Number of clusters does not match with the number of selected areas in condensed_tree

[cyr31000]

Hi,

I have started to use hdbscan for a couple of weeks. Sometimes, I got for examples 3 clusters, but when I plot the condensed_tree with the option select_, clusters= True, I have seen that 6 clusters are selected (6 ellipses are drew) in the condensed_tree. It's like sometimes the condensed_tree is not updated. Any ideas? I've checked the corresponding .pyx files but no more informations...
Thank you,

cyr31000

[JelmerBot]

That sounds odd, indeed. Could you provide a small example script that reproduces this behaviour? And which version are you using? The latest release or a more recent branch?

This is the function in the current main branch that decides which ellipses to draw:

hdbscan/hdbscan/plots.py

Lines 235 to 245 in 8ecf239

	def _select_clusters(self):
	points_tree = self._raw_tree[self._raw_tree["child_size"] == 1]
	# Find lowest cluster segment id for each cluster label
	segments = points_tree['parent']
	labels = self._labels[points_tree['child']]
	order = np.argsort(labels)
	groups = np.split(segments[order], np.flatnonzero(np.diff(labels[order]) != 0) + 1)
	return [
	groups[label].min() for label in range(int(labels[order[0]] == -1), len(groups))
	]

It uses the cluster label vector to find the correct segment for each cluster. That cluster label vector is read from the HDBSCAN object each time the condensed_tree_ property is accessed. So, a CondensedTree object can become outdated if the HDBSCAN object changes after its creation:

# create clusterer and tree object
clusterer = HDBSCAN().fit(data)
tree = clusterer.condensed_tree_

# change clustering after tree creation
clusterer.cluster_selection_method='leaf'
clusterer.fit(data)

# outdated figure
tree.plot(select_clusters=True)
# updated figure
clusterer.condensed_tree_.plot(select_clusters=True)