ECO2S

ECO2S
An overview of the Graphical User Interface
15 October 2010
Compiled by
Gerardo Fratini
Antonio Forgione
Department of Forest Sciences and Resources, University of Tuscia, Viterbo, Italy
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Contents
Abstract ................................................................................................................................................ 6
1. ECO2S Start Menu ....................................................................................................................... 7
::Data Logging ............................................................................................................................. 7
::Data Processing.......................................................................................................................... 7
2. ECO2S Menu bar (1) .................................................................................................................... 8
File Menu ......................................................................................................................................... 8
View Menu ....................................................................................................................................... 8
Start Menu .................................................................................................................................... 8
Project Page.................................................................................................................................. 8
Managed/Unmanaged mode ........................................................................................................ 9
Full screen .................................................................................................................................... 9
Status bar ...................................................................................................................................... 9
3. Project Page................................................................................................................................ 10
Raw File Type ............................................................................................................................ 10
Number of ASCII header lines................................................................................................... 11
End of line .................................................................................................................................. 11
Number of bytes per variable ..................................................................................................... 11
Endianess ................................................................................................................................... 11
Custom configuration file .......................................................................................................... 11
Raw file name format ................................................................................................................. 12
Use dynamic parameter file ....................................................................................................... 12
Use ECO2S::Datalogging project file ........................................................................................ 12
Next ............................................................................................................................................ 13
4. Processing Suite Page ................................................................................................................ 14
5. ECO2S Menu bar (2) .................................................................................................................. 15
Tools........................................................................................................................................... 15
Window ...................................................................................................................................... 15
6. ECO2S::RawProcess .................................................................................................................. 16
General Options Tab ...................................................................................................................... 16
Raw data directory ..................................................................................................................... 16
Output directory ......................................................................................................................... 16
Flux averaging interval .............................................................................................................. 17
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Number of files to merge ........................................................................................................... 17
Create continuous dataset........................................................................................................... 17
Missing lines allowance ............................................................................................................. 17
Settings Tab.................................................................................................................................... 19
Wind speed measurement off-set ............................................................................................... 19
Cross-wind correction for sonic temperature ............................................................................. 19
Angle-of-attack correction for wind components (Gill’s only) ................................................. 19
Axis rotation for tilt correction .................................................................................................. 20
Detrending .................................................................................................................................. 21
Time-lag compensation .............................................................................................................. 21
Output all binned (co)spectra ..................................................................................................... 23
Output full cospectra of sonic sensible heat............................................................................... 23
Window for data tapering before fft-ing .................................................................................... 23
Number of frequency bins for spectra reduction ....................................................................... 23
Statistical Tests Tab ....................................................................................................................... 24
7. ECO2S::Meteo ............................................................................................................................ 28
Meteo file(s) type ....................................................................................................................... 29
Data directory............................................................................................................................. 30
File extension ............................................................................................................................. 30
Timestamp refers to ................................................................................................................... 31
Date format ................................................................................................................................ 31
Time format................................................................................................................................ 31
Field separator ............................................................................................................................ 31
Separator policy ......................................................................................................................... 31
Variable Options Tab ..................................................................................................................... 32
8. ECO2S::Tilting ........................................................................................................................... 34
Level 4 statistics file .................................................................................................................. 34
Starting and ending date/time of dataset .................................................................................... 35
Missing lines allowance ............................................................................................................. 35
Number of wind sectors ............................................................................................................. 35
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Minimum number of elements per wind sectors ........................................................................ 35
Maximum average w (per input file).......................................................................................... 35
Minimum average u (per input file) ........................................................................................... 35
Time-varying info file ................................................................................................................ 36
9. ECO2S::Spectra .......................................................................................................................... 37
Binned (co)spectra directory ...................................................................................................... 38
Raw fluxes file ........................................................................................................................... 38
Use external meteo data file ....................................................................................................... 38
Use external virtual meteo data file ........................................................................................... 39
Number of bins of reduced spectra ............................................................................................ 39
Minimum number of spectra samples in each frequency bin .................................................... 39
Minimum sensible heat flux ....................................................................................................... 39
Groups Tab ..................................................................................................................................... 41
10. ECO2S::Fluxes........................................................................................................................ 43
General Info Tab ............................................................................................................................ 43
Level 7 statistics file .................................................................................................................. 43
Create continuous dataset........................................................................................................... 44
Time-varying info file ................................................................................................................ 44
Use external meteo data file ....................................................................................................... 44
Processing Options Tab ................................................................................................................. 45
Axis rotation for tilt correction .................................................................................................. 45
Compensation of density fluctuations ........................................................................................ 46
Add Li7500-related sensible heat components .......................................................................... 46
Correction of sonic temperature for humidity............................................................................ 47
Spectral Corrections Tab ................................................................................................................ 48
High-pass filtering correction .................................................................................................... 50
Post-processing Options Tab ......................................................................................................... 51
Quality check ............................................................................................................................. 51
Footprint estimation ................................................................................................................... 52
References .......................................................................................................................................... 53
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blank page
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Abstract
In this document we provide a quick-look guide describing ECO2S Graphical User Interface (GUI).
The document is intended to help the user to understand the meaning of each entry, in order to
perform a proper Eddy Covariance (EC) processing, according to the data type and to the EC
site/set-up under consideration. The structure of ECO2S and its flow of data processing are
described in a separate document: “ECO2S – A quick introduction and user reference”, to which the
present guide refers often.
Note: In the present version of this document, the tool ECO2S::Timelag is not described, due to
time limitations. However, a quick look to ECO2S::Timelag and ECO2S::RawProcess will show
that there are minor differences between the two. ECO2S::Timelag requires a subset of the settings
of ECO2S::RawProcess. The only new entry here is Use external meteo data file, also described at
p. 38 in the context of ECO2S::Spectra.
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1. ECO2S Start Menu
::Data Logging
This is the main entrance to the ECO2S::Datalogging program. This is a fully-featured program to
acquire Eddy Covariance data. However, currently this software is not embedded into ECO2S
Graphical Interface, thus the button is ineffective. ECO2S::Datalogging is available as a separate
program, distributed on demand with the old name of ECO2Catch.
::Data Processing
This is the main entrance to ECO2S::Dataprocessing. This program allows you to process raw Eddy
Covariance data, to get corrected fluxes and a number of optional outputs, useful for further micro-
meteorological analysis.
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2. ECO2S Menu bar (1)
ECO2S features a rather limited Menu, with standard options that allow you to work with “project
files”, change a few settings and preferences, arrange project windows.
File Menu
As described more in depth in “ECO2S – A quick introduction and user reference”,

