Delta SS1-UM-1.05 User manual

SunScan
Canopy Analysis
System
User Manual
SS1-UM-1.05
Notices
Copyright
All rights reserved. Under the copyright laws, this manual may not be
copied, in whole or in part, without the written consent of Delta-T
Devices Limited. Under the law, copying includes translation into
another language.
Copyright © 1996, Delta-T Devices Limited.
SunData software and canopy theory are Copyright © 1996 John Wood,
Peak Design, Wensley Road, Winster, Derbyshire, U.K.
Acknowledgements
Extracts and illustrations from the Psion Workabout documentation are
Copyright © 1995 Psion PLC, and are reprinted here by kind permission
of Psion PLC.
Trademarks
Psion and the Psion logo are registered trademarks, and Psion
Workabout, 3Link, SSD and Solid State Disk are trademarks of Psion
PLC.
Windows is a registered trademark of Microsoft Corp.
All other trademarks are acknowledged. Some names referred to are
registered trademarks.
CE conformity
The SunScan system conforms to EU regulations regarding
electromagnetic emissions and susceptibility.
The Psion Workabout and its accessories are CE marked by Psion PLC.
The SunScan probe is CE marked by Delta-T Devices Ltd.
Warnings
To maintain conformance to CE standards, the equipment must be used
as described in this manual and in the Psion Workabout User Guide.
Modifications to the equipment may invalidate CE certifications.
Delta-T Devices Ltd reserves the right to change the designs and
specifications of its products at any time without prior notice. The
information in this document is subject to change without notice.
Authors
Edmund Potter, John Wood, Chris Nicholl
Version 1.05 December 1996
Delta-T Devices Ltd
128 Low Road, Burwell, Cambridge, England, U.K.
Contents
Introduction .................................................................................................6
How to use the manuals ............................................................................. 6
Organisation of this manual .......................................................................... 6
The SunScan Canopy Analysis System .................................................... 6
PAR measurements...................................................................................... 6
SunScan probe ............................................................................................. 7
Beam Fraction sensor .................................................................................. 7
Data Collection Terminal .............................................................................. 7
SunData software ......................................................................................... 7
Field accessories .......................................................................................... 7
Getting Started ............................................................................................8
Preliminary checks ..................................................................................... 8
The Workabout and SunScan probe ............................................................ 8
Checking the Workabout hardware .............................................................. 9
Installing the SunData s/w in your PC..................................................... 10
The SunData s/w Diskette .......................................................................... 10
Installing the s/w ......................................................................................... 10
Running SunData...................................................................................... 11
Setting up your PC's COM port .................................................................. 11
Communication checks:........................................................................... 12
SunScan probe to PC ................................................................................. 12
Workabout to PC ........................................................................................ 12
Running SunData in Windows ................................................................. 13
SunScan Tutorial ......................................................................................14
About this tutorial ..................................................................................... 14
What you will learn...................................................................................... 14
Using a portable PC instead of the Workabout .......................................... 14
Working with the Workabout ................................................................... 14
Powering up................................................................................................ 14
Navigating around the Workabout .............................................................. 14
What to do if you get lost ............................................................................ 15
Starting SunData in the Workabout ............................................................ 15
Using a PC instead of the Workabout ..................................................... 16
Starting the PC software............................................................................. 16
Setting up a measurement session ......................................................... 18
Working through the menu options............................................................. 18
File Saving .................................................................................................. 19
"Hot Keys"................................................................................................... 19
Taking readings ........................................................................................ 20
Using the Emulator mode ........................................................................... 20
Without a Beam Fraction Sensor................................................................ 21
Connecting the SunScan probe.................................................................. 21
Connecting the Beam Fraction Sensor....................................................... 22
Measuring Leaf Area Index without a Beam Fraction Sensor .................... 23
Averages..................................................................................................... 24
Reviewing your data file ........................................................................... 24
Transferring the data file to your PC ....................................................... 25
Initiating the file transfer from the Workabout............................................. 26
RS232 communication problems................................................................ 28
Conclusion of the Tutorial........................................................................ 28
SunData Screens on the Workabout ....................................................... 29
SunScan User Manual v 1.05
• 3
Menus and Screens ..................................................................................30
More Psion and file handling notes.........................................................33
Navigating Psion directories and screens ...............................................33
The Workabout User Guide ........................................................................ 33
Navigating the Psion directories and screens............................................. 33
Psion subdirectory usage in file select dialogs ........................................... 34
Re-installing the SunData application icon.................................................. 35
Deleting unwanted Workabout files ............................................................ 35
Flashcards - reformatting ............................................................................ 35
Data memory management .......................................................................36
Configuration and data file handling........................................................36
SunData Configuration files ........................................................................ 36
Data files ..................................................................................................... 37
Displaying data files on your PC ..............................................................38
The .PRN file............................................................................................... 38
The .CSV file ............................................................................................... 38
Data file layouts and data groups ............................................................... 39
Measurement options ...............................................................................41
Experiment design.....................................................................................41
Above-canopy reference requirements....................................................... 41
Canopy type and BFS practicalities ............................................................ 42
Canopy type and LAI estimates .................................................................. 42
Canopy Sampling volume ........................................................................... 42
Preferred light and weather conditions ....................................................... 43
Planning for the sun’s position .................................................................... 43
Advice on Absorption and ELADP values ...............................................44
Absorption................................................................................................... 44
ELADP ........................................................................................................ 44
Relationship between Mean Leaf Angle and ELADP.................................. 45
SunScan System Measurement modes....................................................46
Workabout setup......................................................................................... 46
The Autolog function ................................................................................... 47
Measurement procedures in the field.......................................................48
Probe handling in the field........................................................................... 48
BFS handling in the field ............................................................................. 49
PAR calibrations ......................................................................................... 51
Environmental and moisture protection ...................................................... 53
LAI theory...................................................................................................54
Ingredients of the LAI computation method ............................................54
Derivation of Wood’s SunScan canopy analysis equations...................55
The major assumptions............................................................................... 55
Beer's law for canopy absorption................................................................ 56
Campbell's Ellipsoidal LAD equations......................................................... 56
Transmission of Diffuse Light...................................................................... 56
Modelling the canopy transmission............................................................. 58
Accuracy of LAI calculations ....................................................................... 60
Functions used to model canopy transmission ......................................60
Diffuse light - cosine response sensor ........................................................ 60
Diffuse light - hemispherical response sensor. ........................................... 60
Modelling incomplete PAR absorption and scattering................................. 61
Calculating zenith angles ............................................................................ 62
Summary..................................................................................................... 62
Scientific references..................................................................................62
Technical Reference section....................................................................64
4 •
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Maintenance and repair ............................................................................ 64
Checking the batteries ................................................................................ 64
The SunScan probe batteries ..................................................................... 64
The Workabout batteries ............................................................................ 64
Checking the desiccant .............................................................................. 65
Checking the PAR calibration ..................................................................... 66
Troubleshooting........................................................................................ 67
Psion Workabout ........................................................................................ 67
Problems running the SunData application. ............................................... 67
While running SunData............................................................................... 67
Technical Support..................................................................................... 69
Distributor contact....................................................................................... 69
Direct Delta-T contact................................................................................. 69
Guarantee................................................................................................... 69
Problem Reports......................................................................................... 69
SunScan circuit schematics and data......................................................... 69
Locating version and serial numbers .......................................................... 69
Specifications ........................................................................................... 70
SunScan Probe type SS1 ......................................................................... 70
Beam Fraction Sensor type BF1 .............................................................. 70
Data Collection Terminal type DCT1 (Psion Workabout) ......................... 70
PC as Data Collection device ..................................................................... 70
Carrying Case type SCC1 ........................................................................ 71
Telescopic Tripod type BFT1.................................................................... 71
Spares Kit type SPS1 ............................................................................... 71
Logging Cables........................................................................................... 71
PAR Performance ..................................................................................... 72
Spectral response....................................................................................... 72
Cosine responses of probe and BFS.......................................................... 73
Appendices................................................................................................74
A. Logging the probe as a Linear Quantum Sensor ............................... 74
B. Logging the Beam Fraction sensor..................................................... 75
C. Upgrading the SunScan system.......................................................... 76
D. File transfer between Workabout and PC........................................... 77
Choice of different programs ...................................................................... 77
PsiWin......................................................................................................... 77
SLINK and RCOM ...................................................................................... 78
Example using SLINK................................................................................. 78
Example using RCOM ................................................................................ 80
Documentation of RCOM and SLINK ......................................................... 80
E. Alternative file transfer mechanisms .................................................. 81
Sending a file to a Communication program............................................... 81
Sending a file to a serial printer .................................................................. 81
Using the Workabout COMMS application ................................................. 81
F. Glossary ................................................................................................ 82
Index...........................................................................................................84
SunScan User Manual v 1.05
• 5
Introduction
How to use the manuals
This manual tells you how to use your SunScan Canopy Analyser and its
accessories. Some pages in the Menus and Screens section are "Quick Guides"
which summarise the principal operating modes of the SunScan. They have been
laminated on to durable material so that they can be taken into the field instead of
the full manual. A separate Technical Manual is provided, but you will only need to
refer to it in exceptional circumstances.
If you have purchased the Psion Workabout Data Collection Terminal, you will need
to refer to its Workabout User Guide at first, to learn its basic operations. You may
also want to refer to your PC User Manual when setting it up to communicate with
the SunScan system.
Organisation of this manual
The sections are arranged in a practical order so that you can first of all check the
functioning of the equipment you have received, and then learn how to operate it
proficiently with the tutorials.
After this, there is a discussion of the measurement options that you must consider
when designing your experiments and taking readings in the field. The remainder of
the manual covers such things as the theoretical basis for leaf area index estimates,
and a technical reference section.
As a new user, you are recommended to work methodically through the Getting
Started, and SunScan Tutorial sections. Thereafter you may browse through other
parts of the manual as needed.
The SunScan Canopy Analysis System
Here is a brief overview of the main functions and components of the SunScan
system.
PAR measurements
Fractional interception and Leaf Area Index estimates
The SunScan probe is a portable instrument for measuring the light levels of
photosynthetically active radiation (PAR) in plant canopies. With it, you can
measure the interception of solar radiation by the canopy, and – in some types of
canopy – make estimates of canopy leaf area index (LAI).
PAR mapping
You can quickly take numerous readings to find the average level of PAR beneath
the canopy, for example, or make linear transects of the PAR distribution within the
canopy.
Autolog and Linear Quantum Sensor modes
The SunScan probe may also be left unattended to log the variation in PAR at one
place throughout the course of a day either in its fully functional Autolog mode, or
in its more basic Linear Quantum Sensor mode, connected to a data logger.
6 • Introduction
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SunScan probe
The light sensitive “wand” of the probe is 1 metre long, containing 64 photodiodes
equally spaced along its length. The probe handle contains batteries and electronics
for converting the photodiode outputs into digital PAR readings, which get sent to
your Data Collection Terminal via the RS232 link.
Beam Fraction sensor
The Beam Fraction sensor (BFS) also measures PAR light levels. It is used to
monitor the light incident on the canopy at the same time as you are making
measurements beneath it. The BFS incorporates two photodiodes, one of which can
be shaded from the direct solar beam by the shade ring. This allows the direct and
diffuse components of PAR to be separated, which is necessary for the computation
of LAI.
Data Collection Terminal
To observe and store readings from the SunScan probe, you need the Data Collection
Terminal (a Psion Workabout). The Workabout is a lightweight, robust field unit
with a full alphabetic keyboard for the annotation of readings. It comes with a
removable Flashcard which can be used for data storage and transfer.
You can use a portable PC as a data collection terminal instead, but it is less
convenient for field work.
SunData software
In order for the SunScan probe to communicate with the Workabout or a PC, it needs
software. We pre-install the Workabout's SunData software, and we provide the
SunData PC software on a 3.5 inch diskette which you must load into your PC. The
SunData PC software is a DOS program; it does not require Windows, but it can be
run in a DOS window. Data files are created in an ASCII text format which you can
import into spreadsheets or other applications for analysis on any PC.
Field accessories
The sturdy field Carrying Case is designed to accommodate all the components of
the SunScan system. It has room for an optional tripod mount which is intended
primarily for use with the BFS, but which can equally well be used with the SunScan
probe. Space is also provided for extension cables that may be ordered with the BFS.
SunScan User Manual v 1.05
Introduction • 7
Getting Started
After unpacking the SunScan consignment and checking the contents against the
packing list, you will want to know if everything is functioning correctly. All parts
of the system are checked at our factory before despatch, so you should not
anticipate trouble. If the SunScan carrying case is difficult to open, slacken the
pressure release screw which is built into the carrying case moulding.
If you are an experienced user, the functional checks can be done in a few minutes
with no difficulty. If you are a new user you will have to follow the steps below
carefully and systematically, which will inevitably take somewhat longer.
Check the Data Collection Terminal first (the Psion Workabout), and then use it to
check the SunScan probe. After that, you must install the SunData s/w on your PC.
This will enable you to confirm communications with the probe, and to establish the
data transfer link between the Workabout and your PC. Testing the Beam Fraction
sensor will be left until the tutorial.
Preliminary checks
The following instructions should enable you to do the preliminary checks as quickly
as possible, so explanations will be kept to a minimum.
The Workabout and SunScan probe
Step 1 - Getting a screen display
♦ Unwrap the Workabout.
The screen should be blank.
♦ Press the yellow On/Esc button.
A screen display should appear.
If it does, Step 1 is satisfactory.
If no screen appears, the Workabout may lack power. Proceed to the Workabout
hardware checks below.
If you cannot successfully follow through these procedures, this may be because
some starting condition is no longer set up exactly as it was when the Workabout left
our factory. Do not abandon the tests, but proceed as far as you can through the
successive steps.
Step 2 - Running SunData and communicating with the probe
The screen should be showing some icons, as above. This is the Psion system
screen.
If something else is on-screen, try the following:
♦ Press On/Esc (this will escape from any menus).
♦ Press ∪+X, that is: hold down the grey Psi key ∪ and press X. (This will exit from
any application that is running.)
Warning! Do not Exit from the System screen itself! If you get the Exit System
Screen? dialog press N. If you can't find the SunData application icon, it may have
been lost after exiting the System screen. Proceed immediately to the section on Reinstalling the SunData icon in More Psion and file handling notes to remedy the
situation.
8 • Getting Started
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After some minutes of inactivity, the Workabout screen will automatically blank
itself to save power. Press On/Esc once more to restore the screen display.
♦ Now connect the SunScan probe to the RS232 port at the top of the Workabout.
Leave the BFS sensor disconnected.
♦ Press the yellow arrow keys to select the SunData icon.(A black background
appears round the selected icon label.)
♦ Press the yellow Enter button. (Enter always accepts the selected item.)
The SunData opening screen should
appear, with a heading indicating that a
probe is connected.
♦ Press the red button on the SunScan
probe handle once or twice.
The Workabout screen should change.
If it does, Step 2 is satisfactory.
If you cannot get this step to work, you will have another chance to test the SunScan
probe after you have installed the SunData s/w in your PC.
Step 3 - Switching off the Workabout
♦ Press ∪+X to exit the SunData program.
♦ Press Off.
The screen will go blank.
Checking the Workabout hardware
You should now refer the Psion Workabout User Guide chapters 1 and 2 and start
familiarising yourself with the basic operation of the Psion (you will need to do this
more thoroughly when you reach the tutorial sections).
The Internal drawer
The Workabout hardware installed at despatch is listed below. You can check this by
pressing the drawer release button at the top left corner of the Workabout to open the
battery drawer. Check for:
a) Lithium backup cell installed.
b) One Ni-Cd battery pack installed, and charged.
c) Flashcard in internal drive slot A
The Psion Charger
This provides power to run the Workabout, and at the same time trickle-charges any
Ni-Cd battery that is installed.
♦ Mount the Workabout into its Docking Unit, and connect the charger to it.
The indicator on the front of the Workabout will light up.
Spare Ni-Cd batteries are supplied uncharged. At the first convenient opportunity,
fit them in the Workabout and trickle-charge them fully (overnight).
This completes the initial checks to show that the SunScan probe and Workabout are
functioning. Now you must install the SunData s/w in your PC.
SunScan User Manual v 1.05
Getting Started • 9
Installing the SunData s/w in your PC
In this section you will be told about the SunData s/w, and what you need to do to
get it running on your PC. You will then use it to establish that your PC can
communicate with the SunScan probe.
The SunData s/w Diskette
What the s/w does
The s/w is provided as three groups of programs in separate directories on the
diskette. If you find a README file in the root directory of the diskette, please read
it. It may contain late release information not included in this manual.
SunData PC s/w (in the \PC directory)
You must install this in a PC for transferring data files from the Workabout to the
PC. You can also install it in a (portable) PC to enable the PC to act as a data
collection terminal instead of the Workabout.
SunData Psion s/w (in the \PSION directory)
This is a backup copy of the s/w that is pre-installed in the Workabout. You will not
use this except in the unlikely event of program loss from the Workabout.
Psion communications s/w (in the \COMMS directory)
These are DOS programs provided by Psion which enable you to transfer files
between the PC and Workabout. Full documentation is provided on disk and in the
appendices. They will not be further described in this section.
These programs are essential if you need to restore s/w lost from the Workabout,
(unless you have purchased the optional PsiWin Windows s/w), and of course they
give you alternative methods of transferring data files from the Workabout to your
PC, if you don't want to use SunData's own data file transfer method.
Installing the s/w
Your PC requirements
Your PC needs: DOS 3.3 or higher; a 3.5 inch 1.44 MB diskette drive, and an
available serial port with 9 pin D-connector
You may need to refer to your PC manual to carry out the following tasks: copy a
diskette, create subdirectories, copy files, and run programs from the DOS prompt.
You should make a copy of the SunData s/w diskette immediately for routine use.
Store the original diskette securely, and set the write-protect slider on the diskettes.
Copy all the diskette files to your hard disk drive (HDD). You are recommended to
use the same diskette directory names and to put them all in a parent directory, for
example: \SUNSCAN. At the same time, you should create another directory for
storing SunScan data files, e.g. \SUNSCAN\SSDATA. You may choose alternative
names for any of these directories if you wish.
♦ Insert the SunData diskette in your PC's diskette drive.
♦ Create the required directories on your PC's HDD.
♦ Copy the files from the diskette to the HDD.
♦ Remove the SunData diskette from the disk drive.
No problems should be experienced if you wish to de-install the SunData programs
later. Simply delete all the directories and files that you copied on to your hard disk.
10 • Getting Started
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Running SunData
The program you will run is SUNDATA.EXE (which was in the \PC directory on the
diskette). This will be a quick test just to obtain the opening SunData screens on
your PC.
