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OceanPC Manual Software for Management and

1. SUS A file of minimum and maximum values and their record numbers identified during the use of the PLOT X Y DATA utility FILE TYPES IN OPCPLOT COMPONENT 14 FLE HPG LST NDX WORLD WDB IOC INF 943 page 15 A short file containing the screen coloring instructions for any standard map selected by the user from the DEFINE A MAP menu A plotter file in Hewlett Packard Graphics Language conforming to the 7475A Plotter specification containing all OPCPLOT drawn figures except screen REPLAY images The HPG files can be imported into WordPerfect documents A file that accompanies any WDB file see above containing a list of all the maps that have been defined from the WDB file The entries in the list consists of the names of the index files that contain the addresses of the segments in WDB needed to make a map and information about the boundaries of the map An index file that contains the addresses of all the segments of data in a WDB file needed to draw a single map A coastline file in Micro WORLD DATA BANK II MWDB2 format used by either the MAKE COASTLINE utility or the GENERAL OCEAN MAPPING utility OceanPC is supplied with WORLD WDB which contains the world s coastlines and major islands The GENERAL OCEAN MAPPING utility however has a function that allows the user to substitute any geo referenced data base in WDB format The complete MWDB2 system consists of 1200 indexed line segme
2. 54 IOC INF 943 page 55 CONVERT OUR TO INF EXECUTABLE PROGRAM NAME OUR2INF EXE FUNCTION To convert the individual files generated by the ENTER DIGITAL ROSCOP utility into one file in the format required by the SEARCH DIGITAL ROSCOP utility OUTPUT FORMAT AND USAGE The default output file is ROSIN INF but the user may specify the alternative The output format is compatible with the SEARCH DIGITAL ROSCOP s utility but please be aware of the naming convention required by this utility i e the name must be of the form ROS INF PROCEDURAL NOTES The OUR files must be present in the current directory Ensure that only those files that require conversion are present 55 IOC INF 943 page 56 56 IOC INF 943 page 57 CONVERT DAT TO ICE EXECUTABLE PROGRAM NAME DATCONV EXE FUNCTION To convert the individual files generated by the ENTER OCEANOGRAPHIC DATA utility into one of three standard data exchange formats ICES Format NODC SD1 Format or Blueprint 86 Format INPUT SOURCE FORMAT INFORMATION The Input DAT files must be on the current directory The utility gathers these files together and sorts them The utility aborts if any of these files are in the incorrect format OUTPUT FORMAT AND USAGE The default output file is ENTICE where may be NOD ICE or BLU but the user may specify an alternative The output format is in the exchange format specified NOD NODC SD1 ICE ICES profile Oc
3. instead of the first number For example if the user wants to enter 1232 7 3 IOC INF 943 page 74 ina field with a width of then at the keyboard he must enter 232 so that K32 appears in the file If however the first character in a field that must be overpunched is greater than 1 then overpunching by the ICES algorithm won t work the value is too large In such a case enter R99 6 Records may be stepped through one at a time by pressing ENTER at the record number prompt Press r to reverse direction 74 IOC INF 943 page 75 EXTRACT DATA EXECUTABLE PROGRAM NAME ICE EXT EXE FUNCTION To extract a subset of a ICES Format data file based on year geographic position country ship month day or user specified oceanographic section INPUT SOURCE FORMAT INFORMATION 1 The user specifies the ICES Format data file from which data will be extracted ICE Immediately after the input filename is supplied the program checks to see if ICE exists If so then processing proceeds The program also checks to see if an index file IND has already been created for ICE with the INDEX DATA utility Although an index file is optional its existence speeds up the extraction process Following this the program searches for and extracts data matching the user s criteria OUTPUT FORMAT AND USAGE The subset of data extracted from the ICE file s will be contained in a new ICES Format file EXT
4. PROCEDURAL NOTES 1 There are some undocumented advanced features in the EXTRACT DATA utility that are reflected in screen prompts that refer to a file named MASTER SEL and ZIP files These screen prompts should be ignored by the user 2 The user is initially given a choice between using this program with or without an index file previously created with the INDEX DATA utility If the user selects not to use an index file then the following Notes should be read as if no index file existed 3 If an index file exists the user can extract only for a Year specified as a 2 digit number such as 88 1988 b Geographic position specified within maximum and minimum latitudes N and S respectively and maximum and minimum longitudes E and W respectively c A oceanographic section specified within 1st and 2nd latitudes and 1st and 2nd longitudes describing endpoints of the section and a vertical offset nautical miles from the center line between the endpoints The section must be principally oriented east west 75 IOC INF 943 page 76 if oriented directly north south no data will be extracted due to the simplicity of the algorithm employed 4 If the user is extracting data by position Option PN or section Option SN then the geographic coordinates must be input in the right handed system RHS All latitudes are input as DDMM where D degrees and M minutes northern hemisphere latitudes are positive and southe
5. ICES Format file 10 IOC INF 943 page 11 EXTRACT DATA A utility is provided that allows the user to extract a subset from any ICES Format file based on year position or location within a user defined corridor This later concept is important in creating synthetic data sections for instance to be used by the ATLAST program described below DISPLAY DATA OceanPC provides several methods to display the oceanographic data as station maps oceanographic profiles or contoured property plots GENERAL OCEAN MAPPING A multi purpose marine mapping utility is provided The utility uses ASCII data files in a simple format that resembles a ship s log The utility also recognizes ICES Format files and many other ASCH and binary data formats drawing maps of the ocean or analytical results The maps can contain notations and symbols depicting the locations of sampling sites or cruises as well as ocean fronts buoy trajectories and other useful information Because the plottable files can be posted on electronic bulletin boards the utility offers a way to communicate maps of marine research activities and of important ocean features to the scientific community ICES DATA DISPLAY FORMATED DATA LIST A utility is provided that reformats a ICE file into a visually pleasing form for subsequent printing or publication FIND DATA LIMITS A utility is provided to examine an ICES Format file to determine the minimum and maximum values for the geogra
6. Information Document No 943 Copenhagen June 1993 107 pp IOC INF 943 page 4 IOC INF 943 page 5 TABLE OF CONTENTS OceanPC LICENSE AGREEMEIN RE TABLE RN RE INTRODUCTION RE NEEN ACKNOWLEDGMENTS ee INQUIRTES Ee LEI KEE OceanPC s WORKING DATA FORMATS NENNEN MESS BOR Vacaciones einen eene BELUEPRINT S6 FORMAT E DIGITAL ROSC OP FORMAT E GEOGRAPHIC COORDINATES ans KEY ENTRY AND FILENAME CONVENTIONS 00 000020000000200002000000020000000000000 OVERVIEW OF COMPONENTS tan CAPTURE OCEANOGRAPHIC amp ROSCOP DATA MANUAL DATAENTR EE ENTER OCEANOGRAPHIC DATA scsi CONVERT DAT TO ICE OR BLU OR NOD esec ENTER DIGLIALROSCOPS 2 22 aa IMPORT amp EXPORT STRANGER FORMATS nnensessensensensennennennennennennennn IMPORT NODC SDVSD2 DATA EXPORT NODC SD1 DATA cosida idad dianas IMPORT NODC CD ROM DATA oococcccnccinononnonacnonnononinnnononaonoricnnononionos IMPORT BLUEPRINT DA TA EXPORT COMMA SEPARATED DATA nnnnsnenne CONVERT COMMA SEPARATED DATA TO SURFER QUALITY CONTROL amp UTILITIES este een BK IOC INF 943 page 6 OCIS e RE E 10 SUMMARIZE STATIONS IN PEE aussen 10 SUMMARIZE DATA IN FILE eege 10 CHECK DATA degen eege ee dree 10 PLOT Y DATA dat AAA 10 EX TRAC DATA ee 11 DISPLAY DATAE ee 11 GENERAL OCEAN MAPPING cccsssccssssccsscccesseccsscccsseceessesessacecssaeeessaees 11 ICES DATA DISPLAY coooonoconncnonanononcnonnnnonananonanaconnnnononanonanano
7. Line where 180 W Long and 180 E Long coincide the above conventions must be observed the internal logic of the OPCPLOT code recognizes and handles the special transformations required and no substitutions or coordinate conversions by the user are expected Please see the OPCLOT Manual for a detailed description of the OPCPLOT format and of the other data file formats recognized by OPCPLOT 78 IOC INF 943 page 79 FIND DATA RANGES EXECUTABLE PROGRAM NAME LIMITS EXE FUNCTION To examine an ICES Data file and report the extreme latitudinal and longitudinal limits of the stations INPUT SOURCE FORMAT INFORMATION The code inputs an ICES Data file name OUTPUT FORMAT AND USAGE Northern most and southern most latitudes eastern most and western most longitudes In addition the maximum and minimum values of all observed parameters in the data file are reported including information on which parameters are not included Output is in a LIM file which can be utilised by both STAPLOT and TSLOOK to enable automatic scaling features PROCEDURAL NOTES 1 Although used for automatic range purposes the utility also serves as a useful check on extreme outliers The record numbers of all maximum values are also reported thus allowing convenient identification using ICE EDT EXE 79 IOC INF 943 page 80 80 IOC INF 943 page 81 MAKE COASTLINE FILE EXECUTABLE PROGRAM NAME WDB EXE FUNCTION To create a coastline file named WOR
8. National Oceanographic Data Center NODC oceanographic data file in SD1 or SD formats CD ROM NODC 20 to ICES Format INPUT SOURCE FORMAT INFORMATION The user specifies an input file which must be in the NODC SD1 or SD2 formats OUTPUT FORMAT AND USAGE On the same directory location where the input SD1 SD2 file was located the utility creates the new ICES Format file ICE PROCEDURAL NOTES Conversion is direct without intermediate formats 41 IOC INF 943 page 42 42 IOC INF 943 page 43 EXPORT NODC SD1 DATA EXECUTABLE PROGRAM NAME ICE NODC EXE FUNCTION To export data from OceanPC ICES Format to the NODC SD1 format used by the U S National Oceanographic Data Center INPUT SOURCE FORMAT INFORMATION The user specifies a Standard Profile file to be converted to SD1 format ICE OUTPUT FORMAT AND USAGE The utility exports a file in NODC SD1 format NOD The utility also exports a secondary file that contains any data in the OceanPC data file that could not be contained in the data fields of the SD1 format for example Total Nitrogen chlorophyll a SUP The SUP file is similar in format to Blueprint 86 Format or the GF3 Format PROCEDURAL NOTES Conversion is direct without intermediate formats 43 IOC INF 943 page 44 44 IOC INF 943 page 45 IMPORT NODC CD ROM DATA EXECUTABLE PROGRAM NAME CD ICE EXE FUNCTION The utility allows the user to import salinity temperature data files fro
9. OUR TO INF utility OUT A family of output files in various formats produced as reports by utilities in the system FISUM OUT A text file created by the FISUM utility that summarizes the contents of a ICE file in terms of vessels years stations and cruises represented ROS STA OUT A text file created by the STASUM utility The entries in the file describe the numbers of stations for each parameter in each Marsden Square ROS1 OUT A text file created by the SEARCH DIGITAL ROSCOP s utility containing the extracted ROSCOP forms ROS2 0UT A text file created by the SEARCH DIGITAL ROSCOP s utility containing cruise headers and information on the availability of the data STASUM OUT A text file created by the STASUM utility that summarizes all the parameters at each oceanographic station STO When the user has completed a session with the MAKE X Y PLOT utility one option offered by the program is the creation of a quick look file that contains the essential information to re create the left hand scatter plot of the 3 plots usually made The STO file is created to contain screen coordinates of the data points and appropriate data pointers SUP When the EXPORT NODC SD2 DATA utility creates a NOD file from a ICE file there may be items of data which cannot be accommodated in the NOD file The EXPORT utility also creates a SUP file to contain these extra data formatted similar to Blueprint 86 Format
