Hi! I’m running into an unusual error when I try to plot the result from the ff code:
# Download reanalysis data
woa_o2 = xr.open_mfdataset(['https://www.ncei.noaa.gov/thredds-ocean/dodsC/ncei/woa/oxygen/all/1.00/woa18_all_o06_01.nc'], decode_times=False)
obs_grid = xr.Dataset({"lat": (["lat"], woa_o2.lat.data), "lon": (["lon"], woa_o2.lon.data)})
obs_lev = woa_o2.depth.data
# Download CMIP data
cat_url = "https://storage.googleapis.com/cmip6/pangeo-cmip6-noQC.json"
col = intake.open_esm_datastore(cat_url)
cat = col.search(table_id='Omon', activity_id='CMIP', experiment_id='historical', variable_id=['thetao','so'],
grid_label='gn', member_id='r1i1p1f1', source_id='MPI-ESM1-2-LR')
cmip6_compiled = cat.to_dataset_dict(zarr_kwargs={'consolidated':True, 'decode_times': True, 'use_cftime': True}, preprocess=combined_preprocessing)
basins = regionmask.defined_regions.natural_earth.ocean_basins_50
subset_temp = {}
for k, ds in cmip6_compiled.items():
if 'member_id' in ds.dims:
ds = ds.isel(member_id=0).unify_chunks()
for key, value in ds.items():
mask = merged_mask(basins,ds[key])
var_masked = ds[key].where(mask == 2)
regridder = xe.Regridder(var_masked, obs_grid, 'nearest_s2d')
var_regridded = regridder(var_masked)
var_subset = var_regridded.sel(time=slice('2014-01-01','2014-12-31'))
var_subset = var_subset.sel(lon=slice(-130,-110),lat=slice(30,45)).mean(dim='time').squeeze()
# Save data into xarray Dataset
var_name = key + "_subset"
subset_temp[var_name] = var_subset
subset = xr.Dataset(subset_temp)
# Interpolate into common vertical grid using xgcm
grid = Grid(subset, coords={'Z': {'center': 'lev'}}, periodic=False)
for varname, varvalue in subset.items():
var_interp = grid.transform(subset[varname], 'Z', obs_lev, target_data=None, method='linear')
var_subset_plot = var_interp.sel(lev=10).squeeze()
var_subset can be plotted but when I try with var_subset_plot:
plt.figure(figsize=(8,4))
ax = plt.axes(projection=ccrs.Mercator())
var_subset_plot.plot.pcolormesh(yincrease=True, x='lon', y='lat', levels=31, ax=ax, robust=True, add_colorbar=False, transform=ccrs.PlateCarree())
the ff error appears:
TypeError Traceback (most recent call last)
<ipython-input-18-ed50ece6f080> in <module>
1 plt.figure(figsize=(8,4))
2 ax = plt.axes(projection=ccrs.Mercator())
----> 3 var_subset_plot.plot.pcolormesh(yincrease=True, x='lon', y='lat', levels=31, ax=ax, robust=True, add_colorbar=False, transform=ccrs.PlateCarree())
/srv/conda/envs/notebook/lib/python3.8/site-packages/xarray/plot/plot.py in plotmethod(_PlotMethods_obj, x, y, figsize, size, aspect, ax, row, col, col_wrap, xincrease, yincrease, add_colorbar, add_labels, vmin, vmax, cmap, colors, center, robust, extend, levels, infer_intervals, subplot_kws, cbar_ax, cbar_kwargs, xscale, yscale, xticks, yticks, xlim, ylim, norm, **kwargs)
1306 for arg in ["_PlotMethods_obj", "newplotfunc", "kwargs"]:
1307 del allargs[arg]
-> 1308 return newplotfunc(**allargs)
1309
1310 # Add to class _PlotMethods
/srv/conda/envs/notebook/lib/python3.8/site-packages/xarray/plot/plot.py in newplotfunc(darray, x, y, figsize, size, aspect, ax, row, col, col_wrap, xincrease, yincrease, add_colorbar, add_labels, vmin, vmax, cmap, center, robust, extend, levels, infer_intervals, colors, subplot_kws, cbar_ax, cbar_kwargs, xscale, yscale, xticks, yticks, xlim, ylim, norm, **kwargs)
1170
1171 # Pass the data as a masked ndarray too
-> 1172 zval = darray.to_masked_array(copy=False)
1173
1174 # Replace pd.Intervals if contained in xval or yval.
