[46d50ca] | 1 | """ |
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| 2 | This software was developed by the University of Tennessee as part of the |
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| 3 | Distributed Data Analysis of Neutron Scattering Experiments (DANSE) |
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| 4 | project funded by the US National Science Foundation. |
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| 5 | |
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| 6 | See the license text in license.txt |
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| 7 | |
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| 8 | copyright 2010, University of Tennessee |
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| 9 | """ |
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| 10 | import unittest |
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[6939bd4] | 11 | import numpy, math |
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[8c9ffde] | 12 | from sas.dataloader.loader import Loader |
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| 13 | from sas.dataloader.data_info import Data1D |
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| 14 | from sas.invariant import invariant |
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[46d50ca] | 15 | |
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| 16 | class TestLinearFit(unittest.TestCase): |
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| 17 | """ |
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| 18 | Test Line fit |
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| 19 | """ |
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| 20 | def setUp(self): |
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| 21 | x = numpy.asarray([1.,2.,3.,4.,5.,6.,7.,8.,9.]) |
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| 22 | y = numpy.asarray([1.,2.,3.,4.,5.,6.,7.,8.,9.]) |
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| 23 | dy = y/10.0 |
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| 24 | |
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| 25 | self.data = Data1D(x=x,y=y,dy=dy) |
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| 26 | |
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| 27 | def test_fit_linear_data(self): |
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| 28 | """ |
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| 29 | Simple linear fit |
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| 30 | """ |
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| 31 | |
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| 32 | # Create invariant object. Background and scale left as defaults. |
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[aafa962] | 33 | fit = invariant.Extrapolator(data=self.data) |
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[bdd162f] | 34 | #a,b = fit.fit() |
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| 35 | p, dp = fit.fit() |
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[46d50ca] | 36 | |
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| 37 | # Test results |
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[bdd162f] | 38 | self.assertAlmostEquals(p[0], 1.0, 5) |
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| 39 | self.assertAlmostEquals(p[1], 0.0, 5) |
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[46d50ca] | 40 | |
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| 41 | def test_fit_linear_data_with_noise(self): |
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| 42 | """ |
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| 43 | Simple linear fit with noise |
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| 44 | """ |
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| 45 | import random, math |
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| 46 | |
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| 47 | for i in range(len(self.data.y)): |
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[bdd162f] | 48 | self.data.y[i] = self.data.y[i]+.1*(random.random()-0.5) |
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[46d50ca] | 49 | |
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| 50 | # Create invariant object. Background and scale left as defaults. |
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[aafa962] | 51 | fit = invariant.Extrapolator(data=self.data) |
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[bdd162f] | 52 | p, dp = fit.fit() |
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[46d50ca] | 53 | |
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| 54 | # Test results |
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[bdd162f] | 55 | self.assertTrue(math.fabs(p[0]-1.0)<0.05) |
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| 56 | self.assertTrue(math.fabs(p[1])<0.1) |
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| 57 | |
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| 58 | def test_fit_with_fixed_parameter(self): |
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| 59 | """ |
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| 60 | Linear fit for y=ax+b where a is fixed. |
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| 61 | """ |
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| 62 | # Create invariant object. Background and scale left as defaults. |
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| 63 | fit = invariant.Extrapolator(data=self.data) |
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| 64 | p, dp = fit.fit(power=-1.0) |
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| 65 | |
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| 66 | # Test results |
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| 67 | self.assertAlmostEquals(p[0], 1.0, 5) |
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| 68 | self.assertAlmostEquals(p[1], 0.0, 5) |
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| 69 | |
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| 70 | def test_fit_linear_data_with_noise_and_fixed_par(self): |
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| 71 | """ |
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| 72 | Simple linear fit with noise |
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| 73 | """ |
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| 74 | import random, math |
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| 75 | |
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| 76 | for i in range(len(self.data.y)): |
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| 77 | self.data.y[i] = self.data.y[i]+.1*(random.random()-0.5) |
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| 78 | |
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| 79 | # Create invariant object. Background and scale left as defaults. |
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| 80 | fit = invariant.Extrapolator(data=self.data) |
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| 81 | p, dp = fit.fit(power=-1.0) |
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| 82 | |
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| 83 | # Test results |
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| 84 | self.assertTrue(math.fabs(p[0]-1.0)<0.05) |
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| 85 | self.assertTrue(math.fabs(p[1])<0.1) |
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| 86 | |
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| 87 | |
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| 88 | |