10. Y X Pressure and Y Pressure monitor screen scatter plots where X and Y are any two parameters in a file selected by the user and to flag suspect data points for subsequent closer examination by the EDIT DATA function The following screen types are supported CGA EGA MCGA VGA INPUT SOURCE FORMAT INFORMATION The user specifies a data file from which the three scatter plots will be created ICE OUTPUT FORMAT AND USAGE 1 The utility creates two files containing suspect data a An ASCI file containing data identified by the user as suspect during viewing of X Y scatter plots ERR The ERR file is also sent to the originator for confirmation of any corrections made b An ASCII file SUS is automatically made by the utility containing all maximum and minimum data values along with their record number SUS c The SUS file also contains the record of the entire station that has a suspect value if so selected 2 The utility also creates an ASCII file that contains the information contained in the basic X Y plot STO In subsequent sessions with the X Y DATA PLOT utility this STO file can be specified instead of the ICE file for more rapid display of the X Y plot In this case however the other plots are not provided but on pointing to individual dots a listing of the displayed parameters in the station centered on the values of this point are printed on the screen 69 IOC INF 943 page 70 PROCE
11. as the source and destination respectively INSTALLATION PROCEDURE The installation process is started by loading Disk 1 in your computer e g in drive A and typing A OPCINST lt ENTER gt The contents of the diskettes files are unpacked into the appropriate directories by the installation program A prompt is given when you need to change diskettes if in fact installation is from diskette On completion of the installation the installation program loads the OceanPC menu program IOCOPC which is placed in directory OCEAN_PC On future sessions of OceanPC then you may start up by changing to this directory and type IOCOPC Alternatively you may place IOCOPC EXE in a directory included in your PATH IOCOPC will then automatically find the correct directory if on the current drive If not you will have to specify this INSTALLATION FROM HARD DISK VIA INTERNET If you have downloaded your OceanPC files by file transfer protocol over INTERNET then the floppy disk is any drive on which the installation files are resident For example if you have copied your files to the drive C hard disk then this is your floppy disk However please note that the installation files MUST be in the root directory of the required drive otherwise you will get FILE NOT FOUND messages OBTAINING OceanPC THROUGH INTERNET OceanPC is maintained on the Public Unix server on the ICES computer in Copenhagen and is therefore retrievable over INTERNET anony
12. finished surmounted by a command line prompt When some commands are answered the command line is replaced by specific questions relating to that command Other commands cause the screen to go blank while various text messages and additional questions to scroll by A detailed description of OPCPLOT is contained in the OPCPLOT Manual a separate volume included with the OceanPC documentation The following brief descriptions of all the principal OPCPLOT commands is an overview of program structure DEFINE MAP To set up the geographic dimensions of a map to be drawn A menu of standard maps will be offered but the user can also define a non standard map within the limits of any of the standard maps Once the answers to a few questions have been supplied the map will be drawn on the screen ZOOM To select a rectangular subarea from the map on the screen so that it can be expanded to fill the screen PLOT To name a particular OPCPLOT data file to be drawn on a map This command cannot be used until a base map has been drawn on the screen with either the DEFINE Map command or the REPLAY command OPCPLOT recognizes about 20 different data file formats selected from major oceanographic programs or systems GRATICULE To draw a latitude longitude graticule on a map KEY To display a set of map boundaries corresponding to the various regional maps available through the DEFINE Command 77 IOC INF 943 page 78 TITLE To write a title in a
13. frame at the bottom of the map SAVE To save the map on the screen to disk The REPLAY command can subsequently be used to recall the map to the screen REPLAY To recall to the screen a previously SAVED screen UTILITY A set of short useful programs for creating converting or listing OPCPLOT files MARK A set of routines that allow the user to place labels or user specified figures in existing files or in new files When a data file has been plotted to the screen the user could for mstance use MARK options to add more information to the same file MARK is a powerful and flexible part of OPCPLOT that can be used to increase the readability of various files or to enhance the resulting maps for purposes of publishing COLOR To fill the various land and water boundary polygons with appropriate colors END To exit the OPCPLOT utility and return to the operating system The user is also offered the option here to re name the Hewlett Packard Graphics Language plotter file extension HPG that has been created in background or to send the HPG file to a plotter OPCPLOT COORDINATE SYSTEM OPCPLOT uses latitude and longitude in decimal degrees format for instance 93 34478 W Long is an acceptable longitude value Further the OPCPLOT globe extends left to right from 180 W Longitude to 180 E longitude and top to bottom from 90 N Lat to 90 S Lat Even for those data sets which may wrap over the International Date
14. install in this way then please make sure that the files are loaded into the correct directories This can be done by typing OPCI d OPC2 d Contents of File OPC1 EXE All executable programs EXE and source codes BAS used in OceanPC with the exception of the OPCPLOT system Contents of File OPC2 EXE Sample hydrochemistry data files digital ROSCOP files and the OPCPLOT system files There are two sample hydrochemistry data files supplied with OceanPC These will help you get started and allow you to see the capabilities of OceanPC These data files are OPC1 ICE this is a section from 20 W worked by the Dutch Research vessel TYRO during a World Ocean Circulation Experiment WOCE cruise in 1990 OPC2 ICE this is a survey conducted by the English Research Vessel CHALLENGER during the United Kingdom North Sea Project in 1988 17 IOC INF 943 page 18 INSTALLATION PROCEDURES FOR OceanPC When you install the system by using the program OPCINST EXE the following directories will be created on the drive you specify ocean_pc with sub directories opcplot rosc exec bas data NOTE You will need about 4 MB of free disk space for this installation INSTALLATION FROM FLOPPY DISKETTE To allow the installation to proceed you need to input the drive letters for your floppy drive and the hard disk drive to which you want to install OceanPC If you press RETURN floppy drive A and hard disk C will be assumed
15. key to return to continuous processing of the data file 5 When using the E operating choice see above the cursor appears on the screen after the plots are drawn and lt ESCAPE gt has been pressed It will appear only on the left hand X Y plot This enables the user by means of the cursor keys to locate the actual record and station pertaining to any particular dot in the X Y plot a Pressing lt ENTER gt stores a single record in SUS b Pressing lt TAB gt stores the whole station in SUS 6 No matter which operating options have been selected E S or any other key the next user action after help screen F5 is the specification of the data filename 7 Ifyou are unsure of the data ranges applicable to your data set use either the default values and examine the SUS file on completion to ascertain if any data are out of range Alternatively you may first run LIMITS and answer the relevant prompt when invited to do so 70 IOC INF 943 page 71 8 When using operating options E or S memory limitations dictate that the vertical resolution is reduced to that of CGA Fh IOC INF 943 page 72 72 IOC INF 943 page 73 EDIT DATA EXECUTABLE PROGRAM NAME ICE EDT EXE FUNCTION To perform data editing on OceanPC standard profile format files using error reports and suspect data lists generated by other quality control routines INPUT SOURCE FORMAT INFORMATION the user selects a ICES Format file to be edite
16. on diskette or electronic mail to ICES or your National or World Data Centre who will check and edit the information Information sent to ICES will be merged with its existing cruise information data bank which is used in conjunction with the SEARCH digital ROSCOP s utility in this system PROCEDURAL NOTES 1 Start by looking at the various pages These are accessible by pressing the function keys listed on the bottomline of each page Try the 4 cursor and the HOME and END keys 2 Once you start entering information into a field you must complete your entry by pressing lt RETURN gt Until you do this you will find that the cursor and function keys not F10 respond only with a BEEP 3 Corrections to your entries may be done using text editor facilities available from F5 Text strings of maximum length 79 may be entered Use the editor if you wish to exceed the designated field length 4 When you have entered the cruise information you should make a backup of your file s and send a copy on diskette either directly to ICES or through your national data center If you send directly to ICES a hard copy of the information will be passed to your National Oceanographic Data Center and ICES will return your diskette with the latest digital ROSCOP information 39 IOC INF 943 page 40 40 IOC INF 943 page 41 APPENDIX B IMPORT AND EXPORT DATA IMPORT NODC SD1 SD2 DATA EXECUTABLE PROGRAM NAME NODC ICE EXE FUNCTION To import any
17. re sure that OPCPLOT has been successfully installed and is running 19 IOC INF 943 page 20 20 IOC INF 943 page 21 REFERENCES Brown M L 1993 OPCPLOT Oceanographic Mapping Software for the World s Seas Version 1 7 June 1993 OCS Report MMS 93 0020 U S Department of the Interior Minerals Management Service Gulf of Mexico Regional Office New Orleans LA 65 pp Golden Software Inc 1993 SURFER User Manual Boulder Colorado IOC 1991a OCEAN PC Inventory of Software and Products for the Display and Analysis of Marine Data The Shoebox IOC INF 878 13 April 1991 Intergovernmental Oceanographic Commission UNESCO Paris 37 pp IOC 1991b Manual on International Oceanographic Data Exchange Manual and Guides 9 Revised Edition Intergovernmental Oceanographic Commission UNESCO Paris Lascaratos A J Daskalakis L Perivoliotis and N Vlastos 1990 SEASPECT A software package for Oceanographic Time Series Analysis University of Athens NODC 1991 CD ROMs NODC 02 and NODC 03 Global Ocean Temperature and Salinity Profiles National Oceanographic Data Center Washington DC July 1991 14 pp documentation and CD s Pospeschil F and Riveria A Micro World Data Bank II Global coastline and political boundary data for use on PC microcomputers For information contact Fred Pospeschil 3108 Jackson St Bellevue NE 68005 Telephone number 402 291 0795 6 9 PM Central Time Rhines P B 1992 ATLAST
