James Clarke Ross Cruise AMT13 CTD Processing
Sampling strategy
A total of 78 successful CTD casts were made during the cruise. Rosette bottles were fired throughout the water column on the upcast of most profiles. Data were measured at 24 Hz by a PC running SEASAVE, Sea-Bird's data acquisition software. The raw data files were supplied to BODC after the cruise.
Originator's processing
Only a subset of files had been partially processed on board during the cruise. The raw data were therefore reprocessed at BODC to produce a homogeneous set of CTD data files for this cruise. BODC used the latest version of the SeaBird Processing software available at the time to process the raw binary data files (DAT files) based on information held in the sensor configuration files (CON files), and bottle firing files (BL).
BODC post-processing and screening
BODC used the latest version of the SeaBird Processing software available at the time to process the raw binary data files (DAT files) based on information held in the sensor configuration files (CON files), and bottle firing files (BL).
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Sea-Bird processing
The CON files were first checked for any changes which may have occurred during the cruise, with the exception of the transmissometer coefficients that changed on a cast by cast basis to account for source decay, none were made. The information was also cross checked against information held in the sensors' calibration reports.
The following SeaBird routines were then carried out using SBE Data Processing software version 5.30a: DATCNV, CELLTM, FILTER, LOOPEDIT, DERIVE, BINAVG, STRIP. After CELLTM was run, tests were carried out to check whether an alignment of the conductivity sensor was necessary. No lag was observed. Details of the routines and settings used were as follows:
DATCNV converts the raw data into engineering units. Both down and upcasts were selected. All channels were selected for transfer.
The manufacturer's calibration for the fluorometer was applied during Sea-Bird processing as follows:
Nominal chl-a conc (µg/l) = (0.009 * 10 voltage ) - 0.016 CELLTM was run on the DATCNV output using SeaBird's recommended settings of alpha= 0.03 and Tau=7.
FILTER was run on pressure using a low pass time constant of 0.15 seconds.
LOOPEDIT was run in order to minimise the marked wake effect linked to ship rolling observed on recent cruises.
DERIVE, BINAVG and STRIP were then run to derive the salinity and oxygen concentration, reduce the data to 2Hz and strip redundant channels from the final sets of ASCII files.
Conversion of transmissometer voltages to beam attenuation
There were no air and blocked path readings provided for this cruise. So the transmissometer output was not processed to transmissance or attenuance during SeaBird processing but retained as a voltage. The conversion to attenuance was carried out after transfer, screening and loading to the database.
Conversion of PAR sensor voltages to irradiance
The PAR sensor output was not processed to irradiance units during SeaBird processing but retained as a voltage. The conversion to irradiance was carried out after transfer, screening and loading to the database.
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Reformatting
The data were converted from Sea-Bird ASCII format into BODC internal format (PXF) using BODC transfer function 357. The following table shows how the variables within the Sea-Bird files were mapped to appropriate BODC parameter codes:
Sea-Bird Parameter Name Units Description BODC Parameter Code Units Comments Pressure, Digiquartz dbar CTD pressure PRESPR01 dbar - Temperature [ITS-90] °C Temperature of water column by CTD sensor 1 TEMPCU01 °C - Temperature, 2 [ITS-90] °C Temperature of water column by CTD sensor 2 TEMPCU02 °C - Salinity - Practical salinity of the water body by CTD sensor 1 PSALCU01 - - Salinity, 2 - Practical salinity of the water body by CTD sensor 2 PSALCU02 - - Oxygen µmol kg -1 Dissolved oxygen concentration DOXYSU01 µmol l -1 Converted from µmol kg -1 to µmol l -1 using sigma-T during transfer Fluorescence mg m -3 Nominal chl-a concentration CPHLPM01 mg m -3 Manufacturer's calibration applied during processing Voltage 4 V