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[46d50ca] | 89 | class TestInvariantCalculator(unittest.TestCase): |
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| 90 | """ |
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[bdd162f] | 91 | Test main functionality of the Invariant calculator |
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[46d50ca] | 92 | """ |
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| 93 | def setUp(self): |
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[be577e7] | 94 | data = Loader().load("latex_smeared_slit.xml") |
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| 95 | self.data = data[0] |
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[8a9f699] | 96 | self.data.dxl = None |
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[46d50ca] | 97 | |
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| 98 | def test_initial_data_processing(self): |
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| 99 | """ |
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| 100 | Test whether the background and scale are handled properly |
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| 101 | when creating an InvariantCalculator object |
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| 102 | """ |
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| 103 | length = len(self.data.x) |
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| 104 | self.assertEqual(length, len(self.data.y)) |
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| 105 | inv = invariant.InvariantCalculator(self.data) |
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| 106 | |
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| 107 | self.assertEqual(length, len(inv._data.x)) |
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| 108 | self.assertEqual(inv._data.x[0], self.data.x[0]) |
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| 109 | |
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| 110 | # Now the same thing with a background value |
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| 111 | bck = 0.1 |
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| 112 | inv = invariant.InvariantCalculator(self.data, background=bck) |
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| 113 | self.assertEqual(inv._background, bck) |
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| 114 | |
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| 115 | self.assertEqual(length, len(inv._data.x)) |
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| 116 | self.assertEqual(inv._data.y[0]+bck, self.data.y[0]) |
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| 117 | |
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| 118 | # Now the same thing with a scale value |
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| 119 | scale = 0.1 |
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| 120 | inv = invariant.InvariantCalculator(self.data, scale=scale) |
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| 121 | self.assertEqual(inv._scale, scale) |
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| 122 | |
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| 123 | self.assertEqual(length, len(inv._data.x)) |
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| 124 | self.assertAlmostEqual(inv._data.y[0]/scale, self.data.y[0],7) |
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| 125 | |
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| 126 | |
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| 127 | def test_incompatible_data_class(self): |
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| 128 | """ |
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| 129 | Check that only classes that inherit from Data1D are allowed as data. |
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| 130 | """ |
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| 131 | class Incompatible(): |
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| 132 | pass |
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| 133 | self.assertRaises(ValueError, invariant.InvariantCalculator, Incompatible()) |
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[bdd162f] | 134 | |
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| 135 | def test_error_treatment(self): |
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| 136 | x = numpy.asarray(numpy.asarray([0,1,2,3])) |
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| 137 | y = numpy.asarray(numpy.asarray([1,1,1,1])) |
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| 138 | |
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| 139 | # These are all the values of the dy array that would cause |
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| 140 | # us to set all dy values to 1.0 at __init__ time. |
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| 141 | dy_list = [ [], None, [0,0,0,0] ] |
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| 142 | |
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| 143 | for dy in dy_list: |
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| 144 | data = Data1D(x=x, y=y, dy=dy) |
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| 145 | inv = invariant.InvariantCalculator(data) |
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| 146 | self.assertEqual(len(inv._data.x), len(inv._data.dy)) |
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| 147 | self.assertEqual(len(inv._data.dy), 4) |
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| 148 | for i in range(4): |
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| 149 | self.assertEqual(inv._data.dy[i],1) |
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| 150 | |
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| 151 | def test_qstar_low_q_guinier(self): |
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| 152 | """ |
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| 153 | Test low-q extrapolation with a Guinier |
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| 154 | """ |
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| 155 | inv = invariant.InvariantCalculator(self.data) |
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| 156 | |
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| 157 | # Basic sanity check |
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| 158 | _qstar = inv.get_qstar() |
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| 159 | qstar, dqstar = inv.get_qstar_with_error() |
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| 160 | self.assertEqual(qstar, _qstar) |
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| 161 | |
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| 162 | # Low-Q Extrapolation |
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| 163 | # Check that the returned invariant is what we expect given |
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| 164 | # the result we got without extrapolation |
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| 165 | inv.set_extrapolation('low', npts=10, function='guinier') |
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| 166 | qs_extr, dqs_extr = inv.get_qstar_with_error('low') |
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| 167 | delta_qs_extr, delta_dqs_extr = inv.get_qstar_low() |
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| 168 | |
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| 169 | self.assertEqual(qs_extr, _qstar+delta_qs_extr) |
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| 170 | self.assertEqual(dqs_extr, math.sqrt(dqstar*dqstar + delta_dqs_extr*delta_dqs_extr)) |