18. the GENERAL OCEAN MAPPING utility is written to require an EGA monitor or better A desirable optional hardware item is a CD ROM reader for access to large data sets SOFTWARE The system assumes only that the user has MS DOS but the following software additions are desirable QUICKBASIC Version 4 5 To enable the user to modify existing utilities or create new ones compatible with OceanPC code The QBASIC Interpreter that is included with DOS 5 1 is also useful SURFER A commercial gridding and contouring program can accept oceanographic data and coastline geographic data files from OceanPC utilities Golden Software Inc 1990 ATLAST The public domain oceanographic data analysis package Rhines 1991 available from the Jet Propulsion Laboratory in California Any word processing program that can import HPGL plotter files into documents such as WordPerfect This allows the user to produce publication quality graphics from the GENERAL OCEAN MAPPING utility SECONDARY DISTRIBUTION The complete OceanPC system is being distributed as both executable codes and source codes see below The IOC requests that primary users share the system with secondary users ONLY if the programs have remained unchanged If primary users have changed any of the programs they are asked to refer potential new users to the IOC OceanPC Program Officer see above for system diskettes or to the INTERNET locale for file downloading IOC INF 943 pag
19. which covered only the Pacific Ocean may also be available to the user but it is not convertible with this utility 45 IOC INF 943 page 46 3 When the NODC updates NODC 02 and NODC 03 in late 1993 or early 1994 the re numbered CD s will contain nutrient data and the format may be changed so compatibility with the present OceanPC software is not guaranteed 46 IOC INF 943 page 47 IMPORT BLUEPRINT DATA EXECUTABLE PROGRAM NAME BLU ICE EXE FUNCTION To import Blueprint 86 Format oceanographic data into OceanPC This conversion is the bridge between Blueprint files created by the ENTER OCEANOGRAPHIC DATA function if the user did not elect to create ICE files initially and the rest of the OceanPC system which requires ICE files INPUT SOURCE FORMAT INFORMATION The user specifies the name of the Blueprint 86 Format file to be converted BLU OUTPUT FORMAT AND USAGE The utility creates the ICES Format data file ICE which is now available for all quality control display and mapping functions in OceanPC PROCEDURAL NOTES 1 No further use of the Blueprint format is made in OCEANPC but it is presented here as a demonstration what a user specified format accommodating any desired parameter may look like The structure of this format is basically that used in ICES for contaminant data storage This format is also in use for flexible data management purposes in some institutions where the ability to expand data ty
20. DURAL NOTES 1 When the opening title screen is presented on the screen the user can enter F5 to be presented with several operating choices The following information summarizes these choices lt E gt Ifthe user exits the F5 help screen by hitting E then the utility will subsequently draw all three scatter plots of the data i e X Y X Pressure and Y Pressure After the plots have been drawn a cursor appears for individual data point examination lt S gt If the user exits the FS help screen by hitting S then the utility just replays a saved X Y plot from a STO file lt ANY OTHER KEY gt If the user exits the FS help screen by hitting any other key than E or S then the utility draws the same three scatter plots as for E but no cross hair cursor is provided This option is for simple viewing purposes only 2 If the E or S options has been chosen inconsistent patterns or outliers can be pointed to in the X Y portion of the plot with the cross hair cursor and saved in the ERR file These points can therefore be corrected or flagged with the EDIT DATA function 3 When exiting this function the user will be given the option of saving the X Y plot to a STO file for re viewing at a later stage This is particularly useful if several pairs of parameters have to be viewed 4 When running the utility you will notice that progress through the data file is continuous To stop on each station press the spacebar press any other
21. IOC INF 943 Paris 30 July 1993 English Only OceanPC Manual Software for Management and International Exchange of Oceanographic Data June 1993 Intergovernmental Oceanographic Commission United Nations Educational Scientific and Cultural Organization IOC INF 943 page 1 OceanPC LICENSE AGREEMENT The goal of OceanPC is to promote the exchange of free software and the ideas contained therein that will in turn help promote the free exchange of oceanographic data within the IODE system The ideas within the programs are possibly more important than the programs themselves therefore OceanPC must only be provided along with the corresponding source code Modified source and executables must be clearly identified as such as the original authors will not provide any support whatsoever for versions of OceanPC which they have not released Although users are free to submit bug fixes or improvements to the OceanPC project office TERMS AND CONDITIONS FOR COPYING DISTRIBUTION AND MODIFICATION 1 The OceanPC software is copyrighted 2 The software is provided free of charge 3 The software is provided without any form of warranty 4 You may copy and distribute verbatim copies of OceanPC source code and executables as you receive it in any medium provided that you also provide a copy of this notice It is not permitted to change this notice 5 You may copy and distribute OceanPC in part or whole or any derivative of it in
22. LD BLN in SURFER format for use with either SURFER or the MAKE STATION PLOT utility INPUT SOURCE FORMAT INFORMATION Based on latitude longitude limits supplied by the user the utility examines the master coastline file WORLD WDB located in the OPCPLOT subdirectory and extracts only those segments of the data needed to draw the needed coastline 5 levels of resolution can be chosen but the invitation to provide data on state boundaries and rivers should be ignored as this is not available in the version of world wdb provided with OceanPC OUTPUT FORMAT AND USAGE An ASCII coastline file in SURFER format Output is in a file named COAST BLN which is the default file name assumed by STAPLOT PROCEDURAL NOTES Latitude and longitude limits for the new map are supplied by the user 81 IOC INF 943 page 82 82 IOC INF 943 page 83 MAKE STATION MAP EXECUTABLE PROGRAM NAME STAPLOT EXE FUNCTION To create a map of all the stations in a ICES Format data file with an optional coastline INPUT SOURCE FORMAT INFORMATION 1 The user specifies a ICES Format file to be mapped TCE 2 Ifa file named WORLD BLN optionally created by the user with the MAKE COASTLINE FILE utility then the coastline is also drawn on the map OUTPUT FORMAT AND USAGE On the video monitor the code draws a geographic coordinate map of the locations of stations contained in the file If available a coastline is drawn No direct hard copy plotting capab
23. MITTED ABOVE BE LIABLE TO YOU FOR DAMAGES INCLUDING ANY GENERAL SPECIAL INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES END OF TERMS AND CONDITIONS IOC INF 943 page 3 VERSION This Manual describes the use of Version 2 0 of OceanPC As new versions are released the Intergovernmental Oceanographic Commission IOC will inform registered users by mailed announcements and through notices on electronic bulletin boards DISCLAIMER This report has been technically reviewed by the IOC and approved for publication Approval does not signify that the contents necessarily reflect the views and policies of the IOC nor does mention of trade names or commercial products constitute endorsement or recommendation for use MANUAL AVAILABILITY Additional copies of this manual and the OceanPC software files may be obtained at the following address OceanPC Project Officer Intergovernmental Oceanographic Commission 1 rue Miollis Paris 75732 FRANCE RECOMMENDED CITATION OceanPC Working Group 1993 OceanPC Manual Software for Management and International Exchange of Oceanographic Data Intergovernmental Oceanographic Commission
24. ODC SD1 format The ICES Format contains a number of chemical parameters additional to those in the NODC format Whenever this utility encounters such parameters it stores them in a separate file SUP where they are identified by the 4 digit GF3 code IMPORT NODC CD ROM DATA A utility is provided that converts data from the U S National Oceanographic Data Center CD ROM s NODC 02 and NODC 03 see Appendix G to ICES Format Both of these CD s are derived from the NODC SD2 format files but they contain only salinity and temperature data with necessary station header information CD ROM NODC 01 which covered only the Pacific Ocean may also be available to the user but it is not convertible with this utility When future CD ROM sets may become available their formats may be different again requiring additional conversion utilities Further complicating the issue of data formats will be the release in 1994 or early 1995 of updates to CD ROM s NODC 02 and 8 IOC INF 943 page 9 NODC 03 including nutrient data These updates vill have new CD numbers and they vill have a different format from SD1 SD2 and the abridged data format used on NODC 02 and NODC 03 IMPORT BLUEPRINT DATA A utility is provided that converts Blueprint 86 Format to ICES Format Although most users will want to create data in ICES Format immediately using the ENTER Oceanographic DATA utility this routine is also provided for pre existing Blueprint 86 For
25. RY The first way to enter your marine data or index information into the system is by manual key entry There are two utilities in OCEAN PC that allow you to do this ENTER OCEANOGRAPHIC DATA A utility is provided that allows the user to enter directly from the keyboard the data from oceanographic casts or of course selected values from STD CTD casts into an intermediate format with a filename extension of DAT CONVERT DAT TO ICE OR BLU OR NOD Immediately after using the above utility the user can employ this utility to convert the intermediate DAT file to any of the following formats ICES Format Blueprint 86 Format or NODC SD1 Format ENTER DIGITAL ROSCOP s An ICES utility is provided that allows the user to manually create the international standard index form called a digital ROSCOP IH The digital ROSCOP forms created by ENTER digital ROSCOP are the basis for index searches with another utility named SEARCH digital ROSCOP s Through digital ROSCOP searching the user can locate vessels institutions and researchers where particular data may reside This utility creates an intermediate file with filename OUR containing the key entered information IMPORT amp EXPORT STRANGER FORMATS IOC INF 943 page 8 Another way to enter data into the system is by means of a set of data conversion utilities already provided in OceanPC The OceanPC Working Group will continue to improve the system by adding necessary co
26. Release 3 5 A World Ocean Atlas of Hydrography Nutrients and Chemical Tracers University of Washington School of Oceanography Technical Report 91 1 Release 3 5 vi 10 92 41 pp To obtain a copy of the ATLAST software please contact NASA PODAAC ME 300 323 Attention Ms Ruby Lassanyi Jet Propulsion Laboratory 4800 Oak Grove Drive Pasadena CA 91109 USA Telephone 818 354 0906 Omnet PO DAAC JPL Internet RAL stans span nasa gov Technical questions regarding ATLAST applications should be addressed to 21 IOC INF 943 page 22 Dr Peter Rhines School of Oceanography WB 10 University of Washington Seattle WA 98195 USA Telephone 206 543 0593 Omnet P RHINES Internet rhines ocean washington edu 22 IOC INF 943 page 23 FIGURE CAPTIONS Figure 1 Overview of initial OCEAN PC system Due to the multiplicity of potential applications programs and data sets that could be part of an OCEAN PC the system will not be a tightly integrated system but instead only be able to provide basic tools and modules for data entry analysis and display Figure 2 Example plot from OPCPLOT This figure shows ocean front and boundary features position of the Loop Current derived from NOAA satellite SST data for April 27 1989 by Evans Hamilton Inc The data were downloaded from the OMNET GULF MEX bulletin board and plotted with OPCPLOT Figure 3 Example of listing of digital ROSCOP entries produced by ICES ROSEARCH prog
