MRG: Extract measurement date and age for NIRX files

mne/io/nirx/nirx.py

@@ -6,6 +6,7 @@
 import glob as glob
 import re as re
 import os.path as op
+import datetime as dt
 
 import numpy as np
 
@@ -15,8 +16,7 @@
 from ..meas_info import create_info, _format_dig_points
 from ...annotations import Annotations
 from ...transforms import apply_trans, _get_trans
-from ...utils import logger, verbose, fill_doc
-from ...utils import warn
+from ...utils import logger, verbose, fill_doc, warn
 
 
 @fill_doc
@@ -118,22 +118,47 @@ def __init__(self, fname, preload=False, verbose=None):
 
         # Parse required header fields
 
+        # Extract measurement date and time
+        datetime_str = hdr['GeneralInfo']['Date'] + hdr['GeneralInfo']['Time']
+        meas_date = None
+        # Several formats have been observed so we try each in turn
+        for dt_code in ['"%a, %b %d, %Y""%H:%M:%S.%f"',
+                        '"%a, %d %b %Y""%H:%M:%S.%f"']:
+            try:
+                meas_date = dt.datetime.strptime(datetime_str, dt_code)
+                meas_date = meas_date.replace(tzinfo=dt.timezone.utc)
+                break
+            except ValueError:
+                pass
+        if meas_date is None:
+            warn("Extraction of measurement date from NIRX file failed. "
+                 "This can be caused by files saved in certain locales. "
+                 "Please report this as a github issue. "
+                 "The date is being set to January 1st, 2000, "
+                 "instead of {}".format(datetime_str))
+            meas_date = dt.datetime(2000, 1, 1, 0, 0, 0,
+                                    tzinfo=dt.timezone.utc)
+
         # Extract frequencies of light used by machine
         fnirs_wavelengths = [int(s) for s in
                              re.findall(r'(\d+)',
-                             hdr['ImagingParameters']['Wavelengths'])]
+                                        hdr['ImagingParameters'][
+                                            'Wavelengths'])]
 
         # Extract source-detectors
         sources = np.asarray([int(s) for s in re.findall(r'(\d+)-\d+:\d+',
-                              hdr['DataStructure']['S-D-Key'])], int)
+                                                         hdr['DataStructure'][
+                                                             'S-D-Key'])], int)
         detectors = np.asarray([int(s) for s in re.findall(r'\d+-(\d+):\d+',
-                                hdr['DataStructure']['S-D-Key'])], int)
+                                                           hdr['DataStructure']
+                                                           ['S-D-Key'])],
+                               int)
 
         # Determine if short channels are present and on which detectors
         if 'shortbundles' in hdr['ImagingParameters']:
             short_det = [int(s) for s in
                          re.findall(r'(\d+)',
-                         hdr['ImagingParameters']['ShortDetIndex'])]
+                                    hdr['ImagingParameters']['ShortDetIndex'])]
             short_det = np.array(short_det, int)
         else:
             short_det = []
@@ -150,6 +175,7 @@ def __init__(self, fname, preload=False, verbose=None):
         # Note: NIRX also records "Study Type", "Experiment History",
         #       "Additional Notes", "Contact Information" and this information
         #       is currently discarded
+        # NIRStar does not record an id, or handedness by default
         subject_info = {}
         names = inf['name'].split()
         if len(names) > 0:
@@ -161,7 +187,6 @@ def __init__(self, fname, preload=False, verbose=None):
         if len(names) > 2:
             subject_info['middle_name'] = \
                 inf['name'].split()[-2].replace("\"", "")
-        # subject_info['birthday'] = inf['age']  # TODO: not formatted properly
         subject_info['sex'] = inf['gender'].replace("\"", "")
         # Recode values
         if subject_info['sex'] in {'M', 'Male', '1'}:
@@ -170,7 +195,9 @@ def __init__(self, fname, preload=False, verbose=None):
             subject_info['sex'] = FIFF.FIFFV_SUBJ_SEX_FEMALE
         else:
             subject_info['sex'] = FIFF.FIFFV_SUBJ_SEX_UNKNOWN
-        # NIRStar does not record an id, or handedness by default
+        subject_info['birthday'] = (meas_date.year - int(inf['age']),
+                                    meas_date.month,
+                                    meas_date.day)
 
         # Read information about probe/montage/optodes
         # A word on terminology used here:
@@ -219,10 +246,11 @@ def __init__(self, fname, preload=False, verbose=None):
         req_ind = req_ind.astype(int)
 
