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Georg-August University of Göttingen Chair for
Computer Graphics and Ecological Informatics Büsgenweg
4, 37077 Göttingen, Germany http://www.uni-goettingen.de/en/67072.html |
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Tutorial and Workshop
"Modelling with
GroIMP and XL"
combined
with the 5th GroIMP user and developer meeting
Date: 27 – 29 February 2012
XL and GroIMP
tutorial for beginners: 27
Feb., 9:15 h – 15:00 h
Tutorial for
advanced XL and GroIMP users: 27
Feb., 16:00 h – 28 Feb., 12:00 h
GroIMP user and
developer meeting: 28 Feb.,
13:00 h – 14:00 h
Workshop dinner: 28
Feb., 19:00 h
Workshop: 28
Feb., 14:00 h – 29 Feb., 12:00 h
Location:
Forest Growth, Büsgenweg 4, 37077
Room CIP I
Contact: Winfried
Kurth, Chair
for Computer Graphics and Ecological Informatics
Georg-August University of
Göttingen, Büsgenweg 4, 37077 Göttingen, Germany
Tel. +49–551–399715, Fax
+49–551–393465, E-mail wk(at)informatik.uni-goettingen.de
Programme
Monday, 27 February 2012
9:00 Opening,
Introduction
9:10 W.
Kurth: Introduction
to rule-based programming, L-systems and XL
[pdf]
10:15 Coffee break
10:30 W. Kurth:
Basic examples
in XL (part 1) [pdf]
11:30 R.
Hemmerling and K. Smoleňová: How to model a daisy in 1/2 hour [textures,
archived files]
12:00 Lunch
13:30 W. Kurth:
Basic examples
in XL (part 2) [pdf]
14:30 Simple
branched structures and rendered plants modelled with XL (team work)
15:00 Coffee break and/or Small team sessions
15:45 W.
Kurth: Interpretive
rules and instantiation rules [pdf]
16:15 M. Henke:
A
closer look at some examples from the grogra.de gallery
16:45 W. Kurth
and G. Buck-Sorlin: Using the
radiation model of GroIMP [pdf]
17:30 Using the
radiation model (team work)
18:00
Questions and answers and/or Small team sessions
- ca. 18:30
Tuesday, 28 February
9:00 R.
Hemmerling: The
ODE framework of GroIMP
10:00 G.
Buck-Sorlin: GPUFlux
– a new radiation model using the GPU
[pdf]
10:30 Coffee break
10:45 Y.
Ong: MTG format,
import and visualization in GroIMP, and statistical analysis
11:30 GroIMP user and developer meeting
12:30 Lunch
Workshop
"Modelling with GroIMP and XL – recent results"
13:30 J. Evers:
Simulating
light interception in Australian wide-row wheat systems
14:15 V.
Sarlikioti and L. Pagès: Exploring
root developmental plasticity to soil nutrients in three-dimensional architectural
modelling of the root system
15:00 Coffee break
15:15 R.
Hemmerling: Specification
of chemical formulæ in XL with operator overloading
16:00 T. W.
Chen: Modelling
cucumber plants (project outline)
16:15 K.
Smoleňová, M. Henke and C. Ding: GreenLab
in XL – usage and more
16:45 Coffee break
17:00 M. Henke
and K. Smoleňová: Component-based
modelling within GroIMP
17:30 G. Buck-Sorlin, P. Guillermin, M. Delaire, Fatoumata Sané, Christian le-Morvan: Towards a multi-scaled functional-structural model of apple, linking ecophysiology at the fruit and branch scales
- ca. 18:15
19:00 Workshop
dinner @ Kartoffelhaus, Goetheallee 8
Wednesday, 29 February
9:00 F. Schöler: Introducing
basic boolean set operations for GroIMP
9:30 P. Surový, A. Yoshimoto, N. A. Ribeiro: Comparison
of pruning regimes for Stone pine (Pinus
pinea L.) using a functional-structural plant model written in XL [pdf] (remote video / audio life presentation from
10:15 Coffee
break
10:45 S. Paulus: The
benefit of plant models for laser generated data [pdf]
11:15 All: Conclusions and future projects
End of tutorials/workshop: 29 Feb., 12:00 h
Abstracts of
workshop contributions
Gerhard
Buck-Sorlin, Pascale Guillermin, Mickaël Delaire, F. Sané, Ch. le-Morvan (Agrocampus
Ouest,
Towards a multi-scaled functional-structural model of apple, linking
ecophysiology at the fruit and branch scales
A lot of data on eco-physiological processes in apple
(Malus x domestica) exists, concerning various aspects of fruit growth and
development, fruit quality, leaf photosynthesis etc. However, despite the
wealth of data and studies many processes leading to (interannual and
intra-arboreal) heterogeneity in quantity of fruit production as well as fruit
quality are only poorly understood at the branch level. Current
Functional-Structural Plant Models of apple have targeted canopy architecture,
i.e. development of vegetative structures. Here we will present a concept to
apply the FSPM paradigm to the simulation of assimilation (source), transport
and consumption (sink) of carbon in the context of a static structure
representing the fruit-bearing branch.
