1 | """ |
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2 | Unit tests for the new recursive cansas reader |
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3 | """ |
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4 | import os |
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5 | import sys |
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6 | import unittest |
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7 | import logging |
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8 | import warnings |
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9 | if sys.version_info[0] >= 3: |
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10 | from io import StringIO |
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11 | else: |
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12 | from StringIO import StringIO |
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13 | |
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14 | from lxml import etree |
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15 | from lxml.etree import XMLSyntaxError |
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16 | from xml.dom import minidom |
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17 | |
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18 | import sas.sascalc.dataloader.readers.cansas_reader as cansas |
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19 | from sas.sascalc.dataloader.file_reader_base_class import decode |
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20 | from sas.sascalc.dataloader.loader import Loader |
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21 | from sas.sascalc.dataloader.data_info import Data1D, Data2D |
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22 | from sas.sascalc.dataloader.readers.xml_reader import XMLreader |
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23 | from sas.sascalc.dataloader.readers.cansas_reader import Reader |
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24 | from sas.sascalc.dataloader.readers.cansas_constants import CansasConstants |
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25 | |
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26 | logger = logging.getLogger(__name__) |
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27 | |
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28 | warnings.simplefilter("ignore") |
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29 | |
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30 | CANSAS_FORMAT = CansasConstants.CANSAS_FORMAT |
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31 | CANSAS_NS = CansasConstants.CANSAS_NS |
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32 | |
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33 | |
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34 | def find(filename): |
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35 | return os.path.join(os.path.dirname(__file__), filename) |
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36 | |
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37 | |
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38 | class cansas_reader_xml(unittest.TestCase): |
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39 | |
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40 | def setUp(self): |
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41 | self.loader = Loader() |
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42 | self.xml_valid = find("cansas_test_modified.xml") |
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43 | self.xml_invalid = find("cansas_test.xml") |
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44 | self.cansas1d_badunits = find("cansas1d_badunits.xml") |
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45 | self.cansas1d = find("cansas1d.xml") |
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46 | self.cansas1d_slit = find("cansas1d_slit.xml") |
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47 | self.cansas1d_units = find("cansas1d_units.xml") |
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48 | self.cansas1d_notitle = find("cansas1d_notitle.xml") |
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49 | self.isis_1_0 = find("ISIS_1_0.xml") |
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50 | self.isis_1_1 = find("ISIS_1_1.xml") |
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51 | self.isis_1_1_notrans = find("ISIS_1_1_notrans.xml") |
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52 | self.isis_1_1_doubletrans = find("ISIS_1_1_doubletrans.xml") |
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53 | self.schema_1_0 = find("cansas1d_v1_0.xsd") |
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54 | self.schema_1_1 = find("cansas1d_v1_1.xsd") |
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55 | self.write_1_0_filename = find("isis_1_0_write_test.xml") |
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56 | self.write_1_1_filename = find("isis_1_1_write_test.xml") |
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57 | |
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58 | def get_number_of_entries(self, dictionary, name, i): |
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59 | if dictionary.get(name) is not None: |
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60 | i += 1 |
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61 | name = name.split("_")[0] |
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62 | name += "_{0}".format(i) |
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63 | name = self.get_number_of_entries(dictionary, name, i) |
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64 | return name |
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65 | |
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66 | def test_invalid_xml(self): |
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67 | """ |
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68 | Should fail gracefully and send a message to logger.info() |
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69 | """ |
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70 | invalid = StringIO('<a><c></b></a>') |
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71 | self.assertRaises(XMLSyntaxError, lambda: XMLreader(invalid)) |
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72 | |
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73 | def test_xml_validate(self): |
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74 | string = "<xsd:schema xmlns:xsd=\"http://www.w3.org/2001/XMLSchema\">\n" |
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75 | string += "\t<xsd:element name=\"a\" type=\"AType\"/>\n" |
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76 | string += "\t<xsd:complexType name=\"AType\">\n" |
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77 | string += "\t\t<xsd:sequence>\n" |
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78 | string += "\t\t\t<xsd:element name=\"b\" type=\"xsd:string\" />\n" |
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79 | string += "\t\t</xsd:sequence>\n" |
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80 | string += "\t</xsd:complexType>\n" |
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81 | string += "</xsd:schema>" |
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82 | f = StringIO(string) |
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83 | xmlschema_doc = etree.parse(f) |
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84 | xmlschema = etree.XMLSchema(xmlschema_doc) |
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85 | valid = etree.parse(StringIO('<a><b></b></a>')) |
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86 | invalid = etree.parse(StringIO('<a><c></c></a>')) |
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87 | self.assertTrue(xmlschema.validate(valid)) |
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88 | self.assertFalse(xmlschema.validate(invalid)) |
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89 | |
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90 | def test_real_xml(self): |
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91 | reader = XMLreader(self.xml_valid, self.schema_1_0) |
