| 1 | """ |
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| 2 | Unit tests for data manipulations |
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| 3 | """ |
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| 4 | from __future__ import print_function |
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| 5 | |
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| 6 | import unittest |
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| 7 | import math |
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| 8 | import numpy as np |
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| 9 | from sas.sascalc.dataloader.loader import Loader |
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| 10 | from sas.sascalc.dataloader.readers.IgorReader import Reader as IgorReader |
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| 11 | from sas.sascalc.dataloader.readers.abs_reader import Reader as AbsReader |
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| 12 | from sas.sascalc.dataloader.readers.hfir1d_reader import Reader as HFIRReader |
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| 13 | from sas.sascalc.dataloader.readers.danse_reader import Reader as DANSEReader |
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| 14 | from sas.sascalc.dataloader.readers.cansas_reader import Reader as CANSASReader |
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| 15 | |
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| 16 | from sas.sascalc.dataloader.data_info import Data1D |
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| 17 | |
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| 18 | import os.path |
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| 19 | |
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| 20 | |
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| 21 | class abs_reader(unittest.TestCase): |
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| 22 | |
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| 23 | def setUp(self): |
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| 24 | reader = AbsReader() |
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| 25 | self.data = reader.read("jan08002.ABS") |
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| 26 | |
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| 27 | def test_abs_checkdata(self): |
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| 28 | """ |
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| 29 | Check the data content to see whether |
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| 30 | it matches the specific file we loaded. |
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| 31 | Check the units too to see whether the |
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| 32 | Data1D defaults changed. Otherwise the |
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| 33 | tests won't pass |
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| 34 | """ |
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| 35 | self.assertEqual(self.data.filename, "jan08002.ABS") |
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| 36 | self.assertEqual(self.data.meta_data['loader'], "IGOR 1D") |
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| 37 | |
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| 38 | self.assertEqual(self.data.source.wavelength_unit, 'A') |
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| 39 | self.assertEqual(self.data.source.wavelength, 6.0) |
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| 40 | |
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| 41 | self.assertEqual(self.data.detector[0].distance_unit, 'mm') |
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| 42 | self.assertEqual(self.data.detector[0].distance, 1000.0) |
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| 43 | |
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| 44 | self.assertEqual(self.data.sample.transmission, 0.5667) |
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| 45 | |
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| 46 | self.assertEqual(self.data.detector[0].beam_center_unit, 'mm') |
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| 47 | center_x = 114.58*5.0 |
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| 48 | center_y = 64.22*5.0 |
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| 49 | self.assertEqual(self.data.detector[0].beam_center.x, center_x) |
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| 50 | self.assertEqual(self.data.detector[0].beam_center.y, center_y) |
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| 51 | |
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| 52 | self.assertEqual(self.data.y_unit, '1/cm') |
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| 53 | self.assertEqual(self.data.x[0], 0.002618) |
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| 54 | self.assertEqual(self.data.x[1], 0.007854) |
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| 55 | self.assertEqual(self.data.x[2], 0.01309) |
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| 56 | self.assertEqual(self.data.x[126], 0.5828) |
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| 57 | |
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| 58 | self.assertEqual(self.data.y[0], 0.02198) |
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| 59 | self.assertEqual(self.data.y[1], 0.02201) |
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| 60 | self.assertEqual(self.data.y[2], 0.02695) |
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| 61 | self.assertEqual(self.data.y[126], 0.2958) |
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| 62 | |
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| 63 | self.assertEqual(self.data.dy[0], 0.002704) |
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| 64 | self.assertEqual(self.data.dy[1], 0.001643) |
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| 65 | self.assertEqual(self.data.dy[2], 0.002452) |
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| 66 | self.assertEqual(self.data.dy[126], 1) |
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| 67 | |
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| 68 | def test_checkdata2(self): |
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| 69 | self.assertEqual(self.data.dy[126], 1) |
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| 70 | |
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| 71 | def test_generic_loader(self): |
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| 72 | # the generic loader should work as well |
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| 73 | data = Loader().load("jan08002.ABS") |
