Topology in neuroscience
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import pandas as pd
import numpy as np
import pickle as pkl
data_folder = "../data/"
stim_file = "Stiminfo_PVCre_2021_0012_s06_e14.csv"
stim = pd.read_csv(data_folder+stim_file)
spike_times_file = "Spiketimes_PVCre_2021_0012_s06_e14.npy"
spike_times = np.load(data_folder+spike_times_file, allow_pickle=True)
active = [len(spike_times[i]) > 0 for i in range(len(spike_times))]
spike_times = spike_times[np.where(active)]
num_unit = len(spike_times)
num_trial = len(stim)
# sort by firing rate
num_spike = list(map(len, spike_times))
# num_spike = np.array([len(spike_times[i]) for i in range(len(spike_times))])
spike_times = spike_times[np.argsort(num_spike)[::-1]]
files = ['stim_data.pkl', 'spike_data.pkl', 'corr_data.pkl']
for file_name in files:
print(file_name)
file = open(file_name, 'rb')
data = pkl.load(file)
print(data.keys())
for key, value in data.items():
globals()[key] = value
file.close()
def pkl_save(filename:str, object:object):
file = open(filename+'.pkl', 'wb')
pkl.dump(object, file, pkl.HIGHEST_PROTOCOL)
file.close()
def pkl_load(filename:str):
file = open(filename+'.pkl', 'rb')
a = pkl.load(file)
file.close()
return a