From DOS
♦ Change to the directory on your hard disk which holds the SUNDATA.EXE file.
♦ At the DOS prompt, type: SUNDATA then ↵ or Return or Enter to run it.
The opening SunData screen will appear. SunData is running. You should see a
starting plaque similar to this:
♦ Press the Tab key ( →| ) to select either <Color> or <Monochrome>,
then press ↵ to expose the first working screen (see below)
You will not see this starting plaque again, but you will always be able to choose
your screen mode from the system settings in the program.
The first working screen will look like this:
For the moment, ignore the connection instruction at the bottom of the screen,
because you need to tell your PC which COM port to use for the SunScan Probe.
Setting up your PC's COM port
♦ Press Alt+S, then Y
The System Settings dialog box will appear:
♦ Use the arrow keys to toggle between the
available COM port options.
♦ Press the Tab key ( →| ) twice to move to <OK> , then press ↵
(You can also move there with ↑↓, Enter, or Shift+Tab.)
SunScan User Manual v 1.05
Getting Started • 11
Communication checks:
SunScan probe to PC
For this test you will need the SunScan probe, and the SunData PC s/w running in
your PC to the stage described above.
♦ Now connect the SunScan probe coiled cable to the COM port you have just
specified, and press ↵ again.
The CONNECT option will be activated, and the screen will change to report the
connection.
♦ On the SunScan probe handle, press the red "GO" button once or twice.
Further changes to the screen will occur.
Communication between the probe and your PC has now been demonstrated. Don't
worry if some of the numbers on the screen appear to be nonsense at this stage. You
will get a chance to set the probe up properly in the Tutorial section.
The SunData probe is supplied with alkaline batteries installed. The power is always
on, but the consumption is so low that new batteries will last for up to 1 year. After
taking readings with the probe, its battery voltage is reported in the screen title. The
cut-off voltage is 4700 mV.
Navigating and selecting options in the PC s/w
If you got lost in any of the above instructions, try again, using the following general
principles for moving around the screen:
a) Select an option by moving the highlighted cursor to it. Use the arrow keys or the
Tab key to move between options. Half-tone highlights indicate that options are
not available at that moment.
b) Accept the selected option by pressing ↵ or Return or Enter
c) Escape from, or cancel, a selection by pressing Esc
Menus at the top of the screen can be selected by pressing Alt + the highlighted letter
key (or using the arrow keys), otherwise the options at the bottom of the screen are
selected.
If you are familiar with the concept of "hot-keys", you will find them listed in the
menu dialog boxes, and you can use them straight away.
To exit or quit SunData
♦ Press Alt+F then X, or Alt+Q then Q
The program will return you to the DOS prompt.
Workabout to PC
For the moment, if the Workabout and SunScan probe have responded to the Getting
Started operations, then the preliminary tests are complete.
Later on in the Tutorial section you will learn how to transfer data files from the
Workabout to the PC. If you ever need to transfer the program files from the PC to
the Workabout, this is dealt with in the appendices.
12 • Getting Started
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Running SunData in Windows
At this stage you may wish to install the SunData program so that it runs from within
Windows.
In Windows 3.11
The SunData diskette also contains SUNDATA.PIF and SUNDATA.ICO files for use
with Windows.
♦ In Windows Program Manager, select File, New, Program Item
♦ Specify SunScan for the Description, SUNDATA.PIF for the Command Line, your
program directory name for the Working Directory, and SUNDATA.ICO for the
Icon File.
Program Manager will then display the SunScan Icon.
Later on you can refine this arrangement, and call the program from a data
directory, but for the present it will get you started.
♦ To run SunData: double click on the SunScan icon to run SunScan full screen.
♦ To exit: press Alt+F, X, or Alt+Q, Q
In Windows 95
SunData will run from a Windows 95 DOS command prompt, or from an MS-DOS
mode DOS session launched from Windows 95. Do not try to run it under a
Windows 95 non MS-DOS mode DOS session. Then follow the general principles
given above for Windows 3.11.
SunScan User Manual v 1.05
Getting Started • 13
SunScan Tutorial
About this tutorial
What you will learn
This tutorial takes you step by step through the processes of setting up and taking
readings with the SunScan probe, and then transferring the data files to a computer
for analysis. It is divided into two parts, each of which should take about 20 to 30
minutes. For the first part you will need access to the Psion Workabout and its User
Guide, or to a portable computer if you are using that instead. The second part
requires access to the SunScan probe, the Beam Fraction Sensor if it is available, and
a computer for collecting and analysing the data files.
Using a portable PC instead of the Workabout
The SunScan can be controlled using either a Psion Workabout or a portable PC
computer. The instructions in this tutorial show the specific keypresses and SunData
screens for the Psion Workabout, but the layout of menus and the operating
principles are broadly similar if you’re using a portable computer instead. Read the
sections with the PC logo in the margin.
♦ Instructions for you to follow are bulleted like this one.
Working with the Workabout
Powering up
If you haven't already done this in the Getting Started section, you should check that
the Workabout has a suitable power supply. This is explained in the introductory
section of its manual, page 3 onwards.
♦ Press the yellow On/Esc button.
The Workabout screen should become visible.
If not, refer to the Troubleshooting section on page 17 of the Workabout manual.
♦ Check the Workabout’s battery status by pressing Ctrl+Shift+B (hold down the
grey Ctrl and Shift buttons, then press B).
Navigating around the Workabout
Each time it powers up, the Workabout returns you to the same place in the
application you were last working on. Once you’ve got used to it, this is a very
useful feature, but it can be quite confusing when you first start. You may be
anywhere, in any application, and switching the Workabout off and on again won’t
get you back to the start.
♦ Exit any current application by pressing ∪+X. (Hold down ∪ then press X)
This will take you to the Psion System
Screen. You should see a display
something like this. (If you can't find the
SunData icon, see Getting Started for
help).
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Warning! If you were already in the Psion System Screen, you’ll see a message Exit
System Screen? Press N, so that you stay in the System Screen.
From this point you can launch SunData, the SunScan application, but first it is a
good idea to familiarise yourself with the Workabout’s keyboard. The main uses of
the keys are explained in the Workabout user Guide on pages 10 and 11.
The following keys are particularly important for the Workabout:
Menu
Pops up a menu of options relevant to your current activity
↑
Move the cursor up and down menu options, or adjust the value of a setup parameter
↓
← →
Cycle through the available settings for a menu option
Enter
Carry out highlighted activity, choose menu option or accept highlighted
setting
On/Esc
Exit from current activity or menu, abandoning any changes
Tab
Gives you and expanded range of choices, especially in file operations
What to do if you get lost
The important thing to remember is that you can get out of any menu by pressing
On/Esc, and out of any application by pressing ∪+X. This should get you back to the
Psion System Screen, as shown above. If things get really stuck, you may have to
reset the Workabout, as explained in its manual on page 20.
Starting SunData in the Workabout
♦ In the System Screen, use the arrow keys to highlight the SunData application,
and then press Enter.
SunData will load and then flash up
communicating as it tries to connect to
the probe. Since you haven’t yet
connected the probe, it will let you know
that Communications failed, and display
this screen (the title screen):
Now, you need to tell SunData to work in Emulator mode.
♦ Press Menu and then use the ← →
arrow keys to select the Settings menu,
which will look like this:
♦ Use the ↑↓ arrow keys to highlight
SunScan Probe, and press Enter to pop
up a dialog box with options on which sensors you have attached.
♦ Use the ← → arrow keys to change the
Data from: setting to emulator like
this:
♦ Set the Ext sensor to BFS so that a
Beam Fraction Sensor will also be
emulated.
♦ Press Enter to accept this setting and return to the title screen.
SunScan User Manual v 1.05
SunScan Tutorial • 15
Using a PC instead of the Workabout
Starting the PC software
Skip this section if you are using the Psion. Refer to the section in Getting Started
for details on starting the PC version of the SunData software. This should bring
you to the PC title screen. You will then set the probe into its emulator mode for the
first part of the tutorial, as follows:
♦ Press Alt+S to drop down the Settings menu
as shown.
♦ Move to the SunScan Probe option using the
↑↓ arrow keys, and accept it by pressing
Enter or ↵
The SunScan Probe dialog box will appear.
♦ Use the Tab or ↑↓ keys to highlight the Data from field.
♦ Use the ←→ keys to toggle between the options in the field
♦ Select the Emulator option
♦ Move to the External Sensor field,
select the BFS option (it will be
emulated too)
♦ Move to the <OK> field and press
Enter or ↵
The menu line at the bottom of the screen will now show only the CONTINUE option.
♦ Press Enter or ↵ to get the following screen:
In the Setting up instructions that follow, you must interpret the Psion Workabout
instructions appropriately for your PC's environment. Don't forget the general rules:
a) Select an option by moving the highlighted cursor to it. Use the arrow keys or the
Tab key to move between options. Half-tone highlights indicate that options are
not available at that moment.
b) Accept the selected option by pressing ↵ or Return or Enter
c) Escape from, or cancel, a selection by pressing Esc
Menus at the top of the screen can be selected by pressing Alt and the highlighted
letter key (or moving the cursor to it with the arrow keys), otherwise the options at
the bottom of the screen are selected.
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SunScan User Manual v 1.05
SunScan Tutorial • 17
Setting up a measurement session
Working through the menu options
In normal use the SunData software calculates Leaf Area Index (LAI) based on
readings from the SunScan probe and from the Beam Fraction Sensor (if fitted).
These calculations also require information about the distribution of leaf angles and
absorption of light by leaves within the canopy and knowledge of the solar angle
calculated from the time of day and local latitude and longitude.
SunScan probe
Average PAR within canopy
Beam fraction
PAR above canopy
Ratio of Direct to Total light
ELADP setting
Leaf Angle Distribution
Absorption setting
Leaf PAR Absorption
Time and date
Latitude setting
ï
ï
Leaf Area Index
ï
ï
ü
Solar zenith angle
Longitude setting
Before it can make sensible calculations of the Leaf Area Index, SunData needs to
know what values to use for the above settings.
♦ Press Menu, use the ← → arrow keys to
select the Settings menu, and the ↑↓
keys to highlight Site, and press Enter.
Type in a Name for your present site, and
set the Latitude and Longitude by
pressing Del and typing in the
appropriate values. When everything is
correct, to accept it
♦ Press Menu again, then select Time & Date and press Enter. Now set the local
time and date in the dialog box. You also need to set the appropriate offset from
GMT for your time zone. Set Local time is GMT to between -12.0 and +13.0
hours. Remember to make allowance for any special seasonal offsets, such as
“Summer Time”, “Daylight Saving”. For example: British Summer Time is
GMT+1, India is GMT+5.5, and USA EST is GMT - 5.0.
♦ Press Enter to accept the settings and return to the Title screen.
Note: The date and time formats can be changed, but for the moment just get the
information correct. To change am to pm, select it, and press p (or a).
♦ Use the ← → arrow keys to set the Absorption to
0.85. Set the ELADP (Ellipsoidal Leaf Angle
Distribution Parameter) to 1. Press Enter to accept
these settings.
Later sections in Measurement Options and LAI Theory give explanations and
advice on choosing values for these parameters.
♦ Set the Display format to LAI. Leave the ‘Sample’ and ‘Plot’ names unchanged.
The options for Display (LAI, PAR and All) have an important effect on the display
of readings but they also interact with the setting for Ext sensor (BFS or none) to
determine the sequence of readings required.
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You will go through these different combinations later in the tutorial, and there is
also a route map in the Menus and Screens section.
These settings can be stored as a Configuration. Saving a number of configurations
enables you to switch quickly between the different set-ups necessary at different
sites, or when analysing the canopy of different crops with different characteristics.
Note: The Workabout’s file structure is very similar to a standard DOS system.
Files, such as SunData configuration and data files, are stored in hierarchical subdirectories either in the Internal Disk (part of the Workabout memory configured as
a disk, called drive M), or on the Solid State Disks (SSDs) A and B.
♦ Press Menu, File, Save Config’n.
Type in an appropriate Name for the
configuration. This will save it into the
\SUN\ directory on the Internal disk,
which for the moment will be
satisfactory.
Note: The Tab key is very useful when setting options generally - it pops up a
scrollable list of all the options available. It is particularly important when saving
and loading files, as it calls up a full list of all existing files and directories for you
to scroll through. Use On/Esc to exit from these directories.
Since you are just about to start taking readings, you also need to tell SunData the
name of the file you want to use for storing the data, and what file format you want
the readings to be stored in.
Press Menu, File, Data Storage, Enter. The default file setting is A:\DATA.PRN.
This will give you an easily Printable text file. If you prefer to work with
spreadsheets, choose the data file type Comma separated. For the Disk, specify A,
and for the moment ignore B and C. Do not put data files into the internal memory:
the space there is needed for other things.
File Saving
As soon as you have opened a data file, the SunData program looks after it for you.
The file will be automatically saved whenever you exit the SunData program or
when the Workabout is switched off. When SunData is re-started, the most recently
used file is automatically re-opened. New data will be appended to it - not
overwriting earlier data.
If you want to start a new file, type a new file name in the Store data to sub-screen.
"Hot Keys"
You may have noticed in the menus that many of the commands have a short-cut or
Hot Key combination, for example the dialog box obtained by Menu, File, Data
Storage, Enter can be invoked from the main SunData program simply by pressing
∪+D.
Try these out from time to time as you become more familiar with SunData program.
Note however that if you are already in a dialog box, you will need to On/Esc from
it before the Hot Key will work.
SunScan User Manual v 1.05
SunScan Tutorial • 19
Taking readings
Using the Emulator mode
You have now configured all the settings necessary to start taking readings,
including setting SunData into emulator mode, with BFS, and setting the display to
LAI At its simplest, you only need to press Enter twice to take, display and store
each Leaf Area Index reading, and the values it is derived from:
♦ Press Enter once to
collect and display an
(emulated) reading.
♦ Press Enter again to
store that reading, and
return to the Next
Reading screen.
....or possibly
Use the ← → arrow keys
to select DISCARD before
pressing Enter, in which
case the reading will not
be stored, ...and
optionally
♦ Use the ← → arrow
keys to select NOTE
before pressing Enter, so that you can add a note to the reading before it is stored.
Reading labels uniquely
identify each reading.
They can be edited in the
Next Reading screen by
using the ↑ key.
Current time, and
calculated solar angle.
Spread of
readings from
individual
photodiodes
along the probe
wand.
PAR in µmol.m-2.s-1
above the canopy,
measured by Beam
Fraction sensor.
PAR within the
canopy, measured by
the SunScan probe
(or emulated).
Fraction of PAR in the
direct solar beam compared
to total incident PAR
(Direct + Diffuse) above
the canopy.
20 • SunScan Tutorial
Leaf Area Index, calculated from
the readings shown and the
parameters entered earlier.
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♦ Now Set the Display to PAR (Menu,
Settings, Display, Enter)
The procedure for taking, displaying and
storing a reading stays the same, but the
reading display and the data stored
change to reflect the new setting:
This screen is the same if you change the Display to All, but the stored data also
includes readings from all 64 individual photodiodes.
Note: if you’re using a portable computer to control the SunScan, then the All
setting will actually display the 64 (emulated) photodiode readings.
Without a Beam Fraction Sensor
♦ Change the SunScan probe, Ext sensor to none. (Menu, Settings, SunScan
probe, Enter)
The reading procedure is still the same
two-step process (read, store, read,
store...) without a Beam Fraction Sensor
- as long as you have the Display set to
PAR or All. However, the screen displays
only the average PAR reading from the
SunScan probe and the spread of the
photodiode readings.
Things get more complicated if you want to take Leaf Area Index readings without a
Beam Fraction sensor. SunData still needs measurements of the Incident PAR and
the Beam Fraction, so you have to make them using the SunScan probe itself. We’ll
go into the details of this procedure later on, once you have got the SunScan probe
connected.
Connecting the SunScan probe
By now you should have a reasonable familiarity with using the Workabout, and
how the SunData menus work, so it is time to try taking some readings with the
SunScan probe connected.
♦ Plug the coiled serial cable from the probe into the RS232 connector at the top
right of the Workabout.
♦ Use Menu, Settings, Display, Enter, and set the display to PAR.
♦ Use Menu, Settings, SunScan probe, Enter, to set the Data from: to SunScan
probe.
♦ For the moment, even if you have a BFS, set the Ext sensor: to none. Press
Enter to accept these settings.
SunData should display a version number at the top of the opening screen. If you see
Communications failed, you will need to recheck the connections.
If you don't get this far but get messages saying the serial port is in use, you must set
the Remote link to off. Exit from the SunData program if necessary (∪+X). From the
Psion System screen, press Menu, Spec, Remote link, Enter, and select Off. Then
restart SunData.
♦ Press Enter in the Next Reading screen.
SunScan User Manual v 1.05
SunScan Tutorial • 21
This time you will see the value of the PAR reading from the probe. Now is a good
time to play around with the system a bit, shine a light on the probe, or take it
outside and poke it into a few canopies.
♦ Press the red (GO) button to store the reading. Take a few more readings,
pressing Enter or the red button, and using NOTE, so that you store a few
annotated readings to your data file.
You may hear occasional beeps as you take readings. These are to help you keep
track of the reading process without constantly having to look at the Workabout: one
beep for READ, a double beep for STORE.(If you hate beeps, they can be turned off
- later!)
Connecting the Beam Fraction Sensor
If you have got a Beam Fraction Sensor...
♦ Screw the BFS connector into the socket at the back of the SunScan probe.
♦ In Menu, Settings, SunScan probe, Enter, set the Ext sensor: to BFS. Press
Enter to accept this setting.
♦ Use Menu, Settings, Display, Enter, and set the display to LAI.
Now when you take readings, you will see a value of the Leaf Area Index.
Mount the BFS above the
canopy, with the arrow facing
North, level, and with the
Shade ring adjusted so that it
casts a shadow over the more
northerly photodiode .
SunScan probe
held level within the
canopy being
measured.
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By now you may have accumulated quite a lot of readings in Data.PRN the default
data file. There is no harm in this, but you may want to put further test results into
new file, or maybe try out a .CSV file. If so, follow the Data Storage instructions a
few pages back.
Measuring Leaf Area Index without a Beam Fraction Sensor
This is the most complicated of the combinations of probe and display settings. The
Measurement Options sections discusses in detail the conditions for which it is
possible and desirable to make this measurement.
♦ set the Ext sensor: to none.
The Next Reading screen now includes
extra options for reading INCIDENT and
B FRAC - and it won’t let you proceed
with a READ until you’ve taken these
readings.
♦ Highlight B FRAC and press Enter.
