This encoding uses the toolbox developed by eccodes and it is adapted to encode Moana TD sensor netcdf files, generally obtained from processing raw Moana TD files with moana-qc. There is the option of using one of three templates:
- BUFR template for Temperature and salinity profile observed by sub-surface profiling floats (subfloat, 315003)
- BUFR template for representation of data derived from a ship based lowered instrument measuring subsurface seawater temperature, salinity and current profiles (ship, 315007)
- BUFR template for representation of observations from a single glider trajectory profile (glider, 315012, work in process).
At the moment we provide the option to decide if only the final upcast should be extracted (upcast=True), or the full deployment (upcast=False).
Additionally, as default we are only using Moana TD sensor data that have passed all the Quality Control tests (QC_flag=1). However, data that failed a test but can probably be classified as good data can also be used (QC_flag=[1,2]). To see more about Moana TD sensor quality control please visit the moana-qc repository.
To install the toolbox and additional requirements please use the following instructions.
Make sure that you have installed eccodes. Instructions here
Then follow these steps.
pip install -r requirements/default.txtpython setup.py installBuild image from scratch using the provided files Dockerfile and geteccodes.sh.
docker build -t moana-bufrtools:v1.0.0 .docker run -ti moana-bufrtools:v1.0.0Note: Don't forget to mount the volumes where your data is located i.e.,
docker run -v /DATA/PATH:/DATA/PATH moana-bufrtools:v1.0.0
The proposed GTS_encode is tailored to Moana TD sensors netcdf formatting. This means, the script uses attributes that are encountered in the sensor netcdf files. Below we present a quick example of how to run the code, the user should provide the input file path and the centre code (Code Table C-11). The default options are to extract only the upcast (upcast=True) and quality control data that passed all the tests (QC_flag=1). The output would be an encoded bufr file in the same folder and the same name as the input file with .bufr extension. The output file can be validated using one of the following tools (aws or ecmwf)
from GTS_encode.GTS_encode import GTS_encode_subfloat, GTS_encode_ship, GTS_encode_glider
file = "../../data/MOANA_0058_434_230228081912_qc.nc"
centre_code = 69 # MetService Centre code from table Code Table C-11 69 -> Wellington (RSMC)
GTS=GTS_encode_subfloat(file, centre_code, upcast=True, QC_flag=1) #upcast True if only upcast is neededor
GTS= GTS_encode_ship(file, centre_code, upcast=True, QC_flag=1)or
GTS= GTS_encode_glider(file, centre_code, upcast=True, QC_flag=1)GTS.run()Useful functions to support the encoding of Moana TD sensors
- inflection_data - Identification of inflection points
- extract_upcast - Extraction of upcast measurements
- pres - conversion of depth (m) to pressure (Pa)
Examples of output file. The .bufr output file was decoded and validated for each template generating the following csv files:
Includes classes to encode the data into GTS/BUFR format. This codes are tailored for Moana TD sensors format, changes might be needed if the netcdf format is different, but it should be straightforward. Probably could be fixed with a configuration file.
