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Sunfleck User Manual - manuals.decagon.com

1. Anderson M C 1971 Radiation and crop structure In Plant Photosynthetic Production Manual of Methods eds A Sestak J Catsky and P G Jarvis Junk The Hague pp 412 66 Campbell G S 1977 An Introduction to Environmental Physics Springer Verlag New York Inc New York 159 pp Campbell G S 1986 Extinction coefficients for radiation in plant canopies calculated using an ellipsoidal inclination angle distribution Agric For Meteorol 36 317 21 Campbell G S and Norman J M 1988 The description and measurement of plant canopy structure in Plant Canopies Their Growth Form and Function ed G Russell Society for Experimental Biology Seminar Series 29 Cambridge University Press New York Goudriaan J 1977 Crop Micrometeorology A Simulation Study Center for Agriculture Publication Documentation Wageningen The Netherlands Lang A R G 1986 Leaf area and average leaf angle from transmission of direct sunlight Aust J Bot 34 349 355 69 Lang A R G 1987 Simplified estimate of leaf area index from transmittance of the sun s beam Agric For Meteorol 41 179 186 Lang A R G 1991 Application of some of Cauchy s theorems to estimation of surface areas of leaves needles and branches of plants and light transmittance Agric For Meteorol 54 in press Lang A R G McMurtrie R E and Benson M L 1991 Validity of leaf area indices of Pinus radiata forests estimated fr
2. Light intensity and sunfleck size distributions in plant canopies Agron J 75 481 8 Norman J M and Welles J M 1983 Radiative transfer in an array of canopies Agron J 63 743 8 Raison R J Benson M L Myers B J Khanna K McMurtrie R E and Lang A R G 1991 Dynamics of Pinus radiata foliage in relation to water and nitrogen stress Il Needle loss and temporal changes in total foliage mass For Ecol Manag accepted Ross J 1981 The Radiation Regime and Architecture of Plant Stands Junk The Hague 391 Pp 71 Welles J M 1990 Some indirect methods of estimating canopy structure nstrumentation for studying vegetation canopies for remote sensing in optical and thermal infrared regions Eds N S Goel and J M Norman Remote Sensing Reviews Harwood Academic Publishers London pp 31 43 72 References Anderson M C 1966 Stand structure and light penetration Il A theoretical analysis J Appl Ecol 3 41 54 Anderson M C 1970 Radiation climate crop architecture and photosynthesis in Prediction and Measurement of Photosynthetic Productivity p 71 78 Setlik J ed Pudoc Wageningen Bonhomme R and Chartier P 1972 The interpretation and automatic measurement of hemispherical photographs to obtain sunlit foliage and gap frequency Israel J Agric Res 22 53 61 Bonhomme R Varlet Grancher C and Chartier P 1974 The use of hemispherical photographs f
3. Q Move to the SunView directory CD SunView and type COPY A SUNVIEW EXE Q Put the original SunView disk in a safe place Q To run the SunView program type CD SUNVIEW then SUNVIEW Connecting the RS 232 Cable An optically isolated RS 232 cable is included with each Ceptometer This cable is specifically designed for use with the instrument and should be used whenever the operator wishes to download data to a computer Other cables will not provide correct data output One end of the RS 232 cable houses a 9 pin connector Secure this connector to the 9 pin receptacle on the Ceptometer The other end of the cable houses a 25 pin connector which needs to be connected to the serial port of the computer at COM1 If you are unsure which port is COM1 see your computer operator s manual Note You may use a 25 to 9 pin adapter to interface with your computer if needed however the 9 pin end of the RS 232 cable must be connected to the Ceptometer for correct operation 61 Downloading Memory to a Computer Prepare your computer to receive data with the SunView software or the BASIC program described earlier Press the function key until the display pointer is stationed at function 8 then press the B key to send the data to the computer The sample numbers on the display will continually update until the transaction is complete This transaction can be interrupted at any time by pressing the A key Running SunView Software
4. The SunView program displays data under four headings Index Time PAR and Sunfleck The Index column refers to the data set number as it was stored in the Ceptometer s memory After the required data has been sent press F2 to save Press F1 to exit If printing is a necessary application data sets will need to be copied to a user provided spreadsheet Some instructions for importing to these spreadsheets are listed below Microsoft Excel To export data to Excel include a CSV extension when naming a file You can load the file into Excel by selecting File Open Lotus 123 To export data to Lotus 123 include a PRN extension when naming a file You can load the file into Lotus 123 by selecting File lmport Numbers Borland s Quattro To export data to Quattro include a PRN extension when naming a file You can load the file into Quattro by selecting Tools Import Then select Comma amp delimited ascii for the file format 62 10 Maintenance Changing the Batteries The Ceptometer does not have a power switch The microprocessor is always on to maintain the memory and update the clock but the display closes after 7 minutes without keyboard activity The instrument uses 5 AA type batteries When the batteries are low an indicator will appear when the Ceptometer is activated the letters LO to the left of the display Press any button to clear the display The instrument may be used and although it will con
5. To take a reading level the board with the protractor parallel with the sun azimuth and adjust the soda straw watching its shadow on a surface below its end When light shines through the straw onto the surface read the angle from the protractor Figure 2 Protractor Straw zenith angle device 12 Calculation The formulas for calculating elevation angle are relatively straightforward The zenith angle is calculated from 8 arccos sin L sin D cos L cos D cos 0 2618 t t 1 where L is the latitude D is the solar declination t is the time and t is the time of solar noon The earth turns at a rate of 0 2618 radians per hour so the 0 2618 factor converts hours to radians Time t is in hours standard local time ranging from 0 to 24 Latitude of site is easily found in an atlas Solar declination ranges from 0 409 radians 23 45 degrees at summer solstice to 0 409 radians 23 45 degrees at winter solstice It can be calculated from D arcsin 0 39785 sin 4 869 0 0172 J 0 03345 sin 6 224 0 0172 J 2 where J is the day of the year Some values are given in Table 1 The time of solar noon is calculated from t 12 LC ET 3 where LC is the longitude correction and ET is the Equation of Time LC is 4 minutes or 1 15 hour for each degree east of the standard meridian and 1 15 hour for each degree west of the standard meridian Standard meridians are at 0 15 30 345 degrees Generally
6. percentage of the sensors exposed to a radiation level greater than the set threshold For a more detailed discussion of sunfleck fraction please refer to page 43 of this manual The A key is the sample key The B key averages the readings and sends the averaged reading to memory Before making sunfleck fraction measurements a threshold will need to be set Refer to function seven 20 Function 3 Unattended PAR Measurement and Display of PAR Memory This function displays previously stored PAR readings and measures PAR unattended Stored readings can be read by pressing either the A or B keys The A key displays progressively earlier readings while the B key displays progressively later readings The readings are shown on the right of the display and the time of sampling is displayed on the left To begin the unattended reading mode press the A and B keys simultaneously The Ceptometer will display the auto mode indicator Refer to Figure 9 Every minute the instrument will automatically sample PAR and sunflecks but the display will only show PAR Function 4 is identical to function 3 and will only show sunflecks Each half hour the thirty samples will be averaged and stored in memory The Ceptometer will remain in automatic mode until either the A or B key is pressed 8 7 6 5 3 2 q A Figure 8 Time and Stored Reading 8 7 6 5 4 3 2 1 A Figure 9 Unattended PAR Indicator 4 21 Function 4
7. 1974 Since K 1 for zenith angles near 57 degrees the inversion of equation 1 is simple and gives L In te 3 If a sunfleck measurement is made when the zenith angle is about 57 degrees equation 3 can be used directly to find L If measurements of the transmission coefficient t are made at several elevation angles a simple method from Lang 1987 can be used 49 The measurements of t are used to compute y cos In To These are regressed on in radians giving a slope B and an intercept A The leaf area index is given by L 2 A B 4 An approximate value for x is x exp B 0 4L Example Sunfleck readings were obtained as follows degree radian cos In t 35 0 61 i 1 28 41 0 72 1 29 55 1 32 xr U gt Note can be measured by placing a stick of length y vertically in the ground and measuring the shadow length x on a horizontal surface tan Q x y so tan 1 x y 50 A more precise method for finding x is as follows We would like to find values for x and L which minimize F X Int KL subject to the constraint x gt 0 where qt are transmission coefficients measured at several zenith angles and qt K are the extinction coefficients for the corresponding angles A BASIC computer program which finds L and x from measured sunfleck fraction data is outlined on the following page 51 A Computer Program to Find LAI and LAD 10 20 35 30 40 5
