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1. l 7 e 8 e THUNEN Woo Digitalization sponsored 43 by Thunen Institut TASA OISCAUNGS SAS afg ICES STATUTORY MEETING 1993 6s Grnek C M 1993 C 17 ar Fisshersi pad SKAGEX ATLAS a software package for the presentation of results of the International Experiment in Skagerrak 1990 1991 by 5 Marek Ostrowski The Institute of Oceanology PAN Sopot ul Powstancow Warszawy 55 i Poland ABSTRACT The Skagerrak International Experiment SKAGEX was carried out in the Skagerrak Kattegat in the period of 1990 1991 It involved four field surveys with up to 17 vessels performing simultaneous oceanographic measurements at sea The resulting data set covers a wide range of environmental parameters from hydrography to marine chemistry and biology It comprises results from more than 2000 oceanographic stations with samples being taken at multiple depth levels In order to make this huge dataset easy accessible to all scientists participating in the experiment a software package has been written that integrates functionality of a database with the presentation methods typical for o oceanographic applications such as XY charts sections time plots and horizontal distributions maps This presentation based on the user s manual of the SKAGEX Atlas demonstrates its basic features and gives examples of its use in studies on synoptic scale variability in Skagerrak and Kattegat It indicates also in what ways the use of this softwar2. one example of its use will be shown on the poster session during the ICES meeting Ostrowski at all 1993 However the import facilities are not yet documented neither sufficiently tested for their inclusion in the next release of the SKAGEX atlas package References Ostrowski M Danielssen D S Svendsen E Application of the SKAGEX Atlas package in studies of long water mass variability along a section in Skagerrak The poster to be displayed during the theme session Computers in Fishery Research the ICES Meeting 1993 Dublin About this version of Skagex Atlas Version 3 of the SKAGEX ATLAS is based on the results from the experiment downloaded from ICES database in January 1993 The data are subdivided into the four following categories SKAGEXI with 1586 stations from 18 May to 25 June 1990 SKAGEX II with 127 stations from 10 to 17 September 1990 SKAGEX III with 98 stations from 12 to 20 January 1991 SKAGEX IV with 299 stations from 17 to 20 May 1991 In contrast to previous versions there is no separation into chemical and physical datasets all data relevant to a selected station are accessible in the same database The field structure for each database is given below Depth Temperature ee Salinity aD Potential temperature Density Potential density Oxygen Phosphate Phosphorus Silicate Nitrate Nitrite Ammonia Nitrogen Chlorophyll A Installation l The package runs on PC machines with pr
3. the given reference level If the requested level is Not present than a value interpolated linearly from the two neighbouring layers is taken instead When all data points are found the result is sent to SURFER to be interpolated onto an evenly spaced grid and the result of that is plotted in terms of isolines The position of the grid on the map its size and few other parameters necessary for the proper definition of the interpolation process are stored i in the so called region file The file with settings adjusted for the Skagerrak region named SKAG REG is already prepared on the home directory of the atlas package Fig 8 This file must always be assigned to inventory window before a map can be produced ASSIGN REGION command The MAKE command triggers the map creation process There are two variants of this command MAKE FOR ALL produces one map for all oceanographic stations selected to the inventory window MAKE FOR EACH instead makes a separate map for each line from the selection window Suppose that during the selection stage the following lines have been entered ll Rec 296 01334 90 0S 26 01 00 0 7 90 05 28 20 00 0 06 00 E o3 00 E 10 00 12 00 E 58 30 N B 30 N 58 00 N 58 00 N s7 30 N 30 N 57 00 H 57 00 H S8 30 N 38200 2 N SSNAN 3 5 00 N Fig 8 Ship positions of all the stations occupied in Skagerrak between 26 and 28 May 1990 The rectangle surrounding the select
4. the transect picture in centimetres or forces a constant number of kilometres per centimetre Step sets the distance between neighbouring descriptions in the selected units On the depth axis the units are always i in meters The grid item selects the number of grid points along the horizontal and depth axis respectively Higher values usually produce more exact results but calculation takes more time The Depth column has also min and max entries for selecting the minimum and maximum depth of a transect and a break option which tells at what depth the vertical scale should change To obtain the upper 100 meters of the water column enlarged five times one should set break to 100 and rate to 0 2 If break is set to 0 no change i in scale occurs In the third column min max and step items set a minimum a maximum and a step between isolines of a selected variable correspondingly The err relative error item has the meaning only when minimum curvature method is selected otherwise it is ignored MAP menus The MAPS menu provides tools and methods for the construction of horizontal distributions of environmental variables from stations present in the inventory list The process begins with so called slicing operation The user selects via RANGES REFERENCES command the reference variable usually the depth The database engine program from the atlas package fulfils the request by browsing all oceanographic stations inside the inventory window at
