import pandas as pd
import numpy as np
from sklearn.preprocessing import StandardScaler
from sklearn.decomposition import PCA
import matplotlib.pyplot as plt
from matplotlib.colors import ListedColormap
from sklearn.linear_model import LogisticRegression
from sklearn.discriminant_analysis import LinearDiscriminantAnalysis as LDA
from sklearn.datasets import make_moons
from sklearn.datasets import make_circles
from sklearn.decomposition import KernelPCA
from scipy.spatial.distance import pdist, squareform
from scipy import exp
from scipy.linalg import eigh
from matplotlib.ticker import FormatStrFormatter

# for sklearn 0.18's alternative syntax
from distutils.version import LooseVersion as Version
from sklearn import __version__ as sklearn_version
if Version(sklearn_version) < '0.18':
    from sklearn.grid_search import train_test_split
    from sklearn.lda import LDA
else:
    from sklearn.model_selection import train_test_split
    from sklearn.discriminant_analysis import LinearDiscriminantAnalysis as LDA


#############################################################################
print(50 * '=')
print('Section: Unsupervised dimensionality reduction'
      ' via principal component analysis')
print(50 * '-')

df_wine = pd.read_csv('https://archive.ics.uci.edu/ml/'
                      'machine-learning-databases/wine/wine.data',
                      header=None)

df_wine.columns = ['Class label', 'Alcohol', 'Malic acid', 'Ash',
                   'Alcalinity of ash', 'Magnesium', 'Total phenols',
                   'Flavanoids', 'Nonflavanoid phenols', 'Proanthocyanins',
                   'Color intensity', 'Hue',
                   'OD280/OD315 of diluted wines', 'Proline']

print('Wine data excerpt:\n\n:', df_wine.head())


X, y = df_wine.iloc[:, 1:].values, df_wine.iloc[:, 0].values

X_train, X_test, y_train, y_test = \
    train_test_split(X, y, test_size=0.3, random_state=0)

sc = StandardScaler()
X_train_std = sc.fit_transform(X_train)
X_test_std = sc.transform(X_test)

cov_mat = np.cov(X_train_std.T)
eigen_vals, eigen_vecs = np.linalg.eig(cov_mat)

print('\nEigenvalues \n%s' % eigen_vals)


#############################################################################
print(50 * '=')
print('Section: Total and explained variance')
print(50 * '-')

tot = sum(eigen_vals)
var_exp = [(i / tot) for i in sorted(eigen_vals, reverse=True)]
cum_var_exp = np.cumsum(var_exp)

plt.bar(range(1, 14), var_exp, alpha=0.5, align='center',
        label='individual explained variance')
plt.step(range(1, 14), cum_var_exp, where='mid',
         label='cumulative explained variance')
plt.ylabel('Explained variance ratio')
plt.xlabel('Principal components')
plt.legend(loc='best')
# plt.tight_layout()
# plt.savefig('./figures/pca1.png', dpi=300)
plt.show()

import pandas as pd
import numpy as np
from sklearn.preprocessing import StandardScaler
from sklearn.decomposition import PCA
import matplotlib.pyplot as plt
from matplotlib.colors import ListedColormap
from sklearn.linear_model import LogisticRegression
from sklearn.discriminant_analysis import LinearDiscriminantAnalysis as LDA
from sklearn.datasets import make_moons
from sklearn.datasets import make_circles
from sklearn.decomposition import KernelPCA
from scipy.spatial.distance import pdist, squareform
from scipy import exp
from scipy.linalg import eigh
from matplotlib.ticker import FormatStrFormatter

# for sklearn 0.18's alternative syntax
from distutils.version import LooseVersion as Version
from sklearn import __version__ as sklearn_version
if Version(sklearn_version) < '0.18':
    from sklearn.grid_search import train_test_split
    from sklearn.lda import LDA
else:
    from sklearn.model_selection import train_test_split
    from sklearn.discriminant_analysis import LinearDiscriminantAnalysis as LDA


#############################################################################
print(50 * '=')
print('Section: Unsupervised dimensionality reduction'
      ' via principal component analysis')
print(50 * '-')

df_wine = pd.read_csv('https://archive.ics.uci.edu/ml/'
                      'machine-learning-databases/wine/wine.data',
                      header=None)

df_wine.columns = ['Class label', 'Alcohol', 'Malic acid', 'Ash',
                   'Alcalinity of ash', 'Magnesium', 'Total phenols',
                   'Flavanoids', 'Nonflavanoid phenols', 'Proanthocyanins',
                   'Color intensity', 'Hue',
                   'OD280/OD315 of diluted wines', 'Proline']

print('Wine data excerpt:\n\n:', df_wine.head())


X, y = df_wine.iloc[:, 1:].values, df_wine.iloc[:, 0].values

X_train, X_test, y_train, y_test = \
    train_test_split(X, y, test_size=0.3, random_state=0)

sc = StandardScaler()
X_train_std = sc.fit_transform(X_train)
X_test_std = sc.transform(X_test)

cov_mat = np.cov(X_train_std.T)
eigen_vals, eigen_vecs = np.linalg.eig(cov_mat)

print('\nEigenvalues \n%s' % eigen_vals)


#############################################################################
print(50 * '=')
print('Section: Total and explained variance')
print(50 * '-')

tot = sum(eigen_vals)
var_exp = [(i / tot) for i in sorted(eigen_vals, reverse=True)]
cum_var_exp = np.cumsum(var_exp)

plt.bar(range(1, 14), var_exp, alpha=0.5, align='center',
        label='individual explained variance')
plt.step(range(1, 14), cum_var_exp, where='mid',
         label='cumulative explained variance')
plt.ylabel('Explained variance ratio')
plt.xlabel('Principal components')
plt.legend(loc='best')
# plt.tight_layout()
# plt.savefig('./figures/pca1.png', dpi=300)
plt.show()

# for sklearn 0.18's alternative syntax ############################################################################# ############################################################################# # plt.tight_layout() # plt.savefig('./figures/pca1.png', dpi=300)