[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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[3a473ef] | 10 | |
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| 11 | import os.path |
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[46d50ca] | 12 | import unittest |
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[9a5097c] | 13 | import math |
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| 14 | import numpy as np |
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[b699768] | 15 | from sas.sascalc.dataloader.loader import Loader |
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| 16 | from sas.sascalc.dataloader.data_info import Data1D |
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| 17 | |
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| 18 | from sas.sascalc.invariant import invariant |
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[3a473ef] | 19 | |
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| 20 | |
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| 21 | def find(filename): |
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| 22 | return os.path.join(os.path.dirname(__file__), filename) |
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| 23 | |
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| 24 | |
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[46d50ca] | 25 | class TestLinearFit(unittest.TestCase): |
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| 26 | """ |
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| 27 | Test Line fit |
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| 28 | """ |
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| 29 | def setUp(self): |
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[9a5097c] | 30 | x = np.asarray([1.,2.,3.,4.,5.,6.,7.,8.,9.]) |
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| 31 | y = np.asarray([1.,2.,3.,4.,5.,6.,7.,8.,9.]) |
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[46d50ca] | 32 | dy = y/10.0 |
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| 33 | |
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| 34 | self.data = Data1D(x=x,y=y,dy=dy) |
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| 35 | |
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| 36 | def test_fit_linear_data(self): |
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| 37 | """ |
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| 38 | Simple linear fit |
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| 39 | """ |
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| 40 | |
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| 41 | # Create invariant object. Background and scale left as defaults. |
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[aafa962] | 42 | fit = invariant.Extrapolator(data=self.data) |
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[bdd162f] | 43 | #a,b = fit.fit() |
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| 44 | p, dp = fit.fit() |
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[46d50ca] | 45 | |
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| 46 | # Test results |
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[bdd162f] | 47 | self.assertAlmostEquals(p[0], 1.0, 5) |
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| 48 | self.assertAlmostEquals(p[1], 0.0, 5) |
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[46d50ca] | 49 | |
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| 50 | def test_fit_linear_data_with_noise(self): |
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| 51 | """ |
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| 52 | Simple linear fit with noise |
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| 53 | """ |
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| 54 | import random, math |
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| 55 | |
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| 56 | for i in range(len(self.data.y)): |
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[bdd162f] | 57 | self.data.y[i] = self.data.y[i]+.1*(random.random()-0.5) |
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[46d50ca] | 58 | |
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| 59 | # Create invariant object. Background and scale left as defaults. |
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[aafa962] | 60 | fit = invariant.Extrapolator(data=self.data) |
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[bdd162f] | 61 | p, dp = fit.fit() |
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[46d50ca] | 62 | |
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| 63 | # Test results |
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[bdd162f] | 64 | self.assertTrue(math.fabs(p[0]-1.0)<0.05) |
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| 65 | self.assertTrue(math.fabs(p[1])<0.1) |
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| 66 | |
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| 67 | def test_fit_with_fixed_parameter(self): |
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| 68 | """ |
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| 69 | Linear fit for y=ax+b where a is fixed. |
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| 70 | """ |
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| 71 | # Create invariant object. Background and scale left as defaults. |
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| 72 | fit = invariant.Extrapolator(data=self.data) |
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| 73 | p, dp = fit.fit(power=-1.0) |
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| 74 | |
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| 75 | # Test results |
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| 76 | self.assertAlmostEquals(p[0], 1.0, 5) |
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| 77 | self.assertAlmostEquals(p[1], 0.0, 5) |
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| 78 | |
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| 79 | def test_fit_linear_data_with_noise_and_fixed_par(self): |
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| 80 | """ |
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| 81 | Simple linear fit with noise |
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| 82 | """ |
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| 83 | import random, math |
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| 84 | |
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| 85 | for i in range(len(self.data.y)): |
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| 86 | self.data.y[i] = self.data.y[i]+.1*(random.random()-0.5) |
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| 87 | |
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| 88 | # Create invariant object. Background and scale left as defaults. |
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| 89 | fit = invariant.Extrapolator(data=self.data) |
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| 90 | p, dp = fit.fit(power=-1.0) |
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| 91 | |
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| 92 | # Test results |