5. these variables is made through the SELECT AXES command SETUP CHART sets options for axis orientation line style etc The plot can be stored in SURFER compatible format STORE PLOT SECTIONS menu This menu provides methods for the creation of vertical section or time plot along the route or within the time span from the inventory list The order of stations to be plotted will be the same as that of the inventory and should be designed during the data selection stage There is no limitation to one ship sections only Time depth diagrams are also possible if the selection is confined to one station at different dates Selection of the variable for transect and interpolation method is made through the SECTIONS menu Vertical axis is always set to depth the horizontal axis can be either time or distance Interpolation is done by the SURFER package and the result is written to a file In the case of sections of the best results seem to be obtained when using the minimum curvature interpolation method Before triggering interpolation MAKE command one should select a variable to display SELECT VARIABLE command and set appropriate ranges Figure 7 shows the layout of the selection form which appears in response to the RANGES command Fig 7 Transect selection form The form is arranged i in three columns the first for the horizontal axis second for the vertical and the third showing selected variables The item scale selects the size of
6. 9 5 7 33 3 11008 5 57927 2 18053 0 4B 3 LATAN TRT TTAN TT TEAL Fig 2 The selection window with SELECT menus in the foreground The first step in the data selection is the choice of the relevant database Make your choice by pressing i Alt F8 or Alt e followed by D and pick the appropriate item from the list in fig 3 The VARIABLE command will show a list of variables from the selected database tet There are cases when the order of stations on inventory list has to be different from that of the database In the databases all data are sorted by the ship name than subsequent stations increase with time This order may be altered by selection of one of the options available on the SORT ORDER selection list The following orderings are provided time longitude latitude latitude than longitude longitude than latitude longitude than time latitude than time longitude then latitude than time latitude then longitude than time 2 3 5 7 E na 3 Al E Gd M meh Fig 3 Selection of database from the selection window n PIES SHE ORULENTR EL pr atermstien en the program 3 ae g i See eae 7 38 3 17 83 5 52 27 18 34 0 Fig 4 A dialog for selection of ship time span and geographical range To complete the selection one must also specify a time span a rectangle in geographical space and the names of ships which are to be included in the search You can construct
7. compound queries by chaining several rectangles and time periods to the one list Suppose that one wants to select the data collected by all participating ships on May 27 1990 By pressing or Insert button fig 2 a new dialog window appears on screen fig 4 The asterisk i the min minimal field symbolises selection of all stations regardless of heir position in the ae ship coordinates To specify a particular date one should alter the value in the Date min field The date is entered in the inverse order year first than month and day There must be exactly three pairs of digits per entry each pair being separated by any character symbol you wish Thus 900527 90 05 27 90 05 27 are all legal whereas 90052 is not The same holds true for Time and Lon Lat longitude latitude entries There always must be six digits denoting in the case of time hours minutes and seconds and in the case of geographical position degrees minutes and tens of a minute The max fi elds may stay blank By setting them one selects a date time of the day longitude or latitude ranges for the selection rather than single values Valid ship names for this version of SKAGEX atlas are ARGOS HUMBOLDT ATAIR HYDROMET TISELIUS J HJORT A VEIMAR L TITOV DANNEVIG OCEANIA G O SARS SIEDLECKI THORSON SVANIC MOSBY _ BRAARUD All must be in capital letters Two remaining objects from the input form are included to limit the search to oceanographic stations t