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| 171 | |
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| 172 | # We don't expect the extrapolated invariant to be very far from the |
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| 173 | # result without extrapolation. Let's test for a result within 10%. |
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| 174 | self.assertTrue(math.fabs(qs_extr-qstar)/qstar<0.1) |
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| 175 | |
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| 176 | # Check that the two results are consistent within errors |
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| 177 | # Note that the error on the extrapolated value takes into account |
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| 178 | # a systematic error for the fact that we may not know the shape of I(q) at low Q. |
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| 179 | self.assertTrue(math.fabs(qs_extr-qstar)<dqs_extr) |
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| 180 | |
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| 181 | def test_qstar_low_q_power_law(self): |
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| 182 | """ |
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| 183 | Test low-q extrapolation with a power law |
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| 184 | """ |
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| 185 | inv = invariant.InvariantCalculator(self.data) |
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| 186 | |
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| 187 | # Basic sanity check |
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| 188 | _qstar = inv.get_qstar() |
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| 189 | qstar, dqstar = inv.get_qstar_with_error() |
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| 190 | self.assertEqual(qstar, _qstar) |
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| 191 | |
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| 192 | # Low-Q Extrapolation |
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| 193 | # Check that the returned invariant is what we expect given |
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| 194 | inv.set_extrapolation('low', npts=10, function='power_law') |
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| 195 | qs_extr, dqs_extr = inv.get_qstar_with_error('low') |
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| 196 | delta_qs_extr, delta_dqs_extr = inv.get_qstar_low() |
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| 197 | |
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[8c9ffde] | 198 | # A fit using SasView gives 0.0655 for the value of the exponent |
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[bdd162f] | 199 | self.assertAlmostEqual(inv._low_extrapolation_function.power, 0.0655, 3) |
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| 200 | |
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| 201 | if False: |
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| 202 | npts = len(inv._data.x)-1 |
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| 203 | import matplotlib.pyplot as plt |
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| 204 | plt.loglog(inv._data.x[:npts], inv._data.y[:npts], 'o', label='Original data', markersize=10) |
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| 205 | plt.loglog(inv._data.x[:npts], inv._low_extrapolation_function.evaluate_model(inv._data.x[:npts]), 'r', label='Fitted line') |
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| 206 | plt.legend() |
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| 207 | plt.show() |
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| 208 | |
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| 209 | self.assertEqual(qs_extr, _qstar+delta_qs_extr) |
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[6574940a] | 210 | self.assertAlmostEqual(dqs_extr, math.sqrt(dqstar*dqstar + delta_dqs_extr*delta_dqs_extr), 15) |
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[bdd162f] | 211 | |
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| 212 | # We don't expect the extrapolated invariant to be very far from the |
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| 213 | # result without extrapolation. Let's test for a result within 10%. |
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| 214 | self.assertTrue(math.fabs(qs_extr-qstar)/qstar<0.1) |
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| 215 | |
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| 216 | # Check that the two results are consistent within errors |
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| 217 | # Note that the error on the extrapolated value takes into account |
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| 218 | # a systematic error for the fact that we may not know the shape of I(q) at low Q. |
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| 219 | self.assertTrue(math.fabs(qs_extr-qstar)<dqs_extr) |
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| 220 | |
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| 221 | def test_qstar_high_q(self): |
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| 222 | """ |
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| 223 | Test high-q extrapolation |
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| 224 | """ |
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| 225 | inv = invariant.InvariantCalculator(self.data) |
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| 226 | |
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| 227 | # Basic sanity check |
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| 228 | _qstar = inv.get_qstar() |
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| 229 | qstar, dqstar = inv.get_qstar_with_error() |
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| 230 | self.assertEqual(qstar, _qstar) |
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| 231 | |
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| 232 | # High-Q Extrapolation |
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| 233 | # Check that the returned invariant is what we expect given |
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| 234 | # the result we got without extrapolation |
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| 235 | inv.set_extrapolation('high', npts=20, function='power_law') |
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| 236 | qs_extr, dqs_extr = inv.get_qstar_with_error('high') |
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| 237 | delta_qs_extr, delta_dqs_extr = inv.get_qstar_high() |
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| 238 | |
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[8c9ffde] | 239 | # From previous analysis using SasView, we expect an exponent of about 3 |
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[bdd162f] | 240 | self.assertTrue(math.fabs(inv._high_extrapolation_function.power-3)<0.1) |
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| 241 | |
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| 242 | self.assertEqual(qs_extr, _qstar+delta_qs_extr) |
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[c4f79f0] | 243 | self.assertAlmostEqual(dqs_extr, math.sqrt(dqstar*dqstar + delta_dqs_extr*delta_dqs_extr), 10) |
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[bdd162f] | 244 | |
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| 245 | # We don't expect the extrapolated invariant to be very far from the |
