Import A Plant From An MTG​#

A MultiScaleTreeGraph (MTG) stores a plant's organs and their relationships. Use it when you already have a measured or generated architecture. The models and value connections are the same as in One multiscale plant; the MTG supplies the objects and records which organ each one belongs to.

Install MultiScaleTreeGraph in your project to run this example. We create a small MTG here so no external data file is needed:

using PlantSimEngine, MultiScaleTreeGraph, DataFrames
using PlantSimEngine.Examples

root = Node(NodeMTG("/", :Plant, 1, 0))
leaf_1 = Node(root, NodeMTG("/", :Leaf, 1, 1))
leaf_2 = Node(root, NodeMTG("/", :Leaf, 2, 1))
leaf_1[:carbon_biomass] = 50.0
leaf_2[:carbon_biomass] = 100.0

The / links describe leaves as components at a finer scale than the plant; this reduced architecture omits stems and petioles. For an existing MTG file, replace these lines with root = read_mtg("my_plant.mtg"). Inspect its symbols first: this example uses :Plant and :Leaf, but your file may use different names.

Choose which attributes become simulation state​#

PlantSimEngine imports each node's ID and parent automatically. By default, it uses the MTG symbol, such as :Leaf, as the object's scale label. It does not automatically copy numerical attributes into Status, where models read and store their values. The function below chooses the initial values to import: each leaf's carbon biomass in this example.

initial_status(node) = MultiScaleTreeGraph.symbol(node) == :Leaf ?
    Status(carbon_biomass=node[:carbon_biomass]) : Status()

model = CompositeModel(
    root;
    status=initial_status,
    applications=(
        ModelSpec(ToyLeafSurfaceModel(0.02);
            name=:leaf_surface, on=Many(scale=:Leaf)),
        ModelSpec(ToyPlantLeafSurfaceModel();
            name=:plant_surface, on=One(scale=:Plant),
            inputs=(leaf_surfaces=Many(
                scale=:Leaf, within=Subtree(),
                application=:leaf_surface, var=:surface,
            ),)),
    ),
)

DataFrames.select(DataFrame(Diagnostics.explain_objects(model)), :id, :scale, :parent)

The teaching leaf model uses carbon biomass in g C and a specific leaf area of 0.02 m² per g C. It gives leaf areas of 1 and 2 m², whose sum is 3 m²:

simulation = run!(model; outputs=:all)
plant_area = final_state(simulation, One(scale=:Plant)).surface
plant_area

Keep the link to the MTG when the plant grows​#

CompositeModel(root; ...) keeps the relationship between MTG nodes and simulation objects. Use object_id(model, leaf_1) to find the object for a node. When you create an organ with add_organ!, PlantSimEngine reuses your initial_status function to set its initial values. The new node must have the attributes this function reads, or the function must supply suitable initial values itself. See Growth within a time step.

Use objects_from_mtg(root; status=initial_status) when you only want a list of Objects to assemble yourself. It does not keep the node-to-object lookup needed to find nodes or create new organs through the MTG later.