Downwelling PAR sensor voltage LVLTPD01 V - Voltage 5 V Upwelling PAR sensor voltage LVLTPU01 V - Voltage 6 V Light Back-Scattering Sensor voltage NVLTST01 V No calibration details - only available as raw voltage Voltage 7 V Transmissometer voltage TVLTDR01 V - - - Practical salinity of the water body by CTD sensor 1 - sample calibrated PSALCC01 - PSALCU01 calibrated against bench salinometer data - - Practical salinity of the water body by CTD sensor 2 - sample calibrated PSALCC02 - PSALCU02 calibrated against bench salinometer data - - Dissolved oxygen concentration - sample calibrated DOXYSC01 µmol l -1 DOXYSU01 calibrated against Winkler titration data - - Fluorometer - sample calibrated CPHLPS01 mg m -3 CPHLPM01 calibrated against fluorometric chlorophyll-a data - - Downwelling sub-surface PAR irradiance IRRDPP01 µE m -2 s -1 Generated using manufacturer's calibration - - Upwelling sub-surface PAR irradiance IRRUPP01 µE m -2 s -1 Generated using manufacturer's calibration - - Beam attenuance ATTNDR01 m -1 Generated using manufacturer's calibration - - Oxygen saturation OXYSSC01 % Generated by BODC using the Benson and Krause (1984) algorithm wioth parameters DOXYSC01, PSALCC01 and TEMPCU01 - - Potential temperature POTMCV01 °C Generated by BODC using UNESCO Report 38 (1981) algorithm with parameters PRESPR01, PSALCC01 and TEMPCU01 - - Sigma-theta SIGTPR02 kg m -3 Generated by BODC using the Fofonoff and Millard (1982) algorithm with parameters PSALCC02 and POTMCV02 - - Potential temperature POTMCV02 °C Only for cast A13_04. Generated by BODC using UNESCO Report 38 (1981) algorithm with parameters PRESPR01, PSALCC02 and TEMPCU02 - - Sigma-theta SIGTPR01 kg m -3 Only for cast A13_04. Generated by BODC using the Fofonoff and Millard (1982) algorithm with parameters PSALCC01 and POTMCV01 -
References
Benson, B.B. and Krause, D., 1984. The concentration and isotopic fractionation of oxygen dissolved in freshwater and seawater in equilibrium with the atmosphere. Limnol. Oceanogr., 29(3), 620-632
Fofonoff, N.P. and Millard, R.C., 1983. Algorithms for computations of fundamental properties of seawater. UNESCO Technical Papers in Marine Science No. 44, 53pp.
UNESCO, 1981. Background papers and supporting data on the International Equation of State of Seawater 1980. UNESCO Technical Papers in Marine Science No. 38, 192pp
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Screening
The PXF data were compared with the original data files to ensure that no errors had been introduced during the conversion process. Reformatted CTD data were transferred onto a graphics work station for visualisation using the in-house editor EDSERPLO. Downcasts and upcasts were differentiated and the limits manually flagged. No data values were edited or deleted. Flagging was achieved by modification of the associated BODC quality control flag for suspect or null values.
As experienced in AMT12, the transmissometer malfunctioned in high temperatures and produced poor data. The casts affected were from 31 to 54.
The dissolved oxygen data for AMT13_45 were suspect - this has been excluded from the final data set.
The primary temperature (TEMPCU01) and salinity (PSALCU01) channels were suspect for the whole profile of cast 04. Dissolved oxygen (DOXYSU01) and oxygen saturation (OXYSSC01) were also suspect for this cast.
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Banking
Once quality control screening was complete, the CTD downcasts were banked. Finally, the data were binned against pressure at 1 dbar increments with flagged data excluded from the bin averaging. The primary salinity, temperature, density and potential temperature channels were retained as the best quality data channels from the two sensors, except for casts A13_04 and A13_45 where the secondary channels were the best quality data channels. In the absence of calibration coefficients the LBSS voltages were not banked but are available on request from the archived full parameter set series.
Voltage conversions
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PAR sub-surface irradiance
The PAR sensor raw voltages have been converted to PAR irradiance values in units of µE m -2 s -1 using supplied manufacturer's calibration coefficients.