ECO2S::Dataprocessing is organized in “processing projects”. Each processing project files retains
all choices made by the user on which data to process and how to process them. You can handle
project as usual: New Project, Open, Open Recent, Save, Save as, Close act on the project file in the
common way. ECO2S project files are plain text files organized in INI format. Refer to the quick
introduction document for more details. The “Quit” button closes ECO2S.
View Menu
Start Menu
Click here to return to ECO2S Start Menu.
Project Page
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Takes you to the Project Page, where you enter general information, common to all following
processing steps.
Managed/Unmanaged mode
Not yet active, this option will allow to work in “supervised mode” (managed) or “expert mode”
(unmanaged). In “supervised mode” several options will be disabled and ECO2S will make some
choices for you, depending on your Eddy Covariance set-up and on the raw files. This is intended to
guide inexpert (or undecided) users to process data in a relatively safe way. The “expert mode” will
turn on all options and all their combinations, thereby also allowing more flexible usage, but also
exposing to unsuitable or even incorrect procedures.
Full screen
Shows ECO2S window on full screen.
Status bar
Shows/hide the status bar, where some activity logging is shown, along with the current date and
time and with the software version.
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3. Project Page
When you enter ECO2S::Dataprocessing, you are first introduced to the “Project Page”, where you
are asked to enter some general information, common to any following data processing. Here you
enter a Title and an ID for the current processing project. Note that the ID will be attached to all
output file names, thus you’d better choose a short one.
Raw File Type
Select here the type of raw files you are going to process. Several options are available:
 Standard Ene: raw files created by ECO2Catch, refer to “ECO2S – A quick introduction
and user reference” for an introduction to this raw file type.
 Native Streams: unmodified anemometric data streams. Native Streams can be collected
using ECO2Catch, but also with any simple serial monitor. In this release, supported Native
Streams are those from R3, HS, WindMaster sonics by Gill Instruments ltd. (Lymington,
Hampshire, England) and USA-1 by Metek GmbH (Elmshorn, Germany). Native serial
binary streams from the CSAT-3 by Campbell Scientific Inc. (North Logan, UT, USA) will
be supported starting from the next release.
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 Generic ASCII: select this option to process raw files available as (not too complicated)
ASCII tables. Comma-, semi-column-, space- and tab- separated data columns are
supported.
 Binary Alteddy: binary files generated by Alteddy.
 Binary EddySoft: SLT files generated by EddyMeas, the data acquisition tool of the
EddySoft package by the Max Planck Institute for Biogeochemistry, Jena, Germany.
 Binary EdiRe: SLT files generated by EdiRe data software by the University of Edinburg,
Edinburg, UK. Note that EdiRe and EddySoft SLT files differ mainly for the format of the
binary header.
 Generic binary: generic binary format, for which details must be specified in the right
column (see below). This feature is still an “alpha version”, please report any bug or
difficulty you may encounter while using it.
Number of ASCII header lines
Applicable to all binary formats, allows to specify an eventual number of ASCII header lines in the
raw files.
End of line
Line terminator for the ASCII header lines (for binary files).
Number of bytes per variable
Here you specify the number of bytes used for each data value (for binary files).
Endianess
Specify here the order of meaningfulness of the bytes in each binary word. If in doubt, refer to the
developer of your data acquisition software. Most of the times “Little endian” applies.
Custom configuration file
Applicable when either EddySoft or EdiRe SLT binary data files are selected, it prompts you to
select a configuration file that is needed to interpret and convert the raw files. For EddySoft files the
relevant CFG file (produced by EddyMeas at acquisition time) must be selected. For EdiRe files,
the configuration file is a “processing list” containing, at least, the “Extract” and “Linear”
commands for all variables contained in the raw files. Refer to the documentation of the two
software if in doubt.
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Raw file name format
Here you must provide a prototype for the raw file names that ECO2S will use to extract timestamp
information. Refer to “ECO2S – A quick introduction and user reference” for details on how to
provide such prototype.
Use dynamic parameter file
Use this checkbox, and the related “Load…” button, to select a file with time-varying site/station
parameters. This requires some more explanations. As already mentioned, ECO2S::Dataprocessing
is particularly suited to process ENE files. Each ENE file contains acquisition-time information
about the site (e.g. the height of the canopy) and the set-up of the Eddy Covariance station (e.g. the
measurement height). Such parameters can change along the dataset, e.g. think about the canopy
height of a crop field: if the user updated ECO2S::Datalogging settings with current values, any
change in the acquisition-time parameters is automatically accounted for, because each ENE file is
processed with its corresponding parameters. However, if you are processing raw files of any other
type, you cannot automatically associate different values of acquisition-time parameters to different
raw files. A way around, is to provide a file that contains the time series of acquisition-time
parameters, if those are known to change along the dataset under consideration. Such file must be
created (currently outside ECO2S, e.g. with a spreadsheet) in a predefined format, described in
“ECO2S – A quick introduction and user reference”.
Use ECO2S::Datalogging project file
Use this checkbox, and the related “Load…” button to provide ECO2S with the proper “acquisition
project file”. Several cases can be envisaged here (refer to “ECO2S – A quick introduction and user
reference” for a more comprehensive description):
 You are processing ENE files and there are acquisition-time parameters changing along the
dataset: in this case, uncheck this option. Files will be processed using file-specific
acquisition-time parameters. It is the best way to process your data.
 You are processing ENE files but acquisition-time parameters did not change during
acquisition of your dataset: in this case, you can speed up the processing procedure, by
doing this: 1) unzip any ENE file; 2) locate the INI file extracted for the ENE archive; 3)
Use the “Load…” button to select this file; 4) check in the right (multi-)panel that all
information have been retrieved correctly; 5) in case any information was not retrieved
correctly, change it as needed and save the “ECO2S::datalogging project file” using the
buttons on the bottom-right corner of the right panel. By doing so, ECO2S will not read
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acquisition-time parameters from each ENE file, rather will use those provided in the file
you just loaded. This will speed up the processing a little.
 You are not processing ENE files: in this case you must use a (virtual) “ECO2S::datalogging
project file”; most likely you don’t have one, so you must fill completely the multi-panel on
the right side (if you were acquiring raw data with ECO2Catch, you would have entered the
same information at acquisition-time). For an overview of content of the right-side multi-
panel, refer to the “ECO2S – A quick introduction and user reference”. Once you have filled
at least all green (=mandatory) fields, save the file with the buttons on the bottom-right
corner. The saved file will appear on the “Load…” entry; such acquisition-time information
will be used for the processing, unless they are bypassed by the time-varying parameters file
(see Use dynamic parameter file).
Next
This button activates if all mandatory fields have been entered. It takes you to the suite of
processing software. The information you entered so far will be used by most of the following
software, so make sure everything is set correctly.
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4. Processing Suite Page
By clicking “Next” in the Project Page, you have been taken to the Processing Suite Page, the place
where you will actually process your data. Remember that you can go back to the Start Menu or to
the Project Page from the View Menu, as well as from the corresponding icons in the tool bar.
The Processing Suite Page is characterised by the Software Menu on the left side, where you can
select the software you want to use. As you can read in more details in the “ECO2S – A quick
introduction and user reference”, in ECO2S corrected fluxes are obtained from raw data through a
series of – at least – two steps: the raw data processing (performed by ECO2S::RawProcess) and the
flux calculation (performed by ECO2S::Fluxes). A number of other tools are available for: 1)
optimizing time-lag estimations (ECO2S::Timelag); 2) formatting high-quality meteorological data
(ECO2S::Meteo); 3) calculating planar-fit rotation matrices (ECO2S::Tilting) and 4) analysing
turbulence co-spectra (ECO2S::Spectra). When you enter the Processing Suite, you are prompted to
ECO2S::RawProcess that is normally the starting point of the data processing. You can pass to
another tool by clicking on the related icon. Note that the “Run” button under the menu is
contextual, thus it will attempt to run the software that is currently active.
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5. ECO2S Menu bar (2)
Tools
The screenshot in the previous page shows ECO2S Output Console (the black window on the right),
that you can show/hide by checking/un-checking it from the Tools Menu in the Menu bar.
Window
Use options in this menu to arrange, visualize or close open windows. ECO2S is intended to be
multi-project, meaning that it will allow you to work on more than one processing project at a time.
Presently, however, known bugs related to this capability prevent a safe use, thus in this preliminary
release this option is switched off. The Window menu options are anyway fully operative.
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6. ECO2S::RawProcess
General Options Tab
As already mentioned, and described in more details in the “ECO2S – A quick introduction and user
reference”, ECO2S::RawProcess is the software that imports raw files and calculates main statistics
(such as mean values, standard deviations, covariances, skewness, kurtosis), that are used for the
calculation of corrected fluxes with ECO2S::Fluxes. It performs some standard Eddy Covariance
processing, such as de-spiking, cross-wind correction, angle-of-attack correction, 2D rotations for
tilt correction, time-lag compensation. In addition, it performs a thorough statistical screening of
raw time series reporting the corresponding flags, calculates tentative fluxes, derives values for
meteorological variables, calculates (on demand) spectra and co-spectra and performs the so-called
stationarity test.
In the General Option Tab, you provide some general information, listed hereafter. Remember that
green fields are mandatory.
Raw data directory
Use the “Browse…” button to locate the folder where your raw files are stored. If files are
organised in subfolders (e.g. monthly sub-folders), locate the parent folder and check the “Search in
subfolder” button. In this software version, depending on how raw files are named and organised in
folders, they might be processed in an order that is different than the chronological one. However,
an option is available for rearranging them in the proper chronological order (see “Create
continuous dataset” below). In the following release, files will be processed directly in
chronological order, regardless of their position or naming criteria.
Output directory
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Use the “Browse…” button to select the main output directory. Keep in mind that
ECO2S::RawProcess will create several subfolders in the selected parent folder and put output files
in there. Note also that this field, similar to output directories in other parts of the suite, is editable
directly from the GUI, without the need of using the “Browse…” button. When editing in such a
way, make sure that the path you type is compatible with your OS file system.
Flux averaging interval
Enter here the time period over which you want fluxes to be averaged, in minutes. Flux averaging
intervals can different from the duration of the raw files. Refer to “ECO2S – A quick introduction
and user reference” for details on how to better exploit your data files and get fluxes averaged over
any time period. Entering 0 (zero) minutes will cause ECO2S::RawProcess to process considering
the duration of each raw file as the flux averaging period.
Number of files to merge
Specify here how many files shall be merged and considered as one only file, for the purpose of
flux computation. This entry must be harmonized with the Flux averaging interval, as better
explained in the “ECO2S – A quick introduction and user reference”.
Create continuous dataset
If checked, ECO2S::RawProcess attempts to create a dataset going from the date/time of the first
raw file, to the date/time of the last one, using the “Flux averaging period” as a time step. Hence,
keep in mind that the very first (in a chronological sense) raw file should have a “correct”
timestamp, with respect to the time series you have in mind. If there are not enough data for
calculating fluxes for any time step, ECO2S::RawProcess will fill the corresponding output line
with an error code. Finally, checking this option forces the software to organize output data lines
chronologically. If the option is unchecked, instead, output files will contain only data lines
corresponding to time periods for which enough data are available for calculating corresponding
fluxes. However, in the current release we cannot assure that in all conditions the data lines will be
ordered chronologically. This will surely be the case when alphabetic and chronological orders
match, but in other cases – such as when files are organised in subfolders – the alphabetic order
may be prioritized. In both case (option checked or unchecked) ECO2S::RawProcess will
automatically adjust timestamps of files that are not coherent with the timeline defined by the flux
averaging period, so that the time structure of the output datasets is regular.
Missing lines allowance
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Each raw file will be tested for the number of data lines contained. Select here the maximum
amount of missing line (in percent) that is acceptable. Raw files with a larger amount of missing
lines will be ignored.
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Settings Tab
In this tab you make choices on how to process raw files.
Wind speed measurement off-set
If you know a systematic bias in the determination of any wind speed components, you can allow
ECO2S::RawProcess to account for it by specifying it here.
Cross-wind correction for sonic temperature
Check this option if you want ECO2S::RawProcess to apply the cross-wind correction to the
estimated sonic temperature. The correction is applied at the raw data level - that is, sample by
sample - after (Liu et al., 2001, Eqs. 3-9). However, the “humidity correction” term of their Eq. 3 is
not applied here, rather it is postponed and applied on the statistics that involve sonic temperature,
following a suggestion by (van Dijk et al., 2004, p. 36). Note that several anemometer models
include the correction in the firmware, so that the output temperature is already compensated for
cross-wind. In this release, it is left up to the user to avoid double accounting, by assuring coherence
between the anemometric measurement and the processing settings.
Angle-of-attack correction for wind components (Gill’s only)
The angle-of-attack correction refers a procedure that attempts to eliminate the error in the wind
speed measurements, due to an imperfect (co)sine response of the anemometer. This imperfection is
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due mostly to the self-sheltering of the transducers and to the flow distortion induced by the frame
of the anemometer. The correction, currently available only for Gill’s anemometers (WindMaster,
WindMaster Pro, R2, R3 and R3-50, R3-100), is implemented after (Nakai et al., 2006, Eqs. 3-6),
and the routine used is derived from the original routine available in Taro Nakai’s web page,
patched to be embedded in ECO2S. It is worth to underline that the application of this correction is
virtually independent (Taro Nakai, personal communication) from the internal correction “applied
to calibrate out the affects of the transducers and head framework” (cited from the R3/R3A User
Manual, Gill Instruments Ltd.). Thus, whether you acquired “CALIBRATED” or
“UNCALIBRATED” wind components, you may decide to apply the present correction as well.
Axis rotation for tilt correction
Tilt correction refers to the procedure that attempts to compensate for the misalignment of the sonic
anemometer with respect to the local streamlines coordinate system. Four options are available in
ECO2S::RawProcess, all implemented after (Wilczak et al., 2001):
 DR on raw data (before detrending): double-rotation about the z and y axis, to nullify the
vertical and lateral wind components and align the x-axes with the (run-specific) mean wind
vector. The procedure is applied following (Wilczak et al., 2001, Eqs. 22-29). If you choose
this option, rotations are applied at the raw data level, before the time series are detrended.
 DR on statistics (after detrending): same rotation as above, but not applied to the raw data,
rather directly to the relevant statistics (mean values and covariances).
 TR on statistics (after detrending): include the DR on statistics, plus a third rotation to

