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CXSFIT --- User Manual

1. MASS FLT NLINES Mass of each line DATA FLT NFRAME NLINES NTRACK Temperature TEMP STR a ERROR FLT NFRAME NLINES NTRACK Error in above DATA FLT NFRAME NLINES NTRACK Intensity INTENSITY STR ERROR FLT NFRAME NLINES NTRACK Error in above WAVELENGTH STR DATA FLT NFRAME NLINES NTRACK Wavelength ERROR FLT NFRAME NLINES NTRACK Error in above DATA FLT NFRAME NLINES NTRACK Rotation VROT STR A ERROR FLT NFRAME NLINES NTRACK Error in above BASELINE STR DATA FLT NFRAME NTRACK Baseline ERROR FLT NFRAME NTRACK Error in above lt 0 Failed FIT STATUS INT NFRAME NTRACK z Notattempted j i 1 Good fit gt l Poor fit WSHIFT FLT NFRAME NTRACK Wavelength shift on the fly calibration only WLFP FLT NFRAME NTRACK Wavelength of first fitted pixel on the fly calibration only 60 B External file formats B 1 Spectra spc file An spc file contains calibrated spectra instrument functions geometry information etc It is an IDL Savefile format and contains a data structure as detailed in appendix A 1 The files can be loaded saved from the Spectra menu see section 2 1 3 or from the command line see section 6 B 2 Fit settings fit file The fit settings file can be saved and loaded from the Fit menu and contain both the history information and the currently displayed option Unlike the other files generated by CXSFIT these files are
2. 1 Clear results buffer i i i No Estimates y Self Mapping Estimates o 522 524 526 530 532 534 Previous Frame Estimates w Self Mapping with baseline 528 Wavelength nm Neighbouring Track Estimates D14 2 87350 m Frame 612 48 8630 s 5 23E 16 Ph 529 388 nm 1 612 CVI 8 7 529 273 nn 5061 7 eV 1 57E 16 Ph Figure 3 Overview of CXSFIT graphical layout The general screen layout of CXSFIT is shown in figure 3 Spectra appear to the left of the main window and fitting parameters to the right The track and frame being displayed can be adjusted with slider widgets below the spectrum for more information on this area see section 2 2 To the right of this are nine panels with the various fit options these are discussed at length throughout sections 2 and 3 Other tabs are present allowing for the inspection of the various measured quantities these are discussed in section 2 7 Options exist in the view menu to have these other windows be free floating at the users preference The details of each of the dropdown menus are given below 2 1 1 File menu The file menu of CXSFIT is show in figure 4 From this menu File view Spectra Fit 1t is possible to Load Ctrl L Save Ctrl 5 e Load Load a previous entire analysis data options and Save as results in from an external file default extension cxf Print Spectrum see appendix B mer e Save Save the entire sessio
3. Number of Tracks 14 1 D14 R z phi 2 87 0 29 302 0 Orig 4 31 0 27 349 3 2 D12 R z phi 3 04 0 26 303 5 Orig 4 31 0 27 349 4 3 D11 R z phi 3 12 0 25 304 2 Orig 4 31 0 27 349 4 4 D10 R z phi 3 19 0 23 304 8 Orig 4 31 0 27 349 4 5 D9 R z phi 3 27 0 22 305 6 Orig 4 30 0 27 349 4 6 D8 R z phi 3 34 0 21 306 3 Orig 4 30 0 27 349 4 7 D7 R z phi 3 41 0 19 306 9 Orig 4 30 0 27 349 4 8 D6 R z phi 3 48 0 18 307 6 Orig 4 30 0 27 349 4 9 D5 R z phi 3 55 0 17 308 2 Orig 4 30 0 27 349 4 10 D4 R z phi 3 62 0 16 308 8 Orig 4 30 0 27 349 4 4 Figure 7 Textual information about the spectra inside CXSFIT Option available from the spectra menu discussed in this section It should be noted that the Load Save and Save as buttons here do not store the results of the fit but rather the parameter settings and the complete history of parameter settings used in the current analysis the rationale behind this is discussed in detail in section 4 The fit menu also has a Library option which works like the Load button but goes to a centrally located repository of pre prepared param eter settings The parameter settings are stored as fit files the format is detailed in appendix B The fit menu also contains the options to ac Fit Results External tually do fitting T
4. Previous frame estimates in the Fit Mode panel Do afit Do another fit Turn on Neighbouring estimates in the Fit Mode panel Doa fit Do another fit Check for poor data a Switch to Mark fits as poor in the Fit Mode panel b Set up criteria to mark the fits as poor c Do a fit really just marks fits as poor d Switch to Refit Failed Frames in the Fit Mode panel e Ensure the Include poor fits option is selected f Turn on Previous frame estimates in the Fit Mode panel g Doa fit h Repeat as necessary Strategy for automatic reference line determination The strategy given here is typical of one which would be used to automatically deter mine the position of the reference line and then do a wavelength recalibration based on it This strategy is also suitable for automation and can be replayed from one his tory recipe file 1 Set up initial estimates which includes a reference line with a position specified in pixels Make sure the reference line is selected in the Data Params panel Make sure the position of the reference line is free Switch to Multiple Frame Fit in the Fit Mode panel Doa fit Switch to Extract Pixel Reference mode in the Fit Mode panel 43 10 11 12 Do a fit actually just extract the results from the previous fit Inspect the reference positi
5. Figure 12 Options for what to display on spectrum plot Note that the colour scheme can be changed from the Colour Scheme option in the View menu The colours given above are the default colour scheme for CXSFIT Black on White and is the colour scheme used throughout this document 2 3 Fit modes The fit mode of CXSFIT is set inside the fit parameters panel see figures 13 15 and can take one of five values 13 Single Frame Fit Multiple Frame Fit e Refit Failed Frames e Extract Pixel Reference e Mark Fits as Poor Extracting the pixel reference and marking fits as poor are more advanced uses of CXSFIT and are discussed in sections 3 5 and 3 7 2 respectively The other three options are discussed below sections 2 3 1 2 3 3 Options also exist to use previous fits as initial estimates the options are e no estimates use estimates from the other panels as normal e previous frame estimates for each fit use the results from the previous frame on the same track for the initial estimates e neighbouring track estimates use an average of the tracks on each side or simply the one neighbouring track if a track is at the edge e self mapping estimates use the same parameters as the current fit found typically used after a good fit has been found more parameters are made free than would have converged allowing fine tuning e self mapping with baseline as above but with a baseline See sec
6. Flat Select line CVI 8 7 Change name ova 8 7 Preset values Remove This Line Param al Unit Lower Upper Fix Value Height 1 476854 Ph m2 sr nm s ER inf 1 Centre 29 200 m p vavao lint 4 Temperature 2500 00 ev lio vena list r Mass 2 100 amu Select F Autodetect Height _ Suppress Line v Active Line Passive Line Theoretical wavelength 529 059 rm Figure 16 Line details panel initial estimates and bounds At the top of this panel the number of lines can be selected along with whether to use a flat or linear baseline Below this is a droplist which allows one to select which line to view edit In this case the line called CVI 8 7 has been selected The line names are arbitrary but are limited to eight characters for display purposes Beside the droplist 1s a text box allowing the name of the line to be changed By default lines start off being called Line 1 Line 2 etc Below the line name is an option allowing preset values to be selected Inside this box are known charge exchange and passive lines selecting one of these will set the current line s name mass and theoretical wavelength values to accepted values It will also put the line position at the theoretical wavelength set its height to whatever the currently viewed spectra is at this value and set the temperature to 150eV 18 Beside the line selection box is an option to remove the line This wi
7. Fonck et al 1983 Boileau et al 1989 Summers and von Hellermann 1993 is a very advanced diagnostic tool which can routinely deliver local temperature and rotation information from a fu sion plasma With further work impurity concentrations and associated quantities e g Ze may also be determined We note specifically that for the next generation fusion experiment ITER active charge exchange recombination spectroscopy has been identified as the sole diagnostic for the measurement of the density of the fusion ash He von Hellermann et al 1996 The strength of charge exchange spectroscopy is based on a comprehensive back ground of supporting atomic data giving effective emission rates neutral beam stopping calculations calculations of effective beam emission rates and populations of excited states Summers 2004 Just as important is the experience gained on many of today s fusion devices which apply CXRS as a routine tool One part of this experience is an intimate knowledge of accompanying background spectra and use of this knowledge to provide routine analysis CXSFIT is the current practical implementation dealing with the full subtlety and complexity of the spectra Our complex spectra are superpositions of passive and active spectra The former consists of broad band continuum radiation along with emission from a narrow layer of low ionisation stages emitted close to the plasma boundary Atomic and plasma mod elling may deliv
8. He and N composite spectra The text in this section is based largely on this publication 1 50 100 150 200 250 300 350 400 450 500 550 2 0x1017 1 5x1017 1 0x1017 intvensiy PO M ST NM 57 5 0x1016 Wavelength nm Figure 2 Example of composite CVI and NeX spectrum observed for JET shot 68822 The dominant features from left to right are the NeX CX feature the Bell reference line the CVI CX feature and the CIII edge line The individual components show that a large number of sub dominant lines must also be fitted in order to correctly understand the data Description Wavelength Transition Relative height CVICX 5290 59 8 gt 7 NeX CX 5248 97 11 10 CII 5257 24 D7 2 4 Fy 2 1 0 CII 5259 06 D52 34 F2 0 686 CII 5259 71 Dsn gt Fo 0 728 Cll 5249 11 5p P gt 4d D Cll 5304 62 7g 5f NeVI 5287 27 8k gt 7i 1 0 NeVI 5280 72 8i gt 7h 0 59 NeVI 523945 8h Tg 0 23 Ne 5294 43 Ne 5291 50 Ne 5284 50 Ne 5278 18 Ne 5275 03 Ne 5267 79 a These lines appear in the outer parts of low temperature plasma and are simply classified as Ne lines of intermediate charge states Ne Ne Table 1 C and Ne lines in the spectral range of the 8 7 CVICX line and the 11 10 NeX CX line 1 2 Historical information The present implementation CXSFIT is built upon almost two decades of experience gained by von Hellermann and co workers at JET Until CXSFIT the p
