| 1 | """ |
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| 2 | Unit tests for specific models |
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| 3 | @author: Mathieu Doucet / UTK |
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| 4 | """ |
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| 5 | |
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| 6 | import unittest, math, time |
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| 7 | |
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| 8 | # Disable "missing docstring" complaint |
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| 9 | # pylint: disable-msg=C0111 |
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| 10 | # Disable "too many methods" complaint |
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| 11 | # pylint: disable-msg=R0904 |
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| 12 | # Disable "could be a function" complaint |
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| 13 | # pylint: disable-msg=R0201 |
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| 14 | |
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| 15 | try: |
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| 16 | import VolumeCanvas |
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| 17 | print "Testing local version" |
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| 18 | except: |
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| 19 | import sys |
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| 20 | print sys.exc_value |
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| 21 | #testing the version that is working on |
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| 22 | print "Testing installed version" |
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| 23 | import sas.sascalc.realspace.VolumeCanvas as VolumeCanvas |
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| 24 | |
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| 25 | class TestRealSpaceModel(unittest.TestCase): |
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| 26 | """ Unit tests for sphere model """ |
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| 27 | |
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| 28 | def setUp(self): |
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| 29 | self.model = VolumeCanvas.VolumeCanvas() |
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| 30 | self.model.add('cylinder', 'cyl') |
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| 31 | self.model.add('sphere', 'sph') |
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| 32 | self.model.add('ellipsoid', 'elli') |
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| 33 | self.model.add('singlehelix', 'shelix') |
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| 34 | |
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| 35 | def testAdding(self): |
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| 36 | self.assertEqual('cyl', self.model.add('cylinder', 'cyl')) |
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| 37 | |
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| 38 | def testDeleting(self): |
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| 39 | self.model.add('ellipsoid','elli2') |
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| 40 | self.model.delete('elli2') |
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| 41 | self.assert_('elli2' not in self.model.getShapeList()) |
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| 42 | |
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| 43 | def testsetParam(self): |
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| 44 | self.model.setParam('q_max', 0.2) |
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| 45 | self.model.setParam('shelix.radius_helix', 12) |
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| 46 | |
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| 47 | def testgetParamList(self): |
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| 48 | #print self.model.getParamList() |
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| 49 | #print self.model.getParamList('shelix') |
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| 50 | pass |
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| 51 | |
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| 52 | def testPr_Iq(self): |
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| 53 | self.model.getPr() |
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| 54 | #print "pr is calculated", self.model.hasPr |
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| 55 | result = self.model.getIq(0.1) |
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| 56 | #print "I(0.1) is calculated: ", result |
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| 57 | |
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| 58 | class TestSphere(unittest.TestCase): |
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| 59 | """ Unit tests for sphere model """ |
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| 60 | |
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| 61 | def setUp(self): |
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| 62 | self.canvas = VolumeCanvas.VolumeCanvas() |
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| 63 | |
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| 64 | |
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| 65 | def testSetQmax(self): |
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| 66 | old_value = self.canvas.getParam('q_max') |
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| 67 | new_value = old_value + 0.1 |
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| 68 | self.canvas.setParam('q_max', new_value) |
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| 69 | self.assertEqual(self.canvas.getParam("Q_MAx"), new_value) |
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| 70 | |
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| 71 | def testSetDensity(self): |
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| 72 | self.canvas.setParam('lores_density', 0.1) |
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| 73 | handle = self.canvas.add('sphere') |
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| 74 | self.canvas.setParam("%s.radius" % handle, 5.0) |
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| 75 | vol = 4/3*math.pi*5*5*5 |
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| 76 | npts_1 = vol/0.1 |
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| 77 | value_1 = self.canvas.getIq(0.001) |
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| 78 | |
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| 79 | # Change density, the answer should be the same |
