LMG01_03 Cruise Data Report Mar 18 - Apr 14 2001 Table of Contents Introduction 3 Distribution CD-ROM 3 CD-ROM Directory Stucture 4 Data Formats and Field Descriptions 5 RVDAS Raw Data Set 5 File Naming Conventions 5 File Structure and Channel ID's 5 Underway Instrument Group 5 Navigation Instrument Group 5 Navigational Data Formats 6 Underway Data Formats 10 JGOF Data Format 12 CTD and ADCP Data Archives 13 Instrument Calibrations 14 Additional Information 14 Acquisition Problems and Events 15 Introduction The LMG data acquisition systems continuously log data from several instruments and subsystems throughout the cruise. This document describes the format of that data and its location on the distribution CD. It also contains important information including sensor calibrations, which may affect how this data is processed. Be sure to examine the Acquisition Events and Problems portion of the document. Distribution CD-ROM The data collected during this cruise is distributed on a CD-ROM written in ISO9660 level-1 format. This data format has strict requirements on filenames and organization. However, it is readable by virtually every computing platform. In order to relax the filename requirements and to increase available space on the CD-ROM, almost all data is compressed using the methods described below. While the filename of the archive must follow ISO9660 guidelines, the files in the archive can any names whatsoever. Be aware that some cross-platform file nameing issues can still arise. Data acquired and hosted by the Research Vessel Data Acquisition System (RVDAS) is compressed using UNIX "g-zip" compression. G-zipped files have a ".gz" filename extension. In addition, certain collections of data are then archived using the UNIX "tar" utility. Tools are available on all platforms for decompressing and de-archiving these formats. Virtually any UNIX system will have the gzip and tar utilities. On the Macintosh platform, Stuffit Expander will open a tar archive and decompress gzipped files. For Windows9X, WinZip or pkzip are the most common utilities. It is often useful to know exactly how an archive was produced when expanding its contents. All tar files were created on an SGI using the following commands: tar cvf archive-filename files-to-be-archived To create a list of the files in the archive on a UNIX platform: tar tvf archive-filename > contents.list To extract the files from the archive on a UNIX platform: tar xvf archive-filename files-to-extract G-zipped files will have a ".gz" extension on the filename. These files can be decompressed after de-archiving, using: gunzip filename.gz Data acquired by standalone DOS workstations is compressed using pkzip compatible commands. The same utilities mentioned above for gzip archives will also decompress pkzip compatible archives. CD-ROM Directory Stucture The names in the first column below represent directories or files on the root level of the CD-ROM. Directory names are followed by a "/". The second column represents the files or data archives available on level down in the directory heirarchy. The third column is a description of the archives or files in the second column. ADCP/ adcp.zip raw pingdata and configuration files from ADCP Calibrations/ *.jpg scanned instrument calibration sheets sensor.xls Excel spreadsheet of sensor serial #'s and cal dates. CTD/ ctd.zip raw and converted files from the CTD *.dat raw data files *.cnv data files converted to ascii *B.cnv converted files modified by BINAVG post processing *.hdr header files *.con configuration files *.btl bottle files *.nav navigation files #d.cnv data files with downcast data only. Isobars/ *.gif Isobar image files received during the cruise JGOF/ jgof.tar JGOF formated data Map/ *.jpg image of