""" Unit tests for the new recursive cansas reader """ import os import sys import unittest import logging import warnings if sys.version_info[0] >= 3: from io import StringIO else: from StringIO import StringIO from lxml import etree from lxml.etree import XMLSyntaxError from xml.dom import minidom import sas.sascalc.dataloader.readers.cansas_reader as cansas from sas.sascalc.dataloader.file_reader_base_class import decode from sas.sascalc.dataloader.loader import Loader from sas.sascalc.dataloader.data_info import Data1D, Data2D from sas.sascalc.dataloader.readers.xml_reader import XMLreader from sas.sascalc.dataloader.readers.cansas_reader import Reader from sas.sascalc.dataloader.readers.cansas_constants import CansasConstants logger = logging.getLogger(__name__) warnings.simplefilter("ignore") CANSAS_FORMAT = CansasConstants.CANSAS_FORMAT CANSAS_NS = CansasConstants.CANSAS_NS def find(filename): return os.path.join(os.path.dirname(__file__), filename) class cansas_reader_xml(unittest.TestCase): def setUp(self): self.loader = Loader() self.xml_valid = find("cansas_test_modified.xml") self.xml_invalid = find("cansas_test.xml") self.cansas1d_badunits = find("cansas1d_badunits.xml") self.cansas1d = find("cansas1d.xml") self.cansas1d_slit = find("cansas1d_slit.xml") self.cansas1d_units = find("cansas1d_units.xml") self.cansas1d_notitle = find("cansas1d_notitle.xml") self.isis_1_0 = find("ISIS_1_0.xml") self.isis_1_1 = find("ISIS_1_1.xml") self.isis_1_1_notrans = find("ISIS_1_1_notrans.xml") self.isis_1_1_doubletrans = find("ISIS_1_1_doubletrans.xml") self.schema_1_0 = find("cansas1d_v1_0.xsd") self.schema_1_1 = find("cansas1d_v1_1.xsd") self.write_1_0_filename = find("isis_1_0_write_test.xml") self.write_1_1_filename = find("isis_1_1_write_test.xml") def get_number_of_entries(self, dictionary, name, i): if dictionary.get(name) is not None: i += 1 name = name.split("_")[0] name += "_{0}".format(i) name = self.get_number_of_entries(dictionary, name, i) return name def test_invalid_xml(self): """ Should fail gracefully and send a message to logger.info() """ invalid = StringIO('') self.assertRaises(XMLSyntaxError, lambda: XMLreader(invalid)) def test_xml_validate(self): string = "\n" string += "\t\n" string += "\t\n" string += "\t\t\n" string += "\t\t\t\n" string += "\t\t\n" string += "\t\n" string += "" f = StringIO(string) xmlschema_doc = etree.parse(f) xmlschema = etree.XMLSchema(xmlschema_doc) valid = etree.parse(StringIO('')) invalid = etree.parse(StringIO('')) self.assertTrue(xmlschema.validate(valid)) self.assertFalse(xmlschema.validate(invalid)) def test_real_xml(self): reader = XMLreader(self.xml_valid, self.schema_1_0) valid = reader.validate_xml() self.assertTrue(valid) def _check_data(self, data): self.assertTrue(data.title == "TK49 c10_SANS") self.assertTrue(data.x.size == 138) self.assertTrue(len(data.meta_data) == 3) self.assertTrue(data.detector[0].distance_unit == "mm") self.assertTrue(data.detector[1].distance_unit == "mm") self.assertTrue(data.detector[0].name == "HAB") self.assertTrue(data.detector[1].name == "main-detector-bank") self.assertTrue(data.detector[0].distance == 575.0) self.assertAlmostEqual(data.detector[1].distance, 4145.02) self.assertTrue(data.process[0].name == "Mantid generated CanSAS1D XML") self.assertTrue(data.meta_data["xmlpreprocess"] is not None) def _check_data_1_1(self, data): spectrum = data.trans_spectrum[0] self.assertTrue(len(spectrum.wavelength) == 138) def test_cansas_xml(self): xmlreader = XMLreader(self.isis_1_1, self.schema_1_1) valid = xmlreader.validate_xml() xmlreader.set_processing_instructions() self.assertTrue(valid) reader_generic = Loader() dataloader = reader_generic.load(self.isis_1_1) reader_cansas = Reader() cansasreader = reader_cansas.read(self.isis_1_1) for i in range(len(dataloader)): self._check_data(dataloader[i]) self._check_data_1_1(dataloader[i]) self._check_data(cansasreader[i]) self._check_data_1_1(cansasreader[i]) reader_generic.save(self.write_1_1_filename, dataloader[i], None) reader2 = Loader() self.assertTrue(os.path.isfile(self.write_1_1_filename)) return_data = reader2.load(self.write_1_1_filename) written_data = return_data[0] self._check_data(written_data) if os.path.isfile(self.write_1_1_filename): os.remove(self.write_1_1_filename) def test_double_trans_spectra(self): xmlreader = XMLreader(self.isis_1_1_doubletrans, self.schema_1_1) self.assertTrue(xmlreader.validate_xml()) reader = Loader() data = reader.load(self.isis_1_1_doubletrans) for item in data: self._check_data(item) def test_entry_name_recurse(self): test_values = [1,2,3,4,5,6] base_key = "key" d = {} for value in test_values: new_key = self.get_number_of_entries(d, base_key, i = 0) d[new_key] = value self.assertTrue(len(d) == 6) def test_load_cansas_file(self): reader1 = XMLreader(self.xml_valid, self.schema_1_0) self.assertTrue(reader1.validate_xml()) reader2 = XMLreader(self.xml_invalid, self.schema_1_0) self.assertFalse(reader2.validate_xml()) reader3 = XMLreader(self.xml_valid, self.schema_1_1) self.assertFalse(reader3.validate_xml()) reader4 = XMLreader(self.xml_invalid, self.schema_1_1) self.assertFalse(reader4.validate_xml()) reader5 = XMLreader(self.isis_1_0, self.schema_1_0) self.assertTrue(reader5.validate_xml()) reader6 = XMLreader(self.isis_1_1, self.schema_1_1) self.assertTrue(reader6.validate_xml()) reader7 = XMLreader(self.isis_1_1, self.schema_1_0) self.assertFalse(reader7.validate_xml()) def test_invalid_cansas(self): list = self.loader.load(self.cansas1d_notitle) data = list[0] self.assertTrue(data.x.size == 2) self.assertTrue(len(data.meta_data) == 2) self.assertTrue(len(data.errors) == 1) self.assertTrue(data.detector[0].distance_unit == "mm") self.assertTrue(data.detector[0].name == "fictional hybrid") self.assertTrue(data.detector[0].distance == 4150) def test_old_cansas_files(self): reader1 = XMLreader(self.cansas1d, self.schema_1_0) self.assertTrue(reader1.validate_xml()) file_loader = Loader() file_loader.load(self.cansas1d) reader2 = XMLreader(self.cansas1d_units, self.schema_1_0) self.assertTrue(reader2.validate_xml()) reader3 = XMLreader(self.cansas1d_badunits, self.schema_1_0) self.assertTrue(reader3.validate_xml()) reader4 = XMLreader(self.cansas1d_slit, self.schema_1_0) self.assertTrue(reader4.validate_xml()) def test_save_cansas_v1_0(self): xmlreader = XMLreader(self.isis_1_0, self.schema_1_0) self.assertTrue(xmlreader.validate_xml()) reader_generic = Loader() dataloader = reader_generic.load(self.isis_1_0) reader_cansas = Reader() cansasreader = reader_cansas.read(self.isis_1_0) for i in range(len(dataloader)): self._check_data(dataloader[i]) self._check_data(cansasreader[i]) reader_generic.save(self.write_1_0_filename, dataloader[i], None) reader2 = Reader() self.assertTrue(os.path.isfile(self.write_1_0_filename)) return_data = reader2.read(self.write_1_0_filename) written_data = return_data[0] xmlreader = XMLreader(self.write_1_0_filename, self.schema_1_0) self.assertTrue(xmlreader.validate_xml()) self._check_data(written_data) if os.path.isfile(self.write_1_0_filename): os.remove(self.write_1_0_filename) def test_processing_instructions(self): reader = XMLreader(self.isis_1_1, self.schema_1_1) valid = reader.validate_xml() if valid: # find the processing instructions and make into a dictionary dic = self.get_processing_instructions(reader) self.assertEqual(dic, {'xml-stylesheet': 'type="text/xsl" href="cansas1d.xsl" '}) xml = "" xmldoc = minidom.parseString(xml) # take the processing instructions and put them back in xmldoc = self.set_processing_instructions(xmldoc, dic) xmldoc.toprettyxml() def set_processing_instructions(self, minidom_object, dic): xmlroot = minidom_object.firstChild for item in dic: pi = minidom_object.createProcessingInstruction(item, dic[item]) minidom_object.insertBefore(pi, xmlroot) return