ISAS-Tool Version 6 : User's manual
Contents
1. za lt A for plotting level in meter to be plotted by post oa if PLOT_LI 0 no plot str_plot_lev 5 38 8 2 log files of the standardisation step 8 2 1 message file gt gt gt gt gt gt gt Running ISAS_V6 STD Last update 20 Dec 2011 16 03 12 Configuration files climref home5 garo arivo software isas isas_ana confstd_v5c3 climref bathy hnome5 garo arivo software isas isas_ana confstd_v5c3 climref area hnome5 garo arivo software isas isas_ana confstd_v5c3 areadef Type_list PR_PF PR_CT PR_MO PR_TE RAW data directory net luarca export homel DATA_WORK NRTOAGLO1 STD data directory net luarca export homel std_data_NRT arglv6NRT_PR STD Type PR_PF 31 files found net luarca export homel DATA_WORK NRTOAGLO1 2011 CO_NRTOAGLO1_20110101_PR_PF nce net luarca export homel DATA_WORK NRTOAGLO1 2011 CO_NRTOAGLO1_20110102_PR_PF nc net luarca export homel DATA_WORK NRTOAGLO1 2011 CO_NRTOAGLO1_20110103_PR_PF nc net luarca export homel DATA_WORK NRTOAGLO1 2011 CO_NRTOAGLO1_20110104_PR_PF nc net luarca export homel DATA_WORK NRTOAGLO1 2011 CO_NRTOAGLO1_20110131_PR _PF nc XKKKXKXXX Xk File 1 XKKKKXKXXX Starting STD_convprof Starting STD_read_ Prof File processed CO_NRTOAGLO1_ 20110101 PR _PF Number of profiles found in file 2271 Number of profiles with valid position time 271 STD_read_xxdata output selection of raw adjusted profi2. File net spineg export home ebrion ISAS ANALYSES ARGLV5TEST EXP_MODIF_LEST std 2010 S T_expmodlest_20100600_PR_PF nc 0 data File net spineg export home ebrion ISAS ANALYSES ARGLV5TEST EXP_MODIF_LEST std 2010 S T_expmodlest_20100600_TSG nc 0 data area 102 nb_data 0 nb_prof_tot 0 processing time 0 04 sec KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK XXXX Starting area 103 File net spineg export home ebrion ISAS ANALYSES ARGLV5TEST EXP_MODIF_LEST std 2010 S T_expmodlest_20100600_PR_PF nc 0 data File net spineg export home ebrion ISAS ANALYSES ARGLV5TEST EXP_MODIF_LEST std 2010 S T_expmodlest_20100600_TSG nc 223 data 0 data removed on type criteria Ok NCW_data_hdr Ok NCW_data_var Ok NCW_data_mult OK NCW_OA_field area 103 nb_data 223 nb_prof_tot 1614 processing time 26 75 sec KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK 42 ISAS_V5 3b PREOA processing done 8 4 log and error file for the Analysis fortran step 8 4 1 error file Run OA_20100615_PSAL OA Version 5 1 PARAM PSAL nb_area 32 Configuration files used A priori variance homel caparmor fgaillar OA CONFSTD V5C3 arglv502_ann_STD_PSAL nc Covariance scales homel caparmor fgaillar OA CONFSTD V5C3 ARV09FDS_ann_COVS nc Bathymetry homel caparmor fgaillar OA CONFSTD V5C3 bathy_GLOBAL05_v5c2 nc Parameters for optima
3. STD_list_hyd Not used yet STD_conv_raw STD_conv_raw Creates standard files from STD_read_ PR raw profiles Coriolis or user defined NC STD_read_TS files STD_read_hyd 1 Extracts valid profiles from RAW file STD_count 2 Computes depths when only pressure is STD_deph provided 3 Adds climatology mean and std profiles and checks profile against climatology and looks for spikes 4 Interpolates to standard levels STD_clim_check STD_spike_check STD_plt_err STD_vert_bins STD_vert_ext_TS STD_vert_interp 25 STD_TS_control_plot STD_PR_control_plot ISAS_MSG Var2analyse count_data NCR_OA field STD_red_list Provide a list of profiles to average none 1 looks for platforms with multiple profiles 2 tests vicinity of multiple profiles 3 defines the groups of profiles STD_red_mean Compute average profiles count_data Averages profiles from the same platform UT_prof_avg according to list provided by STD_red_list STD_read_PR STD_read_PR ISAS_MSG Reads and extracts valid profiles QC area var2analyse and time period from file FILE_raw_i STD_read_PR_data Select raw values or adjusted values count_data STD_red_list STD_red_mean STD_read_PR data Select valid data according to QC list and none fill_value Raw data are Profiles data STD_read_TS Reads and extracts valid profiles from time ISAS_MSG series files var2analyse STD_read_TS_data count_data STD_read_TS_dat
4. no 1 2 fact Variance 5 12 QC Max Mx std 1 1 Cov_max if gt 1 no oversampling test 2 11 oversample alpha fct_test If fct_test lt 10 increases error in the whole area 21 4 2 1 2 data Contains the fld and dat files created and optionnally copied by PREOA Those files will be completed by OA 4 2 2 Running ISAS_f90 The program can be run in interactive mode cd my_DIR_ANA_f90 calculateur isas_f90 OA_main lt config TEMP_2011 in It can also be launched in batch mode this allows to loop over dates and parameters The way batches are run is machine dependent Examples are given here for SGI ICE 8200 To process launch the batch with qsub my_DIR_ANA_F90 batch my_batch where my_batch is as follows and be created in the directory batch bin csh cd to the directory you submitted your job cd home1 caparmor toto OARUN myanalysis get the path for library MKL source usr share modules init csh module load intel comp 11 1 073 module load netcdf intel 3 6 3 11 1 073 date foreach year 2011 foreach month 09 10 11 foreach param TEMP PSAL export home1 toto 0A versions isas f90 V6 2 s8 0A main lt config param year month 15 in end end end At the end of the job a log message like my_batch o appears in the directory my_DIR_ANA_F90 batch It is a summary of the information written in the log files in the directoy err and log d
5. gal o LEV_SURF level of standardisation EV_SURF 0 20 Ex 37 Definition of the erro multiplicative factor for the surface processing RR_COEF 1 5 2 EH ole le le o PREOA Preprocessing ole ole ANA_AREA_LIST list of geographical areas to analyze str_listarea_ana 101 141 201 241 301 388 401 403 501 506 ole AMPL_OA time interval around date of analysis in days data from jest dtime_ana to jest dtime_ana will be used S str_dtime_ana 41 str_dtime_ana 41 QU QU Levels selected for the analysis str_deph_ana 1 no selection keep all the levels str_deph_ana 0 5 20 100 list of STD levels to analyze the closest standard levels will be selected str_dep_ana 1 o str_qcmax_ana max STD QC taken into account scale QC_interp str_qcmax_ana 4 o Instrument type excluded INST_EXCL_LIST 1 800 900 exclude XBTs of all types s INST_EXCL_LIST str_list_excl_inst 1 800 900 ole ole After PREOA copies NetCDF files on the remote computer and creates config files 1 yes o o str_copy_preoa 1 le ole POSTOA Post Processing le QU Analysis name ANA_NAME ARGLV6XX clim_ref_oa M month or clim_ref_oa Y year clim_ref_oa M Spatial filtering allowed on point with err gt err_max str_filter_errmax 80
