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Ellipsis handling #168

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228e83f
ellipsis handling; resolves #93
alimanfoo Oct 25, 2017
b9cd024
minor conciseness
alimanfoo Oct 26, 2017
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71 changes: 68 additions & 3 deletions zarr/tests/test_core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -123,6 +123,12 @@ def test_array_1d(self):
assert_array_equal(a[:10], z[:10])
assert_array_equal(a[10:20], z[10:20])
assert_array_equal(a[-10:], z[-10:])
assert_array_equal(a[:10, ...], z[:10, ...])
assert_array_equal(a[10:20, ...], z[10:20, ...])
assert_array_equal(a[-10:, ...], z[-10:, ...])
assert_array_equal(a[..., :10], z[..., :10])
assert_array_equal(a[..., 10:20], z[..., 10:20])
assert_array_equal(a[..., -10:], z[..., -10:])
# ...across chunk boundaries...
assert_array_equal(a[:110], z[:110])
assert_array_equal(a[190:310], z[190:310])
Expand All @@ -135,6 +141,18 @@ def test_array_1d(self):
eq(a[42], z[np.int32(42)])
eq(a[42], z[np.uint64(42)])
eq(a[42], z[np.uint32(42)])
# too many indices
with assert_raises(IndexError):
z[:, :]
with assert_raises(IndexError):
z[0, :]
with assert_raises(IndexError):
z[:, 0]
with assert_raises(IndexError):
z[0, 0]
# only single ellipsis allowed
with assert_raises(IndexError):
z[..., ...]

# check partial assignment
b = np.arange(1e5, 2e5)
Expand Down Expand Up @@ -194,37 +212,84 @@ def test_array_2d(self):
eq(a.nbytes, z.nbytes)
eq(50, z.nchunks_initialized)

# check slicing
# check array-like
assert_array_equal(a, np.array(z))

# check slicing

# total slice
assert_array_equal(a, z[:])
assert_array_equal(a, z[...])
# noinspection PyTypeChecker
assert_array_equal(a, z[slice(None)])

# slice first dimension
assert_array_equal(a[:10], z[:10])
assert_array_equal(a[10:20], z[10:20])
assert_array_equal(a[-10:], z[-10:])
assert_array_equal(a[:10, :], z[:10, :])
assert_array_equal(a[10:20, :], z[10:20, :])
assert_array_equal(a[-10:, :], z[-10:, :])
assert_array_equal(a[:10, ...], z[:10, ...])
assert_array_equal(a[10:20, ...], z[10:20, ...])
assert_array_equal(a[-10:, ...], z[-10:, ...])
assert_array_equal(a[:10, :, ...], z[:10, :, ...])
assert_array_equal(a[10:20, :, ...], z[10:20, :, ...])
assert_array_equal(a[-10:, :, ...], z[-10:, :, ...])

# slice second dimension
assert_array_equal(a[:, :2], z[:, :2])
assert_array_equal(a[:, 2:4], z[:, 2:4])
assert_array_equal(a[:, -2:], z[:, -2:])
assert_array_equal(a[..., :2], z[..., :2])
assert_array_equal(a[..., 2:4], z[..., 2:4])
assert_array_equal(a[..., -2:], z[..., -2:])
assert_array_equal(a[:, ..., :2], z[:, ..., :2])
assert_array_equal(a[:, ..., 2:4], z[:, ..., 2:4])
assert_array_equal(a[:, ..., -2:], z[:, ..., -2:])

# slice both dimensions
assert_array_equal(a[:10, :2], z[:10, :2])
assert_array_equal(a[10:20, 2:4], z[10:20, 2:4])
assert_array_equal(a[-10:, -2:], z[-10:, -2:])
# ...across chunk boundaries...

# slicing across chunk boundaries
assert_array_equal(a[:110], z[:110])
assert_array_equal(a[190:310], z[190:310])
assert_array_equal(a[-110:], z[-110:])
assert_array_equal(a[:110, :], z[:110, :])
assert_array_equal(a[190:310, :], z[190:310, :])
assert_array_equal(a[-110:, :], z[-110:, :])
assert_array_equal(a[:, :3], z[:, :3])
assert_array_equal(a[:, 3:7], z[:, 3:7])
assert_array_equal(a[:, -3:], z[:, -3:])
assert_array_equal(a[:110, :3], z[:110, :3])
assert_array_equal(a[190:310, 3:7], z[190:310, 3:7])
assert_array_equal(a[-110:, -3:], z[-110:, -3:])
# single item

# single row/col/item
assert_array_equal(a[0], z[0])
assert_array_equal(a[-1], z[-1])
assert_array_equal(a[:, 0], z[:, 0])
assert_array_equal(a[:, -1], z[:, -1])
eq(a[0, 0], z[0, 0])
eq(a[-1, -1], z[-1, -1])

# too many indices
with assert_raises(IndexError):
z[:, :, :]
with assert_raises(IndexError):
z[0, :, :]
with assert_raises(IndexError):
z[:, 0, :]
with assert_raises(IndexError):
z[:, :, 0]
with assert_raises(IndexError):
z[0, 0, 0]
# only single ellipsis allowed
with assert_raises(IndexError):
z[..., ...]

