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Final data

Final CTD data have passed through the CalCOFI quality control process and are considered the best data we provide. After standard SBE Data Processing (Seabird's data processing suite) tuned for our SBE 911 or 911+, the CTD asc files are additionally processed by SIO-CalCOFI in-house software (BtlVsCTD). Averaged (4-sec or 1m binavg) CTD sensor data are matched with corresponding bottle data and corrected two ways: cruise-corrected and station-corrected.

The final CTD.csvs include three versions of sensor data:

  1. SBE-processed data; no bottle corrections applied
  2. Cruise-corrected CTD data (column labels '_CruiseCorr'); cruise-corrected data are CTD sensor data corrected using regression coefficients derived from 4-sec ave sensor data vs bottle data comparisons for the entire cruise (all casts with bottle samples; n=~1400; fliers omitted).
  3. Station-corrected CTD data (column labels '_StaCorr') are CTD sensor data corrected using regression coefficients generated dynamically for each cast, 1m binavg sensor data vs bottle data (n=~20; fliers omitted). Since sensor behavior may vary from station-to-station, station-corrected CTD data for salinity, oxygen, estimated NO3, estimated chlorophyll-a; corrected using the individual cast bottle samples station-corrected CTD sensor data are considered the best, particularly for estimated nitrate.

06 Oct 2017 - uploaded revised FinalQC zips for 1402SH, 1404OS, & 1407NH with relabeled .asc voltage headers & filenames; data unchanged

20 Sep 2017 - added FinalQC CTD data for 1611SR, including RINKO III O2 data

05 Sep 2017 - added prelim CTD data for 1708SR, fixing NO3 import error on casts 008 & 009

28 Jun 2017 - corrections to 1504SH & 1507OC Raw CTD cast data, updated pressure coefficients; new CTDCast.zips posted

27 Jun 2017 - corrections to 1604SH Raw CTD cast data, casts 001-025 xmlcon files corrected pressure coefficients; new zip posted

22 May 2017 - corrections to 1507OC & 1511OC Final CTD data

1507OC - longitude noise on casts 001, 013, 018, 027, 029, 031, 044, 046, 055, 060, 062, 067 corrected.
1511OC - bad downcast surface data flagged on cast 016 & 017 due to pump issues. (thanks Sharon)

27 Apr 2017 - added 1704SH raw & preliminary CTD data

22 Mar 2017 - corrections to 1601RL CTDCast & finalQC CTD+Bottle data

Casts 099 did not merge properly with bottle data in the previous version due to sta mislabeling in the CTD .hdr file. The newest 20-1601RL_CTDFinalQC.zip has corrected CTD.csvs and plot for Cast 099. Cast 099 line.sta was mislabel sta 63.3 50.0 so the raw CTD.hex file and processed .asc & .csv files have been corrected; there is a new 20-1601RL_CTDCast.zip.

16 Mar 2017 - 1411NH CTD Data Update

CalCOFI 1411NH CTD files have been renamed using the new schema; sta 071 was re-merge with bottle data excluding 4 bad bottle oxygens - sta-corrected CTD oxygens should be much improved for this station. New plots were done including secondary sensor downcast and upcast plots.

CalCOFI 1202NH CTD data have been reprocessed into 82-column CTD.csvs; filenames have been updated to YY-YYMMSC_LLLLSSSS_###DU; .asc voltages have been relabeled. Cast 004-007 sta-corrected oxygens have been recalculated after eliminated bad 270m bottle data from sta.csvs.

15 Mar 2017 - New Final CTD Data

1601RL CTD+Bottle Data Online

Earlier additions and changes

2015 cruises (1501, 1504, 1507, 1511) CTD fies renamed using the new schema - YY-YYMMSC_LLLLSSSS_###DU. Also sensor voltage columns have been relabled in the .asc files but original .asc files have also been archived. 

2012 cruises: 1210, 1207, 1203 have been re-processed into 82-column datacode-friendly format. Data are unchanged from previous final data but additional columns have been added to the CTD.csvs. Also primary and secondary sensor plots have been generated and archived.

This tabulation was started 16Mar2017 and will be updated frequently. Changes to CTD data are listed on the CTD Processing Summary web page for each cruise. Please refer to individual cruise pages for additional detailed information on CTD data processing, re-processing, and re-formatting.

