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#!/usr/bin/env python
"""Tests of the geometry package."""
from numpy import array, take, newaxis
from math import sqrt
from cogent.util.unit_test import TestCase, main
from cogent.maths.geometry import center_of_mass_one_array, \
center_of_mass_two_array, center_of_mass, distance, sphere_points
__author__ = "Sandra Smit"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Sandra Smit", "Rob Knight"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Sandra Smit"
__email__ = "sandra.smit@colorado.edu"
__status__ = "Production"
class CenterOfMassTests(TestCase):
"""Tests for the center of mass functions"""
def setUp(self):
"""setUp for all CenterOfMass tests"""
self.simple = array([[1, 1, 1], [3, 1, 1], [2, 3, 2]])
self.simple_list = [[1, 1, 1], [3, 1, 1], [2, 3, 2]]
self.more_weight = array([[1, 1, 3], [3, 1, 3], [2, 3, 50]])
self.square = array([[1, 1, 25], [3, 1, 25], [3, 3, 25], [1, 3, 25]])
self.square_odd = array([[1, 1, 25], [3, 1, 4], [3, 3, 25], [1, 3, 4]])
self.sec_weight = array([[1, 25, 1], [3, 25, 1], [3, 25, 3], [1, 25, 3]])
def test_center_of_mass_one_array(self):
"""center_of_mass_one_array should behave correctly"""
com1 = center_of_mass_one_array
self.assertEqual(com1(self.simple), array([2, 2]))
self.assertEqual(com1(self.simple_list), array([2, 2]))
self.assertFloatEqual(com1(self.more_weight), array([2, 2.785714]))
self.assertEqual(com1(self.square), array([2, 2]))
self.assertEqual(com1(self.square_odd), array([2, 2]))
self.assertEqual(com1(self.sec_weight, 1), array([2, 2]))
def test_CoM_one_array_wrong(self):
"""center_of_mass_one_array should fail on wrong input"""
com1 = center_of_mass_one_array
self.assertRaises(TypeError, com1, self.simple, 'a') #weight_idx wrong
self.assertRaises(IndexError, com1, self.simple, 100) #w_idx out of range
self.assertRaises(IndexError, com1, [1, 2, 3], 2) #shape[1] out of range
def test_center_of_mass_two_array(self):
"""center_of_mass_two_array should behave correctly"""
com2 = center_of_mass_two_array
coor = take(self.square_odd, (0, 1), 1)
weights = take(self.square_odd, (2,), 1)
self.assertEqual(com2(coor, weights), array([2, 2]))
weights = weights.ravel()
self.assertEqual(com2(coor, weights), array([2, 2]))
def test_CoM_two_array_wrong(self):
"""center_of_mass_two_array should fail on wrong input"""
com2 = center_of_mass_two_array
weights = [1, 2]
self.assertRaises(TypeError, com2, self.simple, 'a') #weight_idx wrong
self.assertRaises(ValueError, com2, self.simple, weights) #not aligned
def test_center_of_mass(self):
"""center_of_mass should make right choice between functional methods
"""
com = center_of_mass
com1 = center_of_mass_one_array
com2 = center_of_mass_two_array
self.assertEqual(com(self.simple), com1(self.simple))
self.assertFloatEqual(com(self.more_weight), com1(self.more_weight))
self.assertEqual(com(self.sec_weight, 1), com1(self.sec_weight, 1))
coor = take(self.square_odd, (0, 1), 1)
weights = take(self.square_odd, (2,), 1)
self.assertEqual(com(coor, weights), com2(coor, weights))
weights = weights.ravel()
self.assertEqual(com(coor, weights), com2(coor, weights))
def test_distance(self):
"""distance should return Euclidean distance correctly."""
#for single dimension, should return difference
a1 = array([3])
a2 = array([-1])
self.assertEqual(distance(a1, a2), 4)
#for two dimensions, should work e.g. for 3, 4, 5 triangle
a1 = array([0, 0])
a2 = array([3, 4])
self.assertEqual(distance(a1, a2), 5)
#vector should be the same as itself for any dimensions
a1 = array([1.3, 23, 5.4, 2.6, -1.2])
self.assertEqual(distance(a1, a1), 0)
#should match hand-calculated case for an array
a1 = array([[1, -2], [3, 4]])
a2 = array([[1, 0], [-1, 2.5]])
self.assertEqual(distance(a1, a1), 0)
self.assertEqual(distance(a2, a2), 0)
self.assertEqual(distance(a1, a2), distance(a2, a1))
self.assertFloatEqual(distance(a1, a2), sqrt(22.25))
def test_sphere_points(self):
"""tests sphere points"""
self.assertEquals(sphere_points(1), array([[ 1., 0., 0.]]))
# def test_coords_to_symmetry(self):
# """tests symmetry expansion (TODO)"""
# pass
#
# def test_coords_to_crystal(self):
# """tests crystal expansion (TODO)"""
# pass
if __name__ == '__main__':
main()
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