Preliminary CTD and Water Sampling Summary
Sarah Zimmermann, WHOI
A total of 157 CTD stations with bottom depths ranging from 30m--2300m were collected from the Chukchi and western Beaufort Seas. Water samples were taken at 117 of these stations. Water sample measurements typically included dissolved oxygen, salinity, nutrients, chlorophyll and phyopigments. In addition, O18, dissolved organic carbon, particulate organic carbon, total CO2, alkalinity, and radium samples were collected during particular sections. CTD casts typically went to within 5m of the ocean floor; however, during the eddy survey and on comparison casts for the mooring sensors, it was not necessary to take the CTD to the ocean bottom.
CTD and water sample data were collected using the USCGC Healy’s Seabird 911+ system operating at 24Hz scan rate, with a 24 position rosette package and 24 12-liter Niskin bottles. In addition to a dual set of pumped temperature and conductivity sensors, the CTD had a SBE43 oxygen sensor pumped in-line with the primary temperature and conductivity sensors, a WetLabs CST transmissometer, an Aquatraka fluorometer, and a Benthos altimeter. Fortunately, a backup frame, CTD and auxiliary sensors were also provided because we were required to change out the CTD and the altimeter during the cruise. See the appendix for sensor serial numbers, calibration dates and position on frame.
CTD Data Acquisition and Processing Procedures
Upon reaching the station, the rosette was brought out of the hanger, the CTD was powered on and data acquisition started. The transmissometer and fluorometer windows were cleaned immediately before each deployment. The sensors were soaked for three minutes at 10m after the pumps turned on. The CTD frame was then raised back to the near-surface (between 2m and 5m) and lowered at 30m/min to 100m and then at 60m/min. The descent rate was slowed to 30m/min approximately 60m off the ocean floor, and slowed further at 10m off the bottom. Depending on sea state, maximum CTD depths were within 1 to 5m of the ocean bottom. The bottom bottle was fired immediately and subsequent bottles were closed after waiting 30 seconds at each stop. The ‘surface’ bottle was taken at 10m to avoid the extremely large surface gradients and the change in water properties due to ship’s presence (for example, the propeller wash). The CTD was turned off after the package was landed on deck, the water sampler rinsed with fresh water and the package returned to the heated hanger for sampling.
The CTD data were acquired and processed with Seabird software on a PC platform with further processing using Matlab-based routines. Acquisition occurred real -time through a conducting cable from the CTD to a PC running Seasave-Win32_V5_31a. The ship’s GPS position was added to each data scan via the NMEA interface. Upon completion of the station, the data were copied via the ship’s network to the processing PC. Seabird’s windows based processing software, SBEDataProcessing-Win32_V5_29b, was then used to produce 1db averaged downcast and upcast profiles. The standard processing steps followed at sea were: sensor alignment through advancing conductivity; spike removal; a correction for the thermal mass of the temperature sensors; filtering; removal of pressure reversals; calculation of oxygen; averaging to 1 db levels; calculation of other derived properties; and the file separation between downcast and upcast profiles.
Final processing was completed using Matlab to calibrate, plot and remove spikes in the data. Both conductivity sensors and the oxygen sensor were calibrated to the water samples and the calibration applied to the down and upcasts. The data were plotted station by station and density inversions in the downcast identified. A 0.004 kg/m3 criteria was used to identify density inversions at depths over 10m. The top 10m were not examined for density inversions. The inversions were interpolated over in the primary temperature and conductivity sensor data, and the derived properties (salinity, density, theta) were recalculated. The interpolations are listed in the appendix. The fluorometer and transmissometer are unprocessed.
CTD and Water Sample Data Files
The file naming scheme starts with a ‘d’ or ‘u’ to indicate downcast or upcast and follows with five digits, ‘dSSSCC.*’, where SSSCC is a 3-digit station number (SSS) and 2-digit cast number (CC). Repeat casts (cast 2 and cast 3) were performed to collect radium samples. Occasionally the repeat cast would be performed out of sequence, ie we moved onto 4 new stations and then came back for the radium cast.
