WIP: Set physical range to digital range for stim channels (mne-tools…

…#5160)

* Set physical range to digital range for stim channels (so that the scaling factor is 1)

* Scale up stim channel values if diff between max and min is less than 1

* Apply scaling only to data channels

* Don't scale stim channel for BDF files

* Move scaling up

* Get data index right

* Add GitHub PR and whats_new

* Fix for preload=False

* Add test with small BDF file

* FIX: Use testing

* PEP8

doc/whats_new.rst

@@ -246,6 +246,8 @@ Bug
 
 - Fix bug in :meth:`mne.SourceEstimate.get_peak` and :meth:`mne.VolSourceEstimate.get_peak` when there is only a single time point by `Marijn van Vliet`_
 
+- Fix bug in :func:`mne.io.read_raw_edf` when reading BDF files stimulus channels are now not scaled anymore by `Clemens Brunner`_
+
 API
 ~~~
 

mne/datasets/utils.py

@@ -235,7 +235,7 @@ def _data_path(path=None, force_update=False, update_path=True, download=True,
     path = _get_path(path, key, name)
     # To update the testing or misc dataset, push commits, then make a new
     # release on GitHub. Then update the "releases" variable:
-    releases = dict(testing='0.47', misc='0.3')
+    releases = dict(testing='0.49', misc='0.3')
     # And also update the "hashes['testing']" variable below.
 
     # To update any other dataset, update the data archive itself (upload
@@ -315,7 +315,7 @@ def _data_path(path=None, force_update=False, update_path=True, download=True,
         sample='fc2d5b9eb0a144b1d6ba84dc3b983602',
         somato='77a7601948c9e38d2da52446e2eab10f',
         spm='9f43f67150e3b694b523a21eb929ea75',
-        testing='fc64b5cd163ea4dd19d8434a7a6d02be',
+        testing='52b017611bedbedb22ff9f464e895aa7',
         multimodal='26ec847ae9ab80f58f204d09e2c08367',
         visual_92_categories=['74f50bbeb65740903eadc229c9fa759f',
                               '203410a98afc9df9ae8ba9f933370e20'],

mne/io/edf/edf.py

@@ -272,15 +272,22 @@ def _read_segment_file(self, data, idx, fi, start, stop, cals, mult):
                     assert ch_data.shape == (len(ch_data), buf_len)
                     data[ii, d_sidx:d_eidx] = ch_data.ravel()[r_sidx:r_eidx]
 
-        data *= cal.T[idx]  # scale
-        data += offsets[idx]  # offset
-        data *= gains.T[idx]  # apply units gain last
-
         # only try to read the stim channel if it's not None and it's
         # actually one of the requested channels
         idx = np.arange(self.info['nchan'])[idx]  # slice -> ints
         read_size = len(r_lims) * buf_len
         stim_channel_idx = np.where(idx == stim_channel)[0]
+
+        if subtype == 'bdf':
+            # do not scale stim channel (see gh-5160)
+            stim_idx = np.where(np.arange(self.info['nchan']) == stim_channel)
+            cal[0, stim_idx[0]] = 1
+            offsets[stim_idx[0], 0] = 0
+            gains[0, stim_idx[0]] = 1
+        data *= cal.T[idx]
+        data += offsets[idx]
+        data *= gains.T[idx]
+
         if stim_channel is not None and len(stim_channel_idx) > 0:
             if annot and annotmap:
                 evts = _read_annot(annot, annotmap, sfreq,

mne/io/edf/tests/test_edf.py

@@ -47,6 +47,7 @@
 edf_overlap_annot_path = op.join(data_path, 'EDF',
                                  'test_edf_overlapping_annotations.edf')
 edf_reduced = op.join(data_path, 'EDF', 'test_reduced.edf')
+bdf_stim_channel_path = op.join(data_path, 'BDF', 'test_bdf_stim_channel.bdf')
 
 
 eog = ['REOG', 'LEOG', 'IEOG']
@@ -75,11 +76,31 @@ def test_bdf_data():
     assert_true((raw_py.info['chs'][63]['loc']).any())
 
 
+@testing.requires_testing_data
 def test_bdf_stim_channel():
-    """Test if last channel is detected as STIM by default."""
+    """Test BDF stim channel."""
+    # test if last channel is detected as STIM by default
     raw_py = _test_raw_reader(read_raw_edf, input_fname=bdf_path)
     assert_true(channel_type(raw_py.info, raw_py.info["nchan"] - 1) == 'stim')
 
+    # test BDF file with wrong scaling info in header - this should be ignored
+    # for BDF stim channels
+    events = [[242, 0, 4],
+              [310, 0, 2],
+              [952, 0, 1],
+              [1606, 0, 1],
+              [2249, 0, 1],
+              [2900, 0, 1],
+              [3537, 0, 1],
+              [4162, 0, 1],
+              [4790, 0, 1]]
+    raw = read_raw_edf(bdf_stim_channel_path, preload=True)
+    bdf_events = find_events(raw)
+    assert_array_equal(events, bdf_events)
+    raw = read_raw_edf(bdf_stim_channel_path, preload=False)
+    bdf_events = find_events(raw)
+    assert_array_equal(events, bdf_events)
+
 
 @testing.requires_testing_data
 def test_edf_overlapping_annotations():