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_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_cansas_xml(self):
filename = "isis_1_1_write_test.xml"
xmlreader = XMLreader(self.isis_1_1, self.schema_1_1)
valid = xmlreader.validate_xml()
xmlreader.set_processing_instructions()
self.assertTrue(valid)
fo = open(self.isis_1_1)
str = fo.read()
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(filename, dataloader[i], None)
fo = open(filename)
str = fo.read()
reader2 = Loader()
return_data = reader2.load(filename)
written_data = return_data[0]
self._check_data(written_data)
def test_cansas_xml(self):
filename = "isis_1_1_write_test.xml"
xmlreader = XMLreader(self.isis_1_1, self.schema_1_1)
valid = xmlreader.validate_xml()
xmlreader.set_processing_instructions()
self.assertTrue(valid)
fo = open(self.isis_1_1)
str = fo.read()
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(filename, dataloader[i], None)
fo = open(filename)
str = fo.read()
reader2 = Loader()
return_data = reader2.load(filename)
written_data = return_data[0]
self._check_data(written_data)
class cansas_reader_xml(unittest.TestCase):
def setUp(self):
self.loader = Loader()
self.cansas_reader = Reader()
self.xml_reader = XMLreader()
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")
self.write_filename = find("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('<a><c></b></a>')
self.assertRaises(XMLSyntaxError, lambda: XMLreader(invalid))
def test_xml_validate(self):
string = "<xsd:schema xmlns:xsd=\"http://www.w3.org/2001/XMLSchema\">\n"
string += "\t<xsd:element name=\"a\" type=\"AType\"/>\n"
string += "\t<xsd:complexType name=\"AType\">\n"
string += "\t\t<xsd:sequence>\n"
string += "\t\t\t<xsd:element name=\"b\" type=\"xsd:string\" />\n"
string += "\t\t</xsd:sequence>\n"
string += "\t</xsd:complexType>\n"
string += "</xsd:schema>"
f = StringIO(string)
xmlschema_doc = etree.parse(f)
xmlschema = etree.XMLSchema(xmlschema_doc)
valid = etree.parse(StringIO('<a><b></b></a>'))
invalid = etree.parse(StringIO('<a><c></c></a>'))
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):
self.xml_reader.set_xml_file(self.isis_1_1)
self.xml_reader.set_schema(self.schema_1_1)
self.xml_reader.set_processing_instructions()
self.assertTrue(self.xml_reader.validate_xml())
dataloader = self.loader.load(self.isis_1_1)
cansasreader = self.cansas_reader.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])
self.loader.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):
self.xml_reader.set_xml_file(self.cansas1d)
self.xml_reader.set_schema(self.schema_1_0)
self.assertTrue(self.xml_reader.validate_xml())
data = self.loader.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):
self.xml_reader.set_xml_file(self.cansas1d)
self.xml_reader.set_schema(self.schema_1_0)
self.assertTrue(self.xml_reader.validate_xml())
self.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())
dataloader = self.loader.load(self.isis_1_0)
cansasreader = self.cansas_reader.read(self.isis_1_0)
for i in range(len(dataloader)):
self._check_data(dataloader[i])
self._check_data(cansasreader[i])
self.loader.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):
self.xml_reader.set_xml_file(self.isis_1_1)
self.xml_reader.set_schema(self.schema_1_1)
if self.xml_reader.validate_xml():
# find the processing instructions and make into a dictionary
dic = self.get_processing_instructions(self.xml_reader)
self.assertEqual(
dic,
{'xml-stylesheet': 'type="text/xsl" href="cansas1d.xsl" '})
xml = "<test><a><b><c></c></b></a></test>"
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
def test_generic_loader(self):
# the generic loader should work as well
data = self.loader.load(find("cansas1d.xml"))
self.assertEqual(len(data), 1)
self.assertEqual(data[0].meta_data['loader'], "CanSAS XML 1D")
def test_cansas_checkdata(self):
self.data_list = self.loader.load(find("cansas1d.xml"))
self.data = self.data_list[0]
self.assertEqual(self.data.filename, "cansas1d.xml")
self._checkdata()
def _checkdata(self):
"""
Check the data content to see whether
it matches the specific file we loaded.