Raw CTD Acquisition Files from Seabird Sea-Save
SSSCC.dat raw data
SSSCC.hdr header file
SSSCC.bl bottle trip scan numbers
SSSCC.con configuration file
SSSCC.mrk mark scan numbers, used to indicate start of down cast, bottom of cast, end of cast. Also used to mark the comparison stops during the CTD comparison casts where FSI EMCTDs and SBE Microcats were attached to the rosette frame.
Processed CTD Files
dSSSCC.cnv down 1 db averaged file is Seabird format
dSSSCC_ct1.csv down 1 db averaged file is JOSS format, comma delimited, and can be read using EXCEL
uSSSCC.cnv up 1 db averaged file in Seabird format
uSSSCC_ct1.csv up 1 db averaged file in JOSS format, comma delimited, and can be read using EXCEL
Water Sample File
HLY0404_HY1.csv water sample file with merged ctd data
CTD Data Quality
The CTD, rosette and niskin bottles performed well. The CTD temperature and conductivity sensors performed to their specified accuracy. The only equipment problems experienced were with leaks in the connections, and the failure of the first altimeter. The auxiliary-4 CTD bulkhead connector leaked repeatedly even after the cable was changed out. Due to this, the CTD body was swapped out before station 61, but all the sensors were kept in their same configuration and plugged into the spare CTD. Removing the CTD with the bad auxillary-4 connector revealed the modem bulkhead connector also had a slow leak. These connectors were replaced although we never needed to switch back to this CTD. The altimeter was changed out shortly afterwards for station 64. It was not reading full scale (~98.5m) when it was over 100m from the ocean floor and during the bottom approach of station 63 the altimeter was reading 4m as the package touched the bottom. The altimeter base appeared damaged although we had not experienced any event that would have caused this damage. Perhaps the damage had been received earlier but only now, cycling in the cold and to greater pressure, it became affected by the damage?
The CTD wire was reterminated once, after station 83. The CTD had swung strongly in the block and in addition to this high-tension event there was an earlier kink in the wire. As a safety measure it was decided to reterminate the wire.
The CTD touched the bottom during stations 63 and 77, both at slow speed and without any change to the calibrations.
The pumps were frozen at the start of station 111, cast 2. The CTD was recovered and the pumps thawed before redeployment. After this the hangar door was lowered further and the gap between door and floor was covered to try and keep the floor at a warmer temperature. The pumps did not freeze again.
These were the major issues for the CTD, however, the complete list of station comments is included in the appendix.
On deck pressure was examined for stations 1 to 49 to determine if a mean pressure offset existed. Typically there was an offset of 0.3db before the cast and –0.2db after the cast. The CTD is powered up just before the cast, and typically the CTD pressure drifts from 0.4 towards 0 during the pre-cast time on deck. Based on this, it appears a longer warm-up period could be used and that there is no pressure bias.
The primary and secondary temperature sensors were compared using the data from the bottle stops. They show a mean difference of less than 0.0005 degC. This inter-comparison supports the stated instrument accuracy of 0.001degC without requiring a post-cruise calibration.
The conductivity sensors were very stable, requiring only one calibration during the cruise and providing the stated accuracy of 0.002 psu. Stations 1 to 111 were used in the fit. Surface values were used in the fit to obtain a slope over the range of conductivities; however, the majority of observations discarded by the iterative fitting routine (acceptable residual criteria was less than 2.5 x STD) were from the high salinity gradient water in the upper 50m.
Sensor Slope Bias STD mS/cm Number of Obs
Primary 1.00016 -0.00358 0.0012 306 of 555
Secondary 0.99959 0.01003 0.0011 284 of 555
The oxygen sensor was also quite stable with one calibration performed for the cruise. The data were calibrated to the water samples, using stations 1 to 96. The calibration method followed the Seabird Application Note Number 64-2. This method determines two of the six coefficients, Soc and Voffset. The other coefficients were left at their laboratory calibration settings. All water samples were used in an iterative fitting routine (acceptable residual criteria was less than 2.5 x STD). The standard deviation of the calculated oxygen (using the same observations that passed the fitting criteria) was 0.05 ml/l.