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| 246 | # result without extrapolation. Let's test for a result within 10%. |
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| 247 | #TODO: verify whether this test really makes sense |
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| 248 | #self.assertTrue(math.fabs(qs_extr-qstar)/qstar<0.1) |
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| 249 | |
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| 250 | # Check that the two results are consistent within errors |
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| 251 | self.assertTrue(math.fabs(qs_extr-qstar)<dqs_extr) |
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| 252 | |
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| 253 | def test_qstar_full_q(self): |
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| 254 | """ |
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| 255 | Test high-q extrapolation |
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| 256 | """ |
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| 257 | inv = invariant.InvariantCalculator(self.data) |
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| 258 | |
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| 259 | # Basic sanity check |
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| 260 | _qstar = inv.get_qstar() |
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| 261 | qstar, dqstar = inv.get_qstar_with_error() |
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| 262 | self.assertEqual(qstar, _qstar) |
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| 263 | |
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| 264 | # High-Q Extrapolation |
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| 265 | # Check that the returned invariant is what we expect given |
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| 266 | # the result we got without extrapolation |
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| 267 | inv.set_extrapolation('low', npts=10, function='guinier') |
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| 268 | inv.set_extrapolation('high', npts=20, function='power_law') |
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| 269 | qs_extr, dqs_extr = inv.get_qstar_with_error('both') |
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| 270 | delta_qs_low, delta_dqs_low = inv.get_qstar_low() |
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| 271 | delta_qs_hi, delta_dqs_hi = inv.get_qstar_high() |
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| 272 | |
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| 273 | self.assertAlmostEqual(qs_extr, _qstar+delta_qs_low+delta_qs_hi, 8) |
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[97700d7] | 274 | self.assertAlmostEqual(dqs_extr, math.sqrt(dqstar*dqstar + delta_dqs_low*delta_dqs_low \ |
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| 275 | + delta_dqs_hi*delta_dqs_hi), 8) |
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[bdd162f] | 276 | |
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| 277 | # We don't expect the extrapolated invariant to be very far from the |
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| 278 | # result without extrapolation. Let's test for a result within 10%. |
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| 279 | #TODO: verify whether this test really makes sense |
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| 280 | #self.assertTrue(math.fabs(qs_extr-qstar)/qstar<0.1) |
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| 281 | |
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| 282 | # Check that the two results are consistent within errors |
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| 283 | self.assertTrue(math.fabs(qs_extr-qstar)<dqs_extr) |
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| 284 | |
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[c75a8ed] | 285 | def _check_values(to_check, reference, tolerance=0.05): |
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| 286 | self.assertTrue( math.fabs(to_check-reference)/reference < tolerance, msg="Tested value = "+str(to_check) ) |
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| 287 | |
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| 288 | # The following values should be replaced by values pulled from IGOR |
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| 289 | # Volume Fraction: |
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| 290 | v, dv = inv.get_volume_fraction_with_error(1, None) |
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| 291 | _check_values(v, 1.88737914186e-15) |
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| 292 | |
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| 293 | v_l, dv_l = inv.get_volume_fraction_with_error(1, 'low') |
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| 294 | _check_values(v_l, 1.94289029309e-15) |
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| 295 | |
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| 296 | v_h, dv_h = inv.get_volume_fraction_with_error(1, 'high') |
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| 297 | _check_values(v_h, 6.99440505514e-15) |
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| 298 | |
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| 299 | v_b, dv_b = inv.get_volume_fraction_with_error(1, 'both') |
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| 300 | _check_values(v_b, 6.99440505514e-15) |
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| 301 | |
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| 302 | # Specific Surface: |
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| 303 | s, ds = inv.get_surface_with_error(1, 1, None) |
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| 304 | _check_values(s, 3.1603095786e-09) |
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| 305 | |
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| 306 | s_l, ds_l = inv.get_surface_with_error(1, 1, 'low') |
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| 307 | _check_values(s_l, 3.1603095786e-09) |
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| 308 | |
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| 309 | s_h, ds_h = inv.get_surface_with_error(1, 1, 'high') |
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| 310 | _check_values(s_h, 3.1603095786e-09) |
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| 311 | |
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| 312 | s_b, ds_b = inv.get_surface_with_error(1, 1, 'both') |
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| 313 | _check_values(s_b, 3.1603095786e-09) |
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| 314 | |
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| 315 | |
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[bdd162f] | 316 | def test_bad_parameter_name(self): |
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| 317 | """ |
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| 318 | The set_extrapolation method checks that the name of the extrapolation |
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| 319 | function and the name of the q-range to extrapolate (high/low) is |
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| 320 | recognized. |
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| 321 | """ |
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| 322 | inv = invariant.InvariantCalculator(self.data) |
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| 323 | self.assertRaises(ValueError, inv.set_extrapolation, 'low', npts=4, function='not_a_name') |
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| 324 | self.assertRaises(ValueError, inv.set_extrapolation, 'not_a_range', npts=4, function='guinier') |
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| 325 | self.assertRaises(ValueError, inv.set_extrapolation, 'high', npts=4, function='guinier') |
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[46d50ca] | 326 | |
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[6939bd4] | 327 | |
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| 328 | class TestGuinierExtrapolation(unittest.TestCase): |
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| 329 | """ |
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| 330 | Generate a Guinier distribution and verify that the extrapolation |
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| 331 | produce the correct ditribution. |
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| 332 | """ |
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| 333 | |
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| 334 | def setUp(self): |
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| 335 | """ |
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| 336 | Generate a Guinier distribution. After extrapolating, we will |
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| 337 | verify that we obtain the scale and rg parameters |
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| 338 | """ |
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| 339 | self.scale = 1.5 |
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[aafa962] | 340 | self.rg = 30.0 |
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[6939bd4] | 341 | x = numpy.arange(0.0001, 0.1, 0.0001) |
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| 342 | y = numpy.asarray([self.scale * math.exp( -(q*self.rg)**2 / 3.0 ) for q in x]) |
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| 343 | dy = y*.1 |
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| 344 | self.data = Data1D(x=x, y=y, dy=dy) |
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| 345 | |
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| 346 | def test_low_q(self): |
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| 347 | """ |
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| 348 | Invariant with low-Q extrapolation |
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| 349 | """ |
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| 350 | # Create invariant object. Background and scale left as defaults. |
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| 351 | inv = invariant.InvariantCalculator(data=self.data) |
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| 352 | # Set the extrapolation parameters for the low-Q range |
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| 353 | inv.set_extrapolation(range='low', npts=20, function='guinier') |
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| 354 | |
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| 355 | self.assertEqual(inv._low_extrapolation_npts, 20) |
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[aafa962] | 356 | self.assertEqual(inv._low_extrapolation_function.__class__, invariant.Guinier) |
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[6939bd4] | 357 | |
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| 358 | # Data boundaries for fiiting |
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| 359 | qmin = inv._data.x[0] |
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| 360 | qmax = inv._data.x[inv._low_extrapolation_npts - 1] |
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| 361 | |
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| 362 | # Extrapolate the low-Q data |
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[bdd162f] | 363 | inv._fit(model=inv._low_extrapolation_function, |
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[6939bd4] | 364 | qmin=qmin, |
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| 365 | qmax=qmax, |
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| 366 | power=inv._low_extrapolation_power) |
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[bdd162f] | 367 | self.assertAlmostEqual(self.scale, inv._low_extrapolation_function.scale, 6) |
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| 368 | self.assertAlmostEqual(self.rg, inv._low_extrapolation_function.radius, 6) |
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[6939bd4] | 369 | |
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| 370 | |
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| 371 | class TestPowerLawExtrapolation(unittest.TestCase): |
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| 372 | """ |
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| 373 | Generate a power law distribution and verify that the extrapolation |
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| 374 | produce the correct ditribution. |
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| 375 | """ |
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| 376 | |
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| 377 | def setUp(self): |
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| 378 | """ |
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| 379 | Generate a power law distribution. After extrapolating, we will |
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| 380 | verify that we obtain the scale and m parameters |
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| 381 | """ |
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| 382 | self.scale = 1.5 |
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| 383 | self.m = 3.0 |
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| 384 | x = numpy.arange(0.0001, 0.1, 0.0001) |
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| 385 | y = numpy.asarray([self.scale * math.pow(q ,-1.0*self.m) for q in x]) |
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| 386 | dy = y*.1 |
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| 387 | self.data = Data1D(x=x, y=y, dy=dy) |
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| 388 | |
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| 389 | def test_low_q(self): |
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| 390 | """ |
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| 391 | Invariant with low-Q extrapolation |
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| 392 | """ |
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| 393 | # Create invariant object. Background and scale left as defaults. |
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| 394 | inv = invariant.InvariantCalculator(data=self.data) |
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| 395 | # Set the extrapolation parameters for the low-Q range |
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| 396 | inv.set_extrapolation(range='low', npts=20, function='power_law') |
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| 397 | |
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| 398 | self.assertEqual(inv._low_extrapolation_npts, 20) |
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[aafa962] | 399 | self.assertEqual(inv._low_extrapolation_function.__class__, invariant.PowerLaw) |
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[6939bd4] | 400 | |
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| 401 | # Data boundaries for fitting |
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| 402 | qmin = inv._data.x[0] |
