User Guide

Version 1.0.0
 DRAFT - SExI-FS Training Workshop, Sembawa 10-12 May 2005

Table of Content

Table of Content ................................................................................................................2

List of Figures ....................................................................................................................4

1. General Information..................................................................................................7
1.1. Overview ............................................................................................................. 7
1.2. The SExI-FS Software ......................................................................................... 8
1.3. The Minimum Requirement................................................................................. 8

2. Getting Started...........................................................................................................9
2.1. Installation .......................................................................................................... 9
2.2. Running SExI-FS............................................................................................... 12
2.3. Main Window .................................................................................................... 13
2.3.1. File Menu .................................................................................................. 14
2.3.2. Simulation Menu....................................................................................... 14
2.3.3. Statistic Chart Menu ................................................................................. 15
2.3.4. Window Menu .......................................................................................... 16
2.3.5. Help Menu ................................................................................................ 16
2.3.6. Simulation List Window ........................................................................... 16
2.3.7. Simulation Control Window ..................................................................... 17
2.3.8. Vertical View Window ............................................................................. 18
2.3.9. Trees 3D Visualization ............................................................................. 19
2.3.10. Forest 3D Visualization ............................................................................ 20

3. User’s Manual ..........................................................................................................21

3.1. Create New Simulation ..................................................................................... 21
3.2. Simulation Plot Setting ..................................................................................... 27
3.2.1. Aboveground Setting ................................................................................ 28
3.2.2. Belowground Setting ................................................................................ 32
3.3. Species Parameters Settings ............................................................................. 32
3.3.1. Set Species List ......................................................................................... 33
3.3.2. Species characteristic ................................................................................ 34
3.3.3. Light Sensitivity........................................................................................ 35
3.3.4. Growth Function ....................................................................................... 36
3.3.5. Allometric Relations ................................................................................. 37
3.3.6. Dynamic Test ............................................................................................ 38
3.4. Scenario Setting ................................................................................................ 40

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3.4.1. Simulation Scenario .................................................................................. 40

3.4.2. Species Scenario ....................................................................................... 41
3.5. Initial Stand....................................................................................................... 42
3.5.1. Regular Plantation..................................................................................... 42
3.5.2. Random Plantation.................................................................................... 43
3.5.3. Manual Plantation ..................................................................................... 44
3.6. Running the Simulation..................................................................................... 45
3.6.1. Run Simulation ......................................................................................... 45
3.6.2. Stop simulation ......................................................................................... 46
3.6.3. Remove Simulation................................................................................... 46
3.6.4. Duplicate Simulation ................................................................................ 47
3.6.5. Save Simulation ........................................................................................ 48
3.6.6. Open Simulation ....................................................................................... 49

4. Simulation Results ...................................................................................................51

4.1. Vertical Projection 2D of Tree Plot.................................................................. 51
4.1.1. Tree Paint Options .................................................................................... 52
4.1.2. Tree’s Info................................................................................................. 52
4.1.3. Overlay Map ............................................................................................. 52
4.1.4. Cut the Trees ............................................................................................. 53
4.1.5. Tree’s Object Inspector............................................................................. 53
4.2. Horizontal Projection 2D of Tree Plot ............................................................. 53
4.3. View 3D Visualization....................................................................................... 54
4.4. View 3D Animation ........................................................................................... 55
4.5. 3D Visualization Window Menus...................................................................... 56
4.5.1. Snaphot ..................................................................................................... 56
4.5.2. Rendering Mode........................................................................................ 56
4.5.3. Show 3D Component Part ........................................................................ 57
4.6. Hemispherical Photograph............................................................................... 57
4.7. Statistical Data.................................................................................................. 59
4.7.1. Bar chart.................................................................................................... 60
4.7.2. Line chart .................................................................................................. 60
4.7.3. Scatter plot ................................................................................................ 61

5. Appendix A...............................................................................................................62
a. File type ............................................................................................................ 62
i. Simulation (*.s)................................................................................................. 62
ii. Simulation data (*.txt) ...................................................................................... 62
iii. Simulation setting (*.xml) ............................................................................ 62

6. Index..........................................................................................................................63
6.1. Order By Alphabet ............................................................................................ 63

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List of Figures

Figure 1: Introduction Window ..............................................................................9

Figure 2:Install Folder Option Window ................................................................10
Figure 3: Shortcut Folder Option Window ...........................................................10
Figure 4: Pre-Install Summary Window...............................................................11
Figure 5: Finish Installation .................................................................................11
Figure 6: SExI-FS in Window's Start Menu .........................................................12
Figure 7: SExI Splash Screen .............................................................................12
Figure 8: Main Window. ......................................................................................13
Figure 9: Menu Bar, Pull Down Menu, and Title Bar Description ........................13
Figure 10: File Menu ...........................................................................................14
Figure 11: Simulation Menu ................................................................................14
Figure 12: Statistic Chart Menu...........................................................................15
Figure 13: Window Menu ....................................................................................16
Figure 14: Simulation List Window......................................................................17
Figure 15: Simulation Control Window................................................................17
Figure 16: Vertical View Window ........................................................................18
Figure 17: Global Menu ......................................................................................19
Figure 18: Tree's Menu .......................................................................................19
Figure 19: Trees 3D visualization........................................................................20
Figure 20: Forest 3D visualization.......................................................................20
Figure 21: File Menu ...........................................................................................21
Figure 22: Source Simulation Dialog...................................................................21
Figure 23:Simulation Description Dialog .............................................................22
Figure 24 Aboveground Setting ..........................................................................22
Figure 25 Belowground Setting...........................................................................23
Figure 26: Tree Species Setting Dialog ..............................................................24
Figure 27 Detail Species Setting.........................................................................24
Figure 28: Initial Stand Dialog.............................................................................25
Figure 29: Summary Dialog ................................................................................26
Figure 30: Simulation List Window......................................................................26
Figure 31: Simulation Control Window................................................................26
Figure 32: Simulation Menu ................................................................................27
Figure 33: Forest Simulation Panel.....................................................................27
Figure 34: Area Size ...........................................................................................28
Figure 35:Light Setting Panel..............................................................................28
Figure 36: Horizon Projection of Beams Vector ..................................................29
Figure 37: Vertical Projection of Beams Vector ..................................................29
Figure 38: Light Map for Recruitment Test Shown in SExI GUI ..........................31
Figure 39: Belowground Setting Panel................................................................32
Figure 40 Species Description List......................................................................33

