[1.3.52] 2025-10-02

- Fixed a bug in the maize phytomer creation function where the scale could be left uninitialized, leading to undefined behavior.
- Removed a duplicate code block in the tomato phytomer creation function.
- Added new apple fruiting wall plant model (`apple_fruitingwall`)
- Fixed fruit set probability calculation when skipping flower stages - now applies compound probability (flower bud break × fruit set) when jumping directly from BUD_ACTIVE to BUD_FRUITING
- Fixed child shoot insertion angle calculation to properly account for parent petiole position using angular offset
- Updated pistachio tree parameters for improved canopy structure

- Fixed vector bounds checking for write flags (`write_depth`, `write_norm_depth`, `write_segmentation_mask`)
- Fixed initialization of write flag vectors in `xmlGetValues()` - vectors are now properly sized when no XML values are present
- Fixed initialization of write flag vectors when adding new rigs via `addRig()`
- Updated bounding box writing calls to include `classes.txt` filename parameter matching new Radiation API
- Merged in many project builder bug fixes and updates

Co-authored-by: Sean Banks <[email protected]>

Author: bnbailey-psl

doc/CHANGELOG.md

@@ -1,5 +1,22 @@
 # Changelog
 
+# [1.3.52] 2025-10-02
+
+## Plant Architecture
+- Fixed a bug in the maize phytomer creation function where the scale could be left uninitialized, leading to undefined behavior.
+- Removed a duplicate code block in the tomato phytomer creation function.
+- Added new apple fruiting wall plant model (`apple_fruitingwall`)
+- Fixed fruit set probability calculation when skipping flower stages - now applies compound probability (flower bud break × fruit set) when jumping directly from BUD_ACTIVE to BUD_FRUITING
+- Fixed child shoot insertion angle calculation to properly account for parent petiole position using angular offset
+- Updated pistachio tree parameters for improved canopy structure
+
+## Project Builder
+- Fixed vector bounds checking for write flags (`write_depth`, `write_norm_depth`, `write_segmentation_mask`)
+- Fixed initialization of write flag vectors in `xmlGetValues()` - vectors are now properly sized when no XML values are present
+- Fixed initialization of write flag vectors when adding new rigs via `addRig()`
+- Updated bounding box writing calls to include `classes.txt` filename parameter matching new Radiation API
+- Merged in many project builder bug fixes and updates
+
 # [1.3.51] 2025-09-25
 
 - Added 'validation' page in documentation

doc/Validation.dox

@@ -2883,6 +2883,10 @@ class PlantArchitecture {
 
     uint buildAppleTree(const helios::vec3 &base_position);
 
+    void initializeAppleFruitingWallShoots();
+
+    uint buildAppleFruitingWall(const helios::vec3 &base_position);
+
     void initializeAsparagusShoots();
 
     uint buildAsparagusPlant(const helios::vec3 &base_position);

doc/images/validation/redbud_leaf_temperature_validation.png

@@ -565,7 +565,7 @@ uint MaizeEarPrototype(helios::Context *context_ptr, uint subdivisions) {
 void MaizePhytomerCreationFunction(std::shared_ptr<Phytomer> phytomer, uint shoot_node_index, uint parent_shoot_node_index, uint shoot_max_nodes, float plant_age) {
 
     // set leaf scale based on position along the shoot
-    float scale;
+    float scale = 1.f;
     if (shoot_node_index <= 5) {
         scale = fmin(1.f, 0.7 + 0.3 * float(shoot_node_index) / 5.f);
         phytomer->scaleInternodeMaxLength(scale);
@@ -887,10 +887,6 @@ void TomatoPhytomerCreationFunction(std::shared_ptr<Phytomer> phytomer, uint sho
         phytomer->setFloralBudState(BUD_DEAD);
         phytomer->setVegetativeBudState(BUD_DEAD);
     }
-    if (phytomer->rank > 1) {
-        phytomer->setFloralBudState(BUD_DEAD);
-        phytomer->setVegetativeBudState(BUD_DEAD);
-    }
 
