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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 achieve this.
ds
---------------------------------------------------------------------------
gaierror Traceback (most recent call last)
File /usr/lib/python3/dist-packages/urllib3/connection.py:198, in HTTPConnection._new_conn(self)
197 try:
--> 198 sock = connection.create_connection(
199 (self._dns_host, self.port),
200 self.timeout,
201 source_address=self.source_address,
202 socket_options=self.socket_options,
203 )
204 except socket.gaierror as e:
File /usr/lib/python3/dist-packages/urllib3/util/connection.py:60, in create_connection(address, timeout, source_address, socket_options)
58 raise LocationParseError(f"'{host}', label empty or too long") from None
---> 60 for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM):
61 af, socktype, proto, canonname, sa = res
File /usr/lib/python3.13/socket.py:977, in getaddrinfo(host, port, family, type, proto, flags)
976 addrlist = []
--> 977 for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
978 af, socktype, proto, canonname, sa = res
gaierror: [Errno -2] Name or service not known
The above exception was the direct cause of the following exception:
NameResolutionError Traceback (most recent call last)
File /usr/lib/python3/dist-packages/urllib3/connectionpool.py:787, in HTTPConnectionPool.urlopen(self, method, url, body, headers, retries, redirect, assert_same_host, timeout, pool_timeout, release_conn, chunked, body_pos, preload_content, decode_content, **response_kw)
786 # Make the request on the HTTPConnection object
--> 787 response = self._make_request(
788 conn,
789 method,
790 url,
791 timeout=timeout_obj,
792 body=body,
793 headers=headers,
794 chunked=chunked,
795 retries=retries,
796 response_conn=response_conn,
797 preload_content=preload_content,
798 decode_content=decode_content,
799 **response_kw,
800 )
802 # Everything went great!
File /usr/lib/python3/dist-packages/urllib3/connectionpool.py:488, in HTTPConnectionPool._make_request(self, conn, method, url, body, headers, retries, timeout, chunked, response_conn, preload_content, decode_content, enforce_content_length)
487 new_e = _wrap_proxy_error(new_e, conn.proxy.scheme)
--> 488 raise new_e
490 # conn.request() calls http.client.*.request, not the method in
491 # urllib3.request. It also calls makefile (recv) on the socket.
File /usr/lib/python3/dist-packages/urllib3/connectionpool.py:464, in HTTPConnectionPool._make_request(self, conn, method, url, body, headers, retries, timeout, chunked, response_conn, preload_content, decode_content, enforce_content_length)
463 try:
--> 464 self._validate_conn(conn)
465 except (SocketTimeout, BaseSSLError) as e:
File /usr/lib/python3/dist-packages/urllib3/connectionpool.py:1093, in HTTPSConnectionPool._validate_conn(self, conn)
1092 if conn.is_closed:
-> 1093 conn.connect()
1095 # TODO revise this, see https://github.com/urllib3/urllib3/issues/2791
File /usr/lib/python3/dist-packages/urllib3/connection.py:704, in HTTPSConnection.connect(self)
703 sock: socket.socket | ssl.SSLSocket
--> 704 self.sock = sock = self._new_conn()
705 server_hostname: str = self.host
File /usr/lib/python3/dist-packages/urllib3/connection.py:205, in HTTPConnection._new_conn(self)
204 except socket.gaierror as e:
--> 205 raise NameResolutionError(self.host, self, e) from e
206 except SocketTimeout as e:
NameResolutionError: <urllib3.connection.HTTPSConnection object at 0x7f28ba297620>: Failed to resolve 'github.com' ([Errno -2] Name or service not known)
The above exception was the direct cause of the following exception:
MaxRetryError Traceback (most recent call last)
File /usr/lib/python3/dist-packages/requests/adapters.py:667, in HTTPAdapter.send(self, request, stream, timeout, verify, cert, proxies)
666 try:
--> 667 resp = conn.urlopen(
668 method=request.method,
669 url=url,
670 body=request.body,
671 headers=request.headers,
672 redirect=False,
673 assert_same_host=False,
674 preload_content=False,
675 decode_content=False,
676 retries=self.max_retries,
677 timeout=timeout,
678 chunked=chunked,
679 )
681 except (ProtocolError, OSError) as err:
File /usr/lib/python3/dist-packages/urllib3/connectionpool.py:841, in HTTPConnectionPool.urlopen(self, method, url, body, headers, retries, redirect, assert_same_host, timeout, pool_timeout, release_conn, chunked, body_pos, preload_content, decode_content, **response_kw)
839 new_e = ProtocolError("Connection aborted.", new_e)
--> 841 retries = retries.increment(
842 method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2]
843 )
844 retries.sleep()
File /usr/lib/python3/dist-packages/urllib3/util/retry.py:519, in Retry.increment(self, method, url, response, error, _pool, _stacktrace)
518 reason = error or ResponseError(cause)
--> 519 raise MaxRetryError(_pool, url, reason) from reason # type: ignore[arg-type]
521 log.debug("Incremented Retry for (url='%s'): %r", url, new_retry)
MaxRetryError: HTTPSConnectionPool(host='github.com', port=443): Max retries exceeded with url: /pydata/xarray-data/raw/master/ROMS_example.nc (Caused by NameResolutionError("<urllib3.connection.HTTPSConnection object at 0x7f28ba297620>: Failed to resolve 'github.com' ([Errno -2] Name or service not known)"))
During handling of the above exception, another exception occurred:
ConnectionError Traceback (most recent call last)
Cell In[2], line 2
1 # load in the file
----> 2 ds = xr.tutorial.open_dataset("ROMS_example.nc", chunks={"ocean_time": 1})
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 achieve this.
