Data files

In this section we describe how to review logged data on the instrument and how to download those files to a computer for further analysis. In addition, we review the contents of data files, including the header and footer. To access data files on the instrument, click Files.

Viewing data on the instrument

On the Files page, you will see your newly-finished file at the top of the list. To view the contents of your file before downloading it, press the graph icon under Actions.

You will first be prompted to choose an ID Tag to view the data for that collar.

After selecting your ID Tag, the data will be displayed below the ID Tag menu, beginning with the default Review Metadata option. A number of variables will be displayed. To the right of Review Metadata, you can also change the display for each of the individual repetitions within each ID Tag (assuming you took >1 repetition at a single ID Tag). s

In addition to reviewing metadata, you may also review your flux data (Review Fluxes) or review the averages of your measured variables (Review Averages).

Downloading data from the instrument

While the Smart Chamber software allows a convenient interface for viewing your data, you may also download your file for advanced analysis with SoilFluxPro Software, or for viewing, visualization, and/or analysis in your statistical software of choice. Your data file(s) will be downloaded to the directory specified by your browser. You can modify this location in your browser settings.

The following section describes the structure of files downloaded from your Smart Chamber with a data dictionary that describes variable names from the files and how those variables are displayed in the interface software.

Data file structure

Files downloaded from the Smart Chamber are broken into four sections: Header, Data, Summary, and Footer variables.

Header

Header variables provide a summary of variables that are taken directly from the Smart Chamber or gas analyzer, and values that are set in the Smart Chamber interface software.

Listing 4‑1. The Header provides a summary of variables.

Copy 
{ "name": "garden_soil_flux",
"remark": "garden next to <span class="text-nowrap mc-variable product_names.LI-COR variable">LI-COR</span> greenhouse",
"date":1561126635,
"datasets":  [ 
{ "measurement_1":
    {
        "remark": "Collar 1",
        "reps":
            {
"REP_1": {
    "header":{
        "Chamber":"82s-1015",
        "Version":"1.5",
        "InstrumentModel":"li870",
        "InstrumentSerialNumber":"ssa-1022",
        "Date":"2019-06-21 15:18:10",
        "RepNum":1,
        "DeadBand":20,
        "Area":318,
        "Offset":3,
        "ChamVolume":4244.1,
        "IrgaVolume":99.42,
        "TotalVolume":5297.52,
        "gps_time":1561148290,
        "latitude":40.8568,
        "longitude":-96.6571,
        "gps_hdop":0.76,
        "altitude":367.8,
        "gps_sats":13,
        "TimeZone":"CST6CDT"
    },    

Labels

A fifth section, called Labels, is used to map variables between the Smart Chamber software and data files with SoilFluxPro, but these definitions have no impact on your measurements.

Copy 
"labels":{
    "area":"Area",
    "volume":"TotalVolume",
    "deadband":"DeadBand",
    "etime":"timestamp",
    "pressure":"chamber_p",
    "temperature":"chamber_t",
    "h2o":"h2o"
},

Data

Data variables, if recorded, are recorded once per second for as many seconds as there are in the duration of the observation Many of these variables can be viewed in real time from the Home Screen and can also be viewed in the File Viewer. Summary variables show the initial value, mean, and range of the same variables recorded as Data variables.

Listing 4‑2. The Data is toward the top of a measurement repitition. It begins with time, followed by data records that correspond to each point in the timestamp.