6. globatt_init NCW _data_hdr NCW_data_var NCW_OA field PREOA _file_list Builds dates list corresponding to STD files none PREOA_append Appends new dataset to structures OAHDR and OAVAR none PREOA select none PREOA_copy_file Copies dat and fld NetCdf files created by PREOA on the remote computer Creates the config file with list of NetCDF files to use and copiesthem to the remote computer PREOA_copy_list PREOA_copy_list Copy a list of files from dir_in to dir_out none POSTOA_main 1 Collects data from all area files and saves a unique data file 2 Merge field areas to form the global anomaly Filters the field and error where error is above threshold Add to climatology and save the final global parameter fieldFilters field and error on area boundaries where error is above threshold rep_definition flddat_init NCR_data PREOA select NCW data hdr NCW_data_var NCR_OA field POSTOA filter NCW_OA field POSTOA filter Filters field and error on area boundaries where error is above threshold none 5 2 1 PREOA_main m Main function to prepare the dataset that will be used to perform the analysis over each area and for one parameter All data within the area mask and the time interval defined by date AMPL_OA are selected Two classes of files are created he temporary files fld and dat e The fld files contain the empty anom
7. Input arguments config_fname full name of the configuration file DATE_INPUT date of the analyse format dd mm yyyy dd could be equal to 0 if you consider the full month mm DAY_NUMBER number of day for the analysis STD_main input argument If you want to consider the full month mm set DAY NUMBER to 0 i_pass i_pass 1 for a strict window profile selection in order to detect suspicious one i_pass 2 for an enlarged window as the suspicious one are considered controlled and get off the raw set if needed Generally STD_main is made first with i_pass 1 The alerted profiles are controlled Then a second run of STD is made with i_pass 2 PLOT_DISP Plotting option makes figure visible or not the figure are saved anyway PLOT_DISP 0 no display PLOT_DISP 1 display Output arguments There is no output argument The standardisation is made and the standardised files are created with the name and in the directory defined in the config_fname 5 2 Pre and Post analysis PREOA POSTOA The main programs are PREOA_main and POSTOA_main PREOA_main prepares the dataset that will be used to rep_definition perform the analysis for the parameter and NCR_OA field the list of areas prescribed in the config file PREOA_file_list All data within the area area mask and the NCR_data time interval defined by date dtime_ana PREOA_append are selected PREOA select 27 PREOA_copy_file
8. an analysis of june 2010 only in the Atlantic Top from left to rigth data position and anomaly at 5m depth Bottom from left to rigth field and error at 5m depth 24 5 Matlab_isas 5 1 The pre processing of data files STD program This step reads the NetCdf files provided by Coriolis or prepared by the user according to a specific format Profiles with valid data are selected and depth is computed if not present in the file then two automatic controls are performed comparison to climatology and spike detection Points that fails the control are not used Finally the profiles are interpolated on the analysis standard levels and the final STD NetCdf files are saved The main program is STD_main m calls STD_main Main function to prepare the dataset forthe STD list PR analysis STD list TS reads Raw files and creates STD files STD_list_hyd STD_conv_raw Syntax STD_red_list STD_main config_fname STD_red_mean DATE_INPUT DAY_NUMBER i_pass rep_definition PLOT_DISP ISAS_MSG flddat_init var2analyse count_data NCW data hdr NCW_data_var NCW data mult STD list PR Builds list of raw files to read and the list of none the corresponding standardised files The files are downloaded from Coriolis database in NetCDF Argo format for daily files STD list TS Build list of Time series raw files to read and none the list of the corresponding standardised files The raw files must be in NetCDF Gosud format
9. and residuals used by all the areas e In DIR_RESU field the NetCDF file fld that contains the global 3D gridded fields and error File naming convention is as follows myanalysis YYYYMMDD_typ_PARAM nc myanalysis analysis identifier ANA_NAME in the config file YYYYMMDD analysis day if DD 00 analysis month typ identifier dat ou fld PARAM the parameter TEMP or PSAL The processing can be checked by looking at the log files and plots The log file has the following naming convention and an example is given in the annexe 8 5 postoa_mess_PARAM_yyyymmdd_Y YY YMMDDHHMMSS asc 23 where PARAM is the parameter PSAL TEMP yyyymma is the analysis date YYYYMMDD is the date when the pre processing has been run HHMMSS is the hour when the pre processing has been run The plots are stored in DIR_RUN plotisas postoa The nomenclature is postoa_myanalysis_yyyymmdd_PARAM png where myanalysis is the analysis identifier ANA_NAME in the config file yyyymmdd is the analysis date PARAM is the parameter PSAL TEMP Each plot contains four axes as shown in the figure 8 e the data position e the error e the anomaly e the final field data position 20100615 Anomaly depth 5 100 l 1 0 1 2 3 100 100 50 0 50 100 0 100 20100615 PSAL Field depth 5 20100615 PSAL Error depth 5 100 80 60 40 20 100 0 100 Figure 8 example of post processing plot from
10. climatology alpha_clim_1 2 tolerance to take into account strong stratification crit_spike_1 100 100 criteria for spike detection Example for an anlaysis of temperature and Salinity 2 check the alert plots and flag with QC 4 or 8 the data considered wrong 3 perform a second pass with high values of the criteria example in the configuration file Data rejected by the tests are not used to produce the STD files but the corresponding value might be interpolated from the neighboring valid points When all data from a profile are rejected the profile no longer appears in STD Examples for running STD Define the configuration file config_fname my_DIR_ANA confisas config_isas_ana txt Then launch STD_main config_fname dd mm yyyy nb_days ipass plot_display with the set of input argument as follow 14 E to process 10 days starting on july 14 2011 first pass dd 14 mm 07 yyyy 2011 nb_days 10 ipass 1 plot_display 1 E to process a full month ex july 2006 dd 0 mm 07 yyyy 2011 nb_days 0 or anything this value is ignored An example of perl script to run STD_main over several month and years is given in the doc directory 3 3 Outputs 3 3 1 Data files on standard levels Results are writen as NetCDF files in the directory DIR_RESU std The naming convention is as follows ST_CCCCCCCC_YYYYMMDD_PR_TT nc ST identifies STD data CCCCCCCC the dataset name