8. e may be extended to other oceanographic datasets Introduction The international marine experiment in Skagerrak SKAGEX was conducted in a series of field surveys between May 1990 and May 1991 During each survey scientist from nine nations from boards of the research vessels were conducting an extensive programme of the in situ sampling that included hydrophysical chemical as well as _ biological parameters One of the main aims of SKAGEX was the recognition of the time variations of the Skagerrak Kattegat water masses in the short synoptic scales In accord with that a regular sampling programme covering carefully selected net of stations was being carried out once in every three days There was eight main sections spanning the Danish Swedish and Norwegian coasts beginning from the whereabouts of the Laso Island in the East towards the western most section extending i into the North Sea domain On all sections the vessels operated simultaneously with spacing between the stations in i the range of 5 nautical miles In addition to that in particular during the SKAGEX I May June 1990 other ships not involved directly with sampling on the sections were collecting samples at additional locations bringing the total number of ships at sea during the most sampling intensive days to the 17 The observations were also made in the days between the obligatory sections The was no detailed scheme of investigation during the
9. een of Skagex atlas amas showing WINDOWS menus in the renani and information window in the background Work with the atlas i is subdivided into the three distinct stages e data selection stage 1 e processing stage e presentation of results The databases of the atlas contain almost all physical and chemical data available from the SKAGEX experiment The access to the required portion of this dataset is possible by definition of a time span geographical range and ship name data selection stage Selected data are then processed as horizontal distributions maps transects and time depth plots processing stage In most cases results of processing are stored to files and to examine the result one needs to call the appropriate viewing or printing function after the processing result presentation Data selection stage As the first step in an attempt to access the SKAGEX dataset one must select the variables time span and location for the data For making selections the atlas provides a special selection window To activate this window you need to press Alt F9 or select the QUERIES NEW INVENTORY command from the main menu A window will appear on the screen fig 2 It has its own menu bar with two menus SELECT and FILES a list box where you can see your selections and four buttons Insert Moa Delete and Span ihtiar Se v 5 a ie 7 SS SSS LA TINUS dod BEES sa 57933 8 11931 5 57 32 3 11 26 0 572932 0 111
10. hat meet certain conditions The item Query type specifies the relation of the selection to the variables If all recs condition is in effect all data sets will be included regardless of the values set in the variable box F8 key On selected vars only the stations with the checked variables present are included during the search On Non missing condition only those stations and selected variables are included that have no missing values embedded inside their datasets Records condition limits the search to a chosen record range from the currently active database When it is blank all the database content will be searched When selection is done retum to the selection window is accomplished by clicking either the Ascending or Descending button The first forces forward the second backward order of the resulting inventory list The new selection is appended to the list that occupies the central part of the selection window A bar running across this list shows in inverse an item currently selected The selected item can be deleted or modified by clicking the appropriate button fig 3 Pressing the Open button or P letter on the keyboard terminates data selection and triggers the search for selected stations in the database The first and immediate result of this search is a list of oceanographic stations matching the selection Only the stations from this list called hereafter the inventory provide the data for subsequent processing To av
11. he others the front most one There are several types of windows but most of them have these things in common e atitle bar e aclose box e a window number 1 to 9 The close box of a window is the box in the upper left corner Click this box to quickly close the window Or choose WINDOW CLOSE or press Alt F3 The title bar the topmost horizontal bar ofa window contains the name of the window and the window number You can drag the title bar to move the window around The zoom box of a window appears in the upper right corner of a data window If the icon in that comer is an up arrow you can click the arrow to enlarge the window to the largest size possible If the icon is a doubleheaded arrow the window is already at its maximum size In that case clicking it returns the window to its previous size To zoom a data window from the keyboard choose WINDOW ZOOM or press F5 Data windows also return to the unzoomed state following each call to the database engine or graphic routines A window number i is displayed in the upper right border You can make a window active and thereby bring it to the top of the heap by pressing Alt in combination with l the window number For example if selection window LEGS MQR window is 5 but has got buried under the other windows Alt 5 brings it to the front Scroll bars are horizontal or vertical bars that are visible on the bottom and right sides of an active data window You use these bars with a mo
