[959eb01] | 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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[7b50f14] | 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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[959eb01] | 13 | |
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| 14 | from lxml import etree |
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[17e257b5] | 15 | from lxml.etree import XMLSyntaxError |
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[959eb01] | 16 | from xml.dom import minidom |
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| 17 | |
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[574adc7] | 18 | import sas.sascalc.dataloader.readers.cansas_reader as cansas |
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[f00072f] | 19 | from sas.sascalc.dataloader.file_reader_base_class import decode |
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[574adc7] | 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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[959eb01] | 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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[f53d684] | 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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[959eb01] | 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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[f53d684] | 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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[959eb01] | 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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[56dac0b] | 70 | invalid = StringIO('<a><c></b></a>') |
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[17e257b5] | 71 | self.assertRaises(XMLSyntaxError, lambda: XMLreader(invalid)) |
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[959eb01] | 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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[56dac0b] | 82 | f = StringIO(string) |
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[959eb01] | 83 | xmlschema_doc = etree.parse(f) |
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| 84 | xmlschema = etree.XMLSchema(xmlschema_doc) |
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[56dac0b] | 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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[959eb01] | 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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[058f6c3] | 93 | self.assertTrue(valid) |
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[959eb01] | 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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[7432acb] | 106 | self.assertTrue(data.meta_data["xmlpreprocess"] is not None) |
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[959eb01] | 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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[17c9436] | 126 | reader_generic.save(self.write_1_1_filename, dataloader[i], None) |
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[959eb01] | 127 | reader2 = Loader() |
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[1fc50fb2] | 128 | self.assertTrue(os.path.isfile(self.write_1_1_filename)) |
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[17c9436] | 129 | return_data = reader2.load(self.write_1_1_filename) |
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[959eb01] | 130 | written_data = return_data[0] |
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| 131 | self._check_data(written_data) |
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[17c9436] | 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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[959eb01] | 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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[17c9436] | 182 | file_loader.load(self.cansas1d) |
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[959eb01] | 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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[058f6c3] | 192 | self.assertTrue(xmlreader.validate_xml()) |
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[959eb01] | 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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[17c9436] | 200 | reader_generic.save(self.write_1_0_filename, dataloader[i], None) |
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[959eb01] | 201 | reader2 = Reader() |
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[1fc50fb2] | 202 | self.assertTrue(os.path.isfile(self.write_1_0_filename)) |
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[17c9436] | 203 | return_data = reader2.read(self.write_1_0_filename) |
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[959eb01] | 204 | written_data = return_data[0] |
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[058f6c3] | 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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[959eb01] | 207 | self._check_data(written_data) |
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[17c9436] | 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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[959eb01] | 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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[17c9436] | 215 | # find the processing instructions and make into a dictionary |
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[959eb01] | 216 | dic = self.get_processing_instructions(reader) |
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[56dac0b] | 217 | self.assertEqual(dic, {'xml-stylesheet': |
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| 218 | 'type="text/xsl" href="cansas1d.xsl" '}) |
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[959eb01] | 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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[17c9436] | 223 | # take the processing instructions and put them back in |
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[959eb01] | 224 | xmldoc = self.set_processing_instructions(xmldoc, dic) |
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[17c9436] | 225 | xmldoc.toprettyxml() |
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[959eb01] | 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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[f00072f] | 241 | pi_string = decode(etree.tostring(pi)) |
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[959eb01] | 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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[f53d684] | 256 | self.datafile_basic = find("simpleexamplefile.h5") |
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[7fd5e2a] | 257 | self.datafile_multiplesasentry = find( |
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| 258 | "test_data//nxcansas_1Dand2D_multisasentry.h5") |
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[2ca5d57b] | 259 | self.datafile_multiplesasdata = find( |
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| 260 | "test_data//nxcansas_1Dand2D_multisasdata.h5") |
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[7fd5e2a] | 261 | self.datafile_multiplesasdata_multiplesasentry = find( |
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| 262 | "test_data//nxcansas_1Dand2D_multisasentry_multisasdata.h5") |
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[959eb01] | 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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[7fd5e2a] | 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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[959eb01] | 279 | |
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[2ca5d57b] | 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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[959eb01] | 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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[7fd5e2a] | 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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[959eb01] | 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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[7fd5e2a] | 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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[959eb01] | 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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[7fd5e2a] | 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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[2ca5d57b] | 334 | self.assertAlmostEqual(data.data[10], 0.465181) |
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[7fd5e2a] | 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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[959eb01] | 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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[17e257b5] | 344 | self.assertAlmostEqual(data.y[40], 0.952749011516985) |
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| 345 | self.assertAlmostEqual(data.x[40], 0.3834415188257777) |
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[959eb01] | 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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[574adc7] | 350 | unittest.main() |
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