11. datacenter There must be one subdirectory per year the user have to create dir_raw and the subdirectory by year The naming convention of the raw files must follow Coriolis recommendations datasetname_yyyymmdd_PR_XX nc where yyyymmdd is the date of the measurments and XX the type of data PR for Profilers CTD dir_std this directory must be created before running the analysis It will hold the data interpolated on the analysis levels The subdirectory by year are created automatically by ISAS Figure 2 Data directories scheme 2 3 The analysis directory Figure 3 Analysis directories scheme It contains 3 subdirectories as shown in the figure 3 11 e dir_confisas e DIR_RESU e DIR_RUN Created by User This directory must be created by the user The model files found in isas doc config_matlab should be copied here and adapted to the user needs and configuration 2 3 1 Confisas directory e isas_matlab env defines the matlab path e config_isas_ana txt holds the data paths and the parameters that define the configuration This file is read by isas_mat Before starting the analysis the matlab paths need to be defined The environment is described in a file isas_matlab env that we recommend be placed in the directory confisas See isas_v6 doc config_matlab for an example To launch type cd confisas source isas_matlab env Hereafter an example of the isas_matl
12. detected during the standardisation step STD 3 Data Pre processing 3 1 Description The first step in the analysis is an interpolation of the raw data on the standard levels of the analysis grid It is partly independent of the analysis in the sense that the dataset produced can be used for different analysis A new QC is introduced it represents the quality of the interpolation the closest to a measured value the lowest the QC flag value To avoid spoiling the analysis with eroneous data a control is performed before the interpolation Finally oversampled points such as repeated fixed points CTD drifting buoys mooring can be averaged reduced into super profiles The processing is detailled below 3 1 1 Detection of erroneous data Two different tests are succesively applied Distance to climatology X A data point will be accepted if the value X verifies Xobs Xclim lt a STD 2x where e Thescalar crit_std in the configuration file has been determined empirically it defines the distance allowed to the climatology e The scalar introduces an additional tolerance relative to the climatology In the vicinity of very strong stratification perfectly good data may differ strongly from the climatology This is taken into account by introducing an additional tolerance proportional to the vertical gradient of the parameter Spike detection A data value is considered as a spike if the following conditions ar
13. field FIELD longitude latitude depth and time ERROR 3D gridded field of error define as percent variance Output arguments No output argument except a message The file is written 32 6 Optimal interpolation f90_isas 6 1 Program list area OA_main f90 Main program for Objective Analysis OA_anaarea Coordinates loop over areas OA_anaarea Analysis of a field on a regular grid for one OA_ncreaddim OA_ncreadstat OA_ncreaddata OA_covini OA_oversamp OA_calsol OA_newrite_fld OA _ncwrite dat pre OA data vector and residuals OA _ncreaddim Reads dimensions in nc file prepared by pre none OA OA_ncreadstat Reads field grid and covariances in nc file none prepared by pre OA OA_ncreaddata Reads data in nc file prepared by pre OA none OA_covini Prepares covariance matrices by computing none the distance dependent part OA_oversamp Computes weights to increase error in case of none oversampling OA_calsol Computes OA solution none X_est X_0 Koa Y Y_0 Koa C_md C_dd R 1 diag C_est R diag data_var where Y_Y_O dino X_est X_0 ana_fld diag C_est ana_var_ps OA_newrite_fld Writes analysis results in nc file prepared by none pre OA gridded field OA_necewrite_dat Writes analysis results in nc file prepared by none 7 References Brion E F Gaillard L Petit de la Vill on T Delcroix G Alory G Reverdin 2011 Collecting and griddin
14. in the configuration file If not run PREOA _creat_configin separately An example of TEMP in and PSAL in is given in the annexe 8 3 1 e A log file 8 3 2 which naming convention is as follows preoa_mess_PARAM_yyyymmdd_YYYYMMDDHHMMSS asc where PARAM is the parameter PSAL TEMP yyyymmd is the analysis date 18 YYYYMMDD is the date when the pre processing has been run HHMMSS is the hour when the pre processing has been run Warning Erase all files from previous runs in preoa directory berore running PREOA The process that copies the files on the fortran computer takes all files found in the directory files from previous runs which have not been overwritten will be taken into acount and may produce inconsistencies area 111 Figure 2 Position of data selected by PREOA to be used for analyzing one area 19 4 2 Analysis The analysis must be run on a computer with fortran compiler Netcdf library and lapack linpack The programs source must be copied from isas_f90 subdirectory into the software directory and compiled for the machine For files from the subdirectory confstd climref must be copied into a directory confstd arglv502_ann_STD_PSAL nc a priori variance for the Salinity arglv502_ann_STD_TEMP nc a priori variance for the Temperature ARVO9FDS_ann_COVS nc Covariance scales caclulated form the Rossby radius bathy_GLOBALO05_v5c2 nc bathymetrie A directory my_DI
15. 1 6 alpha_clim_1 2 crit_spike_1 100 100 le le QU le QU Pass2 crit_std_ clim _2 80 alpha_clim_2 10 crit_spike_2 2000 2000 ale ol le str_crit_std_clim_1 6 str_alpha_clim_1 2 str_crit_spike_1 100 100 str_crit_std_clim_2 80 str_alpha_clim_2 10 str_crit_spike_2 1000 1000 INT_NB_MIN Minimum number of data points for interpolating a profile INT_NB_MIN 5 Parametres for the reduction of nearby profiles str_red_opt24 1 applies 24h average of 1 level profiles RED_DXMAX maximum allowed distance km RED_DTMAX maximum allowed interval of time days str_red_qcmax maximum quality flag of interpolation taking into account to make the m average profiles str_red_opt24 1 RED_DXMAX 15 RED_DTMAX 7 str_red_qcmax 4 NPROF_ MAX Maximum number of raw profiles found to form one std file NPROF_MAX 90000 NTIMS_MAX Maximum number of raw TSG found to form one std file NTIMS_MAX 1000000 le str_plot_std Plotting option for STD no plots summary plot alert plot L FCE plot 2 plot each profile pause _plot_std 1 QU ole le le 0 1 2 3 ia t n o Specifique TSG le le FILE_LIST list of raw files to explore file txt corresponding to the list of TSG files of the DIR_RAW_ROOT_TSG ILE_LIST TS_raw_list txt QU
16. 4 1 1 Running PREOA After setting the parameters in the preoa block of the configuration file PREOA can be launched in the matlab window e config fname my_DIR_ANA confisas config_isas_ana txt e launch PREOA_main config_fname dd mm yyyy parameter plot_display An example of perl script to run PREOA_main over several months and years is given in lisas_v6 perl preoa pl 4 1 2 The output PREOA outputs are e the temporary files fld and dat for each area placed in the directory DIR_RUN preoa The fld files contain the empty anomaly filled for the area on the grid The dat files contain the data to be used by the analysis Naming convention are as follows OA_YYYYMMDD _ iarea_typ_PARAM nc OA identifier for optimal analyse YYYYMMDD analysis date iarea area number typ identifier dat ou fld PARAM TEMP ou PSAL e A copy of the dat and fld files in the data subdirectory of DIR_ OA_CALCUL if option copy_preoa 1 is set in the configuration file If not run the matlab script PREOA_copy_file separately DIR_OA_CALCUL is the directory of analysis created in the fortran computer for the analysis step It is defined in the configuration file e The files TEMP in and PSAL in that contain the list of the areas to be processed These files are created by the program PREOA_creat_configin and copied in the subdirectory config of DIR_OA_CALCUL if option creat_in_preoa 1 is set
