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Fixes ensembling with sigmoid #6588

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merged 4 commits into from
Jun 8, 2023
Merged

Fixes ensembling with sigmoid #6588

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9f7fe69
ens sigm
myron Jun 7, 2023
f51fd55
Merge remote-tracking branch 'upstream/dev' into ensem_sigm
myron Jun 7, 2023
6d727ba
update sigmoid handling for ensembling
myron Jun 7, 2023
d6371a3
Merge branch 'dev' into ensem_sigm
wyli Jun 8, 2023
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3 changes: 3 additions & 0 deletions monai/apps/auto3dseg/auto_runner.py
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Original file line number Diff line number Diff line change
Expand Up @@ -292,6 +292,9 @@ def __init__(
self.search_space: dict[str, dict[str, Any]] = {}
self.hpo_tasks = 0

if "sigmoid" not in self.kwargs and "sigmoid" in self.data_src_cfg:
self.kwargs["sigmoid"] = self.data_src_cfg["sigmoid"]

def read_cache(self):
"""
Check if the intermediate result is cached after each step in the current working directory
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8 changes: 2 additions & 6 deletions monai/apps/auto3dseg/ensemble_builder.py
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Expand Up @@ -586,14 +586,10 @@ def ensemble(self):
if len(infer_files) == 0:
logger.info("No testing files for inference is provided. Ensembler ending.")
return
infer_files = (
partition_dataset(data=infer_files, shuffle=False, num_partitions=len(infer_files))[self.rank]
if self.rank < len(infer_files)
else []
)
infer_files = [infer_files[self.rank]] if self.rank < len(infer_files) else []
else:
infer_files = partition_dataset(
data=infer_files, shuffle=False, num_partitions=self.world_size, even_divisible=True
data=infer_files, shuffle=False, num_partitions=self.world_size, even_divisible=False
)[self.rank]

# TO DO: Add some function in ensembler for infer_files update?
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