Please note that 'prelim' files are Seasave-processed asc data; preliminary bottle-corrected CTD+bottle data may also be included; 'cast' files are raw CTD cast files; 'final' are combine Seasave-processed asc data with bottle-corrected CTD data & bottle data.
Reprocessing of older CTD data files is currently underway, adding data-quality code columns and data codes on bad or missing data ("9") or questionable data ("8"). Data values should not have changed from previously published final CTD data. But the total number of columns in the updated CTD.csvs have changed from 65 to 82. "Final" CTD archives are 65 or 66 column format; "finalQC" CTD data files are 82-columns.
Refer to the CTD.csv data format webpage: 65-column index; 82-column index for columns added.
     
WINTER       SPRING       SUMMER       AUTUMN      

2017

  1701RL
FinalQC
cast
        1704SH
prelim
cast
        1708SR
prelim
cast
  1607 75 Station Pattern       1711SR   1607 75 Station Pattern      

2016

  1601RL
FinalQC
cast
        1604SH
FinalQC
cast
        1607OS
FinalQC
cast
  1607 75 Station Pattern       1611SR
FinalQC
cast•
  1611 75 Station Pattern      

2015

  1501NH
finalQC
cast
        1504NH
finalQC
cast
  1504NH 70 Station Pattern       1507OC
FinalQC
cast
  1202 75 Station Pattern       1511OC
FinalQC
cast•
  1202 75 Station Pattern      

2014

 

1402SH
finalQC
cast

  1402SH36StationTrack100       1404OS
finalQC
cast
  1404OS 75 Station Pattern       1407NH
finalQC
cast
  1407NH 75 Station Pattern       1411NH
finalQC
cast
  1411NH 75 Station Pattern      

2013

 

1301SH
finalQC
cast

        1304SH
finalQC
cast
        1307NH
finalQC
cast
   1307NH 75 Station Pattern       1311NH
finalQC
cast
  1311NH 75 Station Pattern      

2012

 

1202NH
finalQC
cast

  1202 75 Station Pattern       1203SH
finalQC
cast
  1203SH 75 Station Pattern       1207OS
finalQC
cast
   1207OS 75 Station Pattern       1210NH
finalQC
cast
rinko
  1210NH 75 Station Pattern      

2011

 

1101NH
final
cast

        1104SH
final
cast
   75 Station Pattern       1108NH
final
cast
   75 Station Pattern       1110NH
final
cast
   75 Station Pattern      

2010

 

1001NH
finalQC
cast

          1004MF
final
cast
   75 Station Pattern       1008NH
final
cast
   75 Station Pattern       1011NH
final
cast
   75 Station Pattern      

2009

 

0901NH
final
cast

  anchor       0903JD
final
cast
  anchor       0907M2
final
cast
  anchor       0911NH
final
cast
  anchor      

2008

 

0801JD
final
cast

  0801Map       0804JD
final
cast
  0804Map       0808NH
final
cast
  0808Map       0810NH
final
cast
  0810Map      

2007

 

0701JD
final
cast

  0701Map       0704JD
final
cast
  0804Map       0707NH
final
cast
  0808Map       0711NH
final
cast
  0810Map      

2006

 

0602JD
final
cast

  0601Map       0604JD
final
cast
  0604Map       0607NH
final
cast
  0607Map       0610RR
final
cast
  0610Map      

2005

 

0501JD
final
cast

  0501Map       0504NH
final
cast
  0804Map       0507NH
final
cast
  0507Map       0511NH
final
cast
  0511Map      

2004

 

0401JD
final
cast

  0401Map       0404NH
prelim
cast
  0404Map       0407JD
prelim
cast
  0408Map       0411RR
final
cast
  0411Map      

2003

 

0302JD
prelim
cast

  0302Map       0304RR
final•
cast
  0304Map       0307NH
final•
cast
  0307Map       0310NH
final•
cast
  0310Map      

2002

 

0201JD
final•
cast

  0201Map       0204JD
final•
cast
  0204Map       0207NH
final•
cast
  0207Map       0211NH
final•
cast
  0211Map      

2001

 

0101JD
final•
cast

  0101Map       0104JD
final•
cast
  0104Map       0107NH
final•
cast
  0107Map       0110NH
final•
cast
  0110Map      

2000

 

0001NH
final•
cast

  0001Map       0004JD
final•
cast
  0004Map       0007NH
final•
cast
  0007Map       0010NH
final•
cast
  0010Map      

 

The CTD Database is currently under reconstruction. The files on this web page are database-import-ready csvs which combine 1m bin-averaged CTD sensor data with rosette bottle data. The addition of data-quality code columns requires older (than 2013) archived cruises be reformatted with data code columns added. Currently, the original CTD+bottle data 62-column data files (YY-YYMMSS_CTDFinal.zip) are being reprocessed to insure consistency of the csv format. Data codes (see the CTD Database Index for key) are added to the QC columns to flag bad or questionable CTD sensor data. These data-quality codes may be used to exclude bad or questionable data during queries.  Original data values should not change, only the format from 62 to 82 columns.