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| 403 | qmax = inv._data.x[inv._low_extrapolation_npts - 1] |
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| 404 | |
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| 405 | # Extrapolate the low-Q data |
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[bdd162f] | 406 | inv._fit(model=inv._low_extrapolation_function, |
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[6939bd4] | 407 | qmin=qmin, |
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| 408 | qmax=qmax, |
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| 409 | power=inv._low_extrapolation_power) |
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| 410 | |
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[bdd162f] | 411 | self.assertAlmostEqual(self.scale, inv._low_extrapolation_function.scale, 6) |
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| 412 | self.assertAlmostEqual(self.m, inv._low_extrapolation_function.power, 6) |
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[aafa962] | 413 | |
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| 414 | class TestLinearization(unittest.TestCase): |
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| 415 | |
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| 416 | def test_guinier_incompatible_length(self): |
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| 417 | g = invariant.Guinier() |
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[76c1727] | 418 | data_in = Data1D(x=[1], y=[1,2], dy=None) |
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| 419 | self.assertRaises(AssertionError, g.linearize_data, data_in) |
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| 420 | data_in = Data1D(x=[1,1], y=[1,2], dy=[1]) |
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| 421 | self.assertRaises(AssertionError, g.linearize_data, data_in) |
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[aafa962] | 422 | |
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| 423 | def test_linearization(self): |
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| 424 | """ |
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| 425 | Check that the linearization process filters out points |
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| 426 | that can't be transformed |
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| 427 | """ |
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| 428 | x = numpy.asarray(numpy.asarray([0,1,2,3])) |
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| 429 | y = numpy.asarray(numpy.asarray([1,1,1,1])) |
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| 430 | g = invariant.Guinier() |
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[76c1727] | 431 | data_in = Data1D(x=x, y=y) |
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| 432 | data_out = g.linearize_data(data_in) |
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| 433 | x_out, y_out, dy_out = data_out.x, data_out.y, data_out.dy |
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[aafa962] | 434 | self.assertEqual(len(x_out), 3) |
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| 435 | self.assertEqual(len(y_out), 3) |
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| 436 | self.assertEqual(len(dy_out), 3) |
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[bdd162f] | 437 | |
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| 438 | def test_allowed_bins(self): |
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| 439 | x = numpy.asarray(numpy.asarray([0,1,2,3])) |
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| 440 | y = numpy.asarray(numpy.asarray([1,1,1,1])) |
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| 441 | dy = numpy.asarray(numpy.asarray([1,1,1,1])) |
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| 442 | g = invariant.Guinier() |
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| 443 | data = Data1D(x=x, y=y, dy=dy) |
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| 444 | self.assertEqual(g.get_allowed_bins(data), [False, True, True, True]) |
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| 445 | |
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| 446 | data = Data1D(x=y, y=x, dy=dy) |
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| 447 | self.assertEqual(g.get_allowed_bins(data), [False, True, True, True]) |
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[97603c0] | 448 | |
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[bdd162f] | 449 | data = Data1D(x=dy, y=y, dy=x) |
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| 450 | self.assertEqual(g.get_allowed_bins(data), [False, True, True, True]) |
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[97603c0] | 451 | |
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| 452 | class TestDataExtraLow(unittest.TestCase): |
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| 453 | """ |
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| 454 | Generate a Guinier distribution and verify that the extrapolation |
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| 455 | produce the correct ditribution. Tested if the data generated by the |
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| 456 | invariant calculator is correct |
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| 457 | """ |
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| 458 | |
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| 459 | def setUp(self): |
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| 460 | """ |
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| 461 | Generate a Guinier distribution. After extrapolating, we will |
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| 462 | verify that we obtain the scale and rg parameters |
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| 463 | """ |
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| 464 | self.scale = 1.5 |
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| 465 | self.rg = 30.0 |
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| 466 | x = numpy.arange(0.0001, 0.1, 0.0001) |
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| 467 | y = numpy.asarray([self.scale * math.exp( -(q*self.rg)**2 / 3.0 ) for q in x]) |
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| 468 | dy = y*.1 |
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| 469 | self.data = Data1D(x=x, y=y, dy=dy) |
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| 470 | |
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| 471 | def test_low_q(self): |
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| 472 | """ |
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| 473 | Invariant with low-Q extrapolation with no slit smear |
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| 474 | """ |
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| 475 | # Create invariant object. Background and scale left as defaults. |
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| 476 | inv = invariant.InvariantCalculator(data=self.data) |
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| 477 | # Set the extrapolation parameters for the low-Q range |
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[bdd162f] | 478 | inv.set_extrapolation(range='low', npts=10, function='guinier') |
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[97603c0] | 479 | |
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[bdd162f] | 480 | self.assertEqual(inv._low_extrapolation_npts, 10) |
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[97603c0] | 481 | self.assertEqual(inv._low_extrapolation_function.__class__, invariant.Guinier) |
