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WinDOAS 2.1 - The BIRA

1. Calibration Fit Parameters Continuous function xO IV x1 IV x2 EE x4 BE Insert Tix Pox Pais ra poe rs Remove HemovE tems ccs o Predefined parameters Offset and slit function parameters SFP are predefined parameters i e parameters with reserved symbols not defined by the user In our example the selected line shape is the error function convolution of a gaussian and a boxcar which is described by 2 SFP parameters SFP 1 for the gaussian FWHM and SFP 2 for the boxcar width SFP 3 and SFP 4 are ignored for this type of line shape even though they are checked Again in this case a better accuracy is obtained when limiting the number of free parameters according to the information content of spectra After optimisation it has been found that best results are obtained when fixing the boxcar width SEP 2 to 0 55 nm the gaussian FWHM SFP 1 therefore accounting for the wavelength dependency of the slit function is initialised to 0 3 nm in order to speed up the convergence of the algorithm it s recommended to initialise fit parameters to a value close to the real one Page 41 WinDOAS 2 1 Quickstart February 2001 Analysis windows properties Calibration description Harestua project Figure 5 12 Calibration Fit Parameters Predefined parameters Shift and Stretch Shift and stretch can be applied either on the control spectrum symbol Spectrum in this case ot
2. Molecules are characterised by their cross section They are represented by symbols previously defined in the Workspace Environment tree see chapter 6 WinDOAS uses these symbols to build cross section files filters gt Cross section files names must imperatively start with the symbol name as prefix followed by the underscore character gt There is no constraint on the cross section file extension the default one used by WinDOAS for creating cross sections files filters starts with xs Page 67 The Projects Tree Inserting a new cross section Figure 7 16 Analysis Windows Properties Inserting A New Cross Section List of files depending on the selected cross section List of available cross sections gt ixi ring qv xs WinDOAS 2 1 February 2001 To insert a new cross section in the Molecules pages 1 right click the Insert option from the property sheet the usual Open Files Windows dialog box appears with as Files of type the list of available cross sections this list is build from the list of symbols previously defined in the Workspace Environment tree and is updated after each new insertion in otder that two identical symbols are not defined in the same analysis configuration Open Cross sections Files Tx loki as sf GE F qa ring ss ixi nng 2s ixi ning gs e nng gk 38 nng kgw ss ixi nng Lxs ixi nng hrg ss File name Files of type
3. L DIES Analysis Program for Windows E WINDOAS Doc SUM S ample sample wds H Eiles View Edit Projects Tools Windows Help Figure 5 6 ls cil facies TS a Graphs a AE Description of the 255 T Lai sample wds configuration HAC osano Harestua H 2000_060 spe Bruxelles file H 2000 OB1 spe User defined symbols o HA_2000_062 spe H 2000 063 spe Analysis Windows Bro Oclo OHP Raw Spectra HP_2000_057 spe HP_2000_058 spe HP_2000_059 spe HP_2000_060 spe HP_2000_061 spe HP_2000_062 spe Analysis Windows bro R DOAS Analysis Program for Windows 14 03 The Projects tree includes two projects Harestua and OHP corresponding to UV measurements performed by IASB BIRA respectively at the ground based stations of Harestua Norway 60 N and OHP France 44 N Two analysis windows BrO and OCIO have been defined for the Harestua project we will focus mainly on the BrO one In the Workspace Environment tree are defined all symbols used in the analysis configuration of both projects Page 37 WinDOAS 2 1 Quickstart February 2001 Analysis Setup For Calibration interval 330 390 nm BrO Retrieval Spectral window 346 359 nm l Main Cross sections Harestua project Source Shift Files on the disk Harestua applied project nm O GOME FM 221K and 241K Io corrected 0 03 03241 10 xs and 03221_10 xs NO GOME FM 221K and 293K Io corrected 0
4. The Shift and Stretch Pages Figure 7 33 Analysis Windows Properties Calibration Shift and Stretch Page The O3 and ring cross sections defined in the Molecules page are shifted with the solar spectrum The Gaps Page The Outputs Page The Projects Tree For the configuration of these pages refer to the previous section 7 6 page 72 In order to avoid the interpolation of the spectrum to calibrate it is recommended to fit the shift of the high resolution solar spectrum represented by the symbol Ref In this case all cross sections defined in the Molecules page have to be shifted with the solar Spectrum Analysis windows properties Calibration description Harestua project Molecules Continuous functions Predefined parameters Shift and Stretch Caps Outputs Cross Sections and spectrum Q3241 Ref rind Shift fit Stretch fit Scaling fit Cancel Help This page is not active for the wavelength calibration procedure in the current vetsion of the programme If the calibration 1s applied on all spectra Run Calibration option in Analysis Windows Properties this page allows checking individual fitting results slant columns and standard deviations Page 79 WinDOAS 2 1 February 2001 The WinDOAS Tools 8 The WinDOAS Tools This chapter covers the main features supported by WinDOAS about convolution and describes the three off line tools included in the software gt the Con
5. Supported line shapes WinDOAS supports the following line shapes for convolution The Gaussian line The usual standard expression used to approximate instrumental slit shape functions is the Gaussian function The Gaussian is the exact line shape in the diffraction limit i e in the case of an infinitely thin entrance slit The normalised Gaussian is given by Page 27 WinDOAS 2 1 Description of The Algorithms February 2001 The Error Function The 2n Lorentz n 1 n 4 TheVoigt Profile Function Page 28 2 ne CXDIi ANT p a G x where e xis the distance from the line centre Oo In2 5 a and o Gaussian half width If the Gaussian can be used as a good approximation for the slit function when a thin entrance slit is used then for a large entrance slit the slit function can be approximated by the convolution of a boxcar and a Gaussian function The expression to use is erf a a 1 x A x A E x a A E where A is half the pixel size and erf x is the well known error function usually defined in text books by erf x exp d This line shape is a generalisation of the well known Lorentzian function n I It is useful to approximate slit functions having shapes differing significantly from the Gaussian one Low order 2n Lorentz can mimic line shapes having large wings typically the Lorentzian profile or line shapes hav
6. V Refi Ref2 Automatic C File Min 1346 Max 359 Files Reference 1 data harestua haggh0S5u_35 ref Browse Reference 2 80 deg i 2 deg Residuals Browse Molecules Continuous functions Predefined parameters Shift and Stretch Gaps Outputs 2 Diff Orthog Interp Convol AMF Fitdisplay 4 No2ch Differential XS Interpolate Mone Bro Differential XS Interpolate Insert Cross section o4 None Interpolate Bemove 1 Ref ting Differential XS interpolate Remove ERES E S Properties d oe _ 7 Right click shortcut menus This dialog box is dedicated to the parameterisation of the main spectral analysis The possibilities of analysis configuration are very large This section describes the main components of the Analysis windows properties dialog box Next section will guide you in the definition of parameters to fit A reference spectrum is assumed to be correctly wavelength calibrated If a wavelength calibration correction is applied anyway on this spectrum cross sections are re interpolated on the new grid WinDOAS gives the possibility to define two reference spectra Reference 1 and Reference If only one reference spectrum is specified it is used as control spectrum te the J spectrum in the Beer Lambert law If two reference spectra are given the wavelength calibration is applied only on the first one Reference 1 the shift between both reference spectra is then determined using
7. Raw S Jungfraujoch Projects Tree sees spe OHP i Analysis Windows Harestua Spectrum Residual Offset res fit BO Bruxelles Oclo User defined symbols OHP 03241 Raw Spectra Bro es ing HP2000_03_06 spe o4 c patties Create folder Analysis Windows ring Insert Path bro Oclo 03221 Remove Del k ie Rename 350 355 350 355 Wor no Hide OfKS P ace 03202 03221 fit resol fit 03241 fit ring fit 1 resol Show Hidden items Environment 03273 Browse gt res Tree ELT NAM Jai Reference for BrO analysis window 12 45 Remove all Items Reference for Oclo analysis window 12 45 Expand all Collapse all Project Harestua 350 355 350 355 File e windoas doc sum data t D d Date and Time 29 02 2000 06 28 13 Bro fit Ho2cb fit Polynomial Win Record 1 45 ata OW Zenith angle 89 700 Exposure time 0 000 sec Scans taken into account 0 Detector temperature 0 000 Sun azimuthal angle 1 000 ALIGNMENT OF REFERENCE 1 ON REFERENCE 2 350 355 Analysis window BrO 4 DOAS Analysis Program for Windows Right click Graphs Status Bar Shortcut Window Menu The WinDOAS user interface is a Multiple Document Interface MDI including the following components gt four main child windows 1 the Workspace Environment window 2 the Projects window 3 the Data window 4 the Graphs window a menu bat a toolbar a status bar right click sh
8. Windows Properties Shift and Stretch Page 4 5 Delta values Page 74 WinDOAS 2 1 February 2001 pg Molecules Continuous functions Predefined parameters Shift and Stretch Gans Outputs Cross Sections and spectrum Spectrum 03221 03241 Bro Fi mi E zh store 5c store Err store Columns of this page are activated only if the Analysis button is checked in the ASCII Results tab page of Project properties see page 62 You can check individual results to save in the output file shift Sh store stretch St store and scaling Sc store If the Err store column is checked the standard deviations of fitted parameters shift stretch and or scaling are saved in the output file Be Molecules Continuous functions Predefined parameters Shift and Stretch Gaps Outputs Cross Sections and spectrum Spectrum a3221 03241 Bra In this page you can specify the initial value of the fitting parameters these are used by the NLLS algorithm Shifts are expressed in the unit selected in the Analysis tab page of Projects properties see page 57 There is one column for each kind of parameter shift stretch order 1 stretch order 2 scaling order 1 scaling order 2 Note that in case the fit of these parameters is disabled in page 1 5 non zero initial shift values are still applied ae Molecules Continuous functions Predefined parameters Shift and Stretch Gaps Outputs Cross Sect
9. a NLLS fitting approach in order to align cross sections on the second reference spectrum Reference WinDOAS allows selecting different control spectra from the current data file by specifying a range in SZA option Automatic in the Reference selection frame For each twilight the spectrum in the file with the SZA closer to the one specified by the user will be selected as control spectrum If the SZA range is lower than SZA supported by the current file the spectrum in the file with the minimum SZA will be selected for both twilights Page 65 WinDOAS 2 1 The Projects Tree February 2001 Calibration To calibrate the reference spectrum select Ref only in the list proposed by the Calibration frame The wavelength interval on which the calibration procedure is applied is selected in the Calibration page of Projects properties see page 58 It can be different from the one selected for spectra analysis The option Spectra only is useful for tropospheric measurements where no reference spectrum is needed The option Reftspectra allows applying a calibration correction on both reference spectrum and spectra to analyse This option has been designed to handle spectra recorded with unstable unthermostated instruments where the spectral resolution can vary a lot from one spectrum to another In this case the resolutions of both spectra are matched to the resolution of the less resolved spectrum and the absorption cross sections can be conv
10. 03 no2cb i0gome xs and n0296 10 xs BrO Wahner 228K 0 17 bro_228wah xs O4 Hermans et al 04 chris xs Ring created according to ref 5 using ring xs WinDOAS Ring tools Wavelength calibration A preliminary calibration has been performed in laboratory Uvcal clb It is corrected through NLLS fitting of the control spectrum a spectrum measured in minimal conditions of absorption w r t the high resolution solar reference spectrum by Chance and Spurr 5 In this case the instrument slit function line shape is best represented by an error function integrated gaussians A preliminaty wavelength dependency of the slit function has been calculated sfpO fullslf in order to convolute cross sections to use in the definition of spectral analysis windows This analysis setup is mainly based on recommendations established from previous studies e g ref 1 and improved according to the type of intstrument and measurements Defining Symbols The symbols defined in the WorkSpace Environment tree must match the first characters of the cross section files those characters are immediately followed by an underscore in the cross section file name To insert symbols in the Workspace Environment tree select the predefined User defined symbol node and right click the Insert item command or use the Insert key You can specify a short description for each symbol if you want Projects Properties Select the Harestua project node in the Projec
11. Extra data can then be requested according to your selection The configuration of parameters to fit is done in the dialog box called by the way of the Fit Parameters pushbutton Spectra compares the observed and calculated spectra Fits displays fits of Ring effect and or atmospheric absorptions if any Residual displays the residual of the fit shift SFP displays the wavelength dependency of the shift and slit function parameters fitted over the selected wavelength window Page 59 WinDOAS 2 1 The Projects Tree February 2001 Project properties GOME Spectra Analysis Filtering Calibration Undersampling Slit Function ASCII Results Figure 7 8 Project Properties The Undersampling Tab Page Solar ref file fgwindoas cd rdataWewkpna vac ktz Method Fixe phase kai shift 0 008 Cancel Help Method See the Undersampling topic in 4 6 section to get further details about undersampling correction In this page three methods are proposed From file Undersampling cross sections are provided in files like usual cross sections These files might be created using the WinDOAS Undersampling tool see 8 5 Fixed phase WinDOAS uses the information derived from the NLLS wavelength calibration and slit function determination to create the undersampling cross sections with a fixed value of the shift The selection of this method is recommended Automatic phase The undersampling cross sections
12. Help For geolocation coordinates WinDOAS applies the following conventions gt longitudes are positive eastwards negative westwards latitudes are positive northwards negative southwards The Site name abbreviation two characters only is used to start the name of overpass files when no output file name is imposed by the user The Altitude field is used to calculate moon positions 6 3 User Defined Symbols Properties Figure 6 3 User defined Symbols Properties Symbol description Bra cross section vahner 228K Cancel Help Cross sections symbols can be completed with a short description 6 4 Handling Items in the WorkSpace Environment Tree Note that only one item can be selected at the same time in the tree Use right click shortcut menus to handle items in the WorkSpace Environment tree The deletion of an item observation site or user defined symbol 1s possible only if the symbol is not used in the configuration of a project or an analysis window Page 50 WinDOAS 2 1 February 2001 7 The Projects Tree 1 1 Description of the Projects Tree Figure 7 1 Main Components of The Projects Tree Project Directories structure User defined folder Spectra file The Projects Tree This chapter describes the organisation the handling and the configuration of the different kinds of items in the Projects tree It covers VVV WV the management of files and directories s
13. Predef V Refi Ref2 Beeeeen en nnn nn nnn Reference 2 o deg l 2 dead Residuals Browse Molecules Continuous functions Predefined parameters Shift and Stretch Gaps Outputs fir Diff Orthog Interp Convol No2ch Differential XS Interpolate Mone Differential XS Fit display Interpolate o4 None Interpolate Mone ring Differential XS Interpolate None EB i c ont ow Analysis Windows This dialog box is dedicated to the configuration of a spectral analysis window Properties In the above window we have specified the fitting interval for BrO 346 359 nm We have checked the option Automatic in the Reference selection frame This means that a different control spectrum is automatically retrieved from the current data file for each twilight The selection is performed around 80 SZA cfr the SZA range specified in Reference The wavelength calibration is applied on the spectrum specified in Reference 1 the shift between both reference spectra is determined using a NLLS fitting approach and applied to align cross sections on the control spectrum The structure of the Analysis Windows Properties pages is very similar to the one used for the calibration and already defined above Molecules pages In these pages the absorption cross sections needed in the BrO fitting interval see the BrO analysis setup page 38 are listed and associated parameters are defined Differential
14. Properties Shift and Stretch Page 1 5 Molecules Continuous functions Predefined parameters shift and Stretch Gaps Outputs 35 Figure 5 16 EH Analysis Windows Spectrum D 000e 00 0 00 Properties 0 00 0 00 Shift and Stretch Page 3 5 Running Analysis To analyse a spectra file select it in the Projects tree and right click the Run Analysis command Note if you right click Run Analysis command from the parent node the command will be performed on all spectra files defined in the selected project Page 44 WinDOAS 2 1 February 2001 Quickstart Fi 5 1 7 L DIES Analysis Program for Windows E WINDOAS Doc SUM S ample sample wds igu re i Files View Edit Projects Tools Windows Help C se e e ajal i lt lt gt gt 1 gt n e A PH Projects Be x FN Workspace Environment EN Calibration applied on project Harestua window BD F Running Analysis Wavelength calibration OHP Window n pix lembda Niter Shift 110136 332 9 5 2 10 221 338 9 5 3 10 307 344 9 4 1 902e 00 2 381 e 02 4 10 394 350 9 4 5 10 483 356 9 5 T DOAS Analysis Program for Windows 11 21 Harestua Observation Sites Raw Spectra User defined symbols HA_2000_058 spe HA 2000 059 spe Complete fit Residual ring fit 03244 fit H 2000_O60 spe l Alli HA 2000 061 spe Bemove Del H 2000 062 spe Hide H 20
