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Merged
wyli merged 4 commits into from
Mar 1, 2022
Merged

Update CSVDataset in dataset.py #3529

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1ba2a83
Update CSVDataset in dataset.py
nvahmadi Dec 21, 2021
eb45470
Update dataset.py
wyli Mar 1, 2022
e4ead32
Merge branch 'dev' into dev
wyli Mar 1, 2022
ec9ae20
Update iterable_dataset.py
wyli Mar 1, 2022
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4 changes: 3 additions & 1 deletion monai/data/dataset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1342,6 +1342,7 @@ class CSVDataset(Dataset):
be the new column name, the `value` is the names of columns to combine. for example:
`col_groups={"ehr": [f"ehr_{i}" for i in range(10)], "meta": ["meta_1", "meta_2"]}`
transform: transform to apply on the loaded items of a dictionary data.
kwargs_read_csv: dictionary args to pass to pandas `read_csv` function.
kwargs: additional arguments for `pandas.merge()` API to join tables.

.. deprecated:: 0.8.0
Expand All @@ -1358,13 +1359,14 @@ def __init__(
col_types: Optional[Dict[str, Optional[Dict[str, Any]]]] = None,
col_groups: Optional[Dict[str, Sequence[str]]] = None,
transform: Optional[Callable] = None,
kwargs_read_csv: Optional[Dict] = None,
**kwargs,
):
srcs = (src,) if not isinstance(src, (tuple, list)) else src
dfs: List = []
for i in srcs:
if isinstance(i, str):
dfs.append(pd.read_csv(i))
dfs.append(pd.read_csv(i, **kwargs_read_csv) if kwargs_read_csv else pd.read_csv(i))
elif isinstance(i, pd.DataFrame):
dfs.append(i)
else:
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5 changes: 4 additions & 1 deletion monai/data/iterable_dataset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -176,6 +176,7 @@ class CSVIterableDataset(IterableDataset):
seed: random seed to initialize the random state for all the workers if `shuffle` is True,
set `seed += 1` in every iter() call, refer to the PyTorch idea:
https://github.com/pytorch/pytorch/blob/v1.10.0/torch/utils/data/distributed.py#L98.
kwargs_read_csv: dictionary args to pass to pandas `read_csv` function. Default to ``{"chunksize", chunksize}``.
kwargs: additional arguments for `pandas.merge()` API to join tables.

.. deprecated:: 0.8.0
Expand All @@ -195,6 +196,7 @@ def __init__(
transform: Optional[Callable] = None,
shuffle: bool = False,
seed: int = 0,
kwargs_read_csv: Optional[Dict] = None,
**kwargs,
):
self.src = src
Expand All @@ -205,6 +207,7 @@ def __init__(
self.col_groups = col_groups
self.shuffle = shuffle
self.seed = seed
self.kwargs_read_csv = kwargs_read_csv or {"chunksize", chunksize}
# in case treating deprecated arg `filename` as kwargs, remove it from `kwargs`
kwargs.pop("filename", None)
self.kwargs = kwargs
Expand All @@ -230,7 +233,7 @@ def reset(self, src: Optional[Union[Union[str, Sequence[str]], Union[Iterable, S
self.iters = []
for i in srcs:
if isinstance(i, str):
self.iters.append(pd.read_csv(i, chunksize=self.chunksize))
self.iters.append(pd.read_csv(i, **self.kwargs_read_csv))
elif isinstance(i, Iterable):
self.iters.append(i)
else:
Expand Down