CTD data archives labeled with "QC" (YY-YYMMSS_FinalQC.zip) or "DB" (YY-YYMMSS_FinalDB.zip) are the latest format. Individual database-ready csvs will be available for each cruise so users can update an existing database on whatever platform they prefer. The addition of these new columns should not change the data presented in the earlier formats. But when a sensor measurement is data coded "9", data derived for it will change to "NaN" - estimated NO3 from the ISUS sensor, for example. Refer to the CTD Database Index and the CTD.csv with QC Index pages for columns and descriptions. As older CTD data are reprocessed to add the QC columns and data codes, the list of database-ready csvs will be updated.

 Please note that filenames have or will change to match the current CTD data distribution format. CTD.csvs processed with IEH-formatted bottle data (all cruises prior to 2012) will have an "I" denoting "IEH" in the filenames before "D.csv" or "U.csv": e.g. 20-1104SH_093301200_049Id.csv.
Preliminary versions of the 2017 database csvs are available by request (This email address is being protected from spambots. You need JavaScript enabled to view it.) but this page only lists final versions.

Two versions of the CTD final data for each cruise (YY-YY is year, MM is month, SS is ship code):

  • YY-YYMMSS_CTDFinalDB = two file subset of CTDFinalQC complete archive: datacoded downcast bottle-corrected CTD data with bottle data csv & upcast bottle-corrected CTD data plus bottle data csv.
  • YY-YYMMSS_CTDFinalQC = standard final CTD & CTD+Btl data files available on Cruise Summary pages and Recent CTD Data page. It is also made available here since it includes the database-ready CTD+Btl csvs plus plots, CTD asc & hdr files and metadata. Individual station CTD+Btl.csvs, same database-ready format, are in the csv subdirectory. 
  • Under revision - YYYY_CTDFinalQC: includes all CTD+Btl csvs for the year in two files - upcast+bottle data, downcast+bottle data - these are currently being rebuilt, stay tuned
Year Winter Cruise Spring Cruise Summer Cruise Autumn Cruise
2017  20-1701RL_CTDFinalDB
20-1701RL_CTDFinalQC
     
2016  20-1601RL_CTDFinalDB
20-1601RL_CTDFinalQC
20-1604SH_CTDFinalDB
20-1604SH_CTDFinalQC
20-1607OS_CTDFinalDB
20-1607OS_CTDFinalQC

20-1611SR_CTDFinalDB
20-1611SR_CTDFinalQC

2015  20-1501NH_CTDFinalDB
20-1501NH_CTDFinalQC
20-1504NH_CTDFinalDB
20-1504NH_CTDFinalQC
20-1507OC_CTDFinalDB
20-1507OC_CTDFinalQC
20-1511OC_CTDFinalDB
20-1511OC_CTDFinalQC
2014  20-1402SH_CTDFinalDB
20-1402SH_CTDFinalQC
20-1404OS_CTDFinalDB
20-1404OS_CTDFinalQC
20-1407NH_CTDFinalDB
20-1407NH_CTDFinalQC
20-1411NH_CTDFinalDB
20-1411NH_CTDFinalQC
2013  20-1301SH_CTDFinalDB
20-1301SH_CTDFinalQC
20-1304SH_CTDFinalDB
20-1304SH_CTDFinalQC
20-1307NH_CTDFinalDB
20-1307NH_CTDFinalQC
20-1311NH_CTDFinalDB
20-1311NH_CTDFinalQC
2012  20-1202NH_CTDFinalDB
20-1202NH_CTDFinalQC
20-1203SH_CTDFinalDB
20-1203SH_CTDFinalQC
20-1207OS_CTDFinalDB
20-1207OS_CTDFinalQC
20-1210NH_CTDFinalDB
20-1210NH_CTDFinalQC
2011 20-1101NH_CTDFinalDB
20-1101NH_CTDFinalQC
20-1104SH_CTDFinalDB
20-1104SH_CTDFinalQC
20-1108NH_CTDFinalDB
20-1108NH_CTDFinalQC
20-1110NH_CTDFinalDB
20-1110NH_CTDFinalQC
2010 20-1001NH_CTDFinalDB
20-1001NH_CTDFinalQC
     
2009        
2008        
2007        
2006        
2005        

 

CTD Database Development Notes

Please note as of mid-2015, a revision of the CTD database is currently underway. With additional data quality code columns added to the CTD+bottle csvs offered as final processed data, new files are being created by re-processing the CTD archives. Measurement values should remain unchanged but the format is being updated.

