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len() function for COO objects #68

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merged 3 commits into from Jan 10, 2018

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@nils-werner
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nils-werner commented Jan 10, 2018

Quite trivial really, implements the len() operation following NumPy's convention of

len(array) == array.shape[0]
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hameerabbasi commented Jan 10, 2018

Seems fine, however it would be really nice to have docstrings for these, and if possible, tests.

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nils-werner commented Jan 10, 2018

Added them

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hameerabbasi commented Jan 10, 2018

Well, this looks good. Let me know if you're finished working on it, and I'll review and merge (don't want to be too fast this time).

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nils-werner commented Jan 10, 2018

This is ready to be merged.

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mrocklin commented Jan 10, 2018

Agreed.

@mrocklin mrocklin merged commit 988c6a3 into pydata:master Jan 10, 2018

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mrocklin commented Jan 10, 2018

Thanks @nils-werner !

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nils-werner commented Jan 10, 2018

One unexpected sideeffect of this:

numpy.array(sparse_arr)

now magically works!

x = sparse.random((20, 30))
np.allclose(x.todense(), np.array(x))    # True
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hameerabbasi commented Jan 10, 2018

I'm going to assume it's really slow. Do we have any benchmarks for this?

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nils-werner commented Jan 10, 2018

Yes, it's very very slow.

If I understand it correctly, numpy.array(x) looks for buffer and __array_interface__ when creating an array from an object. If it doesn't find one it simply iterates over it.

What if we implement __array_interface__ that calls self.todense()?

@property
def __array_interface__(self):
    return {
        'shape': self.shape,
        'data': self.todense(),
        'typestr': self.dtype.str,
    }

Before

x = sparse.random((20, 30, 20))

%timeit numpy.array(x)
# 1.48 s ± 25.5 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
%timeit x.todense()
# 11.6 µs ± 40.3 ns per loop (mean ± std. dev. of 7 runs, 100000 loops each)
numpy.allclose(x, x.todense)
# True

After

%timeit numpy.array(x)
# 23 µs ± 392 ns per loop (mean ± std. dev. of 7 runs, 10000 loops each)
numpy.allclose(x, x.todense)
# True

I can't explain where the 2x slowdown (11 vs 23 us) comes from though...

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hameerabbasi commented Jan 10, 2018

A pull request would be welcome. Also, your data is too small. Maybe it's just the overhead.

@nils-werner nils-werner deleted the nils-werner:len branch Jan 15, 2018

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