Gulf Stream Currents¶
Overview¶
An example that uses ipyleaflet to reproduce style of visualization used in the New York Times article
In the Atlantic Ocean, Subtle Shifts Hint at Dramatic Dangers (March 2, 20121).
- Open an Intake catalogue reference Sea Surface Height data
- Make a geographic map of the data using ipyleaflet
Prerequisites¶
| Concepts | Importance | Notes |
|---|---|---|
| Xarray | Helpful | |
| Dask | Helpful | |
| Intake | Helpful | |
| ipyleaflet | Helpful |
- Time to learn: 15 minutes
Imports¶
from ipyleaflet import Map, TileLayer, basemaps
from ipyleaflet.velocity import Velocity
from intake import open_catalogLoad Data¶
The Copernicus Monitoring Environment Marine Service (CMEMS) is a large repository of ocean products including in-situ observations, satellite based remote sensing data, and numerical model output.
We want to look at altimeter satellite data to show the Sea Level Anomalies (SLA) for the global ocean. The particular data product is called Global Ocean Gridded L4 Sea Surface Heights and Derived Variables Reprocessed (1993-Ongoing) (SEALEVEL
This dataset is available as an analysis-ready on the Pangeo Cloud Data Catalog
cat = open_catalog("https://raw.githubusercontent.com/pangeo-data/pangeo-datastore/master/intake-catalogs/ocean.yaml")
cat["sea_surface_height"]<intake_xarray.xzarr.ZarrSource at 0x7f2731ad4590>This dataset is marked “requester pays” which means we have do an addtional step if we are not already on Pangeo Hub on the Google Cloud Platform.
Working with requester pays data¶
Several of the datasets within the Pangeo cloud data catalog are contained in requester pays storage buckets. This means that a user requesting data must provide their own billing project (created and authenticated through Google Cloud Platform) to be billed for the charges associated with accessing a dataset. To set up an GCP billing project and use it for authentication in applications:
Create a project on GCP; if this is the first time using GCP, a prompt will appear to choose a Google account to link to all GCP-related activities.
Create a Cloud Billing account associated with the project and enable billing for the project through this account.
Using Google Cloud IAM, add the Service Usage Consumer role to your account, which enables it to make billed requests on the behalf of the project. Through command line, install the Google Cloud SDK; this can be done using conda:
conda install -c conda-forge google-cloud-sdkInitialize the
gcloudcommand line interface, logging into the account used to create the aforementioned project and selecting it as the default project; this will allow the project to be used for requester pays access through the command line:
gcloud init```
Finally, use
gcloudto establish application default credentials; this will allow the project to be used for requester pays access through applications:gcloud auth application-default login
ds = cat["sea_surface_height"].to_dask()
ds---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
Cell In[3], line 1
----> 1 ds = cat["sea_surface_height"].to_dask()
2 ds
File ~/micromamba/envs/po-cookbook-dev/lib/python3.13/site-packages/intake_xarray/base.py:8, in IntakeXarraySourceAdapter.to_dask(self)
6 def to_dask(self):
7 if "chunks" not in self.reader.kwargs:
----> 8 return self.reader(chunks={}).read()
9 else:
10 return self.reader.read()
File ~/micromamba/envs/po-cookbook-dev/lib/python3.13/site-packages/intake/readers/readers.py:121, in BaseReader.read(self, *args, **kwargs)
119 kw.update(kwargs)
120 args = kw.pop("args", ()) or args
--> 121 return self._read(*args, **kw)
File ~/micromamba/envs/po-cookbook-dev/lib/python3.13/site-packages/intake/readers/readers.py:1327, in XArrayDatasetReader._read(self, data, open_local, **kw)
1325 f = fsspec.open(data.url, **(data.storage_options or {})).open()