nullify the cross-stream Reynolds stress, following (Wilczak et al., 2001, Eqs. 30-33).
 Planar fit (after detrending): this is an alternative way to align the coordinate system to
the (long-term) mean local streamlines. It is implemented here following (Wilczak et al.,
2001, Eqs. 35 and 42-47).
Note that selecting a method applied on statistics (all but the first one), causes ECO2S::RawProcess
not to perform any rotation. In fact, these rotations are applied later, by ECO2S::Fluxes. This is
because ECO2S::RawProcess is intended to act on the raw data in order to calculate well defined
statistics. Any further processing is done in subsequent steps. Thus, the main difference between the
first and the second method, is that the second is applied after time series have been detrended.
Rotation angles, however, are always calculated with un-detrended wind components.
If you do not want to correct for such possible problem, uncheck this entry.
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Detrending
Detrending, or high-pass filtering, can be performed in ECO2S::RawProcess, by any of the

following four options:
 Block average: it is the simple act of subtracting mean values from the time series,
calculated on the whole averaging period.
 Linear detrending: consists in calculating fluctuations of each variable about a linear trend,
calculated on the whole averaging period.
 Running mean: a local mean is defined at each time step by:
1
vi vi 1  (v i  v i  n ) (1)
n
In Eq. (1) as each new number is added into the average, the one n before is dropped out of
it, so each new number is the average of the last n old numbers. n is defined by the filter
time constant  , expressed in seconds: n    f a , with f a being the acquisition frequency
(Hz). Fluctuations are then calculated around such local mean values.
 Exponentially-weighted average: similar to the previous one, but here the local mean is
defined by the weighted average of the current data point and the previous average:
vi  (1  a)vi  avi 1 (2)
with the weight a given by the exponential:
t
ae 
(3)
where  is again the filter time constant and t  1 / f a .
Note that the last two methods require you to enter a “filter time constant”, that gets a different
meaning in the two cases. In both cases, the higher the time constant, the smaller the frequency
range that the filter cuts off.
Time-lag compensation
This entry provides several methods to compensate the time-lag between anemometric and gas
concentration time series, that might be due to several reasons (transient time of gases into a
sampling line, sensors separation, electronics delays). Depending on the causes of the possible time-
lags, different options might be more suited:
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 Do not compensate: if you uncheck this entry, no time-lag compensation will be performed.
This choice, that helps speeding up the data processing, might be suitable only in case of
wind/concentration sensors placed very closed to each other, with rather sustained winds
that minimize the transit time between the sensors and with gas analysers that do not need a
sampling line to take the air parcels to the measuring cell.
 Constant: this is a preferred option over the previous one, in the same situations described
above. You have already set a tentative time-lag for each of the gases in Project Page (or at
acquisition time in case of ENE files). This values will be used to synchronise wind and gas
concentration time series. This option might be suitable also for a not-so-accurate flux
calculation (e.g. for checking the status of the acquisition), in case of larger time-lags
induced by the presence of a sampling line, typical of closed-path gas analysers.
 Max covariance with default: this is the most common way to determine and compensate
the time-lags. With this procedure, also referred to as “circular covariance”, the best time-
lag estimation is determined by maximizing the covariance between the vertical wind speed
and the gas concentration time series, within a range of plausible time-lags, defined by the
minimum and maximum time-lags you have set in the Project Page (or at acquisition time in
case of ENE files). If a maximum is not attained for the covariance within the window of
plausible time-lags (that is, if the series of covariances is monotone), a default value is used,
that is the one you set as the nominal time-lag in the Project Page.
 Max covariance without default: same as above, but here the time-lags corresponding to
the maximum covariance are used in any case, even if covariances are monotone functions
of the plausible time-lags. In such cases the maximum covariance is found at one extreme of
the time-lag window and corresponding time-lag is either the minimum or the maximum
that you have set in the Project Page. The difference between this method and the former
one is probably not critical for narrowed time-lag windows, but it becomes more and more
important (and correspondingly affects fluxes) as the range of plausible time-lags becomes
larger.
 Time-lag optimiser: this option requires you to run, first, ECO2S::Timelag. This software,
specifically designed for determining water vapour time-lags in closed-path EC systems,
attempts to calculate a functional relation (an exponential one) between the best time-lag
estimation - and of the plausible time-lag window - and ambient relative humidity, that
largely affects the dynamic of water vapour inside the sampling line (Ibrom et al., 2007a;
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Ibrom et al., 2007b). In doing this, it also provides best estimates for CO2, as well as proper
plausible time-lag windows. If you choose this option, after running ECO2S::Timelag you
must provide here the “Time-lag optimizer file” (the main output of ECO2S::Timelag) as
well as the relevant meteo file, from which relative humidity values are retrieved.
Output all binned (co)spectra
Check this option if you want ECO2S to calculate spectra and cospectra for all relevant variables
and fluxes. This option, that considerably increases the processing time (about 70% longer), must
be selected if you want to apply certain spectral correction schemes for low-pass filtering
correction. This issue is particularly critical for closed-path systems, although open-path systems
are not unaffected by high-frequency losses.
Output full cospectra of sonic sensible heat
This option, also indispensable in case of certain spectral correction schemes available in
ECO2S::Fluxes, is meant to output the full (i.e., not binned) co-spectrum of vertical velocity with
sonic temperature, that – assuming spectral similarity – can be considered as a reference
atmospheric cospectrum for all passive scalars, with the property of being unaffected (or minimally
affected) by artificial high-frequency attenuation.
Window for data tapering before fft-ing
If you selected either spectral output, here you can select the shape of the filter applied to the time
series before calculating their Discrete Fourier Transforms. The time-domain data windowing, or
tapering, is meant to reduce the among-frequencies leakages while estimating discrete spectra.
Different window shapes trade off in different ways between the peakedness and the narrowness of
the leakage function, although the final effects are rather similar to the purposes of micro-
meteorological analyses. For a thorough discussion of the topic see, e.g., (Press et al., 1996 Ch. 13,
pp. 545 – 549).
Number of frequency bins for spectra reduction
Set here the number of (logarithmically equally spaced) frequency bins for reducing spectra and
cospectra. The binning procedure is primarily meant to eliminate much of the medium and high-
frequency noise to highlight main slopes of (co)spectra. It also has the important side effect of
dramatically reducing the amount of disk space required to store spectral data, while retaining most
the information contained in it.
23
Statistical Tests Tab
This part of the GUI is devoted to the statistical tests that can be performed on the raw time series.
All tests here are implemented after (Vickers and Mahrt, 1997 Par. 6). Tests are selectable on the
left side of the tab. Use the “Select/Deselect All” checkbox for a quick selection. Note that in this
release, tests are implemented only for anemometric variables and for CO2/H2O time series (i.e., not
for methane and nitrous oxide). Where applicable, each time series gets a separate flag from each
test. There are cases, however, when the test is applied only to certain variables, or variable
combinations. Test results are presented as “hard flags” and “soft flags”, defining severe and
moderate deviations from ideal, respectively. For their detailed definition for each test refer to
(Vickers and Mahrt, 1997).
Results of the tests shall be used to take decisions about retaining or discarding the results obtained
from each raw file. ECO2S::RawProcess will not discard time series according to the test results, it
is left up to the user to do so on the final outputs. This is because criteria of selection policy are
hardly defined and partly subjective. Furthermore, reasons for hard-flags should be evaluated in
details, because sometimes unusual but yet plausible conditions may lead to artificial hard-flags
(Vickers and Mahrt, 1997).
All tests have some parameters that can be changed by the user in the corresponding sub-tab, while
other parameters have been hard-set in the code, to trade-off flexibility and complexity of the
interface. However, we appreciate suggestions in this respect. ECO2S::RawProcess proposes default
24
values for all settable parameters, based on the reference paper. However, users should customize
those values according to their EC set-up and site characteristics. ECO2S::RawProcess defaults can
always be restored by clicking the “Set Defaults” button on the bottom right corner. Here it follows
a brief description of the tests:
 Spike detection/removal: selecting this option, time series will be tested for the number of
spikes and flagged if this number is beyond a certain (user selectable) threshold. In doing so,
spikes are removed and replaced by linear interpolation of neighbouring data points. In the
GUI you must set:
o Max consecutive outliers: maximum number of consecutive outliers to