27. VERT COMMA SEPARATED DATA TO SURFER OR SPREADSHEET APPENDIX C DATA QUALITY CONTROL AND UTILITIES ssscsscsccssssssssssccsssssssesssssseen SOR EE A a N N A AT AT AT T AT ET AT SA SUMMARIZE STATIONS IN FILE EE SUMMARIZE DATA TIN EIEE sea Quali CHECK DATA NE re eRe PLOT XY DAT X L Arr Art r Pat a Ar ri r Aai a Pace EDI DATA ee APPENDIX D DISPLAY DATA N GENERAL OCEAN MAPPING oo oiono ociioncioconiicornicn coincidan FIND DATARANGES na MAKE COASTLINE FILE ee MAKE EH RL ER E APPENDIX E SEARCH DIGITAL ROSCOBS u a APPENDIX F ICES OCEANOGRAPHIC DATA CENTRE DATA EXCHANGE FORMA Pt APPENDIX G CD ROM NODC 02 amp 03 FORMAT DOCUMENTATION EE APPENDIX H NODC SD1 amp SD2 FORMAT DOCUMENTATION orita IOC INF 943 page 1 INTRODUCTION OVERVIEW OceanPC is an Intergovernmental Oceanographic Commission IOC project to organize a system of free or inexpensive software for processing of oceanographic data principally oceanographic profile data on IBM compatible microcomputers Using OceanPC you can 1 Key enter various types of oceanographic observations from your own files 2 Merge your own data with historical data from other ships and nations to create a local or regional Oceanographic Atlas 3 Analyze display print and plot the merged data and 4 Exchange data with oceanographers and National Data Centers around the world OCEAN PC accommodates the wide diversity of data types formats and applications of oceano
28. al SURFER program This figure shows the distribution of Norwegian profile data for 1985 held by ICES Figure 9 Example of gridding and contouring capabilities of the commercial SURFER program for oceanographic data The variable gridded and contoured in this figure is the ratio of the phosphate in the surface waters of the southeastern North Sea in February 1987 relative to January 1935 36 Note the enrichment of 4 to 5 times near the mouth of the Rhine River 24 IOC INF 943 page 37 APPENDIX A MANUAL DATA ENTRY ENTER OCEANOGRAPHIC DATA EXECUTABLE PROGRAM NAME ENTICE EXE FUNCTION This utility provides you with the means to enter oceanographic chemistry data into a structured computer file Most parameters normally collected at profile stations are included It is ergonomically designed to help data entry personnel to reach maximum speed efficiently and is particularly suitable for digitizing large data sets INPUT SOURCE FORMAT INFORMATION Manually enter the oceanographic data for each station location time temperature salinity and nutrients using original cruise reports logs data sheets or other historical data OUTPUT FORMAT AND USAGE Each use of this utility produces ASCII files that record your key entries which have an extension DAT where the refers to the originators 4 character station number One DAT file is produced for every station This file can be re read by ENTICE allowing you to make corr
29. am except as expressly provided under this OceanPC License Any attempt otherwise to copy modify sublicense distribute or transfer the Program is void and will automatically terminate your rights to use the Program under this License However parties who have received copies or rights to use copies from you under this General Public License will not have their licenses terminated so long as such parties remain in full compliance 8 You may charge a fee for the physical act of transferring a copy 9 By copying distributing or modifying the Program or any work based on the Program you indicate your acceptance of this license to do so and all its terms and conditions NO WARRANTY 10 BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE THERE IS NO WARRANTY FOR THE PROGRAM TO THE EXTENT PERMITTED BY APPLICABLE LAW EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND OR OTHER PARTIES PROVIDE THE PROGRAM AS IS WITHOUT WARRANTY OF ANY KIND EITHER EXPRESSED OR IMPLIED INCLUDING BUT NOT LIMITED TO THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU SHOULD THE PROGRAM PROVE DEFECTIVE YOU ASSUME THE COST OF ALL NECESSARY SERVICING REPAIR OR CORRECTION 11 IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER OR ANY OTHER PARTY WHO MAY MODIFY AND OR REDISTRIBUTE THE PROGRAM AS PER
30. cate the specific ATLAST format The OceanPC utility always assigns the digit 3 By chance data files in NODC SD2 format from CD ROM NODC 20 also use the filename convention DAT 12 ERR EXT FLT ICE IND INF LST LIM IOC INF 943 page 13 A file that lists the record numbers of suspect data in a Standard Profile file The ERR files are created by the CHECK DATA FAST utility An extract of data in ICES format from another larger ICE file The EXT file has been created by the EXTRACT DATA utility A file of selected data values taken from a comma separated data file The data are separated by a space or any user specified character in a FLT file and it has only 2 or 3 parameters per record as opposed to the 24 parameters in the long version of a CSV file These 2 or 3 parameters are specially selected by the user for export to SURFER 2 parameters are used by SURFER s graphics utility and 3 parameters latitude longitude and an oceanographic variable are used for data gridding and contouring The Standard Profile format for oceanographic data designed and used by the International Council for the Exploration of the Seas ICES This format is also the central standard format for the OceanPC system which borrows many of the ICES data management programs An index file to a ICES Format file Each record in the IND file contains information about a single station contai
31. d ICE OUTPUT FORMAT AND USAGE Based on the corrections made by the user at the keyboard the utility automatically updates the specified data file PROCEDURAL NOTES 1 ICE EDT EXE operates in random access mode on the ASCII ICES Format data files This is possible due to the fixed length of the ICES Format records You can make changes on data files of any length and changes are recorded without the need to re save the file The changes are made immediately to the selected file and there is automatic backup so BE CAREFUL 2 The user will be prompted for the record number s of the suspect data Useful information about record numbers and ranges of record numbers can be obtained from the files FISUM OUT and STASUM OUT if they have been generated for the data file FISUM OUT is generated by the SUMMARIZE STATIONS IN FILE utility STASUM OUT is generated by the SUMMARIZE ALL DATA IN FILE utility 3 Instead of designating a specific data record number for editing the user can respond 2 lt ENTER gt The utility will automatically open the appropriate ERR file if it exists for the ICE file and begin stepping through the suspect data records listed in ERR 4 Changes to entries in any Master Record are automatically made in all individual data records associated with that Master Record 5 If the value you wish to enter to a field is larger than the field this requires an overpunch which is generated by a entering a
32. d format Processing will abort here if the file is not a 24 field CSV file 2 It is common practice to consider data doublets as consisting of an independent variable the x value or abscissa and a dependant variable the y value or ordinate This notation is used by the utility when the user is selecting data for use with a spreadsheet or database manager program 3 When selecting either doublets or triplets the user is given the following capabilities 51 IOC INF 943 page 52 a Choice of selecting winter December to March data only b Choice of selecting only data within a certain depth band relative to the surface c Choice of selecting only data within a certain depth band relative to the bottom 4 When selecting data doublets the following automatic data management functions can be selected by the user a Summation of nitrite and nitrate c Grouping of independent variable values into specific intervals for instance to create a bar graph where the abscissa plots the midpoints of the intervals and the ordinate plots the average values of the dependant values d Pick the upper limit of the highest abscissa interval i e put an upper limit on the abscissa of a bar graph 52 IOC INF 943 page 53 CONVERT COMMA SEPARATED DATA TO ATLAST FORMAT EXECUTABLE PROGRAM NAME CSV ATL EXE FUNCTION To convert a comma separated data file CSV to the ATLAST format INPUT SOURCE FORMAT INFORMATION The code inp
33. d summary of all the data in a Standard Profile file down to the individual parameters measured at each station depth Optionally it can also produce a report file summarizing the cruises by different ships and or an automatic digital ROSCOP III file CHECK DATA A utility is provided that checks for a number of common errors and problems This utility produces an output file ERR compatible with the system file editor see EDIT A FILE below Thus records failing the tests can be corrected or flagged as necessary PLOT X Y DATA A utility is provided that lets the user examine one or more scatter plots to see patterns in the data Depending on the options employed the user can flag outlier data points for later examination by an edit utility EDIT DATA A utility is provided that edits ICES Format data records To use this utility the user must already know the record number s of questionable data This can be obtained by use of any of the following other OceanPC utilities PLOT X Y DATA Use of this utility results in a ERR error file that flags suspect data CHECK DATA Use of this utility results in a ERR error file that flags suspect data SUMMARIZE STATIONS IN FILE and SUMMARIZE DATA IN FILE Use of this either of these utilities allows the user to visually spot questionable data records Using the ERR error tag file as a guide the user can examine correct or discard the questionable oceanographic data in a
34. e 4 SYSTEM ARCHITECTURE The OceanPC system is provided as a set of executable programs source codes and a menu program Using the installation procedures provided below the system will install as follows Hard Disk e g C 3 AAA OCEAN PC Executable menu program amp ASCII 2 program manual 3 AA EXEC All executable programs except 3 OPCPLOT 3 AA BAS All program source codes 3 AA DATA Data files for OceanPC 3 AA ROSC Digital ROSCOP data 3 A OPCPLOT Program and files for GENERAL OCEAN MAPPING utility BASIC CONCEPTS OceanPC s WORKING DATA FORMATS ICES FORMAT OCEAN PC performs all of its display and analysis functions for oceanographic data using a single standard format at the heart of the system At present that format is the fixed record punch card ASCII format used by the International Council for the Exploration of the Seas ICES called ICES Standard Profile Format referred to throughout this manual as ICES FORMAT see Appendix F To use OceanPC it is required that existing data be converted to ICES Format and that new data be entered into the system in ICES Format ICES Format has been used for many years so it has some older features such as overpunches for negative temperatures and redundant information for each depth level However many useful software programs are available which require ICES Format and the format is suitable for many types of ocean station data including water te
