Selected List of Sensor Suppliers
1
Cole-Parmer Instrument Company
7425 North Oak Park Avenue
Niles, IL 60714
Phone: 708-647-7600
FAX: 708-549-1700
APPLICATION NOTE
LI-6400 Portable Photosynthesis System
Omega Engineering, Inc.
P.O. Box 4047
Stamford, CT 06907-0047
Phone: 203-359-1660
FAX: 203-359-7700
Rotronic Instrument Corp.
7 High Street
Huntington, NY 11743
Phone: 516-427-3994
FAX: 516-427-3902
Vaisala Inc.
100 Commerce Way
Woburn, MA 01801-1068
Phone: 617-933-4500
FAX: 617-933-8029
Yellow Springs Instruments
1725 Brannum Lane
P.O. Box 465
Yellow Springs, OH 45387
Phone: 513-767-7241
FAX: 513-767-9353
Configuring and Operating the
LI-6400 Portable Photosynthesis
System with External Sensors
Introduction
Follow these 6 steps to set up the auxiliary port and
the software:
It is sometimes desirable to log auxiliary sensor
data while running the LI-6400 system. For
example, a user may wish to monitor conditions
outside the leaf cuvette during measurement of
photosynthesis. Furthermore, some users may
want to control chamber conditions such as
temperature or photosynthetically active radiation
(PAR) based on external conditions. In this note
we demonstrate how to connect a humidity sensor
and an air temperature sensor to the LI–6400; we
then give an example of how the LI– 6400
chamber conditions may be controlled using inputs
from one or several external sensors. Finally, we
make some comments concerning continuous
unattended logging.
Using an External Humidity and Air
Temperature Sensor with the
LI–6400
The Vaisala Humitter 50Y* relative humidity and
air temperature probe (Vaisala, Woburn, MA) is
used here as an example of an external sensor
because it is simple to connect to the LI–6400 and
program the spare channels for it. However, other
humidity probes or temperature sensors (such as
thermocouples) may be more suitable for these
measurements depending on your requirements.
The user is only limited by the range of the
differential input channels (±5V) and the resolution requirements of the experiment (low resolution = 270 µV and high resolution = 60 µV with
AvgTime= 4).
There are two general steps to using external
sensors with the LI–6400: 1) properly connecting
the sensor wires to the 37–pin auxiliary port, and
2) configuring the LI–6400 software to process the
signals.
1.
2.
3.
4.
5.
6.
Connect the external sensors to the auxiliary
port.
Add the spare analog channels being used to
the Configuration File.
Change the Compute List File to accomodate the new calculations and store the
results.
Edit and store the Displays File to include
external sensors.
Edit and store the LogList to record the
additional sensor information.
Store the Configuration File with the new
Compute List, Displays, and LogList.
NOTE: The procedure for configuring the system
software requires OPEN version 2.0 or greater, and
may vary between different software versions. The
description given here is for OPEN software
version 2.0.
1.
Connect the external sensors to the auxiliary port.
Pin assignments for the 37-pin auxiliary port are
given in Appendix C of the LI-6400 Primer. The
pin numbers are stamped on the connector. In this
example we have configured the connector to use
differential input channels 20 and 21 (Figure 1).
The differential ground of the sensors is tied to the
digital ground because the Vaisala 50Y has no
separate ground.
2.
Add the spare channels to the Configuration File.
From the initial startup screen go to the Config
Menu and enter the Config Editor. Press Add (f2)
and the Master List of configuration options will
appear. Scroll to the UserChan= command and
press Select (f5). Repeat this process of adding a
®
LI-COR, inc.
●
Environmental Division ● 4421 Superior Street ● P.O. Box 4425
Phone: 402-467-3576 ● FAX: 402-467-2819
Toll-free 1-800-447-3576 (U.S. & Canada)
●
Lincoln, Nebraska 68504 USA
* A list of suppliers is given at the end of this note.
®
1
6.
19 18 17 16 15 14 13 12 11 10 9
8
7
6
5
4
3
2
Store the new Config File.
1
37 36 35 34 33 32 31 30 29 28 27 26 25 24 23 22 21 20
Yellow
Green
Green
Brown
Violet
Vaisala Humitter 50Y
HUMITTER
P1620016
Figure 1. Connecting the Vaisala Humitter 50Y to the LI–6400 37–pin auxiliary port.