12. ion limits the region in which maps will be plotted The region shown here has been defined in the file SKAG REG and displayed on screen using VIEW ASSIGNED REGION option from the MAPS menus 900604 900506 900607 900609 The first line stands for selection of all vessels in the database between 4th to 6th June 1990 whereas the second between 7th and 9 June When this query is sent to the MAKE FOR ALL command thanonly one map with averaged results from all casts from 4th to 9th June will be made The MAKE FOR EACH command will create the two separate synoptic maps of both periods respectively This command is very convenient when large number of maps to show synoptic variability is required The query file LEGS MQR provides the selection of stations allowing for creation of the maps covering all SKAGEX I The maps are made in two forms as isoline plots and colour raster maps displayable on the computer s screen None of these are shown after the interpolation One must use one of the commands from the CHARTS menus on the main menu bar to display the results on the screen or plotting device FILE menus SAVE and SAVE TO commands allow to store the current state ofan inventory window into a selection file MQR Next time such a file is loaded all the assignments and setting applied to this window so far will be restored The GET REC command copies parameters of the oceanographic station pointed by the selection bar to the prog
13. l datasets available between 26 and 28 05 1990 900610 800812 000002 2358S8 os 00 e PEKEE 58 00 N 57 00 N aa 08 00 E 10 00 E Hitrate at Depth 30 sS Fig 14 Distribution of nitrates interpolated from all datasets available between 10 and 12 06 1990 15 The program will than show in colours the horizontal distribution of interpolated parameter on top of the contour map of Skagerrak Pressing the space bar moves to a new distribution Fig 13 and 14 show a sample distributions of nitrates at the depth of 30 meters obtained when a driver file NO3 30 LGT is used in the dialog box from fig 14 Windows management Windows Most of what you see and do in the program manager happens i in a window A window is a screen area that you can open close move resize and overlap You can have up to nine windows open in the program manager but only one window can be active at any time The active window is the one that you re currently working in Any command from the local menu bar you choose or text you type generally applies only to the active window If you have the same query open in several windows the action will apply to the file everywhere that it s open You can spot the active window easily It s the one with the double lined border around it The active window always has a close box in the upper corner If your windows are overlapping the active window is always the one on top of all t
14. ocessors 80286 or higher All programs and data take about 12 MB memory on your hard disk The package can be executed even on small notebooks provided that there is enough conventional memory more than 560 KB and a numeric processor is installed To install the package insert the disk labelled 3 not 1 into floppy drive log onto that drive and type UNPACK X where X stands for the letter of your hard drive The decompressing utility UNZIP EXE will ask you to change installation diskettes three times more The atlas creates a path SKX on the root directory of your hard drive To run it one should change to this path and type the command SKX Always run SKX program from this directory The atlas program uses a large portion of conventional memory during execution and its is not safe to run it from within the memory resident utility suchas Norton Commander or XTPRO The package behaves correctly under Microsoft Windows 3 1 only when is executed in full screen mode The new version of the Atlas similarly to older ones requires the SURFER package Golden Softw are 5 ver 4 0 1989 If this product is not present or not registered the program issues the following waming Error during initialisation invalid item PRN To register SURFER go to OPTIONS DIRECTORIES and type in its proper path Basic operations and screen layout The main screen of the atlas consists of the top menu bar from where commands are selected and the statu
