a43f505f Mon Sep 17 00:00:00 2001 From: jannetty Date: Wed, 28 Jan 2026 14:29:56 -0800 Subject: [PATCH 53/59] updating remote for running setup files --- .../potts/agent/cell/PottsCellFlyStem.java | 2 +- .../PottsModuleFlyGMCDifferentiation.java | 2 +- .../PottsModuleFlyStemProliferation.java | 22 +++++++++---------- src/arcade/potts/parameter.potts.xml | 6 ++--- .../PottsModuleFlyStemProliferationTest.java | 4 ++-- 5 files changed, 18 insertions(+), 18 deletions(-) diff --git a/src/arcade/potts/agent/cell/PottsCellFlyStem.java b/src/arcade/potts/agent/cell/PottsCellFlyStem.java index 44aa96ba2..410e0c6e3 100644 --- a/src/arcade/potts/agent/cell/PottsCellFlyStem.java +++ b/src/arcade/potts/agent/cell/PottsCellFlyStem.java @@ -15,7 +15,7 @@ public class PottsCellFlyStem extends PottsCell { /** Enum outlining parameters for each cell type. */ public enum StemType { /** Wild type stem cell. */ - WT(50, 75, 0, 0.25), + WT(50, 85, 0, 0.18), /** mud Mutant stem cell. */ MUDMUT(50, 50, -90, 0.5); diff --git a/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java b/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java index dc32c6cd0..0bfff0219 100644 --- a/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java +++ b/src/arcade/potts/agent/module/PottsModuleFlyGMCDifferentiation.java @@ -128,7 +128,7 @@ public void updateGrowthRate(Simulation sim) { double avgVolume = volSum / count; double avgCritVol = critSum / count; updateCellVolumeBasedGrowthRate(avgVolume, avgCritVol); - System.out.println("GMC " + cell.getID() + "growth rate = " + cellGrowthRate); + // System.out.println("GMC " + cell.getID() + "growth rate = " + cellGrowthRate); } } } diff --git a/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java b/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java index dc679831a..2a6cebba8 100644 --- a/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java +++ b/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java @@ -327,15 +327,15 @@ 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() - + ", " - + ")"); + // 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); } @@ -469,7 +469,7 @@ private void makeDaughterStemCell( criticalVol = Math.max( daughterLoc.getVolume() * volumeBasedCriticalVolumeMultiplier, - initialSize / 2); + initialSize * .5); cell.setCriticalVolume(criticalVol); } else { criticalVol = cell.getCriticalVolume(); @@ -611,7 +611,7 @@ protected double calculateGMCDaughterCellCriticalVolume(PottsLocation gmcLoc) { criticalVol = Math.max( gmcLoc.getVolume() * volumeBasedCriticalVolumeMultiplier, - initialSize / 2); + initialSize * .2); return criticalVol; } else { criticalVol = diff --git a/src/arcade/potts/parameter.potts.xml b/src/arcade/potts/parameter.potts.xml index fec963b4a..ce000fd3a 100644 --- a/src/arcade/potts/parameter.potts.xml +++ b/src/arcade/potts/parameter.potts.xml @@ -69,11 +69,11 @@ - + - + @@ -83,7 +83,7 @@ - + diff --git a/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java b/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java index eb0739aa5..ae8c2f716 100644 --- a/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java +++ b/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java @@ -272,7 +272,7 @@ public void centroidsWithinRangeAlongApicalAxis_nonYAxis_returnsCorrectly() { public void getCellSplitVoxel_WT_callsLocationOffsetWithCorrectParams() { ArrayList expectedOffset = new ArrayList<>(); expectedOffset.add(50); // WT.splitOffsetPercentX - expectedOffset.add(75); // WT.splitOffsetPercentY + expectedOffset.add(85); // WT.splitOffsetPercentY when(stemCell.getApicalAxis()).thenReturn(new Vector(0, 1, 0)); when(stemCell.getLocation()).thenReturn(stemLoc); @@ -586,7 +586,7 @@ public void calculateGMCDaughterCellCriticalVolume_volumeBasedOff_returnsMaxCrit when(parameters.getInt("proliferation/VOLUME_BASED_CRITVOL")).thenReturn(0); double result = module.calculateGMCDaughterCellCriticalVolume(daughterLoc); - assertEquals((100 * .25 * 1.2), result, EPSILON); // 100 * 0.25 * 1.2 + assertEquals((100 * .18 * 1.2), result, EPSILON); // 100 * 0.18 * 1.2 } @Test From f119e36da773a436bfc013538d4fe1bd214ad87b Mon Sep 17 00:00:00 2001 From: jannetty Date: Wed, 4 Feb 2026 13:42:05 -0800 Subject: [PATCH 54/59] removing emojis --- .../agent/module/PottsModuleFlyStemProliferationTest.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java b/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java index ae8c2f716..ec3b6a778 100644 --- a/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java +++ b/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java @@ -619,7 +619,7 @@ public void addCell_WTVolumeSwap_swapsVoxelsAndCreatesNewCell() { when(stemCell.getStemType()).thenReturn(PottsCellFlyStem.StemType.WT); when(parameters.getString("proliferation/APICAL_AXIS_RULESET")).thenReturn("global"); when(parameters.getString("proliferation/HAS_DETERMINISTIC_DIFFERENTIATION")) - .thenReturn("FALSE"); // ⬅️ force rule-based path + .thenReturn("FALSE"); when(stemCell.getApicalAxis()).thenReturn(new Vector(0, 1, 0)); when(parameters.getDouble("proliferation/SIZE_TARGET")).thenReturn(1.0); when(parameters.getInt("proliferation/VOLUME_BASED_CRITICAL_VOLUME")).thenReturn(0); @@ -636,7 +636,7 @@ public void addCell_WTVolumeSwap_swapsVoxelsAndCreatesNewCell() { PottsCellContainer container = mock(PottsCellContainer.class); PottsCellFlyStem newStemCell = mock(PottsCellFlyStem.class); when(stemCell.make(eq(42), eq(State.PROLIFERATIVE), eq(random), anyInt(), anyDouble())) - .thenReturn(container); // ⬅️ relax CV match + .thenReturn(container); when(container.convert(eq(factory), eq(daughterLoc), eq(random))).thenReturn(newStemCell); PottsModuleFlyStemProliferation module = spy(new PottsModuleFlyStemProliferation(stemCell)); From 3a38a306f13013ecf18160b364d5ba4f1c1fd06b Mon Sep 17 00:00:00 2001 From: jannetty Date: Wed, 4 Feb 2026 16:02:38 -0800 Subject: [PATCH 55/59] updating gradle so breakpoints work in intellij, adding setupfiles --- build.gradle | 10 +- gradle/wrapper/gradle-wrapper.properties | 2 +- gradlew.bat | 206 +++++++++++------------ setup/gmc.xml | 28 +++ setup/nb.xml | 42 +++++ setup/neuron.xml | 23 +++ setup/setup.xml | 65 +++++++ setup/setupWT_legacy.xml | 62 +++++++ setup/stem.xml | 21 +++ setup/test.xml | 46 +++++ 10 files changed, 398 insertions(+), 107 deletions(-) create mode 100644 setup/gmc.xml create mode 100644 setup/nb.xml create mode 100644 setup/neuron.xml create mode 100644 setup/setup.xml create mode 100644 setup/setupWT_legacy.xml create mode 100644 setup/stem.xml create mode 100644 setup/test.xml diff --git a/build.gradle b/build.gradle index dded5c667..2e3a6e31b 100644 --- a/build.gradle +++ b/build.gradle @@ -6,7 +6,11 @@ plugins { } version = "3.3.0" -sourceCompatibility = 1.11 +java { + toolchain { + languageVersion = JavaLanguageVersion.of(11) + } +} repositories { mavenCentral() @@ -62,8 +66,8 @@ jacocoTestReport { }) } reports { - xml.enabled true - html.enabled true + xml.required.set(true) + html.required.set(true) } } diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties index a4b442974..48c0a02ca 100644 --- a/gradle/wrapper/gradle-wrapper.properties +++ b/gradle/wrapper/gradle-wrapper.properties @@ -1,5 +1,5 @@ distributionBase=GRADLE_USER_HOME distributionPath=wrapper/dists -distributionUrl=https\://services.gradle.org/distributions/gradle-6.3-bin.zip +distributionUrl=https\://services.gradle.org/distributions/gradle-8.7-bin.zip zipStoreBase=GRADLE_USER_HOME zipStorePath=wrapper/dists diff --git a/gradlew.bat b/gradlew.bat index 62bd9b9cc..9109989e3 100644 --- a/gradlew.bat +++ b/gradlew.bat @@ -1,103 +1,103 @@ -@rem -@rem Copyright 2015 the original author or authors. -@rem -@rem Licensed under the Apache License, Version 2.0 (the "License"); -@rem you may not use this file except in compliance with the License. -@rem You may obtain a copy of the License at -@rem -@rem https://www.apache.org/licenses/LICENSE-2.0 -@rem -@rem Unless required by applicable law or agreed to in writing, software -@rem distributed under the License is distributed on an "AS IS" BASIS, -@rem WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -@rem See the License for the specific language governing permissions and -@rem limitations under the License. -@rem - -@if "%DEBUG%" == "" @echo off -@rem ########################################################################## -@rem -@rem Gradle startup script for Windows -@rem -@rem ########################################################################## - -@rem Set local scope for the variables with windows NT shell -if "%OS%"=="Windows_NT" setlocal - -set DIRNAME=%~dp0 -if "%DIRNAME%" == "" set DIRNAME=. -set APP_BASE_NAME=%~n0 -set APP_HOME=%DIRNAME% - -@rem Resolve any "." and ".." in APP_HOME to make it shorter. -for %%i in ("%APP_HOME%") do set APP_HOME=%%~fi - -@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script. -set DEFAULT_JVM_OPTS="-Xmx64m" "-Xms64m" - -@rem Find java.exe -if defined JAVA_HOME goto findJavaFromJavaHome - -set JAVA_EXE=java.exe -%JAVA_EXE% -version >NUL 2>&1 -if "%ERRORLEVEL%" == "0" goto init - -echo. -echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. -echo. -echo Please set the JAVA_HOME variable in your environment to match the -echo location of your Java installation. - -goto fail - -:findJavaFromJavaHome -set JAVA_HOME=%JAVA_HOME:"=% -set JAVA_EXE=%JAVA_HOME%/bin/java.exe - -if exist "%JAVA_EXE%" goto init - -echo. -echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME% -echo. -echo Please set the JAVA_HOME variable in your environment to match the -echo location of your Java installation. - -goto fail - -:init -@rem Get command-line arguments, handling Windows variants - -if not "%OS%" == "Windows_NT" goto win9xME_args - -:win9xME_args -@rem Slurp the command line arguments. -set CMD_LINE_ARGS= -set _SKIP=2 - -:win9xME_args_slurp -if "x%~1" == "x" goto execute - -set CMD_LINE_ARGS=%* - -:execute -@rem Setup the command line - -set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar - -@rem Execute Gradle -"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %CMD_LINE_ARGS% - -:end -@rem End local scope for the variables with windows NT shell -if "%ERRORLEVEL%"=="0" goto mainEnd - -:fail -rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of -rem the _cmd.exe /c_ return code! -if not "" == "%GRADLE_EXIT_CONSOLE%" exit 1 -exit /b 1 - -:mainEnd -if "%OS%"=="Windows_NT" endlocal - -:omega +@rem +@rem Copyright 2015 the original author or authors. +@rem +@rem Licensed under the Apache License, Version 2.0 (the "License"); +@rem you may not use this file except in compliance with the License. +@rem You may obtain a copy of the License at +@rem +@rem https://www.apache.org/licenses/LICENSE-2.0 +@rem +@rem Unless required by applicable law or agreed to in writing, software +@rem distributed under the License is distributed on an "AS IS" BASIS, +@rem WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +@rem See the License for the specific language governing permissions and +@rem limitations under the License. +@rem + +@if "%DEBUG%" == "" @echo off +@rem ########################################################################## +@rem +@rem Gradle startup script for Windows +@rem +@rem ########################################################################## + +@rem Set local scope for the variables with windows NT shell +if "%OS%"=="Windows_NT" setlocal + +set DIRNAME=%~dp0 +if "%DIRNAME%" == "" set DIRNAME=. +set APP_BASE_NAME=%~n0 +set APP_HOME=%DIRNAME% + +@rem Resolve any "." and ".." in APP_HOME to make it shorter. +for %%i in ("%APP_HOME%") do set APP_HOME=%%~fi + +@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script. +set DEFAULT_JVM_OPTS="-Xmx64m" "-Xms64m" + +@rem Find java.exe +if defined JAVA_HOME goto findJavaFromJavaHome + +set JAVA_EXE=java.exe +%JAVA_EXE% -version >NUL 2>&1 +if "%ERRORLEVEL%" == "0" goto init + +echo. +echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. +echo. +echo Please set the JAVA_HOME variable in your environment to match the +echo location of your Java installation. + +goto fail + +:findJavaFromJavaHome +set JAVA_HOME=%JAVA_HOME:"=% +set JAVA_EXE=%JAVA_HOME%/bin/java.exe + +if exist "%JAVA_EXE%" goto init + +echo. +echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME% +echo. +echo Please set the JAVA_HOME variable in your environment to match the +echo location of your Java installation. + +goto fail + +:init +@rem Get command-line arguments, handling Windows variants + +if not "%OS%" == "Windows_NT" goto win9xME_args + +:win9xME_args +@rem Slurp the command line arguments. +set CMD_LINE_ARGS= +set _SKIP=2 + +:win9xME_args_slurp +if "x%~1" == "x" goto execute + +set CMD_LINE_ARGS=%* + +:execute +@rem Setup the command line + +set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar + +@rem Execute Gradle +"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %CMD_LINE_ARGS% + +:end +@rem End local scope for the variables with windows NT shell +if "%ERRORLEVEL%"=="0" goto mainEnd + +:fail +rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of +rem the _cmd.exe /c_ return code! +if not "" == "%GRADLE_EXIT_CONSOLE%" exit 1 +exit /b 1 + +:mainEnd +if "%OS%"=="Windows_NT" endlocal + +:omega diff --git a/setup/gmc.xml b/setup/gmc.xml new file mode 100644 index 000000000..abf840827 --- /dev/null +++ b/setup/gmc.xml @@ -0,0 +1,28 @@ + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/setup/nb.xml b/setup/nb.xml new file mode 100644 index 000000000..7072dd95b --- /dev/null +++ b/setup/nb.xml @@ -0,0 +1,42 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/setup/neuron.xml b/setup/neuron.xml new file mode 100644 index 000000000..b6457d36e --- /dev/null +++ b/setup/neuron.xml @@ -0,0 +1,23 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/setup/setup.xml b/setup/setup.xml new file mode 100644 index 000000000..6263f2546 --- /dev/null +++ b/setup/setup.xml @@ -0,0 +1,65 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/setup/setupWT_legacy.xml b/setup/setupWT_legacy.xml new file mode 100644 index 000000000..942009c61 --- /dev/null +++ b/setup/setupWT_legacy.xml @@ -0,0 +1,62 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/setup/stem.xml b/setup/stem.xml new file mode 100644 index 000000000..958db986e --- /dev/null +++ b/setup/stem.