Sensor Soc Voffset STD Number of Obs
Oxygen 4.0268e-01 –0.4434 0.006 oxy/phi 422 out of 560
0.05 ml/l 422 out of 560
The fluorometer data were not processed.
The transmissometer data were not processed. A log of the full scale in-air and blocked in-air readings were measured from 7 September to 16 September. They show little change over this period. The full scale in-air reading had a range from 4.56 to 4.8 volts with a more consistent reading after the transmissometer had been powered on for a few minutes. The blocked reading had a range of 0.048 to 0.056 volts. The window was cleaned with de-ionized water prior to each cast.
Water Sample Acquisition and Processing Procedures
Salts, Nutrients, Oxygen, and Water Sample File Preparation
Please see odfhly0404.doc
Chlorophyll samples have been collected from casts covering 106 of the stations occupied during the 2004 SBI Mooring cruise. Six to nine depths per cast have been sampled and processed. In addition, samples have been processed from 8 stations, that were collected during underway analysis (Sharon Smith). Data entry into the data server has been made following quality control checks on spreadsheet information. Highest chlorophyll concentrations for the cruise (8.2 mg Chl/l) occurred at station 36. Chlorophyll samples were filtered onto 25 mm GF/F filters and extracted for 24 hours in 90% acetone and determined fluorometrically (Evans and O’Reilly, 1983; Holm-Hansen et al., 1965).
Evans, C.A. and J.E. O’Reilly. 1983. A Handbook for the Measurement of Chlorophyll a in Netplankton and Nannoplankton. Biomass Handbook No. 9. N.O.A.A.
Holm-Hansen, O., C.J. Lorenzen, R.W. Holmes, and J. D. Strickland. 1965. Fluorometric determination of chlorophyll. J. Cons. Cons. Int. Explor. Mer 30:3-15.
Dissolved organic carbon (DOC) samples were taken on all CTD lines and during the eddy survery. Full depth profiles were conducted with 375 total samples taken. These samples will be stored frozen until they can be return to the lab for analysis. Total CO2 and alkalinity samples were taken on all lines at the surface only, with the exception of the eddy profile in which full depth profiles were taken for both. 210 samples were taken for TCO2 and Alkalinity. Particulate Organic Carbon (POC) samples were taken during the eddy survery. 120 samples were taken at full depth ranges throughout the eddy work and will also be analyzed once returned to lab with the DOC, TCO2 and alkalinity samples. The main objective of the cruise was to quantify the total carbon transport that occurs in an eddy moving from the shelf break into the Canada Basin and with the excellent high resolution sampling that was conducted in the eddy it is very likely that the objective will be fully accomplished.
A1 CTD Configuration
Pressure 0639 001 to 060
Primary Temperature 2796 02Jul04 001 to 157
Primary Conductivity 2545 02Jul04 001 to 157
Secondary Temperature 2824 02Jul04 001 to 157
Secondary Conductivity 2568 02Jul04 001 to 157
Oxygen SBE43 459 30Jun04 001 to 157
Trans. Wetlabs CST CST-390-DR 20Nov03 001 to 157
Fluor. MKIII Aquatracka 088233 21Jan04 001 to 157
Benthos Alt. PSA-916D 872 default 001 to 064
Pressure 0638 5Mar04 061 to 157
Benthos Alt. PSA-916D 843 default 064 to 157
Main CTD is horizontally mounted at base of CTD frame. 24 bottle rosette with 12 liter Niskin bottles and SBE Rosette. Oxygen is in line with primary temperature and conductivity. Both T+C pairs have pumped flow. Fluorometer and transmissometer are not pumped systems.
After swapping out CTD 0639, Jim Schmidt replaced the modem and auxiliary-4 (v6 and v7 channel) bulkhead connectors. The swap was made because auxiliary-4 connector was leaking, but it was discovered after the swap that the modem connector had also leaked.