8. If the ELE mode is used the instrument will not function properly and will need to be recalibrated Cleaning the Probe The white surface of the probe should always be clean to insure accurate readings To clean the probe use a small amount of alcohol and a soft cloth Rub the surface until it is clean 64 11 Return and Repair Should anything ever go wrong with the Ceptometer Decagon will repair it Just follow the instructions below for returning the instrument Q Before returning the Ceptometer call our offices for a Return Materials Authorization Number RMA Include this number on all correspondence regarding the repair of your instrument Q With your return please include your RMA a complete return address the name and department of the person responsible for the Ceptometer a repair budget for non warranty instruments and a purchase order number Q Pack the Ceptometer carefully and mail to Decagon Devices Inc NE 1525 Merman Drive Pullman WA 99163 To avoid damage during shipping return the instrument in the case in which it was shipped or place adequate padding around it NEVER SHIP THE CEPTOMETER WITH THE BATTERIES INSTALLED 65 12 Questions and Answers Q When should remove the batteries from my instrument O Always remove the batteries before shipping or traveling with the Ceptometer If the batteries are shifted during transit data will be lost and cannot be retrieved Damage to th
9. Unattended Sunfleck Measurement and Display of Sunfleck Memory Function four displays previously stored sunfleck readings and measures sunflecks unattended This function is similar to function three and the keys are used in the same way As in function two a threshold should be set before sunfleck measurements are taken Refer to function seven Function 5 Continuous Sunfleck and PAR Readings Function five continuously samples both PAR and Sunfleck and displays the readings The PAR measurement is shown on the right of the display and the sunfleck measurement is shown on the left As measurement conditions change so will the readings but they may be held by pressing the A key Pressing the A key again will release the values Held values can be sent to memory by pressing the B key and stored values can then be viewed by using functions three and four 8 7 6 4 3 2 1 59f 35 Figure 10 Continuous Sunfleck and PAR measurements Function 6 Setting the Time When a measurement is stored in memory the time in hours and minutes will be stored along with it Function six can be used to set the Ceptometer to the correct time The A key controls the hour value and the B key controls the minutes The clock can be set by either moving one hour or minute at a time by pressing the key once or moving rapidly by holding down the key 8 1 05 00 25 Figure 11 Time Setting 23 Function 7 Setting the Thresho
10. determine other canopy characteristics Note When using sunflecks for inversions it is critical that the instrument be placed in exactly the same location for each reading It is therefore strongly recommended the unattended mode of data collection be used The sunfleck measurement can also be used to determine intercepted radiation for a canopy 44 The sunfleck measurement is faster than the PAR measurement since the sunfleck measurement does not require finding the ratio of measurements below the canopy to measurements above it It also has advantages on days where incoming radiation varies over short time periods since light levels needed for making calculations are all measured at one time The method cannot be used on overcast days or in canopies with overlapping penumbra since it relies on distinct shadows to make the measurement Penumbra are the partial shadows which surround the shadows of objects illuminated by the sun or any other source of finite size and are the result of the sun not being a point source of light Setting the Threshold A proper threshold level must be established before accurate sunfleck measurements can be made At each sunfleck measurement the sensors in the probe are scanned by the microprocessor and the reading of each sensor is compared to the established threshold The microprocessor counts the number of sensors above the threshold divides this value by the total number of sensors in the
11. of day or at positions within the canopy that directly minimize the clumping effects 29 A uw a Figure 1 Randomly Dispersed L Le ae Let Ae G OP Figure 2 Underdispersed L gt Le DARA Figure 3 Overdispersed L lt L 30 6 Applications The Sunfleck Ceptometer is useful for a number of applications including the measurement of average and intercepted PAR and the recording of sunfleck occurrences From these measurements canopy structure can be estimated PAR PAR photosynthetically active radiation is generally considered to be the radiation in the 400 to 700 nanometer waveband It represents the portion of the spectrum that plants can use for photosynthesis In the PAR waveband irradiances can vary from full sun to almost zero over the space of a few centimeters and reliable measurement of PAR requires many samples at many locations under the canopy Measuring Average and Intercepted PAR Monteith 1977 observed that dry matter production of a plant canopy is directly related to the amount of photosynthetically useful radiation intercepted by the canopy Dry matter production is modeled as the product of three terms P efS where P is the amount of dry matter produced S is the flux density of incident radiation intercepted by the crop and e is a conversion efficiency Conversion efficiency and fractional interception are determined by crop physiology and management 31 Incident solar radi
12. sunflecks 100 Zenith angle refers to the angle the sun makes with respect to a line vertical to the earth s surface A full description of zenith angle and how to measure it begins on page 11 A number of expressions have been proposed for K The most useful is from Campbell 1986 where the angle distribution of canopy elements is assumed to be ellipsoidal One can picture the angle distribution of area in a plant canopy to be similar to the angle distribution of area on the surface of oblate or prolate spheroids or spheres 48 The equation for K is x tan o x 1 744 x 1 182 2 The parameter x is the ratio of the length of the horizontal to the vertical axis of the spheroid and can be measured as the ratio of the projected area of an average canopy element on a horizontal plane to its projection on a vertical plane Extinction coefficient is plotted as a function of zenith angle for various values of x See figure 16 At a zenith angle of about 57 degrees the extinction coefficient is near unity for all canopies When leaves are horizontal large X the extinction coefficient K is unity for all elevation angles but as X decreases K becomes smaller at large zenith angles and larger at small zenith angles Equation 1 can be used in various ways to determine the leaf area index and possibly also the leaf angle distribution function for a canopy The simplest application is that of Bonhomme et al
13. 0 60 70 80 90 100 110 120 130 140 150 160 170 S1 180 190 200 210 220 230 240 250 260 270 280 290 300 from Sunfleck Fraction Measurements REM ELLIPSOIDAL EXTINCTION COEFFICIENT DEF FNK Z X SQR X X Z Z x 1 774 x 1 182 0 733 REM Z IS TAN ZENITH ANGLE REM eee Pl 3 14159 DX 0 1 INPUT NUMBER OF ZENITH ANGLES NZ DIM Z NZ T NZ FOR l 1 TO NZ PRINT ZENITH ANGLE I DEGREES INPUT Z PRINT TRANSMISSION AT Z 1 DEG INPUT T I Z I TAN Z PI 180 T l LOG T I NEXT REM FIND X USING BISECTION METHOD XMAX 10 XMIN 1 X 1 1 0 S2 0 S3 0 S4 0 FOR J 1 TO NZ TZ Z J KB FNK TZ X DK FNK TZ X DX KB S1 KB T J S2 S2 KB KB S3 S3 KB DK S4 S4 DK T J NEXT F S2 S4 S1 S3_ PRINT X F IF F lt 0 THEN XMIN X ELSE XMAX X X XMAX XMIN 2 IF XMAX XMIN gt 01 THEN GOTO 140 REM FIND LAI AND PRINT RESULTS L S1 S2 PRINT LEAF AREA INDEX L PRINT RATIO OF VERTICAL TO HORIZONTAL PROJECTIONS X PRINT PRINT ZENITH ANG MEASURED T PREDICTED T FOR J 1 TO NZ PRINT ATN Z J 180 PI EXP T J EXP FNK Z J X L NEXT 52 Correction of Sunfleck and Intercepted Radiation for Sun Angle Sunfleck fraction t measured at one zenith angle can be used to predict sunfleck fraction or radiation interception for other zenith angles For example a measurement might be made at 32 from which cover 1 transmission at 0 is to be calculated F
