from_mlab_linkage — SciPy v1.15.2 Manual (original) (raw)

scipy.cluster.hierarchy.

scipy.cluster.hierarchy.from_mlab_linkage(Z)[source]#

Convert a linkage matrix generated by MATLAB(TM) to a new linkage matrix compatible with this module.

The conversion does two things:

• the indices are converted from 1..N to 0..(N-1) form, and
• a fourth column Z[:,3] is added where Z[i,3] represents the number of original observations (leaves) in the non-singleton cluster i.

This function is useful when loading in linkages from legacy data files generated by MATLAB.

Parameters:

Zndarray

A linkage matrix generated by MATLAB(TM).

Returns:

ZSndarray

A linkage matrix compatible with scipy.cluster.hierarchy.

See also

linkage

for a description of what a linkage matrix is.

to_mlab_linkage

transform from SciPy to MATLAB format.

Examples

import numpy as np from scipy.cluster.hierarchy import ward, from_mlab_linkage

Given a linkage matrix in MATLAB format mZ, we can usescipy.cluster.hierarchy.from_mlab_linkage to import it into SciPy format:

mZ = np.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]])

Z = from_mlab_linkage(mZ) 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. ]])

As expected, the linkage matrix Z returned includes an additional column counting the number of original samples in each cluster. Also, all cluster indices are reduced by 1 (MATLAB format uses 1-indexing, whereas SciPy uses 0-indexing).