PlantLibrary.cpp

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#include "CollisionDetection.h"
#include "PlantArchitecture.h"
 
using namespace helios;
 
float PlantArchitecture::getParameterValue(const std::map<std::string, float> &build_parameters, const std::string &parameter_name, float default_value, float min_value, float max_value, const std::string &parameter_description) const {
 
    // Check if parameter is specified in the map
    auto it = build_parameters.find(parameter_name);
    if (it == build_parameters.end()) {
        // Parameter not specified, use default
        return default_value;
    }
 
    float value = it->second;
 
    // Validate parameter is within valid range
    if (value < min_value || value > max_value) {
        helios_runtime_error("ERROR (PlantArchitecture::getParameterValue): build parameter '" + parameter_name + "' (" + parameter_description + ") has value " + std::to_string(value) + " which is outside the valid range [" +
                             std::to_string(min_value) + ", " + std::to_string(max_value) + "].");
    }
 
    return value;
}
 
void PlantArchitecture::initializePlantModelRegistrations() {
    // Register all available plant models
    registerPlantModel("almond", [this]() { initializeAlmondTreeShoots(); }, [this](const helios::vec3 &pos) { return buildAlmondTree(pos); }, "tree");
 
    registerPlantModel("almond_aldrich", [this]() { initializeAlmondTreeAldrichShoots(); }, [this](const helios::vec3 &pos) { return buildAlmondTreeAldrich(pos); }, "tree");
 
    registerPlantModel("almond_wood_colony", [this]() { initializeAlmondTreeWoodColonyShoots(); }, [this](const helios::vec3 &pos) { return buildAlmondTreeWoodColony(pos); }, "tree");
 
    registerPlantModel("apple", [this]() { initializeAppleTreeShoots(); }, [this](const helios::vec3 &pos) { return buildAppleTree(pos); }, "tree");
 
    registerPlantModel("apple_fruitingwall", [this]() { initializeAppleFruitingWallShoots(); }, [this](const helios::vec3 &pos) { return buildAppleFruitingWall(pos); }, "tree");
 
    registerPlantModel("asparagus", [this]() { initializeAsparagusShoots(); }, [this](const helios::vec3 &pos) { return buildAsparagusPlant(pos); });
 
    registerPlantModel("bindweed", [this]() { initializeBindweedShoots(); }, [this](const helios::vec3 &pos) { return buildBindweedPlant(pos); }, "weed");
 
    registerPlantModel("bean", [this]() { initializeBeanShoots(); }, [this](const helios::vec3 &pos) { return buildBeanPlant(pos); });
 
    registerPlantModel("bougainvillea", [this]() { initializeBougainvilleaShoots(); }, [this](const helios::vec3 &pos) { return buildBougainvilleaPlant(pos); });
 
    registerPlantModel("capsicum", [this]() { initializeCapsicumShoots(); }, [this](const helios::vec3 &pos) { return buildCapsicumPlant(pos); });
 
    registerPlantModel("cheeseweed", [this]() { initializeCheeseweedShoots(); }, [this](const helios::vec3 &pos) { return buildCheeseweedPlant(pos); }, "weed");
 
    registerPlantModel("cowpea", [this]() { initializeCowpeaShoots(); }, [this](const helios::vec3 &pos) { return buildCowpeaPlant(pos); });
 
    registerPlantModel("grapevine_VSP", [this]() { initializeGrapevineVSPShoots(); }, [this](const helios::vec3 &pos) { return buildGrapevineVSP(pos); });
 
    registerPlantModel("grapevine_Wye", [this]() { initializeGrapevineWyeShoots(); }, [this](const helios::vec3 &pos) { return buildGrapevineWye(pos); });
 
    registerPlantModel("groundcherryweed", [this]() { initializeGroundCherryWeedShoots(); }, [this](const helios::vec3 &pos) { return buildGroundCherryWeedPlant(pos); }, "weed");
 
    registerPlantModel("maize", [this]() { initializeMaizeShoots(); }, [this](const helios::vec3 &pos) { return buildMaizePlant(pos); });
 
    registerPlantModel("olive", [this]() { initializeOliveTreeShoots(); }, [this](const helios::vec3 &pos) { return buildOliveTree(pos); }, "tree");
 
    registerPlantModel("pistachio", [this]() { initializePistachioTreeShoots(); }, [this](const helios::vec3 &pos) { return buildPistachioTree(pos); }, "tree");
 
    registerPlantModel("puncturevine", [this]() { initializePuncturevineShoots(); }, [this](const helios::vec3 &pos) { return buildPuncturevinePlant(pos); }, "weed");
 
    registerPlantModel("easternredbud", [this]() { initializeEasternRedbudShoots(); }, [this](const helios::vec3 &pos) { return buildEasternRedbudPlant(pos); }, "tree");
 
    registerPlantModel("rice", [this]() { initializeRiceShoots(); }, [this](const helios::vec3 &pos) { return buildRicePlant(pos); });
 
    registerPlantModel("butterlettuce", [this]() { initializeButterLettuceShoots(); }, [this](const helios::vec3 &pos) { return buildButterLettucePlant(pos); });
 
    registerPlantModel("sorghum", [this]() { initializeSorghumShoots(); }, [this](const helios::vec3 &pos) { return buildSorghumPlant(pos); });
 
    registerPlantModel("soybean", [this]() { initializeSoybeanShoots(); }, [this](const helios::vec3 &pos) { return buildSoybeanPlant(pos); });
 
    registerPlantModel("strawberry", [this]() { initializeStrawberryShoots(); }, [this](const helios::vec3 &pos) { return buildStrawberryPlant(pos); });
 
    registerPlantModel("sugarbeet", [this]() { initializeSugarbeetShoots(); }, [this](const helios::vec3 &pos) { return buildSugarbeetPlant(pos); });
 
    registerPlantModel("tomato", [this]() { initializeTomatoShoots(); }, [this](const helios::vec3 &pos) { return buildTomatoPlant(pos); });
 
    registerPlantModel("cherrytomato", [this]() { initializeCherryTomatoShoots(); }, [this](const helios::vec3 &pos) { return buildCherryTomatoPlant(pos); });
 
    registerPlantModel("walnut", [this]() { initializeWalnutTreeShoots(); }, [this](const helios::vec3 &pos) { return buildWalnutTree(pos); }, "tree");
 
    registerPlantModel("wheat", [this]() { initializeWheatShoots(); }, [this](const helios::vec3 &pos) { return buildWheatPlant(pos); });
}
 
void PlantArchitecture::loadPlantModelFromLibrary(const std::string &plant_label) {
 
    current_plant_model = plant_label;
    initializeDefaultShoots(plant_label);
}
 
std::vector<std::string> PlantArchitecture::getAvailablePlantModels() const {
    std::vector<std::string> models;
    models.reserve(shoot_initializers.size());
    for (const auto &pair: shoot_initializers) {
        models.push_back(pair.first);
    }
    return models;
}
 
uint PlantArchitecture::buildPlantInstanceFromLibrary(const helios::vec3 &base_position, float age, const std::map<std::string, float> &build_parameters) {
 
    if (current_plant_model.empty()) {
        helios_runtime_error("ERROR (PlantArchitecture::buildPlantInstanceFromLibrary): current plant model has not been initialized from library. You must call loadPlantModelFromLibrary() first.");
    }
 
    // Find the plant builder function
    auto builder_it = plant_builders.find(current_plant_model);
    if (builder_it == plant_builders.end()) {
        helios_runtime_error("ERROR (PlantArchitecture::buildPlantInstanceFromLibrary): plant label of " + current_plant_model + " does not exist in the library.");
    }
 
    // Set current build parameters so builder functions can access them
    current_build_parameters = build_parameters;
 
    // Call the builder function
    uint plantID = builder_it->second(base_position);
 
    // Clear build parameters after use
    current_build_parameters.clear();
 
    plant_instances.at(plantID).plant_name = current_plant_model;
 
    // Rename organ materials that were created with the temporary "custom" plant name during the
    // build (geometry is constructed before plant_name is set, so renameAutoMaterial() in
    // PlantArchitecture.cpp tags them "custom_<organ>"). Rewrite the "custom_" prefix to the model
    // name so materials get descriptive labels like "bean_trifoliate_leaf".
    if (current_plant_model != "custom") {
        std::vector<std::string> material_labels = context_ptr->listMaterials();
        std::string old_prefix = "custom_";
        for (const auto &label: material_labels) {
            if (label.substr(0, old_prefix.size()) == old_prefix) {
                std::string new_label = current_plant_model + "_" + label.substr(old_prefix.size());
                if (!context_ptr->doesMaterialExist(new_label)) {
                    context_ptr->renameMaterial(label, new_label);
                }
            }
        }
    }
 
    // Update plant_name object data if enabled (geometry was built with temporary "custom" name)
    if (output_object_data.at("plant_name")) {
        std::vector<uint> plant_primitives = getAllPlantObjectIDs(plantID);
        for (uint objID: plant_primitives) {
            if (context_ptr->doesObjectDataExist(objID, "plant_name")) {
                context_ptr->setObjectData(objID, "plant_name", current_plant_model);
            }
        }
    }
 
    // Set plant_type object data if enabled
    if (output_object_data.at("plant_type")) {
        std::string plant_type = "herbaceous"; // Default type
        auto type_it = plant_type_map.find(current_plant_model);
        if (type_it != plant_type_map.end()) {
            plant_type = type_it->second;
        }
        std::vector<uint> plant_primitives = getAllPlantObjectIDs(plantID);
        context_ptr->setObjectData(plant_primitives, "plant_type", plant_type);
    }
 
    // Register plant with per-tree BVH collision detection if enabled
    if (collision_detection_enabled && collision_detection_ptr != nullptr && collision_detection_ptr->isTreeBasedBVHEnabled()) {
        std::vector<uint> plant_primitives = getPlantCollisionRelevantObjectIDs(plantID);
        if (!plant_primitives.empty()) {
            collision_detection_ptr->registerTree(plantID, plant_primitives);
        }
    }
 
    if (age > 0) {
        advanceTime(plantID, age);
    }
 
    return plantID;
}
 
ShootParameters PlantArchitecture::getCurrentShootParameters(const std::string &shoot_type_label) {
 
    if (shoot_types.find(shoot_type_label) == shoot_types.end()) {
        helios_runtime_error("ERROR (PlantArchitecture::getCurrentShootParameters): shoot type label of " + shoot_type_label + " does not exist in the current shoot parameters.");
    }
 
    return shoot_types.at(shoot_type_label);
}
 
std::map<std::string, ShootParameters> PlantArchitecture::getCurrentShootParameters() {
    if (shoot_types.empty()) {
        std::cerr
                << "WARNING (PlantArchitecture::getCurrentShootParameters): No plant models have been loaded. You need to first load a plant model from the library (see loadPlantModelFromLibrary()) or manually add shoot parameters (see updateCurrentShootParameters())."
                << std::endl;
    }
    return shoot_types;
}
 
std::map<std::string, PhytomerParameters> PlantArchitecture::getCurrentPhytomerParameters() {
    if (shoot_types.empty()) {
        std::cerr
                << "WARNING (PlantArchitecture::getCurrentPhytomerParameters): No plant models have been loaded. You need to first load a plant model from the library (see loadPlantModelFromLibrary()) or manually add shoot parameters (see updateCurrentShootParameters())."
                << std::endl;
    }
    std::map<std::string, PhytomerParameters> phytomer_parameters;
    for (const auto &type: shoot_types) {
        phytomer_parameters[type.first] = type.second.phytomer_parameters;
    }
    return phytomer_parameters;
}
 
std::vector<std::string> PlantArchitecture::listShootTypeLabels() const {
    if (shoot_types.empty()) {
        helios_runtime_error(
                "ERROR (PlantArchitecture::listShootTypeLabels): No plant model has been loaded. You must call loadPlantModelFromLibrary() first, or use listShootTypeLabels(plant_model_name) to query a specific model, or use listShootTypeLabels(plantID) to query a plant instance.");
    }
 
    std::vector<std::string> labels;
    labels.reserve(shoot_types.size());
 
    for (const auto &pair: shoot_types) {
        labels.push_back(pair.first);
    }
 
    return labels;
}
 
std::vector<std::string> PlantArchitecture::listShootTypeLabels(const std::string &plant_model_name) {
    // Validate model exists before modifying state
    auto init_it = shoot_initializers.find(plant_model_name);
    if (init_it == shoot_initializers.end()) {
        helios_runtime_error("ERROR (PlantArchitecture::listShootTypeLabels): plant model '" + plant_model_name + "' does not exist in the library. Use getAvailablePlantModels() to see available plant models.");
    }
 
    // Save current state
    std::string saved_plant_model = current_plant_model;
    std::map<std::string, ShootParameters> saved_shoot_types = shoot_types;
 
    // Load target plant model to extract shoot types
    try {
        initializeDefaultShoots(plant_model_name);
 
        // Extract shoot type labels
        std::vector<std::string> labels;
        labels.reserve(shoot_types.size());
        for (const auto &pair: shoot_types) {
            labels.push_back(pair.first);
        }
 
        // Restore original state
        current_plant_model = saved_plant_model;
        shoot_types = saved_shoot_types;
 
        return labels;
    } catch (...) {
        // Restore state even on exception
        current_plant_model = saved_plant_model;
        shoot_types = saved_shoot_types;
        throw;
    }
}
 
void PlantArchitecture::updateCurrentShootParameters(const std::string &shoot_type_label, const ShootParameters &params) {
    shoot_types[shoot_type_label] = params;
}
 
void PlantArchitecture::updateCurrentShootParameters(const std::map<std::string, ShootParameters> &params) {
    shoot_types = params;
}
 
void PlantArchitecture::initializeDefaultShoots(const std::string &plant_label) {
 
    // Clear existing shoot types to prevent contamination between plant models
    shoot_types.clear();
 
    // Find the shoot initializer function
    auto init_it = shoot_initializers.find(plant_label);
    if (init_it == shoot_initializers.end()) {
        helios_runtime_error("ERROR (PlantArchitecture::loadPlantModelFromLibrary): plant label of " + plant_label + " does not exist in the library.");
    }
 
    // Call the initializer function
    init_it->second();
}
 
void PlantArchitecture::registerPlantModel(const std::string &name, std::function<void()> shoot_init, std::function<uint(const helios::vec3 &)> plant_build, const std::string &plant_type) {
    shoot_initializers[name] = shoot_init;
    plant_builders[name] = plant_build;
    plant_type_map[name] = plant_type;
}
 
void PlantArchitecture::initializeAlmondTreeShoots() {
 
    // ---- Leaf Prototype ---- //
 
    LeafPrototype leaf_prototype(context_ptr->getRandomGenerator());
    leaf_prototype.leaf_texture_file[0] = "AlmondLeaf.png";
    leaf_prototype.leaf_aspect_ratio = 0.33f;
    leaf_prototype.midrib_fold_fraction = 0.1f;
    leaf_prototype.longitudinal_curvature = 0.05;
    leaf_prototype.lateral_curvature = 0.1f;
    leaf_prototype.subdivisions = 1;
    leaf_prototype.unique_prototypes = 1;
 
    // ---- Phytomer Parameters ---- //
 
    PhytomerParameters phytomer_parameters_almond(context_ptr->getRandomGenerator());
 
    phytomer_parameters_almond.internode.pitch = 3;
    phytomer_parameters_almond.internode.phyllotactic_angle.uniformDistribution(120, 160);
    phytomer_parameters_almond.internode.radius_initial = 0.002;
    phytomer_parameters_almond.internode.length_segments = 1;
    phytomer_parameters_almond.internode.image_texture = "AlmondBark.jpg";
    phytomer_parameters_almond.internode.max_floral_buds_per_petiole = 1; //
 
    phytomer_parameters_almond.petiole.petioles_per_internode = 1;
    phytomer_parameters_almond.petiole.pitch.uniformDistribution(-145, -90);
    phytomer_parameters_almond.petiole.taper = 0.1;
    phytomer_parameters_almond.petiole.curvature = 0;
    phytomer_parameters_almond.petiole.length = 0.04;
    phytomer_parameters_almond.petiole.radius = 0.0005;
    phytomer_parameters_almond.petiole.length_segments = 1;
    phytomer_parameters_almond.petiole.radial_subdivisions = 3;
    phytomer_parameters_almond.petiole.color = make_RGBcolor(0.61, 0.5, 0.24);
 
    phytomer_parameters_almond.leaf.leaves_per_petiole = 1;
    phytomer_parameters_almond.leaf.roll.uniformDistribution(-10, 10);
    phytomer_parameters_almond.leaf.prototype_scale = 0.12;
    phytomer_parameters_almond.leaf.prototype = leaf_prototype;
 
    phytomer_parameters_almond.peduncle.length = 0.002;
    phytomer_parameters_almond.peduncle.radius = 0.0005;
    phytomer_parameters_almond.peduncle.pitch = 80;
    phytomer_parameters_almond.peduncle.roll = 90;
    phytomer_parameters_almond.peduncle.length_segments = 1;
    phytomer_parameters_almond.petiole.radial_subdivisions = 3;
 
    phytomer_parameters_almond.inflorescence.flowers_per_peduncle = 1;
    phytomer_parameters_almond.inflorescence.pitch = 0;
    phytomer_parameters_almond.inflorescence.roll = 0;
    phytomer_parameters_almond.inflorescence.flower_prototype_scale = 0.04;
    phytomer_parameters_almond.inflorescence.flower_prototype_function = AlmondFlowerPrototype;
    phytomer_parameters_almond.inflorescence.fruit_prototype_scale = 0.04;
    phytomer_parameters_almond.inflorescence.fruit_prototype_function = AlmondFruitPrototype;
 
    // ---- Shoot Parameters ---- //
 
    // Trunk
    ShootParameters shoot_parameters_trunk(context_ptr->getRandomGenerator());
    shoot_parameters_trunk.phytomer_parameters = phytomer_parameters_almond;
    shoot_parameters_trunk.phytomer_parameters.internode.pitch = 0;
    shoot_parameters_trunk.phytomer_parameters.internode.phyllotactic_angle = 0;
    shoot_parameters_trunk.phytomer_parameters.internode.radius_initial = 0.005;
    shoot_parameters_trunk.phytomer_parameters.internode.radial_subdivisions = 24;
    shoot_parameters_trunk.max_nodes = 20;
    shoot_parameters_trunk.girth_area_factor = 10.f;
    shoot_parameters_trunk.vegetative_bud_break_probability_min = 0;
    shoot_parameters_trunk.vegetative_bud_break_time = 0;
    shoot_parameters_trunk.tortuosity = 1;
    shoot_parameters_trunk.internode_length_max = 0.04;
    shoot_parameters_trunk.internode_length_decay_rate = 0;
    shoot_parameters_trunk.defineChildShootTypes({"scaffold"}, {1});
 
    // Proleptic shoots
    ShootParameters shoot_parameters_proleptic(context_ptr->getRandomGenerator());
    shoot_parameters_proleptic.phytomer_parameters = phytomer_parameters_almond;
    shoot_parameters_proleptic.phytomer_parameters.internode.color = make_RGBcolor(0.3, 0.2, 0.2);
    shoot_parameters_proleptic.phytomer_parameters.internode.radial_subdivisions = 5;
    shoot_parameters_proleptic.phytomer_parameters.phytomer_creation_function = AlmondPhytomerCreationFunction;
    shoot_parameters_proleptic.phytomer_parameters.phytomer_callback_function = AlmondPhytomerCallbackFunction;
    shoot_parameters_proleptic.max_nodes = 60;
    shoot_parameters_proleptic.max_nodes_per_season = 20;
    shoot_parameters_proleptic.phyllochron_min = 1;
    shoot_parameters_proleptic.elongation_rate_max = 0.3;
    shoot_parameters_proleptic.girth_area_factor = 6.f;
    shoot_parameters_proleptic.vegetative_bud_break_probability_min = 0.1;
    shoot_parameters_proleptic.vegetative_bud_break_probability_max = 0.5;
    shoot_parameters_proleptic.vegetative_bud_break_probability_decay_rate = 0.15;
    shoot_parameters_proleptic.vegetative_bud_break_time = 0;
    shoot_parameters_proleptic.gravitropic_curvature = 250;
    shoot_parameters_proleptic.tortuosity = 3.5;
    shoot_parameters_proleptic.insertion_angle_tip.uniformDistribution(25, 30);
    shoot_parameters_proleptic.insertion_angle_decay_rate = 15;
    shoot_parameters_proleptic.internode_length_max = 0.03;
    shoot_parameters_proleptic.internode_length_min = 0.002;
    shoot_parameters_proleptic.internode_length_decay_rate = 0.002;
    shoot_parameters_proleptic.fruit_set_probability = 0.4;
    shoot_parameters_proleptic.flower_bud_break_probability = 0.3;
    shoot_parameters_proleptic.max_terminal_floral_buds = 3;
    shoot_parameters_proleptic.flowers_require_dormancy = true;
    shoot_parameters_proleptic.growth_requires_dormancy = true;
    shoot_parameters_proleptic.determinate_shoot_growth = false;
    shoot_parameters_proleptic.defineChildShootTypes({"proleptic", "sylleptic"}, {1.0, 0.});
 
    // Sylleptic shoots
    ShootParameters shoot_parameters_sylleptic = shoot_parameters_proleptic;
    //    shoot_parameters_sylleptic.phytomer_parameters.internode.color = RGB::red;
    shoot_parameters_sylleptic.phytomer_parameters.internode.image_texture = "";
    shoot_parameters_sylleptic.phytomer_parameters.leaf.prototype_scale = 0.14;
    shoot_parameters_sylleptic.phytomer_parameters.leaf.pitch.uniformDistribution(-45, -20);
    shoot_parameters_sylleptic.insertion_angle_tip = 0;
    shoot_parameters_sylleptic.insertion_angle_decay_rate = 0;
    shoot_parameters_sylleptic.phyllochron_min = 1;
    shoot_parameters_sylleptic.vegetative_bud_break_probability_min = 0.0;
    shoot_parameters_sylleptic.vegetative_bud_break_probability_max = 0.7;
    shoot_parameters_sylleptic.gravitropic_curvature = 600;
    shoot_parameters_sylleptic.internode_length_max = 0.02;
    shoot_parameters_sylleptic.flowers_require_dormancy = true;
    shoot_parameters_sylleptic.growth_requires_dormancy = true;
    shoot_parameters_sylleptic.defineChildShootTypes({"proleptic"}, {1.0});
 
    // Main scaffolds
    ShootParameters shoot_parameters_scaffold = shoot_parameters_proleptic;
    //    shoot_parameters_scaffold.phytomer_parameters.internode.color = RGB::blue;
    shoot_parameters_scaffold.phytomer_parameters.internode.radial_subdivisions = 10;
    shoot_parameters_scaffold.max_nodes = 40;
    shoot_parameters_scaffold.gravitropic_curvature = 150;
    // shoot_parameters_scaffold.internode_length_max = 0.02;
    shoot_parameters_scaffold.tortuosity = 1.;
    shoot_parameters_scaffold.defineChildShootTypes({"proleptic"}, {1.0});
 
    defineShootType("trunk", shoot_parameters_trunk);
    defineShootType("scaffold", shoot_parameters_scaffold);
    defineShootType("proleptic", shoot_parameters_proleptic);
    defineShootType("sylleptic", shoot_parameters_sylleptic);
}
 
uint PlantArchitecture::buildAlmondTree(const helios::vec3 &base_position) {
 
    if (shoot_types.empty()) {
        // automatically initialize almond tree shoots
        initializeAlmondTreeShoots();
    }
 
    // Get training system parameters (with defaults matching original hard-coded values)
    auto trunk_height = getParameterValue(current_build_parameters, "trunk_height", 0.6f, 0.1f, 3.f, "total trunk height in meters");
    auto num_scaffolds = uint(getParameterValue(current_build_parameters, "num_scaffolds", 4.f, 2.f, 8.f, "number of scaffold branches"));
    auto scaffold_angle = getParameterValue(current_build_parameters, "scaffold_angle", 40.f, 20.f, 70.f, "scaffold branch angle in degrees");
 
    // Calculate trunk nodes based on desired height and internode length
    float trunk_internode_length = 0.03f; // Default internode length for almond
    uint trunk_nodes = uint(trunk_height / trunk_internode_length);
    if (trunk_nodes < 1)
        trunk_nodes = 1;
 
    // Fixed training parameters (not user-customizable)
    float trunk_radius = 0.015f;
    float scaffold_radius = 0.007f;
    float scaffold_length = 0.06f;
 
    uint plantID = addPlantInstance(base_position, 0);
 
    //    enableEpicormicChildShoots(plantID,"sylleptic",0.001);
 
    uint uID_trunk = addBaseStemShoot(plantID, trunk_nodes, make_AxisRotation(context_ptr->randu(0.f, 0.05f * M_PI), context_ptr->randu(0.f, 2.f * M_PI), 0.f * M_PI), trunk_radius, trunk_internode_length, 1.f, 1.f, 0, "trunk");
    appendPhytomerToShoot(plantID, uID_trunk, shoot_types.at("trunk").phytomer_parameters, 0.01, 0.01, 1, 1);
 
    plant_instances.at(plantID).shoot_tree.at(uID_trunk)->meristem_is_alive = false;
 
    auto phytomers = plant_instances.at(plantID).shoot_tree.at(uID_trunk)->phytomers;
    for (const auto &phytomer: phytomers) {
        phytomer->removeLeaf();
        phytomer->setVegetativeBudState(BUD_DEAD);
        phytomer->setFloralBudState(BUD_DEAD);
    }
 
    // Hard-coded scaffold node range (not user-customizable)
    uint scaffold_nodes_min = 5;
    uint scaffold_nodes_max = 5;
 
    for (int i = 0; i < num_scaffolds; i++) {
        float pitch = deg2rad(scaffold_angle) + context_ptr->randu(-0.1f, 0.1f); // Small randomness around specified angle
        uint scaffold_nodes = context_ptr->randu(int(scaffold_nodes_min), int(scaffold_nodes_max));
        uint uID_shoot = addChildShoot(plantID, uID_trunk, getShootNodeCount(plantID, uID_trunk) - i - 1, scaffold_nodes, make_AxisRotation(pitch, (float(i) + context_ptr->randu(-0.2f, 0.2f)) / float(num_scaffolds) * 2 * M_PI, 0), scaffold_radius,
                                       scaffold_length, 1.f, 1.f, 0.5, "scaffold", 0);
    }
 
    makePlantDormant(plantID);
 
    setPlantPhenologicalThresholds(plantID, 90, -1, 3, 7, 20, 275, false);
    plant_instances.at(plantID).max_age = 1825;
 
    return plantID;
}
 
void PlantArchitecture::initializeAlmondTreeAldrichShoots() {
 
    // ---- Leaf Prototype ---- //
 
    LeafPrototype leaf_prototype(context_ptr->getRandomGenerator());
    leaf_prototype.leaf_texture_file[0] = "AlmondLeaf.png";
    leaf_prototype.leaf_aspect_ratio = 0.33f;
    leaf_prototype.midrib_fold_fraction = 0.1f;
    leaf_prototype.longitudinal_curvature = 0.05;
    leaf_prototype.lateral_curvature = 0.1f;
    leaf_prototype.subdivisions = 1;
    leaf_prototype.unique_prototypes = 1;
 
    // ---- Phytomer Parameters ---- //
 
    PhytomerParameters phytomer_parameters_almond(context_ptr->getRandomGenerator());
 
    phytomer_parameters_almond.internode.pitch = 3;
    phytomer_parameters_almond.internode.phyllotactic_angle.uniformDistribution(120, 160);
    phytomer_parameters_almond.internode.radius_initial = 0.002;
    phytomer_parameters_almond.internode.length_segments = 1;
    phytomer_parameters_almond.internode.image_texture = "AlmondBark.jpg";
    phytomer_parameters_almond.internode.max_floral_buds_per_petiole = 1; //
 
    phytomer_parameters_almond.petiole.petioles_per_internode = 1;
    phytomer_parameters_almond.petiole.pitch.uniformDistribution(-145, -90);
    phytomer_parameters_almond.petiole.taper = 0.1;
    phytomer_parameters_almond.petiole.curvature = 0;
    phytomer_parameters_almond.petiole.length = 0.04;
    phytomer_parameters_almond.petiole.radius = 0.0005;
    phytomer_parameters_almond.petiole.length_segments = 1;
    phytomer_parameters_almond.petiole.radial_subdivisions = 3;
    phytomer_parameters_almond.petiole.color = make_RGBcolor(0.61, 0.5, 0.24);
 
    phytomer_parameters_almond.leaf.leaves_per_petiole = 1;
    phytomer_parameters_almond.leaf.roll.uniformDistribution(-10, 10);
    phytomer_parameters_almond.leaf.prototype_scale = 0.12;
    phytomer_parameters_almond.leaf.prototype = leaf_prototype;
 
    phytomer_parameters_almond.peduncle.length = 0.002;
    phytomer_parameters_almond.peduncle.radius = 0.0005;
    phytomer_parameters_almond.peduncle.pitch = 80;
    phytomer_parameters_almond.peduncle.roll = 90;
    phytomer_parameters_almond.peduncle.length_segments = 1;
    phytomer_parameters_almond.petiole.radial_subdivisions = 3;
 
    phytomer_parameters_almond.inflorescence.flowers_per_peduncle = 1;
    phytomer_parameters_almond.inflorescence.pitch = 0;
    phytomer_parameters_almond.inflorescence.roll = 0;
    phytomer_parameters_almond.inflorescence.flower_prototype_scale = 0.04;
    phytomer_parameters_almond.inflorescence.flower_prototype_function = AlmondFlowerPrototype;
    phytomer_parameters_almond.inflorescence.fruit_prototype_scale = 0.04;
    phytomer_parameters_almond.inflorescence.fruit_prototype_function = AlmondFruitPrototype;
 
    // ---- Shoot Parameters ---- //
 
    // Trunk
    ShootParameters shoot_parameters_trunk(context_ptr->getRandomGenerator());
    shoot_parameters_trunk.phytomer_parameters = phytomer_parameters_almond;
    shoot_parameters_trunk.phytomer_parameters.internode.pitch = 0;
    shoot_parameters_trunk.phytomer_parameters.internode.phyllotactic_angle = 0;
    shoot_parameters_trunk.phytomer_parameters.internode.radius_initial = 0.005;
    shoot_parameters_trunk.phytomer_parameters.internode.radial_subdivisions = 24;
    shoot_parameters_trunk.max_nodes = 20;
    shoot_parameters_trunk.girth_area_factor = 8.f;
    shoot_parameters_trunk.vegetative_bud_break_probability_min = 0;
    shoot_parameters_trunk.vegetative_bud_break_time = 0;
    shoot_parameters_trunk.tortuosity = .5;
    shoot_parameters_trunk.internode_length_max = 0.05;
    shoot_parameters_trunk.internode_length_decay_rate = 0;
    shoot_parameters_trunk.defineChildShootTypes({"scaffold"}, {1});
 
