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1353 optional progress bar for lmdbdataset #1354

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Merged
wyli merged 2 commits into from
Dec 11, 2020
Merged

1353 optional progress bar for lmdbdataset #1354

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a82d9f5
fixes #1353
wyli Dec 11, 2020
549a172
Merge branch 'master' into 1353-lmdbdataset-pbar
wyli Dec 11, 2020
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7 changes: 5 additions & 2 deletions monai/data/dataset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -321,6 +321,7 @@ def __init__(
cache_dir: Union[Path, str] = "cache",
hash_func: Callable[..., bytes] = pickle_hashing,
db_name: str = "monai_cache",
progress: bool = True,
pickle_protocol=pickle.HIGHEST_PROTOCOL,
lmdb_kwargs: Optional[dict] = None,
) -> None:
Expand All @@ -338,6 +339,7 @@ def __init__(
hash_func: a callable to compute hash from data items to be cached.
defaults to `monai.data.utils.pickle_hashing`.
db_name: lmdb database file name. Defaults to "monai_cache".
progress: whether to display a progress bar.
pickle_protocol: pickle protocol version. Defaults to pickle.HIGHEST_PROTOCOL.
https://docs.python.org/3/library/pickle.html#pickle-protocols
lmdb_kwargs: additional keyword arguments to the lmdb environment.
Expand All @@ -352,15 +354,16 @@ def __init__(
if not self.lmdb_kwargs.get("map_size", 0):
self.lmdb_kwargs["map_size"] = 1024 ** 4 # default map_size
self._read_env = None
self.progress = progress
print(f"Accessing lmdb file: {self.db_file.absolute()}.")

def _fill_cache_start_reader(self):
# create cache
print(f"Accessing lmdb file: {self.db_file.absolute()}.")
self.lmdb_kwargs["readonly"] = False
env = lmdb.open(path=f"{self.db_file}", subdir=False, **self.lmdb_kwargs)
if not has_tqdm:
warnings.warn("LMDBDataset: tqdm is not installed. not displaying the caching progress.")
for item in tqdm(self.data) if has_tqdm else self.data:
for item in tqdm(self.data) if has_tqdm and self.progress else self.data:
key = self.hash_func(item)
done, retry, val = False, 5, None
while not done and retry > 0:
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8 changes: 6 additions & 2 deletions tests/test_lmdbdataset.py
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Expand Up @@ -144,11 +144,15 @@ def test_shape(self, transform, expected_shape, kwargs=None):
]

cache_dir = os.path.join(os.path.join(tempdir, "cache"), "data")
dataset_precached = LMDBDataset(data=test_data, transform=transform, cache_dir=cache_dir, **kwargs)
dataset_precached = LMDBDataset(
data=test_data, transform=transform, progress=False, cache_dir=cache_dir, **kwargs
)
data1_precached = dataset_precached[0]
data2_precached = dataset_precached[1]

dataset_postcached = LMDBDataset(data=test_data, transform=transform, cache_dir=cache_dir, **kwargs)
dataset_postcached = LMDBDataset(
data=test_data, transform=transform, progress=False, cache_dir=cache_dir, **kwargs
)
data1_postcached = dataset_postcached[0]
data2_postcached = dataset_postcached[1]

Expand Down