[FIX] Fix logging in adni to bids (#1181)

* refactor slightly the logging configuration logic * re-configure the clinica logger in child processes (not optimal but better) * Update clinica/iotools/converters/adni_to_bids/adni_utils.py Co-authored-by: AliceJoubert <[email protected]> --------- Co-authored-by: AliceJoubert <[email protected]>
aramis-lab · May 17, 2024 · 7f7a0b4 · 7f7a0b4
1 parent 0871d35
commit 7f7a0b4
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Showing 2 changed files with 34 additions and 16 deletions.
diff --git a/clinica/cmdline.py b/clinica/cmdline.py
@@ -32,29 +32,24 @@ def setup_logging(verbose: bool = False) -> None:
             (0 (default): WARNING, 1: INFO, 2: DEBUG)
     """
     import logging
-    import sys
-    from logging.handlers import RotatingFileHandler as RFHandler
-
-    import nipype
-    from colorlog import ColoredFormatter, StreamHandler
 
     logging_level = "DEBUG" if verbose else "INFO"
-
     # Root logger configuration.
     root_logger = logging.getLogger()
     root_logger.setLevel(logging_level)
-
     # Clinica logger configuration.
-    clinica_logger = logging.getLogger("clinica")
-    clinica_logger.setLevel(logging_level)
-    console_handler = StreamHandler(stream=sys.stdout)
-    console_handler.setFormatter(
-        ColoredFormatter("%(log_color)s%(asctime)s:%(levelname)s:%(message)s")
-    )
-    clinica_logger.addHandler(console_handler)
-
+    setup_clinica_logging(logging_level)
     # Nipype logger configuration.
-    # Monkey-patch nipype to use Python's RFH logger.
+    setup_nipype_logging()
+
+
+def setup_nipype_logging():
+    """Monkey-patch nipype to use Python's RFH logger."""
+    import logging
+    from logging.handlers import RotatingFileHandler as RFHandler
+
+    import nipype
+
     nipype.utils.logger.RFHandler = RFHandler
     # Setup debug logging to file.
     nipype.config.enable_debug_mode()
@@ -74,6 +69,21 @@ def setup_logging(verbose: bool = False) -> None:
     nipype_logger.addHandler(logging.NullHandler())
 
 
+def setup_clinica_logging(logging_level: str):
+    import logging
+    import sys
+
+    from colorlog import ColoredFormatter, StreamHandler
+
+    clinica_logger = logging.getLogger("clinica")
+    clinica_logger.setLevel(logging_level)
+    console_handler = StreamHandler(stream=sys.stdout)
+    console_handler.setFormatter(
+        ColoredFormatter("%(log_color)s%(asctime)s:%(levelname)s:%(message)s")
+    )
+    clinica_logger.addHandler(console_handler)
+
+
 @click.group(context_settings=CONTEXT_SETTINGS)
 @click.version_option(version=clinica.__version__)
 @click.option("-v", "--verbose", is_flag=True, help="Increase logging verbosity.")

diff --git a/clinica/iotools/converters/adni_to_bids/adni_utils.py b/clinica/iotools/converters/adni_to_bids/adni_utils.py
@@ -1344,12 +1344,20 @@ def create_file(
 
     import numpy as np
 
+    from clinica.cmdline import setup_clinica_logging
     from clinica.iotools.bids_utils import run_dcm2niix
     from clinica.iotools.converter_utils import viscode_to_session
     from clinica.iotools.utils.data_handling import center_nifti_origin
     from clinica.utils.pet import ReconstructionMethod, Tracer
     from clinica.utils.stream import cprint
 
+    # This function is executed in a multiprocessing context
+    # such that we need to re-configure the clinica logger in the child processes.
+    # Note that logging messages could easily be lost (for example when logging
+    # to a file from two different processes). A better solution would be to
+    # implement a logging process consuming logging messages from a multiprocessing.Queue...
+    setup_clinica_logging("INFO")
+
     modality_specific = {
         "t1": {
             "output_path": "anat",