[Fix] Concatenate raw objects with annotations (#5851)

Fix #5839, #5555 

This PR fixes the fact that `raw_A.append(raw_B)` ignores `meas_date` and
supposes that the buffers of `raw_A` and `raw_B` where captured one right
after the other.

Author: massich

doc/whats_new.rst

@@ -54,6 +54,8 @@ Changelog
 Bug
 ~~~
 
+- Fix :meth:`mne.io.Raw.append` annotations miss-alignment  by `Joan Massich`_
+
 - Fix :func:`mne.io.read_raw_edf` reading duplicate channel names by `Larry Eisenman`_
 
 - Fix :func:`set_bipolar_reference` in the case of generating all bipolar combinations and also in the case of repeated channels in both lists (anode and cathode) by `Cristóbal Moënne-Loccoz`_
@@ -3142,4 +3144,4 @@ of commits):
 
 .. _Larry Eisenman:  https://github.com/lneisenman
 
-.. _Stanislas Chambon: https://github.com/Slasnista
+.. _Stanislas Chambon: https://github.com/Slasnista

mne/io/base.py

@@ -2127,8 +2127,12 @@ def append(self, raws, preload=None):
         edge_samps = list()
         for ri, r in enumerate(raws):
             n_samples = self.last_samp - self.first_samp + 1
+            r_annot = Annotations(onset=r.annotations.onset - r._first_time,
+                                  duration=r.annotations.duration,
+                                  description=r.annotations.description,
+                                  orig_time=None)
             annotations = _combine_annotations(
-                annotations, r.annotations, n_samples,
+                annotations, r_annot, n_samples,
                 self.first_samp, r.first_samp,
                 self.info['sfreq'], self.info['meas_date'])
             edge_samps.append(sum(self._last_samps) -

mne/io/fiff/raw.py

@@ -112,7 +112,7 @@ def __init__(self, fname, allow_maxshield=False, preload=False,
                     self.annotations, r.annotations,
                     n_samples, self.first_samp, r.first_samp,
                     r.info['sfreq'], self.info['meas_date'])
-                self.set_annotations(annotations, False)
+                self.set_annotations(annotations, emit_warning=False)
                 n_samples += r.last_samp - r.first_samp + 1
 
         # Add annotations for in-data skips

mne/io/tests/test_raw.py

@@ -281,3 +281,46 @@ def test_get_data_reject():
         assert log.getvalue().strip() == msg
     assert data.shape == (len(ch_names), 2560)  # shape doesn't change
     assert np.isnan(data).sum() == 3072  # but NaNs are introduced instead
+
+
+def test_5839():
+    """Test concatenating raw objects with annotations."""
+    # Global Time 0         1         2         3         4
+    #             .
+    #      raw_A  |---------XXXXXXXXXX
+    #      annot  |--------------AA
+    #    latency  .         0    0    1    1    2    2    3
+    #             .              5    0    5    0    5    0
+    #
+    #      raw_B  .                   |---------YYYYYYYYYY
+    #      annot  .                   |--------------AA
+    #    latency  .                             0         1
+    #             .                                  5    0
+    #             .
+    #     output  |---------XXXXXXXXXXYYYYYYYYYY
+    #      annot  |--------------AA---|----AA
+    #    latency  .         0    0    1    1    2    2    3
+    #             .              5    0    5    0    5    0
+    #
+    EXPECTED_ONSET = [1.5, 2.5, 2., 2.]
+    EXPECTED_DURATION = [0.2, 0.2, 0., 0.]
+    EXPECTED_DESCRIPTION = ['dummy', 'dummy', 'BAD boundary', 'EDGE boundary']
+
+    def raw_factory(meas_date):
+        raw = RawArray(data=np.empty((10, 10)),
+                       info=create_info(ch_names=10, sfreq=10., ),
+                       first_samp=10)
+        raw.info['meas_date'] = meas_date
+        raw.set_annotations(annotations=Annotations(onset=[.5],
+                                                    duration=[.2],
+                                                    description='dummy',
+                                                    orig_time=None))
+        return raw
+
+    raw_A, raw_B = [raw_factory((x, 0)) for x in [0, 2]]
+    raw_A.append(raw_B)
+
+    assert_array_equal(raw_A.annotations.onset, EXPECTED_ONSET)
+    assert_array_equal(raw_A.annotations.duration, EXPECTED_DURATION)
+    assert_array_equal(raw_A.annotations.description, EXPECTED_DESCRIPTION)
+    assert raw_A.annotations.orig_time == 0.0