| 1 | """ |
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| 2 | Implementation of the use-case from a usage perspective. |
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| 3 | TODO: check the return values to perform actual unit testing. |
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| 4 | """ |
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| 5 | import unittest |
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| 6 | import numpy |
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| 7 | from DataLoader.loader import Loader |
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| 8 | from sans.invariant import invariant |
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| 9 | |
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| 10 | class Data1D: |
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| 11 | print "I am not of type Dataloader.Data1D" |
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| 12 | |
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| 13 | class TestInvPolySphere(unittest.TestCase): |
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| 14 | """ |
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| 15 | Test unsmeared data for invariant computation |
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| 16 | """ |
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| 17 | def setUp(self): |
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| 18 | self.data = Loader().load("PolySpheres.txt") |
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| 19 | |
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| 20 | def test_wrong_data(self): |
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| 21 | """ test receiving Data1D not of type loader""" |
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| 22 | |
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| 23 | wrong_data= Data1D() |
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| 24 | try: |
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| 25 | self.assertRaises(ValueError,invariant.InvariantCalculator(wrong_data)) |
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| 26 | except ValueError, msg: |
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| 27 | print "test pass "+ str(msg) |
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| 28 | else: raise ValueError, "fail to raise exception when expected" |
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| 29 | |
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| 30 | |
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| 31 | def test_use_case_1(self): |
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| 32 | """ |
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| 33 | Invariant without extrapolation |
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| 34 | """ |
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| 35 | # Create invariant object. Background and scale left as defaults. |
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| 36 | inv = invariant.InvariantCalculator(data=self.data) |
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| 37 | |
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| 38 | # We have to be able to tell the InvariantCalculator whether we want the |
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| 39 | # extrapolation or not. By default, when the user doesn't specify, we |
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| 40 | # should compute Q* without extrapolation. That's what should be done in __init__. |
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| 41 | |
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| 42 | # We call get_qstar() with no argument, which signifies that we do NOT |
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| 43 | # want extrapolation. |
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| 44 | qstar = inv.get_qstar() |
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| 45 | |
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| 46 | # The volume fraction and surface use Q*. That means that the following |
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| 47 | # methods should check that Q* has been computed. If not, it should |
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| 48 | # compute it by calling get_qstare(), leaving the parameters as default. |
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| 49 | v, dv = inv.get_volume_fraction_with_error(contrast=2.6e-6) |
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| 50 | s, ds = inv.get_surface_with_error(contrast=2.6e-6, porod_const=2) |
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| 51 | |
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| 52 | # Test results |
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| 53 | self.assertAlmostEquals(qstar, 7.48959e-5,2) |
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| 54 | self.assertAlmostEquals(v, 0.005644689) |
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| 55 | self.assertAlmostEquals(s, 9.42e+2,2) |
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| 56 | |
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| 57 | def test_use_case_2(self): |
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| 58 | """ |
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| 59 | Invariant without extrapolation. Invariant, volume fraction and surface |
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| 60 | are given with errors. |
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| 61 | """ |
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| 62 | # Create invariant object. Background and scale left as defaults. |
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| 63 | inv = invariant.InvariantCalculator(data=self.data) |
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| 64 | |
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| 65 | # Get the invariant with errors |
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| 66 | qstar, qstar_err = inv.get_qstar_with_error() |
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| 67 | |
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| 68 | # The volume fraction and surface use Q*. That means that the following |
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| 69 | # methods should check that Q* has been computed. If not, it should |
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| 70 | # compute it by calling get_qstare(), leaving the parameters as default. |
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| 71 | v, dv = inv.get_volume_fraction_with_error(contrast=2.6e-6) |
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| 72 | s, ds = inv.get_surface_with_error(contrast=2.6e-6, porod_const=2) |
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| 73 | # Test results |
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| 74 | self.assertAlmostEquals(qstar, 7.48959e-5,2) |
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| 75 | self.assertAlmostEquals(v, 0.005644689) |
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| 76 | self.assertAlmostEquals(s, 9.42e+2,2) |
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| 77 | |
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| 78 | |
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| 79 | def test_use_case_3(self): |
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| 80 | """ |
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| 81 | Invariant with low-Q extrapolation |