define a spike. If more than n consecutive data points are found outside the
plausibility range, they are not detected as a spike;
o Plausibility range: the amplitude of the range around the window mean,
expressed as multiples of the window standard deviation;
o Accepted amount of spikes: The percentage of spikes, respect to the total

number of data points, defining the threshold to flag the each variable.
 Amplitude resolution: this test assesses whether the number of different values that each
variable takes throughout the time series covers homogeneously enough the range of its
variations. This range is defined by the minimum among: 1) the difference between the
maximum and the minimum value assumed by the variable and 2) n times the standard
deviation of the variable in the time series. Here you must set:
o Range of variation: The multiples of the window standard deviations (n)

defining the range of variations for each variable;
o Number of bins: The number of bins in which the range of variation must be
divided;
o Accepted amount of empty bins: The percentage of empty bins over

which each variable is flagged for a too low amplitude resolution.
 Drop-outs: this test detects whether each variable temporarily sticks on some value
throughout the time series. It is assessed by considering if how many consecutive data points
stay in the same bin (as defined above). Extreme bins (as opposed to central bins) are
expected to have smaller numbers of consecutive data points, thus thresholds are defined
differently for extreme and central bins. You must set:
25
o Percentile defining extreme bins: The percentile that distinguishes
extreme vs. central bins. For example, choosing 10%, the central bins will be those
between the 10th and the 90th percentiles. The remaining bins are considered as
extreme bins.
o Accepted central drop-outs: The threshold percentage of central drop-

outs, beyond which the variable is flagged for too many drop-outs;
o Accepted extreme drop-outs: The threshold percentage of extreme drop-

outs, beyond which the variable is flagged for too many drop-outs.
 Absolute limits: tests the time series for single values exceeding plausible physical ranges.
Here you must set:
o Max horizontal velocity: the maximum plausible horizontal velocity,

calculated from the combination of the two wind components in the anemometer’s
coordinate framework.
o Max vertical wind component: the maximum plausible vertical wind

component. Note that the very raw vertical wind component is used here, before any
compensation for tilt correction. This implies that if the anemometer is sensibly tilted
with respect to local streamlines, a part of the horizontal component may folds into
the vertical one, that would thus result seriously biased. This means that an important
sequence of raw files flagged for too high vertical wind, might be a sign of an
improper installation of the anemometer.
o Min/Max Ts: maximum and minimum values of sonic temperature, used as a

proxy for air temperature. Set these values large enough to include plausible extreme
values. Consider that the test is performed on the raw data, not on 30 min average
values.
o Min/Max CO2/H2O concentration: set here plausible ranges of gas

concentrations (expressed as mole fractions), considering the peculiarities of your
site.
 Skewness and kurtosis: selecting this test, skewness and kurtosis for the whole time series
are evaluated against acceptance ranges that you must set in the GUI. In the GUI you set:
o Lower/Higher limits for hard/soft flagging for