/srv/conda/envs/notebook/lib/python3.8/site-packages/xarray/core/dataarray.py in to_masked_array(self, copy)
2785 Masked where invalid values (nan or inf) occur.
2786 """
-> 2787 values = self.to_numpy() # only compute lazy arrays once
2788 isnull = pd.isnull(values)
2789 return np.ma.MaskedArray(data=values, mask=isnull, copy=copy)
/srv/conda/envs/notebook/lib/python3.8/site-packages/xarray/core/dataarray.py in to_numpy(self)
666 DataArray.data
667 """
--> 668 return self.variable.to_numpy()
669
670 def as_numpy(self: T_DataArray) -> T_DataArray:
/srv/conda/envs/notebook/lib/python3.8/site-packages/xarray/core/variable.py in to_numpy(self)
1074 # TODO first attempt to call .to_numpy() once some libraries implement it
1075 if isinstance(data, dask_array_type):
-> 1076 data = data.compute()
1077 if isinstance(data, cupy_array_type):
1078 data = data.get()
/srv/conda/envs/notebook/lib/python3.8/site-packages/dask/base.py in compute(self, **kwargs)
277 dask.base.compute
278 """
--> 279 (result,) = compute(self, traverse=False, **kwargs)
280 return result
281
/srv/conda/envs/notebook/lib/python3.8/site-packages/dask/base.py in compute(*args, **kwargs)
559 postcomputes.append(x.__dask_postcompute__())
560
--> 561 results = schedule(dsk, keys, **kwargs)
562 return repack([f(r, *a) for r, (f, a) in zip(results, postcomputes)])
563
/srv/conda/envs/notebook/lib/python3.8/site-packages/distributed/client.py in get(self, dsk, keys, restrictions, loose_restrictions, resources, sync, asynchronous, direct, retries, priority, fifo_timeout, actors, **kwargs)
2682 should_rejoin = False
2683 try:
-> 2684 results = self.gather(packed, asynchronous=asynchronous, direct=direct)
2685 finally:
2686 for f in futures.values():
/srv/conda/envs/notebook/lib/python3.8/site-packages/distributed/client.py in gather(self, futures, errors, direct, asynchronous)
1991 else:
1992 local_worker = None
-> 1993 return self.sync(
1994 self._gather,
1995 futures,
/srv/conda/envs/notebook/lib/python3.8/site-packages/distributed/client.py in sync(self, func, asynchronous, callback_timeout, *args, **kwargs)
837 return future
838 else:
--> 839 return sync(
840 self.loop, func, *args, callback_timeout=callback_timeout, **kwargs
841 )
/srv/conda/envs/notebook/lib/python3.8/site-packages/distributed/utils.py in sync(loop, func, callback_timeout, *args, **kwargs)
338 if error[0]:
339 typ, exc, tb = error[0]
--> 340 raise exc.with_traceback(tb)
341 else:
342 return result[0]
/srv/conda/envs/notebook/lib/python3.8/site-packages/distributed/utils.py in f()
322 if callback_timeout is not None:
323 future = asyncio.wait_for(future, callback_timeout)
--> 324 result[0] = yield future
325 except Exception as exc:
326 error[0] = sys.exc_info()
/srv/conda/envs/notebook/lib/python3.8/site-packages/tornado/gen.py in run(self)
760
761 try:
--> 762 value = future.result()
763 except Exception:
764 exc_info = sys.exc_info()
/srv/conda/envs/notebook/lib/python3.8/site-packages/distributed/client.py in _gather(self, futures, errors, direct, local_worker)
1856 exc = CancelledError(key)
1857 else:
-> 1858 raise exception.with_traceback(traceback)
1859 raise exc
1860 if errors == "skip":
/srv/conda/envs/notebook/lib/python3.8/site-packages/dask/optimization.py in __call__()
961 if not len(args) == len(self.inkeys):
962 raise ValueError("Expected %d args, got %d" % (len(self.inkeys), len(args)))
--> 963 return core.get(self.dsk, self.outkey, dict(zip(self.inkeys, args)))
964
965 def __reduce__(self):
/srv/conda/envs/notebook/lib/python3.8/site-packages/dask/core.py in get()
149 for key in toposort(dsk):
150 task = dsk[key]
--> 151 result = _execute_task(task, cache)
152 cache[key] = result
153 result = _execute_task(out, cache)
/srv/conda/envs/notebook/lib/python3.8/site-packages/dask/core.py in _execute_task()
119 # temporaries by their reference count and can execute certain
120 # operations in-place.
--> 121 return func(*(_execute_task(a, cache) for a in args))
122 elif not ishashable(arg):
123 return arg
TypeError: interp_1d_linear() got an unexpected keyword argument 'bypass_checks'
I’ve tried looking through xarray and dask but I can’t seem to find where the error is pointing to specifically. I would appreciate any insights, thank you!
Package versions:
xarray='0.19.0'
dask='2021.1.1'
dask-gateway='0.9.0'
intake='0.6.0'
intake-esm='2021.1.15'
cmip6-preprocessing='0.5.0'
xesmf='0.5.1'
xgcm='0.5.3.dev28+g95f4f33'
regionmask='0.8.1.dev1+g0872147'
Cartopy='0.19.0.post1'
matplotlib='3.3.4'
Thanks for the tip Deepak! I’ll double check how I use 