cruise track map *.ps cruise track map for plotting Report/ report.doc a copy of this report in Microsoft Word97 format report.txt a copy of this report in ASCII text format crurptlmg.doc a cruise report prepared by the Chief Scientist / additional science data in 3 subdirectories RVDAS/ nav.tar navigational data archive of ship's instrumentation uw.tar underway data archive of ship's instrumentation Utility/ mac/ contains expander.sit, a utility for de-archiving on the Mac winzip/ contains WinZip installer, a utilitity for de-archiving under Windows acdc3224.exe installation file shareware image viewer Data Formats and Field Descriptions RVDAS Raw Data Set File Naming Conventions RVDAS data files are named following the convention: [Vessel][Channel_ID].d### * The Vessel fields contains the initals of the vessels name, for example: LMG. * The Channel_ID is a 4-character code representing the instrument of system being logged, for example: met1 (meteorology) * ### is the Julian day during which the data is logged. (GMT time base) File Structure and Channel ID's RVDAS data is divided into two broad categories, Underway and Navigation. The groups are abbreviated "uw" and "nav". Thus, these two subdirectories exist under the top-level rvdas directory. The instruments and their associated Channel ID's are organized as shown. Each data file is g-zipped. Underway Instrument Group * Knudsen Sonar - lknu * Meteorological - lmet * Thermosalinograph - ltsg * ADCP - ladc * Sound Velocity Probe - lsvp Navigation Instrument Group * Ashtech GPS - lash * Trimble P-Code GPS - lpcd * Trimble NT200 GPS - tgps * Gyrocompass - lgyr Time Stamps All RVDAS data is time stamped in the following format before it is written to disk. The timestamp is found at the beginning of each logged data string. YY+DDD:HH:MM:SS.SSS [data stream from instrument] Where, YY: two-digit year (Y2K note: if >= 70 add 1900; if < 70, add 2000) DDD: Julian Day HH: two digit GMT hours MM: two digit GMT minutes SS.SSS: seconds, with millisecond resolution, GMT Navigational Data Formats Yokogawa Gyroscope - LMGlgyr.d### Example: 00+040:00:00:02.108 $HEHDT,308.5,T*21 00+040:00:00:02.447 $HEROT,029.0,A*20 $HEHDT - True Heading Fields: 1. Time and date stamp, yy+jjj:hh:mm:ss.sss 2. $HEHDT, NEMA sentence label 3. Heading in degrees received from vessel gyro compass (###.#) 4. T flag for True Heading, checksum (T*##) $HEROT - Rate of Turn Fields: 1. Time and date stamp, yy+jjj:hh:mm:ss.sss 2. #HEROT: NEMA sentence label 3. Rate of turn, degrees/minute, negative values represent bow turn to port. (###.#) 4. Status: A = Data Valid, checksum (A*##) Trimble Centurion PCODE GPS - LMGlpcd.d### Example: 00+040:00:00:00.465 $GPGGA,000002.925,6139.9970,S,05949.3634,W,3,06,1.3,029.6,M,... ...-018.8,M,,*41 00+040:00:00:00.575 $GPGLL,6139.9970,S,05949.3634,W,000002.925,A*3E 00+040:00:00:00.645 $GPVTG,161.7,T,150.0,M,010.9,N,020.2,K*43 $ GPGGA - Global Positioning System Fix Data Fields: 1. Time and date stamp, yy+jjj:hh:mm:ss.sss 2. $GPGGA, NEMA sentence label 3. UTC of position fix (hhmmss.ss) 4. Latitude in degrees with decimal minutes (####.##) 5. Hemisphere Flag: either N or S 6. Longitude in degrees with decimal minutes (#####.##) 7. Hemisphere Flag: either E or W 8. GPS quality indicator (0=Invalid fix or not available, 1=GPS available, 2=DGPS available) 9. Number of GPS satellites in use (##) 10. Horizontal dilution of precision (HDOP), (#.#) 11. Antenna height above/below mean-sea-level (geoid), (#.#) 12. Units for antenna height (M = Meters) 13. Geoidal Separation1 14. Units for Geoidal Separation (M = Meters) 15. Null field (for differential GPS use) 16. Checksum (*##) 1Geoidal Separation: the difference between the WGS-84 earth ellipsoid and mean-sea-level (geoid). A negative value represents mean-sea-level below ellipsoid. $GPGLL - Geographic Position - Latitiude/Logitude Fields: 1. Time and date stamp, yy+jjj:hh:mm:ss.sss 2. Latitude (####.