SELMATER User Manual
Contents
1. window For time series you can only extract observed data Fig 16 5 9 3 The Output directory This is used to describe the directory where the extracted files are to be loaded It is possible to copy all the extracted files in one directory or to keep the same directory tree than the one of the CD ROM If the output directory does not exist the software creates it IM amer March 2001 22 Fig 15 SELMATER Output window for vertical profiles 3 output formats available data observed or interpolated to standard levels SelMater Ea County Ship Parameten Fig 16 SELMATER Output format for time series Only MEDATLAS output format and observed data are available FP mer March 2001 23 5 10 Running the Extraction Two possibilities are offered either the extraction of data and plotting of the positions or the simple plotting of the positions Once all the selection criteria and the output description are entered press the Extract button to run the plotting and the extraction of data from the MATER CD ROM or the Position button to run only the plotting of data from the MATER CD ROM In both cases the displayed screen during the extraction is the geographical map Fig 17 the number of extracted files and stations are respectively displayed in the fields Selected files and Selected stations The location of2. Direction de la Technologie Marine et des Syst mes d Informations Auteurs Mich le FICHAUT Michel LAROUR Gilbert MAUDIRE 30 mars 2001 SISMER R INT TMSI SISMER ISIB SIS 01 042 SELMATER DATA SELECTION FROM THE MATER DATA BASE SUMMARY 1 INTRODUCTION 3 2 SUPPORTED PLATFORM 4 3 INSTALLING AND RUNNING THE SOFTWARE 4 4 GETTING STARTED 4 5 USING THE SOFTWARE 6 5 1 The Map window souder in en kd ann erre vio va d ea 6 5 1 1 Zoom Shore line and 6 5 1 2 Geographical selection 6 5 1 3 Modification of the selection 7 Soc Resule kouraa tad alee a 8 5 2 Data Type window 1 8 5 3 The Cruise WiINdOW s s ssssseussnenneununennunnnnnnununnnnunnnnnnnnnnnnn unane nnna 11 54 The Time wIndOW ue rrocenicunde sca xuch ce cas rue ito autunno 12 5 5 The Country WINAOW vuusivmvusuins vaasa via uida au wan vau 13 5 6 TNE SHIP WIBOOW vaasan 14 5 7 The Parameter window cernere 15 56 The Flag WINAOW iussisti ava vus res
3. buttons Add level and Remove level At least two standard levels are reguired to perform the interpolation calculation If some levels are added they are automatically ordered gt The button Extrapolate at first standard level surface must be checked only if the first standard level is near the surface It gives the possibility for extrapolating the first upper level when there are data between the second level and the surface or at the second level but not at the first level In that case the surface value is assigned to the first observed value if the corresponding depth do not exceed the second standard level IM amer March 2001 21 This possibility allows to do not reject the profiles for further computations like the geopotential if the observations begin near the surface For example with respectively 0 and 5 dbar as standard levels and no data at 0 dbar an observed value at 3 dbar will be assigned at 0 dbar However if no data exists above 5 1 dbar the two first levels will keep the default value The surface extrapolation requires to have selected at least two standard levels gt If the button is not checked no extrapolation is made at the upper level The button Extrapolate at first standard level surface is checked by default when you start SELMATER software When you want to extract data interpolated to standard levels you must only keep the data flag to good through the Flag
4. selection button is not pressed there will be no selection on the ship The list on the left hand side contains all the ship referenced on the CD ROM sorted by alphabetic order of their codes in fact the two first characters of the ship code are the country code so the ship are sorted by countries On the right hand side is the list of the ship you have selected You can add or remove ship from the list you want to keep in the output files by using the right add and left remove arrows or by double clicking in the lists In the example below all the cruises from the AEGAEO will be selected Map Data type Cruise Time County Ship Parameter Flag Output Visu Ship selection Available Keep in output files POSEIDON 364E AEGAEO 29DB ODON DE BUEN 29GD GARCIA DEL CID 28HE HESPERIDES 35EU EUROPE 35GP GEORGES PETIT SUROIT TETHYS II URANIA Fig 11 SELMATER Ship window Selection of data collected from the AEGAEO IM amer March 2001 15 5 7 The Parameter window This window is to perform selection on the measured parameters to be selected Fig 12 It is only available for Vertical profiles data First click the Parameter selection button to validate or invalidate parameter criterion If the Parameter selection button is not pressed all the parameters will be selected The list on the left hand side contains all the parameters codes name