Auxiliary Sensor Configuration 1, Stations 1 to 59
Auxiliary 1 V0 Fluorometer
Auxiliary 2 V2 Free
Auxiliary 3 V4 Transmissometer
Auxiliary 4 V6 Altimeter
Auxiliary Sensor Configuration 2, Stations 60 to 157
Auxiliary 1 V0 Fluorometer
Auxiliary 2 V2 Altimeter
Auxiliary 3 V4 Transmissometer
Auxiliary 4 V6 Oxygen
Filename Stations Change
Hly0404_1.con 00101 to 05901 First setup
Hly0404_2.con 06001 Changed voltage channels
Hly0404_3.con 06101 to 06401 Changed pressure housing
Hly0404_4.con 06002 and 06501 to 15701 Changed altimeter
Primary Temperature 3.5”
Primary Conductivity 5.5”
Primary Pump 6.5”
Oxygen SBE43 6”
Secondary Temperature 3.5”
Secondary Conductivity 5.5”
Secondary Pump 6.5”
Trans. Wetlabs CST 2.75”
Fluor. Aquatracker 4”
Bottle bottom 24.25”
Bottle mid-point 24.25”+19.5”
Distance between Temperature Sensors 7”
Tubing Lengths in Primary system:
Conductivity to Oxygen 2.5”
Oxygen to Pump 4.5”
Tubing Lengths in Secondary system:
Conductivity to Pump 6.5”
A2 Individual Station Notes
Notes from station logsheets and processing:
1301 Did not get within altimeter range of bottom.
1401 Did not get within altimeter range of bottom.
1502 Radium and EMCTD comparison cast. EMCTDs s/n1313(BS7) and s/n1346(BS8).
1503 Radium and EMCTD comparison cast. EMCTDs s/n1313(BS7) and s/n1346(BS8).
1601 EMCTD comparison cast. EMCTDs s/n1355(BS3) and s/n1337(BS4).
1701 EMCTD comparison cast. EMCTDs s/n1337(BS2) and s/n1363(BS4).
1801 EMCTD comparison cast. EMCTDs s/n1355(BS3) and s/n1341(BS5).
1901 EMCTD comparison cast. EMCTDs s/n1337 (BS2) and s/n1341(BS5).
2001 MicroCat comparison cast. Microcats s/n 2131(BS1) and s/n 2132 (BS2).
2101 MicroCat comparison cast. Microcats s/n 2139(BS6).
Wire kinked while taking up slack prior to deployment.
2201 MicroCat comparison cast. Microcats s/n 2135(BS3), s/n2136(BS4), and s/n2137(BS5)
2301 Oxygen sensor not properly soaked. Only waited at 5m until pump turned on.
2401 Oxygen sensor not properly soaked. Only waited at 5m until pump turned on.
3001 Niskin 2 closed without waiting for 30second wait so closed niskin 3 at same depth. CTD tags will be left for both niskins but water samples should be merged with niskin 3 because they were drawn from this niskin.
Surface mark is actually at 30db.
3301 T1-T2 difference looks larger than normal. May be due to jellyfish tentacles (seen on frame), or due to large swell in shallow water with large gradients. Later (station ??) a small blob of jelly-fish material freed from tubing between C2 and pump.
3401 Bottom mark is 5m off the bottom of cast.
3801 Did not wait 30 sec on Niskin 3
3901 Niskin1 was deployed with bottom cap closed. No samples from nikin1 but tag is in file.
4501 Niskin 2 and 3, top vents not closed.
Gelatinous material removed from tubing between C2 and pump.
Software indicated pump was on while on deck prior to cast.
4601 Prior to cast flushed sensors again. This time a glob of gelatinous material appeared in tubing between secondary conductivity cell and pump. The material was removed, tube re-attached, and cast looked better.
4701 Quite a bit of jellyfish material on frame, including CTD intake.
5001 Originally named 05201. Filenames and *.hdr changed afterwards. Bottom depth also added to header file after the cast.
5201 Niskin1 did not close, not sampled.
5603 Mark taken 5 m above max CTD depth.
5801 Ryan noticed altimeter is not reading full scale anymore…off by 5m at surface and bottom depth (altimeter plus ctd depth) are 5m less than the bathymeter and seabeam depth (however it does read +4 of the adcp depth).
