changed for multiple repros

open_nixio.py

@@ -22,7 +22,6 @@ def open_nixio(nix_file, avg_opt):
     feature_dict = {}
     for feat in mt.features:
         feature_dict.update({feat.data.name[16:]: mt.features[feat.data.name].data[:]})
-
     #  Spike data in intervals of comb position + speed
     intervals_dict = defaultdict(list)
     for idx, position in enumerate(comb_pos):
@@ -40,5 +39,6 @@ def open_nixio(nix_file, avg_opt):
 
     #  Spike data at baseline
     # comb_baseline = spikes[(spikes < comb_pos[0])]
-
+    embed()
+    quit()
     return curr_comb, intervals_dict

open_nixio_new.py

@@ -0,0 +1,40 @@
+import nixio as nix
+from IPython import embed
+from collections import defaultdict
+import numpy as np
+
+nix_file = '/home/sachgau/Documents/combproject/comb_data/2018-11-16-ag/2018-11-16-ag.nix'
+
+
+f = nix.File.open(nix_file, nix.FileMode.ReadOnly)
+b = f.blocks[0]  # first block
+mt = b.multi_tags['moving object-1']
+comb_pos = mt.positions[:]
+comb_ext = np.array(mt.extents[:])
+spikes = b.data_arrays["Spikes-1"][:]
+
+feature_dict = {}
+for feat in mt.features:
+    feature_dict.update({feat.data.name[16:]: mt.features[feat.data.name].data[:]})
+
+tags = b.tags
+for tag in tags:
+    if tag.name.startswith('Baseline'):
+        continue
+    repro_pos, = tag.position
+    repro_ext, = tag.extent
+
+    tag_idx = np.where(np.logical_and(repro_pos < comb_pos, comb_pos < (repro_pos+repro_ext)))
+    embed()
+    quit()
+    tag_idx_pos = comb_pos[np.logical_and(repro_pos < comb_pos, comb_pos < (repro_pos + repro_ext))]
+
+
+intervals_dict = defaultdict(list)
+for idx, position in enumerate(comb_pos):
+    if idx == (len(comb_pos)-1):
+        break
+    curr_speed = feature_dict['speed'][idx]
+    curr_pos = comb_pos[idx]
+    curr_dir = feature_dict['direction'][idx]
+    curr_spikes = spikes[(spikes < comb_pos[idx + 1]) & (spikes > comb_pos[idx])]

raster_plot.py

@@ -31,10 +31,10 @@ cell_name = sys.argv[1].split('/')[-2]
 
 curr_comb, intervals_dict = open_nixio(sys.argv[1], sys.argv[2])
 
-spike_repeats = []
+
 for (speed, direct, comb) in intervals_dict:
     s_trials = intervals_dict[(speed, direct, comb)]
-
+    spike_repeats = []
     for trial in intervals_dict[(speed, direct, comb)]:
         spike_train = trial[1]
         spike_train = spike_train - spike_train[0]  # changing spike train to start at 0 (subtracting baseline)
@@ -46,3 +46,4 @@ for (speed, direct, comb) in intervals_dict:
     ax.set_xlabel('Time (s)')
     ax.set_ylabel('Trials')
     plt.show()
+    plt.close