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Description
openedon Mar 28, 2017
I have an xarray dataset with the following structure:
<xarray.Dataset>
Dimensions: (face: 13, i: 4320, j: 4320, k: 90, time: 1)
Coordinates:
* k (k) int64 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 ...
* j (j) float64 0.0 1.0 2.0 3.0 4.0 5.0 6.0 7.0 8.0 9.0 10.0 11.0 ...
* i (i) int64 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 ...
* face (face) int64 0 1 2 3 4 5 6 7 8 9 10 11 12
iter (time) int64 487152
* time (time) int64 487152
XC (face, j, i) >f4 -114.932 -114.932 -114.932 -114.932 -114.932 ...
YC (face, j, i) >f4 -88.1771 -88.1801 -88.183 -88.1859 -88.1888 ...
Z (k) >f4 -0.5 -1.57 -2.79 -4.185 -5.78 -7.595 -9.66 -12.01 ...
Data variables:
Theta (time, k, face, j, i) >f4 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 ...
Salt (time, k, face, j, i) >f4 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 ...
This is an enormous dataset from a ocean simulation using a faceted curvilinear grid. The longitudes latitudes, and depths of the data are encoded by the variables 'XC' and 'YC'.
I am trying, unsuccessfully, to use geoviews to visualize this data. Here is what I am doing:
import geoviews as gv
gvds_from_xr = gv.Dataset(ds, kdims=['XC', 'YC', 'Z', 'time'], vdims=['Theta', 'Salt'])
gvds_from_xr.to(gv.Image, ['XC', 'YC'])This raises the error
ValueError: dimensions or multi-index levels ['Z'] do not exist
If I try
gvds_from_xr = gv.Dataset(ds, kdims=['XC', 'YC', 'k', 'time'], vdims=['Theta', 'Salt'])
gvds_from_xr.to(gv.Image, ['XC', 'YC'])(replacing physical dimension 'Z' with logical dimension 'k') I get the following stack trace:
ValueErrorTraceback (most recent call last)
<ipython-input-27-02d44a5c1c08> in <module>()
2 get_ipython().magic(u"time gvds_from_xr = gv.Dataset(ds, kdims=['XC', 'YC', 'k', 'time'], vdims=['Theta', 'Salt'])")
3 print(gvds_from_xr)
----> 4 get_ipython().magic(u"time gvds_from_xr.to(gv.Image, ['XC', 'YC'])")
/home/rpa/.conda/envs/lagrangian_vorticity/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc in magic(self, arg_s)
2156 magic_name, _, magic_arg_s = arg_s.partition(' ')
2157 magic_name = magic_name.lstrip(prefilter.ESC_MAGIC)
-> 2158 return self.run_line_magic(magic_name, magic_arg_s)
2159
2160 #-------------------------------------------------------------------------
/home/rpa/.conda/envs/lagrangian_vorticity/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc in run_line_magic(self, magic_name, line)
2077 kwargs['local_ns'] = sys._getframe(stack_depth).f_locals
2078 with self.builtin_trap:
-> 2079 result = fn(*args,**kwargs)
2080 return result
2081
<decorator-gen-59> in time(self, line, cell, local_ns)
/home/rpa/.conda/envs/lagrangian_vorticity/lib/python2.7/site-packages/IPython/core/magic.pyc in <lambda>(f, *a, **k)
186 # but it's overkill for just that one bit of state.
