scipy.cluster.hierarchy.to_mlab_linkage

scipy.cluster.hierarchy.to_mlab_linkage(Z)

Convert a linkage matrix to a MATLAB(TM) compatible one.

Converts a linkage matrix Z generated by the linkage function of this module to a MATLAB(TM) compatible one. The return linkage matrix has the last column removed and the cluster indices are converted to 1..N indexing.

Parameters:

Z : ndarray

A linkage matrix generated by scipy.cluster.hierarchy.

Returns:

to_mlab_linkage : ndarray

A linkage matrix compatible with MATLAB(TM)’s hierarchical clustering functions.

The return linkage matrix has the last column removed and the cluster indices are converted to 1..N indexing.

See also

linkage

for a description of what a linkage matrix is.

from_mlab_linkage

transform from Matlab to Scipy format.

Examples

>>> from scipy.cluster.hierarchy import ward, to_mlab_linkage
>>> from scipy.spatial.distance import pdist

>>> X = [[0, 0], [0, 1], [1, 0],
...      [0, 4], [0, 3], [1, 4],
...      [4, 0], [3, 0], [4, 1],
...      [4, 4], [3, 4], [4, 3]]

>>> Z = ward(pdist(X))
>>> Z
array([[ 0.        ,  1.        ,  1.        ,  2.        ],
       [ 3.        ,  4.        ,  1.        ,  2.        ],
       [ 6.        ,  7.        ,  1.        ,  2.        ],
       [ 9.        , 10.        ,  1.        ,  2.        ],
       [ 2.        , 12.        ,  1.29099445,  3.        ],
       [ 5.        , 13.        ,  1.29099445,  3.        ],
       [ 8.        , 14.        ,  1.29099445,  3.        ],
       [11.        , 15.        ,  1.29099445,  3.        ],
       [16.        , 17.        ,  5.77350269,  6.        ],
       [18.        , 19.        ,  5.77350269,  6.        ],
       [20.        , 21.        ,  8.16496581, 12.        ]])

After a linkage matrix Z has been created, we can use scipy.cluster.hierarchy.to_mlab_linkage to convert it into MATLAB format:

>>> mZ = to_mlab_linkage(Z)
>>> mZ
array([[  1.        ,   2.        ,   1.        ],
       [  4.        ,   5.        ,   1.        ],
       [  7.        ,   8.        ,   1.        ],
       [ 10.        ,  11.        ,   1.        ],
       [  3.        ,  13.        ,   1.29099445],
       [  6.        ,  14.        ,   1.29099445],
       [  9.        ,  15.        ,   1.29099445],
       [ 12.        ,  16.        ,   1.29099445],
       [ 17.        ,  18.        ,   5.77350269],
       [ 19.        ,  20.        ,   5.77350269],
       [ 21.        ,  22.        ,   8.16496581]])

The new linkage matrix mZ uses 1-indexing for all the clusters (instead of 0-indexing). Also, the last column of the original linkage matrix has been dropped.