##) 3. Hemisphere Flag: either N or S 4. Logitude (#####.##) 5. Hemisphere Flag: either E or W 6. UTC of position (hhmmss.ss) 7. Status: A = Data Valid, checksum (A*##) $GPVTG - Track Made Good and Speed over Ground Fields: 1. Time and date stamp, yy+jjj:hh:mm:ss.sss 2. $GPVTG, NEMA sentence label 3. Track, degrees true (#.#) 4. T flag for True 5. Track, degrees magnetic (#.#) 6. M flag for Magnetic 7. Speed over Ground, knots (#.#) 8. N flag for Knots 9. Speed over Ground, km/hr (#.#) 10. K flag for km/hr, Checksum (K*##) Ashtech ADU2 GPS Attitude System - LMGlash.d### Example: 00+077:23:59:59.130 $PASHR,ATT,518412.0,130.72,+001.96,+002.50,0.0024,0.0171,0*2D 00+077:23:59:59.291 $GPGGA,235959.00,6507.5960,S,06444.3192,W,1,08,01.1,+00082,M,,M,,*7E $PASHR,ATT Fields: 1. Time and date stamp, yy+jjj:hh:mm:ss.sss 2. $PASHR,ATT sentence label 3. UTC of position fix 4. Heading in degrees 5. Pitch in degrees 6. Roll in degrees 7. MRMS (measurement RMS error) in meters 8. BRMS (baseline RMS error) in meters 9. Attitude reset flag $GPGGA Fields: 1. Time and date stamp, yy+jjj:hh:mm:ss.sss 2. $GPGGA sentence label 3. UTC of position fix 4. Latitude in degrees, minutes and fraction of minutes 5. Latitude Sector, N-North, S-South 6. Longitude in degrees, minutes and fraction of minutes 7. Longitude Sector, N-North, S-South 8. Raw/differential position, n n = 1, Raw; position is not differential corrected n = 2, position is deferentially corrected n = 9, position computed using almanac information 9. Number of SVs used in position computation 10. HDOP - horizontal dilution of precision, pp.p = 00.0 to 99.9 11. GPS Sensor-computed altitude, saaaaa s = "+" or "-" aaaaa = Altitude 00000 to 30000 meters above WGS-84 reference ellipsiod. Trimble NT2100 GPS - LMGtgps.d### Example: 00+040:00:00:00.065 $GPGLL,6139.96,S,05949.42,W,000002,A 00+040:00:00:00.212 $GPVHW,246,T,234,M,012.3,N,022.8,K 00+040:00:00:00.213 $GPVTG,161,T,149,M,009.6,N,017.8,K 00+040:00:00:00.285 $GPZDA,000002,09,02,2000,00,00 00+040:00:00:00.865 $GPBWC,000003,6209.70,S,05824.00,W,127.2,T,115.3,M,050.1,N,014 00+040:00:00:00.985 $GPGGA,000003,6139.961,S,05949.422,W,1,6,001.64,-00036,M,00000,M,, $GPGGA - Global Positioning System Fix Data Fields: 1. Time and date stamp, yy+jjj:hh:mm:ss.sss 2. $GPGGA, NEMA sentence label 3. UTC of position fix (hhmmss.ss) 4. Latitude in degrees with decimal minutes (####.##) 5. Hemisphere Flag: either N or S 6. Longitude in degrees with decimal minutes (#####.##) 7. Hemisphere Flag: either E or W 8. GPS quality indicator (0=Invalid fix or not available, 1=GPS available, 2=DGPS available) 9. Number of GPS satellites in use (##) 10. Horizontal dilution of precision (HDOP), (#.#) 11. Antenna height above/below mean-sea-level (geoid), (#.#) 12. Units for antenna height (M = Meters) 13. Geoidal Separation1 14. Units for Geoidal Separation (M = Meters) 15. Age of differential GPS data, number of seconds since last SC104 Type 1 or 9 update. 16. Differental reference station ID (####) 1Geoidal Separation: the difference between the WGS-84 earth ellipsoid and mean-sea-level (geoid). A negative value represents mean-sea-level below ellipsoid. $GPGLL - Geographic Position - Latitiude/Logitude Fields: 1. Time and date stamp, yy+jjj:hh:mm:ss.sss 2. Latitude (####.##) 3. Hemisphere Flag: either N or S 4. Logitude (#####.##) 5. Hemisphere Flag: either E or W 6. UTC of position (hhmmss.ss) 7. Status: A = Data Valid $GPVTG - Track Made Good and Speed over Ground Fields: 1. Time and date stamp, yy+jjj:hh:mm:ss.sss 2. $GPVTG, NEMA sentence label 3. Track, degrees true (#.