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[python] Fix ExperimentDataPipe length #1221

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merged 3 commits into from
Jul 8, 2024
Merged

[python] Fix ExperimentDataPipe length #1221

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e6ab9f0
Fix ExperimentDataPipe length
ebezzi Jul 3, 2024
68c1fe1
Update api/python/cellxgene_census/src/cellxgene_census/experimental/…
ebezzi Jul 3, 2024
75dc638
Update api/python/cellxgene_census/tests/experimental/ml/test_pytorch.py
ebezzi Jul 5, 2024
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3 changes: 2 additions & 1 deletion api/python/cellxgene_census/src/cellxgene_census/experimental/ml/pytorch.py
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Original file line number Diff line number Diff line change
Expand Up @@ -631,7 +631,8 @@ def __len__(self) -> int:
self._init()
assert self._obs_joinids is not None

return len(self._obs_joinids)
div, rem = divmod(len(self._obs_joinids), self.batch_size)
return div + bool(rem)

def __getitem__(self, index: int) -> ObsAndXDatum:
raise NotImplementedError("IterDataPipe can only be iterated")
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20 changes: 20 additions & 0 deletions api/python/cellxgene_census/tests/experimental/ml/test_pytorch.py
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Expand Up @@ -519,6 +519,26 @@ def test_experiment_dataloader__batched(soma_experiment: Experiment, use_eager_f
assert batch[1].tolist() == [[0, 0], [1, 1], [2, 2]]


@pytest.mark.experimental
# noinspection PyTestParametrized,DuplicatedCode
@pytest.mark.parametrize(
"obs_range,var_range,X_value_gen,use_eager_fetch",
[(10, 3, pytorch_x_value_gen, use_eager_fetch) for use_eager_fetch in (True, False)],
)
def test_experiment_dataloader__batched_length(soma_experiment: Experiment, use_eager_fetch: bool) -> None:
dp = ExperimentDataPipe(
soma_experiment,
measurement_name="RNA",
X_name="raw",
obs_column_names=["label"],
batch_size=3,
shuffle=False,
use_eager_fetch=use_eager_fetch,
)
dl = experiment_dataloader(dp)
assert len(dl) == len(list(dl))


@pytest.mark.experimental
# noinspection PyTestParametrized,DuplicatedCode
@pytest.mark.parametrize(
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