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Co-simulation with OpenAlea and GroIMP for cross-platform functional-structural plant modelling

Long Q., Pradal C., Kurth W.. 2020. In : Kahlen Katrin (ed.), Chen Tsu-Wei (ed.), Fricke Andreas (ed.), Stützel Hartmut (ed.). Book of abstracts of the 9th International Conference on Functional-Structural Plant Models: FSPM2020, 5 - 9 October 2020. Hanovre : Institute of Horticultural Production Systems, p. 97-98. International Conference on Functional-Structural Plant Models (FSPM 2020), 2020-10-05/2020-10-09, (Allemagne).

Introduction - Within the FSPM community, different teams of researchers have specialized on different processes. Thus there is an increasing wish to re-use the diverse simulation packages which were already created but which are usually implemented within different software environments, often not directly compatible with each other. The OpenAlea platform (Pradal et al., 2008) was developed as an environment to connect and reuse components with specific functionality in a scientific workflow environment. However, not all widely-used FSPM-related tools are already available from OpenAlea. In our work, we created an interface between OpenAlea and the FSPM platform GroIMP (Kniemeyer, 2008). The latter contains some dedicated tools, among them a simulator for light distribution and interception, based on stochastic path tracing. This radiation model is interesting due to its accuracy, its spectral capabilities and because it is already used in different applications. To demonstrate the technical usability of our interface, we took an established simulator for the growth and structural development of apple trees, MAppleT (Costes et al., 2008), which is already accessible from OpenAlea but which does not include a radiation model on its own. By exporting the generated tree structures from MAppleT via OpenAlea to GroIMP, we were able to employ GroIMP's light model on them and to reimport the structures with added information on "absorbed light" at phytomer level. Within OpenAlea, photosynthesis was then calculated and tentatively assumed effects on organ sizes could be visualized. Our conceptual contributions are a generic web architecture and the bidirectional matching between two different multiscale formalisms for topology and geometry in FSPMs. OpenAlea - OpenAlea emphasizes modularity and reuse by using a central data structure, the MTG (Godin and Caraglio, 1998). This enables indirect communication between the components that are integrated in the platform, using a blackboard architecture. It captures the multiscale organization of plant canopies, particularly its topology. Various properties can also be stored at the different scales. MTG vertices are topological elements that represent modular parts of a plant (e.g., axis, phytomer, organ). The neighborhood of each element is stored in the MTG as well as its associated properties. Geometrical elements are stored separately in an external scene graph for efficiency but are available from a property of the MTG. GroIMP - In GroIMP, a scene, including virtual plants, is represented as a rooted graph which can be an MTG in the sense of Godin and Caraglio (1998). At the same time, it has the semantics of a scene graph (a well-known data model in computer graphics). In contrast to the MTG in OpenAlea, it contains all information about the scene including geometry. Its nodes can represent geometrical objects (e.g., standing for plant organs), light sources, spatial transformations (e.g., rotations), or they are abstract nodes used purely for replacement purposes during development. The development of scenes, including plants, is modelled by parallel graph rewriting: Rules are applied by substituting in every timestep all instances of graphs which occur as left-hand side of a rule by the corresponding right-hand side. L-systems, operating on strings, can be subsumed as special cases under this formalism. The Interface - Although the data models of OpenAlea and GroIMP were both derived from the same mathematical concept, the implemented data structures of both platforms differ in several aspects. To bridge the gap between them, a data extractor from OpenAlea to GroIMP has first to combine the topological (MTG) with the geometrical information and to build a scene graph where the global positional information of each object is split into the transformation matrices of its predecessors (in the graph) and of itself. Furthermore, the scale information, represented by an indexing of nod...

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