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| 93 | self.assertTrue(math.fabs(p[0]-1.0)<0.05) |
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| 94 | self.assertTrue(math.fabs(p[1])<0.1) |
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| 95 | |
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| 96 | |
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| 97 | |
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[46d50ca] | 98 | class TestInvariantCalculator(unittest.TestCase): |
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| 99 | """ |
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[bdd162f] | 100 | Test main functionality of the Invariant calculator |
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[46d50ca] | 101 | """ |
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| 102 | def setUp(self): |
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[3a473ef] | 103 | data = Loader().load(find("latex_smeared_slit.xml")) |
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[be577e7] | 104 | self.data = data[0] |
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[8a9f699] | 105 | self.data.dxl = None |
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[46d50ca] | 106 | |
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| 107 | def test_initial_data_processing(self): |
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| 108 | """ |
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| 109 | Test whether the background and scale are handled properly |
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| 110 | when creating an InvariantCalculator object |
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| 111 | """ |
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| 112 | length = len(self.data.x) |
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| 113 | self.assertEqual(length, len(self.data.y)) |
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| 114 | inv = invariant.InvariantCalculator(self.data) |
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| 115 | |
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| 116 | self.assertEqual(length, len(inv._data.x)) |
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| 117 | self.assertEqual(inv._data.x[0], self.data.x[0]) |
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| 118 | |
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| 119 | # Now the same thing with a background value |
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| 120 | bck = 0.1 |
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| 121 | inv = invariant.InvariantCalculator(self.data, background=bck) |
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| 122 | self.assertEqual(inv._background, bck) |
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| 123 | |
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| 124 | self.assertEqual(length, len(inv._data.x)) |
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| 125 | self.assertEqual(inv._data.y[0]+bck, self.data.y[0]) |
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| 126 | |
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| 127 | # Now the same thing with a scale value |
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| 128 | scale = 0.1 |
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| 129 | inv = invariant.InvariantCalculator(self.data, scale=scale) |
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| 130 | self.assertEqual(inv._scale, scale) |
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| 131 | |
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| 132 | self.assertEqual(length, len(inv._data.x)) |
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| 133 | self.assertAlmostEqual(inv._data.y[0]/scale, self.data.y[0],7) |
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| 134 | |
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| 135 | |
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| 136 | def test_incompatible_data_class(self): |
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| 137 | """ |
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| 138 | Check that only classes that inherit from Data1D are allowed as data. |
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| 139 | """ |
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| 140 | class Incompatible(): |
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| 141 | pass |
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| 142 | self.assertRaises(ValueError, invariant.InvariantCalculator, Incompatible()) |
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[bdd162f] | 143 | |
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| 144 | def test_error_treatment(self): |
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[9a5097c] | 145 | x = np.asarray(np.asarray([0,1,2,3])) |
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| 146 | y = np.asarray(np.asarray([1,1,1,1])) |
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[bdd162f] | 147 | |
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| 148 | # These are all the values of the dy array that would cause |
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| 149 | # us to set all dy values to 1.0 at __init__ time. |
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| 150 | dy_list = [ [], None, [0,0,0,0] ] |
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| 151 | |
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| 152 | for dy in dy_list: |
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| 153 | data = Data1D(x=x, y=y, dy=dy) |
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| 154 | inv = invariant.InvariantCalculator(data) |
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| 155 | self.assertEqual(len(inv._data.x), len(inv._data.dy)) |
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| 156 | self.assertEqual(len(inv._data.dy), 4) |
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| 157 | for i in range(4): |
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| 158 | self.assertEqual(inv._data.dy[i],1) |
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| 159 | |
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| 160 | def test_qstar_low_q_guinier(self): |
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| 161 | """ |
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| 162 | Test low-q extrapolation with a Guinier |
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| 163 | """ |
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| 164 | inv = invariant.InvariantCalculator(self.data) |
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| 165 | |
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| 166 | # Basic sanity check |
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| 167 | _qstar = inv.get_qstar() |
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| 168 | qstar, dqstar = inv.get_qstar_with_error() |
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| 169 | self.assertEqual(qstar, _qstar) |
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| 170 | |
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| 171 | # Low-Q Extrapolation |
