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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:174, in HTTPConnection._new_conn(self)
173 try:
--> 174 conn = connection.create_connection(
175 (self._dns_host, self.port), self.timeout, **extra_kw
176 )
178 except SocketTimeout:
File /usr/lib/python3/dist-packages/urllib3/util/connection.py:73, in create_connection(address, timeout, source_address, socket_options)
69 return six.raise_from(
70 LocationParseError("'%s', label empty or too long" % host), None
71 )
---> 73 for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM):
74 af, socktype, proto, canonname, sa = res
File /usr/lib/python3.12/socket.py:964, in getaddrinfo(host, port, family, type, proto, flags)
963 addrlist = []
--> 964 for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
965 af, socktype, proto, canonname, sa = res
gaierror: [Errno -3] Temporary failure in name resolution
During handling of the above exception, another exception occurred:
NewConnectionError Traceback (most recent call last)
File /usr/lib/python3/dist-packages/urllib3/connectionpool.py:716, in HTTPConnectionPool.urlopen(self, method, url, body, headers, retries, redirect, assert_same_host, timeout, pool_timeout, release_conn, chunked, body_pos, **response_kw)
715 # Make the request on the httplib connection object.
--> 716 httplib_response = self._make_request(
717 conn,
718 method,
719 url,
720 timeout=timeout_obj,
721 body=body,
722 headers=headers,
723 chunked=chunked,
724 )
726 # If we're going to release the connection in ``finally:``, then
727 # the response doesn't need to know about the connection. Otherwise
728 # it will also try to release it and we'll have a double-release
729 # mess.
File /usr/lib/python3/dist-packages/urllib3/connectionpool.py:405, in HTTPConnectionPool._make_request(self, conn, method, url, timeout, chunked, **httplib_request_kw)
404 try:
--> 405 self._validate_conn(conn)
406 except (SocketTimeout, BaseSSLError) as e:
407 # Py2 raises this as a BaseSSLError, Py3 raises it as socket timeout.
File /usr/lib/python3/dist-packages/urllib3/connectionpool.py:1059, in HTTPSConnectionPool._validate_conn(self, conn)
1058 if not getattr(conn, "sock", None): # AppEngine might not have `.sock`
-> 1059 conn.connect()
1061 if not conn.is_verified:
File /usr/lib/python3/dist-packages/urllib3/connection.py:363, in HTTPSConnection.connect(self)
361 def connect(self):
362 # Add certificate verification
--> 363 self.sock = conn = self._new_conn()
364 hostname = self.host
File /usr/lib/python3/dist-packages/urllib3/connection.py:186, in HTTPConnection._new_conn(self)
185 except SocketError as e:
--> 186 raise NewConnectionError(
187 self, "Failed to establish a new connection: %s" % e
188 )
190 return conn
NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f1ac89c7c50>: Failed to establish a new connection: [Errno -3] Temporary failure in name resolution
During handling of the above exception, another exception occurred:
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:800, in HTTPConnectionPool.urlopen(self, method, url, body, headers, retries, redirect, assert_same_host, timeout, pool_timeout, release_conn, chunked, body_pos, **response_kw)
798 e = ProtocolError("Connection aborted.", e)
--> 800 retries = retries.increment(
801 method, url, error=e, _pool=self, _stacktrace=sys.exc_info()[2]
802 )
803 retries.sleep()
File /usr/lib/python3/dist-packages/urllib3/util/retry.py:592, in Retry.increment(self, method, url, response, error, _pool, _stacktrace)
591 if new_retry.is_exhausted():
--> 592 raise MaxRetryError(_pool, url, error or ResponseError(cause))
594 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 NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f1ac89c7c50>: Failed to establish a new connection: [Errno -3] Temporary failure in name resolution'))
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:161, in open_dataset(name, cache, cache_dir, engine, **kws)
158 url = f"{base_url}/raw/{version}/{path.name}"
160 # retrieve the file
--> 161 filepath = pooch.retrieve(url=url, known_hash=None, path=cache_dir)
162 ds = _open_dataset(filepath, engine=engine, **kws)
163 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:208, in HTTPDownloader.__call__(self, url, output_file, pooch, check_only)
206 output_file = open(output_file, "w+b")
207 try:
--> 208 response = requests.get(url, **kwargs)
209 response.raise_for_status()
210 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 NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f1ac89c7c50>: Failed to establish a new connection: [Errno -3] Temporary failure in name resolution'))
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
[ ]:
