You can run this notebook in a live session or view it on Github.

# ROMS Ocean Model Example

The Regional Ocean Modeling System (ROMS) is an open source hydrodynamic model that is used for simulating currents and water properties in coastal and estuarine regions. ROMS is one of a few standard ocean models, and it has an active user community.

ROMS uses a regular C-Grid in the horizontal, similar to other structured grid ocean and atmospheric models, and a stretched vertical coordinate (see the ROMS documentation for more details). Both of these require special treatment when using `xarray` to analyze ROMS ocean model output. This example notebook shows how to create a lazily evaluated vertical coordinate, and make some basic plots. The `xgcm` package is required to do analysis that is aware of the horizontal C-Grid.

    [1]:

    import numpy as np
    import cartopy.crs as ccrs
    import cartopy.feature as cfeature
    import matplotlib.pyplot as plt
    %matplotlib inline

    import xarray as xr

Load a sample ROMS file. This is a subset of a full model available at

    http://barataria.tamu.edu/thredds/catalog.html?dataset=txla_hindcast_agg

The subsetting was done using the following command on one of the output files:

    #open dataset
    ds = xr.open_dataset('/d2/shared/TXLA_ROMS/output_20yr_obc/2001/ocean_his_0015.nc')

    # Turn on chunking to activate dask and parallelize read/write.
    ds = ds.chunk({'ocean_time': 1})

    # Pick out some of the variables that will be included as coordinates
    ds = ds.set_coords(['Cs_r', 'Cs_w', 'hc', 'h', 'Vtransform'])

    # Select a a subset of variables. Salt will be visualized, zeta is used to
    # calculate the vertical coordinate
    variables = ['salt', 'zeta']
    ds[variables].isel(ocean_time=slice(47, None, 7*24),
                       xi_rho=slice(300, None)).to_netcdf('ROMS_example.nc', mode='w')

So, the `ROMS_example.nc` file contains a subset of the grid, one 3D variable, and two time steps.

## Load in ROMS dataset as an xarray object

    [2]:

    # load in the file
    ds = xr.tutorial.open_dataset('ROMS_example.nc', chunks={'ocean_time': 1})

    # This is a way to turn on chunking and lazy evaluation. Opening with mfdataset, or
    # setting the chunking in the open_dataset would also achive this.
    ds

    ---------------------------------------------------------------------------
    FileNotFoundError                         Traceback (most recent call last)
    <ipython-input-2-f6e5aae51f8e> in <module>
          1 # load in the file
    ----> 2 ds = xr.tutorial.open_dataset('ROMS_example.nc', chunks={'ocean_time': 1})
          3
          4 # This is a way to turn on chunking and lazy evaluation. Opening with mfdataset, or
          5 # setting the chunking in the open_dataset would also achive this.

    /build/python-xarray-kTVyut/python-xarray-0.15.0/xarray/tutorial.py in open_dataset(name, cache, cache_dir, github_url, branch, **kws)
         76         # May want to add an option to remove it.
         77         if not _os.path.isdir(longdir):
    ---> 78             _os.mkdir(longdir)
         79
         80         url = "/".join((github_url, "raw", branch, fullname))

    FileNotFoundError: [Errno 2] No such file or directory: '/sbuild-nonexistent/.xarray_tutorial_data'

## Add a lazilly calculated vertical coordinates

Write equations to calculate the vertical coordinate. These will be only evaluated when data is requested. Information about the ROMS vertical coordinate can be found (here)[https://www.myroms.org/wiki/Vertical_S-coordinate]

In short, for `Vtransform==2` as used in this example,

\(Z_0 = (h_c \, S + h \,C) / (h_c + h)\)

\(z = Z_0 (\zeta + h) + \zeta\)

where the variables are defined as in the link above.