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| 482 | |
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| 483 | # Data boundaries for fiiting |
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| 484 | qmin = inv._data.x[0] |
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| 485 | qmax = inv._data.x[inv._low_extrapolation_npts - 1] |
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| 486 | |
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| 487 | # Extrapolate the low-Q data |
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[bdd162f] | 488 | inv._fit(model=inv._low_extrapolation_function, |
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[97603c0] | 489 | qmin=qmin, |
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| 490 | qmax=qmax, |
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| 491 | power=inv._low_extrapolation_power) |
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[bdd162f] | 492 | self.assertAlmostEqual(self.scale, inv._low_extrapolation_function.scale, 6) |
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| 493 | self.assertAlmostEqual(self.rg, inv._low_extrapolation_function.radius, 6) |
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[97603c0] | 494 | |
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| 495 | qstar = inv.get_qstar(extrapolation='low') |
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| 496 | test_y = inv._low_extrapolation_function.evaluate_model(x=self.data.x) |
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| 497 | for i in range(len(self.data.x)): |
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[c75a8ed] | 498 | value = math.fabs(test_y[i]-self.data.y[i])/self.data.y[i] |
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[97603c0] | 499 | self.assert_(value < 0.001) |
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| 500 | |
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[76c1727] | 501 | class TestDataExtraLowSlitGuinier(unittest.TestCase): |
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| 502 | """ |
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| 503 | for a smear data, test that the fitting go through |
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[c75a8ed] | 504 | real data for atleast the 2 first points |
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[76c1727] | 505 | """ |
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| 506 | |
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| 507 | def setUp(self): |
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| 508 | """ |
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| 509 | Generate a Guinier distribution. After extrapolating, we will |
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| 510 | verify that we obtain the scale and rg parameters |
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| 511 | """ |
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| 512 | self.scale = 1.5 |
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| 513 | self.rg = 30.0 |
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| 514 | x = numpy.arange(0.0001, 0.1, 0.0001) |
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| 515 | y = numpy.asarray([self.scale * math.exp( -(q*self.rg)**2 / 3.0 ) for q in x]) |
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| 516 | dy = y*.1 |
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| 517 | self.data = Data1D(x=x, y=y, dy=dy) |
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| 518 | self.npts = len(x)-10 |
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| 519 | |
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| 520 | def test_low_q(self): |
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| 521 | """ |
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| 522 | Invariant with low-Q extrapolation with slit smear |
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| 523 | """ |
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| 524 | # Create invariant object. Background and scale left as defaults. |
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| 525 | inv = invariant.InvariantCalculator(data=self.data) |
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| 526 | # Set the extrapolation parameters for the low-Q range |
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| 527 | inv.set_extrapolation(range='low', npts=self.npts, function='guinier') |
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| 528 | |
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| 529 | self.assertEqual(inv._low_extrapolation_npts, self.npts) |
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[97603c0] | 530 | self.assertEqual(inv._low_extrapolation_function.__class__, invariant.Guinier) |
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| 531 | |
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| 532 | # Data boundaries for fiiting |
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| 533 | qmin = inv._data.x[0] |
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| 534 | qmax = inv._data.x[inv._low_extrapolation_npts - 1] |
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| 535 | |
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| 536 | # Extrapolate the low-Q data |
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[bdd162f] | 537 | inv._fit(model=inv._low_extrapolation_function, |
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[97603c0] | 538 | qmin=qmin, |
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| 539 | qmax=qmax, |
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| 540 | power=inv._low_extrapolation_power) |
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| 541 | |
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| 542 | |
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| 543 | qstar = inv.get_qstar(extrapolation='low') |
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[c75a8ed] | 544 | |
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[76c1727] | 545 | test_y = inv._low_extrapolation_function.evaluate_model(x=self.data.x[:inv._low_extrapolation_npts]) |
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[c75a8ed] | 546 | self.assert_(len(test_y) == len(self.data.y[:inv._low_extrapolation_npts])) |
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[97603c0] | 547 | |
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[76c1727] | 548 | for i in range(inv._low_extrapolation_npts): |
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[c75a8ed] | 549 | value = math.fabs(test_y[i]-self.data.y[i])/self.data.y[i] |
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[97603c0] | 550 | self.assert_(value < 0.001) |
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| 551 | |
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[76c1727] | 552 | def test_low_data(self): |
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| 553 | """ |
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| 554 | Invariant with low-Q extrapolation with slit smear |
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| 555 | """ |
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| 556 | # Create invariant object. Background and scale left as defaults. |
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| 557 | inv = invariant.InvariantCalculator(data=self.data) |
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| 558 | # Set the extrapolation parameters for the low-Q range |
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| 559 | inv.set_extrapolation(range='low', npts=self.npts, function='guinier') |