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| 172 | # Check that the returned invariant is what we expect given |
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| 173 | # the result we got without extrapolation |
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| 174 | inv.set_extrapolation('low', npts=10, function='guinier') |
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| 175 | qs_extr, dqs_extr = inv.get_qstar_with_error('low') |
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| 176 | delta_qs_extr, delta_dqs_extr = inv.get_qstar_low() |
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| 177 | |
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| 178 | self.assertEqual(qs_extr, _qstar+delta_qs_extr) |
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| 179 | self.assertEqual(dqs_extr, math.sqrt(dqstar*dqstar + delta_dqs_extr*delta_dqs_extr)) |
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| 180 | |
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| 181 | # We don't expect the extrapolated invariant to be very far from the |
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| 182 | # result without extrapolation. Let's test for a result within 10%. |
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| 183 | self.assertTrue(math.fabs(qs_extr-qstar)/qstar<0.1) |
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| 184 | |
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| 185 | # Check that the two results are consistent within errors |
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| 186 | # Note that the error on the extrapolated value takes into account |
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| 187 | # a systematic error for the fact that we may not know the shape of I(q) at low Q. |
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| 188 | self.assertTrue(math.fabs(qs_extr-qstar)<dqs_extr) |
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| 189 | |
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| 190 | def test_qstar_low_q_power_law(self): |
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| 191 | """ |
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| 192 | Test low-q extrapolation with a power law |
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| 193 | """ |
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| 194 | inv = invariant.InvariantCalculator(self.data) |
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| 195 | |
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| 196 | # Basic sanity check |
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| 197 | _qstar = inv.get_qstar() |
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| 198 | qstar, dqstar = inv.get_qstar_with_error() |
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| 199 | self.assertEqual(qstar, _qstar) |
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| 200 | |
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| 201 | # Low-Q Extrapolation |
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| 202 | # Check that the returned invariant is what we expect given |
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| 203 | inv.set_extrapolation('low', npts=10, function='power_law') |
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| 204 | qs_extr, dqs_extr = inv.get_qstar_with_error('low') |
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| 205 | delta_qs_extr, delta_dqs_extr = inv.get_qstar_low() |
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| 206 | |
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[8c9ffde] | 207 | # A fit using SasView gives 0.0655 for the value of the exponent |
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[bdd162f] | 208 | self.assertAlmostEqual(inv._low_extrapolation_function.power, 0.0655, 3) |
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| 209 | |
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| 210 | if False: |
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| 211 | npts = len(inv._data.x)-1 |
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| 212 | import matplotlib.pyplot as plt |
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| 213 | plt.loglog(inv._data.x[:npts], inv._data.y[:npts], 'o', label='Original data', markersize=10) |
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| 214 | plt.loglog(inv._data.x[:npts], inv._low_extrapolation_function.evaluate_model(inv._data.x[:npts]), 'r', label='Fitted line') |
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| 215 | plt.legend() |
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| 216 | plt.show() |
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| 217 | |
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| 218 | self.assertEqual(qs_extr, _qstar+delta_qs_extr) |
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[6574940a] | 219 | self.assertAlmostEqual(dqs_extr, math.sqrt(dqstar*dqstar + delta_dqs_extr*delta_dqs_extr), 15) |
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[bdd162f] | 220 | |
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| 221 | # We don't expect the extrapolated invariant to be very far from the |
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| 222 | # result without extrapolation. Let's test for a result within 10%. |
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| 223 | self.assertTrue(math.fabs(qs_extr-qstar)/qstar<0.1) |
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| 224 | |
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| 225 | # Check that the two results are consistent within errors |
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| 226 | # Note that the error on the extrapolated value takes into account |
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| 227 | # a systematic error for the fact that we may not know the shape of I(q) at low Q. |
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| 228 | self.assertTrue(math.fabs(qs_extr-qstar)<dqs_extr) |
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| 229 | |
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| 230 | def test_qstar_high_q(self): |
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| 231 | """ |
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| 232 | Test high-q extrapolation |
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| 233 | """ |
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| 234 | inv = invariant.InvariantCalculator(self.data) |
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| 235 | |
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| 236 | # Basic sanity check |
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| 237 | _qstar = inv.get_qstar() |
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| 238 | qstar, dqstar = inv.get_qstar_with_error() |
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| 239 | self.assertEqual(qstar, _qstar) |
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| 240 | |
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| 241 | # High-Q Extrapolation |
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| 242 | # Check that the returned invariant is what we expect given |
