



     GP2-05-KA
     NOAA Ship KA'IMIMOANA
     San Diego, CA - Galapagos, Ecuador - Manzanillo, Mexico
     April 5 - May 11, 2005

     Chief Scientist: Dave Zimmerman
     Survey Department: ST Shawn Gendron
     CTD Personnel: ST Shawn Gendron, Patrick Rafter
     Final Processing: K. McTaggart


     ACQUISITION: 

     Fifty-three CTD profiles were collected at 49 stations during this cruise.
     Twenty-seven profiles were collected from 12N to 8S along the northern 
     trackline and 110W.  Twenty-six profiles were collected from 8S to 13N 
     along 125W and northern trackline.  The majority of casts were to 1000m.
     Seven casts were deep (>3000m) and 4 were shallow (400m).  There was one 
     test cast (500m) at the start of the cruise to test the termination but 
     these data were neither archived or processed.

     PMC's Sea-Bird 9plus CTD s/n 09P13807-0439 (pressure s/n 59788) was used
     for all casts during this cruise, along with primary temp sensor s/n 1710 
     and primary cond sensors s/n 1467 (casts 0011-0121), and s/n 524 (casts 
     0131-0491).  An SBE 43 oxygen sensor (s/n 313) was installed in line with 
     the primary TC pair.  Secondary temp sensor s/n 4211 and secondary cond 
     sensor s/n 1537 were used for all casts.

     The CTD was mounted in the TAO spare custom 24-bottle frame with TAO SBE 
     carousel pylon s/n 407.  The CTD data stream was passed through TAO 11plus
     deck unit s/n 376 with factory settings.  Digitized data were sent
     to a new Dell personal computer using Windows XP OS equipped with SBE's
     SEASOFT Windows acquisition software.  Calibrated data were displayed
     in fixed listing and graphical form in real-time, as well as stored in
     raw form onto hard disk.  Backups of the raw data were made on a Sony thumb
     drive and DVD.   DVDs were returned to PMEL for post-cruise processing.

     Apparently the air-bleed hole in the y-piece of the primary plumbing was
     clogged during casts 0011-0141.  Then the air-bleed hole in the y-piece
     of the secondary plumbing was clogged intermittently throughout the rest
     of the cruise.  Air in the plumbing results in low surface salinities
     and bad oxygen data as deep as 60 dbar.  It was noted that the pumps
     even shut off after soaking at 10 m.  Also, during cast 0481, the tubing
     at the top of the primary conductivity cell wasn’t secured and the data
     for this cast were bad.


     SALINITY SAMPLES:
   
     No duplicate samples were taken this cruise.  Salinity analysis was 
     performed using Guildline Autosal 8400B salinometer s/n 61.667, Ocean
     Scientific ACI2000, and IAPSO standard seawater batch #P143 dated February
     2003.  The bath temperature was set to 24 degrees Celsius.  Only 8 samples
     are collected per cast instead of 12, and no samples are collected 
     from the half-degree stations between 3N-3S.  Raw data were archived along 
     with CTD data on CD.  

     At PMEL, ACI2000 .dat files were ammended in Excel such that only 1 header
     line, 1 standard correction line, and 3 salinity lines per sample were
     included in the file.  Corrected salinity values were fixed to 4 decimal
     places and the file overwritten in the NT folder as a space delimited file.


     OXYGEN SAMPLES:

     Oxygen samples were collected and analysed at sea by Eric Gehrie of 
     University of Chicago.  Final results were emailed to KEM by Eric on June
     7, 2005.


     CONDUCTIVITY CALIBRATION:
   
     GP205S.CAL of secondary sensor data (te 4211, co 1537) was created at PMEL  
     and used to calibrate stations 1-14 and 48.  Primary sensor data (te 1710,
     co 524) was used to calibrate stations 15-47 and 49.

     Final pressure and temperature calibrations were pre-cruise.  A viscous
     heating correction of -0.0006 C was applied to each temperature sensor
     but both drift corrections were near zero.

     The best fit was determined using CALCOP0 for secondary sensor casts 1-49:

     number of points used   247
     total number of points  287
     % of points used in fit 86.06
     fit standard deviation  0.00194
     fit bias                -0.01315362
     fit co pressure fudge   6.1756615e-007
     min fit slope           1.0005676
     max fit slope           1.0005676

     CALCOP1 was the best fit for the primary sensor, casts 13-49:

     number of points used   169
     total number of points  206
     % of points used in fit 82.04
     fit standard deviation  0.001753
     fit bias                -0.0044737858
     fit co pressure fudge   3.8782887e-007
     min fit slope           0.99997246
     max fit slope           1.0000748

     Slope and bias correction values were applied to CTD burst data and 
     converted directly into netCDF format using CALMSTR and CLB_EPS on 
     PC Pacific.  Final calibrations, including oxygen, were applied using
     CALCTD_K and CALCLO_K.  Calibrated data files were converted to netCDF
     format using CNV_EPSO.f and CLB_EPSO.f.  



     OXYGEN CALIBRATION:

     Following the same procedures as GP504-KA, primary sensor data were
     extracted from the .BTL files using SBECAL1K.f.  Because oxygens were
     drawn from some Niskins where salinities were not drawn, ALLSALT.TXT
     in the /oxy folder was padded in those cases with sample salinities of 
     -9.9999.  Then sample salinities were matched to CTD records by 
     station/sample number using ADDSALK.f.  Sample oxygen data were matched 
     to CTD records by station/sample number using ADDOXYK.f.  -9's were used 
     for missing sample salinities and oxygens.