    // Proleptic shoots
    ShootParameters shoot_parameters_proleptic(context_ptr->getRandomGenerator());
    shoot_parameters_proleptic.phytomer_parameters = phytomer_parameters_almond;
    shoot_parameters_proleptic.phytomer_parameters.internode.color = make_RGBcolor(0.3, 0.2, 0.2);
    shoot_parameters_proleptic.phytomer_parameters.internode.radial_subdivisions = 5;
    shoot_parameters_proleptic.phytomer_parameters.phytomer_creation_function = AlmondPhytomerCreationFunction;
    shoot_parameters_proleptic.phytomer_parameters.phytomer_callback_function = AlmondPhytomerCallbackFunction;
    shoot_parameters_proleptic.max_nodes = 25;
    shoot_parameters_proleptic.max_nodes_per_season = 15;
    shoot_parameters_proleptic.phyllochron_min = 1;
    shoot_parameters_proleptic.elongation_rate_max = 0.3;
    shoot_parameters_proleptic.girth_area_factor = 8.f;
    shoot_parameters_proleptic.vegetative_bud_break_probability_min = 0.1;
    shoot_parameters_proleptic.vegetative_bud_break_probability_max = 0.5;
    shoot_parameters_proleptic.vegetative_bud_break_probability_decay_rate = 0.15;
    shoot_parameters_proleptic.vegetative_bud_break_time = 0;
    shoot_parameters_proleptic.gravitropic_curvature = 450;
    shoot_parameters_proleptic.tortuosity = 2.5;
    shoot_parameters_proleptic.insertion_angle_tip.uniformDistribution(5, 30);
    shoot_parameters_proleptic.insertion_angle_decay_rate = 5;
    shoot_parameters_proleptic.internode_length_max = 0.025;
    shoot_parameters_proleptic.internode_length_min = 0.002;
    shoot_parameters_proleptic.internode_length_decay_rate = 0.002;
    shoot_parameters_proleptic.fruit_set_probability = 0.4;
    shoot_parameters_proleptic.flower_bud_break_probability = 0.3;
    shoot_parameters_proleptic.max_terminal_floral_buds = 3;
    shoot_parameters_proleptic.flowers_require_dormancy = true;
    shoot_parameters_proleptic.growth_requires_dormancy = true;
    shoot_parameters_proleptic.determinate_shoot_growth = false;
    shoot_parameters_proleptic.defineChildShootTypes({"proleptic", "sylleptic"}, {1.0, 0.});
 
    // Sylleptic shoots
    ShootParameters shoot_parameters_sylleptic = shoot_parameters_proleptic;
    //    shoot_parameters_sylleptic.phytomer_parameters.internode.color = RGB::red;
    shoot_parameters_sylleptic.phytomer_parameters.internode.image_texture = "";
    shoot_parameters_sylleptic.phytomer_parameters.leaf.prototype_scale = 0.12;
    shoot_parameters_sylleptic.phytomer_parameters.leaf.pitch.uniformDistribution(-45, -20);
    shoot_parameters_sylleptic.insertion_angle_tip = 0;
    shoot_parameters_sylleptic.insertion_angle_decay_rate = 0;
    shoot_parameters_sylleptic.phyllochron_min = 1;
    shoot_parameters_sylleptic.vegetative_bud_break_probability_min = 0.0;
    shoot_parameters_proleptic.vegetative_bud_break_probability_max = 0.6;
    shoot_parameters_sylleptic.gravitropic_curvature = 600;
    shoot_parameters_sylleptic.internode_length_max = 0.02;
    shoot_parameters_sylleptic.flowers_require_dormancy = true;
    shoot_parameters_sylleptic.growth_requires_dormancy = true;
    shoot_parameters_sylleptic.defineChildShootTypes({"proleptic"}, {1.0});
 
    // Main scaffolds
    ShootParameters shoot_parameters_scaffold = shoot_parameters_proleptic;
    //    shoot_parameters_scaffold.phytomer_parameters.internode.color = RGB::blue;
    shoot_parameters_scaffold.phytomer_parameters.internode.radial_subdivisions = 10;
    shoot_parameters_scaffold.max_nodes = 20;
    shoot_parameters_scaffold.gravitropic_curvature = 200;
    shoot_parameters_scaffold.internode_length_max = 0.02;
    shoot_parameters_scaffold.tortuosity = 0.5;
    shoot_parameters_scaffold.defineChildShootTypes({"proleptic"}, {1.0});
 
    defineShootType("trunk", shoot_parameters_trunk);
    defineShootType("scaffold", shoot_parameters_scaffold);
    defineShootType("proleptic", shoot_parameters_proleptic);
    defineShootType("sylleptic", shoot_parameters_sylleptic);
}
 
uint PlantArchitecture::buildAlmondTreeAldrich(const helios::vec3 &base_position) {
 
    if (shoot_types.empty()) {
        // automatically initialize almond tree shoots
        initializeAlmondTreeShoots();
    }
 
    uint plantID = addPlantInstance(base_position, 0);
 
    //    enableEpicormicChildShoots(plantID,"sylleptic",0.001);
 
    uint uID_trunk = addBaseStemShoot(plantID, 19, make_AxisRotation(context_ptr->randu(0.f, 0.05f * M_PI), context_ptr->randu(0.f, 2.f * M_PI), 0.f * M_PI), 0.015, 0.03, 1.f, 1.f, 0, "trunk");
    appendPhytomerToShoot(plantID, uID_trunk, shoot_types.at("trunk").phytomer_parameters, 0.01, 0.01, 1, 1);
 
    plant_instances.at(plantID).shoot_tree.at(uID_trunk)->meristem_is_alive = false;
 
    auto phytomers = plant_instances.at(plantID).shoot_tree.at(uID_trunk)->phytomers;
    for (const auto &phytomer: phytomers) {
        phytomer->removeLeaf();
        phytomer->setVegetativeBudState(BUD_DEAD);
        phytomer->setFloralBudState(BUD_DEAD);
    }
 
    uint Nscaffolds = 4; // context_ptr->randu(4,5);
 
    for (int i = 0; i < Nscaffolds; i++) {
        float pitch = context_ptr->randu(deg2rad(5), deg2rad(35));
        uint uID_shoot = addChildShoot(plantID, uID_trunk, getShootNodeCount(plantID, uID_trunk) - i - 1, context_ptr->randu(7, 9), make_AxisRotation(pitch, (float(i) + context_ptr->randu(-0.2f, 0.2f)) / float(Nscaffolds) * 2 * M_PI, 0), 0.007, 0.06,
                                       1.f, 1.f, 0.5, "scaffold", 0);
    }
 
    makePlantDormant(plantID);
 
    setPlantPhenologicalThresholds(plantID, 90, -1, 3, 7, 20, 275, false);
    plant_instances.at(plantID).max_age = 1825;
 
    return plantID;
}
 
 
void PlantArchitecture::initializeAlmondTreeWoodColonyShoots() {
 
    // ---- Leaf Prototype ---- //
 
    LeafPrototype leaf_prototype(context_ptr->getRandomGenerator());
    leaf_prototype.leaf_texture_file[0] = "AlmondLeaf.png";
    leaf_prototype.leaf_aspect_ratio = 0.33f;
    leaf_prototype.midrib_fold_fraction = 0.1f;
    leaf_prototype.longitudinal_curvature = 0.05;
    leaf_prototype.lateral_curvature = 0.1f;
    leaf_prototype.subdivisions = 1;
    leaf_prototype.unique_prototypes = 1;
 
    // ---- Phytomer Parameters ---- //
 
    PhytomerParameters phytomer_parameters_almond(context_ptr->getRandomGenerator());
 
    phytomer_parameters_almond.internode.pitch = 3;
    phytomer_parameters_almond.internode.phyllotactic_angle.uniformDistribution(120, 160);
    phytomer_parameters_almond.internode.radius_initial = 0.002;
    phytomer_parameters_almond.internode.length_segments = 1;
    phytomer_parameters_almond.internode.image_texture = "AlmondBark.jpg";
    phytomer_parameters_almond.internode.max_floral_buds_per_petiole = 1; //
 
    phytomer_parameters_almond.petiole.petioles_per_internode = 1;
    phytomer_parameters_almond.petiole.pitch.uniformDistribution(-145, -90);
    phytomer_parameters_almond.petiole.taper = 0.1;
    phytomer_parameters_almond.petiole.curvature = 0;
    phytomer_parameters_almond.petiole.length = 0.04;
    phytomer_parameters_almond.petiole.radius = 0.0005;
    phytomer_parameters_almond.petiole.length_segments = 1;
    phytomer_parameters_almond.petiole.radial_subdivisions = 3;
    phytomer_parameters_almond.petiole.color = make_RGBcolor(0.61, 0.5, 0.24);
 
    phytomer_parameters_almond.leaf.leaves_per_petiole = 1;
    phytomer_parameters_almond.leaf.roll.uniformDistribution(-10, 10);
    phytomer_parameters_almond.leaf.prototype_scale = 0.12;
    phytomer_parameters_almond.leaf.prototype = leaf_prototype;
 
    phytomer_parameters_almond.peduncle.length = 0.002;
    phytomer_parameters_almond.peduncle.radius = 0.0005;
    phytomer_parameters_almond.peduncle.pitch = 80;
    phytomer_parameters_almond.peduncle.roll = 90;
    phytomer_parameters_almond.peduncle.length_segments = 1;
    phytomer_parameters_almond.petiole.radial_subdivisions = 3;
 
    phytomer_parameters_almond.inflorescence.flowers_per_peduncle = 1;
    phytomer_parameters_almond.inflorescence.pitch = 0;
    phytomer_parameters_almond.inflorescence.roll = 0;
    phytomer_parameters_almond.inflorescence.flower_prototype_scale = 0.04;
    phytomer_parameters_almond.inflorescence.flower_prototype_function = AlmondFlowerPrototype;
    phytomer_parameters_almond.inflorescence.fruit_prototype_scale = 0.04;
    phytomer_parameters_almond.inflorescence.fruit_prototype_function = AlmondFruitPrototype;
 
    // ---- Shoot Parameters ---- //
 
    // Trunk
    ShootParameters shoot_parameters_trunk(context_ptr->getRandomGenerator());
    shoot_parameters_trunk.phytomer_parameters = phytomer_parameters_almond;
    shoot_parameters_trunk.phytomer_parameters.internode.pitch = 0;
    shoot_parameters_trunk.phytomer_parameters.internode.phyllotactic_angle = 0;
    shoot_parameters_trunk.phytomer_parameters.internode.radius_initial = 0.005;
    shoot_parameters_trunk.phytomer_parameters.internode.radial_subdivisions = 24;
    shoot_parameters_trunk.max_nodes = 15;
    shoot_parameters_trunk.girth_area_factor = 10.f;
    shoot_parameters_trunk.vegetative_bud_break_probability_min = 0;
    shoot_parameters_trunk.vegetative_bud_break_time = 0;
    shoot_parameters_trunk.tortuosity = 1;
    shoot_parameters_trunk.internode_length_max = 0.0325;
    shoot_parameters_trunk.internode_length_decay_rate = 0;
    shoot_parameters_trunk.defineChildShootTypes({"scaffold"}, {1});
 
    // Proleptic shoots
    ShootParameters shoot_parameters_proleptic(context_ptr->getRandomGenerator());
    shoot_parameters_proleptic.phytomer_parameters = phytomer_parameters_almond;
    shoot_parameters_proleptic.phytomer_parameters.internode.color = make_RGBcolor(0.3, 0.2, 0.2);
    shoot_parameters_proleptic.phytomer_parameters.internode.radial_subdivisions = 5;
    shoot_parameters_proleptic.phytomer_parameters.phytomer_creation_function = AlmondPhytomerCreationFunction;
    shoot_parameters_proleptic.phytomer_parameters.phytomer_callback_function = AlmondPhytomerCallbackFunction;
    shoot_parameters_proleptic.max_nodes = 20;
    shoot_parameters_proleptic.max_nodes_per_season = 15;
    shoot_parameters_proleptic.phyllochron_min = 1;
    shoot_parameters_proleptic.elongation_rate_max = 0.3;
    shoot_parameters_proleptic.girth_area_factor = 8.f;
    shoot_parameters_proleptic.vegetative_bud_break_probability_min = 0.1;
    shoot_parameters_proleptic.vegetative_bud_break_probability_max = 0.5;
    shoot_parameters_proleptic.vegetative_bud_break_probability_decay_rate = 0.15;
    shoot_parameters_proleptic.vegetative_bud_break_time = 0;
    shoot_parameters_proleptic.gravitropic_curvature = 150;
    shoot_parameters_proleptic.tortuosity = 3;
    shoot_parameters_proleptic.insertion_angle_tip.uniformDistribution(30, 75);
    shoot_parameters_proleptic.insertion_angle_decay_rate = 17.5;
    shoot_parameters_proleptic.internode_length_max = 0.02;
    shoot_parameters_proleptic.internode_length_min = 0.002;
    shoot_parameters_proleptic.internode_length_decay_rate = 0.002;
    shoot_parameters_proleptic.fruit_set_probability = 0.4;
    shoot_parameters_proleptic.flower_bud_break_probability = 0.3;
    shoot_parameters_proleptic.max_terminal_floral_buds = 3;
    shoot_parameters_proleptic.flowers_require_dormancy = true;
    shoot_parameters_proleptic.growth_requires_dormancy = true;
    shoot_parameters_proleptic.determinate_shoot_growth = false;
    shoot_parameters_proleptic.defineChildShootTypes({"proleptic", "sylleptic"}, {1.0, 0.});
 
    // Sylleptic shoots
    ShootParameters shoot_parameters_sylleptic = shoot_parameters_proleptic;
    //    shoot_parameters_sylleptic.phytomer_parameters.internode.color = RGB::red;
    shoot_parameters_sylleptic.phytomer_parameters.internode.image_texture = "";
    shoot_parameters_sylleptic.phytomer_parameters.leaf.prototype_scale = 0.12;
    shoot_parameters_sylleptic.phytomer_parameters.leaf.pitch.uniformDistribution(-45, -20);
    shoot_parameters_sylleptic.insertion_angle_tip = 0;
    shoot_parameters_sylleptic.insertion_angle_decay_rate = 0;
    shoot_parameters_sylleptic.phyllochron_min = 1;
    shoot_parameters_sylleptic.vegetative_bud_break_probability_min = 0.0;
    shoot_parameters_proleptic.vegetative_bud_break_probability_max = 0.6;
    shoot_parameters_sylleptic.gravitropic_curvature = 600;
    shoot_parameters_sylleptic.internode_length_max = 0.02;
    shoot_parameters_sylleptic.flowers_require_dormancy = true;
    shoot_parameters_sylleptic.growth_requires_dormancy = true;
    shoot_parameters_sylleptic.defineChildShootTypes({"proleptic"}, {1.0});
 
    // Main scaffolds
    ShootParameters shoot_parameters_scaffold = shoot_parameters_proleptic;
    //    shoot_parameters_scaffold.phytomer_parameters.internode.color = RGB::blue;
    shoot_parameters_scaffold.phytomer_parameters.internode.radial_subdivisions = 10;
    shoot_parameters_scaffold.max_nodes = 15;
    shoot_parameters_scaffold.gravitropic_curvature = 100;
    shoot_parameters_scaffold.internode_length_max = 0.02;
    shoot_parameters_scaffold.tortuosity = 1.;
    shoot_parameters_scaffold.defineChildShootTypes({"proleptic"}, {1.0});
 
    defineShootType("trunk", shoot_parameters_trunk);
    defineShootType("scaffold", shoot_parameters_scaffold);
    defineShootType("proleptic", shoot_parameters_proleptic);
    defineShootType("sylleptic", shoot_parameters_sylleptic);
}
 
uint PlantArchitecture::buildAlmondTreeWoodColony(const helios::vec3 &base_position) {
 
    if (shoot_types.empty()) {
        // automatically initialize almond tree shoots
        initializeAlmondTreeShoots();
    }
 
    uint plantID = addPlantInstance(base_position, 0);
 
    //    enableEpicormicChildShoots(plantID,"sylleptic",0.001);
 
    uint uID_trunk = addBaseStemShoot(plantID, 14, make_AxisRotation(context_ptr->randu(0.f, 0.05f * M_PI), context_ptr->randu(0.f, 2.f * M_PI), 0.f * M_PI), 0.015, 0.03, 1.f, 1.f, 0, "trunk");
    appendPhytomerToShoot(plantID, uID_trunk, shoot_types.at("trunk").phytomer_parameters, 0.01, 0.01, 1, 1);
 
    plant_instances.at(plantID).shoot_tree.at(uID_trunk)->meristem_is_alive = false;
 
    auto phytomers = plant_instances.at(plantID).shoot_tree.at(uID_trunk)->phytomers;
    for (const auto &phytomer: phytomers) {
        phytomer->removeLeaf();
        phytomer->setVegetativeBudState(BUD_DEAD);
        phytomer->setFloralBudState(BUD_DEAD);
    }
 
    uint Nscaffolds = 5; // context_ptr->randu(4,5);
 
    for (int i = 0; i < Nscaffolds; i++) {
        float pitch = context_ptr->randu(deg2rad(45), deg2rad(60));
        uint uID_shoot = addChildShoot(plantID, uID_trunk, getShootNodeCount(plantID, uID_trunk) - i - 1, context_ptr->randu(7, 9), make_AxisRotation(pitch, (float(i) + context_ptr->randu(-0.2f, 0.2f)) / float(Nscaffolds) * 2 * M_PI, 0), 0.007, 0.06,
                                       1.f, 1.f, 0.5, "scaffold", 0);
    }
 
    makePlantDormant(plantID);
 
    setPlantPhenologicalThresholds(plantID, 90, -1, 3, 7, 20, 275, false);
    plant_instances.at(plantID).max_age = 1825;
 
    return plantID;
}
 
void PlantArchitecture::initializeAppleTreeShoots() {
 
    // ---- Leaf Prototype ---- //
 
    LeafPrototype leaf_prototype(context_ptr->getRandomGenerator());
    leaf_prototype.leaf_texture_file[0] = "AppleLeaf.png";
    leaf_prototype.leaf_aspect_ratio = 0.6f;
    leaf_prototype.midrib_fold_fraction = 0.4f;
    leaf_prototype.longitudinal_curvature = -0.3f;
    leaf_prototype.lateral_curvature = 0.1f;
    leaf_prototype.subdivisions = 3;
    leaf_prototype.unique_prototypes = 1;
 
    // ---- Phytomer Parameters ---- //
 
    PhytomerParameters phytomer_parameters_apple(context_ptr->getRandomGenerator());
 
    phytomer_parameters_apple.internode.pitch = 0;
    phytomer_parameters_apple.internode.phyllotactic_angle.uniformDistribution(130, 145);
    phytomer_parameters_apple.internode.radius_initial = 0.004;
    phytomer_parameters_apple.internode.length_segments = 1;
    phytomer_parameters_apple.internode.image_texture = "AppleBark.jpg";
    phytomer_parameters_apple.internode.max_floral_buds_per_petiole = 1;
 
    phytomer_parameters_apple.petiole.petioles_per_internode = 1;
    phytomer_parameters_apple.petiole.pitch.uniformDistribution(-40, -25);
    phytomer_parameters_apple.petiole.taper = 0.1;
    phytomer_parameters_apple.petiole.curvature = 0;
    phytomer_parameters_apple.petiole.length = 0.04;
    phytomer_parameters_apple.petiole.radius = 0.00075;
    phytomer_parameters_apple.petiole.length_segments = 1;
    phytomer_parameters_apple.petiole.radial_subdivisions = 3;
    phytomer_parameters_apple.petiole.color = make_RGBcolor(0.61, 0.5, 0.24);
 
    phytomer_parameters_apple.leaf.leaves_per_petiole = 1;
    phytomer_parameters_apple.leaf.prototype_scale = 0.12;
    phytomer_parameters_apple.leaf.prototype = leaf_prototype;
 
    phytomer_parameters_apple.peduncle.length = 0.04;
    phytomer_parameters_apple.peduncle.radius = 0.001;
    phytomer_parameters_apple.peduncle.pitch = 90;
    phytomer_parameters_apple.peduncle.roll = 90;
    phytomer_parameters_apple.peduncle.length_segments = 1;
 
    phytomer_parameters_apple.inflorescence.flowers_per_peduncle = 1;
    phytomer_parameters_apple.inflorescence.pitch = 0;
    phytomer_parameters_apple.inflorescence.roll = 0;
    phytomer_parameters_apple.inflorescence.flower_prototype_scale = 0.03;
    phytomer_parameters_apple.inflorescence.flower_prototype_function = AppleFlowerPrototype;
    phytomer_parameters_apple.inflorescence.fruit_prototype_scale = 0.1;
    phytomer_parameters_apple.inflorescence.fruit_prototype_function = AppleFruitPrototype;
    phytomer_parameters_apple.inflorescence.fruit_gravity_factor_fraction = 0.5;
 
    // ---- Shoot Parameters ---- //
 
    // Trunk
    ShootParameters shoot_parameters_trunk(context_ptr->getRandomGenerator());
    shoot_parameters_trunk.phytomer_parameters = phytomer_parameters_apple;
    shoot_parameters_trunk.phytomer_parameters.internode.phyllotactic_angle = 0;
    shoot_parameters_trunk.phytomer_parameters.internode.radius_initial = 0.01;
    shoot_parameters_trunk.phytomer_parameters.internode.radial_subdivisions = 24;
    shoot_parameters_trunk.max_nodes = 20;
    shoot_parameters_trunk.girth_area_factor = 5.f;
    shoot_parameters_trunk.vegetative_bud_break_probability_min = 0;
    shoot_parameters_trunk.vegetative_bud_break_time = 0;
    shoot_parameters_trunk.tortuosity = 1;
    shoot_parameters_trunk.internode_length_max = 0.05;
    shoot_parameters_trunk.internode_length_decay_rate = 0;
    shoot_parameters_trunk.defineChildShootTypes({"proleptic"}, {1});
 
    // Proleptic shoots
    ShootParameters shoot_parameters_proleptic(context_ptr->getRandomGenerator());
    shoot_parameters_proleptic.phytomer_parameters = phytomer_parameters_apple;
    shoot_parameters_proleptic.phytomer_parameters.internode.color = make_RGBcolor(0.3, 0.2, 0.2);
    shoot_parameters_proleptic.phytomer_parameters.phytomer_creation_function = ApplePhytomerCreationFunction;
    shoot_parameters_proleptic.max_nodes = 40;
    shoot_parameters_proleptic.max_nodes_per_season = 20;
    shoot_parameters_proleptic.phyllochron_min = 2.0;
    shoot_parameters_proleptic.elongation_rate_max = 0.15;
    shoot_parameters_proleptic.girth_area_factor = 7.f;
    shoot_parameters_proleptic.vegetative_bud_break_probability_min = 0.1;
    shoot_parameters_proleptic.vegetative_bud_break_probability_decay_rate = 0.4;
    shoot_parameters_proleptic.vegetative_bud_break_time = 0;
    shoot_parameters_proleptic.gravitropic_curvature.uniformDistribution(450, 500);
    shoot_parameters_proleptic.tortuosity = 3;
    shoot_parameters_proleptic.insertion_angle_tip.uniformDistribution(30, 40);
    shoot_parameters_proleptic.insertion_angle_decay_rate = 20;
    shoot_parameters_proleptic.internode_length_max = 0.04;
    shoot_parameters_proleptic.internode_length_min = 0.01;
    shoot_parameters_proleptic.internode_length_decay_rate = 0.004;
    shoot_parameters_proleptic.fruit_set_probability = 0.3;
    shoot_parameters_proleptic.flower_bud_break_probability = 0.3;
    shoot_parameters_proleptic.max_terminal_floral_buds = 1;
    shoot_parameters_proleptic.flowers_require_dormancy = true;
    shoot_parameters_proleptic.growth_requires_dormancy = true;
    shoot_parameters_proleptic.determinate_shoot_growth = false;
    shoot_parameters_proleptic.defineChildShootTypes({"proleptic"}, {1.0});
 
    defineShootType("trunk", shoot_parameters_trunk);
    defineShootType("proleptic", shoot_parameters_proleptic);
}
 
uint PlantArchitecture::buildAppleTree(const helios::vec3 &base_position) {
 
    if (shoot_types.empty()) {
        // automatically initialize apple tree shoots
        initializeAppleTreeShoots();
    }
 
    // Get training system parameters (with defaults matching original hard-coded values)
    auto trunk_height = getParameterValue(current_build_parameters, "trunk_height", 0.8f, 0.1f, 3.f, "total trunk height in meters");
    auto num_scaffolds = uint(getParameterValue(current_build_parameters, "num_scaffolds", 4.f, 2.f, 8.f, "number of scaffold branches"));
    auto scaffold_angle = getParameterValue(current_build_parameters, "scaffold_angle", 40.f, 20.f, 70.f, "scaffold branch angle in degrees");
 
    // Calculate trunk nodes based on desired height and internode length
    float trunk_internode_length = 0.04f; // Default internode length for apple
    uint trunk_nodes = uint(trunk_height / trunk_internode_length);
    if (trunk_nodes < 1)
        trunk_nodes = 1;
 
    // Fixed training parameters (not user-customizable)
    float trunk_radius = 0.015f;
    float scaffold_radius = 0.005f;
    float scaffold_length = 0.04f;
 
    uint plantID = addPlantInstance(base_position, 0);
 
    uint uID_trunk = addBaseStemShoot(plantID, trunk_nodes, make_AxisRotation(context_ptr->randu(0.f, 0.05f * M_PI), context_ptr->randu(0.f, 2.f * M_PI), 0.f * M_PI), trunk_radius, trunk_internode_length, 1.f, 1.f, 0, "trunk");
    appendPhytomerToShoot(plantID, uID_trunk, shoot_types.at("trunk").phytomer_parameters, 0, 0.01, 1, 1);
 
    plant_instances.at(plantID).shoot_tree.at(uID_trunk)->meristem_is_alive = false;
 
    auto phytomers = plant_instances.at(plantID).shoot_tree.at(uID_trunk)->phytomers;
    for (const auto &phytomer: phytomers) {
        phytomer->removeLeaf();
        phytomer->setVegetativeBudState(BUD_DEAD);
        phytomer->setFloralBudState(BUD_DEAD);
    }
 
    // Hard-coded scaffold node range (not user-customizable)
    uint scaffold_nodes_min = 7;
    uint scaffold_nodes_max = 9;
 
    for (int i = 0; i < num_scaffolds; i++) {
        float pitch = deg2rad(scaffold_angle) + context_ptr->randu(-0.1f, 0.1f); // Small randomness around specified angle
        uint scaffold_nodes = context_ptr->randu(int(scaffold_nodes_min), int(scaffold_nodes_max));
        uint uID_shoot = addChildShoot(plantID, uID_trunk, getShootNodeCount(plantID, uID_trunk) - i - 1, scaffold_nodes, make_AxisRotation(pitch, (float(i) + context_ptr->randu(-0.2f, 0.2f)) / float(num_scaffolds) * 2 * M_PI, 0), scaffold_radius,
                                       scaffold_length, 1.f, 1.f, 0.5, "proleptic", 0);
    }
 
    makePlantDormant(plantID);
 
    setPlantPhenologicalThresholds(plantID, 165, -1, 3, 7, 30, 200, false);
    plant_instances.at(plantID).max_age = 1460;
 
    return plantID;
}
 
void PlantArchitecture::initializeAppleFruitingWallShoots() {
 
    // ---- Leaf Prototype ---- //
 
    LeafPrototype leaf_prototype(context_ptr->getRandomGenerator());
    leaf_prototype.leaf_texture_file[0] = "AppleLeaf.png";
    leaf_prototype.leaf_aspect_ratio = 0.6f;
    leaf_prototype.midrib_fold_fraction = 0.4f;
    leaf_prototype.longitudinal_curvature = -0.3f;
    leaf_prototype.lateral_curvature = 0.1f;
    leaf_prototype.subdivisions = 3;
    leaf_prototype.unique_prototypes = 1;
 
    // ---- Phytomer Parameters ---- //
 
    PhytomerParameters phytomer_parameters_apple(context_ptr->getRandomGenerator());
 
    phytomer_parameters_apple.internode.pitch = 0;
    phytomer_parameters_apple.internode.phyllotactic_angle.uniformDistribution(130, 145);
    phytomer_parameters_apple.internode.radius_initial = 0.004;
    phytomer_parameters_apple.internode.length_segments = 1;
    phytomer_parameters_apple.internode.image_texture = "AppleBark.jpg";
    phytomer_parameters_apple.internode.max_floral_buds_per_petiole = 1;
 
    phytomer_parameters_apple.petiole.petioles_per_internode = 1;
    phytomer_parameters_apple.petiole.pitch.uniformDistribution(-40, -25);
    phytomer_parameters_apple.petiole.taper = 0.1;
    phytomer_parameters_apple.petiole.curvature = 0;
    phytomer_parameters_apple.petiole.length = 0.04;
    phytomer_parameters_apple.petiole.radius = 0.00075;
    phytomer_parameters_apple.petiole.length_segments = 1;
    phytomer_parameters_apple.petiole.radial_subdivisions = 3;
    phytomer_parameters_apple.petiole.color = make_RGBcolor(0.61, 0.5, 0.24);
 
    phytomer_parameters_apple.leaf.leaves_per_petiole = 1;
    phytomer_parameters_apple.leaf.prototype_scale = 0.12;
    phytomer_parameters_apple.leaf.prototype = leaf_prototype;
 
    phytomer_parameters_apple.peduncle.length = 0.04;
    phytomer_parameters_apple.peduncle.radius = 0.001;
    phytomer_parameters_apple.peduncle.pitch = 90;
    phytomer_parameters_apple.peduncle.roll = 90;
    phytomer_parameters_apple.peduncle.length_segments = 1;
 
    phytomer_parameters_apple.inflorescence.flowers_per_peduncle = 1;
    phytomer_parameters_apple.inflorescence.pitch = 0;
    phytomer_parameters_apple.inflorescence.roll = 0;
    phytomer_parameters_apple.inflorescence.flower_prototype_scale = 0.03;
    phytomer_parameters_apple.inflorescence.flower_prototype_function = AppleFlowerPrototype;
    phytomer_parameters_apple.inflorescence.fruit_prototype_scale = 0.1;
    phytomer_parameters_apple.inflorescence.fruit_prototype_function = AppleFruitPrototype;
    phytomer_parameters_apple.inflorescence.fruit_gravity_factor_fraction = 0.5;
 
    // ---- Shoot Parameters ---- //
 
    // Trunk
    ShootParameters shoot_parameters_trunk(context_ptr->getRandomGenerator());
    shoot_parameters_trunk.phytomer_parameters = phytomer_parameters_apple;
    shoot_parameters_trunk.phytomer_parameters.internode.phyllotactic_angle.uniformDistribution(175, 185);
    shoot_parameters_trunk.phytomer_parameters.internode.radius_initial = 0.01;
    shoot_parameters_trunk.phytomer_parameters.internode.radial_subdivisions = 24;
    shoot_parameters_trunk.max_nodes = 30;
    shoot_parameters_trunk.girth_area_factor = 5.f;
    shoot_parameters_trunk.vegetative_bud_break_probability_min = 0;
    shoot_parameters_trunk.vegetative_bud_break_time = 0;
    shoot_parameters_trunk.tortuosity = 0.5;
    shoot_parameters_trunk.internode_length_max = 0.05;
    shoot_parameters_trunk.internode_length_decay_rate = 0;
    shoot_parameters_trunk.defineChildShootTypes({"lateral"}, {1});
 
    // Proleptic shoots
    ShootParameters shoot_parameters_proleptic(context_ptr->getRandomGenerator());
    shoot_parameters_proleptic.phytomer_parameters = phytomer_parameters_apple;
    shoot_parameters_proleptic.phytomer_parameters.internode.color = make_RGBcolor(0.3, 0.2, 0.2);
    shoot_parameters_proleptic.phytomer_parameters.phytomer_creation_function = ApplePhytomerCreationFunction;
    shoot_parameters_proleptic.max_nodes = 20;
    shoot_parameters_proleptic.max_nodes_per_season = 20;
    shoot_parameters_proleptic.phyllochron_min = 2.0;
    shoot_parameters_proleptic.elongation_rate_max = 0.15;
    shoot_parameters_proleptic.girth_area_factor = 7.f;
    shoot_parameters_proleptic.vegetative_bud_break_probability_min = 0.1;
    shoot_parameters_proleptic.vegetative_bud_break_probability_decay_rate = 0.4;
    shoot_parameters_proleptic.vegetative_bud_break_time = 0;
    shoot_parameters_proleptic.gravitropic_curvature.uniformDistribution(550, 700);
    shoot_parameters_proleptic.tortuosity = 3;
    shoot_parameters_proleptic.insertion_angle_tip.uniformDistribution(70, 110);
    shoot_parameters_proleptic.insertion_angle_decay_rate = 20;
    shoot_parameters_proleptic.internode_length_max = 0.04;
    shoot_parameters_proleptic.internode_length_min = 0.01;
    shoot_parameters_proleptic.internode_length_decay_rate = 0.004;
    shoot_parameters_proleptic.fruit_set_probability = 0.3;
    shoot_parameters_proleptic.flower_bud_break_probability = 0.3;
    shoot_parameters_proleptic.max_terminal_floral_buds = 1;
    shoot_parameters_proleptic.flowers_require_dormancy = true;
    shoot_parameters_proleptic.growth_requires_dormancy = true;
    shoot_parameters_proleptic.determinate_shoot_growth = false;
    shoot_parameters_proleptic.defineChildShootTypes({"proleptic"}, {1.0});
 