15. Spectra W Fits W Residual w shift sFP Number af zub vvindaws 10 Fit parameters Wavelength Calibration Wavelength calibration and instrumental slit function characterisation are And Slit Function performed using a non linear least squares NLLS fitting approach where Characterization measured intensities are fitted to a high resolution solar atlas spectrum degraded to the resolution of the instrument The wavelength interval used for this calibration must be specified in the Window limits nm box This interval is subdivided in a number of equally spaced sub windows and shift and slit function parameters SFP are fitted using the NLLS approach in each interval The shifts values determined in all sub windows are then used to reconstruct an accurate wavelength registration Similarly the wavelength dependent slit function is determined by polynomial fitting through individual SFP values These two information are subsequently used e g to build undersampling cross sections The current tab page comprises the following fields and buttons for configuring calibration Page 58 WinDOAS 2 1 February 2001 Solar reference spectrum Line Shape Selection Display Solar ref file Analysis Method Fit SFP Display Polynomial degree Window limits Number of sub windows Fit Parameters The Projects Tree the solar reference spectrum see remarks below the fitting method can be different from the one u
16. U A log over A under A Undersampling cross sections can be pre calculated using the WinDOAS undersampling tool or they can be calculated in real time just after the wavelength calibration procedure using the corrected wavelength grid and the characterised slit function Page 31 WinDOAS 2 1 February 2001 Quickstart 5 Quickstart When starting WinDOAS two empty windows Projects and Workspace Environment appear inside the main program window This chapter describes how to create a project insert files and display spectra Using a predefined configuration provided with the package setup for BrO retrieval it guides you step by step towards the complete configuration of a project All needed input files spectra and cross sections can be found in the directory Data on the distributed disk 9 1 Creating a Project Creating a New To create a new project item in the Projects tree Project 1 select Projects New command from the menu bar 2 rename the created new project item for example give it the name my first project 3 a dialog box with Projects properties appears a DES Analysis Program for Windows Figure 9 1 Files View Edit Projects Tools Windows Help aS Creating a new project my first project Raw Spectra Project properties my first project i21 x Analysis Windows Spectra Analysis Fiterng Calibration Undersampling instrumental sit Function A
17. a Project for BrO Retrieval Configuring A Project The configuration of a project requires the following steps For Spectra Analysis 1 define in the Workspace Environment tree all relevant symbols related to the cross sections files that will be used in the analysis 2 call back the Projects properties dialog box to parameterise the wavelength calibration procedure and to setup analysis options independent of the spectral window fitting method unit for shifts 3 create an Analysis Window item in the Projects tree for each spectral window to process and parameterise it These steps are described through the example file Sample wds provided with the package Page 36 WinDOAS 2 1 February 2001 Quickstart Description of The file sample wds in the WinDOAS folder contains the configuration of a sample wds project for BrO retrieval This file should have been copied to your hard disk l during the installation procedure see section 2 2 Change paths Before using the sample wds file you may probably change paths The fastest way to do it is to edit the file and check the All paths section Piece of content of the sample wds configuration file All paths 0 c windoas data harestua 40 1l c windoas data harestua spectra 7 4 c windoas 2 6 c windoas data ohp spectra 6 7 c windoas data ohp 14 Loading sample wds file Use Files Open command from the menu bar or the equivalent button in the toolbar
18. applications developed with WinDOAS is saved in ASCII files The default extension for WinDOAS configuration files is wds You can Open an existing configuration file using the options sequence Files Open from the menu bar or the icon Open from the toolbar The same result will be obtained easier by double clicking on the name of any file with extension wds For that apply the following instructions in My Computer or Windows Explorer window apply the command View Options from the menu bar select the File Types tab page click New Type pushbutton enter WinDOAS as Description of type enter wds as Associated extension click New pushbutton to open a New Action popup window enter WinDOAS as Action use Browse pushbutton to search for WinDOAS program in your path tree click OK click Change Icon pushbutton and then Browse pushbutton to search for WinDOAS program select WinDOAS icon Click ok Page 9 WinDOAS 2 1 February 2001 Description of The User Interface 3 Description of The User Interface 3 1 The User Interface Components Figure 3 1 The WinDOAS Menu User Interface Bar Toolbar in DITS Analysis Program for Windows E WINDOAS Doc SUM Data sample wds Files View Edit Projects Tools Windows Help S Alo il a gt mif gt n e BN Projects olx FN Workspace Environment a a rn x Harestua Observation Sites
19. are calculated at each iteration of the analysis procedure using the fitted value for the shift between control and measured spectra This method is rather time consuming and only applicable for testing purposes Shift The Shift field operates only in Fixed phase method Solar ref file In Fixed phase and Automatic phase undersampling cross sections are calculated from a high resolution solar spectrum convoluted on an oversampled and an undersampled grid with the instrument slit function see the Supported line shapes page 27 If you don t want to correct for undersampling Select File method and for all the Analysis Windows see page 72 defined under the current project uncheck the fitting of undersampling cross sections in the Predefined parameters page in intensity fitting mode or remove Usampl1 and Usampz2 cross sections symbols from the Molecules page in optical density fitting Page 60 WinDOAS 2 1 February 2001 The Projects Tree Project properties Harestua Figure 7 9 Project Properties The Instrumental Tab Page lr 1 touc ELE pe AharestuaWlvcal clb LI ome ee In the Instrumental page you must specify the format of the spectra files to process The fields to fill in depend on the selected format For a detailed description of a specific format or to include a new spectra files format contact authors A preliminary calibration is expected in the Calibration file field Instrumental corr
20. as renames the current WinDOAS application Print prints the content of the active Graphs or Data window Print Setup selects and set up the printer Exit exits WinDOAS Edit for the moment this option only includes the Goto sub option giving direct access to any record in the current open spectra file Projects global operations on the Projects tree New creates a new project in the Projects tree Remove All removes all projects from the Projects tree Run Analysis applies analysis on all files of all projects Run Calibration applies wavelength calibration on all files of all projects Tools gives access to WinDOAS tools Page 12 WinDOAS 2 1 February 2001 Description of The User Interface Windows Organization View calls back the selected child window Windows usual Windows options for organising child windows in the current application or activating the selected child window Online Help Help gives access to online help 3 4 The Toolbar First Next New Save Zoom out spectrum spectrum Continue Stop yy yy o oe Figure dip mmm alal Open Print Goto Previous Last Pause spectrum spectrum The WinDOAS toolbar proposes several shortcuts that allow easy access to the following options Application Control New starts a new WinDOAS application Open opens an existing WinDOAS application Save saves the current WinDOAS application Printing Print prints the content of the active Graphs or Data window Display Zoom out
21. band 000 Humber of iterations 0 High Pass Filtering Filter Type hone Cancel Help Spectra and cross sections can be filtered using one of the filters proposed in the Filtering tab page Kaiser Boxcar Gaussian Triangular Savitzky Golay Odd even pixels correction Binomial VVVVVV NV According to the selected filter different fields must be filled in The selected Page 57 WinDOAS 2 1 The Projects Tree February 2001 filtering can be disabled for individual cross sections in the Analysis windows properties dialog box see page 70 Select filter type None if you want to disable spectra and cross sections filtering The program supports low pass and high pass filtering In the latter case cross sections are filtered by subtracting a fitted polynomial or a smooth spectrum calculated by filtering the original cross sections a high number of times Differential cross sections can be obtained by this way For the moment high pass filtering is supporting only in optical density fitting mode Project properties Harestua instrumental SlitFunction ASCIResuts wasa AMESResuts Spectra Analysis Filtering Calibration Undersampling wA Figure 7 7 Project Properties The Calibration Tab Page Solar ref file e Wdataixs hrikurucz urd kt Analysis Method Optical density fitting Fit SFP Error function Polynomial degree Window limits mmm Display I
22. been inserted under the predefined Raw Spectra node To display the complete file path select the file name item in the Projects tree and right click the Properties option a DES Analysis Program for Windows Figure 5 2 fies Yen ect Ioe Wr HOB lejals FA Workspace Environment Spectra files properties E my first project El Raw Spectra H 2000 057 spe HA 2000 058 spe Remove H 2000 058 spe Hide HA 2000 060 spe Show Hidden tems HA_2000_061 spe HA 2000 062 spe Browse spectra Analysis Windows Export in ASCII RonAnalvsis Run Calibration Expand all Collapse all Raw Spectra File Properties Dont create files names automatically Raw Spectra EWINDOAS DociSUMSample HarestualiSpectratHA_2000_058 spe Cancel Help Edit properties of the selected item 12 04 Don t worry about the Don t create files names automatically for the moment When the format includes record names and dark currents you can check this button to replace default WinDOAS record names and dark currents file names by yours The format in this example doesn t use record names and dark currents Browsing Spectra To browse spectra 1 open Graphs and Data windows with the View command in the menu bar resize and organise windows at your best convenience 2 select a spectra file item and right click the command Browse Spectra Page 34 WinDOAS 2 1 February 2001 Figure 5 Browsing spectra Handling Graphs Figure 5
23. control spectrum and each spectrum to analyse and use this information to convolute cross sections in real time To apply this select as Slit Function type a wavelength and temperature dependent one enter the appropriate file and check the button Apply Fwhm correction Note that this method is heavy in processing time Project properties Harestua EAE Figure 7 11 Project Properties Spectra Analysis Fitering Calibration Undersampling Instrumental Slit Function ASCH Results NASA AMES Results The ASCII Results Tab Page 5 e Analysis Fluxes 330 350 380 M Calibration Cic 380 330 Date amp time YY MMDDhhrr Date ODM mg v Time hh mm sxj Fractionnal day Output Files Format This page is dedicated to the selection of calibration and analysis results to output gt when the Analysis button is checked the selection of the results file and the selection of fields to output are enabled The program produces tabbed separated columns ASCII files that you can easily load in spreadsheets like Excel There is one line per processed spectrum and the first line is reserved fot columns titles gt when the Calibration button is checked wavelength calibration results are saved before analysis results Lines start with the semicolon character Page 62 WinDOAS 2 1 February 2001 The Projects Tree Automatic Creation Of The Output Path or File pushbutton allows you to locate
24. cross sections are generated by orthogonalisation to an otthogonal base defined in the Continuous function page In order to avoid cotrelation between cross sections of similar shapes e g when treating temperature effects by including two or several cross sections of the same species these cross sections can be orthogonalised with respect to each other Continuous functions page In this page the polynomial used for fitting the smooth part of the absorbance is defined An orthogonal base is built with the main components of the polynomial in order to calculate differential cross sections To build the otthogonal base right click the Properties command Page 43 WinDOAS 2 1 Quickstart February 2001 Predefined parameters page Among the available predefined parameters we have selected the components of the offset second order Shift and Stretch pages Shift and stretch 1st order applied to the spectrum are selected for fitting In these pages a shift value to be applied not fitted to the O cross section is also defined Note that several cross sections can be grouped together To access the configuration menu right click the Properties command The units of the shift values are selected in Projects properties in the Analysis page Molecules Continuous functions Predefined parameters Shift and Stretch Gaps Outputs is Figure 5 15 shift fit Stretch fit Scaling fit Analysis Windows Spectrum 1st order Mone
25. defined in the Filter tab page of Projects properties otherwise WinDOAS 2 1 February 2001 Interpolation Convolution AMF The Projects Tree a cross section in the selected cross section is orthogonalised to the the proposed list otthogonal base if defined and to another cross section defined in the list orthogonalisation in cascade is allowed In the latter case you can avoid any correlation between two cross sections for example two O3 cross sections measured at different temperatures The list of available cross sections includes all cross sections symbols defined in the Molecules page except the one selected It is updated as cross sections symbols are added in or removed from this page This column describes the action to perform on the selected cross section None the selected cross section is assumed to be correctly aligned on the reference spectrum grid so no action has to be performed on the cross section for example a user defined undersampling cross section in optical density fitting Interpolate this is the usual choice the selected cross section a pre convoluted ot a high resolution one has to be interpolated on the grid of the reference spectrum Convolute Std this option gives the possibility to convolute a cross section in real time using either the information on calibration and slit function provided by the wavelength calibration procedure or the user defined slit function specified in the Sli
26. foreseen for cross sections files a file name in the format imposed by WinDOAS as described in section Configuration of the Fitting Parameters page 67 WinDOAS inserts in the output file a header describing how the convoluted filtered spectra have been created To disable header writing check the Remove header button in tools dialog boxes Results of the Convolution and the Ring tools are displayed in the Graphs window Page 81 WinDOAS 2 1 The WinDOAS Tools February 2001 8 3 The Convolution Filtering Tool The Convolution Filtering tool gives the possibility gt toapply a convolution with Jj correction gt to introduce a shift by shifting the calibration grid before convolution gt to create an effective slit function taking into account the finite resolution of the source spectrum using a FT deconvolution method gt to filter the convoluted cross section before saving it Convolution Filtering tool options are distributed in three pages general general options convolution type input output files slit function selection and parameterisation of the slit function filtering selection and parametetisation of the filter Convolution Filtering tool Ei Figure 8 1 Convolution Filtering Tool General sit function Fittering The General Tab Convolution type l correction T shift oos ru Page Conversion vac to Air hd Sone se 18 molem input file cstaws HmosOSs241 vac Output fil
27. graph zoom in is performed by clicking and dragging the mouse ovet the wanted screen area this shortcut recovers the original size of the active graph Spectra Browsing Goto direct access to a given record in the current spectra file p g 8l p First spectrum goes back to the first spectrum in the current file Previous spectrum goes back to the previous spectrum in the current file this button speeds up the spectra browsing when held down Next spectrum goes to the next spectrum in the current file this button also speeds up the spectra browsing when held down Last spectrum goes to the last spectrum in the current file Continue continues the paused spectra browsing or analysis Pause in non stop spectra browsing or analysis marks a pause Stop stops spectra browsing or analysis Page 13 WinDOAS 2 1 Description of The User Interface February 2001 3 5 The Status Bar The status bar is divided in three sections online help a short help text is displayed as a menu bar command or a shortcut menu option is pointed out with the cursor graphs coordinates the current coordinates in user units are displayed as the cursor is moved on the graph time section the current time is displayed with an accuracy of 1 minute 3 6 The Shortcut Menus Page 14 Menu commands and toolbar buttons are completed in right click shortcut menus The options proposed in the shortcut menus depend on the calling object the Data window a
28. offset values can be easily interpreted relatively to the absolute intensity of the spectrum percent offset Page 24 WinDOAS 2 1 February 2001 Description of The Algorithms Ring Effect The so called Ring effect arises in the atmosphere due to inelastic scattering processes mainly Rotational Raman Scattering RRS by molecular O and N2 Roughly speaking it manifests itself by a broadening of the solar and atmospheric spectral features present in measured spectra This broadening typically reduces the depth of thin solar and atmospheric absorption features by several percents Hence it has a strong impact on spectroscopic measurements using the DOAS method and requires appropriate correction to be implemented in retrieval algorithms This is especially true for minor absorbers like BrO or OCIO for which weak absorption features can be completely masked by Ring structures In DOAS the Ring effect is usually accounted for as an absorber Ring cross sections can be obtained from different sources for example Vountas et al 13 Chance et al 5 WinDOAS implements a tool for the calculation of Ring cross section using the method described by Chance et al 5 The approach consists in a simple convolution of a solar source spectrum using calculated RRS cross sections Refer to section 4 6 for a brief description of the way this method is implemented Undersampling The undersampling is a well known problem of GOME see Ref 4 It
