minor code cleanup

Author: Thinh Nguyen

elements_ephys/ephys.py

@@ -205,15 +205,15 @@ class LFP(dj.Imported):
     ---
     lfp_sampling_rate: float        # (Hz)
     lfp_time_stamps: longblob       # (s) timestamps with respect to the start of the recording (recording_timestamp)
-    lfp_mean: longblob              # (mV) mean of LFP across electrodes - shape (time,)
+    lfp_mean: longblob              # (uV) mean of LFP across electrodes - shape (time,)
     """
 
     class Electrode(dj.Part):
         definition = """
         -> master
         -> probe.ElectrodeConfig.Electrode  
         ---
-        lfp: longblob               # (mV) recorded lfp at this electrode 
+        lfp: longblob               # (uV) recorded lfp at this electrode 
         """
 
     # Only store LFP for every 9th channel, due to high channel density, close-by channels exhibit highly similar LFP
@@ -431,8 +431,8 @@ class Electrode(dj.Part):
         -> master
         -> probe.ElectrodeConfig.Electrode  
         --- 
-        waveform_mean: longblob   # mean over all spikes
-        waveforms=null: longblob  # (spike x sample) waveform of each spike at each electrode
+        waveform_mean: longblob   # (uV) mean over all spikes
+        waveforms=null: longblob  # (uV) (spike x sample) waveform of each spike at each electrode
         """
 
     @property

elements_ephys/readers/openephys.py

@@ -114,11 +114,11 @@ def __init__(self, processor):
     @property
     def ap_data(self):
         """
-        AP data concatenated across recordings. Shape: (channel x sample)
+        AP data concatenated across recordings. Shape: (sample x channel)
         Channels' gains (bit_volts) applied - unit: uV
         """
         if self._ap_data is None:
-            self._ap_data = np.hstack([s.signal for s in self.ap_analog_signals])
+            self._ap_data = np.hstack([s.signal for s in self.ap_analog_signals]).T
             self._ap_data = self._ap_data * self.ap_meta['channels_gains']
         return self._ap_data
 
@@ -131,11 +131,11 @@ def ap_timestamps(self):
     @property
     def lfp_data(self):
         """
-        LFP data concatenated across recordings. Shape: (channel x sample)
+        LFP data concatenated across recordings. Shape: (sample x channel)
         Channels' gains (bit_volts) applied - unit: uV
         """
         if self._lfp_data is None:
-            self._lfp_data = np.hstack([s.signal for s in self.lfp_analog_signals])
+            self._lfp_data = np.hstack([s.signal for s in self.lfp_analog_signals]).T
             self._lfp_data = self._lfp_data * self.lfp_meta['channels_gains']
         return self._lfp_data
 

elements_ephys/readers/spikeglx.py

@@ -39,6 +39,10 @@ def apmeta(self):
 
     @property
     def apdata(self):
+        """
+        AP data: (sample x channel)
+        Channels' gains (bit_volts) applied - unit: uV
+        """
         if self._apdata is None:
             self._apdata = self._read_bin(self.root_dir / (self.root_name + '.ap.bin'))
             self._apdata = self._apdata * self.get_channel_bit_volts('ap')
@@ -52,6 +56,10 @@ def lfmeta(self):
 
     @property
     def lfdata(self):
+        """
+        LFP data: (sample x channel)
+        Channels' gains (bit_volts) applied - unit: uV
+        """
         if self._lfdata is None:
             self._lfdata = self._read_bin(self.root_dir / (self.root_name + '.lf.bin'))
             self._lfdata = self._lfdata * self.get_channel_bit_volts('lf')