simplify_hierarchy and CondensedTree._select_clusters optimisations #677
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This PR simplifies and optimises the
CondensedTree._select_clustersandsimplify_hierarchyfunctions. It turns out that thesimplify_hierarchyoperation reduces to iterating over thecluster_treein reverse order (so children are processed before their parents).The PR introduces one behavioural change to
simplify_hierarchy. Density values are no longer updated when two leaves combine into one. This change ensures that the resulting leaf-combination retains its full density range. Consequently, the resulting simplified tree more accurately reflects the persistence threshold. Only when a leaf merges into a non-leaf are the leaf's density values updated to avoid breaking the condensed tree plot. Those points can have densities higher than the non-leaf's birth density, resulting in child clusters breaking off from a parent cluster before its icicle ends.