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| 74 | self.assertEqual(data.meta_data['loader'], "IGOR 1D") |
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| 75 | |
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| 76 | |
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| 77 | class hfir_reader(unittest.TestCase): |
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| 78 | |
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| 79 | def setUp(self): |
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| 80 | reader = HFIRReader() |
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| 81 | self.data = reader.read("S2-30dq.d1d") |
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| 82 | |
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| 83 | def test_hfir_checkdata(self): |
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| 84 | """ |
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| 85 | Check the data content to see whether |
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| 86 | it matches the specific file we loaded. |
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| 87 | """ |
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| 88 | self.assertEqual(self.data.filename, "S2-30dq.d1d") |
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| 89 | # THIS FILE FORMAT IS CURRENTLY READ BY THE ASCII READER |
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| 90 | self.assertEqual(self.data.meta_data['loader'], "HFIR 1D") |
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| 91 | self.assertEqual(len(self.data.x), 134) |
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| 92 | self.assertEqual(len(self.data.y), 134) |
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| 93 | # Q I dI dQ |
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| 94 | # Point 1: 0.003014 0.003010 0.000315 0.008249 |
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| 95 | self.assertEqual(self.data.x[1], 0.003014) |
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| 96 | self.assertEqual(self.data.y[1], 0.003010) |
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| 97 | self.assertEqual(self.data.dy[1], 0.000315) |
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| 98 | self.assertEqual(self.data.dx[1], 0.008249) |
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| 99 | |
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| 100 | def test_generic_loader(self): |
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| 101 | # the generic loader should work as well |
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| 102 | data = Loader().load("S2-30dq.d1d") |
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| 103 | self.assertEqual(data.meta_data['loader'], "HFIR 1D") |
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| 104 | |
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| 105 | |
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| 106 | class igor_reader(unittest.TestCase): |
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| 107 | |
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| 108 | def setUp(self): |
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| 109 | # the IgorReader should be able to read this filetype |
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| 110 | # if it can't, stop here. |
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| 111 | reader = IgorReader() |
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| 112 | self.data = reader.read("MAR07232_rest.ASC") |
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| 113 | |
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| 114 | def test_igor_checkdata(self): |
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| 115 | """ |
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| 116 | Check the data content to see whether |
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| 117 | it matches the specific file we loaded. |
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| 118 | Check the units too to see whether the |
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| 119 | Data1D defaults changed. Otherwise the |
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| 120 | tests won't pass |
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| 121 | """ |
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| 122 | self.assertEqual(self.data.filename, "MAR07232_rest.ASC") |
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| 123 | self.assertEqual(self.data.meta_data['loader'], "IGOR 2D") |
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| 124 | |
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| 125 | self.assertEqual(self.data.source.wavelength_unit, 'A') |
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| 126 | self.assertEqual(self.data.source.wavelength, 8.4) |
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| 127 | |
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| 128 | self.assertEqual(self.data.detector[0].distance_unit, 'mm') |
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| 129 | self.assertEqual(self.data.detector[0].distance, 13705) |
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| 130 | |
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| 131 | self.assertEqual(self.data.sample.transmission, 0.84357) |
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| 132 | |
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| 133 | self.assertEqual(self.data.detector[0].beam_center_unit, 'mm') |
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| 134 | center_x = (68.76 - 1)*5.0 |
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| 135 | center_y = (62.47 - 1)*5.0 |
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| 136 | self.assertEqual(self.data.detector[0].beam_center.x, center_x) |
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| 137 | self.assertEqual(self.data.detector[0].beam_center.y, center_y) |
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| 138 | |
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| 139 | self.assertEqual(self.data.I_unit, '1/cm') |
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| 140 | # 3 points should be suffcient to check that the data is in column |
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| 141 | # major order. |
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| 142 | np.testing.assert_almost_equal(self.data.data[0:3], |
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| 143 | [0.279783, 0.28951, 0.167634]) |
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| 144 | np.testing.assert_almost_equal(self.data.qx_data[0:3], |
