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 0x7fa7ec92cec0>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:760, 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)
748 decoders = _resolve_decoders_kwargs(
749 decode_cf,
750 open_backend_dataset_parameters=backend.open_dataset_parameters,
(...) 756 decode_coords=decode_coords,
757 )
759 overwrite_encoded_chunks = kwargs.pop("overwrite_encoded_chunks", None)
--> 760 backend_ds = backend.open_dataset(
761 filename_or_obj,
762 drop_variables=drop_variables,
763 **decoders,
764 **kwargs,
765 )
766 ds = _dataset_from_backend_dataset(
767 backend_ds,
768 filename_or_obj,
(...) 779 **kwargs,
780 )
781 return ds
File ~/micromamba/envs/po-cookbook-dev/lib/python3.13/site-packages/xarray/backends/zarr.py:1654, 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)
1652 filename_or_obj = _normalize_path(filename_or_obj)
1653 if not store:
-> 1654 store = ZarrStore.open_group(
1655 filename_or_obj,
1656 group=group,
1657 mode=mode,
1658 synchronizer=synchronizer,
1659 consolidated=consolidated,
1660 consolidate_on_close=False,
1661 chunk_store=chunk_store,
1662 storage_options=storage_options,
1663 zarr_version=zarr_version,
1664 use_zarr_fill_value_as_mask=None,
1665 zarr_format=zarr_format,
1666 cache_members=cache_members,
1667 )
1669 store_entrypoint = StoreBackendEntrypoint()
1670 with close_on_error(store):
File ~/micromamba/envs/po-cookbook-dev/lib/python3.13/site-packages/xarray/backends/zarr.py:714, 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)
688 @classmethod
689 def open_group(
690 cls,
(...) 707 cache_members: bool = True,
708 ):
709 (
710 zarr_group,
711 consolidate_on_close,
712 close_store_on_close,
713 use_zarr_fill_value_as_mask,
--> 714 ) = _get_open_params(
715 store=store,
716 mode=mode,
717 synchronizer=synchronizer,
718 group=group,
719 consolidated=consolidated,
720 consolidate_on_close=consolidate_on_close,
721 chunk_store=chunk_store,
722 storage_options=storage_options,
723 zarr_version=zarr_version,
724 use_zarr_fill_value_as_mask=use_zarr_fill_value_as_mask,
725 zarr_format=zarr_format,
726 )
728 return cls(
729 zarr_group,
730 mode,
(...) 739 cache_members=cache_members,
740 )
File ~/micromamba/envs/po-cookbook-dev/lib/python3.13/site-packages/xarray/backends/zarr.py:1858, 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)
1854 group = open_kwargs.pop("path")
1856 if consolidated:
1857 # TODO: an option to pass the metadata_key keyword
-> 1858 zarr_root_group = zarr.open_consolidated(store, **open_kwargs)
1859 elif consolidated is None:
1860 # same but with more error handling in case no consolidated metadata found
1861 try:
File ~/micromamba/envs/po-cookbook-dev/lib/python3.13/site-packages/zarr/api/synchronous.py:231, in open_consolidated(use_consolidated, *args, **kwargs)
226 def open_consolidated(*args: Any, use_consolidated: Literal[True] = True, **kwargs: Any) -> Group:
227 """
228 Alias for :func:`open_group` with ``use_consolidated=True``.
229 """
230 return Group(
--> 231 sync(async_api.open_consolidated(*args, use_consolidated=use_consolidated, **kwargs))
232 )
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:408, in open_consolidated(use_consolidated, *args, **kwargs)
403 if use_consolidated is not True:
404 raise TypeError(
405 "'use_consolidated' must be 'True' in 'open_consolidated'. Use 'open' with "
406 "'use_consolidated=False' to bypass consolidated metadata."
407 )
--> 408 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:857, in open_group(store, mode, cache_attrs, synchronizer, path, chunk_store, storage_options, zarr_version, zarr_format, meta_array, attributes, use_consolidated)
855 try:
856 if mode in _READ_MODES:
--> 857 return await AsyncGroup.open(
858 store_path, zarr_format=zarr_format, use_consolidated=use_consolidated
859 )
860 except (KeyError, FileNotFoundError):
861 pass
File ~/micromamba/envs/po-cookbook-dev/lib/python3.13/site-packages/zarr/core/group.py:559, in AsyncGroup.open(cls, store, zarr_format, use_consolidated)
552 raise FileNotFoundError(store_path)
553 elif zarr_format is None:
554 (
555 zarr_json_bytes,
556 zgroup_bytes,
557 zattrs_bytes,
558 maybe_consolidated_metadata_bytes,
--> 559 ) = await asyncio.gather(
560 (store_path / ZARR_JSON).get(),
561 (store_path / ZGROUP_JSON).get(),
562 (store_path / ZATTRS_JSON).get(),
563 (store_path / str(consolidated_key)).get(),
564 )
565 if zarr_json_bytes is not None and zgroup_bytes is not None:
566 # warn and favor v3
567 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:168, in StorePath.get(self, prototype, byte_range)
166 if prototype is None:
167 prototype = default_buffer_prototype()
--> 168 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:299, in FsspecStore.get(self, key, prototype, byte_range)
297 try:
298 if byte_range is None:
--> 299 value = prototype.buffer.from_bytes(await self.fs._cat_file(path))
300 elif isinstance(byte_range, RangeByteRequest):
301 value = prototype.buffer.from_bytes(
302 await self.fs._cat_file(
303 path,
(...) 306 )
307 )
File ~/micromamba/envs/po-cookbook-dev/lib/python3.13/site-packages/gcsfs/core.py:1119, in GCSFileSystem._cat_file(self, path, start, end, **kwargs)
1117 else:
1118 head = {}
-> 1119 headers, out = await self._call("GET", u2, headers=head)
1120 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/.zgroup?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