14. 22 Feb 9 40 0 261 0 238 Feb 19 50 0 202 0 232 Mar 1 60 0 138 0 208 Mar 11 70 0 071 0 170 Mar 21 80 0 002 0 122 Mar 31 90 0 067 0 072 Apr 10 100 0 133 0 024 Apr 20 110 0 196 0 017 Apr 30 120 0 253 0 046 May 10 130 0 304 0 060 May 20 140 0 346 0 059 May 30 150 0 378 0 043 Jun 9 160 0 399 0 015 Jun 19 170 0 409 0 019 Jun 29 180 0 406 0 055 Jul 9 190 0 392 0 085 Jul 19 200 0 366 0 103 Jul 29 210 0 331 0 107 Aug 8 220 0 286 0 094 Aug 18 230 0 233 0 065 Aug 28 240 0 174 0 022 Sep 7 250 0 111 0 031 Sep 17 260 0 045 0 089 Sep 27 270 0 023 0 147 Oct 7 280 0 091 0 201 Oct 17 290 0 157 0 243 Oct 27 300 0 219 0 268 Nov 6 310 0 275 0 273 Nov 16 320 0 324 0 255 Nov 26 330 0 363 0 213 Dec 6 340 0 391 0 151 Dec 16 350 0 406 0 075 Dec 26 360 0 408 0 007 15 4 Keyboard Operation This section is designed to familiarize the user with the Ceptometer s function keys More in depth discussion of the methods described briefly here can be found later in this chapter Overview of Functions Function 1 PAR Measurement A is the sample button and B averages the readings and sends them to memory Function 2 Sunfleck Measurement A is the sample button and B averages the readings and sends them to Function 3 Views previously stored PAR readings and reads PAR and sunflecks unattended Function 4 Views previously stored sunfleck readings and reads sunflecks and PAR unattended Function 5 Continuously sam
15. 63 Line 60 Prints the contents of t to the screen Line 70 Prints the contents of t to the file numbered 2 Line 80 Prompts the program to go to line 40 Line 85 Prompts the program to resume running on the line where an error was detected 58 Executing the BASIC Program Write and save the BASIC program to disk then execute it in the following way to avoid any communication buffer overflow problems If the program were called Sunread type gwbasic sunread C 15000 at the prompt This allocates 15 000 bytes to the RS 232 receiver buffers and allows enough room for a full interface with the Ceptometer s memory Note When running the program and saving data to disk check to see that there is at least 40K left on the disk A full interface of 1200 data points requires 22K of disk space 59 Sunfleck SunView Software Backing Up and Running SunView from Floppy Disk Before using the SunView program from a floppy disk make a backup copy Q Insert a blank formatted disk into drive A OY Place the SunView disk in drive B O Type COPY B SUNVIEW EXE A To run SunView from a floppy disk Q Place the floppy disk in drive A O Type A SUNVIEW Note Put the original SunView disk in a safe place Always run the program from a backup copy 60 Installing SunView to the Hard Drive Q Place the SunView disk in drive A Q Move to your hard drive and make a SunView directory by typing MD SUNVIEW
16. Radiation for Sun Angle Example 9 Interfacing with a Computer Connections BASIC Program Notes on the BASIC Program Executing the BASIC Program Sunfleck SunView Software Backing Up and Running SunView from Floppy Disk Installing SunView to the Hard Drive Connecting the RS 232 Cable Downloading Memory to a Computer Running SunView Software 10 Maintenance Changing the Batteries Recalibrating the Sensors Cleaning the Probe 11 Return and Repair 12 Questions and Answers Appendix A Additional Information References 45 46 47 48 48 49 51 53 54 54 57 58 58 59 60 61 61 62 62 63 63 64 65 65 65 66 67 70 74 1 Introduction The Sunfleck Ceptometer is a battery operated PAR sensor used for data collection in plant and forestry canopy research It will enable the user to collect and store radiation data in the 400 700 nm PAR region The Ceptometer is easy to use and will give accurate results when properly maintained About This Guide Included in this manual are instructions for operation and calibration of the Ceptometer along with guidelines to help you maintain and care for your instrument Please read all of these instructions before operating the Ceptometer to insure that the instrument performs to its full potential Warranty The Ceptometer has a 30 day satisfaction guarantee and a one year warranty on parts and labor To validate your warranty please complete and return the warranty card includ
17. Sunfleck PAR Ceptometer Operator s Manual Table of Contents 1 2 3 Introduction About This Guide Warranty Customer Service Information Seller s Liability About the Sunfleck Ceptometer Getting Started Installing the Batteries Calibration Finding the Zenith Angle of the Sun Direct Measurement Calculation Example Calculation 4 Keyboard Operation 5 6 Overview of Functions Function 1 PAR Measurement Function 2 Sunfleck Measurement Function 3 Unattended PAR Measurement Function 4 Unattended Sunfleck Measurement Function 5 Continuous Sunfleck and PAR Readings Function 6 Setting the Time Function 7 Setting the Threshold Function 8 Send Erase Memory and Individual Sensor Dump Measurement Tips Discussion of the Effects of Non Random Distribution of Canopy Elements of LAI Measurement in situ Applications PAR Measuring Averaged and Intercepted PAR Sampling for Fractional Interception Unattended Recording of Transmitted PAR Survey Sampling of Average Line PAR Using PAR to Determine Leaf Area Index Applications and Examples Final Comments Spectral and Cosine Response ONOnDAARAHRA 31 31 31 33 36 37 37 41 42 42 7 Sunflecks Setting the Threshold Sampling for Sunfleck Fraction Unattended Recording of Sunfleck Fraction Survey Sampling of Sunfleck Fraction 8 The Theory of Sunflecks and Canopy Structure Example Computer Program to Find LAI and LAD Correction of Sunfleck and Intercepted
18. ation is the only environmental factor If f and S are monitored over the period of growth of a crop and P is measured at harvest e can be determined The results of experimental treatments or the influence of genetics can be interpreted in terms of their effect on e and f The radiation incident on a canopy can be absorbed by the canopy transmitted through the canopy and absorbed or reflected at the soil surface or reflected by the canopy In principle only PAR absorbed by the canopy is useful in producing dry matter so f should be the fractional absorption If t is the fraction of incident radiation transmitted by the canopy r is the fraction of incident radiation reflected to a sensor above the canopy and r is the reflectance of the soil surface then the absorbed radiation fraction is calculated from f 1 t r tr 1 The last two terms are often ignored and fractional interception is approximated by f 1 t 2 The error resulting from this approximation is usually small when t r and r are measured in the PAR waveband because most of the PAR is absorbed The error becomes much more significant when measurements of total solar radiation are used because of large scattering coefficients of leaves for near infrared radiation 32 As a first order estimate of error assume that r 1 t r tr 3 where r is the reflectance of the vegetation The first equation becomes f 1 t 1 4r 4 The error resul
19. can be assumed and x be set equal to 1 For a zenith angle of 30 degrees this gives K 0 577 Substituting these values into equation 4 results in L 5 2 40 Final Comments While leaf area estimates can be made under either clear or overcast skies the clear sky estimate requires that you guess a value for x The overcast sky measurement may therefore be more reliable Spatial variability is a big problem in canopies and measurements at several locations should always be used to determine LAI Spectral and Cosine Response The Ceptometer is limited in ideal PAR response because of its deficiencies in the blue spectrum These deficiencies are insignificant when working with normal plant canopy environments and solar radiation However the Ceptometer should not be used as an absolute PAR sensor when the environment being studied has a significant blue emphasis in its radiation composition Examples of this blue component would include the measurement of blue skies while the sensors are shaded from direct beam radiation or artificial lighting that contains a strong blue component like metal halide The two graphs on the following pages show the responses of the Ceptometer sensors Spectral response of the photodiodes lies almost entirely within the PAR waveband The response approximates an ideal quantum response but drops to zero at about 680 nm rather than 700 nm and is somewhat low in the blue region If the radiation is entir
20. ce Picea sitchensis Bong Carr V Radiation penetration theory and a test case J Appl Ecol 12 839 878 Norman J M and Welles J M 1983 Radiative transfer in an array of canopies Agron J 75 481 488 75 Norman J M Miller E E and Tanner C B 1971 Light intensity and sunfleck size distributions in plant canopies Agron J 63 743 748 Norman J M Perry S G Fraser A B and Mach W 1979 Remote sensing of canopy structure Proc 14th Conf Agric For Meteor p 184 185 Am Meteor Soc Boston Philip J R 1965 The distribution of foliage density with foliage angle estimated from inclined point quadrat observations Aust J Bot 13 357 366 Pierce L L and Running S W 1988 Rapid estimation of coniferous forest leaf area index using a portable integration radiometer Ecology Ross J 1981 The Radiation Regime and Architecture of Plant Stands W Junk The Hague 391 p Shell G S G and Lang A R G 1975 Description of leaf orientation and heliotropic response of sunflower using directional statistics Agric Meteor 15 33 48 Vanderbilt V C 1985 Measuring plant canopy structure Remote Sensing Environ 18 281 294 Vanderbilt V C Bauer M E and Silva L F 1979 Prediction of solar irradiance distribution in a wheat canopy using a laser technique Agric Meteor 20 147 160 Warren Wilson J 1959 Analysis of the spatial distribution of fo