15. oid repetition of selection each time the data are requested they should be saved to a file before the data search FILES SAVE command lets you save the selection asa file with extension MQR To load that selection again press F9 or use QUERIES OPEN command from the main menu Data processing stage x The stations conforming to the selection condition are returned in the inventory window which occupies the same position on the screen as th former selection window from where the search was called The window displays a list of selected oceanographic stations The horizontal bar points toa record arene selected Ane 2 oe 7 33 0 11231 5 57 32 3 1126 8 7 32 0 34 19 5 57231 3 11008 5 57027 9 19 54 0 Fig 5 Inventory window with station selection for database SKAGEX I vessel Oceania date 27 05 1990 with SHIP TRACK menus in the foreground All data processing operations are relevant to the displayed selection of stations The following operations are available Viewing the map of positions of all the stations included in the selection SHIP TRACK menus Viewing the station s data as numbers on the screen RECORDS menus Plotting two selected variables simultaneously RECORDS menus Storing station data to a file RECORDS menus Making a vertical section of a variable along the path along all stations from the inv entory list SECTIONS menus Creating a map at chosen depths for a selected variable MAP menus St
16. ong the Oceania route on 27 05 1990 13 wee 997 OE EN ere r ee aor nce y OE 1 1 an n 7 5 Fig 11 Distribution of nutrients along the r v Oceania route on 27 05 1993 The plot was retrieved from the file OCNO3275 PLS using VIEW SECTIONS command from the CHARTS menus The maps created through the MAKE FOR EACH command cannot be found on the current directory Instead the program creates a subdirectory with the user given name and a special driver file with the extension LGT All maps resulting from this command are put to that directory being given numeral file names increasing with the order of their creation i e 001 PLM 002 PLM To view sucha collection on the computer screen give the name of the proper driver file in VIEW DISTRIBUTIONS dialog accessible from RESULTS menus on the main menu bar Fig 12 NNN NIN ANY WES ote 57733 0 11 32 5 57032 3 57032 0 57 38 3 changes UME ALES ESO ERENCE ISG PER SER ECRE SSL LG Fig 12 The dialog box for displaying the colle mh ich will be displayed with lowest value on the colour scale and Step sets the threshold value before color 11928 0 1194955 11008 5 10 54 0 ection of maps The item Min se 14 e value which _ 300526 800528 000001 235958 06 00 E ne 10 00 E 22 00 E s8 00 N 4 08 00 E 10 00 E Nitrate at Denth 30 Range Fig 13 Distribution of nitrates interpolated from al
17. oring current settings of inventory window variable selection plot axis choice etc to MQR file SHIP TRACK menus This menu displays on the map the positions of ships included in thei inventory list The picture can be stored to a file in the SURFER compatible format and used as hard copy STORE command Rec 884780875 90 05 27 06 00 0 90 05 27 22 00 0 08 00 E 12 00 E 58 30 N 58 30 N 57 30 N 30 N S7 00 H S7 00 H sain 08 00 E 08 00 E 10 00 E 12 00 E Fig 6 Ship s track of Oceania on 27 05 1990 The result of SHIP TRACK VIEW command RECORDS menu The record menus provides operations on a single oceanographic station selection The station is selected by moving a selection bar up and down the inventory list To view data in the numeric form press the VIEW DATA command The STORE DATA command allows you to store the data from a selected station in a text file The command OPTIONS MISCELLANEOUS from the main menu affects the output by forcing an appropriate separator between the numbers and a symbol replacing missing data values To obtain the file in CSV format compatible with popular spreadsheet packages one should select a comma as delimiter The VARIABLES command selects variables for output those unselected will not appear on the output PLOT command displays a picture containing two X Y plots for any combination of variables accessible in the database Selection of
18. ram clipboard from where they can be retrieved into another selection window on the screen Presentation of results The results of transects and maps are stored in files under names given by the user The group of maps created via MAPS MAKE FOR EACH commands are accessible through a special driver file with extension LOG To display on the screen or to plot a single map or transect use the commands from CHARTS menus on the main menu bar Each of the commands from this menu asks for the file name of an item produced during the data processing stage and starts appropriate plotting routine The help 12 system invoked by pressing F1 when CHARTS menus has been selected gives detailed instruction on how to use these commands Fig 9 EAK ISIE os 2 oD 4 z OO ae EN ais ror E i Fig 9 The CHARTS menus with the help information on PLOT TRACK command displayed in the right bottom corner If the ship track from fig 6 was used to create a vertical section of nitrates along Oceania route from 27 05 1990 and the result is stored under the name OCNO3275 PLS then to have this result displayed on the screen select VIEW SECTION command and pick this name from all files with th extension PLS Fig 10 Fig 11 shows the resulting plot AG Pad Do OST EF US nS ob oP PM je x 3 CEs am a RSDR ATNI Lowen Fig 10 Selection of the file OCNO3275 PLS containing the section of nitrates al