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| 145 | [-0.01849072, -0.01821785, -0.01794498]) |
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| 146 | np.testing.assert_almost_equal(self.data.qy_data[0:3], |
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| 147 | [-0.01677435, -0.01677435, -0.01677435]) |
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| 148 | |
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| 149 | def test_generic_loader(self): |
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| 150 | # the generic loader should direct the file to IgorReader as well |
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| 151 | data = Loader().load("MAR07232_rest.ASC") |
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| 152 | self.assertEqual(data.meta_data['loader'], "IGOR 2D") |
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| 153 | |
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| 154 | |
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| 155 | class danse_reader(unittest.TestCase): |
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| 156 | |
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| 157 | def setUp(self): |
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| 158 | reader = DANSEReader() |
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| 159 | self.data = reader.read("MP_New.sans") |
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| 160 | |
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| 161 | def test_checkdata(self): |
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| 162 | """ |
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| 163 | Check the data content to see whether |
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| 164 | it matches the specific file we loaded. |
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| 165 | Check the units too to see whether the |
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| 166 | Data1D defaults changed. Otherwise the |
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| 167 | tests won't pass |
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| 168 | """ |
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| 169 | self.assertEqual(self.data.filename, "MP_New.sans") |
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| 170 | self.assertEqual(self.data.meta_data['loader'], "DANSE") |
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| 171 | |
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| 172 | self.assertEqual(self.data.source.wavelength_unit, 'A') |
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| 173 | self.assertEqual(self.data.source.wavelength, 7.5) |
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| 174 | |
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| 175 | self.assertEqual(self.data.detector[0].distance_unit, 'mm') |
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| 176 | self.assertAlmostEqual(self.data.detector[0].distance, 5414.99, 3) |
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| 177 | |
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| 178 | self.assertEqual(self.data.detector[0].beam_center_unit, 'mm') |
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| 179 | center_x = 68.74*5.0 |
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| 180 | center_y = 64.77*5.0 |
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| 181 | self.assertEqual(self.data.detector[0].beam_center.x, center_x) |
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| 182 | self.assertEqual(self.data.detector[0].beam_center.y, center_y) |
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| 183 | |
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| 184 | self.assertEqual(self.data.I_unit, '1/cm') |
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| 185 | self.assertEqual(self.data.data[0], 1.57831) |
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| 186 | self.assertEqual(self.data.data[1], 2.70983) |
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| 187 | self.assertEqual(self.data.data[2], 3.83422) |
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| 188 | |
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| 189 | self.assertEqual(self.data.err_data[0], 1.37607) |
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| 190 | self.assertEqual(self.data.err_data[1], 1.77569) |
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| 191 | self.assertEqual(self.data.err_data[2], 2.06313) |
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| 192 | |
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| 193 | def test_generic_loader(self): |
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| 194 | # the generic loader should work as well |
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| 195 | data = Loader().load("MP_New.sans") |
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| 196 | self.assertEqual(data.meta_data['loader'], "DANSE") |
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| 197 | |
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| 198 | |
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| 199 | class cansas_reader(unittest.TestCase): |
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| 200 | |
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| 201 | def setUp(self): |
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| 202 | reader = CANSASReader() |
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| 203 | data = reader.read("cansas1d.xml") |
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| 204 | self.data = data[0] |
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| 205 | |
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| 206 | def test_generic_loader(self): |
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| 207 | # the generic loader should work as well |
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| 208 | data = Loader().load("cansas1d.xml") |
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| 209 | self.assertEqual(data[0].meta_data['loader'], "CanSAS XML 1D") |
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| 210 | |
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| 211 | def test_cansas_checkdata(self): |
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| 212 | self.assertEqual(self.data.filename, "cansas1d.xml") |
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| 213 | self._checkdata() |
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| 214 | |
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| 215 | def _checkdata(self): |
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| 216 | """ |
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| 217 | Check the data content to see whether |