1326 return open_dataset(f, **kw)
-> 1327 return open_dataset(data.url, **kw)
File ~/micromamba/envs/po-cookbook-dev/lib/python3.13/site-packages/xarray/backends/api.py:715, in open_dataset(filename_or_obj, engine, chunks, cache, decode_cf, mask_and_scale, decode_times, decode_timedelta, use_cftime, concat_characters, decode_coords, drop_variables, create_default_indexes, inline_array, chunked_array_type, from_array_kwargs, backend_kwargs, **kwargs)
703 decoders = _resolve_decoders_kwargs(
704 decode_cf,
705 open_backend_dataset_parameters=backend.open_dataset_parameters,
(...) 711 decode_coords=decode_coords,
712 )
714 overwrite_encoded_chunks = kwargs.pop("overwrite_encoded_chunks", None)
--> 715 backend_ds = backend.open_dataset(
716 filename_or_obj,
717 drop_variables=drop_variables,
718 **decoders,
719 **kwargs,
720 )
721 ds = _dataset_from_backend_dataset(
722 backend_ds,
723 filename_or_obj,
(...) 734 **kwargs,
735 )
736 return ds
File ~/micromamba/envs/po-cookbook-dev/lib/python3.13/site-packages/xarray/backends/zarr.py:1587, in ZarrBackendEntrypoint.open_dataset(self, filename_or_obj, mask_and_scale, decode_times, concat_characters, decode_coords, drop_variables, use_cftime, decode_timedelta, group, mode, synchronizer, consolidated, chunk_store, storage_options, zarr_version, zarr_format, store, engine, use_zarr_fill_value_as_mask, cache_members)
1585 filename_or_obj = _normalize_path(filename_or_obj)
1586 if not store:
-> 1587 store = ZarrStore.open_group(
1588 filename_or_obj,
1589 group=group,
1590 mode=mode,
1591 synchronizer=synchronizer,
1592 consolidated=consolidated,
1593 consolidate_on_close=False,
1594 chunk_store=chunk_store,
1595 storage_options=storage_options,
1596 zarr_version=zarr_version,
1597 use_zarr_fill_value_as_mask=None,
1598 zarr_format=zarr_format,
1599 cache_members=cache_members,
1600 )
1602 store_entrypoint = StoreBackendEntrypoint()
1603 with close_on_error(store):
File ~/micromamba/envs/po-cookbook-dev/lib/python3.13/site-packages/xarray/backends/zarr.py:664, in ZarrStore.open_group(cls, store, mode, synchronizer, group, consolidated, consolidate_on_close, chunk_store, storage_options, append_dim, write_region, safe_chunks, align_chunks, zarr_version, zarr_format, use_zarr_fill_value_as_mask, write_empty, cache_members)
638 @classmethod
639 def open_group(
640 cls,
(...) 657 cache_members: bool = True,
658 ):
659 (
660 zarr_group,
661 consolidate_on_close,
662 close_store_on_close,
663 use_zarr_fill_value_as_mask,
--> 664 ) = _get_open_params(
665 store=store,
666 mode=mode,
667 synchronizer=synchronizer,
668 group=group,
669 consolidated=consolidated,
670 consolidate_on_close=consolidate_on_close,
671 chunk_store=chunk_store,
672 storage_options=storage_options,
673 zarr_version=zarr_version,
674 use_zarr_fill_value_as_mask=use_zarr_fill_value_as_mask,
675 zarr_format=zarr_format,
676 )
678 return cls(
679 zarr_group,
680 mode,
(...) 689 cache_members=cache_members,
690 )
File ~/micromamba/envs/po-cookbook-dev/lib/python3.13/site-packages/xarray/backends/zarr.py:1791, in _get_open_params(store, mode, synchronizer, group, consolidated, consolidate_on_close, chunk_store, storage_options, zarr_version, use_zarr_fill_value_as_mask, zarr_format)
1787 group = open_kwargs.pop("path")
1789 if consolidated:
1790 # TODO: an option to pass the metadata_key keyword
-> 1791 zarr_root_group = zarr.open_consolidated(store, **open_kwargs)
1792 elif consolidated is None:
1793 # same but with more error handling in case no consolidated metadata found
1794 try:
File ~/micromamba/envs/po-cookbook-dev/lib/python3.13/site-packages/zarr/api/synchronous.py:222, in open_consolidated(use_consolidated, *args, **kwargs)
217 def open_consolidated(*args: Any, use_consolidated: Literal[True] = True, **kwargs: Any) -> Group:
218 """
