Merge pull request #1609 from h-mayorquin/fix_time_metadata

Add timing metadata for `SpikeGLXRawIO`

Author: zm711

neo/rawio/spikeglxrawio.py

@@ -224,14 +224,25 @@ def _parse_header(self):
         spike_channels = np.array(spike_channels, dtype=_spike_channel_dtype)
 
         # deal with nb_segment and t_start/t_stop per segment
-        self._t_starts = {seg_index: 0.0 for seg_index in range(nb_segment)}
+
+        self._t_starts = {stream_name: {} for stream_name in stream_names}
         self._t_stops = {seg_index: 0.0 for seg_index in range(nb_segment)}
-        for seg_index in range(nb_segment):
-            for stream_name in stream_names:
+        
+        for stream_name in stream_names:
+            for seg_index in range(nb_segment):
                 info = self.signals_info_dict[seg_index, stream_name]
+
+                frame_start = float(info["meta"]["firstSample"])
+                sampling_frequency = info["sampling_rate"]
+                t_start = frame_start / sampling_frequency
+                                
+                self._t_starts[stream_name][seg_index] = t_start 
                 t_stop = info["sample_length"] / info["sampling_rate"]
                 self._t_stops[seg_index] = max(self._t_stops[seg_index], t_stop)
 
+                
+
+
         # fille into header dict
         self.header = {}
         self.header["nb_block"] = 1
@@ -276,7 +287,8 @@ def _segment_t_stop(self, block_index, seg_index):
         return self._t_stops[seg_index]
 
     def _get_signal_t_start(self, block_index, seg_index, stream_index):
-        return 0.0
+        stream_name = self.header["signal_streams"][stream_index]["name"]
+        return self._t_starts[stream_name][seg_index]
 
     def _event_count(self, event_channel_idx, block_index=None, seg_index=None):
         timestamps, _, _ = self._get_event_timestamps(block_index, seg_index, event_channel_idx, None, None)

neo/test/rawiotest/test_spikeglxrawio.py

@@ -112,6 +112,65 @@ def test_nidq_digital_channel(self):
         atol = 0.001
         assert np.allclose(on_diff, 1, atol=atol)
 
+    def test_t_start_reading(self):
+        """Test that t_start values are correctly read for all streams and segments."""
+        
+        # Expected t_start values for each stream and segment
+        expected_t_starts = {
+            'imec0.ap': {
+                0: 15.319535472007237,
+                1: 15.339535431281986,
+                2: 21.284723325294053,
+                3: 21.3047232845688
+            },
+            'imec1.ap': {
+                0: 15.319554693264516,
+                1: 15.339521518106308,
+                2: 21.284735282142822,
+                3: 21.304702106984614
+            },
+            'imec0.lf': {
+                0: 15.3191688060872,
+                1: 15.339168765361949,
+                2: 21.284356659374016,
+                3: 21.304356618648765
+            },
+            'imec1.lf': {
+                0: 15.319321358082725,
+                1: 15.339321516521915,
+                2: 21.284568614155827,
+                3: 21.30456877259502
+            }
+        }
+        
+        # Initialize the RawIO
+        rawio = SpikeGLXRawIO(self.get_local_path("spikeglx/multi_trigger_multi_gate/SpikeGLX/5-19-2022-CI4"))
+        rawio.parse_header()
+        
+        # Get list of stream names
+        stream_names = rawio.header["signal_streams"]["name"]
+        
+        # Test t_start for each stream and segment
+        for stream_name, expected_values in expected_t_starts.items():
+            # Get stream index
+            stream_index = list(stream_names).index(stream_name)
+            
+            # Check each segment
+            for seg_index, expected_t_start in expected_values.items():
+                actual_t_start = rawio.get_signal_t_start(
+                    block_index=0,
+                    seg_index=seg_index,
+                    stream_index=stream_index
+                )
+                
+                # Use numpy.testing for proper float comparison
+                np.testing.assert_allclose(
+                    actual_t_start,
+                    expected_t_start,
+                    rtol=1e-9,
+                    atol=1e-9,
+                    err_msg=f"Mismatch in t_start for stream '{stream_name}', segment {seg_index}"
+                )
 
 if __name__ == "__main__":
     unittest.main()