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#!/usr/bin/env python
import os, tempfile
import numpy as np
try:
from cogent.util.unit_test import TestCase, main
except ImportError:
from zenpdb.cogent.util.unit_test import TestCase, main
__author__ = "Marcin Cieslik"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__contributors__ = ["Marcin Cieslik"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Marcin Cieslik"
__email__ = "mpc4p@virginia.edu"
__status__ = "Development"
class KDTreeTest(TestCase):
"""Tests KD-Trees"""
def setUp(self):
self.arr = np.random.random(3000).reshape((1000, 3))
self.point = np.random.random(3)
self.center = np.array([0.5, 0.5, 0.5])
def test_0import(self):
# sort by name
"""tests if can import ckd3 cython extension."""
global ckd3
from cogent.maths.spatial import ckd3
assert 'KDTree' in dir(ckd3)
def test_instance(self):
"""check if KDTree instance behaves correctly."""
kdt = ckd3.KDTree(self.arr)
self.assertEquals(kdt.dims, 3)
def assig():
kdt.dims = 4
self.assertRaises(AttributeError, assig)
self.assertEquals(kdt.dims, 3)
self.assertEquals(kdt.pnts, 1000)
def test_knn(self):
"""testing k-nearest neighbors.
"""
sqd = np.sum(np.power((self.arr - self.point), 2), axis=1)
sorted_idx = sqd.argsort()
kdt = ckd3.KDTree(self.arr)
points, dists = kdt.knn(self.point, 5)
self.assertEqualItems(sorted_idx[:5], points)
def test_rn(self):
"""testing neighbors within radius.
"""
sqd = np.sum(np.power((self.arr - self.point), 2), axis=1)
sqd = sqd[sqd <= 0.05]
sqd.sort()
kdt = ckd3.KDTree(self.arr)
points, dists = kdt.rn(self.point, 0.05)
dists.sort()
self.assertFloatEqual(dists, sqd)
if __name__ == '__main__':
main()
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