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scipy.cluster.hierarchy.

# fclusterdata

scipy.cluster.hierarchy.fclusterdata(X, t, criterion='inconsistent', metric='euclidean', depth=2, method='single', R=None)

  Cluster observation data using a given metric.

  Clusters the original observations in the n-by-m data matrix X (n observations in m dimensions), using the euclidean distance metric to calculate distances between original observations, performs hierarchical clustering using the single linkage algorithm, and forms flat clusters using the inconsistency method with t as the cut-off threshold.

  A 1-D array `T` of length `n` is returned. `T[i]` is the index of the flat cluster to which the original observation `i` belongs.

  Parameters:
    X(N, M) ndarray

      N by M data matrix with N observations in M dimensions.

    t scalar
      For criteria ‘inconsistent’, ‘distance’ or ‘monocrit’,

        this is the threshold to apply when forming flat clusters.

      For ‘maxclust’ or ‘maxclust_monocrit’ criteria,

        this would be max number of clusters requested.

    criterion str, optional

      Specifies the criterion for forming flat clusters. Valid values are ‘inconsistent’ (default), ‘distance’, or ‘maxclust’ cluster formation algorithms. See `fcluster` for descriptions.

    metric str or function, optional

      The distance metric for calculating pairwise distances. See `distance.pdist` for descriptions and linkage to verify compatibility with the linkage method.

    depth int, optional

      The maximum depth for the inconsistency calculation. See `inconsistent` for more information.

    method str, optional

      The linkage method to use (single, complete, average, weighted, median centroid, ward). See `linkage` for more information. Default is “single”.

    R ndarray, optional

      The inconsistency matrix. It will be computed if necessary if it is not passed.

  Returns:
    fclusterdata ndarray

      A vector of length n. T[i] is the flat cluster number to which original observation i belongs.

  See also

  `scipy.spatial.distance.pdist`

    pairwise distance metrics

  Notes

  This function is similar to the MATLAB function `clusterdata`.

  `fclusterdata` 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.

  Library | CPU | GPU
  --- | --- | ---
  NumPy | ✅ | n/a
  CuPy | n/a | ⛔
  PyTorch | ✅ | ⛔
  JAX | ⚠️ no JIT | ⛔
  Dask | ⚠️ computes graph | n/a

  See Support for the array API standard for more information.

  Examples

      >>> from scipy.cluster.hierarchy import fclusterdata

  This is a convenience method that abstracts all the steps to perform in a typical SciPy’s hierarchical clustering workflow.

  - Transform the input data into a condensed matrix with `scipy.spatial.distance.pdist`.

  - Apply a clustering method.

  - Obtain flat clusters at a user defined distance threshold `t` using `scipy.cluster.hierarchy.fcluster`.

      >>> 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]]

      >>> fclusterdata(X, t=1)
      array([3, 3, 3, 4, 4, 4, 2, 2, 2, 1, 1, 1], dtype=int32)

  The output here (for the dataset `X`, distance threshold `t`, and the default settings) is four clusters with three data points each.