9. Js Figure 34 Writing JET data A PPFUID must be specified along with a DDA Note that if writing public PPFs then the DDA must conform with the standards shown in table 2 and the correct DDA will be filled in automatically it is not possible to override this for a public PPF If 47 Instrument Element KSSA KS7A KS5B KS5C KS5D KSSE C He N CXSM CXPM CXDM CXFM CXGM CXHM Be CXS4 CXP4 CXD4 CXF4 CXG4 CXH4 Ne CXS6 CXP6 CXD6 CXF6 CXG6 CXH6 Ar CXS8 CXP8 CXD8 CXF8 CXG8 CXH8 Table 2 DDA naming conventions writing a private PPF then the DDA can be anything Note also that special permission is required to write public PPFs First and last frames can also be specified these are filled in by default based on where data exist but can be overridden Also the radial chords to write can also be overridden Like the start and end time these are by default based on where data are present but tracks with poor data can be turned off if necessary The PPF written is compatible with the JET version of CHEAP written in Fortran 5 1 3 Running headless from the command line The program u cxs bin cxsfit_batch pl is a wrapper to CXSFIT so that a non graphical instance of CXSFIT can be run in batch mode This program should be used if incorporating CXSFIT into other processing schemes or used by itself from the command line Its core function is to allow CXSFIT to run without the requirement for it to display anything on screen It
10. Reading JET data 46 internal wavelength recalibration based on the position of the reference line but if nec essary one can specify these at the reading stage There is also an option to downsample data this will take successive N frames and add them together to form a longer frame This feature simulates running the diagnostic on a slower time resolution to collect more data per frame but isn t perfect with regards to the increase in readout noise etc Note that entering a value of 1 is equivalent to having the option turned off Finally due to a problem with XCAM CCDs there is an option to input a number which will unscramble the data Determination of this number must be done manually but it is noted that the preview in show option is useful for this If required all of the extra options input can be saved in a opt file see appendix B This will save all of the options with the exception of the shot number and diagnostic The options used to read data which eventually produced an output PPF can also be read via the PPF button 5 1 2 Writing data The window to write JET data is shown in figure 34 Save Data Jof x PPFUID jetpp StatusFlag O wmchecked First Frame 78 Last Frame 1025 Override radial chords to be written to PPF F is 22 8 3 JT BAD 13 880 F BIE 3 1 M HIS 33 19 M BS 3 22m F p8 3 34s FB Gola M B6 348a OM p5 3 5 J B4 3 6203 F 53 3 69m F 5 3 72m Pin ns 1 track 14
11. as well as the radial chords the interface is very similar to the JET panel see section 5 1 2 Save Data Figure 38 Writing TEXTOR data 32 A directory name must be given for all of the UFILEs to be output to this defaults to a standard TEXTOR naming convention by default but can be overridden A directory is and any directories above it are created if necessary This directory is compatible with the TEXTOR version of CHEAP implemented in Matlab In addition there is a button to Write main CX line output to TPD This will take the line indicated as the CX line set via the data parameters panel see e g figure 17 and send its various parameters to the TEXTOR Physics Database TPD This is also done remotely via the web but permissions are only granted if physically using a computer at TEXTOR This system in reality simply copies several of the UFILES to a web server 53 6 Command line usage When CXSFIT is called from the command line of a UNIX terminal a number of differ ent arguments can be passed to it these are discussed here The individual commands are processed in order and essentially simulate the user haven driven the graphical in terface Because of this the order of arguments is important Throughout this documentation it is assumed that the CXSFIT command from a UNIX terminal is simply cxsfit where appropriate aliasing or PATH environment variables have been set up Note that some of
12. database This option is machine specific see section 5 for more details on the implementation at each site Options appear in the Fit menu see section 2 1 4 to reload histories from PPFs or Level 1 shotfiles The entire history can be cleared from the fit menu and more advanced history op tions appear when explicitly viewing the history information discussed below 4 1 Viewing history information This history information can be viewed by selecting the option in the Fit menu see section 2 1 4 This pops up a window as shown in figure 32 The main content of the window is identical to the parameter settings as displayed in the main CXSFIT window These panels allow inspection of each history entry The entry to be viewed is chosen from the droplist at the top of the window in this case the seventh step is being viewed For more advanced usage it is sometimes convenient to edit the history this can be done in a number of ways Any history entry can simply be modified this will alter the history and when a replay is subsequently done the modified history will be played This is useful if e g the user wanted to modify some small detail in the middle of the steps but didn t want to go through the trouble of repeating all the steps Note however that each entry has to be modified manually so if the fitted pixel range had to be changed then it would need to be changed for each item in the history It is also possible to delet
13. has no knowledge of the vertical extent of the plasma and thus can not interpolate in flux coordinates Furthermore it is interpolating in R only something which can lead to more subtle errors if two lines of sight have different heights or inclination angles 3 7 Poor fits 3 7 1 Poorly fitted data Whilst doing a fit CXSFIT will identify fits as poor if various convergence criteria are not found with regards to the data being fitted On the contour plots see section 2 7 these fits are marked with a cross rather than a dot When in refit mode see section 2 3 3 an option exists to either refit only frames with failed fits or also frames with poor fits Selecting this option allows for the cleaning up of data It is also possible to mark other data points as being poor based on different criteria these are discussed below 3 7 2 Marking fits as poor Several options exist for marking fits as poor The most commonly used one is to find poor fits based on outliers in time Figure 28 shows the options available for this It al lows the selection of a specific quantity temperature intensity velocity or background and the selection of a specific line an option exists for all lines and no line can be selected when the background is the quantity of interest Criteria are then set for how high a point has to be above both points on either side of it or how far below A further option exists to specify whether data values are used for these
14. line it is possible to remove it by pressing the delete key this is equivalent to pressing the Remove this line button on the initial estimates panel see section 2 4 Whilst the mouse is moving around the spectrum display the program will select the closest fitted line note not initial estimate and show its name and calculated pa rameters below the spectrum If the fitted line centres option is activated see section 2 2 1 then a box will also be put around the centre mark of the line If it also possible to select a line by moving across the line centres at the top of the plot in this case the In this context dragging means to move the mouse with the button held down Unless specialist software has been installed to allow the mouse to be controlled from the keyboard 37 program only pays attention to x coordinates when selecting the closest line which can often make things simpler Right clicking on the spectrum plot at any point will insert a new line at that posi tion By default the line will be given a position and height of where the mouse was clicked Its temperature will be arbitrarily set to 150eV If CXSFIT has a line within its wavelength database at the wavelength which was clicked the line will be issued an appropriate name mass and theoretical wavelength If not then it will be set to an unknown carbon line It is possible to zoom in on the spectrum by holding a modifier key typically shift or ctrl while
15. make panels float An example of the spectrum contained in the main window was shown in figure 3 section 2 1 and an example of it free floating is shown in figure 11 This shows the original data in black the spectral fit in blue and the individual fit components in magenta Also shown are the pixel bounds green and line centres magenta The various data can be turned on and off for a full list of the different options see below section 2 2 1 Below the spectrum the current track and frame can be changed using the sliders which also displays the nominal radius of the spectrum and the recorded time An 11 asterisk is put next to the word Frame if the beam is considered to be on see section 5 for machine specific implementations Also shown are the current position of the mouse cursor and the line closest to the mouse courser along with its parameters The initial estimates pixel ranges etc can also be manipulated with the mouse and zooming features are available for a more detailed description of mouse usage see section 3 8 Pixel un 1 50 100 150 200 250 300 350 400 450 500 550 a 8x10 8x10 4x10 2x10 Intenaity Ph m art nm a Wavelength nm 4x10 Fi 2x10 2 o D ne 2x10 4x10 522 524 526 528 530 532 534 Wavelength nm D8 3 34314 m Frame 625 48 9930 s 1 95E 16 Ph 527 060 nm 6 625 BeII Ref 527 063 mm lcd 150 0 eV 5 14E 15 Ph Figure 11 E
16. number of machine specific locations see section 5 for details Individual quantities can also be written to ASCII files or UFILES IDL savefiles can also be written suitable for inspection plotting inside an interactive IDL session Write AUG shotfile Write JET ppf Write TEXTOR ufile set Write individual ufile Write IDL savefile Write ASCII file Ctrl W Figure 9 Results menu External 2 1 6 External menu The external menu see figure 10 allows the user to read in external 7 or angular frequency estimates from previously road written results These reading routines are machine specific Save Save as see section 5 for details There are also options to view the currently stored exter nal estimates these will pop up panels similar to the results display panels which are discussed in section 2 7 As for Read Ti from AUG shotfile Read Ti from JET PPF Read Ti from ufile Read AF from AUG shotfile each of the menus the user can Load or Save external esti mates to local files For a discussion as to how external estimates are used Read AF from JET PPF Read AF from ufile Display External Ti within CXSFIT see section 3 6 Display External AF Figure 10 External menu 2 2 Displaying spectra Spectra and individual fits are displayed in the spectrum win dow which can either be docked into the main CXSFIT window or free floating see section 2 1 2 for information on how to