Older information about database development is described below:

Starting with CalCOFI 0907M2, the BTLvsCTD program (developed by SIO-CalCOFI) generates several database-friendly csvs. With Seasave Data Processing software v7.19, sensor calibration coefficients are embedded as xml data in the .hdr file.  BTLvsCTD.exe parses the .hdr for all stations into three csvs: hdr.csv, xmlcoeff.csv, & span.csv.

  • The .hdr csv includes the cast information such as date, time, line, sta, lat & lon, sensor configuration, and all Seasave data processing modules and coefficients applied.
  • The span.csv is a tabulation of the min and max values for each sensor, extracted from the .hdr file. This file/table will be useful for automating basic data-quality controls and sensor behavior assessments, allowing data processors to query data ranges for validity.
  • The last file is xmlcoeff.csv, a tabulation of the coefficients for sensor.

Starting with 0907, the first cruise to use dual SBE43 O2 sensors so the data tables will have these columns by default. Earlier cruises, using single O2 sensors will auto-fill the tables, leaving the second O2 columns blank. 
Since sensor installation may vary from cruise to cruise and sensors may occupy different voltage channels, the voltage references v1 v2 v3... are replaced by TransV FluorV AltV... whenever possible.This requirement required a revision of BTLvsCTD.exe dated 9 Nov 2009 since I had originally maintained the voltage # in respect to sensor.  But this creates a database import problem; v0_Trans, v1_Fluor will not integrate with v0_Fluor, v1_Trans so both are renamed TransV FluorV, removing the specific voltage # reference.

Currently, relabeling of the voltage channels is offline since it creates data reprocessing issues. You will have to refer to the hdr file to determine which sensor occupies the 8 voltage channels (V0-V7). We try to keep the channels consistent unless deploying test sensors for performance assessment. Like the RINKO Oxygen Optode on 1210NH.

  • V0 = Transmissometer
  • V1 = Fluorometer
  • V2 = PAR
  • V3 = Altimeter
  • V4 = Primary Oxygen
  • V5 = Secondary Oxygen
  • V6 = ISUS Nitrate
  • V7 = pH
  • V15 = Surface PAR, when made available by the vessel; SIO's was retired

BTLvsCTD.exe's main module also generates bottle-corrected upcast and downcast csvs, merging all the individual station up and down csvs into two files.  A dbcoeff.csv file is generated tabulating the cruise-ave bottle vs CTD coefficients as well as the station regression coefficients (each station's CTD data are regressed against bottle samples from that station, reducing the station-to-station variability witnessed using the cruise-ave coefficients).  If bottle data are not available then only cruise-ave coefficients are used to correct the CTD data.

BTLvsCTD.exe has a module to automatically relabel the v0 v1 v2... to the sensor voltage in all .asc files. (I plan on using the hdr to automate this but currently the table in BTLvsCTD tabulating voltages vs sensor is used.)

BTLvsCTD.exe has a file renaming module that renames all dYYMM###.asc & .hdr, uYYMM###.asc & .hdr files to web-format YYMM_LLLLSSSS_###d.asc & .hdr, YYMM_LLLLSSSS_###u.asc & u.hdr.

The CalCOFI CTD Database format is currently being revised (Sept 2015). Data quality columns for each sensors are being added to the database tables to flag questionable or bad data. Until this version is available, the original CTD database links will be available below.

Review the database index for column descriptions.
2005-2012 MS Access database - 2005 - 2012 final bottle-corrected CTD database

The CTD database is constructed or updated from each cruises' CTD cast files after bottle-corrections have been applied. Two tables - upcast & downcast - are in the database along with bottle data used to calibrate the sensors. Note that typically three columns are available for each sensor: Seasave-only processed sensor data - no bottle correction applied; cruise-corrected ("CruiseCorr") = bottle-corrected sensor data using coefficients derived from regressing all bottle data to sensor data; station-corrected ("StaCorr") = bottle-corrected sensor data using coefficients derived from regressing only the current station's bottle data to sensor data. Station-corrected sensor data is considered the best when 20 or more bottle samples are available to calibrate the sensor measurements. Station-correcting helps eliminate the station-to-station variability in certain sensor, particularly the ISUS when a new lamp is installed and experiencing "burn-in" drift.