Check the units too to see whether the
Data1D defaults changed. Otherwise the
tests won't pass
"""
self.assertEqual(len(self.data_list), 1)
self.assertEqual(self.data.run[0], "1234")
self.assertEqual(self.data.meta_data['loader'], "CanSAS XML 1D")
# Data
self.assertEqual(len(self.data.x), 2)
self.assertEqual(self.data.x_unit, 'A^{-1}')
self.assertEqual(self.data.y_unit, 'cm^{-1}')
self.assertAlmostEqual(self.data.x[0], 0.02, 6)
self.assertAlmostEqual(self.data.y[0], 1000, 6)
self.assertAlmostEqual(self.data.dx[0], 0.01, 6)
self.assertAlmostEqual(self.data.dy[0], 3, 6)
self.assertAlmostEqual(self.data.x[1], 0.03, 6)
self.assertAlmostEqual(self.data.y[1], 1001.0)
self.assertAlmostEqual(self.data.dx[1], 0.02, 6)
self.assertAlmostEqual(self.data.dy[1], 4, 6)
self.assertEqual(self.data.run_name['1234'], 'run name')
self.assertEqual(self.data.title, "Test title")
# Sample info
self.assertEqual(self.data.sample.ID, "SI600-new-long")
self.assertEqual(self.data.sample.name, "my sample")
self.assertEqual(self.data.sample.thickness_unit, 'mm')
self.assertAlmostEqual(self.data.sample.thickness, 1.03)
self.assertAlmostEqual(self.data.sample.transmission, 0.327)
self.assertEqual(self.data.sample.temperature_unit, 'C')
self.assertEqual(self.data.sample.temperature, 0)
self.assertEqual(self.data.sample.position_unit, 'mm')
self.assertEqual(self.data.sample.position.x, 10)
self.assertEqual(self.data.sample.position.y, 0)
self.assertEqual(self.data.sample.orientation_unit, 'degree')
self.assertAlmostEqual(self.data.sample.orientation.x, 22.5, 6)
self.assertAlmostEqual(self.data.sample.orientation.y, 0.02, 6)
self.assertEqual(
self.data.sample.details[0],
"http://chemtools.chem.soton.ac.uk/projects/blog/blogs.php/bit_id/2720"
)
self.assertEqual(self.data.sample.details[1], "Some text here")
# Instrument info
self.assertEqual(self.data.instrument, "canSAS instrument")
# Source
self.assertEqual(self.data.source.radiation, "neutron")
self.assertEqual(self.data.source.beam_size_unit, "mm")
self.assertEqual(self.data.source.beam_size_name, "bm")
self.assertEqual(self.data.source.beam_size.x, 12)
self.assertEqual(self.data.source.beam_size.y, 13)
self.assertEqual(self.data.source.beam_shape, "disc")
self.assertEqual(self.data.source.wavelength_unit, "A")
self.assertEqual(self.data.source.wavelength, 6)
self.assertEqual(self.data.source.wavelength_max_unit, "nm")
self.assertAlmostEqual(self.data.source.wavelength_max, 1.0)
self.assertEqual(self.data.source.wavelength_min_unit, "nm")
self.assertAlmostEqual(self.data.source.wavelength_min, 0.22)
self.assertEqual(self.data.source.wavelength_spread_unit, "percent")
self.assertEqual(self.data.source.wavelength_spread, 14.3)
# Collimation
_found1 = False
_found2 = False
self.assertEqual(self.data.collimation[0].length, 123.)
