File size: 5,393 Bytes
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import pickle as pkl
from medimeta import MedIMeta
from torchcross.data.metadataset import (
FewShotMetaDataset,
SubTaskRandomFewShotMetaDataset,
)
from torchcross.data.task import Task
overwrite = False
def available_tasks(data_path) -> list[tuple[str, str]]:
task_dict = MedIMeta.get_available_tasks(data_path)
return [(dataset, task) for dataset, tasks in task_dict.items() for task in tasks]
def create_few_shot_tasks(
data_path,
dataset_id: str,
task_name: str,
n_support: int,
n_query: int,
length: int,
split: str | list[str] | None = None,
) -> list[Task]:
task_source = MedIMeta(data_path, dataset_id, task_name, split=split)
few_shot = FewShotMetaDataset(
task_source, None, n_support, n_query, length=length, output_indices=True
)
print(
f"Creating {length} few-shot tasks for: {dataset_id} {task_name} {n_support} {n_query}"
)
try:
print("Length: ", len(few_shot))
except ValueError:
print("Length: None")
task_list = [t for t in few_shot]
print("Total: ", len(task_list))
return task_list
def create_random_few_shot_tasks(
data_path,
dataset_id: str,
task_name: str,
n_support_min: int,
n_support_max: int,
n_query: int,
length: int,
split: str | list[str] | None = None,
) -> list[Task]:
task_source = MedIMeta(data_path, dataset_id, task_name, split=split)
few_shot = SubTaskRandomFewShotMetaDataset(
task_source,
None,
n_support_samples_per_class_min=n_support_min,
n_support_samples_per_class_max=n_support_max,
n_query_samples_per_class=n_query,
length=length,
output_indices=True,
)
print(
f"Creating {length} few-shot tasks for: {dataset_id} {task_name} {n_support_min}-{n_support_max} {n_query}"
)
try:
print("Length: ", len(few_shot))
except ValueError:
print("Length: None")
task_list = [t for t in few_shot]
print("Total: ", len(task_list))
return task_list
def save_few_shot_tasks(data_path, save_path=None, split=None):
n_query = 10
length = 100
os.makedirs(save_path, exist_ok=True)
# create few-shot instances for all tasks and all nshot values
# and save them to pkl files
for dataset, task in available_tasks(data_path):
for n_support in [1, 2, 3, 5, 7, 10, 15, 20, 25, 30]:
few_shot_tasks = create_few_shot_tasks(
data_path, dataset, task, n_support, n_query, length, split
)
if few_shot_tasks is None:
continue
file_name = f"{task}_{n_support}_{n_query}_{length}.pkl"
if split is not None:
if isinstance(split, str):
file_name = f"{file_name[:-4]}_{split}.pkl"
else:
file_name = f"{file_name[:-4]}_{'-'.join(split)}.pkl"
file_path = os.path.join(save_path, dataset, file_name)
os.makedirs(os.path.dirname(file_path), exist_ok=True)
if os.path.exists(file_path) and not overwrite:
raise FileExistsError(
f"File {file_name} already exists. Set overwrite to True to overwrite."
)
with open(file_path, "wb") as f:
pkl.dump(few_shot_tasks, f)
def save_random_few_shot_tasks(data_path, save_path=None, split=None):
n_query = 10
length = 1000
n_support_min = 1
n_support_max = 10
os.makedirs(save_path, exist_ok=True)
for dataset, task in available_tasks(data_path):
few_shot_tasks = create_random_few_shot_tasks(
data_path,
dataset,
task,
n_support_min,
n_support_max,
n_query,
length,
split,
)
if few_shot_tasks is None:
continue
file_name = f"{task}_{n_support_min}-{n_support_max}_{n_query}_{length}.pkl"
if split is not None:
if isinstance(split, str):
file_name = f"{file_name[:-4]}_{split}.pkl"
else:
file_name = f"{file_name[:-4]}_{'-'.join(split)}.pkl"
file_path = os.path.join(save_path, dataset, file_name)
os.makedirs(os.path.dirname(file_path), exist_ok=True)
if os.path.exists(file_path) and not overwrite:
raise FileExistsError(
f"File {file_name} already exists. Set overwrite to True to overwrite."
)
with open(file_path, "wb") as f:
pkl.dump(few_shot_tasks, f)
def main():
import argparse
parser = argparse.ArgumentParser()
parser.add_argument("--data_path", type=str, default="data/MedIMeta")
parser.add_argument("--save_path", type=str, default="data/MedIMeta_presampled2")
parser.add_argument("--split", type=str, default=None)
args = parser.parse_args()
data_path = args.data_path
save_path = args.save_path
split = args.split
if split is not None:
split = split.split("-")
if isinstance(split, list) and len(split) == 1:
split = split[0]
print("Available tasks:")
print(available_tasks(data_path))
save_few_shot_tasks(data_path, save_path, split)
save_random_few_shot_tasks(data_path, save_path, split)
if __name__ == "__main__":
main()
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