Hold the probe level above the canopy as
before, but now cast a small shadow over
part of the probe. Don't hold the shade too
close to the probe - otherwise it will cut
out some of the diffuse light as well.
SunData looks at the readings from the
photodiodes and uses the lowest value to
calculate the Diffuse component of the
incident light. It uses the highest
photodiode values to calculate the Total
incident, and uses these two values to
calculate and display the Beam Fraction:
Note: SunData uses this value for the Beam Fraction to increase the accuracy of
the calculation of Leaf Area Index, as explained in the LAI Theory section.
However, this is a secondary effect, and you should not worry unduly about the
second decimal place for the Beam Fraction value.
♦ Press Enter or the red button to STORE the Beam Fraction reading.
You can now continue to take readings with the probe and display the LAI as before
- that is, until the light conditions change, when you will need to retake the Beam
Fraction readings. If you wish to recheck only the incident light reading, you can do
so as follows:
♦ Hold the probe level above the canopy, and make sure as little as possible of your
own outline is being seen by the probe.
♦ Use the ← → arrow keys to highlight INCIDENT, and press Enter.
SunData will display the reading from
the probe:
♦ Press Enter or the red button to store
this as the Incident PAR reading.
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SunScan Tutorial • 23
Averages
SunData can calculate and store the average of all the samples in a plot, as well as
retaining each actual reading.
♦ In the Reading screen, use the ← →
arrow keys to highlight the AVERAGE
option and press Enter.
You can then store, discard or add a note to
this average. After taking an average,
SunData will automatically increment the plot number.
In the LAI mode SunData calculates the following averages of the samples in the
plot:
• The average of all the Total incident light readings.
• The average of all the transmitted fractions (transmitted light/incident light ) for
each sample.
• The average of all the calculated LAIs for each sample.
In the PAR or All modes, the averages calculated are:
• The average of all the BFS Total readings (if the BFS is present).
• The average of all the SunScan probe readings.
Reviewing your data file
As soon as you have taken a few readings, you may want to look back over the
results before you transfer your data file to a PC. To review your file:
♦ Press Menu, File, Review, Enter (or
∪+V) to call up the dialog box as
shown.
You will be prompted with the current
data file name.
♦ Press Enter to accept it.
The data file should now be visible. If it is cluttered with "" and ,, it is a .CSV file,
and you may format it for clarity. See below.
Owing to the small size of the Workabout screen you must scroll up and down or
sideways to view the whole extent of the file.
♦ Use the arrow keys for scrolling in
continuous motion.
♦ Use Shift+ the arrow keys to step a
screen at a time.
♦ Use ∪+ arrow keys to move to the
ends of a file.
♦ Press Menu for the list of hot keys, and other options.
These hot keys will take you to the top or bottom of the file, or allow you to zoom in
to three levels of magnification.
Note: you can in fact review the contents of any data file stored in the Workabout.
Just use the dialog box to choose a different file name.
If you have selected a comma separated (.CSV) data file instead of the default print
(.PRN) file, either
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♦ Select Format CSV: Yes in the Review dialog box
or from the file itself
♦ Press Menu, Format CSV, Enter (or ∪+F)
This command in fact toggles between the formatted and unformatted states, and the
terminology changes accordingly.
Press On/Esc to exit from any of the dialogs, or from the reviewed file itself.
Note: if you’re using a portable computer to control the SunScan, the file is fitted
into one screen width, and you will be able to see a bigger area of the screen. You
can move throughout the file using ↑↓ PgUp, PgDn, Home, and End keys. You can
also view data files with any other text reading or spreadsheet application.
Transferring the data file to your PC
Now is the time to practice transferring a data file from the Workabout to your PC.
You will run SunData in the Workabout and SunData on the PC, and send the file
via the RS232 serial connection.
The SunData File Transfer system is intended only for transferring data files from
the Workabout to a PC. You can't use it for non data files, nor for transfers from the
PC to the Workabout. Other types of file transfer can be done with the utility
programs referred to in the appendices.
Of course, if you are using a portable PC as a Data Collection Terminal instead of
the Workabout, your data files will already be on the hard disk, and you won't need
to do this.
From the Workabout
On the Workabout:
♦ Disconnect the SunScan probe coiled cable from the RS232 port on the
Workabout. Plug the (uncoiled) SunScan comms cable into the Workabout. For
the moment leave the remote end of the comms cable not connected to your PC.
If you get a "Failed to open Serial port in use" message, press On/Esc to clear the
message, then press ∪+L from the system screen. The Remote Link dialog box will
appear from which you must set the link to Off, and press Enter to accept it.
SunData should now run.
To the PC
Now proceed to your PC. If you haven't done so already, you should run SunData
and set up your PC's COM port as described in the Getting Started section of this
manual (access the System Settings dialog box by Alt+S then Y, or Ctrl Y).
♦ Connect the SunScan (uncoiled) comms cable to the COM port you have
specified.
♦ Select Alt+File, File Transfer, ↵
This calls up the File Transfer box which lets you specify the directory on your PC
into which you want the data file transferred. The current choice of directory is
shown in the top line.
If you want to change it, use the commands shown below.
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SunScan Tutorial • 25
Navigating in the File Transfer box
• The Tab key (➙❘) will move you from one <field> to the next, in sequence.
Shift+Tab takes you back a step.
• The <Dirs/Drives> area shows you other drives that can be accessed. Use the ↑↓
arrows and press ↵ to select the drive or directory you want.
• "Sliders" on the side of the box give you an indication of where you are in the
complete list.
• ". ." takes you to the parent directory.
• "." Returns you to the current directory File box.
• The <Files> area shows you the filenames that are already used in that directory.
Use the ↑↓ or ←→ arrows to view the complete file listing.
You can't select or change these filenames here - they are listed so that you can see
what files you already have. Specifying the filename you want to save is done in the
next steps on the Workabout. Don't worry about over-writing an existing file, you
will be warned if this is about to happen.
You can quit this process at any stage by pressing Esc on your PC, or by selecting
<Cancel> and ↵.
♦ When satisfied with your choice of directory, select <Receive> and press ↵.
A "Waiting for Data . . " message will appear in the files box.
Now move back to the Workabout for the final stage.
Initiating the file transfer from the Workabout
With SunData running in the Workabout:
♦ Press Menu, File, File Transfer, Enter or (∪+R), for the file transfer dialog box.
You will be prompted with the current data file Name and Disk, but you could
choose any data file in the Workabout by following the on-screen prompts. For this
example we will continue with the A:\Data.prn file illustrated.
Now is your chance to specify the
filename you want the file saved as. If you
are happy with the send file Name, then
leave the save as showing ✳.✳.
♦ If you want to change the name, use the ↑↓ arrows to select save as, and type in
your preferred filename.
♦ Press Enter.
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You will immediately get a "Sending" message showing the progress of the transfer
until it is completed, after which you will be returned to the SunData program.
If you have no more to do, you can exit SunData with ∪+X and disconnect the
RS232 comms cable.
If the process is not going according to plan, and you suspect problems with the
RS232 link, see the section below for help.
Meanwhile, on the PC...
Simultaneously with the sending message on the Workabout, you will see the file
being written on the PC screen, and a final confirmatory message that the file has
been sent correctly, if all was well.
♦ Press Esc twice to exit the file transfer process, and then exit the SunData
program too (Alt+F, X).
The data file has now been copied to your PC, into the directory you have specified.
From there you can easily import it into spreadsheets or other applications for
presentation or further analysis.
In a later section (More Psion and file handling notes) you can find out how to
clean up your Flashcard by deleting files you have transferred to your PC.
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SunScan Tutorial • 27
RS232 communication problems
RS232 links between computers are notorious for giving difficulties, because there is
no completely accepted international standard for them. If you are getting error
messages which indicate the link is not working properly, then the difficulties may
occur in a number of areas.
• The physical connections (the comms cable, the computer serial ports) may be
incorrect or defective.
• The RS232 data parameters of the sending and receiving computers must be
matched. (SunData takes care of the Baud rate, parity, and other data bit settings
for you, so this should not be the problem).
• Even if the above settings and connections are correct, the computers may be
sensitive to the exact order in which components are plugged in and the programs
run.
Try the following systematic process to resolve problems:
♦ Exit from the SunData programs and disconnect the comms cable from the
Workabout and PC.
♦ Switch off the Workabout and the PC.
♦ Work through the instructions above again exactly in the order they are
presented, double checking the physical connection of the comms cable and the
COM port setting of your PC. Preferably work in DOS only.
The above instructions have worked successfully on a variety of portable and
desktop computers, with processors from 286s to Pentiums, and DOS versions from
4.0 to 6.2.
If you still have difficulty, try making the connections in a different order, or try
different PCs if they are available, or contact your agent or supplier, or Delta-T
Devices for technical support. If you are successful, make a note of the exact
process.
Conclusion of the Tutorial
By now you have used the SunScan to take practice readings in the emulator mode,
and you have set up the configuration to take readings with the probe itself in a
variety of modes (PAR, LAI and All). You have stored readings and been able to
review the data file and transfer it to the hard disk of your PC. These are the basic
operations which should enable you to explore other capabilities (such as the
Autolog mode, for example) without further detailed instruction.
If you are now keen to think about the practicalities of your next experiment then
skip to the section on Measurement Options. If not, you could consolidate your
familiarity with the Workabout and its file handling concepts in the next sections.
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SunData Screens on the Workabout
Note: these screens
are only required if you
are measuring Leaf
Area Index (LAI), and
you do not have a
Beam Fraction sensor
attached to the probe.
Note: screen display and data stored
will be different from this if the Menu,
Settings, Display option is set to
either PAR or All instead of LAI.
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SunScan Tutorial • 29
Menus and Screens
The following table shows the menu options and settings for the Psion Workabout.
Menus for SunData PC software follow a similar layout.
File
Data
Storage
Transfer
Save
Config’n
Restore
Config’n
Name
≤ 8 chars.
Type in name (and subdirectory) for the data file. .PRN or .CSV
extensions are added automatically, depending on data type.
Press Tab to display a list of files and directories on the specified
Disk. These can be selected too.
Disk
A, B or
Internal
A and B refer to the Solid State Disks - see Workabout manual
page 12. Internal refers to the Workabout memory (RAM).
Subdirectory usage needs care! See User Manual.
Type
Print
File is a directly printable, ASCII file with appropriate formatting.
Comma
separated
File type is best for spreadsheets. Fields are enclosed in commas,
text in "...".
send file
Name
Data.prn
Prompts with current data file name, but any other name can be
selected, with Tab or ← →.
Disk
see above
save as
✳.✳
✳
Type another name, or the "send file Name" will be used by
default.
Name
≤ 8 chars.
Type in name for configuration file. Extension .CFG is added
automatically. Press Tab to display a list of files and directories on
the specified Disk.
Disk
see above
Disk
Review
Use ← → or press Tab to display a list of possible .CFG files from
which to restore.
Name
see above
View data file on the Workabout screen. Prompts with current data
file name. Select other names with Tab or ← →
Name
Disk
see above
Format
.CSV
Yes, No
Yes hides the ",,," in a .CSV file. Has no effect on a .PRN file.
Menu
Zoom
Top of File
Bottom of file
Format CSV
Quit
For manoeuvring. Press Menu within a reviewed file. Gives rapid
scrolling, zooming to different magnifications, format/unformat of
.CSV files, and quitting the reviewed file.
Also, Shift+ arrow keys moves one screen at a time. ∪+↑
↑↓ moves
to end of file
Exit the SunData program
Exit
Settings
SunScan
probe
Data from:
SunScan
probe
Light readings are collected from the SunScan probe.
emulator
Light readings are generated by the SunData software - used for
test purposes and for the Tutorial.
Ext sensor: BFS
none
Constants
Absorption 0.5 to 1.0
ELADP
30 • Menus and Screens
0 to 1024
Incident PAR and beam fraction readings are collected from a
Beam Fraction sensor attached to the SunScan probe.
No external sensor is connected, and readings for incident PAR
and beam fraction (if required) have to be measured using the
SunScan probe itself.
Set the leaf PAR absorption. 0.85 is typical.
Set the Ellipsoidal Leaf Angle Distribution Parameter, which
models the leaf angles within the canopy. 1 corresponds to a
random spherical distribution, 0 to vertical, and 1024 to horizontal.
Use 1 as default.
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Settings
Titles
(contd.)
Site
Time &
Date
Display
Title
≤ 40 chars.
Title name is stored in the data file heading, and is displayed on
the Title screen.
Group
≤ 40 chars.
Name for a group of readings. A new name (or setting change)
starts a new group.
Site Name
≤ 40 chars.
Name of your measurement site.
Latitude
-90°° to +90°°
Latitude of your measurement site. Use negative numbers south
of equator.
Longitude
-180°° to
+180°°
Longitude of your measurement site. Use negative numbers east
of Greenwich meridian.
Local time
Set clock to the time at the measurement site.
Date
Today’s date.
Local time
is GMT
-12.0 to +13.0 Offset of local time zone from GMT. Remember to include
Display:
LAI
provision for any local “Summer” time etc.
Display:
Solar Zenith
Incident PAR
Transmitted PAR
Beam Fraction
Utils
Calibrate
Photodiode spread
Leaf Area Index
PAR
Display:
All
Same as for PAR, but individual readings stored to the data file.
'Sample'
name
≤ 6 chars.
Change name if ‘Sample’ is not appropriate.
'Plot' name
≤ 6 chars.
Change name if ‘Plot’ is not appropriate.
Transmitted PAR
Incident total PAR
Incident diffuse PAR
Photodiode spread
Restore
Factory
Calibration
Restores each photodiode's calibration coefficient as determined
by Delta-T.
Recalibrate
SunScan
Calculate and reset the individual photodiode calibration
coefficients using the Beam Fraction sensor as a reference.
SunScan will operate unattended in whatever mode has been setup. Complete all the screen entries then press Enter to initiate
Autolog process.
Autolog
(setup
screen)
Start
Date, time
Type in start date and time. These can be in the past 24 hours to
allow alignment with particular periods.
Stop
Date, time
Type in date and time to finish. Must be in the future.
Read
interval
hh:mm:ss
Type in the sampling interval. Every reading is stored.
Minimum 00:00:01, maximum 23:59:59.
Average
interval
hh:mm:ss
Stores averages at the specified interval. Should be a multiple of
the read interval. Zero gives no averages.
Ignore
nighttime?
yes, no
Yes: readings are not taken at night.
No: readings are continuous.
Sleep, (or
Off)
Blanks the screen. This is the usual condition. Press On/Esc to reawaken it.
Cancel
Stops the Autolog process on demand.
(progress
screen)
Comms
Test
Dumb terminal mode. Factory setup use only.
About
Displays Psion SunData s/w version, and the battery voltage and
status for both the SunScan probe and Workabout.
SunScan User Manual v 1.05
Menus and Screens • 31
Quit
32 • Menus and Screens
Exit the SunData program
Document code: SS1-UM-1.05
More Psion and file handling notes
Navigating Psion directories and screens
The Workabout User Guide
At this stage you may want to learn more about operating the Workabout, so you
should refer again to the Workabout User Guide in which the following subjects are
well covered.
• Keyboard and LCD screen - pages 8,9
• Key functions and combination keypresses - pages 10,11
• The System Screen and Menus and dialogs - pages 38-42
• Solid State Disk drives - pages 12, 35
• Basic operation and troubleshooting - pages 13,14,16,17-20
When the User Guide refers to "application developers" and functions under
"application control", this means that Delta-T and the SunData program may use
some of the keys for special functions.
Warning! Look at "Changing the system-wide settings" - pages 23-24, but for the
moment do not change any of these! They may well make the SunData screens look
or behave somewhat differently from the examples in the SunScan documentation.
General principles
Remember the general rules for moving around Psion screens:
• The cursor (inverse video) highlights an available option
• Move the cursor with the yellow arrow keys to select options
• Press Enter to accept an option
• Press Menu to view lists of menus
• Press Tab to view alternative choices
• Press On/Esc to exit from menus or screens without changing them
• Press ∪+X to exit from any application
• Press Off to switch off
• Press On/Esc to resume exactly where you were before switching off
• Press Shift+On/Esc for Help (but not in SunData screens).
"Hot keys"
You will see that many menu options provide a hot key combination for rapid access
- for example pressing ∪+L in the Psion System Screen will take you straight into the
Remote Link dialog box. This is often a very convenient form of "shorthand" for
keyboard operations when you have learnt them. Note though, that the hot keys are
application specific - pressing ∪+L in the SunData program will take you to the
Autolog function.
Navigating the Psion directories and screens
The Workabout's file directories are structured just like DOS, but because the Psion
screen is much more limited for space, the method of displaying and navigating
around the directories is illustrated in the following examples.
SunScan User Manual v 1.05
More Psion and file handling notes • 33
This is the Psion System screen. If you
cant see the application you want, use the
yellow left or right arrow keys to scroll
through the range.
To get to the directories press
Menu, then the yellow arrow keys
to select Disk, Directory, and then
press Enter
Warning! Do not Exit (∪
∪+X ) from the
System screen otherwise you will get this
Psion Logo startup screen and lose your
SunData icon. Avoid this screen! To get
back to the System screen follow the
directions: press Menu, then select
System screen, and press Enter. Then
refer below to re-install the SunData
application icon.
This symbol indicates the parent
directory. To move there, select it,
and press Enter.
This shows the Disk and subdirectory
you are in, whose files are listed in the
bottom panel.
The files in the subdirectory are
listed here. To operate on the
highlighted file press Menu for
various options.
To scroll through other disks,
press the yellow left or right arrow
This is the root directory of the
Internal Disk.
To scroll through the list, press the
up or down arrow keys.
Psion subdirectory usage in file select dialogs
In the Workabout file selection dialogs, you are only presented with information
about the file name and the drive it is on. No subdirectory information is given, and
this can cause confusion.
You can see which subdirectory you are currently working in by pressing Tab to
bring up the file directory display.
If you change the filename or drive in the dialog, you should be aware that the
Workabout takes the subdirectory information from the original file, unless you
specify otherwise. For example, if you copy a file from the root directory on drive A:
to another drive, it will be copied into the root directory of the drive you are copying
to.
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To copy to another subdirectory, you must add that information to the filename you
choose. If you only put a subdirectory name in the filename field, then the
Workabout will use the original filename, but with the new subdirectory. A
subdirectory name always starts and ends with “\”, for example \SUN\. If you are in
any doubt about what is happening, include the complete subdirectory path and
filename (but not the drive) in the filename field.
Re-installing the SunData application icon
If the Psion Logo Start-up screen (see previous page) has been accessed, the
SunData application may not be automatically re-installed on returning to the Psion
System screen, and the SunData icon will no longer be shown.
