add rectify, cv, serial correlation

helperFunctions.py

@@ -3,6 +3,8 @@ import pyrelacs.DataLoader as dl
 import numpy as np
 import matplotlib.pyplot as plt
 from warnings import warn
+import scipy.stats
+
 
 def get_subfolder_paths(basepath):
     subfolders = []
@@ -212,4 +214,35 @@ def plot_frequency_curve(cell_data, save_path: str = None, indices: list = None)
         plt.show()
     else:
         plt.savefig(save_path + "mean_frequency_curves.png")
-    plt.close()
+    plt.close()
+
+
+def rectify(x):
+    if x < 0:
+        return 0
+    return x
+
+
+def calculate_coefficient_of_variation(spiketimes: list) -> float:
+    # CV (stddev of ISI divided by mean ISI (np.diff(spiketimes))
+    isi = np.diff(spiketimes)
+    std = np.std(isi)
+    mean = np.mean(isi)
+
+    return std/mean
+
+
+def calculate_serial_correlation(spiketimes: list, max_lag: int) -> list:
+    isi = np.diff(spiketimes)
+    if len(spiketimes) < max_lag + 1:
+        raise ValueError("Given list to short, with given max_lag")
+
+    cor = []
+    for lag in range(max_lag):
+        lag = lag + 1
+        first = isi[:-lag]
+        second = isi[lag:]
+
+        cor.append(np.corrcoef(first, second)[0][1])
+
+    return cor