Functions for processing BGC-Argo data:

• Download raw data
• Extract SST, SSS, depth of maximum chlorophyll
• Compute MLD, nitracline depth
• Hierarchical clustering and Principal component analyses of oceanographic parameters
• Mask Longhurst's biogeochemical provinces to each float profile
• Filter for outliers
• Match Phytoplankton Functional Types with each profile

BGC-Argo track within the North Atlantic

Seasonal variation of PFT within the North Atlantic

BGC-ARGO & PFT data mining pipeline

Requirement:

• Anaconda
• Account on: https://data.marine.copernicus.eu/

One-time setup:

Create new anaconda environment:

conda create --name argo_pft --file argo_pft.txt

Setup OPenDAP:

python config_opendap_MAC.py

Data mining:

Activate conda environment:

conda activate argo_pft

Download BGC-Argo example

./argo_download_ifremer.py --float 1902380 –export

Calculate habitat-defining variables:

./HDV_calculate.py

Match phytoplankton functional type with HDV files:

./PFT_download.py

Download script usage

./argo_download_ifremer.py --help
usage: argo_download_ifremer.py [-h] [--float FLOAT [FLOAT ...]] [--lat LAT LAT] [--lon LON LON] [--start START] [--end END] [--sensor SENSOR [SENSOR ...]] [--folder FOLDER] [--skip] [--export] [--plot] [--overwrite]

options:
  -h, --help            show this help message and exit
  --float FLOAT [FLOAT ...]
                        WMOID number/list
  --lat LAT LAT         Latitude range: lower upper (within -90 to 90)
  --lon LON LON         Longitude range: lower upper (within either -180 to 180 or 0 to 360)
  --start START         Start date: datetime object
  --end END             End date: datetime object
  --sensor SENSOR [SENSOR ...]
                        Specify required sensors: PRES, TEMP, PSAL, DOXY, CHLA, BBP700, PH_IN_SITU_TOTAL, and NITRATE
  --folder FOLDER       File download folder
  --skip                Return list of file names, skip download
  --export              Export .nc files to .csv files
  --plot                Plotting trajectories
  --overwrite           Overwrite existing files