Re-installing SunData is quite simple. From the Psion system screen:
♦ Press Menu, Disk, Directory, Enter and make sure that the files SunData.app
and Sys$8087.ldd are present in the \SUN\ directory on the Internal Disk. Press
On/Esc to return to the System screen.
♦ Press Menu, Apps, Install, Enter, Tab, then move to \SUN\ and press Enter, then
select SunData.app and press Enter.
You will now see the Install dialog box with Filename SunData.app specified.
♦ Check that Disk is specified as Internal. The Position of the icon in the System
screen can be specified too. When all the settings in the dialog box are
satisfactory, press Enter to accept them.
The Sundata icon should now be present in the System screen.
The identical process can be used subsequently for installing an upgraded version of
the SunData.app program if one is issued.
Deleting unwanted Workabout files
You can delete files from the either the internal memory or the SSDs of the
Workabout using its own file handling procedures as follows:
♦ On the Workabout, exit from SunData (if necessary) by pressing ∪+X.
♦ In the System Screen, press Menu, Disk, Directory, Enter.
♦ Press ← or → to select Disk [A] (or whichever Disk your file is on).
♦ Press ↑ or ↓ to highlight the filename of the file you want to delete.
♦ Press Menu, Delete file, Enter, then respond to the confirmatory dialogue box.
You will find that no extra space is created on your SSD by deleting the files. The
only way to liberate space on the SSD is to re-format it after removing all valuable
files from it.
Flashcards - reformatting
The Flashcard (SSD) medium (unlike the Workabout internal memory) is such a
secure form of data storage that the only way to make it rewriteable is to reformat it.
If your Flashcard drive directory shows much less free space than the you would
expect from the difference between 256K (the full amount) and the files shown on it,
then you may want to reformat it. Check this with:
♦ Menu, Disk, Directory, Enter, then select the drive with ← or →
Reformatting will destroy any files left on the Flashcard. Make sure you have
already transferred all valuable data files to a PC using SunData's file transfer
procedure.
SunScan User Manual v 1.05
More Psion and file handling notes • 35
If you have other (non-data) files you want to keep, copy them to the internal drive,
or to another Flashcard for temporary storage (don't forget to copy them back and
delete them immediately afterwards), alternatively copy them to your PC using
RCOM or SLINK, or the PsiWin program if you have it.
♦ On the Workabout, exit from SunData (if necessary) by pressing ∪+X.
♦ In the System Screen, press Menu, Disk, Format disk, Enter.
Then follow the instructions and prompts carefully.
Warning! Reformatting is an irrevocable process - you will get on-screen warnings
that files will be deleted. Also, do not format the Internal drive - you will lose your
SunData program!
Data memory management
The memory space taken up by a given number of readings can't be specified exactly
because it depends on how many notes have been included, the number of data
groups used, whether the file is a .PRN or a .CSV file, and so on. The following
estimates will however give you a useful guide when planning experiments.
For the standard 256K Flashcard, about 2500-3000 readings can be stored in the LAI
and PAR modes. This reduces to about 400-500 in the All mode, which retains the
64 individual diode values for each reading. The optional 1 Mb Flashcard can
accommodate about four times these amounts.
You can check the available memory space on your Flashcard from the Psion system
menus as indicated in the previous paragraph. Bear in mind the note about creating
space on the Flashcard.
Warning! Don't be tempted to store data files in the internal memory even though it
may appear to have plenty of free space. The SunData program uses a lot of this
space when running, and will refuse to run without it.
Configuration and data file handling
Opening and closing files in the SunData programs follows a somewhat different
routine from that used by applications run in desktop PCs because of the
Workabout's Solid State Disks.
Two sorts of files are involved: data files which are used for storing measurements
made by the SunScan; and configuration files, in which you can retain the settings of
different sites and experiments.
SunData Configuration files
Configuration files contain information on the state of the SunData program, which
includes the following Settings menu and readings information:
• SunScan probe and External sensor settings
• Site and local time details.
• Leaf constants (Absorption and leaf angle distribution parameters).
• Display mode for readings (LAI, PAR or All).
• Title and reading Group names.
• The Plot and Sample numbers of the last reading taken.
• The filename, subdirectory and file type (.PRN or .CSV) for data storage.
36 • More Psion and file handling notes
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Default .cfg
Every time you exit the SunData program, the program state is stored in the file Default.cfg. This configuration is restored when the SunData program is next run,
which means that you start again exactly where you finished last time.
Configuration files can help you if you want to alternate between different sites with
different settings. Set up the appropriate titles, settings and data file information for
each site you have, and save them to separate configuration files. Use a separate data
file for each site.
When you visit a site, Restore its configuration file before you start taking readings
there, and Save it again when you finish. Do this each time you visit a site. This will
give you a separate data file for each site, and the readings will follow on
sequentially within each file, as if you had been at that site without interruption.
Creating a configuration file
You create a configuration file by saving it with a specific file name.
♦ Run SunData in the Workabout, and set up as many of the above details as you
can establish beforehand (press Menu, Settings, etc; and Menu, File, Data
storage, etc).
♦ Press Menu, File, Save Config'n, Enter. You will be prompted for a name and
Disk location.
♦ Press ← → or Tab to survey the subdirectory in which your file will be saved.
Specify a different name from any of these to create a new file, or select one of
the existing files (which will then be overwritten).
Restoring a configuration
♦ In the SunData program on the Workabout, proceed to Menu, File,
RestoreConfig'n. Press ← → or Tab to survey the list, and then select the .cfg
file that you want to restore.
Data files
A data file is automatically opened whenever you enter SunData. The initial default
file name is A:\DATA.PRN. When you take readings, they are appended to this file,
that is to say the new readings are added to the end of it, and do not overwrite it.
The value of this feature will become apparent when you want to alternate between
plots with different measurement displays. Your data files will be easier to read and
process if they contain only measurements of one type. However, there is absolutely
no restriction on what types of readings a data file can accept.
When you switch off, the file is automatically saved. You cannot forget to save, and
thereby lose readings. When you switch on again, the same file is open ready to
receive more data. There is no "data file close" command.
Changing the data file
If you want to store data in a different file (or change the file type from .PRN to
.CSV) at any time, you must specify a different filename and type (and location) for
it.
♦ Select Menu, File, Data storage, Enter for the appropriate dialog box. You can
either create a new filename, or select an existing file to append the data to it.
Don't forget that a Configuration contains the filename of the data file it uses. When
changing from plot to plot, you may prefer simply to restore a different
configuration.
SunScan User Manual v 1.05
More Psion and file handling notes • 37
Displaying data files on your PC
As soon as you have transferred data files from the Workabout to your PC (or have
created them on a portable PC) you will want to analyse and print them for your
records.
The .PRN file
The .PRN file format contains ASCII characters which can be read by a wide range
of text reading programs, and by some spreadsheets. An example printout is shown
below.
Created by SunData for Workabout v0.11
Title
:Demonstration
Location :Burwell, Cambridge
Latitude :52.2N
Longitude :0.4W
1996-05-19
Local time is GMT+1 Hrs
SunScan probe emulator
Ext sensor:BFS
Leaf Angle Distn Parameter: 1.5
Group
1 :Presentation
Time
Plot
15:51:12
15:51:59
15:52:08
15:52:16
15:52:24
Sample Trans- Spread
mitted
1
1
1
1
1
1
2
3
4
5
270.9
189.6
1047.5
63.4
1225.3
Average of
5 readings:
Incident light: 2000.0
0.13
0.14
0.15
0.14
0.15
Leaf Absorption : 0.85
Incident
Beam Zenith
frac Angle
LAI Notes
2000.0
2000.0
2000.0
2000.0
2000.0
0.65
0.65
0.65
0.65
0.65
2.7 Notes appear here.
3.2
0.8
4.7
0.6
Transmitted fraction:0.28
46.5
46.6
46.6
46.6
46.6
LAI:
2.4
The .CSV file
The Comma Separated Value format is a common format where ASCII characters
are separated into fields by commas, and text is identified by being enclosed in "...".
This greatly simplifies importing the files into spreadsheets for further analysis and
printout. The example below was created in Microsoft Excel 5.0
Created by SunData for Workabout v0.11
Title :
Demonstration2
Location : Burwell, Cambridge
Latitude : 52.0N
Longitude :0.1W
19/05/96
Local time is GMT+1 Hrs
SunScan probe emulator
Ext sensor: None
Leaf Angle Distn Parameter:
Group 1 : Presentation2
Time
Plot
15:56:54
15:57:54
15:58:00
15:58:05
15:58:09
15:58:15
Average of
Incident light:
Sample
Transmitted
2.5 Leaf Absorption :
Spread
Incident
1662.4
1
1
1
1
1
1
2
3
4
5
754.2
142.9
203.4
255.4
701.4
Zenith
Angle
LAI
Notes
0.37
0.15
0.15
0.15
0.17
0.13
5 readings:
1662.4 Transmitted fraction
38 • More Psion and file handling notes
Beam
frac
0.9
Beam Fraction measm't
47.5
47.5
47.5
47.5
47.5
0.25 LAI
0.9
2.9
2.5
2.2
1
1.9
Document code: SS1-UM-1.05
Data file layouts and data groups
If you want to get a good idea of how the data files will look, you can run the PC
SunData program in the emulator mode. The general presentation of the results on
screen will be similar to that in the eventual data file.
The one major exception to this is in the All mode when the 64 individual
photodiode readings are listed. On the PC screen they are shown as 4 rows of 16
values, whereas in the .CSV data files they occupy 64 adjacent columns (from handle
to tip of the probe) to the right of the notes field.
A single data file can contain a mixture of layouts. The column headings will be
different for different combinations of equipment (BFS or not) and measurement
(LAI or PAR or All) that you have chosen. Each time there is a change, the headings
and titles will be revised to start a new group and give you a complete "audit trail"
for your measurements. Each group contains readings with exactly the same settings.
When a new group is started, you can create a group title for it from Menu,
Settings, Titles, Enter. The group title is automatically cleared when a new group is
formed.
Group numbering
Data groups are numbered sequentially, starting from group 1 when the data file is
created. You can't edit the group number (in the way that you can edit Plot and
Sample numbers), but you can give it a title.
The group number is incremented automatically whenever you re-start the SunData
program after exiting, or when you change a critical setting, that is:
• any parameter in the Settings menu
• any data or configuration file change.
SunScan User Manual v 1.05
More Psion and file handling notes • 39
Measurement options
Experiment design
This section discusses the factors that bear on the experimental objectives you wish
to achieve. It should help you answer questions like:
• What equipment do I need?
• What readings must be taken?
• Will I have to wait for particular times of day or weather conditions?
The type of study you propose to do will determine the time of year and duration of
the experiment, and whether you are interested, for example, in monitoring growth
by interception of solar radiation, or perhaps in the canopy structure as well.
Some canopies types (the non-uniform ones) preclude the use of the SunScan’s
direct LAI readout. You could, however, characterise the 3-dimensional light
distribution within your canopy at different heights, or along transects through it. For
brevity we will call this approach “PAR mapping” in the discussion below
Answers to the above questions are complicated, but the following tables should
give you a good appreciation of the main issues involved.
Above-canopy reference requirements
This refers to measurements of PAR incident on the canopy, made at the same time
as the below-canopy measurements. The question is whether to use a BFS.
Beam Fraction sensor
A BFS connected to the SunScan probe provides the best option, because you can
operate with fewest restrictions. However, with some canopy types this may not be
practical.
The next best option is to use the SunScan probe (without the BFS) sequentially
above and below the canopy, but you may be restricted to times when the light levels
are not changing fast.
Independent PAR sensor
If that method is not practical either, you may have to rely on independent records of
incident PAR from a separate sensor. In addition to slowly changing light levels, you
may also have to average measurements in each place over periods of a few minutes,
furthermore the direct LAI readout is not available. This is the least convenient
situation, and it will not always be considered in the analysis below.
You cannot currently use the SunData software to merge independent records of
transmitted PAR and incident PAR to get LAI.
Direct and Diffuse components
Assuming that you make your above-canopy measurements on the SunScan (with or
without a BFS), then the next table summarises whether you need to measure the
Direct and Diffuse components of the incident light. If you do not need the separate
components, you benefit because the BFS is quicker to set up (there is no need to readjust its shade ring, once it has been set up correctly).
Type of study
Fractional interception
LAI
PAR mapping
SunScan User Manual v 1.05
Incident PAR
Total only
Yes
No
Yes
Incident PAR
Direct & Diffuse components
No
Yes
Possibly
Measurement options • 41
Canopy type and BFS practicalities
Canopy type is the next variable to be considered. As a general guide, the abovecanopy reference measurements should be made close to, or above, the position of
the SunScan probe. Tall canopies will undoubtedly exercise your ingenuity in
achieving this! If you want to use the BFS for LAI readings you must be able to see
the top of it to set the shade ring correctly.
Canopy
type
Low
Low
High
High
High
Options
Comments
BFS connected, with extension
cables, if necessary.
No BFS
Best, but long cables need
management
Slower. Needs slow-changing light
conditions
Good when possible. Checking BFS
shade ring difficult.
Needs steady light conditions.
Clearing light may be partly shaded.
Needs slow-changing light, and
possibly time average readings. LAI
readings not available.
Devise a portable BFS mount. Use
extension cables.
Use clearings to get out from under
the canopy. (No BFS required)
Use independent sensor for above
canopy PAR.
Canopy type and LAI estimates
Some types of canopy do not conform well to the assumptions about canopy
structure used by the SunScan in calculating LAI. The following table will give you
an initial idea of whether it is applicable to your canopy. You should read the
chapter on the LAI theory for a fuller appreciation of the subject. Some guidance on
specifying values for the typical leaf angle (the ELADP parameter) and leaf
absorptivity of your canopy comes later in this section.
Canopy type
Low, uniform (e.g. cereal crops, trial
plots)
Low, regular but not uniform (e.g.
row crops)
Isolated trees or bushes (e.g.
orchard trees)
sparse vegetation (e.g. scrub)
high, uniform , not clumped (e.g.
some timber plantations)
high, clumped vegetation (e.g.
natural woodland)
Comments
Good for LAI
Absolute LAI dubious. May show valid trends. PAR
mapping
PAR mapping only
PAR mapping only
In principle good for LAI, but practical difficulties for
above-canopy reference
PAR mapping only
Canopy Sampling volume
It is useful to be aware of the volume of the canopy that the SunScan is "seeing"
when calculating LAI, so you can take this into account when planning your
sampling scheme.
With the Direct beam, the SunScan only sees the canopy elements along a 1 metre
wide sheet between the probe and the sun. With Diffuse light, the SunScan sees a
much larger volume, covering a region centred on the probe, extending out
approximately as far as the canopy is high, but with the canopy above the probe
making the greatest contribution. These two very different sampling volumes are
measured in the same proportions as the incident Direct and Diffuse light.
42 • Measurement options
Document code: SS1-UM-1.05
This means that in strong sun (high Beam Fraction) the canopy volume sampled is
fairly small and well defined. As the Beam Fraction decreases, the volume sampled
increases, and has less well defined limits.
Preferred light and weather conditions
These also will significantly influence your field operations.
Limitation
Time of day
Solar zenith angle
Incident light level absolute
Light level - rate of
change
Full overcast, or full
sun in blue sky
Comments
Preferably within 3 hours either side of solar noon depending on
the location and season, to meet the next two conditions.
Measurements are easier when the sun is high. Probe and BFS
levelling errors become larger beyond zenith angles of greater
than 60°, especially for LAI
Preferably above about 200 µmol.m-2.s-1. Accuracy degrades
below this figure.
With the BFS, avoid only the very fastest changes between bright
sun and cloud.
With no BFS: slow-changing conditions needed.. For LAI, with no
BFS, slow change of direct and diffuse components.
SunScan LAI model copes with both, but full sun will usually give
the best results. Broken cloud is also satisfactory.
Planning for the sun’s position
The SunData software on the PC contains a useful calculator for solar zenith angles
on any date, to help you plan appropriate times to make your measurements. This
can be accessed from the Utilities menu Alt+Utilities, Zenith calculator. The default
values are taken from the Site Settings you are currently using, but can be changed
within the solar predictor without affecting any settings elsewhere in the program.
SunScan User Manual v 1.05
Measurement options • 43
Advice on Absorption and ELADP values
Absorption
Absorption is the percentage of incident PAR that is absorbed by the leaf.
Most leaves have Absorption values in the range 0.8 - 0.9, so the default value of
0.85 will usually be appropriate.
Only adjust the Absorption value if you have good reason to, for example if you are
working with very thick, dark leaves, or very thin transparent ones.
If you set the Absorption value to 1.0, the LAI calculations will be equivalent to
simpler models that assume completely black leaves.
ELADP
ELADP is the Ellipsoidal Leaf Angle Distribution Parameter.
The ELADP is a way of characterising the horizontal or vertical tendency of leaves
in a canopy.
The canopy leaf elements are assumed to be
distributed in space in the same directions and
proportions as the surface area of an ellipsoid of
revolution, symmetrical about the vertical axis.
The Leaf Angle Distribution can then be
described by a single parameter, the ratio of the
Horizontal to Vertical axes of the Ellipsoid.
V
H
ELADP = H V
This is also equal to the ratio of the vertically projected area to the horizontally
projected area of the ellipsoid (or of the canopy elements).
• An ELADP of 1.0 gives a spherical Leaf Angle Distribution, where all leaf angles
are equally represented.
• A high ELADP (e.g. 1024) represents a broad flat ellipsoid, i.e. the leaf elements
are all horizontal
• A low ELADP (0.0) represents a tall thin ellipsoid, i.e. all the leaf elements are
vertical.
Most crops have ELADPs in the range 0.5 - 2.0.
Setting ELADP
The default setting of 1.0 (spherical leaf angle distribution) is a good starting point.
If you are unable to estimate the ELADP any other way, set ELADP to 1.0. You can
check how much this affects your results in the field by making several
measurements in one place within a canopy using different ELADP values, and
comparing the LAI values calculated.
44 • Measurement options
Document code: SS1-UM-1.05
Estimating ELADP in the field
If the canopy shows a clear predominance of horizontal or vertical leaves, then
choose a small volume of the canopy that is representative. Count the number of
leaves that are at more than 45° from the vertical (i.e. mostly horizontal), and the
number of leaves that are less than 45° from the vertical. If the leaves are curved,
pick the angle at the widest part of the leaf. The ELADP can be estimated as the
number of horizontal leaves (Nh) divided by the number of vertical leaves (Nv),
multiplied by π/2 (1.6).
ELADP =
π Nh
2 Nv
The factor π/2 comes from the fact that the vertical leaves are distributed about the
vertical axis, so for any light ray, some will be seen face-on, and some edge-on. In
effect, the ellipsoidal distribution is being further approximated as a cylindrical
distribution.