5. the geographical criteria If the Geographical selection button is not pressed there will be no geographical selection 5 1 1 Zoom Shore line and Bathymetry The background of the map can be modified by zooming and displaying the bathymetry On the left hand side of the map use the al Zoom out EN Zoom in button for zooming The shore line the 200 and 1000 isobaths and the selected stations can be added or deleted from the map when clicking on the corresponding buttons on top of the map 5 1 2 Geographical selection There are two ways for creating a geographical area e by drawing the area with the mouse on the screen after clicking on the e button by entering manually the coordinate and then press the Create button The input format for the latitude is N S99 99 99 and for the longitude E W999 99 99 in degrees minutes and hundreds of minutes Fig 4 4 March 2001 It is possible to create several geographical areas SelMater v v Fig 4 SELMATER Map window 5 1 3 Modification of the selection FECI diiit County Ship paramere M 2 P ner March 2001 Fig 5 Modify a geographical area You can modify an area by re sizing it with the mouse or by changing manually the coordinates and then press the Modify button Fig 5 You can delete an area by selecting it with the mouse and then press the Del key on your keyboard 5 1 4 Result Two count
6. the stations are drawn on the map as the extraction progresses During the extraction and the plotting it is possible to use the Zoom buttons SelMater x Map Data type Cruise Time Country Ship Parameter Flag Dutput Visu Gesaraphicallselection Shore line v 1000m v 200m F Stations Limits Selected files is _ Selected stations 71 amp san stations n Fig 17 SELMATER window during the extraction Pressing the Cancel button aborts the extraction If you need to do another selection you can delete all the previous criteria IM amer March 2001 24 by pressing the Clear button Everything is deleted from all the windows except the output directory of the Output window cce Coo D 5 11 The Visu window This window is used to visualize the vertical profile data that have been extracted from the CD ROM Fig 18 20 and 21 This window is divided into two sub windows gt Data sub window used to described and select the data you want to plot Fig 18 gt Graph sub window used to plot the selected data Fig 20 21 and 22 5 11 1 The data sub window i SelMater X Map Data type Cruise Time Country Ship Parameter Flag Output Visu Data Graph Data Directory Cruise c tmpenl MTPII MATER CNL 4PR96 MTPII MATER CNL
7. APRS N MTPII MATER CNL APR98 MTPII MATER CNL AUGS x Min MTPII MATER CNL JANS TEMP MTPII MATER CNL 8 MTPII MATER CNL JUL96 Max Ss MTPII MATER CNL JUNS MTPII MATER CNL JUN98 MTPII MATER CNL MARSB MTPII MATER CNL MAR38 MTPII MATER CNL MAYS6 Y Min ka MTPII MATER CNL MAYS MTPII MATER CNL1 JUN96 Fig 18 SELMATER Visu window Data sub window 5 11 1 1 Selecting the data The data directory is the directory where are the vertical profiles to plot The files to be plotted must be at the MEDATLAS format You must IM ner March 2001 25 select the directory by using the button Once you have selected the directory you need all the cruises found in it are listed in the cruise list You need to select at least one cruise that you want to plot in the cruise list You can select several cruises in the list using the Shift key of your Key board for consecutive selection or Ctrl key of your key board for non consecutive selection Fig 19 MTPII MATER CNL APR36 MTPII MATER CNL JUN97 MTPII MATER CNL1 JUN96 Fig 19 Non consecutive cruise selection with the Ctrl key and consecutive cruise selection with the Shift key m mer March 2001 26 5 11 1 2 Selecting the parameters to plot The X and Y parameters of the graph can be selected in a list using the down black arrows By default pressure is given as the Y parameter but it can be replaced by any others from the lis
