pass tox tests

Author: AlanKuurstra

heudiconv/tests/test_utils.py

@@ -229,7 +229,7 @@ def test_strptime_dcm_da_tm(tm: str, tm_fmt: str, offset: str, offset_fmt: str)
     da_fmt = "%Y%m%d"
     target = datetime.strptime(da + tm + offset, da_fmt + tm_fmt + offset_fmt)
     ds = dcm.dataset.Dataset()
-    ds["AcquisitionDate"] = dcm.DataElement("AcquisitionDate","DA",da)
+    ds["AcquisitionDate"] = dcm.DataElement("AcquisitionDate", "DA", da)
     ds["AcquisitionTime"] = dcm.DataElement("AcquisitionTime", "TM", tm)
     if offset:
         ds[(0x0008, 0x0201)] = dcm.DataElement((0x0008, 0x0201), "SH", offset)
@@ -269,7 +269,7 @@ def test_strptime_dcm_dt(dt: str, dt_fmt: str, offset: str, offset_fmt: str) ->
     else:
         target = datetime.strptime(dt + offset, dt_fmt + offset_fmt)
     ds = dcm.dataset.Dataset()
-    ds["AcquisitionDateTime"] = dcm.DataElement("AcquisitionDateTime","DT", dt)
+    ds["AcquisitionDateTime"] = dcm.DataElement("AcquisitionDateTime", "DT", dt)
     if offset:
         ds[(0x0008, 0x0201)] = dcm.DataElement((0x0008, 0x0201), "SH", offset)
     assert strptime_dcm_dt(ds, "AcquisitionDateTime") == target

heudiconv/utils.py

@@ -670,7 +670,7 @@ def get_datetime(date: str, time: str, *, microseconds: bool = True) -> str:
     return datetime_str
 
 
-def strptime_micr(date_string: str, fmt: str) -> datetime:
+def strptime_micr(date_string: str, fmt: str) -> datetime.datetime:
     r"""
     Decorate strptime while supporting optional [.%f] in the format at the end
 
@@ -691,15 +691,20 @@ def strptime_micr(date_string: str, fmt: str) -> datetime:
     return datetime.datetime.strptime(date_string, fmt)
 
 
-def datetime_utc_offset(datetime_obj: datetime, utc_offset: str):
+def datetime_utc_offset(datetime_obj: datetime.datetime, utc_offset: str) -> datetime.datetime:
     """set the datetime's tzinfo by parsing an utc offset string"""
-    sign, hours, minutes = re.match(r"([+\-]?)(\d{2})(\d{2})", utc_offset).groups()
+    # https://dicom.innolitics.com/ciods/electromyogram/sop-common/00080201
+    extract_offset = re.match(r"([+\-]?)(\d{2})(\d{2})", utc_offset)
+    if extract_offset is None:
+        raise ValueError(f"utc offset {utc_offset} is not valid")
+    sign, hours, minutes = extract_offset.groups()
     sign = -1 if sign == '-' else 1
     hours, minutes = int(hours), int(minutes)
     tzinfo = datetime.timezone(sign * datetime.timedelta(hours=hours, minutes=minutes))
     return datetime_obj.replace(tzinfo=tzinfo)
 
-def strptime(datetime_string: str, fmts: list[str]) -> datetime:
+
+def strptime(datetime_string: str, fmts: list[str]) -> datetime.datetime:
     r"""
     Try datetime.strptime on a list of formats returning the first successful attempt.
 
@@ -718,7 +723,8 @@ def strptime(datetime_string: str, fmts: list[str]) -> datetime:
             pass
     raise ValueError(f"Unable to parse datetime string: {datetime_str}")
 
-def strptime_bids(datetime_string: str) -> datetime:
+
+def strptime_bids(datetime_string: str) -> datetime.datetime:
     r"""
     Create a datetime object from a bids datetime string.
 
@@ -732,7 +738,8 @@ def strptime_bids(datetime_string: str) -> datetime:
     datetime_obj = strptime(datetime_string, fmts)
     return datetime_obj
 
-def strptime_dcm_da_tm(dcm_data: dcm.Dataset, da_tag: TagType, tm_tag: TagType) -> datetime:
+
+def strptime_dcm_da_tm(dcm_data: dcm.Dataset, da_tag: TagType, tm_tag: TagType) -> datetime.datetime:
     r"""
     Create a datetime object from a dicom DA tag and TM tag.
 
@@ -756,12 +763,13 @@ def strptime_dcm_da_tm(dcm_data: dcm.Dataset, da_tag: TagType, tm_tag: TagType)
 
     datetime_obj = datetime.datetime.combine(date.date(), time.time())
 
-    if utc_offset_dcm := dcm_data.get([0x0008, 0x0201]):
+    if utc_offset_dcm := dcm_data.get((0x0008, 0x0201)):
         utc_offset = utc_offset_dcm.value.strip()
         datetime_obj = datetime_utc_offset(datetime_obj, utc_offset) if utc_offset else datetime_obj
     return datetime_obj
 
-def strptime_dcm_dt(dcm_data: dcm.Dataset, dt_tag: TagType) -> datetime:
+
+def strptime_dcm_dt(dcm_data: dcm.Dataset, dt_tag: TagType) -> datetime.datetime:
     r"""
     Create a datetime object from a dicom DT tag.
 
@@ -779,13 +787,13 @@ def strptime_dcm_dt(dcm_data: dcm.Dataset, dt_tag: TagType) -> datetime:
             "%Y", "%Y%m", "%Y%m%d", "%Y%m%d%H", "%Y%m%d%H%M", "%Y%m%d%H%M%S", "%Y%m%d%H%M%S.%f"]
     datetime_obj = strptime(datetime_str, fmts)
 
-    if utc_offset_dcm := dcm_data.get([0x0008, 0x0201]):
+    if utc_offset_dcm := dcm_data.get((0x0008, 0x0201)):
         if utc_offset := utc_offset_dcm.value.strip():
-             datetime_obj2 = datetime_utc_offset(datetime_obj, utc_offset)
-             if datetime_obj.tzinfo and datetime_obj2 != datetime_obj:
-                 lgr.warning("Unexpectedly previously parsed datetime %s contains zoneinfo which is different from the one obtained from DICOMs UTFOffset field: %s", datetime_obj, datetime_obj2)
-             else:
-                 datetime_obj = datetime_obj2 
+            datetime_obj2 = datetime_utc_offset(datetime_obj, utc_offset)
+            if datetime_obj.tzinfo and datetime_obj2 != datetime_obj:
+                lgr.warning("Unexpectedly previously parsed datetime %s contains zoneinfo which is different from the one obtained from DICOMs UTFOffset field: %s", datetime_obj, datetime_obj2)
+            else:
+                datetime_obj = datetime_obj2
     return datetime_obj