29. on the solar spectrum symbol Ref in this case In otder to avoid the need to interpolate the control spectrum we recommend for the wavelength calibration shifting the high resolution solar spectrum instead of the control one Note that in this case the cross section s defined in the Molecules page must be shifted together with the solar spectrum To change the selection or add another item in the list of shifted quantities right click the Properties command Analysis windows properties Calibration description Harestua project Figure 5 13 Calibration Fit Parameters Shift and Stretch 03241 Ref ring M SET IdETTIGVE EMO We NIENS Analysis Window Properties Creating a New Analysis To create a new Analysis Windows item in the Projects tree Window Item in the 1 select the predefined Analysis Windows node and right click the Insert Projects Tree item command 2 rename the created new Analysis Windows item for example give it the name BrO a dialog box with Analysis window properties appeats Page 42 WinDOAS 2 1 February 2001 Quickstart Analysis windows properties BrO Harestua project Figure 5 14 Calibration Ret only Reference selection Fitting interval nm Analysis windows properties Min 1346 Max 359 Reference 1 datatharestuatha99h085u_35 ref Browse Display v Spectrum vw Polyn v Fits v Residual vw
30. satellite measurements only in the User defined symbols section the user must define the list of all relevant symbols that will be used in the configuration of projects and analysis windows These symbols are needed to build cross sections files filters to link AMF and cross section files to name result files and for internal manipulations This chapter describes how to manipulate and configure Observation Sites and User defined symbols items in the Workspace Environment tree Figure 6 1 Pl Workspace Environment E E ES E Observation Sites ee Jungfraujoch The Workspace Environment Tree v Harestua i Bruxelles User defined symbols 6 1 Creating a New Item in the Workspace Environment Tree Creating a new item inthe 1 select the parent node in the tree Observation Sites or User defined Workspace Environment symbols node MEE 2 right click to open the associated shortcut menu and select the Insert Item option or use the Insert button on the keyboard 3 replace the new item text by the name of your choice 4 validate to open the properties dialog box for configuring the object Page 49 WinDOAS 2 1 The Workspace Environment Tree February 2001 6 2 Observation Sites Properties Figure 6 2 Observation Site Properties Longitude in degrees positive eastward 10 753 i Latitude in degrees positive northward 60 217 Site name abbreviation HA Altitude meters 600 000 Cancel
31. selected tree an item that was already existing Dialog boxes settings 4004 5018 5037 Field is out of d d range The pointed variable is out of the specified range 4005 Field s is empty or invalid 4010 Polynomial degree of s should be a positive integer and a multiple of 2 4011 Filter width should be an odd strictly positive number 4012 Filter order should be an even strictly positive number 4013 s should be strictly positive 4015 Format filter is invalid 4018 The number of points used for computing a polynomial should be strictly larger than the requested degree for the polynomial The indicated field must be filled in or contains an invalid value Directory structures handling 4016 You should validate path changes before selecting files You can not manipulate files in a directory structure before inserting the path in the Projects tree use the OK pushbutton to validate the path selection 4017 Selection of files and files only is requested Page 89 WinDOAS 2 1 Annexes February 2001 In Paths Properties dialog boxes right click shortcut menus are enabled for files items only Files handling 5007 File s not found 5013 Can t open file s in writing mode WinDOAS can t open the indicated file verify the path file 5010 File s is empty or not large enough The indicated file is empty ot doesn t contain the expected data Analysis error messages 5014 No automatic reference selection can be perf
32. 00 063 spe Show Hidden items Analysis Windows Browse spectra Export in ASCII Run Calibration 1 Expand all Collapse all 330 360 330 360 330 360 330 360 Shift applied SFP 2 applied Properties 330 360 Calibration applied on project Harestua window BrO 1 992e 00 4 968e 02 2 114e 00 2 192e 02 1 693e 00 1 878e 02 1 634e 00 3 544e 02 The first step of the program consists in applying in each sub interval of the calibration window a NLLS fit between the Reference 1 spectrum see Analysis Windows properties page 43 and the high resolution solar spectrum in order to determine the wavelength dependency of the shift and the fitted SFP the Gaussian FWHM of an error function in this case and then to optimise the calibration The Graphs window displays gt VV V WV the Reference 1 spectrum compared to the high resolution solar spectrum convoluted with the calculated resolution of the instrument the normalised residual the ring and the ozone contributions to the optical density the wavelength dependency of the shift the wavelength dependency of SFP 1 SFP 2 has been fixed Page 45 Quickstart Figure 5 18 Running Analysis Spectrum to analyse Figure 5 19 Running Analysis Control spectrum alignment on the Reference 1 spectrum Page 46 WinDOAS 2 1 February 2001 in DIES Analysis Program for Windows E WINDOAS Doc SUM S ample sample wds Files View Edit
33. 000 061 spe H 2000 052 spe H 2000 053 spe Analysis Windows OHP PN Analysis of in BrO window fei Observation Sites User defined symbols Running Analysis Spectrum Residual res fit Analysis results PN Analysis of in BrO window Bro fit 350 355 350 355 350 355 03221 fit resol fit 03241 fit Bro fit 350 355 Bro fit Ho2cb fit Pohmomial DOAS Analysis Program for Windows 12 18 The absorption cross sections ate interpolated on the control spectrum grid Then the program starts the spectral fitting in the BrO window according to the method selected in the Analysis page of Projects properties Columns densities of all selected species are retrieved Once the analysis is completed residuals and fitting results are displayed in the Graphs window The retrieved parameters are displayed in the Data window We have zoomed the BrO fit If we go on the program will perform the spectral fitting in the OCIO window Page 47 WinDOAS 2 1 February 2001 The Workspace Environment Tree 6 The Workspace Environment Tree The Workspace Environment tree contains two sections gt in the Observation Sites section the user can define a list of observation sites specified by their geolocation coordinates These are used for cotrecting zenith angles data or performing a spectra selection balloons and
34. 0_056 spe SMPTE HA 2000 064 HA 2000 063 Cancel o cme Help HA 2000 58 Browse spectra Export in ASCII Run Calibration 7 3 Handling Items In The Projects Tree Use right click shortcut menus to handle items in the Projects tree Note that only one item can be selected at the same time in the tree Page 53 The Projects Tree Common options Projects Analysis Windows Spectra files Remove Rename Remove all items Hide Show hidden items Copy Cut Paste WinDOAS 2 1 February 2001 removes the selected item from the Projects tree renames the selected item removes all child items under the selected node hides the selected item files folders directories or analysis windows without loosing its properties hidden items are not considered for the spectra analysis recovers under the selected node all previously child items files folders directories or analysis windows these operations are supported for analysis windows and projects nodes but not for files and folders when pasting an item in another configuration file the list of symbols is updated if needed Right click the Properties option to open the Project properties dialog box and to configure the selected project Select the following Projects commands in the menu bar New Remove All View cross sections Properties Insert item Sort items See previous section 7 4 Project Properties Pa
35. 1 spe H 2000 062 spe H 2000 053 spe Analysis Windows DUM MMOL NER dE OHP 0 027 wesssssssoesscsssececoccecuseecseeunssssses esseceeelevecccecccheecibeeccccccecccccece g TNR E N ROME LAE g 0021 JA een Mx EDD HP nated n Data OF xi Reference for BrO analysis window 14 38 SZA 80 3667 i 2l Reference for Oclo analysis window 14 38 SZA 80 3667 i Measured Calculated Project Higgs T r EET EEEE EEEN File AharestualspectradHA 2000 060 spe Date and Time 29 02 2000 06 28 13 m m Ber Record 3 38 Zenith angle 89 629 Exposure time 0 000 sec avelength nm Scans taken into account 0 E xl AZ DOAS Analysis Program for Windows no 2038 The program then searches in the file for a spectrum to use as control spectrum for the current twilight In the Data window you can see the record number and the SZA of the selected spectrum In this case the same control spectrum will be used in BrO and OCIO analysis windows The alignment between the control spectrum and the reference is determined using a NLLS fit in both spectral analysis windows and the result of the fit is displayed WinDOAS 2 1 February 2001 Quickstart L DIES Analysis Program for Windows E WINDOAS Doc SUM AS ample sample wds H Files View Edit Projects Tools Windows Help Figure 5 20 ne S slal ial ul n e iN Projects E ICI XJ Harestua Raw Spectra H 2000 D058 spe H 2000 053 spe H 2000 O60 spe H 2
36. 3 Structure of the slant column fitting module Page 19 Description of The Algorithms Page 20 b low pass and high pass filtering optional Non linear parameters initialization NLLS fit y Modify NL parameters according to the NLLS fit using a gradient search algorithm m combined with a linearization of the fitting function Marquardt Levenberg Solve linear problem LLS fit Minimization of the residual R for linear parameters using SVD method Eu Residual R fitted parameters including SCD standard deviations Figure 4 4 Structure of the coupled linear non linear least squares algorithm used in the slant column fitting module and in the wavelength calibration module WinDOAS 2 1 February 2001 WinDOAS 2 1 February 2001 Description of The Algorithms 4 3 Slant column fitting The Beer Lambert The Beer Lambert law describes the extinction of the solar radiation in an law absorbing atmosphere I A 71 A exp 6 eq 1 where I A is the solar spectrum after absorption Io A is the extraterrestrial solar spectrum Oi are the relevant cross sections of the absorbing species with wavelength and temperature dependent structures Ci are the unknown species column densities The logarithm of the ratio of the control spectrum 75 A and the measured spectrum 7 A is denoted optical density or optical thicknes
37. 4 Zoom in Se 3 L DITS Analysis Program for Windows bservation Sites User defined symbols my first project B Raw Spectra P H 2000 057 spe H 2000 058 spe HA 2000 053 spe H 2000 060 spe i HA 2000_061 spe po HA 2000 062 spe i Analysis Windows Quickstart 360 Wavelength nm L DES Analysis Program for Windows Observation Sites User defined symbols my first project Raw Spectra H 2000 057 spe H 2000 058 spe H 2000 053 spe H 2000 O50 spe H 2000 051 spe HA_2000_062 spe Analysis Windows The first record is displayed in the Graphs window The Data window displays available data on the current record Use appropriate buttons in the toolbar to move in the file lal x PN Spectra E WINDOAS Doc SUM S ample Harestua S pectra HA_2000_058 spe 2 39 SZA 90 44 ol x 360 Wavelength nm You can perform zooms using the mouse If the main Graphs window contains several graphs this is not the case in this example you can click in graph frames to redraw spectra in separate windows and then perform zoom Page 35 WinDOAS 2 1 Quickstart February 2001 H a DES Analysis Program for Windows BEE Figu re 9 5 Files View Edit Projects Tools Windows Help se tal S amp I ma ii e PN Workspace Environment i l xd PN Spectra E WINDOAS Doc SUM S ample Harestua Spectra HA_2000_058 spe 1 39 SZA 90 96 Dixi Obser
38. A AMES Research Centre is an ASCII based reporting system which includes several categories of self described data formats The Ames format is used to provide for example the NDSC database WinDOAS can output results in the Ames format for four molecules NO Os slant and vertical columns BrO and OCIO slant columns only using the template NASAAMES HDR provided with the program For each molecule you can select the analysis window in which the results to output ate calculated The selected analysis window must include a symbol whose syntax is exactly the same as the indicated one As for ASCII results you can specify in the usual Windows Save dialog box the name of an output file or just the word automatic In the latter case WinDOAS will create automatically output files names according to the syntax described above but will use the UVV extension instead of the ASC one Page 64 WinDOAS 2 1 February 2001 The Projects Tree The Instrument and Experiment fields must be filled in They will be used in place of INSTR and EXPERIMENT macros edit the NASA AMES HDR file when building the Ames file header 7 5 Analysis Windows Properties Figure 7 13 Analysis Windows Properties Reference Spectra Analysis windows properties BrO Harestua project Calibration Ret only Reference selection Fitting interval nm Display v Spectrum V Polyn v Fits v Residual vw Predef
39. Com Cross Sections Dam Com Usamp1 and Usamp2 are predefined symbols Handling cross sections items in the list Differential cross sections Page 68 gt Usamp Cross Sections Usarnp _ 3 2 x x ing Cross Sections ring s k OclO Cross Sections Ocli set 2 select in the Files of type list the cross section you want to insert 3 in the cut down list of files select the file containing the cross section to fit To control or modify the cross section file associated to a cross section symbol defined in the Molecules pages right click the Properties of the selected symbol To remove a cross section from the list select the cross section symbol and right click the Remove option The option is greyed if another cross section is otthogonalised to the selected one or if the selected symbol is used in the Shift and Stretch pages Differential cross sections can be generated either by orthogonalisation or high pass filtering according to the definition or not of an orthogonal base formed with the component vectors generally a base of order 2 of the polynomial defined in the Continuous functions page see the next section page 70 There are three possible choices None use the original cross section Differential XS generate a differential cross section gt byotthogonalisation if an orthogonal base is defined in the Continuous functions page gt using high pass filtering options
40. EEEE A E A E E ounces 26 4 5 Wavelength calibration and slit function characterisation esssesessesessesseseseesessestssrsrssesrerrstesestesrsrerrsreseess 2T LU ME Gioco UD Zu d UTEM TRU RR EEE EAO 27 FUE TOOL Eo o 30 81777 217 127 10 E777 a X 31 8e Ccup 4 peccet 33 Oa Creatas q PtOJCGUani sui ath op patas dd ot Ut utis uet bab tre t Ds p ates 33 CEU END TG a sodomie Du cta aed aca aaa Mcd MEE 23 IAM MT 34 I SDA L A AA T E A A E PEA E E T T S A EEA 34 TA GUAT AE I E EAT A cin I A E EAS aD E eaa S 35 ST U O E EE T A TET ETTO 36 52 Example Configuration ofa Project tor BrO Retrieval ier PE o Po Ee lotbed io Linee 36 COMME AA Doro Por S DOTEA NEUE acabe edic aaa videi elect pesti issus 36 DO OO SODES sss Tira etis esti eec o edi etse d te dera ipii oleae EN a Bf zinam S T OF DTI ROTTA PNE 38 ID T EAA T EAS NAA EA EA E A T AEE NE T OE 38 EI BE PE 38 PANG SIS WOW Ur ND 42 TE AIA I NP pEE 44 6 THE WORKSPACE ENVIRONMENT TREE eene nennen nnne 49 6 1 Creating a New Item in the Workspace Environment Tree oet itii irato tne Horne reto 49 OZ XODsesyation sites PTOP OT E at uie datio mee optet een tette nde lod Dui Mk A T 50 Go DserDenned Syrabols Properties oina a aR EA E A E a dees 50 6 4 Handling Items in the WorkSpace Environment Tree iude ee pedes br bedient 50 LHERROJECIS TREE ceruan e E eut E 51 Jh dHOCSCHDHOMOL the Projects LEGO aique
41. Projects Tools Windows Help C se E amp I4 pli a GES BEE PN Workspace E PN Spectra harestua spectra HA_2000_060 spe i 3 38 SZA 89 6294 iof x Harestua Observation Sites Raw Spectra User defined symbols HA 2000 058 spe H 2000 059 spe HA 2000_060 spe H 2000 O51 spe H 2000 052 spe H 2000 053 spe Analysis Windows OHP 30000 24000 e 18000 o 12000 WN Data Reference for BrO analysis window 1 38 SZA 58 18 6000 Reference for Oclo analysis window 1 38 SZA 58 1 Project Harestua File Aharestualspectra HA 2 Date and Time 29 02 2000 06 28 13 Record 3 38 Zenith angle 89 629 Exposure time 0 000 sec Wavelength nm Scans taken into account 0 xl DOAS Analysis Program for Windows Tr 53 The program searches for the first spectrum to analyse in the selected file and displays it L DITS Analysis Program for Windows E WINDOAS Doc SUM S ample sample wds Files View Edit Projects Tools Windows Help C ae amp I4 44 gt gt ed P ii e A Projects Ioj x IN workspace Go on nment Pl Reference 2 alignment on reference 1 in BrO analysis window 0 438178 ml x Harestua bservation Sites Raw Spectra User defined symbols H 2000 058 spe H 2000 053 spe HA_2000_060 spe H 2000 06
42. S EEEE EEEE teed sas td eodera eddie canh es bo desc epselii epos tud os 78 LG TIT TH UIDI NR 78 LAC SUL ANG T0 POON ririri re R nesiaeactetiiead ancmenit a pattem 79 DDO ADS PARC T M sats 79 IDE T E L E E E A A E E E 79 THE WINDOAS TOOLS taiea eaa eto aara OEE eee E 81 Dl Sapore aE ADES aaae r E E A E EO OARE 81 Uu UNDOUE TUST OTI ces a E N nana AT NE T ae 81 eo The Convolution Pireno Tool deut n E ca aaa da Mead 82 EE 577547 WR Mr TRECE 82 E TT GION Ta NT LADEN 43 PEU E IURI AE T Mm TE 64 P MB NE Sire o sina sass tssen yesvesahia lanes tlaca satu tadeoehed ida chatetuisnas aaa Sata blacticsn as aie sas uiulsdd a ak Satta nen MMs cetcloaal encase 84 Bo hel ndettamolhe TOOL dessous tas ni tute desea ctesit Eu tauren Ceara 86 ANNEXES c Fa ere ee ee a Im et cet een 87 Dl PIESTNE aeaa a a a Dsbodun dada iunt Rt dee 97 7 77 7 Men E P 87 E M 87 OUTS DOT UIE rt 87 e A ET A MEME 87 P p 88 SU JUNTUNEN RE NAE RE 88 Oey Troubles Hoot enen E E A E AO REE TEE 89 AMF ASCII BrO Cic DOAS ERS FT FWHM GOME IASB BIRA MDI nm NDSC NLLS OHP RAM RMS RRS SCD SFP SVD SZA VCD Acronyms and abbreviations Air Mass Factor American Standard Code for Information Interchange Bromine monoxide Colour Index Differential Optical Absorption Spectroscopy European Remote Sensing Satellite Fourier Tr