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Figure 41: Species Characteristic Setting ...........................................................33

Figure 42: Light Sensitivity Setting......................................................................35
Figure 43: Light Stress Graphic ..........................................................................35
Figure 44: Growth Function Panel ......................................................................37
Figure 45:Profile Function Panel.........................................................................38
Figure 46: Dynamic Test Panel...........................................................................38
Figure 47: Artificial Light Map .............................................................................39
Figure 48: Age Dialog Box ..................................................................................39
Figure 49: 3D Tree Visualization.........................................................................40
Figure 50: Plot Scenario Setting Panel ...............................................................41
Figure 51: Species Scenario Panel.....................................................................41
Figure 52 Initial Stand with Regular Plantation ...................................................42
Figure 53 Plantation Pattern Editor .....................................................................43
Figure 54 Regular Plantation 3x6m.....................................................................43
Figure 55: Random Plantation ............................................................................44
Figure 56: Manual Plantation. .............................................................................45
Figure 57: Remove Tree .....................................................................................45
Figure 58: Simulation Control Window................................................................46
Figure 59: Stop Menu in Simulation Menu ..........................................................46
Figure 60: Remove Option in Simulation Options ...............................................47
Figure 61: Remove Menu in Simulation Menu ....................................................47
Figure 62: Remove Confirmation ........................................................................47
Figure 63: Duplicate Option in Simulation Options..............................................48
Figure 64: Duplicate Menu in Simulation Menu ..................................................48
Figure 65: Save Option on File Menu .................................................................48
Figure 66: Save File Dialog.................................................................................49
Figure 67: File Menu ...........................................................................................49
Figure 68: File Open Dialog ................................................................................50
Figure 69: Vertical Projection Option ..................................................................51
Figure 70: Vertical View Window ........................................................................51
Figure 71 2D Tree Paint Options Menu ..............................................................52
Figure 72: Show Tree’s Info menu ......................................................................52
Figure 73 Overlay Map Option Menu Figure 74 Light Map (left) and Root Map
(Right) Overlay 52
Figure 75: Remove Tree in Vertical View............................................................53
Figure 76: Object Inspector Option Figure 77: Object Inspector ...................53
Figure 78: Horizontal Projection View .................................................................53
Figure 79 Horizontal View Menu .........................................................................53
Figure 80: 3D View in Simulation Menu Figure 81: Virtual Forest Setting. ......54
Figure 82: Wireframe Crown and Land in Virtual Forest .....................................55
Figure 83: Leafy and Textured Tree Crown 3D visualization ..............................55
Figure 84:Virtual Control Window .......................................................................55
Figure 85: 3D Option Menu from Vertical View Window .....................................55
Figure 86: Snapshot Setting Box ........................................................................56
Figure 87: Snapshot Window ..............................................................................56
Figure 88: Tree in Transparent Mode .................................................................56

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Figure 89:Tree in Solid Mode..............................................................................56

Figure 90: Tree Branches View...........................................................................57
Figure 91: Hemiphot Menu in Vertical View Window ..........................................57
Figure 92 Hemiphot Window...............................................................................58
Figure 93: Hemiphot Table .................................................................................59
Figure 94: Statistic Chart Menu for Overall Simulation List.................................59
Figure 95: Data Option in Simulation Options .....................................................59
Figure 96: Tree Stat Option ................................................................................60
Figure 97: Bar Chart Variables ...........................................................................60
Figure 98: Bar Chart ...........................................................................................60
Figure 99: Line Chart Variables ..........................................................................61
Figure 100: Basal Area in Line Chart ..................................................................61
Figure 101: Scatter Plot Variables ......................................................................61
Figure 102: Scatter Plot ......................................................................................61

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Chapter

1. General Information

General Information 1
1.1. Overview
The SExI forest simulator focuses on tree-tree interactions in a mixed multi-species agroforest.
The high level of structural complexity of such traditional agroforestry systems defies classical
forestry approaches when it comes to optimizing management practices. To cope with this
complexity, farmers have adopted a tree-by-tree management approach, which is closer to
gardening than to any usual tropical forestry or estate crop management model. Individual tree
care and regular tending takes the form of seedlings transplanting, selective cleaning and felling,
adjusted harvesting intensity.
Farmers’ approach appears to be in line with two basic tenets of biology: first, individuals are all
different with behavior and physiology that result from a unique combination of genetic and
environmental influence, and second, interactions are inherently local. Based on the same
premises a computer model was developed to explore different management scenarios.
The model uses an object-oriented approach where each tree is represented by an instance of a
generic class of tree. The simulated object trees, mimicking real trees, interact through modifying
their neighbors' environment. These modifications are mediated through two major resources:
space and light. A 3D representation of a one-hectare plot of forest serves as the grounds for the
simulation of this competition.
The major objective of such a model is to get a coherent dynamic representation of a complex
system, where complexity refers here to the assemblage of locally interacting individuals with
different properties more than to the complexity of the elementary processes involved. The model
provides insight on what are the critical processes and parameters of the dynamic of the system.
It should also allow exploring prospective management scenarios, help assessing the relevance
of present management techniques etc.
Model sensitivity tests confirm the importance of the parameters related to tree geometry. This
directly stems from the fact that competition is simulated by means of spatial interactions, so that
anything that alters either the shape, the size, or the relative position of the trees have direct
impact on the outcome of the competition and therefore on the growth dynamic. These
elementary influences are usually straightforward but their effect at different times and scales are
difficult to predict without simulating because of the numerous feedback loops at work and the
non-linear dynamics of the system. To illustrate this, let’s examine very simple cases. By
simulating growth in a mono-specific stand of regularly spaced trees planted at increasing
densities, we observe the following response. Planting at medium density translates into growth
in height of the trees in the center of the plot being superior to that of border trees, which is a
response to the increasingly limited access to light of the trees in the center of the plot. When
planting density is increased further though, growth in height of the trees in the center of the plot
becomes less than their neighbors: the level of competition is so high that these trees get
overtopped and suppressed by border trees in more favorable position with respect to access to
light. Another simple test shows that ability to respond to low light availability by enhanced growth

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in height (a response, which occurs at the expense of growth in diameter) appears to be

advantageous under specific conditions and disadvantageous under others. If all species in the
mixture share the same ability and the same sensitivity to light level then this potential
competitive advantage turns out to be disadvantageous both for individual tree growth and for
overall plot productivity. But when trees with different sensitivity to light level or different ability to
alter their allocation of growth between height and diameter occur in a mixture then this capacity
proves to be an effective competitive advantage for individual species. By accelerating the
establishment of a multi-strata structure it also increases the overall productivity of the plot
through better allocation of spatial resources. Similarly, rather counter intuitively, an increased
growth rate for a given crown size appears to be an advantage for a species under certain
circumstances but not all: under very crowded conditions large crowns (showing low efficiency in
terms of light and space utilization) can show competitive advantage by suffering less from crown
encroachment and shading out competitor more efficiently. These are but a few examples of the
insight such generic models can bring.
More direct application of the model include comparing alternative scenarios in terms of financial
return for instance involving rotational versus permanent agroforests, etc.