CalCOFI CTD Database Data Summary
Column Header Units Description
ID Number/Long Integer Database assigned index
Project Text CalCOFI
Study Text Cruise YYMMSS
Ord_Occ Number/Integer Station order
Event_Num Number/Integer CTD-at-depth Event Number
Cast_ID Text Cruise_OrderOccupied_Up or Down
Date_Time_UTC Date/Time CTD-At-Depth GPS UTC
Date_Time_PST Date/Time CTD-At-Depth Computer PST
Lat_Dec Number/Double GPS Decimal Latitude (always N)
Lon_Dec Number/Double GPS Decimal Longitude (always W)
Sta_ID Text CalCOFI Line Station
Line Number/Double CalCOFI Line
Sta Number/Double CalCOFI Station
Depth Number/Double Depth in meters
Pressure Number/Double Pressure in decibars
Temp1 Number/Double CTD Sensor 1 Temperature deg C
Temp2 Number/Double CTD Sensor 2 Temperature deg C
TempAve Number/Double Ave CTD Sensor 1+2 Temperature deg C
Salt1 Number/Double CTD Temp 1+Conductivity 1 Salinity PSU
Salt1_Corr Number/Double CTD Temp 1+Conductivity 1 Salinity PSU Bottle Offset Corrected
Salt2 Number/Double CTD Temp 2+Conductivity 2 Salinity PSU
Salt2_Corr Number/Double CTD Temp 2+Conductivity 2 Salinity PSU Bottle Offset Corrected
SaltAve_Corr Number/Double CTD Primary+Secondary Salinity Bottle-corrected Average
Ox1 Number/Double CTD Primary Oxygen mL/L
Ox1_CruiseCorr Number/Double CTD Primary Oxygen mL/L, regression corrected using all O2 bottles
Ox1_StaCorr Number/Double CTD Primary Oxygen mL/L, regression corrected using matching station O2 bottles
Ox2 Number/Double CTD Secondary Oxygen mL/L
Ox2_CruiseCorr Number/Double CTD Secondary Oxygen mL/L, regression corrected using all O2 bottles
Ox2_StaCorr Number/Double CTD Secondary Oxygen mL/L, regression corrected using matching station O2 bottles
OxAve_StaCorr Number/Double CTD Station-corrected Primary+Secondary Oxygen Average mL/L
FluorV Number/Double Fluorometer Voltage
EstChl_CruiseCorr Number/Double Fluorometer Estimated Chl, regression calc'd using all cruise chlorophyll-a samples
EstChl_StaCorr Number/Double Fluorometer Estimated Chl, regression calc'd using matching sta chlorophyll-a samples
ISUSV Number/Double ISUS Nitrate Sensor Voltage
EstNO3_CruiseCorr Number/Double ISUS Estimated NO3, regression calc'd using all cruise NO3 samples
EstNO3_StaCorr Number/Double ISUS Estimated NO3, regression calc'd using matching sta NO3 samples
SigThetaTS1 Number/Double Sigma-theta, primary sensors, Seabird algorithm
SigThetaTS2 Number/Double Sigma-theta, secondary sensors, Seabird algorithm
BAT Number/Double Transmissometer Beam Attenuation Coefficient, Seabird algorithm
XMiss Number/Double Transmissometer %Transmission, Seabird algorithm
SPAR Number/Double Surface Photoradiometer Irradiance (unavailable on NOAA vessels)
PAR Number/Double CTD Insitu Photoradiometer Irradiance, Seabird algorithm
PoT1 Number/Double Primary Potential Temperature, Seabird algorithm
PoT2 Number/Double Secondary Potential Temperature , Seabird algorithm
DynHt Number/Double Dynamic Height, Seabird algorithm
SVA Number/Double Specific Volume Anomaly, Seabird algorithm
OxSat1 Number/Double Primary O2 Saturation, Seabird algorithm
OxSat2 Number/Double Secondary O2 Saturation, Seabird algorithm
BTL_Depth Number/Single Bottle Depth
BTL_Temp Number/Single Bottle Temperature (should match CTD Primary Temperature)
SaltB Number/Single Bottle Salinity
OxB Number/Single Bottle Oxygen
Chl-a Number/Single Bottle Chlorophyll-a
Phaeo Number/Single Bottle Phaeopigments
NO3 Number/Single Bottle Nitrate
NO2 Number/Single Bottle Nitrite
NH4 Number/Single Bottle Ammonium
PO4 Number/Single Bottle Phosphate
SIL Number/Single Bottle Silicate

CalCOFI processes our CTD casts using the guidelines recommended by Seabird for our 911+ sensor array and depths. Please refer to the CTD Data Processing Protocol web page for the Seasoft modules applied. This page describes the in-house software used to merge CTD sensor data with bottle data, derive bottle corrections to apply to sensor data, & CTD data flagging. Also explained is the organization of data and metadata files distributed online as preliminary & final data products.
Files referenced: '.asc' & '.hdr' files are Seasoft-generated CTD data files. All other files referenced are SIO-CalCOFI data files generated at-sea and ashore from data acquistion & analysis software and SIO-CalCOFI-developed in-house software. SIO-CalCOFI's data processing methods, file formats, and metadata descriptions are available on the Data FormatsMethods web pages.

