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How to create a custom index

How to create a custom index#

Warning

This feature is highly experimental. Support for custom indexes has been introduced in v2022.06.0 and is still incomplete. API is subject to change without deprecation notice. However we encourage you to experiment and report issues that arise.

Xarray’s built-in support for label-based indexing (e.g. ds.sel(latitude=40, method=”nearest”)) and alignment operations relies on pandas.Index objects. Pandas Indexes are powerful and suitable for many applications but also have some limitations:

  • it only works with 1-dimensional coordinates where explicit labels are fully loaded in memory

  • it is hard to reuse it with irregular data for which there exist more efficient, tree-based structures to perform data selection

  • it doesn’t support extra metadata that may be required for indexing and alignment (e.g., a coordinate reference system)

Fortunately, Xarray now allows extending this functionality with custom indexes, which can be implemented in 3rd-party libraries.

The Index base class#

Every Xarray index must inherit from the Index base class. It is for example the case of Xarray built-in PandasIndex and PandasMultiIndex subclasses, which wrap pandas.Index and pandas.MultiIndex respectively.

The Index API closely follows the Dataset and DataArray API, e.g., for an index to support DataArray.sel() it needs to implement Index.sel(), to support DataArray.stack() and DataArray.unstack() it needs to implement Index.stack() and Index.unstack(), etc.

Some guidelines and examples are given below. More details can be found in the documented Index API.

Minimal requirements#

Every index must at least implement the Index.from_variables() class method, which is used by Xarray to build a new index instance from one or more existing coordinates in a Dataset or DataArray.

Since any collection of coordinates can be passed to that method (i.e., the number, order and dimensions of the coordinates are all arbitrary), it is the responsibility of the index to check the consistency and validity of those input coordinates.

For example, PandasIndex accepts only one coordinate and PandasMultiIndex accepts one or more 1-dimensional coordinates that must all share the same dimension. Other, custom indexes need not have the same constraints, e.g.,

  • a georeferenced raster index which only accepts two 1-d coordinates with distinct dimensions

  • a staggered grid index which takes coordinates with different dimension name suffixes (e.g., “_c” and “_l” for center and left)

Optional requirements#

Pretty much everything else is optional. Depending on the method, in the absence of a (re)implementation, an index will either raise a NotImplementedError or won’t do anything specific (just drop, pass or copy itself from/to the resulting Dataset or DataArray).

For example, you can just skip re-implementing Index.rename() if there is no internal attribute or object to rename according to the new desired coordinate or dimension names. In the case of PandasIndex, we rename the underlying pandas.Index object and/or update the PandasIndex.dim attribute since the associated dimension name has been changed.

Wrap index data as coordinate data#

In some cases it is possible to reuse the index’s underlying object or structure as coordinate data and hence avoid data duplication.

For PandasIndex and PandasMultiIndex, we leverage the fact that pandas.Index objects expose some array-like API. In Xarray we use some wrappers around those underlying objects as a thin compatibility layer to preserve dtypes, handle explicit and n-dimensional indexing, etc.

Other structures like tree-based indexes (e.g., kd-tree) may differ too much from arrays to reuse it as coordinate data.

If the index data can be reused as coordinate data, the Index subclass should implement Index.create_variables(). This method accepts a dictionary of variable names as keys and Variable objects as values (used for propagating variable metadata) and should return a dictionary of new Variable or IndexVariable objects.

Data selection#

For an index to support label-based selection, it needs to at least implement Index.sel(). This method accepts a dictionary of labels where the keys are coordinate names (already filtered for the current index) and the values can be pretty much anything (e.g., a slice, a tuple, a list, a numpy array, a Variable or a DataArray). It is the responsibility of the index to properly handle those input labels.

Index.sel() must return an instance of IndexSelResult. The latter is a small data class that holds positional indexers (indices) and that may also hold new variables, new indexes, names of variables or indexes to drop, names of dimensions to rename, etc. For example, this is useful in the case of PandasMultiIndex as it allows Xarray to convert it into a single PandasIndex when only one level remains after the selection.

The IndexSelResult class is also used to merge results from label-based selection performed by different indexes. Note that it is now possible to have two distinct indexes for two 1-d coordinates sharing the same dimension, but it is not currently possible to use those two indexes in the same call to Dataset.sel().

Optionally, the index may also implement Index.isel(). In the case of PandasIndex we use it to create a new index object by just indexing the underlying pandas.Index object. In other cases this may not be possible, e.g., a kd-tree object may not be easily indexed. If Index.isel() is not implemented, the index in just dropped in the DataArray or Dataset resulting from the selection.

Alignment#

For an index to support alignment, it needs to implement:

  • Index.equals(), which compares the index with another index and returns either True or False

  • Index.join(), which combines the index with another index and returns a new Index object

  • Index.reindex_like(), which queries the index with another index and returns positional indexers that are used to re-index Dataset or DataArray variables along one or more dimensions

Xarray ensures that those three methods are called with an index of the same type as argument.

Meta-indexes#

Nothing prevents writing a custom Xarray index that itself encapsulates other Xarray index(es). We call such index a “meta-index”.

Here is a small example of a meta-index for geospatial, raster datasets (i.e., regularly spaced 2-dimensional data) that internally relies on two PandasIndex instances for the x and y dimensions respectively:

from xarray import Index
from xarray.core.indexes import PandasIndex
from xarray.core.indexing import merge_sel_results


class RasterIndex(Index):
    def __init__(self, xy_indexes):
        assert len(xy_indexes) == 2

        # must have two distinct dimensions
        dim = [idx.dim for idx in xy_indexes.values()]
        assert dim[0] != dim[1]

        self._xy_indexes = xy_indexes

    @classmethod
    def from_variables(cls, variables):
        assert len(variables) == 2

        xy_indexes = {
            k: PandasIndex.from_variables({k: v}) for k, v in variables.items()
        }

        return cls(xy_indexes)

    def create_variables(self, variables):
        idx_variables = {}

        for index in self._xy_indexes.values():
            idx_variables.update(index.create_variables(variables))

        return idx_variables

    def sel(self, labels):
        results = []

        for k, index in self._xy_indexes.items():
            if k in labels:
                results.append(index.sel({k: labels[k]}))

        return merge_sel_results(results)

This basic index only supports label-based selection. Providing a full-featured index by implementing the other Index methods should be pretty straightforward for this example, though.

This example is also not very useful unless we add some extra functionality on top of the two encapsulated PandasIndex objects, such as a coordinate reference system.

How to use a custom index#

You can use Dataset.set_xindex() or DataArray.set_xindex() to assign a custom index to a Dataset or DataArray, e.g., using the RasterIndex above:

import numpy as np
import xarray as xr

da = xr.DataArray(
    np.random.uniform(size=(100, 50)),
    coords={"x": ("x", np.arange(50)), "y": ("y", np.arange(100))},
    dims=("y", "x"),
)

# Xarray create default indexes for the 'x' and 'y' coordinates
# we first need to explicitly drop it
da = da.drop_indexes(["x", "y"])

# Build a RasterIndex from the 'x' and 'y' coordinates
da_raster = da.set_xindex(["x", "y"], RasterIndex)

# RasterIndex now takes care of label-based selection
selected = da_raster.sel(x=10, y=slice(20, 50))
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