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92 | valid = reader.validate_xml() |
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93 | self.assertTrue(valid) |
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94 | |
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95 | def _check_data(self, data): |
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96 | self.assertTrue(data.title == "TK49 c10_SANS") |
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97 | self.assertTrue(data.x.size == 138) |
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98 | self.assertTrue(len(data.meta_data) == 3) |
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99 | self.assertTrue(data.detector[0].distance_unit == "mm") |
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100 | self.assertTrue(data.detector[1].distance_unit == "mm") |
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101 | self.assertTrue(data.detector[0].name == "HAB") |
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102 | self.assertTrue(data.detector[1].name == "main-detector-bank") |
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103 | self.assertTrue(data.detector[0].distance == 575.0) |
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104 | self.assertAlmostEqual(data.detector[1].distance, 4145.02) |
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105 | self.assertTrue(data.process[0].name == "Mantid generated CanSAS1D XML") |
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106 | self.assertTrue(data.meta_data["xmlpreprocess"] is not None) |
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107 | |
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108 | def _check_data_1_1(self, data): |
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109 | spectrum = data.trans_spectrum[0] |
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110 | self.assertTrue(len(spectrum.wavelength) == 138) |
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111 | |
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112 | def test_cansas_xml(self): |
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113 | xmlreader = XMLreader(self.isis_1_1, self.schema_1_1) |
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114 | valid = xmlreader.validate_xml() |
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115 | xmlreader.set_processing_instructions() |
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116 | self.assertTrue(valid) |
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117 | reader_generic = Loader() |
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118 | dataloader = reader_generic.load(self.isis_1_1) |
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119 | reader_cansas = Reader() |
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120 | cansasreader = reader_cansas.read(self.isis_1_1) |
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121 | for i in range(len(dataloader)): |
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122 | self._check_data(dataloader[i]) |
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123 | self._check_data_1_1(dataloader[i]) |
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124 | self._check_data(cansasreader[i]) |
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125 | self._check_data_1_1(cansasreader[i]) |
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126 | reader_generic.save(self.write_1_1_filename, dataloader[i], None) |
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127 | reader2 = Loader() |
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128 | self.assertTrue(os.path.isfile(self.write_1_1_filename)) |
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129 | return_data = reader2.load(self.write_1_1_filename) |
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130 | written_data = return_data[0] |
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131 | self._check_data(written_data) |
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132 | if os.path.isfile(self.write_1_1_filename): |
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133 | os.remove(self.write_1_1_filename) |
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134 | |
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135 | def test_double_trans_spectra(self): |
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136 | xmlreader = XMLreader(self.isis_1_1_doubletrans, self.schema_1_1) |
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137 | self.assertTrue(xmlreader.validate_xml()) |
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138 | reader = Loader() |
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139 | data = reader.load(self.isis_1_1_doubletrans) |
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140 | for item in data: |
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141 | self._check_data(item) |
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142 | |
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143 | def test_entry_name_recurse(self): |
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144 | test_values = [1,2,3,4,5,6] |
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145 | base_key = "key" |
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146 | d = {} |
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147 | for value in test_values: |
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148 | new_key = self.get_number_of_entries(d, base_key, i = 0) |
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149 | d[new_key] = value |
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150 | self.assertTrue(len(d) == 6) |
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151 | |
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152 | def test_load_cansas_file(self): |
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153 | reader1 = XMLreader(self.xml_valid, self.schema_1_0) |
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154 | self.assertTrue(reader1.validate_xml()) |
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155 | reader2 = XMLreader(self.xml_invalid, self.schema_1_0) |
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156 | self.assertFalse(reader2.validate_xml()) |
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157 | reader3 = XMLreader(self.xml_valid, self.schema_1_1) |
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158 | self.assertFalse(reader3.validate_xml()) |
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159 | reader4 = XMLreader(self.xml_invalid, self.schema_1_1) |
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160 | self.assertFalse(reader4.validate_xml()) |
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161 | reader5 = XMLreader(self.isis_1_0, self.schema_1_0) |
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162 | self.assertTrue(reader5.validate_xml()) |
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163 | reader6 = XMLreader(self.isis_1_1, self.schema_1_1) |
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164 | self.assertTrue(reader6.validate_xml()) |
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165 | reader7 = XMLreader(self.isis_1_1, self.schema_1_0) |
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166 | self.assertFalse(reader7.validate_xml()) |
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167 | |
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168 | def test_invalid_cansas(self): |
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169 | list = self.loader.load(self.cansas1d_notitle) |
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170 | data = list[0] |
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171 | self.assertTrue(data.x.size == 2) |
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172 | self.assertTrue(len(data.meta_data) == 2) |
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173 | self.assertTrue(len(data.errors) == 1) |
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174 | self.assertTrue(data.detector[0].distance_unit == "mm") |
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175 | self.assertTrue(data.detector[0].name == "fictional hybrid") |
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176 | self.assertTrue(data.detector[0].distance == 4150) |