Unplugged oxygen and altimeter cable from CTD and found connection had been leaking again. Cleaned up, reattached and redeployed.
5901 No spare Y-cable available but since the aux-2 bulkhead connector was free we removed Y-cable and plugged altimeter into the aux-2, and left oxygen in aux-4. New configuration file made: HLY0404_2.con Altimeter is now changed from V6 to V2 and Oxygen is changed from V7 to V6.
6001 Oxygen data bad. Yes connection leaked again (aux-4).
Swapped out CTD body (s/n 638 for 639) but kept all the same sensors. Turns out the modem connection also had corrosion from leaking. No clear problem seen on bulkhead connectors…pins on Aux-4 look slightly bent. New configuration file: HLY0404_3.con. The pressure casing we’ve switched to had a blown fuse and bulkhead connector during the last leg. Rob Palmeres could tell us what happened in particular. He got it back into working order with MSTs. Jim Schmidt replaced the aux-4 and modem bulkhead connectors in the removed CTD (s/n639).
6101 Data look good with new pressure housing.
6201 Pump on while on deck before cast.
6301 Bottom contact (at slow speed). Altimeter read 4m and then touched bottom- altimeter was reading incorrectly.
6401 Careful bottom approach: flat bottom, no ship-rock, altimeter read 6m and then switched to 99. Did not touch bottom, but expect altimeter has ~ 4m offset.
Altimeter changed out after cast.
6002 First cast with spare altimeter. Taken after 6401. Originally saved as 00602.* Changed back to 06002.* No bottles
6501 Altimeter reading fine.
6902 Originally saved file as 0690.* After cast files were renamed back to 06902.*
7401 Auxiliary-4 connector cleaned after cast. Pins were green, showing seawater had been leaking in. Connector was examined because V7 was reading non-zero (only oxygen is plugged into this connector so only V6 should have reading). However, there were no spikes in the data to indicate a problem.
7601 Niskin 3 was closed at an un-intended depth so was not sampled.
7701 Bottom contact. Ship lost power 8m above bottom. Ship drift/ wire angle change brought the CTD in contact with the bottom. The package may have even dragged along the bottom. Power was restored in ~2 minutes. Cast was restarted (?) bottom bottle tripped and continued with uptrace as normal. Primary and secondary conductivity differences were small- does not appear to shifted calibration.
7801 Altimeter went from 4.5 to 98 at bottom. Maybe due to slope, maybe altimeter problem? Altimeter was late in finding the bottom (28m off bottom).
8301 Wire stressed during wait at 5m. A big swell raised package and lowered tension of wire on block and then quickly released package, putting a shock on the wire. Data looks spiky and shows 5 m density inversion but this is most likely due to mixing by package/ ship prop in the high gradient water with big swells. Station 8401 performed next and then it was decided to reterminate wire (outer armor shows slight gaps and there is a kink from an earlier cast ) and go back and repeat this station (calling the repeat 8304).
8304 Follows station 8401, back at station 83. First cast with reterminated wire. Looks fine. Seas have also calmed down slightly. Voltage channel 7 is free, but shows voltage on this cast. Aux-4 connector (oxygen plugged in here: V6 and V7) cleaned after cast but does not appear noticeably wet. Oxygen trace looks fine. Cast is named 04 to differentiate from naming scheme of radium casts (02 and 03), although there are no radium casts at this station.
8501 Voltage channel 7 shows small noise. Connector left as is, not checked.
8502 Voltage channel 7 reads 0 all cast but voltage channel 5 now has small noise. Connector left as is, not checked.
8601 Voltage channel 5 shows small noise again. Connector left as is, not checked.
8701 No more noise on any of the free channels (v1,v3,v5,v7).
9001 Niskin 1 not tripped at right depth (too early, ~10 off bottom). Not sampled. 2nd mark scan also not at bottom. 3rd mark scan is at bottom.
