unable to pickle scipy.spatial.KDTree objects

Question

I have a code where I build a huge tree and I need to save it for later use. Unluckily it seems I cannot pickle scipy.spatial.KDTree objects.

In fact, when I run this:

import pickle
import scipy.spatial
tree=scipy.spatial.KDTree([[1,2,3]])
pickle.dump(tree,open('tree.p','wb'))

I get the error:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib64/python2.7/pickle.py", line 1370, in dump
    Pickler(file, protocol).dump(obj)
  File "/usr/lib64/python2.7/pickle.py", line 224, in dump
    self.save(obj)
  File "/usr/lib64/python2.7/pickle.py", line 331, in save
    self.save_reduce(obj=obj, *rv)
  File "/usr/lib64/python2.7/pickle.py", line 419, in save_reduce
    save(state)
  File "/usr/lib64/python2.7/pickle.py", line 286, in save
    f(self, obj) # Call unbound method with explicit self
  File "/usr/lib64/python2.7/pickle.py", line 649, in save_dict
    self._batch_setitems(obj.iteritems())
  File "/usr/lib64/python2.7/pickle.py", line 663, in _batch_setitems
    save(v)
  File "/usr/lib64/python2.7/pickle.py", line 331, in save
    self.save_reduce(obj=obj, *rv)
  File "/usr/lib64/python2.7/pickle.py", line 401, in save_reduce
    save(args)
  File "/usr/lib64/python2.7/pickle.py", line 286, in save
    f(self, obj) # Call unbound method with explicit self
  File "/usr/lib64/python2.7/pickle.py", line 562, in save_tuple
    save(element)
  File "/usr/lib64/python2.7/pickle.py", line 286, in save
    f(self, obj) # Call unbound method with explicit self
  File "/usr/lib64/python2.7/pickle.py", line 748, in save_global
    (obj, module, name))     pickle.PicklingError: Can't pickle <class 'scipy.spatial.kdtree.leafnode'>: it's not found as scipy.spatial.kdtree.leafnode

Given this, is there a way to pickle it? or at least to save a part of the object that can be used to rebuild the tree fastly? Otherwise, are there other fast options besides scipy.spatial.KDTree?

Answer 1

Use cKDTree instead of KDTree as follows:

import pickle
import scipy.spatial
tree=scipy.spatial.cKDTree([[1,2,3]])
pickle.dump(tree,open('tree.p','wb'))