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177 | |
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178 | def test_old_cansas_files(self): |
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179 | reader1 = XMLreader(self.cansas1d, self.schema_1_0) |
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180 | self.assertTrue(reader1.validate_xml()) |
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181 | file_loader = Loader() |
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182 | file_loader.load(self.cansas1d) |
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183 | reader2 = XMLreader(self.cansas1d_units, self.schema_1_0) |
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184 | self.assertTrue(reader2.validate_xml()) |
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185 | reader3 = XMLreader(self.cansas1d_badunits, self.schema_1_0) |
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186 | self.assertTrue(reader3.validate_xml()) |
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187 | reader4 = XMLreader(self.cansas1d_slit, self.schema_1_0) |
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188 | self.assertTrue(reader4.validate_xml()) |
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189 | |
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190 | def test_save_cansas_v1_0(self): |
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191 | xmlreader = XMLreader(self.isis_1_0, self.schema_1_0) |
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192 | self.assertTrue(xmlreader.validate_xml()) |
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193 | reader_generic = Loader() |
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194 | dataloader = reader_generic.load(self.isis_1_0) |
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195 | reader_cansas = Reader() |
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196 | cansasreader = reader_cansas.read(self.isis_1_0) |
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197 | for i in range(len(dataloader)): |
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198 | self._check_data(dataloader[i]) |
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199 | self._check_data(cansasreader[i]) |
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200 | reader_generic.save(self.write_1_0_filename, dataloader[i], None) |
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201 | reader2 = Reader() |
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202 | self.assertTrue(os.path.isfile(self.write_1_0_filename)) |
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203 | return_data = reader2.read(self.write_1_0_filename) |
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204 | written_data = return_data[0] |
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205 | xmlreader = XMLreader(self.write_1_0_filename, self.schema_1_0) |
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206 | self.assertTrue(xmlreader.validate_xml()) |
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207 | self._check_data(written_data) |
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208 | if os.path.isfile(self.write_1_0_filename): |
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209 | os.remove(self.write_1_0_filename) |
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210 | |
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211 | def test_processing_instructions(self): |
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212 | reader = XMLreader(self.isis_1_1, self.schema_1_1) |
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213 | valid = reader.validate_xml() |
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214 | if valid: |
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215 | # find the processing instructions and make into a dictionary |
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216 | dic = self.get_processing_instructions(reader) |
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217 | self.assertEqual(dic, {'xml-stylesheet': |
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218 | 'type="text/xsl" href="cansas1d.xsl" '}) |
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219 | |
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220 | xml = "<test><a><b><c></c></b></a></test>" |
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221 | xmldoc = minidom.parseString(xml) |
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222 | |
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223 | # take the processing instructions and put them back in |
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224 | xmldoc = self.set_processing_instructions(xmldoc, dic) |
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225 | xmldoc.toprettyxml() |
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226 | |
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227 | def set_processing_instructions(self, minidom_object, dic): |
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228 | xmlroot = minidom_object.firstChild |
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229 | for item in dic: |
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230 | pi = minidom_object.createProcessingInstruction(item, dic[item]) |
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231 | minidom_object.insertBefore(pi, xmlroot) |
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232 | return minidom_object |
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233 | |
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234 | def get_processing_instructions(self, xml_reader_object): |
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235 | dict = {} |
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236 | pi = xml_reader_object.xmlroot.getprevious() |
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237 | i = 0 |
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238 | while pi is not None: |
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239 | attr = {} |
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240 | pi_name = "" |
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241 | pi_string = decode(etree.tostring(pi)) |
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242 | if isinstance(pi_string, str): |
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243 | pi_string = pi_string.replace("<?", "").replace("?>", "") |
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244 | split = pi_string.split(" ", 1) |
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245 | pi_name = split[0] |
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246 | attr = split[1] |
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247 | dict[pi_name] = attr |
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248 | pi = pi.getprevious() |
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249 | return dict |
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250 | |
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251 | |
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252 | class cansas_reader_hdf5(unittest.TestCase): |
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253 | |
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254 | def setUp(self): |
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255 | self.loader = Loader() |
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256 | self.datafile_basic = find("simpleexamplefile.h5") |
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257 | self.datafile_multiplesasentry = find( |
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258 | "test_data//nxcansas_1Dand2D_multisasentry.h5") |
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259 | self.datafile_multiplesasdata = find( |
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260 | "test_data//nxcansas_1Dand2D_multisasdata.h5") |
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261 | self.datafile_multiplesasdata_multiplesasentry = find( |
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262 | "test_data//nxcansas_1Dand2D_multisasentry_multisasdata.h5") |
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263 | |
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264 | def test_real_data(self): |