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| 80 | self.canvas.setParam('lores_density', 0.2) |
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| 81 | npts_2 = vol/0.2 |
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| 82 | value_2 = self.canvas.getIq(0.001) |
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| 83 | |
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| 84 | self.assert_( (value_1-value_2)/value_1 < 0.1) |
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| 85 | |
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| 86 | def testSetDensityTiming(self): |
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| 87 | """Testing change in computation time with density""" |
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| 88 | handle = self.canvas.add('sphere') |
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| 89 | self.canvas.setParam("%s.radius" % handle, 15.0) |
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| 90 | |
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| 91 | self.canvas.setParam('lores_density', 0.6) |
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| 92 | t_0 = time.time() |
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| 93 | self.canvas.getIq(0.001) |
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| 94 | t_1 = time.time()-t_0 |
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| 95 | |
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| 96 | # Change density, the answer should be the same |
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| 97 | self.canvas.setParam('lores_density', 0.1) |
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| 98 | t_0 = time.time() |
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| 99 | self.canvas.getIq(0.001) |
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| 100 | t_2 = time.time()-t_0 |
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| 101 | |
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| 102 | self.assert_( t_2 < t_1 and (t_1-t_2)/t_2 > 2) |
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| 103 | |
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| 104 | def testGetParamList(self): |
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| 105 | """ Test GetParamList on empty canvas""" |
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| 106 | self.assert_('lores_density' in self.canvas.getParamList()) |
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| 107 | handle = self.canvas.add('sphere') |
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| 108 | |
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| 109 | def testGetParamListWithShape(self): |
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| 110 | """ Test GetParamList on filled canvas""" |
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| 111 | self.canvas.add('sphere') |
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| 112 | self.assert_('lores_density' in self.canvas.getParamList()) |
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| 113 | |
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| 114 | def testAdd(self): |
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| 115 | handle = "s1" |
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| 116 | self.assertEqual(handle, self.canvas.add('sphere', handle)) |
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| 117 | |
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| 118 | #TODO: test for current list of shape |
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| 119 | self.assertEqual( [handle] , self.canvas.getShapeList()) |
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| 120 | |
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| 121 | def testSetRadius(self): |
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| 122 | handle = self.canvas.add('sphere') |
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| 123 | self.canvas.setParam("%s.rAdius" % handle, 24.0) |
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| 124 | self.assertEqual(self.canvas.getParam("%s.rAdius" % handle), 24.0) |
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| 125 | |
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| 126 | def testGetIq(self): |
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| 127 | """ Test the output of I(q) to the analytical solution |
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| 128 | If the normalization is wrong, we will have to fix it. |
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| 129 | |
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| 130 | getIq() should call getPr() behind the scenes so that |
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| 131 | the user doesnt have to do it if he doesn't need to. |
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| 132 | """ |
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| 133 | from sas.models.SphereModel import SphereModel |
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| 134 | sphere = SphereModel() |
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| 135 | sphere.setParam('radius', 10.0) |
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| 136 | sphere.setParam('contrast', 1.0) |
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| 137 | sphere.setParam('background', 0.0) |
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| 138 | sphere.setParam('scale', 1.0) |
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| 139 | |
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| 140 | handle = self.canvas.add('sphere') |
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| 141 | self.canvas.setParam('%s.radius' % handle, 10.0) |
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| 142 | self.canvas.setParam('%s.contrast' % handle, 1.0) |
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| 143 | |
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| 144 | |
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| 145 | sim_1 = self.canvas.getIq(0.001) |
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| 146 | ana_1 = sphere.run(0.001) |
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| 147 | sim_2 = self.canvas.getIq(0.01) |
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| 148 | ana_2 = sphere.run(0.01) |
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| 149 | |
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| 150 | # test the shape of the curve (calculate relative error |
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| 151 | # on the output and it should be compatible with zero |
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| 152 | # THIS WILL DEPEND ON THE NUMBER OF SPACE POINTS: |
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| 153 | # that why we need some error analysis. |