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| 218 | it matches the specific file we loaded. |
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| 219 | Check the units too to see whether the |
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| 220 | Data1D defaults changed. Otherwise the |
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| 221 | tests won't pass |
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| 222 | """ |
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| 223 | self.assertEqual(self.data.run[0], "1234") |
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| 224 | self.assertEqual(self.data.meta_data['loader'], "CanSAS XML 1D") |
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| 225 | |
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| 226 | # Data |
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| 227 | self.assertEqual(len(self.data.x), 2) |
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| 228 | self.assertEqual(self.data.x_unit, '1/A') |
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| 229 | self.assertEqual(self.data.y_unit, '1/cm') |
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| 230 | self.assertAlmostEqual(self.data.x[0], 0.02, 6) |
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| 231 | self.assertAlmostEqual(self.data.y[0], 1000, 6) |
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| 232 | self.assertAlmostEqual(self.data.dx[0], 0.01, 6) |
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| 233 | self.assertAlmostEqual(self.data.dy[0], 3, 6) |
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| 234 | self.assertAlmostEqual(self.data.x[1], 0.03, 6) |
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| 235 | self.assertAlmostEqual(self.data.y[1], 1001.0) |
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| 236 | self.assertAlmostEqual(self.data.dx[1], 0.02, 6) |
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| 237 | self.assertAlmostEqual(self.data.dy[1], 4, 6) |
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| 238 | self.assertEqual(self.data.run_name['1234'], 'run name') |
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| 239 | self.assertEqual(self.data.title, "Test title") |
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| 240 | |
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| 241 | # Sample info |
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| 242 | self.assertEqual(self.data.sample.ID, "SI600-new-long") |
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| 243 | self.assertEqual(self.data.sample.name, "my sample") |
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| 244 | self.assertEqual(self.data.sample.thickness_unit, 'mm') |
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| 245 | self.assertAlmostEqual(self.data.sample.thickness, 1.03) |
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| 246 | |
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| 247 | self.assertAlmostEqual(self.data.sample.transmission, 0.327) |
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| 248 | |
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| 249 | self.assertEqual(self.data.sample.temperature_unit, 'C') |
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| 250 | self.assertEqual(self.data.sample.temperature, 0) |
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| 251 | |
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| 252 | self.assertEqual(self.data.sample.position_unit, 'mm') |
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| 253 | self.assertEqual(self.data.sample.position.x, 10) |
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| 254 | self.assertEqual(self.data.sample.position.y, 0) |
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| 255 | |
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| 256 | self.assertEqual(self.data.sample.orientation_unit, 'degree') |
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| 257 | self.assertAlmostEqual(self.data.sample.orientation.x, 22.5, 6) |
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| 258 | self.assertAlmostEqual(self.data.sample.orientation.y, 0.02, 6) |
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| 259 | |
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| 260 | self.assertEqual(self.data.sample.details[0], "http://chemtools.chem.soton.ac.uk/projects/blog/blogs.php/bit_id/2720") |
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| 261 | self.assertEqual(self.data.sample.details[1], "Some text here") |
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| 262 | |
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| 263 | # Instrument info |
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| 264 | self.assertEqual(self.data.instrument, "canSAS instrument") |
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| 265 | |
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| 266 | # Source |
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| 267 | self.assertEqual(self.data.source.radiation, "neutron") |
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| 268 | |
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| 269 | self.assertEqual(self.data.source.beam_size_unit, "mm") |
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| 270 | self.assertEqual(self.data.source.beam_size_name, "bm") |
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| 271 | self.assertEqual(self.data.source.beam_size.x, 12) |
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| 272 | self.assertEqual(self.data.source.beam_size.y, 13) |
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| 273 | |
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| 274 | self.assertEqual(self.data.source.beam_shape, "disc") |
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| 275 | |
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| 276 | self.assertEqual(self.data.source.wavelength_unit, "A") |
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| 277 | self.assertEqual(self.data.source.wavelength, 6) |
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| 278 | |
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| 279 | self.assertEqual(self.data.source.wavelength_max_unit, "nm") |
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| 280 | self.assertAlmostEqual(self.data.source.wavelength_max, 1.0) |
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| 281 | self.assertEqual(self.data.source.wavelength_min_unit, "nm") |
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| 282 | self.assertAlmostEqual(self.data.source.wavelength_min, 0.22) |
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| 283 | self.assertEqual(self.data.source.wavelength_spread_unit, "percent") |