17. Nb_data 263 Nb_ovsamp 89 fact_mult 1 00 fact_mult2 1 00 ano_max 13 727 inov min 3 563 inov max 0 830 fld min 1 742 fld max 0 006 err_min 21 487 err max 100 000 cond 0 1237E 01 cpu Analysis 0 044 ARR End area err_min_ tot 20 867 err max _ tot 100 000 cpu total area 0 380 KKKKKKKKKKKKKKKKKKKK 8 5 log file of the post processing steps gt gt gt gt gt gt gt Running ISAS_V6 POSTOA 15 Nov 2011 10 02 05 ARGLV6NRT PSAL 20110115 dir_oaf90_tmp net caparmor nas mnt data2 homel fgaillar OARUN arglv6NRT data 2011 PSAL dir_OA_ field net luarca export homel analysis_NRT arglv6NRT ISAS_RESU field 20 dir_OA_ data net luarca export homel analysis_NRT arglv6NRT ISAS_RESU data 2011 dir _clim home5 garo arivo software isas isas_ana confstd_v5c3 climref AREA_LIMITS 81 00 90 00 180 00 180 00 44 filter_err_max 80 AMPL_OA 41 0 Area 504 missing on remote computer Area 505 missing on remote computer Area 506 missing on remote computer gt gt gt gt Copy terminated in 105 067581 sec 176 area found Number of OA data 27136 Ok NCW_data_hdr Ok NCW_data_var gt gt gt gt Processing time for data 15 35 Processing time for field anomaly 55 92 Processing time for smoothing 347 15 Processing time for absolute field 76 18 45
18. R_ANA_F90 must be created for each specific analysis This directory must exist before launching preoa with option 1 for the file copying see previous section 4 2 1 Analysis subdirectory on the fortran computer The analysis directory is shown in the Figure 7 my_DIR_ANA_F90 is automatically created by the pre processing step the path and name is defined in the configuration file as DIR_OA_CALCUL Two directories have to be created by the user in the fortran computer e ISAS_F90 contains all the fortran scripts e confstd contains the annual variance and covariance and the bathymetry 20 Figure 7 post processing directories scheme 4 2 1 1 config Contains the list of area created and automatically copied here by the preprocessing step for each parameter Nomenclature is PARAM in where PARAM is the parameter analysed Theses files contains the list of NetCDF files to be processed An example is given in the annexes 8 3 1 It should also contain the configuration file for the analysis TEMP cnf or PSAL cnf created here by the user An example is shown below Provided by User TEMP home2 mycomputer user OA run CONFSTD ISASW_51_STD_TEMP nc home2 mycomputer user OA run CONFSTD ISASW_5_ann_COVS nc home2 mycomputer user OA run CONFSTD bathy_GLOBAL05_V5_0 nc 300 30021 covar_Is x yt in km km days 21 covar_ms_t in days 114 var_weigh LS MS UR 1101 X y Z t covariance dependency 1 yes 0
19. YYYYMMDD the date of observation if day 00 file contains the whole month PR identifies profile data TT the data types according to Coriolis convention 3 3 2 Listing log file The log files can be found in DIR_RUN logisas For an analysis standardization step there is two log files which names start with e std_mess the detailled logfile e std_summary the summary log file The suffix of each file name is composed of the date of the std data followed by the date of the run For example the detailled logfile for a standardisation of july 2011 running in august 2011 the 12 will be std_mess_ 20110714 20110812 asc Two examples of both log files are given in the Annexes 8 2 1 8 2 2 3 3 3 Control plots Different types of plots can be found in DIR_RUN plotisas std 15 Standard plot level PLOT_CONV 1 The nomenclature is ST_myanalysis_yyyymmdd_PR_XX png with yyyymmdd the standardisation date XX the data type PR for Profiler CTD A plot showing all profiles is produced for both Temperature and Salinity if it is the parameter aanlyzed as shown in figure 4 IvVENRT_20110100_PR_PF psal ay 1000 p 1000 1200 1200 1400 1400 1600 1600 1800 j 1800 2000 2000 5 Figure 1 Example of standard plot level High level plot PLOT_CONV gt 1 The plot shown in figure 5 shows for each analysed p
20. _135_dat_PSAL OA_20100615_136_dat_PSAL OA_20100615_137_dat_PSAL OA_20100615_138_dat_PSAL OA_20100615_140_dat_PSAL OA_20100615_141_ dat _PSAL 8 3 2 log file gt gt gt gt gt gt gt Last update STD_PRO net spineg export home ebrion ISAS ANALYSES ARGLVSTEST EXP_ MODIF _LEST STD_TIMSER net spineg export home ebrion ISAS ANALYSES ARGLV5TEST EXP_MODIF_LES1 PREOA net spineg export home ebrion ISAS ANALYSES ARGLV5TEST EXP_MODIF_LES1 preoa nb area 41 nb_std 5 param TEMP File dates 20100500 ne nc nc nc nc nc nc nc nc nc nc nc nc nc nc nc nc nc nc nc ne nc nc nc nc nc nc nc nc nc nc nc Running ISAS_V5 3b PREOA 30 May 2011 14 18 32 std std ISAS_RUN 41 20100600 20100700 20100800 20100000 File types PR_PF TSG XXX X Starting area 101 File net spineg export home ebrion ISAS ANALYSES ARGLV5TEST EXP_MODIF_LEST std 2010 S T_expmodlest_20100600_PR_PF nc 7 data File net spineg export home ebrion ISAS ANALYSES ARGLV5TEST EXP_MODIF_LEST std 2010 S T_expmodlest_20100600_TSG nc 278 data 0 data removed on type criteria Ok NCW_data_hdr Ok NCW_data_var Ok NCW_data_mult OK NCW_OA_field area 101 nb_data 285 nb_prof_tot 3281 processing time 33 55 sec KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK KK KKK EK x xx Starting area 102
21. a e STDVAR structure of data of the file fnam_data e STDQC structure with QC and DCref information reduction of the read file 5 3 2 NCR_OA_field m Reads parameter field and coordinates from nc file Function lon_ana lat_ana dep_ana param_OA pct_var NCR_OA_field file_nc_OA PARAM list_level ilim jlim Input arguments e file_nc_OA full name of the file to be read e PARAM parameter name PSAL TEMP optional arguments e list_level list of depth levels to be read absent read all the depth levels 30 0 read only the coordinates 1 read all the depth levels n read depth levels from 1 to n else read depth levels listed in list_level e ilim min and max latitude to be read if absent all the latitude domain is read e jlim min and max longitude to be read if absent all the longitude domain is read Output arguments e lon_ana longitude read in the field file e lat_ana latitude read in the field file e dep_ana depth read in the field file e param_OA data read corresponding to the parameter PARAM e pct_var variance percentage corresponding to the parameter PARAM 5 3 3 NCW_data_hdr m Write headers metadata and their atytributes in data file that is created here msg_error NCW_data_hdr ncfile_name GLOB_ATT STDHDR Input arguments e ncfile_name the full name of the file to be created e GLOB_ATT global attributes structures e STDHDR structure with metadata and global attributes