21. ction eight is passed the reading will be lost and must be made again Prepare the computer or other external device to receive the data Press the B key to send the individual sensor readings to the prepared file Refer to chapter nine for more information about interfacing with a computer POO IS Figure 15 Sending Memory to an External Device 2 64 26 5 Measurement Tips Q When measuring with the Ceptometer the instrument should be kept fairly level This is less critical below the canopy however it should be followed as closely as possible as some of the radiation below the canopy may be direct beam Q Since light below a canopy is extremely variable several samples are necessary for reliable averages Q When using sunfleck inversion methods the instrument should be left in the same position If the instrument is moved errors may result in data collection Q In canopies with clumped or row structures it is important to take samples that show no favoring of within row or between row areas In these cases it is best to sample with the probe of the Ceptometer placed perpendicular to the row If row spacing is different from the probe length the probe can be placed diagonally to get a representative sample Q In tall canopies and canopies having small leaves overlapping penumbra make measurements of sunfleck fraction unreliable Inversion to obtain leaf area index must therefore be performed using
22. e BASIC program outlined in this chapter The Ceptometer s communication protocol is Q Baud Rate 1200 Parity even m Q Data Bits 7 Q Stop Bits 1 Ceptometer data is output as comma separated values The output signal is as follows 5V ov Start Do Dy a D7 Parity Stop LSB 56 Connections for the 9 pin connector are IN e BASIC Program 5 10 20 40 45 50 60 70 80 85 INPUT NAME OF DATE FILE DF OPEN COM1 1200 CS DS CD AS 1 OPEN DF FOR OUTPUT AS 2 T INPUT 1 1 ON ERROR GOTO 85 IF T CHR 127 THEN T CHR 63 PRINT T PRINT 2 T GOTO 40 RESUME 57 Notes on the BASIC Program Line 1 Prompts the program to go to line 85 if an error occurs during the execution of the program Line 5 Displays NAME OF DATA FILE and assigns it to the variable DF Line 10 Opens communication device 1as file number 1 The baud rate is 1200 parity is set to the default value the number of data bits is set to the default value the stop bit is set to the default value the request to send is suppressed and CS clear to send DS data set ready and CD carrier detect are set so as not to allow them to time out Line 20 Opens DF and creates a file number 2 to receive data Line 40 Inputs one character at a time from the file numbered 1 to the file or variable t Line 50 Checks the contents of t If it is equal to 127 it is changed to
23. e battery clips is alsoa possibility if the batteries are shifted Q Can the data gather with the Ceptometer be saved to an external device O Yes Data collected and stored in the Ceptometer memory can be downloaded to a disk file using a BASIC program or the SunView software included with the instrument Please refer to page 63 of this manual for instructions on downloading the Ceptometer Q Can send individual PAR readings to an external device O Yes However this option will not work if any data is stored in memory Please refer to page 26 of this manual for instructions on this option 66 Can use the automatic threshold setting in the single sensor mode No The automatic threshold setting cannot be used in the single sensor mode The threshold must be manually set before using this option Please refer to page 25 of this manual for more details PLL does not appear on the display after have calibrated What should do First try your calibration technique again Remember to hold the keys down simultaneously to avoid any errors Refer to page 10 of this manual for detailed instructions on calibration If this does not work contact Decagon for technical assistance accidentally recalibrated my instrument in the ELE mode instead of the H mode What should do Recalibrate the Ceptometer making sure to calibrate in the H mode Refer to page 65 of this manual for instructions on recalibra
24. ed in this manual It is necessary for Decagon to have your current mailing address and telephone number in case we need to send updated product information to you Customer Service Information If you ever have questions concerning the Ceptometer or need assistance regarding your instrument please call our toll free customer service number between 8 a m and 5 p m Monday through Friday Pacific Time 1 800 755 2751 Seller s Liability Seller warrants new equipment of its own manufacture against defective workmanship and materials for a period of one year from date of receipt of equipment the results of ordinary wear and tear neglect misuse accident and excessive deterioration due to corrosion from any cause not to be considered a defect but Seller s liability for defective parts shall in no event exceed the furnishing of replacement parts f o b the factory where originally manufactured Material and equipment covered hereby which is not manufactured by Seller shall not be liable to Buyer for loss damage or injuries to persons including death or to property or things whatsoever kind including but not without limitation loss of anticipated profits occasioned by or arising out of the installation operation use misuse nonuse repair or replacement of said material and equipment or out of the use of any method or process for which the same may be employed The use of this equipment constitutes Buyer s acceptance of t
25. either be calculated from time of day or measured directly This section suggests methods for finding the zenith angle of the sun Direct Measurement The zenith angle is the angle the sun makes with respect to a line vertical to the earth s surface For zenith angle the point directly overhead would be defined as 0 and the horizon defined as 90 For elevation angle the point directly overhead would be defined as 90 and the horizon 0 The simplest method for measuring zenith angle is to construct a device as shown in Figure 1 from two pieces of wood placed at right angles to each other The top edge of the vertical piece should be 10 centimeters above the top surface of the horizontal piece and the horizontal piece should be 20 to 30 centimeters long Mount a bubble level and a ruler on the horizontal piece To measure zenith angle level the horizontal piece with the vertical piece perpendicular to the sun azimuth and measure the length of the shadow on the horizontal ruler The zenith angle is calculated from 6 arctan x 10 where x is the shadow length cm and 10 is the height of the vertical piece 11 Figure 1 Board Scale zenith angle device Another simple method is to attach a protractor to a small board mount a bubble level on the board to the level of the protractor and attach the end of a soda straw with a pin to the center of the protractor so that the straw can pivot across the face of the protractor
26. ely blue skylight the GaAsP photodiode reads about 20 lower than the PAR sensor but under normal sun and light cloudy skies or in crop canopies errors due to limited spectral response are negligible 41 009 wu yHusjaneny oos 00r asuodsay aalejay 42 06 OL s 16 p ajbuy yyueZz 09 os Ov oe oz OL 02 70 S20 08 0 S80 06 0 S60 00 oney esuodsey 43 7 Sunflecks Sunflecks refer to the bright areas under the canopy where direct beam solar radiation penetrates without dissipation by the canopy The size shape duration and peak photon flux of a sunfleck depends on the height and precise arrangement of vegetation within the canopy as well as the position of the sun in the sky Fraction measurements of a ground covered by sunflecks can be used with inverse methods to determine important characteristics of canopy structure The sun approximates a point source of radiation which can be used on clear days to probe the canopy and obtain information on canopy cover and canopy geometry The information needed to determine these canopy properties is the fraction of the area under the canopy which is covered by sunflecks or the gap fraction of the canopy For canopy cover only measurements at high sun angles are needed since cover is the fraction of the ground covered by a vertical projection of the canopy onto it Sunfleck measurements at several sun angles are needed to
27. f f in equation 1 can vary with sun elevation since t depends on elevation angle Fractional interception should be an integrated value averaged over the growing season While the reading obtained at a particular time is closely related to this average value readings need to be taken over a full day to find the true integrated value of t Two measurements are needed T at various times of the day and S integrated over these same times We recommend that the data for S be obtained by recording the output of another Ceptometer or a SunLink PAR Probe Both instruments have identical spectral and cosine responses A PAR point sensor may also be used or the data may be obtained by calculating PAR from incident solar radiation To do so multiply the total short wave flux density W m by 2 1 to convert to umol m s This calculation can be verified by comparing these estimates to spot measurements with the Ceptometer placed above the plant canopy To obtain data for T support the Ceptometer in the canopy select function three and press the A and B keys simultaneously Readings will be taken automatically every minute and then averaged and stored in memory every 30 minutes Press either the A key or the B key to stop logging Readings can be reviewed by pressing the A and B keys to move back and forth through the memory 36 Survey Sampling of Average Line PAR Select function five The value appearing to the right of the displa