1.2. The SExI-FS Software

SExI-FS software is available on the Internet. It can be downloaded for free from
http://www.worldagroforestry.org/sea/Products/AFModels/SExI. The software is available on
various installation file, packaged for any Platform or Operating System.
SExI-FS is targeted to be platform independent. It’s developed in Java Programming Language,
so it should be able to run on any platform that supports Java Virtual Machine (JVM). The
information about Java Programming Languages and Java Virtual Machine can be accessed
through http://java.sun.com.

1.3. The Minimum Requirement

The minimum requirements to run the 3D visualization of SexI-FS are:
1. 60 MB Hard disk space (Included JVM)
2. VGA card with 3D graphics accelerator.
3. 128MB Ram
4. PII 600MHz or equivalent

The minimum requirements to run SexI-FS without 3D Visualization are:

1. 60 MB Hard disk space
2. Pentium PC 133Mhz
3. 32MB of RAM

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Chapter

2. Getting Started

Getting Started 2
The software is available in two packages, one that includes the Java Virtual Machine (JVM) and
the other without (smaller size). If you do not have a Java virtual machine installed on your
computer, be sure to get the package that includes one.

2.1. Installation
Below are the installation steps:
Step 1. Introduction Window.
This window displays general information about the software that will be installed. Press the Next
button to continue.

Figure 1: Introduction Window

Step 2. Choose Installation Directory window.

The default directory is C:/Program Files/SExI-FS. You can change the default directory by either
press the Choose… button to select the installation directory, or type the directory name in the
directory path field. Press the Next button to continue.

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Figure 2:Install Folder Option Window

Step 3. Choose Shortcut Folder Window

This window provides the setting options for shortcut icon. You can choose the place of icon
either in new program group, in an existing program group, in the start menu, on the desktop, in
the quick launch bar, or leave it without creating the icon. You can set whether these icons will be
created for all users or not. Press the Next button to continue.

Figure 3: Shortcut Folder Option Window

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Step 4. Pre-Installation Summary window.

Review the pre–installation summary. Click Previous button if you need to reset the installation
setting. And after, press the Install button to start the installation process.

Figure 4: Pre-Install Summary Window

Step 5. Installation window.

If it’s done, you can start to use the software.

Figure 5: Finish Installation

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2.2. Running SExI-FS

To run the SExI-FS, you can press Start button, and then select Programs, and select SExI-FS,
and then select SExI-FS shortcut icon (see Figure 6). This is assuming that you use MS Windows
Operating System and you choose default installation setting. For the other platforms it might
have different GUI.

Figure 6: SExI-FS in Window's Start Menu

If it works, the splash screen will show.

Figure 7: SExI Splash Screen

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2.3. Main Window

The main window is a desktop window that contains all simulation GUI window such as the
Simulation List, the Simulation Control, the Simulation Setting, the Vertical Projection of
Forest, etc. Some windows might show up outside the SExI-FS desktop (ex. 3D Visualization
window). The main window contains a menu bar to interact and work with the system.
Pull-
Tool Title
Down
Bar Bar
Menu

Simulation Simulation
List Panel Setting
Panel

Simulation
Horizontal
Control
View Panel
Panel

Line
Chart
Panel
Vertical
View
Panel Scatter
Plot
Chart

Bar
Chart

Figure 8: Main Window.

SExI-FS Title Simulation Statistic Window Minimize Maximize Exit

Logo Bar Menu Chart Menu Button Button Button
Menu

File
Menu Help
Menu

Add New Auto Run

Icon Icon

Figure 9: Menu Bar, Pull Down Menu, and Title Bar Description

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2.3.1.File Menu

Figure 10: File Menu

The File menu has submenus for interacting with input and output file:
• New Simulation
Select this option to create new simulation.
• Open
Select this option to load the simulation file produced by SExI-FS
• Save
Select this option to save the selected simulation on the Simulation List window.
• Exit
Select this option to quit SExI-FS.

2.3.2.Simulation Menu

Figure 11: Simulation Menu

The Simulation menu is a tool for working with the simulations. It’s connected to an active
simulation (highlighted) on the Simulation List window. You can access a similar menu by right

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clicking the mouse when the pointer is on the highlighted item in the simulation list. Below are the
submenus:
• Setting
This will show the Simulation Setting window.
• Start
Select this option to start simulation. Be sure to set the simulation time in the
Simulation Control window before running the simulation.
• Stop
Select this option to stop simulation.
• Vertical Projection
Select this option to open the Vertical Projection View of the tree stand.
• 3D View
Select this option to open the 3D Visualization of the tree stand.
• Data
Select this option to show the statistical chart of the simulation data. The available types of
chart are:
‰ Scatter plot
A scatter plot or scatter graph is a graph used in statistics to visually display and
compare two sets of related quantitative, or numerical, data by displaying only finitely
many points, each having a coordinate on a horizontal and a vertical axis.
‰ Line chart
A line chart is a graphic representation of quantitative information by means of a
chart in which a series of data points are connected by a continuous line.
‰ Bar chart
A bar chart is a chart with rectangular bars of lengths usually proportional to the
magnitudes or frequencies of what they represent.
‰ Export Data
Here you can export the data for further analysis using other statistical software. This
will export the data on TXT file format with tab separated row data.
• Remove
This option will remove the selected simulation

2.3.3.Statistic Chart Menu

Figure 12: Statistic Chart Menu

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This Statistical Chart Menu is applied for the whole simulation data on the Simulation
List window. It has the following menu items:
• Scatter plot
• Bar
• Line

2.3.4.Window Menu

Figure 13: Window Menu

This is an optional menu for window setting and controlling the system:
• Memory Monitor
This option will show the memory allocation used by this system over time dynamically.
• Look and Feel
This option will change the graphic appearance of the software. There are six options of
Look and Feel: Java, Macintosh, Motif, Windows, Liquid, and Kunststoff style. The
available styles are Java, Motif, and Windows style. The Java style is the default look and
feel.
Look and feel refers to design aspects of a graphical user interface - in terms of shapes,
layout, typefaces, etc (the "look"); and, the behavior of dynamic elements such as
buttons, boxes, and menus (the "feel"). It is used in reference to both software and
websites.
• Themes
This option is an additional menu to the Look and Feel menu. If you choose the default
Java look and feel, then the available options are Default, Aqua, Charcoal and Emerald.
This selection will change appearance color of the application such as the background
color, pointer color, etc.