8. OPHYLL 4 2 MICRON FIL CHLOROPHYLL 4 20 MICRON FI CPHL CHLOROPHYLL TOTAL milliarz DARK CARBON ABSORPTION DFCw NUMBER OF SW DINOFLAGELL DOPW DISSOLVED ORGANIC PHOSPH DOX1 DISSOLVED OXYGEN ml l DOX2 DISSOLVED OXYGEN micromole DOXY DISSOLVED OXYGEN millimole r DTCw NUMBER OF SW DIATOMS 10 DXAP DIADINOXANTHINE rilligram mz EFTw DISSOLVED CFC11 ERROR 4 EF2w DISSOLVED CFC12 ERROR 4 EF3w DISSOLVED CFC113 ERROR gt CORG DISSOLVED ORGANIC RON E Fig 12 SELMATER Parameter window Selection of vertical profiles containing Temperature and or salinity and or dissolved oxygen in ml l If you need the files containing Pressure AND Temperature AND Salinity AND Dissolved oxygen in ml l check the Select stations which contains ALL the selected parameters button 5 8 The Flag window This window is to perform selection on the quality of the MATER data to be selected This option is important to allow any processing on the data with no detected anomalies QC flag 1 In the MEDATLAS format the quality flags are found at three different levels e In the station header to qualify the Time Latitude Longitude and Depth of the station e In the station header to qualify the global quality of the profile and the global quality of one parameter in the profile e Inthe data to qualify each data point M remer March 2001 17 MEDATLAS flag scale i
9. aa Gras a 16 5 9 our HE 19 5 9 1 The Output Format 19 5 9 2 The O tput type eee re po En eee e TOR 20 5 9 8 The Output directory once eor avi 21 5 10 Running the 55 udin tremit edes ta Qu sa dE Gu 23 5 11 The VISU WING OW iaceret vede sta taret cu ome a enu a aa Raak 24 5 11 1 data nnne nnne nnn nnns 24 5 11 2 The graph 26 5 12 Printing or the MAD iecore ron np Tq feri ici SN SUD PE Ue 28 6 REFEBENGCES 28 f remer March 2001 1 Introduction The MATER CR ROM is an electronic publication of the data collected in the Mediterranean sea in the frame of the MAST III MTP I MATER project A software to extract data from the CD ROM and to store them on the user computer is also included on the medium This software SELMATER can select data according to several criteria e data type Vertical profiles of CTD Bottle XBT Current profilers and Time series of Current meters Thermistor chains Drifting buoys Sediment traps measured parameters quality flag period year month date geographical location ship source cou
10. d the CD ROM the following window is opened Fig 1 IM amer March 2001 O x Copyright MATER GROUP 2001 5 inside Fig 1 Window which is automatically opened when reading the MATER CD If you click on Documentation you will open the HTML documentation about the CD ROM if you click on Data extraction you will run the SELMATER software which allows to perform data extraction from the CD ROM It opens the following windows Fig 2 SelMater 1al SelMater ELS Engish CRB inside Fig 2 First window of the SELMATER software M remer March 2001 If you click on the language you want to use the first screen of the software is opened 5 Using the software The different choices proposed to the user are presented as tabs on the screen Fig 3 Cruise Time Country Ship aramee Flag Output Visu Fig 3 Tabs of the SELMATER software All the tabs and buttons will give you the different possibilities for selecting and extracting the data Click on the tab you need to open the corresponding window Before performing any data extraction it is necessary to define at least the data type and the output directory On most of the buttons of the windows a context help is available 5 1 The Map window This window is to perform geographical selection of the data Fig 4 First click the Geographical selection button to validate or invalidate
11. e e Flag equal to 1 good or 5 modified during the QC for Time Latitude and Longitude of the stations e Any values for the quality flag of the bottom depth of the stations e Any values for the Global profile and Global parameter quality flags e Flag equal to 1 good for the measured parameters SelMater ale all Di E ele Fig 14 SELMATER Flag window for time series Selection on the parameter flags or the data flags is not allowed In the example of Fig 14 the time series data selected will have e Flag equal to 1 good or 5 modified during the QC for Time Latitude and Longitude of the stations e Any values for the quality flag of the bottom depth of the stations e Any values for the Global profile quality flag FP mer March 2001 19 5 9 Output window This window is used to describe the output of the selection from the CD ROM The Output format The Output type observed levels or interpolated to standard levels gt The Output directory The output window is different for vertical profiles and for times series More possibilities are available for selection of vertical profiles Fig 15 than for selection of time series Fig 16 Before executing the extraction the output format the output type and the output directory MUST be entered The MEDATLAS format and observed data as output type are the default values 5 9 1 The Output Format For vertical pr