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| 284 | self.assertEqual(self.data.source.wavelength_spread, 14.3) |
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| 285 | |
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| 286 | # Collimation |
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| 287 | _found1 = False |
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| 288 | _found2 = False |
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| 289 | self.assertEqual(self.data.collimation[0].length, 123.) |
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| 290 | self.assertEqual(self.data.collimation[0].name, 'test coll name') |
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| 291 | |
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| 292 | for item in self.data.collimation[0].aperture: |
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| 293 | self.assertEqual(item.size_unit,'mm') |
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| 294 | self.assertEqual(item.distance_unit,'mm') |
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| 295 | |
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| 296 | if item.size.x == 50 \ |
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| 297 | and item.distance == 11000.0 \ |
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| 298 | and item.name == 'source' \ |
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| 299 | and item.type == 'radius': |
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| 300 | _found1 = True |
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| 301 | elif item.size.x == 1.0 \ |
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| 302 | and item.name == 'sample' \ |
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| 303 | and item.type == 'radius': |
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| 304 | _found2 = True |
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| 305 | |
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| 306 | if _found1 == False or _found2 == False: |
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| 307 | raise RuntimeError, "Could not find all data %s %s" % (_found1, _found2) |
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| 308 | |
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| 309 | # Detector |
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| 310 | self.assertEqual(self.data.detector[0].name, "fictional hybrid") |
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| 311 | self.assertEqual(self.data.detector[0].distance_unit, "mm") |
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| 312 | self.assertEqual(self.data.detector[0].distance, 4150) |
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| 313 | |
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| 314 | self.assertEqual(self.data.detector[0].orientation_unit, "degree") |
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| 315 | self.assertAlmostEqual(self.data.detector[0].orientation.x, 1.0, 6) |
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| 316 | self.assertEqual(self.data.detector[0].orientation.y, 0.0) |
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| 317 | self.assertEqual(self.data.detector[0].orientation.z, 0.0) |
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| 318 | |
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| 319 | self.assertEqual(self.data.detector[0].offset_unit, "m") |
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| 320 | self.assertEqual(self.data.detector[0].offset.x, .001) |
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| 321 | self.assertEqual(self.data.detector[0].offset.y, .002) |
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| 322 | self.assertEqual(self.data.detector[0].offset.z, None) |
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| 323 | |
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| 324 | self.assertEqual(self.data.detector[0].beam_center_unit, "mm") |
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| 325 | self.assertEqual(self.data.detector[0].beam_center.x, 322.64) |
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| 326 | self.assertEqual(self.data.detector[0].beam_center.y, 327.68) |
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| 327 | self.assertEqual(self.data.detector[0].beam_center.z, None) |
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| 328 | |
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| 329 | self.assertEqual(self.data.detector[0].pixel_size_unit, "mm") |
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| 330 | self.assertEqual(self.data.detector[0].pixel_size.x, 5) |
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| 331 | self.assertEqual(self.data.detector[0].pixel_size.y, 5) |
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| 332 | self.assertEqual(self.data.detector[0].pixel_size.z, None) |
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| 333 | |
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| 334 | # Process |
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| 335 | _found_term1 = False |
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| 336 | _found_term2 = False |
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| 337 | for item in self.data.process: |
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| 338 | self.assertTrue(item.name in ['NCNR-IGOR', 'spol']) |
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| 339 | self.assertTrue(item.date in ['04-Sep-2007 18:35:02', |
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| 340 | '03-SEP-2006 11:42:47']) |
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| 341 | print(item.term) |
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| 342 | for t in item.term: |
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| 343 | if (t['name'] == "ABS:DSTAND" |
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| 344 | and t['unit'] == 'mm' |
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| 345 | and float(t['value']) == 1.0): |
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| 346 | _found_term2 = True |
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| 347 | elif (t['name'] == "radialstep" |
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| 348 | and t['unit'] == 'mm' |
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| 349 | and float(t['value']) == 10.0): |
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| 350 | _found_term1 = True |
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| 351 | |
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| 352 | if _found_term1 == False or _found_term2 == False: |
