L-Py, an open L-systems framework in Python

International audienceL-systems were conceived as a mathematical framework for modeling growth of plants. In this paper, we present L-Py, a simulation software that mixes L-systems construction with the Python high-level modeling language. In addition to this software module, an integrated visual development environment has been developed that facilitates the creation of plant models. In particular, easy to use optimization tools have been integrated. Thanks to Python and its modular approach, this framework makes it possible to integrate a variety of tools defined in different modeling context, in particular tools from the OpenAlea platform. Additionally, it can be integrated as a simple growth simulation module into more complex computational pipelines

PlantGL : a Python-based geometric library for 3D plant modelling at different scales

In this paper, we present PlantGL, an open-source graphic toolkit for the creation, simulation and analysis of 3D virtual plants. This C++ geometric library is embedded in the Python language which makes it a powerful user-interactive platform for plant modelling in various biological application domains. PlantGL makes it possible to build and manipulate geometric models of plants or plant parts, ranging from tissues and organs to plant populations. Based on a scene graph augmented with primitives dedicated to plant representation, several methods are provided to create plant architectures from either field measurements or procedural algorithms. Because they reveal particularly useful in plant design and analysis, special attention has been paid to the definition and use of branching system envelopes. Several examples from different modelling applications illustrate how PlantGL can be used to construct, analyse or manipulate geometric models at different scales

OpenAlea 2.0: Architecture of an integrated modeling environment on the web

International audiencePlant modeling is based on the use of a diverse set of design paradigms (L-systems, visual programming, imperative languages or sketch-based interfaces). In this poster, the architecture of a new multi-paradigm and integrated modeling environment is presented. This desktop application will become a distributed web application, allowing to run simulations on a cloud computing system and share virtual experiments on the web. The modeling environment will run on a web browser using HTML5 and WebGL technologies

L-Py: An L-System Simulation Framework for Modeling Plant Architecture Development Based on a Dynamic Language

The study of plant development requires increasingly powerful modeling tools to help understand and simulate the growth and functioning of plants. In the last decade, the formalism of L-systems has emerged as a major paradigm for modeling plant development. Previous implementations of this formalism were made based on static languages, i.e., languages that require explicit definition of variable types before using them. These languages are often efficient but involve quite a lot of syntactic overhead, thus restricting the flexibility of use for modelers. In this work, we present an adaptation of L-systems to the Python language, a popular and powerful open-license dynamic language. We show that the use of dynamic language properties makes it possible to enhance the development of plant growth models: (i) by keeping a simple syntax while allowing for high-level programming constructs, (ii) by making code execution easy and avoiding compilation overhead, (iii) by allowing a high-level of model reusability and the building of complex modular models, and (iv) by providing powerful solutions to integrate MTG data-structures (that are a common way to represent plants at several scales) into L-systems and thus enabling to use a wide spectrum of computer tools based on MTGs developed for plant architecture. We then illustrate the use of L-Py in real applications to build complex models or to teach plant modeling in the classroom

OpenAlea: A visual programming and component-based software platform for plant modeling

International audienceAs illustrated by the approaches presented during the 5th FSPM workshop (Prusinkiewicz and Hanan 2007, and this issue), the development of functional-structural plant models requires an increasing amount of computer modeling. All these models are developed by different teams in various contexts and with different goals. Efficient and flexible computational frameworks are required to augment the interaction between these models, their reusability, and the possibility to compare them on identical datasets. In this paper, we present an open-source platform, OpenAlea, that provides a user-friendly environment for modelers, and advanced deployment methods. OpenAlea allows researchers to build models using a visual programming interface and provides a set of tools and models dedicated to plant modeling. Models and algorithms are embedded in OpenAlea components with well defined input and output interfaces that can be easily interconnected to form more complex models and define more macroscopic components. The system architecture is based on the use of a general purpose, high-level, object-oriented script language, Python, widely used in other scientific areas. We briefly present the rationale that underlies the architectural design of this system and we illustrate the use of the platform to assemble several heterogeneous model components and to rapidly prototype a complex modeling scenario

A Plastic, Dynamic and Reducible 3D Geometric Model for Simulating Gramineous Leaves

International audienceUnlike trees, the 3D architecture of gramineous plants is much more related to the shapes of its leaves than the arrangement of its branches. Many modelling efforts have thus concentrated on correctly capturing its complex shape at different stages and use them as scalable geometric primitives. Still, additional control of such objects is needed in the context of Functional Structural Modelling. The objective of this work is to propose a plastic and dynamic 3D leaf model that is well suited for such uses, still able to capture a variety of observed static shapes. Leaf shape is modeled by a parametric surface describing leaf midrib curvature, leaf width variation, undulation of leaf margins and twist along the midrib. Meshes can be generated from these surfaces, and reduced using a decimation algorithm. The model can be fitted with data or with curves drawn by user interaction. Morphological operators are defined and allows for plastic deformation of the control curves. The dynamics of shape acquisition can also be specified, and combined with morphological operators to sim- ulate various scenarios of evolution and responses to stresses. The capabilities of the model are demonstrated through several cases of use. Future directions of research are thought to be a better integration of mechanical or physiological constraints that would reduce the model plasticity but avoid user-induced unrealistic simulation