Merge branch 'master' of https://whale.am28.uni-tuebingen.de/git/jgrewe/gp_neurobio

FG
wb

code/read_chirp_data.py

@@ -1,5 +1,7 @@
 import numpy as np
 import os
+import nixio as nix
+from IPython import embed
 
 
 def read_chirp_spikes(dataset):
@@ -85,10 +87,37 @@ def read_chirp_times(dataset):
     return chirp_times
 
 
+def read_chirp_stimulus(dataset):
+    base = dataset.split(os.path.sep)[-1] + ".nix"
+    nix_file = nix.File.open(os.path.join(dataset, base), nix.FileMode.ReadOnly)
+    b = nix_file.blocks[0]
+    data = {}
+    for t in b.tags:
+        if "Chirps" in t.name:
+            stims = []
+            index = int(t.name.split("_")[-1])
+            df = t.metadata["RePro-Info"]["settings"]["deltaf"]
+            cs = t.metadata["RePro-Info"]["settings"]["chirpsize"]
+            stim_da = t.references["GlobalEFieldStimulus"]
+            si = stim_da.dimensions[0].sampling_interval
+            for mt in b.multi_tags:
+                if mt.positions[0] >= t.position[0] and \
+                   mt.positions[0] < (t.position[0] + t.extent[0]):
+                    break
+            for i in range(len(mt.positions)):
+                start_index = int(mt.positions[i] / si)
+                end_index = int((mt.positions[i] + mt.extents[i]) / si) - 1
+                stim = stim_da[start_index:end_index]
+                time = stim_da.dimensions[0].axis(len(stim)) + mt.positions[i]
+                stims.append((time, stim))
+            data[(index, df, cs)] = stims
+    nix_file.close()
+    return data
+
 if __name__ == "__main__":
     data_dir = "../data"
-    dataset = "2018-11-09-ad-invivo-1"
+    dataset = "2018-11-20-ad-invivo-1"
-    spikes = load_chirp_spikes(os.path.join(data_dir, dataset))
+    #spikes = load_chirp_spikes(os.path.join(data_dir, dataset))
-    chirp_times = load_chirp_times(os.path.join(data_dir, dataset))
+    #chirp_times = load_chirp_times(os.path.join(data_dir, dataset))
-    chirp_eod = load_chirp_eod(os.path.join(data_dir, dataset))
+    #chirp_eod = load_chirp_eod(os.path.join(data_dir, dataset))
-
+    stim = read_chirp_stimulus(os.path.join(data_dir, dataset))