# check partial assignment
b = np.arange(10000, 20000).reshape((1000, 10))
z[190:310, 3:7] = b[190:310, 3:7]
Expand Down
21 changes: 15 additions & 6 deletions zarr/tests/test_util.py
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Original file line number Diff line number Diff line change
Expand Up @@ -111,18 +111,17 @@ def test_normalize_array_selection():
eq((slice(0, 100),), normalize_array_selection(slice(None), (100,)))
eq((slice(0, 100),), normalize_array_selection(slice(None, 100), (100,)))
eq((slice(0, 100),), normalize_array_selection(slice(0, None), (100,)))
eq((slice(0, 100),), normalize_array_selection((slice(None), Ellipsis), (100,)))
eq((slice(0, 100),), normalize_array_selection((Ellipsis, slice(None)), (100,)))

# 2D, single item
eq((0, 0), normalize_array_selection((0, 0), (100, 100)))
eq((99, 1), normalize_array_selection((-1, 1), (100, 100)))

# 2D, single col/row
eq((0, slice(0, 100)), normalize_array_selection((0, slice(None)),
(100, 100)))
eq((0, slice(0, 100)), normalize_array_selection((0,),
(100, 100)))
eq((slice(0, 100), 0), normalize_array_selection((slice(None), 0),
(100, 100)))
eq((0, slice(0, 100)), normalize_array_selection((0, slice(None)), (100, 100)))
eq((0, slice(0, 100)), normalize_array_selection((0,), (100, 100)))
eq((slice(0, 100), 0), normalize_array_selection((slice(None), 0), (100, 100)))

# 2D slice
eq((slice(0, 100), slice(0, 100)),
Expand All @@ -131,6 +130,16 @@ def test_normalize_array_selection():
normalize_array_selection(slice(None), (100, 100)))
eq((slice(0, 100), slice(0, 100)),
normalize_array_selection((slice(None), slice(None)), (100, 100)))
eq((slice(0, 100), slice(0, 100)),
normalize_array_selection((Ellipsis, slice(None)), (100, 100)))
eq((slice(0, 100), slice(0, 100)),
normalize_array_selection((slice(None), Ellipsis), (100, 100)))
eq((slice(0, 100), slice(0, 100)),
normalize_array_selection((slice(None), Ellipsis, slice(None)), (100, 100)))
eq((slice(0, 100), slice(0, 100)),
normalize_array_selection((Ellipsis, slice(None), slice(None)), (100, 100)))
eq((slice(0, 100), slice(0, 100)),
normalize_array_selection((slice(None), slice(None), Ellipsis), (100, 100)))

with assert_raises(TypeError):
normalize_array_selection('foo', (100,))
Expand Down
53 changes: 32 additions & 21 deletions zarr/util.py
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Original file line number Diff line number Diff line change
Expand Up @@ -192,29 +192,40 @@ def normalize_array_selection(item, shape):
"""Convenience function to normalize a selection within an array with
the given `shape`."""

# normalize item
if isinstance(item, numbers.Integral):
item = (int(item),)
elif isinstance(item, slice):
# ensure tuple
if not isinstance(item, tuple):
item = (item,)
elif item == Ellipsis:
item = (slice(None),)

# handle tuple of indices/slices
if isinstance(item, tuple):

# determine start and stop indices for all axes
selection = tuple(normalize_axis_selection(i, l)
for i, l in zip(item, shape))

# fill out selection if not completely specified
if len(selection) < len(shape):
selection += tuple(slice(0, l) for l in shape[len(selection):])

return selection

else:
raise TypeError('expected indices or slice, found: %r' % item)
# handle ellipsis
n_ellipsis = sum(1 for i in item if i == Ellipsis)
if n_ellipsis > 1:
raise IndexError("an index can only have a single ellipsis ('...')")
elif n_ellipsis == 1:
n_items_l = item.index(Ellipsis) # items to left of ellipsis
n_items_r = len(item) - (n_items_l + 1) # items to right of ellipsis
n_items = len(item) - 1 # all non-ellipsis items
if n_items >= len(shape):
# ellipsis does nothing, just remove it
item = tuple(i for i in item if i != Ellipsis)
else:
# replace ellipsis with as many slices are needed for number of dims
new_item = item[:n_items_l] + ((slice(None),) * (len(shape) - n_items))
if n_items_r:
new_item += item[-n_items_r:]
item = new_item

# check dimensionality
if len(item) > len(shape):
raise IndexError('too many indices for array')

# determine start and stop indices for all axes
selection = tuple(normalize_axis_selection(i, l) for i, l in zip(item, shape))

# fill out selection if not completely specified
if len(selection) < len(shape):
selection += tuple(slice(0, l) for l in shape[len(selection):])

return selection


def get_chunk_range(selection, chunks):
Expand Down