LI-COR LI-6800 User manual

Using Background Programs
on the LI-6800 Portable Photosynthesis System
Version 1.4

Using Background Programs
on the LI-6800 Portable Photosynthesis System
for Bluestem OS™ version 1.4
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Publication Number: 977-18536
Created on: Tuesday, January 28, 2020.
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Contents
Section 1. Things you should know
Nomenclature and symbols 1-1
Python 1-2
If you don't know Python 1-2
Pay attention to the hints 1-3
If you do know Python 1-6
Consider using VNC 1-8
Section 2. Overview
Work flows 2-3
A tour 2-4
Start an existing BP 2-4
Build a new BP 2-6
Section 3. Some examples
Early morning FoFm 3-1
Variations on AutoLog 3-5
Timing 3-5
Log until sundown 3-7
Varying the log interval 3-10
Monitoring match mode 3-18
Record and replay a time series 3-20
Section 4. Response curves
Basic 4-1
Multiple controls 4-5
Higher dimensions 4-8
Variable stability wait times 4-14
Section 5. Using dialogs

Section 6. Screen reference
The Open/New screen 6-1
The Build screen 6-2
The Set screen 6-5
The Start screen 6-6
The Monitor screen 6-8
Set screen interface tools 6-9
Simple objects 6-9
Control table 6-11
Data dictionary 6-12
Control dictionary 6-13
Status dictionary 6-13
Debug mode 6-14
Directory information 6-15
Saving BPs 6-17
Section 7. Step reference
# - comment 7-1
ASSIGN 7-1
Value or expression 7-1
Data Dictionary value 7-3
Status Dictionary value 7-4
(Advanced) Topic and Key 7-5
(Advanced) XML value 7-9
AUTOENV 7-10
BREAK 7-13
CALL and DEFINE 7-13
Variable scope 7-13
Passing by value or reference 7-13
DIALOG 7-15
Grid items 7-16
_dlg variables 7-20
Things to consider 7-21
EXEC 7-22
Local vs global 7-22
GROUP 7-23
IF, ELSE IF, ELSE 7-24
LOG 7-25
Open file 7-25
Record remark 7-26
Record data 7-26
Close file 7-26
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LOOP 7-27
Count 7-27
Duration 7-28
List 7-29
File 7-29
PROPERTIES 7-31
RETURN 7-31
RUN 7-31
SETCONTROL 7-32
SHOW 7-33
TABLE 7-34
Structure of a TABLE variable 7-35
Custom executions 7-37
WAIT 7-37
Duration 7-38
Stability 7-38
Until 7-39
Event 7-41
WHILE 7-42
Appendix A. Control dictionary map
Appendix B. Status dictionary map
Appendix C. The list_utility module

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Section 1.
Things you should know
A Background Program (BP) is a collection of steps that will execute on the
LI-6800 console “in the background” to accomplish various tasks. These steps can
be put together with tools provided on the console’s user interface.
While BPs can do the same things as conventional AutoPrograms, they have three
significant advantages: 1) you can make your own BPs, 2) the scope of what can be
done via a BP exceeds what can be done with an AutoProgram, 3) any number of
BPs can be run simultaneously.
Some background information will help you be successful with background pro-
grams.
Nomenclature and symbols
We use some terminology and some highlights in this document that are explained
here.
lAutoProgram - The traditional LI-6800 method of running automated logging,
etc.
lBP - Background Program. The subject of this document
lOpen,New,Start, etc. - Refers to a button on the interface.
lOpen/New,Build,Set,Monitor - Refers to a tab label, or the screen associated
with that tab label.
lLOOP,SETCONTROL,WAIT - A BP step.
lLOOP [Duration] - A BP step of a particular sub-type.
1-1Using LI-6800 Background Programs

