pydata / pydata/xarray

N-dimensional boolean indexing

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API design design question
Dominant language
Python
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Description

Currently, the docs state that boolean indexing is only possible with 1-dimensional arrays:
http://xarray.pydata.org/en/stable/indexing.html

However, I often have the case where I'd like to convert a subset of an xarray to a dataframe.
Usually, I would call e.g.:

data = xrds.stack(observations=["dim1", "dim2", "dim3"])
data = data.isel(~ data.missing)
df = data.to_dataframe()

However, this approach is incredibly slow and memory-demanding, since it creates a MultiIndex of every possible coordinate in the array.

Describe the solution you'd like
A better approach would be to directly allow index selection with the boolean array:

data = xrds.isel(~ xrds.missing, dim="observations")
df = data.to_dataframe()

This way, it is possible to

  1. Identify the resulting coordinates with np.argwhere()
  2. Directly use the underlying array for fancy indexing: variable.data[mask]

Additional context
I created a proof-of-concept that works for my projects:
https://gist.github.com/Hoeze/c746ea1e5fef40d99997f765c48d3c0d
Some important lines are those:

def core_dim_locs_from_cond(cond, new_dim_name, core_dims=None) -> List[Tuple[str, xr.DataArray]]:
    [...]
    core_dim_locs = np.argwhere(cond.data)
    if isinstance(core_dim_locs, dask.array.core.Array):
        core_dim_locs = core_dim_locs.persist().compute_chunk_sizes()

def subset_variable(variable, core_dim_locs, new_dim_name, mask=None):
    [...]
    subset = dask.array.asanyarray(variable.data)[mask]
    # force-set chunk size from known chunks
    chunk_sizes = core_dim_locs[0][1].chunks[0]
    subset._chunks = (chunk_sizes, *subset._chunks[1:])

As a result, I would expect something like this:
image

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the indexing documentation and the isel/to_dataframe examples in the issue, then review the proof-of-concept, especially core_dim_locs_from_cond and subset_variable. Compare the proposed np.argwhere and underlying-array indexing behavior, including the dask case. Done means n-dimensional boolean selection works without constructing every possible coordinate and preserves usable coordinates for to_dataframe.

Written by the indexing model from the issue text.

Assessment

Tech stack
numpy, pandas, python
Domain
data
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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