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| 154 | self.assert_( (sim_2*ana_1/sim_1 - ana_2)/ana_2 < 0.1) |
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| 155 | |
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| 156 | # test the absolute amplitude |
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| 157 | self.assert_( math.fabs(sim_2-ana_2)/ana_2 < 0.1) |
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| 158 | |
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| 159 | def testGetIq2(self): |
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| 160 | """ Test two different q values |
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| 161 | """ |
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| 162 | handle = self.canvas.add('sphere') |
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| 163 | self.canvas.setParam('%s.radius' % handle, 10.0) |
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| 164 | |
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| 165 | sim_1 = self.canvas.getIq(0.001) |
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| 166 | sim_2 = self.canvas.getIq(0.01) |
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| 167 | |
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| 168 | self.assertNotAlmostEqual(sim_2, sim_1, 3) |
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| 169 | |
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| 170 | def testGetIq_Identical(self): |
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| 171 | """ Test for identical model / no param change |
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| 172 | """ |
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| 173 | handle = self.canvas.add('sphere') |
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| 174 | self.canvas.setParam('%s.radius' % handle, 10.0) |
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| 175 | |
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| 176 | sim_1 = self.canvas.getIq(0.01) |
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| 177 | sim_2 = self.canvas.getIq(0.01) |
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| 178 | |
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| 179 | self.assertEqual(sim_2, sim_1) |
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| 180 | |
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| 181 | def testGetIq_Identical2(self): |
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| 182 | """ Test for identical model after a parameter change |
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| 183 | Should be different only of the space points |
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| 184 | are regenerated and the random seed is different |
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| 185 | """ |
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| 186 | handle = self.canvas.add('sphere') |
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| 187 | self.canvas.setParam('%s.radius' % handle, 10.0) |
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| 188 | |
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| 189 | self.canvas.setParam('lores_density', 0.1) |
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| 190 | sim_1 = self.canvas.getIq(0.01) |
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| 191 | |
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| 192 | # Try to fool the code by changing to a different value |
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| 193 | self.canvas.setParam('lores_density', 0.2) |
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| 194 | self.canvas.getIq(0.01) |
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| 195 | |
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| 196 | self.canvas.setParam('lores_density', 0.1) |
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| 197 | sim_2 = self.canvas.getIq(0.01) |
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| 198 | |
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| 199 | self.assert_((sim_2-sim_1)/sim_1<0.05) |
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| 200 | |
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| 201 | def testGetIq_time(self): |
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| 202 | """ Time profile |
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| 203 | """ |
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| 204 | handle = self.canvas.add('sphere') |
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| 205 | self.canvas.setParam('%s.radius' % handle, 15.0) |
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| 206 | |
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| 207 | |
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| 208 | self.canvas.setParam('lores_density', 0.1) |
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| 209 | t_0 = time.time() |
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| 210 | sim_1 = self.canvas.getIq(0.01) |
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| 211 | delta_1 = time.time()-t_0 |
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| 212 | |
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| 213 | self.canvas.setParam('lores_density', 0.1) |
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| 214 | |
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| 215 | t_0 = time.time() |
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| 216 | sim_2 = self.canvas.getIq(0.01) |
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| 217 | delta_2 = time.time()-t_0 |
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| 218 | |
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| 219 | self.assert_((delta_2-delta_1)/delta_1<0.05) |
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| 220 | |
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| 221 | |
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| 222 | def testGetPr(self): |
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| 223 | """Compare the output of P(r) to the theoretical value""" |
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| 224 | #TODO: find a way to compare you P(r) to the known |
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| 225 | # analytical value. |
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| 226 | pass |
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| 227 | |
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| 228 | def testLogic1(self): |
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| 229 | """ Test that the internal logic is set so that the user |
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| 230 | get the right output after changing a parameter |