28. gime in sunflower Jerusalem artichoke and corn and soybean canopies using actual stand structure data Agric Meteor 12 229 247 Levy E B and Madden E A 1933 The point method of pasture analysis New Zeal J Agric 46 267 279 Mann J E Curry G L and Sharpe P H 1979 Light interception by isolated plants Agric Meteor 20 205 214 74 Mann J E Curry G L DeMichele D W and Baker D N 1980 Light penetration in row crop with random plant spacing Agron J 72 131 142 Marquardt D W 1963 An algorithm for least squares estimation of nonlinear parameters J Soc Ind Appl Math 11 431 444 Menke W 1984 Geophysical Data Analysis Discrete Inverse Theory Academic Press New York 260 p Monsi M and Saeki T 1953 Uber den Lichtfaktor in den Pflanzengesellschaften und seine Bedeutung fur die Stoffproduktion Jap J Bot 14 22 52 Monteith J L 1965 Light distribution and photosynthesis in field crops Ann Bot 29 17 37 Monteith J L 1973 Principles of Environmental Physics Edward Arnold London 241 p Nilson J M 1971 A theoretical analysis of frequency of gaps in plant stands Agric Meteor 8 25 38 Norman J M 1979 Modeling the complete crop canopy in Modification of the Aerial Environment of Plants p 249 277 B J Bardield and J F Gerber eds ASAE St Joseph Michigan Norman J M and Jarvis P G 1975 Photosynthesis in Sitka spru
29. gs stored in the instrument s memory To find r invert the Ceptometer at a height of 1 2 meters above the crop canopy Leveling is not critical for this measurement since the radiation reaching the sensor is not directional Clear the display by pressing the A key Press the A key a second time to take a reading The display shows the R value Multiple readings are not necessary since R is not usually variable Press the B key twice to store the reading in memory Calculate r from equation 6 using the previously recorded S value To find r invert the Ceptometer over the soil below the canopy and take measurements at several locations Average and store these measurements as before This reading is the value U Calculate r from equation 7 using U and T A value in the range of 0 1 to 0 2 should be obtained but it is possible that the light level below the canopy will be so low that U will not be accurately measured If a value outside of the expected range is obtained there will be negligible error in f by assuming r 0 15 As mentioned before evaluation of intercepted radiation normally involves the measurement of t Only measurements below the canopy have been discussed Obviously measurements throughout the canopy are possible Profiles of interception with height can be useful in determining at what location most of the photosynthesis is occurring in the canopy 35 Unattended Recording of Transmitted PAR The value o
30. he 4 A 1 0 47f 39 Applications and Examples PAR was measured above a barley canopy of 391umol m s on an overcast day The average of several measurements below the canopy was 62 umol m21 The transmission t is therefore 62 391 0 159 Since the day was overcast f 0 If a 0 9 then A 0 86 From equation 4 L n 0 159 0 86 2 14 Because the measurement was made under overcast skies it was not necessary to have canopy structure information or solar elevation angle Measurements on overcast days are the simplest for LAI determination and do not require assumptions about canopy structure The next example uses measurements on a sunny day 1614 umol m s was measured above a pea canopy and 80 umol m s under the canopy The fraction of PAR transmitted by the canopy was therefore t 80 1614 0 05 The solar zenith angle was 30 The fraction of diffuse radiation was measured by switching the Ceptometer to single sensor mode and taking a reading with the leveled probe in full sun and another reading with the sensor at the tip of the probe shaded by a 10 centimeter diameter shade at a distance of about 1 meter The ratio of the shaded to unshaded readings was 0 119 which is the diffuse PAR fraction The beam fraction was f 1 fj 0 881 The A value for equation 4 is again 0 86 x for the canopy is unknown but unless leaves have obvious horizontal or vertical tendencies a spherical distribution
31. he terms set forth in this warranty There are no understandings representations or warranties of any kind express implied statutory or otherwise including but without limitation the implied warranties of merchantability and fitness for a particular purpose not expressly set forth herein 2 About the Ceptometer The Sunfleck PAR Ceptometer is a battery operated PAR sensor used for data collection in plant and forestry canopy research Model SF 80 has 80 independent sensors located in a weather proof enclosure at one centimeter intervals along a sensor probe Model SF 40 has 40 sensors located in the same manner The datalogger is capable of either hand held push button operation or stand alone measurements of light in plant canopies The sensors measure PAR Photosynthetically Active Radiation in the 400 to 700 nanometer waveband Units of measurement for the instrument are umol m 251 The Ceptometer has two main modes of operation In the first the average photon flux density of PAR on the probe is measured In the second the fraction of the probe in sunflecks is measured and reported Other modes allow continuous display of readings on a single sensor and stand alone data collection in both modes The datalogger averages and stores measurements and dumps them to a computer when field measurements are complete The biggest problem with making reliable measurements of light in plant canopies is the extreme light level variati
32. instrument reads 100 0 in full sun but it also reads 100 0 in full shade since it determines the percentages by comparing the highest reading on the probe It is only when there is variation along the probe that it can detect sunflecks Sampling for Sunfleck Fraction Sampling for sunfleck fraction is similar to sampling PAR under the canopy Select function two Place the probe under the canopy and press the A key Many samples are needed because of the large spatial variation in sunfleck fraction Leveling is not important for sunfleck measurements and it is sometimes desirable to tip the probe in the direction of the sun when sun angles are low so that a larger reading is obtained The sunfleck fraction is shown on the right of the display and the number of samples taken is shown on the left After 10 to 20 samples are taken press the B key to average and display the reading 46 The number of samples needed for a given precision can be estimated using equation 8 on page 34 To store the reading press the B key again In the sampling modes of functions one through five both PAR and sunfleck fraction are read averaged and stored but only one reading PAR in function one and three and sunfleck fraction in function two and four is displayed Unattended Recording of Sunfleck Fraction To record sunfleck fraction unattended select function four Press the A and B keys simultaneously to begin readings Readings will be taken eve
33. iton Calibrating in the ELE mode will not damage the instrument but will put it in the single sensor mode meaning that only one sensor at the probe tip will respond to light Future readings in this mode will not be accurate The display is reading LO What does this mean A LO reading indicates that the batteries are running low Press any key to clear the display The instrument may be used as normal however the batteries should be replaced as soon as possible 67 Q O Pressing keys on the keypad does not activate the display What should do Reset the batteries in the battery pack Refer to page 64 of this manual for instructions If this does not solve the problem the instrument will need to be sent for repair Refer to chapter 11 for return and repair instructions The following is a list of problems that may indicate other complications with the Ceptometer If any of these problems should occur the instrument may need to be returned for repair Please contact Decagon first for technical assistance O The instrument powers up but seems to stick when trying to scroll through functions The instrument powers up but the display fades a and flickers After calibration the instrument reads low light readings but will not read above low light readings 68 Appendix A Additional Information The following is a list of references that offer more detail concerning plant canopy characteristics