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| 243 | # the result we got without extrapolation |
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| 244 | inv.set_extrapolation('high', npts=20, function='power_law') |
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| 245 | qs_extr, dqs_extr = inv.get_qstar_with_error('high') |
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| 246 | delta_qs_extr, delta_dqs_extr = inv.get_qstar_high() |
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| 247 | |
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[8c9ffde] | 248 | # From previous analysis using SasView, we expect an exponent of about 3 |
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[bdd162f] | 249 | self.assertTrue(math.fabs(inv._high_extrapolation_function.power-3)<0.1) |
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| 250 | |
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| 251 | self.assertEqual(qs_extr, _qstar+delta_qs_extr) |
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[c4f79f0] | 252 | self.assertAlmostEqual(dqs_extr, math.sqrt(dqstar*dqstar + delta_dqs_extr*delta_dqs_extr), 10) |
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[bdd162f] | 253 | |
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| 254 | # We don't expect the extrapolated invariant to be very far from the |
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| 255 | # result without extrapolation. Let's test for a result within 10%. |
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| 256 | #TODO: verify whether this test really makes sense |
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| 257 | #self.assertTrue(math.fabs(qs_extr-qstar)/qstar<0.1) |
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| 258 | |
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| 259 | # Check that the two results are consistent within errors |
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| 260 | self.assertTrue(math.fabs(qs_extr-qstar)<dqs_extr) |
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| 261 | |
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| 262 | def test_qstar_full_q(self): |
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| 263 | """ |
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| 264 | Test high-q extrapolation |
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| 265 | """ |
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| 266 | inv = invariant.InvariantCalculator(self.data) |
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| 267 | |
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| 268 | # Basic sanity check |
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| 269 | _qstar = inv.get_qstar() |
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| 270 | qstar, dqstar = inv.get_qstar_with_error() |
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| 271 | self.assertEqual(qstar, _qstar) |
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| 272 | |
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| 273 | # High-Q Extrapolation |
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| 274 | # Check that the returned invariant is what we expect given |
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| 275 | # the result we got without extrapolation |
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| 276 | inv.set_extrapolation('low', npts=10, function='guinier') |
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| 277 | inv.set_extrapolation('high', npts=20, function='power_law') |
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| 278 | qs_extr, dqs_extr = inv.get_qstar_with_error('both') |
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| 279 | delta_qs_low, delta_dqs_low = inv.get_qstar_low() |
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| 280 | delta_qs_hi, delta_dqs_hi = inv.get_qstar_high() |
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| 281 | |
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| 282 | self.assertAlmostEqual(qs_extr, _qstar+delta_qs_low+delta_qs_hi, 8) |
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[97700d7] | 283 | self.assertAlmostEqual(dqs_extr, math.sqrt(dqstar*dqstar + delta_dqs_low*delta_dqs_low \ |
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| 284 | + delta_dqs_hi*delta_dqs_hi), 8) |
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[bdd162f] | 285 | |
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| 286 | # We don't expect the extrapolated invariant to be very far from the |
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| 287 | # result without extrapolation. Let's test for a result within 10%. |
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| 288 | #TODO: verify whether this test really makes sense |
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| 289 | #self.assertTrue(math.fabs(qs_extr-qstar)/qstar<0.1) |
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| 290 | |
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| 291 | # Check that the two results are consistent within errors |
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| 292 | self.assertTrue(math.fabs(qs_extr-qstar)<dqs_extr) |
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| 293 | |
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[c75a8ed] | 294 | def _check_values(to_check, reference, tolerance=0.05): |
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| 295 | self.assertTrue( math.fabs(to_check-reference)/reference < tolerance, msg="Tested value = "+str(to_check) ) |
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| 296 | |
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| 297 | # The following values should be replaced by values pulled from IGOR |
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| 298 | # Volume Fraction: |
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| 299 | v, dv = inv.get_volume_fraction_with_error(1, None) |
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| 300 | _check_values(v, 1.88737914186e-15) |
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| 301 | |
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| 302 | v_l, dv_l = inv.get_volume_fraction_with_error(1, 'low') |
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| 303 | _check_values(v_l, 1.94289029309e-15) |
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| 304 | |
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| 305 | v_h, dv_h = inv.get_volume_fraction_with_error(1, 'high') |
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| 306 | _check_values(v_h, 6.99440505514e-15) |
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| 307 | |
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| 308 | v_b, dv_b = inv.get_volume_fraction_with_error(1, 'both') |
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| 309 | _check_values(v_b, 6.99440505514e-15) |
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| 310 | |
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| 311 | # Specific Surface: |
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| 312 | s, ds = inv.get_surface_with_error(1, 1, None) |
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| 313 | _check_values(s, 3.1603095786e-09) |