skewness/kurtosis: maximum and minimum accepted values for the statistical
26
moments. Limits for hard-flags shall contain those for soft-flags. Default values are
those suggested by (Vickers and Mahrt, 1997).
 Discontinuites: discontinuities in the time series are detected using the Haar transform that
calculates the difference in some quantity over two half-window means. Large values of the
transform identify changes that are coherent on the scale of the window and hence
potentially detect discontinuities that lead to semi-permanent changes as opposed to sharp
changes associated with smaller-scale fluctuations (Vickers and Mahrt, 1997). In the GUI
you must set the limits for hard- and soft-flagging individual variables for discontinuites.
Refer to the cited publication for more details.
 Time-lags: this test flags CO2/H2O time series if the maximal w-covariances, determined
via the covariance maximization procedure described above (see the “Max covariance with
default” option for time-lag compensation) and evaluated over a predefined time-lag
window, are too different from those calculated for the suggested time-lags. That is, the
mismatch between fluxes calculated with the expected time lags and with the “actual” time
lags is too large. In the GUI, you set acceptable percentage of mismatch to hard- and soft-
flag the file.
 Angle-of-attack: if selected, this test calculates sample-wise angle of attacks throughout the
file and flags it if the percentage of angles-of-attack exceeding a user-defined range is
beyond a (user-selected) threshold.
 Steadiness of horizontal wind: this test assesses whether the along-wind and cross-wind
components of the wind vector undergo a systematic reduction (increase) throughout the
file. If the quadratic combination of such systematic variations is beyond the limit that you
set in the GUI, the file is hard-flagged for instationary horizontal wind (cf. Vickers and
Mahrt, 1997, Par. 6g).
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7. ECO2S::Meteo
General Options Tab
This tool of ECO2S allows you to reformat high-quality meteorological files into a suitable format
that is importable by all other software of the suite. High quality meteo data are expected to be
available as values averaged over a certain time interval, typically - but not necessarily - 30 minutes
and to be provided as data lines featuring a timestamp at the beginning. ECO2S::Meteo is able to
import an undefined number of meteo files and to merge them into a unique time series, basing on
the timestamps. Note that the association of meteo data with all results calculated from raw data, is
done basing on the time stamp. Thus, make sure that the time series you implicitly define with the
Flux averaging interval and the time stamp of the first raw file, matches with the time series of the
data file. A smarter association of meteo data lines with results obtained from raw data is planned
for a next release.
ECO2S meteo file format is characterised by the presence of an header (where variable labels and
units are specified) by a standard (ISO) timestamp format and by the fact that all meteo files have
the same number of fields and the same order for all supported (meteo and auxiliary) variables. This
choice in general implies an abundance of useless “error codes” for the variables that are not
available in the original data files. However, for yearly datasets, the amount of disk space required
is negligible with respect to current computer capabilities. On the other side, this format allows a
straightforward usage of meteo files collected from different stations (or from the same station in
different configurations), within and outside ECO2S.
ECO2S::Meteo allows to reformat three different types of meteo files: files collected with Campbell
Scientific dataloggers (such as CR10x, CR3000, CR5000) and meteo files formatted according to
the specifications of the FLUXNET database, either in TXT or CSV style, as specified below.
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Meteo file(s) type
Here you specify the type of meteo files you want to reformat.
 Campbell dataloggers: choose this options if your meteo files have been collected with a
Campbell datalogger, with a format similar to that showed in Figure 1. In this release, the
format allowed for the meteo data of this file type is rather strict. ECO2S team is currently
working to make it more flexible.
Figure 1. Sample meteo file as acquired with a Campbell datalogger CR10x.
In this file type, the first field in each data line must be an alphanumeric identifier of the
datalogger, then the date follows in the form of year (4 digits), DOY (3 digits), time
(HHMM, but accepted also HMM and MM) and then the data values. In the example shown
in Figure 1 fields are separated by commas, but this is user-selectable (see below).
 FLUXNET TXT form: it is likely that you have already submitted meteo files to the
FLUXNET databases. If so, you should be familiar with the standardized meteo data format
of this database; perhaps your meteo files are already formatted in either the TXT or CSV
style. Figure 2 shows an example of a meteo file formatted according to the TXT format:
Figure 2. Sample meteo file as formatted in FLUXNET-TXT style.
Here we recognize several elements: a two-lines header, where variable labels and units are
reported. Note that variable labels must be specified, as standardized in the FLUXNET
database otherwise they are not recognized by the software. On the contrary, the units line is
not interpreted. Data are expected to be expressed in FLUXNET standard units.
29
Data lines are expected to start with a timestamp, whose format can be specified in the GUI
(see below), and then continue with data values in the order specified in the header. Black
spaces are allowed between the field separator and the actual values. The field separator can
also be specified (see later).
 FLUXNET CSV form: The main difference between the present format and the previous
one is the shape of the header. See Figure 3:
Figure 3. Sample meteo file as formatted in FLUXNET-CSV style.
All that ECO2S::Meteo requires is that the list of the variables is in the 4th line and the actual
data lines start from the 10th. For the rest, the file is treated in exactly the same way as a
FLUXNET-TXT file. In the following release, the distinction between the two file types will
be eliminated and more file description capabilities will be provided to the users.
Note that FLUXNET-CSV files can be obtained from Microsoft Excel native format (“.xls”),
by saving the data file (using Excel) as “values delimited by the list separator”. The actual
list separator depends on the Excel settings in your computer and it is likely to be comma,
semi-column, tab or space. You will be able to specify it to ECO2S::Meteo later on.
For both FLUXNET types, note that pressure is expressed in kPa, while ECO2S uses hPa.
As a consequence, ECO2S automatically and silently performs the conversion, assuming that
the pressure values read from the file are in kPa.
Data directory
Specify here the directory where ECO2S::Meteo will look for valid meteo files. The software will
attempt to import all files with the extension specified later. In the case of Campbell datalogger
files, the presence of the logger identifier will assure that extraneous files are ignored, while there is
not (yet) such control on either FLUXNET file types, so it is strongly suggested to create a separate
folder where only the meteo files of interest are collected.
File extension
30
Specify here the extension (without the “dot”) of the meteo files. All files with the specified
extension will be considered as valid meteo files. Where applicable, ECO 2S::Meteo will attempt to
understand whether the file is actually a meteo one. Note, however, that in this software version the
control over improper files is not fully implemented, so finding extraneous files with the selected
extension may result in a software crash.
Output directory
Set the directory where you want ECO2S::Meteo to place its output, constituted by the reformatted
meteo file and by a log file of performed operations.
Timestamp refers to
Indicate here whether the timestamp of the meteo data lines refers to the end or to the beginning of
the averaging period. Remember that, if the case, ECO2S will modify the timestamps so that they
always refer to the end of the averaging periods. This is the policy adopted throughout the software
suite.
Date format
Only applicable to FLUXNET data files. Here you must specify the date format of the data lines.
For details on how to correctly describe timestamps, refer to “ECO2S – A quick introduction and
user reference”, in the section describing the definition of raw file name prototype.
Time format
Same as above, but for the time.
Field separator
Here you must specify which character shall be considered as the field separator in the data files.
Separator policy
This option is not implemented yet. It is intended to specify to ECO2S::Meteo how to behave in
case two or more consecutive separators are found. Currently, two or more separators are
considered as being only one.
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Variable Options Tab
If you selected the “Campbell datalogger” as the meteo file type, now you have to specify the nature
and order of the meteorological variables in your file(s). Note that units cannot be chosen freely,
rather must match those specified in the GUI for each variable. This is especially critical for a
subset of meteo variables that are actually used by ECO2S and expected to be expressed in
predefined units. These are: air temperature (in °C), air pressure (in hPa), relative humidity (in %),
global radiation (in W m-2), net radiation (in W m-2) and PPFD (in mol m-2 s-1). All other
supported variables might be present in your file with different units. However, consider that the
units reported in the output file header are those expected by ECO2S, thus having different actual
units would turn out in an inconsistency between the header and the content of the file. A much
better way would be to first convert units into ECO2S units, and then use ECO2S::Meteo to perform
the file format conversion. It is planned for a later release that ECO2S will allow to change variable
units, too. Finally, note that a maximum of 19 “custom” variables is available, to handle variables
that are present in your meteo files but that are not foreseen in the ECO2S standard set. For each
variable not belonging to the ECO2S set, select an “Optional” one. You will then find those
variables ordered as optional ones in the last 19 columns of the output meteo file. Currently,
ECO2S::Meteo does not allow entering explicit name/units for those variables. Keep this in mind
when storing your files somewhere for a later use: a small table with the correspondence of ECO 2S
“Optional” variables and their actual meaning might help in the future. It is planned for the next
release, to allow the user to explicitly enter a name and units for variables beyond the standard set.
In the “Variable order” table you can add or deleted rows (corresponding to data columns in the
meteo file), by using the “+ Add a variable” and “- Remove a variable” buttons. The aim is to
describe the order of the variables as they come in the meteo file, excluding the timestamp that is
32
always expected to initiate the data line. When you click on the “+ Add a variable” button, a new
row is added (under the currently focused row or as the first row if none is focused) with the
message “PLEASE SPECIFY VARIABLE”: click there and specify the new variable. Add and
remove rows as needed if you enter the wrong sequence. Note that the GUI does not allow you to
enter the same variable name more than once. If you do have replicates of the same variable, where
applicable use the repetitions foreseen in the standard set (such as PPFD, PPFD2, PPFD3), or use
“Opt ##” names (with ## going from 2 to 20).
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8. ECO2S::Tilting
General Options Tab
ECO2S::Tilting is primarily intended for calculating sector-wise planar fit rotation matrices, in the
framework of coordinate rotations for correcting anemometer tilting with respect to local
streamlines. It also outputs the fitting plane(s) coefficients on a separate file. ECO2S::Tilting starts
from an intermediate statistics file produced by ECO2S::RawProcess (statistics at Level 4) and
performs the calculations for a user-defined number of equally (angularly) wide wind sectors.
Below you can read more details about the GUI fields that must be entered prior of running this
tool.
Level 4 statistics file
Here you must select the appropriate statistics file, produced by ECO2S::RawProcess, to be used for
planar fit rotation calculation. Statistics at Level 4 are calculated on raw time series, after the de-
spiking, cross-wind correction and angle of attack correction (if any of these are requested). Note
that the planar fit matrices calculation requires only the mean (un-rotated) wind components in the
anemometer’s Cartesian coordinate system. Note also that ECO2S will pre-compile this field for
you with the appropriate statistics file, at the end of the ECO2S::RawProcess run. However, you are
always free to change that pre-selection using the “Browse…” button to load another file.
Output directory
34
Here you select the directory where to save the output files. Also this field is pre-compiled by
ECO2S, so that all output files from the same processing project are properly organized in one main
folder. However, same as above, you are always free to select a different output folder.
Starting and ending date/time of dataset
Planar fit calculations must be performed using wind data relating to a time period when the
anemometer was not moved and did not undergo major dislocations. Normally, a time period of 3 to
6 weeks is enough for calculating planar fit coefficients, depending on the number of sectors.
ECO2S::Tilting allows you to select the starting/ending timestamps of the time period used for
calculating planar fit coefficients, that of course must fall (at least partially) within the period of the
available statistics (that is, within the period of the processed raw files).
Missing lines allowance
Similar to the same setting in ECO2S::RawProcess. Each raw file will be tested for the number of
data lines contained. Select here the maximum amount of missing line (in percent) that is
acceptable. Raw files with a larger amount of missing lines will be ignored.
Number of wind sectors
Enter here the number of wind sectors for which you want to calculate rotation matrices, up to a
maximum of 32 sectors. Each sector has an angular wideness given by 360° divided by the selected
number of sectors. Sectors are numbered in clockwise direction, the first one starting from North
(0°). In principle, a higher number of sectors allows a better representation in complex topographies
but requires a higher number of statistics available.
Minimum number of elements per wind sectors
Planar fit calculation is performed for each wind sector, for which a minimum number of statistics
is available. This threshold must be specified here. For sectors for which rotation matrices are not
calculated because there are not enough data, in the next processing step ECO2S::Flux will
automatically switch to DR (double rotation) applied on statistics.
Maximum average w (per input file)
Here and in the following entry, you specify boundaries to acceptable values of average wind
components. Specifically, here you can set a maximum average vertical wind component.
Minimum average u (per input file)
Similar to the previous one but to set a minimum value for the horizontal wind speed.
35
Time-varying info file
If in the Project Page you checked the option for using a “dynamic parameter file”, or if you are
processing ENE files without using a common ECO2S::Datalogging project file, you will find this
field mandatory. Here you must enter the path of the file containing the time series of acquisition-
time parameters. This file, generated by ECO2S::RawProcess, is named eco2s_ID_ini_info.csv
(where ID is the ID of the project, that you entered in the Project Page) and is stored in the sub-
folder ..\eco2s_aux, automatically created inside the chosen main output folder. The file is
generated in any case, but it is only needed when there could be acquisition-time parameters
changing along the dataset. Once more, at the end of the ECO2S::RawProcess you should find this
field pre-compiled with the path of the file produced in the same run. You can however modify it at
your convenience.
36
9. ECO2S::Spectra
General Options Tab
This tool of ECO2S is used to perform an analysis of spectra derived from raw data, in order to
determine the cut-off frequencies of the eddy covariance system under consideration, for the
purpose of in-situ or mixed analytic/in-situ spectral corrections. The rationale of the analysis and
the details of the implementations follow closely the methodology proposed by (Ibrom et al.,
2007a). The tool focuses on the assessment of the attenuation of gas concentration spectra at the
high-frequency range, considering sonic temperature spectra as a proxy to the real gas spectra
(assuming spectral similarity). High-frequency attenuation is due to the sum of several factors,
some of which are inherent to the eddy covariance set-up (e.g., the finite time/space resolution of
instruments, the transit of air parcels through a sampling line), while others are attributable to the
micrometeorological conditions (e.g. relative humidity) or to the management of the flux station
(e.g. aging of the sampling lines, see Mammarella et al., 2009). Because the environmental relative
humidity was shown to be a major driver of spectral attenuation of water vapour signals in closed-
path systems, while it is not the case for CO2, ECO2S performs the spectral analysis in different
ways for the two scalars. For water vapour, using all available spectra, an ensemble cut-off
frequency is determined for ten relative humidity classes. Of course there are cases, when relative
humidity is not a major driver of spectral attenuation, for example when open-path gas analysers are
37
used. In such cases, ECO2S still determines a set of RH-dependent cut-off frequencies. This is not
harmful: simply, cut-offs will not show a detectable dependency on RH. A drawback, however, is
that a considerable amount of spectra must be available, given that they will be sorted in ten RH-
classes and then averaged to derive ensemble cut-off frequencies.
For CO2, instead, ECO2S allows to determine different ensemble cut-off frequencies for different
time periods, as specified below.
Similar to ECO2S::tilting, also ECO2S::Spectra starts from partial results created by