Copy 
"data":{
    "timestamp":[0,1,2,3,4,5,6,7,8,9,10,11,12,13,
        14,15,16,17,18,19,20,21,22,23,24,25,26,
        27,28,29,30,31,32,33,34,35,36,37,38,39,
        40,41,42,43,44,45,46,47,48,49,50,51,52,
        53,54,55,56,57,58,59,60,61,62,63,64,65,
        66,67,68,69,70,71,72,73,74,75,76,77,78,
        79,80,81,82,83,84,85,86,87,88,89,90,91,
        92,93,94,95,96,97,98,99,100,101,102,103,
        104,105,106,107,108,109,110,111,112,113,
        114,115,116,117,118,119],
    "chamber_p":[96.5794,96.5559,96.5727,96.5841,96.5938,
        96.5515,96.5955,96.5829,96.623,96.5866,96.5963,
        96.589,96.5819,96.5908,96.5872,96.5848,96.5805,
        96.5861,96.5742,96.5835,96.5717,96.5888,96.5964,
        96.5466,96.5838,96.5868,96.5735,96.5861,96.6204,
        96.5755,96.6027,96.5908,96.5674,96.6072,96.5866,
        96.5675,96.5452,96.58,96.5775,96.5953,96.6406,
        96.5856,96.615,96.5872,96.5466,96.5783,96.6087,
        96.5734,96.5909,96.5718,96.5651,96.5722,96.5807,
        96.606,96.5936,96.5969,96.6092,96.5958,96.5906,
        96.545,96.6203,96.5843,96.5727,96.5853,96.5818,
        96.5645,96.5917,96.6016,96.5971,96.5741,96.5902,
        96.5839,96.6054,96.5858,96.5811,96.586,96.5742,
        96.5882,96.5714,96.5803,96.6093,96.5794,96.5917,
        96.6259,96.5965,96.6331,96.591,96.6118,96.5825,
        96.579,96.6206,96.6176,96.5867,96.6159,96.6021,
        96.5732,96.5802,96.6038,96.5985,96.5872,96.5866,
        96.592,96.615,96.6237,96.6067,96.5917,96.6047,
        96.5758,96.6095,96.5721,96.6007,96.5757,96.5748,
        96.5908,96.5736,96.5991,96.5903,96.5908,96.6057,
        96.6216],
    ...

Summary

Summary variables are taken from your Smart Chamber, displayed in the Diagnostics page, or are entered in the Measurement Settings section of the user interface software. After a measurement is completed, these variables can be viewed in the File Viewer under Review Metadata in the same format as in data files.

Listing 4‑3. The Summary are readings taken by the Smart Chamber.

Copy 
"summary":{
    "timestamp":[0,59.5,119],
    "chamber_p":[96.5675,96.5891,0.0956268],
    "chamber_p_t":[42.4249,43.1838,1.45625],
    "chamber_t":[31.7913,31.4581,0.429932],
    "soil_t":[9999,9999,0],
    "soilp_c":[0.105,0.105833,0.002],
    "soilp_m":[0.412909,0.416333,0.012],
    "soilp_t":[33.7455,34.1667,0.400002],
    "co2":[407.552,465.22,108.547],
    "co2_wet":[396.912,446.847,96.9495],
    "h2o":[26.1346,39.2463,16.9272],
    "cell_t":[51.4534,51.4569,0.0199013],
    "cell_p":[95.7688,95.7761,0.0236053],
    "flow_rate":[0.741264,0.741002,0.00915241]
},

Footer

Lastly, the Footer variables give fluxes and other processed data calculated from SoilFluxPro™ Software. Three variables are presented at the top of this section, followed by flux data for the individual gases being measured.

Listing 4‑4. The Footer gives fluxes and other data that has been calculated. Gases are identified by name.

Copy 
"footer":{
    "P_o":96.5878,
    "T_o":31.9038,
    "W_o":29.32,
    "fluxes":[{
        "name":"ch4",
        "F_o":0.0868594,
        "F_cv":4.71688,
        "t_o":24.5392,
        "C_o":1918.24,
        "a":0.00138232,
        "C_x":1928.44,
        "iter":5,
        "sei":0.045308,
        "ses":0.000647258,
        "r2":0.813923,
        "slope":0.0141046,
        "domain":98,
        "n":99
        },
        {
        "name":"co2",
        "F_o":5.41461,
        "F_cv":1.35554,
        "t_o":-2.62295,
        "C_o":396.007,
        "a":0.00171484,
        "C_x":908.734,
        "iter":2,
        "sei":0.495223,
        "ses":0.00707461,
        "r2":0.992023,
        "slope":0.879245,
        "domain":98,
        "n":99
        }]
    }

More information on these variables can be found in the SoilFluxPro™ Software manual, available at www.licor.com/env/support.

Data dictionary

The following tables provide a detailed description of how the variables from each section of the data file are represented in the user interface software, and how these variables are defined.

Header variables

Data File Variable Interface Variable Definition
Chamber Name Smart Chamber serial number.
Version Version Smart Chamber software version.
DeviceType LI-7810, LI-7820, or LI-870 LI-COR analyzer(s).
DeviceName TG10/TG20-xxxxx or SSA-xxxx Analyzer serial number(s) (if using LI-COR analyzer).
Date - Timestamp for when the repetition begins.
RepNum - Repetition number.
DeadBand Deadband Dead band (seconds).
Area Soil Area Soil collar area (cm2).
Offset Collar Offset Soil collar height (cm).
ChamVolume Chamber Smart Chamber system volume (cm3).
IrgaVolume IRGA(s) Gas analyzer optical bench volume (cm3). This reported value also includes tubing volume.
TotalVolume Total Total system volume (cm3; calculated as IrgaVolume + ChamVolume + (Offset * Area))
gps_time - GPS Time (seconds since 05 Jan 1980).
latitude Lat Soil collar latitude (degrees).
longitude Long Soil collar longitude (degrees).
gps_hdop HDOP GPS dilution of precision (see Troubleshooting).
altitude Altitude Soil collar altitude (meters above sea level).
gps_sats # Satellites Number of GPS satellites being used to calculate GPS data.
TimeZone Timezone User-set time zone.