     // set leaf and internode scale based on position along the shoot
     float leaf_scale = fmin(1.f, 0.5 + 0.5 * plant_age / 10.f);

plugins/plantarchitecture/include/PlantArchitecture.h

@@ -4598,13 +4598,19 @@ void PlantArchitecture::advanceTime(const std::vector<uint> &plantIDs, float tim
                             if (shoot->shoot_parameters.phytomer_parameters.inflorescence.fruit_prototype_function != nullptr) {
                                 if ((fbud.state == BUD_FLOWER_OPEN && plant_instance.dd_to_fruit_set >= 0.f) ||
                                     // flower opened and fruit set is enabled
-                                    (fbud.state == BUD_ACTIVE && plant_instance.dd_to_flower_initiation < 0.f && plant_instance.dd_to_flower_opening < 0.f && plant_instance.dd_to_fruit_set >= 0.f) ||
-                                    // jumped straight to fruit set with no flowering
+                                    (fbud.state == BUD_ACTIVE && plant_instance.dd_to_flower_initiation < 0.f && (plant_instance.dd_to_flower_opening < 0.f || shoot->shoot_parameters.phytomer_parameters.inflorescence.flower_prototype_function == nullptr) && plant_instance.dd_to_fruit_set >= 0.f) ||
+                                    // jumped straight to fruit set with no flowering (either flower opening disabled OR no flower prototype defined)
                                     (fbud.state == BUD_FLOWER_CLOSED && plant_instance.dd_to_flower_opening < 0.f && plant_instance.dd_to_fruit_set >= 0.f)) {
                                     // jumped from closed flower to fruit set with no flower opening
                                     if (fbud.time_counter >= plant_instance.dd_to_fruit_set) {
                                         fbud.time_counter = 0;
-                                        if (context_ptr->randu() < shoot->shoot_parameters.fruit_set_probability.val()) {
+                                        // When skipping flowering entirely (BUD_ACTIVE -> BUD_FRUITING), apply compound probability
+                                        float fruit_set_prob = shoot->shoot_parameters.fruit_set_probability.val();
+                                        if (fbud.state == BUD_ACTIVE) {
+                                            // Apply compound probability: flower_bud_break_probability * fruit_set_probability
+                                            fruit_set_prob *= shoot->shoot_parameters.flower_bud_break_probability.val();
+                                        }
+                                        if (context_ptr->randu() < fruit_set_prob) {
                                             phytomer->setFloralBudState(BUD_FRUITING, fbud);
                                         } else {
                                             phytomer->setFloralBudState(BUD_DEAD, fbud);
@@ -4697,7 +4703,9 @@ void PlantArchitecture::advanceTime(const std::vector<uint> &plantIDs, float tim
                                 //                                new_shoot_parameters->insertion_angle_tip.resample();
                                 //                            }
                                 float insertion_angle_adjustment = fmin(shoot->shoot_parameters.insertion_angle_tip.val() + shoot->shoot_parameters.insertion_angle_decay_rate.val() * float(parent_node_count - phytomer->shoot_index.x - 1), 90.f);
-                                AxisRotation base_rotation = make_AxisRotation(deg2rad(insertion_angle_adjustment), deg2rad(new_shoot_parameters->base_yaw.val()), deg2rad(new_shoot_parameters->base_roll.val()));
+                                // Calculate angular offset for child shoot based on parent petiole position
+                                float budrot = float(parent_petiole_index) * 2.f * PI_F / float(phytomer->axillary_vegetative_buds.size());
+                                AxisRotation base_rotation = make_AxisRotation(deg2rad(insertion_angle_adjustment), deg2rad(new_shoot_parameters->base_yaw.val()) + budrot, deg2rad(new_shoot_parameters->base_roll.val()));
                                 new_shoot_parameters->base_yaw.resample();
                                 if (shoot->shoot_parameters.insertion_angle_decay_rate.val() == 0) {
                                     shoot->shoot_parameters.insertion_angle_tip.resample();