Ocean Carbon and Biogeochemistry: Data System

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MedFlux cruise: EN416 April 2006
CTD profile data processing notes

PI: Cindy Lee (SUNY Stony Brook)

13 February 2007: Prepared for OCB data system by Terry McKee (PO Dept, WHOI) and Cyndy Chandler, OCB DMO (WHOI).

Details of CTD data processing steps:

The shipboard SeaBird CTD processing was done by Lynne Butler (URI), and she authored several documents providing details about the CTD and Niskin bottle data processing steps. The original MS Word documents have been converted to PDF files, but are otherwise identical to her original files.

Cast Log and Information (PDF file)
R/V Endeavor CTD station shipboard procedures (PDF file)
CTD system configuration details (PDF file)

Processing configurations/variables used for EN416 Cindy Lee,
contributed by Lynne Butler,
Ship’s Oceanographic Technician, R/V Endeavor.

Original set up of CTD: V0=Xmiss, V2=Altimeter, V3=PAR, V4=DO1, V5=DO2, V7=ECOFluor, V9=SPAR

Before CTD001 PAR removed from V3
Before CTD002 ECO Fluor moved from V7 to V3. Alt moved from V2 to V6, PAR moved from V3 to V7.
Before CTD003, 8, 12, 17, 18 & 19 - Alt & PAR removed. Niskins in positions 8-12 removed. HPSS canisters installed in their place. After cast, restored to normal w/ HPSS canisters removed & all Niskins reinstalled. See EN416/CTD/CTDLog416.xls or copies of Logsheets
Before CTD004 & 14 PAR installed on V6. After cast PAR removed.

Confile A CTD001 V0=Xmiss, V1=nothing, V2=Altimeter?, V3=nothing=blank PAR cable,V4=DO1, V5=DO2, V6=part of ECO Fluorometer, V7=ECOFluor, V9=SPAR

Confile B CTD002 V0=Xmiss, V1=nothing, V2= part of ECO Fluorometer, V3= ECOFluor, V4=DO1, V5=DO2, V6=Altimeter, V7=PAR, V9=SPAR

Confile HPSS CTD003, 8, 12, 17, 18, 19: V0=Xmiss, V1=nothing, V2= part of ECO Fluorometer, V3= ECOFluor, V4=DO1, V5=DO2, V6=FGP Pressure0, V7=FGP Pressure1, V9=SPAR

Confile C CTD004 V0=Xmiss, V1=nothing, V2= part of ECO Fluorometer, V3= ECOFluor, V4=DO1, V5=DO2, V6=PAR, V7=nothing, V9=SPAR

Xmiss= WET Labs C-Star Transmissometer
Fluor= WET Labs ECO Fluorometer
PAR=Biopherical PAR
Alt=Benthos Altimeter
DO1=SBE43 Oxygen1
DO2= SBE43 Oxygen 2
Due to the nature of the sensors, DO1 & DO2 do not track exactly although they are comparable.
SPAR=Biospherical Surface PAR Temperature and Conductivity as well as all other SBE CTD sensors are calibrated w/in the last year.

416Datcnv_a casts w/ altimeter on V2 (CTD001)

X Process scans to end of file. Scans to skip over 0. Binary output, up & down, Both bottle & data to list. Scans marked with bottle confirm bit. Scan range offset 0. Scan range duration 2. Do not merge separate header file.
Scan Count, Time Elapsed (s), Pressure Digiquartz (db), Depth seawater (m), Temp 1, Temp 2, Temp Diff, Cond 1, Cond 2, Cond Diff, V0 Xmiss V, Beam Attenuation C-Star, Beam Transmission C-Star, V2 Altimeter V, Altimeter, V4, Oxygen V SBE43 1, V5, Oxygen V SBE43 2, V7, Fluorescence WETLab ECOFL, Pump Status, Latitude, Longitude, Bottles Fired.

416Datcnv_b casts w/ altimeter & PAR sensor

X Process scans to end of file. Scans to skip over 0. Binary output, up& down, Both bottle & data to list. Scans marked with bottle confirm bit. Scan range offset 0. Scan range duration 2. Do not merge separate header file.
Scan Count, Time Elapsed (s), Pressure Digiquartz (db), Depth seawater (m), Temp 1, Temp 2, Temp Diff, Cond 1, Cond 2, Cond Diff, V0, Beam Attenuation C-Star, Beam Transmission C-Star, V3, Fluorescence WETLab ECOFL, V4, Oxygen V SBE43 1, V5, Oxygen V SBE43 2, V6 Altimeter V, Altimeter, V7 PAR V, Irradiance, Pump Status, Latitude, Longitude, Bottles Fired.

