Hanan, J. S.

Wang, Y.

University of Queensland eSpace

FSPM04  ORAL PRESENTATIONS - SESSION 8 
 
4th International Workshop on Functional-Structural Plant Models, 7-11 june 2004 –Montpellier, France 
Edited by C. Godin et al., pp. 407-411 
Floradig: a configurable program for capturing plant architecture 
Jim Hanan,Yicai Wang 
Advanced Computational Modelling Centre, University of Queensland, Australia 
 
Floradig is computer software for measuring and recording plant architecture and how it changes 
over time. It is generic in that it can be configured to collect plant architecture data for any species of 
plant at any level of detail. It uses a systematic, hierarchical, approach to address the modular nature 
of plants in which complex architectures are constructed from limited sets of components. In addition, 
Floradig allows records to be made of the positions on plants of associated entities such as insects, 
infections, damage, and droplets of pesticides. This software demonstration will show how Floradig 
can be configured for different components at various levels of abstraction. The recommended 
procedure for data entry will be demonstrated, including audible prompting by the program. The use 
of automated error checking, structural comparisons and animation of data collected over time for 
ensuring data integrity will be shown. The user can also configure the data to be calculated from the 
input points and output to a file suitable for import to databases or spreadsheets. A new feature is the 
ability to produce output in AMAPmod MTG format [1]. 
 
The System 
The hardware for working with Floradig consists of a personal computer (PC) running Microsoft 
Windows 95, 98 or 2000 and one of a number of compatible 3D digitisers such as a GTCO GP12 
sonic digitiser, or a Polhemus FastTrak or IsoTrak magnetic digitiser.  
 
The Floradig program allows you to capture change in a plant’s architecture by recording 
snapshots, or instances, of 3D structure on a series of dates.  It is recommended that all instances of a 
single plant are accumulated in a single file, which increases in size each time the plant is digitised 
(Figure 1). Following this approach, there will be one data file for each plant in any particular 
experiment. 
 
 
Figure 1 Plant Manager Window 
 
Each time a plant is digitised, the geometry of its architecture is recorded as 3D coordinates for a 
set of points in a hierarchical structure (Figure 2).  Each point should be at a pre-defined and easily-
recognised location on the plant such as at a node or the tip of a leaf.  The user provides a settings file 
that contains a list of codes for different components and types and the number of points to be 
recorded for each. Floradig labels the xyz coordinates for each point according to its component type 
and the component’s topological position. 
J. Hanan et al. 
SESSION 7 – ORAL PRESENTATIONS 
408 
  
Figure 2 Hierarchy Window 
In most cases, digitising proceeds upward from the base of a plant.  The series of nodes up the 
main stem is digitised, followed by the components attached at each node from the bottom up.  
Branching topology is captured by starting a new series of nodes attached to the parent node of each 
branch.  Components within branches are then added in the same fashion as for the main stem.  The 
components and types within components are selected from a menu using the keyboard.  Floradig 
prompts for the number of points to be digitised for the selected component.  
 
 
Figure 3 Graphics Window.  In this example, flowers are shown as yellow, developing fruit as pale blue, and 
mature fruit as red. 
To help in checking for errors you can activate a 3D graphics reconstruction of the data (Figure 3) 
that can be rotated and viewed from any angle.  Different instances of the same plant can be compared 
in this way and in text format.  Menu commands allow data to be cut and pasted, comments to be 
recorded, branching topology to be navigated and files to be saved.  The 3D coordinate data can be 
converted into angles and lengths according to instructions in the settings file (*.ini) before being 
exported in a delimited text format (*.txt) suitable for importing into database, spreadsheet and 
statistics programs. 
 
Configuring Floradig 
Floradig is configured to suit a particular study by creating a settings file having an .ini extension 
(Figure 4). The settings in the file are arranged in 5 sections: Session, Digitising, Graphics, Output 
Floradig: a configurable program for capturing plant architecture 
ORAL PRESENTATIONS - SESSION 7 
409
Control and Component Definitions. A text-editing program such as Notepad should be used to 
customise the Output Control and Component Definitions settings.  
 
The Component Definitions section allows you to specify the components and types within 
components that may be digitised, the number of points to be digitised for each type, what values to 
calculate and write to file, and what graphics to display. This section of the file consists of an arbitrary 
number of 3-line definitions. In each line, the first two items give the component name and type 
separated by spaces. The name must be one of those found in Table 1 and the corresponding code is 
the shorthand used to select the component via the keyboard during operation of Floradig. The type 
can be any number from 0 to 9. 
 
