Merge pull request #518 from SpikeInterface/fix_h5_sorted

Fix h5 unsorted channel_ids in get_traces
SpikeInterface · Dec 8, 2020 · c935458 · c935458
2 parents c8a7fb8 + 2946f9b
commit c935458
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Showing 5 changed files with 19 additions and 14 deletions.
diff --git a/spikeextractors/extractors/maxoneextractors/maxoneextractors.py b/spikeextractors/extractors/maxoneextractors/maxoneextractors.py
@@ -103,9 +103,10 @@ def get_sampling_frequency(self):
     def get_traces(self, channel_ids=None, start_frame=None, end_frame=None):
         if np.array(channel_ids).size > 1:
             if np.any(np.diff(channel_ids) < 0):
-                sorted_idx = np.argsort(channel_ids)
-                recordings = self._signals[np.sort(channel_ids), start_frame:end_frame]
-                return (recordings[sorted_idx] * self._lsb).astype('float')
+                sorted_channel_ids = np.sort(channel_ids)
+                sorted_idx = np.array([list(sorted_channel_ids).index(ch) for ch in channel_ids])
+                recordings = (self._signals[sorted_channel_ids, start_frame:end_frame] * self._lsb).astype('float32')
+                return recordings[sorted_idx]
             else:
                 return (self._signals[np.array(channel_ids), start_frame:end_frame] * self._lsb).astype('float32')
         else:

diff --git a/spikeextractors/extractors/mcsh5recordingextractor/mcsh5recordingextractor.py b/spikeextractors/extractors/mcsh5recordingextractor/mcsh5recordingextractor.py
@@ -83,8 +83,9 @@ def get_traces(self, channel_ids=None, start_frame=None, end_frame=None):
 
         if np.array(channel_idxs).size > 1:
             if np.any(np.diff(channel_idxs) < 0):
-                sorted_idx = np.argsort(channel_idxs)
-                recordings = stream.get('ChannelData')[np.sort(channel_idxs), start_frame:end_frame]
+                sorted_channel_ids = np.sort(channel_idxs)
+                sorted_idx = np.array([list(sorted_channel_ids).index(ch) for ch in channel_idxs])
+                recordings = stream.get('ChannelData')[sorted_channel_ids, start_frame:end_frame]
                 return recordings[sorted_idx] * conv
             else:
                 return stream.get('ChannelData')[np.sort(channel_idxs), start_frame:end_frame] * conv

diff --git a/spikeextractors/extractors/mea1kextractors/mea1kextractors.py b/spikeextractors/extractors/mea1kextractors/mea1kextractors.py
@@ -184,9 +184,10 @@ def get_sampling_frequency(self):
     def get_traces(self, channel_ids=None, start_frame=None, end_frame=None):
         if np.array(channel_ids).size > 1:
             if np.any(np.diff(channel_ids) < 0):
-                sorted_idx = np.argsort(channel_ids)
-                recordings = self._signals[np.sort(channel_ids), start_frame:end_frame]
-                return recordings[sorted_idx].astype('float')
+                sorted_channel_ids = np.sort(channel_ids)
+                sorted_idx = np.array([list(sorted_channel_ids).index(ch) for ch in channel_ids])
+                recordings = (self._signals[sorted_channel_ids, start_frame:end_frame] * self._lsb).astype('float32')
+                return recordings[sorted_idx]
             else:
                 return (self._signals[np.array(channel_ids), start_frame:end_frame] * self._lsb).astype('float32')
         else:

diff --git a/spikeextractors/extractors/mearecextractors/mearecextractors.py b/spikeextractors/extractors/mearecextractors/mearecextractors.py
@@ -77,13 +77,14 @@ def get_sampling_frequency(self):
     @check_get_traces_args
     def get_traces(self, channel_ids=None, start_frame=None, end_frame=None):
         if np.any(np.diff(channel_ids) < 0):
-            sorted_idx = np.argsort(channel_ids)
-            recordings = self._recordings[start_frame:end_frame, np.sort(channel_ids)]
-            return np.array(recordings[sorted_idx]).transpose()
+            sorted_channel_ids = np.sort(channel_ids)
+            sorted_idx = np.array([list(sorted_channel_ids).index(ch) for ch in channel_ids])
+            recordings = self._recordings[start_frame:end_frame, sorted_channel_ids]
+            return np.array(recordings[:, sorted_idx]).T
         else:
             if sorted(channel_ids) == channel_ids and np.all(np.diff(channel_ids) == 1):
                 channel_ids = slice(channel_ids[0], channel_ids[0] + len(channel_ids))
-            return np.array(self._recordings[start_frame:end_frame, channel_ids]).transpose()
+            return np.array(self._recordings[start_frame:end_frame, channel_ids]).T
 
     @staticmethod
     def write_recording(recording, save_path, check_suffix=True):

diff --git a/spikeextractors/extractors/nwbextractors/nwbextractors.py b/spikeextractors/extractors/nwbextractors/nwbextractors.py
@@ -287,8 +287,9 @@ def get_traces(self, channel_ids=None, start_frame=None, end_frame=None):
             if np.array(channel_ids).size > 1 and np.any(np.diff(channel_ids) < 0):
                 # get around h5py constraint that it does not allow datasets
                 # to be indexed out of order
-                sorted_idx = np.argsort(channel_inds)
-                recordings = es.data[start_frame:end_frame, np.sort(channel_inds)].T
+                sorted_channel_ids = np.sort(channel_ids)
+                sorted_idx = np.array([list(sorted_channel_ids).index(ch) for ch in channel_ids])
+                recordings = es.data[start_frame:end_frame, sorted_channel_ids].T
                 traces = recordings[sorted_idx, :]
             else:
                 traces = es.data[start_frame:end_frame, channel_inds].T