34. lay corresponding indicates the selected function Note Regardless of the mode both Sunfleck and PAR readings are stored in final memory The functions only alter the displayed readings Figure 4 Function Indicator Arrow 18 Function 1 PAR Measurement Press the function key until the display arrow is pointing to number one In this mode the A key is the sample key Each time this key is pressed the Ceptometer will take a new PAR reading The previous readings will be saved in a short term memory until an average is taken The sample number is shown on the left side of the display and the PAR measurement is shown on the right 8 7 6 5 4 3 2 1 A Figure 5 Sample Number and PAR Measurement When the B key is pressed all the accumulated readings will be averaged and the average PAR will be displayed 8 7 6 5 4 3 2 hoj Figure 6 Average PAR 19 Pressing the B key a second time will store the average reading in memory Pressing the A key clears all readings and resets the sample counter If the A key is pressed before the average reading is stored in memory the average will be erased 2 1 8 7 6 5 4 3 Figure 7 Memory Indicator Indicates 11 readings stored in memory Function 2 Sunfleck Measurement Function two is similar to function one but the number appearing on the right side of the display is the sunfleck fraction Sunfleck fraction is given as a
35. ld Function seven is used to set the threshold and determine whether one or all of the sensors will be sampled For applications of the threshold and line vs single sensor operation refer to chapter six beginning on page 31 of this manual Threshold refers to the lowest PAR value in umoles that will be sampled Any number below the chosen value will not be counted in the measurement Pressing the A key sets the threshold manually it will be set equal to half of the highest reading of any sensor on the probe The letter H is shown on the display to indicate a threshold function along with the threshold setting in umol ms H 28 Figure 12 Threshold Indicator and Setting 8 7 A The B key is used for both automatic threshold and single sensor setting In the automatic threshold mode the Ceptometer will find the highest light reading on the probe and set the threshold at half of that value lf there is a difference in light along the probe the sunfleck reading will be displayed as a percentage less than 100 if the lower value falls below the threshold If the light on the probe is even the reading will be 100 percent regardless of the strength of the light and assuming the reading is greater than the set threshold 24 In the single sensor mode only one sensor at the tip of the probe will respond to light This allows the instrument to be used as a point sensor In this mode the readings in functions one through five wi
36. liage by two dimensional point quadrats New Phytol 58 92 101 76 Warren Wilson J 1963 Estimation of foliage denseness and foliage angle by inclined point quadrats Aust J Bot 11 95 105 Warren Wilson J 1965 Stand structure and light penetration Analysis by point quadrats J Appl Ecol 2 383 390 Warren Wilson J 1967 Stand structure and light penetration Ill Sunlit foliage area J Appl Ecol 4 159 165 77
37. ll be single sensor readings The sunfleck reading will be either 1 or 0 indicating that the reading is above or below the manually set threshold Pressing the B key shifts between automatic threshold and single sensor settings The automatic threshold is indicated by an H followed by two dashes on the display When the single sensor setting is chosen the display will read ELE NOTE The automatic threshold cannot be used in the single sensor mode The threshold must be manually set before using this option 5 4 3 2 1 Figure 13 Automatic Threshold Indicator 8 7 6 A 8 7 6 5 ELE Figure 14 Single Sensor Indicator 25 Function 8 Send Erase Memory and Individual Sensor Dump Function eight is used to send stored readings to an external device or to erase the memory Pressing the B key sends the data via an RS 232 interface cable to the external device The sample numbers on the display will continually update until the transaction is complete This transaction can be interrupted at any time by pressing the A key To erase the memory hold down the A key and press the B key If the memory is empty individual sensor PAR readings may be sent to an external device This option will not work if any data is stored in the memory To send these readings select function five Choose desired values by pressing the A key to hold them Return to function eight This move must be direct if fun
38. measurements of transmitted PAR 27 Discussion of the Effects of Non Random Distribution of Canopy Elements on LAI Measurements in situ There has been much discussion concerning inversion methods to obtain leaf area index Since all inversion methods rely on the assumption that elements of a canopy are randomly dispersed in space errors in the measurement of leaf area index may result from a non random arrangement of canopy elements This is especially true for canopies with heliotropic leaves conifer forests row crops before canopy closure or for canopies which never close as in desert vegetation The degree of error in measurement is a result of the canopy s deviation from this random dispersion assumption In past studies LAI has been used to relate both actual biomass area and the interception of PAR by a plant canopy Chen et al 1991 have proposed another view regarding LAI in which L the actual biomass area was related to a new term L which represents the actual orientation of the canopy elements relating to the interception of PAR at a given angle In situ measurements of LAI using hemispherical photography were equated with this new term effective plant area index L which was defined as L QL where L represents the actual leaf area index equal to a harvested leaf area measurement and refers to a clumping index resluting from the non random distribution of canopy elements 28 When a canopy di
39. nce the light below the canopy is extremely variable several samples at different locations will be necessary for a reliable reading The number of necessary samples can be determined by taking for example 10 readings and computing the coefficient of variation from CV Z x x n 1 2 S 8 where n is the number of samples taken The error in any measurement of t will be CV divided by the square root of the number of samples Usually a number around 10 should suffice Press the A key to take a reading Each of the readings will appear on the left of the display In canopies with a clumped or row structure it is important that samples show no favor of between row or within row areas It is best to sample with the probe perpendicular to the row If the row spacing is different from the probe length the probe can be placed diagonally to get a representative sample The readings taken can be averaged by pressing the B key This reading is the T value Pressing the B key a second time stores the reading in memory The fractional transmission for the canopy t can now be calculated from equation 5 34 This calculation would normally be generated by a computer program after the data from all of the samples have been sent to the computer However it is important to set up some kind of sampling scheme beforehand or keep detailed notes of sampled areas of the field plot or treatment so that they can be compared to the readin
40. om transmittances of the sun s beam Agric For Meteorol accepted Lang A R G and McMurtrie R E 1991 Total leaf areas of single trees of Eucalyptus grandis estimated from transmittance of the sun s beam Agric For Meteorol accepted Lang A R G and Xiang Yueqin 1986 Estimation of leaf area index from transmission of direct sunlight in discontinuous canopies Agric For Meteorol 37 229 43 Lang A R G Xiang Yueqin and Norman J M 1985 Crop structure and the penetration of direct sunlight Agric For Meteorol 35 83 101 Lemur R 1973 A method for simulating the direct solar radiation regime in sunflower Jerusalem artichoke corn and soybean canopies using actual stand structure data Agric Meteorol 12 229 47 70 Norman J M 1979 Modeling the complete crop canopy in Modification of the Aerial Environment of Crops eds B J Barfield and J Gerber American Society of Agricultural Engineers St Joseph MI pp 249 77 Norman J M and Campbell G S 1989 Canopy structure Plant physiological ecology Field methods and instrumentation R E Pearcy J R Ehleringer H A Mooney and P W Rundel eds London Chapman and Hall pp 301 325 Norman J M and Jarvis P G 1974 Photosynthesis in Sitka Spruce Picea sitchensis Bong Carr Ill Measurements of canopy structure and interception of radiation J Appl Ecol 11 375 98 Norman J M Miller E E and Tanner C B 1971
41. on of the measurements In the PAR waveband irradiances can vary from full sun to almost zero over the space of a few centimeters and a reliable measurement of average PAR requires many samples at many locations under the plant canopy The Ceptometer provides an easy way of obtaining the necessary number of samples for light measurement The instrument s 80 sensor probe is inserted into the canopy and a microprocessor scans the sensors In the sample mode the Ceptometer displays a reading an average of the readings of all sensors each time the sample button is pushed and the user discerns when to average the accumulated readings and store them in memory In the auto mode the unattended Ceptometer takes readings every minute then averages and stores accumulated readings every 30 minutes The Sunfleck application of the Ceptometer is an added bonus Sunflecks are the bright areas under the canopy where direct beam solar radiation penetrates without attenuation by the canopy The fraction of the ground covered by sunflecks is a useful measurement for determining canopy cover Sunfleck fraction measurements can also be used with inverse methods to determine important characteristics of canopy structure These will be discussed later in the manual Sampling averaging and auto mode operation features for the sunfleck fraction mode are similar to those in the PAR mode The Ceptometer can be operated in environments with temperatures f