         # Generate meaningful channel names
-        def prepend(list, str):
+        def prepend(li, str):
             str += '{0}'
-            list = [str.format(i) for i in list]
-            return(list)
+            li = [str.format(i) for i in li]
+            return li
+
         snames = prepend(sources[req_ind], 'S')
         dnames = prepend(detectors[req_ind], '_D')
         sdnames = [m + str(n) for m, n in zip(snames, dnames)]
@@ -235,6 +263,7 @@ def prepend(list, str):
                            samplingrate,
                            ch_types='fnirs_cw_amplitude')
         info.update(subject_info=subject_info, dig=dig)
+        info['meas_date'] = meas_date
 
         # Store channel, source, and detector locations
         # The channel location is stored in the first 3 entries of loc.

mne/io/nirx/tests/test_nirx.py

@@ -6,6 +6,7 @@
 import os.path as op
 import shutil
 import os
+import datetime as dt
 
 import pytest
 from numpy.testing import assert_allclose, assert_array_equal
@@ -79,6 +80,8 @@ def test_nirx_15_2_short():
     # Test data import
     assert raw._data.shape == (26, 145)
     assert raw.info['sfreq'] == 12.5
+    assert raw.info['meas_date'] == dt.datetime(2019, 8, 23, 7, 37, 4, 540000,
+                                                tzinfo=dt.timezone.utc)
 
     # Test channel naming
     assert raw.info['ch_names'][:4] == ["S1_D1 760", "S1_D1 850",
@@ -92,7 +95,8 @@ def test_nirx_15_2_short():
     # Test info import
     assert raw.info['subject_info'] == dict(sex=1, first_name="MNE",
                                             middle_name="Test",
-                                            last_name="Recording")
+                                            last_name="Recording",
+                                            birthday=(2014, 8, 23))
 
     # Test distance between optodes matches values from
     # nirsite https://github.com/mne-tools/mne-testing-data/pull/51
@@ -179,8 +183,10 @@ def test_nirx_15_3_short():
     assert raw.info['chs'][1]['loc'][9] == 850
 
     # Test info import
-    assert raw.info['subject_info'] == dict(
-        sex=0, first_name="testMontage\\0ATestMontage")
+    assert raw.info['subject_info'] == dict(birthday=(2020, 8, 18),
+                                            sex=0,
+                                            first_name="testMontage\\0A"
+                                                       "TestMontage")
 
     # Test distance between optodes matches values from
     # https://github.com/mne-tools/mne-testing-data/pull/72
@@ -257,7 +263,8 @@ def test_encoding(tmpdir):
         for line in hdr:
             fid.write(line)
     # smoke test
-    read_raw_nirx(fname)
+    with pytest.raises(RuntimeWarning, match='Extraction of measurement date'):
+        read_raw_nirx(fname)
 
 
 @requires_testing_data
@@ -268,16 +275,20 @@ def test_nirx_15_2():
     # Test data import
     assert raw._data.shape == (64, 67)
     assert raw.info['sfreq'] == 3.90625
+    assert raw.info['meas_date'] == dt.datetime(2019, 10, 2, 9, 8, 47, 511000,
+                                                tzinfo=dt.timezone.utc)
 
     # Test channel naming
     assert raw.info['ch_names'][:4] == ["S1_D1 760", "S1_D1 850",
                                         "S1_D10 760", "S1_D10 850"]
 
     # Test info import
-    assert raw.info['subject_info'] == dict(sex=1, first_name="TestRecording")
+    assert raw.info['subject_info'] == dict(sex=1, first_name="TestRecording",
+                                            birthday=(1989, 10, 2))
 
     # Test trigger events
     assert_array_equal(raw.annotations.description, ['4.0', '6.0', '2.0'])
+    print(raw.annotations.onset)
 
     # Test location of detectors
     allowed_dist_error = 0.0002
@@ -312,6 +323,9 @@ def test_nirx_15_0():
     # Test data import
     assert raw._data.shape == (20, 92)
     assert raw.info['sfreq'] == 6.25
+    assert raw.info['meas_date'] == dt.datetime(2019, 10, 27, 13, 53, 34,
+                                                209000,
+                                                tzinfo=dt.timezone.utc)
 
     # Test channel naming
     assert raw.info['ch_names'][:12] == ["S1_D1 760", "S1_D1 850",
@@ -322,7 +336,8 @@ def test_nirx_15_0():
                                          "S6_D6 760", "S6_D6 850"]
 
     # Test info import
-    assert raw.info['subject_info'] == {'first_name': 'NIRX',
+    assert raw.info['subject_info'] == {'birthday': (2004, 10, 27),
+                                        'first_name': 'NIRX',
                                         'last_name': 'Test',
                                         'sex': FIFF.FIFFV_SUBJ_SEX_UNKNOWN}