Access the "X_Sensors Config" file again by selecting Config
Editor in the Config Menu. Press labels and then press
StoreAs (f5). Name the file "X_Sensors Config" if it is not
already named. It should look similar to the following list
(depending, of course, on the optional accessories you may
have installed):
UserChan= 20 5 0
UserChan= 21 5 0
LightSource= “Sun+Sky” 1.0 0.19
user channel to the config list 1 more time. You will have two
entries that appear as UserChan= 0 0 0. Highlight the first
entry and press Edit. Press 0, 5, then L. Your entry will now
appear as
UserChan= 20 5 0
Edit the remaining channel to look like this:
UserChan= 21 5 0 (Press 1, 5, L)
User channels 20 and 21 are now configured for the humidity
and temperature sensors, respectively; they use differential
ground number 5 (which is tied to the digital ground on pin
20); and the resolution is set to low (0).
store it in a new file name. Let’s call this new Compute List
file “X_Sensors Compute”. When you Quit the Editor and are
asked if you want to implement this new file, type Y for yes.
For further information about Compute List Files see LI-6400
Technical Note #2 - Defining Equations for OPEN.
4.
Since we want to view the status of our sensors in the New
Measurements Display, enter New Msmnts from the OPEN
screen, and press the Display Editor function key (level 6, f4).
Follow these steps to add and store the two new sensors to a
display definition:
Store this as “X_Sensors Config” by pressing the labels key
and then choosing StoreAs (f5). Press the labels key and
then choose OK (f5) to implement this Config file. For further
information about config files see LI-6400 Technical Note #3.
3.
Change the compute list to accomodate the new
calculations.
Select User Compute List Editor from the Config Menu. Add
channels 20 and 21, plus decimal time to the Compute List.
Assign decimal time to user variable ID 01; user variable ID's
91 and 92 will be the humidity and temperature, respectively.
Below is a sample of how the first 3 items in the Compute List
can be programmed to accomplish this (include all spaces):
##92F2 “xTair” “external temperature”
“chan21_mv * 0.1 – 40”
“Hrs” will allow us to record the observation time in decimal
hours, which we will need when plotting data against time.
“xRH and “xTair” are the values of external humidity and air
temperature, respectively.
Store this new compute list file by pressing Escape and S to
2
●
Press Display Editor (f4).
●
Press Add (f2) to add an additional display line.
●
Use the arrow keys to highlight xRH.
●
Press Select (f5).
●
Select xTair, then Escape to quit after adding the two
variables.
●
##01F5 “Hrs” “Decimal hrs. of OBS Time”
“$ GETTDS TIME ROT 3600. / SWAP 60. / + +”
##91F1 “xRH” “external humidity”
“chan20_mv * 0.1”
Add the external sensors to the Display file.
5.
Press OK (f5). When prompted to store the changes,
press Y. Name the new Display file “X_Sensors Displays”, and press Select. When you return to the New
Measurements screen, you can put this line on the screen
by pressing the letter associated with this new line. The
new line will be displayed at the end of the Display
Editor list.
Edit and store a new LogList file.
In order to log data from the external sensors, we must edit the
LogList file. While still in New Msmnts, select the Loglist
Editor function key (level 5, f5).
Add and store the new channels to the LogList file according
to the procedure outlined in the Primer on pages 4-9 and 4-10.
When finished, name this new LogList file “X_Sensors
Output”.
AREA= 6
STOMRAT= 1
ComputeList= “X_Sensors Compute”
Displays= “X_Sensors Display”
StripDefs= “Photo & CV” (or whatever you want this to be)
LogFormat= “X_Sensors Output”
Continuous Unattended Recording with the
LI–6400.
Recording continuous unattended measurements is as simple
as enabling the AutoLog program (see the LI– 6400 Primer,
pages 4–11 and 4–12) and logging samples at fixed intervals
for any specified number of samples. Alternatively, when Log
is pressed, if you do not enter a file name and press Escape at
the prompt, data can be logged to memory or to the COM port.
If you log data to the COM port, you must run a program on
your PC (such as the LI-COR 1000-90 COMM program) to
capture the incoming ASCII data.