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| 82 | """ |
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| 83 | # Create invariant object. Background and scale left as defaults. |
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| 84 | inv = invariant.InvariantCalculator(data=self.data) |
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| 85 | |
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| 86 | # Set the extrapolation parameters for the low-Q range |
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| 87 | |
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| 88 | # The npts parameter should have a good default. |
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| 89 | # The range parameter should be 'high' or 'low' |
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| 90 | # The function parameter should default to None. If it is None, |
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| 91 | # the method should pick a good default (Guinier at low-Q and 1/q^4 at high-Q). |
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| 92 | # The method should also check for consistency of the extrapolation and function |
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| 93 | # parameters. For instance, you might not want to allow 'high' and 'guinier'. |
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| 94 | # The power parameter (not shown below) should default to 4. |
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| 95 | inv.set_extrapolation(range='low', npts=10, function='guinier') |
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| 96 | |
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| 97 | # The version of the call without error |
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| 98 | # At this point, we could still compute Q* without extrapolation by calling |
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| 99 | # get_qstar with arguments, or with extrapolation=None. |
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| 100 | qstar = inv.get_qstar(extrapolation='low') |
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| 101 | |
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| 102 | # The version of the call with error |
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| 103 | qstar, qstar_err = inv.get_qstar_with_error(extrapolation='low') |
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| 104 | |
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| 105 | # Get the volume fraction and surface |
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| 106 | v, dv = inv.get_volume_fraction_with_error(contrast=2.6e-6) |
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| 107 | s, ds = inv.get_surface_with_error(contrast=2.6e-6, porod_const=2) |
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| 108 | |
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| 109 | # Test results |
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| 110 | self.assertAlmostEquals(qstar, 7.49e-5) |
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| 111 | self.assertAlmostEquals(v, 0.005648401) |
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| 112 | self.assertAlmostEquals(s, 9.42e+2,2) |
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| 113 | |
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| 114 | def test_use_case_4(self): |
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| 115 | """ |
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| 116 | Invariant with high-Q extrapolation |
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| 117 | """ |
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| 118 | # Create invariant object. Background and scale left as defaults. |
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| 119 | inv = invariant.InvariantCalculator(data=self.data) |
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| 120 | |
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| 121 | # Set the extrapolation parameters for the high-Q range |
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| 122 | inv.set_extrapolation(range='high', npts=10, function='power_law', power=4) |
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| 123 | |
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| 124 | # The version of the call without error |
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| 125 | # The function parameter defaults to None, then is picked to be 'power_law' for extrapolation='high' |
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| 126 | qstar = inv.get_qstar(extrapolation='high') |
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| 127 | |
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| 128 | # The version of the call with error |
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| 129 | qstar, qstar_err = inv.get_qstar_with_error(extrapolation='high') |
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| 130 | |
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| 131 | # Get the volume fraction and surface |
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| 132 | v, dv = inv.get_volume_fraction_with_error(contrast=2.6e-6) |
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| 133 | s, ds = inv.get_surface_with_error(contrast=2.6e-6, porod_const=2) |
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| 134 | |
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| 135 | # Test results |
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| 136 | self.assertAlmostEquals(qstar, 7.49e-5,2) |
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| 137 | self.assertAlmostEquals(v, 0.005952674) |
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| 138 | self.assertAlmostEquals(s, 9.42e+2,2) |
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| 139 | |
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| 140 | def test_use_case_5(self): |
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| 141 | """ |
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| 142 | Invariant with both high- and low-Q extrapolation |
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| 143 | """ |
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| 144 | # Create invariant object. Background and scale left as defaults. |
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| 145 | inv = invariant.InvariantCalculator(data=self.data) |
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| 146 | |
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| 147 | # Set the extrapolation parameters for the low- and high-Q ranges |
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| 148 | inv.set_extrapolation(range='low', npts=10, function='guinier') |
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| 149 | inv.set_extrapolation(range='high', npts=10, function='power_law', power=4) |
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| 150 | |
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| 151 | # The version of the call without error |
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| 152 | # The function parameter defaults to None, then is picked to be 'power_law' for extrapolation='high' |
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| 153 | qstar = inv.get_qstar(extrapolation='both') |
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| 154 | |
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| 155 | # The version of the call with error |
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| 156 | qstar, qstar_err = inv.get_qstar_with_error(extrapolation='both') |