9601 Did not wait 30 seconds before tripping surface bottle.
11101 Extra tag (24th niskin) not sampled- remove tag.
11102 First dunking the pumps never came on due to freezing. CTD was brought back into hanger and flushed with warm water and then with warm saline water. CTD was then redeployed, leaving syringes full of warm saline water on as long as possible, removing just before it was lowered into the water. Initially this was called 11103 but was renamed to 11102.
11201 Paused at 210m for a few minutes on downcast because wire was rubbing side on A-frame.
11601 Initially put into water with syringes still attached. Brought out, syringes taken off and restarted.
12101 Thermometer for measuring oxygen temperature out of range on very cold water
12502 CTD drifted lower while tripping all the bottles for radium samples. Niskins 13 and 14 not sampled due to change in depth. CTD depth readjusted after niskin 14.
12902 Niskin 10 leaking.
14401 Large number of jellyfish-parts on CTD frame. May have affected transmissometer.
Notes on Bottles
00101 3 Did not wait 30 seconds before closing niskin
00201 1 Did not close. Lanyard hooked over pin 1 and 24
00201 14 Did not close. But closed after tugging on lanyard.
00601 1 Mistake: wrong depth, no samples drawn.
01201 2 Mistake: wrong depth, no samples drawn.
03801 3 Did not wait 30 seconds before closing niskin
03901 1 Deployed with bottom endcap closed
04501 2 Top vent not closed
04501 3 Top vent not closed
05201 1 Tripped but did not close.
09601 9 Did not wait 30 seconds before closing niskin
12101 Thermometer for measuring oxygen temperature out of range on very cold water
12902 10 Niskin leaking
A3 Interpolation List
This list contains the pressure intervals over which the primary temperature and conductivity data were linearly interpolated over.
Station Start (db) End(db)