22. a Select valid data from TimeSeries Nc file none according to area and QC list STD_read_hyd Not used STD_count counts valid profiles and redefine flags none STD_deph Compute depth when only pressure is NCR_OA field provided by interpolating the depth pressure profile of the nearest grid point of the climatology STD clim_check Check each profile against climatology using the standard deviation Eliminated data are flagged 4 none STD_spike_check Check spikes in each profile The spike test looks for 1 a significative change in the sign of the first derivative 2 high values of the second derivative normalized Eliminated data are flagged 5 none STD_plt_err Plot and save error plots none STD_vert_bins Averages the data into bins centered on STD UT_vert_bin 26 levels STD_vert_ext_TS Extrapolate the TSG data from the level of none measurement up to the surface STD_vert_interp Interpolate profiles when nb_data points gt none NB_INT_MIN Flags the data according to interval betwen data points Increase error by a factor sqrt QC STD_control_plot_PR Control plot for profiles none STD_control_plot_TS Control plot for time series none 5 1 1 STD_main m Main function to prepare the dataset for the analysis reads Raw files and creates STD files Syntax STD_main config_fname DATE_INPUT DAY_NUMBER i_pass PLOT_DISP
23. ab env file usr bin sh setenv MATHOME net triagoz export homel matlab matlab_last setenv TOOLBOXPATH net triagoz export homel matlab outils_matlab m_mapl 4 setenv MATLAB MATHOME tayuh set path MATLAB path Configuration ISAS setenv ISAS_ANA HOME homel toto lulu prog_ISAS svn trunk matlab_isas setenv ISAS_ANA_ PATH ISAS_ANA HOME functions ISAS ANA HOME tools echo Toolbox ISAS ANA svn OK setenv MATLABPATH ISAS_ANA_PATH TOOLBOXPATH Furthermore the various paths of the analysis the file names and the different parameters must be defined This is done through the configuration file config_isas_ana txt that we recommend be placed in the directory confisas An example of configuration file is given in isas_v6 doc config_matlab and is reported in the annexe 8 1 12 2 3 2 Results Directory DIR_RESU This directory contains the analysis results in two subdirectories e field contains the 3D field and error on the regular grid e data contains the data used by the analysis and the residuals 2 3 3 Directory of calculation DIR_RUN This directory contains the analysis run information in subdirectories e preoa contains the pre processed fields ready to be read in the analysis step e logisas contains the log files e plotisas contains the plots created during the runs e alert contains the alert lists of suspicious profiles
24. ality control QC was performed QC was performed good data QC was performed probably good data QC was performed probably bad data QC was performed bad data The value was changed as a result of QC Interpolated value The value is missing o QU o o o o ole L O1 amp WNEF le QU ole QC_TS flags ok Temp and Psal QC_ZP flags ok Pres and depth QC_XY flags ok Position and date Temporarilly two sets char for Argo num for TSG uses also error max to select data QC_TS 125 QC_ZP 0 125 QC_XY 0 125 QC_TS_num 1 2 5 QC_ZP_num 0 1 2 5 QC_XY_num 0 1 2 5 o oP ol le LA RR_MAX_PRES 20 RR_MAX_TEMP RR_MAX_PSAL 1 He ti ole Parameters for profiles controls Criteria for comparaison with climatology and spike detection The processing is performed in two passes so 2 values are proposed The maximum deviation realtive to the reference climatology is defined y crit_std_clim that sets the number of standard deviations allowed for climatology comparison alpha_clim that add a tolerance to take into account the strong stratifications crit_spike that sets the number of standard deviations allowed for spike detection Number of ae O oP a de AP oP AO 36 QU value depending on the number of variable analysed le le Passl recommended values for TEMP and PSAL parameter analysis crit_std_clim_
25. aly fields for the area on the grid e The dat files contain the data to be used by the analysis Syntax PREOA_main config_fname DATE_EST PARAM PLOT_DISP Input arguments e config fname full name of the configuration file e DATE_EST date of the analyse format dd mm yyyy e PARAM parameter to be pre processed PSAL TEMP DOXY PLOT_DISP 0 no display PLOT_DISP 1 display 28 PLOT_DISP Plotting option makes figure visible or not the figure are saved anyway Output arguments No output argument The pre processing is made Pre processed files are created with the name and in the directory defined in config_fname 5 2 2 POSTOA_main m The area files created by PREOA and completed by the analysis OA are processed to form global fld and dat files POSTOA_main e Collects data from all area files and saves a unique data file e Merges field areas to form the global anomaly A smoothing of the areas boundaries can be made where error is above a specified threshold Finally the anomaly is added to climatology to form the final field of the analyzed parameter Syntax POSTOA_main config_fname DATE_EST PARAM PLOT_DISP Input arguments e config fname full name of the configuration file e DATE_EST date of the analyse format dd mm yyyy e PARAM parameter to be pre processed PSAL TEMP DOXY e PLOT_DISP Plotting option makes figure visible or not the figu
26. alysis dates and parameters e models of batch and config files for the fortran part all files defining the standard configuration and statistics used by the analysis Gaillard 2011 2 1 3 Matlab scripts matlab_isas Provided by ISAS Contains the matlab scripts for version nn used for the data pre processing and the analysis pre and post processing 2 1 4 Fortran programs f90_isas This directory contains the source codes A makefile and executable for SGI Altrix is provided Although isas_f90 is part of ISAS chain it has to be copied in the fortran computer tree structure see 4 2 1 CO 2 2 The data directories 2 2 1 The datasets We briefly describe here the characteristics of the data types taken into account at the moment These dataset have different accuracy resolution and sampling that depend mostly on the sensor and on the storage and transmission system used Temperature and salinity measurements are obtained from autonomous instruments drifting or anchored or from instruments deployed with a ship The data are transmitted in real time by satellite or in delayed mode The main characteristics of the most common instruments are given below 2 2 2 Profiling floats The autonomous floats are part of the ARGO program they collect vertical profiles of temperature and salinity as a function of pressure between their maximum pressure usually 2000 dbars and the surface At the end of the profile that takes nea