Sensor s/n Calibration BODC cal ref 08 IRRDPP01 = 0.0423 * exp (LVLTDP01 * 5.125 - 7.557) 3293 12 IRRUPP01 = 0.0423 * exp (LVLTUP01 * 5.091 - 8.879) 3143 -
Attenuance
The transmissometer raw voltages have been converted to attenuance values in units of m -1 using manufacturer air/dark/pure water voltages converted to calibration coefficients as per Sea-Bird Application Note No.7 . No air/dark voltages were provided from the cruise so coefficients have been calculated with the most recent dark/air voltages being those provided by the manufacturer.
M = (T w / (W 0 - Y 0 ) * (A 0 - Y 0 ) / (A 1 - Y 1 ) B = -M * Y 1 where
Stainless steel T w = % transmission for pure water 100% W 0 = voltage output in pure water 4.2009 V A 0 = manufacturer's air voltage 4.7810 V Y 0 = manufacturer's blocked path voltage 0.0184 V A 1 = cruise air voltage not available - used A 0 Y 1 = cruise blocked path voltage not available - used Y 0 Sensor s/n Calibration BODC cal ref 161-2642-03 ATTNDR01 = -1 / 0.25 * ln (TVLTDR01 * 0.23909 - 0.004399) 3343
Field Calibrations
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Pressure
The pressure sensor has been calibrated at BODC against pressures reading in air.
Casts Calibration BODC cal ref All PRESPR01 calibrated = PRESPR01 raw - 0.517 2983 -
Temperature
No reversing thermometer data were available for AMT13, so the CTD sensor data have not been calibrated against another dataset. Temperature readings from the two temperature sensors were almost identical and no other independent measurements of better quality were available. No further correction was therefore applied to the data.
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Salinity
Bench salinometer data were provided by UKORS. Some analyses were carried out on-board, but some problems were encountered with the instrument. As a result, the remaining samples were sent to SOC and analysed after the cruise.
The salinometer data were compared with CTD values from primary and secondary sensors on the upcast at the time of bottle firing. Analysis of the data showed that the samples measured on-board produced less consistent relationships with the CTD sensor data. Although only 10 samples were available from the post-cruise sample analysis, it was decided to calibrate the sensors using these samples only. This produced the following calibrations which have been applied to the CTD data.
Casts Calibration N R 2 BODC cal ref All PSALCC01 = 0.998289 * PSALCU01 + 0.0517 10 1.0 3163 All PSALCU02 = 1.000660 * PSALCU02 - 0.0236 10 1.0 3164 -
Dissolved oxygen
The oxygen sensor calibrations have been carried out using dissolved oxygen data from Winkler titrations (provided by Nikki Gist, Plymouth Marine Laboratory). Examination of the calibration data set showed a clear problem with the sensor of drift throughout the cruise. The change of sensor on casts A13_55 and A13_56 shows the poor accuracy of the SBE45 s/n 0013 during the cruise. Since the drift was so pronounced and where the Winkler titration dataset provided a good number of samples from each day the sensor was calibrated on a daily basis. This corrected for much of the observed drift.
Casts A13_03, A13_04, A13_07, A13_09 to A13_12, A13_42 and A13_76 to A13_78 have not had a calibration applied to the oxygen sensor data.
