xarray DataArray attributes breaking grdimage #1578
Description
Description of the problem
When trying to plot a timeslice of a field from an open xarray DataSet with the coordinates time, latitude, and longitude, I get a warning indicating the presence of a datacube, and a ValueError in accessors.py expecting 2 values but getting none. I found that this problem disappears when I perform an operation on the DataArray, e.g. multiplying with 1. The only thing that seems to change with this operation is that the attributes in xarray are dropped.
Full code that generated the error
Using the original DataArray:
print(ds['msl'].isel(time=i))
<xarray.DataArray 'msl' (latitude: 89, longitude: 241)>
array([[102200.34 , 102197.32 , 102193.22 , ..., 101123.69 , 101133.4 ,
101143.98 ],
[102182.86 , 102179.41 , 102176.59 , ..., 101061.734, 101072.31 ,
101083.1 ],
[102170.555, 102166.234, 102161.92 , ..., 100998.49 , 101009.28 ,
101020.08 ],
...,
[101951.47 , 101926.21 , 101900.52 , ..., 101845.7 , 101869.66 ,
101891.67 ],
[102002.19 , 101976.51 , 101950.17 , ..., 101921.25 , 101941.1 ,
101961.83 ],
[102049.89 , 102023.99 , 101997.445, ..., 101993.34 , 102012.984,
102031.98 ]], dtype=float32)
Coordinates:
* longitude (longitude) float32 150.0 150.2 150.5 150.8 ... 209.5 209.8 210.0
* latitude (latitude) float32 72.0 71.75 71.5 71.25 ... 50.5 50.25 50.0
time datetime64[ns] 1996-11-04T06:00:00
Attributes:
units: Pa
long_name: Mean sea level pressure
standard_name: air_pressure_at_mean_sea_level
Breaks:
ds = xr.open_dataset(data_path) #
fig = pygmt.Figure()
msl=ds['msl'].isel(time=i)
fig.grdimage(grid=msl)
fig.show()Using the DataArray multiplied by 1:
print(ds['msl'].isel(time=i)*1)
<xarray.DataArray 'msl' (latitude: 89, longitude: 241)>
array([[102200.34 , 102197.32 , 102193.22 , ..., 101123.69 , 101133.4 ,
101143.98 ],
[102182.86 , 102179.41 , 102176.59 , ..., 101061.734, 101072.31 ,
101083.1 ],
[102170.555, 102166.234, 102161.92 , ..., 100998.49 , 101009.28 ,
101020.08 ],
...,
[101951.47 , 101926.21 , 101900.52 , ..., 101845.7 , 101869.66 ,
101891.67 ],
[102002.19 , 101976.51 , 101950.17 , ..., 101921.25 , 101941.1 ,
101961.83 ],
[102049.89 , 102023.99 , 101997.445, ..., 101993.34 , 102012.984,
102031.98 ]], dtype=float32)
Coordinates:
* longitude (longitude) float32 150.0 150.2 150.5 150.8 ... 209.5 209.8 210.0
* latitude (latitude) float32 72.0 71.75 71.5 71.25 ... 50.5 50.25 50.0
time datetime64[ns] 1996-11-04T06:00:00
Works:
ds = xr.open_dataset(data_path)
fig = pygmt.Figure()
msl=ds['msl'].isel(time=i)*1
fig.grdimage(grid=msl)
fig.show()
Full error message
grdinfo [WARNING]: Detected a data cube (/Users/rfische1/Documents/UMD/Assistantship/POLARA/data/ERA5/ERA5_1995-2020-2.nc) but -Q not set - skipping
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
/var/folders/hh/2wq7ys4544ngb10v0y46_f_h0000gr/T/ipykernel_12727/718688776.py in <module>
5 msl=ds['msl'].isel(time=i)
6
----> 7 fig.grdimage(
8 grid=msl
9 )
~/opt/anaconda3/envs/name/lib/python3.8/site-packages/pygmt/helpers/decorators.py in new_module(*args, **kwargs)