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| 353 | raise RuntimeError, "Could not find all process terms %s %s" % (_found_term1, _found_term2) |
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| 354 | |
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| 355 | def test_writer(self): |
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| 356 | r = CANSASReader() |
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| 357 | |
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| 358 | filename = "write_test.xml" |
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| 359 | r.write(filename, self.data) |
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| 360 | data = Loader().load(filename) |
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| 361 | self.data = data[0] |
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| 362 | self.assertEqual(self.data.filename, filename) |
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| 363 | self._checkdata() |
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| 364 | if os.path.isfile(filename): |
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| 365 | os.remove(filename) |
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| 366 | |
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| 367 | def test_units(self): |
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| 368 | """ |
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| 369 | Check units. |
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| 370 | Note that not all units are available. |
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| 371 | """ |
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| 372 | filename = "cansas1d_units.xml" |
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| 373 | data = CANSASReader().read(filename) |
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| 374 | self.data = data[0] |
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| 375 | self.assertEqual(self.data.filename, filename) |
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| 376 | self._checkdata() |
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| 377 | |
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| 378 | def test_badunits(self): |
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| 379 | """ |
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| 380 | Check units. |
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| 381 | Note that not all units are available. |
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| 382 | """ |
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| 383 | filename = "cansas1d_badunits.xml" |
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| 384 | data = CANSASReader().read(filename) |
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| 385 | self.data = data[0] |
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| 386 | self.assertEqual(self.data.filename, filename) |
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| 387 | # The followed should not have been loaded |
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| 388 | self.assertAlmostEqual(self.data.sample.thickness, 0.00103) |
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| 389 | # This one should |
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| 390 | self.assertAlmostEqual(self.data.sample.transmission, 0.327) |
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| 391 | |
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| 392 | self.assertEqual(self.data.meta_data['loader'], "CanSAS XML 1D") |
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| 393 | print(self.data.errors) |
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| 394 | self.assertEqual(len(self.data.errors), 1) |
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| 395 | |
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| 396 | def test_slits(self): |
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| 397 | """ |
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| 398 | Check slit data |
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| 399 | """ |
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| 400 | filename = "cansas1d_slit.xml" |
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| 401 | data = CANSASReader().read(filename) |
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| 402 | self.data = data[0] |
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| 403 | self.assertEqual(self.data.filename, filename) |
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| 404 | self.assertEqual(self.data.run[0], "1234") |
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| 405 | |
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| 406 | # Data |
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| 407 | self.assertEqual(len(self.data.x), 2) |
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| 408 | self.assertEqual(self.data.x_unit, '1/A') |
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| 409 | self.assertEqual(self.data.y_unit, '1/cm') |
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| 410 | self.assertEqual(self.data.x[0], 0.02) |
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| 411 | self.assertEqual(self.data.y[0], 1000) |
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| 412 | self.assertEqual(self.data.dxl[0], 0.005) |
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| 413 | self.assertEqual(self.data.dxw[0], 0.001) |
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| 414 | self.assertEqual(self.data.dy[0], 3) |
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| 415 | self.assertEqual(self.data.x[1], 0.03) |
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| 416 | self.assertAlmostEquals(self.data.y[1], 1001.0) |
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| 417 | self.assertEqual(self.data.dx, None) |
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| 418 | self.assertEqual(self.data.dxl[1], 0.005) |
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| 419 | self.assertEqual(self.data.dxw[1], 0.001) |
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| 420 | self.assertEqual(self.data.dy[1], 4) |
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| 421 | self.assertEqual(self.data.run_name['1234'], 'run name') |
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| 422 | self.assertEqual(self.data.title, "Test title") |
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| 423 | |
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| 424 | |
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| 425 | if __name__ == '__main__': |
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| 426 | unittest.main() |
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