self.assertEqual(self.data.collimation[0].name, 'test coll name')
for item in self.data.collimation[0].aperture:
self.assertEqual(item.size_unit, 'mm')
self.assertEqual(item.distance_unit, 'mm')
if item.size.x == 50 \
and item.distance == 11000.0 \
and item.name == 'source' \
and item.type == 'radius':
_found1 = True
elif item.size.x == 1.0 \
and item.name == 'sample' \
and item.type == 'radius':
_found2 = True
if not _found1 or not _found2:
raise RuntimeError("Could not find all data %s %s" %
(_found1, _found2))
# Detector
self.assertEqual(self.data.detector[0].name, "fictional hybrid")
self.assertEqual(self.data.detector[0].distance_unit, "mm")
self.assertEqual(self.data.detector[0].distance, 4150)
self.assertEqual(self.data.detector[0].orientation_unit, "degree")
self.assertAlmostEqual(self.data.detector[0].orientation.x, 1.0, 6)
self.assertEqual(self.data.detector[0].orientation.y, 0.0)
self.assertEqual(self.data.detector[0].orientation.z, 0.0)
self.assertEqual(self.data.detector[0].offset_unit, "m")
self.assertEqual(self.data.detector[0].offset.x, .001)
self.assertEqual(self.data.detector[0].offset.y, .002)
self.assertEqual(self.data.detector[0].offset.z, None)
self.assertEqual(self.data.detector[0].beam_center_unit, "mm")
self.assertEqual(self.data.detector[0].beam_center.x, 322.64)
self.assertEqual(self.data.detector[0].beam_center.y, 327.68)
self.assertEqual(self.data.detector[0].beam_center.z, None)
self.assertEqual(self.data.detector[0].pixel_size_unit, "mm")
self.assertEqual(self.data.detector[0].pixel_size.x, 5)
self.assertEqual(self.data.detector[0].pixel_size.y, 5)
self.assertEqual(self.data.detector[0].pixel_size.z, None)
# Process
_found_term1 = False
_found_term2 = False
for item in self.data.process:
self.assertTrue(item.name in ['NCNR-IGOR', 'spol'])
self.assertTrue(
item.date in ['04-Sep-2007 18:35:02', '03-SEP-2006 11:42:47'])
for t in item.term:
if (t['name'] == "ABS:DSTAND" and t['unit'] == 'mm'
and float(t['value']) == 1.0):
_found_term2 = True
elif (t['name'] == "radialstep" and t['unit'] == 'mm'
and float(t['value']) == 10.0):
_found_term1 = True
if not _found_term1 or not _found_term2:
raise RuntimeError("Could not find all process terms %s %s" %
(_found_term1, _found_term2))
def test_writer(self):
filename = "write_test.xml"
data_list = self.loader.load(self.cansas1d)
data = data_list[0]
self.cansas_reader.write(self.write_filename, data)
self.data_list = self.loader.load(self.write_filename)
self.data = self.data_list[0]
self.assertEqual(len(self.data_list), 1)
self.assertEqual(len(self.data_list), len(self.data_list))
self.assertEqual(self.data.filename, filename)
self._checkdata()
if os.path.isfile(self.write_filename):
os.remove(self.write_filename)
def test_units(self):
"""
Check units.
Note that not all units are available.
"""
filename = "cansas1d_units.xml"
self.data_list = self.cansas_reader.read(find(filename))
self.data = self.data_list[0]
self.assertEqual(len(self.data_list), 1)
self.assertEqual(self.data.filename, filename)
self._checkdata()
def test_badunits(self):
"""
Check units.
Note that not all units are available.
"""
filename = "cansas1d_badunits.xml"
self.data_list = self.cansas_reader.read(find(filename))
self.data = self.data_list[0]
self.assertEqual(len(self.data_list), 1)
self.assertEqual(self.data.filename, filename)
# The followed should not have been loaded
self.assertAlmostEqual(self.data.sample.thickness, 0.00103)
# This one should
self.assertAlmostEqual(self.data.sample.transmission, 0.327)
self.assertEqual(self.data.meta_data['loader'], "CanSAS XML 1D")
self.assertEqual(len(self.data.errors), 0)
def test_slits(self):
"""
Check slit data
"""
filename = "cansas1d_slit.xml"
self.data_list = self.cansas_reader.read(find(filename))
self.data = self.data_list[0]
self.assertEqual(len(self.data_list), 1)
self.assertEqual(self.data.filename, filename)
self.assertEqual(self.data.run[0], "1234")
# Data
self.assertEqual(len(self.data.x), 2)
self.assertEqual(self.data.x_unit, 'A^{-1}')
self.assertEqual(self.data.y_unit, 'cm^{-1}')
self.assertEqual(self.data.x[0], 0.02)
self.assertEqual(self.data.y[0], 1000)
self.assertEqual(self.data.dxl[0], 0.005)
self.assertEqual(self.data.dxw[0], 0.001)
self.assertEqual(self.data.dy[0], 3)
self.assertEqual(self.data.x[1], 0.03)
self.assertAlmostEqual(self.data.y[1], 1001.0)
self.assertEqual(self.data.dxl[1], 0.005)
self.assertEqual(self.data.dxw[1], 0.001)
self.assertEqual(self.data.dy[1], 4)
self.assertEqual(self.data.run_name['1234'], 'run name')
self.assertEqual(self.data.title, "Test title")