416Datcnv_c

X Process scans to end of file. Scans to skip over 0. Binary output, up& down, Both bottle & data to list. Scans marked with bottle confirm bit. Scan range offset 0. Scan range duration 2. Do not merge separate header file.
Scan Count, Time Elapsed (s), Pressure Digiquartz (db), Depth seawater (m), Temp 1, Temp 2, Temp Diff, Cond 1, Cond 2, Cond Diff, V0, V3, Beam Attenuation C-Star, Beam Transmission C-Star, Fluorescence WETLab ECOFL, V4, Oxygen V SBE43 1, V5, Oxygen V SBE43 2, Pump Status, Latitude, Longitude, Bottles Fired.

416Datcnv_hpss casts w/ altimeter & PAR sensor

X Process scans to end of file. Scans to skip over 0. Binary output, up& down, Both bottle & data to list. Scans marked with bottle confirm bit. Scan range offset 0. Scan range duration 2.

X Merge separate header file. Scan Count, Time Elapsed (s), Pressure Digiquartz (db), Depth (seawater, m), Temp 1, Temp 2, Temp Diff, Cond 1, Cond 2, Cond Diff, V0, Beam Attenuation C-Star, Beam Transmission C-Star, V3, Fluorescence WETLab ECOFL, V4, Oxygen V SBE43 1, V5, Oxygen V SBE43 2, V6, Pressure FGP0, V7, Pressure FGP1, Pump Status, Latitude, Longitude, Bottles Fired.

416Filter_*
From SBE manual, “FILTER can be run before CELLTM to remove any residual response time between the temperature and conductivity sensors and to minimize digitization noise. On average, a low pass filter with a time constant of 0.03 sec reduces the noise in computed salinity slightly.”
for SBE9/11 SBE9plus, older manualSBE4249.txt suggests
Low pass filter B = 0.15s for pressure
Low pass filter A = 0.03s for conductivity
New SBEDataProcessing_5.32a.pdf suggests only .15 for pressure
Used: B=0.15 for Press, Depth. A=0.03 for Cond 1 & 2 & Diff

SBE Processing configurations used for EN416 Cindy Lee con’t:


416AlignCTD_*
Cond 0.073s (secondary only)
Temp 0
DO 4 (2 at 25C, 5 at 0C) V4, Oxy V pri, V5, OxyV sec

416CellTM_*
for 9+ w/TC duct & pump running at 3000rpm.
Correct both pri & sec conductivity values
alpha = 0.03 1/
beta = 7

LoopEdit (not done for EN416)
Fixed minimum velocity of 0.25m/s.

X Exclude scans marked bad.

416Derive_*
Depth (sw m 43.35Deg N), Salinity 1 & 2 (PSU), Density 1 & 2 (sigma-t, Kg/m^3), Oxygen 1 & 2 (ml/l), Pot Temp 1 & 2 (deg C), Sound Velocity (Chen-Millero m/s), Descent Rate (m/s)

416BinAvg_*
Pressure, 0.5, X Incl #scans/bin, X exclude scans marked bad, skip over 0, Process Downcast only,X Incl surface bin 0, 0, 0

416ASCII_Out_*
Output header & data files, 60 lines/pg, label columns top of file, Semicolon, Julian days, all variables.

416BottleSum_*
Show Min/Max for Avg’d variables, all. Derive: Salinity 1 & 2 (PSU), Density 1 & 2 (sigma-t, Kg/m^3), Oxygen 1 & 2 (ml/l), Pot Temp 1 & 2 (deg C)

OCB DMO processing note:

The OCB DMO used perl scripts to reformat semi-colon delimited (Seabird-processed .asc) files with Seabird parameter names to space-delimited files with OCB ontology parameter names. All data are from primary (T0 and C0) sensors; and a text file recorded the Seabird/OCB parameter name translation, see: ctd_EN416_params.txt

Important: station 19 is an uptrace (no downtrace data reported); These comments regarding stations 18 and 19 were recorded in the CTDCastLogandInfo416.xls file PDF version):

Station 18: "HPSS cast. Trip HPBottles then wait for 10min before ascending. FGP P0 = V6 went from 0 to ~0.77 at ~1300m to 2400m downcast then to 2.2 when tripped at 2400m. V6 decreased during upcast - leak in system for FGP Pressure 0. FGP P1 = V7. Fluorometer has high voltage values during downcast ~1600m+ then also on upcast to ~800m. Tripped carousel positions 9-13 two times because FGP1 didn't change when bottle should have tripped. Stopped acquisition at 500m bottle stop. The maximum of 24 positions had been tripped with still 5 bottles to trip. Those remaining 5 were tripped during CTD019."

Station 19: "HPSS cast. This cast started at 500m after ending CTD018 at 500m bottle-tripping stop during the upcast. The maximum of 24 bottle positions were fired during CTD018 to double check that High Pressure bottle tripped. Thus acquisition had to be restarted to trip remaining bottles. Niskin bottle GOEX109 bottom cap broke before CTD017, replaced w/OTE112."