PlantGeom

Documentation for PlantGeom, a package about everything 3D-related for plants.

The package is designed around MultiScaleTreeGraph for the basic structure of plants (or any 3D object) topology and attributes.

The package provides different functionalities, the main ones being:

IO for the OPF file format (see read_opf and write_opf);
plotting using viz and viz!, optionally using coloring by attribute;
mesh transformations using transform_mesh!

Note that PlantGeom reserves the :geometry attribute in the nodes (e.g. organs). It uses it to store the 3D geometry as a special structure (geometry).

If you want to reproduce the animation, you can look at the code below. Otherwise, please head to the next section.

using CairoMakie, Meshes, PlantGeom, MultiScaleTreeGraph
opf = read_opf(joinpath(dirname(dirname(pathof(PlantGeom))),"test","files","simple_plant.opf"))

# First, we compute the 3D coordinates for each node in the MTG:
transform!(opf, refmesh_to_mesh!)
# And compute the max z of each node based on their mesh:
transform!(opf, zmax => :z_node, ignore_nothing = true)
# Or the z coordinate of each vertez of each node mesh:
transform!(opf, :geometry => (x -> [Meshes.coords(i)z for i in Meshes.vertices(x.mesh)]) => :z_vertex, ignore_nothing = true)


# Then we make a Makie figure:
f = Figure()
ga = f[1, 1]
gb = f[1, 2]

ax1 = Axis(ga[1, 1])
ax2 = Axis3(gb[1, 1], aspect = :data, title = "3D representation (mesh)", elevation = 0.15π, azimuth = 0.3π)
hidedecorations!(ax2)

# We can make a diagram out of the MTG, and coloring using the z coordinates attribute:
diagram!(ax1, opf, color = :z_node)
hidedecorations!(ax1)
ax1.title = "MultiscaleTreeGraph diagram"

# And a 3d representation:

viz!(opf, color = :z_vertex)

# And making a little animation out of it:
CairoMakie.record(f, "plant_animation.mp4", 1:120) do frame
    ax2.azimuth[] = 0.3π + 0.3 * sin(2π * frame / 120)
end