17. together This allows a line selection on one panel to modify the line selection on another or zooming on one panel to also zoom all the others Whether these things are locked can be toggled on and off individually 2 8 Global Switches Figure 21 shows the global switches panel where features of the program can be turned on and off This will cause relevant boxes to be sensitised or de sensitised as appropri ate Most of this can also be achieved by turning individually options on and off e g you can turn parameter bounds off in global switches or simply go through every bound setting them to inf inf and have the same effect A number of the global switches are also duplicated on other panels e g in the reduced areas panel figure 18 in section 2 5 1ts possible to turn on and off the global switch directly This is simply a further convenience to the user and the two buttons do the same thing 24 E al Ji E r r Figure 21 Global switches panel 25 3 Advanced use of CXSFIT 3 1 Track Specific Options Figure 22 shows track specific options for CXSFIT Namely whether to fit a track or whether to suppress lines or not The shift fields are deactivated in the figure shown but are discussed in section 3 4 The fit track option requests whether or not when in multiple frame fit section 2 3 2 or refit failed frame mode section 2 3 3 particular tracks should be fitted when the Fit all tracks option is selecte
18. wavelength can also be input this wavelength is necessary to convert a wavelength shift into a rotation in the case of an active line It also plays an important role if on the fly wavelength calibration is going to be performed with a reference line see section 3 3 for details on this procedure Note again that the Select Line droplist box should be used to specify which initial estimates are to be viewed edited Also note that the initial estimates can be adjusted and lines inserted graphically see section 3 8 for more information 2 5 Pixel range and blind areas There are two ways to deselect data in CXSFIT one using pixel ranges and the other using reduced areas The reasons for these two methods existing are partly historic Figure 17 shows the panel where pixel ranges can be adjusted These are the solid green bars which can be displayed on the spectrum see section 2 2 1 These can either be set by entering data in the text boxes or moved about on the screen with the mouse see section 3 8 The other important use this range has is to allow the spectrum plot to be scaled according to only the data being used see section 2 1 2 meaning that noisy data towards the end of a spectrum will not dominate the Y scaling of the plotted spectrum Figure 18 shows the panel which allows reduced areas to be set These regions do not need to be specified at the edges of the spectra and can be used to remove noisy unfittable data The ca
19. 1996 Diagnostics for Experimental Fusion Reactors I Edited by Stott et al Plenum Press N Y 321 von Hellermann M G Bertschinger G Biel W Giroud C Jaspers R Jupen C Marchuk O O Mullane M Summers H P Whiteford A and Zastrow K D 2005 Physica Scripta T120 19 von Hellermann M 2005 ITER Active Charge Exchange Spectroscopy CXRS and Beam Emission Spectroscopy BES MSE with Diagnostic Neutral Beam DNB un der EFDA contract not publicly available contact mgvh rijnh nl 56 A Internal data structures A 1 Spectrum data structure NAME STG machine name AUG JET TEXTOR MACHINE STR PATH STG path to machine info cxrsfit lt mach gt DATAFORMAT STG AUGSF PPF NAME STG CER for identifying data source PECTROMETER TR ot SPECTRO 4 INFO STG descriptive string INPUT FILE STG full path name for local file input SHOT_NR LNG shot number NPIXEL LNG number of pixels NTRACK LNG number of tracks NFRAME LNG number of frames NINST LNG number of instrument functions Elements above are used to initialise structure elements below are added automatically WLENGTH FLT spectrometer nominal central wavelength in Angstroms SLIT FLT spectrometer slit width in microns LOS_NAME STG NTRAC Names of each track R POS FLT NTRAC crossing point of LOS with beam used as a zero order position of fitted parameters z POS FLT NTRA
20. 24 This then overrides the initial estimate setting for the reference line position Note that using the pre determined position for the position of the reference line is distinct from using it for the track to track pixel shifts but it is common to use both options together The position which will be used is also shown in figure 27 269 202 and is also shown on the reference time traces 3 6 External estimates CXSFIT can read data from other analyses in order to given initial estimates to parame ters This is limited to the main charge exchange line temperature and rotation External estimates can be read via the external menu see section 2 1 6 These options are also quite machine specific see section 5 since they are reading in external data After the data has been read it can be displayed in a standard contour plot also from the exter nal menu In order to have CXSFIT use the data during a fit the global switch must be turned on for either both of external Ti and external AF If the temperature rotation 32 1s set to fixed then CXSFIT will force the parameters to be the external ones otherwise they will only be used as initial estimates Interpolation in time and space is done inside CXSFIT however this is limited in that CXSFIT has no knowledge of the plasma centre so will typically extrapolate tem perature upwards through it as opposed to letting it turn over In addition and perhaps more importantly CXSFIT
21. 69 replay write jetppf cxfm quit cxsfit readoptions cxfm 66870 ks5c 66870 settings cxfm 66870 replay write jetppf cxfm quit cxsfit readoptions cxfm 66871 ks5c 66871 settings cxfm 66871 replay write jetppf cxfm quit 55 References Afrosimov V V Gordeev Yu S Zinovev A N and Korotkov A 1978 JETP Lett 28 500 Boileau A von Hellermann M G Horton L D Spence J and Summers H P 1989 Plasma Phys Contr Fusion 31 779 Fonck R J Darrow D S and Jaehnig K P 1983 Phys Rev A 29 3288 Gormezano C Sips A C C Luce T C Ide S Becoulet A Litaudon X Isayama A Hobirk J Wade M R Oikawa T Prater R Zvonkov A Lloyd B Suzuki T Barbato E Bonoli P Phillips C K Vdovin V Joffrin E Casper T Ferron J Mazon D Moreau D Bundy R Kessel C Fukuyama A Hayashi N Imbeaux F Murakami M Polevoi A R and St John HE Nuclear Fusion 47 S285 Isler R C 1977 Phys Rev Lett 38 1359 Summers H P and von Hellermann M 1993 Atomic and Plasma Material Interac tion Processes in Controlled Thermonuclear Fusion Edited by Janev Elsevier Science Publishers 87 117 Summers H P 2004 The ADAS User Manual version 2 6 http adas phys strath ac uk Tunklev M Breger P Giinther K von Hellermann M K nig R O Mullane M and Zas trow K D 1999 Plasma Phys Contr Fusion 41 985 von Hellermann M Core W G F Howman A Juper C Konig R W T Stamp ME Summers H P Thomas P R and Zastrow K D
22. ADAS R 07 01 ADAS Atomic Data and Analysis Structure A D Whiteford M G von Hellermann L D Horton and K D Zastrow CXSFIT User Manual 08 November 2007 This communication has been prepared for discussion within the ADAS and OPEN ADAS community It is subject to change without notice Please contact the authors before referencing it in peer reviewed literature 1995 2009 The ADAS Project Germany CXSFIT User Manual 8th November 2007 A D Whiteford M G von Hellermann L D Horton and K D Zastrow 1 ADAS 2 FOM Institute for Plasma Physics Rijnhuizen Department of Physics Association EURATOM FOM University of Strathclyde Member of Trilateral Euregio Cluster 107 Rottenrow PO Box 1207 Glasgow G4 ONG 3430 BE Nieuwegein UK The Netherlands 3 Max Planck Institut f r Plasmaphysik 4 Euratom UKAEA Fusion Association EURATOM IPP Association Culham Science Centre D 85748 Garching Abingdon OX14 3DB UK Contents 1 Introduction and Background 3 1 1 Fitting charge exchange spectra 1 2 Historical information Ls o a A er General use of CXSFIT 2 1 Screen layout and dropdown menus Zabel HS MeNR SE 4 372 4 ae Pa a di Ee SS 2 1 2 VIEW MENU errar 2 1 3 Spectra Menu e ann dec dy ue deep Esp ins 214 FEMME vs Lie a s A AAA ZAG Results MENU ii ia a g ao eds Be See Be 216 External menu a ra a aa aa 2 2 Display Spectra 20d unina dE ooh ep Le A
23. ASCII in a markup language and can be inspected with a conventional text editor Note that it s also possible to read in fit settings from a PPF or Level 1 shotfile also from the Fit menu see section 2 1 4 B 3 Fit output otp file An otp file contains the output data from a fit temperature intensity etc It is an IDL Savefile format and contains a data structure as detailed in appendix A 4 The files can be loaded saved from the Results menu see section 2 1 5 or from the command line see section 6 B 4 External estimates ext file An external estimates file ext contains the external Ti and AF estimates in an IDL Savefile format The files can be loaded saved from the External menu see section 2 1 6 or from the command line see section 6 B 5 Complete dataset cxf file A cxf file contains everything stored inside CXSFIT at a given point in time with the exception of the display options in an IDL Savefile format It consists of the data structures specified in appendix A The files can be loaded saved from the File menu see section 2 1 1 or from the command line see section 6 These files are the most convenient way to save a shot for either work in the future or for passing to someone else 61 B 6 Extra read options opt file file An extra read options file opt contains read options used to obtain spectra in an IDL Savefile format and suitable to be passed direc
24. CK see R_pos PHI POS FLT NTRACK see R_pos R_ORIG FLT NTRAC position of the origin of the LOS with R_pos z_pos ph_pos to define the LOS z ORIG FLT NTRAC see R_orig PHI_ORIG FLT NTRAC see R_orig TIME FLT NFRAME central time of exposure in seconds EXPOSURE FLT NFRAME duration of exposure of each frame BEAM BYT NFRAME switch for beam on 1 or off 0 DATA FLT NPIXEL NTRACK NFRAME ph m srnm ERROR FLT NPIXEL NTRACK NFRAME Error in above Bit Meaning 1 Dead pixel 2 Saturation INTENSITY STR 3 Unaemned VALIDITY BYT NPIXEL NTRACK NFRAME 6 Undefined 8 Undefined 16 Undefined 32 Undefined 64 Undefined REFERENCE STG text specifying source DATA FLT npixel ntrack wavelength nm WAVELENGTH STR ERROR FLT npixel ntrack Error in above REFERENCE STG text specifying source DATA FLT NPIXEL NTRACK inverse linear dispersion in nm pixel DISPERSION STR ERROR FLT NPIXEL NTRACK Error in above REFERENCE STG text specifying source YO FLT NINST NTRACK relative intensity of individual Gaussians XW FLT NINST NTRACK 1 e half width in Angstroms of individual IU STR z es relative shi t in Angstroms o individual Gaussians in instrument function REFERENCE STG text specifying source 57 A 2 Fit settings data structure FRAME TRACK FITMODE INITIAL FPARAM INT INT PTR PTR PTR Selected frame Selected track MODE STG single
25. E zis P le bide ke a Slee Se a met SD me sut ne Sil Reading data cita ioes teed eee Meee Gee ae Gee de 5 1 2 Witins data es us eb iets odie tear Goat ar dig Gh eg wee A 5 1 3 Running headless from the command line 5 1 4 Automatic processing inloadleveller Deke AU Te Sg a AE Be di ei Ga deju RA BO I ado a 321 Reading data A e far ge a de a aS eee ee br Bee 5 2 2 Writing data Lee Lo Re LR hae to ed e 3s TEXTOR geru gedo e gei alta Dome fa ielas io o ie does eN e AI of bite PE ee amp te ge amp ul 22 WTO data sasia neo ntl re tN eee atte nt 6 Command line usage Gali Basic usager sre tetas A RA OSE ESE Re 6 2 Practical examples 2 4 00 404 4c8 024 Gr va Rat seat See References A Internal data structures A l Spectrum data structure A2 Fit settings data structure 4 228 duo Ba A A KK Ka A 3 History Data Structure AA Output data structure 4 2 4du o LAA A NE AS ar B External file formats B 1 Spectra spe fil vu oa sacr eee eee eo eed Be wee eX B 2 Fit settings f Tt file saose is das a ad ae dada ais B 3 Fit output sotPill s ss fee bbe eee Dee eA B 4 External estimates ext file B 5 Complete dataset cxf file B 6 Extra read options opt filefile 11 1 Introduction and Background Charge Exchange Spectroscopy Isler 1977 Afrosimov et al 1978