If you set ELADP to 1024, and Absorption to 1.0, the LAI calculations will be
equivalent to the simple Beer’s law inversion based on black, horizontal leaves.
Relationship between Mean Leaf Angle and ELADP
Wang & Jarvis (1988) describe the relationship between ELADP and the Mean Leaf
Angle, which is sometimes known from other studies. Their results are summarised
by the following graph:
90
80
70
MLA degrees
60
50
40
30
20
10
0
0.01
0.1
1
10
100
ELADP
SunScan User Manual v 1.05
Measurement options • 45
SunScan System Measurement modes
Workabout setup
With your planned experiments in mind, you should now know what measurements
you want to make, and what equipment you will need. The following section
describes the three display functions that you may use, and gives advice on the
handling of SunData configuration files.
The LAI, PAR and All displays
(Note that the values in the screens below were generated with the emulator for
illustration purposes and may not be very realistic).
LAI display
LAI readings are available only in this mode.
With Beam Fraction sensor
With no BFS
PAR display
This display is most often used for simple light interception measurements which
can later be processed to give values of the fractional interception.
All display
This mode is appropriate for PAR mapping and profiling. Each stored reading
contains the summary readings displayed, plus the 64 individual photodiode
readings. Don't use this mode unless you have to - it will consume data file memory
space much more rapidly!
In the All display on the Workabout, there is not enough room to display the
individual photodiode readings. You can only view these in the File, Review screen,
or after transferring the data file to your PC (but they can be viewed with a PC
connected directly to the SunScan probe instead of the Workabout).
46 • Measurement options
Document code: SS1-UM-1.05
The Autolog function
You can set up the SunScan system to operate automatically in any of its modes, just
as if you were pushing the read, store and average buttons at regular intervals.
Note: don't confuse Autolog with logging the probe as a Linear Quantum sensor, or
with logging the Beam Fraction sensor as an independent sensor. These applications
are dealt with in the Appendices.
From Menu, Utils, Autolog, Enter you will arrive in the Automatic Logging setup
screen:
This is the Autolog setup screen.
Use the ↑↓ keys to select the
choices; edit the prompted values
or use the ↔ keys to toggle
through options presented.
System time in the heading is
constantly updated
You will be prompted with a current
Start time, and 6 hours later Stop time
and date. Edit these appropriately.
Change the read interval to
whatever sampling interval you
want (hh:mm:ss).
Nighttime is defined as when the
sun is more than 6° below the
horizon. SunScan computes this
for you automatically.
If you leave the Average interval at 0
you will not get average summaries.
Any other setting (hh:mm:ss) will
insert average summaries into the data
file at the specified intervals.
The Start time can be set to a time up to 24 hours before the current time! You might
do this for example if you wanted to set up averaging on the hour with sampling at
one minute intervals but the system time had just gone past the hour.
When you are satisfied with your choices, press Enter to accept the screen and
initiate the logging process. After a few minutes the Workabout will sleep and the
screen will go blank. You can safely press Off to blank the screen immediately (it
will not stop the Autolog process). From time to time when a reading is logged, the
screen will briefly show a Logging in progress message.
At any time, if you want to check the status of the Autolog, press On/Esc to access
the screen on the left.
The timing of the next reading (and the Plot and Sample number) will be indicated,
with the current system time. You can either select Sleep, Enter (to continue) or
Cancel, Enter to cancel (stop) the logging session from this screen. If you select
Cancel you must confirm that you want to stop logging by pressing On/Esc.
SunScan User Manual v 1.05
Measurement options • 47
Battery and memory management
When leaving the SunScan probe to Autolog over a few days, the memory space on
the Flashcard will determine how long it can run for, provided the Workabout Ni-Cd
battery is fully charged, and the probe alkaline batteries are not near the end of their
life. Approximate indications of data memory requirements are given in the earlier
Data memory management section.
Warning! If you leave the Workabout in the field for Autologging, you must enclose
it in a bag or container with plenty of desiccant to protect it from the possibility of
internal condensation. If you are using the Beam Fraction sensor as well during the
Autolog process, bear in mind that the shade ring may need occasional
readjustment.
Measurement procedures in the field
Of course it is worth checking the equipment a day or two before your field
experiment for routine matters such as the state of the batteries and the internal
desiccant. See the Technical Reference section for details of these.
Probe handling in the field
Earlier sections in the SunScan User Manual (Measurement options and experiment
design) give you guidance as to what equipment you will need (BFS or not) and
what types of measurement you will make (LAI, PAR, or All). This section helps
with practical comments and advice.
The probe GO button
The red button on the probe handle allows you to initiate and store repetitive
readings from the probe without needing to look at the Workabout display. Listen for
the tones from the Workabout which tell you where you are in the process:
• single beep - initiate READ
• double beep - accept STORE
The GO button functions just like the Enter button on the Workabout, for all menu
options that are presented at the bottom of the screen.
Levelling the probe
The probe is fitted with a miniature bubble level to help you hold it level during the
measurements.
In most situations beneath the canopy, exact levelling of the probe is not critical.
Do your best to minimise your own shading of the probe when taking readings. If the
probe can "see" you, you will be blocking a certain amount of diffuse light from the
sky. Casting a dense shadow on the probe by blocking the direct beam could cause
significant errors.
Your best strategy will be to take as many samples as quickly as you can rather than
aim for perfection with each reading. This will counter the spatial variability of most
canopies, and is especially true if you have to work in unsteady light conditions.
When using the GO button, concentrate on getting the best levelling for the READ
function (single beep) which then "freezes" the reading. It does not matter whether
the probe is level when you press GO the second time to store the reading.
48 • Measurement options
Document code: SS1-UM-1.05
Levelling is most critical when you are using the probe:
• for the incident radiation above the canopy, and
• when then direct solar beam is strong, and
• when the sun is low in the sky.
Use of the tripod
The probe base has a standard camera mount socket for use with the tripod. You will
probably not want to use this routinely, but you could use it, for example, to mount
the probe in one fixed position for taking readings in the Autolog mode during the
course of a day.
The Workabout
Whatever measurements you are taking, you will always have the probe connected
via its coiled cable to your Workabout or other data collection device. The terminal
case and strap supplied with the Workabout should enable you to operate the
keyboard with one hand.
BFS handling in the field
The Beam Fraction sensor is definitely recommended for taking most types of
readings, however the extra cable connection to the SunScan probe does add an
unwelcome practical complication! If, in addition, you are using a portable PC
instead of the Workabout, you may find that a two-person team can cope much better
than a single person working alone.
Diffuse photodiode. In line with
the shade ring pivots
Bubble level.
Desiccant indicator
Align this arrow with North
Total photodiode
Using the tripod
The BFS has a tripod mount, which will probably be the most convenient mounting
method to use above low field canopies (up to about 1.8 m high). If you are working
with canopies higher than this, you will need to devise an alternative mounting
method.
SunScan User Manual v 1.05
Measurement options • 49
Finding North, and setting the shade ring
If you are taking measurements which require only the incident total radiation on
the canopy, you can ignore the compass orientation of the BFS and you should set
the shade ring horizontal so that it is not in use.
If, however, you want the Direct and Diffuse components of the incident radiation,
you must elevate the shade ring so that its shadow falls across the Diffuse sensor
(the one directly in line with the shade ring pivots), covering it completely.
If you are moving the BFS frequently, the compass orientation of the BFS need not
be accurately set to north. If you want the shadow to track correctly for longer
periods of time, set the BFS to point true north more carefully. The same instructions
apply if you are using the BFS in the southern hemisphere.
The shadow may not track perfectly throughout the course of a whole day, owing to
limitations imposed by the simple and robust design of the BFS. You should inspect
the BFS from time to time and readjust the ring if necessary.
In overcast conditions, the exact elevation of the shade ring is not critical (and it is
quite difficult to estimate!). If there is any chance of direct sun breaking through,
you must wait for it to do so before setting the elevation.
Levelling the BFS
The BFS is equipped with a miniature bubble level. The tripod supplied has 3-axis
adjustment to facilitate levelling.
It is more important to level the BFS accurately than the probe.
The usual routine for setting up the tripod will be:
• Orientate the BFS to face true north.
• Level the BFS.
• Elevate the shade ring to bring the shadow completely across the Diffuse sensor
(the northernmost one).
Extension cables, and the location of the BFS
Extension cables of 10, 25 and 50 m can be fitted between the BFS and the probe,
which will extend your range of operation from the BFS. There is a trade-off
between range and convenience: the greater your range, the fewer times you need to
re-site the BFS, but the more time you are likely to spend handling the cable.
Extension cables can be joined together. A combination of two shorter cables may
be preferable to one long one.
You should bear in mind that the SunScan will read the BFS and probe
simultaneously. If the different locations are widely spaced apart, the light levels
could momentarily be different - cloud shadows can easily travel at 20 m.s-1.
The solution is to be aware of this possibility in fast changing conditions and avoid
taking readings at critical moments.
Very long cable lengths may introduce a small systematic error in BFS readings. Up
to 100 metres, this should not be significant (< 10 µmol.m-2.s-1). At 200 metres it
could add about 20 µmol.m-2.s-1 to the readings, which may need subsequent
adjustment .
50 • Measurement options
Document code: SS1-UM-1.05
PAR calibrations
This section describes the basis for the light calibrations used in the SunScan
system, and explains when and how you might want to recalibrate the probe or
restore its factory calibration.
Factory light calibration
The SunScan probe and Beam Fraction Sensor are calibrated to give PAR readings
which match those of a standard PAR quantum sensor in typical bright daylight
conditions.
This matching cannot be made completely reproducible because an ideal PAR
quantum sensor has perfect spectral and cosine responses whereas the SunScan
probe and BFS can only approximate to the ideal. However, for most normal usage,
the SunScan calibration will be perfectly satisfactory, but if you are working under
strong artificial lights (for example) you may need to contact Delta-T for advice.
SunScan readings of LAI and fractional interception depend for their validity on the
ratio of the transmitted light to the incident light rather than their absolute values,
so it is the matching between the probe and the BFS calibration that is important.
Checking the probe/BFS matching
It is good experimental practice to carry out this test in the field before (and after)
taking a lot of readings.
♦ Mount the SunScan probe and your BFS horizontally in uniform sunlight. Place
the shade ring horizontal as well. Make sure the probe and BFS diffusers are
clean.
♦ In the SunData program, select the PAR display (∪
∪+F hot key), and take some
readings.
The display will show you the values of the SunScan probe, BFS Total and BFS
Diffuse sensors. All three values should be approximately the same. Store these
readings, and you will have complete results that you can refer back to later if need
be.
The BFS values should be within about 5% of each other.
Mismatches of this magnitude have only a minor effect on the beam fraction
calculations and hence the LAI. (There is no field method for re-matching the Total
and Diffuse sensors. Contact Delta-T if you have a problem).
The probe and BFS Total readings may be within 5-10% of each other without
greatly contributing to errors in canopies where the transmission is below 50%.
Errors from the mismatch are likely to be swamped by the magnitude of the variation
in the samples. However, if you want to improve the matching, then proceed with the
Recalibrate option.
The Recalibrate option
This option matches your probe to your BFS (you cannot recalibrate the probe if you
do not have a BFS).
♦ Set up the probe and BFS as for the previous test. On the Workabout, access the
Calibrate procedure (∪
∪+C) and select Recalibrate SunScan, then follow the
instructions.
SunScan User Manual v 1.05
Measurement options • 51
You should not expect to have to do this very often. The photodiodes and light
measurement circuits are very stable.
The source of the apparent variability mentioned above is the not quite ideal cosine
and spectral response of the sensors.
Restoring the factory calibration
At any time after carrying out the Recalibrate option you can restore the original
factory calibration. You do not have to set up the probe or BFS in uniform light.
♦ On the Workabout, simply access the Calibrate procedure (∪+C) and select
Restore Factory calibration.
You will briefly see a message confirming that this has been done.
Effect of the shade ring on the BFS
If the above matching tests are carried out with the shade ring elevated (but not
actually casting a shadow on either BFS sensor), you will get different results.
The shade ring blocks about 7% of the diffuse sky light, and none of the direct beam.
In bright sun conditions it will have no significant effect on LAI readings. In
completely overcast conditions it might contribute a small error of up to 0.1 to the
LAI value.
Comparing the calibration with other PAR sensors
You can carry out matching comparisons between the probe and BFS and any other
PAR quantum sensor. You cannot reset the probe values to it, but you can annotate
the readings and retain the comparison information in the SunScan data files.
Routine maintenance and cleaning
The probe diffuser is Perspex. Clean it when necessary with a damp cloth, moistened
with mild detergent, or with IPA (iso propyl alcohol).
The BFS diffusers are also made of Perspex. Clean them very carefully, especially
the groove around the diffusers. Use a fine soft brush to remove any dirt or dust
from the groove - it could affect the accuracy of the cosine response of the sensors.
The "spread" measurement
The "spread" value is a measure of the relative variation of the light along the probe.
This is a useful parameter in light profiling measurements: it is the value of the
standard deviation of the 64 photodiode readings, divided by their mean.
You can check the probe uniformity of calibration at any time by taking a reading in
uniform light. The spread value should be 0.00 or 0.01.
52 • Measurement options
Document code: SS1-UM-1.05
Environmental and moisture protection
You should be aware of the different levels of protection of the components of the
SunScan system to avoid putting them at risk when working outdoors. As with all
field instruments you should minimise, as far as practical their exposure to high or
rapidly changing temperatures.
The SunScan probe and Beam Fraction Sensor
Warning! The probe and BFS are designed to resist dust and water jets (IP65), but
they are not hermetically sealed. They will survive rainfall, but will not survive
being immersed in water.
Avoid any situation where they could be flooded. Internal condensation will be
avoided provided that you keep the desiccant fresh. Inspect the coloured indicator
panels on the housings to check this.
The probe and BFS are reasonably robust, but they do not have a drop test rating. Do
not drop them! Take extra care when carrying the 1 metre-long probe!
The Workabout
The Workabout is dust proof and splash proof (IP54), and has a 1 metre drop test
rating, but does not contain desiccant. Operating conditions are specified as 0% 90% RH, non condensing.
Warning! If you leave the Workabout in the field for Autologging, you must enclose
it in a bag or container with plenty of desiccant to protect it from the possibility of
internal condensation.
SunScan User Manual v 1.05
Measurement options • 53
LAI theory
In this section we shall explain as fully as we can how the SunScan computes its
readings of leaf area index, and what the main limitations and provisos are in
interpreting these for real canopies.
Ingredients of the LAI computation method
There are three broad areas contributing to the final result.
Geometric analysis
The first is the analysis of what happens to a ray of light passing through the canopy.
In order to do this, we have to make some general assumptions about the canopy, i.e.
uniformity, randomness and total absorption by canopy elements. This was done by
Campbell (1986) for a beam of light from a single direction (the Direct solar beam)
passing through a canopy with a generalised ellipsoidal leaf angle distribution
function. This function allows a wide range of different canopy types to be described
by the value of a single parameter ELADP.
Wood then integrated Campbell’s result over the whole sky to give a description of
the transmission of Diffuse light through the same canopy. This is important because
the transmission of Diffuse light is different, and in reality there is usually a
combination of both Direct and Diffuse illumination. In particular, the analysis
shows that Diffuse transmission is strongly dependent on the leaf angle distribution,
a point which has not generally been recognised.
These functions are integrals which do not have direct analytical solutions, so have
to be solved numerically, and computable functions fitted to the results. This has
been done to a high degree of accuracy, improving on Campbell’s original
approximation.
Incomplete absorption - more elaborate analysis
The above analysis based on black leaves is relatively straightforward. However,
real leaves also reflect or scatter some of the light that falls on them. Typically, only
about 85% of the incident light is absorbed. This means that in reality, every leaf
element in the canopy is re-emitting light, as well as absorbing it, which makes the
situation much more complicated.
Because the direction of any particular light ray can be changed by reflection or
scattering, it means the spatial distribution of the light changes through the canopy.
Therefore it is no longer adequate to consider just the vertical component of the light
(as measured by a cosine corrected sensor), the horizontal component must also be
included. This is why Wood’s analysis also considers a hemispherical response
sensor (which measures both horizontal and vertical components).
The relentless advance of computing power has made it possible to model the
situation in ways that were not feasible in the past. By integrating the "black leaf"
analysis into a computer model Wood has calculated the light levels in the canopy
across the whole range of canopy and incident light parameters.
54 • LAI theory
Document code: SS1-UM-1.05
Equation fitting and inversion
The results of the computer modelling, while accurate, are not suitable for use in a
field instrument. It takes many minutes of processing on a fast PC to calculate light
transmission for any given conditions using the model, and the Psion Workabout is
not a fast computer!. The model calculates values of light transmission for a given
LAI, whereas the SunScan measures light transmission. This means that the
functions have to be inverted to work back to LAI, which is more difficult.
To give you immediate results in the field, computable functions have been fitted to
the model data, and it is these that are solved to give LAI to reasonable accuracy
from the parameters measured by the SunScan system.
Note! Wood’s SunScan equations are copyright, and you should not copy them
without written permission unless for purposes of scientific debate or publication, in
which case they should be fully acknowledged.
Theory versus reality
We believe that Wood’s SunScan equations accurately reflect the assumptions that
the modelling is based on.
By far the largest uncertainties are bound to be caused by
• the mismatch between the real canopy architecture and the simplifying
assumptions built into the fundamental analysis
• to a lesser extent the uncertainty in the numerical values of ELADP estimated for
your canopy.
With these caveats, the values of LAI for your canopy, even if of uncertain accuracy,
will provide valid trends for a given canopy (e.g. canopy growth in a season), and
valid comparisons between different canopies of similar architecture (e.g. trial plots
of different cultivars of the same species). If you are able to compare SunScan
estimates with actual harvested samples from time to time, this will enable you to
calibrate out any systematic errors due to your canopy not matching the SunScan
assumptions.
If you wish, you can force the SunScan calculations to be equivalent to older, less
sophisticated inversions by setting some of the parameters to appropriate values.
For example, setting ELADP to 1024 (horizontal leaves) and Absorption to 1.0 will
give you the simple Beer’s law inversion.
Derivation of Wood’s SunScan canopy analysis equations
The major assumptions
• The canopy is an infinite, uniform, horizontal slab, with leaf elements randomly
distributed in proportion to the surface area of an ellipsoid, as described by
Campbell.
• The incident light consists of a component from a point source at a given zenith
angle (the Direct beam); and a Diffuse component of equal intensity from every
point in the sky (Uniform Overcast Sky).
• The canopy either has sufficiently high LAI that light reflected back from the
ground below is negligible, or the reflectance of the ground is similar to that of
the canopy.
