You could start by fixing the basic syntax and other errors:
import os
import glob
import csv
path=r"E:\Users\ConfocalUser\Documents\GitHub\qudi"
files=glob.glob(os.path.join(path,'*.csv'))
xData=[]
yData=[]
for file in files:
print(file)
with open(file,"r") as f_in:
reader=csv.reader(f_in)
next(reader)
for line in reader:
try:
float_1,float_2=float(line[0]),float(line[1])
xData.append(float_1)
yData.append(float_2)
except ValueError:
continue
print('xData:', xData)
print('yData:', yData)
Always test your code first with a few simple fixed test files.