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RF: Use safe resizing for ArraySequence extension #724

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Merged
merged 2 commits into from
Feb 12, 2019
Merged

RF: Use safe resizing for ArraySequence extension #724

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84fa165
TEST: Extending ArraySequences corrupts sliced data
effigies Feb 7, 2019
989e6bb
RF: Use _safe_resize helper function
effigies Feb 8, 2019
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12 changes: 11 additions & 1 deletion nibabel/streamlines/array_sequence.py
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Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,16 @@ def is_ndarray_of_int_or_bool(obj):
np.issubdtype(obj.dtype, np.bool_)))


def _safe_resize(a, shape):
""" Resize an ndarray safely, using minimal memory """
try:
a.resize(shape)
except ValueError:
a = a.copy()
a.resize(shape, refcheck=False)
return a


class _BuildCache(object):
def __init__(self, arr_seq, common_shape, dtype):
self.offsets = list(arr_seq._offsets)
Expand Down Expand Up @@ -196,7 +206,7 @@ def _resize_data_to(self, n_rows, build_cache):
if self._data.size == 0:
self._data = np.empty(new_shape, dtype=build_cache.dtype)
else:
self._data.resize(new_shape)
self._data = _safe_resize(self._data, new_shape)

def shrink_data(self):
self._data.resize((self._get_next_offset(),) + self.common_shape,
Expand Down
4 changes: 4 additions & 0 deletions nibabel/streamlines/tests/test_array_sequence.py
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Expand Up @@ -219,6 +219,10 @@ def test_arraysequence_extend(self):
seq = SEQ_DATA['seq'].copy() # Copy because of in-place modification.
assert_raises(ValueError, seq.extend, data)

# Extend after extracting some slice
working_slice = seq[:2]
seq.extend(ArraySequence(new_data))

def test_arraysequence_getitem(self):
# Get one item
for i, e in enumerate(SEQ_DATA['seq']):
Expand Down