• Of the light intercepted by the leaf element, a fraction a (absorption) is totally
absorbed. The remainder is re-emitted uniformly in all directions.
SunScan User Manual v 1.05
LAI theory • 55
Beer's law for canopy absorption
Beer's law occurs in many situations where events happen at random. In the case of
light absorption by a canopy, it applies to the absorption of incident photons or light
rays. For a uniform infinite randomly distributed canopy of completely absorbing
leaves, it can be shown that the relationship between the transmitted light I, a beam
of incident light I0 and the Leaf Area Index L is given by:
I I 0. exp( K. L )
where K is the extinction coefficient which depends on the leaf angle distribution
and the direction of the beam. K=1 for entirely horizontal leaves.
Campbell's Ellipsoidal LAD equations.
Campbell (1986) derives an equation for the extinction coefficient of leaves
distributed in the same proportions and orientation as the surface of an ellipsoid of
revolution, symmetrical about a vertical axis. The semi vertical axis is a and the semi
horizontal axis is b . There is symmetry about the vertical axis. He relates these to a
single parameter x = b/a. (x is the Ellipsoidal Leaf Angle Distribution Parameter, or
ELADP). The extinction coefficient also depends on the zenith angle of the
incoming direct beam. Canopy elements are assumed to be completely black, and
randomly distributed in a horizontal slab extending to infinity in all directions.
Note: in the following equations derived in MathCad, different conventions are used
for some symbols. Equality is represented by :=, and tan2 (θ) is expressed tan(θ)2 .
The extinction coefficient, K, is calculated as follows:
x
K( x , θ )
x
2
tan( θ )
1.702. ( x
2
1.12 )
Ext'n
Coeff't
0.708
Where:
x is the ELADP
θ is the zenith angle of the direct
beam.
The transmitted fraction of incident
direct light is given by:
τ dir
3
K( 0 , θ )
2
K( 1 , θ )
K( 100 , θ ) 1
0
0°
θ
90°
exp( K ( x , θ ) . L )
where L is the canopy LAI.
Transmission of Diffuse Light
Campbell's analysis applies only to a beam of light from a specific direction, which
is the Direct solar beam in our case. Even under strong sunlight, the Direct fraction
rarely exceeds 80% of the Total incident radiation, so penetration of the Diffuse
component of incident radiation is also important.
There is a misconception that the extinction coefficient for Diffuse light is
independent of canopy Leaf Angle Distribution, but this is not the case as the
following analysis shows. As the following graph also shows, transmission of
Diffuse light does not obey a simple Beer's law curve, so cannot be represented by a
single extinction coefficient, except in the case of a horizontal LAD.
56 • LAI theory
Document code: SS1-UM-1.05
The next section derives the transmission of light from a uniform overcast sky
through a uniform infinite canopy of black leaves of constant LAI with an ellipsoidal
leaf angle distribution.
Let the sky have uniform brightness of 1 per steradian over the hemisphere.
The radiance of a strip around the sky at angle θ is given by:
R 2. π . sin( θ ) . dθ
and the irradiance on a horizontal surface due to that strip is given by
I 0 2. π . sin ( θ ) . cos ( θ ) . dθ
The total irradiance due to the hemisphere is obtained by integrating over the
complete sky area:
π
2
2. π . sin ( θ ) . cos ( θ ) dθ = 1 π
0
For each strip of sky, the transmitted radiation is given by
I I 0. exp( K. L )
where K is the extinction coefficient from Campbell,
so the total transmitted radiation is
π
2
2. π . sin ( θ ) . cos ( θ ) . exp( K( x , θ ) . L ) dθ
I
0
and the transmission fraction τ is given by I/I0
π
τ diff( x , L )
1.
π
2
2. π . sin ( θ ) . cos ( θ ) . exp( K( x , θ ) . L ) dθ
0
This integral was evaluated numerically over the range x = 0 to 1000 and L = 0 to
10, and is graphed below for three different values of x.
SunScan User Manual v 1.05
LAI theory • 57
Diffuse light transmission (cosine corrected sensor)
Transmission
fraction
1
Leaf Angle Distribution
vertical
τ diff ( 0 , L )
spherical
τ diff ( 1 , L )
horizontal
τ diff ( 1000 , L )
vertical
0.1
spherical
0.01
horizontal
0.001
0
2
4
6
L
8
10
Leaf Area Index
Modelling the canopy transmission
Accounting for incomplete absorption of PAR by the canopy elements, and
scattering of light within the canopy is complicated. It is no longer sufficient to
consider only the vertical component of PAR (i.e. as measured by a cosine-corrected
sensor) because scattering effectively transfers power between the horizontal and
vertical components, so the canopy changes the spatial distribution of power in the
PAR flux as it is transmitted down through the canopy and reflected back up.
A multi-stream computer model was set up to calculate these effects as follows.
Assumptions
• The canopy is an infinite, uniform, horizontal slab, with leaf elements randomly
distributed in proportion to the surface area of an ellipsoid, as described by
Campbell.
• The incident light consists of a component from a point source at a given zenith
angle (the Direct Beam); and a Diffuse component of equal intensity from every
point in the sky (Uniform Overcast Sky).
• The canopy either has sufficiently high LAI that light reflected back from the
ground below is negligible, or the reflectance of the ground is similar to that of
the canopy.
• Of the light intercepted by the leaf element, a fraction a (absorption) is totally
absorbed. The remainder is re-emitted uniformly in all directions.
58 • LAI theory
Document code: SS1-UM-1.05
In detail:
• The canopy is divided into horizontal layers of LAI 0.1
• Direct beam absorption by each layer is calculated using Campbell's equation. In
calculating the amount of absorbed light that is re-emitted, the total power in the
direct beam has to be used (i.e. as measured by an integrating hemisphere or a
cosine-corrected sensor perpendicular to the beam). The amount intercepted by
the layer is the difference between the absolute intensity above and below the
layer.
• Diffuse light intercepted by the layer is calculated in a similar way, taking into
account the incident Diffuse light, and the sum of re-emitted light from all other
layers, attenuated by the intervening layers. This is done for both downwelling
and upwelling Diffuse light. A fraction of the Diffuse light absorbed by the layer
is also re-emitted. Again, absolute rather than cosine-corrected intensity
measurements must be used.
• Both cosine-corrected and absolute light measurements are calculated for each
layer, and the model iterated until it converges. This has been done for a range of
different values of zenith angle, Direct/Diffuse ratios, Leaf Angle Distributions
and Absorptions.
Simpler functions have been found to approximate these results, and are used in the
SunData software when inverting transmitted fraction back to LAI. These are
described in detail in the next section.
The canopy model
SunScan User Manual v 1.05
LAI theory • 59
Accuracy of LAI calculations
When used to predict LAI from transmitted fraction, the functions used in the
SunData software are accurate to within ±10% ±0.1 over the range of LAI less than
10 and Zenith Angle less than 60° when compared to the output of the full model.
The errors become larger for highly vertical leaves with a strong low sun, and users
should avoid these conditions if possible.
In practice, the greatest errors are likely to follow from the differences between the
real canopy and the idealised assumptions in the model.
Functions used to model canopy transmission
Diffuse light - cosine response sensor
The transmission of diffuse light through a canopy, as measured by a cosine
corrected sensor, can be modelled by the following functions:
Given:
A( x )
τ diff( x , L )
exp( L )
1
1.38
0.15. x
0.007
B( x )
4.32
2.60. exp( 2.75. x )
C( x )
0.57
0.23. exp( 1.40. x )
3
A( x ) . L . exp
C( x )
B ( x ). L
These curves give maximum errors of 0.009 in τdiff, with a maximum 6% error for
τdiff greater than 0.01 over the range L = 0 to 10 and x = 0 to 1000.
Diffuse light - hemispherical response sensor.
The previous analysis of diffuse light transmission is appropriate for a cosinecorrected sensor as it only considers the vertical component of the incident and
transmitted light. This works as long as the leaf absorption in the PAR band is
complete, and there is no scattering of the incoming light.
When we consider leaves with incomplete PAR absorption, some of the absorbed
light is re-emitted in different directions to the original incoming light. Because of
this we have to account for all of the incoming light, both horizontal and vertical
components, and also be aware that the spatial intensity distribution of the light is
modified by the canopy and varies through the canopy depending on the canopy leaf
angle distribution.
The above analysis is now repeated to find the transmission of uniform diffuse light
as measured by a sensor with a hemispherical response. The equivalent equation for
the transmission fraction is:
π
τ spher ( x , L )
60 • LAI theory
1 .
2. π
2
2. π . sin ( θ ) . exp( K( x , θ ) . L ) dθ
0
Document code: SS1-UM-1.05
This was again calculated numerically and curves fitted to the data with similar
accuracy as above. The curves fitted are:
Given:
τ spher ( x , L )
exp
0.4. exp( 0.1. x ) . ( atan( 0.9. x )
P( x )
1
Q( x )
0.255. atan( x )
R( x )
exp( x )
Q( x )
P ( x ). L
0.95 )
0.6
R( x ) . ln( 1
L)
Diffuse light transmission (hemispherical response sensor)
Transmission
fraction
1
Leaf Angle
Distribution
Vertical
τ spher ( 0 , L )
Spherical
τ spher ( 1 , L )
Horizontal
τ spher ( 1000 , L )
Vertical
0.1
Spherical
0.01
Horizontal
0.001
0
2
4
6
L
8
10
Leaf Area Index
Modelling incomplete PAR absorption and scattering
Radiation models have been used for many years to calculate the effects of scattering
in the canopy e.g. Norman & Jarvis (1975). Wood's model incorporates Campbell’s
ellipsoidal leaf angle distribution and the effects this has on transmission of both
Direct and Diffuse light.
The model splits the canopy into layers of LAI 0.1, extending to a sufficient depth to
absorb all of the incident light. Incident light above the top layer was a known
fraction of Direct (at a given zenith angle) and Diffuse light. The amount of light
absorbed by a layer, assuming completely black leaves, was calculated. The fraction
of this absorbed light re-emitted by the leaves was then assumed to be re-emitted in
all directions uniformly (see Monteith & Unsworth, 1990, p85 onwards) .
The light level at any point in the canopy is then the light calculated assuming
complete absorption, plus the sum of the light re-emitted by each canopy layer,
attenuated by the intervening layers.
These calculations had to take full account of both horizontal and vertical light
components. This involved an iterative solution and a lot of computer time. Finally,
the light intensity as measured by a cosine corrected sensor was calculated.
SunScan User Manual v 1.05
LAI theory • 61
The results were then analysed in terms of La, the LAI of a canopy of black leaves
that would give the same transmission as a canopy of LAI L assuming incomplete
absorption, all other factors being equal.
L a L. ( 1
g( 1
a) )
L is the "true" LAI, La is the LAI that when used in the black leaf model, gives the
same transmission as L used in the complete model. a is the leaf absorptivity in the
PAR band.
The function g varied with all the other parameters in a complex way, but most
strongly with x, the leaf angle distribution parameter, and with solar zenith angle for
the direct beam. The following equations represent quite a crude approximation to
the full model, but give satisfactory results for most situations. If any given
transmission fraction is inverted using the approximation, the LAI calculated is
within ±10% ±0.1 of the "true" LAI indicated by the full model, except for x near 0
(extreme vertical leaves) and zenith angle > 60 ° (strong low sun).
For diffuse light:
g diff 0.5
For direct beam:
g dir exp( 1.5. x ) .
0.2
0.7. zen
2
5
0.2. zen
0.3
where: x is the ellipsoidal leaf angle distribution parameter
zen is the solar zenith angle in radians.
The full equation thus becomes:
τ f b. exp
+ 1
K ( x , θ ). 1
f b . exp
La
g dir. ( 1
a ) . L ...
3.
A ( x ) . L a exp
Direct part
C( x )
B ( x ). L a
Diffuse
This looks hard to invert to get LAI from τ, but an iterative solution is fairly
straightforward given the computing power, and is much simpler than the full
numerical solution.
Calculating zenith angles
Zenith angles are calculated from latitude, longitude, and local time using standard
astronomical equations as given in Practical Astronomy. These give zenith angles
accurate to better than 0.1° and times of sunrise or sunset to within a few seconds.
Summary
A computer model has been created which calculates accurately the transmitted light
below the canopy based on the assumptions given. This has been run over the whole
range of each of the different variables, i.e. Direct beam angle, Direct beam fraction,
Leaf Angle Distribution, Leaf Absorption and Leaf Area Index. The results of these
runs, taking many hours of computer time, have been collected and functions found
to fit them.
These approximating functions are used in the SunData software to predict LAI from
the measured inputs in the field. The LAI values calculated by the SunData software
are within ± 10% ± 0.1 of the LAI that would have been calculated by the full
model.
Scientific references
Campbell G S (1986). Extinction coefficients for radiation in plant canopies using
an ellipsoidal inclination angle distribution. Agric. For. Meteor., 36:317-321.
62 • LAI theory
Document code: SS1-UM-1.05
Daughty, Craig S T (1990). Direct measurements of canopy structure. Remote
Sensing Reviews 1990 vol 5(1) pp 45 - 60.
Diffey B L (ed).(1989) Radiation Measurement in Photobiology. Academic Press.
Goudriaan J (1977). Crop Micrometeorology: A Simulation Study. Centre for
Agricultural Publication Documentation, Wageningen, Netherlands.
Jones, Hamlyn G. (1992) Plants and Microclimate second edition. CUP.
Lang A R G & Xiang Yueqin (1986). Estimation of leaf area index from
transmission of direct sunlight in discontinuous canopies. Agric. For. Meteor.
35:83-101.
Lang A R G, Xiang Yueqin, & Norman J M (1985). Crop structure and the
penetration of direct sunlight. Agric. For. Meteorol. 35:83-101.
Marshall B and Woodward F I (eds). (1985) Instrumentation for Environmental
Physiology. SEB Seminar series 22, CUP.
Monteith J L & Unsworth M H. (1990) Principles of Environmental Physics second
edition. Edward Arnold (Hodder & Stoughton).
Norman J M & Welles J M (1983). Radiative transfer in an array of canopies.
Agron. J. 63:743-748.
Norman J M and Jarvis P G (1975). Photosynthesis in Sitca Spruce (Picea sitchensis
(Bong) Carr.) V. Radiation penetration theory and a test case. J. Appl. Ecol.,
12:839-878
Russel G, Marshall B and Jarvis P (eds). (1989) Plant Canopies, their Growth, Form
& Function. SEB Seminar series 31, CUP, Cambridge
Wang Y P and Jarvis P G (1988). Mean leaf angles for the ellipsoidal inclination
angle distribution. Agric. For. Meteor., 43:319-321.
Welles J M (1990). Some indirect methods of estimating canopy structure. Remote
Sensing Reviews 1990 vol 5(1) pp 31 - 43.
SunScan User Manual v 1.05
LAI theory • 63
Technical Reference section
Maintenance and repair
Checking the batteries
The SunScan system requires batteries within the probe and in the Workabout. The
Beam Fraction sensor does not require batteries because it draws its power from the
probe.
The SunScan probe batteries
The probe is powered by 4 AA size alkaline cells mounted within the probe handle.
With typical use, these batteries should last from 6 - 12 months. The probe circuit
automatically "sleeps" when no readings are being taken. There is no probe on/off
switch.
Checking the probe battery level
Connect the probe to the Workabout, and from the SunData program take a reading
with the probe (any light reading will do - it is required only to activate the battery
sensing circuit).
Then press ∪+B (or Menu,Utils,About). The screen display will show various
version numbers plus a Battery mV reading.
Replace the batteries if the reading is 4700 mV or less. A reading of 5000 mV or
above indicates that the batteries are healthy. You will get an on-screen warning if
the batteries are low. When this happens replace them as soon as you can.
If you get a 0 mV reading, the probe has not been read. Take a light reading, and try
∪+B again.
Probe battery life
With a fresh set of batteries in the probe, you could take about 300,000 readings. If
you took no readings, the batteries would last for about 6-12 months.
Warning! If you are likely to store the probe for a long period, you should remove
the batteries.
Replacing the probe batteries
You must dismantle the probe handle. Disconnect the BFS and the probe's RS232
cable. The baseplate of the probe is secured to the handle by 4 cross-head corner
screws. Unscrew these to remove the handle, whilst carefully supporting the probe.
The battery holder can now be prised out of its compartment, and the batteries
changed.
The Workabout batteries
Checking the Workabout battery levels
The Workabout is supplied with a rechargeable Ni-Cd battery pack and a Lithium
back-up battery installed. Press Shift+Ctrl+B to display the Psion Battery info
screen. You will be warned when the batteries get low. Switch off and recharge the
batteries as soon as possible.
For full details on the care and maintenance of the Workabout's batteries you should
refer to the Workabout User Guide pages 2-5, but the following brief notes will get
you started.
64 • Technical Reference section
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Workabout battery management
When you receive the Workabout, the installed battery pack may not be fully
charged. Connect the Workabout to the Docking unit and Charger immediately, so
that charging can proceed whilst you are learning to use the SunScan.
The charger is a trickle-charger and may take 14 hours to fully recharge the battery
pack. A fully charged Ni-Cd battery should easily give 2 or 3 full days use in the
field. You must then recharge the Workabout overnight if you want to continue with
daily use in the field.
Warning! In general, Ni-Cd batteries prefer to be fully discharged before being
recharged. Do not leave them continuously trickle-charging.
If you ordered a spare Ni-Cd battery pack it will not be charged initially. Charge it as
soon as you have the opportunity, so that you can replace an exhausted one without
delay.
To gain access to the batteries, open the battery drawer by pressing the black button
at the top left corner of the Workabout very firmly.
The Workabout will run equally well from 2 AA alkaline cells. Carry some of these
with you if there is any chance that your Ni-Cd will become exhausted when no
mains power is available for recharging.
Warning! Don't leave the Workabout without a main battery for more than a day or
two. Its back-up cell will last for several days only.
Beyond this time you may lose data in the internal memory (but Flashcard data will
not be affected).
If you get low battery warnings, even after fully charging the Ni-Cd pack, these can
be reset by removing and then replacing the pack.
Checking the desiccant
Both the SunScan probe and Beam Fraction sensor contain desiccant packs to
prevent internal condensation of moisture when they are used outside. The dryness
of the desiccant is indicated by a coloured panel on the outside of each housing. Blue
indicates dry, pink indicates that renewal is needed. The Workabout does not contain
desiccant.
Refreshing the desiccant
The desiccant pack can be regenerated by heating. Remove the pack from the probe
or BFS and heat the pack in an oven for a few hours at about 140ºC, then allow it to
cool down away from moisture before reinstalling it.