219 Alias for :func:`open_group` with ``use_consolidated=True``.
220 """
221 return Group(
--> 222 sync(async_api.open_consolidated(*args, use_consolidated=use_consolidated, **kwargs))
223 )
File ~/micromamba/envs/po-cookbook-dev/lib/python3.13/site-packages/zarr/core/sync.py:163, in sync(coro, loop, timeout)
160 return_result = next(iter(finished)).result()
162 if isinstance(return_result, BaseException):
--> 163 raise return_result
164 else:
165 return return_result
File ~/micromamba/envs/po-cookbook-dev/lib/python3.13/site-packages/zarr/core/sync.py:119, in _runner(coro)
114 """
115 Await a coroutine and return the result of running it. If awaiting the coroutine raises an
116 exception, the exception will be returned.
117 """
118 try:
--> 119 return await coro
120 except Exception as ex:
121 return ex
File ~/micromamba/envs/po-cookbook-dev/lib/python3.13/site-packages/zarr/api/asynchronous.py:382, in open_consolidated(use_consolidated, *args, **kwargs)
377 if use_consolidated is not True:
378 raise TypeError(
379 "'use_consolidated' must be 'True' in 'open_consolidated'. Use 'open' with "
380 "'use_consolidated=False' to bypass consolidated metadata."
381 )
--> 382 return await open_group(*args, use_consolidated=use_consolidated, **kwargs)
File ~/micromamba/envs/po-cookbook-dev/lib/python3.13/site-packages/zarr/api/asynchronous.py:845, in open_group(store, mode, cache_attrs, synchronizer, path, chunk_store, storage_options, zarr_version, zarr_format, meta_array, attributes, use_consolidated)
843 try:
844 if mode in _READ_MODES:
--> 845 return await AsyncGroup.open(
846 store_path, zarr_format=zarr_format, use_consolidated=use_consolidated
847 )
848 except (KeyError, FileNotFoundError):
849 pass
File ~/micromamba/envs/po-cookbook-dev/lib/python3.13/site-packages/zarr/core/group.py:542, in AsyncGroup.open(cls, store, zarr_format, use_consolidated)
535 raise FileNotFoundError(store_path)
536 elif zarr_format is None:
537 (
538 zarr_json_bytes,
539 zgroup_bytes,
540 zattrs_bytes,
541 maybe_consolidated_metadata_bytes,
--> 542 ) = await asyncio.gather(
543 (store_path / ZARR_JSON).get(),
544 (store_path / ZGROUP_JSON).get(),
545 (store_path / ZATTRS_JSON).get(),
546 (store_path / str(consolidated_key)).get(),
547 )
548 if zarr_json_bytes is not None and zgroup_bytes is not None:
549 # warn and favor v3
550 msg = f"Both zarr.json (Zarr format 3) and .zgroup (Zarr format 2) metadata objects exist at {store_path}. Zarr format 3 will be used."