26. E 2 2 1 Display options 22 e ar LS de a ra 2 3 GE AN UES eu eria k o Eee ds KS i AE ce A 23 1 Single frame fit sor o hes rs Gh r ie ses 23 2 M l plefgame fita ode Data a a en Jen re 2 3 3 Refit TANCE frames lt sue de di e e tetes 2 4 Initial estimates and bounds 2 5 Pixel range and blind areas ses oh rest Bee os Gee Ghee Gras Gris os 2 6 Parameter coupling 2 44 8 dol ca amp Sod qe RS al Spe See Be we 24 Examining results as desa See ee Pe es 2 8 Global Switches 2 x 304 00 240428 ba TRS RE Tee Advanced use of CXSFIT 3 1 Track Specific Options a bon a ai rada a ES 3 29 Other track estimates lt lt 4 4 Krons ds oh a Ai Ad 3 3 In place wavelength calibration 3 4 Wav l nethSits 4 4 444 ne au k 2 44444 45 6h ee he sta 3 5 Automatic determination of reference line position 3 6 E l tn l stindl sk zilas t Apt ie Mein Pt wD Arig ca 5 Ol POO GUS stl adds det dr Stadt di trais isti ra 3 7 1 Poorly fitted data 4 bo biel he k s ie 3 7 2 Marking fits as poor gt Sids AAA 3 8 GUI mouse and keyboard shortcuts 39 NAG ODUONS ge Gola E di 4 Histories recipes and automated processing 4 1 Viewing history information 42 o IR RR oP beret OT ne 4 3 Strategy for cleaning wp data lt iu e a 4 4 Strategy for automatic reference line determination 5 Machine Specific Information Del J
27. IT e View Pixel References Displays automatically determined position of the refer ence line see section 3 3 for more details on this e Save defaults Saves all the options set in the view menu to a file cxsfit dat so that they are used in all subsequent sessions 2 1 3 Spectra menu The spectra menu see figure 6 controls the reading of spectra from data sources See section 5 for details of ma chine specific reading options and appendix A 1 for details of the internal data structure for spectra This menu also allows spectra to be saved loaded to local files see also ap pendix B The spectra information option allows textual information to be shown about a spectrum as illustrated in figure 7 The shortcut key ctrl R is automatically set de pending on what computer system CXSFIT is running on 2 1 4 Fit menu The fit menu see figure 8 controls the process of fitting Spectra Fit Results Exter Load Save Save as Read AUG shotfile Read TEXTOR TW Read JET JPF Ctrl R Spectra information Figure 6 Spectra menu data and saving the parameter sets The parameters themselves are set in various panels CXF Spectra Information olx Machine JET Shot 70312 Diagnostic ks5c Vavelength Setting 5270 00 Number of Frames 1066 Time Range 38 6030 gt 53 4030 s Beam on for 948 frames Beam on between frame 78 t 43 5230s and frame 1025 t 52 9930s
28. OFF AREAS PTR MIN_VALUES MAX_VALUES PTYPE T Linked to global switch T 10 Reduced area is on LT 10 Min range of reduced area LT 10 Max range of reduced area T 10 O pixels 1 nm Hm m HH FIXED_ESTIMATES COUPLED_ PARAMETERS AUTOMATIC_AMPLITUDE_ESTIMATES EXTERNAL_TRACK_ESTIMATES EXTERNAL_TI_ESTIMATES GLOBSW PTR EXTERNAL _AF ESTIMATES REDUCED_AREA_ACTIVATION SUPPRESS GAUSSIAN ACTIVATION PARAMETER BOUNDS_ACTIVATION PEDESTAL_FUNCTION_ACTIVATION PIXEL_CORRECTIONS_ACTIVATION Allow parameters to be fixed Activate coupled parameters Turn on automatic amp estimates Turn on external track estimates Turn on external Ti estimates Turn on external AF estimates Turn on reduced areas feature Turn on suppressed guassians Turn on paramater bounds T Unused Turn on pixel correction options A E E AAA AA D AA A 3 1 A 3 History Data Structure This history data structure is simply a pointer array with each element pointing to a structure as described above See section 4 for more details on the history settings 59 A 4 Output data structure CODE STG Code use to do the fit e g ks4fit MACHINE STG Machine e g AUG SPECTROMETER STG Spectrometer e g CER SHOT_NR LNG Shot number NTRACK LNG Number of tracks NFRAME LNG Number of frames NLINES LNG Number of lines Elements above are used to initialise structure elements below are added automatically
29. an also be supplied some information is filled in by default but other information can be added The shotfile diagnostic designation is automatically deter mined from the original instrument and corresponds to the information in table 3 The shotfile written is compatible with the AUG version of CHEAP written in IDL 5 3 TEXTOR 5 3 1 Reading data Data can be read from the TEXTOR Web Umbrella TWU system from the option in the spectra menu see section 2 1 3 as shown in figure 37 The only inputs are 50 Save Data ausu Figure 36 Writing AUG data System type Level 0 Diagnostic Level 1 Diagnostic Core charge exchange CER CEZ Core charge exchange CHR CHZ Edge charge exchange CMR CMZ Lithium beam LIA LIT Table 3 AUG naming conventions 51 a diagnostic 1 e Kamera and a pulse number The TWU system is completely web based so unlike JET and AUG data the TEXTOR data can be read equally well from any machine with an internet connection Note that this reading stage does reading of the various TWU signals to handle calibration of the data determination of instrument functions and association with geometry Read Data Figure 37 Reading TEXTOR data 5 3 2 Writing data The results can be written to a TEXTOR compatible UFILE set from the option in the results menu see section 2 1 5 as shown in figure 38 As can be seen it s possible to override the first and last frame which should be written
30. and beam energies are between 50 and 70 keV amu For ITER a negative ion diagnostic neutral beam with energy of 100 ke V amu and a power of about 2 MW is proposed von Hellermann 2005 Gormezano et al 2007 A key strategy for a robust and unique spectral interpretation is the modelling of the passive components in particular the PCX feature For details of thee passive emis sion processes see Tunklev ef al 1999 In the example shown the PCX width and its Doppler shift are no longer free parameters but are fixed to the temperature and velocity of the ACX component close to the plasma boundary Empirically it was proven that although the PCX component being a line of sight integrated spectrum has not neces sarily a Gaussian line shape it can be approximated by a combination of a Doppler shifted Gaussian feature located at approximately a minor radius of r a 0 95 and an unshifted edge component CVI ice Note that modelling as opposed to just fitting of the PCX amplitude requires as input a modelling of the neutral density as donor for the passive CX process The neutral density in most cases is not known better than within a factor of 2 see Tunklev 1999 A longstanding experience in CX analysis also exists for the NeX CX spectrum which is comparable to the main CX spectrum for CVI n 8 lt n 7 The main reason is the close vicinity in the same spectral range at 5248 97 and 5290 59 respectively allowing simultaneous measureme
31. criteria or the error bar limits Care should be taken when using error bar limits since bad data often have very large error bars and so will not be found if limits of error bars are investigated Figure 29 shows the option to find poor fits based on the reference pixel see section 3 3 for details on the reference pixel This will find any points which have a reference pixel which is more than X pixels from the mean reference position for each track Note that the mean reference position is calculated by only using good fits This gives the feature that once data have been excluded the mean can change then other data can be outside of the range An option exists to recursively apply the algorithm until convergence is achieved with respect to this feature As with finding outliers data values or error bar ranges can be used when checking the data 33 Figure 28 Finding poor fits based on outliers 34 Figure 29 Finding poor fits based on the reference pixel 35 Figure 30 shows the options for finding outliers based on monotonic temperature values This is the only option which works on all the tracks of a given frame to find poor data Besides specifying error bars or data values no further options exist The algorithm simply checks for an increase in temperature with radius and marks that fit as poor This has the limitation that it may be the other data point which is too low as such this option is less safe for automatic processin
32. d The suppress line options only work in multiple or refit mode this specifies on a track by track basis whether or not the Suppress line button for each line has any effect or not Fit Mode Data Params Line Details Global Switches Coupled Params NAG Options Red Area Other Tracks Track Options Use relative pixel shifts for reference line J Use axtomatic estimates from cache 8 F Fit Shift Suppress Track 9 F Fit Track F Suppress lines Shift Track 10 f Fit Track F Suppress lines Shift 2 3 Track 11 F Fit Track F Suppress lines Shift p es Track 12 J Fit Track M Suppress lines Shift 2 66 Track 13 Fit Track _ Suppress lines Shift p es Track 14 1 Fit Track Suppress lines Shift p s Note Pixel Shifting only applies to the reference line if the initial estimate is given in pixels Figure 22 Track options panel This latter option is typically used to suppress a passive line near the edge due to not being able to distinguish it from the active line The line is set as suppressed in the In single frame fit mode these boxes are ignored 26 Line details panel and then only the suppress lines boxes on the outer tracks are set to actually suppress the line 3 2 Other track estimates The other tracks estimate panel is shown in figure 23 This panel allows the results from one track to be imposed on other tracks The
33. dragging over the spectrum window Holding a modifier and right clicking will unzoom back to the default view 3 9 NAG options The options passed to the underlying NAG routine E04UPF can be changed from the NAG Options Panel shown in figure 31 Normally these should be left at their default values The values which can be changed are e Major Print Level The amount of output produced on screen for each major iteration the default of 0 implies no output e Minor Print Level The amount of output produced on screen for each minor iteration the default of 0 implies no output e Verify Level Verification that gradients will be checked on each iteration the default of 1 implies no checking which makes the code run faster e Function Precision Control over what NAG sees as the inherent error in the cal culation of the spectra e Major Iteration Limit The number of major iterations which will be tested before the fitting algorithm gives up e Step Limit How far the algorithm will move on each step Smaller values work best on rapidly varying functions but need a better initial solution NAG recom mends a number typically between 0 01 and 2 e Line Search Tolerance A specification of how accurate a search should be per formed along the search direction Thttp www nag com numeric FL manual19 pdf E04 E04UNF_ 119 pdf 38 e Optimality Tolerance How good a solution is required Can be thought o
