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Geometry Concepts in PlantGeom

Overview

PlantGeom provides a framework for representing, manipulating, and visualizing 3D plant architecture. This page introduces the key concepts behind PlantGeom's approach to geometry handling.

Reference Mesh Design Philosophy

Most plants contain many similar organs - think of hundreds of leaves on a tree that share the same basic shape but differ in size and orientation. PlantGeom leverages this biological pattern through its reference mesh approach:

  1. Define a single reference mesh for each organ type (e.g., a generic leaf shape)
  2. Apply transformations (scaling, rotation, translation) to position each instance

This approach offers significant benefits:

  • Memory efficiency: Store one mesh instead of hundreds of copies
  • Smaller file sizes: OPF files store only unique reference meshes plus transformations
  • Performance: Operations can be applied to reference meshes once rather than to many instances

For highly specialized shapes that can't be derived from a reference (like wheat leaves with complex curvatures), PlantGeom can still use direct mesh representations.

Key Components

PlantGeom's geometry system consists of three main components:

  1. RefMesh: A reference mesh with a unique identifier and the mesh data
  2. Geometry: A container that links a RefMesh to a node and stores transformation information
  3. Transformations: Operations that scale, rotate, and position instances of reference meshes

MTG Integration

Geometries in PlantGeom are attached to nodes in a Multi-scale Tree Graph (MTG) that represents plant topology:

# Attaching geometry to an MTG node
node.geometry = Geometry(ref_mesh=some_ref_mesh, transformation=some_transformation)

Documentation Structure

To learn more about PlantGeom's geometry features:

  • Reference Meshes: Learn how to create and work with reference meshes
  • Building Plant Models: Step-by-step guide to constructing complete plant geometries
  • Merging Meshes: Tools for combining geometries at different scales

File Format Support

PlantGeom works with several file formats:

  • OPF: Open Plant Format - combines MTG structure and geometry efficiently
  • OBJ/PLY/STL: Common 3D mesh formats

Basic Usage Example

using PlantGeom
using CairoMakie

# Load a plant model with geometry
mtg = read_opf("path/to/plant.opf")

# Visualize
fig = Figure()
ax = Axis3(fig[1, 1])
viz!(ax, mtg)
fig

For more visualization options, see the 3D recipes section.