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from multiprocessing import Pool
from typing import Union, Tuple
import numpy as np
from batchgenerators.utilities.file_and_folder_operations import *
from nnunetv2.configuration import default_num_processes
from nnunetv2.paths import nnUNet_results
from nnunetv2.utilities.dataset_name_id_conversion import maybe_convert_to_dataset_name
def convert_trainer_plans_config_to_identifier(trainer_name, plans_identifier, configuration):
return f'{trainer_name}__{plans_identifier}__{configuration}'
def convert_identifier_to_trainer_plans_config(identifier: str):
return os.path.basename(identifier).split('__')
def get_output_folder(dataset_name_or_id: Union[str, int], trainer_name: str = 'nnUNetTrainer',
plans_identifier: str = 'nnUNetPlans', configuration: str = '3d_fullres',
fold: Union[str, int] = None) -> str:
tmp = join(nnUNet_results, maybe_convert_to_dataset_name(dataset_name_or_id),
convert_trainer_plans_config_to_identifier(trainer_name, plans_identifier, configuration))
if fold is not None:
tmp = join(tmp, f'fold_{fold}')
return tmp
def parse_dataset_trainer_plans_configuration_from_path(path: str):
folders = split_path(path)
# this here can be a little tricky because we are making assumptions. Let's hope this never fails lol
# safer to make this depend on two conditions, the fold_x and the DatasetXXX
# first let's see if some fold_X is present
fold_x_present = [i.startswith('fold_') for i in folders]
if any(fold_x_present):
idx = fold_x_present.index(True)
# OK now two entries before that there should be DatasetXXX
assert len(folders[:idx]) >= 2, 'Bad path, cannot extract what I need. Your path needs to be at least ' \
'DatasetXXX/MODULE__PLANS__CONFIGURATION for this to work'
if folders[idx - 2].startswith('Dataset'):
splitted = folders[idx - 1].split('__')
assert len(splitted) == 3, 'Bad path, cannot extract what I need. Your path needs to be at least ' \
'DatasetXXX/MODULE__PLANS__CONFIGURATION for this to work'
return folders[idx - 2], *splitted
else:
# we can only check for dataset followed by a string that is separable into three strings by splitting with '__'
# look for DatasetXXX
dataset_folder = [i.startswith('Dataset') for i in folders]
if any(dataset_folder):
idx = dataset_folder.index(True)
assert len(folders) >= (idx + 1), 'Bad path, cannot extract what I need. Your path needs to be at least ' \
'DatasetXXX/MODULE__PLANS__CONFIGURATION for this to work'
splitted = folders[idx + 1].split('__')
assert len(splitted) == 3, 'Bad path, cannot extract what I need. Your path needs to be at least ' \
'DatasetXXX/MODULE__PLANS__CONFIGURATION for this to work'
return folders[idx], *splitted
def get_ensemble_name(model1_folder, model2_folder, folds: Tuple[int, ...]):
identifier = 'ensemble___' + os.path.basename(model1_folder) + '___' + \
os.path.basename(model2_folder) + '___' + folds_tuple_to_string(folds)
return identifier
def get_ensemble_name_from_d_tr_c(dataset, tr1, p1, c1, tr2, p2, c2, folds: Tuple[int, ...]):
model1_folder = get_output_folder(dataset, tr1, p1, c1)
model2_folder = get_output_folder(dataset, tr2, p2, c2)
get_ensemble_name(model1_folder, model2_folder, folds)
def convert_ensemble_folder_to_model_identifiers_and_folds(ensemble_folder: str):
prefix, *models, folds = os.path.basename(ensemble_folder).split('___')
return models, folds
def folds_tuple_to_string(folds: Union[List[int], Tuple[int, ...]]):
s = str(folds[0])
for f in folds[1:]:
s += f"_{f}"
return s
def folds_string_to_tuple(folds_string: str):
folds = folds_string.split('_')
res = []
for f in folds:
try:
res.append(int(f))
except ValueError:
res.append(f)
return res
def check_workers_alive_and_busy(export_pool: Pool, worker_list: List, results_list: List, allowed_num_queued: int = 0):
"""
returns True if the number of results that are not ready is greater than the number of available workers + allowed_num_queued
"""
alive = [i.is_alive() for i in worker_list]
if not all(alive):
raise RuntimeError('Some background workers are no longer alive')
not_ready = [not i.ready() for i in results_list]
if sum(not_ready) >= (len(export_pool._pool) + allowed_num_queued):
return True
return False
if __name__ == '__main__':
### well at this point I could just write tests...
path = '/home/fabian/results/nnUNet_remake/Dataset002_Heart/nnUNetModule__nnUNetPlans__3d_fullres'
print(parse_dataset_trainer_plans_configuration_from_path(path))
path = 'Dataset002_Heart/nnUNetModule__nnUNetPlans__3d_fullres'
print(parse_dataset_trainer_plans_configuration_from_path(path))
path = '/home/fabian/results/nnUNet_remake/Dataset002_Heart/nnUNetModule__nnUNetPlans__3d_fullres/fold_all'
print(parse_dataset_trainer_plans_configuration_from_path(path))
try:
path = '/home/fabian/results/nnUNet_remake/Dataset002_Heart/'
print(parse_dataset_trainer_plans_configuration_from_path(path))
except AssertionError:
print('yayy, assertion works')
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