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 > 4.15 NetCDF into ODV

4.15 Importing Coriolis NetCDF Operational Marine Data (Argo Profilers/GTSPP/SOOP) into ODV

  • Exercise Title:  Importing Coriolis NetCDF Operational Marine Data (Argo Profilers/GTSPP/SOOP) into ODV

  • Abstract:  In this exercise you'll learn two ways to put Coriolis NetCDF data into ODV:

    • First, you'll add it to an existing ODV collection of WOD profiles (made in the previous exercise).  This collection uses the WOD structure, a standard item in ODV. 

    • Second, you'll create a new, empty ODV collection and import the Coriolis data.  This collection uses the Argo profile structure, a standard item in ODV.

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

    • N/A

  • Required Software:

  • Other Resources: 

    • pfl_2005_2011_liberia_wod.odv - Profile data collection, made in ODV from WOD data.  If you don't have it, then use your bottle data collection in exactly the same way.

    • argo_xbt_ctd_20120801_20130801_liberia_any_good_coriolis.tgz  - Downloaded in the previous exercise; not necessary to unzip

  • Author:  Murray Brown

  • Version:  August 2013

1.  Run ODV and open the existing profile collection for Liberia (or the bottle collection if you don't have the profiles).
2.  Select IMPORT > ARGO FORMATS > FLOAT PROFILES.
3.  Navigate to the folder LIBERIA > DATA > OCEAN > CORIOLIS and select the file argo_xbt_ctd_20120801_20130801_liberia_any_good_coriolis.tgz.  You might have to use ALL FILES to see it, because the ODV interface doesn't include TGZ as an allowable format, but it does work.
4.  This Data Import window open.  All of the "Source File Variables" on the right are from the Coriolis file.  All of the "Target Collection Variables" are already included in the structure of the collection.

ODV examines the two collections and compares them for exact matches.  Only one is found, Salinity [psu], and it is marked with an asterisk (*).

Now we need to find other exact matches, or set up conversions to make matches.  Look over the sources list, and you'll find that over half of them are concerned with adjustments (adj.) or errors, or both.  We don't have places for them in the target collection now, and we'll ignore them.  In fact, only the first 6 on the source side are of interest.

NOTE:  There will be much more to say about these quality-related fields in the future, as "end to end" data management methods are implemented.  We're taking a short-cut to make this collection now, but expect that you must deal with many or all of these other fields in your career.

5.  Depth can be calculated from pressure:
  • Select these 2 variables
  • Click CONVERT
  • Select the PRESSURE >> DEPTH conversion formula

Then click OK.  Asterisks will appear by the 2 variables to indicate they have been matched up.

6.  The 2 temperature variables are the same, just spelled differently.  Select both of them and click ASSOCIATE.  The asterisks appear.
7.  Oxygen is like the pressure/depth pair; a conversion is needed.  Select them and find the conversion formula for UMOL/KG to ML/L.  Then click OK.  The asterisks appear.
8.  These associations (i.e. equalities) can also be made:
  • CHLOROPHYLL [MG M-3] = CHLOROPHYLL [UG/L]
  • LIGHT ATTENTUATION COEFFICIENT [M-1] = TRANSMISSIVITY [M-1]

The asterisks appear.

9.  Now you have 6 variables on the left and right, matched up.  Just click OK to procede.
10.  Some measurements may be identified by ODV (through locations, times and/or other identification) as duplicates.  Accept any replacements that are discovered in this way.
11.  You should see the new stations added to the map, as red dots.

When you see this message, click OK.

12.  Reply YES.
13.  And here is your combined collection.  You can easily see the ship-of-opportunity lines, which confirm the addition.
14.  If you're wondering about how the variou data sources are identified in the cobined collection, right-click on the station map, and select STATION SELECTION CRITERIA.

In the NAME/RANGE tab you can find all of the stations:

  • The Coriolis stations are usually identified by 6-character WMO stations codes, as you see in the top 2 items. 
  • The earlier stations from the WOD are identified by 14-character codes, as you see in the bottom 3 items. 
  • Some miscellaneous codes also sometimes appear, as you see in the middle 5 items
14.  The new data are already in the collection, so you should consider changing the collection name to indicate a new time-span.  You can do this manually, by changing the names of the *.odv file and the associated data folder, after you close the combined collection. 
15.  The above steps illustrate the great power of ODV to accept data from many different formats/systems, with the flexible import module.  This will because much more apparent to you, and become an essential tool, as you make progress with data collections and sources.
16.  In ODV, select FILE > NEW
17.  Navigate to the folder PRODUCTS > ODV > COLLECTIONS > PROFILES and enter the name argo_xbt_ctd_20120801_20130801_liberia_any_good_coriolis (which is the same name as the data file).
18.  In this list of available collection structures, select ARGO PROFILE, and click OK.
19.  After the new, empty collection is created, select IMPORT > ARGO FORMAT > FLOAT PROFILES
20.  Navigate to the folder LIBERIA > DATA > CORIOLIS and select argo_xbt_ctd_20120801_20130801_liberia_any_good_coriolis.tgz.  You might have to use ALL FILES to see it, because the ODV interface doesn't include TGZ as an allowable format, but it does work.
21.  When this IMPORT OPTIONS window opens, you can see that everything is matched up, because the incoming structure is the same as the target structure.

Click OK.

22.  The dataset loads, and you'll see this map of red dots.
23.  And here is your new collection, which should be the same map as the original in Coriolis.
24.  The extreme ease of making this collection is by design, and you should take advantage of the existing structures to make most collections easy to make.  The collection is complete now, and already saved for use.  That completes the methods to add recent operational data to ODV.