27. arameter most of the time Salinity and Temperature the data standardized red and the raw data blue CO ST 0040701 RLA 1798588 p mbetet pe 40 H e0 F BOK XK KEM XK EK KM Q a T x Xy i 80 L F 1000 4 wet 1200F ki 7 a ape 1400 F 1600 1800 F i 4 2000 a z 180 o Figure 5 example of high level plot The red cross are the data standardised the blue one 16 represents the raw data Alerts When data points are excluded a plot is created in the directory alert std Figure 6 The profile reference is added to the list in the directory alert list Eror clim or spike lat 36 67 lon 179 42 doret 18557376 platt 2900550 tAz Error clim or spike lat 7 19 lon 28 83 doret 18117261 platt 6900596 t A 1 Figure 6 example of alert plots Temperature and salinity data points in blue climatology in black corrected standard deviation criteria as dashed line In red the points excluded by the climatology test and in green the points excluded by the spike test The plot title gives the DC reference of the profile 17 4 Analysis 4 1 Preprocessing PREOA PREOA select the data that will be used to perform the analysis over each area All data within the area mask and the time interval defined by date AMPL_OA are selected At this stage data might be excluded on the instrument type criteria INST_EXCL_LIST
28. ccident E 33 Ge PUN INE ES eeii nenna ai eadera aaa aaa aa bation aa eaaa aiaa aia aa aeaa E Eaa SEa ERE 34 8 1 CORTE ADAM OL ES tee ae ae Pen et E TE E E aye Sennen 34 8 2 log files of the standardisation step enssosseeeseeseessessoessesseessersessssssessesssessensorssrssensoessesseesee 39 8 3 output files of the pre processing step eesereeseeessessressessessreserssenseesorssenseeserssseessseessseesssees 41 8 4 log and error file for the Analysis fortran step eseseseeeessessessssssesseesoessesseessesseeseessesseessseee 43 8 5 log file of the post processing SOS ennemies 44 1 INTRODUCTION ISAS In Situ Analysis System is an analysis tool for producing gridded scalar fields At the moment it is set to process temperature and salinity Originally designed for the synthesis of ARGO dataset it has been tested for the first time on the POMME area in the North East Atlantic in 2000 it was later extended to the Atlantic and the Global ocean as the Argo array was setting up It is developed and maintained at LPO Laboratoire de Physique des Oc ans within the Argo Observing Service SO ARGO where it is used for research purposes on ocean variability ISAS is made available to the Coriolis datacenter for exploitation in operational mode The analysis is performed on the datasets prepared by Coriolis according to Argo recommendations for data quality control and NetCDF format A set of background and statistical informat
29. e A ISAS Tool Version 6 User s manual E Brion F Gaillard Rapport LPO 12 01 Laboratoire de Physique de Oc ans UMR 6523 Auteur Mise a jour Date F Gaillard Cr ation du document V4 beta 03 02 2007 R Charraudeau V4 00 Version fran aise 23 11 2007 F Gaillard V4 01 Version fran aise 11 02 2008 F Gaillard V4 1b English version 19 03 2008 F Gaillard Minor corrections 25 09 2008 F Gaillard V5 1 18 06 2009 E Brion V6 beta 10 06 2011 F Gaillard V6 05 01 2012 Table of Contents 1 INTRODUCTION susie asc pale lees a ee ao a E om aon DeatAGN 7 2 General presentatiO Minerin crane ican eo er Ore 8 2 1 ROT By ae TOR datent amino 8 2 2 The HE CN na notons 10 2 3 Theanalysis AO nissan nn dis 11 2 Data Pre proces SIO renion E E NA nae TE T EEAO 15 AR DECO admire are aera RAR eee 13 3 2 PAINE SUD isesi aaea academe 14 Sh NS en aan ao One el in idee 15 Ce a a li ae 18 4 1 Preprocessing PREOA tue ne tm to E 18 ae a ie aca aes esl cn leo nn 20 4 3 Post Processing POS PUA haine nent 23 PAU BET LE RC dS me er E re a E eee 25 5 1 The pre processing of data files STD Progra s n0scseserevacesaneiesssasnseumanweniaerevectanannmavnaiens 25 5 2 Pre and Post a alysis PREOA POS TOA Joerie eneen aaisa 27 DEE EO E E E E E E E Sti rene Sereno E E eer dede 29 6 Optimal interpolation 190 ER ni a e ee a eS 33 6 1 Propran Se anne ec nt oc EEE ERSTES 33 7 EE E nt a
30. e filled e Change of sign of the first derivative for at least one point before or after the point 13 e Second derivative criteria normalized by the median in the vicinity of the point 2 6 P SZ median z gt crit _ spike SZ 3 1 2 Interpolation The high resolution data are bin averaged on the standard levels then the remaining levels are interpolated new Quality Code QC is set to the data related to the interpolation quality The more the initial data is close to the interpolated one the better the QC is To eliminate interpolated pointd which sem too far from the measurement levels one can select the str_qcmax_ana level see PREOA part in the configuration file 3 1 3 Reduction superobs Data from the same platform which are close in time and space are averaged The control parameters defined in the configuration file are RED DXMAX Minimum distance in kilometers RED_DTMAX Minimum time difference in days RED QCMAX maximum QC flag after standardization 3 2 Running STD After setting the parameters of the STD block in the configuration file STD_ main can be launched in the matlab execution window STD files may remain on a daily sampling or data within a month can be grouped The climatological tests can be applied at two levels The recommended procedure is 1 perform a first pass with rather strict parameters crit_std clim _1 6 distance allowed to
31. etailed in the following 4 2 3 Outputs 4 2 3 1 err Created by ISAS Contains a short log file with the list of processes files and any error message issued by the 22 program This file must be screened carefully to check that the processing has ended normally An example is given in the Annexes 8 4 1 The log file contain statistical information on the processing for each area and each level of analysis An example is given in the Annexes 8 4 2 4 2 3 3 data files The analysis results are stored in the directory data with the fld and dat data files that now contain the gridded anomaly fields and corresponding error and the data residuals respectively 4 3 Post Processing POSTOA During this last part of the processing the program concatenates all processed areas and datasets It also convert anomalies to absolute values The files are read in DIR_OA_CALCUXL here my_DIR_ANA_F90 data and results are written in DIR_ANA_RESU here DIR_RESU 4 3 1 Running POSTOA POSTOA is launched with the same arguments as PREOA In the matlab window e config_fname my_DIR_ANA confisas config_isas_ana txt e launch POSTOA_main config_fname dd mm yyyy parameter plot_display An example of perl script to run POSTOA_main over several month and years is given in the doc directory 4 3 2 Outputs The results are saved in two files e In DIR_RESU data the NetcCDF dat file that contains the data