2.3.5.Help Menu
In Help menu, you can see SexI-FS version.

2.3.6.Simulation List Window

Simulation List window is the simulations holder. It contains the list of active simulations
in the system. The window displays current status of each simulation such as the simulation
progress, age, and population of the trees. The Auto Run option allows you to run a series of

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simulations in a batch mode. Double click on one of simulation line, and the Simulation Control
window will show up.

Figure 14: Simulation List Window.

2.3.7.Simulation Control Window

Figure 15: Simulation Control Window

This window displays the status and control buttons of the current simulation

Setting: click this button to open Simulation Setting window.

Start: click this button to start simulation.

Stop: click this button to stop simulation.

Vertical Projection: click this button to open Vertical View window.

3D View: click this button to open the Forest 3D Viewer window.

Statistic Chart: click this button to open the Statistic Chart window.

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2.3.8.Vertical View Window

Figure 16: Vertical View Window

This window displays the plot of trees stand in vertical projection. You can see a popup menu on
this window by right clicking in this window. There are two group of popup menu in this panel:
Plot Menu and Tree Menu. The Plot Menu will show up if you right click in the planting area, but
if you select the tree then do the right click, then the Tree Menu will show up. The Plot menu has
some options to interact with the plot and to change its appearance:
• Paint
Select this option to change the drawing mode of crown shape projection either in outline,
opaque, transparent, or shading mode. See 4.1.1: Tree Paint for more information.
• Show
Select this option to view tree’s info, like ID, Label, CP, and CF. See 4.1.2,
• Overlay Map
Select this option to see the overlay map. See Overlay Map for more information.
• Plant
Select this option to plant a tree on a selected point.
• Zoom In
Select this option to examine closely the stand.
• Zoom Out
Select this option to have a wider view of the stand.

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Figure 17: Global Menu

Tree menu group has some control menus for the selected trees:
• Horizontal View
Select this option to view the trees from north, east, south, or west projection.
• Hemiphot
Select this option to view the hemispherical photograph of the canopy gap on the selected
tree position. See chapter 4.6: Hemispherical Photograph for further information.
• Remove
Select this option to view the hemispherical photograph of the canopy gap on the selected
tree position. See chapter 4.1.4: Cut the Trees for further information
• Show 3D
Select this option to view the selected trees in 3D visualization. See chapter 4.4: View 3D
Animation for further information
• Tree Stat
Select this option to see the statistic chart of the selected tree individually.
• Object Inspector
Select this option to view the tree’s properties. See 4.1.5: Tree’s Object Inspector for more
information.

Figure 18: Tree's Menu

2.3.9.Trees 3D Visualization
This window displays the 3D visualization of the trees.
Optionally, the crown can be shown in solid or wire frame

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mode. The detail of the tree menu will be discussed in 4.4:View 3D Animation.

2.3.10. Forest 3D Visualization

This window displays the 3D visualization of the whole trees. You can view it from any
direction interactively. In this panel, you can set the crown to be rendered in leafy, solid,
or wire frame mode. You can set also the land to be rendered in wire frame or solid
mode. For further information, see in 4.3: View 3D .

Figure 19: Forest 3D visualization

Figure 20: Trees 3D visualization

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Chapter

3. User’s Manual

User’s Manual 3
3.1. Create New Simulation
There are several ways to create a simulation. These are:

a. On the menu bar click Add New menu bar.

b. In the File Menu, select New Simulation menu.

Figure 21: File Menu

After you gone through one of those steps, the Create New Simulation Wizard will show.
Follow these steps:
• On Source Simulation dialog, you will be asked whether you want to load an existing
simulation or create a new simulation.
If you choose to load an existing simulation, the Browse button will be active, and you can
browse your computer to search for the saved file.

Figure 22: Source Simulation Dialog

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• Click Next button, and Simulation Description dialog will show.

In this wizard dialog, the simulation’s description will show. You may change simulation’s
Name and Area Size. The area size default is 100x100 m.

Figure 23:Simulation Description Dialog

Clicking on “Detail” will show up the detail setting for the plot, Aboveground and Belowground
Setting. The explanation about those parameters is to be found in section 3.2 Simulation Plot
Setting.

Figure 24 Aboveground Setting

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Figure 25 Belowground Setting

• After the plot setting, Clicking Next button will bring you to Tree Species Setting.

Add the species by clicking button. The species description item will be added to the list.
Then, double click on the species item that you have added and the detail setting for the
species will show up. Detail explanation about species parameter is covered under section
3.3 Species Parameter Setting

Click to remove selected species and lick on to remove ALL species in the list. If you
have previously saved species descriptions then click to load the species description
file. And click on “Save” button to save the current species list into a file.

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Figure 26: Tree Species Setting Dialog

Figure 27 Detail Species Setting

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• Click Next button to go to Initial Planting Area dialog, Figure 288.

There are three ways to plant the trees into the plot: plant randomly, manually, or orderly.
Detail explanation about this Initial Plantation is given in section 3.5. Initial Stand.

Planting
Area

Figure 28: Initial Stand Dialog

• Click Next button, and the Summary dialog will show.

The last option is to choose weather you want to run the simulation later or run it
immediately.
The auto run option is for batch mode run.

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Figure 29: Summary Dialog

• Click Finish button. The simulation description item will be added to the Simulation List
window.

Figure 30: Simulation List Window

If you choose the “Run Later” option before the simulation plot will be stopped at its initial stage.
You can run this simulation by double clicking the simulation item on the list, and The Simulation
Control window will show up (Figure 31). Fill the Iteration Setting field with the length of

simulation you wish to run in year, then click start button .

Figure 31: Simulation Control Window

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You can reset the default setting for the plot and the species by clicking the Setting icon. You
access this shortcut by clicking on the “Simulation” menu on the main window or right clicking the
simulation description item on the simulation list.

Figure 32: Simulation Menu

Next section will describe in detail the settings for the Simulation Plot and Tree Species.

