Discrete Water Column Measurements

Identifies the Latitude position passed to the NMEA interface at the time of the start of the cast from the ship’s primary GPS. Should always be in the form DD MM.MM N

The original filename specified at time of collection. (1) FileName will end in .hdr if the ‘Merge separate HDR file ‘option was used to process in Data Conversion (2) FileName will end in .hex if the original header at collection time was not altered AND the cast was collected on or after Jan 1, 2012 (3) FileName will end in .dat

The version of Seabird’s SEASAVE software used to acquire the raw cast data

The serial number of the Primary Temperature probe used on the CTD at the time of collection. Used by SBE Data Processing as a QA/QC measure to help ensure proper XMLCON file is used to process the data file – warning issued on steps computing engineering units is no match found

The serial number of the Primary Conductivity probe used on the CTD at the time of collection. Used by SBE Data Processing as a QA/QC measure to help ensure proper XMLCON file is used to process the data file – warning issued on steps computing engineering units is no match found

Number of bytes used by each scan line to capture all sensor data as represented in HEX

Number of active voltage sensors being collected at time of data acquisition. Voltage sensors include

• Oxygen sensors

• Fluorescence

• Beam Transmission

• Altimeter

Indicates whether the Deck Unit is averaging the cast data prior to being written to file.

(1) Value of 1 indicates all values are written to output file

(2) Max value for SBE-9plus cannot exceed 24

* - It is NOT desirable to allow averaging of cast data at the deck unit level as it lowers data resolution

Date and time of the cast in the LOCAL time of the machine. This time is only supplied for reference purposes. Should NMEA UTC (Time) not be available, user should use System UTC as backup rather than this field as the time zone cannot be determined from the data itself for this entry

Identifies the Latitude position passed to the NMEA interface at the time of the start of the cast from the ship’s primary GPS. Should always be in the form

DD MM.MM N

Identifies the Latitude position passed to the NMEA interface at the time of the start of the cast from the ship’s primary GPS. Should always be in the form

DDD MM.MM W

The UTC time at which the start of the cast occurred. Value will depend upon selected NMEA sentence in deck unit dip switch setup:

• GGA or RMC will yield Date and Time data

• GLL will yield only a time

*NOTE - Most deck units on NOAA Ships are set to look for the GGA signal

Value set for the storage of position data to the cast. Must be set to at least append to HDR, default is append to Every Scan

* NOTE – With this option set , the user must set Latitude and/or Longitude as a desired output variable to see its value listed in the cast row data, normally we do not include this data

Identifies the name of the platform used to collect the data. The name of the ship should be spelled out in all capital letters and start one space after the identifier colon. Valid ship names for MSLabs include the following:

• PISCES

• OREGON II

• GORDON GUNTER

• SOUTHERN JOURNEY

• CARETTA

• GANDY

• HST

Identifies the cruise number that the data was collected on as a 4 digit number.For Oregon II this should be the sequential cruise number of the ship over its entire lifespan with appropriate leading zero placeholders. For all other vessels it should be in the form YYNN where:

• YY = last two digits of the year the survey was conducted – for 2015 this would be 15

• NN = the sequential trip of the vessel within that calendar year – 2nd trip would be designated 02

Ex. ** Cruise: 1502

This is the Pascagoula Station number where the cast was conducted. It should always be 3-digits (pad with 0 to ensure minimum length of 3 characters is met)

This represents the valid cast number of the hydrocast taken at a station, not the attempt. Used to indicate if more than 1 valid cast is done at the station

This is the manually recorded Latitude position as observed from a GPS display at the time of the start of the cast. It is entered as a failsafe in case the NMEA Interface does not capture a valid Latitude position

This is the manually recorded Longitude position as observed from a GPS display at the time of the start of the cast. It is entered as a failsafe in case the NMEA Interface does not capture a valid Latitude position

Value should only be populated if the station is a valid SEAMAP designated station. Valid entries are in the following form:

• If TRAWL

o First character one of the following

¿ W- West Delta

¿ E- East Delta

¿ T – Texas

o Characters 2 and 3 are numeric and represent the Shrimp Stat Zone the station resides in as a two digit value

o Characters 4 and 5 are numeric and represent the sequential station contained within that Shrimp Stat Zone

