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#!/usr/bin/env python
from cogent.util.unit_test import TestCase, main
from numpy import array, sqrt, size
from cogent.cluster.nmds import NMDS, metaNMDS
from cogent.maths.distance_transform import dist_euclidean
__author__ = "Justin Kuczynski"
__copyright__ = "Copyright 2007-2016, The Cogent Project"
__credits__ = ["Justin Kuczynski"]
__license__ = "GPL"
__version__ = "1.9"
__maintainer__ = "Justin Kuczynski"
__email__ = "justinak@gmail.com"
__status__ = "Development"
class NMDSTests(TestCase):
"""test the nonmetric_scaling module, using floating point numpy arrays
"""
def setUp(self):
"""creates inputs"""
self.mtx = array([[0,3,4,8],
[3,0,1,27],
[4,1,0,3.5],
[8,27,3.5,0]],'d')
self.nm = NMDS(self.mtx, verbosity=0)
def test_getStress(self):
"""stress should be small
this is preliminary, better to check for convergence to similar states
with random starting points enabled"""
stress = self.nm.getStress()
self.assertLessThan(stress, 1e-1)
def test_getPoints(self):
"""points should be of the right number and dimensionality
this is preliminary, better to check for convergence to similar states
with random starting points enabled"""
pts = self.nm.getPoints()
self.assertEqual(size(pts, 0), 4)
self.assertEqual(size(pts, 1), 2)
def test_metaNMDS(self):
"""l19 data should give stress below .13"""
ptmtx = array(
[[7,1,0,0,0,0,0,0,0],
[4,2,0,0,0,1,0,0,0],
[2,4,0,0,0,1,0,0,0],
[1,7,0,0,0,0,0,0,0],
[0,8,0,0,0,0,0,0,0],
[0,7,1,0,0,0,0,0,0],#idx 5
[0,4,2,0,0,0,2,0,0],
[0,2,4,0,0,0,1,0,0],
[0,1,7,0,0,0,0,0,0],
[0,0,8,0,0,0,0,0,0],
[0,0,7,1,0,0,0,0,0],#idx 10
[0,0,4,2,0,0,0,3,0],
[0,0,2,4,0,0,0,1,0],
[0,0,1,7,0,0,0,0,0],
[0,0,0,8,0,0,0,0,0],
[0,0,0,7,1,0,0,0,0],#idx 15
[0,0,0,4,2,0,0,0,4],
[0,0,0,2,4,0,0,0,1],
[0,0,0,1,7,0,0,0,0]], 'float')
distmtx = dist_euclidean(ptmtx)
nm = metaNMDS(1, distmtx, verbosity=0)
self.assertLessThan(nm.getStress(), .13)
if __name__ == '__main__':
main()
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