43. SCIResutts NASA AMES Results Format ASCII X Observation site Not Specified v Detector Size Format Data to read with spectra EZE Line v Zenith angle I Decimal time C Column IV Date DD MM YYYY TT lembda Instr function Calibration file AHarestuaWlvcal clb DOAS Analysis Program for Windows o0 eS The Projects properties dialog box includes several categories of options dedicated to the configuration of a project for analysis Example spectra files are provided in ASCII format A complete record is defined per file line and includes the following data the SZA the measurement date the fractional time and a 1024 pixels spectrum In the Instrumental page specify the Detector Size 1024 check the Line button in the Format frame and check the Zenith angle Date and Decimal time buttons in the Data to read with spectra frame Use the Calibration File Page 33 WinDOAS 2 1 Quickstart February 2001 button to locate the wavelength calibration in the Harestua sub directory of the Data folder If no wavelength calibration file is given pixels numbers will be used as abscissa Click OK Inserting Files To insert files under the new project 1 select the predefined Raw Spectra node and right click Insert files to open the usual Open Files Windows dialog box 2 locate and select some spectra files default extension is SPE for example in the Harestua Spectra sub directory File names have
44. WinDOAS 2 1 Software User Manual Caroline FAYT Michel VAN ROOZENDAEL February 2001 BIRA IASB WinDOAS 2 1 Software User Manual February 2001 WinDOAS is distributed without any restrictions In case of publications making use of WinDOAS please mention the following authors in the acknowledgements Michel VAN ROOZENDAEL Michelv oma be Caroline FAYT Caroline fayt oma be Phone number 32 2 373 04 16 Fax number 32 2 374 84 23 Mail address IASB BIRA Avenue Circulaire 3 B 1180 UCCLE BELGIUM Users may also contact the authors for spectra format adaptations remarks suggestions and technical support 1 Table of Contents INTRODUC TION mE 7 ls Purpose Or tne DOCUtieitexul deno oen a ER E h Io cde ambas estat i M eA DE sus 7 125 uNGtCtences cse sce tendi Dem EUR RM NM Ad ROME y lov CONer ew OF tbe DOCU BE oreet OQ DIN RA vor etd deci c 8 INSTALLING WIND OAS cncic5 si RM 9 2 ROMS Ee Mea Farchware REG SRI CE S cot oda aided oboe loca satedes onusta te tuts en ione 9 Paa SAA O P M M 9 2 2 Associate sa Tile Extension with WinD OU AS siodipuesnwe us etie ait tori ai Doi epi pi AUR Les pP RA RS UE 9 DESCRIPTION OF THE USER INTERFACE ccccccscceeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeesseeeeeeeeeees 11 Ot SZbhedscrinterface Componer e O ENET ad dig dise tunedtacs 11 2 2 Lae Bout Main Window sl WERDONS et bittet betonte ted ataca atop aat tureecatenardeutreucauniaes 12 Th
45. al organization of the processor The structures of the wavelength calibration and slant column fitting modules are given in Figures 2 and 3 while the coupled linear non linear least squares fitting algorithm is sketched in Figure 4 WinDOAS 2 1 February 2001 Description of The Algorithms Initial wavelength calibration A Control spectrum I A Cross sections o Pre processing Wavelength calibration wc and slit function characterisation SFP Apply NLLS fit to high resolution Frauhnofer reference spectrum see Fig 2 Apply wavelength calibration Convolute and or interpolate o using wc and SFP Select fitting method DOAS Intensity fitting Processing Load spectra Slant columns fitting Apply a NLLS fit to deduce slant columns densities of fitted absorbers see Fig 3 l Interpolation of AMF on the spectra SZA l Convert Slant columns into Vertical columns VCD SCD AMF All fitted parameters SCD and VCD Standard deviations Figure 4 1 Overall structure of the spectral analysis programme Page 17 Description of The Algorithms Page 18 Initial wavelength calibration A Control spectrum S High resolution solar spectrum Cross sections o Select calibration interval and split into V sub windows Select fitting method DOAS Intensity fit
46. amme itself see section 4 5 Moreover shift and stretch parameters can be fitted in order to obtain a best match of the absorption structures In automatic reference selection mode a spectrum is selected in the current file as J absorption cross sections are aligned with this spectrum based on the determination of the shift between Jp and a reference spectrum the spectrum with the correct calibration Interpolation Convolution In the usual case cross sections ate pre convoluted and interpolated on an appropriate wavelength grid prior to the analysis However the programme also authorises the direct use of high resolution cross sections which can be convoluted in real time with a predefined slit function or with the slit function determined by the wavelength calibration process Standard and J convolution types are supported see Offline tools described in section 4 6 Differential cross sections The aim of calculating differential absorption cross sections is to separate narrow spectral features from unstructured absorption not useful in the DOAS method Differential cross sections can be obtained either by orthogonalisation with respect to an orthogonal base formed with the component vectors of the polynomial term or by high pass filtering In the latter case the same high pass filter is applied to spectra and absorption cross sections High pass filtering 1s presently only supported in optical density fitting mode DOAS mode Low p
47. and all Collapse all Right click shortcut menu Page 51 WinDOAS 2 1 The Projects Tree February 2001 7 2 Directories and Files Management Spectra Files To insert one or several spectra files in the Projects tree 1 select the predefined Raw Spectra node under the parent project 2 right click the Insert files command 3 in the usual Open Files Windows dialog box locate the source path and select the spectra files Note that the file path doesn t appear in the tree If you right click the Properties command you can display this path User defined Folders You can organise spectra files in folders structures To create a new folder item right click the Insert folders from the predefined Raw Spectra node and give it a name The new folder item has the same properties as the predefined Raw Spectra node i e you can insert spectra files in this folder or create a new level of folders Directories structures For large amount of files creation and handling of spectra files and folder items in the Projects tree can become too heavy In this case you have the possibility to insert directory structures instead of spectra files To insert a directory structure in the Projects tree select the predefined Raw Spectra node under the parent project or a user defined folder and right click the Insert Path options The following dialog box appears Figure 7 2 Insert Change path Inserting a Direc
48. ansform Full Width at Half Maximum Global Ozone Monitoring Experiment Belgian Institute for Space Aeronomy Multiple Document Interface nanometers Network for the Detection of Stratospheric Change Non Linear Least Squares Observatoire de Haute Provence France Random Access Memoty Root Mean Square Rotational Raman Scattering Slant Column Densities Slit Function Parameter Singular Value Decomposition Solar Zenith Angle Vertical Column Densities WinDOAS 2 1 February 2001 Introduction 1 Introduction 1 1 Purpose of the Document WinDOAS is a software developed at IASB BIRA for analysis of UV visible spectra by the method of Differential Optical Absorption Spectroscopy DOAS 12 It takes the advantage of the experiment acquired by IASB BIRA from early nineties in DOAS measurements and analysis Several European groups of the DOAS community contribute also to the improvement and the evolution of the software by their helpful suggestions applications and inter comparison exercise A separate version GWinDOAS has been developed for GOME Global Ozone Monitoring Experiment a nadir viewing UV visible spectrometer aboard on the European satellite ERS 2 GOME measures the solar radiation back scattered from the atmosphere in the spectral range 230 800 nm with a high spectral resolution allowing the observation of minor trace gases implied in the ozone depletion like BrO 1 2 References 1 Aliwell S et al Mid latitu
49. arises Correction 0m the poor sampling ratio of the GOME instrument 2 to 3 pixels FWHM of the resolution of the spectrometer which results in a lost of spectral information when interpolating earthshine spectra during the DOAS fitting process To some extent the problem can be corrected by using an ad hoc cross section obtained by simulating the effect based on a high resolution solar reference 4 Undersampling cross sections can be pre calculated using the WinDOAS undersampling tool see section 4 6 or they can be calculated in real time just after the wavelength calibration procedure using the corrected grid and the determined slit function Standard Deviations Standard deviations are calculated directly from the SVD algorithm for linear of The Fitted Parameters see ref 11 and from the Marquardt Levenberg algorithm for non Parameters linear parameters see ref 2 They are weighted by the 7 previously divided by the square root of the number of degrees of freedom N N Window width Fit Filter width where Window width is the width of the current spectral window Filter width is the total effective width of the filter low pass and high pass nFit is the total number of fitted parameters linear and non linear Page 25 WinDOAS 2 1 Description of The Algorithms February 2001 AMF The conversion of slant column densities SCD to vertical columns VCD is obtained after division by an appropriate geometrical facto
50. ass filtering Low pass filters can be applied to both spectra and absorption cross sections A large choice of filters is proposed see section 4 6 Wavelength dependent Absorption cross sections can be replaced by geometrically corrected cross AMF sections that take into account the wavelength dependency of the AMF The correction is based on the following equation log I5 log I o A AMF 0 SZA AMF A SZA 9 C SZA C SZA where SZA and SZA are respectively the SZA of the measured spectrum J and the reference spectrum Jp if applicable AMF A SZA and AMF A SZAg ate the wavelength dependent AMF calculated in SZA and SZA AMF A SZA a SZA b SZA A tn SZA A A Onr and Op in the formula above is a high resolution cross section C SZA and C SZA y are photochemical coefficients calculated respectively in SZA and SZA Page 23 WinDOAS 2 1 Description of The Algorithms February 2001 Polynomial A polynomial function is required to account for the smooth part of the atmospheric attenuation Rayleigh and Mie scattering In WinDOAS the order of the fitted polynomial can be set up to degree 5 Differential cross sections can be obtained either by orthogonalisation to an otthogonal base formed with the component vectors of the polynomial using Gram Schmitt s algorithm or by high pass filtering see above Shift and Stretch Shift and stretch parameters allow correcting for possible misalignment betw
51. ate Remove We take the absorption of Os and ring into account To obtain differential cross sections otthogonalise them to the orthogonal base defined in the Continuous functions page Remove Allitems Properties Cancel Help To insert a new cross section in this page right click the Insert Cross section Page 40 WinDOAS 2 1 February 2001 Quickstart command In this example differential cross sections are obtained by orthogonalisation to an orthogonal base formed with polynomial terms defined in the Continuous functions page Analysis windows properties Calibration description Harestua project Figure 5 10 Molecules Continuous functions Predefined parameters Shift and Stretch Gaps Outputs Calibration Fit Parameters 22 Molecules Page 2 2 Cross Sections Cc Delta 2e19 E 045 0 001 The densities of Os and ring are fixed respectively to 2e19 and 0 15 mol cm E Continuous functions The smooth component of the differential absorbance is fitted by a polynomial The selection of the degree of the polynomial is made in the Continuous functions page To build an orthogonal base as needed for calculating differential cross sections right click Properties command Analysis windows properties Calibration description Harestua project Figure 5 11 Molecules Continuous functions Predetined parameters Shift and Stretch Gaps Outputs
52. boxes see section 7 6 The ASCII Results tab page proposes the following list of spectra related information items Select those that are available in your spectra files Spec No the record number Name the record name Date amp time YYYYMMDDhhmmss measurement date and time in the specified format Date DD MM YYYY measurement date Time hh mm ss measurement time Year the year of data Day number the day number Fractional day the fractional day number Fractional time the fractional time Page 63 WinDOAS 2 1 The Projects Tree February 2001 Scans the number of scans Tint the exposure time SZA SZA Chi Square the y for each analysis window RMS the RMS for each analysis window Tdet the detector temperature Sky obs information of the sky during the current measurement Ref SZA the SZA of the control spectrum if this data is known Longitude longitude of the observation site Latitude latitude of the observation site Altitude altitude of the observation site Figure 7 12 Project Project properties Harestua MA Properties Spectra Analysis Filtering Calibration LInderszarmplina Instrumental Sit Function ASCI Results NASA AMES Results The NASA AMES Results Tab Page EX boAsDocisUM Samples Save Inatrument Reticon PDA EGAG v MASA AMES results Experiment SESAME 95 NO rejection test Moz wot saved co vet saved O3 Not saved ll o v The NAS
53. concerned constituent Both are used for calculating the synthetic optical density in the formula of l correction convolution see page 29 These fields are hidden if Jp correction is not used Figure 8 2 Convolution Filtering Tool General Slit function Fitering Convolution The Slit Function Tab Slit function type Gaussian Page Gaussian FH Jo B5 nm Deconvolution Slit function type Fie slit function file Remove header Cancel Help This page is dedicated to the selection and the parameterisation of the convolution slit function Refer to section 8 1 for a list of possible choices Deconvolution If the selected convolution slit function doesn t imply a wavelength dependency of the resolution a deconvolution slit function can also be defined In this case the high resolution cross section is convoluted using an effective slit function obtained from the FT of convolution and deconvolution slit functions If you don t want to specify a deconvolution slit function select option File as Deconvolution slit function type and let the Deconvolution slit function field empty Options in this page are ignored if the convolution type None is selected in the General tab page of the current tool According to the selected convolution and deconvolution slit functions types WinDOAS presents different fields to fill in Page 83 WinDOAS 2 1 The WinDOAS Tools February 2001 Convolutio
54. de observations of the seasonal variation of BrO 1 Zenith sky measurements Geophys Res Letter 24 1195 1198 1997 2 Bevington P R Data reduction and error analysis for the physical sciences Mc Graw Hill Book Company 2 3 Burrows J P et al Atmospheric remote sensing reference data from GOME Part 2 Temperature dependent absorption cross sections of O3 in the 231 794 nm range JOSRT 1998 4 Chance K Analysis of BrO measurements from the Global Ozone Monitoring Experiment Geophys Res Lett 25 3335 3338 1998 5 Chance K and Spurr R J D Ring effect studies Rayleigh scattering including molecular parameters for rotational Raman scattering and the Fraunhofer spectrum Applhed Optics 36 5224 5230 1997 6 Hermans C et al Absorption Cross Sections of Atmospheric Constituents NO O2 and H20 ESPR 6 3 151 158 1999 7 Kaiser J F and W A Reed Data smoothing using low pass digital filters Rev Sci Instrum Vol 48 1447 1457 1977 3 Kuntz M a new implementation of the Humlicek algorithm for the calculation of the Voigt Profile Function JOSRT Vol 57 no 6 pp 819 824 1997 9 Kurucz R L I Furenlid J Brault and L Testerman Solar flux atlas from 296 nm to 1300 nm National Solar Observatory Atlas No 1 1984 10 NDSC Database User s Manual June 1999 11 Press et al Numerical Recipes in C Cambridge University Press 1988 1991 12 Platt U in Air Monitorin
55. e wetsharestusios vaczeirxs 0 00000 Calibration Wdetatharestuavealcls 000000 Solar spectrum Watalnarestuaiurlt tz Remove header NNI The Convolution Type Three options are proposed for convolution None no convolution the original cross section is just interpolated on the final grid Standard usual convolution convolution integral is calculated using method of trapezes Io correction standard convolution with p correction Conversion The program gives the possibility to convert before convolution the original wavelength calibration of the input cross section file from the air to the vacuum ot inversely from the vacuum to the air Page 82 WinDOAS 2 1 February 2001 The WinDOAS Tools Requested Files Names Input file the name of the high resolution cross section file to interpolate or convolute Output file the name of the resulting interpolated ot convoluted cross section file Calibration the wavelength grid on which the original cross section input file must be interpolated ot convoluted Shifting the Convoluted You can specify in field Shift the shift in nm to apply to the convoluted cross Cross Section section In order to avoid interpolation after convolution this shift is applied on the calibration grid before convolution Io correction The fields Solar spectrum and Conc are respectively the name of the high resolution solat spectrum file and the scaling column density of the
56. e Environment Workspace 1T 7ngdol tuto tori eot uceae tae dia ctae bite edpde Sedet Ede eed 12 TTC ni co Se 717177 RSEN NOME ENS 12 CEP sages tee aia di ca alee es ENOTE tue casa ana Cat td tran da cated can sa cupesta guyana ia 12 TE GAPIS MAO M Dm 12 2 92 Heo Meni DAE aia aa T EE ON TT N 12 24 SIBe OOIDIP ae O O Pa E 13 9 9 VEBe Status DAtathustbansddu ated an aha ttm TE Lut suas Vee tain de 14 20 hheoloBcut NMORUS s eos eiiie iSS Rd he ti S Bias sini bane LL sp v i esee 14 DESCRIPTION OF THE ALGORITHMS eeeeeeeeeeeeeeen nennen nnne nnn nnn nnn nnn 15 Ase Man NWA LO AS I INTES estos idee remitido en ors naso liar eti daten n vara rri editos ala aed 15 42 Blockdnetrani Structure OF the DEOBTAITDIPIG uoo irato tee betae se haste p Det babuit deu beste cse ds ce 16 4 5 alant colum H tessera noa beoe nita asd aste otor deus bt DU atre esit OR uta TAA 21 Ea E ANC 21 TOAD AE A AI pred 21 I 19 7 77 AN EEA E EOE E SE OT E A T EE A OAE E 22 de NT ANN ES od ont md tamen A N A a a a a 22 PA AT A EE 22 FOO I EE PR EE 24 STONE SHOT PT 24 9 73 CONC ON ET M Po 24 Rnd T 25 Uder sampun 087 2177717 ERE sss shitssa asst sig abdvb R aa natiaaidxs 25 Sanada Dianon OF LPEE TRA PUTE EEA TAO AEE EEEO T ETA 25 AME na M 26 E Display OFS Dect A A EN