12. ers give the number of selected files and stations This counters are updated as the extraction progresses 5 2 The Data Type window This window is to perform selection on the data type you must first select either Vertical profiles or Time series to run the selection Fig 6 Map Data type Cruise Time Country Ship Parameter Flag Output Visu Water bottles stations CTD stations Bathythermographs Current profilers eg ADCP Fig 6 SELMATER Data type window If only the Vertical profiles button is pressed all the vertical profiles data types will be selected If you want to select only some of the vertical profiles data type click on the button s corresponding to the data type you want to select If only the Time series button is pressed all the time series data types will be selected If you want to select only some of the time series data IM amer March 2001 type click on the button s corresponding to the data type you want to select On the following example only current meters time series will be selected on the CD ROM Fig 7 SelMater x Map Data type Cruise Time Country Ship Parameter Flag Output Visu C Vertical profiles Time series Sediment traps Surface drifters drifting buoys Neutrally buoyant floats Thermistor chains Fig 7 Selection of current meters time series The data types match the different senso
13. ntry cruise name or cruise identifier The data can be extracted at the observed levels or at interpolated standard levels Under three different formats which are either the MEDATLAS format or a simple CSV format with separator which can be easily included in a spreadsheet or Ocean Data View format to be able to include the selected data into the ODV software Schlitzer 2000 Schlitzer 2001 In addition SELMATER allows to visualize the vertical profiles Further information about the cruises the data sets the MEDATLAS format and the quality checks applied beforehand to the data can be found on the html documentation of the CD ROM IM amer March 2001 2 Supported platform The SELMATER released with the MATER CD Rom is supported on the following environments Microsoft Windows 95 Windows 98 Microsoft Windows Millenium Hardware and software requirements for these supported platforms are Processor Pentium 266 or above AMD K6 or above Memory 2 Mb minim 64 Mb recommended Display SVGA 256 colors minimum Additional device CD Rom drive 4 x speed minimum 3 Installing and running the software No installation is required To run the software insert the MATER CD Rom in the CD Rom drive Remark If after a minute the SELMATER first windows is not displayed try to run the autorun inf file manually double click on this file in the windows Explorer utility 4 Getting started When you rea
14. ofiles you can choose between 3 output formats Fig 15 gt MEDATLAS format auto descriptive ASCII format see the html documentation for a complete description gt CSV Comma Separated Values format a simple format with semicolons separator which can be easily included in a spreadsheet umn number ME 7 First parameter Na Flag of the first parameter DATLAS flag scale N ParameterN N 1 Flag of parameter N MEDATLAS flag scale gt ODV Ocean Data View text format to be able to import the extracted data into the ODV software which is available for Windows on the CDROM IM amer March 2001 20 Content ruise name tation number ta type for CTD XBT or B for Bottle tation date titude ongitude ottom depth ii essure ag of the pressure irst parameter poo ag of first ODV flag scale Column number F tri IA S Z e Jg MS 5 g Jg lt 02 6 arameter Tj lag of parameter N The ODV flag scale is the following 0 Good 1 Unknown 4 Questionable 8 Bad For time series only the MEDATLAS output format is available Fig 16 5 9 2 Output type For vertical profiles the observed data can be extracted from the CD ROM or the data can be interpolated to standard levels Fig 15 The default standard levels are those defined in the MEDATLAS climatology but it is possible to add or to suppress some levels using the