42. or determining the leaf area index of young crops Photosynthitica 8 299 301 Caldwell M M Harris G W and Dzurec R S 1983 A fiber optic point quadrat system for improved accuracy in vegetation sampling Oecologic 59 417 418 Campbell G S 1986 Extinction coefficients for radiation in plant canopies using an ellipsoidal inclination angle distribution Agric For Meteor 36 317 321 Charles Edwards D A and Thormley J H M 1973 Light interception by an isolated plant a simple model Ann Bot 37 919 928 73 Chazdon R L and Pearcy R W 1991 The importance of sunflecks for forest understory plants Bio Science 41 760 766 Fuchs M and Stanhill G 1980 Row structure and foliage geometry as determinants of the interception of light rays in a sorghum row canopy Plant Cell and Environment 3 175 182 Lang A R G 1973 Leaf orientation of a cotton plant Agric Meteor 11 37 51 Lang A R G and Shell G S G 1976 Sunlit areas and angular distribution of sunflower leaves for plants in single and multiple rows Agric Meteor 16 5 15 Lang A R G Xiang Yuegin and Norman J M 1985 Crop structure and the penetration of direct sunlight Agric For Meteor 35 83 101 Lang A R G 1987 Simplified estimate of leaf area index from transmittance of the sun s beam Agric For Meteor 41 179 186 Lemeur R 1973 A method for stimulating the direct solar radiation re
43. ples PAR and sunflecks and displays readings Function 6 Sets the Sunfleck to the correct time The A key controls the hours and the B key controls the minutes Function 7 Sets single element mode for point sensor use and sets the sunfleck threshold Downloads and erases memory 16 The Ceptometer is controlled by the three keys on the cover located just below the display The key on the left is the function key and is used to switch functions Keys A and B located in the middle and right of the cover respectively affect the Ceptometer s mode of operation within a function All of the Ceptometer s modes are mapped out on the keyboard When the batteries are installed the Ceptometer s microprocessor is always on to update the clock check the keyboard and maintain the memory but the display closes after 7 minutes without keyboard operation Any button may be pressed to activate the display Q 5 8 7 6 4 3 2 1 AA 1 PAR sample average 2 Sunfleck sample average 3 Auto PAR read read 4 Auto Sunfleck read read 5 Continuous hold store 6 Time set hours minutes 7 Threshold or set Single Sensor set 8 Erase or Send send SUNFLECK CEPTOMETER Pullman WA Made in USA erase Figure 3 Cover of the Sunfleck Ceptometer 17 Any of the eight functions of the Ceptometer may be selected by pressing the function key A small arrow above the disp
44. probe and then displays the reading as a percentage Two types of threshold settings are possible When a sample is taken by the instrument in the automatic threshold setting the microprocessor scans the set of readings finds the highest one and sets the threshold at half of this value If the highest light value on the probe changes as different samples are taken the threshold will also change As long as the sunflecks are large enough for at least one sensor to be in full sun the automatic threshold setting is the simplest and most reliable setting to use It also measures the correct size of sunflecks with penumbra as long as they do not overlap 45 The manually set threshold must be used for dense canopies when there is a possibility that not even one sensor will be in full sun during a scan Select function seven and press the A key The probe is scanned and the threshold is set at half of the value of the highest sensor reading The threshold value is displayed in umol ms If a different threshold level is desired select the location of the probe when the A key is pressed The manually set threshold will remain until it is reset The user should experiment with the manual threshold mode before taking serious data as it may take some time to learn to use this setting effectively Measurements of low sunfleck fraction which cause the Ceptometer to register a high value are an indication that this mode may need to be used The
45. ps will be visible as the cover is lifted Place the batteries in the battery clips making sure to orient them correctly as indicated by the diagrams on the battery clip Replace the cover and the four screws Note When shipping the Ceptometer always remove the batteries to prevent damage to the battery clips When using the Ceptometer in the field the user may wish to download data to a portable personal computer rough terrain may cause the batteries to shift and data may be lost Calibration Each time the batteries are replaced or installed for the first time the Ceptometer s sensors must be recalibrated Calibration must be performed in bright even sunlight on a cloudless day Shift to function seven by pressing the function key until the display pointer is stationed at function7 Hold down buttons A and B simultaneously and press the function key The letter PLL will appear on the left side of the display This indicates that the probe has been correctly calibrated If these letters do not appear refer to the troubleshooting section of this manual Note Be sure to recalibrate the Ceptometer in the H mode of function seven and not the ELE mode If the ELE mode is used the instrument will not function properly and will need to be recalibrated 10 Finding the Zenith Angle of the Sun Zenith angle of the sun is required for inversion of canopy light transmission data to determine leaf area index Zenith angle can
46. rom 30 to 50 C and relative humidities up to 100 The instrument comes with a standard RS 232 interface cable for easy connection to a user provided computer The Sunfleck provides fast reading and averaging data and stores over 1 000 data sets Each stored data set includes time PAR and sunfleck percentage regardless of the operating mode Biomass production in plant communities is directly related to PAR interception The Ceptometer provides the user with the measurements needed to interpret field experiments Leaf area index and canopy cover can be estimated from measurements of intercepted PAR The Ceptometer may also aid the user in understanding the importance of sunflecks in the photosynthesis and growth of forest understory plants and crops by recording their occurrance Other Ceptometer applications include water stress studies crop and canopy modeling plant disease and environmental research and fertilizer and pesticide efficacy studies 3 Getting Started There are a few things to consider before beginning measurements with the Ceptometer These consist of installing the batteries calibrating the instrument and finding the zenith angle of the sun Installing the Batteries The Ceptometer s batteries are shipped separate of the instrument and must be installed before operation To install the batteries remove the four screws in the corners of the instrument s cover and lift the cover carefully The battery cli
47. rom equation 1 In t In Tt K K p 5 so 1 O t O5 P 6 Calculate p from equation 2 p x tan x tan 2 7 If 0 p x x tan If x is not Known assume x 1 Example From the previous measurements find the canopy cover Take 35 t 0 21 and x 0 9 p 0 92 0 92 tan 35 0 79 1 0 0 21979 0 29 Cover 1 t 0 1 0 29 0 71 53 Intercepted radiation averaged over an entire day can be estimated from f 1 8 where ta is the transmission coefficient averaged over all elevation angles ta can be calculated from IN ta uL 9 where u and v are functions of x which can be calculated from u 1 0 33 exp 0 57x 10 v 1 0 3 exp 0 97x 11 The following table shows typical values of u and v Table 2 Values for u and v for equation 9 54 Combining equations 1 and 9 gives where q uL K Example Calculate a value for fractional daily interception for the crop in the previous examples u 1 0 33exp 0 57 x0 9 0 80 v 1 0 3exp 0 97 x0 9 0 87 0 9 tan 35 1 14 K z 0 59 0 9 1 774 0 9 1 182 1 94 0 13 0 80 x 2 64 213 0 59 t4 0 21 0 15 f 1 1 1 0 12 0 85 55 9 Interfacing with a Computer Data collected and stored in the Ceptometer s memory can be downloaded to a disk file using the SunView software included with your instrument or th