35. eanPC compatible and BLU Blueprint 86 PROCEDURAL NOTES The DAT files must be present in the current directory Ensure that only those files that require conversion are present 57 IOC INF 943 page 58 58 IOC INF 943 page 59 APPENDIX C DATA QUALITY CONTROL AND UTILITIES SORT DATA EXECUTABLE PROGRAM NAME ICESORT EXE FUNCTION To sort an existing data file to a new data file INPUT SOURCE FORMAT INFORMATION The use specifies the input file name ICE OUTPUT FORMAT AND USAGE Because the output file is also in OceanPC format the user must specify a new filename to avoid overwriting the old file PROCEDURAL NOTES 1 The utility allows the user to specify any or all of the following fields to sort on Station number Country Ship Year 2 digit e g 88 not 1988 Month Day Hour 2 Because the program makes use of SORT EXE which is supplied with DOS this must be available either in current directory or in path It also means that there is an upper limit to the number of stations that can be sorted For sorting on only 2 keys approximately 15 000 stations may be sorted 59 IOC INF 943 page 60 60 IOC INF 943 page 61 INDEX DATA EXECUTABLE PROGRAM NAME INDEX EXE FUNCTION To create an ASCII index file to the locations of records in a data file Although not required if the user subsequently uses the EXTRACT DATA function then the index file created here will speed up the extraction proces
36. ections or additions if necessary Once you have completed your data entry session you may erase the DAT files but first REMEMBER to convert them to a standard format in one file using DATCONV DATCONV is accessible from ENTICE and converts your entered data to any of three formats ICES profile Blueprint 86 and NODC SD1 PROCEDURAL NOTES 1 The utility checks the keyed data for consistency as it is entered and places the data in an intermediate format Blueprint 86 Format that precedes conversion to the selected final output format 2 Quick guide to Function Keys Fl Master record F2 Data cycles 1 to 22 first 11 parameters shift F2 Data cycles 1 to 22 last 4 parameters depth for info only F3 Data cycles 22 to 44 first 11 parameters 37 IOC INF 943 page 38 shift F3 Data cycles 22 to 44 last 4 parameters depth for info only shift F4 Doubtful data quality marker point to field before pressing F10 Completes this session saves data into Blueprint 86 Format file readable by ENTICE Esc Press two or three times to abort without save Cursors Use cursor keys to navigate to fields Tab Press to move to beginning of next column Ctrl D Delete entry and shuffle fields up Ctrl E Expand i e create a space and shuffle fields down Others All numeric keys plus delete lt and are permissible assuming permitted by the data entry checks 4 Hints a Once a field is filled the cursor moves to
37. graphic data A wide variety of improvements to OCEAN PC are desirable particularly more flexible interfacing between large standard systems Users are encouraged to contact IOC if they have special needs for software or data sets or can contribute software to the system Within the original project constraint of providing a reasonably sized low cost system the project team will work toward incorporating additional components into succeeding versions of OceanPC ACKNOWLEDGMENTS The following people participated in the assembly of the OceanPC system Dr Murray Brown U S Minerals Management Service Dr Harry Dooley Mr Garry Hopwood International Council for the Exploration of the Seas Dr Doug McLain Chairman U S NOAA Center for Ocean Analysis and Prediction Mr John Withrow IOC Program Officer Intergovernmental Oceanographic Commission INQUIRIES IOC INF 943 page 2 To make inquiries to obtain additional copies of this Manual or to obtain a set of 3 1 4 inch high density system installation diskettes please write to OceanPC Project Officer IOC UNESCO 1 rue Miollis 75732 Paris Cedex FRANCE IOC INF 943 page 3 SYSTEM INFORMATION HARDWARE OCEAN PC has been designed for low cost operation on XT and AT microcomputers with the MS DOS operating system Versions 3 x and higher All but one of the utilities has been written to run on a CGA monitor or a monochrome monitor running in CGA emulation mode Only
38. gt Nitrite lt 7 gt Day lt 19 gt Ammonium lt 8 gt Time lt 20 gt Total Nitrogen lt 9 gt Sounding lt 21 gt Hydrogen Sulphide lt 10 gt Observation depth lt 22 gt pH lt 11 gt Temperature lt 23 gt Alkalinity lt 12 gt Salinity lt 24 gt Chlorophyll a 49 IOC INF 943 page 50 The units of measurement are described in Appendix F Any missing values in the original file are represented in the CSV file by 9 PROCEDURAL NOTES 1 When the opening title page of the utility appears the user can use the F5 key to a See a listing of the data fields that will be in the new CSV file the same listing shown above The left hand 12 fields can be considered the short form of the CSV while all 24 fields can be considered the long form b Change the fields separator from a comma to any other ASCII character Whichever key the user hits when leaving the above Table is subsequently used by utility as the fields separator in the output file 2 After the user specifies the ICE file to be converted to CSV he is given the choice between a short form output and a long form output referring to 12 vs 24 output fields In responding a lt ENTER gt short form output b lt ANY OTHER KEY gt long form output 50 IOC INF 943 page 51 CONVERT COMMA SEPARATED DATA TO SURFER OR SPREADSHEET FORMAT EXECUTABLE PROGRAM NAME CSV SUR EXE FUNCTION To select information from a comma separated file and
39. he names of the data files available to you Select the ones you want 4 The fourth screen requests information concerning the volume of output There are 3 possibilities a Full digital ROSCOP information including number of stations b Brief information providing a compact layout and c A summary of the extracted forms You can make extracts of the digital ROSCOP files based on any or all of the 11 fields of the digital ROSCOP form and within each field searches are by free text Don t worry about upper and lower case Searches using OR AND NOT statements are possible the menu shows you the defaults HELP is accessible from the Selection Menu and will give you more information about this Also accessible from the Selection Menu are lists of digital ROSCOP parameters and the means to view Marsden squares from maps of the World Digital ROSCOP parameters and Marsden squares are both used extensively in the data set so if you are not familiar with them you will get more enjoyment from this utility if you take a look at the lists maps 86 IOC INF 943 page 87 APPENDIX F ICES OCEANOGRAPHIC DATA CENTRE DATA EXCHANGE FORMATS 87 IOC INF 943 page 88 88 89 IOC INF 943 page 89 IOC INF 943 page 90 APPENDIX G CD ROM NODC 02 amp 03 FORMAT DOCUMENTATION 90 91 IOC INF 943 page 91 IOC INF 943 page 92 APPENDIX H NODC SD1 amp SD2 FORMAT DOCUMENTATION 92
40. ility is provided but the user can use a screen capture facility to transfer the screen image to a word processing program PROCEDURAL NOTES 1 The user will be prompted for the geographic limits of the map of stations which can easily obtained by using the FIND GEOGRAPHIC RANGE utility In all cases default values corresponding to the North Atlantic Ocean will also be offered If the user does not want the North Atlantic defaults the geographic coordinates must be input in the right handed system RHS All latitudes are input as DDMM where D degrees and M minutes northern hemisphere latitudes are positive and southern hemisphere latitudes are negative All longitudes are input as DDDMM western hemisphere longitudes are negative and eastern hemisphere longitudes are positive For example 56 degrees 8 minutes North would be input as 5608 112 degrees 40 minutes West would be input as 11240 2 The coastline is plotted after all the ocean stations have been plotted by pressing lt SPACE gt when the stations are finished Otherwise press lt ESCAPE gt to skip the coastlines and to leave the utility program 83 IOC INF 943 page 84 84 IOC INF 943 page 85 APPENDIX E SEARCH DIGITAL ROSCOPS EXECUTABLE PROGRAM NAME ROSEARCH EXE FUNCTION This is a utility to make selections of Cruise Summary Reports digital ROSCOP s based on user specified search criteria Ten years of cruises the 1980 s is supplied with OCEANPC Da
41. ing the presence absence of each oceanographic parameter at each depth at each station STASUM OUT 2 ASCII cruise summary where the utility divides data from specific vessels into cruises based on assumptions provided by the user about the length of time between periods of at sea activity ROS OUT DAT 3 digital ROSCOP file ROSDA INF PROCEDURAL NOTES 1 Enter the filename with extension 2 The screen prompt text for output report refers to a user supplied word or phrase that will appear in the output report for ease of later identification 65 IOC INF 943 page 66 3 The screen prompt referring to lt A gt means that if the user types in A at this point then the output will be formatted for an A4 paper otherwise A5 will be assumed 66 IOC INF 943 page 67 QUALITY CHECK DATA EXECUTABLE PROGRAM NAME ICESQC EXE FUNCTION To perform a fast quality control check of a data file As its name suggests this utility carries out basic quality control of Standard Profile data files INPUT SOURCE FORMAT INFORMATION The user specifies the data file to be examined ICE OUTPUT FORMAT AND USAGE The utility creates an ASCII file that notes on a record by record basis all of the suspect records ERR Subsequently if the utility EDIT DATA is being used this ERR file can be used to point toward the suspect values for individual correction or flagging as necessary PROCEDURAL NOTES 1 ICESQC EXE chec
42. ks for the following problems a Illegal record types b Illegal record lengths must be 80 characters c Minutes values greater or equal to 60 d Ship speed checks The ICESQC utility flags negative shipspeeds suspect speeds greater than 20 and less than 40 knots and gross speed errors greater than 40 knots Ship speed checks require that the data be sorted by ship and time using ICESORT For this consistent station numbering in a data set is encouraged as a redundant checking parameter This procedure often reveals points on land but is double checked using the STAPLOT which produces a track map e Decreasing depth of observations at a single station This is often a symptom of merging several stations under the one header a common error for data exported from a data base table f Sounding is greater than the deepest observation depth Assumes units are meters and decibars respectively 67 IOC INF 943 page 68 g Warnings of density instabilities are given if option lt G gt is given on startup The flags are for 1 Slight instabilities greater than 0 1 and less than 0 5 and 2 Large instabilities greater than 0 5 h It checks that minutes do not exceed 60 or months do not exceed 12 2 Many other profile consistency checks are possible including checks for unrealistic oxygen saturation 68 IOC INF 943 page 69 PLOT X Y DATA EXECUTABLE PROGRAM NAME TSLOOK EXE FUNCTION To examine a set of X
43. m the U S National Oceanographic Data Center CD ROM set entitled Global Ocean Temperature and Salinity Profiles CD ROM s NODC 02 and NODC 03 INPUT SOURCE FORMAT INFORMATION Use the software that accompanies the CD ROM to download selected temperature salinity T S data files to a hard disk This utility will then convert the CD ROM data to ICES Format The data on the CD ROM s are contained in 6 different types of files 1 T S data from Nansen casts these data are called SD2 on the CD but they are not the same format as the real SD2 data also available at the NODC SD2 data from NODC can also be imported into OceanPC with a different utility program NODC ICE EXE 2 T S data from low resolution conductivity salinity temperature depth data profiles STD 3 Four different types of bathythermograph data MBT XBT SBT and IGT Of these only the first two data types can be imported with this utility i e only the T S data not temperature only data These first two data types have identical formats OUTPUT FORMAT AND USAGE The user specifies the filename for the new ICES Format data file ICE which will be placed in the same hard disk directory where the input file was located PROCEDURAL NOTES 1 The NODC CD ROM s 2 and 3 contain only salinity and or temperature data by location date time and depth The data are derived from the much larger SD2 data files but the nutrient data are omitted 2 The CD ROM NODC 01