32. file nine std_summary 20110701 _20111109102322 lt lt lt lt lt lt Final number of profiles per type lt lt lt lt lt lt before time space reduction after reduction lt lt lt Nfound NokST NnoZ Nalert N_pstd NS NT NST Total lt gt 9494 9471 12 5 9459 0 236 8826 9062 ST_arglv6NRT_20110700_PR_PF nc lt gt 1635 1426 131 1 1295 0 10 250 260 ST_arglv6NRT_20110700_PR_ CT nc lt gt 2796 2796 0 0 2796 0 55 395 450 ST_arglv6NRT_20110700_PR_MO nc lt gt 113857 36266 0 0 36266 0 535 2048 2583 ST_arglv6NRT_20110700_PR_TE nc 8 3 output files of the pre processing step 8 3 1 List of area processed example with a PSAL in data 2010 PSAL log 2010 PSAL config PSAL cnf 32 OA_20100615_101_dat_PSAL OA_20100615_103_dat_PSAL OA_20100615_105_dat_PSAL OA_20100615_106_dat_PSAL OA_20100615_107_dat_PSAL OA_20100615_109_dat_PSAL OA_20100615_110_dat_PSAL OA_20100615_111_dat_PSAL OA_20100615_112_dat_PSAL OA_20100615_113_dat_PSAL OA_20100615_115_dat_PSAL OA_20100615_116_dat_PSAL OA_20100615_117_dat_PSAL OA_20100615_118_dat_PSAL OA_20100615_120_dat_PSAL OA_20100615_ 122 dat _PSAL OA_20100615_ 123 dat _PSAL OA_20100615_ 124 dat _PSAL OA_20100615_125 dat _PSAL OA_20100615_ 126 dat _PSAL OA_20100615_127_dat_PSAL OA_20100615_129_dat_PSAL OA_20100615_130_dat_PSAL OA_20100615_131_dat_PSAL OA_20100615_133_dat_PSAL OA_20100615_134 dat_PSAL OA_20100615
33. g complementary in situ SST SSS data for the calibration and validation of SMOS Article in the Newsletter Mercator Coriolis april 2011 Brion E F Gaillard 2011 ISAS Tool Version 6 programs Rapport LPO Brion E F Gaillard 2011 ISAS Tool Version 6 User s manual Rapport LPO 33 Gaillard F 2011 ISAS Tool Version 6 Configuration Rapport LPO Gaillard F E Autret VThierry P Galaup C Coatanoan and T Loubrieu 2009 Quality control of large Argo data sets JOAT Vol 26 No 2 337 351 Bretherton F R Davis and C Fandry 1976 A technique for objective analysis and design of oceanic experiments applied to Mode 73 Deep Sea Research 23 1B 559 582 Charraudeau R and F Gaillard 2007 ISAS_V4 Mise en place de la configuration Rapport LPO 07 09 88 p 8 ANNEXES 8 1 Configuration file ole QU Configuration file for ISAS V6 F Gaillard LPO Ifremer E Brion LPO CNRS QU QU QU ole Attention no space within lines unless necessary ol ole Language EN or FR LANG En Metadata information for NC files DATA _SET YYYYYYY INSTITUTION XX IFREMER PROJECT_NAME MyP rogName DATA _MANAGER YOU SOURCE ISAS V6 Q fo ole ole Directory and file names for standard configuration ol ole Configuration files Climatology STD areas o
34. ion required to complement the observations are provided with the software as part of the configuration For each analysis date the results are provided in two NetCDF files one holding the data and analysis residuals the other holding the gridded fields and estimation error expressed as percentage of a priori variance This document describes how to implement the ISAS software The main steps of the process are detailed and examples of configuration files are provided The statistical method used to produce the estimate and the specific choices performed to implement the method are described in the Method and Configuration document corresponding to the appropriate ISAS version 2 General presentation Producing a gridded field with a large dataset downloaded from a datacenter as Coriolis requires several preliminary operations before being able to perform the analysis Two main tasks have been identified 1 Definition of the configuration files that include bathymetry area limits and masks as well as climatology mean state and associated variance They are provided in the defined confstd directory 2 Preprocessing of the data files to perform elementary checks and interpolates the data on standard levels This is performed by the STD function The analysis optimal interpolation itself is divided in 3 elementary operations e PREOA preparation of files and assembly of the datasets needed by the analysis e OA Optimal interpola
35. l estimation Large scale covariance x y t 300000 0 300000 0 30 0 Meso scale covariance t 30 0 Variance weights LS MS UR 1 0 2 0 6 0 Covariances used x y Z t 1101 Factor multiplying apr var 1 5 qc_max mx_std 5 12 Oversampling cov_max alpha fct_test 0 98000 2 00 11 0 Analysis name 0A_20100615_101_dat_PSAL Analysis name 0A_20100615_103_dat_PSAL Analysis name 0A_20100615_105_dat_PSAL Analysis name 0A_20100615_106_dat_PSAL Analysis name 0A_20100615_107_dat_PSAL Analysis name 0A_20100615_109_dat_PSAL Analysis name OA_20100615_141_dat_PSAL 4 50828230381012 8 4 2 log file Example for the file OA_20100615_101_dat_PSAL log 43 HN Area 101 Nb_profiles 285 Nb_level 152 Nb_analysis points nlon nlat 71 90 Nb_Bathy points nlon nlat 720 545 OA_anaarea statistics OK OA_anaarea data OK cpu distance calculations 0 068 Level 1 Nb_ana_points 3240 Nb_data 272 Nb_ovsamp 89 fact_mult 1 00 fact_mult2 1 00 ano_max 16 123 inov min 3 747 inov max 0 837 fla min 1 733 fld max 0 005 err min 20 867 err max 100 000 cond 0 1230E 01 cpu Analysis 0 052 Level 2 Nb_ana_points 3240 Nb_data 263 Nb_ovsamp 89 fact_mult 1 00 fact_mult2 1 00 ano_max 14 609 inov min 3 551 inov max 0 841 flid min 1 720 fld max 0 007 err_min 21 434 err max 100 000 cond 0 1092E 01 cpu Analysis 0 048 Level 3 Nb_ana_points 3240
36. le IR_CONFSTD net toto export homel arivo software isas isas_ ana confstd_v 5637 nam_clim arglv502 nam_std arglv502_ann_STD nam_bathy bathy_GLOBALO5_v5c2 nc RAW DATA Raw data directory and files prefix for profiles Coriolis files DIR_RAW_ROOT_PRC net mymachine export home1 DATA_WORK NRTOAGL01 PRF_RAW_PRC CO_NRTOAGLO1_ Raw data directory and files prefix for profiles User files hydro or profilers SDIR_RAW_ROOT_PRU net mymachine export homel DATA_WORK NRTOAGLO1 34 o ao ole iw le Raw o o CP en tof o le S ole le O PRFE_STI T IR_STD D RF_RAW_PRU CO_NRTOAGLO1_ Raw data directory and files prefix for time series TSG IR_RAW_ROOT_TSG net toto export homel SOERE CTDO2 TSGRecherche NRTGV2_nc data directory and files prefix for time series buoys RA data directory and files prefix for time series moorings RA V_ROOT_TSB Y_ROOT_TSM DATA STD data directory and files prefix for Profiles _ROOT_PR net mymachine export homel std_data_NRT isasv6xx_PR PRF_STD Prefix for std files D_ PR ST_isasv6xx_ STD data directory and files prefix for TIMESERIES J IR_STI PRF_STI D_ROOT_TS net mymachine export homel std_data_NRT isasv6xx_TS D_TS ST_isasv6xx_ Analysis o OUD O oe Directory for 90 computer TR_OA_CALCUL net ca
37. les Variable psal Nb raw profiles QC ok 127 Nb elements QC ok 16063 Nb adj profiles QC ok 144 Nb elements QC ok 11293 Variable temp Nb raw profiles QC ok 125 Nb elements QC ok 16253 Nb adj profiles QC ok 146 Nb elements QC ok 11497 Variable pres Nb raw profiles QC ok 125 Nb elements QC ok 16255 Nb adj profiles QC ok 146 Nb elements QC ok 11518 the variable deph does not exist STD_read_Prof end Number of profiles with valid S T data good QC and no NaN 271 39 distribution per type S 0 Te S T 264 Number of profiles without deph before 271 Number of profi distribution per type S 0 les with valid S T data Tete ly Number of profiles with std alert S Number of profiles with valid S T data distribution per type S 0 Interpolation on std_levels a caer A S T 264 0 Le 20 S T 264 Number of profiles with valid S T data good QC and distribution per type S 0 T 7 S T 264 271 profiles CPU time total seconds 87 84 CPU read 0 36 deph 26 62 STD check 533 KKKKKKKK File 2 KaKKKKKKK after 0 good QC and good QC and no NaN 271 no NaN 271 no NaN 271 83 Stdlev 34 01 Starting STD_convprof Starting STD_read_Prof File processed CO_NRTOAGLO1_20110102_PR_PF Number of profiles found in file 12592 Number of profiles with valid position time 252 8 2 2 summary