57. easured intensities to the solar spectrum The algorithm can take into account molecular absorption and offset cotrection The derived values of the shift are used to reconstruct an accurate waveleneth registration The instrumental slit function is characterised by fitting the parameters usually the FWHM of a selected line shape see the Supported line shapes in next section The wavelength dependency of the slit function is determined by polynomial fitting through the individual slit function parameters SFP found in the different sub intervals By fitting different parameters on both sides of a Voigt profile function the program accounts for the possible asymmetry of the slit function 46 Off line tools Convolution Filtering Tool Definition The convolution of a spectrum S by an instrumental slit function F is given by the following integral f A S A F A A da This integral is calculated by decomposition of the surface area in trapezes The integral interval is defined by the width of the slit function 6 x FWHM In otder to speed up the convolution algorithm analytical slit functions are pre calculated on a suitable wavelength grid 6 pixels at FWHM and then interpolated on the grid of the spectrum For Gaussian and error function line shapes a FFT algorithm is used to calculate analytically the integral in situations requesting optimisation of the processing time e g within the wavelength calibration procedure
58. ecause of a bad configuration or bad input verify the content of your cross sections files and the initial values of parameters to fit Page 90 WinDOAS 2 1 February 2001 Annexes 5032 5034 5035 5036 5048 Zenith angle 2f not found in file s AMF not computed Interpolation error on SZA occuts when calculating AMF Bad wavelength scale in file os Calibration of s is not the same as reference one Interpolation error because of non increasing abscisses The wavelength calibration of the indicated file is not the expected one Verify the size and the content of the wavelength calibration file The file mustn t contain blank lines The slit function is sampled at higher resolution than the original cross section The cross section will be interpolated on the slit function grid Continue anyway For convolution the slit function is expected to be interpolated on the grid of the cross section except if the resolution of the grid of the cross section is poorer than the one of the slit function in this case the cross section must be interpolated Allocation error messages 5005 5006 Allocation error V os V old od Free memory error s 008x Internal problem in the allocation release of some WinDOAS objects contact authors Page 91
59. ected in the Shift and Stretch page it can not be removed anymore from the Molecules page Modifying the selection You can modify at any time a selection of symbols in the Shift and Stretch page by right clicking the Properties option from this selection to call back the dialog box in figure 7 21 Molecules Continuous functions Predefined parameters Shift and Stretch Gaps Outputs js Figure 7 22 Analysis Windows Properties Cross Sections and spectrum shift fit Stretch fit Scaling fit Spectrum 1st order Mone Shift and Stretch Page 1 5 o3221 03241 Bra Selecting fitting When you have selected the appropriate symbols you must specify which parameters parameters to fit for this selection in columns of page 1 5 Stretch and scaling parameters can be fitted using a polynomial expression of order 1 or 2 Select option None in columns Stretch fit and Scaling fit if you don t want to fit these parameters Uncheck the button in the Shift fit column if you don t want to fit the shift Note that when you disable the fit of one of these parameters the associated initial value defined in page 3 5 is still applied to the selected cross section or spectrum Page 73 The Projects Tree Figure 7 23 Analysis Windows Properties Shift and Stretch Page 2 5 Output selection Figure 7 24 Analysis Windows Properties Shift and Stretch Page 3 5 Initial values of the fitting parameters Figure 7 25 Analysis
60. ections can be applied on spectra those are divided by the vector given in the Instr function field The Observation site field is used to re calculate SZA from geolocation coordinates given in the Workspace Environment tree and to build automatic output file names see The ASCII Results Tab Page page 63 Figure 7 10 Project Properties The Slit Function Tab Page J My Data cross sections and amp MFYS HEWuruczWur Error function wavelength dependent T Cy PackagesWyinDossiDataiHarestuaisfpl fullslf O 55 Page 61 WinDOAS 2 1 The Projects Tree February 2001 WinDOAS gives the possibility to convolute cross sections in real time using the information provided by the wavelength calibration procedure If you don t want to characterise the slit function cross sections can be convoluted before spectra analysis using the line shape specified in the Slit Function tab page Note that in this case it is preferable to use pre convoluted cross sections obtained using the Convolution Filtering tool see section 8 3 Refer to the same section for a list of all possible slit function types Fields to fill in depend on the selected slit function type The Solar ref file entry field must be filled in if the convolution with Jp correction is requested for at least one cross section If the dependence of the slit function with the detector temperature is known WinDOAS can determine the difference of resolution between the
61. ee of polynomial by checking the appropriate buttons in the Fit column Fitting the undersampling The way the undersampling correction is implemented slightly differs depending on the fitting method DOAS or intensity fitting If the undersampling correction method in the Undersampling tab page of Project properties see page 60 is set to File in DOAS fitting enter undersampling cross sections files as any other cross sections in the Molecules page using Usamp1 and Usamp2 predefined symbols in Intensity fitting right click the Properties option from Usamp1 and Usamp2 symbols in the Predefined parameters page to specify or update the user defined undersampling cross sections files Check Usamp1 and or Usamp2 buttons in the Fit column in all cases of undersampling correction except in File method under DOAS fitting Fitting the common In case systematic structures are identified in the residuals a common residual residual cross section can be created and introduced in the spectral analysis As for the undersampling correction the implementation depends on the fitting method in DOAS fitting enter the common residual cross section file as any other cross sections in the Molecules page using the Com predefined symbol in Intensity fitting right click the Properties option from the Com symbol in the Predefined parameters page to specify or update the user defined common residual cross section file Check the Com button in the Fit colu
62. een the various spectral items involved in the data evaluation ie measured and reference spectra as well as absorption cross sections Shift and stretch parameters may be fitted or simply applied to any kind of spectral item according to the following equation a b A Ag A Ag whete A the wavelength calibration Ao the centre wavelength of the current spectral window a the fitted shift the fitted stretch first order C the fitted stretch second order Offset Correction An ideal spectrometer in an ideal atmosphere would measure the part of the sunlight that has been elastically scattered by air molecules and particles in the zenith direction In a real experiment however a number of possible additional soutces of signal may add up to the ideal Rayleigh Mie contribution leading to offset the measured intensity by a certain amount In addition to the Ring effect which is to a first approximation a natural source of offset instrumental sources of offset also need to be considered like stray light in the spectrometer and dark current of the detector This is the purpose of the offset parameter which we defined as follows I A offset A I Io A exp 1 A with offset A a b A Ag c Ay where Ag is the centre wavelength of the spectral analysis window a b and c are the fitted parameters and the mean intensity in the current spectral analysis window Due to the normalisation by 7 the
63. end on the selected slit function type About the algorithm The ring cross section is calculated as the ratio of the rotational Raman spectrum by the solar spectrum R S see section 4 6 page 30 The algorithm is described in ref 5 Because of a double convolution this algorithm can be very slow depending on the resolution of the solar spectrum and the grid on which the cross section is calculated A resolution of 0 05 nm for the solar spectrum is a good compromise The possibilities to calculate the second order R2 S2 and molecular ring cross sections have been implemented The output file The output file contains four columns the input wavelength calibration the calculated ring cross section the interpolated Raman spectrum the convoluted solar spectrum ab od ad When this file is used as cross section for spectra analysis WinDOAS loads only the two first columns except if the Convolution Ring see section 7 6 action is requested In this case the program uses the Raman and the solar spectra Page 85 The WinDOAS Tools WinDOAS 2 1 February 2001 8 9 The Undersampling Tool Page 86 Figure 8 5 The Undersampling Tool Requested data Undersampling tool fgometwsWlsampl xs Output file Phase 2 figometes Wsamp2 xs Solar spectrum ecidata xs hrkurucziKurl ac Calibration t aomeveiCalib clb Slit Function Slit Function type Gaussian Gaussian FvvHIM 0 165 nm Anal
64. ental SitFunction ASCIResuts NASA AMESResutts Spectra Analysis Filtering Calibration Undersampling The Analysis Tab Page Analysis Method Optical density tting Least Squares fit Noweighting rm shift and stretch units IINE Interpolation lspine gr Cancel Help Page 56 WinDOAS 2 1 February 2001 The Projects Tree The Analysis Method Shift and stretch units Interpolation Least Squares Fit Figure 7 6 Project Properties The Filtering Tab Page In the Analysis tab page you can select the retrieval method among three possible choices gt Optical density fitting gt Intensity fitting Marquardt Levenberg SVD gt Intensity fitting Full Marquardt Levenberg These methods differ by the way the Beer Lambert s equation is expressed and solved Details are given in section 4 3 Selection of the unit Pixels or Nanometers in which shift and stretch parameters are expressed Linear and cubic Spline interpolations are implemented Spline interpolation 1s selected by default The fit can be weighted if uncertainties on measurements ate known Instrumental and Statistical weighting options are foreseen but not yet implemented Project properties Harestua Instrumental Sit Function ASCiIResuts MASsA AMESResuts Spectra Analysis Fitering Calibration Undersampling Low Pass Filtering Fiter Type kaiser Cutott freq 050 Tolerance dB 80 00 Pass
65. entry fields To remove a gap select it in the Gap column and right click the Remove option In these pages you can select for each cross section defined in the Molecules pages see page 67 which analysis results to save in the ASCII output file s Columns are activated only if the Analysis button is checked in the ASCII Results tab page of Project properties see page 62 Ima Molecules Continuous functions Fredefined parameters Shift and Stretch Gaps Outputs Sint Col a wx g BE 1 Eo or gm Er x Y Cross Sections Residual Cal Sint Err Sint Fact ajel Page 75 WinDOAS 2 1 The Projects Tree February 2001 Slant Columns and AMFs Check buttons of Sint Col and Sint Err columns if you want to output respectively the calculated slant column and the standard deviation of the selected species Buttons in AMFs column ate activated only if an AMF dependency has been selected in the Molecules pages see page 69 In the Sint Fact column you can specify scaling factors that will be applied on slant columns and standard deviations before safe keeping in the output file The Residual Col column gives you the possibility to enter a value for the residual column amount of the selected species in the reference spectrum this value is used in the calculation of the vertical column Molecules Continuous functions Predefined parameters Shift and Stretch Gaps Outputs 22 Figure 7 29 Analysis E Wi
66. es The resulting information is subsequently used in the programme e g to convolute cross sections ot build undersampling cross sections In the example the Calibration page is configured as follows Project properties Harestua Figure 5 8 Projects properties The Calibration page AhareztuaWcurn ktz Optical density fitting Eres m Solar ref file use this button to locate the high resolution solar spectrum Analysis Method the fitting method used for wavelength calibration can be Page 39 WinDOAS 2 1 Quickstart February 2001 different from the one selected for spectra evaluation in the Analysis tab page see above Fit SFP this button is checked in order to fit the resolution of the slit function in this case the Error function line shape is selected Display check boxes in the frame to display the indicated graphs Polynomial degree the degree of the polynomial used in the final determination of the wavelength registration shift and the wavelength dependent slit function SFP Window limits the complete calibration interval Number of the number of calibration sub intervals sub windows Calibration Fit Parameters The Fit Parameters button calls another dialog box with several pages of options The four following pages have been parameterised Molecules specification of the absorption cross sections included in the spectral analysis Continuous functions polynomial fitting the smoot
67. es below Molecules Continuous functions Predefined parameters Shift and Stretch Gaps Outputs fir Val delta Fit store Err store a Offset Constant al n 0 004 Otfset Order 1 ma 0 0 004 i Offset Order 2 Iz D 0 004 Com ES D 0 004 sd ajel Check buttons in the Fit column for selecting the fitting parameters Val init and Val delta are respectively the initial value and the convergence factor parameters used by the NLLS algorithm In general these values should not be modified except in case of convergence problems Fit store and Err store columns are activated only if the Analysis button is checked in the ASCII Results tab page of Project properties see page 62 In these columns you can check individual results and standard deviations of fitted parameters Molecules Continuous functions Predefined parameters Shift and Stretch Gaps Outputs 22 ah Offset Order 1 D n 1 Offset Order2 D n Cam El ajel Page 71 WinDOAS 2 1 The Projects Tree February 2001 If the non linear algorithm does not converge you can fix the range of plausible values for the selected parameter If Val min and Val max are set to 0 no range condition is applied Fitting the offset WinDOAS allows fitting an instrumental offset e g due to incorrect correction of the dark current or residual stray light Polynomial offsets of order 0 1 and 2 ate supported Select the degr
68. f a polynomial of degree k over at least k 1 data points around each point in the spectrum Binomial convolution with a filter function formed with the binomial coefficients calculated using the recursive Pascal s triangle algorithm High pass filters are obtained by subtraction or division of low pass filtered data from the original spectrum Ring Tool WinDOAS implements a tool to calculate Ring cross section according to the algorithm described by Chance and Spurr 1997 5 The approach consists in a simple convolution of a solar source spectrum using calculated rotational Raman scattering Ors cross sections Ring cross sections are calculated from the ratio of the rotational Raman spectrum by the solar spectrum Raman Solar according to the following first order optically thin development for Ring effect I Ig RR S Iy exp 2 log Ip RRS log lo T log Ig log 1 RRS Ip log lo T Ring log 1 a RRS Ip a RRS Ip b RRS Ip with Ig Rayleigh scattered intensity RRS Rotational Raman scattered intensity gt Ring cross section 1 order RRS Is Raman Solar Page 30 WinDOAS 2 1 February 2001 Undersampling Tool Description of The Algorithms The WinDOAS Ring effect tool calculates the first and the second term of the Taylor expansion Spectra are convoluted using a user specified slit function WinDOAS can also generate Ring cross sections accounting for molecular absorption m
69. formats to use for AMF files are described in Annex Fit display This column is active only if the Fits button is checked in the Display frame of the current dialog box It allows selecting which cross sections fits are to be displayed Filter This column is active only if a low pass filter has been selected in the Filtering tab page of Project properties see page 57 It allows defining individually which cross sections are to be filtered Cc Fit If you uncheck the fit of a cross section the weight of the cross section in the optical density is fixed at the concentration value given in the Ce Init column see the next column Cc Init If the selected cross section is not fitted the Cc Fit button is unchecked this is the fixed concentration value to take into account in the optical density This is also the initial concentration value for the non linear algorithm in intensity fitting Cc Delta This is the delta value used by the non linear algorithm to calculate numerically partial derivatives of the fitting function for the selected non linear parameter in intensity fitting It determines the accuracy with which the algorithm approaches the minimum for this parameter The default value shouldn t be modified except if the system seems not to converge This column is active only if the Convolute I0 option has been selected for a cross section This is the concentration of the cross section used to calculate the Cc IO theoretical opt
70. g by Spectroscopic Techniques Chap 2 ed Markus W Sigrist Chemical Analysis Serzes Vol 127 p 27 84 1994 13 Vountas M V V Rozanov and J P Burrows Ring effect Impact of Rotational Raman Scattering on Radiative Transfer in Earth s Atmosphere Page 7 Introduction WinDOAS 2 1 February 2001 JORST Vol 57 no 6 pp 819 824 1997 14 Wahner A et al Absorption cross section of BrO between 312 and 385 nm at 298 and 223 K Chem Phys Lett 152 507 510 1988 1 3 Overview of the Document Chapter 2 Installing WinDOAS Chapter 3 Description of The User Interface Chapter 4 Description of The Algorithms Chapter 5 Quickstart Chapter 6 The Workspace Environment Tree Chapter 7 The Projects Tree Chapter 8 The WinDOAS Tools Chapter 9 Annexes Page 8 This chapter covers system and hardware requirements and guide you in the installation of the software This chapter covers the main components of the WinDOAS user interface the four child windows the menu bar the toolbar the status bar the right click shortcut menus VVVVV This chapter summarises the main features of WinDOAS and describes the structure of the programme and the nature of the coded algorithms This chapter describes how to create a project insert files and display spectra Using a predefined configuration provided with the package set up for BrO retrieval it guides you step by step towards comple
