"""
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("", "").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()