Move datetime to new util function and add test.

Author: tsalo

heudiconv/bids.py

@@ -21,6 +21,7 @@
     json_dumps_pretty,
     set_readonly,
     is_readonly,
+    get_datetime,
 )
 
 lgr = logging.getLogger(__name__)
@@ -407,8 +408,7 @@ def get_formatted_scans_key_row(dcm_fn):
     try:
         date = dcm_data.ContentDate
         time = dcm_data.ContentTime
-        td = time + ':' + date
-        acq_time = datetime.strptime(td, '%H%M%S.%f:%Y%m%d').isoformat()
+        acq_time = get_datetime(date, time)
     except (AttributeError, ValueError) as exc:
         lgr.warning("Failed to get date/time for the content: %s", str(exc))
         acq_time = ''

heudiconv/tests/test_utils.py

@@ -10,6 +10,7 @@
     load_json,
     create_tree,
     save_json,
+    get_datetime,
     JSONDecodeError)
 
 import pytest
@@ -85,3 +86,17 @@ def test_load_json(tmpdir, caplog):
     save_json(valid_json_file, vcontent)
 
     assert load_json(valid_json_file) == vcontent
+
+
+def test_get_datetime():
+    """
+    Test utils.get_datetime()
+    """
+    date = '20200512'
+    time = '162130'
+    datetime_str = get_datetime(date, time)
+    assert datetime_str == '2020-05-12T16:21:30.000000'
+    date = '20200512'
+    time = '162130.5'
+    datetime_str = get_datetime(date, time)
+    assert datetime_str == '2020-05-12T16:21:30.500000'

heudiconv/utils.py

@@ -13,6 +13,7 @@
 from collections import namedtuple
 from glob import glob
 from subprocess import check_output
+from datetime import datetime
 
 from nipype.utils.filemanip import which
 
@@ -505,3 +506,27 @@ def get_typed_attr(obj, attr, _type, default=None):
     except (TypeError, ValueError):
         return default
     return val
+
+
+def get_datetime(date, time):
+    """
+    Convert date and time from dicom to isoformat.
+
+    Parameters
+    ----------
+    date : str
+        Date in YYYYMMDD format.
+    time : str
+        Time in either HHMMSS.ffffff format or HHMMSS format.
+
+    Returns
+    -------
+    datetime_str : str
+        Combined date and time in ISO format, with milliseconds.
+    """
+    if '.' not in time:
+        # add milliseconds if not available
+        time += '.000'
+    td = time + ':' + date
+    datetime_str = datetime.strptime(td, '%H%M%S.%f:%Y%m%d').isoformat()
+    return datetime_str