Stochastic 3D Tree Simulation Using Substructure Instancing

Tree growth is simulated using a stochastic model of organogenesis that is faithful to botanical knowledge. This model is based on the concept of bud "physiological age", on the statistical description of the transition from one physiological age to another as well as of bud death, bud growth and branching processes. In order to enhance simulation efficiency, a recurrent algorithm based on stochastic substructure instancing is proposed. The tree is hierarchically decomposed into substructures that are classified according to their physiological age, and a library of random substructure instances is constructed: the recurrent simulation starts with the simplest peripheral substructures, which are also the physiologically oldest; these substructures are then progressively assembled into more complex substructures, until the tree is completely simulated. When the size of the library of substructure instances is small, the time needed to build a single stochastic tree is much shorter than for a usual tree simul tion that operates on a bud-by-bud basis. in computing a group of trees, the speed gain is even much greater, because the library of substructure instances is built for the first tree, and then is reused for computing subsequent trees. A preliminary sensitivity analysis is carried out according to the size of the library: when the library is large, the simulated distribution of the number of organs fits well with the theoretical mean and variance; the algorithm can thus be tuned in order to obtain accurate predictions. On the other hand, a small library (e.g., with only 2 or 3 instances for each substructure class) is sufficient for generating visually realistic trees. A few examples illustrate the high performance of this algorithm which paves the way for the fast simulation of large forest scenes

Structural Factorization of Plants to Compute their Functional and Architectural Growth

Numerical simulation of plant growth has been facing a bottleneck due to the cumbersome computation implied by the complex plant topological structure. In this article, the authors present a new mathematical model for plant growth, GreenLab, overcoming these difficulties. GreenLab is based on a powerful factorization of the plant structure. Fast simulation algorithms are derived for deterministic and stochastic trees. The computation time no longer depends on the number of organs and grows at most quadratically with the age of the plant. This factorization finds applications to build trees very efficiently, in the context of geometric models, and to compute biomass production and distribution, in the context of functional structural models

Wood specific gravity variations within tree trunk: the case study of Legumes representatives in French Guiana

International audienceOver the past decade, much attention has been devoted to the development of forest biomass estimation methods at a stand scale, leading to the establishment of allometric models (Chave et al., 2014). These allometric equations use a unique wood specific gravity value (WSG) per species, but neglect the within tree variations of WSG found by others (Wiemann & Williamson, 1989).The main objectives of this study are (1) to illustrate the diversity of radial (from pith to bark) and longitudinal (from bottom to top) patterns of WSG variation within and between species, (2) to highlight different trends of WSG radial variations and the possible misinterpretations of these trends due to the effect of heartwood and (3) to link these variations and patterns to the successional status of the species (from pioneer to sciaphilic species).We sampled 33 small trees (10<DBH<15cm) at the Paracou field station in French Guiana, belonging to 14 Legumes species, and to different ecological groups according to light. WSG radial profiles were measured at 3 heights along the trunk, and 2 heights along the crown, of each tree.We observed different radial and longitudinal patterns of WSG variation. Pioneer and heliophilic species show both radial and longitudinal increases in WSG, while shade-tolerant and sciaphilic species show the reverse pattern. Hemi-tolerant species show an intermediate pattern, with WSG increasing radially, but decreasing or increasing longitudinally. Decreasing radial pattern in sciaphilic species is due to the presence of heartwood relatively denser than sapwood. When a corrected WSG is used, sciaphilic species show the same radial pattern as hemi-tolerant species (i.e. increasing) or no radial pattern (i.e. ‘flat’ from pith to bark).Decreasing WSG from bottom to top is a general case, excepted for species with low WSG (i.e pioneers). All studied species tend to the same range of WSG values with height (~ 0.6-0.9), supported by a higher WSG under bark within trunk.We also developed a biomass model, implemented under Xplo software (Griffon et al., 2011) to infer trunk biomass from WSG profiles, allowing comparisons of both single- and varying-WSG models.Wood specific gravity variations within tree trunk: the case study of Legumes representatives in French Guiana

Xtrawood: refining estimation of tree above ground biomass using wood density variations and tree structure

International audienceBackgroundTree above ground biomass (AGB) is currently estimated by tree-level allometrical models that take into account, tree volume estimated from proxy variables of tree size (DBH) and species average wood specific gravity (WSG). These methods are common and realistic from a practical point of view. However, they do not take into account deviance from fixed allometrical trajectories and species or tree level WSG variations. Here, we present Xtrawood software that allows computation of tree AGB according to structure and WSG variations.MethodXtrawood reconstructs tree structure and integrates WSG variations by merging tree structure and WSG data measured at different position in trees, leading to the computation of global AGB and visualization of WSG variation along tree structure. Tree structure is measured according to stem dimensions (length, diameter) and positions within tree, and encoded in Multiscale Tree Graph format (MTG). WSG data is made of radial WSG profiles (1 measure each 0,5 cm from pith to bark) sampled at different heights within whole tree. Xtrawood output are illustrated using a dataset collected on an Amazonian forest ‘biomass dominant species’, Dicorynia guianensis Amsh., also known to exhibit substantial WSG gradients along both radial and vertical axis. 9 trees ranging from 15 to 60 cm DBH were measured by climbers. Each tree was felled and samples were collected at different positions (3 in trunk, 1 to 5 in crown) to record WSG radial profiles.ResultsXtrawood allows computation of tree volume, but also visualization of WSG variations in tree as well as inference of WSG radial profiles at different heights. Output variables are decomposed according to different tree scale and locations (axis, trunk/crown) and easy to extract. Xtrawood results will be compared to those of standard estimation method and can be used to identify positions in trees where WSG value leads to the better estimate of tree AGB.Conclusion/perspectiveXtrawood produces AGB estimate with data from intensive measurements practices. The sampling protocol, used here, remains destructive and time-consuming because Xtrawood is not directly dedicated to forest managers, but to help calibration of realistic sampling strategies. Moreover, Xtrawood offers a way to understand relationships between tree development, WSG variations within tree structure and biomass accumulation in the context of natural forests or plantations. A software demo is available at coffee break

