How should xarray use/support sparse arrays?

[shoyer]

I'm looking forward to being easily able to create sparse xarray objects from pandas: #3206

Are there other xarray APIs that could make good use of sparse arrays, or could make sparse arrays easier to use?

Some ideas:

• to_sparse()/to_dense() methods for converting to/from sparse without requiring using .data
• to_dataframe()/to_series() could grow options for skipping the fill-value in sparse arrays, so they can round-trip MultiIndex data back to pandas
• Serialization to/from netCDF files, using some custom convention (see Sparse arrays #1375 (comment))

[khaeru]

This is very exciting! In energy-economic research (unlike, e.g., earth systems research), data are almost always sparse, so first-class sparse support will be broadly useful.

I'm leaving a comment here (since this seems to be a meta-issue; please link from wherever else, if needed) with two example use-cases. For the moment, #3206 seems to cover them, so I can't name any specific additional features.

1. MESSAGEix is an energy systems optimization model framework, formulated as a linear program.

   • Some variables have many dimensions, for instance, the input coefficient for a technology has the dimensions (node_loc, technology, year_vintage, year_active, mode, node_origin, commodity, level, time, time_origin).
     • In the global version of our model, the technology dimension has over 400 labels.
     • Often two or more dimensions are tied, eg technology='coal power plant' will only take input from (commodity='coal', level='primary energy'); all other combinations of (commodity, level) are empty for this technology.
     • So, this data is inherently sparse.
   • For modeling research, specifying quantities in this way is a good design because (a) it is intuitive to researchers in this domain, and (b) the optimization model is solved using various LP solvers via GAMS, which automatically prune zero rows in the resulting matrices.
   • When we were developing a dask/DAG-based system for model results post-processing, we wanted to use xarray, but had some quantities with tens of millions of elements that were less than 1% full. Here is some test code that triggered MemoryErrors using xarray. We chose to fall back on using a pd.Series subclass that mocks xarray methods.

2. In transportation research, stock models of vehicle fleets are often used.

   • These models always have at least two time dimensions: cohort (the time period in which a vehicle was sold) and period(s) in which it is used (and thus consumes fuel, etc.).
   • Since a vehicle sold in 2020 can't be used in 2015, these data are always triangular w.r.t. these two dimensions. (The dimensions year_vintage and year_active in example Added setup.py which runs unit tests as necessary. #1 above have the same relationship.)
   • Once multiplied by other dimensions (technology; fuel; size or shape or market segment; embodied materials; different variables; model runs across various scenarios or input assumptions) the overhead of dense arrays can become problematic.

[crusaderky]

+1 for the introduction of to_sparse() / to_dense(), but let's please avoid the mistakes that were done with chunk(). DataArray.chunk() is extremely frustrating when you have non-index coords and, 9 times out of 10, you only want to chunk the data and you have to go through the horrid

a = DataArray(a.data.chunk(), dims=a.dims, coords=a.coords, attrs=a.attrs, name=a.name)

Exactly the same issue would apply to to_sparse().

Possibly we could define them as

class DataArray:
    def to_sparse(
        self,
        data: bool = True,
        coords: Union[Iterable[Hashable], bool] = False
    )

class Dataset:
    def to_sparse(
        self,
        data_vars: Union[Iterable[Hashable], bool] = True,
        coords: Union[Iterable[Hashable], bool] = False
    )

same for to_dense() and chunk() (the latter would require a DeprecationWarning for a few release before switching the default for coords from True to False - only to be triggered in presence of dask-backed coords).

[crusaderky]

As already mentioned in #3206, unstack(sparse=True) would be extremely useful.

[crusaderky]

As for NetCDF, instead of a bespoke xarray-only convention, wouldn't it be much better to push a spec extension upstream?

[shoyer]

netCDF has a pretty low-level base spec, with conventions left to higher level docs like CF conventions. Fortunately, there does seems to be a CF convention that would be a good fit for for sparse data in COO format, namely the indexed ragged array representation (example, note the instance_dimension attribute). That's probably the right thing to use for sparse arrays in xarray.

[ivirshup]

Would it be feasible to use the contiguous ragged array spec or the gathering based compression when the COO coordinates are sorted? I think this could be very helpful for read efficiency, though I'm not sure if random writes were a requirement here.

[shoyer]

I like the indexed ragged array representation because it maps directly into sparse’s COO format. I’m sure other formats would be possible, but they would also likely be harder to implement.

[ivirshup]

That's fair. I just think it would be useful to have an assurance that indices are sorted you read them. I don't see how to express this within the CF specs while still looking like a COO array though.

[shoyer]

Yes, it would be useful (eventually) to have lazy loading of sparse arrays from disk, like we want we currently do for dense arrays. This would indeed require knowing that the indices are sorted.

[normanb]

I would be interested in trying to add PDAL (https://pdal.io/) support, is this something of interest in a similar way to the support for rasterio for dense arrays?

[darothen]

Tagging @jeliashi for visibility/collaboration

[fjanoos]

Would it be possible that pd.{Series, DataFrame}.to_xarray() automatically creates a sparse dataarray - or we have a flag in to_xarray which allows controlling for this. I have a very sparse dataframe and everytime I try to convert it to xarray I blow out my memory. Keeping it sparse but logically as a DataArray would be fantastic.

[shoyer]

We have a new "sparse=True" option in xarray.Dataset.from_dataframe for exactly this use case. Pandas's to_xarray() method just calls this method, so it would make sense to forward keyword arguments, too.

…

On Fri, Aug 30, 2019 at 11:53 AM firdaus janoos ***@***.***> wrote: Would it be possible that pd.{Series, DataFrame}.to_xarray() automatically creates a sparse dataarray - or we have a flag in to_xarray which allows controlling for this. I have a very sparse dataframe and everytime I try to convert it to xarray I blow out my memory. Keeping it sparse but logically as a DataArray would be fantastic — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#3213?email_source=notifications&email_token=AAJJFVTD2IWWPE6RTSWPVLDQHFUDTA5CNFSM4ILGYGP2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD5SPPNI#issuecomment-526710709>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAJJFVWEOGEBGXV62QFYU6DQHFUDTANCNFSM4ILGYGPQ> .

[fjanoos]

I cloned the master branch and installed it using 'python setup.py develop'.

When I try to use the sparse data loading functionality as per

oo = xa.Dataset.from_dataframe( my_df, sparse=True )

I get the following error:

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
<ipython-input-9-fce0ca6bc4c2> in <module>
----> 1 oo = xa.Dataset.from_dataframe( poly_df.iloc[:10000], sparse=True )

/mnt/local/xarray/xarray/core/dataset.py in from_dataframe(cls, dataframe, sparse)
   4040 
   4041         if sparse:
-> 4042             obj._set_sparse_data_from_dataframe(dataframe, dims, shape)
   4043         else:
   4044             obj._set_numpy_data_from_dataframe(dataframe, dims, shape)

/mnt/local/xarray/xarray/core/dataset.py in _set_sparse_data_from_dataframe(self, dataframe, dims, shape)
   3936         self, dataframe: pd.DataFrame, dims: tuple, shape: Tuple[int, ...]
   3937     ) -> None:
-> 3938         from sparse import COO
   3939 
   3940         idx = dataframe.index

ModuleNotFoundError: No module named 'sparse'

Any suggestions on what I need to do ?

[dcherian]

conda install -c conda-forge sparse

Basically you need to install https://sparse.pydata.org/en/latest/ using either pip or conda.