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| 314 | |
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| 315 | s_l, ds_l = inv.get_surface_with_error(1, 1, 'low') |
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| 316 | _check_values(s_l, 3.1603095786e-09) |
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| 317 | |
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| 318 | s_h, ds_h = inv.get_surface_with_error(1, 1, 'high') |
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| 319 | _check_values(s_h, 3.1603095786e-09) |
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| 320 | |
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| 321 | s_b, ds_b = inv.get_surface_with_error(1, 1, 'both') |
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| 322 | _check_values(s_b, 3.1603095786e-09) |
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| 323 | |
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| 324 | |
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[bdd162f] | 325 | def test_bad_parameter_name(self): |
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| 326 | """ |
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| 327 | The set_extrapolation method checks that the name of the extrapolation |
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| 328 | function and the name of the q-range to extrapolate (high/low) is |
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| 329 | recognized. |
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| 330 | """ |
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| 331 | inv = invariant.InvariantCalculator(self.data) |
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| 332 | self.assertRaises(ValueError, inv.set_extrapolation, 'low', npts=4, function='not_a_name') |
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| 333 | self.assertRaises(ValueError, inv.set_extrapolation, 'not_a_range', npts=4, function='guinier') |
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| 334 | self.assertRaises(ValueError, inv.set_extrapolation, 'high', npts=4, function='guinier') |
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[46d50ca] | 335 | |
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[6939bd4] | 336 | |
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| 337 | class TestGuinierExtrapolation(unittest.TestCase): |
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| 338 | """ |
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| 339 | Generate a Guinier distribution and verify that the extrapolation |
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| 340 | produce the correct ditribution. |
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| 341 | """ |
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| 342 | |
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| 343 | def setUp(self): |
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| 344 | """ |
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| 345 | Generate a Guinier distribution. After extrapolating, we will |
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| 346 | verify that we obtain the scale and rg parameters |
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| 347 | """ |
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| 348 | self.scale = 1.5 |
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[aafa962] | 349 | self.rg = 30.0 |
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[9a5097c] | 350 | x = np.arange(0.0001, 0.1, 0.0001) |
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| 351 | y = np.asarray([self.scale * math.exp( -(q*self.rg)**2 / 3.0 ) for q in x]) |
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[6939bd4] | 352 | dy = y*.1 |
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| 353 | self.data = Data1D(x=x, y=y, dy=dy) |
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| 354 | |
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| 355 | def test_low_q(self): |
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| 356 | """ |
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| 357 | Invariant with low-Q extrapolation |
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| 358 | """ |
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| 359 | # Create invariant object. Background and scale left as defaults. |
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| 360 | inv = invariant.InvariantCalculator(data=self.data) |
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| 361 | # Set the extrapolation parameters for the low-Q range |
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| 362 | inv.set_extrapolation(range='low', npts=20, function='guinier') |
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| 363 | |
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| 364 | self.assertEqual(inv._low_extrapolation_npts, 20) |
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[aafa962] | 365 | self.assertEqual(inv._low_extrapolation_function.__class__, invariant.Guinier) |
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[6939bd4] | 366 | |
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| 367 | # Data boundaries for fiiting |
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| 368 | qmin = inv._data.x[0] |
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| 369 | qmax = inv._data.x[inv._low_extrapolation_npts - 1] |
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| 370 | |
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| 371 | # Extrapolate the low-Q data |
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[bdd162f] | 372 | inv._fit(model=inv._low_extrapolation_function, |
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[6939bd4] | 373 | qmin=qmin, |
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| 374 | qmax=qmax, |
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| 375 | power=inv._low_extrapolation_power) |
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[bdd162f] | 376 | self.assertAlmostEqual(self.scale, inv._low_extrapolation_function.scale, 6) |
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| 377 | self.assertAlmostEqual(self.rg, inv._low_extrapolation_function.radius, 6) |
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[6939bd4] | 378 | |
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| 379 | |
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| 380 | class TestPowerLawExtrapolation(unittest.TestCase): |
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| 381 | """ |
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| 382 | Generate a power law distribution and verify that the extrapolation |
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| 383 | produce the correct ditribution. |
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| 384 | """ |
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| 385 | |
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| 386 | def setUp(self): |
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| 387 | """ |
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| 388 | Generate a power law distribution. After extrapolating, we will |
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| 389 | verify that we obtain the scale and m parameters |
