Supported biomet file formats

EddyPro supports biomet data in two main formats: embedded in compressed .ghg eddy covariance data files, and as external text files. These are described in detail below.

Biomet data files embedded in .ghg files

The preferred, easiest, and most robust system to store and process biomet data is to collect them with a LI-COR biomet station. When collected through the SmartFlux 2 or 3 System, biomet data are stored in an ASCII, tab-separated file in a format that closely resembles that of the EddyPro data files, featuring a preamble and a header with variable names and units. This biomet file, identified by the suffix -biomet.data, comes with a paired -biomet.metadata file, which describes the format and, more importantly, the content of the file, with identification of the variables, their units, the sampling and averaging rates, etc. This structure closely replicates that of the EddyPro .data and .metadata. If the SmartFlux 2 or 3 System is collecting both eddy and biomet data, all four files are bundled together in a unique file with a .ghg extension containing all data corresponding to every time period of the specified length, and the corresponding metadata.

You can download a sample .ghg file including eddy and biomet files from the LI-COR web site. We suggest taking a few minutes to explore its content of this file. Unzip the file using, for example, 7-zip (after installation, right-click → 7zip → Extract Here) and open any of the files with a text editor. You will quickly figure out the format of both the .data and .metadata files and the organization of the content.

External biomet files

If you don’t have biomet data collected with the .ghg files, or if you want to process data collected as text files, you can still do so by formatting your biomet file(s) as described below.

External biomet files must be formatted (outside EddyPro, for example using MS Excel) in such a way that EddyPro can interpret them without the need to specify anything in the EddyPro interface. This means that extreme care must be given in correctly labeling variables, writing units, defining timestamps, etc.

Following you can find detailed guidelines that should allow you to correctly format your biomet file(s):

• Files are formatted as ASCII, comma-separated files;
• Each data line—terminated by CR/LF (Windows) or by LF (Mac/Linux)—is a record of biomet measurements, identified by a timestamp;
• Each file starts with a 2-line header:
  • In the first line, a label is associated to each data column (including the timestamp) to identify the variable. For the naming convention, refer to the tables below;
  • In the second line, a label is associated with each data column (including the timestamp) to identify the unit of each measurement. For the naming convention, refer to the tables below;
  • Capitalization in the header is irrelevant;
  • Location qualifier: The variable labels in the first line of the header can include as a suffix the “location qualifier” designed by the European Fluxes Database Cluster. The location qualifier is comprised of a numeric triplet in the form _X_Y_Z where X, Y and Z are integer numbers identifying the location of the instrument/sensor that measured the variable. An example of a label with location qualifier is: TA_1_2_3.
  • If you are not required to use the location qualifier, you can simply use the variable label. Note, however, that EddyPro outputs are standardized on the usage of the location qualifier. Any time EddyPro encounters a variable without the qualifier, EddyPro will rename it by adding a default qualifier as a suffix to the label provided. As an example, if the variable is labeled TA, the variable will be identified as TA_0_0_1 in the biomet output. If there are multiple instances of the same variable, the last number of the default qualifier will be increased: TA_0_0_2, …, TA_0_0_5”, …
  • Since the official usage of the location qualifier does not foresee the use of zeros, having zeros in the first two positions of the qualifier in EddyPro’s output is an indication that the variable was provided without qualifier.

• Timestamps: Timestamps can occupy up to 7 (comma-separated) fields, that can appear anywhere in the file (i.e., not necessarily in the first columns). In the first header line, timestamp columns are identified by the labels:

In the second header line, the format of the timestamp is specified according to the following conventions:

Table 2‑1. Timestamp formats for biomet data in EddyPro.

Variable	EddyPro Label	Description of corresponding data
yyyy	year	4-digit integer number
mm	month of year	2-digit integer number, between 01 and 12
ddd	day of year	3-digit integer number, between 001 and 366
dd	day of month	2-digit integer number, between 01 and 31
HH	hour of the day	2-digit integer number between 00 and 23
MM	minute of the hour	2-digit integer number between 00 and 59

The following examples are of valid timestamp headers and data:

Labeling and units conventions for formatting external biomet files:

Table 2‑2. Biomet variables supported by EddyPro.

Variable	EddyPro Label	EddyPro Units	How to Write Units	Other Supported Units
Air Temperature	Ta	K	K	C, cC, F, cF, cK
Atmospheric pressure	Pa	Pa	Pa	hPa, kPa, PSI, Torr, mmHg, Atm, Bar
Relative humidity	RH	%	%	#
Canopy temperature	Tc	K	K	C, cC, F, cF, cK
Air temperature below canopy	Tbc	K	K	C, cC, F, cF, cK
Diffuse radiation	Rd	W m-2	W+1m-2	J s-1 m-2
Reflected radiation	Rr	W m-2	W+1m-2	J s-1 m-2
Global radiation	Rg	W m-2	W+1m-2	J s-1 m-2
Net radiation	Rn	W m-2	W+1m-2	J s-1 m-2
UVA radiation	R_uva	W m-2	W+1m-2	J s-1 m-2
UVB radiation	R_uvb	W m-2	W+1m-2	J s-1 m-2
Longwave incoming radiation	LWin	W m-2	W+1m-2	J s-1 m-2
Longwave outgoing radiation	LWout	W m-2	W+1m-2	J s-1 m-2
Shortwave incoming radiation	SWin	W m-2	W+1m-2	J s-1 m-2
Shortwave outgoing radiation	SWout	W m-2	W+1m-2	J s-1 m-2
Shortwave below canopy	SWbc	W m-2	W+1m-2	J s-1 m-2
Shortwave incoming diffuse	SWdif	W m-2	W+1m-2	J s-1 m-2
Photosynthetic photon flux density	PPFD	μmol m-2 s-1	umol+1m-2s-1	μE m-2 s-1
Diffuse PPFD	PPFDd	μmol m-2 s-1	umol+1m-2s-1	μE m-2 s-1
Reflected PPFD	PPFDr	μmol m-2 s-1	umol+1m-2s-1	μE m-2 s-1
Below Canopy PPFD	PPFDbc	μmol m-2 s-1	umol+1m-2s-1	μE m-2 s-1
Total precipitation	P	m	m	um, μm, mm, cm, km
Rain precipitation	P_rain	m	m	um, μm, mm, cm, km
Snow precipitation	P_snow	m	m	um, μm, mm, cm, km
Snow depth	SNOWd	m	m	um, μm, mm, cm, km
Maximum wind speed	MWS	m s-1	m+1m-1	cm s-1, km h-1
Wind direction	WD	deg. from N	degrees	-
Bole temperature	Tbole	K	K	C, cC, F, cF, cK
SapFlow	SapFlow	g h-1	g+1h-1	-
StemFlow	StemFlow	g h-1	g+1h-1	-
Soil temperature	Ts	K	K	C, cC, F, cF, cK
Soil heat flux	SHF	W m-2	W+1m-2	J s-1 m-2
Soil water content	SWC	m3 m-3	m+3m-3	-