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| 157 | |
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| 158 | # Get the volume fraction and surface |
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| 159 | v, dv = inv.get_volume_fraction_with_error(contrast=2.6e-6) |
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| 160 | s, ds = inv.get_surface_with_error(contrast=2.6e-6, porod_const=2) |
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| 161 | |
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| 162 | # Test results |
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| 163 | self.assertAlmostEquals(qstar, 7.88981e-5,2) |
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| 164 | self.assertAlmostEquals(v, 0.005952674) |
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| 165 | self.assertAlmostEquals(s, 9.42e+2,2) |
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| 166 | |
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| 167 | class TestInvSlitSmear(unittest.TestCase): |
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| 168 | """ |
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| 169 | Test slit smeared data for invariant computation |
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| 170 | """ |
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| 171 | def setUp(self): |
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| 172 | # Data with slit smear |
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| 173 | list = Loader().load("latex_smeared.xml") |
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| 174 | self.data_slit_smear = list[1] |
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| 175 | |
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| 176 | def test_use_case_1(self): |
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| 177 | """ |
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| 178 | Invariant without extrapolation |
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| 179 | """ |
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| 180 | inv = invariant.InvariantCalculator(data=self.data_slit_smear) |
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| 181 | # get invariant |
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| 182 | qstar = inv.get_qstar() |
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| 183 | # Get the volume fraction and surface |
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| 184 | v, dv = inv.get_volume_fraction_with_error(contrast=2.6e-6) |
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| 185 | s, ds = inv.get_surface_with_error(contrast=2.6e-6, porod_const=2) |
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| 186 | # Test results |
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| 187 | self.assertAlmostEquals(qstar, 4.1539e-4) |
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| 188 | self.assertAlmostEquals(v, 0.032164596) |
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| 189 | self.assertAlmostEquals(s, 9.42e+2,2) |
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| 190 | |
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| 191 | def test_use_case_2(self): |
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| 192 | """ |
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| 193 | Invariant without extrapolation. Invariant, volume fraction and surface |
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| 194 | are given with errors. |
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| 195 | """ |
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| 196 | # Create invariant object. Background and scale left as defaults. |
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| 197 | inv = invariant.InvariantCalculator(data=self.data_slit_smear) |
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| 198 | # Get the invariant with errors |
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| 199 | qstar, qstar_err = inv.get_qstar_with_error() |
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| 200 | # Get the volume fraction and surface |
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| 201 | v, dv = inv.get_volume_fraction_with_error(contrast=2.6e-6) |
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| 202 | s, ds = inv.get_surface_with_error(contrast=2.6e-6, porod_const=2) |
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| 203 | # Test results |
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| 204 | self.assertAlmostEquals(qstar, 4.1539e-4) |
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| 205 | self.assertAlmostEquals(v, 0.032164596) |
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| 206 | self.assertAlmostEquals(s, 9.42e+2,2) |
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| 207 | |
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| 208 | def test_use_case_3(self): |
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| 209 | """ |
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| 210 | Invariant with low-Q extrapolation |
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| 211 | """ |
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| 212 | # Create invariant object. Background and scale left as defaults. |
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| 213 | inv = invariant.InvariantCalculator(data=self.data_slit_smear) |
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| 214 | # Set the extrapolation parameters for the low-Q range |
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| 215 | inv.set_extrapolation(range='low', npts=10, function='guinier') |
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| 216 | # The version of the call without error |
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| 217 | # At this point, we could still compute Q* without extrapolation by calling |
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| 218 | # get_qstar with arguments, or with extrapolation=None. |
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| 219 | qstar = inv.get_qstar(extrapolation='low') |
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| 220 | # The version of the call with error |
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| 221 | qstar, qstar_err = inv.get_qstar_with_error(extrapolation='low') |
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| 222 | # Get the volume fraction and surface |
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| 223 | v, dv = inv.get_volume_fraction_with_error(contrast=2.6e-6) |
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| 224 | s, ds = inv.get_surface_with_error(contrast=2.6e-6, porod_const=2) |
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| 225 | |
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| 226 | # Test results |
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| 227 | self.assertAlmostEquals(qstar,4.1534e-4,3) |
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| 228 | self.assertAlmostEquals(v, 0.032164596) |
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| 229 | self.assertAlmostEquals(s, 9.42e+2,2) |
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| 230 | |
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| 231 | def test_use_case_4(self): |
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| 232 | """ |
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| 233 | Invariant with high-Q extrapolation |
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| 234 | """ |