ECO2S::RawProcess. Running ECO2S::Spectra requires that you selected the option Output all
binned (co)spectra in ECO2S::RawProcess, because the tool uses those spectra for the calculations.
The main output of ECO2S::Spectra is a text file reporting the transfer function (TF) parameters for
H2O and CO2, for two different kinds of assumed shaped of the TFs, namely the “Infinite Impulse
Response” (IIR) filter (Ibrom et al., 2007a, Eq. 3) and the one-parameter sigma function described
by (Aubinet et al., 2001, Eq. A.2). In case the non linear regressions implied in the implementation
do not converge, or if there is not a sufficient amount of well characterised spectra, an error code is
returned in the output file. Results of ECO2S::Spectra can be used later, for the calculation of
corrected fluxes with ECO2S::Fluxes.
Similar to the other software in the suite, once ECO2S::RawProcess has completed the run, the GUI
pre-compiles in/out directories and file paths to drive a correct use. You can however always
change these paths using the buttons “Load…” or “Browse…”.
Binned (co)spectra directory
Select here the directory where binned (co)spectra have been stored by ECO2S::RawProccess. In the
normal case, this is a sub-folder named \eco2s_bin_cospectra inside the main output folder
selected in ECO2S::RawProccess.
Raw fluxes file
This file is also generated by ECO2S::RawProccess. It is a tentative calculation of uncorrected

fluxes. Here tentative fluxes of latent heat, sensible heat and CO2 are used to select spectra for
calculating transfer functions (see below).
Output directory
This is the directory where ECO2S::Spectra will put its output files.
Use external meteo data file
38
Check this option (and load the related file) if you have a high-quality meteorological file from
which ambient relative humidity and air temperature will be retrieved. Remember that meteo files
must be formatted using ECO2S::Meteo, before they can be used in ECO2S.
Use external virtual meteo data file
Check this option (and load the related file) if you do not have a high-quality meteorological file,
and thus need to use the meteo values estimated by ECO2S::RawProcess starting from raw files.
From this file, ECO2S::Spectra will retrieve “virtual” ambient relative humidity and air temperature
for its internal need.
Number of bins of reduced spectra
This information must match that set in ECO2S::RawProcess (Number of frequency bins for spectra
reduction). In a following release, the need to re-enter settings already entered elsewhere, will be
eliminated. For the moment, the GUI will take care of pre-compiling this field with the value you
entered in ECO2S::RawProcess.
Minimum number of spectra samples in each frequency bin
Ensemble, binned spectra are evaluated by averaging all available (binned) spectra, sorting them
into time-classes or RH-classes where applicable. If any bins do not contain a sufficient amount of
spectra samples, such bin is not considered in the following processing. Specify here such minimum
value.
Minimum sensible heat flux
Set here a minimum value for the sensible heat flux. Spectra of sonic temperature corresponding to
sensible heat fluxes smaller than the one you set here, will not be considered in the analysis. We
recall that sonic temperature spectrum is considered here as a proxy for the unaffected spectrum of
all atmospheric passive scalars, including gas concentrations.
Minimum (absolute) CO2 flux
Set here a minimum value for the carbon dioxide flux. Spectra corresponding to CO 2 fluxes smaller
than this, will not be considered in the CO2 spectral attenuation analysis.
Minimum latent heat flux
Set here a minimum value for the latent heat flux. Spectra of water vapour corresponding to latent
heat fluxes smaller than this, will not be considered in the water vapour spectral attenuation
analysis.
39
Minimum frequency for fitting low-pass transfer functions
Currently, ECO2S::Spectra only assess spectral attenuations at the high-frequency range. Often, the
behaviours of CO2, H2O and temperature spectra at the low-frequency end differ from each other,
due to different source/sinks behaviours. Thus, when calculating low-pass transfer functions, it is
advisable to eliminate from the regressions the low-frequency range, that anyway is virtually not
affected by the phenomena that cause high-frequency losses.
Maximum frequency for fitting low-pass transfer functions
Spectra of scalar concentrations as measured by IRGAs often show high-frequency noise. Although
ECO2S automatically performs a high-frequency noise elimination, by linearly interpolating and
subtracting the high-frequency (>2Hz) part of ensemble spectra (see Ibrom et al., 2007a), you may
want to limit the calculation of transfer functions to a certain band, that you may possibly determine
by visual inspection of binned spectra calculated by ECO2S::RawProcess. Set here such higher
limit: if you want to consider the full (high frequency) spectral range, insert a large value here (e.g.,
the acquisition frequency will be large enough).
40
Groups Tab
As mentioned above, CO2 transfer functions can be evaluated for different time periods. This option
can be useful to account for the possible effects of , for example, sampling line aging and anyway to
analyse whether there is any systematic change in the spectral attenuation of CO 2 signals. To do
this, ECO2S::Spectra allows you to create different “time groups” within a period of one year, with
a monthly base. You can create up to 12 groups, and each group can contain one to twelve months,
with the constrains that: 1) the same month cannot belong to more than one group and 2) groups
must be chronologically ordered. Some examples:
 To create only one group including the whole year, select January/December as the
Start/Stop months of the first group. This is the default settings. In the output files, you will
then find the same transfer function parameters for all months.
 To create four contiguous and equally long groups: Select January/March for the first group,
then Click on “Add a group” and select April/June, and so on. You will then find the same
transfer function parameters for the months belonging to the same group.
Also consider that:
1) groups do not have to be contiguous (if a month is not included in the groups, an error code
for that month will be reported as output).
41
2) groups can include months, for which you do not have data (spectra). Only groups for which
a sufficient amount of spectra is available will be considered in the calculations. For the
others, error codes will show on output.
42
10. ECO2S::Fluxes
General Info Tab
ECO2S::Fluxes is the last step of data processing, designed to calculate corrected fluxes, starting
from the results obtained in the previous steps. In the easiest case, the whole processing is done
using ECO2S::RawProcess and ECO2S::Fluxes. This is the case when: 1) you do not need to use the
planar fit method to correct for anemometer’s tilting; 2) you do not intend to use an in-situ
correction method for compensating high-frequency losses; 3) you do not have high-quality meteo
files and 4) time-lag estimation is not critical. In any other case, the processing will need to pass
also through one of the tools intended to: 1) calculate planar fit rotation matrices (ECO 2S::Tilting);
2) perform a spectral analysis based measured spectra (ECO2S::Spectra); 3) format meteo files
(ECO2S::Meteo) and 4) assess relative-humidity dependency of water vapour time-lags as well as
calculate a plausibility range of time-lags for CO2 time series (ECO2S::Timelag).
We will see in the following how the results of the other software enter into ECO2S::Fluxes.
Level 7 statistics file
ECO2S::Fluxes starts its calculations from the last intermediate statistics file produced by
ECO2S::RawProcess. At this level, statistics are calculated on raw time series after: de-spiking (if
requested), cross-wind correction (if requested), angle of attack correction (if requested), double-
rotation for tilt correction (if requested); high-pass filtering; time-lag compensation (if requested).
43
The GUI pre-compiles this field (as well as all other file paths and directories, where applicable) at
the successful end of ECO2S::RawProcess run. You can always change the default path by using the
buttons “Load…” or “Browse…”.
Output directory
As usual, this is the directory where ECO2S::Fluxes will store its output files.
Create continuous dataset
Refer to the same option, described at p.17. If you have chosen this option when running
ECO2S::RawProcess, then doing it here is redundant (although not harmful).
Time-varying info file
Refer to the same entry described at p. 36.
Use external meteo data file
Refer to the same entry described at p. 38.
44
Processing Options Tab
Here you will select some processing choices. Some of them shall fit with previous choices, and the
GUI helps you to do so.
Axis rotation for tilt correction
Refer to the description at p. 20 for the available options and a brief explanation. Note that the GUI
here forces you to be consistent with the choices made in ECO2S::RawProcess, in the framework of
the same processing project:
 If you selected the option DR on raw data (before detrending), the double rotation was
applied in ECO2S::RawProcess and no further rotation is allowed. Consistently, the GUI
shows you this as the only option available.
 If you selected either DR on statistics (after detrending), TR on statistics (after detrending)