38. of a standardised file or of a fld analysed file Output arguments No output argument except a message The file is completed 5 3 4 NCW_data_var m Writes data of the variable PARAM in data file Used after NCW_data_hdr that creates the data file Function msg_error NCW_data_var ncfile_name PARAM STDVAR Input arguments e necfile_name full name of the file to be completed File created by NCW_data_hdr e PARAM parameter to be written PSAL TEMP e STDVAR structure with the data of the file ncfile_name for the parameter PARAM Output arguments No output argument except a message The file is completed 31 5 3 5 NCW OA field m This function creates and write the fld NetCDF files These files contains fields 3D grid time lat lon and the time Function msg_error NCW_OA_field OA_filename PARAM GLOB_ATT longitude latitude depth jul_rel FIELD ERROR Input arguments OA_ filename Full name of file to be created PARAM parameter TEMP PSAL TPOT SIGO TEMP_STD PSAL_STD GLOB_ATT structure setting the global attributes longitude Vector of longitudes its length defines the longitude dimension latitude Vector of latitudes its length defines the latitude dimension depth Vector of depth its length defines the depth dimension jul_rel Julian day referenced to the Reference Date Time read in the standardised file most of the time 01 01 1950 FIELD 3D gridded
39. parmor nas mnt data2 homel you OARUN arglv6XX Directory for Analysis results and logs TR_ANA_ALL net mymachine export homel analysis_NRT isasv6xx TR_ANA_RESU net mymachine export homel analysis_NRT isasv6xx ISAS_RESU TR_ANA_RUN net mymachine export homel analysis_NRT isasv6xx ISAS_RUN ole str_area_limits 81 90 180 180 ole STD Standardisation TYP_LIST List of file types to process TYP_LIST PR_CT PR_PF PR_TE PR_XB PR_MO PR_BA STYP_LI GREY_ I le oe U H EH x W H H w mP ro tO u u o al doko Q H E A A ST PR_PF PR_CT PR_MO PR_TE b R 7 R R an IST_STD model_greylist txt Definition of default measurement error associated with each file type used if no error information is found in the file R 0 03 R 0 05 R 0 01 R 0 R 0 203 lt 01 35 R 0 01 R 0 002 RR 0 02 PR_MO_E PR_BH_E TS_TS_E RI RI month_grp 1 all data within a month are grouped no group 0 month_grp 1 Variables to analyse lower case VAR psal temp Variables to analyse specific to timeSeries lower case VARtimser ssps sstp QU o use_adjust 1 use adjusted value if exist else 0 use_adjust_PR 1 use_adjust_TS 0 o Datacenter QC used o o Datacenter QC are the following No qu
40. re are saved anyway PLOT_DISP 0 no display PLOT_DISP 1 display Output arguments No output argument Post processed files are created with the name and in the directory defined in config_fname A control plot is saved in the directory ISAS_RUN plotisas postoa 5 3 Tools These matlab programs are used in each of the three steps standardisation pre and post processing They are sorted in alphanumerical order rep_definition flddat_init var2analyse count_data NCR_OA field NCW _data_hdr NCW_data_var NCW_data_mult 29 NCW_OA field UT_vert_bin 5 3 1 NCR_data m Select usefull data read in STD files or dat files Used in PREOA_main and POSTOA_main m Function STDHDR STDVAR STDQC NCR_data fnam_data PARAM iopt_nan pltnum jlim tab_msk lat_msk lon_msk Input arguments e fnam_adata full name of the file to be read e PARAM parameter name PSAL TEMP e iopt_nan If iopt_nan is set to 1 the program replaces fill_value with NaN optional arguments e pltnum platform number character If pltnum 0 no platform selection e jlim time limits in julian days e tab_msk geographical mask of the considered area only sea 2 only land 0 sea and land 1 e lat msk latitudes of the considered area e lon ms longitudes of the considered area Output arguments e STDHDR structure with metadata and global attributes of the file fnam_dat
41. rly 5 hours the profiler transmits the data to a satellite and dives toward its parking depth 1000 dbars waiting for the next cycle 10 days later Nominal accuracy of the data is assumed to be 0 01 C and 0 01 PSU At present time a vertical profile is described by approximately 100 pts XBT An eXpendable BathyThermograph is launched from a steaming ship It measures temperature and salinity in the case of XCTD The measurement depth is deduced from the XBT fall rate The accuracy is 0 1 C and most XBT reach 800 m CTD This high quality measurement is obtained from a research vessel in the context of a scientific cruise Pressure and temperature sensors are carefully calibrated and water samples are taken to adjust the salinity measurement Standard procedure were defined for the WOCE experiment they lead to accuracies of 0 001 C and 0 001 PSU Time series Time series of pressure temperature and salinity are recorded at high time resolution hours from sensors installed on fixed points mooring or drifting buoys The sensors are similar to those used on the profiling floats The thermosalinographs installed aboard scientific or commercial ships are another type of time series data The sensors are different from profiling floats ones Depth measurement is usually constant The directories Two directories are defined as shown in Fig 2 10 dir_raw contains all raw data downloaded from the Coriolis Provided by User
42. tion or analysis e POSTOA assembly of the final files The various files and programs are organized as indicated in Figure 1 Note that STD PREOA and POSTOA are writen in matlab while OA is in fortran 90 The directories and Configuration files 2 1 The software directories These directories contains all programs and files required to perform the analysis It is organized as follows Figure 1 Program directories scheme 2 1 1 Configuration directory confstd The configuration proposed with ISAS V6 is described in detail in Gaillard et al 2011 The horizontal grid is 2 degree Mercator limited to 80S 90N The vertical levels are given in the Table 1 Standard levels m i 10 300 820 20 2000 Table 1 vertical standard levels The directory confstd contains all files defining the standard configuration and statistics used by the analysis Gaillard 2011 It is organised as follow in the directory climref o Bathymetry o Climatology annual and monthly for the parameter PSAL and TEMP o A priori variances annual for the parameter PSAL and TEMP o Covariance scales annual deduced from rossby radius calculated from the climatology areadef o Definition for analysis areas and masks 2 1 2 Documentation directory doc Provided by ISAS This directory contains e the programs documentation pdf files e models of configuration files for matlab scripts and perl script that allow to loop over different an
Download Pdf Manuals
Related Search