    // lateral shoots
    ShootParameters shoot_parameters_lateral = shoot_parameters_proleptic;
    shoot_parameters_lateral.gravitropic_curvature = 0;
    shoot_parameters_lateral.phytomer_parameters.internode.phyllotactic_angle = 360;
 
    defineShootType("trunk", shoot_parameters_trunk);
    defineShootType("proleptic", shoot_parameters_proleptic);
    defineShootType("lateral", shoot_parameters_lateral);
}
 
uint PlantArchitecture::buildAppleFruitingWall(const helios::vec3 &base_position) {
 
    if (shoot_types.empty()) {
        // automatically initialize apple tree shoots
        initializeAppleFruitingWallShoots();
    }
 
    std::vector<std::vector<vec3>> trellis_points;
 
    std::vector<float> wire_heights{0.75, 1.6, 2.25, 2.8};
    float tree_spacing = 1.2;
 
    trellis_points.reserve(wire_heights.size());
    for (int i = 0; i < wire_heights.size(); i++) {
        trellis_points.push_back(linspace(make_vec3(0, -0.5f * tree_spacing, wire_heights.at(i)), make_vec3(0, 0.5f * tree_spacing, wire_heights.at(i)), 8));
        // context_ptr->addTube( 4, {base_position+trellis_points.back().at(0), base_position+trellis_points.back().back()}, {0.005, 0.005}, {RGB::silver, RGB::silver});
    }
 
    for (int j = 0; j < trellis_points.size(); j++) {
        for (int i = 0; i < trellis_points[j].size(); i++) {
            trellis_points.at(j).at(i) += base_position;
        }
    }
 
    uint plantID = addPlantInstance(base_position, 0);
 
    uint uID_leader = addBaseStemShoot(plantID, std::ceil(wire_heights.back() / 0.1), make_AxisRotation(context_ptr->randu(0, 0.05 * M_PI), 0, 0), shoot_types.at("trunk").phytomer_parameters.internode.radius_initial.val(), 0.09, 1, 1, 0.1, "trunk");
    plant_instances.at(plantID).shoot_tree.at(uID_leader)->meristem_is_alive = false;
    removeShootLeaves(plantID, uID_leader);
    removeShootVegetativeBuds(plantID, uID_leader);
    removeShootFloralBuds(plantID, uID_leader);
 
    for (int i = 0; i < 8; i++) {
        float z;
        if (i == 0) {
            z = wire_heights.front() - 0.1;
        } else {
            z = context_ptr->randu(wire_heights.front() - 0.1, wire_heights.at(wire_heights.size() - 1));
        }
        int node = std::round(z / 0.1) - 1;
        addChildShoot(plantID, uID_leader, node, 8, make_AxisRotation(context_ptr->randu(float(0.45f * M_PI), 0.52f * M_PI), context_ptr->randu(0, 1) * M_PI, M_PI), 0.005, 0.05, 1, 1, 0.5, "lateral");
    }
 
    // Set plant-specific attraction points for this grapevine's trellis system
    setPlantAttractionPoints(plantID, flatten(trellis_points), 45.f, 1.f, 0.8);
 
    setPlantPhenologicalThresholds(plantID, 165, -1, 3, 7, 30, 200, false);
    plant_instances.at(plantID).max_age = 730;
 
    return plantID;
}
 
void PlantArchitecture::initializeAsparagusShoots() {
 
    // ---- Phytomer Parameters ---- //
 
    PhytomerParameters phytomer_parameters(context_ptr->getRandomGenerator());
 
    phytomer_parameters.internode.pitch = 1;
    phytomer_parameters.internode.phyllotactic_angle.uniformDistribution(127.5, 147.5);
    phytomer_parameters.internode.radius_initial = 0.00025;
    phytomer_parameters.internode.max_floral_buds_per_petiole = 0;
    phytomer_parameters.internode.max_vegetative_buds_per_petiole = 1;
    phytomer_parameters.internode.color = RGB::forestgreen;
    phytomer_parameters.internode.length_segments = 2;
 
    phytomer_parameters.petiole.petioles_per_internode = 1;
    phytomer_parameters.petiole.pitch = 90;
    phytomer_parameters.petiole.radius = 0.0001;
    phytomer_parameters.petiole.length = 0.0005;
    phytomer_parameters.petiole.taper = 0.5;
    phytomer_parameters.petiole.curvature = 0;
    phytomer_parameters.petiole.color = phytomer_parameters.internode.color;
    phytomer_parameters.petiole.length_segments = 1;
    phytomer_parameters.petiole.radial_subdivisions = 5;
 
    phytomer_parameters.leaf.leaves_per_petiole = 5;
    phytomer_parameters.leaf.pitch.normalDistribution(-5, 30);
    phytomer_parameters.leaf.yaw = 30;
    phytomer_parameters.leaf.roll = 0;
    phytomer_parameters.leaf.leaflet_offset = 0;
    phytomer_parameters.leaf.leaflet_scale = 0.9;
    phytomer_parameters.leaf.prototype.prototype_function = AsparagusLeafPrototype;
    phytomer_parameters.leaf.prototype_scale.uniformDistribution(0.018, 0.02);
    //    phytomer_parameters.leaf.subdivisions = 6;
 
    phytomer_parameters.peduncle.length = 0.17;
    phytomer_parameters.peduncle.radius = 0.0015;
    phytomer_parameters.peduncle.pitch.uniformDistribution(0, 30);
    phytomer_parameters.peduncle.roll = 90;
    phytomer_parameters.peduncle.curvature.uniformDistribution(50, 250);
    phytomer_parameters.peduncle.length_segments = 6;
    phytomer_parameters.peduncle.radial_subdivisions = 6;
 
    phytomer_parameters.inflorescence.flowers_per_peduncle.uniformDistribution(1, 3);
    phytomer_parameters.inflorescence.flower_offset = 0.;
    phytomer_parameters.inflorescence.pitch.uniformDistribution(50, 70);
    phytomer_parameters.inflorescence.roll.uniformDistribution(-20, 20);
    phytomer_parameters.inflorescence.flower_prototype_scale = 0.015;
    phytomer_parameters.inflorescence.fruit_prototype_scale.uniformDistribution(0.02, 0.025);
    phytomer_parameters.inflorescence.fruit_gravity_factor_fraction.uniformDistribution(0., 0.5);
 
    // ---- Shoot Parameters ---- //
 
    ShootParameters shoot_parameters(context_ptr->getRandomGenerator());
    shoot_parameters.phytomer_parameters = phytomer_parameters;
    shoot_parameters.phytomer_parameters.phytomer_creation_function = AsparagusPhytomerCreationFunction;
 
    shoot_parameters.max_nodes = 20;
    shoot_parameters.insertion_angle_tip.uniformDistribution(40, 70);
    //    shoot_parameters.child_insertion_angle_decay_rate = 0; (default)
    shoot_parameters.internode_length_max = 0.015;
    //    shoot_parameters.child_internode_length_min = 0.0; (default)
    //    shoot_parameters.child_internode_length_decay_rate = 0; (default)
    shoot_parameters.base_roll = 90;
    shoot_parameters.base_yaw.uniformDistribution(-20, 20);
    shoot_parameters.gravitropic_curvature = -200;
 
    shoot_parameters.phyllochron_min = 1;
    shoot_parameters.elongation_rate_max = 0.15;
    //    shoot_parameters.girth_growth_rate = 0.00005;
    shoot_parameters.girth_area_factor = 30;
    shoot_parameters.vegetative_bud_break_time = 5;
    shoot_parameters.vegetative_bud_break_probability_min = 0.25;
    //    shoot_parameters.max_terminal_floral_buds = 0; (default)
    //    shoot_parameters.flower_bud_break_probability.uniformDistribution(0.1, 0.2);
    shoot_parameters.fruit_set_probability = 0.;
    //    shoot_parameters.flowers_require_dormancy = false; (default)
    //    shoot_parameters.growth_requires_dormancy = false; (default)
    //    shoot_parameters.determinate_shoot_growth = true; (default)
 
    shoot_parameters.defineChildShootTypes({"main"}, {1.0});
 
    defineShootType("main", shoot_parameters);
}
 
uint PlantArchitecture::buildAsparagusPlant(const helios::vec3 &base_position) {
 
    if (shoot_types.empty()) {
        // automatically initialize asparagus plant shoots
        initializeAsparagusShoots();
    }
 
    uint plantID = addPlantInstance(base_position, 0);
 
    uint uID_stem = addBaseStemShoot(plantID, 1, make_AxisRotation(0, 0.f, 0.f), 0.0003, 0.015, 1, 0.1, 0.1, "main");
 
    breakPlantDormancy(plantID);
 
    setPlantPhenologicalThresholds(plantID, 0, -1, -1, -1, 5, 100, false);
 
    plant_instances.at(plantID).max_age = 20;
 
    return plantID;
}
 
void PlantArchitecture::initializeBindweedShoots() {
 
    // ---- Phytomer Parameters ---- //
 
    PhytomerParameters phytomer_parameters_bindweed(context_ptr->getRandomGenerator());
 
    phytomer_parameters_bindweed.internode.pitch.uniformDistribution(0, 15);
    phytomer_parameters_bindweed.internode.phyllotactic_angle = 180.f;
    phytomer_parameters_bindweed.internode.radius_initial = 0.0012;
    phytomer_parameters_bindweed.internode.color = make_RGBcolor(0.3, 0.38, 0.21);
    phytomer_parameters_bindweed.internode.length_segments = 1;
 
    phytomer_parameters_bindweed.petiole.petioles_per_internode = 1;
    phytomer_parameters_bindweed.petiole.pitch.uniformDistribution(80, 100);
    phytomer_parameters_bindweed.petiole.radius = 0.001;
    phytomer_parameters_bindweed.petiole.length = 0.006;
    phytomer_parameters_bindweed.petiole.taper = 0;
    phytomer_parameters_bindweed.petiole.curvature = 0;
    phytomer_parameters_bindweed.petiole.color = phytomer_parameters_bindweed.internode.color;
    phytomer_parameters_bindweed.petiole.length_segments = 1;
 
    phytomer_parameters_bindweed.leaf.leaves_per_petiole = 1;
    phytomer_parameters_bindweed.leaf.pitch.uniformDistribution(5, 30);
    phytomer_parameters_bindweed.leaf.yaw = 0;
    phytomer_parameters_bindweed.leaf.roll = 90;
    phytomer_parameters_bindweed.leaf.prototype_scale = 0.05;
    phytomer_parameters_bindweed.leaf.prototype.OBJ_model_file = "BindweedLeaf.obj";
 
    phytomer_parameters_bindweed.peduncle.length = 0.01;
    phytomer_parameters_bindweed.peduncle.radius = 0.0005;
    phytomer_parameters_bindweed.peduncle.color = phytomer_parameters_bindweed.internode.color;
 
    phytomer_parameters_bindweed.inflorescence.flowers_per_peduncle = 1;
    phytomer_parameters_bindweed.inflorescence.pitch = -90.f;
    phytomer_parameters_bindweed.inflorescence.flower_prototype_function = BindweedFlowerPrototype;
    phytomer_parameters_bindweed.inflorescence.flower_prototype_scale = 0.045;
 
    // ---- Shoot Parameters ---- //
 
    ShootParameters shoot_parameters_primary(context_ptr->getRandomGenerator());
    shoot_parameters_primary.phytomer_parameters = phytomer_parameters_bindweed;
    shoot_parameters_primary.vegetative_bud_break_probability_min = 0.1;
    shoot_parameters_primary.vegetative_bud_break_probability_decay_rate = -1.;
    shoot_parameters_primary.vegetative_bud_break_time = 10;
    shoot_parameters_primary.base_roll = 90;
    shoot_parameters_primary.phyllochron_min = 1;
    shoot_parameters_primary.elongation_rate_max = 0.25;
    shoot_parameters_primary.girth_area_factor = 0;
    shoot_parameters_primary.internode_length_max = 0.03;
    shoot_parameters_primary.internode_length_decay_rate = 0;
    shoot_parameters_primary.insertion_angle_tip.uniformDistribution(50, 80);
    shoot_parameters_primary.flowers_require_dormancy = false;
    shoot_parameters_primary.growth_requires_dormancy = false;
    shoot_parameters_primary.flower_bud_break_probability = 0.2;
    shoot_parameters_primary.determinate_shoot_growth = false;
    shoot_parameters_primary.max_nodes = 15;
    shoot_parameters_primary.gravitropic_curvature = 40;
    shoot_parameters_primary.tortuosity = 0;
    shoot_parameters_primary.defineChildShootTypes({"secondary_bindweed"}, {1.f});
 
    ShootParameters shoot_parameters_base = shoot_parameters_primary;
    shoot_parameters_base.phytomer_parameters = phytomer_parameters_bindweed;
    shoot_parameters_base.phytomer_parameters.internode.phyllotactic_angle.uniformDistribution(137.5 - 10, 137.5 + 10);
    shoot_parameters_base.phytomer_parameters.petiole.petioles_per_internode = 0;
    shoot_parameters_base.phytomer_parameters.internode.pitch = 0;
    shoot_parameters_base.phytomer_parameters.petiole.pitch = 0;
    shoot_parameters_base.vegetative_bud_break_probability_min = 1.0;
    shoot_parameters_base.vegetative_bud_break_time = 2;
    shoot_parameters_base.phyllochron_min = 2;
    shoot_parameters_base.elongation_rate_max = 0.15;
    shoot_parameters_base.girth_area_factor = 0.f;
    shoot_parameters_base.gravitropic_curvature = 0;
    shoot_parameters_base.internode_length_max = 0.01;
    shoot_parameters_base.internode_length_decay_rate = 0;
    shoot_parameters_base.insertion_angle_tip = 95;
    shoot_parameters_base.insertion_angle_decay_rate = 0;
    shoot_parameters_base.flowers_require_dormancy = false;
    shoot_parameters_base.growth_requires_dormancy = false;
    shoot_parameters_base.flower_bud_break_probability = 0.0;
    shoot_parameters_base.max_nodes.uniformDistribution(3, 5);
    shoot_parameters_base.defineChildShootTypes({"primary_bindweed"}, {1.f});
 
    ShootParameters shoot_parameters_children = shoot_parameters_primary;
    shoot_parameters_children.base_roll = 0;
 
    defineShootType("base_bindweed", shoot_parameters_base);
    defineShootType("primary_bindweed", shoot_parameters_primary);
    defineShootType("secondary_bindweed", shoot_parameters_children);
}
 
uint PlantArchitecture::buildBindweedPlant(const helios::vec3 &base_position) {
 
    if (shoot_types.empty()) {
        // automatically initialize bindweed plant shoots
        initializeBindweedShoots();
    }
 
    uint plantID = addPlantInstance(base_position, 0);
 
    uint uID_stem = addBaseStemShoot(plantID, 3, make_AxisRotation(0, 0.f, 0.f), 0.001, 0.001, 1, 1, 0, "base_bindweed");
 
    breakPlantDormancy(plantID);
 
    setPlantPhenologicalThresholds(plantID, 0, -1, 14, -1, -1, 1000, false);
 
    plant_instances.at(plantID).max_age = 50;
 
    return plantID;
}
 
void PlantArchitecture::initializeBeanShoots() {
 
    // ---- Leaf Prototype ---- //
 
    LeafPrototype leaf_prototype_trifoliate(context_ptr->getRandomGenerator());
    leaf_prototype_trifoliate.leaf_texture_file[0] = "BeanLeaf_tip.png";
    leaf_prototype_trifoliate.leaf_texture_file[-1] = "BeanLeaf_left_centered.png";
    leaf_prototype_trifoliate.leaf_texture_file[1] = "BeanLeaf_right_centered.png";
    leaf_prototype_trifoliate.leaf_aspect_ratio = 1.f;
    leaf_prototype_trifoliate.midrib_fold_fraction = 0.2;
    leaf_prototype_trifoliate.longitudinal_curvature.uniformDistribution(-0.3f, -0.2f);
    leaf_prototype_trifoliate.lateral_curvature = -1.f;
    leaf_prototype_trifoliate.subdivisions = 6;
    leaf_prototype_trifoliate.unique_prototypes = 5;
    leaf_prototype_trifoliate.build_petiolule = true;
 
    LeafPrototype leaf_prototype_unifoliate = leaf_prototype_trifoliate;
    leaf_prototype_unifoliate.leaf_texture_file.clear();
    leaf_prototype_unifoliate.leaf_texture_file[0] = "BeanLeaf_unifoliate_centered.png";
    leaf_prototype_unifoliate.unique_prototypes = 2;
 
    // ---- Phytomer Parameters ---- //
 
    PhytomerParameters phytomer_parameters_trifoliate(context_ptr->getRandomGenerator());
 
    phytomer_parameters_trifoliate.internode.pitch = 20;
    phytomer_parameters_trifoliate.internode.phyllotactic_angle.uniformDistribution(145, 215);
    phytomer_parameters_trifoliate.internode.radius_initial = 0.001;
    phytomer_parameters_trifoliate.internode.max_floral_buds_per_petiole = 1;
    phytomer_parameters_trifoliate.internode.max_vegetative_buds_per_petiole = 1;
    phytomer_parameters_trifoliate.internode.color = make_RGBcolor(0.2, 0.25, 0.05);
    phytomer_parameters_trifoliate.internode.length_segments = 2;
 
    phytomer_parameters_trifoliate.petiole.petioles_per_internode = 1;
    phytomer_parameters_trifoliate.petiole.pitch.uniformDistribution(20, 50);
    phytomer_parameters_trifoliate.petiole.radius = 0.0015;
    phytomer_parameters_trifoliate.petiole.length.uniformDistribution(0.1, 0.14);
    phytomer_parameters_trifoliate.petiole.taper = 0.;
    phytomer_parameters_trifoliate.petiole.curvature.uniformDistribution(-100, 200);
    phytomer_parameters_trifoliate.petiole.color = make_RGBcolor(0.28, 0.35, 0.07);
    phytomer_parameters_trifoliate.petiole.length_segments = 5;
    phytomer_parameters_trifoliate.petiole.radial_subdivisions = 6;
 
    phytomer_parameters_trifoliate.leaf.leaves_per_petiole = 3;
    phytomer_parameters_trifoliate.leaf.pitch.normalDistribution(0, 20);
    phytomer_parameters_trifoliate.leaf.yaw = 10;
    phytomer_parameters_trifoliate.leaf.roll = -15;
    phytomer_parameters_trifoliate.leaf.leaflet_offset = 0.3;
    phytomer_parameters_trifoliate.leaf.leaflet_scale = 0.9;
    phytomer_parameters_trifoliate.leaf.prototype_scale.uniformDistribution(0.09, 0.11);
    phytomer_parameters_trifoliate.leaf.prototype = leaf_prototype_trifoliate;
 
    phytomer_parameters_trifoliate.peduncle.length = 0.04;
    phytomer_parameters_trifoliate.peduncle.radius = 0.00075;
    phytomer_parameters_trifoliate.peduncle.pitch.uniformDistribution(0, 40);
    phytomer_parameters_trifoliate.peduncle.roll = 90;
    phytomer_parameters_trifoliate.peduncle.curvature.uniformDistribution(-500, 500);
    phytomer_parameters_trifoliate.peduncle.color = phytomer_parameters_trifoliate.petiole.color;
    phytomer_parameters_trifoliate.peduncle.length_segments = 1;
    phytomer_parameters_trifoliate.peduncle.radial_subdivisions = 6;
 
    phytomer_parameters_trifoliate.inflorescence.flowers_per_peduncle.uniformDistribution(1, 4);
    phytomer_parameters_trifoliate.inflorescence.flower_offset = 0.2;
    phytomer_parameters_trifoliate.inflorescence.pitch.uniformDistribution(50, 70);
    phytomer_parameters_trifoliate.inflorescence.roll.uniformDistribution(-20, 20);
    phytomer_parameters_trifoliate.inflorescence.flower_prototype_scale = 0.03;
    phytomer_parameters_trifoliate.inflorescence.flower_prototype_function = BeanFlowerPrototype;
    phytomer_parameters_trifoliate.inflorescence.fruit_prototype_scale.uniformDistribution(0.15, 0.2);
    phytomer_parameters_trifoliate.inflorescence.fruit_prototype_function = BeanFruitPrototype;
    phytomer_parameters_trifoliate.inflorescence.fruit_gravity_factor_fraction.uniformDistribution(0.8, 1.0);
 
    PhytomerParameters phytomer_parameters_unifoliate = phytomer_parameters_trifoliate;
    phytomer_parameters_unifoliate.internode.pitch = 0;
    phytomer_parameters_unifoliate.internode.max_vegetative_buds_per_petiole = 1;
    phytomer_parameters_unifoliate.internode.max_floral_buds_per_petiole = 0;
    phytomer_parameters_unifoliate.petiole.petioles_per_internode = 2;
    phytomer_parameters_unifoliate.petiole.length = 0.0001;
    phytomer_parameters_unifoliate.petiole.radius = 0.0004;
    phytomer_parameters_unifoliate.petiole.pitch.uniformDistribution(50, 70);
    phytomer_parameters_unifoliate.leaf.leaves_per_petiole = 1;
    phytomer_parameters_unifoliate.leaf.prototype_scale = 0.04;
    phytomer_parameters_unifoliate.leaf.pitch.uniformDistribution(-10, 10);
    phytomer_parameters_unifoliate.leaf.prototype = leaf_prototype_unifoliate;
 
    // ---- Shoot Parameters ---- //
 
    ShootParameters shoot_parameters_trifoliate(context_ptr->getRandomGenerator());
    shoot_parameters_trifoliate.phytomer_parameters = phytomer_parameters_trifoliate;
    shoot_parameters_trifoliate.phytomer_parameters.phytomer_creation_function = BeanPhytomerCreationFunction;
 
    shoot_parameters_trifoliate.max_nodes = 25;
    shoot_parameters_trifoliate.insertion_angle_tip.uniformDistribution(40, 60);
    //    shoot_parameters_trifoliate.child_insertion_angle_decay_rate = 0; (default)
    shoot_parameters_trifoliate.internode_length_max = 0.025;
    //    shoot_parameters_trifoliate.child_internode_length_min = 0.0; (default)
    //    shoot_parameters_trifoliate.child_internode_length_decay_rate = 0; (default)
    shoot_parameters_trifoliate.base_roll = 90;
    shoot_parameters_trifoliate.base_yaw.uniformDistribution(-20, 20);
    shoot_parameters_trifoliate.gravitropic_curvature = 200;
 
    shoot_parameters_trifoliate.phyllochron_min = 2;
    shoot_parameters_trifoliate.elongation_rate_max = 0.1;
    shoot_parameters_trifoliate.girth_area_factor = 1.5f;
    shoot_parameters_trifoliate.vegetative_bud_break_time = 15;
    shoot_parameters_trifoliate.vegetative_bud_break_probability_min = 0.1;
    shoot_parameters_trifoliate.vegetative_bud_break_probability_decay_rate = -0.4;
    //    shoot_parameters_trifoliate.max_terminal_floral_buds = 0; (default)
    shoot_parameters_trifoliate.flower_bud_break_probability.uniformDistribution(0.3, 0.4);
    shoot_parameters_trifoliate.fruit_set_probability = 0.4;
    //    shoot_parameters_trifoliate.flowers_require_dormancy = false; (default)
    //    shoot_parameters_trifoliate.growth_requires_dormancy = false; (default)
    //    shoot_parameters_trifoliate.determinate_shoot_growth = true; (default)
 
    shoot_parameters_trifoliate.defineChildShootTypes({"trifoliate"}, {1.0});
 
 
    ShootParameters shoot_parameters_unifoliate = shoot_parameters_trifoliate;
    shoot_parameters_unifoliate.phytomer_parameters = phytomer_parameters_unifoliate;
    shoot_parameters_unifoliate.phytomer_parameters.phytomer_creation_function = nullptr;
    shoot_parameters_unifoliate.max_nodes = 1;
    shoot_parameters_unifoliate.girth_area_factor = 1.f;
    shoot_parameters_unifoliate.vegetative_bud_break_probability_min = 1.0;
    shoot_parameters_unifoliate.flower_bud_break_probability = 0;
    shoot_parameters_unifoliate.insertion_angle_tip = 50;
    shoot_parameters_unifoliate.insertion_angle_decay_rate = 0;
    shoot_parameters_unifoliate.vegetative_bud_break_time = 8;
    shoot_parameters_unifoliate.defineChildShootTypes({"trifoliate"}, {1.0});
 
    defineShootType("unifoliate", shoot_parameters_unifoliate);
    defineShootType("trifoliate", shoot_parameters_trifoliate);
}
 
uint PlantArchitecture::buildBeanPlant(const helios::vec3 &base_position) {
 
    if (shoot_types.empty()) {
        // automatically initialize bean plant shoots
        initializeBeanShoots();
    }
 
    uint plantID = addPlantInstance(base_position, 0);
 
    AxisRotation base_rotation = make_AxisRotation(context_ptr->randu(0.f, 0.05f * M_PI), context_ptr->randu(0.f, 2.f * M_PI), context_ptr->randu(0.f, 2.f * M_PI));
    uint uID_unifoliate = addBaseStemShoot(plantID, 1, base_rotation, 0.0005, 0.03, 0.01, 0.01, 0, "unifoliate");
 
    appendShoot(plantID, uID_unifoliate, 1, make_AxisRotation(0, 0, 0.5f * M_PI), shoot_types.at("trifoliate").phytomer_parameters.internode.radius_initial.val(), shoot_types.at("trifoliate").internode_length_max.val(), 0.1, 0.1, 0, "trifoliate");
 
    breakPlantDormancy(plantID);
 
    setPlantPhenologicalThresholds(plantID, 0, 40, 5, 5, 30, 1000, false);
 
    plant_instances.at(plantID).max_age = 365;
 
    return plantID;
}
 
void PlantArchitecture::initializeBougainvilleaShoots() {
 
    // ---- Leaf Prototype ---- //
 
    LeafPrototype leaf_prototype(context_ptr->getRandomGenerator());
    leaf_prototype.leaf_texture_file[0] = "CapsicumLeaf.png";
    leaf_prototype.leaf_aspect_ratio = 0.8f;
    leaf_prototype.midrib_fold_fraction = 0.2f;
    leaf_prototype.longitudinal_curvature.uniformDistribution(-0.15, -0.05f);
    leaf_prototype.lateral_curvature = -0.25f;
    leaf_prototype.wave_period = 0.35f;
    leaf_prototype.wave_amplitude = 0.1f;
    leaf_prototype.subdivisions = 7;
    leaf_prototype.unique_prototypes = 5;
 
    // ---- Phytomer Parameters ---- //
 
    PhytomerParameters phytomer_parameters(context_ptr->getRandomGenerator());
 
    phytomer_parameters.internode.pitch = 10;
    phytomer_parameters.internode.phyllotactic_angle.uniformDistribution(160, 190);
    phytomer_parameters.internode.radius_initial = 0.001;
    phytomer_parameters.internode.color = make_RGBcolor(0.213, 0.270, 0.056);
    phytomer_parameters.internode.length_segments = 1;
 
    phytomer_parameters.petiole.petioles_per_internode = 1;
    phytomer_parameters.petiole.pitch.uniformDistribution(-60, -40);
    phytomer_parameters.petiole.radius = 0.0001;
    phytomer_parameters.petiole.length = 0.0001;
    phytomer_parameters.petiole.taper = 1;
    phytomer_parameters.petiole.curvature = 0;
    phytomer_parameters.petiole.color = phytomer_parameters.internode.color;
    phytomer_parameters.petiole.length_segments = 1;
 
    phytomer_parameters.leaf.leaves_per_petiole = 1;
    phytomer_parameters.leaf.pitch = 0;
    phytomer_parameters.leaf.yaw = 10;
    phytomer_parameters.leaf.roll = 0;
    phytomer_parameters.leaf.prototype_scale.uniformDistribution(0.08, 0.12);
    phytomer_parameters.leaf.prototype = leaf_prototype;
 
    phytomer_parameters.peduncle.length = 0.15;
    phytomer_parameters.peduncle.radius = 0.0015;
    phytomer_parameters.peduncle.pitch.uniformDistribution(70, 90);
    phytomer_parameters.peduncle.roll.uniformDistribution(0, 180);
    phytomer_parameters.peduncle.curvature.uniformDistribution(-200, 200);
    phytomer_parameters.peduncle.color = phytomer_parameters.internode.color;
    phytomer_parameters.peduncle.length_segments = 3;
    phytomer_parameters.peduncle.radial_subdivisions = 6;
 
    phytomer_parameters.inflorescence.flowers_per_peduncle.uniformDistribution(4, 6);
    phytomer_parameters.inflorescence.pitch = 80;
    phytomer_parameters.inflorescence.roll.uniformDistribution(-180, 180);
    phytomer_parameters.inflorescence.flower_prototype_scale = 0.05;
    phytomer_parameters.inflorescence.flower_prototype_function = BougainvilleaFlowerPrototype;
    phytomer_parameters.inflorescence.unique_prototypes = 1;
    phytomer_parameters.inflorescence.flower_offset = 0.12;
 
    // ---- Shoot Parameters ---- //
 
    ShootParameters shoot_parameters(context_ptr->getRandomGenerator());
    shoot_parameters.phytomer_parameters = phytomer_parameters;
 
    shoot_parameters.max_nodes = 60;
    shoot_parameters.insertion_angle_tip = 25;
    shoot_parameters.insertion_angle_decay_rate = 0;
    shoot_parameters.internode_length_max = 0.04;
    shoot_parameters.internode_length_min = 0.0;
    shoot_parameters.internode_length_decay_rate = 0;
    shoot_parameters.base_roll = 90;
    shoot_parameters.base_yaw.uniformDistribution(-20, 20);
    shoot_parameters.gravitropic_curvature = 500;
    shoot_parameters.tortuosity = 3;
 
    shoot_parameters.phyllochron_min = 2.75;
    shoot_parameters.elongation_rate_max = 0.1;
    shoot_parameters.girth_area_factor = 1.f;
    shoot_parameters.vegetative_bud_break_time = 30;
    shoot_parameters.vegetative_bud_break_probability_min = 0.075;
    shoot_parameters.vegetative_bud_break_probability_decay_rate = 0.8;
    shoot_parameters.flower_bud_break_probability = 0.5;
    shoot_parameters.flowers_require_dormancy = false;
    shoot_parameters.growth_requires_dormancy = false;
    shoot_parameters.determinate_shoot_growth = false;
 
    shoot_parameters.defineChildShootTypes({"secondary"}, {1.0});
 
    defineShootType("mainstem", shoot_parameters);
 
    ShootParameters shoot_parameters_secondary = shoot_parameters;
    shoot_parameters_secondary.max_nodes = 15;
 
    defineShootType("secondary", shoot_parameters_secondary);
}
 
uint PlantArchitecture::buildBougainvilleaPlant(const helios::vec3 &base_position) {
 
    if (shoot_types.empty()) {
        // automatically initialize bougainvillea plant shoots
        initializeBougainvilleaShoots();
    }
 
    uint plantID = addPlantInstance(base_position, 0);
 
