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Allow indexing with None to expand dimensions #83

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merged 1 commit into from
Aug 4, 2022
Merged

Allow indexing with None to expand dimensions #83

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23 changes: 20 additions & 3 deletions cubed/core/ops.py
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Original file line number Diff line number Diff line change
Expand Up @@ -165,6 +165,18 @@ def elemwise(func, *args, dtype=None):


def index(x, key):
if not isinstance(key, tuple):
key = (key,)

# Remove None values, to be filled in with expand_dims at end
where_none = [i for i, ind in enumerate(key) if ind is None]
for i, a in enumerate(where_none):
n = sum(isinstance(ind, Integral) for ind in key[:a])
if n:
where_none[i] -= n
key = tuple(ind for ind in key if ind is not None)

# Replace ellipsis with slices
selection = replace_ellipsis(key, x.shape)

# Use a Zarr BasicIndexer just to find the resulting array shape
Expand All @@ -185,14 +197,12 @@ def index(x, key):
else:
raise NotImplementedError(f"Index not supported: {key}")

from cubed.core.ops import map_direct

# memory allocated by reading one chunk from input array
# note that although the output chunk will overlap multiple input chunks, zarr will
# read the chunks in series, reusing the buffer
extra_required_mem = x.chunkmem

return map_direct(
out = map_direct(
func,
x,
shape=shape,
Expand All @@ -203,6 +213,13 @@ def index(x, key):
offsets=offsets,
)

for axis in where_none:
from cubed.array_api.manipulation_functions import expand_dims

out = expand_dims(out, axis=axis)

return out


def _read_index_chunk(x, *arrays, source_chunks=None, offsets=None, block_id=None):
array = arrays[0]
Expand Down
14 changes: 9 additions & 5 deletions cubed/tests/test_array_api.py
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Original file line number Diff line number Diff line change
Expand Up @@ -162,13 +162,13 @@ def test_negative(spec, executor):
# Indexing


@pytest.mark.parametrize("i", [6])
@pytest.mark.parametrize("i", [6, (6, None)])
def test_index_1d(spec, i):
a = xp.arange(12, chunks=(4,), spec=spec)
assert_array_equal(a[i].compute(), np.arange(12)[i])


@pytest.mark.parametrize("i", [(2, 3)])
@pytest.mark.parametrize("i", [(2, 3), (None, 2, 3)])
def test_index_2d(spec, i):
a = xp.asarray(
[[1, 2, 3, 4], [5, 6, 7, 8], [9, 10, 11, 12], [13, 14, 15, 16]],
Expand All @@ -186,22 +186,26 @@ def test_slice_1d(spec, sl):


@pytest.mark.parametrize(
"sl0, sl1",
"sl",
[
(slice(None), slice(2, 4)),
(slice(3), slice(2, None)),
(slice(1, None), slice(4)),
(slice(1, 3), slice(None)),
(slice(None), slice(2, 4)),
(None, slice(None), slice(2, 4)), # add a new dimension
(slice(None), None, slice(2, 4)), # add a new dimension
(slice(None), slice(2, 4), None), # add a new dimension
],
)
def test_slice_2d(spec, sl0, sl1):
def test_slice_2d(spec, sl):
a = xp.asarray(
[[1, 2, 3, 4], [5, 6, 7, 8], [9, 10, 11, 12], [13, 14, 15, 16]],
chunks=(2, 2),
spec=spec,
)
x = np.array([[1, 2, 3, 4], [5, 6, 7, 8], [9, 10, 11, 12], [13, 14, 15, 16]])
assert_array_equal(a[sl0, sl1].compute(), x[sl0, sl1])
assert_array_equal(a[sl].compute(), x[sl])


def test_slice_unsupported_step(spec):
Expand Down