There are three classes:
- Category 15 – Oceanographic report sequence
- Sequence 003 – Temperature and salinity profile observed by profile floats
| 315003 | Subsurface float Template |
|---|---|
| Identification | |
| 001087 | WMO Marine observing platform extended identifier |
| 001085 | Observing platform manufacturers model |
| 001086 | Observing platform manufacturers serial number |
| 002036 | Buoy type |
| 002148 | Data collection and/or location system |
| Float information | |
| 002149 | Type of data buoy |
| 022055 | Float cycle number |
| 022056 | Direction of profile |
| 022067 | Instrument type for water temperature profile measurement |
| 301011 | Date |
| 301012 | Time |
| 301021 | Latitude and longitude (high accuracy) |
| 008080 | Qualifier for quality class |
| 033050 | Global GTSPP quality class |
| Profile Measurements | |
| 109000 | Delayed replication of 9 descriptors |
| 031002 | Extended delayed descriptor replication factor |
| 007065 | Water pressure |
| 008080 | Qualifier for quality class |
| 033050 | Global GTSPP quality class |
| 022045 | Subsurface sea temperature |
| 008080 | Qualifier for quality class |
| 033050 | GTSPP quality class |
| 022064 | Salinity |
| 008080 | Qualifier for quality class |
| 033050 | GTSPP quality class |
- Category 15 – Oceanographic report sequence
- Sequence 007 – Representation of data derived from a ship based lowered instrument measuring subsurface seawater temperature, salinity and current profiles
| 315003 | Ship Template |
|---|---|
| 301003 | Ship's call sign and motion |
| Extended identification | |
| 001019 | Long station or site name |
| 001103 | IMO Number |
| 001087 | WMO marine observing platflorm extended identifier |
| Cruise/ship line information | |
| 001036 | Agency in chage of operating the observing platform |
| 001115 | Identifier of the cruise or mission under which the data were collected |
| 001080 | Ship line number according to SOOP |
| 005036 | Ship transect number according to SOOP |
| 301011 | Year, month, day |
| 301012 | Hour, minute |
| 301021 | Latitude/Longitude (high accuracy) |
| Profile Information | |
| 001079 | Unique identifier for the profile |
| 001023 | Observation sequence number |
| 022063 | Total water depth |
| Surface Pressure | |
| 101000 | Delayed replication of 1 descriptor |
| 031000 | Short delayed descriptor replication factor |
| 302001 | Pressure and 3-hour pressure change |
| Waves | |
| 101000 | Delayed replication of 1 descriptor |
| 031000 | Short delayed descriptor replication factor |
| 302021 | Waves |
| Temperature and humidity data | |
| 101000 | Delayed replication of 1 descriptor |
| 031000 | Short delayed descriptor replication factor |
| 302052 | Ship temperature and humidity data |
| Wind data | |
| 101000 | Delayed replication of 1 descriptor |
| 031000 | Short delayed descriptor replication factor |
| 302059 | Ship wind data |
| Surface temperature, salinity and current | |
| 022067 | Instrument type for water temperature/salinity profile measurement |
| 002171 | Instrument serial number for water temperature profile measurement |
| 302090 | Sea/water temperature high precision (surface) |
| 306033 | Surface salinity |
| 306034 | Surface current |
| 002171 | Instrument serial number for water temperature profile measurement (set to missing) |
| 022067 | Instrument type for water temperature/salinity profile measurement (set to missing) |
| Temperature and salinity profile data | |
| 002038 | Method of water temperature and/or salinity measurement |
| 022067 | Instrument type for water temperature /salinity profile measurement |
| 022068 | Water temperature profile recorder types |
| 002171 | Instrument serial number for water temperature profile measurement |
| 002033 | Method of salinity/depth measurement |
| 002032 | Indicator for digitization |
| 022056 | Direction of profile |
| 003011 | Method of depth calculation |
| 306035 | Temperature and salinity profile |
| Current profile data | |
| 107000 | Delayed replication of 7 descriptors |
| 031000 | Short delayed descriptor replication factor |
| 002032 | Indicator for digitization |
| 003010 | Method of sea/water current measurement |
| 002031 | Duration and time of current measurement |
| 002040 | Method of removing velocity and motion of platform from current |
| 022056 | Direction of profile |
| 003011 | Method of depth calculation |
| 306036 | Current profile |
| Dissolved oxygen profile data | |
| 104000 | Delayed replication of 4 descriptors |
| 031000 | Short delayed descriptor replication factor |
| 002032 | Indicator for digitization |
| 003012 | Instrument type/sensor for dissolved oxygen measurement |