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| 560 | |
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| 561 | self.assertEqual(inv._low_extrapolation_npts, self.npts) |
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| 562 | self.assertEqual(inv._low_extrapolation_function.__class__, invariant.Guinier) |
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| 563 | |
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| 564 | # Data boundaries for fiiting |
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| 565 | qmin = inv._data.x[0] |
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| 566 | qmax = inv._data.x[inv._low_extrapolation_npts - 1] |
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| 567 | |
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| 568 | # Extrapolate the low-Q data |
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[bdd162f] | 569 | inv._fit(model=inv._low_extrapolation_function, |
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[76c1727] | 570 | qmin=qmin, |
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| 571 | qmax=qmax, |
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| 572 | power=inv._low_extrapolation_power) |
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| 573 | |
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| 574 | |
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| 575 | qstar = inv.get_qstar(extrapolation='low') |
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| 576 | #Compution the y 's coming out of the invariant when computing extrapolated |
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| 577 | #low data . expect the fit engine to have been already called and the guinier |
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| 578 | # to have the radius and the scale fitted |
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[c75a8ed] | 579 | data_in_range = inv.get_extra_data_low(q_start=self.data.x[0], |
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| 580 | npts = inv._low_extrapolation_npts) |
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[76c1727] | 581 | test_y = data_in_range.y |
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[c75a8ed] | 582 | self.assert_(len(test_y) == len(self.data.y[:inv._low_extrapolation_npts])) |
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[76c1727] | 583 | for i in range(inv._low_extrapolation_npts): |
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[c75a8ed] | 584 | value = math.fabs(test_y[i]-self.data.y[i])/self.data.y[i] |
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[76c1727] | 585 | self.assert_(value < 0.001) |
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[c75a8ed] | 586 | |
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[97603c0] | 587 | |
---|
[76c1727] | 588 | class TestDataExtraHighSlitPowerLaw(unittest.TestCase): |
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| 589 | """ |
---|
| 590 | for a smear data, test that the fitting go through |
---|
[c75a8ed] | 591 | real data for atleast the 2 first points |
---|
[76c1727] | 592 | """ |
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| 593 | |
---|
| 594 | def setUp(self): |
---|
| 595 | """ |
---|
| 596 | Generate a Guinier distribution. After extrapolating, we will |
---|
| 597 | verify that we obtain the scale and rg parameters |
---|
| 598 | """ |
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| 599 | self.scale = 1.5 |
---|
| 600 | self.m = 3.0 |
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| 601 | x = numpy.arange(0.0001, 0.1, 0.0001) |
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| 602 | y = numpy.asarray([self.scale * math.pow(q ,-1.0*self.m) for q in x]) |
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| 603 | dy = y*.1 |
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| 604 | self.data = Data1D(x=x, y=y, dy=dy) |
---|
| 605 | self.npts = 20 |
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| 606 | |
---|
| 607 | def test_high_q(self): |
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| 608 | """ |
---|
| 609 | Invariant with high-Q extrapolation with slit smear |
---|
| 610 | """ |
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| 611 | # Create invariant object. Background and scale left as defaults. |
---|
| 612 | inv = invariant.InvariantCalculator(data=self.data) |
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| 613 | # Set the extrapolation parameters for the low-Q range |
---|
| 614 | inv.set_extrapolation(range='high', npts=self.npts, function='power_law') |
---|
| 615 | |
---|
| 616 | self.assertEqual(inv._high_extrapolation_npts, self.npts) |
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| 617 | self.assertEqual(inv._high_extrapolation_function.__class__, invariant.PowerLaw) |
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| 618 | |
---|
| 619 | # Data boundaries for fiiting |
---|
| 620 | xlen = len(self.data.x) |
---|
| 621 | start = xlen - inv._high_extrapolation_npts |
---|
| 622 | qmin = inv._data.x[start] |
---|
| 623 | qmax = inv._data.x[xlen-1] |
---|
| 624 | |
---|
| 625 | # Extrapolate the high-Q data |
---|
[bdd162f] | 626 | inv._fit(model=inv._high_extrapolation_function, |
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[76c1727] | 627 | qmin=qmin, |
---|
| 628 | qmax=qmax, |
---|
| 629 | power=inv._high_extrapolation_power) |
---|
| 630 | |
---|
| 631 | |
---|
| 632 | qstar = inv.get_qstar(extrapolation='high') |
---|
| 633 | |
---|
| 634 | test_y = inv._high_extrapolation_function.evaluate_model(x=self.data.x[start: ]) |
---|
[c75a8ed] | 635 | self.assert_(len(test_y) == len(self.data.y[start:])) |
---|
[76c1727] | 636 | |
---|
| 637 | for i in range(len(self.data.x[start:])): |
---|
[c75a8ed] | 638 | value = math.fabs(test_y[i]-self.data.y[start+i])/self.data.y[start+i] |
---|
[76c1727] | 639 | self.assert_(value < 0.001) |
---|
| 640 | |
---|
| 641 | def test_high_data(self): |
---|
| 642 | """ |
---|
| 643 | Invariant with low-Q extrapolation with slit smear |
---|
| 644 | """ |
---|
| 645 | # Create invariant object. Background and scale left as defaults. |
---|
| 646 | inv = invariant.InvariantCalculator(data=self.data) |
---|
| 647 | # Set the extrapolation parameters for the low-Q range |
---|
| 648 | inv.set_extrapolation(range='high', npts=self.npts, function='power_law') |
---|
| 649 | |
---|
| 650 | self.assertEqual(inv._high_extrapolation_npts, self.npts) |
---|
| 651 | self.assertEqual(inv._high_extrapolation_function.__class__, invariant.PowerLaw) |
---|
| 652 | |
---|
| 653 | # Data boundaries for fiiting |
---|
| 654 | xlen = len(self.data.x) |
---|
| 655 | start = xlen - inv._high_extrapolation_npts |
---|
| 656 | qmin = inv._data.x[start] |
---|
| 657 | qmax = inv._data.x[xlen-1] |
---|
| 658 | |
---|
| 659 | # Extrapolate the high-Q data |
---|
[bdd162f] | 660 | inv._fit(model=inv._high_extrapolation_function, |
---|
[76c1727] | 661 | qmin=qmin, |
---|
| 662 | qmax=qmax, |
---|
| 663 | power=inv._high_extrapolation_power) |
---|
| 664 | |
---|
| 665 | qstar = inv.get_qstar(extrapolation='high') |
---|
| 666 | |
---|
[c75a8ed] | 667 | data_in_range= inv.get_extra_data_high(q_end = max(self.data.x), |
---|
| 668 | npts = inv._high_extrapolation_npts) |
---|
[76c1727] | 669 | test_y = data_in_range.y |
---|
[c75a8ed] | 670 | self.assert_(len(test_y) == len(self.data.y[start:])) |
---|
| 671 | temp = self.data.y[start:] |
---|
[76c1727] | 672 | |
---|
| 673 | for i in range(len(self.data.x[start:])): |
---|
| 674 | value = math.fabs(test_y[i]- temp[i])/temp[i] |
---|
[c75a8ed] | 675 | self.assert_(value < 0.001) |
---|
[76c1727] | 676 | |
---|