71. ge 54 to create a new project item in the Projects tree to remove all projects items from the Projects tree displays in the main Graphs window all cross sections defined in the selected analysis window opens the Analysis windows properties dialog box and parameterise the selected analysis window inserts a new analysis windows item in the parent project sorts the analysis windows list in alphabetic order Options for configuring projects are separated according to the category they belong to among the following pages of the Projects Properties dialog box Spectra Analysis Filtering Calibration Undersampling selection of spectra to analyse selection of the analysis method selection of a filtering method to apply to spectra and absorption cross sections wavelength calibration and slit function characterisation selection of a method for calculating undersampling cross sections WinDOAS 2 1 February 2001 Figure 7 4 Project Properties The Spectra Tab Page Spectra selection Geolocation coordinates The Projects Tree Instrumental specification of the spectra files format and instrumental corrections Slit function definition of a slit function for convoluting cross sections in real time ASCII results output file configuration NASA AMES output configuration specific NDSC format results Project properties Harestua Instrumental Slit Function ASCII Resul
72. graph or any item in the Workspace Environment ot Projects trees WinDOAS 2 1 February 2001 Description of The Algorithms 4 Description of The Algorithms This chapter summarises the main features of WinDOAS and describes the structure of the programme and the nature of the coded algorithms 4 1 Main WinDOAS features Analysis Calibration And Slit Function Characterization Cross Sections Handling Undersampling Y Y Y V WV DOAS intensity fitting modes shift stretch fully configurable for any spectral item cross section or spectrum possibility to filter spectra and cross sections before analysis supported filters include Kaiser gaussian boxcar Savitsky Golay possibility to define gaps within fitting intervals e g to eliminate bad pixels possibility to fit an instrumental offset possibility to work either in pixel or in wavelength nm units possibility to define several configurations of spectral windows under a project wavelength calibration and instrumental slit function characterisation using a non linear least squares NLLS fitting approach where measured intensities are fitted to a high resolution solar spectrum degraded to the resolution of the instrument The fitting method DOAS or intensity fitting can be chosen different from the method used in the analysis possibility to correct for atmospheric absorption and Ring effect supports different analytical line shapes as described i
73. gth calibration of the reference spectrum 1f it has been requested in the configuration of analysis windows saves the content of the original file to a new file in ASCII format in the Windows Save dialog box you can specify the name of the output file or automatic In the latter case the original file name will be kept but the extension will be changed into ASC uses the configuration of calibration defined in the Project properties see page 58 to apply it on spectra in the selected file Accotding to the selected item in a project these actions are carried out by the way of shortcut menus gt on the selected spectra file gt onall spectra files of a user defined folder and or directories structure gt onall spectra files of the selected project They can be applied on all projects defined in the Projects tree using the Projects Run Analysis and Run Calibration commands from the menu bar And finally you can call back the Properties of a sub directory item select spectra files to process in the Files list and right click to perform action Insert Change path Path to inset EWVNDOAS Doc SUM SampletHarestuatspectra Folder name spectra File filter SERE Files list H4_2000_051 spe H4_2000_055 spe H4_2000_065 H4 _2000_052 spe amp 2000 53 spe H amp 2000 O60 A 2000 54 spe HA 2 600 61 i i 2000 055 Ae H4 _2000_062 H Ln Analysis Mildcards characters 7 may be used HA_200
74. h part of the spectrum Predefined parameters selection of predefined fit parameters Shift and Stretch definition of shift and stretch parameters Molecules In these pages we specify which absorption cross sections are to be included in the fitting procedure absorbing correcting terms in this case ozone and ring For best results and given the usually limited information content over individual sub windows it is recommended to limit the number of free parameters as follows First try and fit the cross section term s freely looking at the retrieved values in each interval The usual situation is that spectral signatures are such that the information content largely differs from one interval to another Look at results in the best windows and fix the absorber amount to a mean value derived from these particular intervals in our example the O3 column density has been fixed to 2 e19 mol cm Although this way of working implicitly assumes that the Os absorption is constant over the whole calibration interval which is not necessarily true this is usually the best compromise Analysis windows properties Calibration description Harestua project Figure 5 9 Molecules Continuous functions Predefined parameters Shift and Stretch Gaps Outputs Calibration Fit Parameters TA Molecules Diff Orthog Fit display Interp Convol Page 1 2 Differential XS interpolate Differential XS Interpol
75. ical depth in convolution with correction The Continuous In this page check the components in x or x of the polynomial fitting the Functions Page continuous part of spectra to analyse Molecules Continuous functions Precetined parameters Shift and Stretch Gaps Outputs Figure 7 17 Analysis Windows Properties Iw x2 ted ew Jw x1 Continuous functions If you want to calculate differential cross sections by orthogonalisation you must create an orthogonal base see page 69 For that right click the Properties option to open the following dialog box and select in the list of available components the ones that will be used to create the orthogonal base Page 70 WinDOAS 2 1 February 2001 Figure 7 18 Analysis Windows Properties Creating an orthogonal base The Predefined Parameters Pages Figure 7 19 Analysis Windows Properties Predefined parameters Page 1 2 Figure 7 20 Analysis Windows Properties Predefined parameters Page 2 2 The Projects Tree Orthogonal base Available Selected xO ES gt Use B ana ERI pushbuttons to move items from one list to the other Cancel Help WinDOAS proposes several predefined fitting parameters gt offset gt undersampling Usamp1 and Usamp2 gt scaling factor for the control spectrum Sol gt common residuals Com Options for configuring these parameters are distributed in two pages see figur
76. ing a plat top high order degree The generic expression for this function is g P 7 5 i g with o the half width at half maximum and x the distance from the line centre The Voigt profile function is the convolution of a Gaussian and a Lorentzian function This function is used in a wide range of contexts and the optimisation of its computation has recetved much attention The Voigt profile is usually expressed as Key ERU x t y dt where x is the distance from the line centre in units of Gaussian half widths and y is the ratio of the Gaussian to the Lorentzian half width Numerous ways have been proposed to compute the Voigt function A recent and rather efficient algorithm has been recently described by Kuntz see ref 8 WinDOAS 2 1 February 2001 Description of The Algorithms WinDOAS accepts also any user defined slit function provided in an ASCII file Finally the program can account for the wavelength dependency of the slit function characterised by the wavelength calibration procedure except for the Voigt profile function Correction for the Solar The Ip correction arises because of the difference in cross sections measured in IyEffect the laboratory with a smooth light source and those seen by the atmosphere with a structured solar light source Johnston unpublished results Basically the Io spectrum is the highly structured solar Fraunhofer spectrum and the DOAS technique attempts to remo
77. ions and spectrum Spectrum 03221 03241 St delta 2 Sc delta 0 004 0 004 0 001 0 001 0 001 0 001 Sc delta 2 0 001 0 004 0 001 Bra In the fourth page you can specify a convergence parameter delta for each parameter to fit This value is used by the NLLS algorithm e g to numerically calculate partial derivatives of the fitting function WinDOAS 2 1 February 2001 Figure 7 26 Analysis Windows Properties Shift and Stretch Page 5 5 Convergence control The Gaps Page Figure 7 27 Analysis Windows Properties Gaps Insert a gap Remove a gap The Outputs Pages Figure 7 28 Analysis Windows Properties Outputs Page 1 2 The Projects Tree E Molecules Continuous functions Predefined parameters Shift and Stretch Gaps Outputs Cross Sections and spectrum Spectrum 03221 03241 sh min nm Sh max nm Bra In case of convergence problems or for safety reasons the range of values allowed for the shift can be limited to a specified interval Gaps can be defined to eliminate pixels or groups of pixels from the fitting interval Molecules Continuous functions Predetined parameters Shift and Stretch Gaps Outputs Max Value nm To insert a gap right click the Insert option and fill in Min Value and Max Value columns with the gap limits expressed in nanometers The first column is automatically updated after validation of the
78. mn in intensity fitting only Fitting a scaling factor for Check the Sol button in the Fit column of Predefined parameters page the control spectrum The Shift and Stretch In WinDOAS you can fit or apply a shift a stretch and or a scaling factor for Pages any spectral item spectra and cross sections In the Shift and Stretch pages five pages in total you can select spectra the spectrum to analyse or the control one and cross sections to shift Page 72 WinDOAS 2 1 February 2001 The Projects Tree Inserting a cross section To fit or apply a shift and or a stretch to a cross section right click the Insert to shift option from the Shift and Stretch pages to open the following dialog box Set of cross sections for shift and stretch Figure 7 21 Analysis Windows Properties Available Selected Selecting a cross section to shift Cancel Help This dialog box presents the list of symbols defined in the Molecules page and completed with the Spectrum and Ref symbols these latter two symbols usually refer respectively to the spectrum to analyse and the control one You can select the cross section to shift in this list If you select several symbols the same shift and stretch parameters will be applied to all items of the selection After validation of the selection WinDOAS automatically updates the list on the left so that a symbol can not be selected twice Note that when a cross section symbol has been sel
79. n Filtering tool Figure 8 3 Convolution Filtering Tool The Filtering Tab Page The presentation of this tab page is the same as the Filtering one of Project properties see page 57 The parameterisation is different according to the selected filter type The filter type None disables the filtering of the convoluted CfOSS section Low pass and high pass filtering are supported In the latter case the user can choose between dividing the original spectrum by the smoothed one or subtracting the smoothed spectrum from the original one 8 4 The Ring Tool Ring tool J figome xe ring_ xs gu edatavs hrkurczWur ds ktz B E f gemetcsiCalib cl it Figure 8 4 The Ring Tool II Jetdataixs hrino wib No2_cb air Gaussian 5 Page 84 WinDOAS 2 1 February 2001 The WinDOAS Tools Requested data The Ring tool dialog box is simpler than the Convolution Filtering one Requested data are Ring type selection of the type of ring cross section to calculate solar or molecular Output file the name of the calculated ring cross section file the second order is optional Solar spectrum the high resolution solar spectrum Calibration the calibration on which the ring cross section has to be calculated Cross section this field is requested for calculating molecular ring cross sections Slit Function type the convolution slit function to select in the list 8 1 parameters to fill in dep
80. n section 4 6 possibility to calculate differential absorption cross sections by otthogonalisation or high pass filtering possibility to correct cross sections using wavelength dependent AMF possibility to fix the column density of any selected species possibility to convolute cross sections in real time using a user defined slit function or the information on calibration and slit function provided by the wavelength calibration procedure possibility to handle a difference of resolution between measured and control spectra possibility to build undersampling cross sections using the information derived from the NLLS wavelength calibration Page 15 WinDOAS 2 1 Description of The Algorithms February 2001 Output Tools The output is fully configurable Analysis results are saved in tabbed columns ASCII files easily loadable in most spreadsheet programmes Convolution Filtering tool standard and o corrected convolutions are supported possibility to create an effective slit function taking into account the finite resolution of the source spectrum using a FT deconvolution method Ring tool calculates Ring effect cross sections Rotational Raman Scattering approach Undersampling tool generates undersampling cross sections 4 2 Block diagram structure of the programme Page 16 The overall structure of the programme is schematically described in the following figures Figure 1 describes the gener
81. ndows Properties Cross Sections Wr Col gue T v v 1 z Outputs m rj Page 2 2 ajel Vertical Columns Buttons in Vrt Col and Vrt Err columns are activated only if an AMF dependency has been selected in the Molecules pages see page 69 In Vrt Fact column you can specify scaling factors to apply on vertical columns and standard deviations 7 1 Configuration of the Wavelength Calibration procedure The wavelength calibration facility developed in WinDOAS is based on a NLLS fitting procedure where the shift between the spectrum to calibrate and a highly accurate solar reference spectrum is determined on a series of equally spaced short intervals The procedure also allows characterising the instrumental slit function through fitting of user defined Slit Function Parameters SFP The wavelength calibration can be applied to any kind of spectrum the reference spectra or spectra to analyse The wavelength calibration uses the same property sheet as the one described in Analysis windows properties You can access this property sheet by clicking the Fit parameters button on the Calibration page of Project properties see page 58 Refer to previous section 7 6 for a detailed description of options page pet page This section describes aspects particular to the parameterisation of the calibration The Molecules pages The Molecules pages allow introducing correcting absorbers that may optimise the accuracy of the wavelength calibrati
82. olecular Ring effect using a Taylor expansion of the Beer Lambert s law RRS aed Ip exp tos ORS ly l To3 Ons I Ors Io T03 Ors In this last expression the Ring effect has been separated in a Fraunhofer filling in contribution pure Ring effect and a molecular filling in contribution molecular Ring effect Accordingly molecular Ring effect cross sections are calculated from a source spectrum given by the product of the solar intensity by the molecular absorption cross section of Os in this case The problem of the undersampling can be corrected by using an ad hoc cross section obtained by simulating the effect based on a high resolution solar reference Oversampled and undersampled spectra are calculated as follows U A A over AA under A where over A A is a high resolution solar spectrum convoluted on its original grid and interpolated on the final grid A A under A is a high resolution solar spectrum convoluted on grid 2 and subsequently interpolated on the final grid A A Residuals are improved by adding a second phase of undersampling U A over A under A The above formulas are valid in intensity fitting mode In DOAS fitting the optical density is expressed as a function of the logarithm of the ratio of the measured intensities Hence the two equations above must be replaced respectively by the following ones U A A log over A A under A
83. oluted in real time to the same effective resolution see 7 6 Select None if you don t want to correct the wavelength calibration of the reference spectrum Fitting interval This is the spectral interval where the current analysis configuration is applied Display After completion of the analysis WinDOAS can display graphically gt the normalised spectra before analysis gt the calculated residuals gt the fitting results for each species and for predefined parameters offset undersampling gt the continuum part fitted by a polynomial Check the appropriate buttons for selecting the graphs you want WinDOAS to display An individual selection of cross sections and predefined parameters can still be performed see section 7 6 Files Reference Reference spectra see above Residuals If you want to perform further studies on residuals you can specify the name of an output file in which calculated residuals will be saved A line of the resulting file contains the calculated residual for a spectrum record Fitting Parameters The user must define the fitting parameters in the appropriate pages of the property sheet at the bottom of the Analysis windows properties dialog box The different pages are Molecules definition and configuration of the list of cross sections to fit Continuous specification of the degree of the polynomial fitting the functions continuous component of the absorbance Predefined this page pro