    [3]:

    if ds.Vtransform == 1:
        Zo_rho = ds.hc * (ds.s_rho - ds.Cs_r) + ds.Cs_r * ds.h
        z_rho = Zo_rho + ds.zeta * (1 + Zo_rho/ds.h)
    elif ds.Vtransform == 2:
        Zo_rho = (ds.hc * ds.s_rho + ds.Cs_r * ds.h) / (ds.hc + ds.h)
        z_rho = ds.zeta + (ds.zeta + ds.h) * Zo_rho

    ds.coords['z_rho'] = z_rho.transpose()   # needing transpose seems to be an xarray bug
    ds.salt

    ---------------------------------------------------------------------------
    NameError                                 Traceback (most recent call last)
    <ipython-input-3-8742ef454e3d> in <module>
    ----> 1 if ds.Vtransform == 1:
          2     Zo_rho = ds.hc * (ds.s_rho - ds.Cs_r) + ds.Cs_r * ds.h
          3     z_rho = Zo_rho + ds.zeta * (1 + Zo_rho/ds.h)
          4 elif ds.Vtransform == 2:
          5     Zo_rho = (ds.hc * ds.s_rho + ds.Cs_r * ds.h) / (ds.hc + ds.h)

    NameError: name 'ds' is not defined

## A naive vertical slice

Create a slice using the s-coordinate as the vertical dimension is typically not very informative.

    [4]:

    ds.salt.isel(xi_rho=50, ocean_time=0).plot()

    ---------------------------------------------------------------------------
    NameError                                 Traceback (most recent call last)
    <ipython-input-4-215db57e17ae> in <module>
    ----> 1 ds.salt.isel(xi_rho=50, ocean_time=0).plot()

    NameError: name 'ds' is not defined

We can feed coordinate information to the plot method to give a more informative cross-section that uses the depths. Note that we did not need to slice the depth or longitude information separately, this was done automatically as the variable was sliced.

    [5]:

    section = ds.salt.isel(xi_rho=50, eta_rho=slice(0, 167), ocean_time=0)
    section.plot(x='lon_rho', y='z_rho', figsize=(15, 6), clim=(25, 35))
    plt.ylim([-100, 1]);

    ---------------------------------------------------------------------------
    NameError                                 Traceback (most recent call last)
    <ipython-input-5-5e678d0c6dcd> in <module>
    ----> 1 section = ds.salt.isel(xi_rho=50, eta_rho=slice(0, 167), ocean_time=0)
          2 section.plot(x='lon_rho', y='z_rho', figsize=(15, 6), clim=(25, 35))
          3 plt.ylim([-100, 1]);

    NameError: name 'ds' is not defined

## A plan view

Now make a naive plan view, without any projection information, just using lon/lat as x/y. This looks OK, but will appear compressed because lon and lat do not have an aspect constrained by the projection.

    [6]:

    ds.salt.isel(s_rho=-1, ocean_time=0).plot(x='lon_rho', y='lat_rho')

    ---------------------------------------------------------------------------
    NameError                                 Traceback (most recent call last)
    <ipython-input-6-fe9c0d0f0fde> in <module>
    ----> 1 ds.salt.isel(s_rho=-1, ocean_time=0).plot(x='lon_rho', y='lat_rho')

    NameError: name 'ds' is not defined

And let’s use a projection to make it nicer, and add a coast.

    [7]:

    proj = ccrs.LambertConformal(central_longitude=-92, central_latitude=29)
    fig = plt.figure(figsize=(15, 5))
    ax = plt.axes(projection=proj)
    ds.salt.isel(s_rho=-1, ocean_time=0).plot(x='lon_rho', y='lat_rho',
                                              transform=ccrs.PlateCarree())

    coast_10m = cfeature.NaturalEarthFeature('physical', 'land', '10m',
                                            edgecolor='k', facecolor='0.8')
    ax.add_feature(coast_10m)

    ---------------------------------------------------------------------------
    NameError                                 Traceback (most recent call last)
    <ipython-input-7-2ca15b1d780f> in <module>
          2 fig = plt.figure(figsize=(15, 5))
          3 ax = plt.axes(projection=proj)
    ----> 4 ds.salt.isel(s_rho=-1, ocean_time=0).plot(x='lon_rho', y='lat_rho',
          5                                           transform=ccrs.PlateCarree())
          6

    NameError: name 'ds' is not defined

    [ ]: