Error while importing scipy.spatial.distance in python

Question

While I am running this code in ubuntu 14.04, I want to calculate the cosine distance of an array with scipy.spatial.distance. But it is throwing me an error in importing scipy.spatial.distance.

import numpy as np
import scipy
from scipy.spatial.distance import pdist


x=np.array([[[-0.22008298,  0.28819615,  0.09895946,  0.16789497,  0.02379252,
   -0.25700486,  0.1628186,   0.12296761,  0.01750283]],

 [[ 0.29891527,  0.17249978, -0.10084602, -0.16522293,  0.06811064,
    0.07434326, -0.19697316, -0.22199543,  0.07647966]],

 [[-0.04112297,  0.13392878, -0.06575392,  0.0893533,   0.22577047,
    0.00289264,  0.09996213,  0.17324321,  0.08673526]]])


B =x.transpose(1,2,0).reshape(-1,x.shape[0])
print(B.shape) 
print (B.ndim)
#array.astype(int)
print(B)
y=1-(pdist(B, metric='cosine'))
print(y)

It is throwing this error,

     Traceback (most recent call last):
  File "cos1.py", line 3, in <module>
    from scipy.spatial.distance import pdist
  File "/home/mayesha/venv/local/lib/python2.7/site-packages/scipy/spatial/__init__.py", line 94, in <module>
    from .kdtree import *
  File "/home/mayesha/venv/local/lib/python2.7/site-packages/scipy/spatial/kdtree.py", line 8, in <module>
    import scipy.sparse
  File "/home/mayesha/venv/local/lib/python2.7/site-packages/scipy/sparse/__init__.py", line 229, in <module>
    from .csr import *
  File "/home/mayesha/venv/local/lib/python2.7/site-packages/scipy/sparse/csr.py", line 20, in <module>
    from .compressed import _cs_matrix
  File "/home/mayesha/venv/local/lib/python2.7/site-packages/scipy/sparse/compressed.py", line 11, in <module>
    from scipy._lib._util import _prune_array
  File "/home/mayesha/venv/local/lib/python2.7/site-packages/scipy/_lib/_util.py", line 9, in <module>
    import inspect
  File "/usr/lib/python2.7/inspect.py", line 37, in <module>
    import dis
  File "/home/mayesha/dis.py", line 2, in <module>
    from scipy.spatial.distance import pdist
  File "/home/mayesha/venv/local/lib/python2.7/site-packages/scipy/spatial/distance.py", line 119, in <module>
    from scipy._lib._util import _asarray_validated
ImportError: cannot import name _asarray_validated

I am using virtual environment with pip. Can someone help me. Thanks in advance.

Answer 1

Installing package sklearn solved my problem.

Answer 2

pip install -U scipy

This will solve your issue. I have tried and it did for me. You might get an error that scikit-learn is not installed properly. If you get that error, you can first run:

pip install -U scikit-learn

and then rerun the above code.