    AxisRotation base_rotation = make_AxisRotation(0, context_ptr->randu(0.f, 2.f * M_PI), context_ptr->randu(0.f, 2.f * M_PI));
    uint uID_stem = addBaseStemShoot(plantID, 3, base_rotation, 0.002, shoot_types.at("mainstem").internode_length_max.val(), 0.01, 0.01, 0, "mainstem");
 
    removeShootVegetativeBuds(plantID, uID_stem);
    removeShootFloralBuds(plantID, uID_stem);
    removeShootLeaves(plantID, uID_stem);
 
    breakPlantDormancy(plantID);
 
    setPlantPhenologicalThresholds(plantID, 0, -1, 75, 1000, 1000, 1000, false);
 
    plant_instances.at(plantID).max_age = 365;
 
    return plantID;
}
 
void PlantArchitecture::initializeCapsicumShoots() {
 
    // ---- Leaf Prototype ---- //
 
    LeafPrototype leaf_prototype(context_ptr->getRandomGenerator());
    leaf_prototype.leaf_texture_file[0] = "CapsicumLeaf.png";
    leaf_prototype.leaf_aspect_ratio = 0.45f;
    leaf_prototype.midrib_fold_fraction = 0.1f;
    leaf_prototype.longitudinal_curvature.uniformDistribution(-0.15, -0.05f);
    leaf_prototype.lateral_curvature = -0.15f;
    leaf_prototype.wave_period = 0.35f;
    leaf_prototype.wave_amplitude = 0.0f;
    leaf_prototype.subdivisions = 5;
    leaf_prototype.unique_prototypes = 5;
 
    // ---- Phytomer Parameters ---- //
 
    PhytomerParameters phytomer_parameters(context_ptr->getRandomGenerator());
 
    phytomer_parameters.internode.pitch = 10;
    phytomer_parameters.internode.phyllotactic_angle.uniformDistribution(137.5 - 10, 137.5 + 10);
    phytomer_parameters.internode.radius_initial = 0.001;
    phytomer_parameters.internode.color = make_RGBcolor(0.213, 0.270, 0.056);
    phytomer_parameters.internode.length_segments = 1;
 
    phytomer_parameters.petiole.petioles_per_internode = 1;
    phytomer_parameters.petiole.pitch.uniformDistribution(-60, -40);
    phytomer_parameters.petiole.radius = 0.0001;
    phytomer_parameters.petiole.length = 0.0001;
    phytomer_parameters.petiole.taper = 1;
    phytomer_parameters.petiole.curvature = 0;
    phytomer_parameters.petiole.color = phytomer_parameters.internode.color;
    phytomer_parameters.petiole.length_segments = 1;
 
    phytomer_parameters.leaf.leaves_per_petiole = 1;
    phytomer_parameters.leaf.pitch = 0;
    phytomer_parameters.leaf.yaw = 10;
    phytomer_parameters.leaf.roll = 0;
    phytomer_parameters.leaf.prototype_scale.uniformDistribution(0.12, 0.15);
    phytomer_parameters.leaf.prototype = leaf_prototype;
 
    phytomer_parameters.peduncle.length = 0.01;
    phytomer_parameters.peduncle.radius = 0.001;
    phytomer_parameters.peduncle.pitch.uniformDistribution(10, 30);
    phytomer_parameters.peduncle.roll = 0;
    phytomer_parameters.peduncle.curvature = -700;
    phytomer_parameters.peduncle.color = phytomer_parameters.internode.color;
    phytomer_parameters.peduncle.length_segments = 3;
    phytomer_parameters.peduncle.radial_subdivisions = 6;
 
    phytomer_parameters.inflorescence.flowers_per_peduncle = 1;
    phytomer_parameters.inflorescence.pitch = 20;
    phytomer_parameters.inflorescence.roll.uniformDistribution(-30, 30);
    phytomer_parameters.inflorescence.flower_prototype_scale = 0.025;
    phytomer_parameters.inflorescence.flower_prototype_function = AlmondFlowerPrototype;
    phytomer_parameters.inflorescence.fruit_prototype_scale.uniformDistribution(0.12, 0.16);
    phytomer_parameters.inflorescence.fruit_prototype_function = CapsicumFruitPrototype;
    phytomer_parameters.inflorescence.fruit_gravity_factor_fraction = 0.9;
    phytomer_parameters.inflorescence.unique_prototypes = 10;
 
    PhytomerParameters phytomer_parameters_secondary = phytomer_parameters;
 
    // ---- Shoot Parameters ---- //
 
    ShootParameters shoot_parameters(context_ptr->getRandomGenerator());
    shoot_parameters.phytomer_parameters = phytomer_parameters;
    shoot_parameters.phytomer_parameters.phytomer_creation_function = CapsicumPhytomerCreationFunction;
 
    shoot_parameters.max_nodes = 30;
    shoot_parameters.insertion_angle_tip = 35;
    shoot_parameters.insertion_angle_decay_rate = 0;
    shoot_parameters.internode_length_max = 0.04;
    shoot_parameters.internode_length_min = 0.0;
    shoot_parameters.internode_length_decay_rate = 0;
    shoot_parameters.base_roll = 90;
    shoot_parameters.base_yaw.uniformDistribution(-20, 20);
    shoot_parameters.gravitropic_curvature = 300;
    shoot_parameters.tortuosity = 3;
 
    shoot_parameters.phyllochron_min = 3;
    shoot_parameters.elongation_rate_max = 0.1;
    shoot_parameters.girth_area_factor = 2.f;
    shoot_parameters.vegetative_bud_break_time = 30;
    shoot_parameters.vegetative_bud_break_probability_min = 0.4;
    shoot_parameters.vegetative_bud_break_probability_decay_rate = 0;
    shoot_parameters.flower_bud_break_probability = 0.5;
    shoot_parameters.fruit_set_probability = 0.05;
    shoot_parameters.flowers_require_dormancy = false;
    shoot_parameters.growth_requires_dormancy = false;
    shoot_parameters.determinate_shoot_growth = true;
 
    shoot_parameters.defineChildShootTypes({"secondary"}, {1.0});
 
    defineShootType("mainstem", shoot_parameters);
 
    ShootParameters shoot_parameters_secondary = shoot_parameters;
    shoot_parameters_secondary.phytomer_parameters = phytomer_parameters_secondary;
    shoot_parameters_secondary.max_nodes = 7;
    shoot_parameters_secondary.phyllochron_min = 6;
    shoot_parameters_secondary.vegetative_bud_break_probability_min = 0.2;
 
    defineShootType("secondary", shoot_parameters_secondary);
}
 
uint PlantArchitecture::buildCapsicumPlant(const helios::vec3 &base_position) {
 
    if (shoot_types.empty()) {
        // automatically initialize capsicum plant shoots
        initializeCapsicumShoots();
    }
 
    uint plantID = addPlantInstance(base_position, 0);
 
    AxisRotation base_rotation = make_AxisRotation(0, context_ptr->randu(0.f, 2.f * M_PI), context_ptr->randu(0.f, 2.f * M_PI));
    uint uID_stem = addBaseStemShoot(plantID, 1, base_rotation, 0.002, shoot_types.at("mainstem").internode_length_max.val(), 0.01, 0.01, 0, "mainstem");
 
    breakPlantDormancy(plantID);
 
    setPlantPhenologicalThresholds(plantID, 0, -1, -1, 75, 14, 1000, false);
 
    plant_instances.at(plantID).max_age = 365;
 
    return plantID;
}
 
void PlantArchitecture::initializeCheeseweedShoots() {
 
    // ---- Leaf Prototype ---- //
 
    LeafPrototype leaf_prototype(context_ptr->getRandomGenerator());
    leaf_prototype.OBJ_model_file = "CheeseweedLeaf.obj";
 
    // ---- Phytomer Parameters ---- //
 
    PhytomerParameters phytomer_parameters_cheeseweed(context_ptr->getRandomGenerator());
 
    phytomer_parameters_cheeseweed.internode.pitch = 0;
    phytomer_parameters_cheeseweed.internode.phyllotactic_angle.uniformDistribution(127.5f, 147.5);
    phytomer_parameters_cheeseweed.internode.radius_initial = 0.0005;
    phytomer_parameters_cheeseweed.internode.color = make_RGBcolor(0.60, 0.65, 0.40);
    phytomer_parameters_cheeseweed.internode.length_segments = 1;
 
    phytomer_parameters_cheeseweed.petiole.petioles_per_internode = 1;
    phytomer_parameters_cheeseweed.petiole.pitch.uniformDistribution(45, 75);
    phytomer_parameters_cheeseweed.petiole.radius = 0.0005;
    phytomer_parameters_cheeseweed.petiole.length.uniformDistribution(0.02, 0.06);
    phytomer_parameters_cheeseweed.petiole.taper = 0;
    phytomer_parameters_cheeseweed.petiole.curvature = -300;
    phytomer_parameters_cheeseweed.petiole.length_segments = 5;
    phytomer_parameters_cheeseweed.petiole.color = phytomer_parameters_cheeseweed.internode.color;
 
    phytomer_parameters_cheeseweed.leaf.leaves_per_petiole = 1;
    phytomer_parameters_cheeseweed.leaf.pitch.uniformDistribution(-30, 0);
    phytomer_parameters_cheeseweed.leaf.yaw = 0;
    phytomer_parameters_cheeseweed.leaf.roll = 0;
    phytomer_parameters_cheeseweed.leaf.prototype_scale = 0.035;
    phytomer_parameters_cheeseweed.leaf.prototype = leaf_prototype;
 
    // ---- Shoot Parameters ---- //
 
    ShootParameters shoot_parameters_base(context_ptr->getRandomGenerator());
    shoot_parameters_base.phytomer_parameters = phytomer_parameters_cheeseweed;
    shoot_parameters_base.vegetative_bud_break_probability_min = 0.2;
    shoot_parameters_base.vegetative_bud_break_time = 6;
    shoot_parameters_base.phyllochron_min = 2;
    shoot_parameters_base.elongation_rate_max = 0.1;
    shoot_parameters_base.girth_area_factor = 10.f;
    shoot_parameters_base.gravitropic_curvature = 0;
    shoot_parameters_base.internode_length_max = 0.0015;
    shoot_parameters_base.internode_length_decay_rate = 0;
    shoot_parameters_base.flowers_require_dormancy = false;
    shoot_parameters_base.growth_requires_dormancy = false;
    shoot_parameters_base.flower_bud_break_probability = 0.;
    shoot_parameters_base.max_nodes = 8;
 
    defineShootType("base", shoot_parameters_base);
}
 
uint PlantArchitecture::buildCheeseweedPlant(const helios::vec3 &base_position) {
 
    if (shoot_types.empty()) {
        // automatically initialize cheeseweed plant shoots
        initializeCheeseweedShoots();
    }
 
    uint plantID = addPlantInstance(base_position, 0);
 
    uint uID_stem = addBaseStemShoot(plantID, 1, make_AxisRotation(0, 0.f, 0.f), 0.0001, 0.0025, 0.1, 0.1, 0, "base");
 
    breakPlantDormancy(plantID);
 
    setPlantPhenologicalThresholds(plantID, 0, -1, -1, -1, -1, 1000, false);
 
    plant_instances.at(plantID).max_age = 40;
 
    return plantID;
}
 
void PlantArchitecture::initializeCowpeaShoots() {
 
    // ---- Leaf Prototype ---- //
 
    LeafPrototype leaf_prototype_trifoliate(context_ptr->getRandomGenerator());
    leaf_prototype_trifoliate.leaf_texture_file[0] = "CowpeaLeaf_tip_centered.png";
    leaf_prototype_trifoliate.leaf_texture_file[-1] = "CowpeaLeaf_left_centered.png";
    leaf_prototype_trifoliate.leaf_texture_file[1] = "CowpeaLeaf_right_centered.png";
    leaf_prototype_trifoliate.leaf_aspect_ratio = 0.7f;
    leaf_prototype_trifoliate.midrib_fold_fraction = 0.2;
    leaf_prototype_trifoliate.longitudinal_curvature.uniformDistribution(-0.3f, -0.1f);
    leaf_prototype_trifoliate.lateral_curvature = -0.4f;
    leaf_prototype_trifoliate.subdivisions = 6;
    leaf_prototype_trifoliate.unique_prototypes = 5;
    leaf_prototype_trifoliate.build_petiolule = true;
 
    LeafPrototype leaf_prototype_unifoliate = leaf_prototype_trifoliate;
    leaf_prototype_unifoliate.leaf_texture_file.clear();
    leaf_prototype_unifoliate.leaf_texture_file[0] = "CowpeaLeaf_unifoliate_centered.png";
 
    // ---- Phytomer Parameters ---- //
 
    PhytomerParameters phytomer_parameters_trifoliate(context_ptr->getRandomGenerator());
 
    phytomer_parameters_trifoliate.internode.pitch = 20;
    phytomer_parameters_trifoliate.internode.phyllotactic_angle.uniformDistribution(145, 215);
    phytomer_parameters_trifoliate.internode.radius_initial = 0.0015;
    phytomer_parameters_trifoliate.internode.max_floral_buds_per_petiole = 1;
    phytomer_parameters_trifoliate.internode.max_vegetative_buds_per_petiole = 1;
    phytomer_parameters_trifoliate.internode.color = make_RGBcolor(0.15, 0.2, 0.1);
    phytomer_parameters_trifoliate.internode.length_segments = 2;
 
    phytomer_parameters_trifoliate.petiole.petioles_per_internode = 1;
    phytomer_parameters_trifoliate.petiole.pitch.uniformDistribution(45, 60);
    phytomer_parameters_trifoliate.petiole.radius = 0.0018;
    phytomer_parameters_trifoliate.petiole.length.uniformDistribution(0.06, 0.08);
    phytomer_parameters_trifoliate.petiole.taper = 0.25;
    phytomer_parameters_trifoliate.petiole.curvature.uniformDistribution(-200, -50);
    phytomer_parameters_trifoliate.petiole.color = make_RGBcolor(0.2, 0.25, 0.06);
    phytomer_parameters_trifoliate.petiole.length_segments = 5;
    phytomer_parameters_trifoliate.petiole.radial_subdivisions = 6;
 
    phytomer_parameters_trifoliate.leaf.leaves_per_petiole = 3;
    phytomer_parameters_trifoliate.leaf.pitch.normalDistribution(45, 20);
    phytomer_parameters_trifoliate.leaf.yaw = 10;
    phytomer_parameters_trifoliate.leaf.roll = -15;
    phytomer_parameters_trifoliate.leaf.leaflet_offset = 0.4;
    phytomer_parameters_trifoliate.leaf.leaflet_scale = 0.9;
    phytomer_parameters_trifoliate.leaf.prototype_scale.uniformDistribution(0.09, 0.12);
    phytomer_parameters_trifoliate.leaf.prototype = leaf_prototype_trifoliate;
 
    phytomer_parameters_trifoliate.peduncle.length.uniformDistribution(0.3, 0.4);
    phytomer_parameters_trifoliate.peduncle.radius = 0.00225;
    phytomer_parameters_trifoliate.peduncle.pitch.uniformDistribution(0, 30);
    phytomer_parameters_trifoliate.peduncle.roll = 90;
    phytomer_parameters_trifoliate.peduncle.curvature.uniformDistribution(125, 200);
    phytomer_parameters_trifoliate.peduncle.color = make_RGBcolor(0.17, 0.213, 0.051);
    phytomer_parameters_trifoliate.peduncle.length_segments = 6;
    phytomer_parameters_trifoliate.peduncle.radial_subdivisions = 6;
 
    phytomer_parameters_trifoliate.inflorescence.flowers_per_peduncle.uniformDistribution(1, 3);
    phytomer_parameters_trifoliate.inflorescence.flower_offset = 0.05;
    phytomer_parameters_trifoliate.inflorescence.pitch.uniformDistribution(40, 60);
    phytomer_parameters_trifoliate.inflorescence.roll.uniformDistribution(-20, 20);
    phytomer_parameters_trifoliate.inflorescence.flower_prototype_scale = 0.03;
    phytomer_parameters_trifoliate.inflorescence.flower_prototype_function = CowpeaFlowerPrototype;
    phytomer_parameters_trifoliate.inflorescence.fruit_prototype_scale.uniformDistribution(0.09, 0.1);
    phytomer_parameters_trifoliate.inflorescence.fruit_prototype_function = CowpeaFruitPrototype;
    phytomer_parameters_trifoliate.inflorescence.fruit_gravity_factor_fraction.uniformDistribution(0.5, 0.7);
 
    PhytomerParameters phytomer_parameters_unifoliate = phytomer_parameters_trifoliate;
    phytomer_parameters_unifoliate.internode.pitch = 0;
    phytomer_parameters_unifoliate.internode.max_vegetative_buds_per_petiole = 1;
    phytomer_parameters_unifoliate.internode.max_floral_buds_per_petiole = 0;
    phytomer_parameters_unifoliate.petiole.petioles_per_internode = 2;
    phytomer_parameters_unifoliate.petiole.length = 0.0001;
    phytomer_parameters_unifoliate.petiole.radius = 0.0004;
    phytomer_parameters_unifoliate.petiole.pitch.uniformDistribution(60, 80);
    phytomer_parameters_unifoliate.leaf.leaves_per_petiole = 1;
    phytomer_parameters_unifoliate.leaf.prototype_scale = 0.02;
    phytomer_parameters_unifoliate.leaf.pitch.uniformDistribution(-10, 10);
    phytomer_parameters_unifoliate.leaf.prototype = leaf_prototype_unifoliate;
 
    // ---- Shoot Parameters ---- //
 
    ShootParameters shoot_parameters_trifoliate(context_ptr->getRandomGenerator());
    shoot_parameters_trifoliate.phytomer_parameters = phytomer_parameters_trifoliate;
    shoot_parameters_trifoliate.phytomer_parameters.phytomer_creation_function = CowpeaPhytomerCreationFunction;
 
    shoot_parameters_trifoliate.max_nodes = 20;
    shoot_parameters_trifoliate.insertion_angle_tip.uniformDistribution(40, 60);
    //    shoot_parameters_trifoliate.child_insertion_angle_decay_rate = 0; (default)
    shoot_parameters_trifoliate.internode_length_max = 0.025;
    //    shoot_parameters_trifoliate.child_internode_length_min = 0.0; (default)
    //    shoot_parameters_trifoliate.child_internode_length_decay_rate = 0; (default)
    shoot_parameters_trifoliate.base_roll = 90;
    shoot_parameters_trifoliate.base_yaw.uniformDistribution(-20, 20);
    shoot_parameters_trifoliate.gravitropic_curvature = 200;
 
    shoot_parameters_trifoliate.phyllochron_min = 2;
    shoot_parameters_trifoliate.elongation_rate_max = 0.1;
    shoot_parameters_trifoliate.girth_area_factor = 1.5f;
    shoot_parameters_trifoliate.vegetative_bud_break_time = 10;
    shoot_parameters_trifoliate.vegetative_bud_break_probability_min = 0.2;
    shoot_parameters_trifoliate.vegetative_bud_break_probability_decay_rate = -0.4;
    //    shoot_parameters_trifoliate.max_terminal_floral_buds = 0; (default)
    shoot_parameters_trifoliate.flower_bud_break_probability.uniformDistribution(0.1, 0.15);
    shoot_parameters_trifoliate.fruit_set_probability = 0.4;
    //    shoot_parameters_trifoliate.flowers_require_dormancy = false; (default)
    //    shoot_parameters_trifoliate.growth_requires_dormancy = false; (default)
    //    shoot_parameters_trifoliate.determinate_shoot_growth = true; (default)
 
    shoot_parameters_trifoliate.defineChildShootTypes({"trifoliate"}, {1.0});
 
 
    ShootParameters shoot_parameters_unifoliate = shoot_parameters_trifoliate;
    shoot_parameters_unifoliate.phytomer_parameters = phytomer_parameters_unifoliate;
    shoot_parameters_unifoliate.max_nodes = 1;
    shoot_parameters_unifoliate.girth_area_factor = 1.f;
    shoot_parameters_unifoliate.vegetative_bud_break_probability_min = 1;
    shoot_parameters_unifoliate.flower_bud_break_probability = 0;
    shoot_parameters_unifoliate.insertion_angle_tip = 40;
    shoot_parameters_unifoliate.insertion_angle_decay_rate = 0;
    shoot_parameters_unifoliate.vegetative_bud_break_time = 8;
    shoot_parameters_unifoliate.defineChildShootTypes({"trifoliate"}, {1.0});
 
    defineShootType("unifoliate", shoot_parameters_unifoliate);
    defineShootType("trifoliate", shoot_parameters_trifoliate);
}
 
uint PlantArchitecture::buildCowpeaPlant(const helios::vec3 &base_position) {
 
    if (shoot_types.empty()) {
        // automatically initialize cowpea plant shoots
        initializeCowpeaShoots();
    }
 
    uint plantID = addPlantInstance(base_position, 0);
 
    AxisRotation base_rotation = make_AxisRotation(context_ptr->randu(0.f, 0.05f * M_PI), context_ptr->randu(0.f, 2.f * M_PI), context_ptr->randu(0.f, 2.f * M_PI));
    uint uID_unifoliate = addBaseStemShoot(plantID, 1, base_rotation, 0.0005, 0.03, 0.01, 0.01, 0, "unifoliate");
 
    appendShoot(plantID, uID_unifoliate, 1, make_AxisRotation(0, 0, 0.5f * M_PI), shoot_types.at("trifoliate").phytomer_parameters.internode.radius_initial.val(), shoot_types.at("trifoliate").internode_length_max.val(), 0.1, 0.1, 0, "trifoliate");
 
    breakPlantDormancy(plantID);
 
    setPlantPhenologicalThresholds(plantID, 0, 40, 5, 5, 30, 1000, false);
 
    plant_instances.at(plantID).max_age = 365;
 
    return plantID;
}
 
void PlantArchitecture::initializeGrapevineVSPShoots() {
 
    // ---- Leaf Prototype ---- //
 
    LeafPrototype leaf_prototype(context_ptr->getRandomGenerator());
    leaf_prototype.leaf_texture_file[0] = "GrapeLeaf.png";
    leaf_prototype.leaf_aspect_ratio = 1.f;
    leaf_prototype.midrib_fold_fraction = 0.3f;
    leaf_prototype.longitudinal_curvature.uniformDistribution(-0.4, 0.4);
    leaf_prototype.lateral_curvature = 0;
    leaf_prototype.wave_period = 0.3f;
    leaf_prototype.wave_amplitude = 0.1f;
    leaf_prototype.subdivisions = 5;
    leaf_prototype.unique_prototypes = 10;
    leaf_prototype.leaf_offset = make_vec3(-0.3, 0, 0);
 
    // ---- Phytomer Parameters ---- //
 
    PhytomerParameters phytomer_parameters_grapevine(context_ptr->getRandomGenerator());
 
    phytomer_parameters_grapevine.internode.pitch = 20;
    phytomer_parameters_grapevine.internode.phyllotactic_angle.uniformDistribution(160, 200);
    phytomer_parameters_grapevine.internode.radius_initial = 0.003;
    phytomer_parameters_grapevine.internode.color = make_RGBcolor(0.23, 0.13, 0.062);
    phytomer_parameters_grapevine.internode.length_segments = 1;
    phytomer_parameters_grapevine.internode.max_floral_buds_per_petiole = 1;
    phytomer_parameters_grapevine.internode.max_vegetative_buds_per_petiole = 1;
 
    phytomer_parameters_grapevine.petiole.petioles_per_internode = 1;
    phytomer_parameters_grapevine.petiole.color = make_RGBcolor(0.13, 0.066, 0.03);
    phytomer_parameters_grapevine.petiole.pitch.uniformDistribution(45, 70);
    phytomer_parameters_grapevine.petiole.radius = 0.0025;
    phytomer_parameters_grapevine.petiole.length = 0.1;
    phytomer_parameters_grapevine.petiole.taper = 0;
    phytomer_parameters_grapevine.petiole.curvature = 0;
    phytomer_parameters_grapevine.petiole.length_segments = 1;
 
    phytomer_parameters_grapevine.leaf.leaves_per_petiole = 1;
    phytomer_parameters_grapevine.leaf.pitch.uniformDistribution(-110, -80);
    phytomer_parameters_grapevine.leaf.yaw.uniformDistribution(-20, 20);
    phytomer_parameters_grapevine.leaf.roll.uniformDistribution(-5, 5);
    phytomer_parameters_grapevine.leaf.prototype_scale = 0.2;
    phytomer_parameters_grapevine.leaf.prototype = leaf_prototype;
 
    phytomer_parameters_grapevine.peduncle.length = 0.08;
    phytomer_parameters_grapevine.peduncle.pitch.uniformDistribution(50, 90);
    phytomer_parameters_grapevine.peduncle.color = make_RGBcolor(0.32, 0.05, 0.13);
 
    phytomer_parameters_grapevine.inflorescence.flowers_per_peduncle = 1;
    phytomer_parameters_grapevine.inflorescence.pitch = 0;
    //    phytomer_parameters_grapevine.inflorescence.flower_prototype_function = GrapevineFlowerPrototype;
    phytomer_parameters_grapevine.inflorescence.flower_prototype_scale = 0.04;
    phytomer_parameters_grapevine.inflorescence.fruit_prototype_function = GrapevineFruitPrototype;
    phytomer_parameters_grapevine.inflorescence.fruit_prototype_scale = 0.04;
    phytomer_parameters_grapevine.inflorescence.fruit_gravity_factor_fraction = 0.7;
 
    phytomer_parameters_grapevine.phytomer_creation_function = GrapevinePhytomerCreationFunction;
    //    phytomer_parameters_grapevine.phytomer_callback_function = GrapevinePhytomerCallbackFunction;
 
    // ---- Shoot Parameters ---- //
 
    ShootParameters shoot_parameters_main(context_ptr->getRandomGenerator());
    shoot_parameters_main.phytomer_parameters = phytomer_parameters_grapevine;
    shoot_parameters_main.vegetative_bud_break_probability_min = 0.075;
    shoot_parameters_main.vegetative_bud_break_probability_decay_rate = 1.;
    shoot_parameters_main.vegetative_bud_break_time = 30;
    shoot_parameters_main.phyllochron_min.uniformDistribution(1.75, 2.25);
    shoot_parameters_main.elongation_rate_max = 0.15;
    shoot_parameters_main.girth_area_factor = 1.f;
    shoot_parameters_main.gravitropic_curvature = 400;
    shoot_parameters_main.tortuosity = 15;
    shoot_parameters_main.internode_length_max.uniformDistribution(0.06, 0.08);
    shoot_parameters_main.internode_length_decay_rate = 0;
    shoot_parameters_main.insertion_angle_tip = 45;
    shoot_parameters_main.insertion_angle_decay_rate = 0;
    shoot_parameters_main.flowers_require_dormancy = false;
    shoot_parameters_main.growth_requires_dormancy = false;
    shoot_parameters_main.determinate_shoot_growth = false;
    shoot_parameters_main.max_terminal_floral_buds = 0;
    shoot_parameters_main.flower_bud_break_probability = 0.5;
    shoot_parameters_main.fruit_set_probability = 0.2;
    shoot_parameters_main.max_nodes = 20;
    shoot_parameters_main.base_roll.uniformDistribution(90 - 25, 90 + 25);
    shoot_parameters_main.base_yaw = 0;
 
    ShootParameters shoot_parameters_cane = shoot_parameters_main;
    //    shoot_parameters_cane.phytomer_parameters.internode.image_texture = "GrapeBark.jpg";
    shoot_parameters_cane.phytomer_parameters.internode.pitch = 0;
    shoot_parameters_cane.phytomer_parameters.internode.radial_subdivisions = 15;
    shoot_parameters_cane.phytomer_parameters.internode.max_floral_buds_per_petiole = 0;
    shoot_parameters_cane.phytomer_parameters.internode.phyllotactic_angle = 0;
    shoot_parameters_cane.insertion_angle_tip.uniformDistribution(60, 120);
    shoot_parameters_cane.girth_area_factor = 0.7f;
    shoot_parameters_cane.max_nodes = 9;
    shoot_parameters_cane.gravitropic_curvature.uniformDistribution(-20, 20);
    shoot_parameters_cane.tortuosity = 1;
    shoot_parameters_cane.gravitropic_curvature = 10;
    shoot_parameters_cane.vegetative_bud_break_probability_min = 0.9;
    shoot_parameters_cane.defineChildShootTypes({"grapevine_shoot"}, {1.f});
 
    ShootParameters shoot_parameters_trunk = shoot_parameters_main;
    shoot_parameters_trunk.phytomer_parameters.internode.image_texture = "GrapeBark.jpg";
    shoot_parameters_trunk.phytomer_parameters.internode.pitch = 0;
    shoot_parameters_trunk.phytomer_parameters.internode.phyllotactic_angle = 0;
    shoot_parameters_trunk.phytomer_parameters.internode.radius_initial = 0.05;
    shoot_parameters_trunk.phytomer_parameters.internode.radial_subdivisions = 25;
    shoot_parameters_trunk.phytomer_parameters.internode.max_floral_buds_per_petiole = 0;
    shoot_parameters_trunk.phyllochron_min = 2.5;
    shoot_parameters_trunk.insertion_angle_tip = 90;
    shoot_parameters_trunk.girth_area_factor = 0;
    shoot_parameters_trunk.max_nodes = 18;
    shoot_parameters_trunk.tortuosity = 0;
    shoot_parameters_trunk.vegetative_bud_break_probability_min = 0;
    shoot_parameters_trunk.defineChildShootTypes({"grapevine_shoot"}, {1.f});
 
    defineShootType("grapevine_trunk", shoot_parameters_trunk);
    defineShootType("grapevine_cane", shoot_parameters_cane);
    defineShootType("grapevine_shoot", shoot_parameters_main);
}
 
uint PlantArchitecture::buildGrapevineVSP(const helios::vec3 &base_position) {
 
    if (shoot_types.empty()) {
        // automatically initialize grapevine plant shoots
        initializeGrapevineVSPShoots();
    }
 
    // Get training system parameters
    auto vine_spacing = getParameterValue(current_build_parameters, "vine_spacing", 2.4f, 0.5f, 5.f, "plant-to-plant spacing in meters");
    auto trunk_height = getParameterValue(current_build_parameters, "trunk_height", 0.1f, 0.05f, 1.f, "total trunk height in meters");
 
    // Calculate trunk nodes based on desired height
    float trunk_internode_length = 0.1f;
    uint trunk_nodes = uint(trunk_height / trunk_internode_length);
    if (trunk_nodes < 1)
        trunk_nodes = 1;
 
    // Calculate cane nodes to span to neighboring plant
    float cane_internode_length = 0.15f;
    float cane_total_length = vine_spacing / 2.f; // Cane extends from center to next plant
    uint cane_nodes = uint(cane_total_length / cane_internode_length);
    if (cane_nodes < 1)
        cane_nodes = 1;
 
    // Fixed training parameters (not user-customizable)
    float cane_radius = 0.005f;
    float cane_pitch_min = float(0.45f * M_PI);
    float cane_pitch_max = float(0.52f * M_PI);
 
    uint plantID = addPlantInstance(base_position, 0);
 
    uint uID_stem = addBaseStemShoot(plantID, trunk_nodes, make_AxisRotation(context_ptr->randu(0, 0.05 * M_PI), 0, 0), shoot_types.at("grapevine_trunk").phytomer_parameters.internode.radius_initial.val(), trunk_internode_length, 1, 1, 0.1,
                                     "grapevine_trunk");
 
    uint uID_cane_L = appendShoot(plantID, uID_stem, cane_nodes, make_AxisRotation(context_ptr->randu(cane_pitch_min, cane_pitch_max), 0, M_PI), cane_radius, cane_internode_length, 1, 1, 0.5, "grapevine_cane");
    uint uID_cane_R = appendShoot(plantID, uID_stem, cane_nodes, make_AxisRotation(context_ptr->randu(cane_pitch_min, cane_pitch_max), M_PI, M_PI), cane_radius, cane_internode_length, 1, 1, 0.5, "grapevine_cane");
 