1A) BTLvsCTD1 Step 1: (files required: sta.csvs with all bottle data columns populated; corrected YYMMcasts.csv, Seasoft-processed non-binavg CTD.asc & .hdr files). Preliminary bottle data ('YYMM###.csv' sta.csvs) are merged with 4-sec-ave (prior-to-bottle-closure) CTD .asc data, creating a single YY-YYMMSS_CTDCSV###-###.csv that is imported into Excel.

1B) Bottle vs CTD sensor data are plotted: primary CTD oxygen vs bottle oxygen ml/L & umol/kg; secondary CTD oxygen vs bottle ml/L & umol/Kg; FlV (usually V1) vs Chl-a; ISUSV (usually V6) vs NO3; CTD Salts > 350m are compared to bottle salts.

Three duplicate spreadsheets are pasted as new sheets to allow sorting and deletion of specific columns (or you can cut-paste specific columns to new sheets, if you prefer)

  • 'Salts > 350m' - all data are sorted by Pr or Depth, Largest to smallest and all rows less than 350m deleted. Two columns are added: bottle salt - CTD Salt00 & bottle salt - CTD Salt 11. Mean, SD, Min, Max, & n are calculated at the bottom of the column. Any values above 0.02 are excluded. The mean values of the bottle minus primary & secondary salts become the offsets.
  •  'Oxygen umol/kg' - for some reason leaving blank fields in the umol/Kg O2 columns can generate "wavy" scatter plots so deleting rows missing bottle oxygen data and missing CTD oxygen sensor data (unusual) is advised. "Fliers" are removed - either bad or questionable bottle or sensor data. Four plots total - Ox1ML vs OxB, Ox2ML vs OxB, Ox1UM vs OxB, Ox2UM vs OxB.
  •  'ISUS vs NO3' - remove missing or 0 ISUS voltages rows and missing bottle NO3 rows then plot & add a trendline.
  •  'Fluorometer voltage vs chl-a' plot can be generated from the main spreadsheet without issue. Or you can create a 'Chl-a' spreadsheet sorted by depth and delete all depths > 200m.

On all plots - all bottle-data fliers, such as mistrips or misdraws, are removed before trendlines added. PDF plots of all regressions are generated plus 400px & 1024px jpgs for posting online. Preliminary regressions and plots are posted since it can take a year for final data to become available. Once final, regression coefficients and plots are updated with new data.
1C) Seasoft 'Split' and 'Binavg' modules are applied to CTD.asc files, generating 1m binavg up & downcast asc files. It is important to verify any mislabeled CTD .hdr files have been corrected before step 2A to insure the matching sta.csv merges properly with CTD.asc. When there's a mismatch, it's usually caused by the cast number (###; aka 'Proc #' or 'Order Occupied') or CalCOFI Line Sta (eg 93.3 120.0) values being mis-entered when the cast starts. It is usually corrected at-sea but the .hdr correction may be lost if the .hex file has not been corrected. It requires the cast's .hex file be corrected using a binary editor (HxD Hex Editor) to stop the error from re-appearing when processed by Seasoft. If corrected, the original CTD cast .hex & .hdr files should be updated into the cast.zip (YYMM###.zip) & the cruise's YYMMSS_CTDCast.zip distributed online, & documented on the 'CTD Updates' web page.

1D) Inspect and correct YYMMcasts.csv & YYMMevents.csv. YYMMevents.csv will require "erase previous event" editing and Line & Sta verification. After YYMMcasts.csv and YYMMevents.csv have been manually corrected, run the DECODR2 'Clean Event Log' module to compare casts.csv order occupied numbering to the eventlog. (JLW usually checks & corrects the YYMMcasts.csv so coordinate with her to avoid duplicating effort).