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| 235 | # Create invariant object. Background and scale left as defaults. |
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| 236 | inv = invariant.InvariantCalculator(data=self.data_slit_smear) |
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| 237 | |
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| 238 | # Set the extrapolation parameters for the high-Q range |
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| 239 | inv.set_extrapolation(range='high', npts=10, function='power_law', power=4) |
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| 240 | |
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| 241 | # The version of the call without error |
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| 242 | # The function parameter defaults to None, then is picked to be 'power_law' for extrapolation='high' |
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| 243 | qstar = inv.get_qstar(extrapolation='high') |
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| 244 | |
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| 245 | # The version of the call with error |
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| 246 | qstar, qstar_err = inv.get_qstar_with_error(extrapolation='high') |
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| 247 | |
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| 248 | # Get the volume fraction and surface |
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| 249 | v, dv = inv.get_volume_fraction_with_error(contrast=2.6e-6) |
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| 250 | s, ds = inv.get_surface_with_error(contrast=2.6e-6, porod_const=2) |
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| 251 | |
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| 252 | # Test results |
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| 253 | self.assertAlmostEquals(qstar, 4.1539e-4) |
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| 254 | self.assertAlmostEquals(v, 0.032164596) |
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| 255 | self.assertAlmostEquals(s, 9.42e+2,2) |
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| 256 | |
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| 257 | def test_use_case_5(self): |
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| 258 | """ |
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| 259 | Invariant with both high- and low-Q extrapolation |
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| 260 | """ |
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| 261 | # Create invariant object. Background and scale left as defaults. |
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| 262 | inv = invariant.InvariantCalculator(data=self.data_slit_smear) |
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| 263 | |
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| 264 | # Set the extrapolation parameters for the low- and high-Q ranges |
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| 265 | inv.set_extrapolation(range='low', npts=10, function='guinier') |
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| 266 | inv.set_extrapolation(range='high', npts=10, function='power_law', power=4) |
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| 267 | |
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| 268 | # The version of the call without error |
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| 269 | # The function parameter defaults to None, then is picked to be 'power_law' for extrapolation='high' |
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| 270 | qstar = inv.get_qstar(extrapolation='both') |
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| 271 | |
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| 272 | # The version of the call with error |
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| 273 | qstar, qstar_err = inv.get_qstar_with_error(extrapolation='both') |
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| 274 | |
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| 275 | # Get the volume fraction and surface |
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| 276 | v, dv = inv.get_volume_fraction_with_error(contrast=2.6e-6) |
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| 277 | s, ds = inv.get_surface_with_error(contrast=2.6e-6, porod_const=2) |
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| 278 | |
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| 279 | # Test results |
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| 280 | self.assertAlmostEquals(qstar, 4.1534e-4,3) |
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| 281 | self.assertAlmostEquals(v, 0.032164596) |
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| 282 | self.assertAlmostEquals(s, 9.42e+2,2) |
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| 283 | |
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| 284 | class TestInvPinholeSmear(unittest.TestCase): |
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| 285 | """ |
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| 286 | Test pinhole smeared data for invariant computation |
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| 287 | """ |
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| 288 | def setUp(self): |
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| 289 | # data with smear info |
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| 290 | list = Loader().load("latex_smeared.xml") |
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| 291 | self.data_q_smear = list[0] |
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| 292 | |
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| 293 | def test_use_case_1(self): |
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| 294 | """ |
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| 295 | Invariant without extrapolation |
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| 296 | """ |
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| 297 | inv = invariant.InvariantCalculator(data=self.data_q_smear) |
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| 298 | qstar = inv.get_qstar() |
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| 299 | |
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| 300 | volume_fraction = inv.get_volume_fraction(contrast=2.6e-6) |
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| 301 | surface = inv.get_surface(contrast=2.6e-6, porod_const=2) |
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| 302 | # Test results |
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| 303 | self.assertAlmostEquals(qstar, 1.361677e-3) |
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| 304 | self.assertAlmostEquals(v, 0.115352622) |
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| 305 | self.assertAlmostEquals(s, 9.42e+2,2) |
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| 306 | |
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| 307 | def test_use_case_2(self): |
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| 308 | """ |
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| 309 | Invariant without extrapolation. Invariant, volume fraction and surface |
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| 310 | are given with errors. |
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| 311 | """ |
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| 312 | # Create invariant object. Background and scale left as defaults. |