Access to the probe handle is as described above for probe battery changing. To
access the Beam Fraction sensor, prise upwards the red plastic strips on the lid, then
undo the four cross-head screws that are revealed.
SunScan User Manual v 1.05
Technical Reference section • 65
Checking the PAR calibration
Various techniques for checking the SunScan system PAR calibration and
consistency are described in the Measurement Options, PAR calibration section,
which you should refer to. This also includes advice on when to use the recalibrate
and restore factory calibration procedures.
Factory calibration method
A standard PAR Quantum sensor provides the reference value of PAR that the Beam
Fraction sensor and the SunScan probe are set up to. This process is carried out
under a near-daylight spectrum lamp in controlled conditions.
Re-setting the factory calibration
The electronic components and photodiodes used in the PAR circuits of the Beam
Fraction sensor and SunScan probe are very stable and are not expected to change
for the lifetime of the instrument.
Circuit adjustment facilities in the Beam Fraction sensor are provided for the initial
factory set-up and are not intended to be used for routine adjustment thereafter. The
probe factory calibration cannot be adjusted without specialist equipment.
Warning! Do not attempt to change the factory calibration without referring back to
Delta-T first. The most likely cause of an apparent change of calibration is physical:
dirt in the grooves around the BFS diffusers, or dirt or staining of the probe diffuser.
If after checking the above you still have:
• a Beam Fraction sensor with badly matched Total and Diffuse outputs, or
• a SunScan probe with an out-of-spec calibration, or individual diode readings that
appear faulty,
please refer back to your agent or the factory.
66 • Technical Reference section
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Troubleshooting
Psion Workabout
There is no SunData Icon in the system screen.
• From the Psion system screen, select Menu, Apps, Install, Enter, Tab, and select
Sundata.app in the \SUN\ subdirectory. If this file does not exist, it must be
copied from the SunScan program disk - refer to the appendix: File Transfer
between Workabout and PC.
The system fails to recognise a Flashcard in the A: or B: drives.
• Make sure the SSD drawer is firmly closed.
The Workabout gives continuous “low battery” warnings, even after fully recharging
the battery pack.
• Remove and then replace the battery pack when it is fully charged. This will reset
the “low battery” warnings.
Problems running the SunData application.
SunData fails to run, with exit code 80.
• The supporting file Sys$8087.ldd is not in the \SUN\ subdirectory. Copy it there
from the SunScan program disk - refer to the installation notes.
SunData reports “serial port in use”.
• Exit the program, and make sure the Remote Link is off. Press Menu, Spec,
Remote Link, Enter, from the system screen.
SunData fails with “insufficient memory” or “insufficient system resources” message.
• Close any other applications that are running. Delete any unnecessary data files
stored on the Internal drive. From the system screen, select Menu, Info, Memory
Info, Enter. If the amount of System memory is shown as more than 80k, reboot
the Workabout (∪+Ctrl+Del) and reinstall the SunData Icon. As a last resort, cold
boot the Workabout (∪+Shift+Ctrl+Del). You will then have to reinstall the
SunData programs from the SunScan program disk - see the complete installation
instructions.
While running SunData
SunData reports “SunScan probe not connected”.
• Check the cable connections. Check the condition of the batteries in the SunScan
probe.
SunData recognises the SunScan probe, but fails to take readings.
• Exit the SunData program, and run it again. If “BFS” is selected as the external
sensor in Menu, Settings, SunScan Probe, Enter, make sure a Beam Fraction
sensor is connected and is exposed to some light.
On running SunData, all the system settings are scrambled.
• The Default.cfg may be corrupted. Exit SunData and delete the file Default.cfg
in the \SUN\ subdirectory.
“Out of memory” reported on drive A:.
• Replace the Flashcard with an empty formatted one and start a new data file.
Transfer the data on the full Flashcard to a PC and reformat it.
SunScan User Manual v 1.05
Technical Reference section • 67
“Insufficient power to write data” reported.
• Recharge the Ni-Cd battery pack, or replace it with a freshly charged Ni-Cd pack
or two AA Alkaline cells.
When transferring files to a PC, data is transferred, but there are repeated checksum or
device IO errors.
• Reboot your PC and start again. See the advice on RS232 communications in the
SunScan Tutorial (p28).
SunScan or BFS give inconsistent light readings.
• Make sure the diffusers are clean and that the desiccant condition indicators are
blue. See the advice on PAR calibration in Measurement Options (p49).
68 • Technical Reference section
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Technical Support
Distributor contact
If you have a problem, please call your local distributor first.
Direct Delta-T contact
You can contact SunScan Technical Support at Delta-T directly on:
Tel: +44 (0)1638 742922
Fax: +44 (0)1638 743155
Email: fi42@delta-t.co.uk
Web site: http://www.delta-t.co.uk/users/fi42
Guarantee
The SunScan system and its components are guaranteed for one year against defects
in manufacture and materials. The guarantee does not cover damage through misuse
or inexpert servicing, or other circumstances beyond our control.
Problem Reports
It will help considerably if you can first fax through as many relevant details as
possible. In particular:
• a description of the fault, its symptoms, or error messages
• what components of the SunScan system you are using
• details of any PC you are using
• software version numbers and hardware serial numbers (see below)
SunScan circuit schematics and data
These are provided in a separate booklet: the SunScan Technical Manual.
Locating version and serial numbers
S/W Diskette:
SunData s/w type SDA1 has the version number on the label.
SunData S/W programs:
In the Workabout, from the SunData program: Menu, Utils, About, Enter
In your PC, from the SunData program: Alt+Utilities, About, Enter
SunScan probe
The serial number label is on the base of the probe handle.
The PROM chip (inside the probe handle) is labelled with its version number. This
can also be seen at the top of the SunData's title screen when the probe is connected.
Beam Fraction Sensor
The serial number label is on the underside of the case.
Psion Workabout:
Serial number is inside its case, at the top of the battery drawer.
SunScan User Manual v 1.05
Technical Reference section • 69
Specifications
SunScan Probe type SS1
Active area
Spectral response
Measurement time
Maximum reading
Resolution
Linearity
Accuracy
Analogue output
Serial interface
Environmental
Size (overall)
Power
1000 x 13 mm wide. Sensor spacing 15.6 mm.
400 - 700 nm (PAR)
120 ms
-2
2500 µmol.m .s-1
-2 -1
0.3 µmol.m .s
better than 1%
+/- 10%
-2
1 mV per µmol.m .s-1
RS232, 9 pin female 'D' connector
protected to IP65, 0° - 60°C working temperature
1300(l) x 100(w) x 130(h) mm
4 x AA Alkaline cells (lifetime up to 1 year)
Beam Fraction Sensor type BF1
Outputs
Maximum range
Cable length
Extension cables
Mounting
Environmental
Size
Power
Total PAR, Diffuse PAR. 1 mV per µmol.m .s-1
-2
2500 µmol.m .s-1
7 m standard
10 m, 25 m, 50 m
1/4 inch Whitworth tripod socket
protected to IP65, 0°...60°C working temperature
160 x 80 x 65 mm (excluding shade ring)
Provided from SunScan (5 - 12 V)
-2
Data Collection Terminal type DCT1 (Psion Workabout)
Full specifications for the Workabout are contained in its User Guide, app B p277.
Screen / keyboard
Data storage
Display options
Environmental
Drop resistance
Power
10 lines x 40 characters / full alphanumeric
Flashcards, 256k or 1Mb - effectively unlimited
a) LAI b) PAR average c) ALL individual sensor readings
IP 54, RH 0%...90% non condensing, -20°...60°C
1 m onto concrete
Ni-Cd pack (up to 15 hours per charge) or 2 x AA Alkaline cells
PC as Data Collection device
Alternatively, the SunScan probe can be operated directly from a PC, minimum
requirements:
• MS-DOS 3.3, and higher
• 512k RAM
• 80 x 25 character display
• RS232 port
• 3.5" FDD
70 • Technical Reference section
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Carrying Case type SCC1
Moulded plastic case with O-ring seal for moisture and dust proofing, including
pressure release valve.
Outside dimensions
Weight
1.40 x 0.44 x 0.16 m
approx 8 kg
Telescopic Tripod type BFT1
3-way head with quick release platform. Geared friction elevator control. Locking
leg catches and brace. Dual Spike/rubber feet.
Max. height
Closed length
Weight
1.73 m
0.68 m
2.5 kg
Spares Kit type SPS1
A detailed list of parts can be supplied on request. The kit includes:
• electrical components which might be subject to breakdown by electrostatic
discharge
• mechanical parts likely to break, be damaged or lost through wear and tear.
Logging Cables
Logger cable for SunScan probe, type SSDL10
10 m cable with connector to attach to SunScan probe, for logging as a linear
quantum sensor.
Logger cable for Beam Fraction sensor type BFDL5
5 m cable with connector to attach to Beam Fraction sensor, for logging Total PAR
and Diffuse PAR outputs.
SunScan User Manual v 1.05
Technical Reference section • 71
PAR Performance
The graphs below show the actual spectral and cosine response curves for the
SunScan system.
Spectral response
The spectral response curve shows that the SunScan response is almost entirely
within the PAR wavelength band of 400 nm - 700 nm. The GaAsP sensors used have
an increased sensitivity towards the red end of the spectrum, but this is compensated
for by the sharp cut-off at 670 nm. In practice, we have found that these sensors read
to within a few percent of an accurate PAR sensor in natural daylight conditions
above or within the canopy. However, if you are working under artificial or strongly
coloured light you should check the SunScan readings against an accurate PAR
sensor if you need to know absolute PAR levels.
SunScan
Spectral response
Ideal
160
relative response %
140
120
100
80
60
40
20
0
350
400
450
500
550
600
650
700
750
w avelength nm
72 • Technical Reference section
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Cosine responses of probe and BFS
The cosine response curves show a diminishing response compared to the ideal at
high zenith angles. For this reason, you should avoid taking measurements when the
sun is strong and near the horizon.
Most studies will be looking at the ratio of incident and transmitted light, and the
graph shows the SunScan and Beam Fraction sensor are very closely matched in
their cosine and spectral responses, so the small deviations from the ideal will not
introduce significant errors.
SunScan system cosine response
Ideal
Actual
Actual / Ideal
1.1
1
relative response
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0
0 10 20 30 40 50 60 70 80 90 0 10 20 30 40 50 60 70 80 90
SunScan probe
SunScan User Manual v 1.05
Zenith angle °
Beam Fraction sensor
Technical Reference section • 73
Appendices
A. Logging the probe as a Linear Quantum Sensor
This application of the SunScan probe turns it into a simple Line Quantum sensor
that can be attached to a data logger. No Data Collection Terminal is used, but you
do require a data logger that can supply power to the probe when taking readings.
The Delta-T DL2e and DL3000 loggers are suitable for this purpose.
If you want to mount the probe on a tripod, a camera mount is provided in the base
of the probe handle. The probe's coiled RS232 cable is not used, and it must be
protected from moisture by enclosing it in a bag with desiccant, for example.
Note: no batteries are required in the probe for this mode, but it does not hurt to
leave them in situ.
Wiring connections
You must use the (optional) special logging cable which plugs into the socket on the
probe handle normally occupied by the Beam Fraction sensor. The cable is 10 metres
long. If you need more length, simply join on extra screened multicore cable of a
similar type. Make sure the joint is weatherproof.
The cores of the probe logging cable have the following functionality:
Core
orange
green
brown
grey
blue
braid
Function
V+ Power supply positive
0V Power supply negative
HI Signal output positive
LO Signal output negative
not used
Screen
Logger Connection
Sensor power positive (switched for warm-up)
Sensor power negative (0V)
Input channel +
Input channel Not connected (see below)
Note: the grey, green and braid are connected internally in the probe handle.
Connecting the braid to an earthing point on the logger could create earth loops, and
is not recommended.
Output
• The output signal is the transmitted PAR irradiance, averaged along the length of
the probe. (Individual photodiode readings are not accessible in the Linear
Quantum Sensor mode.)
• The millivolt output is linear, with a sensitivity of 1 mV = 1 µmol.m-2.s-1.
Maximum output is 2500 mV.
Logger requirements
• The probe requires a voltage supply of 7-15 V dc (unregulated), at about 30 mA
current. The analogue output is enabled when the external voltage is greater than
the battery voltage.
• Configure one channel of the logger for voltage input, with the above sensitivity.
• Use a "warm-up" time of 1 second (the logger must apply the power 1 second
before taking its reading).
• The output voltage will be stable 120 ms after applying external power, and is
updated every 60 ms while external power remains connected.
74 • Appendices
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B. Logging the Beam Fraction sensor
You can log the Beam Fraction sensor in a similar manner, using the (optional)
special logging cable for it. Two outputs are available, corresponding to the Total
incident PAR and Diffuse PAR photodiode readings.
Be aware that the shade ring elevation may need readjustment after an hour or two.
Also, that separately logged incident PAR readings cannot at present be merged
with probe readings of transmitted PAR to give LAI estimates using the SunScan
mathematical model.
Wiring connections
The Beam Fraction sensor logging cable plugs into the BFS cable connector, giving
up to 12 metres distance from the logger. If you need more length, simply join on
extra screened multicore cable of a similar type. Make sure the joint is weatherproof.
The cores of the BFS logging cable have the following functionality:
Core
orange
green
brown
grey
blue
braid
Function
V+ Power supply positive
0V Power supply negative
HI Total PAR signal output
positive
LO Common signal output
negative
HI Diffuse PAR signal output
positive
Screen
Logger Connection
Sensor power positive (switched for warm-up)
Sensor power negative (0V)
Input channel +, for Total PAR
Input channels - common negative
Input channel +, for Diffuse PAR
Frame earth, or 0V
Note: the grey and green are connected internally in the BFS case. The braid is not
connected to any other core.
Output
• The output signals are the Total and the Diffuse PAR irradiance.
• The millivolt outputs are linear, with a sensitivity of 1 mV = 1 µmol.m-2.s-1.
Maximum output is dependent on the supply voltage, and can exceed 2500 mV.
Logger requirements
• The BFS requires a voltage supply of 5-15 V dc (unregulated), at about 1 mA
current.
Warning! Pre-Release Beam Fraction sensors require a regulated voltage supply of
5 V dc (±0.25 V). Refer to Delta-T if you are uncertain about this.
• Configure two logger channels for voltage input, with the above sensitivity.
• Use a "warm-up" time of 1 second (the logger must apply the power 1 second
before taking its reading). Outputs will be stable after 10 ms.
SunScan User Manual v 1.05
Appendices • 75
C. Upgrading the SunScan system
From time to time, new issues of the software programs in the SunScan system may
be released and offered to existing customers. Brief notes follow for what is
involved in installing them.
The SunData PC s/w
New versions of the PC program file SunData.exe will be provided on a floppy
disk. Rename the existing file on your PC's hard disk, then copy the new file across
to the same directory as was previously used.
The Workabout SunData s/w
New versions of the SunData.app file (and any other files needed in the Psion),
must be copied across to the Workabout and the application installed. To do this,
you will need to use the SLINK or RCOM file transfer utilities, or the PsiWin
program if you have it.
Once you have copied across the new program file, you will need to install the
SunData application as described in the section More Psion and file handling notes.
Revision History
Full release versions of hardware, software and documentation are v1.05 or later
(December 1996).
Pre-Release units were issued before this time. A free of charge upgrade has been
offered to all pre-release customers. If you are unsure about the status of your
equipment, please refer to the earlier Technical Support section of this manual for
how to locate version and serial numbers, then contact your agent or Delta-T.
76 • Appendices
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D. File transfer between Workabout and PC
Choice of different programs
For the transfer of data files from the Workabout to a PC, the SunData software that
resides in the Workabout and on your PC provides all you need, but it is specific for
this purpose. There are other occasions however when you may want to transfer
other files between the PC and the Workabout, for example to send an upgraded
version of the SunData.app file to the Workabout.
To do this, there are three routes. We provide two DOS utility programs from Psion
plc on the SunData diskette called SLINK and RCOM. The main difference
between these programs is that RCOM is operated from your PC keyboard with
DOS-like commands, whereas SLINK lets you use the Workabout's own file and
directory screens, and no input is required from the PC. Documentation text files are
included on the SunData diskette.
If you are familiar with the Workabout's screens then you will probably find SLINK
is the easiest route to master quickly.
In addition, we offer as an option the Psion PsiWin program for Windows, which is
an excellent application program for handling communications between PCs and
various computers in the Psion range. Contact your agent or Delta-T if you wish to
purchase a copy.
The Workabout Remote Link
We give you below some notes on using each of these programs. In every case you
must set the Workabout's Remote Link on. Access this from the Psion System screen
with ∪+L, or press Menu, Spec, Remote Link, Enter.
Warning! Don't forget to turn the Remote Link off when you have finished. If you
neglect this, you will get a "Failed to open Serial Port In use" message when you
next try to run SunData in the Workabout.
PsiWin
PsiWin is a well documented program with a full User Manual and on-screen Help.
It uses a screen layout very similar to Windows File Manager. When communication
is established between your PC and the Workabout, you can drag and drop files
between different drives and directories, and of course do very much more
♦ Install and run PsiWin on your PC.
♦ Connect the Workabout to your PC COM port with the SunScan RS232 comms
cable.
♦ On your Workabout, exit from the SunData program if necessary (∪+X). Access
the Remote Link dialog (∪+L) and set the link on, port A and with 19200 Baud.
In PsiWin:
The Setup, Communications... menu deals with COM ports and serial data
parameters. Check that they correspond exactly with those of the Workabout remote
link.
The Setup, Conversions... menu deals with file conversions. This is not needed for
any file transfer. Make sure Conversion is Off.
Window, Refresh is worth doing when verifying that a file has been transferred to a
new drive or directory.
SunScan User Manual v 1.05
Appendices • 77
If PsiWin has difficulty establishing the link to the Workabout at any stage,
powering down PsiWin and the Workabout and physically remaking the RS232
connections before running them again may clear the problem.
Don't forget to turn off the remote link in the Workabout when you have finished.
SLINK and RCOM
The procedure
For maximum safety, to start with, close down all other applications on the PC, and
run everything from the DOS prompt whilst you do this.
Both programs follow a similar procedure in general.
♦ On your PC, copy the RCOM and SLINK files on to your hard disk if you have
not already done so by following the Getting Started section in the User Manual.
♦ On the Workabout, exit the SunData s/w, and set up the Remote Link parameters
in the Psion's system.
♦ Connect the Workabout comms cable between the RS232 port on the Workabout
and the COM1 serial port on your PC. (If you can't use COM1 you must refer to
the program documentation to enable it to use COM2).
♦ Run whichever program you have chosen, and copy the appropriate files across.
