Merge branch 'workflows' into workflows

moseq2_ephys_sync/main.py

@@ -83,10 +83,29 @@ def main_function(base_path, output_dir_name, first_source, second_source, led_l
     # Save the codes for use later
     np.savez('%s/codes.npz' % save_path, first_source_codes=first_source_led_codes, second_source_codes=second_source_led_codes)
 
+
     # Visualize a small chunk of the bit codes. do you see a match? 
     # Codes array should have times in seconds by this point
     plotting.plot_code_chunk(first_source_led_codes, second_source_led_codes, save_path)
 
+    ################################# Load the ephys TTL data #####################################
+
+    ephys_ttl_path = glob('%s/**/TTL_*/' % base_path,recursive = True)[0]
+    channels = np.load('%s/channel_states.npy' % ephys_ttl_path)
+    ephys_timestamps = np.load('%s/timestamps.npy' % ephys_ttl_path)
+
+    ## need to subtract the raw traces' starting timestamp from the TTL timestamps:
+    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_fs = 3e4
+
+    led_fs = 30
+
+
 
 
 
@@ -105,6 +124,7 @@ def main_function(base_path, output_dir_name, first_source, second_source, led_l
 
 
 
+
     #### Make the models! ####
 
     # Rename for clarity.