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| 231 | """ |
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| 232 | |
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| 233 | handle = self.canvas.add('sphere') |
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| 234 | self.canvas.setParam('%s.radius' % handle, 10.0) |
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| 235 | result_1 = self.canvas.getIq(0.1) |
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| 236 | self.canvas.setParam('%s.radius' % handle, 20.0) |
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| 237 | result_2 = self.canvas.getIq(0.1) |
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| 238 | self.assertNotAlmostEqual(result_1, result_2, 2) |
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| 239 | |
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| 240 | class TestCanvas(unittest.TestCase): |
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| 241 | """ Unit tests for all shapes in canvas model """ |
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| 242 | |
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| 243 | def setUp(self): |
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| 244 | self.canvas = VolumeCanvas.VolumeCanvas() |
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| 245 | self.canvas.params['lores_density'] = 0.05 |
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| 246 | |
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| 247 | def testGetIq_cylinder(self): |
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| 248 | handle = self.canvas.add('cylinder','cyl') |
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| 249 | self.canvas.setParam('%s.radius' % handle, 15.0) |
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| 250 | self.canvas.setParam('%s.length' % handle, 50.0) |
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| 251 | self.assertEqual(50,self.canvas.getParam('%s.length'%handle)) |
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| 252 | result_1 = self.canvas.getIq(0.1) |
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| 253 | result_2 = self.canvas.getIq(0.1) |
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| 254 | self.assertEqual(result_1,result_2) |
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| 255 | |
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| 256 | self.canvas.delete(handle) |
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| 257 | handle2 = self.canvas.add('cylinder','cyl2') |
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| 258 | self.assertEqual(40,self.canvas.getParam('%s.length'%handle2)) |
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| 259 | result_3 = self.canvas.getIq(0.1) |
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| 260 | self.assertNotEqual(result_1, result_3) |
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| 261 | |
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| 262 | def testGetIq_ellipsoid(self): |
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| 263 | handle = self.canvas.add('ellipsoid','elli') |
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| 264 | self.canvas.setParam('%s.radius_x' % handle, 35) |
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| 265 | self.canvas.setParam('%s.radius_y' % handle, 20) |
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| 266 | self.canvas.setParam('%s.radius_z' % handle, 10) |
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| 267 | result_1 = self.canvas.getIq(0.1) |
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| 268 | result_2 = self.canvas.getIq(0.1) |
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| 269 | self.assertEqual(result_1,result_2) |
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| 270 | |
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| 271 | self.canvas.delete(handle) |
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| 272 | self.assertEqual(False,self.canvas.hasPr) |
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| 273 | handle2 = self.canvas.add('ellipsoid','elli2') |
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| 274 | result_3 = self.canvas.getIq(0.1) |
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| 275 | self.assertNotEqual(result_1, result_3) |
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| 276 | |
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| 277 | def testGetIq_singlehelix(self): |
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| 278 | handle = self.canvas.add('singlehelix','shelix') |
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| 279 | self.canvas.setParam('%s.radius_helix' % handle, 11) |
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| 280 | self.canvas.setParam('%s.radius_tube' % handle, 4) |
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| 281 | self.canvas.setParam('%s.pitch' % handle, 30) |
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| 282 | self.canvas.setParam('%s.turns' % handle, 3.2) |
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| 283 | result_1 = self.canvas.getIq(0.1) |
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| 284 | result_2 = self.canvas.getIq(0.1) |
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| 285 | self.assertEqual(result_1,result_2) |
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| 286 | |
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| 287 | self.canvas.delete(handle) |
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| 288 | self.assertEqual(False,self.canvas.hasPr) |
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| 289 | handle2 = self.canvas.add('singlehelix','shelix2') |
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| 290 | result_3 = self.canvas.getIq(0.1) |
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| 291 | self.assertNotEqual(result_1, result_3) |
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| 292 | |
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| 293 | class TestOrdering(unittest.TestCase): |
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| 294 | """ Unit tests for all shapes in canvas model """ |
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| 295 | |
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| 296 | def setUp(self): |
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| 297 | from sas.models.CoreShellModel import CoreShellModel |
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| 298 | radius = 15 |
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| 299 | thickness = 5 |
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| 300 | core_vol = 4.0/3.0*math.pi*radius*radius*radius |
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| 301 | outer_radius = radius+thickness |
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| 302 | shell_vol = 4.0/3.0*math.pi*outer_radius*outer_radius*outer_radius - core_vol |
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| 303 | self.shell_sld = -1.0*core_vol/shell_vol |
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| 304 | |
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| 305 | self.canvas = VolumeCanvas.VolumeCanvas() |
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| 306 | self.canvas.params['lores_density'] = 0.1 |
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| 307 | |
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| 308 | # Core shell model |
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| 309 | sphere = CoreShellModel() |
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| 310 | # Core radius |
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| 311 | sphere.setParam('radius', radius) |
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| 312 | # Shell thickness |
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| 313 | sphere.setParam('thickness', thickness) |
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| 314 | sphere.setParam('core_sld', 1.0) |
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| 315 | sphere.setParam('shell_sld', self.shell_sld) |
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| 316 | sphere.setParam('solvent_sld', 0.0) |
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| 317 | sphere.setParam('background', 0.0) |
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| 318 | sphere.setParam('scale', 1.0) |
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| 319 | self.sphere = sphere |
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| 320 | self.radius = radius |
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| 321 | self.outer_radius = outer_radius |
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| 322 | |
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| 323 | def set_coreshell_on_canvas(self, order1=None, order2=None): |
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| 324 | |
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| 325 | handle = self.canvas.add('sphere') |
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| 326 | self.canvas.setParam('%s.radius' % handle, self.outer_radius) |
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| 327 | self.canvas.setParam('%s.contrast' % handle, self.shell_sld) |
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| 328 | if order1 is not None: |
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| 329 | self.canvas.setParam('%s.order' % handle, order1) |
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| 330 | |
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| 331 | handle2 = self.canvas.add('sphere') |
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| 332 | self.canvas.setParam('%s.radius' % handle2, self.radius) |
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| 333 | self.canvas.setParam('%s.contrast' % handle2, 1.0) |
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| 334 | if order2 is not None: |
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| 335 | self.canvas.setParam('%s.order' % handle2, order2) |
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| 336 | |
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| 337 | self.canvas.setParam('scale' , 1.0) |
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| 338 | self.canvas.setParam('background' , 0.0) |
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| 339 | |
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| 340 | |
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| 341 | def testDefaultOrder(self): |
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| 342 | self.set_coreshell_on_canvas() |
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| 343 | |
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| 344 | ana = self.sphere.run(0.05) |
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| 345 | val, err = self.canvas.getIqError(0.05) |
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| 346 | self.assert_(math.fabs(ana-val)<2.0*err) |
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| 347 | |
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| 348 | def testRightOrder(self): |
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| 349 | self.set_coreshell_on_canvas(3.0, 6.0) |
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| 350 | |
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| 351 | ana = self.sphere.run(0.05) |
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| 352 | val, err = self.canvas.getIqError(0.05) |
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| 353 | #print 'right', ana, val, err |
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| 354 | self.assert_(math.fabs(ana-val)/ana < 1.1) |
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| 355 | |
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| 356 | def testWrongOrder(self): |
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| 357 | from sas.models.SphereModel import SphereModel |
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| 358 | self.set_coreshell_on_canvas(1, 0) |
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| 359 | |
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| 360 | # Core shell model |
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| 361 | sphere = SphereModel() |
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| 362 | # Core radius |
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| 363 | sphere.setParam('radius', self.outer_radius) |
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| 364 | # Shell thickness |
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| 365 | sphere.setParam('contrast', self.shell_sld) |
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| 366 | sphere.setParam('background', 0.0) |
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| 367 | sphere.setParam('scale', 1.0) |
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| 368 | |
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| 369 | ana = sphere.run(0.05) |
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| 370 | val, err = self.canvas.getIqError(0.05) |
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| 371 | #print 'wrong', ana, val, err |
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| 372 | self.assert_(math.fabs(ana-val)/ana < 1.1) |
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| 373 | |
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| 374 | |
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| 375 | if __name__ == '__main__': |
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| 376 | unittest.main() |
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