More details on files

Data files are tab-delimited text files, and if you selected the option, .xlsx files. Each file includes a header—which is information that describes the rest of the file.

The logs folder

The contents of the header will depend on whether you selected variables in Check to log as a row in Logging options. Underneath the header is the data from each measurement. Here again, the columns included depend on the variables you choose. You will find some or all of the following:

Header label Description Variables table
Const Gas exchange constants Table 4‑10
FLR Fluorometer computations Table 4‑151
FlrLS Fluorometer light source data Table 4‑81
FlrStats Fluorometer statistics Table 4‑17
GasEx Gas exchange variables Table 4‑18
LQConst Light source constants Table 4‑24
LTConst Leaf temperature constants
LeafQ Light Table 4‑23
MPF MultiPhase flash values Table 4‑301,2
Match Match data Table 4‑262
Meas Measured variables Table 4‑28
Meas2 Additional measured data Table 4‑292
QConst Light source constants Table 4‑32
Raw Raw data Table 4‑332
Stability Stability parameters Table 4‑402
Status Status data Table 4‑38
Status2 Additional status information Table 4‑392
Sys System variables Table 4‑41
UserDef User defined constants  

Remarks are stored in the log files. In text data files, remarks are recorded in the text data file, either in the header information or inline with the other measurements. In Excel files, they are in a separate tab from the measurements (called Remarks). Remarks will always include the time stamp.

The flrevents folder

Data files for each flash made by the fluorometer are stored in the instrument's memory. Inside the folder you'll see text files, and possibly .xlsx files with names like the following examples:






In each of these file names, the first set of capital letters indicates the flash type.

  • RECT is for rectangular flash
  • MPF is for a multiphase flash
  • INDUCTION is an induction event
  • DARK is for the dark pulse.
  • RCRDG is the continuous fluorescence trace.

The first digit is the flash number. Each flash made by the fluorometer is assigned a number, and the number increments once per measurement. The remaining numbers are the date and time stamp, following this convention: yyyymmdd-hh_mm_ss. Year is indicated by yyyy, mm is the month, dd is day, hh is hour, mm is minute, ss is second.

Interpreting a flash data set

If you open a rectangular flash file in Microsoft Excel, you will see something like this:

Fluorometer Serial Number
Fluorometer Settings

The left two columns are information about the flash event. Columns D to H are the fluorescence data.

Table 4‑1. Each flash will have its own file, which includes the following pieces of information.
Column Meaning
Secs Time
DC Actinic light
PFD Photon Flux Density
Code The sequence of the flash that is underway at the time.
  • 2 is the beginning margin
  • 3 is the rectangular flash
  • 4 is Phase 1 of a multiphase flash
  • 5 is Phase 2 of a multiphase flash
  • 6 is Phase 3 of a multiphase flash
  • 7 is the end margin

If you open a typical multiphase flash data set, expect something like this:

The continuous fluorescence trace

When you record the fluorometer trace (Fluorometry > Settings > Measuring), the resulting data file will be stored in the /home/licor/flrevents directory and the name will begin with RCRDG... followed by the date and time that recording began. The resulting file is tab-delimited. The data frequency will be about 2 Hz, except during flash or dark events, in which case it is determined by the output frequency that you specified for the event.


1 1478561051.8 1.80625 113.31 100.013 89.996998089 10.016001911 0.0 1.99973

1 1478561052.4 1.6265 113.091 99.983 90.004796583 9.978183420399999 0.0 1.99973

1 1478561053 1.699 113.041 100.022 90.005496854 10.016503146 0.0 1.99973

1 1478561053.6 2.296 112.79 100.015 89.998797795 10.016202205 0.0 1.99973

1 1478561054.2 2.14475 112.784 99.9829 90.0047065629 9.978173440519999 0.0 1.99973

1 1478561054.8 1.388 113.628 100.01 89.99429853000001 10.01570147 0.0 1.99973

1 1478561055.4 2.45675 113.051 99.9943 90.0146688714 9.97968112575 0.0 1.99973

1 1478561056 1.97575 113.334 99.9834 90.0051566634 9.97822333992 0.0 1.99973

1 1478561056.6 1.7955 112.926 99.9909 90.0119081709 9.978971830919999 0.0 1.99973


Listing 4‑1. The start of the RCRDG... file.

Table 4‑2. Items in a fluorescence recording (RCRDG...) file.
Label Description
CODE Record identifier (see Table 4‑3)
TIME Seconds
FLUOR AC fluorescence
PFD Total photon flux density (µmol m-2 s-1)
RED Red (non-modulated) photon flux density (µmol m-2 s-1)
BLUE Blue photon flux density (µmol m-2 s-1)
FARRED Far red flux fluorescence (µmol m-2 s-1)
REDMODAVG Averaged photon flux density contributed by the modulation (µmol m-2 s-1)
Table 4‑3. CODE values in a fluorescence recording file.
CODE Description
0 Off
1 Normal measuring
2 Pre-flash
3 Rectangle flash
4 MPF, phase 1
5 MPF, phase 2
6 MPF, phase 3
7 Post-flash
11 Pre-dark
12 Dark pulse, Far Red ON (actinic still on)
13 Dark pulse, Actinic off (far red still on)
14 Dark pulse, all off
15 Post-dark

Configuration files, graph definition files, and assorted miscellany

In addition to the data files, the LI-6800 file system includes configuration files, graph definitions, and other files that are either logged information, settings (saved as plain text files), and instructions for the instrument (saved as .py and .json files). You can access all of these when connected to the instrument's file system.

We're interested in the settings—the contents of the configs folder. Since these are plain text files, you can open and edit them in any text editor, so feel free to explore them on your own if you are so inclined.

Copying configuration files is just like moving files in any other computer file system. You'll save the files to your computer, and then load them onto another instrument by placing them in the same directory that they were in originally.


Snapshots are stored in the directory /home/licor/info/snapshots, and are named for the date and time when they occurred. They are .json files, consisting of the latest values for each of a number of topics at the time of the snapshot.

The format of a system snapshot is slightly changed in version 1.5. It is now a single .json map with 5 parts: topics, head, flr, console, tests. The head, console, and flr are new for 2.0. See .

  • Topics - topics and payloads covering most aspects of system operation.
  • Head - complete configuration of the sensor head.
  • Console - complete configuration of the console.
  • Flr - complete configuration of the fluorometer (if any).
  • Tests - latest log of each system warmup test.

Listing 4‑2. The five sections of a snapshot file (topics, head, console, flr, and tests).

    "topics:": {
        "licor/li6850/output/DATA": {
            "TIME": 1604939190,
    "head": {
        "licor": {
            "li6850": {
                "ver": "1.4.3",
    "console": {
        "licor": {
            "li6860": {
                "ver": "1.4.08",
    "flr": {},
    "tests": {
        "Cal_Coeff_Test": [
            "Cal_Coeff_Test started at 2020-11-06 15:20:55",