centroid#
- scipy.cluster.hierarchy.centroid(y)[source]#
Perform centroid/UPGMC linkage.
See
linkagefor more information on the input matrix, return structure, and algorithm.The following are common calling conventions:
Z = centroid(y)Performs centroid/UPGMC linkage on the condensed distance matrix
y.Z = centroid(X)Performs centroid/UPGMC linkage on the observation matrix
Xusing Euclidean distance as the distance metric.
- Parameters:
- yndarray
A condensed distance matrix. A condensed distance matrix is a flat array containing the upper triangular of the distance matrix. This is the form that
pdistreturns. Alternatively, a collection of m observation vectors in n dimensions may be passed as an m by n array.
- Returns:
- Zndarray
A linkage matrix containing the hierarchical clustering. See the
linkagefunction documentation for more information on its structure.
See also
linkagefor advanced creation of hierarchical clusterings.
scipy.spatial.distance.pdistpairwise distance metrics
Notes
centroidhas experimental support for Python Array API Standard compatible backends in addition to NumPy. Please consider testing these features by setting an environment variableSCIPY_ARRAY_API=1and providing CuPy, PyTorch, JAX, or Dask arrays as array arguments. The following combinations of backend and device (or other capability) are supported.Library
CPU
GPU
NumPy
✅
n/a
CuPy
n/a
⛔
PyTorch
✅
⛔
JAX
✅
⛔
Dask
⚠️ merges chunks
n/a
See Support for the array API standard for more information.
Examples
>>> from scipy.cluster.hierarchy import centroid, fcluster >>> from scipy.spatial.distance import pdist
First, we need a toy dataset to play with:
x x x x x x x x x x x x
>>> 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]]
Then, we get a condensed distance matrix from this dataset:
>>> y = pdist(X)
Finally, we can perform the clustering:
>>> Z = centroid(y) >>> Z array([[ 0. , 1. , 1. , 2. ], [ 3. , 4. , 1. , 2. ], [ 9. , 10. , 1. , 2. ], [ 6. , 7. , 1. , 2. ], [ 2. , 12. , 1.11803399, 3. ], [ 5. , 13. , 1.11803399, 3. ], [ 8. , 15. , 1.11803399, 3. ], [11. , 14. , 1.11803399, 3. ], [18. , 19. , 3.33333333, 6. ], [16. , 17. , 3.33333333, 6. ], [20. , 21. , 3.33333333, 12. ]]) # may vary
The linkage matrix
Zrepresents a dendrogram - seescipy.cluster.hierarchy.linkagefor a detailed explanation of its contents.We can use
scipy.cluster.hierarchy.fclusterto see to which cluster each initial point would belong given a distance threshold:>>> fcluster(Z, 0.9, criterion='distance') array([ 7, 8, 9, 10, 11, 12, 1, 2, 3, 4, 5, 6], dtype=int32) # may vary >>> fcluster(Z, 1.1, criterion='distance') array([5, 5, 6, 7, 7, 8, 1, 1, 2, 3, 3, 4], dtype=int32) # may vary >>> fcluster(Z, 2, criterion='distance') array([3, 3, 3, 4, 4, 4, 1, 1, 1, 2, 2, 2], dtype=int32) # may vary >>> fcluster(Z, 4, criterion='distance') array([1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], dtype=int32)
Also,
scipy.cluster.hierarchy.dendrogramcan be used to generate a plot of the dendrogram.