580 )
581 warnings.warn(msg, category=SyntaxWarning, stacklevel=2)
--> 582 return module_func(*args, **kwargs)
583
584 new_module.aliases = aliases
~/opt/anaconda3/envs/name/lib/python3.8/site-packages/pygmt/helpers/decorators.py in new_module(*args, **kwargs)
723 kwargs[arg] = separators[fmt].join(f"{item}" for item in value)
724 # Execute the original function and return its output
--> 725 return module_func(*args, **kwargs)
726
727 return new_module
~/opt/anaconda3/envs/name/lib/python3.8/site-packages/pygmt/src/grdimage.py in grdimage(self, grid, **kwargs)
171 kwargs["I"] = stack.enter_context(shading_context)
172
--> 173 fname = stack.enter_context(file_context)
174 arg_str = " ".join([fname, build_arg_string(kwargs)])
175 lib.call_module("grdimage", arg_str)
~/opt/anaconda3/envs/name/lib/python3.8/contextlib.py in enter_context(self, cm)
423 _cm_type = type(cm)
424 _exit = _cm_type.__exit__
--> 425 result = _cm_type.__enter__(cm)
426 self._push_cm_exit(cm, _exit)
427 return result
~/opt/anaconda3/envs/name/lib/python3.8/contextlib.py in __enter__(self)
111 del self.args, self.kwds, self.func
112 try:
--> 113 return next(self.gen)
114 except StopIteration:
115 raise RuntimeError("generator didn't yield") from None
~/opt/anaconda3/envs/name/lib/python3.8/site-packages/pygmt/clib/session.py in virtualfile_from_grid(self, grid)
1335 >>> # The output is: w e s n z0 z1 dx dy n_columns n_rows reg gtype
1336 """
-> 1337 _gtype = {0: "GMT_GRID_IS_CARTESIAN", 1: "GMT_GRID_IS_GEO"}[grid.gmt.gtype]
1338 _reg = {0: "GMT_GRID_NODE_REG", 1: "GMT_GRID_PIXEL_REG"}[grid.gmt.registration]
1339
~/opt/anaconda3/envs/name/lib/python3.8/site-packages/xarray/core/extensions.py in __get__(self, obj, cls)
34
35 try:
---> 36 accessor_obj = self._accessor(obj)
37 except AttributeError:
38 # __getattr__ on data object will swallow any AttributeErrors
~/opt/anaconda3/envs/name/lib/python3.8/site-packages/pygmt/accessors.py in __init__(self, xarray_obj)
32 # From the shortened summary information of `grdinfo`,
33 # get grid registration in column 10, and grid type in column 11
---> 34 self._registration, self._gtype = map(
35 int, grdinfo(self._source, per_column="n", o="10,11").split()
36 )
ValueError: not enough values to unpack (expected 2, got 0)
System information
Please paste the output of python -c "import pygmt; pygmt.show_versions()":
PyGMT information:
version: v0.4.1
System information:
python: 3.8.11 (default, Aug 6 2021, 08:56:27) [Clang 10.0.0 ]
executable: /Users/name/opt/anaconda3/envs/name/bin/python
machine: macOS-10.16-x86_64-i386-64bit
Dependency information:
numpy: 1.21.2
pandas: 1.3.3
xarray: 0.19.0
netCDF4: 1.5.7
packaging: 21.0
ghostscript: 9.54.0
gmt: 6.2.0
GMT library information:
binary dir: /Users/name/opt/anaconda3/envs/name/bin
cores: 8
grid layout: rows
library path: /Users/name/opt/anaconda3/envs/name/lib/libgmt.dylib
padding: 2
plugin dir: /Users/name/opt/anaconda3/envs/name/lib/gmt/plugins
share dir: /Users/name/opt/anaconda3/envs/name/share/gmt
version: 6.2.0