44. mat files or other specialized uses EXPORT COMMA SEPARATED DATA A utility is provided to convert ICES Format files to a much more easily read comma separated version The resulting flat files are immediately usable by most spreadsheet programs and some database management programs This conversion utility is also provided for any data the user wishes to further transform to the SURFER and ATLAST display and analysis programs CONVERT COMMA SEPARATED DATA TO SURFER FORMAT A utility is provided to translate comma separated data created by the above utility to simpler 2 column or 3 column data files that can be used by the SURFER gridding and contouring program SURFER expects geo referenced parameter data Le X Y Parameter and can produce a wide variety of screen printer and plotter analyses where data contouring or X Y graphs are needed CONVERT COMMA SEPARATED DATA TO ATLAST FORMAT A utility is provided to export data to ATLAST ATLAST is a public domain program that creates color coded station profiles of oceanographic data within an extremely flexible menu environment ATLAST is provided by the Jet Propulsion Laboratory Rhines 1993 with a global data set but the ability to provide additional data from OceanPC should be a significant improvement Conversely visualization of OceanPC cruise data with ATLAST should improve data quality control QUALITY CONTROL amp UTILITIES A major function of any environmental data management sy
45. mous file transfer protocol ftp To obtain OceanPC by this means the following procedure is recommended but note that all instructions are case sensitive 18 IOC INF 943 page 19 ftp server ices inst dk or ftp 129 142 180 10 USER ftp PASSWORD your mail address ftp gt cd dist oceanpc ftp gt binary ftp gt Is ftp gt prompt off ftp gt mget where is are the desired file s ftp gt bye The full ICES digital ROSCOP data set is also available from this server To obtain this follow the above instructions change to directory dist roscop rather than dist oceanpc OBTAINING THE GENERAL OCEAN MAPPING UTILITY THROUGH INTERNET The GENERAL OCEAN MAPPING UTILITY which is included in the entire OceanPC package described above may also be obtained by itself The executable program code OPCPLOT EXE the manual Wordperfect 5 1 or ASCH version and sample files may obtained through anonymous file transfer protocol over INTERNET as follows Access INTERNET by the usual means use lower case letters except as shown ftp atlantic ocean fsu edu Name anonymous Password your internet address readme file appears ftp gt binary ftp gt cd pub Opcplot ftp gt Is lists the files ftp gt mget readme doc opcunpak exe ftp gt bye On your own computer create the directory OPCPLOT copy OPCUNPAK EXE to it then type OPCUNPAK lt RETURN gt to initiate the unpacking of the files OPCUNPAK EXE can be deleted after you
46. mperature salinity oxygen and nutrients Data in ICES Format are in fixed positions and thus easily sorted extracted and output for use in other programs Being a fixed format however ICES Format is not flexible for use with all types of oceanographic variables such as chlorophyll noble gases or trace elements A standard convention in OceanPC and all ICES software programs is that ICES Format files have the filename extension ICE 4 IOC INF 943 page 5 To distinguish all those data formats outside the OceanPC system the common phrase stranger data or stranger formats will be used Importing stranger data into OceanPC is an important activity dealt with at length in this Manual BLUEPRINT 86 FORMAT The Blueprint 86 Format see Appendix A is a more modern format for oceanographic data designed for greater flexibility for many types of ocean observations Blueprint 86 Format has a table at the beginning of the record that contains the names of the variables a Blueprint of what follows The oceanographic parameter codes used by Blueprint 86 Format are the same as those used by the IODE General Format 3 or GF3 IOC 1991b Blueprint S Format can thus contain a virtually unlimited variety of oceanographic variables but at the price of more complicated software than a fixed format such as ICES Format Blueprint 86 Format files usually have the filename extension BLU DIGITAL ROSCOP FORMAT In 1990 the IOC devel
47. ned in a ICE file The availability of an index file greatly speeds up the EXTRACT DATA utility A file of digital ROSCOP information searchable by the SEARCH digital ROSCOP utility ROS INF One of the annual summary files of digital ROSCOP entries supplied with OceanPC where stands for the calendar year e g ROS88 INF for 1988 ROSIN INF A new searchable file of digital ROSCOP information created by the user through key entry with the ENTER DIGITAL ROSCOP s utility followed by using the CONVERT OUR TO INF utility ROSDA INF The unique file automatically created by the STASUM utility to describe the cruise or cruises contained in a ICE file A specially formatted listing of the data in a ICES Format file wherein all the data items and fields are clearly labelled for easy visual inspection created by the FORMATTED DATA LIST utility This small file is generated by the FIND DATA LIMITS utility It contains data on the maximum and minimum values of all parameters in the file and on the geographic coordinates This file is used by the PLOT X Y DATA utility 13 IOC INF 943 page 14 NOD A file in National Oceanographic Data Center SD1 format created from an ICES Format file by the EXPORT NODC SD1 DATA utility OUR The file created by the INPUT DIGITAL ROSCOP s utility It can be submitted directly to a National Ocean Data Center or can be converted to searchable digital ROSCOP format with the CONVERT
48. ng messages are issued to the screen if appropriate concerning the structure of the examined file An ASCII file containing a summary of the cruises in the file based on the activity of different ships FISUM OUT This file also contains the range of record numbers for each cruise which the user could subsequently employ with the EXTRACT DATA function to extract any particular cruise or the EDIT DATA function to make corrections 63 IOC INF 943 page 64 64 IOC INF 943 page 65 SUMMARIZE DATA IN FILE EXECUTABLE PROGRAM NAME STASUM EXE FUNCTION To prepare an extended summary of all the data in a file including the presence absence of all data types at all station depth locations The summary displays the contents of each station showing which of the 17 parameters were measured Contents of each master record are also shown as are the maximum observed depths and the number of observations The utility also produces a summary for each cruise showing the distribution of stations by marsden square and the number of stations in terms of ROSCOP parameters One of the files generated by the utility produces a cruise summary that is compatible with the format produced by ROSEARCH INPUT SOURCE FORMAT INFORMATION The user specifies a data file to be summarized ICE OUTPUT FORMAT AND USAGE Depending on the options selected by the user the utility can provide 1 ASCII table summarizing all the data in the file includ
49. nnnnonananonna conan nononos 11 CHECK KEREN 11 FIND DATA KM 11 MAKE COASTLINE FILE c cccsccsscsssscssccsssccseceseecsesceseceseeeseeeseneess 11 MAKE STATION EE 11 SEARCH DIGITAL RTE 12 DATA FME TY HI EE 13 FILE TYPES IN ICES SOFTWARE COMPONENTS oonococcccnnononanonannnnonanonananonanaccananonos 13 FILE TYPES IN OPCPLOT COMPONENT aussen 16 BRIEF DESCRIPTION OF RELATED SOFTWARE oooooooccccocoooncoonnonnnonnnconnnonnncnnnononncnnncnnnconnnons 17 THE SHOEBOX ENEE ee e 17 MICRO WORLD DATA BANK oir aiii d 17 SEAS 70 KE 17 SURFER eege ee dd dad als 17 ATLAS in 17 CONTENTS OF THE OceanPC DISKETTEG ccccccssscssscsssceseccsesceseceseccseseesnceseees 18 INSTALLATION PROCEDURES FOR OceanPC coocooonccccocccooncnonononnonnnconnnonnnonnncnnncnnnnon 18 INSTALLATION FROM FLOPPY DISKETTE ensennennnennennnen 19 INSTALLATION PROCEDURE u ans 19 INSTALLATION FROM HARD DISK VIA INTERNET 19 OBTAINING OceanPC THROUGH INTERNET 19 OBTAINING THE GENERAL OCEAN MAPPING UTILITY THROUGH INTERNET 22242022 ee Eer EE 20 APPENDIX A MANUAL DATA ENTRY aeree EEA EEA EAEE EEEE is 25 ENTER OCEANOGRAPHIC DATA een 25 ENTER DIGITAL ROSCOPS Ha A 27 APPENDIX B IMPORT AND EXPORT DATA uuu ceeccccccccscccsssccesseeesseecesseccessecesseecessseeesaees 29 IMPORT NODC SD SD DATA ege aR RA AS 29 EXPORT NODE DL DATA ERREGER 31 IMPORT NODC CD ROM DATA 33 IMPORT REITER 35 EXPORT COMMA SEPARATED DATA 37 IOC INF 943 page 7 CON
50. nts in 6 different categories land islands rivers lakes countries states at 5 levels of resolution ranging from a few km s to about 200 km s To reduce plotting time OceanPC uses indexing schemes to identify the necessary line segments during any geographic mapping 15 IOC INF 943 page 16 BRIEF DESCRIPTION OF RELATED SOFTWARE THE SHOEBOX IOC 1991a The Intergovernmental Oceanographic Commission has assembled a catalogue of useful stand alone software programs for marine scientists that can be used in conjunction with OceanPC This catalogue nicknamed The Shoebox can be obtained from Ocean PC Project Officer Intergovernmental Oceanographic Commission UNESCO 1 rue Miollis 75732 Paris cedex FRANCE MICRO WORLD DATA BANK II Popeschil and Riveria ND Based on the much larger World Data Bank Il available from the U S National Technical Information Service this microcomputer version contains digital coastline island country U S state river and lake boundaries The MWDBII system was used as the source for the WORLD WDB file used by several utilities SEASPECT Lascaratos et al 1990 SEASPECT is a software package specially designed for oceanographic time series analysis It contains five main programs which perform data handling and manipulation univariate and rotary spectral analysis The package has initially been developed by and installed at the Department of Applied Physics Laboratory of Mete
51. nversion routines The following conversion utilities are provided IMPORT NODC SD1 SD2 DATA A utility is provided that converts the National Oceanographic Data Center SD1 AND SD2 data formats to the ICES Format This is a useful utility for importing into OceanPC any part of the extensive NODC data holdings in these formats described in Appendix H The utility automatically recognizes which format SD1 or SD2 in which the incoming data are stored The Standard Profile and NODC formats are the most widely used oceanographic data formats in the world today The current holdings go back to 1902 the date of the establishment of the Standard Seawater Service in Copenhagen The present formats were devised in the early 1960s At that time US needs and ICES needs differed slightly and as a result although structurally similar Standard Profile and SD1 SD2 differ in both concept and parameters It is intended that this utility be used in conjunction with the EXPORT NODC SD1 DATA utility which performs the opposite conversion The two utilities allow the user to take advantage of various PC based oceanographic data display products available for either format In mid 1993 the NODC is releasing CD ROM NODC 20 containing many long term transect and long term station data in SD2 format This special CD should not be confused with the NODC CD ROM DATA discussed below EXPORT NODC SD1 DATA A utility is provided that converts the ICES Format to N