3.2. Simulation Plot Setting

Figure 33: Forest Simulation Panel

In Forest Simulation panel (see Figure 33), you must specify the parameter values to be
used, which are:
• Simulation’s Name
Fill the label for current simulation setting
• Area Size

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The default value for plot area is 100.0 x 100.0 m. Click Change button to change the area
size, and the Input New Area Size dialog will show. Type the size of the new area and click
OK.

Figure 34: Area Size

• Random Generator
Type the random seed for the Random Generator. It can be any number.
• Record Tree Profile History
Check if you want to record the tree profile history and show it in 3D visulaization

3.2.1.Aboveground Setting

Figure 35:Light Setting Panel

The parameters are:

• Light Insolation
Light Insolation settings control the level of detail used for exploring the sky vault, i.e. the
number of light beams and their weighting. The number of inclinations and azimuths
defines the number of beams.

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Azimuth is the horizontal component of a direction (compass direction), measured around

the horizon from the North point, toward the East, i.e. clockwise. It is usually measured in
degrees.
Inclination is the angular distance of the orbital plane from the plane of reference (usually
planet's equator or the ecliptic), stated in degrees.

Figure 36: Horizon Projection of Beams Vector

Figure 37: Vertical Projection of Beams Vector

The parameters for insolation are:

‰ Detail Level
There are four options of detail level:
1. Low
If you choose low, the system will set 5 as number azimuths value, and 3
as number of inclinations..
2. Medium
If you choose medium, the system will set 15 as number azimuths value,
and 5 as number of inclinations.

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3. High
If you choose high, the system will set 30 as number azimuths value, and
10 as number of inclinations.
4. Manual (Inactivated)
If you choose manual, you can freely set the number of azimuths and
number of inclinations.
‰ Lowest Zenithal Angle
Lowest Zenithal Angle defines the lowest angle considered for light calculation.
‰ Inclination weighted model
There are three models you can choose from:
1. SOC (Standard Overcast Sky)
This model weights each direction according to surface of sky vault fraction
moreover assuming a decrease in light intensity from zenith to horizon,
using the formula:

Light ( x, α ) = x ∗ [1 + 2 ∗ sin (α )]
1
3

2. UOC (Uniform Overcast Sky)

This model weights each direction according to the relative surface of the
sky vault explored by each beam.
3. None
This option gives equal weight to each direction sampled.
‰ Distance of Interaction
The interaction area is limited by the Distance of Interaction setting. The trees
outside the radius of interaction distance and are not included for current target
calculation.
• Interception
The parameters for interception are:
‰ Crown Permeability
If Crown Permeability checkbox is selected, the crown is considered as partially
transparent (transparency is also referred to as crown porosity in the following).
If Crown Permeability is not selected, it is assumed to be totally opaque.
‰ Trunk InterceptionError! Bookmark not defined.
If Trunk Interception checkbox is selected, the trunk is considered to intercept the
light. If Trunk Interception is not selected, it’s neglected.
• Environment
‰ Topography
If topography is selected, the plot will using the topography data (if it exists), else
the plot is assumed to be flat.
‰ Torus Space
In geometry, a torus (pl. tori) is a doughnut-shaped surface of revolution
generated by revolving a circle about an axis coplanar with the circle. The sphere
is a special case of the torus obtained when the axis of rotation is a diameter of
the circle. If the axis of rotation does not intersect the circle, the torus has a hole
in the middle and resembles a ring doughnut, a hula hoop or an inflated tire. The
other case, when the axis of rotation is a chord of the circle, produces a sort of

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squashed sphere resembling a round cushion. Torus was the Latin word for a
cushion of this shape.
If selected then the plot is assumed to be toric, in such case the plot has no
borders as the trees from one side of the plot act as neighbors for the trees on
the opposite side. If not selected then the plot is limited by the border. (Note that
the area outside the border is considered as an open area).
• Light Map Calculation
There are two options on Light Map Calculation:
‰ Simple
Select Simple if you want to use simple Light Map Calculation
‰ Detail
Select Detail if you want to use detail Light Map Calculation
Light calculation for each grid cell in this module uses Simple Vertical Light Calculation
(cf SLIM part below). The plot is divided into a grid of cells (default size 5 by 5 m). For
each cell at each time step a coarse index of light availability is computed based on
overhead light of target cell and 8 immediate neighbors (a single vertical direction
originating from center of cell is explored for each cell).
The average of canopy openness on each grid cell is used in the recruitment process to
assess suitability of light regime.

Figure 38: Light Map for Recruitment Test Shown in SExI GUI

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3.2.2.Belowground Setting

Figure 39: Belowground Setting Panel

Check the Enable Belowground competitions option to simulate below ground

competitionbetween neighbouring trees. The parameters for root influential zone are explained in
section 3.3 Species Parameters Setting.
Soil fertility is set manually for each cell of a grid covering the plot or read from a text file.
Missing data are interpolated using bilinear 3 dimensional interpolation (Press, Teukolsky et al.
1992). Fertility values vary between 0 and 1; a fertility of one meaning there is no soil fertility
related limitation.
The fertility experienced by a tree will be computed as the average of cells fertility value
of cells within the tree root influential zone.

3.3. Species Parameters Settings

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3.3.1.Set Species List

Figure 40 Species Description List

Add species by clicking button. The species description item will be added to the list.
Next, double click on the species item that you have added and the detail setting for the
species will show up. Detailed explanation about the species parameters is given in section
3.3 Species Parameter Setting

Click to remove selected species and Clicking on will remove all species on the list.
If you have previously saved species descriptions then click to load the file. And click
on “Save” button to save the current species list into a file.
Select the species label on the left tree menu, the right panel will show the detailed species
settings for the selected species.

Figure 41: Species Characteristic Setting

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3.3.2.Species characteristic
The first tab is species characteristic setting. Except Species Name and Species
Description, the parameters are:
• Color.
The color is used for visualization purposes; it’s not the real color of the tree species. This
color is useful to differentiate between species. Click the color to change color.
• Adult age (year)
Type the age of the tree species when it reaches sexual maturity (determines start of
recruitment for non pioneer species, see below)
• Minimum DBH (Diameter at Breast Height)
Enter the initial diameter for newly recruited trees (default is 1 cm dbh)
• Maximum DBH
Enter the maximum diameter of the tree species
• Recruitment
This recruitment rate is the proportion of suitable "gaps” that are filled by a particular
species at each time step. It does not depend on number of adult trees of the same
species. However it is conditional (for non pioneer species) to the presence of at least one
mature adult tree in the stand. Suitability for recruitment is based on minimum and
maximum light levels setting. Location of newly recruited seedling/sapling is randomly
chosen within the range of suitable locations.
The minimum and maximum light levels setting for recruitment are defined on "Light
Sensitivity" part and Light availability map is calculated using two optional method,
accessible under "Forest" > "Light Setting" section.
This method of recruitment refers to natural regeneration ("Natural Recruitment" scenario)
and can be overridden in the management scenario (see below).

