How to create a numpy array to an xarray data array?

Question

I am trying to convert a 3D numpy array to a data array however I am getting an error that I cannot figure out.

I have a 3D numpy array (lat, lon, and time), and I am hoping to convert it into an xarray data array with the dimensions being lat, lon, and time.

The np.random.rand is just to make a reproducible example of a 3D array:

atae = np.random.rand(10,20,30) # 3d array 
lat_atae = np.random.rand(10) # latitude is the same size as the first axis
lon_atae = np.random.rand(20) # longitude is the same size as second axis
time_atae = np.random.rand(30) # time is the 3rd axis


data_xr = xr.DataArray(atae, coords=[{'y': lat_atae,'x': lon_atae,'time': time_atae}], 
                    dims=["y", "x", "time"])


---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-156-8f8f8a1fc7aa> in <module>
----> 1 test = xr.DataArray(atae, coords=[{'y': lat_atae,'x': lon_atae,'time': time_atae}], 
      2                     dims=["y", "x", "time"])
      3 

~/opt/anaconda3/lib/python3.8/site-packages/xarray/core/dataarray.py in __init__(self, data, coords, dims, name, attrs, indexes, fastpath)
    408             data = _check_data_shape(data, coords, dims)
    409             data = as_compatible_data(data)
--> 410             coords, dims = _infer_coords_and_dims(data.shape, coords, dims)
    411             variable = Variable(dims, data, attrs, fastpath=True)
    412             indexes = dict(

~/opt/anaconda3/lib/python3.8/site-packages/xarray/core/dataarray.py in _infer_coords_and_dims(shape, coords, dims)
    104         and len(coords) != len(shape)
    105     ):
--> 106         raise ValueError(
    107             f"coords is not dict-like, but it has {len(coords)} items, "
    108             f"which does not match the {len(shape)} dimensions of the "

ValueError: coords is not dict-like, but it has 1 items, which does not match the 3 dimensions of the data

How do I convert this numpy array into a xarray data array?

StupidWolf · Accepted Answer · 2021-12-11 22:53:18Z

5

You don't need to provide a list for coords, the dictionary is enough :

data_xr = xr.DataArray(atae, 
coords={'y': lat_atae,'x': lon_atae,'time': time_atae}, 
dims=["y", "x", "time"])

answered Dec 11, 2021 at 22:53

StupidWolf

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5 Comments

wabash Over a year ago

Thank you! I will mark this correct . I tried it with my real data though (not np.random.rand), and i get this error unfortunately:

MissingDimensionsError: cannot set variable 'y' with 2-dimensional data without explicit dimension names. Pass a tuple of (dims, data) instead.

. Do you know what that means? Thanks!

StupidWolf Over a year ago

one of your input is an embedded list or 2 dimensional array?

wabash Over a year ago

one of them is a 3d array but I think the other two lon_atae, lat_atae are embedded lists. That might be the problem, should the lists be converted to arrays? Thanks again!

StupidWolf Over a year ago

are they arrays or list? Also if the list is embedded, are you sure the length or lon_atae tallies with your data? you can try list(itertools.chain.from_iterable(lon_atae)) for example

StupidWolf Over a year ago

or np.array(lon_atae).ravel() , i am really guessing your data

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