52. object code or executable form under the terms of Paragraphs 1 and 2 above provided that you also accompany it with the complete corresponding machine readable source code which must be distributed under the terms of Paragraphs 1 4 above 6 You may modify your copy or copies of the Program or any portion of it and copy and distribute such modifications under the terms of Paragraphs 1 4 above provided that you also do the following a cause the modified files to carry prominent notices stating that you changed the files and the date of any change and b cause the whole of any work that you distribute or publish that in whole or in part contains OceanPC or any part thereof either with or without modifications to be licensed at no charge to all third parties under the terms of this OceanPC License except that you may choose to grant warranty protection to some or all third parties at your option Source code for a work means the preferred form of the work for making modifications to it For an executable file complete source code means all the source code for all modules it contains but as a special exception it need not include source code for modules which are standard libraries that accompany the operating system on which the executable file runs or for standard header files or definitions files that accompany that operating system 1 IOC INF 943 page 2 7 You may not copy modify sublicense distribute or transfer the Progr
53. oped the Cruise Summary Report III formerly known as the Report of Observations Samples Collected from Oceanographic Platform for reporting the locations of measurements and samples collected at sea IOC 1991b ICES on the other hand has pioneered in the development of a digital version of ROSCOP parallel in content to ROSCOP III In digital ROSCOPS the report from a cruise would be a single record in a larger ASCII file describing an oceanographic data collection effort A file of some 15 000 digital ROSCOP entries for historical oceanographic cruises in the North Atlantic is available from ICES from the late 1960 s to the present ICES receives about 500 additional digital ROSCOP cruise entries per year The US National Oceanographic Data Center NODC is in the process of providing 6000 additional ROSCOP entries to be digitized The combined ICES NODC file of ROSCOP cruise reports represents only a small portion of the total number of historical oceanographic cruises However only about 15 20 of the cruises documented by ROSCOPS have resulted in nationally or internationally available data Indeed a major objective of the OCEAN PC project is to encourage users to report their cruises in digital ROSCOP form and later to report the observations to National Oceanographic Data Centers and World Data Centers for international exchange digital ROSCOP files have the filename extension INF GEOGRAPHIC COORDINATES Geographic coordinates sho
54. orology and Oceanography of the University of Athens Greece SURFER Golden Software Inc 1990 A commercially purchased data gridding and contouring program in wide use by meteorologists oceanographers and biologists Oceanographic data triplets see the Appendices can be exported from OceanPC to SURFER for gridding and the gridded data can be contoured by either SURFER or the GENERAL OCEAN MAPPING utility ATLAST Rhines 1993 The ATLAST program is an extremely flexible public domain oceanographic sectioning utility Using files of nutrient data from actual historic cruises or artificially constructed sections from general archives for details see the EXTRACT DATA utility the program draws a number of instructive vertical property property plots The utility of the program ranges from basin scale visualization of water masses to bottle by bottle examination of the specific data points A separate Manual is available 16 IOC INF 943 page 17 INSTALLING THE SYSTEM CONTENTS OF THE OceanPC DISKETTES The OCEAN PC system is distributed On 2 1 4 MB 3 1 2 inch floppy diskettes or Over Internet as 3 files in compressed format and a READ ME instructional file The diskettes files are as follows Diskette 1 File OPC1 EXE OPCINST EXE Diskette 2 File OPC2 EXE OPCI EXE and OPC2 EXE are self extracting PKZIP compressed files Please use the installation program OPCINST EXE to unpack the above files If you do not want to
55. pes without resorting to format re design was an important criterion 47 IOC INF 943 page 48 48 IOC INF 943 page 49 EXPORT COMMA SEPARATED DATA EXECUTABLE PROGRAM NAME ICE CSV EXE FUNCTION The utility converts OceanPC standard profile format data to a comma separated version for Easier visual inspection Direct import into many spreadsheet programs and For the CONVERT COMMA SEPARATED DATA TO SURFER FORMAT utility As with most data formats the Standard Profile format is not well suited to use in commercial data base managers or spreadsheet programs Software to read data in this structure has to be fairly sophisticated ICES CSV EXE helps you to circumvent this difficulty by converting Standard Profile format to a flat ascii file of data whose field separator is a comma by default Any character produced by the keyboard may be used as a field separator see below INPUT SOURCE FORMAT INFORMATION The user specifies the OceanPC data file to be converted ICE OUTPUT FORMAT AND USAGE The utility creates a new file CSV wherein each data line contains a sequence of either 12 or 24 see Procedural Note 2 comma separated data fields as follows lt 1 gt Country ship lt 13 gt Oxygen lt 2 gt Station No lt 14 gt Phosphate lt 3 gt Latitude decimal degrees lt 15 gt Total Phosphorus lt 4 gt Longitude decimal degrees lt 16 gt Silicate lt 5 gt Year e g 9 lt 17 gt Nitrate lt 6 gt Month lt 18
56. phic coordinates and for all of the parameters present in the data MAKE COASTLINE FILE A utility is provided that allows the user to create a coastline file in the SURFER format for use with the MAKE STATION MAP utility below MAKE STATION MAP A utility is provided that allows the user to create screen maps of the station locations in ICES Format data file Coastlines can be drawn on the maps using the SURFER coastline data format see above and the relevant geographic limits see above SEARCH DIGITAL ROSCOP s A utility is provided that allows users to search for the existence of historical oceanographic cruises of interest Figure 3 shows an example listing from SEARCH DIGITAL ROSCOP s for cruises that took carbon dioxide measurements Files of digital ROSCOP entries for the years 1980 1989 are included in the OCEAN PC system Additional ROSCOP entries can be obtained through INTERNET as described above 11 IOC INF 943 page 12 DATA FILE TYPES The following listing shows all of the many different file types that the user may eventually find in the OceanPC subdirectories depending on which utilities he uses With few exceptions they are distinguishable by their filename extensions Reference to this listing should facilitate occasional housecleaning of the file or re locating previously created files The first section ICES software components lists files that could be found anywhere the second section OPCPLOT program list
57. ram from ICES file of digital ROSCOP cruise inventories This printout is a partial listing of all digital ROSCOP inventories in the file for which CO observations were made 3954 stations in 81 cruises Figure 4 Examples of temperature salinity profile data in three formats used in OCEAN PC NODC CD ROM ICES Format and Blueprint 86 Formats Figure 5 Temperature salinity plot of oceanographic cast data from NODC CD ROM for Marsden Square 7209 in the western Gulf of Mexico These data were extracted from the CD ROM in SD2 format with the CD ICES program stored in an ICES Profile format file and plotted with the PLOT X Y DATA utility The left panel shows a scatter diagram of temperature from 1 to 35 C versus salinity 30 to 40 ppt while the other panels show temperature center and salinity right plotted against depth pressure from O to 4000 decibars Note the region of very cold water at depths of less than 200 meters pressures less than 200 decibars in the center panel These temperatures appear in error as they do not follow the main pattern of the data The data show the need to plot observation data prior to use in analyses Unless erroneous values are detected and deleted before use any analyses and conclusions based on the data could be in serious error A feature of the PLOT X Y DATA utility is that the user can move a cursor around in the plot to identify the country and ship codes of any particular data point After s
58. rn hemisphere latitudes are negative All longitudes are input as DDDMM western hemisphere longitudes are negative and eastern hemisphere longitudes are positive For example 56 degrees 8 minutes North would be input as 5608 112 degrees 40 minutes West would be input as 11240 5 If no index file exists then the user can also extract for a Country or ship name b Month specified as an integer c Day specified as an integer 76 IOC INF 943 page 77 APPENDIX D DISPLAY DATA GENERAL OCEAN MAPPING EXECUTABLE PROGRAM NAME OPCPLOT EXE INPUT SOURCE FORMAT INFORMATION The program recognizes data files in its own OPCPLOT format ICES Format files and a number of ASCII and binary data files produced by other oceanographic analysis programs including ATLAST and SURFER The OPCPLOT format resembles a ship s log so that the files can be read and recognized visually by the user even before plotting OUTPUT FORMAT AND USAGE On the video monitor the code draws maps of various ocean regions allowed by a menu system The menu can be expanded by the user Direct hard copy plotting capability via HPGL format plotting files is provided screen images can also be captured with a provided command function for later replay with a slideshow utility PROCEDURAL NOTES OPCPLOT is essentially an electronic sketchpad that the user operates interactively Usually the screen consists of a map either in the process of being drawn or just
59. s INPUT SOURCE FORMAT INFORMATION The user specifies a data file to be indexed ICE OUTPUT FORMAT AND USAGE The utility creates a new ASCII file that indexes the user specified data file IND An ASCII file containing the year geographic location and Standard Profile data segment location for every station in ICE PROCEDURAL NOTES 61 IOC INF 943 page 62 62 IOC INF 943 page 63 SUMMARIZE STATIONS IN FILE EXECUTABLE PROGRAM NAME FISUM EXE FUNCTION Examine a data file and prepare a brief summary of all the stations in that file FISUM summarizes the contents of your data set generating one line of output whenever station number or time date ceases to be incrementing A line of output is also triggered by a change in ship platform and a new year This utility is also useful for detecting incorrect entries following data entry with the ENTER OCEANOGRAPHIC DATA utility For example and incorrectly entered country code will be singled out by this utility Other information in the output shows the number of stations with oceanographic profile data records 03 chemistry records 56 or 76 or records with very high levels of nutrients P6 These numbers are the various record identifiers used in the ICES format INPUT SOURCE FORMAT INFORMATION The user specifies the data file to be summarized ICE OUTPUT FORMAT AND USAGE The utility generates two forms of information useful to the user A set of warni
60. s files that would be found only in the OPCPLOT subdirectory FILE TYPES IN ICES SOFTWARE COMPONENTS COAST BLN A coastline file for use by either the MAKE STATION CHART utility or the SURFER program produced by the MAKE COASTLINE FILE utility from the master coastline file WORLD WDB in the OPCPLOT subdirectory BLU The Blueprint 86 Format used as an intermediate data storage medium during the keyboard entry of oceanographic data The user can convert BLU files to ICES Format by the IMPORT BLUEPRINT DATA utility Alternately the user can avoid any use of BLU files by specifying that the output from the INPUT OCEANOGRAPHIC DATA utility be in ICES format CSV A comma separated data file converted from a ICES format file by the EXPORT COMMA SEPARATED DATA utility CSV files are found in two different versions a 12 parameter short version and a 24 parameter long version DAT A file that records the user s key entry information during the use of the INPUT OCEANOGRAPHIC DATA utility By chance binary data files utilized by the ATLAST program also use the filename convention DAT Many DAT file come with ATLAST but new ones con be created by a converting a standard profile file to comma separated format with the EXPORT COMMA SEPARATED DATA UTILITY then b using the CONVERT COMMA SEPARATED DATA TO ATLAST FORMAT utility to complete the conversion The 8th character in the ATLAST filenames should be a digit from 1 4 to indi