• If Plankton

o The character B followed by its numeric number as read from the Plankton grid map

* NOTE – Field is often used incorrectly for other site designation. Stations not meeting above specifications are deemed non-SEAMAP

The initials of the user running the CTD collection software, SEASAVE, at the time of data acquisition

The entire depth , surface to bottom, of the location the cast was conducted

* NOTE – for surveys such as Plankton and Mammals this depth may exceed the cast depth due to sampling protocol. Ex. Plankton only samples to 200 meters to correlate data to Bongo collection but the actual site depth may be much greater

Notes is an optional field that may be populated where applicable. If no notes, header section will skip this line and be one line shorter than a file where a note field was entered. Notes should be entered strictly as text only and be relevant – Ex. CHART DEPTH 1200 meters

Number of columns (sensors) to expect in each row of data. These quantities will be identified beginning at line 28 of the header with the tag #name 0. The final defined variable enumeration will always be one less than the nquan value since the names array starts from position 0, not 1. If the CTD is configured with all sensors this value should be 11 in a processed data file, 9 if the transmissiometer and fluorometer are removed for deepwater work

Number of rows, or depth bins, to expect in the output data.

*NOTE – users should not assume the output will start at the 1 meter depth bin, typical value will be 3.0

Tells user that the units the variable represented by the “name” tag were collected in

The temperature, in degrees C , within the depth bin specified as a named variable within the same data row

The in situ Chlorophyll A value output by the Fluorometer within the depth bin specified as a named variable within the same data row

[mg/m^3] 2010 forward

Measure of water clarity % (Percent) determined by the strength of the signal strength of the 25cm red wavelength of light transmitted from transmitter to receiver of the transmissometer within the depth bin specified as a named variable within the same data row

Measures the speed of sound (meters/second) through the depth bin specified as a named variable within the same data row

The dissolved oxygen in mg/l of the water within the depth bin specified as a named variable within the same data row

The dissolved oxygen value expressed as a percentage of a comparison to a known 100% saturation value of the water within the depth bin specified as a named variable within the same data row

The depth, in meters, at which the variables within the output data row were sampled

The salinity of the water in PSU (Practical Salinity Units) within the depth bin specified as a named variable within the same data row

The salinity of the water in kilograms/meter ^3 within the depth bin specified as a named variable within the same data row

Used to indicate the number of scans averaged into the depth bin specified as a named variable within the same data row. In an ideal circumstance where the CTD traveled at 1 m/s and no scans were rejected the value of nbins should be 24 as the CTD samples at 24Hz. Nbin values of less than 5 should be further examined to determine why scans were omitted by processing

Flag should ALWAYS be the last variable of the output row. This variable is added automatically by SBE Data Processing to indicate whether the data represented for a particular depth bin was deemed acceptable by the processing software. Users should verify all variables output to ensure they fall within acceptable ranges. Span data can be used for these purposes, included in the lines that follow within the header section

0.0000e+00 for good data -9.990e-29 for bad/rejected data

Example: # datcnv_in = C:\OT1505\110.hex C:\OT1505\110.XMLCON

The #datcnv_in tag provides the user of the data with the following information: 1. The name of the raw data file used as the input file for the Data Conversion module – filename in this case was C:\OT1505\110.hex

2. The name of the XMLCON configuration file used with the data to compute/convert raw data to ASCII engineering units

Example: # datcnv_skipover = 4567

The #datcnv_skipover= tag provides the user of the data with the following information:

1. The number of scans removed from the output data by Data Conversion associated with the soak period. This value is input by the user as a parameter 2. Allows user to see if the recommended 3 minute soak period was used • The SBE-9plus CTD samples at a rate of 24 scans per second. For a 3-minute soak period, the value in scans should be 4320 (24 scans a second * 60 seconds in a minute * 3 minutes) • User should compare stated skipover value to 4320 – value used should be equal to or greater than 4320

