Catch age parsing exceptions

Donders-Institute · Apr 25, 2024 · 997b39c · 997b39c
1 parent 5bac582
commit 997b39c
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Showing 2 changed files with 23 additions and 17 deletions.
diff --git a/bidscoin/plugins/dcm2niix2bids.py b/bidscoin/plugins/dcm2niix2bids.py
@@ -531,14 +531,17 @@ def bidscoiner_plugin(session: Path, bidsmap: Bidsmap, bidsses: Path) -> Union[N
 
     # Collect personal data for the participants.tsv file
     if dataformat == 'DICOM':                               # PAR does not contain personal info
-        personals = {}
-        age       = datasource.attributes('PatientAge')     # A string of characters with one of the following formats: nnnD, nnnW, nnnM, nnnY
-        if   age.endswith('D'): age = float(age.rstrip('D')) / 365.2524
-        elif age.endswith('W'): age = float(age.rstrip('W')) / 52.1775
-        elif age.endswith('M'): age = float(age.rstrip('M')) / 12
-        elif age.endswith('Y'): age = float(age.rstrip('Y'))
-        if age and options.get('anon','y') in ('y','yes'):
-            age = int(float(age))
+        age = datasource.attributes('PatientAge')           # A string of characters with one of the following formats: nnnD, nnnW, nnnM, nnnY
+        try:
+            if   age.endswith('D'): age = float(age.rstrip('D')) / 365.2524
+            elif age.endswith('W'): age = float(age.rstrip('W')) / 52.1775
+            elif age.endswith('M'): age = float(age.rstrip('M')) / 12
+            elif age.endswith('Y'): age = float(age.rstrip('Y'))
+            if age and options.get('anon','y') in ('y','yes'):
+                age = int(float(age))
+        except Exception as exc:
+            LOGGER.warning(f"Could not parse age from: {datasource.path}\n{exc}")
+        personals           = {}
         personals['age']    = str(age)
         personals['sex']    = datasource.attributes('PatientSex')
         personals['size']   = datasource.attributes('PatientSize')

diff --git a/bidscoin/plugins/spec2nii2bids.py b/bidscoin/plugins/spec2nii2bids.py
@@ -317,15 +317,18 @@ def bidscoiner_plugin(session: Path, bidsmap: Bidsmap, bidsses: Path) -> Union[N
         try:
             age = dateutil.parser.parse(datasource.attributes('rhr_rh_scan_date')) - dateutil.parser.parse(datasource.attributes('rhe_dateofbirth'))
             age = str(age.days) + 'D'
-        except dateutil.parser.ParserError as dateerror:
+        except dateutil.parser.ParserError as exc:
             pass
-    if   age.endswith('D'): age = float(age.rstrip('D')) / 365.2524
-    elif age.endswith('W'): age = float(age.rstrip('W')) / 52.1775
-    elif age.endswith('M'): age = float(age.rstrip('M')) / 12
-    elif age.endswith('Y'): age = float(age.rstrip('Y'))
-    if age:
-        if options.get('anon',OPTIONS['anon']) in ('y','yes'):
-            age = int(float(age))
-        personals['age'] = str(age)
+    try:
+        if   age.endswith('D'): age = float(age.rstrip('D')) / 365.2524
+        elif age.endswith('W'): age = float(age.rstrip('W')) / 52.1775
+        elif age.endswith('M'): age = float(age.rstrip('M')) / 12
+        elif age.endswith('Y'): age = float(age.rstrip('Y'))
+        if age:
+            if options.get('anon',OPTIONS['anon']) in ('y','yes'):
+                age = int(float(age))
+            personals['age'] = str(age)
+    except Exception as exc:
+        LOGGER.warning(f"Could not parse age from: {datasource.path}\n{exc}")
 
     return personals