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| 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.*") |
|
|
| 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", |
| "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 |
|
|