Data variables

Data File Variable Interface Variable Definition
timestamp - Observation length time (seconds).
chamber_p Chamber Pressure Chamber pressure (kPa).
chamber_p_t - Chamber pressure sensor temperature (°C).
chamber_t Chamber Temperature Chamber temperature (°C).
soil_t Soil Temperature Soil temperature value read from type-E thermocouple port (°C).
soilp_c Soil EC Soil electrical conductivity value from Stevens HydraProbe (S/m).
soilp_m Soil Moisture Soil moisture value from Stevens HydraProbe (m3/m3).
soilp_t Soil Temperature Soil temperature value from Stevens HydraProbe (°C).
ch4 CH4 Methane concentration (ppb) reported from LI-7810.
co2 CO2 Carbon dioxide concentration (ppm) reported from LI-7810 or LI-7815 or LI-870.
h2o H2O Water vapor mole fraction (mmol/mol) reported from LI-7810, LI-7815, or LI-870.
err - Error code from LI-78xx Trace Gas Analyzers. Refer to your trace gas analyzer manual for detailed information about the error code.
cell_t - Optical bench temperature (°C) from LI-870 analyzer.
cell_p - Optical bench pressure (kPa) from LI-870 analyzer.

Summary variables

Data File Variable Interface Variable Definition
timestamp - Initial value, mean, and range of observation length time (seconds).
chamber_p Chamber Pressure Initial value, mean, and range of chamber pressure values (kPa).
chamber_p_t - Initial value, mean, and range of chamber pressure sensor temperature values (°C).
chamber_t Chamber Temperature Initial value, mean, and range of chamber temperature values (°C).
soil_t Soil Temperature Initial value, mean, and range of soil temperature values read from type-E thermocouple port (°C).
soilp_c Soil EC Initial value, mean, and range of soil electrical conductivity values from Stevens HydraProbe (S/m).
soilp_m Soil Moisture Initial value, mean, and range of soil moisture values from Stevens HydraProbe (m3/m3).
soilp_t Soil Temperature Initial value, mean, and range of soil temperature values from Stevens HydraProbe (°C).
n2o N2O Initial value, mean, and range of N2O concentration values (ppb) reported from LI-7820.
ch4 CH4 Initial value, mean, and range of methane concentration values (ppb) reported from LI-7810.
co2 CO2 Initial value, mean, and range of carbon dioxide concentration values (ppm) reported from LI-7810, LI-7815, LI-7820, or LI-870.
co2_wet - From the LI-870 only, the CO2 value not corrected for the presence of water vapor.
h2o H2O Water vapor mole fraction (mmol/mol) reported from LI-7810, LI-7815, or LI-870.
err - Error code from LI-78xx Trace Gas Analyzers. Refer to your trace gas analyzer manual for detailed information about the error code.
cell_t - Optical bench temperature from LI-870 analyzer.

Footer variables

Data File Variable Interface Variable Definition
P_o - Initial chamber pressure (kPa).
T_o - Initial chamber temperature (°C).
W_o - Initial water vapor mole fraction (mmol/mol).
name ch4; co2 Name of gas species being summarized. Used as the prefix in the interface-displayed version of the remaining flux variables.
F_o name_F_o Flux computed from the exponential fit (unit depends on gas species).
F_cv name_F_cv Flux coefficient of variance (%).
t_o name_t_o The t0 term for the exponential fit (seconds).
C_o name_C_o Initial gas concentration (unit depends on gas species).
α name_α The α term for the exponential fit.
C_x name_C_x The term C∞ for the exponential fit.
sei name_sei Standard error of the intercept of the concentration vs. time curve (%).
ses name_ses Standard error of the slope of the concentration vs. time curve (%).
r2 name_r2 Flux correlation coefficient.
slope name_slope Slope of the exponential fit at time t0.
domain name_domain Number of data points in the observation length.
n name_n Number of data points used for exponential curve fitting.