Section 1. Things you should know
Python
Even through BPs are Python files, you do not need to be a Python programmer to
build or run them, since the LI-6800 software provides a graphical user interface
for doing those tasks. However, knowing a little bit of Python syntax can be very
helpful if you wish to design your own BPs and take advantage of some powerful
options that are available. The BP interface contains places where you are invited to
type in values, expressions, variable names, etc., and even if you have no inclination
to become a programmer, some simple knowledge can be very useful to you. For
example, rather than entering in a list of setpoints for light intensity, you might
instead type in something like randomList(50,2000,15), which, when the pro-
gram runs, will generate a randomized list of 15 linearly spaced set points ranging
between 50 and 2000.
If you are not a programmer, the next section is for you.
If you don't know Python
The Python world consists of objects of various types, such as numbers, strings,
lists, and so on. You create and keep track of your objects by assigning them to vari-
ables. Consider these simple examples of Python assignments:
la = 10 apoints to an integer.
lByeBye = 'this is a string' ByeBye points to a string.
lc66 = ["hello", 55, ByeBye] c66 points to a list containing a string, num-
ber, and string.
ldd = True dd points to a boolean.
le_xy = ByeBye+" and " + c66[0] e_xy will be the string 'this is a string and
hello'.
lfff = 'file '+str(a) fff makes a string out of a number, so is = 'file 10'.
lhh = a >15 and dd hh will be False, since a is not greater than 15.
Variable names should start with a letter (a-z or A-Z), and can contain numbers
and underscores (_). Python is case sensitive. There are some keywords you should
avoid when creating variable names (Figure 1-1 on the facing page), but if you acci-
dentally use one, you will be notified when you run the program and you can fix it.
1-2 Using LI-6800 Background Programs

The same name rule also applies to functions. A function is a named collection of
instructions that can be invoked by using the name followed by a list of zero or
more arguments (information passed to the function). Examples:
ldoSomething(a,5,c66) Calls the function doSomething, sending to it three
arguments.
ltryThis() Runs the function tryThis which takes no arguments.
lfff = 'file '+str(a) The function str() makes a string out of a number, so
fff becomes 'file 10' since ais 10.
Some functions only exist for a particular type of object. For those, we use a dot:
object.function(). For example, strings have a replace(x, y) function that replaces all
occurrences of xwith yin that string. So, if the string pointed at by fff is 'file 10',
then
gg = fff.replace('file','cabinet') gg becomes 'cabinet 10'
Figure 1-1. Avoid using these as variable names.
Pay attention to the hints
The interface for configuring steps in a BP frequently contain hints that tell you
what is expected to configure that step. For example, the configuration interface for
the BP step ASSIGN, which lets you create a variable and assign it to an expression
(or other things), is shown in Figure 1-2 on the next page.
Section 1. Things you should know
1-3Pay attention to the hints

Section 1. Things you should know
Figure 1-2. An example of an edit box requiring a variable name.
When an edit box has a hint with 'eval()' in it, it means that entry is going to be
passed to Python's eval() function when the program runs. This allows your entry
to be more complicated than, say, a numeric value. In the example above, the vari-
able is going to be assigned to whatever the eval() returns, regardless of type. In
other settings (Figure 1-3 below), a specific type is required, and that is reflected in
the hint. In the first example below, the entry is 10. It could just as easily be an
expression, like 8+2, or (if you have defined variables xand y)(x+y)/3.14159, or
anything that evaluates to something numeric.
Figure 1-3. Examples of edit boxes with eval() in the hint.
Lists: "Must eval() to a list" means to enter a sequence that is comma separated.
You can use [], or (), or leave them off:
[1,2,3] or (1,2,3) or 1,2,3
1-4 Using LI-6800 Background Programs

In Python, [1,2,3] is a list that can be modified; otherwise, it is a tuple, a list that
cannot be modified. For lists you enter in a BP interface, that distinction is usually
not important. To enter a single valued list, use a trailing comma.
[1,] or (1,) or 1,
Trailing commas like this (1,2,3,) are always allowed, regardless of the size of the
list.
Strings: Take special note of the string example in Figure 1-3 on the previous page.
If you are being asked for a string, such as a color, or a file name, that will be
passed to eval(), and you enter
/home/licor/myfile.txt
eval() will treat that entry like a variable name and you'll see an error. To avoid
that, put single or double quotes around it.
'/home/licor/myfile.txt' or "/home/licor/myfile.txt"
The reason for this is to allow for variable names. For example, you might wish to
programmatically name a new file each time through a loop, so you enter
'/home/licor/myfile'+str(count)+'.txt'
where count is some variable you have defined, giving you a new file each time
through:
/home/licor/myfile0.txt
/home/licor/myfile1.txt
/home/licor/myfile2.txt
Failure to follow the guidance provided in the hint will usually result in an error
(Figure 1-4 on the next page).
Section 1. Things you should know
1-5Pay attention to the hints

