def _read_options(self, group):
source = BytesIO(group.attrs['options'])
element = etree.parse(source).getroot()
reader = OptionsReader()
reader.parse(element)
return reader.get()
def setUp(self):
unittest.TestCase.setUp(self)
self.reader = OptionsReader()
etree.register_namespace('mc', 'http://pymontecarlo.sf.net')
source = BytesIO(b'<mc:options xmlns:mc="http://pymontecarlo.sf.net" name="Test" uuid="51d62e0261f2449eb41a74e4cb4501e0" version="6"><programs><program>dummy</program></programs><beam><mc:pencilBeam aperture="0.0" energy="1234.0" particle="electron"><origin x="0.0" y="0.0" z="1.0" /><direction u="0.0" v="0.0" w="-1.0" /></mc:pencilBeam></beam><geometry><mc:substrate rotation="0.0" tilt="0.0"><materials><mc:material _index="1" density="19300.0" name="Gold"><composition><element weightFraction="1.0" z="79" /></composition></mc:material></materials><body material="1" /></mc:substrate></geometry><detectors><mc:backscatteredElectronEnergyDetector _key="bse"><channels>1000</channels><limits lower="0.0" upper="1234.0" /></mc:backscatteredElectronEnergyDetector></detectors><limits><mc:showersLimit showers="5678" /></limits><models><mc:model name="Rutherford" type="elastic cross section" /></models></mc:options>')
self.element = etree.parse(source).getroot()
class TestOptionsReader(unittest.TestCase):
def setUp(self):
unittest.TestCase.setUp(self)
self.reader = OptionsReader()
etree.register_namespace('mc', 'http://pymontecarlo.sf.net')
source = BytesIO(b'<mc:options xmlns:mc="http://pymontecarlo.sf.net" name="Test" uuid="51d62e0261f2449eb41a74e4cb4501e0" version="6"><programs><program>dummy</program></programs><beam><mc:pencilBeam aperture="0.0" energy="1234.0" particle="electron"><origin x="0.0" y="0.0" z="1.0" /><direction u="0.0" v="0.0" w="-1.0" /></mc:pencilBeam></beam><geometry><mc:substrate rotation="0.0" tilt="0.0"><materials><mc:material _index="1" density="19300.0" name="Gold"><composition><element weightFraction="1.0" z="79" /></composition></mc:material></materials><body material="1" /></mc:substrate></geometry><detectors><mc:backscatteredElectronEnergyDetector _key="bse"><channels>1000</channels><limits lower="0.0" upper="1234.0" /></mc:backscatteredElectronEnergyDetector></detectors><limits><mc:showersLimit showers="5678" /></limits><models><mc:model name="Rutherford" type="elastic cross section" /></models></mc:options>')
self.element = etree.parse(source).getroot()
def tearDown(self):
unittest.TestCase.tearDown(self)
def testcan_parse(self):
self.assertTrue(self.reader.can_parse(self.element))
def testparse(self):
self.reader.parse(self.element)
obj = self.reader.get()
self.assertEqual("Test", obj.name)
self.assertEqual('51d62e0261f2449eb41a74e4cb4501e0', obj.uuid)
self.assertEqual(1, len(obj.programs))
self.assertEqual('dummy', list(obj.programs.aliases())[0])
self.assertAlmostEqual(1234, obj.beam.energy_eV, 4)
self.assertEqual(1, len(obj.detectors))
det = obj.detectors['bse']
self.assertAlmostEqual(0, det.limits_eV[0], 4)
self.assertAlmostEqual(1234, det.limits_eV[1], 4)
self.assertEqual(1000, det.channels)
self.assertEqual(1, len(obj.limits))
limits = list(obj.limits.iterclass(ShowersLimit))
self.assertEqual(1, len(limits))
self.assertEqual(5678, limits[0].showers)
self.assertEqual(1, len(obj.models))
models = list(obj.models.iterclass(ELASTIC_CROSS_SECTION))
self.assertEqual(1, len(models))
self.assertEqual(ELASTIC_CROSS_SECTION.rutherford, models[0])
def append(results, filepath):
with FileLock(filepath), h5py.File(filepath, 'r+') as hdf5file:
# Check UUID of base options
source = BytesIO(hdf5file.attrs['options'])
reader = OptionsReader()
reader.read(source)
options = reader.get()
if options.uuid != results.options.uuid:
raise ValueError('UUID of base options do not match: %s != %s' % \
(options.uuid, results.options.uuid))
# Save results
identifiers = np.array(hdf5file.attrs['identifiers'], 'U').tolist()
for container in results:
identifier = container.options.uuid
identifiers.append(identifier)
group = hdf5file.create_group('result-' + identifier)
# Save each result
for key, result in container.items():
subgroup = group.create_group(key)
handler = find_convert_handler('pymontecarlo.fileformat.results.result',
result, subgroup)
handler.convert(result, subgroup)
# Save options
writer = OptionsWriter()
writer.convert(container.options)
element = writer.get()
group.attrs['options'] = etree.tostring(element)
# Update identifiers
del hdf5file.attrs['identifiers']
hdf5file.attrs.create('identifiers', identifiers,
dtype=h5py.special_dtype(vlen=str))
def fromelement(cls, element):
from pymontecarlo.fileformat.options.options import OptionsReader
reader = OptionsReader()
reader.parse(element)
return reader.get()
def read(cls, source):
from pymontecarlo.fileformat.options.options import OptionsReader
reader = OptionsReader()
reader.read(source)
return reader.get()