Jochem Evers
(Wageningen
Simulating light interception in Australian wide-row wheat systems
To optimize the use of water of a wheat crop in
water-limited environments, wheat can be sown in wide rows of closely spaced
wheat plants. This is done to delay water use and avoid terminal water stress
during grain filling. However, light interception in such systems differs from
regular crop row distances. Therefore, to be able to simulate such wide-row
systems using crop models such as APSIM, its light extinction routines need to
accommodate alternative crop configurations, such as wide rows. Here we show
on-going work on using a GroIMP-based architectural model of wheat development
to analyse the relationship between crop configuration and light interception.
The aim of this work is to improve calculation of light interception in APSIM
such that wide-row wheat systems can be simulated more accurately.
Reinhard Hemmerling (
Specification of chemical
formulæ in XL with operator overloading
Operator overloading is a feature of many programming
languages and allows to define the meaning of operator symbols on user-define
types. In this presentation we will show how certain operators can be defined
in XL that allow to parse chemical reactions, and then solve the reactions
numerically. As an interesting side-effect, specification of chemical reaction
equations can be seen as part of the XL language, and syntax checking of the
compiler is applied to these equations. Two examples will be shown to
demonstrate its use and to verify the results.
Michael
Henke and Katarína Smoleňová (
Component-based modelling within
GroIMP
A framework
for interactive, visual modelling – new tools to tackle problems in plant
science
Modelling has become an essential part of all kinds of scientific activities.
In fact, it could be stated that modelling is the common way to obtain a better
understanding of a system and problems related to it. The interactive modelling
platform GroIMP is a general 3D-modelling software, which has been tailor-made
for use in functional-structural plant modelling. By using the integrated
language XL (a Java-based extended L-system language), various different models
have been developed over the last years, yielding a pool of more or less
specialized, openly accessible models, from which the user community could
actually benefit directly. However, when applied to complex tasks, models still
tend to develop in an intransparent manner, rendering an efficient re-use of
existing components next to impossible. Methods and tools which are commonly
used in software engineering (e.g., component-based programming, graphical
software visualization) can help to overcome this bottleneck.
Stefan
Paulus (
The benefit of plant models for laser generated data
Laserscanning of plants provides highly accurate resolution together with
non-invasive measurements. The resulting point cloud can be used to extract
parameters describing plant status in respect to, e.g., drought stress.
Problems result from plant motion, dimension of deformation caused by growth
and outer influences as well as from insufficient 3D correspondence of scan
parts among each other. This complicates fusion of different sensors and scan
parts and also comparison of data from different dates. Plant models give
solutions to these problems by providing plant-applied coordinate systems that
enable spatio-temporal registration.
Vaia Sarlikioti and Loïc Pagès (INRA
Exploring
root developmental plasticity to soil nutrients in three-dimensional architectural
modelling of the root system
A simple
dynamic root model proposed by Pagès (2011) was
translated to the modelling language XL, using the GroIMP platform and was used
as a base. The objectives of this work were to introduce a new
simplified root architectural model that includes the recognized plasticity
mechanisms of 1) Chemotropism, 2) Inter-Branch distance and 3) Branching
Hierarchy and to investigate the effect of such mechanisms on root architecture
and nutrient uptake for four different nutrient distributions in the soil.
Florian Schöler (
Introducing Basic Boolean Set Operations for GroIMP
This talk
will be about a technical approach to introduce basic Boolean set operations
for the modelling platform GroIMP. Boolean set operations are important in many
fields of application. Their results can, for example, be used to compute the
volume of generated structures. Based on the volume, other physical properties
like the weight or inertia, and also semantic properties like construction
costs (e.g., in CAD) can be derived. It is shown how one can unify or intersect
two or more geometric primitives and how one can compute their difference. The
operations may be inserted as nodes into the RGG-Graph that automatically
gather all accessible primitives. The geometric primitives are amended by a
description of a closed surface as a set of triangles. As an example
application, it is shown how one can compute the volume of complex objects
generated by the Boolean set operations.
Katarína
Smoleňová, Michael Henke and Cong Ding (
GreenLab in XL – usage and more
GreenLab is
a functional-structural plant model that has already been applied to a number
of various plant species. Plant organogenesis is desribed by the dual-scale
automaton formalism and growth is driven by source-sink relations between
plant organs. It will be shown how the formalism of GreenLab and the growth
process can be translated into the language XL. Currently several features of
the deterministic and stochastic version of the GreenLab model are included.
To provide a
user-friendly way for parameter input, an additionally implemented graphical
user interface was developed as part of the modelling platform GroIMP.
Supported is also import and export of parameter files (*.sci) and AMAPSymbol
object shape files (*.smb), both being in use in the open-source GreenLab
software called GreenSciLab.
Peter Surový, A. Yoshimoto
and N. A. Ribeiro:
Comparison
of pruning regimes for Stone pine (Pinus pinea L.) using a
functional-structural plant model
Functional-Structural Plant
Models (FSPM) are becoming important tools for modelling the structure and
growth of plants, including complex organisms like trees. These models combine
the advantages of empirical, mechanistic, and structural models to simulate the
growth of individual plant structures (branches, buds, leaves, etc.). This
approach enables realistic evaluation of the plant’s response – including changes
in structure and growth – to different environmental conditions. We demonstrate
the potential use of these models to evaluate individual tree growth under
different management regimes (pruning). The data used in this study were
obtained from 3-D measurements taken with a FASTRAK Polhemus digitizer, with
specific attention given to bud creation and branching. Each branch segment was
analyzed to estimate its age, enabling us to document annual structural
changes. We use the XL programming language and a GroIMP environment to
simulate and compare different pruning scenarios.