61. stem is quality control Decades of experience with marine data have led ICES to the development of the utilities included below Through various sorting and display methods the user can visualize and organize the data in ways that emphasize inconsistencies or specific patterns indicative of error There is no general plan that will always identify erroneous data rather the user is advised to become familiar with these utility programs and to try them out on a test data in order to recognize the formats and usages of LIST FILES A utility is provided that lists the files in the current directory 9 IOC INF 943 page 10 SORT DATA A utility is provided that performs hierarchical sorting of a ICES Format file to a new user named file Sorting can occur by year country ship date time or station number Files with up to 15 000 stations can be handled irrespective of station size INDEX DATA A utility is provided that can create an index to a Standard Profile file This is useful in speeding up the EXTRACT DATA utility described below SUMMARIZE STATIONS IN FILE A utility is provided that summarizes station by station the contents of a Standard Profile file and checks the structure of the file for consistency Appropriate screen warning messages are issued if a problem is encountered A report file is also produced summarizing the cruises by different ships etc SUMMARIZE DATA IN FILE A utility is provided that produces a detaile
62. ta for other periods can be supplied on request INPUT SOURCE FORMAT INFORMATION 1 The code searches existing digital ROSCOP data files created by the CREATE digital ROSCOP utility The set of digital ROSCOP s provided with OceanPC is contained in files named ROS INF where the wildcards identify the year Thus the file ROS87 INF is the file containing digital ROSCOP s for the year 1987 Z However if the user has previously used ROSEARCH EXE then he also has a digital ROSCOP format file with filename ROSXX INF containing the results of that search This file is also searchable by ROSEARCH EXE giving the possibility of iterative searches OUTPUT FORMAT AND USAGE ROSEARCH creates an ASCII file named ROSXX INF in the same directory as the 1 or more digital ROSCOP files that are being searched The contents and size of ROSXX INF are variable based on switches described below PROCEDURAL NOTES There are four screens in ROSEARCH 1 The first screen is a menu to allow you to enter your search identifiers By pointing to a field and pressing lt ESC gt you get lists of keywords for field you are pointing to In the case 3 of the fields Country Area and digital ROSCOP parameter You can enter the criteria being pointed to directly to your list of Search criteria 2 The second screen reviews what you have done and gives you chance to change your mind 85 IOC INF 943 page 86 3 The third screen displays t
63. the next field Alternatively if you do not want to use all available decimal positions in a field terminate the entry by pressing lt Enter gt no b Type to avoid typing leading zeros eg 7 gives 07 5 Beeps Your computer will beep if you enter a number that is not within the allowed range The greatest control occurs in the depth field these must be entered before any other parameter and must be entered in increasing order 38 IOC INF 943 page 39 ENTER DIGITAL ROSCOPS EXECUTABLE PROGRAM NAME ROSIN EXE FUNCTION This utility is a user friendly form filler for IOC s digital ROSCOP III cruise summaries allowing the user to enter information about a single oceanographic cruise It is completely self contained with built in touch and select maps of Marsden squares to the 1 degree level and lists of digital ROSCOP parameter codes Since digital ROSCOP s are basically free text there are minimal quality checks on each item entered by the user INPUT SOURCE FORMAT INFORMATION The user provides information by direct key entry in some cases by pointing to lists or maps OUTPUT FORMAT AND USAGE ROSIN s OUR output files are convertible to INF files Program OUR2INF EXE which are identical to the archive of digital ROSCOP files provided with the OceanPC system The user can easily set up a searchable data set extending the OceanPC digital ROSCOP collection If you make use of this utility you may send your output
64. to convert it to a flat file compatible with the SURFER program or to spreadsheet program or a database management program This selection process is much more detailed and user controllable than the rudimentary selection options offered by the EXPORT COMMA SEPARATED DATA utility INPUT SOURCE FORMAT INFORMATION The user specifies the file already produced by the EXPORT COMMA SEPARATED DATA utility from which data will be selected and converted CSV OUTPUT FORMAT AND USAGE Based on the user s specifications for selecting data from the CSV file the utility creates a new file FLT in either of two different formats 1 If the user is selecting data to use with the SURFER gridding and contouring program then a triplet of data is required for each record A triplet consists of a Latitude and Longitude and any one of the measured parameters e g salinity These values are separated in the output file only by a space 2 If the user is selecting data to use with a spreadsheet program or a database management program for instance to make a graph or to perform other statistical analysis then a doublet of data is required for each record A doublet consists of any pair of measured parameters e g salinity amp temperature These values are separated in the output file only by a space PROCEDURAL NOTES 1 The program first checks to make sure the input file is a 24 field CSV format rather than the alternate 12 fiel
65. uch searching 1t was determined that these stations have depths in error by a factor of ten probably due to a programming error in the original loading of the data which shifted the depths by one column Figure 6 Temperature salinity plot of the same data as Figure 5 but plotted with the ICE EDT utility The ICE EDT utility allows the user to move a cursor to a particular point on the scatter diagram using either the cursor keys or a mouse to see a detailed listing of the profile data at that point This data set provides another example of the need to edit data prior to use The cursor was placed on one of the apparently anomalous points to the right of the main T S pattern in the panel 23 IOC INF 943 page 24 on the left The cross in the figure is the cursor position After selection of this point the ICE EDT utility listed the profile data on the right The cause of the data problem can be seen as a probable key punch error in the salinity at 690 meters depth At this level the salinity was entered as 35 820 rather than 34 820 which is consistent with values above and below this depth Figure 7 Total number of NODC SD2 stations read from the CD ROM in Marsden Square 7209 These totals were made with the ICES WONDER program named for the question I wonder how many stations there arein The data are plotted with a commercial plotting program Harvard Graphics Figure 8 Example of distribution map made with commerci
66. uld be entered at the various screen prompts by three different methods IOC INF 943 page 6 GENERAL OCEAN MAPPING UTILITY This program complies with the new U S Federal Information Processing Standard for geo referenced data in that the coordinates are given in signed decimal degrees For example 56 degrees 30 minutes North would be input as 56 5 112 degrees 45 minutes West would be input as 112 75 MAKE COASTLINE UTILITY Geographic coordinates are supplied to this program as whole number degrees followed by N E S or W as appropriate e g 40 S ALL OTHER UTILITIES The right handed system RHS is used to respond to all other system program prompts In the RHS all latitudes are input as DDMM where D degrees and M minutes northern hemisphere latitudes are positive and southern hemisphere latitudes are negative All longitudes are input as DDDMM western hemisphere longitudes are negative and eastern hemisphere longitudes are positive For example 56 degrees 8 minutes North would be input as 5608 112 degrees 40 minutes West would be input as 11240 If the user examines the contents of any data files in the OceanPC system caution should be observed in reading the geographic coordinates due to differences in the file storage formats which can be quite different from the keyboard input methods described above KEY ENTRY AND FILENAME CONVENTIONS A convention used in this Manual is the use of lt and gt to bracket specific ke
67. uts a CSV file created by prior use of the EXPORT COMMA SEPARATED DATA function Due to a small limitation on the filenames in the ATLAST program the user must also enter a separate filename for the new data file OUTPUT FORMAT AND USAGE There are 4 different data formats in the ATLAST system Rhines 1992 indicated for each file by a single digit in the 8th place of the filename hence a 7 character limit on the user selectable filename the filename extension is usually DAT The output from CSV ATL EXE corresponds ONLY to Format No 3 so the resulting filename is 3 DAT The ATLAST file contains the following variables in random access basic binary format station latitude longitude pressure temperature salinity oxygen sigma 0 sigma 2 sigma 4 nitrate phosphate and silicate The CSV file from which it was converted contains everything except pressure sigma O sigma 2 and sigma 4 Pressure in decibars is estimated as the depth of the observation in meters sigma 0 is calculated from the salinity oxygen in micromoles per kilogram is calculated from oxygen in milliliters per liter and sigma 0 After these substitutions any other missing values are represented by a value of binary zero PROCEDURAL NOTES 1 The program first checks to make sure the input file is a 24 field CSV format rather than the alternate 12 field format Processing will abort here if the file is not a 24 field CSV file 53 IOC INF 943 page 54
68. ystrokes in the examples quoted in the Manual e g lt ENTER gt means a single stroke on the ENTER key also called the CARRIAGE RETURN key or lt CR gt For example if the utility instructions tell the user to supply the input file ICE then the following key sequence would be a valid response GY3536 ICE lt ENTER gt Where GY3536 is the filename of a data file that does exist and its filename extension is ICE Likewise if the Manual remarks that based on the above entry a file ERR will be created the user knows its complete filename will be GY3536 ERR To avoid constant repetition of format names the Manual frequently uses a simple shorthand based on the filename extension for example ICE a file in the ICES Format BLU a file in the Blueprint 86 Format Etc Where is the user provided filename 6 IOC INF 943 page 7 A later section provides a description of the various file types listed by their usual filename extensions OVERVIEW OF COMPONENTS CAPTURE OCEANOGRAPHIC amp ROSCOP DATA OceanPC provides the user with a wide range of options for capturing data Methods encompass New hard copy data from the ship or lab The user s existing digital data and International and regional digital data available from Oceanographic Data Centers and other sources OceanPC deals with each of these categories of information employing utility programs described below MANUAL DATA ENT

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