    //    makePlantDormant(plantID);
 
    removeShootLeaves(plantID, uID_stem);
    removeShootLeaves(plantID, uID_cane_L);
    removeShootLeaves(plantID, uID_cane_R);
 
    setPlantPhenologicalThresholds(plantID, 165, -1, -1, 45, 45, 200, false);
 
    plant_instances.at(plantID).max_age = 365;
 
    return plantID;
}
 
void PlantArchitecture::initializeGrapevineWyeShoots() {
 
    // ---- Leaf Prototype ---- //
 
    LeafPrototype leaf_prototype(context_ptr->getRandomGenerator());
    leaf_prototype.leaf_texture_file[0] = "GrapeLeaf.png";
    leaf_prototype.leaf_aspect_ratio = 1.f;
    leaf_prototype.midrib_fold_fraction = 0.3f;
    leaf_prototype.longitudinal_curvature.uniformDistribution(-0.4, 0.4);
    leaf_prototype.lateral_curvature = 0;
    leaf_prototype.wave_period = 0.3f;
    leaf_prototype.wave_amplitude = 0.1f;
    leaf_prototype.subdivisions = 5;
    leaf_prototype.unique_prototypes = 10;
    leaf_prototype.leaf_offset = make_vec3(-0.3, 0, 0);
 
    // ---- Phytomer Parameters ---- //
 
    PhytomerParameters phytomer_parameters_grapevine(context_ptr->getRandomGenerator());
 
    phytomer_parameters_grapevine.internode.pitch = 20;
    phytomer_parameters_grapevine.internode.phyllotactic_angle.uniformDistribution(160, 200);
    phytomer_parameters_grapevine.internode.radius_initial = 0.003;
    phytomer_parameters_grapevine.internode.color = make_RGBcolor(0.23, 0.13, 0.062);
    phytomer_parameters_grapevine.internode.length_segments = 1;
    phytomer_parameters_grapevine.internode.max_floral_buds_per_petiole = 1;
    phytomer_parameters_grapevine.internode.max_vegetative_buds_per_petiole = 1;
 
    phytomer_parameters_grapevine.petiole.petioles_per_internode = 1;
    phytomer_parameters_grapevine.petiole.color = make_RGBcolor(0.13, 0.125, 0.03);
    phytomer_parameters_grapevine.petiole.pitch.uniformDistribution(45, 70);
    phytomer_parameters_grapevine.petiole.radius = 0.0025;
    phytomer_parameters_grapevine.petiole.length = 0.1;
    phytomer_parameters_grapevine.petiole.taper = 0;
    phytomer_parameters_grapevine.petiole.curvature = 0;
    phytomer_parameters_grapevine.petiole.length_segments = 1;
 
    phytomer_parameters_grapevine.leaf.leaves_per_petiole = 1;
    phytomer_parameters_grapevine.leaf.pitch.uniformDistribution(-110, -80);
    phytomer_parameters_grapevine.leaf.yaw.uniformDistribution(-20, 20);
    phytomer_parameters_grapevine.leaf.roll.uniformDistribution(-5, 5);
    phytomer_parameters_grapevine.leaf.prototype_scale = 0.2;
    phytomer_parameters_grapevine.leaf.prototype = leaf_prototype;
 
    phytomer_parameters_grapevine.peduncle.length = 0.04;
    phytomer_parameters_grapevine.peduncle.radius = 0.005;
    phytomer_parameters_grapevine.peduncle.color = make_RGBcolor(0.13, 0.125, 0.03);
    phytomer_parameters_grapevine.peduncle.pitch.uniformDistribution(80, 100);
 
    phytomer_parameters_grapevine.inflorescence.flowers_per_peduncle = 1;
    phytomer_parameters_grapevine.inflorescence.pitch = 0;
    //    phytomer_parameters_grapevine.inflorescence.flower_prototype_function = GrapevineFlowerPrototype;
    phytomer_parameters_grapevine.inflorescence.flower_prototype_scale = 0.04;
    phytomer_parameters_grapevine.inflorescence.fruit_prototype_function = GrapevineFruitPrototype;
    phytomer_parameters_grapevine.inflorescence.fruit_prototype_scale = 0.04;
    phytomer_parameters_grapevine.inflorescence.fruit_gravity_factor_fraction = 0.9;
 
    phytomer_parameters_grapevine.phytomer_creation_function = GrapevinePhytomerCreationFunction;
    //    phytomer_parameters_grapevine.phytomer_callback_function = GrapevinePhytomerCallbackFunction;
 
    // ---- Shoot Parameters ---- //
 
    ShootParameters shoot_parameters_main(context_ptr->getRandomGenerator());
    shoot_parameters_main.phytomer_parameters = phytomer_parameters_grapevine;
    shoot_parameters_main.vegetative_bud_break_probability_min = 0.025;
    shoot_parameters_main.vegetative_bud_break_probability_decay_rate = -1.;
    shoot_parameters_main.vegetative_bud_break_time = 30;
    shoot_parameters_main.phyllochron_min.uniformDistribution(2.5, 3.5);
    shoot_parameters_main.elongation_rate_max = 0.15;
    shoot_parameters_main.girth_area_factor = 0.8f;
    shoot_parameters_main.gravitropic_curvature.uniformDistribution(0, 100);
    shoot_parameters_main.tortuosity = 10;
    shoot_parameters_main.internode_length_max.uniformDistribution(0.06, 0.08);
    shoot_parameters_main.internode_length_decay_rate = 0;
    shoot_parameters_main.insertion_angle_tip = 45;
    shoot_parameters_main.insertion_angle_decay_rate = 0;
    shoot_parameters_main.flowers_require_dormancy = false;
    shoot_parameters_main.growth_requires_dormancy = false;
    shoot_parameters_main.determinate_shoot_growth = false;
    shoot_parameters_main.max_terminal_floral_buds = 0;
    shoot_parameters_main.flower_bud_break_probability = 0.5;
    shoot_parameters_main.fruit_set_probability = 0.2;
    shoot_parameters_main.max_nodes.uniformDistribution(14, 18);
    shoot_parameters_main.base_roll.uniformDistribution(90 - 25, 90 + 25);
    shoot_parameters_main.base_yaw.uniformDistribution(-50, 50);
 
    ShootParameters shoot_parameters_cordon = shoot_parameters_main;
    shoot_parameters_cordon.phytomer_parameters.internode.image_texture = "GrapeBark.jpg";
    shoot_parameters_cordon.phytomer_parameters.internode.pitch = 0;
    shoot_parameters_cordon.phytomer_parameters.internode.radial_subdivisions = 15;
    shoot_parameters_cordon.phytomer_parameters.internode.max_floral_buds_per_petiole = 0;
    shoot_parameters_cordon.phytomer_parameters.internode.phyllotactic_angle = 0;
    shoot_parameters_cordon.insertion_angle_tip.uniformDistribution(60, 120);
    shoot_parameters_cordon.girth_area_factor = 3.5f;
    shoot_parameters_cordon.max_nodes = 8;
    shoot_parameters_cordon.tortuosity = 1;
    shoot_parameters_cordon.gravitropic_curvature = 0;
    shoot_parameters_cordon.vegetative_bud_break_probability_min = 0.9;
    shoot_parameters_cordon.base_yaw = 0;
    shoot_parameters_cordon.defineChildShootTypes({"grapevine_shoot"}, {1.f});
 
    ShootParameters shoot_parameters_trunk = shoot_parameters_main;
    shoot_parameters_trunk.phytomer_parameters.internode.image_texture = "GrapeBark.jpg";
    shoot_parameters_trunk.phytomer_parameters.internode.pitch = 0;
    shoot_parameters_trunk.phytomer_parameters.internode.phyllotactic_angle = 0;
    shoot_parameters_trunk.phytomer_parameters.internode.radius_initial = 0.05;
    shoot_parameters_trunk.phytomer_parameters.internode.radial_subdivisions = 25;
    shoot_parameters_trunk.phytomer_parameters.internode.max_floral_buds_per_petiole = 0;
    shoot_parameters_trunk.phyllochron_min = 2.5;
    shoot_parameters_trunk.insertion_angle_tip = 90;
    shoot_parameters_trunk.girth_area_factor = 0;
    shoot_parameters_trunk.max_nodes = 18;
    shoot_parameters_trunk.tortuosity = 2;
    shoot_parameters_trunk.vegetative_bud_break_probability_min = 0;
    shoot_parameters_trunk.defineChildShootTypes({"grapevine_shoot"}, {1.f});
 
    defineShootType("grapevine_trunk", shoot_parameters_trunk);
    defineShootType("grapevine_cordon", shoot_parameters_cordon);
    defineShootType("grapevine_shoot", shoot_parameters_main);
}
 
uint PlantArchitecture::buildGrapevineWye(const helios::vec3 &base_position) {
 
    if (shoot_types.empty()) {
        // automatically initialize grapevine plant shoots
        initializeGrapevineWyeShoots();
    }
 
    // Get training system parameters
    auto trunk_height_total = getParameterValue(current_build_parameters, "trunk_height", 0.165f, 0.05f, 1.f, "total trunk height in meters");
    auto cordon_spacing = getParameterValue(current_build_parameters, "cordon_spacing", 0.6f, 0.2f, 2.f, "spacing between cordon rows in meters");
    auto vine_spacing = getParameterValue(current_build_parameters, "vine_spacing", 1.8f, 0.5f, 5.f, "plant-to-plant spacing in meters");
    auto catch_wire_height = getParameterValue(current_build_parameters, "catch_wire_height", 2.1f, 0.5f, 4.f, "absolute height of catch wires in meters");
 
    // Calculate trunk nodes based on desired height
    float trunk_internode_length = 0.165f / 8.f; // Original was 8 nodes * 0.165m total
    uint trunk_nodes = uint(trunk_height_total / trunk_internode_length);
    if (trunk_nodes < 1)
        trunk_nodes = 1;
 
    // Calculate trellis head height from catch wire height (catch wires above fruiting wires)
    float head_height = catch_wire_height - 0.35f; // Offset to match original geometry
 
    // Fixed training parameters (not user-customizable)
    uint upright_nodes = 3;
    float upright_pitch_min = 42.f;
    float upright_pitch_max = 48.f;
    float upright_radius = 0.03f;
    float upright_length = 0.14f;
    uint cordon_nodes = 8;
    float cordon_radius = 0.02f;
    float cordon_length = 0.11f;
    float catch_wire_offset_1 = 0.15f;
    float catch_wire_offset_2 = 0.35f;
 
    std::vector<std::vector<vec3>> trellis_points;
 
    // fruiting wires
    trellis_points.push_back(linspace(make_vec3(-0.5f * vine_spacing, -0.5f * cordon_spacing, head_height), make_vec3(0.5f * vine_spacing, -0.5f * cordon_spacing, head_height), 8));
    trellis_points.push_back(linspace(make_vec3(-0.5f * vine_spacing, 0.5f * cordon_spacing, head_height), make_vec3(0.5f * vine_spacing, 0.5f * cordon_spacing, head_height), 8));
 
    // first catch wires (these don't exist in a real Wye trellis, but are needed to keep the vines from falling through the wires)
    trellis_points.push_back(linspace(make_vec3(-0.5f * vine_spacing, -0.5f * cordon_spacing - catch_wire_offset_1, catch_wire_height - catch_wire_offset_2),
                                      make_vec3(0.5f * vine_spacing, -0.5f * cordon_spacing - catch_wire_offset_1, catch_wire_height - catch_wire_offset_2), 8));
    trellis_points.push_back(linspace(make_vec3(-0.5f * vine_spacing, 0.5f * cordon_spacing + catch_wire_offset_1, catch_wire_height - catch_wire_offset_2),
                                      make_vec3(0.5f * vine_spacing, 0.5f * cordon_spacing + catch_wire_offset_1, catch_wire_height - catch_wire_offset_2), 8));
 
    // second catch wires (at specified height)
    trellis_points.push_back(linspace(make_vec3(-0.5f * vine_spacing, -0.5f * cordon_spacing - catch_wire_offset_2, catch_wire_height), make_vec3(0.5f * vine_spacing, -0.5f * cordon_spacing - catch_wire_offset_2, catch_wire_height), 8));
    trellis_points.push_back(linspace(make_vec3(-0.5f * vine_spacing, 0.5f * cordon_spacing + catch_wire_offset_2, catch_wire_height), make_vec3(0.5f * vine_spacing, 0.5f * cordon_spacing + catch_wire_offset_2, catch_wire_height), 8));
 
    for (int j = 0; j < trellis_points.size(); j++) {
        for (int i = 0; i < trellis_points[j].size(); i++) {
            trellis_points.at(j).at(i) += base_position;
        }
    }
 
    uint plantID = addPlantInstance(base_position, 0);
 
    // Set plant-specific attraction points for this grapevine's trellis system
    setPlantAttractionPoints(plantID, flatten(trellis_points), 45.f, 0.5f, 0.5);
 
    uint uID_stem = addBaseStemShoot(plantID, trunk_nodes, make_AxisRotation(0., 0, 0), shoot_types.at("grapevine_trunk").phytomer_parameters.internode.radius_initial.val(), trunk_internode_length, 1, 1, 0.1, "grapevine_trunk");
 
    uint uID_upright_L = appendShoot(plantID, uID_stem, upright_nodes, make_AxisRotation(deg2rad(context_ptr->randu(upright_pitch_min, upright_pitch_max)), 0, M_PI), upright_radius, upright_length, 1, 1, 0.2, "grapevine_trunk");
    uint uID_upright_R = appendShoot(plantID, uID_stem, upright_nodes, make_AxisRotation(deg2rad(context_ptr->randu(upright_pitch_min, upright_pitch_max)), M_PI, M_PI), upright_radius, upright_length, 1, 1, 0.2, "grapevine_trunk");
 
    uint uID_cordon_L1 = appendShoot(plantID, uID_upright_L, cordon_nodes, make_AxisRotation(deg2rad(-90), 0.5 * M_PI, -0.2), cordon_radius, cordon_length, 1, 1, 0.5, "grapevine_cordon");
    uint uID_cordon_L2 = appendShoot(plantID, uID_upright_L, cordon_nodes, make_AxisRotation(deg2rad(-90), -0.5 * M_PI, 0.2), cordon_radius, cordon_length, 1, 1, 0.5, "grapevine_cordon");
 
    uint uID_cordon_R1 = appendShoot(plantID, uID_upright_R, cordon_nodes, make_AxisRotation(deg2rad(-90), 0.5 * M_PI, 0.2), cordon_radius, cordon_length, 1, 1, 0.5, "grapevine_cordon");
    uint uID_cordon_R2 = appendShoot(plantID, uID_upright_R, cordon_nodes, make_AxisRotation(deg2rad(-90), -0.5 * M_PI, -0.2), cordon_radius, cordon_length, 1, 1, 0.5, "grapevine_cordon");
 
    removeShootLeaves(plantID, uID_stem);
    removeShootLeaves(plantID, uID_upright_L);
    removeShootLeaves(plantID, uID_upright_R);
    removeShootLeaves(plantID, uID_cordon_L1);
    removeShootLeaves(plantID, uID_cordon_L2);
    removeShootLeaves(plantID, uID_cordon_R1);
    removeShootLeaves(plantID, uID_cordon_R2);
 
    removeShootVegetativeBuds(plantID, uID_upright_L);
    removeShootVegetativeBuds(plantID, uID_upright_R);
 
    setPlantPhenologicalThresholds(plantID, 165, -1, -1, 45, 45, 200, false);
 
    plant_instances.at(plantID).max_age = 365;
 
    return plantID;
}
 
void PlantArchitecture::initializeGroundCherryWeedShoots() {
 
    // ---- Leaf Prototype ---- //
 
    LeafPrototype leaf_prototype(context_ptr->getRandomGenerator());
    leaf_prototype.leaf_texture_file[0] = "GroundCherryLeaf.png";
    leaf_prototype.leaf_aspect_ratio.uniformDistribution(0.3, 0.5);
    leaf_prototype.midrib_fold_fraction = 0.2f;
    leaf_prototype.longitudinal_curvature = 0.1f;
    ;
    leaf_prototype.lateral_curvature = -0.3f;
    leaf_prototype.wave_period = 0.35f;
    leaf_prototype.wave_amplitude = 0.08f;
    leaf_prototype.subdivisions = 6;
    leaf_prototype.unique_prototypes = 5;
 
    // ---- Phytomer Parameters ---- //
 
    PhytomerParameters phytomer_parameters(context_ptr->getRandomGenerator());
 
    phytomer_parameters.internode.pitch = 5;
    phytomer_parameters.internode.phyllotactic_angle = 137.5;
    phytomer_parameters.internode.radius_initial = 0.0005;
    phytomer_parameters.internode.color = make_RGBcolor(0.266, 0.3375, 0.0700);
    phytomer_parameters.internode.length_segments = 1;
 
    phytomer_parameters.petiole.petioles_per_internode = 1;
    phytomer_parameters.petiole.pitch.uniformDistribution(45, 60);
    phytomer_parameters.petiole.radius = 0.0005;
    phytomer_parameters.petiole.length = 0.025;
    phytomer_parameters.petiole.taper = 0.15;
    phytomer_parameters.petiole.curvature.uniformDistribution(-150, -50);
    phytomer_parameters.petiole.color = phytomer_parameters.internode.color;
    phytomer_parameters.petiole.length_segments = 2;
 
    phytomer_parameters.leaf.leaves_per_petiole = 1;
    phytomer_parameters.leaf.pitch.uniformDistribution(-30, 5);
    phytomer_parameters.leaf.yaw = 10;
    phytomer_parameters.leaf.roll = 0;
    phytomer_parameters.leaf.prototype_scale.uniformDistribution(0.06, 0.08);
    phytomer_parameters.leaf.prototype = leaf_prototype;
 
    phytomer_parameters.peduncle.length = 0.01;
    phytomer_parameters.peduncle.radius = 0.001;
    phytomer_parameters.peduncle.pitch = 20;
    phytomer_parameters.peduncle.roll = 0;
    phytomer_parameters.peduncle.curvature = -700;
    phytomer_parameters.peduncle.color = phytomer_parameters.internode.color;
    phytomer_parameters.peduncle.length_segments = 2;
    phytomer_parameters.peduncle.radial_subdivisions = 6;
 
    phytomer_parameters.inflorescence.flowers_per_peduncle = 1;
    phytomer_parameters.inflorescence.pitch = 0;
    phytomer_parameters.inflorescence.roll.uniformDistribution(-30, 30);
    phytomer_parameters.inflorescence.flower_prototype_scale = 0.01;
    phytomer_parameters.inflorescence.flower_prototype_function = BindweedFlowerPrototype;
    phytomer_parameters.inflorescence.fruit_prototype_scale = 0.06;
    // phytomer_parameters.inflorescence.fruit_prototype_function = GroundCherryFruitPrototype;
    phytomer_parameters.inflorescence.fruit_gravity_factor_fraction = 0.75;
 
    // ---- Shoot Parameters ---- //
 
    ShootParameters shoot_parameters(context_ptr->getRandomGenerator());
    shoot_parameters.phytomer_parameters = phytomer_parameters;
    // shoot_parameters.phytomer_parameters.phytomer_creation_function = TomatoPhytomerCreationFunction;
 
    shoot_parameters.max_nodes = 26;
    shoot_parameters.insertion_angle_tip = 50;
    shoot_parameters.insertion_angle_decay_rate = 0;
    shoot_parameters.internode_length_max = 0.015;
    shoot_parameters.internode_length_min = 0.0;
    shoot_parameters.internode_length_decay_rate = 0;
    shoot_parameters.base_roll = 90;
    shoot_parameters.base_yaw.uniformDistribution(-20, 20);
    shoot_parameters.gravitropic_curvature = 700;
    shoot_parameters.tortuosity = 3;
 
    shoot_parameters.phyllochron_min = 1;
    shoot_parameters.elongation_rate_max = 0.1;
    shoot_parameters.girth_area_factor = 2.f;
    shoot_parameters.vegetative_bud_break_time = 10;
    shoot_parameters.vegetative_bud_break_probability_min = 0.1;
    shoot_parameters.vegetative_bud_break_probability_decay_rate = -0.5;
    shoot_parameters.flower_bud_break_probability = 0.25;
    shoot_parameters.fruit_set_probability = 0.5;
    shoot_parameters.flowers_require_dormancy = false;
    shoot_parameters.growth_requires_dormancy = false;
    shoot_parameters.determinate_shoot_growth = false;
 
    shoot_parameters.defineChildShootTypes({"mainstem"}, {1.0});
 
    defineShootType("mainstem", shoot_parameters);
}
 
uint PlantArchitecture::buildGroundCherryWeedPlant(const helios::vec3 &base_position) {
 
    if (shoot_types.empty()) {
        // automatically initialize ground cherry plant shoots
        initializeGroundCherryWeedShoots();
    }
 
    uint plantID = addPlantInstance(base_position, 0);
 
    AxisRotation base_rotation = make_AxisRotation(0, context_ptr->randu(0.f, 2.f * M_PI), context_ptr->randu(0.f, 2.f * M_PI));
    uint uID_stem = addBaseStemShoot(plantID, 1, base_rotation, 0.0025, 0.018, 0.01, 0.01, 0, "mainstem");
 
    breakPlantDormancy(plantID);
 
    setPlantPhenologicalThresholds(plantID, 0, 20, -1, 20, 30, 1000, false);
 
    plant_instances.at(plantID).max_age = 80;
 
    return plantID;
}
 
void PlantArchitecture::initializeMaizeShoots() {
 
    // ---- Leaf Prototype ---- //
 
    LeafPrototype leaf_prototype(context_ptr->getRandomGenerator());
    leaf_prototype.leaf_texture_file[0] = "SorghumLeaf.png";
    leaf_prototype.leaf_aspect_ratio = 0.25f;
    leaf_prototype.midrib_fold_fraction = 0.3f;
    leaf_prototype.longitudinal_curvature.uniformDistribution(-0.45, -0.3);
    leaf_prototype.lateral_curvature = -0.3f;
    ;
    leaf_prototype.petiole_roll = 0.04f;
    leaf_prototype.wave_period = 0.1f;
    leaf_prototype.wave_amplitude = 0.1f;
    leaf_prototype.leaf_buckle_length.uniformDistribution(0.4, 0.6);
    leaf_prototype.leaf_buckle_angle.uniformDistribution(40, 50);
    leaf_prototype.subdivisions = 50;
    leaf_prototype.unique_prototypes = 10;
 
    // ---- Phytomer Parameters ---- //
 
    PhytomerParameters phytomer_parameters_maize(context_ptr->getRandomGenerator());
 
    phytomer_parameters_maize.internode.pitch = 0;
    phytomer_parameters_maize.internode.phyllotactic_angle.uniformDistribution(170, 190);
    phytomer_parameters_maize.internode.radius_initial = 0.0075;
    phytomer_parameters_maize.internode.color = make_RGBcolor(0.126, 0.182, 0.084);
    phytomer_parameters_maize.internode.length_segments = 2;
    phytomer_parameters_maize.internode.radial_subdivisions = 10;
    phytomer_parameters_maize.internode.max_floral_buds_per_petiole = 1;
    phytomer_parameters_maize.internode.max_vegetative_buds_per_petiole = 0;
 
    phytomer_parameters_maize.petiole.petioles_per_internode = 1;
    phytomer_parameters_maize.petiole.pitch.uniformDistribution(-40, -20);
    phytomer_parameters_maize.petiole.radius = 0.0;
    phytomer_parameters_maize.petiole.length = 0.05;
    phytomer_parameters_maize.petiole.taper = 0;
    phytomer_parameters_maize.petiole.curvature = 0;
    phytomer_parameters_maize.petiole.length_segments = 1;
 
    phytomer_parameters_maize.leaf.leaves_per_petiole = 1;
    phytomer_parameters_maize.leaf.pitch = 0;
    phytomer_parameters_maize.leaf.yaw = 0;
    phytomer_parameters_maize.leaf.roll = 0;
    phytomer_parameters_maize.leaf.prototype_scale = 0.6;
    phytomer_parameters_maize.leaf.prototype = leaf_prototype;
 
    phytomer_parameters_maize.peduncle.length = 0.14f;
    phytomer_parameters_maize.peduncle.radius = 0.004;
    phytomer_parameters_maize.peduncle.curvature = 0;
    phytomer_parameters_maize.peduncle.color = phytomer_parameters_maize.internode.color;
    phytomer_parameters_maize.peduncle.radial_subdivisions = 6;
    phytomer_parameters_maize.peduncle.length_segments = 2;
 
    phytomer_parameters_maize.inflorescence.flowers_per_peduncle = 7;
    phytomer_parameters_maize.inflorescence.pitch.uniformDistribution(0, 30);
    phytomer_parameters_maize.inflorescence.roll = 0;
    phytomer_parameters_maize.inflorescence.flower_offset = 0.1;
    phytomer_parameters_maize.inflorescence.fruit_prototype_scale = 0.15;
    phytomer_parameters_maize.inflorescence.fruit_prototype_function = MaizeTasselPrototype;
 
    phytomer_parameters_maize.phytomer_creation_function = MaizePhytomerCreationFunction;
 
    // ---- Shoot Parameters ---- //
 
    ShootParameters shoot_parameters_mainstem(context_ptr->getRandomGenerator());
    shoot_parameters_mainstem.phytomer_parameters = phytomer_parameters_maize;
    shoot_parameters_mainstem.vegetative_bud_break_probability_min = 0.5;
    shoot_parameters_mainstem.flower_bud_break_probability = 1;
    shoot_parameters_mainstem.phyllochron_min = 2;
    shoot_parameters_mainstem.elongation_rate_max = 0.1;
    shoot_parameters_mainstem.girth_area_factor = 6.f;
    shoot_parameters_mainstem.gravitropic_curvature.uniformDistribution(-500, 0);
    shoot_parameters_mainstem.internode_length_max = 0.22;
    shoot_parameters_mainstem.tortuosity = 1.f;
    shoot_parameters_mainstem.internode_length_decay_rate = 0;
    shoot_parameters_mainstem.flowers_require_dormancy = false;
    shoot_parameters_mainstem.growth_requires_dormancy = false;
    shoot_parameters_mainstem.determinate_shoot_growth = false;
    shoot_parameters_mainstem.flower_bud_break_probability = 1.0;
    shoot_parameters_mainstem.fruit_set_probability = 1.0;
    shoot_parameters_mainstem.defineChildShootTypes({"mainstem"}, {1.0});
    shoot_parameters_mainstem.max_nodes = 17;
    shoot_parameters_mainstem.max_terminal_floral_buds = 1;
 
    defineShootType("mainstem", shoot_parameters_mainstem);
}
 
uint PlantArchitecture::buildMaizePlant(const helios::vec3 &base_position) {
 
    if (shoot_types.empty()) {
        // automatically initialize maize plant shoots
        initializeMaizeShoots();
    }
 
    uint plantID = addPlantInstance(base_position, 0);
 
    uint uID_stem = addBaseStemShoot(plantID, 1, make_AxisRotation(context_ptr->randu(0.f, 0.035f * M_PI), context_ptr->randu(0.f, 2.f * M_PI), context_ptr->randu(0.f, 2.f * M_PI)), 0.003, 0.08, 0.01, 0.01, 0.2, "mainstem");
 
    breakPlantDormancy(plantID);
 
    setPlantPhenologicalThresholds(plantID, 0, -1, -1, 4, 10, 1000, false);
 
    plant_instances.at(plantID).max_age = 365;
 
    return plantID;
}
 
void PlantArchitecture::initializeOliveTreeShoots() {
 
    // ---- Leaf Prototype ---- //
 
    LeafPrototype leaf_prototype(context_ptr->getRandomGenerator());
    leaf_prototype.prototype_function = OliveLeafPrototype;
    leaf_prototype.unique_prototypes = 1;
 
    // ---- Phytomer Parameters ---- //
 
    PhytomerParameters phytomer_parameters_olive(context_ptr->getRandomGenerator());
 
    phytomer_parameters_olive.internode.pitch = 0;
    phytomer_parameters_olive.internode.phyllotactic_angle.uniformDistribution(80, 100);
    phytomer_parameters_olive.internode.radius_initial = 0.002;
    phytomer_parameters_olive.internode.length_segments = 1;
    phytomer_parameters_olive.internode.image_texture = "OliveBark.jpg";
    phytomer_parameters_olive.internode.max_floral_buds_per_petiole = 3;
 
    phytomer_parameters_olive.petiole.petioles_per_internode = 2;
    phytomer_parameters_olive.petiole.pitch.uniformDistribution(-40, -20);
    phytomer_parameters_olive.petiole.taper = 0.1;
    phytomer_parameters_olive.petiole.curvature = 0;
    phytomer_parameters_olive.petiole.length = 0.01;
    phytomer_parameters_olive.petiole.radius = 0.0005;
    phytomer_parameters_olive.petiole.length_segments = 1;
    phytomer_parameters_olive.petiole.radial_subdivisions = 3;
    phytomer_parameters_olive.petiole.color = make_RGBcolor(0.61, 0.5, 0.24);
 
    phytomer_parameters_olive.leaf.leaves_per_petiole = 1;
    phytomer_parameters_olive.leaf.prototype_scale = 0.06;
    phytomer_parameters_olive.leaf.prototype = leaf_prototype;
 
    phytomer_parameters_olive.peduncle.length = 0.065;
    phytomer_parameters_olive.peduncle.radius = 0.001;
    phytomer_parameters_olive.peduncle.pitch = 60;
    phytomer_parameters_olive.peduncle.roll = 0;
    phytomer_parameters_olive.peduncle.length_segments = 1;
    phytomer_parameters_olive.peduncle.color = make_RGBcolor(0.7, 0.72, 0.7);
 
    phytomer_parameters_olive.inflorescence.flowers_per_peduncle = 10;
    phytomer_parameters_olive.inflorescence.flower_offset = 0.13;
    phytomer_parameters_olive.inflorescence.pitch.uniformDistribution(80, 100);
    phytomer_parameters_olive.inflorescence.roll.uniformDistribution(0, 360);
    phytomer_parameters_olive.inflorescence.flower_prototype_scale = 0.01;
    //    phytomer_parameters_olive.inflorescence.flower_prototype_function = OliveFlowerPrototype;
    phytomer_parameters_olive.inflorescence.fruit_prototype_scale = 0.025;
    phytomer_parameters_olive.inflorescence.fruit_prototype_function = OliveFruitPrototype;
 
    // ---- Shoot Parameters ---- //
 
    // Trunk
    ShootParameters shoot_parameters_trunk(context_ptr->getRandomGenerator());
    shoot_parameters_trunk.phytomer_parameters = phytomer_parameters_olive;
    shoot_parameters_trunk.phytomer_parameters.internode.phyllotactic_angle = 0;
    shoot_parameters_trunk.phytomer_parameters.internode.radius_initial = 0.015;
    shoot_parameters_trunk.phytomer_parameters.internode.radial_subdivisions = 20;
    shoot_parameters_trunk.max_nodes = 20;
    shoot_parameters_trunk.girth_area_factor = 3.f;
    shoot_parameters_trunk.vegetative_bud_break_probability_min = 0;
    shoot_parameters_trunk.vegetative_bud_break_time = 0;
    shoot_parameters_trunk.tortuosity = 1;
    shoot_parameters_trunk.internode_length_max = 0.05;
    shoot_parameters_trunk.internode_length_decay_rate = 0;
    shoot_parameters_trunk.defineChildShootTypes({"scaffold"}, {1});
 