15. rs which are Seno Vertical profiles Water Bottle stations Ho Bathythermographs BT m3 ADCP vertical profes Time series Sediment trap Current meters including ADCP time series Surface drifters Neutrally buoyant float IM amer March 2001 10 Thermistor chains H72 IM amer March 2001 5 3 11 The Cruise window This window is to perform selection on the cruise name or on the cruise reference Fig 8 First click the Cruise selection button to validate or invalidate the cruise criterion If the Cruise selection button is not pressed there will be no selection on the cruise name or reference The selected cruises will be the cruises which contain the characters of the cruise name or the cruise reference fields The cruise reference is the MEDATLAS format reference of a cruise A cruise names list can be accessed by clicking on the button In this case the Cruise name field is considered as a filter pattern to compute the list if the character is used For example MTPII MATER CNL in the field asks the program to list the cruise name beginning with MTPI MATER CNL The character can only be used at the end of the character string SelMater E ZN x Map Data type Cruise Time Country Ship Parameter Flag Output Visu Cruise selection Cruise name MTPI MATER CNL C Cruise reference C
16. ruise chooser MTPII MATER CNL 4PR96 i MTPII MATER CNL APRS MTPII MATER CNL APR98 MTPII MATER CNL AUGS MTPII MATER CNL JANS MTPII MATER CNL JAN98 MTPII MATER CNL JULS6 MTPII MATER CNL JUN36 MTPII MATER CNL JUNS MTPII MATER CNL JUNSS MTPII MATER CNL MTPII MATFR PNI MARJR zl Cruise chooser s n tee Ce Fig 8 SELMATER Cruise window Selection of data from the MATER CNL cruises IM amer March 2001 12 5 4 Time window This window is to perform selection on the time period or the month of the starting date of the vertical profiles or the time series of the MATER CD ROM Fig 9 First click the Period and or the Month buttons to validate or invalidate the criteria If the Period and the Month buttons are not pressed there will be no selection on the time period of the stations If you want only the profiles or time series starting during 1996 enter 01 01 1996 in the From field and 31 12 1996 in the To field On the following example all the profiles or time series starting in January and March will be selected Map Data type Cruise Time Country Ship Parameter Flag Dutput Visu Time selection Period v Month 02 04 05 06 08 08 10 El aie Fig 9 SELMATER Time window Selection of all the data from January and March A combination of the two criteria is possible
17. s and units referenced on the CD ROM On the right hand side is the list of the parameters you want to extract You can add or remove parameters from the list you want to keep in the output files by using the right add and left remove arrows or by double clicking in the lists As Pressure is the vertical reference it is a mandatory parameter to select and you cannot remove it from the selected list At the screen bottom there is an additional button Select stations which contains ALL the selected parameters which means e if this button is checked the extraction will select the files which contains ALL the selected parameters together else if this button is not checked the files which contains any combination of these selected parameters will be extracted this is the default option In the example below all the files with Pressure AND Temperature AND OR Salinity AND OR Dissolved oxygen in ml l will be selected IM amer March 2001 16 i SelMater x Map Data type Parameter selection Available CHLT CHLOROPHYLL TOTAL milligram 4 CICW NUMBER OF SW CILIATES 10 CO2W DISSOLVED CARBON DIOXYD COCW NUMBER OF SW COCCOLITHO Cruise Time Country Ship Parameter Flag Output Visu Keep in output files PRES SEA PRESSURE sea surface 0 TEMP SEA TEMPERATURE Celsius degre PSAL PRACTICAL SALINITY P S U DOX1 DISSOLVED OXYGEN ml l CPH3 CHLOR