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| 390 | """ |
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| 391 | self.scale = 1.5 |
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| 392 | self.m = 3.0 |
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[9a5097c] | 393 | x = np.arange(0.0001, 0.1, 0.0001) |
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| 394 | y = np.asarray([self.scale * math.pow(q ,-1.0*self.m) for q in x]) |
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[6939bd4] | 395 | dy = y*.1 |
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| 396 | self.data = Data1D(x=x, y=y, dy=dy) |
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| 397 | |
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| 398 | def test_low_q(self): |
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| 399 | """ |
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| 400 | Invariant with low-Q extrapolation |
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| 401 | """ |
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| 402 | # Create invariant object. Background and scale left as defaults. |
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| 403 | inv = invariant.InvariantCalculator(data=self.data) |
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| 404 | # Set the extrapolation parameters for the low-Q range |
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| 405 | inv.set_extrapolation(range='low', npts=20, function='power_law') |
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| 406 | |
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| 407 | self.assertEqual(inv._low_extrapolation_npts, 20) |
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[aafa962] | 408 | self.assertEqual(inv._low_extrapolation_function.__class__, invariant.PowerLaw) |
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[6939bd4] | 409 | |
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| 410 | # Data boundaries for fitting |
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| 411 | qmin = inv._data.x[0] |
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| 412 | qmax = inv._data.x[inv._low_extrapolation_npts - 1] |
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| 413 | |
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| 414 | # Extrapolate the low-Q data |
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[bdd162f] | 415 | inv._fit(model=inv._low_extrapolation_function, |
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[6939bd4] | 416 | qmin=qmin, |
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| 417 | qmax=qmax, |
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| 418 | power=inv._low_extrapolation_power) |
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| 419 | |
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[bdd162f] | 420 | self.assertAlmostEqual(self.scale, inv._low_extrapolation_function.scale, 6) |
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| 421 | self.assertAlmostEqual(self.m, inv._low_extrapolation_function.power, 6) |
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[aafa962] | 422 | |
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| 423 | class TestLinearization(unittest.TestCase): |
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| 424 | |
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| 425 | def test_guinier_incompatible_length(self): |
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| 426 | g = invariant.Guinier() |
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[76c1727] | 427 | data_in = Data1D(x=[1], y=[1,2], dy=None) |
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| 428 | self.assertRaises(AssertionError, g.linearize_data, data_in) |
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| 429 | data_in = Data1D(x=[1,1], y=[1,2], dy=[1]) |
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| 430 | self.assertRaises(AssertionError, g.linearize_data, data_in) |
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[aafa962] | 431 | |
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| 432 | def test_linearization(self): |
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| 433 | """ |
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| 434 | Check that the linearization process filters out points |
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| 435 | that can't be transformed |
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| 436 | """ |
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[9a5097c] | 437 | x = np.asarray(np.asarray([0,1,2,3])) |
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| 438 | y = np.asarray(np.asarray([1,1,1,1])) |
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[aafa962] | 439 | g = invariant.Guinier() |
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[76c1727] | 440 | data_in = Data1D(x=x, y=y) |
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| 441 | data_out = g.linearize_data(data_in) |
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| 442 | x_out, y_out, dy_out = data_out.x, data_out.y, data_out.dy |
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[aafa962] | 443 | self.assertEqual(len(x_out), 3) |
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| 444 | self.assertEqual(len(y_out), 3) |
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| 445 | self.assertEqual(len(dy_out), 3) |
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[bdd162f] | 446 | |
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| 447 | def test_allowed_bins(self): |
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[9a5097c] | 448 | x = np.asarray(np.asarray([0,1,2,3])) |
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| 449 | y = np.asarray(np.asarray([1,1,1,1])) |
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| 450 | dy = np.asarray(np.asarray([1,1,1,1])) |
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[bdd162f] | 451 | g = invariant.Guinier() |
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| 452 | data = Data1D(x=x, y=y, dy=dy) |
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| 453 | self.assertEqual(g.get_allowed_bins(data), [False, True, True, True]) |
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| 454 | |
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| 455 | data = Data1D(x=y, y=x, dy=dy) |
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| 456 | self.assertEqual(g.get_allowed_bins(data), [False, True, True, True]) |
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[97603c0] | 457 | |
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[bdd162f] | 458 | data = Data1D(x=dy, y=y, dy=x) |
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| 459 | self.assertEqual(g.get_allowed_bins(data), [False, True, True, True]) |
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[97603c0] | 460 | |
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| 461 | class TestDataExtraLow(unittest.TestCase): |
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| 462 | """ |
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| 463 | Generate a Guinier distribution and verify that the extrapolation |
