Export to netcdf tutorial

This is a demonstration script for how to export intermediate data from COAsT to netCDF files for later analysis or storage. The tutorial showcases the xarray.to_netcdf() method. http://xarray.pydata.org/en/stable/generated/xarray.Dataset.to_netcdf.html

Begin by importing COAsT and other packages

import coast
import xarray as xr

/usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pydap/lib.py:5: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
/usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('pydap')`.
Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages
/usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('pydap.responses')`.
Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages
/usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pkg_resources/__init__.py:2350: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('pydap')`.
Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages
/usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('pydap.handlers')`.
Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages
/usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pkg_resources/__init__.py:2350: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('pydap')`.
Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages
/usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('pydap.tests')`.
Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages
/usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pkg_resources/__init__.py:2350: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('pydap')`.
Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages
/usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('sphinxcontrib')`.
Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages

Now define some file paths

root = "./"
# And by defining some file paths
dn_files = root + "./example_files/"
fn_nemo_dat = dn_files + "coast_example_nemo_data.nc"
fn_nemo_dom = dn_files + "coast_example_nemo_domain.nc"
config = root + "./config/example_nemo_grid_t.json"
ofile = "example_export_output.nc"  # The target filename for output

We need to load in a NEMO object for doing NEMO things

nemo = coast.Gridded(fn_nemo_dat, fn_nemo_dom, config=config)

/usr/share/miniconda/envs/coast/lib/python3.10/site-packages/xarray/core/dataset.py:282: UserWarning: The specified chunks separate the stored chunks along dimension "time_counter" starting at index 2. This could degrade performance. Instead, consider rechunking after loading.

We can export the whole xr.DataSet to a netCDF file

Other file formats are available. From the documentation:

• NETCDF4: Data is stored in an HDF5 file, using netCDF4 API features.
• NETCDF4_CLASSIC: Data is stored in an HDF5 file, using only netCDF 3 compatible API features.
• NETCDF3_64BIT: 64-bit offset version of the netCDF 3 file format, which fully supports 2+ GB files, but is only compatible with clients linked against netCDF version 3.6.0 or later.
• NETCDF3_CLASSIC: The classic netCDF 3 file format. It does not handle 2+ GB files very well.

Mode - ‘w’ (write) is the default. Other options from the documentation:

• mode ({“w”, “a”}, default: “w”) – Write (‘w’) or append (‘a’) mode.
• If mode=’w’, any existing file at this location will be overwritten.
• If mode=’a’, existing variables will be overwritten.

Similarly xr.DataSets collections of variables or xr.DataArray variables can be exported to netCDF for objects in the TRANSECT, TIDEGAUGE, etc classes.

nemo.dataset.to_netcdf(ofile, mode="w", format="NETCDF4")

Alternatively a single variable (an xr.DataArray object) can be exported

nemo.dataset["temperature"].to_netcdf(ofile, format="NETCDF4")

Check the exported file is as you expect

Perhaps by using ncdump -h example_export_output.nc, or load the file and see that the xarray structure is preserved.

object = xr.open_dataset(ofile)
object.close()  # close file associated with this object