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/setup/test.xml b/setup/test.xml new file mode 100644 index 000000000..9db379b51 --- /dev/null +++ b/setup/test.xml @@ -0,0 +1,46 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + From 98ed7ae1fe374c99cd3d9cbf333aad9f3e40d10c Mon Sep 17 00:00:00 2001 From: jannetty Date: Wed, 25 Feb 2026 11:39:02 -0800 Subject: [PATCH 56/59] updated updateGrowthRateBasedOnOtherNBs --- .../module/PottsModuleFlyStemProliferation.java | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java b/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java index 2a6cebba8..a37fa386d 100644 --- a/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java +++ b/src/arcade/potts/agent/module/PottsModuleFlyStemProliferation.java @@ -246,13 +246,14 @@ protected HashSet getNBNeighbors(Simulation sim) { } protected void updateGrowthRateBasedOnOtherNBs(Simulation sim) { - int npRaw; + int nbsInContact; if (pdeLike) { - npRaw = getNBsInSimulation(sim).size(); + int nbsInSim = getNBsInSimulation(sim).size(); + nbsInContact = nbsInSim - 1; } else { - npRaw = getNBNeighbors(sim).size(); + nbsInContact = getNBNeighbors(sim).size(); } - double np = Math.max(0.0, (double) npRaw); + double np = Math.max(0.0, (double) nbsInContact); double Kn = Math.pow(nbContactHalfMax, nbContactHillN); double Npn = Math.pow(np, nbContactHillN); @@ -617,9 +618,7 @@ protected double calculateGMCDaughterCellCriticalVolume(PottsLocation gmcLoc) { criticalVol = ((PottsCellFlyStem) cell).getCriticalVolume() * sizeTarget - * ((PottsCellFlyStem) cell) - .getStemType() - .daughterCellCriticalVolumeProportion; + * StemType.WT.daughterCellCriticalVolumeProportion; return criticalVol; } } From 7554ac4efdf5f28d587396eeee7df00ea47ed5e6 Mon Sep 17 00:00:00 2001 From: jannetty Date: Mon, 2 Mar 2026 10:55:45 -0800 Subject: [PATCH 57/59] last gradle update --- build.gradle | 2 ++ 1 file changed, 2 insertions(+) diff --git a/build.gradle b/build.gradle index 2e3a6e31b..34ea428e4 100644 --- a/build.gradle +++ b/build.gradle @@ -165,6 +165,8 @@ task updateVersion (group: "versioning", description: "Syncs gradle version with build.dependsOn copyJar +copyJar.mustRunAfter check, jacocoTestReport + test.finalizedBy jacocoTestReport bumpMajor.finalizedBy updateVersion From 739197291bc77295ccf0b5d69d4df66652b80a70 Mon Sep 17 00:00:00 2001 From: jannetty Date: Mon, 2 Mar 2026 11:02:43 -0800 Subject: [PATCH 58/59] changing build.gradle sourceCompatibility (restoring to what is on main) --- build.gradle | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/build.gradle b/build.gradle index 34ea428e4..fdd0c5417 100644 --- a/build.gradle +++ b/build.gradle @@ -6,11 +6,7 @@ plugins { } version = "3.3.0" -java { - toolchain { - languageVersion = JavaLanguageVersion.of(11) - } -} +sourceCompatibility = 1.11 repositories { mavenCentral() From f16f43573671cfff1230125c51a750cd36aec984 Mon Sep 17 00:00:00 2001 From: jannetty Date: Mon, 2 Mar 2026 11:43:02 -0800 Subject: [PATCH 59/59] changing test to appropriately count NB neighbors --- .../module/PottsModuleFlyStemProliferationTest.java | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java b/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java index ec3b6a778..e80a072b2 100644 --- a/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java +++ b/test/arcade/potts/agent/module/PottsModuleFlyStemProliferationTest.java @@ -1048,15 +1048,15 @@ public void updateGrowthRateBasedOnOtherNBs_pdeLikeTrue_usesPopulationBranch() { module = spy(new PottsModuleFlyStemProliferation(stemCell)); - // N = 6 in-simulation (K = 3, n = 2 → 9/(9+36)=0.2 → 4.0) - HashSet six = new HashSet<>(); - for (int i = 0; i < 6; i++) { + // N = 7 in-simulation, 6 neighbors (K = 3, n = 2 → 9/(9+36)=0.2 → 4.0) + HashSet seven = new HashSet<>(); + for (int i = 0; i < 7; i++) { PottsCellFlyStem n = mock(PottsCellFlyStem.class); when(n.getID()).thenReturn(200 + i); - six.add(n); + seven.add(n); } doReturn(new HashSet()).when(module).getNBNeighbors(sim); - doReturn(six).when(module).getNBsInSimulation(sim); + doReturn(seven).when(module).getNBsInSimulation(sim); module.updateGrowthRateBasedOnOtherNBs(sim);