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# Copyright (c) MONAI Consortium
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
import logging
import os
import warnings
from logging.config import fileConfig
from pathlib import Path
import numpy as np
from monai.apps import get_logger
from monai.apps.utils import DEFAULT_FMT
from monai.bundle import ConfigParser
from monai.utils import RankFilter, ensure_tuple
logger = get_logger("VistaCell")
np.set_printoptions(formatter={"float": "{: 0.3f}".format}, suppress=True)
logging.getLogger("torch.nn.parallel.distributed").setLevel(logging.WARNING)
warnings.filterwarnings("ignore", message=".*Divide by zero.*") # intensity transform divide by zero warning
LOGGING_CONFIG = {
"version": 1,
"disable_existing_loggers": False,
"formatters": {"monai_default": {"format": DEFAULT_FMT}},
"loggers": {"VistaCell": {"handlers": ["file", "console"], "level": "DEBUG", "propagate": False}},
"filters": {"rank_filter": {"()": RankFilter}},
"handlers": {
"file": {
"class": "logging.FileHandler",
"filename": "default.log",
"mode": "a", # append or overwrite
"level": "DEBUG",
"formatter": "monai_default",
"filters": ["rank_filter"],
},
"console": {
"class": "logging.StreamHandler",
"level": "INFO",
"formatter": "monai_default",
"filters": ["rank_filter"],
},
},
}
def parsing_bundle_config(config_file, logging_file=None, meta_file=None):
if config_file is not None:
_config_files = ensure_tuple(config_file)
config_root_path = Path(_config_files[0]).parent
for _config_file in _config_files:
_config_file = Path(_config_file)
if _config_file.parent != config_root_path:
logger.warning(
f"Not all config files are in '{config_root_path}'. If logging_file and meta_file are"
f"not specified, '{config_root_path}' will be used as the default config root directory."
)
if not _config_file.is_file():
raise FileNotFoundError(f"Cannot find the config file: {_config_file}.")
else:
config_root_path = Path("configs")
logging_file = str(config_root_path / "logging.conf") if logging_file is None else logging_file
if os.path.exists(logging_file):
fileConfig(logging_file, disable_existing_loggers=False)
parser = ConfigParser()
parser.read_config(config_file)
meta_file = str(config_root_path / "metadata.json") if meta_file is None else meta_file
if isinstance(meta_file, str) and not os.path.exists(meta_file):
logger.error(
f"Cannot find the metadata config file: {meta_file}. "
"Please see: https://docs.monai.io/en/stable/mb_specification.html"
)
else:
parser.read_meta(f=meta_file)
return parser
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