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| 464 | produce the correct ditribution. Tested if the data generated by the |
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| 465 | invariant calculator is correct |
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| 466 | """ |
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| 467 | |
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| 468 | def setUp(self): |
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| 469 | """ |
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| 470 | Generate a Guinier distribution. After extrapolating, we will |
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| 471 | verify that we obtain the scale and rg parameters |
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| 472 | """ |
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| 473 | self.scale = 1.5 |
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| 474 | self.rg = 30.0 |
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[9a5097c] | 475 | x = np.arange(0.0001, 0.1, 0.0001) |
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| 476 | y = np.asarray([self.scale * math.exp( -(q*self.rg)**2 / 3.0 ) for q in x]) |
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[97603c0] | 477 | dy = y*.1 |
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| 478 | self.data = Data1D(x=x, y=y, dy=dy) |
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| 479 | |
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| 480 | def test_low_q(self): |
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| 481 | """ |
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| 482 | Invariant with low-Q extrapolation with no slit smear |
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| 483 | """ |
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| 484 | # Create invariant object. Background and scale left as defaults. |
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| 485 | inv = invariant.InvariantCalculator(data=self.data) |
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| 486 | # Set the extrapolation parameters for the low-Q range |
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[bdd162f] | 487 | inv.set_extrapolation(range='low', npts=10, function='guinier') |
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[97603c0] | 488 | |
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[bdd162f] | 489 | self.assertEqual(inv._low_extrapolation_npts, 10) |
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[97603c0] | 490 | self.assertEqual(inv._low_extrapolation_function.__class__, invariant.Guinier) |
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| 491 | |
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| 492 | # Data boundaries for fiiting |
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| 493 | qmin = inv._data.x[0] |
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| 494 | qmax = inv._data.x[inv._low_extrapolation_npts - 1] |
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| 495 | |
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| 496 | # Extrapolate the low-Q data |
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[bdd162f] | 497 | inv._fit(model=inv._low_extrapolation_function, |
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[97603c0] | 498 | qmin=qmin, |
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| 499 | qmax=qmax, |
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| 500 | power=inv._low_extrapolation_power) |
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[bdd162f] | 501 | self.assertAlmostEqual(self.scale, inv._low_extrapolation_function.scale, 6) |
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| 502 | self.assertAlmostEqual(self.rg, inv._low_extrapolation_function.radius, 6) |
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[97603c0] | 503 | |
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| 504 | qstar = inv.get_qstar(extrapolation='low') |
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| 505 | test_y = inv._low_extrapolation_function.evaluate_model(x=self.data.x) |
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| 506 | for i in range(len(self.data.x)): |
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[c75a8ed] | 507 | value = math.fabs(test_y[i]-self.data.y[i])/self.data.y[i] |
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[97603c0] | 508 | self.assert_(value < 0.001) |
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| 509 | |
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[76c1727] | 510 | class TestDataExtraLowSlitGuinier(unittest.TestCase): |
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| 511 | """ |
---|
| 512 | for a smear data, test that the fitting go through |
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[c75a8ed] | 513 | real data for atleast the 2 first points |
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[76c1727] | 514 | """ |
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| 515 | |
---|
| 516 | def setUp(self): |
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| 517 | """ |
---|
| 518 | Generate a Guinier distribution. After extrapolating, we will |
---|
| 519 | verify that we obtain the scale and rg parameters |
---|
| 520 | """ |
---|
| 521 | self.scale = 1.5 |
---|
| 522 | self.rg = 30.0 |
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[9a5097c] | 523 | x = np.arange(0.0001, 0.1, 0.0001) |
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| 524 | y = np.asarray([self.scale * math.exp( -(q*self.rg)**2 / 3.0 ) for q in x]) |
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[76c1727] | 525 | dy = y*.1 |
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| 526 | self.data = Data1D(x=x, y=y, dy=dy) |
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| 527 | self.npts = len(x)-10 |
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| 528 | |
---|
| 529 | def test_low_q(self): |
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| 530 | """ |
---|
| 531 | Invariant with low-Q extrapolation with slit smear |
---|
| 532 | """ |
---|
| 533 | # Create invariant object. Background and scale left as defaults. |
---|
| 534 | inv = invariant.InvariantCalculator(data=self.data) |
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| 535 | # Set the extrapolation parameters for the low-Q range |
---|
| 536 | inv.set_extrapolation(range='low', npts=self.npts, function='guinier') |
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| 537 | |
---|
| 538 | self.assertEqual(inv._low_extrapolation_npts, self.npts) |
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[97603c0] | 539 | self.assertEqual(inv._low_extrapolation_function.__class__, invariant.Guinier) |
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| 540 | |
---|
| 541 | # Data boundaries for fiiting |
---|
| 542 | qmin = inv._data.x[0] |
---|
| 543 | qmax = inv._data.x[inv._low_extrapolation_npts - 1] |
---|
| 544 | |
---|
| 545 | # Extrapolate the low-Q data |
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[bdd162f] | 546 | inv._fit(model=inv._low_extrapolation_function, |
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[97603c0] | 547 | qmin=qmin, |
