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 0x7f38cd990ec0>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:687, 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, inline_array, chunked_array_type, from_array_kwargs, backend_kwargs, **kwargs)
675 decoders = _resolve_decoders_kwargs(
676 decode_cf,
677 open_backend_dataset_parameters=backend.open_dataset_parameters,
(...) 683 decode_coords=decode_coords,
684 )
686 overwrite_encoded_chunks = kwargs.pop("overwrite_encoded_chunks", None)
--> 687 backend_ds = backend.open_dataset(
688 filename_or_obj,
689 drop_variables=drop_variables,
690 **decoders,
691 **kwargs,
692 )
693 ds = _dataset_from_backend_dataset(
694 backend_ds,
695 filename_or_obj,
(...) 705 **kwargs,
706 )
707 return ds
File ~/micromamba/envs/po-cookbook-dev/lib/python3.13/site-packages/xarray/backends/zarr.py:1578, 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)
1576 filename_or_obj = _normalize_path(filename_or_obj)
1577 if not store:
-> 1578 store = ZarrStore.open_group(
1579 filename_or_obj,
1580 group=group,
1581 mode=mode,
1582 synchronizer=synchronizer,
1583 consolidated=consolidated,
1584 consolidate_on_close=False,
1585 chunk_store=chunk_store,
1586 storage_options=storage_options,
1587 zarr_version=zarr_version,
1588 use_zarr_fill_value_as_mask=None,
1589 zarr_format=zarr_format,
1590 cache_members=cache_members,
1591 )
1593 store_entrypoint = StoreBackendEntrypoint()
1594 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:1777, 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)
1773 group = open_kwargs.pop("path")
1775 if consolidated:
1776 # TODO: an option to pass the metadata_key keyword
-> 1777 zarr_root_group = zarr.open_consolidated(store, **open_kwargs)
1778 elif consolidated is None:
1779 # same but with more error handling in case no consolidated metadata found
1780 try:
File ~/micromamba/envs/po-cookbook-dev/lib/python3.13/site-packages/zarr/api/synchronous.py:217, in open_consolidated(use_consolidated, *args, **kwargs)
212 def open_consolidated(*args: Any, use_consolidated: Literal[True] = True, **kwargs: Any) -> Group:
213 """
214 Alias for :func:`open_group` with ``use_consolidated=True``.
215 """
216 return Group(
--> 217 sync(async_api.open_consolidated(*args, use_consolidated=use_consolidated, **kwargs))
218 )
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:362, in open_consolidated(use_consolidated, *args, **kwargs)
357 if use_consolidated is not True:
358 raise TypeError(
359 "'use_consolidated' must be 'True' in 'open_consolidated'. Use 'open' with "
360 "'use_consolidated=False' to bypass consolidated metadata."
361 )
--> 362 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:825, in open_group(store, mode, cache_attrs, synchronizer, path, chunk_store, storage_options, zarr_version, zarr_format, meta_array, attributes, use_consolidated)
823 try:
824 if mode in _READ_MODES:
--> 825 return await AsyncGroup.open(
826 store_path, zarr_format=zarr_format, use_consolidated=use_consolidated
827 )
828 except (KeyError, FileNotFoundError):
829 pass
File ~/micromamba/envs/po-cookbook-dev/lib/python3.13/site-packages/zarr/core/group.py:538, in AsyncGroup.open(cls, store, zarr_format, use_consolidated)
531 raise FileNotFoundError(store_path)
532 elif zarr_format is None:
533 (
534 zarr_json_bytes,
535 zgroup_bytes,
536 zattrs_bytes,
537 maybe_consolidated_metadata_bytes,
--> 538 ) = await asyncio.gather(
539 (store_path / ZARR_JSON).get(),
540 (store_path / ZGROUP_JSON).get(),
541 (store_path / ZATTRS_JSON).get(),
542 (store_path / str(consolidated_key)).get(),
543 )
544 if zarr_json_bytes is not None and zgroup_bytes is not None:
545 # warn and favor v3
546 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:124, in StorePath.get(self, prototype, byte_range)
122 if prototype is None:
123 prototype = default_buffer_prototype()
--> 124 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:230, in FsspecStore.get(self, key, prototype, byte_range)
228 try:
229 if byte_range is None:
--> 230 value = prototype.buffer.from_bytes(await self.fs._cat_file(path))
231 elif isinstance(byte_range, RangeByteRequest):
232 value = prototype.buffer.from_bytes(
233 await self.fs._cat_file(
234 path,
(...) 237 )
238 )
File ~/micromamba/envs/po-cookbook-dev/lib/python3.13/site-packages/gcsfs/core.py:1115, in GCSFileSystem._cat_file(self, path, start, end, **kwargs)
1113 else:
1114 head = {}
-> 1115 headers, out = await self._call("GET", u2, headers=head)
1116 return out
File ~/micromamba/envs/po-cookbook-dev/lib/python3.13/site-packages/gcsfs/core.py:481, in GCSFileSystem._call(self, method, path, json_out, info_out, *args, **kwargs)
477 async def _call(
478 self, method, path, *args, json_out=False, info_out=False, **kwargs
479 ):
480 logger.debug(f"{method.upper()}: {path}, {args}, {kwargs.get('headers')}")
--> 481 status, headers, info, contents = await self._request(
482 method, path, *args, **kwargs
483 )
484 if json_out:
485 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:474, in GCSFileSystem._request(self, method, path, headers, json, data, *args, **kwargs)
471 info = r.request_info # for debug only
472 contents = await r.read()
--> 474 validate_response(status, contents, path, args)
475 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/zarr.json?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