Python Xarray add DataArray to Dataset -
very simple question can't find answer online. have dataset , want add named dataarray it. dataset.add({"new_array": new_data_array}). know merge , update , concatenate, understanding merge merging 2 or more datasets , concatenate concatenating 2 or more dataarrays form dataarray, , haven't quite understood update yet. i've tried dataset.update({"new_array": new_data_array}) following error.
invalidindexerror: reindexing valid uniquely valued index objects i've tried dataset["new_array"] = new_data_array , same error.
update
i've found out problem of coordinates have duplicate values, didn't know about. coordinates used index, xarray gets confused (understandably) when trying combine shared coordinates. below example works.
names = ["joaquin", "manolo", "xavier"] n = xarray.dataarray([23, 98, 23], coords={"name": names}) print(n) print("======") m = numpy.random.randint(0, 256, (3, 4, 4)).astype(numpy.uint8) mm = xarray.dataarray(m, dims=["name", "row", "column"], coords=[names, range(4), range(4)]) print(mm) print("======") n_dataset = n.rename("number").to_dataset() n_dataset["mm"] = mm print(n_dataset) output:
<xarray.dataarray (name: 3)> array([23, 98, 23]) coordinates: * name (name) <u7 'joaquin' 'manolo' 'xavier' ====== <xarray.dataarray (name: 3, row: 4, column: 4)> array([[[ 55, 63, 250, 211], [204, 151, 164, 237], [182, 24, 211, 12], [183, 220, 35, 78]], [[208, 7, 91, 114], [195, 30, 108, 130], [ 61, 224, 105, 125], [ 65, 1, 132, 137]], [[ 52, 137, 62, 206], [188, 160, 156, 126], [145, 223, 103, 240], [141, 38, 43, 68]]], dtype=uint8) coordinates: * name (name) <u7 'joaquin' 'manolo' 'xavier' * row (row) int64 0 1 2 3 * column (column) int64 0 1 2 3 ====== <xarray.dataset> dimensions: (column: 4, name: 3, row: 4) coordinates: * name (name) object 'joaquin' 'manolo' 'xavier' * row (row) int64 0 1 2 3 * column (column) int64 0 1 2 3 data variables: number (name) int64 23 98 23 mm (name, row, column) uint8 55 63 250 211 204 151 164 237 182 24 ... the above code uses names index. if change code little bit, names has duplicate, names = ["joaquin", "manolo", "joaquin"], invalidindexerror.
code:
names = ["joaquin", "manolo", "joaquin"] n = xarray.dataarray([23, 98, 23], coords={"name": names}) print(n) print("======") m = numpy.random.randint(0, 256, (3, 4, 4)).astype(numpy.uint8) mm = xarray.dataarray(m, dims=["name", "row", "column"], coords=[names, range(4), range(4)]) print(mm) print("======") n_dataset = n.rename("number").to_dataset() n_dataset["mm"] = mm print(n_dataset) output:
<xarray.dataarray (name: 3)> array([23, 98, 23]) coordinates: * name (name) <u7 'joaquin' 'manolo' 'joaquin' ====== <xarray.dataarray (name: 3, row: 4, column: 4)> array([[[247, 3, 20, 141], [ 54, 111, 224, 56], [144, 117, 131, 192], [230, 44, 174, 14]], [[225, 184, 170, 248], [ 57, 105, 165, 70], [220, 228, 238, 17], [ 90, 118, 87, 30]], [[158, 211, 31, 212], [ 63, 172, 190, 254], [165, 163, 184, 22], [ 49, 224, 196, 244]]], dtype=uint8) coordinates: * name (name) <u7 'joaquin' 'manolo' 'joaquin' * row (row) int64 0 1 2 3 * column (column) int64 0 1 2 3 ====== --------------------------------------------------------------------------- invalidindexerror traceback (most recent call last) <ipython-input-12-50863379cefe> in <module>() 8 print("======") 9 n_dataset = n.rename("number").to_dataset() ---> 10 n_dataset["mm"] = mm 11 print(n_dataset) /library/frameworks/python.framework/versions/3.5/lib/python3.5/site-packages/xarray/core/dataset.py in __setitem__(self, key, value) 536 raise notimplementederror('cannot yet use dictionary key ' 537 'to set dataset values') --> 538 self.update({key: value}) 539 540 def __delitem__(self, key): /library/frameworks/python.framework/versions/3.5/lib/python3.5/site-packages/xarray/core/dataset.py in update(self, other, inplace) 1434 dataset. 