The following precautions should be taken when operating the
LI-6400 continuously:
●
The length of time the LI–6400 will run from a single
6400–03 rechargeable battery depends on what is being
powered (see page 2–14 in the LI-6400 Primer). For
long–term operation it is necessary to plug in one fully
charged battery and connect the other battery jack to the
battery charger with the 9960–062 cable.
●
If the interior temperature of the analyzers falls below
the ambient dew point temperature, water will condense
on the interior surfaces of the analyzers. This typically
occurs at night. Therefore, if you run the system outside
during the night it may be wise to configure the block
temperature to track external air temperature, or a
temperature 2 to 5 °C greater than the external temperature. Furthermore, cover the console and sensor head to
prevent dew formation on the instruments.
Now OK this configuration to store your changes and the
system software is ready.
Using External Sensor Inputs to Control Leaf
Chamber Variables
LI–6400 Technical Note #7 (Environmental Control) describes
how to control cuvette variables such as light, temperature,
and humidity from external sensors.
For our example, assume we want to drive the block temperature from the external air temperature sensor that was configured as shown in the section above. Controlling the block
temperature will indirectly control the air temperature in the
cuvette, since both temperatures are coupled by the vigorous
mixing between the optical bench and the cuvette.
From the New Msmnts screen, enter level 2 and press f4 to
open the Temperature Control Options and Targets menu. Use
the arrow keys to highlight Block Temp and press Enter (or
just press B). Enter the target value for the temperature by
typing #92 and pressing Enter, (or just press # and then Enter.
A menu will appear with a list of available target channels,
from which you can select channel 92). This will cause the
block temperature to track the Vaisala external air temperature
sensor.
It may be possible to track external humidity also, depending
on the transpiration rate of the leaf and whether or not you
have a CO2 injector, which provides a greater dynamic range
of flow control. It is not advisable to program the system to
lock in on a variable target while an AutoProgram is controlling that same variable. The AutoLog program should work
fine when the sampling intervals are several minutes apart if
you choose to match the analyzers. A complete discussion of
this subject is found in LI-6400 Technical Note #7 and will not
be covered here.
3
6.
19 18 17 16 15 14 13 12 11 10 9
8
7
6
5
4
3
2
Store the new Config File.
1
37 36 35 34 33 32 31 30 29 28 27 26 25 24 23 22 21 20
Yellow
Green
Green
Brown
Violet
Vaisala Humitter 50Y
HUMITTER
P1620016
Figure 1. Connecting the Vaisala Humitter 50Y to the LI–6400 37–pin auxiliary port.
Access the "X_Sensors Config" file again by selecting Config
Editor in the Config Menu. Press labels and then press
StoreAs (f5). Name the file "X_Sensors Config" if it is not
already named. It should look similar to the following list
(depending, of course, on the optional accessories you may
have installed):
UserChan= 20 5 0
UserChan= 21 5 0
LightSource= “Sun+Sky” 1.0 0.19
user channel to the config list 1 more time. You will have two
entries that appear as UserChan= 0 0 0. Highlight the first
entry and press Edit. Press 0, 5, then L. Your entry will now
appear as
UserChan= 20 5 0
Edit the remaining channel to look like this:
UserChan= 21 5 0 (Press 1, 5, L)
User channels 20 and 21 are now configured for the humidity
and temperature sensors, respectively; they use differential
ground number 5 (which is tied to the digital ground on pin
20); and the resolution is set to low (0).
store it in a new file name. Let’s call this new Compute List
file “X_Sensors Compute”. When you Quit the Editor and are
asked if you want to implement this new file, type Y for yes.
For further information about Compute List Files see LI-6400
Technical Note #2 - Defining Equations for OPEN.
4.
Since we want to view the status of our sensors in the New
Measurements Display, enter New Msmnts from the OPEN
screen, and press the Display Editor function key (level 6, f4).
Follow these steps to add and store the two new sensors to a
display definition:
Store this as “X_Sensors Config” by pressing the labels key
and then choosing StoreAs (f5). Press the labels key and
then choose OK (f5) to implement this Config file. For further
information about config files see LI-6400 Technical Note #3.
3.
Change the compute list to accomodate the new
calculations.