34. dual points than the mouse particularly when the time resolution is very high and the points are close together on screen It 1s not possible to zoom using the cursor keys The scale bar at the right of the contour window can also be adjusted The minimum or maximum value can be dragged up and down with the mouse to compress the colour range into a smaller region This is useful if one or two outliers are skewing the whole plotting range Note also that the contours can be inverted from the view menu section 2 1 2 or by pressing ctrl I This feature is useful when looking for low lying outliers Depending on the machine specific options see section 5 it is possible to click on either the profile or time trace and read in arbitrary data to be plotted in the window This allows e g a D signal to be plotted below the ion temperature to look for correlations with ELMs or similar On the spectrum plots e g figure 11 the mouse has a number of functions It is possible to drag any initial estimate around Dragging near the top of the line will allow the adjustment of the position and height dragging near the side of the line will allow the adjustment of the width temperature Pixel ranges can also be moved as well as reduced areas boundaries see section 2 5 While an element is being dragged the fit parameters panel will switch tabs and line selection if necessary to show the details of the element being changed in real time Whilst dragging a
35. e O and JETPPF or cxsfit settings cxfm 66869 awhitef To re do a fit as it was done from the PPF one could then cxsfit ks5c 66869 settings cxfm 66869 replay To write a ppf e g cxsfit my_session cxf write awhitef cxfm cxsfit my session cxf write jetppf cxfm note that any PPF written from the command line will have a status flag of zero To quit the program after all of the commands issue the command quit e g cxsfit my_session cxf write jetppf cxfm quit 6 2 Practical examples To do a range of shots using a particular recipe file and save them for later inspection it s possible to type something like cxsfit ks5c 66869 path to recipe fit replay save ks5c_66869 cxf quit cxsfit ks5c 66870 path to recipe fit replay save ks5c_66870 cxf quit cxsfit ks5c 66871 path to recipe fit replay save ks5c 66871 cxf quit It s also possible to do a range of shots and just write a PPF at the end cxsfit ks5c 66869 path to recipe fit replay write jetppf cxfm quit cxsfit ks5c 66870 path to recipe fit replay write jetppf cxfm quit cxsfit ks5c 66871 path to recipe fit replay write jetppf cxfm quit For inspection of data which has been queried it s possible to bring it up inside CXSFIT for manual inspection cxsfit readoptions cxfm 66869 ks5c 66869 settings cxfm 66869 replay It s possible to quickly reprocess a list of shots because e g calibration has changed cxsfit readoptions cxfm 66869 ks5c 66869 settings cxfm 668
36. e history entries the current entry can be deleted all of the entries previous to but not including the current entry or all of the entries subsequent to but not including the current entry This allows e g the user to go back to some step and then start again from that point There is also a button to remove all the entries 40 CXF Fit History Figure 32 Example of displaying the fit history 41 before the last clear If the buffer is cleared then history entries previous to this are not required to reproduce the results These entries are automatically discarded when a fit history is saved but are still present for convenience when running CXSFIT Finally at the bottom it is possible to copy the currently selected entry to the main buffer or perform a fit up to the selected entry Note also that there is no cancel option when editing history entries There is an important distinction between the last history entry and the currently displayed parameters Often they will be the same but they don t need to be It s possible to do a fit change the parameter settings and then save the settings In this case the final history entry will be different from the one viewed in the normal CXSFIT window but the history viewing option will still display the actual options used to fit the data 4 2 Recipes Clearly a set of history steps need not be replayed on the same shot they were produced on Using the history from one sh
37. en take the fitted pixel positions of the reference line and find a mean for each track This mean is then used to determine relative shifts between tracks see section 3 4 above and a suggested pixel position for the zero shifted track If the automatically determined pixel shifts are to be used then the use automatic estimates from cache button on the track shift panel see figure 25 above should be pressed This will grey out the manually entered shift boxes To view the pixel position 28 Figure 24 Data parameters panel 29 EE Eeg a peze DC A uz Figure 25 Track options panel with shifts activated 30 Figure 26 Extract reference fit mode 31 which will be used a popup with numbers can be displayed from the view menu see section 2 1 2 as shown in figure 27 The determined pixel position will also be shown on the reference output tab as a solid line running through the time traces Zero shifted track 11 Pixel position 269 202 Relative shifts ale 1 73279 CE 1 78366 3 2 26456 4 2 47977 5 0 964722 6 2 13678 7 0 920807 8 1 76459 9 0 0733032 10 2 12106 11 0 00000 12 2 07346 13 0 00000 14 0 00000 Figure 27 Viewing automatically determined pixels To use the automatically determined pixel position for the zero shifted track the Automatically set reference line to pre determined position button must be pressed on the Data parameters panel see figure
38. er a non local simulation of the line of sight integrated passive spec trum making use of external plasma data as input for collisional radiative processes The active charge exchange recombination contribution is essentially locally emitted at the beam plasma viewing line intersection and allows the key diagnosis of local plasma data In hot fusion plasma with temperatures of several keV the passive spectrum is generally not as strong as the active one In principle the passive and active spectra may be separated by for example beam modulation It is the contention of the current work and all the work it builds on that we must still seek the ability to evaluate the complete superposed complex spectral structure comprising the simultaneous active hot core and passive primarily edge parts The reason for accepting the evaluation of a complex spectral structure requiring comprehensive modelling rather than the ap parent simplicity offered by a subtraction method is that in many cases the seemingly stable background emission is affected by the injection of a neutral beam It is noted that in most of the present fusion devices where CXRS is applied a typical neutral power in excess of 1MW is needed for routine diagnostics and that this is not a first order linear perturbation The dual existence of passive emission spectroscopy representing the plasma edge and the so called active core CXRS spectroscopy is a complex but very intriguing cha
39. es when beam is on F Include Poor Fits BG 9638 itt 4438 JS ficar resalto baifer No Estimates y Self Mapping Estimates y Previous Frame Estimates y Self Mapping with baseline y Neighbouring Track Estimates Figure 15 Refit failed frames mode When in this mode the program will go through any fits which failed in previous fits and attempt to refit them It doesn t make sense to do this without modifying the initial estimates etc or the fit will just fail again The strategies behind this procedure are discussed in detail in section 4 3 A typical procedure might be to do a multiple frame fit and then switch to refit mode with previous frame estimates selected Since this procedure is working on previous results the clear results buffer option is not available CXSFIT has the concept of failed frames and poor fits When refitting failed frames it s also possible to refit ones which CXSFIT considers to be poor by selecting the option in the panel The distinction between a failed fit and a poor fit is of course somewhat arbitrary See section 3 7 for more details on this concept and how to mark a fit as poor 17 2 4 Initial estimates and bounds Figure 16 shows the main panel where the initial estimates and parameter bounds of each line can be adjusted Global Switches Coupled Params NAG Options Red Area Other Tracks Track Options Fit Mode Data Params Number of lines 8 Baseline
40. f as how many significant figures are required in the result the default value of 1 actually makes NAG use its default which is related to machine precision 0 0 1 ies a pa ea cea Figure 31 Nag options panel 39 4 Histories recipes and automated processing CXSFIT records the status of the fit settings panels each time Fit Now is selected Each of these settings are stored in order and the result can be thought of as a history of the steps taken to go from a raw spectroscopic data through to final results temperatures intensities etc This history of steps if made generic enough can be applied to many shots and can then be considered a recipe This section discusses the practical usage of the history both to reprocess data and as fixed recipes Given a saved history and initial data 1 e a fit and spc respectively see section B CXSFIT can reproduce the same results The spectra should be loaded along with the history file The Replay History ctrl H option should then be used and CXSFIT will replay all the steps as before to get the same results The same history file can be used with different initial data if it is re read and calibration has changed However it should be noted that in this case ad hoc corrections to single fits may be slightly different since the initial data have changed but this is not usually the case Typically the fit history is written along with the outputs to the final
41. fied theoretical wavelength as set in the line details panel see section 2 4 Rotations of the other lines are adjusted accordingly The position of the line can also be fixed in which case its not treated as a free parameter but the wavelength re calibration is still done When this feature is used it s possible to ask CXSFIT to either view the initial wavelength grid as read or the automatically generated one This option is present in the view menu see section 2 1 2 3 4 Wavelength shifts If the reference line position is set to fixed see discussion above then it is useful to be able to supply relative shifts between tracks Figure 25 shows the input panel for this feature This allows specification of the shift from one track to another In the example case track 11 has been specified to have a zero shift in terms of the pixel position of the reference line we refer to this as the zero shifted track and all of the others are specified according So if we set the reference line pixel to be 192 03 then on track 11 it would stay as 192 03 and on track 10 it would be 192 03 2 11 189 92 3 5 Automatic determination of reference line position CXSFIT can automatically determine average reference line positions and hence wave length shifts This is a fit mode which looks at previous results as shown in figure 26 This fit mode can only be used after doing an initial fit A track to be zero shifted has to be designated CXSFIT will th