• Min Survival Probability

Min Survival probability (sp) is the survival probability value of a completely suppressed
plant (no growth)
In addition, a systematic mortality is assumed once tree crown size has reached 5% of
normal crown size
• Mortality Curvature
Mortality Curvature modulates the shape of survival probability curve as growth rate is
reduced (higher m values imply higher mortality rates at identical growth rate). Default
value is 15. See documentation for more details.
• 2nd Mortality Probability
2nd Mortality Probability is the probability that a tree dies from a neighbouring tree fall (0 - 1)
if it lies in the sector affected by tree fall. Default value is 50% (see documentation for
further computational details).
• Root Influential Zone Modifier
Species specific factor of root influential zone from default 20*DBH meters

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3.3.3.Light Sensitivity

Figure 42: Light Sensitivity Setting

Here are the parameters that define the light stress factor of the tree growth. The curve
below shows the light stress factor derived from the parameters:
• Growth response to light:
• Minimum Level for Growth to Occur
Input the minimum level for a tree so that the tree can grow.
• Optimum Level for Growth
Input the optimum level for a tree to grow.

Figure 43: Light Stress Graphic

min = Minimum level for growth to occur

opt = Optimum level for growth

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• Recruitment
Once a recruitment decision is made for a tree of a particular species it is randomly
“planted” within the area defined as suitable i.e. which light level is between
minilum_for_recruitment and maxilum_for_recruitment
• Minimum Light Level for Recruitment
• Maximum Light Level for Requirement to Occur

3.3.4.Growth Function
DBH as the function of time (t) uses a Chapman Richards function:

dbh = dbh_max * (1 − e − k *t )
c

Approximating DBH annual increment with the first derivative of DBH with respect to time
(t) one can express dbh increment as a function of current dbh as follows:

⎛ −1
⎞
⎜ ⎛ dbh_init ⎞ c ⎟
dbh_inc = dbh_init * c * k⎜ ⎜⎜ ⎟⎟ − 1⎟
⎜ ⎝ dbh_max ⎠ ⎟
⎝ ⎠
(See SExI-FS Documentation for detail)
The parameter of c and k can be obtained from Non-linear regression of DBH-
DBH_increment plot (see Guide to SExI-FS calibration).

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Figure 44: Growth Function Panel

3.3.5.Allometric Relations
DBH-Height is power function and DBH-Crown Width is linear function.

Height functions
The formula of height follows:
Height = alpha_h * DBH ^ beta _h

Crown Width functions

The formula of crown width follows:
Crown_width = alpha_cr + beta_cr*DBH

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Figure 45:Profile Function Panel

3.3.6.Dynamic Test
Simple test of tree profile evolution over time and light condition can be tested here. Test
Simulation in Dynamic Test.

Figure 46: Dynamic Test Panel

The light option set the average of light received by this tree overtime, neglecting the
spatial distribution of light. Here you can see the effect of light amount on dbh growth over time.

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Artificial Light Map option gives a more advanced test. Here you can set the distribution
of light over the crown by accessing a virtual hemispherical photograph describing the sky vault
as viewed by the tree. Note that this is constant over time (whereas in the real condition it would
be dynamically changing following the tree growth and environment dynamic evolution).

Figure 47: Artificial Light Map

Light Gradient is computed as the average ratio of light between vertical and the series
of inclinations explored. Hence a light-gradient value of 1 would indicate NO light gradient (apart
from the one possibly imposed by the illumination model not considered) while in case of dense
planting with no overhead shade, light gradient would tend towards 0.
Note: check "Use Artificial Map" checkbox to activate the light map. You can check the 3D
animation visualization of the tree growth by clicking the Show 3D button, enter the maximum
age for the tree (see Figure 48: Age Dialog Box) the 3D animation shows the evolution of the tree
profile over time.

Figure 48: Age Dialog Box

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Figure 49: 3D Tree Visualization

3.4. Scenario Setting

Scenario definition may include general rules (“Simulation scenario”) or species specific rules
(”species scenario”).

3.4.1.Simulation Scenario
To change the simulation scenario select Scenario Setting node on the tree menu and the
Scenario Setting panel will appear. The options in simulation scenario are:
• Allow Mortality
Check the Allow Mortality box if you want to allow for mortality while the simulation running.
• Allow Recruitment
Check the Allow Recruitment box if you want to allow for recruitment. Enter the starting
time of recruitment.

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Figure 50: Plot Scenario Setting Panel

3.4.2.Species Scenario
In the species scenario species-specific management options can be set. Select a species
for which you want to edit information by clicking the node under Species Setting node.

Figure 51: Species Scenario Panel

The options that can be chosen in the Species Setting panel are:
• Pioneer Species

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Check the Pioneer Species box if the species is a pioneer species, i.e. a species that will
recruit saplings even if there are no sexually mature trees in the stand.
Conversely, if a species is declared as non pioneer then it is allowed to regenerate only in
the presence of adult trees of the same species.
• Timber Value
Check the Timber valued box if the species has timber value. Input the price (in US$) in the
given box.
• Logging
Check the Logging box if the species can be logged. Input the DBH above (in m) value
when the species is logged.
• Is Produce (fruit, latex, resin)
Check the Is Produce box if the species can produce. The graphic Production per DBH (y)
will show. Input the parameter for function production = (DBH * a) + b.
Input value of producuction days per year. Check also “cut after produce days” box if the
species will be felled (latex producing species) and enter the number of production days
after which the tree will be felled.

3.5. Initial Stand

Once you have set-up a species list for your simulation, you need to plant trees. Go to the
Initial Stand panel on the Simulation Setting window. Go to the Initial Stand panel on the
Simulation Setting window. The Figure 52 below shows the Initial Stand window. There are
three ways to plant the trees into plot:

3.5.1.Regular Plantation

Figure 52 Initial Stand with Regular Plantation

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To plant the trees regularly, use the pattern editor for design the plantation pattern. Click on “Edit
Pattern” button to show the pattern editor. Figure 53 shows the plantation result with current
designed pattern.

