Marine Data Literacy 2.0

Providing instruction for managing, converting, analyzing and displaying oceanographic station data, marine meteorological data, GIS-compatible marine and coastal data or model simulations, and mapped remote sensing imagery

 

 

 

 

Home > 4. Ocean Data View > 4.9 Add CTD to ODV

4.9 Add Seabird CTD Data to an ODV Collection

  • Exercise Title:  Add Seabird CTD Data to an ODV Collection

  • Abstract:  It's very important to be able to add new data to ODV collection, however obtained.  In this exercise you'll learn how to add conductivity-temperature-depth (CTD) data from the popular SeaBird systems.  Formerly a very tedious method was required, but ODV's author has recently added the method shown below, which is so simple that this exercise is probably not even necessary.

  • Preliminary Reading (in OceanTeacher, unless otherwise indicated):

  • Required Software:

  • Other Resources: 

    • ctd_madagascar_asclme_seabird_cnv.zip - CTD data collected from 4 stations off the coast of Madagascar as part of the Agulhas and Somali Current Large Marine Ecosystems Project (ASCLME) project.  CNV format is a special archiving format produced by Seabird processing systems that can be directly imported by ODV

  • Author:  Murray Brown

  • Version:  April 2013

1.  Download the above zipped data file to the folder DATA > OCEAN.  Then unzip it in the same folder to reveal 4 CNV files:
  • sta0860.cnv
  • sta0861.cnv
  • sta0864.cnv
  • sta0865.cnv

Check afterwards to make sure the file has the extension cnv only.  If Windows has added .txt, then remove that additional extension.

2.  A wise scientist always inspects data files, visually, to learn what they contain and to find any possible copy or transcription errors.  Open the largest CNV file, sta0865.cnv in any good ASCII editor.  It has a very large "header" followed by a traditional spreadsheet section.
3.  All of these items above the spreadsheet are metadata.  There are 2 types of metadata:
  • "Use metadata" - Information items needed to process data
  • "Discovery metadata" - Information about datasets needed to find them in larger aggregates or collections

The first lines of the header, identified by *, contain use metadata about the SeaBird system.  Also the items identified NMEA (for National Marine Electronics Association) are possibly plug-in data from a navigation system, providing location and time.

* Sea-Bird SBE 9 Data File:
* FileName = C:\Seabird\CTDData\STA0865.dat
* Software Version Seasave Win32 V 5.30a
* Temperature SN = 2369
* Conductivity SN = 1827
* Number of Bytes Per Scan = 21
* Number of Voltage Words = 3
* Number of Scans Averaged by the Deck Unit = 1
* System UpLoad Time = Aug 31 2008 07:23:08
* NMEA Latitude = 25 55.56 S
* NMEA Longitude = 044 29.10 E
* NMEA UTC (Time) = none
* Store Lat/Lon Data = Append to .NAV File When <Ctrl F7> is Pressed

4.  If your data file does not contain NMEA Latitude and NMEA Longitude values (due possibly to the absence of an integrated navigation system), then use an ASCII editor to enter those values (using the format you see here), usually taken from the station log.  ODV will not process a file without lat and lon values.

In this case, the file contained usable values, so nothing is necessary.

* NMEA Latitude = 25 55.56 S
* NMEA Longitude = 044 29.10 E

5.  Many systems do not automatically receive NMEA UTC (Time) values from its sensors.  In the above example, you can see the value NONE, which is useless.  If you want your collection to have correct date and time values, then you must make the change you see here.  You can find the date/time string at many places in the file; in this case just 3 lines above.

After you make this edit, you can save the file and continue your exploration of it.

* NMEA UTC (Time) = none

               Line before editing

* NMEA UTC (Time) = Aug 31 2008 07:23:08

               Line after editing

6.  The lines identified by ** are discovery metadata, typical of ocean station data. 

** Ship: 14 R/V "Dr. Fridtjof Nansen"
** Station: 0865
** Echodepth: 1158
** Log: 2238.32
** Wind-Dir/Force: 35 07
** Air-Temp (dry): 23
** Weather Sky: 1 1
** Sea : 2

7.  The lines identified by # are mainly use metadata, including parameter identifications ("name" lines), and value ranges ("span" lines).

