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.
{ "name": "garden_soil_flux",
"remark": "garden next to 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.
"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.
"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.
"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.
"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/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. |