     Upcast bottle data were matched to downcast profile data by sigma-2 using
     MATCH_SG2_313K.m.  RUN_OXYGEN_CAL_1.m was used to determine an overall 
     group fit with a station dependent slope.  Final coefficients were stored
     in FINAL.mat (roughly, slope=0.48, bias=-0.55, lag=4.6s, tcor=-0.0054, 
     pcor=0.0001, and weight=0).  98.9% of the 67 data points were used in
     the fit with a standard deviation of 1.74 umol/kg.  Calibrated up/down
     profiles with bottles overplotted were examined to verify the fit using
     PLOT_OX.m.  Although there were up to 20 dbar up/down differences, the lag
     seemed appropriate with few instances of over/undershooting in oxygen, 
     even in high gradient regions.

     For casts 0011-0141, oxygens in the top 60 dbar were replaced with upcast
     oxygens using FIX_OX.m.  


     PROCESSING:

     The following are the standard SEASOFT processing modules used to reduce 
     Sea-Bird CTD data:

     DATCNV converts raw data to engineering units and creates a bottle
     file if a Sea-Bird rosette sampler was used.  Both down and up casts
     are processed.

     ROSSUM averages the bottle data specified in the DATCNV output and 
     derives salinity, theta, and sigma-theta. Bottle data are used
     to calibrate the CTD and O2 sensor post-cruise. 

     WILDEDIT makes two passes through the data in 100 scan bins.  The
     first pass flags points greater than 2 standard deviations; the
     seond pass removes points greater than 20 standard deviations from
     the mean with the flagged points excluded.  Data were kept within 100
     of the mean (i.e. all data).

     FILTER applies a low pass filter to pressure with a time constant of
     0.15 seconds.  In order to produce zero phase (no time shift) the
     filter is first run forward through the file and then run backwards
     through the file.

     CELLTM uses a recursive filter to remove conductivity cell thermal
     mass effects from the measured conductivity.  In areas with steep
     temperature gradients the thermal mass correction is on the order
     of 0.005 psu.  In other areas the correction is negligible.  The
     value used for the thermal anomaly amplitude (alpha) is 0.03.  The
     value used for the thermal anomaly time constant (1/beta) is 7.0.
 
     LOOPEDIT removes scans associated with pressure slowdowns and
     reversals.  If the CTD velocity is less than 0.25 m/s or the pressure
     is not greater than the previous maximum scan, the scan is omitted.

     BINAVG averages the data into 1 db bins.  Each bin is centered around
     a whole pressure value, e.g. the 1 db bin averages scans where pressure
     is between 0.5 db and 1.5 db.  There is no surface bin.

     DERIVE uses 1 db averaged pressure, temperature, and conductivity to
     compute salinity, theta, sigma-theta, and dynamic height.

     TRANS converts the data file from binary to ASCII format.

     Program CALCTD_K.m applied a viscous correction to temperature, calibration
     coefficients to conductivity, and final oxygen coefficients to compute
     oxygen (umol/kg).  Pressure calibrations were pre-cruise.  CALCTD_K.m also  
     computed a calibrated salinity profile.  Deep TS profiles compared well
     with historical profiles for the most part, although casts 0052 and 0081
     were salty by 0.003-0.005 PSU.  Calibrating them more closely with the
     bottles in a grouping of casts 0011-0141 would only make them saltier
     so they were left they are.  Program CNV_EPSO.f converted the calibrated 
     ASCII data files into NetCDF format, filling in the surface to 1 dbar, 
     and computing theta, sigma-t, sigma-theta, and dynamic height.

     Likewise for burst data, program CALCLO_K.m applied post-cruise 
     calibrations to the bottle file (gp205o.fin) and program CLB_EPSO.f
     converted it into NetCDF format.  There were 4 bad sample salinities:
     station 0241 sample 11, 0261 13, 0411 11, and 0451 12.  There were 3
     bad sample oxygens:  station 0051 sample 11, and 0251 samples 108 and
     109.  Bad points were not included in the final bottle data files.

     Final CTD and bottle files were moved to /home/plover/insitu2/DATA/hayes
     /gp205/ctd/ and /bot and included in the MySQL data management tables on
     June 30, 2005.



     JULY 21, 2005

     Calibrated profile data for this cruise include conductivities from 
     secondary sensor s/n 1537 for casts 0011-0141 and 0481; and conductivities
     from primary sensor s/n 524 for casts 0151-0471 and 0491.  This is because
     of intermitently clogged y-bleed valves in the primary and secondary
     plumbing, except for cast 0481 where the tubing was detached from the 
     primary conductivity sensor at the snap fitting.  No changes were made to
     these data on July 21, 2005.

     However, calibrated burst data for this cruise include only primary
     conductivities from sensor s/n 1467 for casts 0011-0121, and from sensor 
     s/n 524 for casts 0131-0491.  This is because the oxygen sensor s/n 313
     was plumbed with the primary TC and calibrated with the primary TC.  
     Upcast data were not affected by the y-bleed problems mentioned above,
     and there is no bottle data for cast 0481.  Only one sample oxygen is
     associated with a bad CTD oxygen (cast 0051 sample 15) from matching 
     upcast values with downcast values for calibration purposes where the
     CTD oxygen trace was affected by the clogged y-bleed valve.  

     \oxy\calclo_k.m was modified to apply only primary conductivity cals
     and rerun to produce gp205o_eps.fin containing all values (n=352).  The
     4 bad sample salts and 3 bad sample oxygens were changed to -9.9s before
     rerunning clb_epso.f for revised PMEL bottle files in NetCDF format.  
     PMEL bottle files don't include CTD salinity or CTD oxygen, just bottle
     data.  gp205o_eps.fin was sent to Eric Gehrie at his request with mention
     of the 8 bad values in an email.