42. g and is more useful when looking at data Figure 30 Finding poor fits based on monotonic temperature values 3 8 GUI mouse and keyboard shortcuts A number of shortcuts exist within the CXSFIT graphical user interface which are dis cussed in other parts of this manual but which are collected here for convenience On the contour plots e g figure 20 it is possible to zoom in on the contour by 36 simply dragging the mouse over the display A box will be drawn indicating the zoom area and when the mouse button is released the selected area will be zoomed in to Both the time traces and the profiles will also change Note that it is possible to select from the view menu see section 2 1 2 whether zooming in on one contour will cause the others to also zoom in or whether each contour can be controlled separately To zoom back out to the default view simply right click on the contour plot Clicking on the contour plot will jump the spectrum window to the selected track frame under the mouse cursor and highlighted with a box If the spectrum window or the contour window are free floating then the selected spectrum will simply be changed but if they are tabbed in the same panel then the spectrum tab will also come to the top Whilst on the contour window it s possible to change the selected point with a box around it with the cursor keys and to select a point by pressing the spacebar This serves as a more precise way to select indivi
43. he most frequently used is Fit oad now ctrl F which takes the parameters set in the Save various panels and does a fit The exact action car Save as ried out depends on the panel settings in particu Yibrary Fit now Ctrl F lar to the selected fit mode see section 2 3 An override is also present allowing a single frame fit to be done ctrl G This is simply a time sav ing feature and is formally equivalent to setting the fit mode to single frame mode doing a fit and then setting the fit mode back to whatever it was before The fit menu also allows the history to be replayed viewed and cleared See section 4 for more information on this Fit now single frame Ctr1 6 Replay history Ctrl H View fit history Clear history Settings from AUG shotfile Settings from JET PPF Figure 8 Fit menu Unrelated to the Flexible Image Transport FIT file format 10 As well as loading settings 1 e histories from a file they can also be recalled from fit results in the machine specific database see section 3 for more information on this 2 1 5 Results menu The results menu shown in figure 9 contains options Results External to save the results of the fitting i e T etc to a num Load ber of places The entire set of results can be saved in Save Save as a res file see appendix B which CXSFIT can re read at a later time or the results can be written to a
44. igure 14 The main options are to select the time window to do the fit between this can be specified by selecting a frame or by typing in a time which will automatically change the selected frame An option also exists to use the beam times for the first and last frames this will take the first frame the beams are on to the last frames the beams are on intermediate frames with no beams can be ignored by selecting the Fit only frames when beam is on option One can also select whether to fit all tracks or only the currently selected track Note however that in Fit all tracks mode of operation the Track Options panel see section 3 1 can exclude particular tracks As with the single frame fit mode one can choose to clear the buffer or not Allowing different temporal regions to be manually selected e g you could fit from frame 100 150 and then from frame 200 250 Figure 14 Multiple frame fit mode 16 2 3 3 Refit failed frames The options available for refitting failed frames are shown in figure 15 These are similar to the options for doing a multiple frame fit in terms of the way spectra are selected for processing Global Switches Coupled Params NAG Options Red Area Other Tracks Track Options Fit Mode Data Params Line Details F Use Beam Times For First Last Frame Bean on 78 t 43 5230s gt 1025 t 52 9930s First frame 360 Last frame 578 _ Fit all tracks Fit only fram
45. isplayed in six panels showing e temperature the temperature of any given line e intensity the intensity of any given line e rotation the rotation in m s or rad s see section 2 1 2 of any given line e wavelength the fitted wavelength of any given line e background the fitted background e reference the pixel position of the reference line see section 3 3 for details The various results either appear as tabs in the main window or can be made to float freely see section 2 1 2 for details Figure 20 shows an example of the temperature of a fit being displayed CXS Fit 0 1 JET KS5C 70312 527 0nm BEE File View Spectra Fit Results External Help Spectrum Paraneters Temperature Intensity Rotation vavelength Background Reference 18 R 6 3 34314 m t 577 48 5130 s peg earal Temperature 3452 18 64 4558 ev Time 48 5130 s ev 6000 38 T T T T T 3 N F S 4000F 7 H 36 E L 5 2000 4 E L U L 28 30 3 2 34 36 38 R m R 3 34314 m 6 24 42 44 46 48 50 52 54 42 44 46 48 50 52 54 Time 9 a Figure 20 Output display of ion temperature The main part of the display is a filled contour plot showing all of the data for the selected line the line to be viewed is selected at the top of the screen Each individual spectrum is a single point on this plot the cursor can be moved over this contour plot and the text at
46. l lenge describing in its entirety the whole plasma environment 1 1 Fitting charge exchange spectra The most frequently exploited CX spectrum is that of CVI at 5290 6 and serves as an introductory illustration of the main strengths but also potential pit falls of CX analysis As in most CX spectra observed in the visible wavelength range the observed CVI spectrum is a composition of several emission features representing the same impurity ion stage involved in different collisional processes within the plasma volume Each of those features is emitted at about the same wavelength and the spectral separation is due to local differences in ion temperature and rotation speeds The composite spectrum figure 1 is described by the superposition of a dominant broad high temperature core feature gt 2 keV which is denoted as the active component active charge exchange ACX Then a medium broad and also lower rotation speed passive CX feature 200eV to 1 keV usually denoted as PCX Finally there is often a narrow low temperature 50eV to 150 eV electron impact component not fitted in the example here The indicated temperature values can vary from machine to machine and also obviously depend on the operation and plasma heating scenario Subject to sufficient neutral beam power the active component should be the dominant feature This applies for example for the case of JET TEXTOR and ASDEX Upgrade where the power levels are around 1MW
47. ll remove the line from the list and adjust all of the other panels accordingly there is no undo function Below these options is a framed area which contains the initial estimates of each parameter height centre and temperature Note that the fit parameter is height and not area but that the fit output see section 2 7 is intensity 1 e area Also note that the position of lines can be set in either nm or pixels To the right of the initial estimates are parameter bounds in the example given they are insensitive this is because the global switch to use parameter bounds is turned off see section 2 8 for information about global switches The string inf should be entered to indicate no upper bound To the right of the parameter bounds are options to set the parameter to be fixed as oppose to free Note also there is a global switch controlling these which must be turned on to use them Below these are the mass of the emitter ion in AMU a value can be entered or an accepted value can be from the dropdown box which will be entered automatically Below the free parameters are options to use an automatic height detection algorithm or to suppress the line Line suppression is also turned on and off on a track by track basis see section 3 1 for details Below this is information as to whether the line is active or passive If it is se lected as active then a nuclear charge ionic charge and upper lower n can be entered A theoretical
48. mulitple refit reference or markpoor FIRST FRAME LNG First frame to fit LAST_FRAME LNG Last frame to fit ALLTRACKS NT Fit all tracks IGNORE_NOBEAM NT Ignore times when beam is off CLEARBUFFER LNG Clear buffer before fit PREVIOUS_FRAME NT Use previous frame estimaes NEIGHBOUR_TRACK NT Use neighbouring track estimates SELF_MAPPING NT Use self mapping estimates SELF_MAPP ING_BACK NT Use self mapping estimates with background USEBEAMS NT Use beam times for fit INCLUDE_POOR LNG Treat poor fits as failed FRAMEADD NT Unused PIXELADD NT Unused NLINES LNG number of lines BASE INT baseline setting O flat 1 linear DESCRIPTION STG 8 character line description HEIGHT FLT Initial height estimate CENTRE FLT Initial position estimate TEMP FLT Initial temperature estimate MASS FLT Mass CENTRE_UNIT LNG 1 nm 0 px HEIGHT_MAX FLT Maximum height value HEIGHT MIN Minimum height value CENTRE_MAX Maximum centre value CENTRE_MIN FLT Minimum centre value TEMP MAX FLT Maximum temperature value LINE STR 8 TEMP _MIN FLT Minimum temperature value AMP_FIXED NT 1 Fixed amplitude WID_FIXED NT 1 Fixed width POS_FIXED NT 1 Fixed position AUTO_AMP LITUDE NT 1 Auto amplitude SUPPRESS NT 1 Suppress line WAVELENGTH FLT Theoretical wavelength UPPER NT Upper n level LOWER NT Lower n level Z0 NT Nuclear charge of receiver Z NT Ionic charge of receiver ACTIVE NT 1 Active Line 0 Passive Line WLENGTH STG Unused PIXMIN INT Minimum pixel
49. n be set as either a function of pixel or of wavelength 19 Figure 17 Data parameters panel 20 being able to set by wavelength is useful when on the fly wavelength calibration will be done see section 3 3 and or when the wavelength range changes from track to track Individual reduced regions can be turned on and off individually and there is a global switch see section 2 8 which can turn them all on or off simultaneously ES DT ie DES EE LEA ce ne sus _m EME proa A MESA p 00 rixots ene mar IES poo pircis Figure 18 Reduced areas panel 21 2 6 Parameter coupling CXSFIT allows the coupling of parameters together in a single fit see figure 19 This allows the width temperature height or centre to be related to each via either a multiplicative factor or additive constant This allows for example the position of non rotating lines to be coupled together to reduced the number of free parameters It also allows the fitting of a group of lines where the intensity ratios and relative positions are known from atomic physics Figure 19 Coupled parameters panel Note the parameter which is coupled is truly height and not area intensity and im portant distinction if coupling lines of different masses and or temperatures Note also that it is possible to do limited quasi coupling across tracks see section 3 2 for details 22 2 7 Examining results The results of fitting are d