6 ds
File /usr/lib/python3/dist-packages/xarray/tutorial.py:167, in open_dataset(name, cache, cache_dir, engine, **kws)
164 downloader = pooch.HTTPDownloader(headers=headers)
166 # retrieve the file
--> 167 filepath = pooch.retrieve(
168 url=url, known_hash=None, path=cache_dir, downloader=downloader
169 )
170 ds = _open_dataset(filepath, engine=engine, **kws)
171 if not cache:
File /usr/lib/python3/dist-packages/pooch/core.py:239, in retrieve(url, known_hash, fname, path, processor, downloader, progressbar)
236 if downloader is None:
237 downloader = choose_downloader(url, progressbar=progressbar)
--> 239 stream_download(url, full_path, known_hash, downloader, pooch=None)
241 if known_hash is None:
242 get_logger().info(
243 "SHA256 hash of downloaded file: %s\n"
244 "Use this value as the 'known_hash' argument of 'pooch.retrieve'"
(...)
247 file_hash(str(full_path)),
248 )
File /usr/lib/python3/dist-packages/pooch/core.py:807, in stream_download(url, fname, known_hash, downloader, pooch, retry_if_failed)
803 try:
804 # Stream the file to a temporary so that we can safely check its
805 # hash before overwriting the original.
806 with temporary_file(path=str(fname.parent)) as tmp:
--> 807 downloader(url, tmp, pooch)
808 hash_matches(tmp, known_hash, strict=True, source=str(fname.name))
809 shutil.move(tmp, str(fname))
File /usr/lib/python3/dist-packages/pooch/downloaders.py:220, in HTTPDownloader.__call__(self, url, output_file, pooch, check_only)
218 # pylint: enable=consider-using-with
219 try:
--> 220 response = requests.get(url, timeout=timeout, **kwargs)
221 response.raise_for_status()
222 content = response.iter_content(chunk_size=self.chunk_size)
File /usr/lib/python3/dist-packages/requests/api.py:73, in get(url, params, **kwargs)
62 def get(url, params=None, **kwargs):
63 r"""Sends a GET request.
64
65 :param url: URL for the new :class:`Request` object.
(...)
70 :rtype: requests.Response
71 """
---> 73 return request("get", url, params=params, **kwargs)
File /usr/lib/python3/dist-packages/requests/api.py:59, in request(method, url, **kwargs)
55 # By using the 'with' statement we are sure the session is closed, thus we
56 # avoid leaving sockets open which can trigger a ResourceWarning in some
57 # cases, and look like a memory leak in others.
58 with sessions.Session() as session:
---> 59 return session.request(method=method, url=url, **kwargs)
File /usr/lib/python3/dist-packages/requests/sessions.py:589, in Session.request(self, method, url, params, data, headers, cookies, files, auth, timeout, allow_redirects, proxies, hooks, stream, verify, cert, json)
584 send_kwargs = {
585 "timeout": timeout,
586 "allow_redirects": allow_redirects,
587 }
588 send_kwargs.update(settings)
--> 589 resp = self.send(prep, **send_kwargs)
591 return resp
File /usr/lib/python3/dist-packages/requests/sessions.py:703, in Session.send(self, request, **kwargs)
700 start = preferred_clock()
702 # Send the request
--> 703 r = adapter.send(request, **kwargs)
705 # Total elapsed time of the request (approximately)
706 elapsed = preferred_clock() - start
File /usr/lib/python3/dist-packages/requests/adapters.py:700, in HTTPAdapter.send(self, request, stream, timeout, verify, cert, proxies)
696 if isinstance(e.reason, _SSLError):
697 # This branch is for urllib3 v1.22 and later.
698 raise SSLError(e, request=request)
--> 700 raise ConnectionError(e, request=request)
702 except ClosedPoolError as e:
703 raise ConnectionError(e, request=request)
ConnectionError: HTTPSConnectionPool(host='github.com', port=443): Max retries exceeded with url: /pydata/xarray-data/raw/master/ROMS_example.nc (Caused by NameResolutionError("<urllib3.connection.HTTPSConnection object at 0x7f28ba297620>: Failed to resolve 'github.com' ([Errno -2] Name or service not known)"))
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)
Cell In[3], line 1
----> 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)
NameError: name 'ds' is not defined
A naive vertical slice¶
Creating 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)
Cell In[4], line 1
----> 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)
Cell In[5], line 1
----> 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)
Cell In[6], line 1
----> 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)
Cell In[7], line 4
2 fig = plt.figure(figsize=(15, 5))
3 ax = plt.axes(projection=proj)
----> 4 ds.salt.isel(s_rho=-1, ocean_time=0).plot(
5 x="lon_rho", y="lat_rho", transform=ccrs.PlateCarree()
6 )
8 coast_10m = cfeature.NaturalEarthFeature(
9 "physical", "land", "10m", edgecolor="k", facecolor="0.8"
10 )
11 ax.add_feature(coast_10m)
NameError: name 'ds' is not defined

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