IndexError: only integers, slices (:), ellipsis (...), numpy.newaxis (None) Error

[joshdunnlime]

Using this example:

from sklearn import datasets
import numpy as np
from classix import CLASSIX

X, y = datasets.make_blobs(n_samples=5000, centers=2, n_features=2, cluster_std=1, random_state=1)
clx = CLASSIX(sorting='pca', radius=0.15, group_merging='density', verbose=1, minPts=13, post_alloc=False)
clx.fit(X)

I am getting the following error:

---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)
<ipython-input-569-bb587af68fc1> in <module>
      5 X, y = datasets.make_blobs(n_samples=5000, centers=2, n_features=2, cluster_std=1, random_state=1)
      6 clx = CLASSIX(sorting='pca', radius=0.15, group_merging='density', verbose=1, minPts=13, post_alloc=False)
----> 7 clx.fit(X)
      8 
      9 X

~/miniconda3/envs/ltf-analysis/lib/python3.8/site-packages/classix/clustering.py in fit(self, data)
    506             self.labels_ = copy.deepcopy(self.groups_)
    507         else:
--> 508             self.labels_ = self.clustering(
    509                 data=self.data,
    510                 agg_labels=self.groups_,

~/miniconda3/envs/ltf-analysis/lib/python3.8/site-packages/classix/clustering.py in clustering(self, data, agg_labels, splist, sorting, radius, method, minPts)
    724             # self.merge_groups = merge_pairs(self.connected_pairs_)
    725 
--> 726         self.merge_groups, self.connected_pairs_ = self.fast_agglomerate(data, splist, radius, method, scale=self.scale)
    727         maxid = max(labels) + 1
    728 

~/miniconda3/envs/ltf-analysis/lib/python3.8/site-packages/classix/merging.py in fast_agglomerate(data, splist, radius, method, scale)
    115             # den1 = splist[int(i), 2] / volume # density(splist[int(i), 2], volume = volume)
    116             for j in select_stps.astype(int):
--> 117                 sp2 = data[splist[j, 0]] # splist[int(j), 3:]
    118 
    119                 c2 = np.linalg.norm(data-sp2, ord=2, axis=-1) <= radius

IndexError: only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

python==3.8.12
classixclustering==0.6.5
numpy==1.22.0
scipy==1.7.3

[chenxinye]

Hi @joshdunnlime

Thanks so much for pointing out this! we just fixed it in the next version 0.6.6. Please use the latest version of classix.
Also, it seems like you do not install Cython properly. Please let us know if you have further questions.

Best,
Xinye

[joshdunnlime]

I'll give it a spin and report back! Thanks for the prompt action!!

[joshdunnlime]

This seems to be working now. It do say that it isn't using Cython but was quick enough anyway for what I was doing.

Many thanks!