James Clarke Ross Cruise AMT14 CTD Processing
Sampling strategy
A total of 89 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 and 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
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Sea-Bird processing
The CON files were first checked for any changes which may have occurred during the cruise. None were made. The information was also crosschecked 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. For reasons which have not been documented output from the LSS6000 sensor and from the secondary temperature and conductivity sensors were omitted from the list of channels output by DATCNV. All other channels were selected. Although DATCNV has since been run again to obtain and preserve an ASCII version of data recorded by the full suite of sensors deployed on the CTD package, the fully processed and QCed version of this CTD dataset does not include data from the secondary sensors nor from the light scatter sensor.
The manufacturer's calibration for the fluorometer was applied during Sea-Bird processing as follows:
Nominal chl-a conc (µg/l) = (0.0113 * 10 voltage ) - 0.032 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 available for this cruise. As a result, the transmissometer reading could not be corrected for source decay and users are advised caution when using absolute attenuance values for this cruise. The calculation of coefficients M and B followed SeaBird Application Note 7 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 4.2220 V A 0 = manufacturer's air voltage 4.4045 V Y 0 = manufacturer's blocked path voltage 0.0185 V A 1 = cruise air voltage not available - used A 0 Y 1 = cruise blocked path voltage not available - used Y 0 -
Reformatting
The data were converted from Sea-Bird ASCII format into BODC internal format (PXF) using BODC transfer function 357. The data were converted to PXF, a BODC internal format. The data were processed from 2Hz averaged down- and upcast data. Sigma-theta was calculated and output from the primary temperature and salinity data channels according to the UNESCO method during the conversion to PXF format. This was used to aid screening of the salinity and temperature data. 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 - - Not transferred during BODC processing Salinity - Practical salinity of the water body by CTD sensor 1 PSALCU01 - - Salinity, 2 - Practical salinity of the water body by CTD sensor 2 - - Not transferred during BODC processing 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 Upwelling PAR sensor voltage LVLTPU01 V Removed on 8 th May 2004 Voltage 4 V Downwelling PAR sensor voltage LVLTPD01 V Replaced upwelling PAR sensor from 8 th May 2004 Voltage 5 V Downwelling PAR sensor voltage LVLTPD01 V Moved to Voltage 4 on 8 th May 2004 Voltage 5 V Cyclops 7 fluorometer voltage FVLTPELN V Added on 8 th May 2004 Voltage 6 V Light Back-Scattering Sensor voltage - - Not transferred during BODC processing Beam Attenuance m -1 Beam attenuance ATTNDR01 m -1 Manufacturer's calibration applied during processing - - Practical salinity of the water body by CTD sensor 1 - sample calibrated PSALCC01 - PSALCU01 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 - - 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 SIGTPR01 kg m -3 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. The data channels were then screened on a graphics workstation using in-house visualisation software. This allows multiple channels to be viewed simultaneously. The start and end-points of the downcast were marked. All spurious and null data were flagged with BODC quality control flags.
The CTD profiles were generally of good quality. However, cast 11 has bad data in the upper 15 db and for cast 87 the quality of the salinity profile is poor, although most bad data and spikes have been flagged prior to binning, users should be advised that the profile should be used with caution.
Oxygen sensor
The profiles have been flagged for noise and spikes but are generally of good quality.
Fluorometer - generally good with the exceptions:
Cast 11: The raw data were constant and negative. So there will be no fluorometer data for that cast.
Casts 1, 12 and 13 were very noisy and the 1Hz data were heavily flagged based on comparison with upcast data. Data from these profiles should be used with caution.
Transmissometer
The transmissometer data are not accurately calibrated as no dark and air voltages were recorded during the cruise to account for source decay along the cruise track. The attenuance values should not be used as absolute values. Casts 12 and 86 have had spikes and anomalous data flagged throughout the water column.
As experienced in AMT12 and 13, the transmissometer malfunctioned in high temperatures and produced poor data. The casts affected were from 39 to 54 and the suspect profiles show large but smooth attenuance maximum at depth as well as strong drifts. The problem is likely related to environmental conditions, for example if temperature or temperature gradients were beyond an acceptable threshold. It is telling that the anomalies are not depth or sensor related but seems to be invariably related to the depth of the thermocline i.e. anomalies are consistently observed at the base of the strong thermocline. The anomalies observed are likely due to a severe case of hysteresis produced by air and water temperature in excess of the instruments operating range (1 to 25 °C).
Up-welling and Down-welling irradiance
Only 8 casts have data for the up-welling PAR sensor.
The down-welling data from casts 19, 44, 71 and 77 were very noisy and the data have been flagged accordingly.
Phycoerythrin fluorometer
Data recorded from cast 26 onwards. The profiles have been flagged for noise in surface waters but in the absence of a calibration sheet are only present as the raw voltage.
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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.
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 11 IRRDPP01 = 0.0423 * exp (LVLTDP01 * 5.331 - 9.267) 3924 10 IRRUPP01 = 0.0423 * exp (LVLTUP01 * 5.195 - 9.036) 3920
Field Calibrations
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Pressure
The pressure sensor has not been calibrated as no values were record in air.
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Temperature
No reversing thermometer data were available for AMT14, 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.
The salinometer data were compared with CTD values from primary sensor on the upcast at the time of bottle firing. Analysis of the data showed that, with the exclusion of 2 outliers, the samples measured on-board produced consistent relationships with the CTD sensor data. A regression analysis was run on the data and showed that there was no linear trend in the data at the 95% confidence level. A simple mean offset, significant at the same confidence level, was applied to the CTD salinities.
Casts Calibration N BODC cal ref All PSALCC01 = PSALCU01 + 0.0026 76 3775 -
Dissolved oxygen
Oxygen calibrations have been carried out using dissolved oxygen data from Winkler titrations (provided by Niki Gist, Plymouth Marine Laboratory). Examination of the calibration data set showed a good correlation with the sensor throughout the cruise.
Casts Calibration N R 2 BODC cal ref All DOXYSC01 = 1.0314 * DOXYSU01 + 5.3147 248 0.994 3794 -
Fluorescence
The CTD fluorometer was calibrated against chlorophyll a concentration extracted from water samples and determined by fluorometric analysis (data originator: A. Poulton, SOC). Nominal chlorophyll concentration recorded on the upcast by the CTD fluorometer at bottle firing depth were extracted from the SeaBird bottle files and compared with extracted values, after exclusion of 6 spurious CTD values and 2 suspect extracted values.
Casts Calibration N R 2 BODC cal ref All CPHLPS01 = 1.66 * CPHLPM01 + 0.09 456 0.673 3918 Residuals (CTD-Extracted) from this calibration ranged between -0.95 and 0.50 mg chl m -3 and 80% of the calibrated CTD fluorometer values were within 0.25 mg chl m -3 of the extracted value. The largest residuals (>0.4 mg chl m -3 ) were observed in the northern and southern part of the transect, outside the subtropical gyres region, and in the upper 50 m of the water column. It is possible that the accuracy of the calibration be improved by splitting the datasets into subgroups. However, an initial attempt to do this by isolating datapoints from stations 15 to 50, had little effect on the quality of the calibration. It was therefore decided in a first instance to apply only one calibration equation for the entire cruise. This calibration was first applied to the data on 10-dec-2004.