3. Allows the user the ability to compute the duration of the soak time based on the following: • Dividing the stated value for skipover by 24 will yield the Elapsed Time to that point in seconds • 4567/24 = 190.3 seconds • 190.3 seconds can be converted to minutes by dividing by 60 • 190.3/60=3.172 Minutes • This can be expressed in minutes and second format a. The integer portion of the value represents whole minutes -> 3 b. The decimal portion of the value multiplied by 60 yields second->.172 * 60 = 10.32 Cast Soak Period was 03:10

4. The computed soak time value can be added to the stated System Upload Time (listed near the beginning of the CTD header section) to compute the time when the actual downcast began in HH:MM:SS format if desired

Example: # datcnv_ox_hysteresis_correction = yes

The # datcnv_ox_hysteresis_correction = tag tells the user whether formulas were applied to the oxygen data to counteract the effects of hysteresis (a retardation of an effect when the forces acting upon a body are changed -as if from viscosity or internal friction).The value should be set to yes to indicate the corrections were applied by the Data Conversion module to the oxygen data.

Example: # alignctd_date = Nov 02 2015 13:27:58, 7.23.2

The #alignctd_date tag provides the user of the data with the following information:

1. The date and time the output data was generated. Time is that of the system used to process the data in the time zone used by the processing computer. Next release of software will update this to a UTC stamp and an update for this document will be sent at that time, current projected date is not known

2. The version of SBE Data Processing used to process the data via Align CTD – version was 7.23.2 in this case

Example : # alignctd_in = C:\OT1505\110.cnv

The #alignctd_in tag provides the user of the data with the name of the data file used as the input file for the Align CTD module – filename in this case was C:\OT1505\110.cnv

Example: # alignctd_adv = c0mS/cm 0.100, c1mS/cm 0.100, sbeox0V 3.000, sbeox1V 3.000, wetStar 3.000, CStarTr0 1.000

The # alignctd_adv tag provides the user with the following information:

1. The shorthand name of each variable a time advance was applied to by the Align CTD module

2. The units associated with each variable a time advance was applied to by the Align CTD module

3. The advance time (in seconds) applied to the variable’s data by the Align CTD module.

Example: # filter_date = Nov 02 2015 13:29:18, 7.23.2

The # filter_date tag provides the user of the data with the following information:

1. The date and time the output data was generated. Time is that of the system used to process the data in the time zone used by the processing computer. Next release of software will update this to a UTC stamp and an update for this document will be sent at that time, current projected date is not known

2. The version of SBE Data Processing used to process the data via Filter – version was 7.23.2 in this case

Example: # filter_in = C:\OT1505\110A.cnv

The # filter_in tag provides the user of the data with the name of the data file used as the input file for the Filter module – filename in this case was C:\OT1505\110A.cnv

Example: # filter_low_pass_tc_A = 0.030

The # filter_low_pass_tc_A is the filter time constant, in seconds, applied to the low pass filter A setting in the SBE Data Processing suite Filter module. This value should be the program’s default value which is 0.030.

Example: # filter_low_pass_tc_B = 0.150

The # filter_low_pass_tc_B tag is the filter time constant, in seconds, applied to the low pass filter B setting in the SBE Data Processing suite Filter module. This value should be the program’s default value which is 0.150.

Example: # filter_low_pass_A_vars =

The # filter_low_pass_A_vars = is used to list any variables, in shorthand notation, that have had the low pass A filter applied to the data. For the SBE-9plus CTD there should be NO variables following the equal sign.

Example: # filter_low_pass_A_vars = prDM

The # filter_low_pass_B_vars = is used to list any variables, in shorthand notation, that have had the low pass B filter applied to the data. For the SBE-9plus CTD there should only be ONE variables following the equal sign - prDM. The prDM shorthand notation represents Presure, Digiquartz sensor in db.