Select User Compute List Editor from the Config Menu. Add
channels 20 and 21, plus decimal time to the Compute List.
Assign decimal time to user variable ID 01; user variable ID's
91 and 92 will be the humidity and temperature, respectively.
Below is a sample of how the first 3 items in the Compute List
can be programmed to accomplish this (include all spaces):
##92F2 “xTair” “external temperature”
“chan21_mv * 0.1 – 40”
“Hrs” will allow us to record the observation time in decimal
hours, which we will need when plotting data against time.
“xRH and “xTair” are the values of external humidity and air
temperature, respectively.
Store this new compute list file by pressing Escape and S to
2
●
Press Display Editor (f4).
●
Press Add (f2) to add an additional display line.
●
Use the arrow keys to highlight xRH.
●
Press Select (f5).
●
Select xTair, then Escape to quit after adding the two
variables.
●
##01F5 “Hrs” “Decimal hrs. of OBS Time”
“$ GETTDS TIME ROT 3600. / SWAP 60. / + +”
##91F1 “xRH” “external humidity”
“chan20_mv * 0.1”
Add the external sensors to the Display file.
5.
Press OK (f5). When prompted to store the changes,
press Y. Name the new Display file “X_Sensors Displays”, and press Select. When you return to the New
Measurements screen, you can put this line on the screen
by pressing the letter associated with this new line. The
new line will be displayed at the end of the Display
Editor list.
Edit and store a new LogList file.
In order to log data from the external sensors, we must edit the
LogList file. While still in New Msmnts, select the Loglist
Editor function key (level 5, f5).
Add and store the new channels to the LogList file according
to the procedure outlined in the Primer on pages 4-9 and 4-10.
When finished, name this new LogList file “X_Sensors
Output”.
AREA= 6
STOMRAT= 1
ComputeList= “X_Sensors Compute”
Displays= “X_Sensors Display”
StripDefs= “Photo & CV” (or whatever you want this to be)
LogFormat= “X_Sensors Output”
Continuous Unattended Recording with the
LI–6400.
Recording continuous unattended measurements is as simple
as enabling the AutoLog program (see the LI– 6400 Primer,
pages 4–11 and 4–12) and logging samples at fixed intervals
for any specified number of samples. Alternatively, when Log
is pressed, if you do not enter a file name and press Escape at
the prompt, data can be logged to memory or to the COM port.
If you log data to the COM port, you must run a program on
your PC (such as the LI-COR 1000-90 COMM program) to
capture the incoming ASCII data.
The following precautions should be taken when operating the
LI-6400 continuously:
●
The length of time the LI–6400 will run from a single
6400–03 rechargeable battery depends on what is being
powered (see page 2–14 in the LI-6400 Primer). For
long–term operation it is necessary to plug in one fully
charged battery and connect the other battery jack to the
battery charger with the 9960–062 cable.
●
If the interior temperature of the analyzers falls below
the ambient dew point temperature, water will condense
on the interior surfaces of the analyzers. This typically
occurs at night. Therefore, if you run the system outside
during the night it may be wise to configure the block
temperature to track external air temperature, or a
temperature 2 to 5 °C greater than the external temperature. Furthermore, cover the console and sensor head to
prevent dew formation on the instruments.
Now OK this configuration to store your changes and the
system software is ready.
Using External Sensor Inputs to Control Leaf
Chamber Variables
LI–6400 Technical Note #7 (Environmental Control) describes
how to control cuvette variables such as light, temperature,
and humidity from external sensors.
For our example, assume we want to drive the block temperature from the external air temperature sensor that was configured as shown in the section above. Controlling the block
temperature will indirectly control the air temperature in the
cuvette, since both temperatures are coupled by the vigorous
mixing between the optical bench and the cuvette.
From the New Msmnts screen, enter level 2 and press f4 to
open the Temperature Control Options and Targets menu. Use
the arrow keys to highlight Block Temp and press Enter (or
just press B). Enter the target value for the temperature by
typing #92 and pressing Enter, (or just press # and then Enter.
A menu will appear with a list of available target channels,
from which you can select channel 92). This will cause the
block temperature to track the Vaisala external air temperature
sensor.