Figure 53 Plantation Pattern Editor

To edit the pattern, just select the species on the right top corner the click on the pattern plot.
Click clear to remove the current pattern.

Figure 54 Regular Plantation 3x6m

If you want to create a regular pattern 3x6m plantation, change the pattern size by clicking
the”change” button. Put the tree on the center of the pattern plot (if you want make sure it was on
the center of the plot, click on “Move to Center” button)

After you edit the pattern, click “Ok” then click “Plant” .

3.5.2.Random Plantation
If you choose plant randomly, the system will plant the species randomly. Check the Select
column on the species you want to plant, type number of tree on Amount column, and click the
Plant button. The system will plant the tree randomly.

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You can plant more than one species. Figure 55 below shows that system will plant ten rubber
trees, ten durian trees, and ten duku trees randomly.

Figure 55: Random Plantation

3.5.3.Manual Plantation
If you choose to plant manually, you must click planting location in the planting area. Select
species that you want to plant, and then click in the planting area on the location where the tree
will be planted. You can plant any number of trees.

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Figure 56: Manual Plantation.

You can delete a tree by selecting it, right clicking, and choosing “delete”. Or click on
“Clear” button if you want to remove all the planted trees.

Figure 57: Remove Tree

3.6. Running the Simulation

3.6.1.Run Simulation
Simulation will be running for a specified number of steps (years). While the simulation is
running, you can see the progress bar that indicates progress of simulation. To begin to run the
simulation, you can click Start menu on Simulation menu or in the Control Simulation window.

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Figure 58: Simulation Control Window

3.6.2.Stop simulation
There are several ways to stop simulation, such as

• Click stop button on Simulation Control window, or

• Select Stop menu on Simulation menu.

Figure 59: Stop Menu in Simulation Menu

3.6.3.Remove Simulation
This command closes the selected simulation on the Simulation List window, and if the
simulation is unsaved, the program will ask whether you want to save the simulation or discard it.
There are two ways to remove simulation from the simulation list:
1. Select the simulation you want to remove. Right click, and option dialog will show, like in
Figure 60, and then select Remove.

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Figure 60: Remove Option in Simulation Options

2. Select the simulation you want to remove from simulation list. Click Simulation menu,
and then select Remove.

Figure 61: Remove Menu in Simulation Menu

After you have done one of those steps, the Remove Confirmation dialog will show, and
click Yes button to remove the selected simulation.

Figure 62: Remove Confirmation

3.6.4.Duplicate Simulation
For analysis reason, it is possible to duplicate a simulation, and run it after changing some
management options. There are two ways to duplicate a simulation:
a) Select the simulation on the Simulation List window that you want to duplicate. Right click
and an option dialog will show, like in Figure 63, and then select Duplicate menu.

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Figure 63: Duplicate Option in Simulation Options

b) Select the simulation you want to duplicate from the Simulation List. Click Simulation
menu, and then select Duplicate menu.

Figure 64: Duplicate Menu in Simulation Menu

3.6.5.Save Simulation
You can save simulation information under two formats: simulation file (*.s) and simulation
setting file (*.xml). Simulation file contains all simulation data including simulation setting and
simulation result data, while simulation setting contains only the simulation setting.
To save the simulation, follow these steps:
1. Select the simulation
2. Click Save option on File menu

Figure 65: Save Option on File Menu

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3. The Save File dialog will appear, like in Figure 66.

Figure 66: Save File Dialog

4. Select the file type on Files of Types: simulation file (*.s) or simulation setting (*.xml).
5. Fill the file name on File Name.
6. Click Save button.

3.6.6.Open Simulation
To open simulation that has been saved before, click the File menu, and select open
menu.

Figure 67: File Menu

The open dialog will show, like in Figure 68 below. Select the location and the file that
you have saved before.

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Figure 68: File Open Dialog

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Chapter

4. Simulation Results

Simulation Output 4
You can explore the simulation output by either inspecting the tree plotting in Two Dimension
(2D) and Three Dimension (3D) graphic or plotting the tree data on statistical chart.

4.1. Vertical Projection 2D of Tree Plot

You can access the shortcut to view vertical projection from simulation menu (see section
2.3.2 Simulation Menu).

Figure 69: Vertical Projection Option

Figure 70: Vertical View Window

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4.1.1.Tree Paint Options

You can set the tree painting on the 2D plot by right click the plot, select “paint”.

Figure 71 2D Tree Paint Options Menu

Default option is paint with Outline mode. You can reset either with opaque, transparent, or
shading mode.

4.1.2.Tree’s Info
You can view the basic info of the plotted trees by selecting the “Show” menu. You can show
either the ID, Species Label, CP index or CF index. see Figure 75.

Figure 72: Show Tree’s Info menu

4.1.3.Overlay Map
The plot can be overlay with either “Light Map” Layer or “Root Influential Zone Map” Layer. To set
the overlay map, select “Overlay Map”
on simulation menu,

Figure 73.

Figure 73 Overlay Map Option Menu Figure 74 Light Map (left) and Root Map (Right) Overlay

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4.1.4.Cut the Trees

On Vertical Projection Plot you can cut (remove) the trees. Select the trees, Right click, and
Select “Remove”. Note that those removed trees are also removed from the simulation and
counted as mortality data.

Figure 75: Remove Tree in Vertical View

4.1.5.Tree’s Object Inspector

This menu will show the technical properties of Tree Object.

Figure 76: Object Inspector Option Figure 77: Object Inspector

4.2. Horizontal Projection 2D of Tree Plot

To view the trees on horizontal projection, select the tree from Vertical Projection Plot, Right
click and select “Horizontal View”. You can view the projection either from North, South, West
or East side.

Figure 78: Horizontal Projection View

Figure 79 Horizontal View Menu

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4.3. View 3D Visualization

You can explore the tree in 3D Graphics. Make sure that you have minimum requirement for
viewing the 3D graphics (see section 1.3 Minimum Requirement). You can access the 3D
Visualization shortcut from Simulation Menu

Figure 80: 3D View in Simulation Menu Figure 81: Virtual Forest Setting.

After you select the “3D View” menu, the Virtual Forest Setting dialog will appear (
Figure 81).
The 3D visualization setting options are:
• Crown type
You can set the Tree Crown rendering type either using Wireframe, Solid or Leafy
modes.
• Land Type
You can set also the Land rendering either using Wireframe or Solid modes.
• Texture
Texture rendering can be applied for each 3D components: Sky, Land, Crown and Trunk
• Topography
Check if you want to enable the topography rendering on 3D Visualization (make sure
that you have applied the topography data)
• Mouse Control
Check if you want to enable moving the 3D Objects using the mouse.