50. n to the current cxf file Figure 4 File menu e Save as As above but prompt for a new filename 7 e Print Spectrum Print the currently displayed spectrum as either an EPS figure or a PNG image e Quit Exit CXSFIT It should be noted that each of the drop down menus with the exception of the view menu see below in CXSFIT contain options to Load Save and Save as These options tend to save whatever else is controlled by that menu The options in the file menu are global and can be thought of as being equivalent to doing individual loading or saving using each menu in turn 2 1 2 View menu The view menu controls how the data are visualised inside CXSFIT Unlike the other menus the view menu does not affect the analysis itself and the way the data are being viewed is not saved with the data The view menu can be seen in figure 5 e Display Various sub options for what should appear in the spectrum plot see section 2 2 1 for more details e Floating Allows the various panels e g spectrum pa rameters temperature rotation etc to float in their own windows e Wavelength Option as to whether to use the wave length scale from the read data or from the on the fly calibration see section 3 3 for more details on this e Rotation Option to show rotations in rad s or m s e Colour Scheme Colour scheme for the spectrum plot black on white View Spectra Fit Res Display Floating Vavele
51. ngth z Rotation Colour Scheme F Contour Scheme F Zoom z View Fit Log View Pixel References Save Defaults Figure 5 View menu either white on black or e Contour Scheme Colour scheme for the contours either a red gradient or a hue gradient Also allows for inversion of the colour scheme useful for finding low value outliers e Zoom Options controlling the zoom display on the spectrum plot only Retain X zoom Keep zoomed x range when a frame track is changed Retain Y zoom Keep zoomed y range when a frame track is changed Zoom Y to fitted pixel range use the pixel fitting range see section 2 5 to autoscale the plots Clear spectrum zoom Unzoom and go back to default view Note see section 3 8 for details on how to zoom using the mouse and section 2 2 for details on viewing the spectra e Lock Options controlling how the results panels are locked together Zooming When one contour e g temperature is zoomed into then all of the other contours follow e g intensity rotation etc Lines When the line being viewed on one contour e g temperature is changed into then all of the other contours follow e g intensity rotation etc Note see section 3 8 for details on how to zoom using the mouse and section 2 7 for details on viewing the results e View Fit Log Displays detailed output from the underlying fitting routine 1 e KS4F
52. nt with the same instrument A number of impurity transport studies were also facilitated by the fact that the behaviour of an intrinsic im purity C could be compared directly with that of a seeded impurity Ne More recently in radiation cooling experiments neon is added as intermediary gas mitigating the power load on plasma walls by enhanced radiation processes 1 50 100 150 200 250 300 350 400 450 500 550 1x107 K TT T T f T 8x10 1 a 1 E c 6x10 L p ki E de a lt 4101 E 2 2x10 Wavelength nm Figure 1 Example of composite CVI spectrum observed for JET shot 70312 The CVI temperatures of the active ACX and passive PCX components are 2811eV and 823eV respectively The twin presence of two CX spectra see figure 2 suggests coupling the two Doppler widths and also their respective Doppler shifts assuming equal ion tempera tures and plasma rotation This method enables the monitoring of very low levels of neon since the only free parameter in the least square minimisation is the NeX spectral amplitude Together with a constraint parameter option permitting only positive am plitude values a twin solution of CX CVI and CX NeX exists for almost any plasma condition A slight modification for the standard CVI setup is required by the super position of additional NeVI lines see table 1 See von Hellermann 2005 for a further discussion of spectra including
53. on which has been determined in the Reference out put panel Go back to multiple frame fit in the Fit Mode panel Turn on Automatically set reference line to pre determined position in the Data Params panel Turn on Use relative pixel shifts for reference line and Use automatic estimates from cache in the Track Options panel Do a fit again and cleanup etc as necessary 44 5 Machine Specific Information 5 1 JET At JET CXSFIT is installed in the cxs account but is available for anyone with ac cess to the JACs to use without any special privileges It can be run by simply typing u cxs bin cxsfit but it is recommended that an alias or similar should be setup For people who produce vast quantities of charge exchange data the intermedi ate files produced can become quite large For this reason an area is available in common cxsfit for such files This area is only available to specified people and should be considered a scratch area not for long term storage and the disk does not benefit from snapshot etc In addition to the interactive CXSFIT program two batch processing programs exist at JET these are e u cxs bin cxsfit batch pl Command to run CXSFIT from the com mand line or from within a script such that no display is required see section 5 1 3 e u cxs bin cxsfit process pl Command to automatically build and submit a loadleveller job to process a series of sho
54. ot on another is termed applying it as a Recipe These recipes are typically unique to a particular instrument wavelength setting and observed species and may also be based on the type of shot being analysed Some of the options present in CXSFIT do not lend themself to being part of a recipe For instance repairing a particular track and frame in one shot can t be applied to a different shot since the chances of the exact same track frame failing is very small A discussion of the recipes for each machine is given in section 5 and information on automatically applying recipes via the command line is provided in section 6 The requirement for histories to be turned into generic recipes is the primary rea son for some of the features of CXSFIT such as automatically determining poor fits automatic determination of the reference line position etc A short discussion of some specific strategies follows in the next sections 4 3 Strategy for cleaning up data The strategy given here is typical of one which is used to do an automated fit with little user interaction The first ten steps were typically the actions manually used at JET in KS4FIT and the final step is an automated approach to identifying outliers and correcting them 1 Set up initial estimates 2 Switch to Multiple Frame Fit in the Fit Mode panel 3 Doa fit 4 Switch to Refit Failed Frames in the Fit Mode panel 42 10 11 4 4 Turn on
55. r system to distribute jobs fairly and in theory one should feel free to submit as many jobs as one likes but in practice this may be considered impolite 49 5 2 AUG 5 2 1 Reading data Data can be read from the AUG Level 0 shotfiles from the option in the spectra menu see section 2 1 3 as shown in figure 35 The only inputs are a diagnostic name and a pulse number Everything else is determined automatically such as dark noise subtrac tion etc Note that this reading stage does reading of the Level 0 shotfile calibration of the data determination of instrument functions and association with geometry Read Data of x Diagnostic CER Pulse 17149 ok Cancel Figure 35 Reading AUG data For the special case of the AUG Li beam diagnostic an extra panel will pop up to do preliminary data analysis and preparation of data This panel is based directly on Li beam analysis software and its description is outwith the scope of this document 5 2 2 Writing data A Level 1 shotfile can be written from the option in the results menu see section 2 1 5 as shown in figure 36 The main input is an experiment which will either be the user s username or AUGD to write a public shotfile Sufficient permissions are required to write a Level 1 AUGD shotfile but no permissions are necessary to write a user shotfile necessary directories etc will be created if they don t already exist in the user s home directory A comment c
56. ractical imple mentation at JET as a TSO based program called KS4FIT written primarily by von Hellermann While the graphical interface and various routine are no longer in use it should be recognised that CXSFIT is largely a re implementation of these ideas In fact the code which does the actually fitting is a variant of this KS4FIT also called KS4FIT which was extracted from JET by von Hellermann and which also appears as the main fitting engine inside the code InSPECtor As well as a modern graphical user interface significant advances have been made with regards to automation of fitting procedure and reproducibility of fits but all of this building on the same core routines and algorithms as were produced at JET and subsequently refined at JET TEXTOR and ASDEX Upgrade 2 General use of CXSFIT 2 1 Screen layout and dropdown menus CXS Fit 0 1 JET KS5C 70312 527 0nm Mi Ei File View Spectra Fit Results External Help Spectrum Paraneters Temperature Intensity Rotation wavelength Background Reference 50 100 150 200 250 300 350 400 450 500 550 Global Switches 1 Coupled Params 1 NAG Options 5x10 U T ld T Red Area Other Tracks Track Options Fit Node Data Parans Line Details Multiple Frame Fit F Use Beam Times For First Last Frame Beam on 78 t 43 5230s gt 1025 t 52 9930s First frame 36 u feso Last frame 570 1 foa Fit all tracks 1 Fit only frames when beam is on
57. range to fit PIXMAX INT Maximum pixel range to fit CXLINE LNG Main CX line 1 indexed 0 None REFLINE LNG Reference line 1 indexed 0 None COSMIC LNG Suppress cosmic bursts 58 MAJPRN LNG Major Print Level see section 3 9 MINPRN LNG Minor Print Level see section 3 9 VERIF LNG Verify Level see section 3 9 FUNPRES FLT Function Precision see section 3 9 MAJIT LNG Major Iteration Limit see section 3 9 STPLIM FLT Step Limit see section 3 9 LINTOL FLT Line Search Tolerance see section 3 9 OPTTOL FLT Optimality Tolerance see section 3 9 NAG PTR COUPLED_ON INT Linked to global switch ONOFF INT 50 Particular coupling is turned on PTYPE INT 50 0 Centre 1 Width 2 Height 3 Ti COUPLED PTR LINE1 INT 50 Line to link to 0 indexed LINE2 INT 50 Line to link from 0 indexed OPERATOR INT 50 O x 1 NUMBE FLT 50 Factor or costant operator dependent SAVETRACK INT 20 Perform fit on this track SUPPRESSLINE INT 20 Suppress lines on this track SAVETRACKS PTR OFFSET FLT 20 Pixel offset value USEOFFSET LNG Use pixel offsets AUTOOFFSET LNG Use pixel offsets from cache ONOFF PTYPE TO_LINE OTHERTRACKS PTR FROM_LINE FROM_TRACK TI_FACTOR AF_FACTOR T 20 Track link is on T 20 0 Ti 1 Intensity 2 AF T 20 Line to go to 0 indexed T 20 Line to come from 0 indexed T 20 Track to come from 0 indexed LT Ti factor LT AF factor AH HH H H REDUCED ON ON