Example: # loopedit_date = Nov 02 2015 13:30:16, 7.23.2

The # loopedit_date tag provides the user of the data with the following information:

1. The date and time the output data was generated. Time is that of the system used to process the data in the time zone used by the processing computer. Next release of software will update this to a UTC stamp and an update for this document will be sent at that time, current projected date is not known

2. The version of SBE Data Processing used to process the data via Loop Edit – version was 7.23.2 in this case

Example: # loopedit_in = C:\OT1505\110AF.cnv

The # loopedit_in tag provides the user of the data with the name of the data file used as the input file for the Loop Edit module – filename in this case was C:\OT1505\110AF.cnv

Example: # loopedit_minVelocity = 0.050

The # loopedit_minVelocity tag is the descent speed of the CTD in meters per second used as the threshold by the Loop Edit module to determine whether a particular scan was associated with ship heave or was valid. The minVelocity tag examines each row of data, or scan line, to ensure the descent rate of the CTD was equal to or greater than 0.050 m/s.

Loop Edit uses this info to add adjust the flag output column. In cases where the scan did not meet the criteria , Loop Edit sets the flag value for the data row to -9.990e-29. If the scan met the requirement and had not been previously flagged as bad, the flag value is set to 0.0000e+00 to indicate a good scan.

Example: # loopedit_surfaceSoak: do not remove

The loopedit_surfaceSoak: tag records the setting associated with computing the number of scans to skip over that are associated with the initial CTD soak. Because the MSLabs protocol is to remove these scans at the Data Conversion module, this flag should always have a value of do not remove after the colon in the tag line.

Example: # loopedit_excl_bad_scans = yes

The loopedit_excl_bad_scans tag shows the value set within the SBE Data Processing LoopEdit module in regards to removing bad scans from the generated output. For MSLabs, this tag should AWAYS show the option of yes indicating that the option was selected within the LoopEdit module setup.

Example: # Derive_date = Nov 02 2015 13:31:35, 7.23.2 [derive_vars = 5]

The # Derive_date tag provides the user of the data with the following information:

1. The date and time the output data was generated. Time is that of the system used to process the data in the time zone used by the processing computer. Next release of software will update this to a UTC stamp and an update for this document will be sent at that time, current projected date is not known

2. The version of SBE Data Processing used to process the data via Derive – version was 7.23.2 in this case

3. The module run within the SBE Data Processing suite. Datcnv is the abbreviation for Data Conversion. All lines beginning with # datcnv_ were generated by that module

4. The number of variables added to the output data by the Derive module. In this case 5 variables were selected. The header itself does not identify them specifically but can be determined from the final named variable set. The five Derive variables are as follows • Oxygen, mg/l • Oxygen, % saturation • Depth, meters • Density, kg/m^3 • Salinity ,PSU

Example: # Derive_in = C:\OT1505\110.hex C:\OT1505\110.XMLCON

The # Derive_in tag provides the user of the data with the following information: 1. The name of the data file used as the input file for the Derive module – filename in this case was C:\OT1505\110AFL.cnv

2. The name of the XMLCON configuration file used with the data to compute/convert raw data to ASCII engineering units

Example: # derive_time_window_docdt = seconds: 2

The # derive_time_window_docdt tag holds the Window size for oxygen derivative calculation (seconds).MSLabs applies the recommended default of a 2 second windows size to all derived variables per Seabird recommendation.

Example: # derive_ox_tau_correction = yes

The # derive_ox_tau_correction tag tells the user whether tau correction was performed on oxygen data. This correction is only applicable if the data contains a SBE43 type oxygen sensor. In cases where Tau correction is set to yes, the Tau formulas are used to derive oxygen values rather than the Window size parameters. These parameters are part of the XMLCON file.

Example: # binavg_date = Nov 02 2015 13:32:48, 7.23.2

The # binavg_date tag provides the user of the data with the following information:

1. The date and time the output data was generated. Time is that of the system used to process the data in the time zone used by the processing computer. Next release of software will update this to a UTC stamp and an update for this document will be sent at that time, current projected date is not known

2. The version of SBE Data Processing used to process the data via Bin Average – version was 7.23.2 in this case

# binavg_in = C:\OT1505\110AFLD.cnv

The # binavg_in tag provides the user of the data with the name of the data file used as the input file for the Bin Average module – filename in this case was C:\OT1505\110AFLD.cnv

# binavg_bintype = meters

The # binavg_bintype tag tells the user the parameter used to bin the data. Meters represents the units associated with the selected variable which was Depth. The variable can be obtained from the list of named variables as discussed previously in this document since there should only be one unique variable whose units are of the specified type shown in the # binavg_bintype tag. For MSLabs, the parameter should AWAYS show meters.