    // Proleptic shoots
    ShootParameters shoot_parameters_proleptic(context_ptr->getRandomGenerator());
    shoot_parameters_proleptic.phytomer_parameters = phytomer_parameters_olive;
    //    shoot_parameters_proleptic.phytomer_parameters.phytomer_creation_function = OlivePhytomerCreationFunction;
    shoot_parameters_proleptic.phytomer_parameters.phytomer_callback_function = OlivePhytomerCallbackFunction;
    shoot_parameters_proleptic.max_nodes.uniformDistribution(16, 24);
    shoot_parameters_proleptic.max_nodes_per_season.uniformDistribution(8, 12);
    shoot_parameters_proleptic.phyllochron_min = 2.0;
    shoot_parameters_proleptic.elongation_rate_max = 0.25;
    shoot_parameters_proleptic.girth_area_factor = 5.f;
    shoot_parameters_proleptic.vegetative_bud_break_probability_min = 0.025;
    shoot_parameters_proleptic.vegetative_bud_break_probability_decay_rate = 1.0;
    shoot_parameters_proleptic.vegetative_bud_break_time = 30;
    shoot_parameters_proleptic.gravitropic_curvature.uniformDistribution(550, 650);
    shoot_parameters_proleptic.tortuosity = 5;
    shoot_parameters_proleptic.insertion_angle_tip.uniformDistribution(35, 40);
    shoot_parameters_proleptic.insertion_angle_decay_rate = 2;
    shoot_parameters_proleptic.internode_length_max = 0.05;
    shoot_parameters_proleptic.internode_length_min = 0.03;
    shoot_parameters_proleptic.internode_length_decay_rate = 0.004;
    shoot_parameters_proleptic.fruit_set_probability = 0.25;
    shoot_parameters_proleptic.flower_bud_break_probability = 0.25;
    shoot_parameters_proleptic.max_terminal_floral_buds = 4;
    shoot_parameters_proleptic.flowers_require_dormancy = true;
    shoot_parameters_proleptic.growth_requires_dormancy = true;
    shoot_parameters_proleptic.determinate_shoot_growth = false;
    shoot_parameters_proleptic.defineChildShootTypes({"proleptic"}, {1.0});
 
    // Main scaffolds
    ShootParameters shoot_parameters_scaffold = shoot_parameters_proleptic;
    shoot_parameters_scaffold.phytomer_parameters.internode.radial_subdivisions = 10;
    shoot_parameters_scaffold.max_nodes = 30;
    shoot_parameters_scaffold.max_nodes_per_season = 10;
    shoot_parameters_scaffold.gravitropic_curvature = 700;
    shoot_parameters_scaffold.internode_length_max = 0.04;
    shoot_parameters_scaffold.tortuosity = 3;
    shoot_parameters_scaffold.defineChildShootTypes({"proleptic"}, {1.0});
 
    defineShootType("trunk", shoot_parameters_trunk);
    defineShootType("scaffold", shoot_parameters_scaffold);
    defineShootType("proleptic", shoot_parameters_proleptic);
}
 
uint PlantArchitecture::buildOliveTree(const helios::vec3 &base_position) {
 
    if (shoot_types.empty()) {
        // automatically initialize olive tree shoots
        initializeOliveTreeShoots();
    }
 
    uint plantID = addPlantInstance(base_position, 0);
 
    uint uID_trunk = addBaseStemShoot(plantID, 19, make_AxisRotation(context_ptr->randu(0.f, 0.025f * M_PI), context_ptr->randu(0.f, 2.f * M_PI), context_ptr->randu(0.f, 2.f * M_PI)),
                                      shoot_types.at("trunk").phytomer_parameters.internode.radius_initial.val(), 0.01, 1.f, 1.f, 0, "trunk");
    appendPhytomerToShoot(plantID, uID_trunk, shoot_types.at("trunk").phytomer_parameters, 0, 0.01, 1, 1);
 
    plant_instances.at(plantID).shoot_tree.at(uID_trunk)->meristem_is_alive = false;
 
    auto phytomers = plant_instances.at(plantID).shoot_tree.at(uID_trunk)->phytomers;
    for (const auto &phytomer: phytomers) {
        phytomer->removeLeaf();
        phytomer->setVegetativeBudState(BUD_DEAD);
        phytomer->setFloralBudState(BUD_DEAD);
    }
 
    uint Nscaffolds = 4; // context_ptr->randu(4,5);
 
    for (int i = 0; i < Nscaffolds; i++) {
        float pitch = context_ptr->randu(deg2rad(30), deg2rad(35));
        uint uID_shoot = addChildShoot(plantID, uID_trunk, getShootNodeCount(plantID, uID_trunk) - i - 1, context_ptr->randu(5, 7), make_AxisRotation(pitch, (float(i) + context_ptr->randu(-0.2f, 0.2f)) / float(Nscaffolds) * 2 * M_PI, 0), 0.007,
                                       shoot_types.at("scaffold").internode_length_max.val(), 1.f, 1.f, 0.5, "scaffold", 0);
    }
 
    makePlantDormant(plantID);
 
    setPlantPhenologicalThresholds(plantID, 165, -1, 3, 7, 20, 200, 600, true);
    plant_instances.at(plantID).max_age = 1825;
 
    return plantID;
}
 
void PlantArchitecture::initializePistachioTreeShoots() {
 
    // ---- Leaf Prototype ---- //
 
    LeafPrototype leaf_prototype(context_ptr->getRandomGenerator());
    leaf_prototype.leaf_texture_file[0] = "PistachioLeaf.png";
    leaf_prototype.leaf_aspect_ratio = 0.6f;
    leaf_prototype.midrib_fold_fraction = 0.;
    leaf_prototype.longitudinal_curvature.uniformDistribution(-0.4, 0.4);
    leaf_prototype.lateral_curvature = 0.;
    leaf_prototype.wave_period = 0.3f;
    leaf_prototype.wave_amplitude = 0.1f;
    leaf_prototype.subdivisions = 3;
    leaf_prototype.unique_prototypes = 5;
 
    // ---- Phytomer Parameters ---- //
 
    PhytomerParameters phytomer_parameters_pistachio(context_ptr->getRandomGenerator());
 
    phytomer_parameters_pistachio.internode.pitch = 0;
    phytomer_parameters_pistachio.internode.phyllotactic_angle.uniformDistribution(160, 200);
    phytomer_parameters_pistachio.internode.radius_initial = 0.002;
    phytomer_parameters_pistachio.internode.length_segments = 1;
    phytomer_parameters_pistachio.internode.image_texture = "OliveBark.jpg";
    phytomer_parameters_pistachio.internode.max_floral_buds_per_petiole = 3;
 
    phytomer_parameters_pistachio.petiole.petioles_per_internode = 1;
    phytomer_parameters_pistachio.petiole.pitch.uniformDistribution(-60, -45);
    phytomer_parameters_pistachio.petiole.taper = 0.1;
    phytomer_parameters_pistachio.petiole.curvature.uniformDistribution(-800, 800);
    phytomer_parameters_pistachio.petiole.length = 0.075;
    phytomer_parameters_pistachio.petiole.radius = 0.001;
    phytomer_parameters_pistachio.petiole.length_segments = 1;
    phytomer_parameters_pistachio.petiole.radial_subdivisions = 3;
    phytomer_parameters_pistachio.petiole.color = make_RGBcolor(0.6, 0.6, 0.4);
 
    phytomer_parameters_pistachio.leaf.leaves_per_petiole = 3;
    phytomer_parameters_pistachio.leaf.prototype_scale = 0.08;
    phytomer_parameters_pistachio.leaf.leaflet_offset = 0.3;
    phytomer_parameters_pistachio.leaf.leaflet_scale = 0.75;
    phytomer_parameters_pistachio.leaf.pitch.uniformDistribution(-20, 20);
    phytomer_parameters_pistachio.leaf.roll.uniformDistribution(-20, 20);
    phytomer_parameters_pistachio.leaf.prototype = leaf_prototype;
 
    phytomer_parameters_pistachio.peduncle.length = 0.1;
    phytomer_parameters_pistachio.peduncle.radius = 0.001;
    phytomer_parameters_pistachio.peduncle.pitch = 60;
    phytomer_parameters_pistachio.peduncle.roll = 0;
    phytomer_parameters_pistachio.peduncle.length_segments = 1;
    phytomer_parameters_pistachio.peduncle.curvature.uniformDistribution(500, 900);
    phytomer_parameters_pistachio.peduncle.color = make_RGBcolor(0.7, 0.72, 0.7);
 
    phytomer_parameters_pistachio.inflorescence.flowers_per_peduncle = 16;
    phytomer_parameters_pistachio.inflorescence.flower_offset = 0.08;
    phytomer_parameters_pistachio.inflorescence.pitch.uniformDistribution(50, 70);
    phytomer_parameters_pistachio.inflorescence.roll.uniformDistribution(0, 360);
    phytomer_parameters_pistachio.inflorescence.flower_prototype_scale = 0.025;
    // phytomer_parameters_pistachio.inflorescence.flower_prototype_function = PistachioFlowerPrototype;
    phytomer_parameters_pistachio.inflorescence.fruit_prototype_scale = 0.025;
    phytomer_parameters_pistachio.inflorescence.fruit_prototype_function = PistachioFruitPrototype;
 
    // ---- Shoot Parameters ---- //
 
    // Trunk
    ShootParameters shoot_parameters_trunk(context_ptr->getRandomGenerator());
    shoot_parameters_trunk.phytomer_parameters = phytomer_parameters_pistachio;
    shoot_parameters_trunk.phytomer_parameters.internode.phyllotactic_angle = 180;
    shoot_parameters_trunk.phytomer_parameters.internode.radius_initial = 0.015;
    shoot_parameters_trunk.phytomer_parameters.internode.radial_subdivisions = 20;
    shoot_parameters_trunk.max_nodes = 20;
    shoot_parameters_trunk.girth_area_factor = 5.f;
    shoot_parameters_trunk.vegetative_bud_break_probability_min = 0;
    shoot_parameters_trunk.vegetative_bud_break_time = 0;
    shoot_parameters_trunk.tortuosity = 0.75;
    shoot_parameters_trunk.internode_length_max = 0.05;
    shoot_parameters_trunk.internode_length_decay_rate = 0;
    shoot_parameters_trunk.defineChildShootTypes({"proleptic"}, {1});
 
    // Proleptic shoots
    ShootParameters shoot_parameters_proleptic(context_ptr->getRandomGenerator());
    shoot_parameters_proleptic.phytomer_parameters = phytomer_parameters_pistachio;
    shoot_parameters_proleptic.phytomer_parameters.phytomer_creation_function = PistachioPhytomerCreationFunction;
    shoot_parameters_proleptic.phytomer_parameters.phytomer_callback_function = PistachioPhytomerCallbackFunction;
    shoot_parameters_proleptic.phytomer_parameters.internode.pitch.uniformDistribution(-15, 15);
    shoot_parameters_proleptic.max_nodes.uniformDistribution(16, 24);
    shoot_parameters_proleptic.max_nodes_per_season.uniformDistribution(8, 10);
    shoot_parameters_proleptic.phyllochron_min = 2.0;
    shoot_parameters_proleptic.elongation_rate_max = 0.25;
    shoot_parameters_proleptic.girth_area_factor = 7.f;
    shoot_parameters_proleptic.vegetative_bud_break_probability_min = 0.1;
    shoot_parameters_proleptic.vegetative_bud_break_probability_decay_rate = 0.7;
    shoot_parameters_proleptic.vegetative_bud_break_time = 0;
    shoot_parameters_proleptic.gravitropic_curvature = 350;
    shoot_parameters_proleptic.tortuosity = 2;
    shoot_parameters_proleptic.insertion_angle_tip.uniformDistribution(45, 55);
    shoot_parameters_proleptic.insertion_angle_decay_rate = 10;
    shoot_parameters_proleptic.internode_length_max = 0.06;
    shoot_parameters_proleptic.internode_length_min = 0.02;
    shoot_parameters_proleptic.internode_length_decay_rate = 0.06;
    shoot_parameters_proleptic.fruit_set_probability = 0.2;
    shoot_parameters_proleptic.flower_bud_break_probability = 0.35;
    shoot_parameters_proleptic.max_terminal_floral_buds = 2;
    shoot_parameters_proleptic.flowers_require_dormancy = true;
    shoot_parameters_proleptic.growth_requires_dormancy = true;
    shoot_parameters_proleptic.determinate_shoot_growth = false;
 
    defineShootType("trunk", shoot_parameters_trunk);
    defineShootType("proleptic", shoot_parameters_proleptic);
}
 
uint PlantArchitecture::buildPistachioTree(const helios::vec3 &base_position) {
 
    if (shoot_types.empty()) {
        // automatically initialize pistachio tree shoots
        initializePistachioTreeShoots();
    }
 
    // Get training system parameters (with defaults matching original hard-coded values)
    auto trunk_height = getParameterValue(current_build_parameters, "trunk_height", 1.0f, 0.1f, 3.f, "total trunk height in meters");
    auto num_scaffolds = uint(getParameterValue(current_build_parameters, "num_scaffolds", 4.f, 2.f, 8.f, "number of scaffold branches"));
    auto scaffold_angle = getParameterValue(current_build_parameters, "scaffold_angle", 50.f, 20.f, 70.f, "scaffold branch angle in degrees");
 
    // Calculate trunk nodes based on desired height and internode length
    float trunk_internode_length = 0.05f; // Default internode length for pistachio
    uint trunk_nodes = uint(trunk_height / trunk_internode_length);
    if (trunk_nodes < 1)
        trunk_nodes = 1;
 
    // Fixed training parameters (not user-customizable)
    float scaffold_radius = 0.007f;
    float scaffold_length = 0.03f;
    uint scaffold_nodes = 5;
 
    uint plantID = addPlantInstance(base_position, 0);
 
    uint uID_trunk = addBaseStemShoot(plantID, trunk_nodes, make_AxisRotation(context_ptr->randu(0.f, 0.05f * M_PI), context_ptr->randu(0.f, 2.f * M_PI), context_ptr->randu(0.f, 2.f * M_PI)),
                                      shoot_types.at("trunk").phytomer_parameters.internode.radius_initial.val(), trunk_internode_length, 1.f, 1.f, 0, "trunk");
    appendPhytomerToShoot(plantID, uID_trunk, shoot_types.at("trunk").phytomer_parameters, 0, 0.01, 1, 1);
 
    plant_instances.at(plantID).shoot_tree.at(uID_trunk)->meristem_is_alive = false;
 
    auto phytomers = plant_instances.at(plantID).shoot_tree.at(uID_trunk)->phytomers;
    for (const auto &phytomer: phytomers) {
        phytomer->removeLeaf();
        phytomer->setVegetativeBudState(BUD_DEAD);
        phytomer->setFloralBudState(BUD_DEAD);
    }
 
    float pitch = deg2rad(scaffold_angle);
    // Four-scaffold training system in cardinal directions
    if (num_scaffolds >= 1) {
        addChildShoot(plantID, uID_trunk, getShootNodeCount(plantID, uID_trunk) - 1, scaffold_nodes, make_AxisRotation(pitch + context_ptr->randu(-0.15f, 0.15f), 0, 0.5 * M_PI + context_ptr->randu(-0.2f, 0.2f)), scaffold_radius, scaffold_length, 1.f,
                      1.f, 0.5, "proleptic", 0);
    }
    if (num_scaffolds >= 2) {
        addChildShoot(plantID, uID_trunk, getShootNodeCount(plantID, uID_trunk) - 1, scaffold_nodes, make_AxisRotation(pitch + context_ptr->randu(-0.15f, 0.15f), M_PI, 0.5 * M_PI + context_ptr->randu(-0.2f, 0.2f)), scaffold_radius, scaffold_length,
                      1.f, 1.f, 0.5, "proleptic", 0);
    }
    if (num_scaffolds >= 3) {
        addChildShoot(plantID, uID_trunk, getShootNodeCount(plantID, uID_trunk) - 2, scaffold_nodes, make_AxisRotation(pitch + context_ptr->randu(-0.15f, 0.15f), 0.5 * M_PI, 0.5 * M_PI + context_ptr->randu(-0.2f, 0.2f)), scaffold_radius,
                      scaffold_length, 1.f, 1.f, 0.5, "proleptic", 0);
    }
    if (num_scaffolds >= 4) {
        addChildShoot(plantID, uID_trunk, getShootNodeCount(plantID, uID_trunk) - 2, scaffold_nodes, make_AxisRotation(pitch + context_ptr->randu(-0.15f, 0.15f), 1.5 * M_PI, 0.5 * M_PI + context_ptr->randu(-0.2f, 0.2f)), scaffold_radius,
                      scaffold_length, 1.f, 1.f, 0.5, "proleptic", 0);
    }
 
 
    makePlantDormant(plantID);
 
    setPlantPhenologicalThresholds(plantID, 165, -1, -1, 7, 20, 200, false);
    plant_instances.at(plantID).max_age = 1460;
 
    return plantID;
}
 
void PlantArchitecture::initializePuncturevineShoots() {
 
    // ---- Leaf Prototype ---- //
 
    LeafPrototype leaf_prototype(context_ptr->getRandomGenerator());
    leaf_prototype.leaf_texture_file[0] = "PuncturevineLeaf.png";
    leaf_prototype.leaf_aspect_ratio = 0.4f;
    leaf_prototype.midrib_fold_fraction = 0.2f;
    leaf_prototype.longitudinal_curvature = -0.1f;
    leaf_prototype.lateral_curvature = 0.4f;
    leaf_prototype.subdivisions = 1;
    leaf_prototype.unique_prototypes = 1;
 
    // ---- Phytomer Parameters ---- //
 
    PhytomerParameters phytomer_parameters_puncturevine(context_ptr->getRandomGenerator());
 
    phytomer_parameters_puncturevine.internode.pitch.uniformDistribution(0, 15);
    phytomer_parameters_puncturevine.internode.phyllotactic_angle = 180.f;
    phytomer_parameters_puncturevine.internode.radius_initial = 0.001;
    phytomer_parameters_puncturevine.internode.color = make_RGBcolor(0.28, 0.18, 0.13);
    phytomer_parameters_puncturevine.internode.length_segments = 1;
 
    phytomer_parameters_puncturevine.petiole.petioles_per_internode = 1;
    phytomer_parameters_puncturevine.petiole.pitch.uniformDistribution(60, 80);
    phytomer_parameters_puncturevine.petiole.radius = 0.0005;
    phytomer_parameters_puncturevine.petiole.length = 0.03;
    phytomer_parameters_puncturevine.petiole.taper = 0;
    phytomer_parameters_puncturevine.petiole.curvature = 0;
    phytomer_parameters_puncturevine.petiole.color = phytomer_parameters_puncturevine.internode.color;
    phytomer_parameters_puncturevine.petiole.length_segments = 1;
 
    phytomer_parameters_puncturevine.leaf.leaves_per_petiole = 11;
    phytomer_parameters_puncturevine.leaf.pitch.uniformDistribution(0, 40);
    phytomer_parameters_puncturevine.leaf.yaw = 30;
    phytomer_parameters_puncturevine.leaf.roll.uniformDistribution(-5, 5);
    phytomer_parameters_puncturevine.leaf.prototype_scale = 0.012;
    phytomer_parameters_puncturevine.leaf.leaflet_offset = 0.18;
    phytomer_parameters_puncturevine.leaf.leaflet_scale = 1;
    phytomer_parameters_puncturevine.leaf.prototype = leaf_prototype;
 
    phytomer_parameters_puncturevine.peduncle.length = 0.001;
    phytomer_parameters_puncturevine.peduncle.color = phytomer_parameters_puncturevine.internode.color;
 
    phytomer_parameters_puncturevine.inflorescence.flowers_per_peduncle = 1;
    phytomer_parameters_puncturevine.inflorescence.pitch = -90.f;
    phytomer_parameters_puncturevine.inflorescence.flower_prototype_function = PuncturevineFlowerPrototype;
    phytomer_parameters_puncturevine.inflorescence.flower_prototype_scale = 0.01;
 
    // ---- Shoot Parameters ---- //
 
    ShootParameters shoot_parameters_primary(context_ptr->getRandomGenerator());
    shoot_parameters_primary.phytomer_parameters = phytomer_parameters_puncturevine;
    shoot_parameters_primary.vegetative_bud_break_probability_min = 0.1;
    shoot_parameters_primary.vegetative_bud_break_probability_decay_rate = 1.f;
    shoot_parameters_primary.vegetative_bud_break_time = 10;
    shoot_parameters_primary.base_roll = 90;
    shoot_parameters_primary.phyllochron_min = 1;
    shoot_parameters_primary.elongation_rate_max = 0.2;
    shoot_parameters_primary.girth_area_factor = 0.f;
    shoot_parameters_primary.internode_length_max = 0.02;
    shoot_parameters_primary.internode_length_decay_rate = 0;
    shoot_parameters_primary.insertion_angle_tip.uniformDistribution(75, 85);
    shoot_parameters_primary.insertion_angle_decay_rate = 0;
    shoot_parameters_primary.flowers_require_dormancy = false;
    shoot_parameters_primary.growth_requires_dormancy = false;
    shoot_parameters_primary.flower_bud_break_probability = 0.2;
    shoot_parameters_primary.determinate_shoot_growth = false;
    shoot_parameters_primary.max_nodes = 15;
    shoot_parameters_primary.gravitropic_curvature = 25;
    shoot_parameters_primary.tortuosity = 0;
    shoot_parameters_primary.defineChildShootTypes({"secondary_puncturevine"}, {1.f});
 
    ShootParameters shoot_parameters_base = shoot_parameters_primary;
    shoot_parameters_base.phytomer_parameters = phytomer_parameters_puncturevine;
    shoot_parameters_base.phytomer_parameters.internode.phyllotactic_angle.uniformDistribution(137.5 - 10, 137.5 + 10);
    shoot_parameters_base.phytomer_parameters.petiole.petioles_per_internode = 0;
    shoot_parameters_base.phytomer_parameters.internode.pitch = 0;
    shoot_parameters_base.phytomer_parameters.petiole.pitch = 0;
    shoot_parameters_base.vegetative_bud_break_probability_min = 1;
    shoot_parameters_base.vegetative_bud_break_time = 2;
    shoot_parameters_base.phyllochron_min = 2;
    shoot_parameters_base.elongation_rate_max = 0.15;
    shoot_parameters_base.gravitropic_curvature = 0;
    shoot_parameters_base.internode_length_max = 0.01;
    shoot_parameters_base.internode_length_decay_rate = 0;
    shoot_parameters_base.insertion_angle_tip = 90;
    shoot_parameters_base.insertion_angle_decay_rate = 0;
    shoot_parameters_base.flowers_require_dormancy = false;
    shoot_parameters_base.growth_requires_dormancy = false;
    shoot_parameters_base.flower_bud_break_probability = 0.0;
    shoot_parameters_base.max_nodes.uniformDistribution(3, 5);
    shoot_parameters_base.defineChildShootTypes({"primary_puncturevine"}, {1.f});
 
    ShootParameters shoot_parameters_children = shoot_parameters_primary;
    shoot_parameters_children.base_roll = 0;
 
    defineShootType("base_puncturevine", shoot_parameters_base);
    defineShootType("primary_puncturevine", shoot_parameters_primary);
    defineShootType("secondary_puncturevine", shoot_parameters_children);
}
 
uint PlantArchitecture::buildPuncturevinePlant(const helios::vec3 &base_position) {
 
    if (shoot_types.empty()) {
        // automatically initialize puncturevine plant shoots
        initializePuncturevineShoots();
    }
 
    uint plantID = addPlantInstance(base_position, 0);
 
    uint uID_stem = addBaseStemShoot(plantID, 3, make_AxisRotation(0, 0.f, 0.f), 0.001, 0.001, 1, 1, 0, "base_puncturevine");
 
    breakPlantDormancy(plantID);
 
    plant_instances.at(plantID).max_age = 45;
 
    setPlantPhenologicalThresholds(plantID, 0, -1, 14, -1, -1, 1000, false);
 
    return plantID;
}
 
void PlantArchitecture::initializeEasternRedbudShoots() {
 
    // ---- Leaf Prototype ---- //
 
    LeafPrototype leaf_prototype(context_ptr->getRandomGenerator());
    leaf_prototype.leaf_texture_file[0] = "RedbudLeaf.png";
    leaf_prototype.leaf_aspect_ratio = 1.f;
    leaf_prototype.midrib_fold_fraction = 0.2f;
    leaf_prototype.longitudinal_curvature = -0.15f;
    leaf_prototype.lateral_curvature = -0.1f;
    leaf_prototype.wave_period = 0.3f;
    leaf_prototype.wave_amplitude = 0.025f;
    leaf_prototype.subdivisions = 5;
    leaf_prototype.unique_prototypes = 5;
    leaf_prototype.leaf_offset = make_vec3(-0.3, 0, 0);
 
    // ---- Phytomer Parameters ---- //
 
    PhytomerParameters phytomer_parameters_redbud(context_ptr->getRandomGenerator());
 
    phytomer_parameters_redbud.internode.pitch = 15;
    phytomer_parameters_redbud.internode.phyllotactic_angle.uniformDistribution(170, 190);
    phytomer_parameters_redbud.internode.radius_initial = 0.0015;
    phytomer_parameters_redbud.internode.image_texture = "WesternRedbudBark.jpg";
    phytomer_parameters_redbud.internode.color.scale(0.3);
    phytomer_parameters_redbud.internode.length_segments = 1;
    phytomer_parameters_redbud.internode.max_floral_buds_per_petiole = 5;
 
    phytomer_parameters_redbud.petiole.petioles_per_internode = 1;
    phytomer_parameters_redbud.petiole.color = make_RGBcolor(0.65, 0.52, 0.39);
    phytomer_parameters_redbud.petiole.pitch.uniformDistribution(20, 40);
    phytomer_parameters_redbud.petiole.radius = 0.002;
    phytomer_parameters_redbud.petiole.length = 0.075;
    phytomer_parameters_redbud.petiole.taper = 0;
    phytomer_parameters_redbud.petiole.curvature = 0;
    phytomer_parameters_redbud.petiole.length_segments = 1;
 
    phytomer_parameters_redbud.leaf.leaves_per_petiole = 1;
    phytomer_parameters_redbud.leaf.pitch.uniformDistribution(-110, -80);
    phytomer_parameters_redbud.leaf.yaw = 0;
    phytomer_parameters_redbud.leaf.roll.uniformDistribution(-5, 5);
    phytomer_parameters_redbud.leaf.prototype_scale = 0.1;
    phytomer_parameters_redbud.leaf.prototype = leaf_prototype;
 
    phytomer_parameters_redbud.peduncle.length = 0.02;
    phytomer_parameters_redbud.peduncle.pitch.uniformDistribution(50, 90);
    phytomer_parameters_redbud.peduncle.color = make_RGBcolor(0.32, 0.05, 0.13);
 
    phytomer_parameters_redbud.inflorescence.flowers_per_peduncle = 1;
    phytomer_parameters_redbud.inflorescence.pitch = 0;
    phytomer_parameters_redbud.inflorescence.flower_prototype_function = RedbudFlowerPrototype;
    phytomer_parameters_redbud.inflorescence.flower_prototype_scale = 0.04;
    phytomer_parameters_redbud.inflorescence.fruit_prototype_function = RedbudFruitPrototype;
    phytomer_parameters_redbud.inflorescence.fruit_prototype_scale = 0.1;
    phytomer_parameters_redbud.inflorescence.fruit_gravity_factor_fraction = 0.7;
 
    phytomer_parameters_redbud.phytomer_creation_function = RedbudPhytomerCreationFunction;
    phytomer_parameters_redbud.phytomer_callback_function = RedbudPhytomerCallbackFunction;
 
    // ---- Shoot Parameters ---- //
 
    ShootParameters shoot_parameters_main(context_ptr->getRandomGenerator());
    shoot_parameters_main.phytomer_parameters = phytomer_parameters_redbud;
    shoot_parameters_main.vegetative_bud_break_probability_min = 1.0;
    shoot_parameters_main.vegetative_bud_break_time = 2;
    shoot_parameters_main.phyllochron_min = 2;
    shoot_parameters_main.elongation_rate_max = 0.1;
    shoot_parameters_main.girth_area_factor = 4.f;
    shoot_parameters_main.gravitropic_curvature = 300;
    shoot_parameters_main.tortuosity = 5;
    shoot_parameters_main.internode_length_max = 0.04;
    shoot_parameters_main.internode_length_decay_rate = 0.005;
    shoot_parameters_main.internode_length_min = 0.01;
    shoot_parameters_main.insertion_angle_tip = 75;
    shoot_parameters_main.insertion_angle_decay_rate = 10;
    shoot_parameters_main.flowers_require_dormancy = true;
    shoot_parameters_main.growth_requires_dormancy = true;
    shoot_parameters_main.determinate_shoot_growth = false;
    shoot_parameters_main.max_terminal_floral_buds = 0;
    shoot_parameters_main.flower_bud_break_probability = 0.8;
    shoot_parameters_main.fruit_set_probability = 0.3;
    shoot_parameters_main.max_nodes = 25;
    shoot_parameters_main.max_nodes_per_season = 10;
    shoot_parameters_main.base_roll = 90;
 
    ShootParameters shoot_parameters_trunk = shoot_parameters_main;
    shoot_parameters_trunk.phytomer_parameters.internode.pitch = 0;
    shoot_parameters_trunk.phytomer_parameters.internode.radial_subdivisions = 15;
    shoot_parameters_trunk.phytomer_parameters.internode.max_floral_buds_per_petiole = 0;
    shoot_parameters_trunk.insertion_angle_tip = 60;
    shoot_parameters_trunk.max_nodes = 75;
    shoot_parameters_trunk.max_nodes_per_season = 10;
    shoot_parameters_trunk.tortuosity = 1.5;
    shoot_parameters_trunk.defineChildShootTypes({"eastern_redbud_shoot"}, {1.f});
 
    defineShootType("eastern_redbud_trunk", shoot_parameters_trunk);
    defineShootType("eastern_redbud_shoot", shoot_parameters_main);
}
 
uint PlantArchitecture::buildEasternRedbudPlant(const helios::vec3 &base_position) {
 
    if (shoot_types.empty()) {
        // automatically initialize redbud plant shoots
        initializeEasternRedbudShoots();
    }
 
    uint plantID = addPlantInstance(base_position, 0);
 
    uint uID_stem = addBaseStemShoot(plantID, 16, make_AxisRotation(context_ptr->randu(0, 0.1 * M_PI), context_ptr->randu(0, 2 * M_PI), context_ptr->randu(0, 2 * M_PI)), 0.0075, 0.05, 1, 1, 0.4, "eastern_redbud_trunk");
 
    makePlantDormant(plantID);
    breakPlantDormancy(plantID);
 
    // leave four vegetative buds on the trunk and remove the rest
    for (auto &phytomer: this->plant_instances.at(plantID).shoot_tree.at(uID_stem)->phytomers) {
        if (phytomer->shoot_index.x < 12) {
            for (auto &petiole: phytomer->axillary_vegetative_buds) {
                for (auto &vbud: petiole) {
                    phytomer->setVegetativeBudState(BUD_DEAD, vbud);
                }
            }
        }
    }
 
    setPlantPhenologicalThresholds(plantID, 165, -1, 3, 7, 30, 200, false);
 
    plant_instances.at(plantID).max_age = 1460;
 
    return plantID;
}
 
void PlantArchitecture::initializeRiceShoots() {
 
    // ---- Leaf Prototype ---- //
 
    LeafPrototype leaf_prototype(context_ptr->getRandomGenerator());
    leaf_prototype.leaf_texture_file[0] = "SorghumLeaf.png";
    leaf_prototype.leaf_aspect_ratio = 0.06f;
    leaf_prototype.midrib_fold_fraction = 0.3f;
    leaf_prototype.longitudinal_curvature.uniformDistribution(-0.2, 0);
    leaf_prototype.lateral_curvature = -0.3;
    leaf_prototype.wave_period = 0.1f;
    leaf_prototype.wave_amplitude = 0.1f;
    leaf_prototype.subdivisions = 20;
    leaf_prototype.unique_prototypes = 10;
 