minidom_object def get_processing_instructions(self, xml_reader_object): dict = {} pi = xml_reader_object.xmlroot.getprevious() i = 0 while pi is not None: attr = {} pi_name = "" pi_string = decode(etree.tostring(pi)) if isinstance(pi_string, str): pi_string = pi_string.replace("", "") split = pi_string.split(" ", 1) pi_name = split[0] attr = split[1] dict[pi_name] = attr pi = pi.getprevious() return dict class cansas_reader_hdf5(unittest.TestCase): def setUp(self): self.loader = Loader() self.datafile_basic = find("simpleexamplefile.h5") self.datafile_multiplesasentry = find( "test_data//nxcansas_1Dand2D_multisasentry.h5") self.datafile_multiplesasdata = find( "test_data//nxcansas_1Dand2D_multisasdata.h5") self.datafile_multiplesasdata_multiplesasentry = find( "test_data//nxcansas_1Dand2D_multisasentry_multisasdata.h5") def test_real_data(self): self.data = self.loader.load(self.datafile_basic) self._check_example_data(self.data[0]) def test_multiple_sasentries(self): self.data = self.loader.load(self.datafile_multiplesasentry) self.assertTrue(len(self.data) == 2) self._check_multiple_data(self.data[0]) self._check_multiple_data(self.data[1]) if isinstance(self.data[0], Data1D): self._check_1d_data(self.data[0]) self._check_2d_data(self.data[1]) else: self._check_1d_data(self.data[1]) self._check_2d_data(self.data[0]) def test_multiple_sasdatas(self): self.data = self.loader.load(self.datafile_multiplesasdata) self.assertTrue(len(self.data) == 2) self._check_multiple_data(self.data[0]) self._check_multiple_data(self.data[1]) if isinstance(self.data[0], Data1D): self._check_1d_data(self.data[0]) self._check_2d_data(self.data[1]) else: self._check_1d_data(self.data[1]) self._check_2d_data(self.data[0]) def test_multiple_sasentries_multiplesasdatas(self): self.data = self.loader.load( self.datafile_multiplesasdata_multiplesasentry) self.assertTrue(len(self.data) == 4) self._check_multiple_data(self.data[0]) self._check_multiple_data(self.data[1]) self._check_multiple_data(self.data[2]) self._check_multiple_data(self.data[3]) for data in self.data: if isinstance(data, Data1D): self._check_1d_data(data) else: self._check_2d_data(data) def _check_multiple_data(self, data): self.assertTrue(data.title == "MH4_5deg_16T_SLOW") self.assertTrue(data.run[0] == '33837') self.assertTrue(len(data.run) == 1) self.assertTrue(data.instrument == "SANS2D") self.assertTrue(data.source.radiation == "Spallation Neutron Source") self.assertTrue(len(data.detector) == 2) self.assertTrue(data.detector[0].name == "rear-detector" or data.detector[1].name == "rear-detector") self.assertTrue(data.detector[0].name == "front-detector" or data.detector[1].name == "front-detector") self.assertAlmostEqual(data.detector[0].distance + data.detector[1].distance, 7230.54, 2) self.assertTrue(data.detector[0].distance_unit == 'mm') self.assertTrue(len(data.trans_spectrum) == 1) def _check_1d_data(self, data): self.assertTrue(len(data.x) == 66) self.assertTrue(len(data.x) == len(data.y)) self.assertTrue(data.dy[10] == 0.207214) self.assertTrue(data.y[10] == 24.1939) self.assertTrue(data.x[10] == 0.00898113) def _check_2d_data(self, data): self.assertTrue(isinstance(data, Data2D)) self.assertTrue(len(data.q_data) == 150*150) self.assertTrue(len(data.q_data) == len(data.data)) self.assertAlmostEqual(data.err_data[10], 0.186723989418) self.assertAlmostEqual(data.data[10], 0.465181) self.assertAlmostEqual(data.qx_data[10], -0.129) self.assertAlmostEqual(data.qy_data[10], -0.149) def _check_example_data(self, data): self.assertTrue(data.title == "") self.assertTrue(data.x.size == 100) self.assertTrue(data._xunit == "A^{-1}") self.assertTrue(data._yunit == "cm^{-1}") self.assertTrue(data.y.size == 100) self.assertAlmostEqual(data.y[40], 0.952749011516985) self.assertAlmostEqual(data.x[40], 0.3834415188257777) self.assertAlmostEqual(len(data.meta_data), 0) if __name__ == '__main__': unittest.main()