[Session] 
InfoTitle=test 
DateFormat=0 
TimeFormat=0 
TestLengthError=87100890 
 
[Digitizing] 
VisitNodeZero=1 
UseDefaultComp=0 
NodePromptingUp=1 
MaxStructuresAtNode=0 
DefaultCompType=2 
DefaultCompIndex=1 
DefaultNodeIndex=0 
 
[Graphics] 
Filename=0 
PlantID=0 
Label=0 
Fill=1 
 
[Output Control] 
Decimal=2 
Minimum Diverg=0.0 
Minimum Pitch=0.0 
Separator=, 
 
[Component Definitions] 
Node 0 Numpoints=3 
Node 0 Output Definitions=I "Length"; W "Width"; R "Radial"; P "Axial"; 
Node 0 Graphics Codes= GC 1 0 0; GS 0 1; GC .4 .7 .3; GW 2; 
Node 1 Numpoints=1 
Node 1 Output Definitions=I "Length"; 
Node 1 Graphics Codes=  GC .4 .7 .3; GW 2; 
Bud 1 Numpoints=1 
Bud 1 Output Definitions=L N 0 "Bud length"; 
Bud 1 Graphics Codes=GC .8 .4 .8; GS N 0 5; 
Leaf 1 Numpoints=5 
Leaf 1 Output Definitions= L 1 4 "Leaf Length"; L 2 3 "Leaf Width";  
Leaf 1 Output Definitions 2= P N 0 1 "Petiole Angle";L 0 1 "Petiole Length"; 
Leaf 1 Graphics Codes=GW .2 GC 0 .7 .1; GS 0 1 2; GT 1 2 3; GT 2 3 4; 
Flower 1 Numpoints=1 
Flower 1 Output Definitions=L N 0 "Flower length"; 
Flower 1 Graphics Codes=GC .4 .7 .3; GS N 0 1; GC 1 1 0.5; GM 0 15;  
Figure 3 A Floradig settings file, Sample.ini 
 
Name Node Bud Leaf Flower Fruit Insect U 1 U 2 U 3 U 4 U 5 
Code N B L F R I X Y Z S T 
Table 1 Component Names and Codes 
 
The first line of each definition sets the number of 3D points to be digitised for that component 
type. There is no limit to the number of points. When digitising, you must remember to enter the 
points in the order you decided on for each component type. In Figure 5, for example, if you enter 
points in the order 0, 1, 2, 4, 3, a later assumption that the length of the lamina may be calculated from 
the second and fifth points to be digitised will be wrong. 
J. Hanan et al. 
SESSION 7 – ORAL PRESENTATIONS 
410 
 
Figure 5 Example of component point positioning by sequence 
 
Nodes are a special case.  If you use two for a node, Floradig will automatically accept the first 
point as the position of the node and will prompt for an "orientation" for the second point. This is a 
point on an imaginary line at right angles to the axis of the stem, passing from the centre of the stem 
out through the node-point. It enables calculation of phyllotactic angles between successive nodes and 
the distance of the orientation-point from the node-point is of no account. If you use three points 
Floradig will prompt for a stem-width-point on the opposite side of the stem from the point for the 
node. 
 
The second group of lines of each Component Definition has the keyword “Output Definitions=” 
followed by a semi colon separated list of definitions specifying what values to calculate and write to 
an export file. The information in the list takes the form: 
<InfoCode> <Index list> "Optional Label"; 
where <InfoCode> specifies the calculation to be performed such as length L, or pitch P <Index 
list> contains the point-identifying numbers required for the calculation, and the optional label is 
used to identify the result of calculation in the export file.  
Similar codes can be used to specify what is drawn in the graphics window. A complete list of 
codes and illustrative diagrams is available in the Floradig manual. For example, in Figure 3, in the 
lines  
 