    // ---- Phytomer Parameters ---- //
 
    PhytomerParameters phytomer_parameters_rice(context_ptr->getRandomGenerator());
 
    phytomer_parameters_rice.internode.pitch = 0;
    phytomer_parameters_rice.internode.phyllotactic_angle.uniformDistribution(67, 77);
    phytomer_parameters_rice.internode.radius_initial = 0.001;
    phytomer_parameters_rice.internode.color = make_RGBcolor(0.27, 0.31, 0.16);
    phytomer_parameters_rice.internode.length_segments = 1;
    phytomer_parameters_rice.internode.radial_subdivisions = 6;
    phytomer_parameters_rice.internode.max_floral_buds_per_petiole = 0;
    phytomer_parameters_rice.internode.max_vegetative_buds_per_petiole = 0;
 
    phytomer_parameters_rice.petiole.petioles_per_internode = 1;
    phytomer_parameters_rice.petiole.pitch.uniformDistribution(-40, 0);
    phytomer_parameters_rice.petiole.radius = 0.0;
    phytomer_parameters_rice.petiole.length = 0.01;
    phytomer_parameters_rice.petiole.taper = 0;
    phytomer_parameters_rice.petiole.curvature = 0;
    phytomer_parameters_rice.petiole.length_segments = 1;
 
    phytomer_parameters_rice.leaf.leaves_per_petiole = 1;
    phytomer_parameters_rice.leaf.pitch = 0;
    phytomer_parameters_rice.leaf.yaw = 0;
    phytomer_parameters_rice.leaf.roll = 0;
    phytomer_parameters_rice.leaf.prototype_scale = 0.15;
    phytomer_parameters_rice.leaf.prototype = leaf_prototype;
 
    phytomer_parameters_rice.peduncle.pitch = 0;
    phytomer_parameters_rice.peduncle.length.uniformDistribution(0.14, 0.18);
    phytomer_parameters_rice.peduncle.radius = 0.0005;
    phytomer_parameters_rice.peduncle.color = phytomer_parameters_rice.internode.color;
    phytomer_parameters_rice.peduncle.curvature.uniformDistribution(-800, -50);
    phytomer_parameters_rice.peduncle.radial_subdivisions = 6;
    phytomer_parameters_rice.peduncle.length_segments = 8;
 
    phytomer_parameters_rice.inflorescence.flowers_per_peduncle = 60;
    phytomer_parameters_rice.inflorescence.pitch.uniformDistribution(20, 25);
    phytomer_parameters_rice.inflorescence.roll = 0;
    phytomer_parameters_rice.inflorescence.fruit_prototype_scale = 0.008;
    phytomer_parameters_rice.inflorescence.flower_offset = 0.012;
    phytomer_parameters_rice.inflorescence.fruit_prototype_function = RiceSpikePrototype;
 
    //    phytomer_parameters_rice.phytomer_creation_function = RicePhytomerCreationFunction;
 
    // ---- Shoot Parameters ---- //
 
    ShootParameters shoot_parameters_mainstem(context_ptr->getRandomGenerator());
    shoot_parameters_mainstem.phytomer_parameters = phytomer_parameters_rice;
    shoot_parameters_mainstem.vegetative_bud_break_probability_min = 0;
    shoot_parameters_mainstem.flower_bud_break_probability = 1;
    shoot_parameters_mainstem.phyllochron_min = 2;
    shoot_parameters_mainstem.elongation_rate_max = 0.1;
    shoot_parameters_mainstem.girth_area_factor = 5.f;
    shoot_parameters_mainstem.gravitropic_curvature.uniformDistribution(-1000, -400);
    shoot_parameters_mainstem.internode_length_max = 0.0075;
    shoot_parameters_mainstem.internode_length_decay_rate = 0;
    shoot_parameters_mainstem.flowers_require_dormancy = false;
    shoot_parameters_mainstem.growth_requires_dormancy = false;
    shoot_parameters_mainstem.determinate_shoot_growth = false;
    shoot_parameters_mainstem.fruit_set_probability = 1.0;
    shoot_parameters_mainstem.defineChildShootTypes({"mainstem"}, {1.0});
    shoot_parameters_mainstem.max_nodes = 30;
    shoot_parameters_mainstem.max_terminal_floral_buds = 5;
 
    defineShootType("mainstem", shoot_parameters_mainstem);
}
 
uint PlantArchitecture::buildRicePlant(const helios::vec3 &base_position) {
 
    if (shoot_types.empty()) {
        // automatically initialize rice plant shoots
        initializeRiceShoots();
    }
 
    uint plantID = addPlantInstance(base_position, 0);
 
    uint uID_stem = addBaseStemShoot(plantID, 1, make_AxisRotation(context_ptr->randu(0.f, 0.1f * M_PI), context_ptr->randu(0.f, 2.f * M_PI), context_ptr->randu(0.f, 2.f * M_PI)), 0.001, 0.0075, 0.01, 0.01, 0, "mainstem");
 
    breakPlantDormancy(plantID);
 
    setPlantPhenologicalThresholds(plantID, 0, -1, -1, 4, 10, 1000, false);
 
    plant_instances.at(plantID).max_age = 365;
 
    return plantID;
}
 
void PlantArchitecture::initializeButterLettuceShoots() {
 
    LeafPrototype leaf_prototype(context_ptr->getRandomGenerator());
    leaf_prototype.leaf_texture_file[0] = "RomaineLettuceLeaf.png";
    leaf_prototype.leaf_aspect_ratio = 0.85f;
    leaf_prototype.midrib_fold_fraction = 0.2f;
    leaf_prototype.longitudinal_curvature.uniformDistribution(-0.2, 0.05);
    leaf_prototype.lateral_curvature = -0.4f;
    leaf_prototype.wave_period.uniformDistribution(0.15, 0.25);
    leaf_prototype.wave_amplitude.uniformDistribution(0.05, 0.1);
    leaf_prototype.subdivisions = 30;
    leaf_prototype.unique_prototypes = 10;
 
    // ---- Phytomer Parameters ---- //
 
    PhytomerParameters phytomer_parameters(context_ptr->getRandomGenerator());
 
    phytomer_parameters.internode.pitch = 0;
    phytomer_parameters.internode.phyllotactic_angle = 137.5;
    phytomer_parameters.internode.radius_initial = 0.02;
    phytomer_parameters.internode.color = make_RGBcolor(0.402, 0.423, 0.413);
    phytomer_parameters.internode.length_segments = 1;
    phytomer_parameters.internode.radial_subdivisions = 10;
 
    phytomer_parameters.petiole.petioles_per_internode = 1;
    phytomer_parameters.petiole.pitch.uniformDistribution(0, 30);
    phytomer_parameters.petiole.radius = 0.001;
    phytomer_parameters.petiole.length = 0.001;
    phytomer_parameters.petiole.length_segments = 1;
    phytomer_parameters.petiole.radial_subdivisions = 3;
    phytomer_parameters.petiole.color = RGB::red;
 
    phytomer_parameters.leaf.leaves_per_petiole = 1;
    phytomer_parameters.leaf.pitch = 10;
    phytomer_parameters.leaf.yaw = 0;
    phytomer_parameters.leaf.roll = 0;
    phytomer_parameters.leaf.prototype_scale.uniformDistribution(0.15, 0.25);
    phytomer_parameters.leaf.prototype = leaf_prototype;
 
    phytomer_parameters.phytomer_creation_function = ButterLettucePhytomerCreationFunction;
 
    // ---- Shoot Parameters ---- //
 
    ShootParameters shoot_parameters_mainstem(context_ptr->getRandomGenerator());
    shoot_parameters_mainstem.phytomer_parameters = phytomer_parameters;
    shoot_parameters_mainstem.vegetative_bud_break_probability_min = 0;
    shoot_parameters_mainstem.phyllochron_min = 2;
    shoot_parameters_mainstem.elongation_rate_max = 0.15;
    shoot_parameters_mainstem.girth_area_factor = 0.f;
    shoot_parameters_mainstem.gravitropic_curvature = 10;
    shoot_parameters_mainstem.internode_length_max = 0.001;
    shoot_parameters_mainstem.internode_length_decay_rate = 0;
    shoot_parameters_mainstem.flowers_require_dormancy = false;
    shoot_parameters_mainstem.growth_requires_dormancy = false;
    shoot_parameters_mainstem.flower_bud_break_probability = 0.0;
    shoot_parameters_mainstem.max_nodes = 25;
 
    defineShootType("mainstem", shoot_parameters_mainstem);
}
 
uint PlantArchitecture::buildButterLettucePlant(const helios::vec3 &base_position) {
 
    if (shoot_types.empty()) {
        // automatically initialize lettuce plant shoots
        initializeButterLettuceShoots();
    }
 
    uint plantID = addPlantInstance(base_position, 0);
 
    uint uID_stem = addBaseStemShoot(plantID, 3, make_AxisRotation(context_ptr->randu(0.f, 0.03f * M_PI), 0.f, context_ptr->randu(0.f, 2.f * M_PI)), 0.005, 0.001, 1, 1, 0, "mainstem");
 
    breakPlantDormancy(plantID);
 
    setPlantPhenologicalThresholds(plantID, 0, -1, -1, -1, -1, 1000, false);
 
    plant_instances.at(plantID).max_age = 365;
 
    return plantID;
}
 
void PlantArchitecture::initializeSorghumShoots() {
 
    // ---- Leaf Prototype ---- //
 
    LeafPrototype leaf_prototype(context_ptr->getRandomGenerator());
    leaf_prototype.leaf_texture_file[0] = "SorghumLeaf.png";
    leaf_prototype.leaf_aspect_ratio = 0.2f;
    leaf_prototype.midrib_fold_fraction = 0.3f;
    leaf_prototype.longitudinal_curvature.uniformDistribution(-0.4, -0.2);
    leaf_prototype.lateral_curvature = -0.3f;
    leaf_prototype.petiole_roll = 0.04f;
    leaf_prototype.wave_period = 0.1f;
    leaf_prototype.wave_amplitude = 0.1f;
    leaf_prototype.leaf_buckle_length.uniformDistribution(0.4, 0.6);
    leaf_prototype.leaf_buckle_angle.uniformDistribution(45, 55);
    leaf_prototype.subdivisions = 50;
    leaf_prototype.unique_prototypes = 10;
 
    // ---- Phytomer Parameters ---- //
 
    PhytomerParameters phytomer_parameters_sorghum(context_ptr->getRandomGenerator());
 
    phytomer_parameters_sorghum.internode.pitch = 0;
    phytomer_parameters_sorghum.internode.phyllotactic_angle.uniformDistribution(170, 190);
    phytomer_parameters_sorghum.internode.radius_initial = 0.003;
    phytomer_parameters_sorghum.internode.color = make_RGBcolor(0.09, 0.13, 0.06);
    phytomer_parameters_sorghum.internode.length_segments = 2;
    phytomer_parameters_sorghum.internode.radial_subdivisions = 10;
    phytomer_parameters_sorghum.internode.max_floral_buds_per_petiole = 0;
    phytomer_parameters_sorghum.internode.max_vegetative_buds_per_petiole = 0;
 
    phytomer_parameters_sorghum.petiole.petioles_per_internode = 1;
    phytomer_parameters_sorghum.petiole.pitch.uniformDistribution(-40, -20);
    phytomer_parameters_sorghum.petiole.radius = 0.0;
    phytomer_parameters_sorghum.petiole.length = 0.05;
    phytomer_parameters_sorghum.petiole.taper = 0;
    phytomer_parameters_sorghum.petiole.curvature = 0;
    phytomer_parameters_sorghum.petiole.length_segments = 1;
 
    phytomer_parameters_sorghum.leaf.leaves_per_petiole = 1;
    phytomer_parameters_sorghum.leaf.pitch = 0;
    phytomer_parameters_sorghum.leaf.yaw = 0;
    phytomer_parameters_sorghum.leaf.roll = 0;
    phytomer_parameters_sorghum.leaf.prototype_scale = 0.6;
    phytomer_parameters_sorghum.leaf.prototype = leaf_prototype;
 
    phytomer_parameters_sorghum.peduncle.length = 0.3;
    phytomer_parameters_sorghum.peduncle.radius = 0.008;
    phytomer_parameters_sorghum.peduncle.color = phytomer_parameters_sorghum.internode.color;
    phytomer_parameters_sorghum.peduncle.radial_subdivisions = 10;
 
    phytomer_parameters_sorghum.inflorescence.flowers_per_peduncle = 1;
    phytomer_parameters_sorghum.inflorescence.pitch = 0;
    phytomer_parameters_sorghum.inflorescence.roll = 0;
    phytomer_parameters_sorghum.inflorescence.fruit_prototype_scale = 0.18;
    phytomer_parameters_sorghum.inflorescence.fruit_prototype_function = SorghumPaniclePrototype;
 
    phytomer_parameters_sorghum.phytomer_creation_function = SorghumPhytomerCreationFunction;
 
    // ---- Shoot Parameters ---- //
 
    ShootParameters shoot_parameters_mainstem(context_ptr->getRandomGenerator());
    shoot_parameters_mainstem.phytomer_parameters = phytomer_parameters_sorghum;
    shoot_parameters_mainstem.vegetative_bud_break_probability_min = 0;
    shoot_parameters_mainstem.flower_bud_break_probability = 1;
    shoot_parameters_mainstem.phyllochron_min = 2;
    shoot_parameters_mainstem.elongation_rate_max = 0.1;
    shoot_parameters_mainstem.girth_area_factor = 5.f;
    shoot_parameters_mainstem.gravitropic_curvature.uniformDistribution(-1000, -400);
    shoot_parameters_mainstem.internode_length_max = 0.26;
    shoot_parameters_mainstem.internode_length_decay_rate = 0;
    shoot_parameters_mainstem.flowers_require_dormancy = false;
    shoot_parameters_mainstem.growth_requires_dormancy = false;
    shoot_parameters_mainstem.determinate_shoot_growth = false;
    shoot_parameters_mainstem.flower_bud_break_probability = 1.0;
    shoot_parameters_mainstem.fruit_set_probability = 1.0;
    shoot_parameters_mainstem.defineChildShootTypes({"mainstem"}, {1.0});
    shoot_parameters_mainstem.max_nodes = 16;
    shoot_parameters_mainstem.max_terminal_floral_buds = 1;
 
    defineShootType("mainstem", shoot_parameters_mainstem);
}
 
uint PlantArchitecture::buildSorghumPlant(const helios::vec3 &base_position) {
 
    if (shoot_types.empty()) {
        // automatically initialize sorghum plant shoots
        initializeSorghumShoots();
    }
 
    uint plantID = addPlantInstance(base_position - make_vec3(0, 0, 0.025), 0);
 
    uint uID_stem = addBaseStemShoot(plantID, 1, make_AxisRotation(context_ptr->randu(0.f, 0.075f * M_PI), context_ptr->randu(0.f, 2.f * M_PI), context_ptr->randu(0.f, 2.f * M_PI)), 0.003, 0.06, 0.01, 0.01, 0, "mainstem");
 
    breakPlantDormancy(plantID);
 
    setPlantPhenologicalThresholds(plantID, 0, -1, -1, 4, 15, 1000, false);
 
    plant_instances.at(plantID).max_age = 365;
 
    return plantID;
}
 
void PlantArchitecture::initializeSoybeanShoots() {
 
    // ---- Leaf Prototype ---- //
 
    LeafPrototype leaf_prototype(context_ptr->getRandomGenerator());
    leaf_prototype.leaf_texture_file[0] = "SoybeanLeaf.png";
    leaf_prototype.leaf_aspect_ratio = 1.f;
    leaf_prototype.midrib_fold_fraction = 0.1f;
    leaf_prototype.longitudinal_curvature.uniformDistribution(0.1, 0.2);
    leaf_prototype.lateral_curvature = 0.45;
    leaf_prototype.subdivisions = 8;
    leaf_prototype.unique_prototypes = 5;
    leaf_prototype.build_petiolule = true;
 
    PhytomerParameters phytomer_parameters_trifoliate(context_ptr->getRandomGenerator());
 
    phytomer_parameters_trifoliate.internode.pitch = 20;
    phytomer_parameters_trifoliate.internode.phyllotactic_angle.uniformDistribution(145, 215);
    phytomer_parameters_trifoliate.internode.radius_initial = 0.002;
    phytomer_parameters_trifoliate.internode.max_floral_buds_per_petiole = 1;
    phytomer_parameters_trifoliate.internode.max_vegetative_buds_per_petiole = 1;
    phytomer_parameters_trifoliate.internode.color = make_RGBcolor(0.2, 0.25, 0.05);
    phytomer_parameters_trifoliate.internode.length_segments = 5;
 
    phytomer_parameters_trifoliate.petiole.petioles_per_internode = 1;
    phytomer_parameters_trifoliate.petiole.pitch.uniformDistribution(15, 40);
    phytomer_parameters_trifoliate.petiole.radius = 0.002;
    phytomer_parameters_trifoliate.petiole.length.uniformDistribution(0.12, 0.16);
    phytomer_parameters_trifoliate.petiole.taper = 0.25;
    phytomer_parameters_trifoliate.petiole.curvature.uniformDistribution(-250, 50);
    phytomer_parameters_trifoliate.petiole.color = phytomer_parameters_trifoliate.internode.color;
    phytomer_parameters_trifoliate.petiole.length_segments = 5;
    phytomer_parameters_trifoliate.petiole.radial_subdivisions = 6;
 
    phytomer_parameters_trifoliate.leaf.leaves_per_petiole = 3;
    phytomer_parameters_trifoliate.leaf.pitch.uniformDistribution(-30, 10);
    phytomer_parameters_trifoliate.leaf.yaw = 10;
    phytomer_parameters_trifoliate.leaf.roll.uniformDistribution(-25, 5);
    phytomer_parameters_trifoliate.leaf.leaflet_offset = 0.5;
    phytomer_parameters_trifoliate.leaf.leaflet_scale = 0.9;
    phytomer_parameters_trifoliate.leaf.prototype_scale.uniformDistribution(0.1, 0.14);
    phytomer_parameters_trifoliate.leaf.prototype = leaf_prototype;
 
    phytomer_parameters_trifoliate.peduncle.length = 0.01;
    phytomer_parameters_trifoliate.peduncle.radius = 0.0005;
    phytomer_parameters_trifoliate.peduncle.pitch.uniformDistribution(0, 40);
    phytomer_parameters_trifoliate.peduncle.roll = 90;
    phytomer_parameters_trifoliate.peduncle.curvature.uniformDistribution(-500, 500);
    phytomer_parameters_trifoliate.peduncle.color = phytomer_parameters_trifoliate.internode.color;
    phytomer_parameters_trifoliate.peduncle.length_segments = 1;
    phytomer_parameters_trifoliate.peduncle.radial_subdivisions = 6;
 
    phytomer_parameters_trifoliate.inflorescence.flowers_per_peduncle.uniformDistribution(1, 4);
    phytomer_parameters_trifoliate.inflorescence.flower_offset = 0.2;
    phytomer_parameters_trifoliate.inflorescence.pitch.uniformDistribution(50, 70);
    phytomer_parameters_trifoliate.inflorescence.roll.uniformDistribution(-20, 20);
    phytomer_parameters_trifoliate.inflorescence.flower_prototype_scale = 0.015;
    phytomer_parameters_trifoliate.inflorescence.flower_prototype_function = SoybeanFlowerPrototype;
    phytomer_parameters_trifoliate.inflorescence.fruit_prototype_scale.uniformDistribution(0.1, 0.12);
    phytomer_parameters_trifoliate.inflorescence.fruit_prototype_function = SoybeanFruitPrototype;
    phytomer_parameters_trifoliate.inflorescence.fruit_gravity_factor_fraction.uniformDistribution(0.8, 1.0);
 
    PhytomerParameters phytomer_parameters_unifoliate = phytomer_parameters_trifoliate;
    phytomer_parameters_unifoliate.internode.pitch = 0;
    phytomer_parameters_unifoliate.internode.max_vegetative_buds_per_petiole = 0;
    phytomer_parameters_unifoliate.internode.max_floral_buds_per_petiole = 0;
    phytomer_parameters_unifoliate.petiole.petioles_per_internode = 2;
    phytomer_parameters_unifoliate.petiole.length = 0.01;
    phytomer_parameters_unifoliate.petiole.radius = 0.001;
    phytomer_parameters_unifoliate.petiole.pitch.uniformDistribution(60, 80);
    phytomer_parameters_unifoliate.leaf.leaves_per_petiole = 1;
    phytomer_parameters_unifoliate.leaf.prototype_scale = 0.02;
    phytomer_parameters_unifoliate.leaf.pitch.uniformDistribution(-10, 10);
    phytomer_parameters_unifoliate.leaf.prototype = leaf_prototype;
 
    // ---- Shoot Parameters ---- //
 
    ShootParameters shoot_parameters_trifoliate(context_ptr->getRandomGenerator());
    shoot_parameters_trifoliate.phytomer_parameters = phytomer_parameters_trifoliate;
    shoot_parameters_trifoliate.phytomer_parameters.phytomer_creation_function = BeanPhytomerCreationFunction;
 
    shoot_parameters_trifoliate.max_nodes = 25;
    shoot_parameters_trifoliate.insertion_angle_tip.uniformDistribution(20, 30);
    //    shoot_parameters_trifoliate.child_insertion_angle_decay_rate = 0; (default)
    shoot_parameters_trifoliate.internode_length_max = 0.035;
    //    shoot_parameters_trifoliate.child_internode_length_min = 0.0; (default)
    //    shoot_parameters_trifoliate.child_internode_length_decay_rate = 0; (default)
    shoot_parameters_trifoliate.base_roll = 90;
    shoot_parameters_trifoliate.base_yaw.uniformDistribution(-20, 20);
    shoot_parameters_trifoliate.gravitropic_curvature = 400;
 
    shoot_parameters_trifoliate.phyllochron_min = 2;
    shoot_parameters_trifoliate.elongation_rate_max = 0.1;
    shoot_parameters_trifoliate.girth_area_factor = 2.f;
    shoot_parameters_trifoliate.vegetative_bud_break_time = 15;
    shoot_parameters_trifoliate.vegetative_bud_break_probability_min = 0.05;
    shoot_parameters_trifoliate.vegetative_bud_break_probability_decay_rate = 0.6;
    //    shoot_parameters_trifoliate.max_terminal_floral_buds = 0; (default)
    shoot_parameters_trifoliate.flower_bud_break_probability.uniformDistribution(0.8, 1.0);
    shoot_parameters_trifoliate.fruit_set_probability = 0.4;
    //    shoot_parameters_trifoliate.flowers_require_dormancy = false; (default)
    //    shoot_parameters_trifoliate.growth_requires_dormancy = false; (default)
    //    shoot_parameters_trifoliate.determinate_shoot_growth = true; (default)
 
    shoot_parameters_trifoliate.defineChildShootTypes({"trifoliate"}, {1.0});
 
 
    ShootParameters shoot_parameters_unifoliate = shoot_parameters_trifoliate;
    shoot_parameters_unifoliate.phytomer_parameters = phytomer_parameters_unifoliate;
    shoot_parameters_unifoliate.max_nodes = 1;
    shoot_parameters_unifoliate.flower_bud_break_probability = 0;
    shoot_parameters_unifoliate.insertion_angle_tip = 0;
    shoot_parameters_unifoliate.insertion_angle_decay_rate = 0;
    shoot_parameters_unifoliate.vegetative_bud_break_time = 8;
    shoot_parameters_unifoliate.defineChildShootTypes({"trifoliate"}, {1.0});
 
    defineShootType("unifoliate", shoot_parameters_unifoliate);
    defineShootType("trifoliate", shoot_parameters_trifoliate);
}
 
uint PlantArchitecture::buildSoybeanPlant(const helios::vec3 &base_position) {
 
    if (shoot_types.empty()) {
        // automatically initialize bean plant shoots
        initializeSoybeanShoots();
    }
 
    uint plantID = addPlantInstance(base_position, 0);
 
    AxisRotation base_rotation = make_AxisRotation(context_ptr->randu(0.f, 0.05f * M_PI), context_ptr->randu(0.f, 2.f * M_PI), context_ptr->randu(0.f, 2.f * M_PI));
    uint uID_unifoliate = addBaseStemShoot(plantID, 1, base_rotation, 0.0005, 0.04, 0.01, 0.01, 0, "unifoliate");
 
    appendShoot(plantID, uID_unifoliate, 1, make_AxisRotation(0, 0, 0.5f * M_PI), shoot_types.at("trifoliate").phytomer_parameters.internode.radius_initial.val(), shoot_types.at("trifoliate").internode_length_max.val(), 0.1, 0.1, 0, "trifoliate");
 
    breakPlantDormancy(plantID);
 
    setPlantPhenologicalThresholds(plantID, 0, 40, 5, 5, 30, 1000, false);
 
    plant_instances.at(plantID).max_age = 365;
 
    return plantID;
}
 
void PlantArchitecture::initializeStrawberryShoots() {
 
    // ---- Leaf Prototype ---- //
 
    LeafPrototype leaf_prototype(context_ptr->getRandomGenerator());
    leaf_prototype.leaf_texture_file[0] = "StrawberryLeaf.png";
    leaf_prototype.leaf_aspect_ratio = 1.f;
    leaf_prototype.midrib_fold_fraction = 0.2f;
    leaf_prototype.longitudinal_curvature = 0.15f;
    leaf_prototype.lateral_curvature = -0.35f;
    leaf_prototype.wave_period = 0.4f;
    leaf_prototype.wave_amplitude = 0.03f;
    leaf_prototype.subdivisions = 6;
    leaf_prototype.unique_prototypes = 10;
 
    // ---- Phytomer Parameters ---- //
 
    PhytomerParameters phytomer_parameters(context_ptr->getRandomGenerator());
 
    phytomer_parameters.internode.pitch = 10;
    phytomer_parameters.internode.phyllotactic_angle.uniformDistribution(80, 100);
    phytomer_parameters.internode.radius_initial = 0.001;
    phytomer_parameters.internode.color = make_RGBcolor(0.15, 0.2, 0.1);
    phytomer_parameters.internode.length_segments = 1;
 
    phytomer_parameters.petiole.petioles_per_internode = 1;
    phytomer_parameters.petiole.pitch.uniformDistribution(10, 45);
    phytomer_parameters.petiole.radius = 0.0025;
    phytomer_parameters.petiole.length.uniformDistribution(0.15, 0.35);
    phytomer_parameters.petiole.taper = 0.5;
    phytomer_parameters.petiole.curvature.uniformDistribution(-150, -50);
    phytomer_parameters.petiole.color = make_RGBcolor(0.18, 0.23, 0.1);
    phytomer_parameters.petiole.length_segments = 5;
 
    phytomer_parameters.leaf.leaves_per_petiole = 3;
    phytomer_parameters.leaf.pitch.uniformDistribution(-35, 0);
    phytomer_parameters.leaf.yaw = -30;
    phytomer_parameters.leaf.roll = -30;
    phytomer_parameters.leaf.leaflet_offset = 0.01;
    phytomer_parameters.leaf.leaflet_scale = 1.0;
    phytomer_parameters.leaf.prototype_scale = 0.12;
    phytomer_parameters.leaf.prototype = leaf_prototype;
 
    phytomer_parameters.peduncle.length.uniformDistribution(0.16, 0.2);
    phytomer_parameters.peduncle.radius = 0.0018;
    phytomer_parameters.peduncle.pitch.uniformDistribution(35, 55);
    phytomer_parameters.peduncle.roll = 90;
    phytomer_parameters.peduncle.curvature = -150;
    phytomer_parameters.peduncle.length_segments = 5;
    phytomer_parameters.peduncle.radial_subdivisions = 6;
    phytomer_parameters.peduncle.color = phytomer_parameters.petiole.color;
 
    phytomer_parameters.inflorescence.flowers_per_peduncle = 1; //.uniformDistribution(1, 2);
    phytomer_parameters.inflorescence.flower_offset = 0.2;
    phytomer_parameters.inflorescence.pitch = 70;
    phytomer_parameters.inflorescence.roll = 90;
    phytomer_parameters.inflorescence.flower_prototype_scale = 0.04;
    phytomer_parameters.inflorescence.flower_prototype_function = StrawberryFlowerPrototype;
    phytomer_parameters.inflorescence.fruit_prototype_scale = 0.085;
    phytomer_parameters.inflorescence.fruit_prototype_function = StrawberryFruitPrototype;
    phytomer_parameters.inflorescence.fruit_gravity_factor_fraction = 0.65;
 
    // ---- Shoot Parameters ---- //
 
    ShootParameters shoot_parameters(context_ptr->getRandomGenerator());
    shoot_parameters.phytomer_parameters = phytomer_parameters;
 
    shoot_parameters.max_nodes = 15;
    shoot_parameters.insertion_angle_tip = 40;
    shoot_parameters.insertion_angle_decay_rate = 0;
    shoot_parameters.internode_length_max = 0.015;
    shoot_parameters.internode_length_decay_rate = 0;
    shoot_parameters.internode_length_min = 0.0;
    shoot_parameters.base_roll = 90;
    shoot_parameters.base_yaw.uniformDistribution(-20, 20);
    shoot_parameters.gravitropic_curvature.uniformDistribution(-10, 0);
    shoot_parameters.tortuosity = 0;
 
    shoot_parameters.phyllochron_min = 2;
    shoot_parameters.elongation_rate_max = 0.1;
    shoot_parameters.girth_area_factor = 2.f;
    shoot_parameters.vegetative_bud_break_time = 15;
    shoot_parameters.vegetative_bud_break_probability_min = 0.;
    shoot_parameters.vegetative_bud_break_probability_decay_rate = -0.5;
    shoot_parameters.flower_bud_break_probability = 1;
    shoot_parameters.fruit_set_probability = 0.3;
    shoot_parameters.flowers_require_dormancy = false;
    shoot_parameters.growth_requires_dormancy = false;
    shoot_parameters.determinate_shoot_growth = true;
 
    shoot_parameters.defineChildShootTypes({"mainstem"}, {1.0});
 
    defineShootType("mainstem", shoot_parameters);
}
 
uint PlantArchitecture::buildStrawberryPlant(const helios::vec3 &base_position) {
 
    if (shoot_types.empty()) {
        // automatically initialize strawberry plant shoots
        initializeStrawberryShoots();
    }
 
    uint plantID = addPlantInstance(base_position, 0);
 
    AxisRotation base_rotation = make_AxisRotation(0, context_ptr->randu(0.f, 2.f * M_PI), context_ptr->randu(0.f, 2.f * M_PI));
    uint uID_stem = addBaseStemShoot(plantID, 1, base_rotation, 0.001, 0.004, 0.01, 0.01, 0, "mainstem");
 
    breakPlantDormancy(plantID);
 
    setPlantPhenologicalThresholds(plantID, 0, 40, 5, 5, 30, 1000, false);
 
    plant_instances.at(plantID).max_age = 120;
 
    return plantID;
}
 
void PlantArchitecture::initializeSugarbeetShoots() {
 
    // ---- Leaf Prototype ---- //
 
    LeafPrototype leaf_prototype(context_ptr->getRandomGenerator());
    leaf_prototype.leaf_texture_file[0] = "SugarbeetLeaf.png";
    leaf_prototype.leaf_aspect_ratio = 0.4f;
    leaf_prototype.midrib_fold_fraction = 0.1f;
    leaf_prototype.longitudinal_curvature = -0.2f;
    leaf_prototype.lateral_curvature = -0.4f;
    leaf_prototype.petiole_roll = 0.75f;
    leaf_prototype.wave_period.uniformDistribution(0.08f, 0.15f);
    leaf_prototype.wave_amplitude.uniformDistribution(0.02, 0.04);
    leaf_prototype.subdivisions = 20;
    ;
    leaf_prototype.unique_prototypes = 10;
 