58. takes as its arguments a recipe file an instrument name a ppfname and a list of shots The shotlist is specified as either individual numbers separated by spaces or a range with a between them Multiple ranges or individual shots and ranges can be specified simultaneously A typical usage might be cxsfit batch pl u cxs cxsfit recipes my_recipe fit V ks5c cxfm 69007 69011 69015 69017 this will read data from ks5c for the shots 69007 69011 69012 69013 69014 69015 and 69017 use the specified recipe and then write the results to a CXFM PPF The parameters can be given in any order If no PPF is specified then the program will simply save a cxf file for each shot to the current directory after it has finished Note that before running cxsfit_batch pl for the first time it is suggested you first run u cxs bin cxsfit process pl setup 8Internally the routine works by redirecting the CXSFIT GUI to a VNC session 48 5 1 4 Automatic processing in loadleveller The program u cxs bin cxsfit_process pl is a wrapper for the see above cxsfit batch pl program which works via loadleveller Its arguments are similar to cxsfit batch pl but it is slightly more focused on producing data in a standard way Before running the program for the first time it is necessary to type u cxs bin cxsfit_process pl setup which will setup some directories etc Instructions and information will be given on screen during the setup process c
59. the examples given here are machine specific 6 1 Basic usage The simplest command is to load data immediately on startup This can be from a JPF TWU or a Level 0 shotfile examples are cxsfit ks5c 66869 cxsfit cer 17818 cxsfit k5 103357 The above uses defaults for reading options to use a saved otp file only relevant for JET AUG doesn t have any extra reading options specify it before the data e g cxsfit path to myfile otp ks5c 66869 In addition to use the settings as used to read data which eventually produced a PPF one can do cxsfit readoptions cxfm 69744 awhitef ks5c 69744 the awhitef is optional To load in any valid CXSFIT file see appendix B just give it at the command line multiple files can be used e g cxsfit my_session cxf Cxsfit my spectra spc cxsfit my spectra spc my settings fit For this feature to work the default CXSFIT file extensions must be used see appendix B To save any CXSFIT file specify it at the command line with the word save before 1t e g to load in a whole session and just save the fit history cxsfit my session cxf save my settings fit or to load data and then save it cxsfit ks5c 66869 save my_spectra spc Again any number of files can be saved To replay a history issue the command replay e g cxsfit ks5c 66869 path to recipe fit replay or cxsfit my session cxf replay 54 to load a history from the PPF cxsfit settings cxfm 66869 defaults to sequenc
60. the top of the screen indicates the selected track with its radius and frame with its time The exact value of the temperature is also displayed along with 3In the present document and on conventional monitors these points can appear as horizontal lines because at high time resolution they are very close together 23 its error Simultaneously the two smaller plots at the left of the screen will change The upper plot displays a profile for the selected time and the lower plot displays a time trace for the selected track Note that zooming in on the contour plot can be achieved by drawing a box with the mouse Also the upper and lower scale can be changed by dragging in the box at the right of the plot which indicates this scale this feature is useful if the scale is being dominated by a small number of outliers Note that poor fits on this contour plot show up as a cross and failed fits show up as an asterisk x The currently selected point is outlined by a box An individual spectrum can be viewed by simply clicking on the point which corresponds to it this will switch the spectrum view menu to the selected point and also bring it to the front 1f the current window is tabbed in the same frame as the spectrum window The selected point can also be moved using the arrow keys and selected using the spacebar see section 3 8 for more information on GUI shortcuts An option in the view menu see section 2 1 2 exists to lock panels
61. tion 4 3 for more details on the practical uses of the latter four options Also note in particular that these options are usually used to repair sets of data with poor or failed frames rather than as an initial estimate at the analysis In particular doing an initial fit with previous frame estimates can lead to results which are incorrect but look plausible at first glance especially if there are a lot of ELMs 2 3 1 Single frame fit The single frame fit mode setting is shown in figure 13 As can be see there are no specific options related to this fitting mode but most of the other panels Data Params Line Details etc still affect the fitting The currently displayed spectrum with the track and frame selected by the sliders see section 2 2 will be the one which is fitted When doing a single frame fit the option to clear the results buffer is present If this option is selected then previous results will be cleared before the fit is done If this option is not selected then it s possible in principle to go through each spectrum in turn doing a fit Doing a single frame fit on a specific frame will also override any other fit which was previously done on this frame allowing the user to manually select outliers or poor fits after a multiple frame fit see below and fix them by hand 14 Figure 13 Single frame fit mode 15 2 3 2 Multiple frame fit Options available for doing a multiple frame fit are shown in f
62. tly to the underlying reading routine The files can be loaded and saved from the machine specific reading panels see section 5 and can also be specified at the command line see section 6 just before data are read at the command line 62
63. ts see section 5 1 4 5 1 1 Reading data Data can be read from the JET JPF system from the option in the spectra menu see section 2 1 3 as shown in figure 33 At the top of the window there is a dropdown to pick the diagnostic name and an entry box to enter the shot number Under normal operation this is all that is required and is the recommended way to read data although further options exist Note that this reading stage does reading of the JPF calibration of the data determination of instrument functions and association with geometry There is an option to preview the data in the SHOW display program This will read the uncalibrated data and feed it into show CXSFIT will automatically determine the first frame to be used as a background by analysing the change in standard deviation by taking subsequent background frames working back in time The default value for this change is 1 5 but this can be over ridden The procedure used can also be viewed graphically by pressing Manual Back ground Analysis this allows the user to specify different percentages and see where the cutoff would be Finally a manual frame can be specified counting from 1 to be used as the first background frame the background frames end at t 40s by definition Towards the bottom of the window a number of boxes appear to manually specify a wavelength pixel pair for each track This is not normally used since CXSFIT can do an 45 Figure 33
64. type of parameter to be linked temperature angular frequency or intensity can be selected as well as the line to which to apply the estimate The track and line to which to apply the estimate is also required Note that if in the initial estimates the specified parameter is set to fixed then the result from the other track is used as a fixed parameter Figure 23 Track options panel This option is typically used when a passive temperature is measured on one track and then the results of this measurement can be applied to every other track In the figure shown the active line is measured on track 12 and then the passive line receives 27 the rotation and temperature from the track 12 measurement See also the previous section where the passive line was turned off on the outer tracks 3 3 In place wavelength calibration For spectrometers where the absolute wavelength calibration is not well known e g most spectrometers at JET CXSFIT can do an on the fly wavelength calibration This works by taking a non rotating line with a known wavelength and fitting this line If the dispersion is known then the entire wavelength calibration can be based on this line position Figure 24 shows this being done via the selection of a Reference line If a reference line is selected then its initial estimate must be given in pixels CXSFIT will then fit this line as normal and then re calculate the wavelength grid based on this line being at its speci
65. xample of a free floating spectrum window 2 2 1 Display options Various display options are available in CXSFIT controlling how the spectra are dis played The total fit and the original data are always turned on but others can be turned on and off Figure 12 shows the options to turn these features on and off The various options are 12 e fitted components magenta displays each fitted component resolved rather than summed e initial components red displays the initial estimates of each line as individual components e initial spectrum red displays the initial estimates on top of the fitted not initial background e pixel Fit Range green displays the pixel fit range as solid bars e highlight Reduced Areas green area shades the reduced areas with a different background e fitted Line Centres magenta displays positions of the line centres across the top of the plot e residuals from Fit displays additional plot in bottom 30 of window e error bars on spectrum displays error bars in original data View Spectra Fit Results External Display F Fitted Components F1 Floating F Initial Components Vavelength Initial Spectrum F3 Rotation w Pixel Fit Range F4 Colour Scheme Highlight Reduced Areas F5 Contour Scheme Fitted Line Centres F6 Zoom Residuals From Fit F7 Lock e Error Bars On Spectrum F8 View Fit Log View Pixel References Save Defaults
66. xsfit_process pl also comes with its own built in help which can be viewed by typing cxsfit process pl help The program takes a recipe file and a list of shots as its minimal arguments an example might be cxsfit process pl V home cxs cxsfit recipes my_ks5c Recipe fit V 69007 69011 69015 69017 note the calling sequence is similar to cxsfit bath pl but the instrument name is not specified rather this 1s inferred from the recipe filename For a discussion as to how the shot ranges work either see the in built help or section 5 1 3 above The program will then construct and submit a loadleveller job which will process each shot in turn and then deposit the results in common cxsfit username as a series Of cxf files and Log files the 1og files correspond to what would have appeared on the terminal during an interactive session of CXSFIT and can be useful in tracking down errors These files can then be opened by hand inspected and a PPF written By default cxsfit process pl will submit one job to the loadleveller system which will do each shot in turn However if the word parallel appears on the command line then one job per shot will be submitted e g cxsfit process pl V home cxs cxsfit recipes my_ks5c Recipe fit V 69007 69011 69015 69017 parallel This decreases the waiting time immensely but if overused could cause other users of the JAC system to complain Note that it is the function of the loadlevelle

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