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| 313 | inv = invariant.InvariantCalculator(data=self.data_q_smear) |
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| 314 | |
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| 315 | # Get the invariant with errors |
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| 316 | qstar, qstar_err = inv.get_qstar_with_error() |
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| 317 | # Get the volume fraction and surface |
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| 318 | v, dv = inv.get_volume_fraction_with_error(contrast=2.6e-6) |
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| 319 | s, ds = inv.get_surface_with_error(contrast=2.6e-6, porod_const=2) |
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| 320 | # Test results |
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| 321 | self.assertAlmostEquals(qstar, 1.361677e-3) |
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| 322 | self.assertAlmostEquals(v, 0.115352622) |
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| 323 | self.assertAlmostEquals(s, 9.42e+2,2) |
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| 324 | |
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| 325 | def test_use_case_3(self): |
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| 326 | """ |
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| 327 | Invariant with low-Q extrapolation |
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| 328 | """ |
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| 329 | # Create invariant object. Background and scale left as defaults. |
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| 330 | inv = invariant.InvariantCalculator(data=self.data_q_smear) |
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| 331 | # Set the extrapolation parameters for the low-Q range |
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| 332 | inv.set_extrapolation(range='low', npts=20, function='guinier') |
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| 333 | # The version of the call without error |
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| 334 | qstar = inv.get_qstar(extrapolation='low') |
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| 335 | # The version of the call with error |
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| 336 | qstar, qstar_err = inv.get_qstar_with_error(extrapolation='low') |
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| 337 | # Get the volume fraction and surface |
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| 338 | v, dv = inv.get_volume_fraction_with_error(contrast=2.6e-6) |
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| 339 | s, ds = inv.get_surface_with_error(contrast=1.0, porod_const=0.08) |
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| 340 | |
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| 341 | # Test results |
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| 342 | self.assertAlmostEquals(qstar, 0.002037677) |
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| 343 | self.assertAlmostEquals(v, 0.115352622) |
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| 344 | self.assertAlmostEquals(s, 9.42e+2,2) |
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| 345 | |
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| 346 | def test_use_case_4(self): |
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| 347 | """ |
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| 348 | Invariant with high-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_q_smear) |
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| 352 | # Set the extrapolation parameters for the high-Q range |
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| 353 | inv.set_extrapolation(range='high', npts=10, function='power_law', power=4) |
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| 354 | # The version of the call without error |
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| 355 | qstar = inv.get_qstar(extrapolation='high') |
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| 356 | # The version of the call with error |
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| 357 | qstar, qstar_err = inv.get_qstar_with_error(extrapolation='high') |
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| 358 | # Get the volume fraction and surface |
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| 359 | v, dv = inv.get_volume_fraction_with_error(contrast=2.6e-6) |
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| 360 | s, ds = inv.get_surface_with_error(contrast=2.6e-6, porod_const=2) |
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| 361 | |
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| 362 | # Test results |
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| 363 | self.assertAlmostEquals(qstar, 1.481677e-3) |
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| 364 | self.assertAlmostEquals(v, 0.127225804) |
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| 365 | self.assertAlmostEquals(s, 9.42e+2,2) |
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| 366 | |
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| 367 | def test_use_case_5(self): |
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| 368 | """ |
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| 369 | Invariant with both high- and low-Q extrapolation |
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| 370 | """ |
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| 371 | # Create invariant object. Background and scale left as defaults. |
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| 372 | inv = invariant.InvariantCalculator(data=self.data_q_smear) |
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| 373 | # Set the extrapolation parameters for the low- and high-Q ranges |
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| 374 | inv.set_extrapolation(range='low', npts=10, function='guinier') |
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| 375 | inv.set_extrapolation(range='high', npts=10, function='power_law', power=4) |
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| 376 | # The version of the call without error |
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| 377 | # The function parameter defaults to None, then is picked to be 'power_law' for extrapolation='high' |
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| 378 | qstar = inv.get_qstar(extrapolation='both') |
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| 379 | # The version of the call with error |
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| 380 | qstar, qstar_err = inv.get_qstar_with_error(extrapolation='both') |
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| 381 | # Get the volume fraction and surface |
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| 382 | v, dv = inv.get_volume_fraction_with_error(contrast=2.6e-6) |
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| 383 | s, ds = inv.get_surface_with_error(contrast=2.6e-6, porod_const=2) |
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| 384 | |
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| 385 | # Test results |
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| 386 | self.assertAlmostEquals(qstar, 0.0021621) |
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| 387 | self.assertAlmostEquals(v, 0.202846825) |
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| 388 | self.assertAlmostEquals(s, 9.42e+2,2) |
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