#) 4. T flag for True 5. Track, degrees magnetic (#.#) 6. M flag for Magnetic 7. Speed over Ground, knots (#.#) 8. N flag for Knots 9. Speed over Ground, km/hr (#.#) 10. K flag for km/hr $GPVHW - Speed Through Water and Heading Fields: 1. Time and date stamp, yy+jjj:hh:mm:ss.sss 2. $GPVHW, NEMA sentence label 3. Heading, degrees True (#.#) 4. T flag for True 5. Heading, degrees Magnetic (#.#) 6. M flag for Magnetic 7. Speed through water, knots (#.#) 8. N flag for Knots` 9. Speed through water, km/hr (#.#) 10. K flag for km/hr $GPZDA - Time and Date Fields: 1. Time and date stamp, yy+jjj:hh:mm:ss.sss 2. $GPZDA, NMEA sentence label 3. UTC time (hhmmss.ss) 4. Day: 01 - 31 (##) 5. Month: 01 - 12 (##) 6. Year (####) 7. Local time zone description1, 00 +/-13 hrs (##) 8. Local time zone minutes description, same sign as local hours (##) 1Zone description is the number of whole hours added to local time to obtain GMT, values are negative for East longitudes. $GPBWC - Bearing and Distance to Waypoint Fields: 1. Time and date stamp, yy+jjj:hh:mm:ss.sss 2. $GPBWC, NEMA sentence label 3. UTC of bearing (hhmmss.ss) 4. Destination waypoint latitude in degrees, decimal minutes (####.##) 5. Hemisphere Flag: N or S 6. Destination waypoint longitude in degrees, decimal minutes (#####.##) 7. Hemisphere Flag: E or W 8. Bearing, degrees true (#.#) 9. T flag for True 10. Bearing, degrees magnetic (#.#) 11. M flag for Magnetic 12. Distance to waypoint in nautical miles (#.#) 13. N flag for Nautical Miles 14. Waypoint ID (###) Underway Data Formats Meteorological - LMGlmet.d### Example: 00+040:00:00:00.928 16-10-97 00:01:19 005.53 005.53 005.69 145 141 005.15 005.12 005.15... ...146 148 004.4 004.4 004.4 94.07 94.06 94.07 0981.40 -0.023 00.292 00.315 Fields: all fields are space delimited 1. Time and date stamp, yy+jjj:hh:mm:ss.sss 2. Instrument Date (dd-mm-yy) 3. Instrument Time (hh:mm:ss) 4. Port wind speed, 10 second running average in m/s 5. Port wind speed, minimum in m/s for 24 hour cycle 6. Port wind speed, maximum in m/s for 24 hour cycle 7. Port wind direction in degrees (degrees) 8. Port wind direction standard deviation in degrees (degrees) 9. Starboard wind speed , 10 second running average in m/s 10. Starboard wind speed, minimum m/s for 24 hour cycle 11. Starboard wind speed, maximum m/s for 24 hour cycle 12. Starboard wind direction in degrees (degrees) 13. Starboard wind direction standard deviation in degrees (degrees) 14. Temperature in degrees Celcius 15. Temperature, minimum in degrees Celcius 16. Temperature, maximum in degrees Celcius 17. Relative humidity in percent 18. Relative humidity in percent, minimum 19. Relative humidity in percent, maximum 20. Barometric pressure in millibars 21. PSP (long wave radiometer) - volts, must apply calibration see below 22. PIR (short wave radiometer) - volts, must apply calibration see below 23. PAR (photo-synthetically active radiation, 400 to 700 nm) - volts, must apply calibration7 Knudsen 320B/R Echosounder - LMGlknu.d### Example: 00+040:14:23:10.880 HF,133.1,LF,133.8 1. Time and date stamp, yy+jjj:hh:mm:ss.sss 2. HF, high frequency (12 kHz) flag 3. High frequency depth in meters (###.#) 4. LF, low frequency (3.5 kHz) flag 5. Low frequency depth in meters (###.#) TSG - LMGltsg.d### Example: 00+040:00:00:06.153 6926 15.8827 0.2010 2.9218 3.239 4.334e-01 Fields: all fields are space delimited 1. Time and date stamp, yy+jjj:hh:mm:ss.sss 2. Scan number 3. Internal water temperature in degrees Celcius 4. Salinity 5. External water temperature in degrees Celcius 6. Transmissometer signal in volts 7. Fluorometer signal in volts ADCP Speed Log - LMGladc.d### Example: 00+040:00:00:00.325 $PUHAW,UVH,3.46,-9.35,160.0 Fields: 1. Time and date stamp, yy+jjj:hh:mm:ss.sss 2. $PUHAW, NEMA sentence label 3. UVH, flags identifying the following fields 4. East/West reference1 layer velocity in knots2 (#.