CTD Processing Summary CalCOFI 1611SR CTD Preliminary Data
Download 1611SR CTD raw cast files zipped Download 1611 Preliminary CTD + bottle data (RINKO O2 still being processed)
General CTD Notes - data acquisition notes, logistics, processing - see below.
Please note that these regressions are generated from preliminary CTD vs bottle data and will be reprocessed once final bottle data are available. CTD temperatures and salinities do not usually change but oxygen, estimated chlorophyll-a, estimated nitrate may change significantly after point-checking. Questionable or mistrip bottle data are removed from these comparisons but may be visible on the CTD.csv plots. For this cruise and future cruises, both primary & secondary sensor profiles vs bottle data will be generated and archived in the downloadable CTD+Bottle data files. These plots are under the "csv-plots\Primary" & "csv-plots\Secondary" subdirectories.
CTD sensor corrections derived by comparing CTD sensor data, 4sec average prior to bottle closure, to bottle samples
Dual T, S, & O2 Primary Sensor Secondary Sensor
Salinity offset (bottle - CTD salinity; > 350m only; Seabird SBE4) -0.00169 -0.00506
Oxygen ml/L (dual Seabird SBE43 on 27 stations; 1-SBE43 & 1- RINKO III on 48 stas, RINKO O2 data available soon) y = 0.9946x+0.0382
R² = 0.9994
y = 1.0199x + 0.0241
R² = 0.9996
Oxygen umol/Kg (dual Seabird SBE43) y = 0.9962x+1.7389
R² = 0.9994
y = 1.0212x + 1.1992
R² = 0.9996
Single sensors Linear Polynomial
Nitrate - ISUS 4sec ave voltage vs Bottle Nitrate (Satlantic MBARI-ISUS v2) y = 31.47x + 0.1785
R² = 0.9618
 
Fluorometer - linear & polynomial regressions

y = 7.513x-0.2674

R² = 0.7601

y = 14.942x2 + 3.3866x - 0.0897

R² = 0.7863

  
 
  Secondary CTD O2 Sensor vs Bottle O2
MBARI-ISUS Voltage vs Bottle NO3 Seapoint Fluorometer Voltage vs Chlorophyll-a
 

CTD Processing Summary CalCOFI 1607OS CTD Preliminary Data
Download 1607OS CTD raw cast files zipped Download 1607 Preliminary CTD + bottle data 
General CTD Notes - data acquisition notes, logistics, processing - see below.
Please note that these regressions are generated from preliminary CTD vs bottle data and will be reprocessed once final bottle data are available. CTD temperatures and salinities do not usually change but oxygen, estimated chlorophyll-a, estimated nitrate may change significantly after point-checking. Questionable or mistrip bottle data are removed from these comparisons but may be visible on the CTD.csv plots. For this cruise and future cruises, both primary & secondary sensor profiles vs bottle data will be generated and archived in the downloadable CTD+Bottle data files. These plots are under the "csv-plots\Primary" & "csv-plots\Secondary" subdirectories.
CTD sensor corrections derived by comparing CTD sensor data, 4sec average prior to bottle closure, to bottle samples
Dual T, S, & O2 Primary Sensor Secondary Sensor
Salinity offset (bottle - CTD salinity; > 350m only; Seabird SBE4) -0.0015 0.0057
Oxygen ml/L (dual Seabird SBE43) y = 1.0544x - 0.0161
R² = 0.9992
y = 1.0537x - 0.0218
R² = 0.9992
Oxygen umol/Kg (dual Seabird SBE43) y = 1.0552x - 0.8115
R² = 0.9992
y = 1.0652x - 0.8115
R² = 0.9992
Single sensors Linear Polynomial
Nitrate - ISUS 4sec ave voltage vs Bottle Nitrate (Satlantic MBARI-ISUS v2) y = 30.449x - 1.4223
R² = 0.9944
 
Fluorometer - linear & polynomial regressions

y = 6.8287x - 0.1561

R² = 0.7598

y = -0.3434x2 + 6.9674x - 0.1628

R² = 0.7598

  
 
  Secondary CTD O2 Sensor vs Bottle O2
MBARI-ISUS Voltage vs Bottle NO3 Wetlabs ECO/FL Fluorometer Voltage vs Chlorophyll-a
 

CTD Processing Summary CalCOFI 1701RL CTD Preliminary Data
Download 1701RL CTD raw cast files zipped Download 1701RL Preliminary CTD + bottle data 

General CTD Notes - data acquisition notes, logistics, processing - see below.
Please note that these regressions are generated from preliminary CTD vs bottle data and will be reprocessed once final bottle data are available. CTD temperatures and salinities do not usually change but oxygen, estimated chlorophyll-a, estimated nitrate may change significantly after point-checking. Questionable or mistrip bottle data are removed from these comparisons but may be visible on the CTD.csv plots. For this cruise and future cruises, both primary & secondary sensor profiles vs bottle data will be generated and archived in the downloadable CTD+Bottle data files. These plots are under the "csv-plots\Primary" & "csv-plots\Secondary" subdirectories.