    // ---- Phytomer Parameters ---- //
 
    PhytomerParameters phytomer_parameters_sugarbeet(context_ptr->getRandomGenerator());
 
    phytomer_parameters_sugarbeet.internode.pitch = 0;
    phytomer_parameters_sugarbeet.internode.phyllotactic_angle = 137.5;
    phytomer_parameters_sugarbeet.internode.radius_initial = 0.005;
    phytomer_parameters_sugarbeet.internode.color = make_RGBcolor(0.44, 0.58, 0.19);
    phytomer_parameters_sugarbeet.internode.length_segments = 1;
    phytomer_parameters_sugarbeet.internode.max_vegetative_buds_per_petiole = 0;
    phytomer_parameters_sugarbeet.internode.max_floral_buds_per_petiole = 0;
 
    phytomer_parameters_sugarbeet.petiole.petioles_per_internode = 1;
    phytomer_parameters_sugarbeet.petiole.pitch.uniformDistribution(0, 40);
    phytomer_parameters_sugarbeet.petiole.radius = 0.005;
    phytomer_parameters_sugarbeet.petiole.length.uniformDistribution(0.15, 0.2);
    phytomer_parameters_sugarbeet.petiole.taper = 0.6;
    phytomer_parameters_sugarbeet.petiole.curvature.uniformDistribution(-300, 100);
    phytomer_parameters_sugarbeet.petiole.color = phytomer_parameters_sugarbeet.internode.color;
    phytomer_parameters_sugarbeet.petiole.length_segments = 8;
 
    phytomer_parameters_sugarbeet.leaf.leaves_per_petiole = 1;
    phytomer_parameters_sugarbeet.leaf.pitch.uniformDistribution(-10, 0);
    phytomer_parameters_sugarbeet.leaf.yaw.uniformDistribution(-5, 5);
    phytomer_parameters_sugarbeet.leaf.roll.uniformDistribution(-15, 15);
    phytomer_parameters_sugarbeet.leaf.prototype_scale.uniformDistribution(0.15, 0.25);
    phytomer_parameters_sugarbeet.leaf.prototype = leaf_prototype;
 
    // ---- Shoot Parameters ---- //
 
    ShootParameters shoot_parameters_mainstem(context_ptr->getRandomGenerator());
    shoot_parameters_mainstem.phytomer_parameters = phytomer_parameters_sugarbeet;
    shoot_parameters_mainstem.vegetative_bud_break_probability_min = 0;
    shoot_parameters_mainstem.phyllochron_min = 2;
    shoot_parameters_mainstem.elongation_rate_max = 0.1;
    shoot_parameters_mainstem.girth_area_factor = 20.f;
    shoot_parameters_mainstem.gravitropic_curvature = 10;
    shoot_parameters_mainstem.internode_length_max = 0.001;
    shoot_parameters_mainstem.internode_length_decay_rate = 0;
    shoot_parameters_mainstem.flowers_require_dormancy = false;
    shoot_parameters_mainstem.growth_requires_dormancy = false;
    shoot_parameters_mainstem.flower_bud_break_probability = 0.0;
    shoot_parameters_mainstem.max_nodes = 30;
 
    defineShootType("mainstem", shoot_parameters_mainstem);
}
 
uint PlantArchitecture::buildSugarbeetPlant(const helios::vec3 &base_position) {
 
    if (shoot_types.empty()) {
        // automatically initialize sugarbeet plant shoots
        initializeSugarbeetShoots();
    }
 
    uint plantID = addPlantInstance(base_position, 0);
 
    uint uID_stem = addBaseStemShoot(plantID, 3, make_AxisRotation(context_ptr->randu(0.f, 0.01f * M_PI), 0.f * context_ptr->randu(0.f, 2.f * M_PI), 0.25f * M_PI), 0.005, 0.001, 1, 1, 0, "mainstem");
 
    breakPlantDormancy(plantID);
 
    setPlantPhenologicalThresholds(plantID, 0, -1, -1, -1, -1, 1000, false);
 
    plant_instances.at(plantID).max_age = 365;
 
    return plantID;
}
 
void PlantArchitecture::initializeTomatoShoots() {
 
    // ---- Leaf Prototype ---- //
 
    LeafPrototype leaf_prototype(context_ptr->getRandomGenerator());
    leaf_prototype.leaf_texture_file[0] = "TomatoLeaf_centered.png";
    leaf_prototype.leaf_aspect_ratio = 0.5f;
    leaf_prototype.midrib_fold_fraction = 0.1f;
    leaf_prototype.longitudinal_curvature.uniformDistribution(-0.45, -0.2f);
    leaf_prototype.lateral_curvature = -0.3f;
    leaf_prototype.wave_period = 0.35f;
    leaf_prototype.wave_amplitude = 0.08f;
    leaf_prototype.subdivisions = 6;
    leaf_prototype.unique_prototypes = 5;
 
    // ---- Phytomer Parameters ---- //
 
    PhytomerParameters phytomer_parameters(context_ptr->getRandomGenerator());
 
    phytomer_parameters.internode.pitch = 10;
    phytomer_parameters.internode.phyllotactic_angle.uniformDistribution(140, 220);
    phytomer_parameters.internode.radius_initial = 0.001;
    phytomer_parameters.internode.color = make_RGBcolor(0.2495, 0.3162, 0.0657);
    phytomer_parameters.internode.length_segments = 1;
 
    phytomer_parameters.petiole.petioles_per_internode = 1;
    phytomer_parameters.petiole.pitch.uniformDistribution(45, 60);
    phytomer_parameters.petiole.radius = 0.002;
    phytomer_parameters.petiole.length = 0.2;
    phytomer_parameters.petiole.taper = 0.25;
    phytomer_parameters.petiole.curvature.uniformDistribution(-150, -50);
    phytomer_parameters.petiole.color = make_RGBcolor(0.3, 0.37, 0.0657);
    phytomer_parameters.petiole.length_segments = 5;
 
    phytomer_parameters.leaf.leaves_per_petiole = 7;
    phytomer_parameters.leaf.pitch.uniformDistribution(-30, 5);
    phytomer_parameters.leaf.yaw = 10;
    phytomer_parameters.leaf.roll = 0;
    phytomer_parameters.leaf.leaflet_offset = 0.15;
    phytomer_parameters.leaf.leaflet_scale = 0.7;
    phytomer_parameters.leaf.prototype_scale.uniformDistribution(0.12, 0.18);
    phytomer_parameters.leaf.prototype = leaf_prototype;
 
    phytomer_parameters.peduncle.length = 0.18;
    phytomer_parameters.peduncle.radius = 0.0015;
    phytomer_parameters.peduncle.pitch = 20;
    phytomer_parameters.peduncle.roll = 0;
    phytomer_parameters.peduncle.curvature = -900;
    phytomer_parameters.peduncle.color = phytomer_parameters.internode.color;
    phytomer_parameters.peduncle.length_segments = 5;
    phytomer_parameters.peduncle.radial_subdivisions = 8;
 
    phytomer_parameters.inflorescence.flowers_per_peduncle = 6;
    phytomer_parameters.inflorescence.flower_offset = 0.15;
    phytomer_parameters.inflorescence.pitch = 80;
    phytomer_parameters.inflorescence.roll = 180;
    phytomer_parameters.inflorescence.flower_prototype_scale = 0.05;
    phytomer_parameters.inflorescence.flower_prototype_function = TomatoFlowerPrototype;
    phytomer_parameters.inflorescence.fruit_prototype_scale = 0.15;
    phytomer_parameters.inflorescence.fruit_prototype_function = TomatoFruitPrototype;
    phytomer_parameters.inflorescence.fruit_gravity_factor_fraction = 0.;
 
    // ---- Shoot Parameters ---- //
 
    ShootParameters shoot_parameters(context_ptr->getRandomGenerator());
    shoot_parameters.phytomer_parameters = phytomer_parameters;
    shoot_parameters.phytomer_parameters.phytomer_creation_function = TomatoPhytomerCreationFunction;
 
    shoot_parameters.max_nodes = 16;
    shoot_parameters.insertion_angle_tip = 30;
    shoot_parameters.insertion_angle_decay_rate = 0;
    shoot_parameters.internode_length_max = 0.04;
    shoot_parameters.internode_length_min = 0.0;
    shoot_parameters.internode_length_decay_rate = 0;
    shoot_parameters.base_roll = 90;
    shoot_parameters.base_yaw.uniformDistribution(-20, 20);
    shoot_parameters.gravitropic_curvature = 150;
    shoot_parameters.tortuosity = 3;
 
    shoot_parameters.phyllochron_min = 2;
    shoot_parameters.elongation_rate_max = 0.1;
    shoot_parameters.girth_area_factor = 2.f;
    shoot_parameters.vegetative_bud_break_time = 30;
    shoot_parameters.vegetative_bud_break_probability_min = 0.25;
    shoot_parameters.vegetative_bud_break_probability_decay_rate = -0.25;
    shoot_parameters.flower_bud_break_probability = 0.2;
    shoot_parameters.fruit_set_probability = 0.8;
    shoot_parameters.flowers_require_dormancy = false;
    shoot_parameters.growth_requires_dormancy = false;
    shoot_parameters.determinate_shoot_growth = true;
 
    shoot_parameters.defineChildShootTypes({"mainstem"}, {1.0});
 
    defineShootType("mainstem", shoot_parameters);
}
 
uint PlantArchitecture::buildTomatoPlant(const helios::vec3 &base_position) {
 
    if (shoot_types.empty()) {
        // automatically initialize tomato plant shoots
        initializeTomatoShoots();
    }
 
    uint plantID = addPlantInstance(base_position, 0);
 
    AxisRotation base_rotation = make_AxisRotation(0, context_ptr->randu(0.f, 2.f * M_PI), context_ptr->randu(0.f, 2.f * M_PI));
    uint uID_stem = addBaseStemShoot(plantID, 1, base_rotation, 0.002, 0.04, 0.01, 0.01, 0, "mainstem");
 
    breakPlantDormancy(plantID);
 
    setPlantPhenologicalThresholds(plantID, 0, 40, 5, 5, 30, 1000, false);
 
    plant_instances.at(plantID).max_age = 365;
 
    return plantID;
}
 
void PlantArchitecture::initializeCherryTomatoShoots() {
 
    // ---- Leaf Prototype ---- //
 
    LeafPrototype leaf_prototype(context_ptr->getRandomGenerator());
    leaf_prototype.leaf_texture_file[0] = "CherryTomatoLeaf.png";
    leaf_prototype.leaf_aspect_ratio = 0.6f;
    leaf_prototype.midrib_fold_fraction = 0.1f;
    leaf_prototype.longitudinal_curvature.uniformDistribution(-0.3, -0.15f);
    leaf_prototype.lateral_curvature = -0.8f;
    leaf_prototype.wave_period = 0.35f;
    leaf_prototype.wave_amplitude = 0.08f;
    leaf_prototype.subdivisions = 7;
    leaf_prototype.unique_prototypes = 5;
 
    // ---- Phytomer Parameters ---- //
 
    PhytomerParameters phytomer_parameters(context_ptr->getRandomGenerator());
 
    phytomer_parameters.internode.pitch = 5;
    phytomer_parameters.internode.phyllotactic_angle.uniformDistribution(14, 220);
    phytomer_parameters.internode.radius_initial = 0.001;
    phytomer_parameters.internode.color = make_RGBcolor(0.2495, 0.3162, 0.0657);
    phytomer_parameters.internode.length_segments = 1;
    phytomer_parameters.internode.radial_subdivisions = 14;
 
    phytomer_parameters.petiole.petioles_per_internode = 1;
    phytomer_parameters.petiole.pitch.uniformDistribution(45, 60);
    phytomer_parameters.petiole.radius = 0.0025;
    phytomer_parameters.petiole.length = 0.25;
    phytomer_parameters.petiole.taper = 0.25;
    phytomer_parameters.petiole.curvature.uniformDistribution(-250, 0);
    phytomer_parameters.petiole.color = make_RGBcolor(0.32, 0.37, 0.12);
    phytomer_parameters.petiole.length_segments = 5;
 
    phytomer_parameters.leaf.leaves_per_petiole = 9;
    phytomer_parameters.leaf.pitch.uniformDistribution(-30, 5);
    phytomer_parameters.leaf.yaw = 10;
    phytomer_parameters.leaf.roll.uniformDistribution(-20, 20);
    phytomer_parameters.leaf.leaflet_offset = 0.22;
    phytomer_parameters.leaf.leaflet_scale = 0.9;
    phytomer_parameters.leaf.prototype_scale.uniformDistribution(0.12, 0.17);
    phytomer_parameters.leaf.prototype = leaf_prototype;
 
    phytomer_parameters.peduncle.length = 0.2;
    phytomer_parameters.peduncle.radius = 0.0015;
    phytomer_parameters.peduncle.pitch = 20;
    phytomer_parameters.peduncle.roll = 0;
    phytomer_parameters.peduncle.curvature = -1000;
    phytomer_parameters.peduncle.color = phytomer_parameters.internode.color;
    phytomer_parameters.peduncle.length_segments = 5;
    phytomer_parameters.peduncle.radial_subdivisions = 8;
 
    phytomer_parameters.inflorescence.flowers_per_peduncle = 6;
    phytomer_parameters.inflorescence.flower_offset = 0.15;
    phytomer_parameters.inflorescence.pitch = 80;
    phytomer_parameters.inflorescence.roll = 180;
    phytomer_parameters.inflorescence.flower_prototype_scale = 0.05;
    phytomer_parameters.inflorescence.flower_prototype_function = TomatoFlowerPrototype;
    phytomer_parameters.inflorescence.fruit_prototype_scale = 0.1;
    phytomer_parameters.inflorescence.fruit_prototype_function = TomatoFruitPrototype;
    phytomer_parameters.inflorescence.fruit_gravity_factor_fraction = 0.2;
 
    // ---- Shoot Parameters ---- //
 
    ShootParameters shoot_parameters(context_ptr->getRandomGenerator());
    shoot_parameters.phytomer_parameters = phytomer_parameters;
    shoot_parameters.phytomer_parameters.phytomer_creation_function = CherryTomatoPhytomerCreationFunction;
    shoot_parameters.phytomer_parameters.phytomer_callback_function = CherryTomatoPhytomerCallbackFunction;
 
    shoot_parameters.max_nodes = 100;
    shoot_parameters.insertion_angle_tip = 30;
    shoot_parameters.insertion_angle_decay_rate = 0;
    shoot_parameters.internode_length_max = 0.04;
    shoot_parameters.internode_length_min = 0.0;
    shoot_parameters.internode_length_decay_rate = 0;
    shoot_parameters.base_roll = 90;
    shoot_parameters.base_yaw.uniformDistribution(-20, 20);
    shoot_parameters.gravitropic_curvature = 800;
    shoot_parameters.tortuosity = 1.5;
 
    shoot_parameters.phyllochron_min = 4;
    shoot_parameters.elongation_rate_max = 0.1;
    shoot_parameters.girth_area_factor = 2.f;
    shoot_parameters.vegetative_bud_break_time = 40;
    shoot_parameters.vegetative_bud_break_probability_min = 0.2;
    shoot_parameters.vegetative_bud_break_probability_decay_rate = 0.;
    shoot_parameters.flower_bud_break_probability = 0.5;
    shoot_parameters.fruit_set_probability = 0.9;
    shoot_parameters.flowers_require_dormancy = false;
    shoot_parameters.growth_requires_dormancy = false;
    shoot_parameters.determinate_shoot_growth = false;
 
    shoot_parameters.defineChildShootTypes({"mainstem"}, {1.0});
 
    defineShootType("mainstem", shoot_parameters);
}
 
uint PlantArchitecture::buildCherryTomatoPlant(const helios::vec3 &base_position) {
 
    if (shoot_types.empty()) {
        // automatically initialize cherry tomato plant shoots
        initializeCherryTomatoShoots();
    }
 
    uint plantID = addPlantInstance(base_position, 0);
 
    AxisRotation base_rotation = make_AxisRotation(0, context_ptr->randu(0.f, 2.f * M_PI), context_ptr->randu(0.f, 2.f * M_PI));
    uint uID_stem = addBaseStemShoot(plantID, 1, base_rotation, 0.002, 0.06, 0.01, 0.01, 0, "mainstem");
 
    breakPlantDormancy(plantID);
 
    setPlantPhenologicalThresholds(plantID, 0, 50, 10, 5, 30, 1000);
 
    plant_instances.at(plantID).max_age = 175;
 
    return plantID;
}
 
void PlantArchitecture::initializeWalnutTreeShoots() {
 
    // ---- Leaf Prototype ---- //
 
    LeafPrototype leaf_prototype(context_ptr->getRandomGenerator());
    leaf_prototype.leaf_texture_file[0] = "WalnutLeaf.png";
    leaf_prototype.leaf_aspect_ratio = 0.5f;
    leaf_prototype.midrib_fold_fraction = 0.15f;
    leaf_prototype.longitudinal_curvature = -0.2f;
    leaf_prototype.lateral_curvature = 0.1f;
    leaf_prototype.wave_period.uniformDistribution(0.08, 0.15);
    leaf_prototype.wave_amplitude.uniformDistribution(0.02, 0.04);
    leaf_prototype.subdivisions = 3;
    leaf_prototype.unique_prototypes = 5;
 
    // ---- Phytomer Parameters ---- //
 
    PhytomerParameters phytomer_parameters_walnut(context_ptr->getRandomGenerator());
 
    phytomer_parameters_walnut.internode.pitch = 0;
    phytomer_parameters_walnut.internode.phyllotactic_angle.uniformDistribution(160, 200);
    phytomer_parameters_walnut.internode.radius_initial = 0.004;
    phytomer_parameters_walnut.internode.length_segments = 1;
    phytomer_parameters_walnut.internode.image_texture = "AppleBark.jpg";
    phytomer_parameters_walnut.internode.max_floral_buds_per_petiole = 3;
 
    phytomer_parameters_walnut.petiole.petioles_per_internode = 1;
    phytomer_parameters_walnut.petiole.pitch.uniformDistribution(-80, -70);
    phytomer_parameters_walnut.petiole.taper = 0.2;
    phytomer_parameters_walnut.petiole.curvature.uniformDistribution(-1000, 0);
    phytomer_parameters_walnut.petiole.length = 0.15;
    phytomer_parameters_walnut.petiole.radius = 0.0015;
    phytomer_parameters_walnut.petiole.length_segments = 5;
    phytomer_parameters_walnut.petiole.radial_subdivisions = 3;
    phytomer_parameters_walnut.petiole.color = make_RGBcolor(0.61, 0.5, 0.24);
 
    phytomer_parameters_walnut.leaf.leaves_per_petiole = 5;
    phytomer_parameters_walnut.leaf.pitch.uniformDistribution(-40, 0);
    phytomer_parameters_walnut.leaf.prototype_scale = 0.14;
    phytomer_parameters_walnut.leaf.leaflet_scale = 0.7;
    phytomer_parameters_walnut.leaf.leaflet_offset = 0.35;
    phytomer_parameters_walnut.leaf.prototype = leaf_prototype;
 
    phytomer_parameters_walnut.peduncle.length = 0.02;
    phytomer_parameters_walnut.peduncle.radius = 0.0005;
    phytomer_parameters_walnut.peduncle.pitch = 90;
    phytomer_parameters_walnut.peduncle.roll = 90;
    phytomer_parameters_walnut.peduncle.length_segments = 1;
 
    phytomer_parameters_walnut.inflorescence.flowers_per_peduncle = 1;
    phytomer_parameters_walnut.inflorescence.pitch = 0;
    phytomer_parameters_walnut.inflorescence.roll = 0;
    phytomer_parameters_walnut.inflorescence.flower_prototype_scale = 0.03;
    phytomer_parameters_walnut.inflorescence.flower_prototype_function = WalnutFlowerPrototype;
    phytomer_parameters_walnut.inflorescence.fruit_prototype_scale = 0.075;
    phytomer_parameters_walnut.inflorescence.fruit_prototype_function = WalnutFruitPrototype;
 
    // ---- Shoot Parameters ---- //
 
    // Trunk
    ShootParameters shoot_parameters_trunk(context_ptr->getRandomGenerator());
    shoot_parameters_trunk.phytomer_parameters = phytomer_parameters_walnut;
    shoot_parameters_trunk.phytomer_parameters.internode.phyllotactic_angle = 0;
    shoot_parameters_trunk.phytomer_parameters.internode.radius_initial = 0.01;
    shoot_parameters_trunk.phytomer_parameters.internode.radial_subdivisions = 24;
    shoot_parameters_trunk.max_nodes = 20;
    shoot_parameters_trunk.girth_area_factor = 5.f;
    shoot_parameters_trunk.vegetative_bud_break_probability_min = 0;
    shoot_parameters_trunk.vegetative_bud_break_time = 0;
    shoot_parameters_trunk.tortuosity = 1;
    shoot_parameters_trunk.internode_length_max = 0.05;
    shoot_parameters_trunk.internode_length_decay_rate = 0;
    shoot_parameters_trunk.defineChildShootTypes({"scaffold"}, {1});
 
    // Proleptic shoots
    ShootParameters shoot_parameters_proleptic(context_ptr->getRandomGenerator());
    shoot_parameters_proleptic.phytomer_parameters = phytomer_parameters_walnut;
    shoot_parameters_proleptic.phytomer_parameters.internode.color = make_RGBcolor(0.3, 0.2, 0.2);
    shoot_parameters_proleptic.phytomer_parameters.phytomer_creation_function = WalnutPhytomerCreationFunction;
    // shoot_parameters_proleptic.phytomer_parameters.phytomer_callback_function = WalnutPhytomerCallbackFunction;
    shoot_parameters_proleptic.max_nodes = 24;
    shoot_parameters_proleptic.max_nodes_per_season = 12;
    shoot_parameters_proleptic.phyllochron_min = 2.;
    shoot_parameters_proleptic.elongation_rate_max = 0.15;
    shoot_parameters_proleptic.girth_area_factor = 9.f;
    shoot_parameters_proleptic.vegetative_bud_break_probability_min = 0.05;
    shoot_parameters_proleptic.vegetative_bud_break_probability_decay_rate = 0.7;
    shoot_parameters_proleptic.vegetative_bud_break_time = 3;
    shoot_parameters_proleptic.gravitropic_curvature = 300;
    shoot_parameters_proleptic.tortuosity = 4;
    shoot_parameters_proleptic.insertion_angle_tip.uniformDistribution(20, 25);
    shoot_parameters_proleptic.insertion_angle_decay_rate = 15;
    shoot_parameters_proleptic.internode_length_max = 0.08;
    shoot_parameters_proleptic.internode_length_min = 0.01;
    shoot_parameters_proleptic.internode_length_decay_rate = 0.006;
    shoot_parameters_proleptic.fruit_set_probability = 0.3;
    shoot_parameters_proleptic.flower_bud_break_probability = 0.3;
    shoot_parameters_proleptic.max_terminal_floral_buds = 4;
    shoot_parameters_proleptic.flowers_require_dormancy = true;
    shoot_parameters_proleptic.growth_requires_dormancy = true;
    shoot_parameters_proleptic.determinate_shoot_growth = false;
    shoot_parameters_proleptic.defineChildShootTypes({"proleptic"}, {1.0});
 
    // Main scaffolds
    ShootParameters shoot_parameters_scaffold = shoot_parameters_proleptic;
    shoot_parameters_scaffold.phytomer_parameters.internode.radial_subdivisions = 10;
    shoot_parameters_scaffold.max_nodes = 30;
    shoot_parameters_scaffold.gravitropic_curvature = 300;
    shoot_parameters_scaffold.internode_length_max = 0.06;
    shoot_parameters_scaffold.tortuosity = 4;
    shoot_parameters_scaffold.defineChildShootTypes({"proleptic"}, {1.0});
 
    defineShootType("trunk", shoot_parameters_trunk);
    defineShootType("scaffold", shoot_parameters_scaffold);
    defineShootType("proleptic", shoot_parameters_proleptic);
}
 
uint PlantArchitecture::buildWalnutTree(const helios::vec3 &base_position) {
 
    if (shoot_types.empty()) {
        // automatically initialize walnut tree shoots
        initializeWalnutTreeShoots();
    }
 
    // Get training system parameters (with defaults matching original hard-coded values)
    auto trunk_height = getParameterValue(current_build_parameters, "trunk_height", 0.8f, 0.1f, 3.f, "total trunk height in meters");
    auto num_scaffolds = uint(getParameterValue(current_build_parameters, "num_scaffolds", 4.f, 2.f, 8.f, "number of scaffold branches"));
    auto scaffold_angle = getParameterValue(current_build_parameters, "scaffold_angle", 40.f, 25.f, 60.f, "scaffold branch angle in degrees");
 
    // Calculate trunk nodes based on desired height and internode length
    float trunk_internode_length = 0.04f; // Default internode length for walnut
    uint trunk_nodes = uint(trunk_height / trunk_internode_length);
    if (trunk_nodes < 1)
        trunk_nodes = 1;
 
    // Fixed training parameters (not user-customizable)
    float scaffold_radius = 0.007f;
    float scaffold_length = 0.06f;
 
    uint plantID = addPlantInstance(base_position, 0);
 
    uint uID_trunk = addBaseStemShoot(plantID, trunk_nodes, make_AxisRotation(context_ptr->randu(0.f, 0.05f * M_PI), context_ptr->randu(0.f, 2.f * M_PI), 0.f * M_PI), shoot_types.at("trunk").phytomer_parameters.internode.radius_initial.val(),
                                      trunk_internode_length, 1.f, 1.f, 0, "trunk");
    appendPhytomerToShoot(plantID, uID_trunk, shoot_types.at("trunk").phytomer_parameters, 0, 0.01, 1, 1);
 
    plant_instances.at(plantID).shoot_tree.at(uID_trunk)->meristem_is_alive = false;
 
    auto phytomers = plant_instances.at(plantID).shoot_tree.at(uID_trunk)->phytomers;
    for (const auto &phytomer: phytomers) {
        phytomer->removeLeaf();
        phytomer->setVegetativeBudState(BUD_DEAD);
        phytomer->setFloralBudState(BUD_DEAD);
    }
 
    // Hard-coded scaffold node range (not user-customizable)
    uint scaffold_nodes_min = 5;
    uint scaffold_nodes_max = 7;
 
    for (int i = 0; i < num_scaffolds; i++) {
        float pitch = deg2rad(scaffold_angle) + context_ptr->randu(-0.1f, 0.1f); // Small randomness around specified angle
        uint scaffold_nodes = context_ptr->randu(int(scaffold_nodes_min), int(scaffold_nodes_max));
        uint uID_shoot = addChildShoot(plantID, uID_trunk, getShootNodeCount(plantID, uID_trunk) - i - 1, scaffold_nodes, make_AxisRotation(pitch, (float(i) + context_ptr->randu(-0.2f, 0.2f)) / float(num_scaffolds) * 2 * M_PI, 0), scaffold_radius,
                                       scaffold_length, 1.f, 1.f, 0.5, "scaffold", 0);
    }
 
    makePlantDormant(plantID);
 
    setPlantPhenologicalThresholds(plantID, 165, -1, 3, 7, 20, 200, false);
 
    plant_instances.at(plantID).max_age = 1460;
 
    return plantID;
}
 
void PlantArchitecture::initializeWheatShoots() {
 
    // ---- Leaf Prototype ---- //
 
    LeafPrototype leaf_prototype(context_ptr->getRandomGenerator());
    leaf_prototype.leaf_texture_file[0] = "SorghumLeaf.png";
    leaf_prototype.leaf_aspect_ratio = 0.1f;
    leaf_prototype.midrib_fold_fraction = 0.3f;
    leaf_prototype.longitudinal_curvature.uniformDistribution(-0.5, -0.1);
    leaf_prototype.lateral_curvature = -0.3;
    leaf_prototype.petiole_roll = 0.04f;
    leaf_prototype.wave_period = 0.1f;
    leaf_prototype.wave_amplitude = 0.1f;
    leaf_prototype.leaf_buckle_length.uniformDistribution(0.5, 0.6);
    leaf_prototype.leaf_buckle_angle.uniformDistribution(25, 35);
    leaf_prototype.subdivisions = 20;
    leaf_prototype.unique_prototypes = 10;
 
    // ---- Phytomer Parameters ---- //
 
    PhytomerParameters phytomer_parameters_wheat(context_ptr->getRandomGenerator());
 
    phytomer_parameters_wheat.internode.pitch = 0;
    phytomer_parameters_wheat.internode.phyllotactic_angle.uniformDistribution(67, 77);
    phytomer_parameters_wheat.internode.radius_initial = 0.001;
    phytomer_parameters_wheat.internode.color = make_RGBcolor(0.27, 0.31, 0.16);
    phytomer_parameters_wheat.internode.length_segments = 1;
    phytomer_parameters_wheat.internode.radial_subdivisions = 6;
    phytomer_parameters_wheat.internode.max_floral_buds_per_petiole = 0;
    phytomer_parameters_wheat.internode.max_vegetative_buds_per_petiole = 0;
 
    phytomer_parameters_wheat.petiole.petioles_per_internode = 1;
    phytomer_parameters_wheat.petiole.pitch.uniformDistribution(-40, -20);
    phytomer_parameters_wheat.petiole.radius = 0.0;
    phytomer_parameters_wheat.petiole.length = 0.005;
    phytomer_parameters_wheat.petiole.taper = 0;
    phytomer_parameters_wheat.petiole.curvature = 0;
    phytomer_parameters_wheat.petiole.length_segments = 1;
 
    phytomer_parameters_wheat.leaf.leaves_per_petiole = 1;
    phytomer_parameters_wheat.leaf.pitch = 0;
    phytomer_parameters_wheat.leaf.yaw = 0;
    phytomer_parameters_wheat.leaf.roll = 0;
    phytomer_parameters_wheat.leaf.prototype_scale = 0.22;
    phytomer_parameters_wheat.leaf.prototype = leaf_prototype;
 
    phytomer_parameters_wheat.peduncle.length = 0.1;
    phytomer_parameters_wheat.peduncle.radius = 0.002;
    phytomer_parameters_wheat.peduncle.color = phytomer_parameters_wheat.internode.color;
    phytomer_parameters_wheat.peduncle.curvature = -100;
    phytomer_parameters_wheat.peduncle.radial_subdivisions = 6;
 
    phytomer_parameters_wheat.inflorescence.flowers_per_peduncle = 1;
    phytomer_parameters_wheat.inflorescence.pitch = 0;
    phytomer_parameters_wheat.inflorescence.roll = 0;
    phytomer_parameters_wheat.inflorescence.fruit_prototype_scale = 0.1;
    phytomer_parameters_wheat.inflorescence.fruit_prototype_function = WheatSpikePrototype;
 
    phytomer_parameters_wheat.phytomer_creation_function = WheatPhytomerCreationFunction;
 
    // ---- Shoot Parameters ---- //
 
    ShootParameters shoot_parameters_mainstem(context_ptr->getRandomGenerator());
    shoot_parameters_mainstem.phytomer_parameters = phytomer_parameters_wheat;
    shoot_parameters_mainstem.vegetative_bud_break_probability_min = 0;
    shoot_parameters_mainstem.flower_bud_break_probability = 1;
    shoot_parameters_mainstem.phyllochron_min = 2;
    shoot_parameters_mainstem.elongation_rate_max = 0.1;
    shoot_parameters_mainstem.girth_area_factor = 6.f;
    shoot_parameters_mainstem.gravitropic_curvature.uniformDistribution(-500, -200);
    shoot_parameters_mainstem.flowers_require_dormancy = false;
    shoot_parameters_mainstem.growth_requires_dormancy = false;
    shoot_parameters_mainstem.determinate_shoot_growth = false;
    shoot_parameters_mainstem.fruit_set_probability = 1.0;
    shoot_parameters_mainstem.defineChildShootTypes({"mainstem"}, {1.0});
    shoot_parameters_mainstem.max_nodes = 20;
    shoot_parameters_mainstem.max_terminal_floral_buds = 1;
 
    defineShootType("mainstem", shoot_parameters_mainstem);
}
 
uint PlantArchitecture::buildWheatPlant(const helios::vec3 &base_position) {
 
    if (shoot_types.empty()) {
        // automatically initialize wheat plant shoots
        initializeWheatShoots();
    }
 
    uint plantID = addPlantInstance(base_position - make_vec3(0, 0, 0.025), 0);
 
    uint uID_stem = addBaseStemShoot(plantID, 1, make_AxisRotation(context_ptr->randu(0.f, 0.05f * M_PI), context_ptr->randu(0.f, 2.f * M_PI), context_ptr->randu(0.f, 2.f * M_PI)), 0.001, 0.025, 0.01, 0.01, 0, "mainstem");
 
    breakPlantDormancy(plantID);
 
    setPlantPhenologicalThresholds(plantID, 0, -1, -1, 4, 10, 1000, false);
 
    plant_instances.at(plantID).max_age = 365;
 
    return plantID;
}