84. on e g the Ring effect when calibrating a scattered light spectrum and Os absorption can be taken into account in the fit Note that these pages are lightened compared to the equivalent pages in the Analysis Windows properties dialog box Page 76 WinDOAS 2 1 February 2001 The Projects Tree Analysis windows properties Calibration description Harestua project Figure 7 30 Analysis Windows Properties Molecules Continuous functions Predefined parameters Shift and Stretch Gaps Outputs pz Calibration Molecules page 1 2 Diff Orthog Fit display Interp Convol Differential XS Interpolate Differential XS This configuration assumes Interpolate the presence of Os and ring structures in the fit Cancel Help To generate cross section column Diff Orthog see page 69 The Fit display column is activated only if the Fits button is checked in the Display frame of the Calibration page of Project properties see page 59 The selected cross section is usually interpolated on the grid of the control reference spectrum If the Interp Convol action is set to Convolute Std the selected cross section is convoluted in real time either with the fitted slit function if Fit SFP button is checked in the Calibration page of Project properties see page 59 or the slit function defined in the Slit Function page of Project properties see page 62 Standard and 10 convolutions are supported ring cros
85. on and a cross section column for each parameter Xj The formula used for calculating wavelength dependent AME is AMF A Ag SZA peA S ZA jo Ay S ZA pe ASZA AA A SZA p An SZA A X SZA pd X SZA X 5 4 Sy SZA p Xy SZA J XSn C SZA ug CZA In Wavelength 2 option the formula is the same but the SZA of the reference spectrum is not taken into account and C is ignored BrO_W228 AMF_SZA no restriction S f by default but it 1s not restrictive Column 1 the wavelength calibration Column 2 the line shape For wavelength dependent slit function types the second column is the parameter dependent on the wavelength slit slf WinDOAS 2 1 February 2001 Annexes 9 2 Troubleshooting This section describes error messages that are popup by WinDOAS Most of them come from a bad configuration or a bad WinDOAS objects handling If you can not solve a problem or if you have detected a bug it s important to contact authors The WinDOAS LOG log file produced by WinDOAS is an important source of information for us A small application with a detailed description of the trouble and the sequence of manipulations leading to it can help us to solve the problem quickly Tree items handling 4001 Impossible to insert s item due to a system limit You have consumed all WinDOAS resources allocated for the kind of object you wanted to insert 4007 Item s already exist You have tried to insert in the
86. orm on this type of file The selected format doesn t support automatic reference selection mode see page 43 because the SZA information is not available 5019 Division by 0 5020 Exp Overflow 5021 Pow Overflow 5022 Log error 5023 Sqrt argument error 5028 Invalid window for calibration g g 5038 Deconvolution slit function width must be lower than convolution one 5039 Slit function should be gaussian or integrated gaussians type for resolution adjustment 5040 Slit function should be gaussian or integrated gaussians type and temperature dependent for resolution adjustment 5041 Can t apply fitting of slit function parameters with calibration and resolution correction 5042 Error with erf function s 5043 Matrix inversion failed 5046 Incompatible options for os 5047 Number of degree of freedom lt 0 reduce the number of parameters or increase the width of the analysis window or reduce the width of filter 5049 Voigt function failed x g y g These errors occur generally in case of bad configuration or bad input Contact authors if you don t find the origin of the error 5024 Bad arguments This error is generally produced after an internal error Contact authors 5025 No convergence after d iterations 5026 Ill conditioned matrix too small singular value found g The algorithm doesn t converge This error can occur occasionally when evaluating a bad spectrum If it is produced systematically it s generally b
87. ortcut menus VVVV These components are further detailed in the following sections Page 11 WinDOAS 2 1 Description of The User Interface February 2001 3 2 The Four Main Windows in WinDOAS The Environment I this window the user should list all relevant symbols that will be used in the Workspace Window configuration of his projects and analysis windows The Observation Sites coordinates are used to re calculate zenith angles For balloons and satellite measurements they allow operating a selection on spectra to analyse according to specified geolocation coordinates the sites The Projects WinDOAS is based on the notion of projects A project can be defined as a set Window of files sharing the same configuration of analysis WinDOAS allows defining several projects in a session giving users the possibility to handle several analysis configurations A project includes the definition of spectral windows and the list of files to analyse with this configuration The Data Window This window displays the available information on the current spectrum and analysis results The Graphs Window Spectra fitting results and in general any kind of graphical information are displayed in the Graphs window 3 3 The Main Menu Bar Application Control Files usual Windows options for applications control New starts anew WinDOAS application Open opens an existing WinDOAS application Save saves the current WinDOAS application Save
88. orthogonal base by right clicking the Properties option from this page see page 70 The Predefined In the parameterisation of the wavelength calibration you can fit offset and slit Parameters Page function parameters SFP Analysis windows properties Calibration description Harestua project Figure 7 32 Analysis Windows Properties Molecules Continuous functions Predefined parameters shift and Stretch Gaps Outputs Calibration eee l Predefined parameters Predefined param Val detta Fit store Errstore Parameterisation for an error function line shape Cancel Help There ate 4 predefined items for SFP SFP 1 SFP 2 SFP 3 and SFP 4 According to the line shape selected in the Calibration page of Project properties see page 59 these parameters are used or ignored SFP 1 SFP 2 SFP 3 SFP 4 Error Boxcar width ignored Ignored function SFP 1 is generally used for fitting the FWHM of the selected line shape The Voigt profile function is the convolution of a Gaussian and a Lorentzian line shapes It can be used for fitting asymmetric line shapes by fitting differently on the left and the right sides the FWHM of the Gaussian resp FWHMy G and FWHMmn G and the Gaussian Lorentzian ratio resp G Li and G Lr If there are several SFP to fit it is generally recommended to fix some of them to an estimated value in order to avoid numerical instabilities Page 78 WinDOAS 2 1 February 2001
89. poses several predefined parameters such as parameters offset undersampline Page 66 WinDOAS 2 1 February 2001 The Projects Tree Shift and Stretch shift and stretch can be applied to any spectral item Gaps gaps can be introduced in the fitting window e g to eliminate bad pixels Outputs selection of the calculated columns densities to save in the output file According to the associated type of parameters the selected page proposes several columns of options to fill in to check or to select from a multiple choice The conviviality of the analysis parameterisation is enhanced by the use of right click shortcut menus to handle lists of items in the different tab pages Because of the complexity of the whole set of options the structure is detailed page after page in the following section 7 6 Configuration of the Fitting Parameters The Molecules Pages The options for defining and configuring the list of cross sections to fit are distributed in two Molecules pages see figures below Molecules Continuous functions Fredefined parameters Shift and Stretch Gaps Outputs pe Figure 7 14 Analysis Windows Properties Ditforthog Intern conval Differential XS Interpalate SZA only Mane Insert ring Differential XS Remove mE 03241 Differential XS Remove All items Molecules Page 1 2 Properties Figure 7 15 Analysis Windows Properties Queue Cc Delta Molecules Page 2 2
90. r or air mass factor AMF VCD SCD AMF For the moment AMF are not calculated by WinDOAS but imported from ASCII files see format in section 9 1 WinDOAS supports options for solar zenith angle dependent AMF wavelength dependent AMF and climatological AMF Graphical Display Of Let us consider the following definitions Spectral Fit Results Joc E and T Iy A exp x with 7 the optical density Accotding to the selected fitting method formulas used to display fitting results are different Definitions used by WinDOAS are described in the following table Optical density l R log T log Tc R T Tc gt R T Te 1 R Te and R log 1 R Tc log T log Tc dic Lis Polynomial R P R P Full Marquardt P R Marquardt SVD log 1 offset I R log 1 offset I R log 1 offset l Page 26 WinDOAS 2 1 February 2001 Description of The Algorithms 4 5 Wavelength calibration and slit function characterisation The wavelength calibration procedure implemented in WinDOAS 1s based on the alignment of the Fraunhofer structures of the control spectrum with those of an accurately calibrated high resolution solar reference atlas that is degraded to the resolution of the instrument as part of a fitting procedure The reference atlas used for this purpose is usually the Kurucz et al 9 spectrum The spectral interval is divided in a number of equally spaced sub windows in which a NLLS fitting algorithm is applied to fit m
91. ross section is simply included as an additional pseudo absorber In DOAS fitting mode WinDOAS minimises residuals of equation 3 using a Marquardt Levenberg non linear least squares NLLS algorithm The method implements a gradient expansion algorithm 2 which is based on the iterative combination of a steepest descent method suitable for approaching the minimum from far away and a linearisation of the fitting function Page 21 WinDOAS 2 1 Description of The Algorithms February 2001 Linear parameters are determined by a Singular Value Decomposition SVD method 11 embedded in the NLLS algorithm Intensity fitting WinDOAS also supports the so called intensity fitting or direct fitting method where measured intensities are directly fitted instead of their logarithms This corresponds to the following equation I A offset A Ig A exp X o c P U eq 4 Two vatiants have been implemented Full Marquardt In this method the Beer Lambert equation is processed without any further linearisation all parameters are treated as non linear parameters with the advantage that some of the derivatives of the fitting function with respect to parameters can be calculated analytically The efficiency of the method depends on the number and type of parameters to fit Best efficiency is usually obtained when a large number of terms are included inside the exponential Marquardt SVD This method involves a decomposition of equa
92. s log I9 4 log 1 4 6 c eq 2 Two fitting analysis methods are implemented DOAS and intensity fitting in WinDOAS They differ in the expression of the fitting function use of the equation 1 or the equation 2 DOAS fitting The DOAS approach is a direct application of the equation 2 High frequency spectral structures of the various absorbing species are used to resolve the corresponding contributions to the total optical density This is obtained using a least square procedure where the slant column densities SCD of the various species are the fitted parameters Large band contributions to the atmospheric attenuation Rayleigh and Mie scattering are accounted for by a low order polynomial function Simply stated the DOAS technique is a linear problem This linearity is unfortunately broken down by the need to account for additional effects namely e small wavelength shifts between and T spectra must be corrected using appropriate shift and stretch parameters e possible instrumental and or atmospheric straylight or residual dark current signal require the introduction of an offset parameter In addition to shift and offset Ring and undersampling effects have to be treated See section 4 4 to have an overview of all parameters to fit Let us consider the modified equation Log I A offset A log Io A X o c P U eq 3 with P the polynomial and U the undersampling cross section Ring effect c
93. s sections can be generated in real time using option Convolute Ring Analysis windows properties Calibration description Harestua project Figure 7 31 Analysis Windows Properties Molecules Continuous functions Predefined parameters Shift and Stretch Gaps Outputs 22 Calibration Molecules page 2 2 Cc Delta T 2e19 0 001 Fa 0 15 0 001 Cross Sections In this configuration the O3 column density is fixed at 2e19 mol cm Cancel Help In order to optimise the accuracy of the calibration and given limitations inherent to the method it is recommended to carry out two passes when a cross section is introduced in the fit 1 in the first pass the column density is fitted button in the Cc Fit column is checked over all the calibration interval a mean value of the concentration is then determined from the sub intervals where the fitting of the cross section has a sense where the spectral information is largest 2 in the second pass the concentration is fixed at the mean value determined at the previous pass See section 7 6 for a complete description of the columns in this page Page 77 WinDOAS 2 1 The Projects Tree February 2001 The Continuous In this page you define the polynomial fitting the continuous component of the Functions Page Spectrum to calibrate To generate differential cross sections by the 9 orthogonalisation method don t forget to build an
94. sed for spectra analysis uncheck the Fit SFP button if you don t want to characterise the slit function specify which graphs to display at the end of the procedure the degree of the polynomial used in the final determination of the wavelength registration shift and the wavelength dependent slit function SFP the wavelength window on which the calibration correction must be applied the number of calibration intervals This pushbutton gives access to a dialog box using a property sheet similar to the one defined in Analysis windows properties in which you can specify parameters to fit and atmospheric absorption to take into account for the fit evaluation This dialog box is detailed in section 7 7 There are two cases to consider 1 You know the slit function of your instrument and you don t want to characterise it once again then you have to provide the Solar ref file field with a solar reference spectrum previously convoluted with the instrument slit function on the grid of the spectrum to calibrate 2 You want to characterise the slit function of your instrument then you must provide the Solar ref file field with a high resolution solar spectrum Because WinDOAS uses FT in order to speed up the NLLS algorithm a high resolution solar spectrum sampled on a constant grid 1s expected When the button Fit SFP is checked you have to select in the list on the right one of the basic line shapes to fit see page 27
95. t Function tab page of Project properties see page 62 If the wavelength calibration slit function characterisation is applied on the control spectrum and spectra to analyse see page 66 the cross section with Interp convol action set to Convolute Std is convoluted with the poorer resolution Convolute I0 the cross section is convoluted with Jp correction using the concentration defined in the column Cc I0 see below Convolute Ring in the same way the program can generate a ring cross section the expected cross section file must be a pre convoluted ring cross section calculated by the WinDOAS Ring tool see section 8 4 on a high resoluted grid If you want to calculate vertical columns or if you want to correct a cross section using wavelength dependent AMF select one of the options proposed in the AMF column option different from the None one and specify an AMF file by right clicking the Properties of the selected cross section Possible choices SZA this is the option usually selected to calculate vertical columns the AMF depends only on the SZA Climatology select this option to introduce climatological AMF the AMF depends on the SZA and the calendar day Wavelength select this option to correct the selected cross section using wavelength dependent AMF modified DOAS Page 69 WinDOAS 2 1 The Projects Tree February 2001 The format of the requested AMF file depends on the option selected in this column The
96. t tinet E totem ENS AAA Sd ads Dittectories and MeS NATET s aco ast seccbacb dtu A d laces iaia las Osan secet acutus N 52 Ro T Ts TRI 52 E T E eM 22 LINES ON STACI NM Rm 52 TANAN 15997177 Cases EEE N OE E O NT NAE EE 53 T Jelanidlingelteris INe Projects TeC nenii a A E T 53 Te SPtOlSGL PODET CS utto eno ohetein a obama api tq rade DM UU n eit Neid 54 We NCCU NAT LOO e casio etu il Ld tetto alse Ua it eU V rd Md US DUXI Rp cU e UAE gaps 55 Freza T AU NACE 56 UDCA WT AD TAO PPM 57 IPO MOVADO NAOT AUC EN E EE Y 58 E NBI ADU AD rr MM E 60 EIE L2 17177177 NAOT rr ve NM ET 61 TOS EDITI III rrr P 61 IET PRINT MU Nur T 62 Lie INAS ACA HES OUS TAO DP UE eciaogtttendteane dit ica tton aru entradas ica tea asta aur OD secure e 64 9 Zdlysis Wind ows PrODS t6Ss ho eost iR bna o du asc a E T a dade 65 76 CouHlsuration ef the Prone Parameters ei uenssaio soin od on od aoa de saut DD ae 67 E 2111 Turo T 67 TAO OMMNUOUS A UR OTE DUC itte duci aeter edet Rote ust aot ceto oor ia fuae pete cose sese eias ERU euius 70 8 UR A CTIA BRI ITI II EST CC 71 THES GU SUV CICD TALES PRENNE fz DGG ADS TARE e Ve IGE UIP UIST CIOS eco so A cad cheats etal A dosh O A ite tede edes dete ti Ult AE 2b Vad Configuration Or the Waveleneth Calibration procedure eio oops opui etfi 76 VEU P 76 DO COMMMUBUS EDITORS
97. te configuration of a project This chapter describes how to manipulate and configure Observation Sites and User defined symbols items in the Workspace Environment tree This chapter describes the organisation the handling and the configuration of the different kinds of items in the Projects tree It covers the management of files and directories structures in the Projects tree the configuration of projects the parameterisation of the analysis the parameterisation of the wavelength calibration VVVV This chapter covers the main features supported by WinDOAS about convolution and describes the three off line tools included in the software gt the Convolution Filtering tool gt the Ring tool for creating Ring effect cross sections gt the Undersampling tool for creating undersampling cross sections Description of the format of input files and troubleshooting WinDOAS 2 1 February 2001 Installing WinDOAS 2 Installing WinDOAS 2 1 System and Hardware Requirements WinDOAS runs under Windows 95 NT A Pentium computer with at least 64 megabytes of RAM is recommended 2 2 Installation The program with the Software User Manual this document and on line help is usually distributed by E mail To install the package just copy the sent files in a dedicated directory The example application described in section 5 2 is available on request 2 3 Associate wds File Extension with WinDOAS The configuration of