Une Contribution Logicielle dédiée la simulation de l'architecture et de la croissance des plantes

Modeling and simulation of plant growth may be assessed in different ways concerning both knowledge and technical means. This research field remains at the intersection of many specialties such as botany, agronomy, physiology, mathematics or computer science. Many works where already leaded in this area which mainly focused on a single one among these specialties. We propose a generalist approach that relies on knowledges coming both from plant biology, mathematics and computer engineering. This study consists in three steps : - Definition of a pure structural model aimed at plant architecture description (AmapSim). This model uses stochastic processes to mimic distributions of branches, shoots and internodes measured on real plants. These processes are ruled through a finite state automaton whose state variable is the physiological age that represents the vigorousness of the buds of the plants during their life. - Definition of a set of software tools ready to host plant simulators (Vitis). This library mainly provides tools to manage a memory plant representation, to manage model parameters and to schedule or connect software parts that may be gathered to build simulators. - Case study of the implementation of AmapSim into Vitis and example of some applications. This step should show how accurate the choice proposed during the previous steps may be. Some results of pure AmapSim simulations will be shown and then some applications where AmapSim is dynamically connected to additional knowledges thanks to Vitis functionalities will be shown. A particular focus will be put on how to add knowledge coming from physiology thus creating functionalstructural applications while connecting structural and physiological software plugins together. This study shows perspectives on how to use AmapSim and how to develop new plugins; on development of new models into Vitis; on the formal study of plant simulators dedicated to the needs of modelers.La modélisation et la simulation de la croissance des plantes peut être abordée selon plusieurs aspects tant pour ce qui concerne la connaissance que les moyens mis en œuvre. Ce champ d'étude se trouve à la croisée de diverses expertises telles que botanique, agronomie, physiologie, mathématique ou informatique. Beaucoup de travaux ont été proposés dans ce domaine dont la plupart sont fortement colorés par une seule de ces spécialités. Nous proposons une approche qui nous semble généraliste et qui s'appuie sur des connaissances provenant conjointement des champs de l'agronomie, des mathématiques et du génie logiciel. Cette étude se décompose en trois étapes : - Proposition d'un modèle purement structural de description de l'architecture des plantes (AmapSim). Ce modèle utilise des processus stochastique pour représenter les distributions de branches, de pousses et d'entre-nœuds observées sur des plantes réelles . Ces processus sont organisés autour d'un automate à états finis dont la variable d'état est l'âge physiologique et qui simule l'évolution de la vigueur des bourgeons de la plante au cours de leur vie. - Définition d'un ensemble d'outils logiciels propres à accueillir des simulateurs de croissance de plante (Vitis). Cette librairie offre des services pour la gestion de la description de plante en cours de simulation, pour la gestion des paramètres des modèles qui édifient la plante et pour la synchronisation et l'échange d'information entre les blocs fonctionnels qui constituent le simulateur. - Développement d'un simulateur d'AmapSim dans Vitis puis de quelques exemples d'applications. Cette étape a pour but de démontrer le bien fondé des choix effectués lors des étapes précedentes. On y montre des résultats de simulation d'AmapSim puis d'applications basées sur AmapSim et agrémentées dynamiquement de connaissances additionnelle grâce aux fonctionnalités de Vitis. On y montre notamment comment ajouter de la connaissance issue du domaine de la physiologie pour créer de applications de type structure-fonction. Ce travail ouvre des perspectives concernant l'utilisation d'AmapSim et le développement de nouveaux plugins ; l'introduction de nouveaux modeles dans Vitis ; la formalisation de la notion de simulateur de plante à l'usage des futurs modélisateur

Rapport de stage de recherche. Zoom sémantique

Dans le cadre de la synthèse d'images, ou infographie, le laboratoire de modélisation du CIRAD a développé le logiciel AMAP, appliqué à l'agriculture et dont les applications commerciales portent essentiellement sur l'élaboration de modèles numériques de plantes. Afin d'accélérer les calculs pour les images contenant un très grand nombre d'objets, une méthode d'optimisation a été mise au point. Cette méthode, le zoom sémantique, permet d'afficher les objets d'une scène avec différents niveaux de précision suivant leur nature et leur situation, ce qui permet de ne consacrer que peu de temps de calcul à des objets peu visible