| 003011 | Method of depth calculation |
| 306037 | Dissolved oxygen profile data |
The glider template is a work in process, here is the latest version Not approved yet:
- Category 15 – Oceanographic report sequence
- Sequence 012 – Observations from a single glider trajectory profile
| 315012 | Glider Template |
|---|---|
| Identification | |
| 301150 | WIGOS identifier* |
| 201129 | Change data width Increase width of following elements by 1 bit |
| 001087 | WMO marine observing platform extended identifier |
| 201000 | Change data width Cancel increase in width |
| 001019 | Long station or site name |
| 001036 | Agency in charge of operating the observing platform |
| 002148 | Data collection and/or location system |
| 001085 | Observing platform manufacturer's model |
| 001086 | Observing platform manufacturer's serial number |
| Surface Pressure | |
| 008021 | Time significance Set to 25, nominal reporting time |
| 301011 | Year, month, day |
| 301013 | Hour, minute, second |
| 301021 | Latitude / longitude (high accuracy) |
| 011104 | True heading of aircraft, ship or other mobile platform |
| 002169 | Anemometer type Set to 2, wind observation through ambient noise (WOTAN) |
| 011002 | Wind speed |
| 011001 | Wind direction |
| 002169 | Anemometer type Set to missing / cancel previous value |
| Ocean Currents | |
| 022032 | Speed of sea surface current |
| 022005 | Direction of sea-surface current |
| 301011 | Year, month, day |
| 301013 | Hour, minute, second |
| 008021 | Time significance Set to 2, time averaged |
| 004025 | Time period or displacement Duration of dive |
| 301021 | Latitude / longitude (high accuracy) |
| 022031 | Speed of current |
| 022004 | Direction of current |
| 008021 | Time significance Set to missing / cancel previous value |
| 005068 | Profile number |
| 001079 | Unique identifier for profile |
| Profile sections | |
| 126000 | Delayed replication of 26 descriptors |
| 031001 | Delayed descriptor replication factor Number of profile sections (e.g. descending, horizontal, ascending) |
| 022056 | Direction of profile 0 (ascending / upwards profile), 1 (descending / downwards profile), or 2 (horizontal) |
| 123000 | Delayed replication of 23 descriptors |
| 031002 | Extended delayed descriptor replication factor |
| 301011 | Year, month, day |
| 301013 | Hour, minute, second |
| 301021 | Latitude / Longitude (high accuracy) |
| 008080 | Qualifier for GTSPP quality flag 20, position |
| 033050 | Global GTSPP quality flag |
| 007062 | Depth below water surface |
| 008080 | Qualifier for GTSPP quality flag 13, water depth at a level |
| 033050 | Global GTSPP quality flag |
| 022065 | Water pressure |
| 008080 | Qualifier for GTSPP quality flag 10, water pressure at a level |
| 033050 | Global GTSPP quality flag |
| 022045 | Sea/water temperature |
| 008080 | Qualifier for GTSPP quality flag 11, water temperature at a level |
| 033050 | Global GTSPP quality flag |
| 022066 | Water conductivity |
| 008080 | Qualifier for GTSPP quality flag 25, water conductivity at a level * |
| 033050 | Global GTSPP quality flag |
| 022064 | Salinity |
| 008080 | Qualifier for GTSPP quality flag 12, salinity at a level |
| 033050 | Global GTSPP quality flag |
| 042016 | Sea water potential density referenced to sea surface* |
| 008080 | Qualifier for GTSPP quality flag 26, sea water potential density at a level |
| 033050 | Global GTSPP quality flag |
* These fields are not available for current tables, these are fields to be added with the glider template
Please see LICENSE for the license under which this code can be shared. Please consider contributing to the code under this repository whenever possible rather then forking or cloning into a new repository so all can benefit from collaborative work. If you need to fork/clone into a new repository, please let us know so we can include any new developments as a community.
Original code base by MetOcean Solutions, a Division of Meteorological Service of New Zealand Ltd, developed as part of the Moana Project. The Moana Project is funded by the New Zealand Ministry of Business, Innovation, and Employment (MBIE) Endeavour Fund.
Contributors to the current version in include: MetOcean Solutions
The Moana TD (Mangōpare) sensor and deck unit hardware were developed by Zebra-Tech, Ltd, Nelson, New Zealand as part of the Moana Project. Sensors are available through https://www.zebra-tech.co.nz/
A fishing vessel, in-situ ocean observing quality control working group is in development through FVON (https://fvon.org/). Please contact either the Moana Project ([email protected]) or FVON (through their website) for more information.