19. s line at the bottom showing names of several keys used for accessing some of the commands immediately In the centre of the screen a window is displayed with information on hydrographic stations during SKAGEX You can zoom that window by pressing F5 drag it around the screen shrink or expand and close remove from the screen The WINDOWS menu on the top bar does operations on windows but most of these functions can be accessed faster by using so called hot keys Names of hot Pe keys are listed to the right of the appropriate command from the menu bar For example to close a window OTN you should press Alt F3 To access the main menu press F10 or hold Alt key while pressing the focused letter of an item you are going to select To quit the program press Alt X or go to the SYSTEM EXIT menu command on the top menu bar This version of the program is provided with the context sensitive help system which can be invoked by pressing F1 Fig 1 shows the main program screen of the atlas with the WINDOWS menus s popped a ormation on the pro vran THE SKAGEN ATLAS Package version 3 0 POSITIONS OF HVOROGRAPHICAL STATIONS BURING SKA SECTION Az Laes _ Sta Lat Lon 4 57228 7 11949 5 57919 3 57018 9 11034 3 57214 0 11026 2 57 1 2 114018 0 57 15 4 1B 45 5 57 15 6 18 49 0 SECTION B Claesa G teborg Friedrtkshaun 57233 0 11931 5 0 2 57 32 3 449260 Sg 3 57932 8 11017 5 5730 3 11008 5 5 aie p Fig E The main scr
20. se times each scientific crew carried out the program according to their national agenda still the data than collected were made available to all participating parties Evaluation of samples and primary processing of on board data were worked up by the participating groups The CTD casts reduced to one metre bins and the water bottle level data for chemistry and biology were submitted to the ICES data management group where they underwent the final quality check and were put together to form a coherent database to be released to the all member institutions This scheme worked well and timely so that by November 1991 only after four months after the last field survey the diskettes containing full SKAGEX dataset with hydrographic and chemical data plus chlorophyll with all surveys included had been supplied to principal scientist from the member institutions Having the database compiled the objectives were set for scientific evaluation of the data Whilst the most evaluation work was to be carried by separate scientific groups in their base laboratories in several topics a close cooperation at international level continued Among such topics were the studies on overall circulation pattern and hydrographic events taking place during SKAGEX To a support this work the author proposed the use of an already existing custom software package developed at IO PAS specially designed to automate the process of the oceanographic cruise resul
21. ts reporting The proposition was accepted by the study group during the group meeting in November 1991 In April 1992 the first version of the package containing the SKAGEX dataset plus presentation software was ready for distribution It was soon followed by a draft copy of an atlas showing the daily variations of the major parameter fields during SKAGEX I It contained over 1000 maps with the horizontal distributions of temperature salinity density nitrate nitrite silicate and phosphate at several depth levels ranging from the surface down to 200 metres The preparation of this atlas including printing and binding was accomplished within a week In the following pages the user s manual for the SKAGEX atlas is presented All examples in the manual relate to Skagerrak and the SKAGEX database The software itself though was written with the general model of oceanographic data in mind and may be reused for other oceanographic datasets without much additional programming effort The basic requirement is that the data supplied must resemble a simple one to many relationship with a station header information containing at least the platform event name the location and the time of measurement as an index and pertaining multiple data cycles on the right hand side of the relation The program imports such data for flat ASCII files and builds in a relational database in its own format The author has tested this system on several datasets
22. use to scroll the contents of the window Click the arrow at either end to scroll one line at a time Keep the mouse button pressed to scroll continuously You can click the shaded area to either side of the scroll box to scroll a page at a time Finally you can drag the scroll box to any spot on the bar to quickly move to a spot in the window relative to the position of the scroll box You can drag any corner to make a window larger or smaller To resize using the keyboard choose SIZE MOVE from the WINDOW Ctr F5 16
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