CTD sensor corrections derived by comparing CTD sensor data, 4sec average prior to bottle closure, to bottle samples
Dual T, S, & O2 Primary Sensor Secondary Sensor
Salinity offset (bottle - CTD salinity; > 350m only; Seabird SBE4) -0.0004 -0.0034
Oxygen ml/L (dual Seabird SBE43; 2° O2 Calib Off) y = 1.0091x-0.0197
R² = 0.9995
y = 1.0559x + 0.0019
R² = 0.9995
Oxygen umol/Kg (dual Seabird SBE43; 2° O2 Calib Off) y =0.0106x+0.9593
R² = 0.9995
y = 1.0575x + 0.1822
R² = 0.9995
Single sensors Linear Polynomial
Nitrate - ISUS 4sec ave voltage vs Bottle NO3 (Frank's Satlantic ISUS v3)
Cast 001 - 020 (pre-calibration)
y = 36.487x - 1.361
R² = 0.9458

y = -18.685x2 + 57.757x - 2.2668

R² = 0.9623

Nitrate - ISUS 4sec ave voltage vs bottle NO3; Cast 021 - 075 (post-calibration) y = 27.587x - 4.030
R² = 0.9708
 
Fluorometer - linear & polynomial regressions

y=7.2233x-0.2435

R² = 0.7822

y = 9.4432x2 + 5.1519x - 0.1638

R² = 0.7863

  
 
  Secondary CTD O2 Sensor vs Bottle O2
MBARI-ISUS Voltage vs Bottle NO3 MBARI-ISUS Voltage vs Bottle NO3
Wetlabs ECO/FL Fluorometer Voltage vs Chlorophyll-a  
 

CTD Updates & Corrections

06 Oct 2017 - uploaded revised FinalQC zips for 1402SH, 1404OS, & 1407NH with relabeled .asc voltage headers & filenames; data unchanged

20 Sep 2017 - added FinalQC CTD data for 1611SR, including RINKO II (secondary) O2 data

05 Sep 2017 - added prelim CTD data for 1708SR, fixing NO3 import error on casts 008 & 009

28 Jun 2017 - corrections to 1504SH & 1507OC Raw CTD cast data, updated pressure coefficients; new CTDCast.zips posted

27 Jun 2017 - corrections to 1604SH Raw CTD cast data, casts 001-025 xmlcon files pressure coefficients corrected; new zip posted

22 May 2017 - corrections to 1507OC & 1511OC Final CTD data

1507OC - longitude noise on casts 001, 013, 018, 027, 029, 031, 044, 046, 055, 060, 062, 067 corrected.
1511OC - bad downcast surface data flagged on cast 016 & 017 due to pump issues. (thanks Sharon)

27 Apr 2017 - added 1704SH raw & preliminary CTD data

22 Mar 2017 - corrections to 1601RL CTDCast & finalQC CTD+Bottle data

Casts 099 did not merge properly with bottle data in the previous version due to sta mislabeling in the CTD .hdr file. The newest 20-1601RL_CTDFinalQC.zip has corrected CTD.csvs and plot for Cast 099. Cast 099 line.sta was mislabel sta 63.3 50.0 so the raw CTD.hex file and processed .asc & .csv files have been corrected; there is a new 20-1601RL_CTDCast.zip.

16 Mar 2017 - 1411NH CTD Data Update

CalCOFI 1411NH CTD files have been renamed using the new schema; sta 071 was re-merge with bottle data excluding 4 bad bottle oxygens - sta-corrected CTD oxygens should be much improved for this station. New plots were done including secondary sensor downcast and upcast plots.

CalCOFI 1202NH CTD data have been reprocessed into 82-column CTD.csvs; filenames have been updated to YY-YYMMSC_LLLLSSSS_###DU; .asc voltages have been relabeled. Cast 004-007 sta-corrected oxygens have been recalculated after eliminated bad 270m bottle data from sta.csvs.

15 Mar 2017 - New Final CTD Data

1601RL CTD+Bottle Data Online

Earlier additions and changes

2015 cruises (1501, 1504, 1507, 1511) CTD fies renamed using the new schema - YY-YYMMSC_LLLLSSSS_###DU. Also sensor voltage columns have been relabled in the .asc files but original .asc files have also been archived. 

2012 cruises: 1210, 1207, 1203 have been re-processed into 82-column datacode-friendly format. Data are unchanged from previous final data but additional columns have been added to the CTD.csvs. Also primary and secondary sensor plots have been generated and archived.

This tabulation was started 16Mar2017 and will be updated frequently. Changes to CTD data are listed on the CTD Processing Summary web page for each cruise. Please refer to individual cruise pages for additional detailed information on CTD data processing, re-processing, and re-formatting.

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