98. the path in which The Output File Name results have to be saved You can specify the name of the output file If you specify automatic as the file name WinDOAS will create automatically output files names depending on the measurement date and the observation site specified in the Instrumental tab page see page Error Reference source not found Error Bookmark not defined as follows lt output path gt XXYYYYMM ASC where output path is the user defined path XX is the abbreviation of the observation site selected in the Instrumental tab page if no observation site is specified the abbreviation XX is used YYYY is the year of measurement MM is the month zeros padded of measurement ASC is the default file extension for ASCII files Fluxes and Colour A flux is the mean signal calculated over seven pixels around the indicated indexes wavelength To output Fluxes specify the central wavelengths separated by the semi colon character For example 330 350 380 will calculate and output fluxes at 330 350 and 380 nm A colour index is the ratio of two fluxes To output colour indexes Cic just write the ratios separated by the semi colon character as in the example below 380 330 380 350 Output Selection In WinDOAS the output is fully configurable The selection of analysis results e g slant column densities or fitted non linear parameters is made individually in Analysis windows properties dialog
99. ting Slant columns fitting see Fig 3 Derive in each interval n The shift between solar et S Fitted slit function parameters SFP SCD of correcting absorbers e g Ring Os Determine the new wavelength calibration wc by polynomial fitting through the N individual shift values Determine wavelength dependency of fitted slit function parameters SFP 4 by polynomial fitting through the N individual SFP values Display calibration results optional Figure 4 2 Structure of the wavelength calibration module WinDOAS 2 1 February 2001 WinDOAS 2 1 February 2001 Description of The Algorithms Module performed at project pre processing level if c matrix can be kept static Cross sections processing c correction with wavelength dependent AMF optional Convolute Interpolate Shift o Low Pass filtering Generate differential o by orthogonalisation or HP filtering Spectra processing Shift I or I Offset correction applied on measured spectra Decompose the fitting function into linear non linear parts according to the selected fitting method NLLS FIT see Fig 4 Residual R Fitted parameters included SCD Standard deviations Figure 4
100. tion 4 in its linear and non linear parts In order to maximise the number of linear terms the equation fitted actually slightly differs from equation 4 the polynomial term is set out of the exponential I A offset A I A P exp U Column densities are still fitted non linearly but polynomial offset and undersampling are calculated using SVD This method is to be preferred over the Full Marquardt method when the configuration is such that most parameters are linear e g in the wavelength calibration procedure 4 4 Fit Parameters Absorption cross The selection of the spectral analysis window determines which absorbers have sections t be included in the fitting procedure Several cross sections of a same absorber can be fitted together for example to account for a temperature dependency of the cross sections In this case WinDOAS provides an option by which two or several cross sections can be mutually orthogonalised using the same Gram Schmitt s algorithm that can be also used to generate differential absorption cross sections In addition to this and upon user request several other manipulations can be applied to absorption cross sections before calculation of the slant column densities These are described below Page 22 WinDOAS 2 1 February 2001 Description of The Algorithms Shift Absorption cross sections are interpolated on the final grid of the control spectrum which may be determined by the progr
101. tories Path ta inset E WMINDOA S Doc SUMSampletHarestua Structure in the Projects Tree Folder name Harestua File filter spe Wildcards characters 7 may be used You can see the impact of this insertion on the Projects tree in Files list o Figure 7 1 spectra are in the Spectra Spectra sub folder Cancel Help vw Include subfolders Use the Browse paths pushbutton to locate the directories structure on your disk and specify a File filter spe is the default extension for spectra files to cut down the list of files The Folder name field indicates the name of the item that will be inserted in the Projects tree and that will give access to the selected path Check the Include subfolders to extend the files selection to subdirectories Before handling spectra files items in the directory structure validate your selection To call back to the dialog box above and change the path or files selection right click the Properties option from the parent directory node Page 52 WinDOAS 2 1 February 2001 The Projects Tree Handling Spectra Four actions ate possible on a spectra file Figure 7 3 Apply analysis on some individual spectra files in the selected sub directory Browse Run Analysis Export in ASCII Run Calibration browses spectra in the selected file analyses spectra using the configuration of the parent project and analysis windows this step includes the cotrection of the wavelen
102. tructures in the Projects tree the configuration of projects the parameterisation of the analysis the parameterisation of the wavelength calibration WinDOAS is based on the notion of projects A project can be defined as a set of files sharing the same configuration of analysis WinDOAS allows defining several projects in a session giving users the possibility to handle several analysis configurations Files can be organised in user defined folders and facilities are provided to manage large amount of files by loading only the directory structure in the tree The organisation of projects analysis windows spectra files and directories in a tree structure completed with the definition of right click shortcut menus at each level of the tree makes the access manipulation and configuration of all these objects very easy m Projects Harestua l Haw Spectra EHE harestua 7 spe rm gt gt H s B spectra spe H 2000 D057 spe H 2000_058 spe H 2000_059 spe H 2000_060 spe H 2000_061 spe H 2000_062 spe 000_070 spe Analysis Windows OHP Haw Spectra HP 2000_057 spe HP 2000_059 spe HP 2000_059 spe HP 2000_060 spe HP 2000_061 spe HP 2000_062 spe Analysis Windows Analysis windows gt bro Insert files Create folder Insert Path Remove Rename Hide Show Hidden hens Browse spectra Export in ASCII Run Analysis Run Calibration Remove all Items Exp
103. ts MA SA AMES Results spectra Analysis Filtering Calibration Undersampling Display M Spectra SZA range deg E hir Max 90 00 Delta 0 00 Spectra M range Iv Data Fits page w xH 4 x 4 W Fits w Pause Geclocations Mode circte area Radius 0 00 km Longitude n n Latitude 0 00 Dark current Cancel Help The Spectra tab page is dedicated to the selection of spectra to display and or to analyse The selection of spectra can be made on SZA specify the SZA range and the SZA step in degrees Spectra N specify a range of record numbers Geolocations specify geolocation coordinates The geolocation coordinates condition is useful for limiting the selection of spectra to a geographic area balloons and satellites measurements Circle area circle area defined by its centre coordinates and its radius Rectangle area rectangle area defined by longitudes and latitudes ranges defines circle area around locations defined in the Observation Sites list of the Workspace environment tree overpasses for satellites measurements Circle area using Obs sites list Let geolocation fields at 0 0 if you don t want to perform this kind of selection Page 55 WinDOAS 2 1 The Projects Tree February 2001 Files option If the selected spectra files format supports record names and dark currents the Names and Dark current buttons must be respecti
104. ts tree and right click the Properties command to open the Projects properties dialog box Options are applied independently to both spectral windows BrO and OCIO defined in the selected project The most important pages in the Projects properties dialog box ate Analysis selection of the analysis method and the unit for shift and stretch parameters Calibration parameterisation of the calibration Analysis Inthe Analysis tab page we have selected Analysis Method Optical density fitting Shift and stretch units Pixels Page 38 WinDOAS 2 1 February 2001 Quickstart Project properties Harestua Figure 5 7 Projects properties SitFunetion ASClResuts NASA AMES Results The Analysis tab page eet Rescate E Optical density fttng H Mowegtna Pes 0 0 0 0 0 0 0 F mie 0 m Wavelength calibration The wavelength calibration interval specified by the Window limits fields is subdivided in a number of equally spaced sub windows In each of these intervals the shift and the slit function parameter s SFP are fitted using a NLLS fitting procedure where a high resolution solar atlas spectrum degraded to the resolution of the instrument is adjusted to the control spectrum The shift values determined in all sub windows are then used to reconstruct an accurate wavelength registration Similarly the wavelength dependent slit function is determined by polynomial fitting through individual SFP valu
105. urier transform and S and S are respectively the convolution and de convolution slit functions Great care is taken in the algorithm to avoid noise corruption effects when taking the ratio of the Fourier transforms Page 29 WinDOAS 2 1 Description of The Algorithms February 2001 Ring Convolution Because of a double convolution the algorithm used to calculate Ring cross sections see the Ring tool topic can be relatively time consuming depending on the resolution of the solar spectrum and the grid on which the cross section has to be calculated A resolution of 0 05 nm for the solar spectrum is a good compromise A solution to speed up the creation of Ring cross sections is to pre calculate a high resolution e g 0 02 nm FWHM Raman spectrum which can be further degraded to any intermediate resolution This feature is currently implemented as an option of the slant column fitting processor Filtering Low pass filters implemented in WinDOAS correspond to a convolution in the pixels domain The following filtering functions are supported gt Kaiser see description of the algorithm in Kaiser and Reed 1977 HE gt Boxcar convolution with a rectangle function this filter consists in averaging the spectrum over several spectral points gt Gaussian convolution with a Gaussian function gt Triangular convolution with a triangle function gt Savitsky Golay the Savitsky Golay filter uses a least square linear regression fit o
106. ust start by the user defined relevant symbol followed by an underscore this restriction does not apply to input cross sections in WinDOAS tools xs by default but it is not restrictive Column 1 the wavelength calibration Column 2 the cross section BrO_W228 XS no restriction ktz by default but it is not restrictive Column 1 the wavelength calibration Column 2 the solar spectrum KUR 01 KTZ no restriction ref by default but it is not restrictive Column 1 the wavelength calibration Column 2 the reference spectrum 80302191 REF Page 87 Annexes Page 88 AMF Analysis windows properties Slit functions Analysis windows properties File name File extension AMF SZA Format WinDOAS 2 1 February 2001 The name of AMF file associated to cross sections implied in the definition of analysis windows must start by the user defined relevant symbol followed by an underscore AMF_SZA for SZA dependent AMF AMF CLI for climatology dependent AMF AMF_WVE for wavelength dependent AMF Column 1 SZA Column 2 AMF AMF_CLI Format 0 JD 1 365 AMF WVE Format Example File name File extension Format Example SZA Climatology dependent AMF have to be provided in a matrix whose first column is SZA grid and first line day number grid Wavelength dependent AMF file should contain 2 parts gt the SZA dependent parameters SZA Ao Ai An Xi o Xn C gt the wavelength calibrati
107. vation Sites User defined symbols Save Graphs Projects E my first project ES E Raw Spectra Bmp file HA 2000 057 spe 6000 H 2000 058 spe HA 2000 059 spe HA 2000 Ob50 spe H 2000 051 spe HA 2000 062 spe Analysis Windows Intensity 3000 360 Wavelength nm o DES nil xi Project my first project File EAWINDOAS Doc SUM Sample Harestua Spectra HA_2000_058 spe Date and Time 27 02 2000 06 22 57 Record 1 39 Zenith angle 90 962 Exposure time 0 000 sec Scans taken into account 0 Detector temperature 0 000 Sun azimuthal angle 1 000 Ki Save the content of the active Graph window in ASCII format 329 816 y 8123 57 12 18 You can print bitmap printing and save in ASCII or bitmap format the content of a graph window In ASCII format spectra are saved with their wavelength calibration and by default a header with the description of the record You can disable the header safe keeping by selecting the ASCII Spectra files without header file type Use the Stop button red circle in the toolbar before coming back to the project configuration Saving Your Work Be sure to save your work at regular intervals using the Save button in the toolbar or the Files Save command from the menu bar The Save As Windows dialog box appears Changes are saved in an ASCII file The default extension for WinDOAS configuration files is wds 5 2 Example Configuration of
108. ve this spectrum by forming the log ratio of two spectra measured at different solar zenith angles thus leaving the atmospheric absorptions However because both of the spectra forming this ratio have been filtered by the instrument function before the calculation of the ratio complete removal of the Fraunhofer structure is not possible This effect may be dealt with to a good approximation by correcting the laboratory measured cross sections with the solar Fraunhofer spectrum Such corrections must be weighted to the column amount of the absorber so a typical maximum column amount of the various absorbers is often used The corrections to the cross sections are made according to the following equation l MUS synth A anaes scale sol A O corrected where synth A is a synthetic absorbing spectrum calculated using uncorrected high resolution cross section and subsequently filtered by the instrument function so A is the filtered solar Fraunhofer spectrum scale is the column amount of the absorber by which the correction is scaled and Ocortected A is the corrected cross section Deconvolution The WinDOAS convolution tool implements a de convolution option In this case the convolution is performed using an effective slit function obtained after Fourier transform manipulation of specified convolution and de convolution functions The effective slit function 1s calculated as follows xl SS o0 LSG where 3 stands for Fo
109. vely checked If these data must be retrieved from files different from the original spectra one the default file path and name are then the same than the original spectra ones but with the respective nms and drk extensions The default record names and dark current files names can be changed in the properties of the associated spectra file item in the Projects tree Display During spectra analysis you can display gt spectra gt fits gt data By default WinDOAS pauses between each display Spectra browsing and analysis can be performed in a non stop way by unchecking the Pause button in the Display frame In this case you can speed up spectra processing by disabling also the Spectra Fits and Data displays The number of graphs to display depends on the number of parameters to fit in your application For each defined analysis window you can select individually the fits to display see section 7 6 page 67 By default WinDOAS displays one eraph at a time in the main Graphs window and you pass from one graph to the other using appropriate toolbar buttons But you can change at your best convenience the number of graphs to display vertically V and horizontally H in one time in the main Graphs window by filling the fields Fits page in the Spectra tab page of Project properties dialog box The maximum number of eraphs per window is limited to 20 Project properties Harestua Figure 7 5 Project Properties Instrum
110. volution Filtering tool gt the Ring tool which allows creating Ring effect cross sections gt the Undersampling tool for creating undersampling cross sections 0 1 Supported line shapes The three tools propose to select the type of the convolution slit function in the following list File Gaussian 2n Lorentz Voigt Error function Gaussian waveleneth dependent 2n Lorentz wavelength dependent Error function wavelength dependent In short WinDOAS dr ee Isi gt accepts any user defined slit function provided in an ASCII file choice 1 gt supports the four basic line shapes described in section 4 6 page 27 choices Zt10 3 gt can take into account the wavelength dependency except for the Voigt profile function of the resolution of the slit function choices 6 to 8 In this case a file expressing the wavelength dependency of the resolution is requested it can have been previously produced by the wavelength calibration and slit function characterisation procedure The parameterisation of the slit function dialog boxes depends on the selected slit function type 8 2 About Files Formats Input files used in the configuration of WinDOAS tools are ASCII files The supported file formats are summarised in Annex 9 1 Output files are ASCII files including the wavelength grid and the convoluted filtered spectrum As these files are generally intended to be used for spectra analysis it is preferable to
111. ysis Analysis method Optical density a shift nim 0 008 Remove header oe oe The problem of undersampling ex for GOME spectra 1s detailed in ref 4 This tool gives the possibility to pre calculate undersampling cross sections using specified slit function and calibration These cross sections can be introduced in the analysis parameterisation by selecting the method File in the Projects Properties see page 60 These cross sections can also be created with the present tool and introduced in the analysis parameterisation as cross section files The Undersampling tool dialog box requests the following data Output files output files names for both phases 1 and 2 of undersampling Solar spectrum the high resolution solar spectrum Calibration Slit Function type Analysis method Shift WinDOAS 2 1 February 2001 9 Annexes 9 1 Files format Calibration File name File extension Tools Format Example Cross Sections File name Analysis windows properties Tools File extension Format Example Solar Spectrum File name File extension Projects properties Format Tools Example Reference spectrum File name File extension Analysis windows properties Format Example Annexes no restriction clb by default but it is not restrictive Column 1 the wavelength calibration ANYTHING CLB For cross sections implied in the definition of analysis windows the file name m

WinDOAS 2.1 - The BIRA

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