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265 | self.data = self.loader.load(self.datafile_basic) |
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266 | self._check_example_data(self.data[0]) |
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267 | |
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268 | def test_multiple_sasentries(self): |
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269 | self.data = self.loader.load(self.datafile_multiplesasentry) |
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270 | self.assertTrue(len(self.data) == 2) |
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271 | self._check_multiple_data(self.data[0]) |
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272 | self._check_multiple_data(self.data[1]) |
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273 | if isinstance(self.data[0], Data1D): |
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274 | self._check_1d_data(self.data[0]) |
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275 | self._check_2d_data(self.data[1]) |
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276 | else: |
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277 | self._check_1d_data(self.data[1]) |
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278 | self._check_2d_data(self.data[0]) |
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279 | |
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280 | def test_multiple_sasdatas(self): |
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281 | self.data = self.loader.load(self.datafile_multiplesasdata) |
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282 | self.assertTrue(len(self.data) == 2) |
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283 | self._check_multiple_data(self.data[0]) |
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284 | self._check_multiple_data(self.data[1]) |
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285 | if isinstance(self.data[0], Data1D): |
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286 | self._check_1d_data(self.data[0]) |
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287 | self._check_2d_data(self.data[1]) |
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288 | else: |
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289 | self._check_1d_data(self.data[1]) |
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290 | self._check_2d_data(self.data[0]) |
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291 | |
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292 | def test_multiple_sasentries_multiplesasdatas(self): |
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293 | self.data = self.loader.load( |
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294 | self.datafile_multiplesasdata_multiplesasentry) |
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295 | self.assertTrue(len(self.data) == 4) |
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296 | self._check_multiple_data(self.data[0]) |
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297 | self._check_multiple_data(self.data[1]) |
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298 | self._check_multiple_data(self.data[2]) |
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299 | self._check_multiple_data(self.data[3]) |
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300 | for data in self.data: |
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301 | if isinstance(data, Data1D): |
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302 | self._check_1d_data(data) |
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303 | else: |
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304 | self._check_2d_data(data) |
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305 | |
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306 | def _check_multiple_data(self, data): |
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307 | self.assertTrue(data.title == "MH4_5deg_16T_SLOW") |
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308 | self.assertTrue(data.run[0] == '33837') |
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309 | self.assertTrue(len(data.run) == 1) |
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310 | self.assertTrue(data.instrument == "SANS2D") |
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311 | self.assertTrue(data.source.radiation == "Spallation Neutron Source") |
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312 | self.assertTrue(len(data.detector) == 2) |
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313 | self.assertTrue(data.detector[0].name == "rear-detector" |
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314 | or data.detector[1].name == "rear-detector") |
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315 | self.assertTrue(data.detector[0].name == "front-detector" |
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316 | or data.detector[1].name == "front-detector") |
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317 | self.assertAlmostEqual(data.detector[0].distance + |
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318 | data.detector[1].distance, 7230.54, 2) |
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319 | self.assertTrue(data.detector[0].distance_unit == 'mm') |
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320 | self.assertTrue(len(data.trans_spectrum) == 1) |
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321 | |
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322 | def _check_1d_data(self, data): |
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323 | self.assertTrue(len(data.x) == 66) |
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324 | self.assertTrue(len(data.x) == len(data.y)) |
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325 | self.assertTrue(data.dy[10] == 0.207214) |
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326 | self.assertTrue(data.y[10] == 24.1939) |
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327 | self.assertTrue(data.x[10] == 0.00898113) |
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328 | |
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329 | def _check_2d_data(self, data): |
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330 | self.assertTrue(isinstance(data, Data2D)) |
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331 | self.assertTrue(len(data.q_data) == 150*150) |
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332 | self.assertTrue(len(data.q_data) == len(data.data)) |
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333 | self.assertAlmostEqual(data.err_data[10], 0.186723989418) |
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334 | self.assertAlmostEqual(data.data[10], 0.465181) |
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335 | self.assertAlmostEqual(data.qx_data[10], -0.129) |
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336 | self.assertAlmostEqual(data.qy_data[10], -0.149) |
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337 | |
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338 | def _check_example_data(self, data): |
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339 | self.assertTrue(data.title == "") |
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340 | self.assertTrue(data.x.size == 100) |
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341 | self.assertTrue(data._xunit == "A^{-1}") |
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342 | self.assertTrue(data._yunit == "cm^{-1}") |
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343 | self.assertTrue(data.y.size == 100) |
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344 | self.assertAlmostEqual(data.y[40], 0.952749011516985) |
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345 | self.assertAlmostEqual(data.x[40], 0.3834415188257777) |
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346 | self.assertAlmostEqual(len(data.meta_data), 0) |
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347 | |
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348 | |
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349 | if __name__ == '__main__': |
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350 | unittest.main() |
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