It may be possible to track external humidity also, depending
on the transpiration rate of the leaf and whether or not you
have a CO2 injector, which provides a greater dynamic range
of flow control. It is not advisable to program the system to
lock in on a variable target while an AutoProgram is controlling that same variable. The AutoLog program should work
fine when the sampling intervals are several minutes apart if
you choose to match the analyzers. A complete discussion of
this subject is found in LI-6400 Technical Note #7 and will not
be covered here.
3
Selected List of Sensor Suppliers
1
Cole-Parmer Instrument Company
7425 North Oak Park Avenue
Niles, IL 60714
Phone: 708-647-7600
FAX: 708-549-1700
APPLICATION NOTE
LI-6400 Portable Photosynthesis System
Omega Engineering, Inc.
P.O. Box 4047
Stamford, CT 06907-0047
Phone: 203-359-1660
FAX: 203-359-7700
Rotronic Instrument Corp.
7 High Street
Huntington, NY 11743
Phone: 516-427-3994
FAX: 516-427-3902
Vaisala Inc.
100 Commerce Way
Woburn, MA 01801-1068
Phone: 617-933-4500
FAX: 617-933-8029
Yellow Springs Instruments
1725 Brannum Lane
P.O. Box 465
Yellow Springs, OH 45387
Phone: 513-767-7241
FAX: 513-767-9353
Configuring and Operating the
LI-6400 Portable Photosynthesis
System with External Sensors
Introduction
Follow these 6 steps to set up the auxiliary port and
the software:
It is sometimes desirable to log auxiliary sensor
data while running the LI-6400 system. For
example, a user may wish to monitor conditions
outside the leaf cuvette during measurement of
photosynthesis. Furthermore, some users may
want to control chamber conditions such as
temperature or photosynthetically active radiation
(PAR) based on external conditions. In this note
we demonstrate how to connect a humidity sensor
and an air temperature sensor to the LI–6400; we
then give an example of how the LI– 6400
chamber conditions may be controlled using inputs
from one or several external sensors. Finally, we
make some comments concerning continuous
unattended logging.
Using an External Humidity and Air
Temperature Sensor with the
LI–6400
The Vaisala Humitter 50Y* relative humidity and
air temperature probe (Vaisala, Woburn, MA) is
used here as an example of an external sensor
because it is simple to connect to the LI–6400 and
program the spare channels for it. However, other
humidity probes or temperature sensors (such as
thermocouples) may be more suitable for these
measurements depending on your requirements.
The user is only limited by the range of the
differential input channels (±5V) and the resolution requirements of the experiment (low resolution = 270 µV and high resolution = 60 µV with
AvgTime= 4).
There are two general steps to using external
sensors with the LI–6400: 1) properly connecting
the sensor wires to the 37–pin auxiliary port, and
2) configuring the LI–6400 software to process the
signals.
1.
2.
3.
4.
5.
6.
Connect the external sensors to the auxiliary
port.
Add the spare analog channels being used to
the Configuration File.
Change the Compute List File to accomodate the new calculations and store the
results.
Edit and store the Displays File to include
external sensors.
Edit and store the LogList to record the
additional sensor information.
Store the Configuration File with the new
Compute List, Displays, and LogList.
NOTE: The procedure for configuring the system
software requires OPEN version 2.0 or greater, and
may vary between different software versions. The
description given here is for OPEN software
version 2.0.
1.
Connect the external sensors to the auxiliary port.
Pin assignments for the 37-pin auxiliary port are
given in Appendix C of the LI-6400 Primer. The
pin numbers are stamped on the connector. In this
example we have configured the connector to use
differential input channels 20 and 21 (Figure 1).
The differential ground of the sensors is tied to the
digital ground because the Vaisala 50Y has no
separate ground.
2.
Add the spare channels to the Configuration File.
From the initial startup screen go to the Config
Menu and enter the Config Editor. Press Add (f2)
and the Master List of configuration options will
appear. Scroll to the UserChan= command and
press Select (f5). Repeat this process of adding a
®
LI-COR, inc.
●
Environmental Division ● 4421 Superior Street ● P.O. Box 4425
Phone: 402-467-3576 ● FAX: 402-467-2819
Toll-free 1-800-447-3576 (U.S. & Canada)
●
Lincoln, Nebraska 68504 USA
* A list of suppliers is given at the end of this note.
®
1