Scipy Interoperability functions¶

 Converts an Higra binary hierarchy to a SciPy linkage matrix. Converts a SciPy linkage matrix to an Higra binary hierarchy.
binary_hierarchy_to_scipy_linkage_matrix(tree, altitudes=None, area=None)[source]

Converts an Higra binary hierarchy to a SciPy linkage matrix.

From SciPy documentation:

An $$n-1$$ by 4 matrix $$Z$$ is returned. At the $$i$$-th iteration, clusters with indices $$Z[i, 0]$$ and $$Z[i, 1]$$ are combined to form cluster $$n+i$$. A cluster with an index less than $$n$$ corresponds to one of the $$n$$ original observations. The distance between clusters $$Z[i, 0]$$ and $$Z[i, 1]$$ is given by $$Z[i, 2]$$. The fourth value $$Z[i, 3]$$ represents the number of original observations in the newly formed cluster.

If altitudes is not specified, the value provided by attribute_regular_altitudes() on tree is used.

If area is not specified, the value provided by attribute_area() on tree is used.

Parameters
• tree – Input tree

• altitudes – Tree nodes altitudes (should be increasing w.r.t tree)

• area – Tree nodes area (should be increasing w.r.t tree)

Returns

scipy_linkage_matrix_to_binary_hierarchy(linkage_matrix)[source]

Converts a SciPy linkage matrix to an Higra binary hierarchy.

The result is composed of

• a tree

• an array containing the altitudes of the tree nodes

• an array containing the area of the tree nodes

Parameters

linkage_matrix – a 2d array as produced by the linkage method of SciPy

Returns

a tuple (tree, altitudes, area)