Section 1. Things you should know
Figure 1-4. This is a one step BP, consisting of a WAIT step. Bad entries (left) and the res-
ulting output in the BP's run log (text at right).
If you do know Python
BP files are Python files (.py). A simple one from one of the upcoming examples is
shown in Listing 1-1 on the facing page.
from bpdefs import ASSIGN, LOOP, SETCONTROL, LOG, Nothing, CheckBox,
Text, Button, DropDown, RadioBtns, EditBox
steps=[
# Assign a variable to an expression: ASSIGN('varname',
exp="expression" [,dlg=Nothing()])
ASSIGN("logint",
exp="lambda x: 30/(1+50*math.exp(-0.03*x))+0"),
# Assign a variable to an expression: ASSIGN('varname',
exp="expression" [,dlg=Nothing()])
ASSIGN("test",
exp="lambda x: x if x >= 1 else 0"),
# Loop through a list: LOOP(list=itemList [,var=varname]
[,mininc=''])
LOOP(list="1500,50,1500",
var="x",
steps=(
# Set a control:
1-6 Using LI-6800 Background Programs

SETCONTROL('target', 'value', 'eval' [,opt_target=''])
SETCONTROL("Qin","x","float"),
# Loop for a duration: LOOP(dur="float"
[,units='Seconds' Second|Minutes|Hours ] [,var=''] [,mininc=''])
LOOP(dur="15",
units="Minutes",
var="t",
mininc="test(logint(t))",
steps=(
# Log a data record:
LOG([avg='Default'] [,match='Default] [,flr='Default']
[flash='Default'])
LOG(avg="Off",
match="Off",
flr="0: Nothing"),
)
),
)
),
]
Listing 1-1. Listing of the file /home/licor/apps/examples/VariableLogInt.py.
A BP file contains one list, which is always named steps. Each item in steps is
created using a constructor, with class names such as ASSIGN, LOOP, LOG, etc.
The line before each constructor contains a comment, showing the options avail-
able for the version of constructor used.
The first thing to know is this: running a BP is not simply a matter of running the
.py file; rather, the .py file is compiled (eval()) to obtain a list of program steps
(steps). The thread that actually executes when a BP uses steps as data as it con-
structs itself.
A second thing to note is that because we are just constructing data in a list, vari-
ables and expressions have to exist at this stage as strings, sometimes even doubly-
quoted strings. The first parameter in ASSIGN, for example, is destined to become a
Python variable (but not yet), so at this stage, it is a quoted string. Similarly, what
will be the object assigned to that variable also starts out as a string. In the two
ASSIGNs above, the assigned objects will become lambda expressions. In summary,
you have to keep in mind that you are writing code that will be sent to a Python's
eval() or exec() statements twice: once to build the step, then later when the step
processes its parameters.
Section 1. Things you should know
1-7If you do know Python

Section 1. Things you should know
Because BP files are .py files, they can be written and/or edited outside of the LI-
6800 console's user interface using any text editor. Ideally, of course, you should
use an editor designed for Python, to eliminate syntax errors in the editing stage.
Consider using VNC
The touch screen keyboard on the LI-6800 console does not lend itself well to typ-
ing long expressions and names that may be needed when developing BPs.
Consider connecting to the LI-6800 with a virtual network computing (VNC)
viewer client when doing BP development. Clients are available for a wide range of
platforms from https://www.realvnc.com/en/connect/download/viewer/
Using a VNC client on your computer allows you to use your computer's keyboard
to enter those long expressions and names.
One hint for doing this is in Figure 1-5 below. When the LI-6800 keyboard (or
keypad) appears for an entry, the VNC client keyboard will not immediately be
“activated”. To do this, you must click in the keypad entry area somewhere to the left
of the entry's last character. (If the entry area is empty, you may have first click on a
couple of keypad buttons to put some characters there, then click to the left of the
last one.)
Figure 1-5. Click in the text to activate the VNC client keyboard.
1-8 Using LI-6800 Background Programs

Section 2.
Overview
As mentioned, a Background Program (BP) is a collection of steps that will execute
on the LI-6800 console "in the background" to accomplish various tasks. These
steps can be put together by the user with tools provided on the console's user inter-
face.
Figure 2-1 below illustrates how to access the BP screens.
Figure 2-1. The Open/New tab of the Background Program interface.
2-1Using LI-6800 Background Programs

Section 2. Overview
The BP environment has five tabs along the bottom: Open/New,Build,Set,Start,
and Monitor.
Open/New - Load BPs from the file system for running or editing.
Build - Assemble a list of program steps fom the menu on the left. Steps can be re-
ordered, moved around, etc.
Set - Each program step has associated parameters that can be edited and adjusted
as needed.
Start - At any point, you can try out all or part of your program. This screen shows
what step is being executed, and shows messages and output generated by the BP as
it runs. You can execute your program in real time or step by step.
Monitor - Similar to the Start screen, but for any running BP.
2-2 Using LI-6800 Background Programs