Casts Calibration N R 2 BODC cal ref A13_01 to A13_02 DOXYSC01 = 1.6072 * DOXYSU01 - 0.2311 9 0.948 6603 A13_05 to A13_06 DOXYSC01 = DOXYSU01 + 86.7859 (sd =1.7531) 19 0.143 6604 A13_08 DOXYSC01 = 2.2852 * DOXYSU01 - 118.9077 11 0.679 6605 A13_13 DOXYSC01 = 1.2621 * DOXYSU01 + 42.4397 7 0.697 6606 A13_14 to A13_16 DOXYSC01 = 1.6872 * DOXYSU01 - 23.668 10 0.893 6607 A13_17 to A13_19 DOXYSC01 = 1.7969 * DOXYSU01 - 34.8284 17 0.788 6608 A13_20 to A13_22 DOXYSC01 = 1.9873 * DOXYSU01 - 59.5409 8 0.910 6609 A13_23 to A13_25 DOXYSC01 = 1.8179 * DOXYSU01 - 26.6879 10 0.992 6610 A13_26 to A13_28 DOXYSC01 = 1.6584 * DOXYSU01 - 5.162 10 0.996 6611 A13_29 to A13_31 DOXYSC01 = 1.6966 * DOXYSU01 - 2.5775 9 0.997 6612 A13_32 DOXYSC01 = 1.7652 * DOXYSU01 + 0.0738 7 0.998 6613 A13_33 to A13_35 DOXYSC01 = 1.9091 * DOXYSU01 - 8.7512 15 0.998 6614 A13_36 to A13_38 DOXYSC01 = 2.1160 * DOXYSU01 - 19.7753 10 0.995 6615 A13_39 to A13_41 DOXYSC01 = 2.1668 * DOXYSU01 - 12.4199 9 0.997 6616 A13_43 to A13_45 DOXYSC01 = 2.3764 * DOXYSU01 - 12.4672 9 1.000 6617 A13_46 to A13_48 DOXYSC01 = 2.4820 * DOXYSU01 - 15.9933 10 0.997 6618 A13_49 to A13_51 DOXYSC01 = 3.0012 * DOXYSU01 - 48.0372 10 0.994 6619 A13_52 to A13_54 DOXYSC01 = 3.5361 * DOXYSU01 - 83.7659 10 0.994 6620 A13_55 to A13_56 DOXYSC01 = DOXYSU01 + 51.56 (±2.17) 9 0.086 6621 A13_57 DOXYSC01 = 3.9667 * DOXYSU01 - 118.2785 5 0.992 6622 A13_58 to A13_60 DOXYSC01 = 4.8638 * DOXYSU01 - 202.1352 10 0.992 6623 A13_61 to A13_63 DOXYSC01 = 4.4150 * DOXYSU01 - 166.8256 9 0.985 6624 A13_64 to A13_66 DOXYSC01 = 3.3921 * DOXYSU01 - 63.6431 10 0.976 6625 A13_67 to A13_69 DOXYSC01 = 3.1397 * DOXYSU01 - 42.9451 15 0.995 6626 A13_70 to A13_72 DOXYSC01 = 2.8050 * DOXYSU01 - 11.0328 10 0.959 6627 A13_73 to A13_75 DOXYSC01 = 2.9869 * DOXYSU01 - 25.5102 14 0.990 6628 -
Fluorescence
The nominal chlorophyll-a values have been calculated from the fluorometer data (with manufacturer's calibration applied) from the up-cast at bottle firing and the fluorometric chlorophyll-a data from sampled bottles. Where samples were not supplied or too few to generate a calibration and could not be grouped with other casts, the fluorometer profiles have not been calibrated. The sampling strategy for the extracted chlorophyll-a dataset used to calibrate the fluorometer focused on the upper water column, therefore the calibration is biased towards these depths. The calibration may not be as reliable below depths ~150m. The extracted chlorophyll-a dataset is available for users to derive their own calibrations should they wish.
Casts Calibration N R 2 BODC cal ref A13_02 to A13_22 CPHLPS01 = 1.4120 * CPHLPM01 52 0.196 6673 A13_24 to A13_41 CPHLPS01 = 1.9320 * CPHLPM01 50 0.578 6674 A13_42 to A13_66 CPHLPS01 = 1.7059 * CPHLPM01 83 0.774 6675 A13_68 to A13_69 CPHLPS01 = 1.6722 * CPHLPM01 10 0.809 6676 A13_71 to A13_72 CPHLPS01 = 1.8222 * CPHLPM01 10 0.761 6677 A13_74 to A13_75 CPHLPS01 = 1.9845 * CPHLPM01 8 0.873 6678 A13_76 to A13_77 CPHLPS01 = 1.5654 * CPHLPM01 5 0.608 6679