187 def magic_deco(arg):
--> 188 call = lambda f, *a, **k: f(*a, **k)
189
190 if callable(arg):
/home/rpa/.conda/envs/lagrangian_vorticity/lib/python2.7/site-packages/IPython/core/magics/execution.pyc in time(self, line, cell, local_ns)
1174 if mode=='eval':
1175 st = clock2()
-> 1176 out = eval(code, glob, local_ns)
1177 end = clock2()
1178 else:
<timed eval> in <module>()
/home/rpa/.conda/envs/lagrangian_vorticity/lib/python2.7/site-packages/geoviews/element/__init__.pyc in __call__(self, *args, **kwargs)
24 if 'crs' not in kwargs and issubclass(group_type, _Element):
25 kwargs['crs'] = self._element.crs
---> 26 return super(GeoConversion, self).__call__(*args, **kwargs)
27
28 def linecontours(self, kdims=None, vdims=None, mdims=None, **kwargs):
/home/rpa/.conda/envs/lagrangian_vorticity/lib/python2.7/site-packages/holoviews/core/data/__init__.pyc in __call__(self, new_type, kdims, vdims, mdims, sort, **kwargs)
92 return element.sort() if sort else element
93 group = selected.groupby(mdims, container_type=HoloMap,
---> 94 group_type=new_type, **params)
95 if sort:
96 return group.map(lambda x: x.sort(), [new_type])
/home/rpa/.conda/envs/lagrangian_vorticity/lib/python2.7/site-packages/holoviews/core/data/__init__.pyc in groupby(self, dimensions, container_type, group_type, dynamic, **kwargs)
409
410 return self.interface.groupby(self, dim_names, container_type,
--> 411 group_type, **kwargs)
412
413 def __len__(self):
/home/rpa/.conda/envs/lagrangian_vorticity/lib/python2.7/site-packages/holoviews/core/data/xarray.pyc in groupby(cls, dataset, dimensions, container_type, group_type, **kwargs)
110 data = [(k, group_type(dataset.data.sel(**dict(zip(dimensions, k))),
111 **group_kwargs))
--> 112 for k in indexes]
113
114 if issubclass(container_type, NdMapping):
/home/rpa/.conda/envs/lagrangian_vorticity/lib/python2.7/site-packages/geoviews/element/geo.pyc in __init__(self, data, **kwargs)
83 elif crs:
84 kwargs['crs'] = crs
---> 85 super(_Element, self).__init__(data, **kwargs)
86
87
/home/rpa/.conda/envs/lagrangian_vorticity/lib/python2.7/site-packages/holoviews/element/raster.pyc in __init__(self, data, **params)
657
658 def __init__(self, data, **params):
--> 659 super(GridImage, self).__init__(data, **params)
660 (l, r), (b, t) = self.interface.range(self, 0), self.interface.range(self, 1)
661 (ys, xs) = self.dimension_values(2, flat=False).shape
/home/rpa/.conda/envs/lagrangian_vorticity/lib/python2.7/site-packages/holoviews/core/data/__init__.pyc in __init__(self, data, **kwargs)
135 datatype=kwargs.get('datatype'))
136 (data, self.interface, dims, extra_kws) = initialized
--> 137 super(Dataset, self).__init__(data, **dict(extra_kws, **dict(kwargs, **dims)))
138 self.interface.validate(self)
139
/home/rpa/.conda/envs/lagrangian_vorticity/lib/python2.7/site-packages/holoviews/core/dimension.pyc in __init__(self, data, **params)
593 for d in params.pop(group)]
594 params[group] = dimensions
--> 595 super(Dimensioned, self).__init__(data, **params)
596 self.ndims = len(self.kdims)
597 cdims = [(d.name, val) for d, val in self.cdims.items()]
/home/rpa/.conda/envs/lagrangian_vorticity/lib/python2.7/site-packages/holoviews/core/dimension.pyc in __init__(self, data, id, **params)
297 params['group'] = long_name
298
--> 299 super(LabelledData, self).__init__(**params)
300 if not group_sanitizer.allowable(self.group):
301 raise ValueError("Supplied group %r contains invalid characters." %
/home/rpa/.conda/envs/lagrangian_vorticity/lib/python2.7/site-packages/param/parameterized.pyc in __init__(self, **params)
1039 self.__generate_name()
1040
-> 1041 self._setup_params(**params)
1042 object_count += 1
1043
/home/rpa/.conda/envs/lagrangian_vorticity/lib/python2.7/site-packages/param/parameterized.pyc in override_initialization(parameterized_instance, *args, **kw)
976 original_initialized=parameterized_instance.initialized
977 parameterized_instance.initialized=False
--> 978 fn(parameterized_instance,*args,**kw)
979 parameterized_instance.initialized=original_initialized
980 return override_initialization
/home/rpa/.conda/envs/lagrangian_vorticity/lib/python2.7/site-packages/param/parameterized.pyc in _setup_params(self, **params)
1439 self.warning("Setting non-parameter attribute %s=%s using a mechanism intended only for parameters",name,val)
1440 # i.e. if not desc it's setting an attribute in __dict__, not a Parameter
-> 1441 setattr(self,name,val)
1442
1443
/home/rpa/.conda/envs/lagrangian_vorticity/lib/python2.7/site-packages/param/__init__.pyc in __set__(self, obj, val)
1151 def __set__(self,obj,val):
1152 """Set to the given value, raising an exception if out of bounds."""
-> 1153 self._check_bounds(val)
1154 super(List,self).__set__(obj,val)
1155
/home/rpa/.conda/envs/lagrangian_vorticity/lib/python2.7/site-packages/param/__init__.pyc in _check_bounds(self, val)
1170 if min_length is not None and max_length is not None:
1171 if not (min_length <= l <= max_length):
-> 1172 raise ValueError("%s: list length must be between %s and %s (inclusive)"%(self._attrib_name,min_length,max_length))
1173 elif min_length is not None:
1174 if not min_length <= l:
ValueError: vdims: list length must be between 1 and 1 (inclusive)
Clearly I am doing something wrong, but I can't figure out what.
Thanks for any help you can provide.
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