48. ry minute automatically and stored in memory every 30 minutes The display will show time on the left and the sunfleck fraction on the right To stop data collection press either the A or B key The readings can be reviewed by pressing the A and B keys to move backward and forward through the memory Survey Sampling of Sunfleck Fraction Select function five A continuous sunfleck fraction is shown on the left of the display Press the A key to hold the reading and the B key to store the reading in memory This mode is often used to check a canopy s variability or to determine which threshold mode to use 47 8 The Theory of Sunflecks and Canopy Structure If the elements of a canopy are randomly distributed in space then the probability of a ray of light or other probe penetrating the canopy without interception can be calculated from theory The probability of penetration without interception is equal to the sunfleck fraction which is the beam transmission coefficient t for the canopy The parameter is the zenith angle of the probe or solar beam t usually varies with zenith angle The transmission coefficient for a canopy of randomly placed elements is exp KL 1 where L is the leaf area index of the canopy area of leaves per unit area of soil surface and K is the extinction coefficient for the canopy which depends on the leaf angle distribution of canopy elements and the zenith angle of the probe t is
49. s model was used to test and fit two simpler models which are more easily inverted Equation 1 is a simple light scattering model suggested by Goudriaan 1988 It gives the fraction of transmitted PAR t ratio of PAR measured below the canopy to PAR above the canopy below a canopy of LAI L as TEF exp VaKL 1 f exp 0 87VaL 1 Here f is the fraction of incident PAR which is beam a is the leaf absorptivity in the PAR band typically around 0 9 and K is the extinction coefficient for the canopy The extinction coefficient can be modeled in various ways Assuming an ellipsoidal angle distribution function Campbell 1986 then x tan o Xx 1 744 x 1 182 2 where 9 is the zenith angle of the sun and x is a leaf angle distribution parameter When x 1 the angle distribution is spherical and K simplifies to i 2cos0 John Norman suggested a different equation for predicting scattered and transmitted PAR A 1 0 47f L 1 ee ee 3 ae 3 where A 0 283 0 785a 0 159a T exp 38 Both equations predict canopy PAR within a few percent of values from the complete Norman Jarvis model Equation 1 is slightly more accurate but equation 3 is much easier to invert to obtain L The difference in accuracy of the two equations is smaller than other incertainties in the method so equation 3 will be used to determine LAI Inverting equation 3 gives t z 1 f 1 inz pa
50. splays random dispersion Q is unity however when a canopy is clumped is not unity In this equation L refers to the actual canopy element orientation For example in a randomly dispersed canopy L would be equal to L figure 1 in an underdispersed canopy clumping L would be greater than L figure 2 and conversely in an overdispersed canopy L would be less than L figure 3 Refer to page 30 for illustrations The purpose of this discussion is to expose the user to possible errors that may occur when making LAI measurements in situ When setting up an experiment the user should carefully examine the desired end result If one is interested in the interception of PAR within a canopy the result of the inversions given in this manual will be correct in reaching L The leaf or plant area index that is calculated through inversion will be an accurate portrayal of the canopy s structure and orientation with respect to light interception In this instance while clumping effects within the canopy remain present these effects do not cause error with regard to light interception and the effective area index for that situation Alternately if the user is interested in obtaining the actual biomass represented by L in this discussion all measurements should be performed so that the effects of clumping are minimized This can be accomplished by modeling the clumping factors of the canopy or by measuring only at certain times
51. time zones run approximately 7 5 to 7 5 degrees either side of a standard meridian but this varies depending on political boundaries so check an atlas to both standard meridian and longitude 13 The Equation of Time is a 15 to 20 minute correction which depends on the day of the year It can be calculated from ET 104 7sino 596 2sin26 4 3sin30 12 7sin4o 4 12 7sin40 429 3coso 2 0cos20 19 3c0S36 3600 where f 279 575 0 986 J p 180 Some values for ET are given in Table 1 Example Calculation Find the zenith angle for Pullman WA at 10 45 PDT on June 30 Convert the time of observation to standard time by subtracting one hour and convert minutes to decimal hours so t 9 75 hours June 30 is J 181 Pullman latitude is 46 77 degrees or 0 816 radians and longitude is 117 2 degrees The standard meridian is 120 degrees The local meridian is 2 8 degrees east of the standard meridian so LC 2 8 15 0 19 hours From equation 4 or Table 1 ET 0 06 hours Equation 3 then gives to 12 0 19 0 06 11 87 Declination from Table 1 or equation 3 is 0 4 radians Substituting these values into equation gives 6 arccos sin 0 816 sin 0 4 cos 0 816 cos 0 4 cos 0 2618 9 75 11 87 0 61 radians or 34 9 degrees 14 Table 1 Solar Declination and Equation of Time Date DOY D rad ET hour Jan 1 1 0 403 0 057 Jan 10 10 0 386 0 123 Jan 20 20 0 355 0 182 Jan 30 30 0 312 0 2
52. ting from using the second equation is approximately equal to r which is typically less than 0 05 in the PAR waveband Since the Ceptometer s sensors are sensitive only to radiation in the PAR waveband equation 2 will generally be accurate for making measurements of intercepted radiation However measurement of the other terms needed for equation 1 is simple and will also be explained Sampling for Fractional Interception Select function one For specific instructions concerning function one refer to page 18 of this manual The measurements needed for fractional interception are those from which t r and r are calculated If S is the PAR reading from an upward facing Ceptometer above the plant canopy R is the reflected PAR above the canopy inverted Ceptometer above the crop T is the upward facing Ceptometer below the plant canopy and U is the reflected PAR from the soil surface then t r and r can be calculated from t T S 5 r R S 6 r U T 7 33 Assume only t needs to be known Measure S above the crop canopy Level the Ceptometer above the canopy using the bubble level and then press the A key The reading appearing on the right of the display is S This value can be stored in memory by pressing the B key twice Press the A key again to clear the display Measure T by placing the Ceptometer below the plant canopy being careful to place it below all of the leaves Try to keep the instrument level Si
53. tinue its normal function the batteries should be replaced as soon as possible To replace the batteries remove the four screws in the cover of the Ceptometer and lift the cover carefully The batteries will be exposed and can be replaced Be sure to orient the batteries correctly The battery clips indicate the direction in which the batteries should be placed The switch to the side of the batteries controls power to the Ceptometer The switch will be closed when the cover is on the instrument and power will be on to maintain the memory and update the clock When the cover is removed the switch opens and the instrument is reset Data will be lost whenever the instrument is reset Only one sensor of the Ceptometer has an absolute calibration the others are calibrated against that sensor by the microprocessor and stored in memory Memory is usually lost when the batteries are replaced and the sensors must be recalibrated 63 Recalibrating the Sensors The sensors should only need recalibration when the batteries are replaced Calibration must be performed in bright even sunlight on a cloudless day Select function seven The display should read H Hold down the A and B keys simultaneously and press the function key The letters PLL will appear on the left of the display indicating that the sensors have been recalibrated Note Be sure to recalibrate the Ceptometer in the H mode of function seven and not the ELE mode
54. y is the average PAR over the length of the probe The value will be updated continuously until the A key is pressed to hold the present reading This reading may be stored in memory by pressing the B key or the user may return to the continuous readings by pressing the A key again Using PAR to Determine Leaf Area Index Ceptometer users may want to use sunfleck measurements to determine plant canopy parameters such as leaf area index and leaf angle distribution The theory for obtaining LAI and leaf angle distribution from these measurements is widely published However the theory is incomplete in some respects and this affects the accuracy of canopy parameters predicted from sunfleck measurements Errors are greatest when LAI is high and or when the canopy is tall The sunfleck inversion fails completely when the sky is overcast and there are no sunflecks Our research has shown that an inversion using transmitted PAR is much more reliable under almost all conditions than an inversion using sunfleck fraction We recommend that this PAR inversion be used instead of the inversion based on sunfleck fraction The PAR measured by the Ceptometer within a plant canopy is a combination of radiation transmitted through the canopy and radiation scattered by leaves within the canopy A complete model of transmission and scattering is given by Norman and Jarvis 1975 but it is very complex and not suitable for inversion 37 The Norman Jarvi

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