Exercise of Data Visualization#
Download the example data (Optional)#
In this practice, we can choose to use the European air quality forecast dataset from CAMS (Copernicus Atmosphere Monitoring Service). You can download this CAMS 2.0 Product Portfolio to see more information on the products. You can follow the instructions below to download the example dataset using python.
Prepare before download#
To download the data, we will use CDS API. The Copernicus website has provided a practical instruction, please follow the steps.
The steps are also described below:
Register an account in ADS here.
Login to the ADS using your account.
Copy the code displayed after login (refresh the page may help) and paste to th file ~/.cdsapirc
Install
A quick fix if you fail to download#
If you fail to download the data or you don’t want to spend time to figure out how to download yourself. We have a already downloaded dataset for you to start the next part.
Read the data#
The file is in netcdf format. We will use xarray package to read the file.
Import the necessary packages:
import xarray as xr
import numpy as np
import matplotlib.pyplot as plt
import cartopy.crs as ccrs
import cartopy.feature as cfeature
ds = xr.open_dataset('../CAMS_ensemble_20240110.nc')
print(ds)
---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
File ~/miniconda3/envs/pybook/lib/python3.10/site-packages/xarray/backends/file_manager.py:211, in CachingFileManager._acquire_with_cache_info(self, needs_lock)
210 try:
--> 211 file = self._cache[self._key]
212 except KeyError:
File ~/miniconda3/envs/pybook/lib/python3.10/site-packages/xarray/backends/lru_cache.py:56, in LRUCache.__getitem__(self, key)
55 with self._lock:
---> 56 value = self._cache[key]
57 self._cache.move_to_end(key)
KeyError: [<class 'netCDF4._netCDF4.Dataset'>, ('/Users/zhuyunye/projects/python/python_tutorial/python_book/CAMS_ensemble_20240110.nc',), 'r', (('clobber', True), ('diskless', False), ('format', 'NETCDF4'), ('persist', False)), '43dfbd6b-b901-4230-aa73-06997f7c8028']
During handling of the above exception, another exception occurred:
FileNotFoundError Traceback (most recent call last)
Cell In[2], line 1
----> 1 ds = xr.open_dataset('../CAMS_ensemble_20240110.nc')
2 print(ds)
File ~/miniconda3/envs/pybook/lib/python3.10/site-packages/xarray/backends/api.py:572, 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)
560 decoders = _resolve_decoders_kwargs(
561 decode_cf,
562 open_backend_dataset_parameters=backend.open_dataset_parameters,
(...)
568 decode_coords=decode_coords,
569 )
571 overwrite_encoded_chunks = kwargs.pop("overwrite_encoded_chunks", None)
--> 572 backend_ds = backend.open_dataset(
573 filename_or_obj,
574 drop_variables=drop_variables,
575 **decoders,
576 **kwargs,
577 )
578 ds = _dataset_from_backend_dataset(
579 backend_ds,
580 filename_or_obj,
(...)
590 **kwargs,
591 )
592 return ds
File ~/miniconda3/envs/pybook/lib/python3.10/site-packages/xarray/backends/netCDF4_.py:593, in NetCDF4BackendEntrypoint.open_dataset(self, filename_or_obj, mask_and_scale, decode_times, concat_characters, decode_coords, drop_variables, use_cftime, decode_timedelta, group, mode, format, clobber, diskless, persist, lock, autoclose)
572 def open_dataset( # type: ignore[override] # allow LSP violation, not supporting **kwargs
573 self,
574 filename_or_obj: str | os.PathLike[Any] | BufferedIOBase | AbstractDataStore,
(...)
590 autoclose=False,
591 ) -> Dataset:
592 filename_or_obj = _normalize_path(filename_or_obj)
--> 593 store = NetCDF4DataStore.open(
594 filename_or_obj,
595 mode=mode,
596 format=format,
597 group=group,
598 clobber=clobber,
599 diskless=diskless,
600 persist=persist,
601 lock=lock,
602 autoclose=autoclose,
603 )
605 store_entrypoint = StoreBackendEntrypoint()
606 with close_on_error(store):
File ~/miniconda3/envs/pybook/lib/python3.10/site-packages/xarray/backends/netCDF4_.py:400, in NetCDF4DataStore.open(cls, filename, mode, format, group, clobber, diskless, persist, lock, lock_maker, autoclose)
394 kwargs = dict(
395 clobber=clobber, diskless=diskless, persist=persist, format=format
396 )
397 manager = CachingFileManager(
398 netCDF4.Dataset, filename, mode=mode, kwargs=kwargs
399 )
--> 400 return cls(manager, group=group, mode=mode, lock=lock, autoclose=autoclose)
File ~/miniconda3/envs/pybook/lib/python3.10/site-packages/xarray/backends/netCDF4_.py:347, in NetCDF4DataStore.__init__(self, manager, group, mode, lock, autoclose)
345 self._group = group
346 self._mode = mode
--> 347 self.format = self.ds.data_model
348 self._filename = self.ds.filepath()
349 self.is_remote = is_remote_uri(self._filename)
File ~/miniconda3/envs/pybook/lib/python3.10/site-packages/xarray/backends/netCDF4_.py:409, in NetCDF4DataStore.ds(self)
407 @property
408 def ds(self):
--> 409 return self._acquire()
File ~/miniconda3/envs/pybook/lib/python3.10/site-packages/xarray/backends/netCDF4_.py:403, in NetCDF4DataStore._acquire(self, needs_lock)
402 def _acquire(self, needs_lock=True):
--> 403 with self._manager.acquire_context(needs_lock) as root:
404 ds = _nc4_require_group(root, self._group, self._mode)
405 return ds
File ~/miniconda3/envs/pybook/lib/python3.10/contextlib.py:135, in _GeneratorContextManager.__enter__(self)
133 del self.args, self.kwds, self.func
134 try:
--> 135 return next(self.gen)
136 except StopIteration:
137 raise RuntimeError("generator didn't yield") from None
File ~/miniconda3/envs/pybook/lib/python3.10/site-packages/xarray/backends/file_manager.py:199, in CachingFileManager.acquire_context(self, needs_lock)
196 @contextlib.contextmanager
197 def acquire_context(self, needs_lock=True):
198 """Context manager for acquiring a file."""
--> 199 file, cached = self._acquire_with_cache_info(needs_lock)
200 try:
201 yield file
File ~/miniconda3/envs/pybook/lib/python3.10/site-packages/xarray/backends/file_manager.py:217, in CachingFileManager._acquire_with_cache_info(self, needs_lock)
215 kwargs = kwargs.copy()
216 kwargs["mode"] = self._mode
--> 217 file = self._opener(*self._args, **kwargs)
218 if self._mode == "w":
219 # ensure file doesn't get overridden when opened again
220 self._mode = "a"
File src/netCDF4/_netCDF4.pyx:2463, in netCDF4._netCDF4.Dataset.__init__()
File src/netCDF4/_netCDF4.pyx:2026, in netCDF4._netCDF4._ensure_nc_success()
FileNotFoundError: [Errno 2] No such file or directory: b'/Users/zhuyunye/projects/python/python_tutorial/python_book/CAMS_ensemble_20240110.nc'
# plot the data in map
fig = plt.figure(figsize=(10, 5))
ax = plt.axes(projection=ccrs.PlateCarree()) # create a GeoAxes object with Plate Carree projection
qm = ds['co_conc'].isel(time=0).plot(ax=ax, transform=ccrs.PlateCarree(),cmap='jet') # plot the data on the GeoAxes object
qm.colorbar.set_label('CO Concentration (\u03bcg/m3)')
ax.coastlines() # add coastlines
plt.show()