or Planar Fit, then ECO2S::RawProcess did not perform any rotation yet, so in principle here
you are able to choose any of the three, but of course not the DR on raw data (before
detrending), that is consistently dimmed and not selectable.
 If you choose Planar Fit, the GUI turns on the mandatory entry Planar fit auxiliary file, that
asks you to enter the rotation matrix file produced by ECO2S::Tilting, recognized by the
name patterns: eco2s_ID_rotmat.txt, with the ID being the ID of the processing project you
entered in the Project Page (see p. 10).
45
Compensation of density fluctuations
This processing option refers to the compensation of air density fluctuations, induced by
temperature, water vapour and pressure fluctuations, that impacts largely carbon dioxide fluxes and,
secondarily, water vapour (hence latent heat) fluxes. The issue is treated in different ways,
depending on the nature of the gas concentration measurement:
 If gas measurements are available as mixing ratios (mole gas per mole of dry air) from a
closed-path system, assuming effective dumping of temperature fluctuations in the sampling
line, there is no need for a density correction, as this measure of concentration is not affected
by dilution/concentration due to water vapour fluctuations (Ibrom et al., 2007b). Thus, in
this release of the software, fluxes are calculated from mixing ratios without any
consideration of air density fluctuations. In the following release, however, ECO2S will be
able to account for any expansion/contraction effects induced by residual temperature
fluctuations in the measuring cell of a closed-path system, provided that fast cell
temperature readings are available.
 If gas measurements are available as mole fractions (mole of gas per more of humid air),
they are tacitly converted to mixing ratios, point-by-point, at the raw data level, by
ECO2S::RawProcess. Thus, in ECO2S::Fluxes they are treated exactly like the case above.
That is, air density fluctuations are neglected.
 If gas measurements are available as mole density, typically the case with open-path gas
analysers, the so-called WPL formulation (Webb et al., 1980) is implemented to include air
density fluctuation effects.
Add Li7500-related sensible heat components
This option, available only for gas measurements taken with the Li-75001 by LI-COR Inc. (Lincoln,
Nebraska, USA), and if the WPL correction was selected, adds a contribution to such correction,
that accounts for extra air density fluctuations, induced by instrument surface heat exchange (Burba
et al., 2008). When only standard measurements are available from the li-7500 (i.e., no fast internal
temperature readings), the correction can be calculated starting from instrument surface temperature
estimations calculated either with a simple or a multiple linear regression(s) (see the cited
reference). Parameters of linear regressions should be assessed for each sensor unit and in each
1
Note that the correction shall not be applied to measurements collected with the Li-7500A.
46
configuration. However, values are available from ad ad-hoc campaign, which are valid within the
limits defined in (Burba et al., 2008). Those values are set by default in ECO2S::Fluxes. If you do
not have better (i.e., unit specific) estimations, such values – that you can retrieve any moment by
using the button “Set defaults” – are to be considered as the best option.
Correction of sonic temperature for humidity
This correction, often referred to as “Schotanus correction”, attempts to correct air temperature
estimations (and all related statistics) that are based on sonic temperature, for the effect of air
humidity on the latter (Schotanus et al., 1983). The humidity correction is applied in ECO2S
following the approach proposed in (van Dijk et al., 2004, p. 31, bullet 10.), that suggest to not
apply it at the raw data level, where individual inaccurate values of the humidity retrieved from fast
hygrometer readings might bias the overall correction. Rather, the correction is applied a posteriori
on averages and covariances. Two slightly different options are available:
 Van Dijk et al. (2004): follows Eqs. 3.49 – 3.53 of the cited article.
 Kaymal and Gaynor (1991): similar to the previous one, calculates the coefficient 0.51 in
Eq. 3.49 of (van Dijk et al., 2004) using a slightly different formulation (Kaimal and
Gaynor, 1991).
47
Spectral Corrections Tab
A separate tab is dedicated to the selection of the spectral correction procedure. Several options are
available, that might be suitable in different situations, depending mainly on the EC setup (analyser,
sampling line, sensors separation, height above the canopy), the ecosystem considered (crop, forest,
wetland) and its climatic conditions (wind regimes, frequency of occurrence of high relative
humidity).
Three methods are implemented following strictly three bibliographic references: a fully analytical
method (Moncrieff et al., 1997), an hybrid analytical/in-situ method (Horst, 1997) and a fully in-situ
method (Ibrom et al., 2007a). Moreover, ECO2S features an original method, that attempts at
refining the one by Ibrom and co-authors. A second original method is under development, visible
in the GUI (labelled as ECO2S II), but not selectable. A brief overview of the options available is
presented hereafter:
 Moncrieff et al. (1997): Following the approach presented in (Moore, 1986), this method
attempts to describe the EC system transfer function acting on the scalar signals, by
providing and analytical formulation of the partial transfer function due to the individual
sources of attenuation (equations in Appendix A of Moncrieff et al., 1997). In
ECO2S::Fluxes these are recalculated at each run, to account for current parameters (e.g.
average wind speed). The overall transfer function is then derived as the product (in the
frequency space) of the individual ones (Eq. 11). This transfer function is applied to
48
analytical scalar flux cospectra (Eqs. 12-18, a reformulation after Kaimal et al., 1972), also
recalculated at each run, to account for atmospheric stratification. Correction factors are
finally derived, from carbon dioxide and water vapour fluxes, following Eq. 10 in
(Moncrieff et al., 1997). This correction method does not need any extra input, as all
functions can be evaluated starting from eddy standard data.
 Horst (1997): Assuming a cospectral shape for scalar fluxes (Eq. 6), Horst derived an
analytical expression for the spectral attenuation (Eq. 11), with parameters depending on the
atmospheric stability regime (  , n m ), as well as on the EC system characteristics as a low-
pass filter (  c ). Note that Eq. 5 in (Horst, 1997) is equal to Eq. 3 in (Ibrom et al., 2007a),
with 2 c  f c1 . Thus, the cut-off frequencies calculated with ECO2S::Spectra (RH-
dependent for water vapour, time-dependent for carbon dioxide), can be used to calculate  c
and apply the Horst’s correction. Accordingly, when selecting this option, the GUI turns on
two extra mandatory entries, namely the Transfer function parameters file and the Cut-off
frequency vs. RH file, both of them created by ECO2S::Spectra. These files have the name
patterns: eco2s_ID_IIR_params.txt and eco2s_ID_cutoff_vs_rh.txt and can be found in the
main output directory selected when running ECO2S::Spectra.
 Ibrom et al. (2007): this is a fully in-situ method. It only assumes a predefined shape for the
system transfer function (identical to the one assumed by Horst), that is adapted to the
current case with the procedure described at p. General Options Tab37. The method requires
the parameterization of a model (Eq. 9 in Ibrom et al., 2007a) for the H2O/CO2 correction
factor, as a function of atmospheric stability, wind speed and cut-off frequency. The
parameterization is performed in ECO2S::Fluxes and needs an extra input file, an
intermediate file created by ECO2S::RawProcess, the “degraded temperatures w-
covariances” file, whose name pattern is: eco2s_ID_vdegT_cov.csv. This file contains a
simulation of the effect of low-pass filtering, performed starting from sonic temperature
time series (taken as a proxy for unaffected scalar turbulent series) and applying the “Infinite
Impulse Response” filter with different cut-off frequencies. Please refer to the original
publication for details on the procedure and its theoretical background. Selecting this
options, the GUI forces you to enter three extra files: the Transfer function parameters file,
the Cut-off frequency vs. RH file and the Degraded temperatures w-covariances file
 ECO2S I: this method, also based on (Ibrom et al., 2007a), differ from the previous one in
that the correction factors are not calculated from a model, rather they are derived by
49
applying the raw-file-specific transfer functions to the full (i.e., not binned) raw-file-specific
cospectrum of wTs . Thus, this option requires that in ECO2S::RawProcess the option to
Output full wT-cospectra (p. 23) , was checked and the GUI forces you to select the
directory where such cospectra have been stored. Furthermore, also in this case the Transfer
function parameters file and the Cut-off frequency vs. RH file must be entered. Finally, this
method allows for a further refinement: checking the option Add analytical portion of TF to
in-situ ones, will cause ECO2S to add the partial analytical transfer functions of (Moncrieff
et al., 1997) that describe the high-frequency losses inherent in the anemometer’s
measurement of temperature spectra. This can be done to account for the fact that the
measured sonic temperature spectrum, assumed as a reference, is actually attenuated at the
high-frequency end from the finite time-space resolution of the anemometer.
 Custom: this method, still in “alpha” version, is intended to allow you to build up your
spectral correction procedure, by combining different options. Because the method is still
highly unstable, it is not described here in details. However, you may attempt to select
“reasonable” options from the GUI, and see the results (and possibly report us any bugs!).
High-pass filtering correction
Checking this option will instruct ECO2S::Fluxes to apply a correction for the low-frequency
attenuation implied by the detrending procedure. ECO2S applies (the inverse of) a transfer function
that depends on the detrending method. Analytical formulations for the method supported in
ECO2S are described, for example, in (Rannik and Vesala, 1999). The information about the
selected detrending method is silently passed from ECO2S::RawProcess to ECO2S::Fluxes.
50
Post-processing Options Tab
In this tab you can select further processing, beyond the calculation of corrected fluxes. Currently,
ECO2S allows the calculation of quality flags for the fluxes and the estimation of the flux footprint.
Quality check
Check this option if you want ECO2S::Fluxes to calculate and output quality flags for sensible heat,
water vapour and CO2 fluxes. Quality flags are calculated following (Foken et al., 2004). For each
averaging period, the procedure involves the execution of two tests - for which individual flags are
calculated - and the combination of such flags into a summary flag, that is the one you will find
beside each flux in the output files. The steady state test (Foken and Wichura, 1996) compares the
statistical parameters determined for the flux averaging period and for short intervals within this
period. The turbulence development test, also described in (Foken and Wichura, 1996), assesses the
turbulent conditions by analyzing the measured integral turbulence characteristics as a function of
the atmospheric stratification and comparing them with a model proposed by (Foken et al., 1991).
In ECO2S, the steady state test is performed by ECO2S::RawProcess, while the turbulence
development test is performed here in ECO2S::Fluxes. Thus, checking this option requires that you
select the file containing the results of the steady state test in the Quality check auxiliary file entry.
This file is stored in the \eco2s_aux subfolder created by ECO2S::RawProcess in its main output
folder and has a name pattern like: eco2s_ID_qc_test.csv, with ID being the identifier of the current
processing project. You shall find the proper file path already pre-compiled by the GUI at the
successful end of the ECO2S::RawProcess run.
51
The overall flag can be calculated according to two different schemes:
 FLUXNET standard (0/1/2): refers to the standard of the FLUXNET database, where the
value “0” means high quality, “1” means poorer quality, but still acceptable for derivation of
annual budgets and “2” suggests to discard the related flux.
 Foken et al. (2004): refers to a different flagging policy, described in (Foken et al., 2004),
that ranks fluxes on a scale from “1”, top quality, to “9” poorer quality.
Footprint estimation
Currently, ECO2S supports two methods for estimating flux footprint. Both methods are one-
dimensional simple parameterizations and the (cross-wind integrated) footprint estimation is
provided as the (upwind) distances from the EC system contributing 70 and 95% to total fluxes,
plus the peak-contribution distance.
 Schuepp et al. 1990: This footprint model, described in (Schuepp et al., 1990), is based on
an analytic solution of the advection-diffusion equation of a scalar in the turbulent boundary
layer (Gash, 1986) and provides a tool for estimating the footprint in neutral and unstable
stratifications, based on the friction velocity, the roughness length and the zero-plane
displacement height. To be completed.
 Kljun et al. 2004: the footprint parameterization described in (Kljun et al., 2004) is based
on a scaling procedure for the flux footprint function, parameterised against footprint
simulations performed with a Lagrangian stochastic model. The parameterisation was
proved to be universally valid (given the value of the roughness length) to a large degree of
accurateness, within the limits explained in the referenced paper (Sect. 3.4), and in a very
wide range of atmospheric stratifications and EC systems heights. In ECO2S::Fluxes, the
footprint estimation is performed following (Kljun et al., 2004, Eq. 7), with parameters set
according their Eqs. 13-16 and using the roughness length available from the time-varying
info file (see p. 44), or from the ECO2S::Datalogging project file. As explained by the
authors, the estimation of the peak distance provided by the parameterisation is closely
similar to the one provided by the full model, while at higher percentages (such as 70% and
especially 95%) the accurateness is slightly reduced, also due to the flatness of the footprint
function at the far limit. The footprint model, however, is not valid for low friction
velocities, thus for u*  0.2 ms 1 the footprint is not estimated and ECO2S::Fluxes reports
an error code on output.
52
References
Aubinet, M., Chermanne, B., Vandenhaute, M., Longdoz, B., Yernaux, M. and Laitat, E., Long term
measurements of water vapour and carbon dioxide fluxes above a mixed forest in Ardenne’s region,
Agricult. For. Met., 108:293–315. 2001
Burba, G.G., Mc Dermitt, D., Grelle, A., Anderson, D.J. and Xu, L., Addressing the influence of
instrument surface heat exchange on the measurements of CO2 flux from open-path gas analyzers,
Glob. Change Biol., 14:1854–1876. 2008
Foken, T., Gockede, M., Mauder, M., Mahrt, L., Amiro, B.D. and Munger, J.W., Post-field quality
control, in Handbook of micrometeorology: a guide for surface flux measurements, pp. 81-108,
edited by X. Lee, et al., publ. by Kluwer, Dordrecht. 2004
Foken, T., Skeib, G. and Richter, S.H., Dependence of the integral turbulence characteristics on the
stability of stratification and their use for Doppler-Sodar measurements, Z. Meteorol., 41:311-315.
1991
Foken, T. and Wichura, B., Tools for quality assessment of surface-based flux measurements,
Agricult. For. Meterol., 78:83-105. 1996
Gash, J.H.C., A note on estimating the effect of a limited fetch on micrometeorological evaporation
measurements, Bound-Lay. Meteorol., 35:409-414. 1986
Horst, T.W., A simple formula for attenuation of eddy fluxes measured with first-order-response
scalar sensors, Bound-Lay. Meteorol., 82:219-233. 1997
Ibrom, A., Dellwik, E., Flyvbjerg, H., Jensen, N.O. and Pilegaard, K., Strong low-pass filtering
effects on water vapour flux measurements with closed-path eddy correlation systems, Agricult.
For. Meterol., 147:140-156. 2007a
Ibrom, A., Dellwik, E., Larse, S.E. and Pilegaard, K., On the use of the Webb-Pearman-Leuning
theory for closed-path eddy correlation measurements, Tellus B, 59(5):937-946. 2007b
Kaimal, J.C. and Gaynor, J.E., Another look at sonic thermometry, Bound-Lay. Meteorol., 56:401-
410. 1991
Kaimal, J.C., Wyngaard, J.C., lzumi, Y. and Cote, O.R., Spectral characteristics of surface-layer
turbulence, Q. J. R. Meteorol. Soc., 98:563-589. 1972
Kljun, N., Calanca, P., Rotach, M.W. and Schmid, H.P., A simple parameterisation for flux
footprint predictions, Bound-Lay. Meteorol., 112:503-523. 2004
Liu, H., Peters, G. and Foken, T., New equations for sonic temperature variance and buoyancy heat
flux with an omnidirectional sonic anemometer, Bound-Lay. Meteorol., 100:459-468. 2001
Mammarella, I., Launiainen, S., Gronholm, T., Keronen, P., Pumpanen, J., Rannik, U. and Vesala,
T., Relative humidity effect on the high-frequency attenuation of water vapour flux measured by a
closed-path eddy covariance system, Journal of Atmospheric and Oceanic Technology, 262009
Moncrieff, J.B., Massheder, J.M., de Bruin, H., Ebers, J., Friborg, T., Heusinkveld, B., Kabat, P.,
Scott, S., Soegaard, H. and Verhoef, A., A system to measure surface fluxes of momentum, sensible
heat, water vapour and carbon dioxide, J. Hydrol., 188-189:589-611. 1997
Moore, C.J., Frequency response corrections for eddy correlation systems, Bound-Lay. Meteorol.,
37:17-35. 1986
53
Nakai, T., van der Molen, M.K., Gash, J.H.C. and Kodama, Y., Correction of sonic anemometer
angle of attack errors, Agricult. For. Meterol., 136:19-30. 2006
Press, W.H., Teukolsky, S.A., Vetterling, W.T. and Flannery, B.P., Numerical Recipes in
FORTRAN 77: The Art of Scientific Computing, Cambridge University Press publ., New York,
1996
Rannik, U. and Vesala, T., Autoregressive filtering versus linear detrending in estimation of fluxes
by the eddy covariance method, Bound-Lay. Meteorol., 91:258-280. 1999
Schotanus, P., Nieuwstadt, F. and de Bruin, H., Temperature measurement with a sonic
anemometer and its application to heat and moisture fluxes, Bound-Lay. Meteorol., 26:81–93. 1983
Schuepp, P.H., Leclerc, M.Y., Macpherson, J.I. and Desjardins, R.L., Footprint prediction of scalar
fluxes from analytical solutions of the diffusion equation, Bound-Lay. Meteorol., 50:355-373. 1990
van Dijk, A., Moene, A.F. and de Bruin, H.A.R., The principles of surface flux physics: theory,
practice and description of the ECPack library, Meteorology and Air Quality Group, Wageningen
University, Wageningen, The Netherlands, 99 pp. 2004
Vickers, D. and Mahrt, L., Quality control and flux sampling problems for tower and aircraft data,
Journal of Atmospheric and Oceanic Technology, 14:512 - 526. 1997
Webb, E.K., Pearman, G.I. and Leuning, R., Correction of flux measurements for density effects due
to heat and water vapour transfer, Q. J. R. Meteorol. Soc., 106 85–100. 1980
Wilczak, J.M., Oncley, S.P. and Stage, S.A., Sonic anemometer tilt correction algorithms., Bound-
Lay. Meteorol., 99:127-150. 2001
54

