json

Standard Format for Graminae

The format is stored in JSON. The aim of this format is to be read and write by MTG datastructure.

First, we focus on two applications: phenotyping and simulation of Graminae.

Metadata

• scales: [(name, index)] with index in [0, N] and name is a string (ontology?)

  • scale 1 : Canopy
  • scale 2 : Plant
  • scale 3 : Axis
  • scale 4 : Phytomer
  • scale 5: Organ

• Module / Label / Symbol (facultatif)

  • name : ontology id, scale

• Plus the Metadata define for RSML

Structure

Raw data-strcucture representing the MTG:

• parent: {vid: vid} the vertex parent of each vertex. -1 when no parent or erase it.

• complex: {vid: vid} the vertex complex of each vertex. For instance, the complex of an axis is its plant that contains it.

• children (optional): {vid: [vid]}. The list of child of a given vertex

• components (optional): {vid: [vid]}. Components of a complex is a list of vertices that belong to a complex (eg axes of a given plant).

• vertices: [vid]. Define the list of all my vertex.

• scales (optional): {vid: int}. The scale id associated to each vertex.

Internal Properties

Internal properties are associated with the graph structure. In our case, the type of these properties are the following:

• label: string. Label of each vertex. The label will describe both the type of element (leaf, stem, plant), plus an index that can represent some information. The label can be associated with an ontology in the metadata field module.
• edge-type: the type of edge that connect an id to its parent (or complex). Edge_type belongs to < (successor), + (ramification), or / (decomposition).

External Properties

External properties are defined for a set of vertices. Some properties are related to an ontology defined in the metadata in property-definitions.

Some property names need to be common to be shares. Standardized properties are defined in the thesaurus.

Main property is the geometry. It is defined at list by a polyline (2 or 3D).

Thesaurus