18. s the following Value Signification No Quality Control Correct Inconsistent with statistics available climatologies Questionable spikes False out of regional scale vertical instability Modified during the QC for the headers only date latitude longitude and depth 6 7 8 Not used 9 No data default value The Flag window is not the same for vertical profiles or time series data For vertical profiles Fig 13 selection can be made on all the type of guality flags of the MEDATLAS format whereas for time series Fig 14 selection can be made only on the flags concerning the station header e g on latitude longitude date and depth of the time series and the global guality of the profile SelMater X Map Data type Cruise Time Country Ship Parameter Flag Output Visu Quality flag selection Station Header Flags to keep Time HOr ea mik ME GI Gi fl v Latitude at il lee Ea EA kS es lee B Longitude 1 E2 E3 Bis fee Ez fag Depth T pr Global Flags to keep Profil IS Pr ME Parameters morei I r v Data Flags to keep boo bene me ma bie me Fig 13 SELMATER Flag window for vertical profiles Selection is allowed all the quality flags of the MEDATLAS format IM amer March 2001 18 In the example of Fig 13 the data selected will hav
19. t 5 11 1 3 Defining the scale of the graph The Min and Max field can be used to fix the minimum and maximum values of X Y parameters if you do not want to use the default ones which are equal to the minimum and maximum X and Y values in the whole selected data set PRESSURE must be entered with negative values 5 11 2 The graph subwindow Once the data you want to plot have been selected you can access to the graph sub window Fig 20 The first time you enter this window nothing is plotted you have to use the buttons on the right hand side of the screen to perform the plot The signification of the buttons is the following If this button is pressed superposed plotting of the profiles when pressing 31 This is the default option If this button is pressed waterfall plot of the profiles when pressing Fi In that case you must defined the shift from one profile to another This shift is given into the parameter unit Fig 21 and gt 22 You can also add the station numbers on the plot Fig Initial plot FP ner March 2001 27 Fig 20 SELMATER Visu window Graph sub window In this example the profiles are superposed You can see on this graph that Pressure is given in negative values for the plotting the values in decibars in the files are multiplied by 1 P nei March 2001 28 Fig 21 SELMATER Visu window Graph sub window In this example the profiles are in a wa
20. terfall plot with 1 CELCIUS degree shift on the X scale and 20 decibars Shift on the Y scale SelMater X Map Data type Cruise Time Country Ship Parameter Flag Output Visu Data Graph 394 8 s ri 5 Shifting in parameter unit x 1 Y 20 F Stations Fig 22 SELMATER Visu window Graph sub window In this example the profiles are in a waterfall plot and the station numbers are plotted also The Zoom In button has been pressed It is possible to use the horizontal and vertical scroll bars to see all the profiles 5 12 Printing of the You can print the map by pressing the Printer button on window The map is printed on the default printer It is just a draft print corresponding to a snapshot of the map displayed on the screen No option are available for printing 6 REFERENCES SCHLITZER R Electronic Atlas of WOCE Hydrographic and Tracer Data Now Available Eos Trans AGU 81 5 45 2000 SCHLITZER R Ocean Data View htto www awi bremerhaven de GEO ODV 2001 er March 2001
21. you can select all the profiles or time series starting in January and March 1996 IM amer March 2001 5 5 13 The Country window This window is to perform selection on the country originator of the MATER data Fig 10 First click the Country selection button to validate or invalidate the country criterion If the Country selection button is not pressed there will be no selection on the country The list on the left hand side contains all the countries referenced on the CD ROM sorted by alphabetic order of the country names The GF3 country codes used in the MEDATLAS format are also given in the list On the right hand side is the list of the countries you have selected You can add or remove countries from the list you want to keep in the output files by using the right add and left remove arrows or by double clicking in the lists In the example below all the cruises from France and Spain will be selected Map Data type Cruise Time Country Ship Parameter Flag Output Visu Country selection Available Keep in output files Fig 10 SELMATER Country window Selection of data collected by French or Spanish institutes IM amer March 2001 5 6 14 Ship window This window is to perform selection on the ship from which the MATER data were collected Fig 11 First click the Ship selection button to validate or invalidate the ship criterion If the Ship
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