ECO2S - An Overview of The Graphical User Interface - 2010!10!15

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An overview of the Graphical User Interface

Department of Forest Sciences and Resources, University of Tuscia, Viterbo, Italy

As described more in depth in “ECO2S – A quick introduction and user reference”,

Click here to return to ECO2S Start Menu.

Shows ECO2S window on full screen.

Raw File Type

 Binary Alteddy: binary files generated by Alteddy.

Number of ASCII header lines

Number of bytes per variable

Custom configuration file

Use dynamic parameter file

Use ECO2S::Datalogging project file

General Options Tab

Raw data directory

Flux averaging interval

Number of files to merge

Create continuous dataset

Missing lines allowance

In this tab you make choices on how to process raw files.

Wind speed measurement off-set

Cross-wind correction for sonic temperature

Angle-of-attack correction for wind components (Gill’s only)

Axis rotation for tilt correction

 TR on statistics (after detrending): include the DR on statistics, plus a third rotation to

Detrending, or high-pass filtering, can be performed in ECO2S::RawProcess, by any of the

 Running mean: a local mean is defined at each time step by:

vi  (1  a)vi  avi 1 (2)

with the weight a given by the exponential:

where  is again the filter time constant and t  1 / f a .

Output all binned (co)spectra

Output full cospectra of sonic sensible heat

Window for data tapering before fft-ing

Number of frequency bins for spectra reduction

o Max consecutive outliers: maximum number of consecutive outliers to

o Accepted amount of spikes: The percentage of spikes, respect to the total

o Range of variation: The multiples of the window standard deviations (n)

o Accepted amount of empty bins: The percentage of empty bins over

o Accepted central drop-outs: The threshold percentage of central drop-

o Accepted extreme drop-outs: The threshold percentage of extreme drop-

o Max horizontal velocity: the maximum plausible horizontal velocity,

o Max vertical wind component: the maximum plausible vertical wind

o Min/Max Ts: maximum and minimum values of sonic temperature, used as a

o Min/Max CO2/H2O concentration: set here plausible ranges of gas

o Lower/Higher limits for hard/soft flagging for

General Options Tab

Figure 1. Sample meteo file as acquired with a Campbell datalogger CR10x.

Figure 2. Sample meteo file as formatted in FLUXNET-TXT style.

Figure 3. Sample meteo file as formatted in FLUXNET-CSV style.

Same as above, but for the time.

General Options Tab

Level 4 statistics file

Starting and ending date/time of dataset

Missing lines allowance

Number of wind sectors

Minimum number of elements per wind sectors

Maximum average w (per input file)