def test_mlab_linkage_conversion_multiple_rows(self):
     # Tests from/to_mlab_linkage on linkage array with multiple rows.
     Zm = np.asarray([[3, 6, 138], [4, 5, 219],
                      [1, 8, 255], [2, 9, 268], [7, 10, 295]])
     Z = np.array([[2., 5., 138., 2.],
                   [3., 4., 219., 2.],
                   [0., 7., 255., 3.],
                   [1., 8., 268., 4.],
                   [6., 9., 295., 6.]],
                   dtype=np.double)
     assert_equal(from_mlab_linkage(Zm), Z)
     assert_equal(to_mlab_linkage(Z), Zm)

 def test_mlab_linkage_conversion_multiple_rows(self):
     # Tests from/to_mlab_linkage on linkage array with multiple rows.
     Zm = np.asarray([[3, 6, 138], [4, 5, 219], [1, 8, 255], [2, 9, 268], [7, 10, 295]])
     Z = np.array(
         [
             [2.0, 5.0, 138.0, 2.0],
             [3.0, 4.0, 219.0, 2.0],
             [0.0, 7.0, 255.0, 3.0],
             [1.0, 8.0, 268.0, 4.0],
             [6.0, 9.0, 295.0, 6.0],
         ],
         dtype=np.double,
     )
     assert_equal(from_mlab_linkage(Zm), Z)
     assert_equal(to_mlab_linkage(Z), Zm)

def show_dendrogram(Z, **kwargs):
    from scipy.cluster.hierarchy import dendrogram, from_mlab_linkage
    from matplotlib import pyplot as plt

    dendrogram(from_mlab_linkage(Z), **kwargs)
    plt.show()

 def test_mlab_linkage_conversion_single_row(self):
     # Tests from/to_mlab_linkage on linkage array with single row.
     Z = np.asarray([[0., 1., 3., 2.]])
     Zm = [[1, 2, 3]]
     assert_equal(from_mlab_linkage(Zm), Z)
     assert_equal(to_mlab_linkage(Z), Zm)

 def test_mlab_linkage_conversion_empty(self):
     # Tests from/to_mlab_linkage on empty linkage array.
     X = np.asarray([])
     assert_equal(from_mlab_linkage([]), X)
     assert_equal(to_mlab_linkage([]), X)

import scipy.cluster.hierarchy as hcluster
import numpy as np
import matplotlib.pyplot as plt

chained_linkage = np.array([[1, 2, 1], [9, 3, 2], [10, 4, 3], [11, 5, 4], [12, 6, 5], [13, 7, 6], [14, 8, 7]])
chained_linkage = hcluster.from_mlab_linkage(chained_linkage)
perfect_linkage = hcluster.from_mlab_linkage(np.array([[1,2,1], [3,4,1], [5,6,1], [7,8,1], [9,10,2], [11,12,2], [13,14,3]]))

hcluster.dendrogram(perfect_linkage, color_threshold=0)
plt.savefig('perfect_linkage.pdf')
plt.close('all')
hcluster.dendrogram(chained_linkage, color_threshold=0)
plt.savefig('worst_case_linkage.pdf')
plt.close('all')

 def check_linkage_q(self, method):
     # Tests linkage(Y, method) on the Q data set.
     Z = linkage(eo['Q-X'], method)
     Zmlab = eo['linkage-Q-%s' % method]
     expectedZ = from_mlab_linkage(Zmlab)
     assert_allclose(Z, expectedZ, atol=1e-06)

 def check_linkage_tdist(self, method):
     # Tests linkage(Y, method) on the tdist data set.
     Z = linkage(_ytdist, method)
     Zmlab = eo['linkage-%s-tdist' % method]
     expectedZ = from_mlab_linkage(Zmlab)
     assert_allclose(Z, expectedZ, atol=1e-10)