# nquan = 12
# nvalues = 1179
# units = specified
# name 0 = scan: Scan Count
# name 1 = prDM: Pressure, Digiquartz [db]
# name 2 = t068C: Temperature [ITS-68, deg C]
# name 3 = c0S/m: Conductivity [S/m]
# name 4 = sbeox0V: Oxygen Voltage, SBE 43
# name 5 = flCUVA: Fluorescence, Chelsea UV Aquatracka [ug/l]
# name 6 = sbeox0ML/L: Oxygen, SBE 43 [ml/l], WS = 2
# name 7 = sal00: Salinity [PSU]
# name 8 = sigma-t00: Density [sigma-t, Kg/m^3 ]
# name 9 = svCM: Sound Velocity [Chen-Millero, m/s]
# name 10 = avgsvCM: Average Sound Velocity [Chen-Millero, m/s], minP = 0, minS = 0, pWS = 20, tWS = 60
# name 11 = flag: flag
# span 0 = 1816, 35605
# span 1 = 4.000, 1182.000
# span 2 = 4.9494, 22.8567
# span 3 = 3.369758, 5.139570
# span 4 = 1.3456, 2.7156
# span 5 = 0.0326, 0.3256
# span 6 = 2.84729, 4.87066
# span 7 = 34.5666, 35.8154
# span 8 = 24.2935, 27.4672
# span 9 = 1487.67, 1530.07
# span 10 = 1501.21, 1529.70
# span 11 = 0.0000e+00, 0.0000e+00
# interval = decibars: 1
# start_time = Aug 31 2008 07:23:08
# bad_flag = -9.990e-29
# sensor 0 = Frequency 0 temperature, 2369, 25-Jul-07
# sensor 1 = Frequency 1 conductivity, 1827, 23-Jun-06, cpcor = -9.5700e-08
# sensor 2 = Frequency 2 pressure, 53966, 17-Jun-93
# sensor 3 = Extrnl Volt 0 Oxygen, SBE, primary, 1102, 17-Oct-06
# sensor 4 = Extrnl Volt 4 Fluorometer, Chelesa UV Aquatracka, 88/2615/119, 1994-12-15
# datcnv_date = Aug 31 2008 08:08:19, 5.30a
# datcnv_in = C:\Seabird\CTDData\sta0865.dat C:\Seabird\SBEDataProcessing-Win32\Seasoft.con
# datcnv_skipover = 0
# wildedit_date = Aug 31 2008 08:08:21, 5.30a
# wildedit_in = C:\Seabird\CTDData\sta0865.cnv
# wildedit_pass1_nstd = 2.0
# wildedit_pass2_nstd = 20.0
# wildedit_pass2_mindelta = 5.000e-003
# wildedit_npoint = 100
# wildedit_vars = prDM t068C c0S/m sbeox0V flCUVA
# wildedit_excl_bad_scans = yes
# celltm_date = Aug 31 2008 08:08:27, 5.30a
# celltm_in = C:\Seabird\CTDData\sta0865.cnv
# celltm_alpha = 0.0300, 0.0000
# celltm_tau = 7.0000, 0.0000
# celltm_temp_sensor_use_for_cond = primary,
# filter_date = Aug 31 2008 08:08:37, 5.30a
# filter_in = C:\Seabird\CTDData\sta0865.cnv
# filter_low_pass_tc_A = 0.030
# filter_low_pass_tc_B = 0.150
# filter_low_pass_A_vars = c0S/m sbeox0V flCUVA
# filter_low_pass_B_vars = prDM
# loopedit_date = Aug 31 2008 08:08:50, 5.30a
# loopedit_in = C:\Seabird\CTDData\sta0865.cnv
# loopedit_minVelocity = 0.250
# loopedit_excl_bad_scans = yes
# Derive_date = Aug 31 2008 08:09:03, 5.30a
# Derive_in = C:\Seabird\CTDData\sta0865.cnv C:\Seabird\SBEDataProcessing-Win32\Seasoft.con
# derive_time_window_docdt = seconds: 2
# binavg_date = Aug 31 2008 08:09:13, 5.30a
# binavg_in = C:\Seabird\CTDData\sta0865.cnv
# binavg_bintype = decibars
# binavg_binsize = 1
# binavg_excl_bad_scans = yes
# binavg_skipover = 0
# binavg_surface_bin = no, min = 0.000, max = 0.000, value = 0.000
# Derive_date = Aug 31 2008 08:09:21, 5.30a
# Derive_in = C:\Seabird\CTDData\sta0865.cnv C:\Seabird\SBEDataProcessing-Win32\Seasoft.con
# file_type = ascii

8.  Follow Panels 7-10 in Creating ODV Collections from World Ocean Database Data to create a new data collection in the folder PRODUCTS > ODV > COLLECTIONS > CTD with the name ctd_madagascar_asclme
9.  But when you are asked for the DEFINITION OF COLLECTION VARIABLES, as you see here, click on CANCEL and do not specify anything.
10.  Here's the empty collection.
11.  Select IMPORT > SEA-BIRD CNV
12.  Navigate to and select one or more of your CNV files.
13.  This small window lets you specify how to import the data. 
  • Check SPLIT DOWN- AND UP-CAST to see both directions, when they are available (not always the case).
  • Don't check SUBSAMPLE if you want to see all the data.  Check it and enter a pressure increment to subsample the data.  For example 10 db would give you data points approximately every 10 meters.
14.  You might be asked here what is the name of the collection.  Navigate to the location and file you created in Panel 8, above.
15.  This information window shows you that the import was successful.  Click OK to close it.
16.  Here's you new data station on the map (slightly zoomed to help you see it).
17.  Use VIEW > LAYOUT TEMPLATES > 1 STATION to see the new data station.  Here, temperature is the selected parameters.
18.  You can use the above method to add other CTD stations.