File ~/micromamba/envs/po-cookbook-dev/lib/python3.13/site-packages/zarr/storage/_common.py:164, in StorePath.get(self, prototype, byte_range)
162 if prototype is None:
163 prototype = default_buffer_prototype()
--> 164 return await self.store.get(self.path, prototype=prototype, byte_range=byte_range)
File ~/micromamba/envs/po-cookbook-dev/lib/python3.13/site-packages/zarr/storage/_fsspec.py:300, in FsspecStore.get(self, key, prototype, byte_range)
298 try:
299 if byte_range is None:
--> 300 value = prototype.buffer.from_bytes(await self.fs._cat_file(path))
301 elif isinstance(byte_range, RangeByteRequest):
302 value = prototype.buffer.from_bytes(
303 await self.fs._cat_file(
304 path,
(...) 307 )
308 )
File ~/micromamba/envs/po-cookbook-dev/lib/python3.13/site-packages/gcsfs/core.py:1117, in GCSFileSystem._cat_file(self, path, start, end, **kwargs)
1115 else:
1116 head = {}
-> 1117 headers, out = await self._call("GET", u2, headers=head)
1118 return out
File ~/micromamba/envs/po-cookbook-dev/lib/python3.13/site-packages/gcsfs/core.py:483, in GCSFileSystem._call(self, method, path, json_out, info_out, *args, **kwargs)
479 async def _call(
480 self, method, path, *args, json_out=False, info_out=False, **kwargs
481 ):
482 logger.debug(f"{method.upper()}: {path}, {args}, {kwargs.get('headers')}")
--> 483 status, headers, info, contents = await self._request(
484 method, path, *args, **kwargs
485 )
486 if json_out:
487 return json.loads(contents)
File ~/micromamba/envs/po-cookbook-dev/lib/python3.13/site-packages/decorator.py:224, in decorate.<locals>.fun(*args, **kw)
222 if not kwsyntax:
223 args, kw = fix(args, kw, sig)
--> 224 return await caller(func, *(extras + args), **kw)
File ~/micromamba/envs/po-cookbook-dev/lib/python3.13/site-packages/gcsfs/retry.py:135, in retry_request(func, retries, *args, **kwargs)
133 if retry > 0:
134 await asyncio.sleep(min(random.random() + 2 ** (retry - 1), 32))
--> 135 return await func(*args, **kwargs)
136 except (
137 HttpError,
138 requests.exceptions.RequestException,
(...) 141 aiohttp.client_exceptions.ClientError,
142 ) as e:
143 if (
144 isinstance(e, HttpError)
145 and e.code == 400
146 and "requester pays" in e.message
147 ):
File ~/micromamba/envs/po-cookbook-dev/lib/python3.13/site-packages/gcsfs/core.py:476, in GCSFileSystem._request(self, method, path, headers, json, data, *args, **kwargs)
473 info = r.request_info # for debug only
474 contents = await r.read()
--> 476 validate_response(status, contents, path, args)
477 return status, headers, info, contents
File ~/micromamba/envs/po-cookbook-dev/lib/python3.13/site-packages/gcsfs/retry.py:120, in validate_response(status, content, path, args)
118 raise requests.exceptions.ProxyError()
119 elif "invalid" in str(msg):
--> 120 raise ValueError(f"Bad Request: {path}\n{msg}")
121 elif error and not isinstance(error, str):
122 raise HttpError(error)
ValueError: Bad Request: https://storage.googleapis.com/download/storage/v1/b/pangeo-cmems-duacs/o/.zmetadata?alt=media
User project specified in the request is invalid.Make a Map¶
center = [35, -50]
zoom = 4
m = Map(center=center, zoom=zoom, interpolation='nearest', basemap=basemaps.Gaode.Satellite)
display_options = {
'velocityType': 'Global Wind',
'displayPosition': 'bottomleft',
'displayEmptyString': 'No wind data'
}
wind = Velocity(
data=ds.isel(time=-1),
zonal_speed='ugos', meridional_speed='vgos',
latitude_dimension='latitude', longitude_dimension='longitude',
velocity_scale=0.2, max_velocity=1,
display_options=display_options
)
m.add_layer(wind)
mSummary¶
In this example we loaded sea level data from an analysis-ready cloud based dataset and made a visualization of that data using mapping library.
Resources and references¶
- This notebook is based on the Pangeo physical oceanography gallery example: https://
gallery .pangeo .io /repos /pangeo -gallery /physical -oceanography /05 _gulf _stream _currents .html