Verify that the file names now appear in the new directories.
♦ Exit from the transfer program on your PC.
♦ Close down the Remote Link on the Workabout.
Example using SLINK
SLINK lets you initiate all the file transfer commands from the Workabout's screens
and menus. Consult the earlier section More Psion and file handling notes first if
you are not adequately familiar with the Psion's routines.
On the Workabout:
♦ Exit from the SunData application (if necessary) by pressing ∪+X.
♦ In the System Screen, press Menu, Spec, Remote Link, and press Enter. Set the
Remote link to On, Baud rate to 9600, and the Port to A. Press Enter to accept.
♦ Connect the RS232 port at the top right of the Workabout to the PC’s COM1
serial port with the SunScan comms cable.
On your PC:
♦ Exit Windows. From the DOS prompt, in the directory holding SLINK.EXE,
type: SLINK ↵
You will get an SLINK acknowledgement like this (or similar):
Psion MC/HC/Series3 File Server Version 1.2 - Copyright (C) Psion Plc 1991
Press Q to Quit
As an example, let us consider how to transfer a new version of the SunData
program to the Workabout from your PC. We will assume you have already copied
the program file SunData.app into a directory called C:\SUNSCAN\PSION on your
Hard Disk.
The same process can be used if you need to re-load the SunData program for any
reason.
SunData.app needs to run from a subdirectory \SUN\ on the Internal drive. You
must create this, if it is not already present.
On the Workabout:
78 • Appendices
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♦ From the Psion System Screen, press Menu, Disk, Directory, Enter.
♦ Press ← → to select the Disk Internal, (or any other Disks or drives).
Note: the Workabout refers to its own drives as Internal and Disk A, B, C etc . The
drives on the PC are referred to as REM::A:, REM::C: (REM = remote).
If no subdirectory \SUN\ exists, then create one as follows:
♦ Select \, the root directory of the Disk Internal
♦ Press Menu, Directory, Make directory, Enter.
♦ For Dir. Name type \SUN and press Enter.
♦ Access the directories again with Menu, Disk, Directory, Enter.
The new subdirectory \SUN\ will now be listed under the root directory of the
Internal Disk.
♦ Now press ← → to move to the REM::C: drive (your PC's hard disk) and enter the
\SUNSCAN\PSION directory.
♦ Press ↑ or ↓ to highlight the file Sundata.app. Don't press Enter!
♦ Press Menu, File, Copy file, Enter.
♦ Complete the dialog box as shown below, noting the general advice.
You must specify the full
subdirectory path of the Disk. Start
and finish with backslashes(\).
If you leave the filename blank after
the backslash, the original filename
will be used. If you want to change
the filename, type in the new
filename, with its extension, after the
directory path.
♦ Press Enter to accept, when you are happy with all the details.
The Workabout will warn you if you have chosen a filename that already exists, and
offer you various options. Otherwise it will proceed, and briefly advise you of the
copying process.
A copy of the file is now in the new location you have specified.
You must also copy across the file Sys$8087.ldd to the same directory on the
Workabout, for the SunData program to run properly. You can do this by a similar
procedure. Finally:
♦ On your PC, quit the SLINK program by typing Q.
♦ On the Workabout, close down the Remote Link: From the System Screen, press
Menu, Spec, Remote Link, and set it to Off, then press Enter.
If the SunData icon does not automatically appear in the Psion System screen, see
More Psion and file handling notes about re-installing SunData as an application.
SunScan User Manual v 1.05
Appendices • 79
Example using RCOM
On the Workabout:
♦ Exit from the SunData application on the Workabout by pressing ∪+X.
♦ In the System Screen, press Menu, Spec, Remote Link, and press Enter. Set the
Remote Link to On, Baud rate to 19200, and the Port to A.
♦ Connect the RS232 port at the top right of the Workabout to the PC’s COM1
serial port using the SunScan comms cable.
From the PC
♦ At the DOS prompt, in the directory holding RCOM.EXE, type: RCOM↵
↵
(Let's assume this is in your C:\SUNSCAN\COMMS directory)
The RCOM prompt "»" followed by the current subdirectory name will appear, in a
DOS-like screen.
You should now be able to get a directory listing of the Workabout Internal Disk on
your PC by typing DIR I: ↵ at the prompt.
Note: in RCOM, the Workabout drives A, B and Internal are mapped onto drives L,
R and I.
♦ If the subdirectory \SUN\ does
not exist you must create it as
follows:
>>C:\SUNSCAN\COMMS>I:↵
>> I:\>md\sun↵
♦ Check the new subdirectory
now exists:
>> I:\>dir↵
♦ Then type
>> I:\>copy
c:\sunscan\psion\*.* I:\sun\↵
This copies both the SunData program sundata.app and sys$8087.ldd, which is
also required, to the Workabout Internal drive subdirectory \SUN\ and confirms the
process. When you have finished:
♦ On your PC, type EXIT↵ to exit from RCOM
♦ On the Workabout, close down the Remote Link: From the System Screen, press
Menu, Spec, Remote Link, and set it to Off, then press Enter.
If the SunData icon does not automatically appear in the Psion System screen, see
More Psion and file handling notes about re-installing SunData as an application.
Documentation of RCOM and SLINK
If you have been successful with the above transfer instructions, you can skip this,
but if you need to know more about either RCOM or SLINK, the SunData s/w
diskette contains text files in the \COMMS directory which explain the operation of
the transfer programs.
• COMMS.TXT gives brief details of the operation of both SLINK and RCOM.
• RCOM.TXT is a text file containing the full RCOM manual.
80 • Appendices
Document code: SS1-UM-1.05
E. Alternative file transfer mechanisms
Sending a file to a Communication program
You can send your files to a communications program such as Windows Terminal or
ProComm. However, if you do this there will be no error checking during the file
transfer.
Connect the Workabout to an appropriate serial port on the PC using the SunScan
RS232 cable or a null modem serial cable.
In the communications program
Set the COM port you are using to 9600 baud, No parity, 8 data bits, 1 stop bit.
Select either hardware (RTS/CTS) or software (XON/XOFF) handshaking.
Select “capture to file” or “receive text file” and the filename you want to store the
data in.
In SunData on the Workabout
Select Menu, File, File Transfer, Enter, and select the file you want to send.
The Workabout will send “start of header” (SOH ASCII 01) followed by the
filename.
After a few seconds, the message “no response from receive program” will appear.
Select continue and the Workabout will send “start of text” (STX ASCII 02) then
continue transmitting the file. You should see this appear on the communications
program screen.
You can stop the transfer by pressing On/Esc on the Workabout, or Ctrl+X in the
communications program.
After the file has been sent, the Workabout will finally send “end of text” (ETX
ASCII 03) and a file checksum value. A few seconds later the message “no
acknowledgement from receive program” will appear. Select Quit.
Now close your file in the communications program.
Sending a file to a serial printer
You can print files out directly to a printer with a serial port. You must set the
printer serial port to 9600 baud, No parity, 8 data bits, 1 stop bit, with either
hardware (RTS/CTS) or software (XON/XOFF) handshaking. This is usually done
by setting switches or jumpers inside the printer, and will be explained in the printer
manual. Connect the printer to the Workabout using the SunScan RS232 cable or a
null modem cable.
Proceed on the Workabout as described in the paragraph above.
Using the Workabout COMMS application
There is a built in communications program accessible from the Workabout system
screen. This supports various protocols including XMODEM and YMODEM, and
will support file transfer via a modem. The use of this is described in the Workabout
manual on pages 52-58.
SunScan User Manual v 1.05
Appendices • 81
F. Glossary
Beam fraction - the fraction of the Total incident PAR in the Direct beam.
Beam Fraction Sensor (BFS) - consists of two PAR sensors and a shade ring, used
for measuring Direct and Diffuse light above the canopy.
Beer’s law - a general law describing transmission through an absorbing medium.
The intensity falls off exponentially with distance through the medium.
Cosine response - the response of a sensor to a ray of light is proportional to the
cosine of the angle of incidence of the ray (measured from the perpendicular to the
sensor surface).
CSV (Comma Separated Variable) a file format intended for importing into
spreadsheet or database programs. Fields are separated by commas, text is enclosed
in quotes.
Data Collection Terminal - the Psion Workabout handheld computer, used for
driving the SunScan probe, and presenting and storing the results.
Diffuse light - light scattered in the atmosphere. It is treated as coming from all parts
of the sky with equal intensity i.e. a Uniform Overcast Sky.
Direct beam - light coming directly from the sun, with no scattering. Usually treated
as if it comes from a point source.
ELADP - see Leaf Angle Distribution
Emulator - a setting in the SunData software that generates random results,
regardless of whether a SunScan probe is connected. Useful for learning to use the
software.
GMT - Greenwich Mean Time, also called Universal Time (UT). The standard time
used for astronomical measurements and calculations.
Hemispherical response - the response of the sensor is equal for all light rays
coming from above the plane of the sensor surface, independent of angle.
LAD - see Leaf Angle Distribution.
LAI - see Leaf Area Index.
Leaf absorption - the fraction of intercepted PAR that is actually absorbed by the
leaf. The remainder is reflected or scattered.
Leaf Angle Distribution - a way of describing the distribution of orientations in
space of the canopy elements. We model this using the Ellipsoidal Leaf Angle
Distribution, which describes the distribution of canopy elements as in the same
proportions as the surface of an ellipsoid. Using this model, a wide range of different
canopy types can be described by a single parameter, the Ellipsoidal Leaf Angle
Distribution Parameter (ELADP), which is the ratio of the horizontal to vertical axes
of the ellipsoid. An ELADP much greater than 1 describes a canopy of mostly
horizontal leaves, an ELADP near 0 describes a canopy of mainly vertical leaves.
Leaf Area Index (LAI) - the surface area of leaf per unit of ground area (assuming
leaves are flat, and including only one side of each leaf). Instruments like the
SunScan cannot differentiate between leaf and stem, so could more correctly be said
to estimate Plant Area Index.
82 • Appendices
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Local time - the time used in your particular time zone. It varies from GMT by an
amount depending on longitude, political boundaries, and any daylight saving time.
Mean Leaf Angle (also Mean Tip Angle, Mean Inclination Angle) is the average
angle of all the leaf elements relative to the horizontal, weighted according to area.
This can be directly related to ELADP.
PAR - Photosynthetically Active Radiation is visible light of wavelength 400 nm 700 nm. It is measured in units of µmol.m-2.s-1 (micromoles per square metre per
second) or formerly µE (micro-Einstein). The normal daylight maximum is a little
over 2000 µmol.m-2.s-1 .
PAR mapping - the study of distribution and variation of PAR within and below a
canopy.
PRN a text file format intended for directly printable output.
Spread - a measure of the relative variation in light intensity along the SunScan
probe. It is calculated as the Standard Deviation divided by the Mean (sometimes
called coefficient of variation).
SunData software- the software used to drive the SunScan probe and calculate and
store the results. There are two versions, one which runs in the Psion Workabout, the
other in an IBM compatible PC. They are functionally very similar.
SunScan probe - the long light sensitive wand and handle used for light readings
within the canopy.
Total PAR - the sum of Direct beam PAR and the Diffuse light PAR.
Transmission fraction - the fraction of incident light that passes through a given
canopy. It can refer to Direct, Diffuse, or Total incident light.
Zenith angle - the angle between the centre of the sun and the point directly
overhead.
SunScan User Manual v 1.05
• 83
Index
A
About ........................................................................ 31
Absorption
incomplete................................................. 52, 56, 59
values .................................................................... 42
Accuracy
LAI ........................................................................ 58
PAR................................................................. 48, 49
All, display................................................................ 44
Appending data......................................................... 19
ASCII text................................................................... 7
Assumptions, theory ........................................... 53, 56
Autolog ........................................................... 6, 31, 45
Average interval........................................................ 31
Averages ................................................................... 24
B
B FRAC .................................................................... 23
Batteries.............................................................. 46, 62
checking .......................................... 9, 12, 14, 65, 66
Beam fraction............................................................ 80
Beam Fraction Sensor..................................... 7, 21, 80
Beeps .................................................................. 22, 46
Beer's Law .......................................................... 43, 80
BFS
extension cables .................................................... 48
field use ................................................................. 47
levelling................................................................. 48
specs...................................................................... 68
C
Calibrate ................................................................... 31
Calibration
factory ............................................................. 49, 64
restore ................................................................ 31
Campbell's equations ................................................ 52
Canopy
model..................................................................... 57
sampling volume ................................................... 40
Canopy types
clumped................................................................. 40
real ........................................................................ 40
Carrying Case ........................................................... 69
CE marks .................................................................... 2
Circuit schematics..................................................... 67
COM ports, PC ......................................................... 11
Comms Test .............................................................. 31
Communication program .......................................... 79
Communications
checks.................................................................... 12
Communications failed ....................................... 15, 21
Compass.................................................................... 47
Configuration files .................................................... 35
Connect..................................................................... 12
84 • Index
Constants............................................................. 18, 30
Continue .................................................................... 16
Copyright .............................................................. 2, 53
Cosine response................................................... 71, 80
CSV files ....................................................... 19, 37, 80
D
Data
groups .................................................................... 38
memory.................................................................. 35
Data Collection Terminal ................................ 7, 68, 80
Data file..................................................................... 36
display ................................................................... 37
layout ..................................................................... 38
Data Storage........................................................ 19, 30
Data.prn............................................................... 19, 36
Default.cfg........................................................... 36, 65
Desiccant................................................................... 63
Diffuse light .................................................. 39, 54, 80
Diffusers.................................................................... 50
Direct beam......................................................... 39, 80
Discard ...................................................................... 21
Display ................................................................ 18, 31
E
ELADP...................................................................... 80
estimating .............................................................. 43
setting .................................................................... 42
Emulator.................................................. 16, 20, 30, 80
Exit............................................................................ 30
Experiment design..................................................... 39
Ext sensor............................................................ 16, 21
Extension cables.................................................... 7, 48
Extinction coefficient ................................................ 54
F
File ............................................................................ 19
Review................................................................... 24
Saving.................................................................... 19
Transfer ........................................................... 25, 75
alternatives ......................................................... 79
dialog ................................................................. 26
Files, Psion
deleting .................................................................. 34
Flashcard ......................................................... 7, 34, 65
Format CSV ........................................................ 25, 30
Fractional interception ................................................ 6
G
GMT.................................................................... 18, 80
GO button............................................................ 12, 46
Group
number................................................................... 38
title......................................................................... 38
Guarantee .................................................................. 67
Document code: SS1-UM-1.05
H
Hemispherical response.......................................58, 80
Hot keys ..............................................................19, 32
I
Inversion....................................................................53
L
LAI, display...............................................................44
LAI, theory................................................................52
Latitude .....................................................................18
Leaf absorption..........................................................80
Leaf Angle Distribution.............................................80
Leaf Area Index.....................................................6, 80
Levelling .............................................................22, 46
Light conditions
preferred ................................................................41
sun position............................................................41
Linear Quantum sensor..........................................6, 72
Local time..................................................................81
Logging
BFS........................................................................73
cables .....................................................................69
Probe......................................................................72
Longitude ..................................................................18
M
Manuals .......................................................................6
Mean Leaf Angle.................................................43, 81
Measurement procedures
field........................................................................46
Memory ...............................................................46, 65
Menus..................................................................18, 30
N
Navigating
Psion ................................................................14, 32
Night time..................................................................31
North, setting.......................................................22, 48
Notes .........................................................................20
P
PAR.......................................................................6, 81
calibration ..................................................49, 50, 64
mapping .......................................................6, 44, 81
profiling .................................................................44
sensor, independent................................................39
Total.......................................................................81
PAR, display .............................................................44
PC
Data Collection ......................................................68
instead of Workabout.................................14, 16, 25
portable..............................................................7, 37
PC software ...............................................................16
Photodiodes.........................................................21, 44
Plot name...................................................................31
PRN files .............................................................37, 81
SunScan User Manual v 1.05
Problem reports ........................................................ 67
Protection, moisture.................................................. 51
Psion
Logo screen........................................................... 33
subdirectories ........................................................ 33
System screen.............................................. 8, 14, 33
PsiWin ...................................................................... 75
Q
Quit........................................................................... 31
R
RCOM ...................................................................... 76
Read interval............................................................. 31
Readings ................................................................... 20
Recalibrate.......................................................... 31, 49
References ................................................................ 61
Remote Link ....................................................... 21, 65
Reset ......................................................................... 15
Restore
calibration ............................................................. 50
Config'n................................................................. 30
Review...................................................................... 30
Revision history ........................................................ 74
RS232
communications .............................................. 28, 66
S
Sample name............................................................. 31
Save Config'n...................................................... 19, 30
Serial numbers .......................................................... 67
Serial printer ............................................................. 79
Settings ............................................................... 16, 18
Shade ring........................................................... 22, 50
Site...................................................................... 18, 31
Sleep ..................................................................... 9, 31
SLINK ...................................................................... 76
Spares kit .................................................................. 69
Specifications............................................................ 68
Spectral response ...................................................... 70
Spread................................................................. 50, 81
Store.......................................................................... 21
SunData s/w........................................................ 74, 81
diskette .................................................................. 10
Icon ................................................................. 34, 65
installation............................................................. 10
SunData.app.............................................................. 65
SunData.exe.............................................................. 11
SunScan probe ................................ 7, 8, 16, 21, 30, 65
specs...................................................................... 68
Sys$8087.ldd ............................................................ 65
T
Tab key ..................................................................... 19
Technical Reference section ..................................... 62
Technical Support..................................................... 67
Time & Date ....................................................... 18, 31
Titles......................................................................... 31
Index • 85
Transfer, file ............................................................. 30
Transmitted fraction.................................................. 81
Tripod Mount...................................................... 47, 69
Troubleshooting.............................................. 8, 27, 65
Tutorial ..................................................................... 14
U
Upgrades................................................................... 74
Utilities ..................................................................... 41
Utils .......................................................................... 31
V
Version numbers ....................................................... 67
W
Warnings
field use ............................. 39, 46, 48, 50, 51, 58, 64
general......................................................... 2, 54, 73
hardware.................................................... 50, 62, 63
86 • Index
software ......................... 8, 10, 15, 32, 34, 35, 45, 75
Weather
preferred ................................................................ 41
Windows, running SunData....................................... 13
Wood's SunScan equations........................................ 53
Workabout....................................................... 8, 47, 65
charger ..................................................................... 9
COMMS ................................................................ 79
hardware .................................................................. 9
keys........................................................................ 15
screens ................................................................... 29
setup ...................................................................... 44
Z
Zenith angle......................................................... 60, 81
Solar Predictor................................................. 41, 60
Zoom ......................................................................... 30
Document code: SS1-UM-1.05