fix log and output folder for dcm2bids_helper

UNFmontreal · Jul 24, 2024 · 386d413 · 386d413
1 parent 1d74109
commit 386d413
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Showing 2 changed files with 15 additions and 10 deletions.
diff --git a/dcm2bids/cli/dcm2bids_helper.py b/dcm2bids/cli/dcm2bids_helper.py
@@ -15,7 +15,6 @@
 from dcm2bids.utils.utils import DEFAULT
 from dcm2bids.utils.tools import dcm2niix_version, check_latest
 from dcm2bids.utils.logger import setup_logging
-from dcm2bids.utils.args import assert_dirs_empty
 from dcm2bids.version import __version__
 
 
@@ -59,12 +58,22 @@ def main():
     """Let's go"""
     parser = _build_arg_parser()
     args = parser.parse_args()
-    out_dir = Path(args.output_dir)
-    log_file = (Path(DEFAULT.output_dir)
-                / DEFAULT.tmp_dir_name
-                / "log"
-                / f"helper_{datetime.now().strftime('%Y%m%d-%H%M%S')}.log")
 
+    out_dir = Path(args.output_dir)
+    if args.output_dir != parser.get_default('output_dir'):
+        out_dir = (Path(args.output_dir)
+                   / DEFAULT.tmp_dir_name
+                   / DEFAULT.helper_dir)
+
+        log_file = (Path(args.output_dir)
+                    / DEFAULT.tmp_dir_name
+                    / "log"
+                    / f"helper_{datetime.now().strftime('%Y%m%d-%H%M%S')}.log")
+    else:
+        log_file = (Path(DEFAULT.output_dir)
+                    / DEFAULT.tmp_dir_name
+                    / "log"
+                    / f"helper_{datetime.now().strftime('%Y%m%d-%H%M%S')}.log")
     if args.nest:
         if isinstance(args.nest, str):
             log_file = Path(
@@ -94,8 +103,6 @@ def main():
     check_latest("dcm2bids")
     check_latest("dcm2niix")
 
-    assert_dirs_empty(parser, args, out_dir)
-
     app = Dcm2niixGen(dicom_dirs=args.dicom_dir, bids_dir=out_dir, helper=True)
 
     rsl = app.run(force=args.overwrite)

diff --git a/dcm2bids/dcm2niix_gen.py b/dcm2bids/dcm2niix_gen.py
@@ -151,8 +151,6 @@ def execute(self):
                 else:
                     self.logger.debug(f"\n{output}")
                     self.logger.info("Check log file for dcm2niix output\n")
-
-
         else:
             for dicomDir in self.dicom_dirs:
                 shutil.copytree(dicomDir, self.output_dir, dirs_exist_ok=True)