Convert ephys times to sec within workflow

moseq2_ephys_sync/ttl.py

@@ -2,6 +2,7 @@
 
 from glob import glob
 import sync
+import pdb
 
 def ttl_workflow(base_path, save_path, num_leds, led_blink_interval, ephys_fs):
     """
@@ -18,12 +19,14 @@ def ttl_workflow(base_path, save_path, num_leds, led_blink_interval, ephys_fs):
     # (This is a bit of a glitch in open ephys, might be able to remove this in future versions)
     continuous_timestamps_path = glob('%s/**/continuous/**/timestamps.npy' % base_path,recursive = True)[0] ## load the continuous stream's timestamps
     continuous_timestamps = np.load(continuous_timestamps_path)
-    ephys_timestamps -= continuous_timestamps[0]  # subract the first timestamp from all TTLs; this way continuous ephys can safely start at 0 samples or seconds
+    ephys_timestamps -= continuous_timestamps[0]   # subract the first timestamp from all TTLs; this way continuous ephys can safely start at 0 samples or seconds
+    ephys_timestamps = ephys_timestamps / ephys_fs
 
     ttl_channels = [-4,-3,-2,-1,1,2,3,4]
+    print('Assuming sync leds in ttl channels 1-4...')
     ttl_bool = np.isin(channels, ttl_channels)
     ephys_events = np.vstack([ephys_timestamps[ttl_bool], abs(channels[ttl_bool])-1, np.sign(channels[ttl_bool])]).T
-    codes, ephys_latencies = sync.events_to_codes(ephys_events, nchannels=num_leds, minCodeTime=(led_blink_interval-1)*ephys_fs)
+    codes, ephys_latencies = sync.events_to_codes(ephys_events, nchannels=num_leds, minCodeTime=(led_blink_interval-1))
     codes = np.asarray(codes)
 
     return codes