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Fixed bug when reading empty object buffer with empty idx list #126

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merged 3 commits into from
Dec 20, 2024
Merged

Fixed bug when reading empty object buffer with empty idx list #126

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a7b5454
Added tests for empty idx lists and sparse idx list with no events in…
Dec 20, 2024
98a1be8
Added fix for bug when reading into empty object buffer with empty id…
Dec 20, 2024
b0b6f97
style: pre-commit fixes
pre-commit-ci[bot] Dec 20, 2024
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5 changes: 3 additions & 2 deletions src/lgdo/lh5/_serializers/read/vector_of_vectors.py
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Original file line number Diff line number Diff line change
Expand Up @@ -189,8 +189,9 @@ def _h5_read_vector_of_vectors(
# if the buffer is partially filled, cumulative_length will be invalid
# (i.e. non monotonically increasing). Let's fix that but filling the
# rest of the array with the length of flattened_data
end = obj_buf_start + n_rows_read
obj_buf.cumulative_length.nda[end:] = obj_buf.cumulative_length.nda[end - 1]
if n_rows_read > 0:
end = obj_buf_start + n_rows_read
obj_buf.cumulative_length.nda[end:] = obj_buf.cumulative_length.nda[end - 1]

return obj_buf, n_rows_read

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14 changes: 14 additions & 0 deletions tests/lh5/test_lh5_store.py
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Original file line number Diff line number Diff line change
Expand Up @@ -292,6 +292,10 @@ def test_read_table_fancy_idx(lh5_file):
assert isinstance(lh5_obj, types.Table)
assert n_rows == 2

lh5_obj, n_rows = store.read("/data/struct/table", lh5_file, idx=[])
assert isinstance(lh5_obj, types.Table)
assert n_rows == 0


def test_read_empty_struct(lh5_file):
store = lh5.LH5Store()
Expand Down Expand Up @@ -468,6 +472,16 @@ def test_read_lgnd_vov_fancy_idx(lgnd_file):
assert (lh5_obj.cumulative_length.nda == [1, 2, 3, 4, 5, 6, 7]).all()
assert (lh5_obj.flattened_data.nda == [40, 60, 64, 60, 64, 28, 60]).all()

lh5_obj, n_rows = store.read("/geds/raw/tracelist", lgnd_file, idx=[])
assert isinstance(lh5_obj, types.VectorOfVectors)
assert n_rows == 0
assert len(lh5_obj) == 0

lh5_obj, n_rows = store.read("/geds/raw/tracelist", [lgnd_file] * 3, idx=[250])
assert isinstance(lh5_obj, types.VectorOfVectors)
assert n_rows == 1
assert len(lh5_obj) == 1


def test_read_array_concatenation(lgnd_file):
store = lh5.LH5Store()
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