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| 548 | qmax=qmax, |
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| 549 | power=inv._low_extrapolation_power) |
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| 550 | |
---|
| 551 | |
---|
| 552 | qstar = inv.get_qstar(extrapolation='low') |
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[c75a8ed] | 553 | |
---|
[76c1727] | 554 | test_y = inv._low_extrapolation_function.evaluate_model(x=self.data.x[:inv._low_extrapolation_npts]) |
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[c75a8ed] | 555 | self.assert_(len(test_y) == len(self.data.y[:inv._low_extrapolation_npts])) |
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[97603c0] | 556 | |
---|
[76c1727] | 557 | for i in range(inv._low_extrapolation_npts): |
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[c75a8ed] | 558 | value = math.fabs(test_y[i]-self.data.y[i])/self.data.y[i] |
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[97603c0] | 559 | self.assert_(value < 0.001) |
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| 560 | |
---|
[76c1727] | 561 | def test_low_data(self): |
---|
| 562 | """ |
---|
| 563 | Invariant with low-Q extrapolation with slit smear |
---|
| 564 | """ |
---|
| 565 | # Create invariant object. Background and scale left as defaults. |
---|
| 566 | inv = invariant.InvariantCalculator(data=self.data) |
---|
| 567 | # Set the extrapolation parameters for the low-Q range |
---|
| 568 | inv.set_extrapolation(range='low', npts=self.npts, function='guinier') |
---|
| 569 | |
---|
| 570 | self.assertEqual(inv._low_extrapolation_npts, self.npts) |
---|
| 571 | self.assertEqual(inv._low_extrapolation_function.__class__, invariant.Guinier) |
---|
| 572 | |
---|
| 573 | # Data boundaries for fiiting |
---|
| 574 | qmin = inv._data.x[0] |
---|
| 575 | qmax = inv._data.x[inv._low_extrapolation_npts - 1] |
---|
| 576 | |
---|
| 577 | # Extrapolate the low-Q data |
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[bdd162f] | 578 | inv._fit(model=inv._low_extrapolation_function, |
---|
[76c1727] | 579 | qmin=qmin, |
---|
| 580 | qmax=qmax, |
---|
| 581 | power=inv._low_extrapolation_power) |
---|
| 582 | |
---|
| 583 | |
---|
| 584 | qstar = inv.get_qstar(extrapolation='low') |
---|
| 585 | #Compution the y 's coming out of the invariant when computing extrapolated |
---|
| 586 | #low data . expect the fit engine to have been already called and the guinier |
---|
| 587 | # to have the radius and the scale fitted |
---|
[c75a8ed] | 588 | data_in_range = inv.get_extra_data_low(q_start=self.data.x[0], |
---|
| 589 | npts = inv._low_extrapolation_npts) |
---|
[76c1727] | 590 | test_y = data_in_range.y |
---|
[c75a8ed] | 591 | self.assert_(len(test_y) == len(self.data.y[:inv._low_extrapolation_npts])) |
---|
[76c1727] | 592 | for i in range(inv._low_extrapolation_npts): |
---|
[c75a8ed] | 593 | value = math.fabs(test_y[i]-self.data.y[i])/self.data.y[i] |
---|
[76c1727] | 594 | self.assert_(value < 0.001) |
---|
[c75a8ed] | 595 | |
---|
[97603c0] | 596 | |
---|
[76c1727] | 597 | class TestDataExtraHighSlitPowerLaw(unittest.TestCase): |
---|
| 598 | """ |
---|
| 599 | for a smear data, test that the fitting go through |
---|
[c75a8ed] | 600 | real data for atleast the 2 first points |
---|
[76c1727] | 601 | """ |
---|
| 602 | |
---|
| 603 | def setUp(self): |
---|
| 604 | """ |
---|
| 605 | Generate a Guinier distribution. After extrapolating, we will |
---|
| 606 | verify that we obtain the scale and rg parameters |
---|
| 607 | """ |
---|
| 608 | self.scale = 1.5 |
---|
| 609 | self.m = 3.0 |
---|
[9a5097c] | 610 | x = np.arange(0.0001, 0.1, 0.0001) |
---|
| 611 | y = np.asarray([self.scale * math.pow(q ,-1.0*self.m) for q in x]) |
---|
[76c1727] | 612 | dy = y*.1 |
---|
| 613 | self.data = Data1D(x=x, y=y, dy=dy) |
---|
| 614 | self.npts = 20 |
---|
| 615 | |
---|
| 616 | def test_high_q(self): |
---|
| 617 | """ |
---|
| 618 | Invariant with high-Q extrapolation with slit smear |
---|
| 619 | """ |
---|
| 620 | # Create invariant object. Background and scale left as defaults. |
---|
| 621 | inv = invariant.InvariantCalculator(data=self.data) |
---|
| 622 | # Set the extrapolation parameters for the low-Q range |
---|
| 623 | inv.set_extrapolation(range='high', npts=self.npts, function='power_law') |
---|
| 624 | |
---|
| 625 | self.assertEqual(inv._high_extrapolation_npts, self.npts) |
---|
| 626 | self.assertEqual(inv._high_extrapolation_function.__class__, invariant.PowerLaw) |
---|
| 627 | |
---|
| 628 | # Data boundaries for fiiting |
---|
| 629 | xlen = len(self.data.x) |
---|
| 630 | start = xlen - inv._high_extrapolation_npts |
---|
| 631 | qmin = inv._data.x[start] |
---|
| 632 | qmax = inv._data.x[xlen-1] |
---|
| 633 | |
---|
| 634 | # Extrapolate the high-Q data |
---|
[bdd162f] | 635 | inv._fit(model=inv._high_extrapolation_function, |
---|
[76c1727] | 636 | qmin=qmin, |
---|
| 637 | qmax=qmax, |
---|
| 638 | power=inv._high_extrapolation_power) |
---|
| 639 | |
---|
| 640 | |
---|
| 641 | qstar = inv.get_qstar(extrapolation='high') |
---|
| 642 | |
---|
| 643 | test_y = inv._high_extrapolation_function.evaluate_model(x=self.data.x[start: ]) |
---|
[c75a8ed] | 644 | self.assert_(len(test_y) == len(self.data.y[start:])) |
---|
[76c1727] | 645 | |
---|
| 646 | for i in range(len(self.data.x[start:])): |
---|
[c75a8ed] | 647 | value = math.fabs(test_y[i]-self.data.y[start+i])/self.data.y[start+i] |
---|
[76c1727] | 648 | self.assert_(value < 0.001) |
---|
| 649 | |
---|
| 650 | def test_high_data(self): |
---|
| 651 | """ |
---|
| 652 | Invariant with low-Q extrapolation with slit smear |
---|
| 653 | """ |
---|
| 654 | # Create invariant object. Background and scale left as defaults. |
---|
| 655 | inv = invariant.InvariantCalculator(data=self.data) |
---|
| 656 | # Set the extrapolation parameters for the low-Q range |
---|
| 657 | inv.set_extrapolation(range='high', npts=self.npts, function='power_law') |
---|
| 658 | |
---|
| 659 | self.assertEqual(inv._high_extrapolation_npts, self.npts) |
---|
| 660 | self.assertEqual(inv._high_extrapolation_function.__class__, invariant.PowerLaw) |
---|
| 661 | |
---|
| 662 | # Data boundaries for fiiting |
---|
| 663 | xlen = len(self.data.x) |
---|
| 664 | start = xlen - inv._high_extrapolation_npts |
---|
| 665 | qmin = inv._data.x[start] |
---|
| 666 | qmax = inv._data.x[xlen-1] |
---|
| 667 | |
---|
| 668 | # Extrapolate the high-Q data |
---|
[bdd162f] | 669 | inv._fit(model=inv._high_extrapolation_function, |
---|
[76c1727] | 670 | qmin=qmin, |
---|
| 671 | qmax=qmax, |
---|
| 672 | power=inv._high_extrapolation_power) |
---|
| 673 | |
---|
| 674 | qstar = inv.get_qstar(extrapolation='high') |
---|
| 675 | |
---|
[c75a8ed] | 676 | data_in_range= inv.get_extra_data_high(q_end = max(self.data.x), |
---|
| 677 | npts = inv._high_extrapolation_npts) |
---|
[76c1727] | 678 | test_y = data_in_range.y |
---|
[c75a8ed] | 679 | self.assert_(len(test_y) == len(self.data.y[start:])) |
---|
| 680 | temp = self.data.y[start:] |
---|
[76c1727] | 681 | |
---|
| 682 | for i in range(len(self.data.x[start:])): |
---|
| 683 | value = math.fabs(test_y[i]- temp[i])/temp[i] |
---|
[c75a8ed] | 684 | self.assert_(value < 0.001) |
---|