xarray.combine_by_coords

xarray.combine_by_coords(datasets, compat='no_conflicts', data_vars='all', coords='different', fill_value=<NA>, join='outer')

Attempt to auto-magically combine the given datasets into one by using dimension coordinates.

This method attempts to combine a group of datasets along any number of dimensions into a single entity by inspecting coords and metadata and using a combination of concat and merge.

Will attempt to order the datasets such that the values in their dimension coordinates are monotonic along all dimensions. If it cannot determine the order in which to concatenate the datasets, it will raise a ValueError. Non-coordinate dimensions will be ignored, as will any coordinate dimensions which do not vary between each dataset.

Aligns coordinates, but different variables on datasets can cause it to fail under some scenarios. In complex cases, you may need to clean up your data and use concat/merge explicitly (also see manual_combine).

Works well if, for example, you have N years of data and M data variables, and each combination of a distinct time period and set of data variables is saved as its own dataset. Also useful for if you have a simulation which is parallelized in multiple dimensions, but has global coordinates saved in each file specifying the positions of points within the global domain.

Parameters

  • datasets (sequence of xarray.Dataset) – Dataset objects to combine.

  • compat ({'identical', 'equals', 'broadcast_equals', 'no_conflicts', 'override'}, optional) –

    String indicating how to compare variables of the same name for potential conflicts:

    • ’broadcast_equals’: all values must be equal when variables are broadcast against each other to ensure common dimensions.

    • ’equals’: all values and dimensions must be the same.

    • ’identical’: all values, dimensions and attributes must be the same.

    • ’no_conflicts’: only values which are not null in both datasets must be equal. The returned dataset then contains the combination of all non-null values.

    • ’override’: skip comparing and pick variable from first dataset

  • data_vars ({'minimal', 'different', 'all' or list of str}, optional) –

    These data variables will be concatenated together:

    • ’minimal’: Only data variables in which the dimension already appears are included.

    • ’different’: Data variables which are not equal (ignoring attributes) across all datasets are also concatenated (as well as all for which dimension already appears). Beware: this option may load the data payload of data variables into memory if they are not already loaded.

    • ’all’: All data variables will be concatenated.

    • list of str: The listed data variables will be concatenated, in addition to the ‘minimal’ data variables.

    If objects are DataArrays, data_vars must be ‘all’.

  • coords ({'minimal', 'different', 'all' or list of str}, optional) – As per the ‘data_vars’ kwarg, but for coordinate variables.

  • fill_value (scalar, optional) – Value to use for newly missing values. If None, raises a ValueError if the passed Datasets do not create a complete hypercube.

  • join ({'outer', 'inner', 'left', 'right', 'exact'}, optional) –

    String indicating how to combine differing indexes (excluding concat_dim) in objects

    • ’outer’: use the union of object indexes

    • ’inner’: use the intersection of object indexes

    • ’left’: use indexes from the first object with each dimension

    • ’right’: use indexes from the last object with each dimension

    • ’exact’: instead of aligning, raise ValueError when indexes to be aligned are not equal

    • ’override’: if indexes are of same size, rewrite indexes to be those of the first object with that dimension. Indexes for the same dimension must have the same size in all objects.

Returns

combined

Return type

xarray.Dataset

See also

concat(), merge(), combine_nested()

Examples

Combining two datasets using their common dimension coordinates. Notice they are concatenated based on the values in their dimension coordinates, not on their position in the list passed to combine_by_coords.

>>> import numpy as np
>>> import xarray as xr

>>> x1 = xr.Dataset(
...     {
...         "temperature": (("y", "x"), 20 * np.random.rand(6).reshape(2, 3)),
...         "precipitation": (("y", "x"), np.random.rand(6).reshape(2, 3)),
...     },
...     coords={"y": [0, 1], "x": [10, 20, 30]},
... )
>>> x2 = xr.Dataset(
...     {
...         "temperature": (("y", "x"), 20 * np.random.rand(6).reshape(2, 3)),
...         "precipitation": (("y", "x"), np.random.rand(6).reshape(2, 3)),
...     },
...     coords={"y": [2, 3], "x": [10, 20, 30]},
... )
>>> x3 = xr.Dataset(
...     {
...         "temperature": (("y", "x"), 20 * np.random.rand(6).reshape(2, 3)),
...         "precipitation": (("y", "x"), np.random.rand(6).reshape(2, 3)),
...     },
...     coords={"y": [2, 3], "x": [40, 50, 60]},
... )

>>> x1
<xarray.Dataset>
Dimensions:        (x: 3, y: 2)
Coordinates:
* y              (y) int64 0 1
* x              (x) int64 10 20 30
Data variables:
    temperature    (y, x) float64 1.654 10.63 7.015 2.543 13.93 9.436
    precipitation  (y, x) float64 0.2136 0.9974 0.7603 0.4679 0.3115 0.945

>>> x2
<xarray.Dataset>
Dimensions:        (x: 3, y: 2)
Coordinates:
* y              (y) int64 2 3
* x              (x) int64 10 20 30
Data variables:
    temperature    (y, x) float64 9.341 0.1251 6.269 7.709 8.82 2.316
    precipitation  (y, x) float64 0.1728 0.1178 0.03018 0.6509 0.06938 0.3792

>>> x3
<xarray.Dataset>
Dimensions:        (x: 3, y: 2)
Coordinates:
* y              (y) int64 2 3
* x              (x) int64 40 50 60
Data variables:
    temperature    (y, x) float64 2.789 2.446 6.551 12.46 2.22 15.96
    precipitation  (y, x) float64 0.4804 0.1902 0.2457 0.6125 0.4654 0.5953

>>> xr.combine_by_coords([x2, x1])
<xarray.Dataset>
Dimensions:        (x: 3, y: 4)
Coordinates:
* x              (x) int64 10 20 30
* y              (y) int64 0 1 2 3
Data variables:
    temperature    (y, x) float64 1.654 10.63 7.015 2.543 ... 7.709 8.82 2.316
    precipitation  (y, x) float64 0.2136 0.9974 0.7603 ... 0.6509 0.06938 0.3792

>>> xr.combine_by_coords([x3, x1])
<xarray.Dataset>
Dimensions:        (x: 6, y: 4)
Coordinates:
* x              (x) int64 10 20 30 40 50 60
* y              (y) int64 0 1 2 3
Data variables:
    temperature    (y, x) float64 1.654 10.63 7.015 nan ... nan 12.46 2.22 15.96
    precipitation  (y, x) float64 0.2136 0.9974 0.7603 ... 0.6125 0.4654 0.5953

>>> xr.combine_by_coords([x3, x1], join="override")
<xarray.Dataset>
Dimensions:        (x: 3, y: 4)
Coordinates:
* x              (x) int64 10 20 30
* y              (y) int64 0 1 2 3
Data variables:
temperature    (y, x) float64 1.654 10.63 7.015 2.543 ... 12.46 2.22 15.96
precipitation  (y, x) float64 0.2136 0.9974 0.7603 ... 0.6125 0.4654 0.5953

>>> xr.combine_by_coords([x1, x2, x3])
<xarray.Dataset>
Dimensions:        (x: 6, y: 4)
Coordinates:
* x              (x) int64 10 20 30 40 50 60
* y              (y) int64 0 1 2 3
Data variables:
temperature    (y, x) float64 1.654 10.63 7.015 nan ... 12.46 2.22 15.96
precipitation  (y, x) float64 0.2136 0.9974 0.7603 ... 0.6125 0.4654 0.5953