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Figure 82: Wireframe Crown and Land in Figure 83: Leafy and Textured Tree Crown 3D
Virtual Forest visualization

Click here to
go forward
Click here
to go up

Click here
Click here
to go left
to go right

Click here to Click here

go backward to go
down

Figure 84:Virtual Control Window

4.4. View 3D Animation

Select a tree or a group of trees on Vertical Projection View window, Right click, and
select show 3D (Figure 85). Make sure you have enabled the “Record Tree Profile History”
option on Simulation Plot Setting (Section 3.2)

Figure 85: 3D Option Menu from Vertical View Window

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4.5. 3D Visualization Window Menus

The 3D window shortcut menus are:

4.5.1.Snaphot
Click here to capture the image from 3D Visualization. Set the scaling factor then click
Ok. The snapshot window will show up. After, you can either save the image or print it .

Figure 86: Snapshot Setting Box

Figure 87: Snapshot Window

4.5.2.Rendering Mode

You can set the rendering mode of the 3D Visualization either using wireframe or solid
mode

Figure 89:Tree in Solid Mode

Figure 88: Tree in Transparent Mode

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4.5.3.Show 3D Component Part

You set the 3D Visualization to show the part of object. You can set either just showing
the crown layer ( ), the branches ( ) or both crown layer and branches ( ).

Figure 90: Tree Branches View

4.6. Hemispherical Photograph

You can view hemispherical photograph model of canopy gap from a tree point of view.
Select a tree on Vertical Projection Plot, Right click, and select “Hemiphot”. The hemiphot window
will show up (Figure 92).

Figure 91: Hemiphot Menu in Vertical View Window

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Figure 92 Hemiphot Window

There are two type of hemiphot map:

- Canopy openness
This represents the canopy openness co;puted at crown base assuming target tree
crown is completely transparent
- Sectoral Light .
Sector light is a smoothed map of canopy openness used to compute anisotropic
gradient affecting crown deformation

You can try to change the light insolation setting for current hemiphot position by opening the
“Setting” tab. click Calculate button to refresh the hemiphot after you change the setting.
You can view the detail value of each hemiphot sector by opening the “Table” tab.

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Figure 93: Hemiphot Table

4.7. Statistical Data

Statistical data output can be accessed either for overall simulation list, for selected
simulation or for each individual tree. To view overall simulation list statistical data, open the
“Statistical Chart” menu on the Main Window menu bar and select the type of the chart.

Figure 94: Statistic Chart Menu for Overall Simulation List

To view the statistical data for each simulation items, select (Highlight) the simulation item on the
simulation list window, right click and select “Statistic Chart”.

Figure 95: Data Option in Simulation Options

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To view statistical data of individual tree, select a tree on the vertical projection plot, Right click,
then select “Tree Statistic” (Figure 104).

Figure 96: Tree Stat Option

4.7.1.Bar chart
Select the variable on the left panel and move it to the x axis panel on the right. The available x
axis variables are DBH (Diameter at Breast Height), Height, CP Index, CF Index.
“Species” and “Simulation” are the grouping variables.
You can view the simulation data of any age by setting the Age field.

Figure 98: Bar Chart

Figure 97: Bar Chart Variables

4.7.2.Line chart
The available variables for Y axis in line charts are: Basal Area (Cross sectional area of tree),
Crown surface, DBH annual, Height, Mortality (number of deaths over a specific time period),
Mortality rate (Mortality relative to the population size), Population, Production (fruit, timber, latex,

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or resin), Recruitment (the count of new members into a population), Recruitment Grid (Number
of available grid cells suitable for recruitment of each species), Recruitment Rate.
Species and Simulation are the group variable
The X axis variable is Age.

Figure 100: Basal Area in Line Chart

Figure 99: Line Chart Variables

4.7.3.Scatter plot
The available variable for X and Y axis are: DBH, Height, Crown Width (2 * Geometric means of
crown radius), Crown Width Max (2 * Max Crown Radius), CP Index, CF Index, Crown Depth,
Crown Depth Ratio (Crown Depth/height), Production.
Species and Simulation are the group variable.

Figure 102: Scatter Plot

Figure 101: Scatter Plot Variables

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Chapter

5. Appendix A

Appendix A 5
a. File type

i. Simulation (*.s)
A full simulation file included the tree and plot data.

ii. Simulation data (*.txt)

Statistical data output is saved on this format

iii. Simulation setting (*.xml)

Plot and Species setting are save on this format

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Chapter

6. Index

Index 6
6.1. Order By Alphabet

F I

Forest Parameter Initial Stand

Area Size · 33 Plant Manually · 50
Azimuth · 35 Plant Randomly · 49
Crown Permeability · 36 Planting Type · 47
Detail Level · 35 Iteration · 31, 85
Detail Light Map Calculation · 37
Distance of Interaction · 36 L
Environment · 36
High Detail Level · 36 Light Gradient · 84
Inactivated Detail Level · 36
Inclination · 35
Inclination Weighted Model · 36 P
Insolation · 34
Interception · 36 plant
Light Map Calculation · 37 manually · 90
Low Detail Level · 35 randomly · 91
Lowest Zenithal Angle · 36 regularly · 86
Manual Detail Level · 36
Medium Detail Level · 36 R
Random Generator · 33
Simple Light Map Calculation · 37 Recruitment · 79
Simulation's Name · 33
SOC · 36 S
Topography · 36
Torus Space · 36 Scenario Setting
Trunk Interception · 36 Allow Mortality · 45
UOC · 36 Allow Recruitment · 46
Logging · 47
Pioneer Species · 47

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Produce · 47 Light · 44
Simulation Scenario · 45 Light Gradient · 44
Species Scenario · 46 Maximum DBH · 40
Timber Value · 47 Minimum DBH · 40
Species Characteristic Minimum Level for Growth to Occur ·
2nd Mortality Probability · 40 41
Adult Age · 40 Minimum Light Level for
Allometric Relations · 43 Recruitment · 42
Artificial Light Map · 44 Recruitment · 40
Color · 40 Recruitment · 41
Crown Width Function · 43 Species Description · 40
Dynamic Test · 43 Species Name · 40
Growth Function · 42 Species Parameters · 40
Height Function · 43 Survival Probability · 40

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