##) 5. North/South reference1 layer velocity in knots2 (#.##) 6. Ship's heading as received from gyrocompass (###.#) 1The reference layer is an average velocity measured in a number of depth "bins". On the LMG, the bins are eight meters wide and bins 3-10 define the reference layer. Hence, the reference layer is the water column from 16-80 meters beneath the ship. 2The speed ouput is water velocity relative to the ship's hull and is therefore opposite of the actual movement of the ship. For example, if the ship's heading is due north, the North/South reference layer velocity is likely to be negative (southernly). SV2000 Sound Velocity Probe - LMGsvp1.d### Example: 00+271:00:01:11.728 1537.56 Fields: 1. Time and date stamp, yy+jjj:hh:mm:ss.sss 2. Sound Velocity in m/s JGOF Data Format The JGOFS data set consists of a single file produced each day named jgDDD.dat.gz where DDD is the Julian day the data was acquired. The ".gz" extension indicates that the individual files are compressed before archiving. The daily file consists of 20 separate columnar fields in text format, which are described below. The JGOFS data set is obtained primarily by applying calibrations to raw data and decimating to whole minute intervals. Note: Null, unused, or unknown fields are filled with 9's in the JGOFS data Field Data Units 01 GMT date dd/mm/yy 02 GMT time hh:mm:ss 03 NGL latitude (negative is South) dd.dddd 04 NGL longitude (negative is West) ddd.dddd 05 speed over ground Knots 06 GPS HDOP - 07 Gyro Heading Degrees (azimuth) 08 course made good NOTE: On the LMG, this is unavailable. course over ground is used instead. Degrees (azimuth) 09 mast PAR ?Einsteins/meters2 sec 10 sea surface temperature (C 11 sea surface conductivity Unavailable on LMG siemens/meter 12 sea surface salinity PSU 13 sea depth (uncorrected, calc. sw sound vel. 1500 m/s) meters 14 true wind speed (port windbird) meters/sec 15 true wind direction (port windbird) degrees (azimuth) 16 ambient air temperature (C 17 relative humidity % 18 barometric pressure mBars 19 sea surface fluorometry Volts (0-5 FSO) 20 not used - CTD Data Archive All CTD data acquired on the cruise can be found in the data.zip archive within the ctd directory. The data for each station consists of four files. Each filename consists of LMG0130# where # is the cast number (1 through 6) or LG0130#B for files post processed with BinAvg or #D files for down cast only data. The type of data in each file is listed below. .dat Actual cast data in SeaBird format. .bl Raw Information pertaining to the water sampling bottles for each cast. .btl Converted information form the water samples .ros Rossette information .nav GPS data for each cast .hdr ASCII "header" containing user specific information for each cast. .con Configuration file used during each cast. .cnv data files processed in ascii format. #b.cnv data files post processed with BinAvg #d.cnv data files process post processed with Loopedit and BinAvg from down cast only. #d.ros rosette data for #d.cnv files. Within the ctd directory, the setup directory contains SeaSoft v4.242, which can be used to replay, display, or manipulate the data. It also includes a Setup.zip file containing the .cfg,.dsp, .con files, and post-processing script used during collection. NOTE: Dates appended to the first 2 casts are incorrect. The first CTD cast set to March 18th is actually March 26th. The second CTD cast set to March 21st is actually March 29th. The remaining 4 casts have the correct dates. The times are supplied via the PCODE GPS and are all correct GMT times. ADCP Data Archive The ADCP files are in ASCII text format and have been compressed using the