from_mlab_linkage — SciPy v1.16.0 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.

Notes

from_mlab_linkage has experimental support for Python Array API Standard compatible backends in addition to NumPy. Please consider testing these features by setting an environment variable SCIPY_ARRAY_API=1 and providing CuPy, PyTorch, JAX, or Dask arrays as array arguments. The following combinations of backend and device (or other capability) are supported.

See Support for the array API standard for more information.

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).