******* ******* ********
101 0 9
201 0 8
501 128 130
601 8 10
601 19 21
603 0 3
603 196 197
701 5 9
701 249 251
701 278 280
702 14 23
702 206 209
703 0 5
703 48 50
801 104 106
901 327 330
902 339 341
1001 28 31
1001 38 40
1301 153 155
1401 456 458
1502 7 9
1502 71 74
1801 771 773
2101 13 18
2201 308 310
2301 33 34
2301 9 11
3101 11 14
4201 4 6
4601 11 15
4601 35 37
4701 52 53
4702 21 23
4702 50 51
4901 30 33
4901 34 35
4902 33 34
5602 0 12
5901 10 12
5901 19 25
6001 6 9
6001 10 12
6001 17 21
6002 5 7
6002 9 11
6201 4 6
6201 66 68
6301 9 11
6301 67 68
6501 4 15
6902 11 13
6902 16 18
7001 180 182
7001 194 196
7101 160 162
7101 206 208
7501 358 360
7701 478 481
7901 39 41
8001 5 7
8001 61 63
8001 23 26
8101 12 14
8101 45 47
8201 4 7
8301 19 21
8301 42 44
8301 45 47
8304 8 10
8701 55 57
8701 62 65
8902 6 12
9101 8 12
9101 111 112
9301 119 121
9501 15 17
9501 135 137
9601 7 12
9601 16 18
9601 46 48
9701 66 68
9701 69 71
9701 89 91
9801 32 35
9801 45 47
9801 144 146
9801 241 243
9901 29 31
9901 32 34
9901 36 38
9901 40 42
10201 171 173
10301 10 12
10401 33 35
10401 36 38
10401 39 41
10401 42 44
10701 10 12
10701 588 591
10801 11 13
11102 10 16
11201 213 216
11401 10 13
11401 19 21
11401 130 132
11401 180 182
11401 187 189
11401 119 121
11401 126 128
11401 234 236
11401 243 245
11401 258 260
11501 117 120
11501 125 129
11501 132 136
11501 141 143
11501 149 152
11501 175 177
11501 228 230
11801 212 214
11901 175 180
11901 210 212
11901 283 285
11901 290 292
12102 11 16
12102 227 229
12102 280 282
12301 43 46
12301 58 60
12301 62 64
12301 80 82
12301 85 87
12301 89 91
12301 105 110
12301 237 239
12301 245 248
12302 45 47
12302 52 54
12302 56 58
12302 302 303
12501 61 63
12501 65 67
12501 69 71
12701 14 16
12701 38 40
12801 51 54
13301 18 20
13301 20 22
13301 24 26
13401 23 25
13501 9 16
13501 16 21
13601 10 12
13601 23 26
13801 35 38
13901 28 30
13901 40 42
13901 43 45
14001 38 40
14201 34 36
14301 34 36
14301 32 34
14401 34 36
14601 37 39
14901 41 42
A4 Seabird Processing Settings
Program/ Module Function
1 SEASAVE Acquire raw data.
2 Data Conversion Convert raw data (*.dat), using the *.con file, selecting ASCII as data conversion format.
Start at scan number of downcast, after the soak. Store files in processed/datcnv
For the *.ros files, use scans marked with bottle confirm bit, 0sec offset, 2sec range duration.
3 Rossete Summary Average the scans associated with each bottle trip to create CTD bottle stop information.
Averaged all values. Derived Oxygen, Oxygen Saturation, Salinity 1 and Salinity 2. Found min/max and STD although this info is not being used in water sample data.
4 Align CTD Advance sensors relative to pressure, depending on sensor response time. Typically secondary conductivity is advanced 0.073seconds and oxygen is advanced +2 to +5 seconds. The primary conductivity is typically already advanced 0.073 seconds by the deck unit.
Confirmed SBE11 deckunit was already advancing both primary and secondary conductivity by 0.073 seconds so only using align to advance oxygen.
Advanced oxygen voltage by 3 seconds.
5 Cell Thermal Mass Perform conductivity cell thermal mass correction to achieve higher salinity accuracy. This step is necessary when salinity accuracy better than 0.01 PSU is desired in regions with steep gradients. Typical values are alpha = 0.03 and 1/beta = 7.0.
Chose to adjust Primary Conductivity with Primary Temperature and to adjust Secondary Conductivity with Secondary Temperature. Used suggested corrections of alpha=0.03 and 1/beta= 7.0
6 Wild Edit Identify scans that have very different values from their neighboring scans.
Chose first pass of 10STD and second pass of 20STD using 100 scans per block (about 4 seconds). All scans are used for STD calculation (after loopedit is run, could exclude those flagged data from the STD calculation). Pressure, T1, T2, C1, C2, OxV, Alt, S1, S2, SndVel, Depth were tested. Did not run procedure on transmissometer, fluorometer or latitude and longitude.
7 Filter Low-pass filter pressure with time constant of
0.15 seconds to increase pressure resolution for Loop Edit. Typically pressure is low passed filtered with 0.15 seconds and conductivity is filtered with 0.03
Applied 0.15 second filter to pressure and 0.03 second filter to conductivities.
8 Loop Edit Mark scans where CTD is moving less than minimum velocity or traveling backwards due to ship roll.
Scans with speeds less than 0m/s are marked bad.
Store files in processed/loopedit.
‘Exclude marked scans’ is checked, meaning scans previously flagged bad will not be used in loopedit calculation.
9 Derive Compute oxygen from oxygen signal (SBE 43); also need conductivity (or salinity), temperature, and pressure.
Derive Oxygen ml/l with 1.0 second window size
10 Bin Average Average data into desired pressure or depth bins.
Pressure averaging, 1db, with interpolation to center the output. Exclude scans marked bad (wildedit, loopedit)t. Output the number of scans in each averaged bin. Process the whole cast, not just the downcast.
11 Derive Compute salinity, density, and other parameters.
Compute salinity 1 and salinity 2, sound velocity, and depth (using 71 Lat).
Store files in processed/derivefull
10 Strip Remove extra columns.
Reduce file to P,T1, T2, C1, C2, OxV, Fl, Tr, Alt, Oxy, Scans per bin, S1, S2, Fl, Alt. Do not include Latitude, Longitude, SndSpd, and Depth
11 Split Create a separate file for down and up cast.
Split files into down and uptrace. Exclude scans marked bad is checked, meaning a scan identified bad in loopedit will not be used to separate the downtrace from the uptrace.