pkzip command. The ADCP data set is broken up into files representing 24 hours of data collection. The files are named pingdata.xxx (xxx representing a day number). Note that these extensions do NOT represent Julian day numbers. Please refer to the DOS (not the compression) date time stamp in the individual pingdata files. During this cruise ADCP collection was modified to produce single ping data in additon to the normal ADCP data set. The large data files produced neccesitated shutting down data collection briefly every 2 days. Any gaps in ADCP data South of King George Island are due to these brief shutdowns. The ADCP system has now been reset to operate normally. Instrument Calibrations The most recent calibration sheets for the TSG, Mast Radiometer and Meteorological Instrumentation have been included on the CD in the cal/ directory. These are scanned image files of the hard copy calibration sheets. A key to match filenames to instruments is shown below. TSG Primary Temperature (Internal) Tsg.jpg TSG Secondary temperature (Sea Water Intake) Tsgtemps.jpg TSG Conductivity Tsgcond.jpg TSG Transmissometer Tsgtrans.gif Sound Velocity Probe- Certification Svp_cert.jpg Sound Velocity Probe- Calibration Svp_cal.jpg Starboard Anemometer StbdWind.jpg Port Anemometer PortWind.jpg Mast Temp/Humidity Humidity.jpg Mast PAR MastPAR.gif Mast PSP MastPSP.gif Mast PIR MastPIR.gif Additional Information The following instrument information may be useful for later analysis. Anemometers (2) R.M.Young Model l 05106, Calibrated by R.M. Young Temperature/Humidity R.M.Young Model 41372VC/VF, Calibrated by R.M. Young Barometer R.M.Young Model 61201, Calibrated by R.M. Young CTD Frequency Connections CTD Freq LMG0103.jpg CTD Voltage Connections CTD Volt LMG0103.jpg CTD Primary Temperature Temp s2444 30Jan01.jpg CTD Secondary Temperature Temp s1542 19Jan01.jpg CTD Primary Conductivity Cond s692 22Aug00.jpg CTD Secondary Conductivity Cond s2048 22Aug00.jpg CTD PAR PAR UW s4470 31Jul00.jpg CTD Transmissometer Trans 407DR 16Nov00.jpg CTD Fluorometer Fluor88093a 18Jun99.jpg Fluor88093b 18Jun99.jpg CTD Dissolved Oxygen DO2 s130412 04May00.jpg CTD Pressure Pres952.jpg Mast PAR BSI model QSR-240P SN 6394. Calibrated March 99 by BSI. Mast Pyranometer PSP Eppley model PSP SN 31701F3. Calibrated August 97 by Eppley Labs. Mast Pyrgeometer PIR Eppley model PIR SN 32031F3. Calibrated September 97 by Eppley Labs. TSG SeaBird model 21. Calibrated by SeaBird Electronics. TSG Remote Temp SeaBird model 3-01/S. Calibrated by SeaBird Electronics. Turner Fluorometer Turner model 10-AU-005 FRTD. Lamp: daylight 10-045, reference filter: 10-052, emission filter: 10-051, excitation filter: 10-050. Calibrated by Turner. Transmissometer Wet Labs model 9903017 C Star 25 cm. SN CST-248DR Calibrated March 17, 2000 by Wet Labs Acquisition Problems and Events This section lists all known problems with acquisition during this cruise including instrument failures, data acquisition system failures and any other factor affecting this data set. The format is jjj:hh:mm (jjj is julian day, hh is hour, and mm is minute). All times are in GMT. 077:17:37 Start RVDA,S Knudsen SONAR 078:03:24 Begin ADCP data acquisition 078:04:00 Start TSG Begin ADCP data acquisition 081:20:52 Switch ADCP to new single ping mode 083:11:20 Shutown TSG & Knudsen at Palmer dock 083:17:07 Change Knudsen sound speed from 1500 to 1459 084:14:09 Restart TSG and Knudsen upon Palmer departure 085:19:49 Change Knudsen sound speed from 1459 to 1449 086:14:43 Change Knudsen sound speed back to 1459 098:12:35 Shutdown TSG and Knudsen at Palmer dock 098:13:05 Switch ADCP back to normal mode 099:14:15 Restart TSG and Knudsen upon Palmer departure 103:01:16 Data collection shutdown at 68West, Strait of Magellan