Leaf 1 Output Definitions= L  1 4 "Leaf Length"; L 2 3 "Leaf Width";  
Leaf 1 Output Definitions 2= P N 0 1 "Petiole Angle";L 0 1 "Petiole Length"; 
 
leaf length is calculated as the distance between points 1 and 4, the width as the distance between 
points 2 and 3, the petiole angle is calculated between the direction of the internode and the vector 
joining points 0 and 1, and the petiole length is calculated as the distance from point 0  to point 1. 
Output 
Floradig can output the data specified by the user either as a flat data file or in MTG format. When 
writing a flat export data file (*.txt) (Figure 6), Floradig attaches a label to every item of data. The 
labels have a multi-level structure that corresponds to the hierarchy of branch-levels in a plant. A 
colon separates the reference numbers of the structures (S) and nodes (N) which connect the base of 
the plant to the node of attachment of a component. The last item in a label defines the component and 
its type. For example: S01N02:S02N01:S01L00; from right to left, S01L00 defines a Leaf, which is 
Structure 01 at (S02N01) Node 01 of the second Structure at (S01N02) Node 2 on the main stem. The 
sequence numbers for structures and nodes are in two-digit fields to facilitate searching and sorting 
when the data have been imported into a database or spreadsheet. Such a data file can be read into a 
database or spreadsheet program, and the structure label will provide the hierarchical information 
needed for detailed analysis. 
0 1 
2 
3 
4 
Floradig: a configurable program for capturing plant architecture 
ORAL PRESENTATIONS - SESSION 7 
411
 
Plant,Treatment,Date,Structure,Component,Type,Level,Label,Value,Comments 
Plant 1, Treat 1,17/02/2000,S00D00:C,I,0,0,PAD-file,,"C:\Digit\Floradig\Demos\Sample.pad" 
Plant 1, Treat 1,17/02/2000,S00D00:C,I,0,0,Definition-file,,"C:\Digit\Floradig\Demos\Sample.ini" 
Plant 1, Treat 1,17/02/2000,S00D00:C,I,0,0,Plant-comment,,"Measured once per week" 
Plant 1, Treat 1,17/02/2000,S00D00:C,I,0,0,Instance-comment,,"Sample 1" 
Plant 1, Treat 1,17/05/2000,S01N00;,C,0,1,Comment,,"Main stem" 
Plant 1, Treat 1,17/02/2000,S01N00;,C,0,1,Comment,,"Base of the plant" 
Plant 1, Treat 1,17/02/2000,S01N01;,N,0,1,Length,121.45 
Plant 1, Treat 1,17/02/2000,S01N01;,N,0,1,Phyllo,-83.04 
Plant 1, Treat 1,17/02/2000,S01N01;,C,0,1,Comment,,"Node 1" 
Plant 1, Treat 1,17/02/2000,S01N01:S01L00;,L,1,2,Leaf Length,83.73 
Plant 1, Treat 1,17/02/2000,S01N01:S01L00;,L,1,2,Leaf Width,36.80 
Plant 1, Treat 1,17/02/2000,S01N01:S01L00;,L,1,2,Comment,,"First leaf" 
Plant 1, Treat 1,17/02/2000,S01N01:S02F00;,F,1,2,Flower length,51.75 
Plant 1, Treat 1,17/02/2000,S01N01:S03F00;,F,1,2,Flower length,44.79 
Plant 1, Treat 1,17/02/2000,S01N01:S04F00;,F,1,2,Flower length,35.53 
Plant 1, Treat 1,17/02/2000,S01N02;,N,0,1,Length,55.17 
Plant 1, Treat 1,17/02/2000,S01N02;,N,0,1,Phyllo,-171.13 
Plant 1, Treat 1,17/02/2000,S01N02:S01L00;,L,1,2,Leaf Length,86.32 
… 
Figure 6 A Floradig export file, Sample_0.txt. 
 
Future Developments 
Future enhancements include the capability to input arbitrary numbers of points for an component 
type, keyboard and menu-based entry of data to associate with a component, and interaction with the 
data through picking from the graphics window. We have a prototype system to allow point-picking 
entry from arbitrary point clouds, such as those produced by a laser scanner. We are always interested 
in hearing users’ ideas on how to improve any aspect of the software. 
 
References 
[1] Godin, C. and Guedon, Y. (2000) AMAPmod Introduction and Reference Manual, V 1.8, CIRAD, 
Montpellier  
[2] Hanan, J and Room, P (2002) Floradig User Manual, CPAI, University of Queensland, Brisbane. 
 


Floradig: a configurable program for capturing plant architecture

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Floradig: a configurable program for capturing plant architecture

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