ecfas 1.0.9

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General Description

• Purpose: Retrieve CMEMS sea-surface height forecasts at the coast (EU-wide) and add other relevant processes to produce a coastal total water-level TWL.
• Output: Netcdf files based on the bulleting date of the execution day (t0) containing coastal time-series for the selected product-region (ARC,MED,IBI,BS,BAL,NWS) for 7 days [t0-2 : t0+5] (dimensions Ncoastalpoints x times)

Installation

We recommend using miniconda.

Create an 'ecfas' virtual environment and install conda dependencies

$ conda create -n 'ecfas' python'>3.8,<3.9' libnetcdf==4.7.3
$ conda activate ecfas
$ conda install -c intel numpy
$ conda install -c fbriol pyfes==2.9.2
$ conda install -c conda-forge proj==7.2.0
$ conda install xarray==0.16
$ conda install geos==3.8.1

Option 1: PIP (current stable release)

$ pip install ecfas

Option 2: Git-Clone and install from sources (current master-branch version)

This option is ideal if you want to edit the code. Clone the repository:

$ git clone [e-mail]:mirazoki/ecfas.git

Change into its directory and install it:

$ cd ecfas
$ pip install -e .

You are now ready to go

External dependencies

• Note: Location of the external files needs to be specified in the configuration file

• Summer masks need to be downloaded from https://nexus.mercator-ocean.fr/repository/moistatics/ECFAS/masks.tar.gz.

• This implementation also requires FES2014 tide data from AVISO. You will need to register for an account, download the data from the AVISO ftp site.

Create a configuration file

Create a file with the following content:

# CMEMS credentials and url for data donload
usr=
pwd=
url=http://nrt.cmems-du.eu/motu-web/Motu
# Directory for outputs
outdir=
# Directory for masks
maskdir=
# Leave blank if do not want any log files (console output only)
logdir=
# FES data, if blank then there is none
fesdir=

Directories paths can be absolute or relative. If relative, they will assumed to be relative to the scripts' running directory.

Usage

Running the workflow

• User guide: The workflow is run separately for each regional domain in Europe, namely NWS,IBI,MED,BAL,BS,ARC (see optional argument -r) For operational purposes (e.g. ECFAS), the workflow should be scheduled at the corresponding daily forecast update time for each domain:

  • NWS: North West Shelf, daily update time: 12:00

  • IBI: Iberian Biscay and Ireland , daily update time: 14:00

  • MED: Mediterranean Sea , daily update time: 20:00

  • BAL: Baltic Sea , daily update time: 22:00

  • BS: Black Sea , daily update time: 12:00

  • ARC: Arctic , daily update time: 04:00

The workflow needs as a minimum the configuration file to run. The optional arguments are the following:

-r <region> : Region, matching the 6 Copernicus Marine Service regional domains (see User guide). Default: NWS

-t <%Y%m%d_%H%M%S>: Bulleting date for the forecast data. Default: Forecast update time of execution day

• Usage: op_workflow -c <config_file> [-r <region>] [-t <%Y%m%d_%H%M%S>] [--reanal] [--debug]

Example call: op_workflow -c ecfas.cnf -r NWS -t 20210427_000000

The debug flag will notably prevent cleaning up of previously downloaded files (which is the default) in order to speed up debugging process.

There are some particularities to 2 of the domains: -For BS water-levels,the FES2014 tides are added because tides are lacking in the CMEMS model -For ARC water-levels, the ocean product in the CMEMS catalogue (ARCTIC_ANALYSIS_FORECAST_PHYS_002_001_A) and the tide and surge model (ARCTIC_ANALYSISFORECAST_PHY_TIDE_002_015) are added together. Some double-counting is expected.

Note: this will access the analysis not the forecast if a date is in the past

• Output: Netcdf files based on the bulleting date of the execution day (t0) containing coastal time-series for the selected product-region (ARC,MED,IBI,BS,BAL,NWS) for 7 days [t0-2 : t0+5] (dimensions Ncoastalpoints x times)

Worflow description

Functions called within main, in this order:

1. motu_download.py: Download fields from CMEMS DU given selected region, timeframe and bulletin date>> CMEMS daily fields to $region/data/*.nc
2. coast_water_level_extract_multiple.py : For the given timeframe [t0-2 : t0+5] (=[tini,tend]), snip fields to prescribed coastal locations and interpolate all variables to common location-times >>CMEMS coastal series to $region/data/tseries_coastal_$bulletindate_$tini_$tend.nc
3. coast_water_level_process.py: Read the time-series and add other releveant coastal WL contributions (tide if not present, wave setup), write out in daily files >> TWL coastal series to $region/timeseries/TScoast_$region_b$bulletindate_$tini_$tend.nc

The files under $region/timeseries/ are the coastal TWL forecasts. These are used in ECFAS to trigger the warning and mapping component of the system.

Test data and checks

Baselines for tests can be found here: https://nexus.mercator-ocean.fr/repository/moistatics/ECFAS

Quality checks:

1. Verification against baseline data:

qual_checks [-h] -o <output_dir> -b <baseline_dir> -r <region> -t <YYmmdd_HHMMSS>

Process input arguments.

optional arguments:
  -h, --help            show this help message and exit
  -o <output_dir>, --outputs <output_dir>
                        Absolute path to output data to be checked
  -b <baseline_dir>, --baselines <baseline_dir>
                        Absolute path to baseline data to be checked against
  -r <region>, --region <region>
                        Region of interest, one of ARC, BAL, BS. IBI, MED, NWS, GLO. Defaults to all
  -t <YYmmdd_HHMMSS>, --t0 <YYmmdd_HHMMSS>
                        Start time t0 in the format YYmmdd_HHMMSS

2. Validation of the resulting time-series

op_validate [-h] -o <output_dir> -r <region> [-s <Y-m-d H-M-S>] [-e <Y-m-d H-M-S>]

Process input arguments.

optional arguments:
  -h, --help            show this help message and exit
  -o <output_dir>, --outputs <output_dir>
                        Absolute path to output data to be checked
  -r <region>, --region <region>
                        Region of interest, one of ARC, BAL, BS. IBI, MED, NWS, GLO. Defaults to all
  -s <Y-m-d H-M-S>, --t-start <Y-m-d H-M-S>
                        Start time in the format Y-m-d H-M-S
  -e <Y-m-d H-M-S>, --t-end <Y-m-d H-M-S>
                        End time in the format Y-m-d H-M-S

Running unit and functional tests

Unit and functional tests are found in the test and functional_test directories respectively

To run the unit and functional tests pip install pytest, py-cov. Then - for example - run

pytest -v -s --log-cli-level=INFO test/*