From 999cd3df306b36ad248b60f59cdcbad9cb7f7b7e Mon Sep 17 00:00:00 2001
From: AliceJoubert <158147135+AliceJoubert@users.noreply.github.com>
Date: Thu, 17 Oct 2024 12:14:15 +0200
Subject: [PATCH] [FIX] Fix logging in OASIS and AIBL converters (#1340)

---
 clinica/iotools/converters/aibl_to_bids/utils/bids.py     | 8 ++++++++
 clinica/iotools/converters/oasis_to_bids/oasis_to_bids.py | 8 ++++++++
 2 files changed, 16 insertions(+)

diff --git a/clinica/iotools/converters/aibl_to_bids/utils/bids.py b/clinica/iotools/converters/aibl_to_bids/utils/bids.py
index 88cfc4327..15a12f21b 100644
--- a/clinica/iotools/converters/aibl_to_bids/utils/bids.py
+++ b/clinica/iotools/converters/aibl_to_bids/utils/bids.py
@@ -630,11 +630,19 @@ def _create_file(
     Path or None :
         Path to file
     """
+    from clinica.cmdline import setup_clinica_logging
     from clinica.iotools.bids_utils import StudyName, bids_id_factory, json_from_dcm
     from clinica.iotools.converter_utils import viscode_to_session
     from clinica.iotools.utils.data_handling import center_nifti_origin
     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")
+
     participant_id = bids_id_factory(StudyName.AIBL).from_original_study_id(
         image.Subjects_ID
     )
diff --git a/clinica/iotools/converters/oasis_to_bids/oasis_to_bids.py b/clinica/iotools/converters/oasis_to_bids/oasis_to_bids.py
index 9f0a1808d..d57ea0e8c 100644
--- a/clinica/iotools/converters/oasis_to_bids/oasis_to_bids.py
+++ b/clinica/iotools/converters/oasis_to_bids/oasis_to_bids.py
@@ -172,9 +172,17 @@ def _create_modality_agnostic_files(self, bids_dir: Path):
 
     @staticmethod
     def convert_single_subject(subj_folder: Path, dest_dir: Path):
+        from clinica.cmdline import setup_clinica_logging
         from clinica.iotools.bids_utils import StudyName, bids_id_factory
         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")
+
         t1_folder = subj_folder / "PROCESSED" / "MPRAGE" / "SUBJ_111"
         cprint(f"Converting {subj_folder.name}", lvl="info")
         participant_id = bids_id_factory(StudyName.OASIS).from_original_study_id(