Example: # binavg_binsize = 1

The # binavg_binsize tag tells the user the size parameter applied to the selected bin type. In this example, a bin size of 1 was selected for the bin type parameter of meters. The combination of the bintype and binsize tags tells the user of the data that the output was averaged by Depth in meters of 1 meter each which is the default protocol for MSLabs.

Example: # binavg_excl_bad_scans = yes

The # binavg_excl_bad_scans tag tells the user whether scans determined as bad during the Bin Average processing were excluded from the output data. For MSLabs, this value should ALWAYS be set as yes.

Example: # binavg_skipover = 0

The # binavg_skipover tag indicates the number of scans skipover at the beginning of the datafile as part of the Bin Average processing done by the SBE Data Processing suite. For MSLabs, this value should always be 0 since the scans associated with the surface scan were removed during the Data Conversion phase of processing.

Example: # binavg_surface_bin = no, min = 0.000, max = 0.000, value = 0.000

The # binavg_surface_bin tag is used to tell the user whether the surface bin was computed automatically, indicated by the word no immediately after the equal sign in the tag, or specified by the user. For MSLabs, the initial parameter should ALWAYS be set to NO as we want the surface bin to be computed from processing rather than specified for a more accurate representation of the data.

The # binavg_surface_bin tag has the following four parameters associated with it:

1. Include surface bin – Allows user to specify whether a range and target be used to calculate a surface bin from the data or if the surface bin should be computed directly from the data. No indicates the surface bin was calculated and any values stated for Surface bin min, max and target were ignored. Yes indicates that a specific starting depth bin is desired and a range and target are specified to use in the computation.

2. Min = <value> - Allows user to specify the desired minimum acceptable surface bin value. The default for the parameter is 0.000 which will be shown within the CTD Header section as a default if the user does not specify a value. If the above parameter Include surface bin is set as NO , any stated value assigned to min=0 was ignored by the Bin Average module.

3. Max = <value> - Allows user to specify the desired maximum acceptable surface bin value. The default for the parameter is 0.000 which will be shown within the CTD Header section as a default if the user does not specify a value. If the above parameter Include surface bin is set as NO , any stated value assigned to min=0 was ignored by the Bin Average module.

4. Value =<value> - Allows user to specify the desired target surface bin value. The default for the parameter is 0.000 which will be shown within the CTD Header section as a default if the user does not specify a value. If the above parameter Include surface bin is set as NO , any stated value assigned to min=0 was ignored by the Bin Average module.

Example: # strip_in = C:\OT1505\110AFLDB.cnv

The # strip_in tag provides the user of the data with the name of the data file used as the input file for the Strip module – filename in this case was C:\OT1505\110AFLDB.cnv

Example: # file_type = ascii

The # file_type = tag tells the user the following information: 1. The format that the output data is written in. For a processed CTD cast, the format should ALWAYS show as ascii. 2. Is an indicator the line in the CTD Header that comes next will be the End of Header marker and no further processing will be applied

IMPORTANT – The name parameters listed earlier in the header represent the FINAL selected variable list. The last module tags listed in the CTD Header Section prior to the #file_type and *END* End of Header marker reflects the variable list as it existed at the point of the last module’s termination.

*END* is a flag used by both the user of the data and the SBE Data Processing suite to indicate the next line contained within the file will begin the output data section.

All subsequent lines will be output data. The user should check the following for QA/QC purposes at this point:

1. The number of data columns, delimited by tabs, should be equal to the #nquan tag near the beginning of the CTD Header. For the example station, nquan = 11 meaning each row show contain 11 data columns

2. The number of data rows following the *END* End of Header flag should be equal to that specified by the # nvalues tag output immediately after the # nquan tag. In this example the stated value is 51, there should be 51 rows of data