import numpy as np #from sklearn.discriminant_analysis import _class_cov,LinearDiscriminantAnalysis from discriminant_analysis import _class_cov,LinearDiscriminantAnalysis X = np.random.rand(1000000, 100) y = np.random.randint(0, 20000, (1000000, )) print len(np.unique(y)) #model=LinearDiscriminantAnalysis(solver='eigen') #model.fit(X,y) _class_cov(X, y, np.array([1.]*20000)/20000)