1435 """ -> 1436 variables, coord_names, dims = dataset_update_method(self, other) 1437 1438 return self._replace_vars_and_dims(variables, coord_names, dims, /library/frameworks/python.framework/versions/3.5/lib/python3.5/site-packages/xarray/core/merge.py in dataset_update_method(dataset, other) 492 priority_arg = 1 493 indexes = dataset.indexes --> 494 return merge_core(objs, priority_arg=priority_arg, indexes=indexes) /library/frameworks/python.framework/versions/3.5/lib/python3.5/site-packages/xarray/core/merge.py in merge_core(objs, compat, join, priority_arg, explicit_coords, indexes) 373 coerced = coerce_pandas_values(objs) 374 aligned = deep_align(coerced, join=join, copy=false, indexes=indexes, --> 375 skip_single_target=true) 376 expanded = expand_variable_dicts(aligned) 377 /library/frameworks/python.framework/versions/3.5/lib/python3.5/site-packages/xarray/core/alignment.py in deep_align(list_of_variable_maps, join, copy, indexes, skip_single_target) 162 163 aligned = partial_align(*targets, join=join, copy=copy, indexes=indexes, --> 164 skip_single_target=skip_single_target) 165 166 key, aligned_obj in zip(keys, aligned): /library/frameworks/python.framework/versions/3.5/lib/python3.5/site-packages/xarray/core/alignment.py in partial_align(*objects, **kwargs) 122 valid_indexers = dict((k, v) k, v in joined_indexes.items() 123 if k in obj.dims) --> 124 result.append(obj.reindex(copy=copy, **valid_indexers)) 125 126 return tuple(result) /library/frameworks/python.framework/versions/3.5/lib/python3.5/site-packages/xarray/core/dataset.py in reindex(self, indexers, method, tolerance, copy, **kw_indexers) 1216 1217 variables = alignment.reindex_variables( -> 1218 self.variables, self.indexes, indexers, method, tolerance, copy=copy) 1219 return self._replace_vars_and_dims(variables) 1220 /library/frameworks/python.framework/versions/3.5/lib/python3.5/site-packages/xarray/core/alignment.py in reindex_variables(variables, indexes, indexers, method, tolerance, copy) 234 target = utils.safe_cast_to_index(indexers[name]) 235 indexer = index.get_indexer(target, method=method, --> 236 **get_indexer_kwargs) 237 238 to_shape[name] = len(target) /library/frameworks/python.framework/versions/3.5/lib/python3.5/site-packages/pandas/indexes/base.py in get_indexer(self, target, method, limit, tolerance) 2080 2081 if not self.is_unique: -> 2082 raise invalidindexerror('reindexing valid uniquely' 2083 ' valued index objects') 2084 invalidindexerror: reindexing valid uniquely valued index objects so it's not bug in xarray such. nevertheless, wasted many hours trying find bug, , wish error message more informative. hope xarray collaborators fix soon. (put in uniqueness check on coordinates before attempting merge.)
in case, method provided answer below still works.
you need make sure dimensions of new dataarray same in dataset. following should work:
dataset['new_array_name'] = new_array here complete example try out:
# create dimensions x = np.linspace(-10,10,10) y = np.linspace(-20,20,20) (yy, xx) = np.meshgrid(y,x) # make 2 different dataarrays equal dimensions var1 = xray.dataarray(np.random.randn(len(x),len(y)),coords=[x, y],dims=['x','y']) var2 = xray.dataarray(-xx**2+yy**2,coords=[x, y],dims=['x','y']) # save 1 dataarray dataset ds = var1.to_dataset(name = 'var1') # add second dataarray existing dataset (ds) ds['var2'] = var2
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