def can_read(self, source):
if hasattr(source, "read"):
element = xmlutil.parse(source)
else:
with FileLock(source), open(source, "rb") as fp:
element = xmlutil.parse(fp)
return self.can_parse(element)
def _load_electronfraction(zipfile, key):
element = xmlutil.parse(zipfile.open(key + '.xml', 'r'))
child = element.find('absorbed')
if child is not None:
absorbed = \
float(child.get('val', 0.0)), float(child.get('unc', 0.0))
else:
absorbed = (0.0, 0.0)
child = element.find('backscattered')
if child is not None:
backscattered = \
float(child.get('val', 0.0)), float(child.get('unc', 0.0))
else:
backscattered = (0.0, 0.0)
child = element.find('transmitted')
if child is not None:
transmitted = \
float(child.get('val', 0.0)), float(child.get('unc', 0.0))
else:
transmitted = (0.0, 0.0)
return ElectronFractionResult(absorbed, backscattered, transmitted)
def _load_showersstatistics(zipfile, key):
element = xmlutil.parse(zipfile.open(key + '.xml', 'r').read())
child = element.find('showers')
if child is not None:
showers = float(child.get('val', 0))
else:
showers = 0
return ShowersStatisticsResult(showers)
def _update_version4(self, filepath):
logging.debug('Updating from "version 4"')
root = xmlutil.parse(filepath)
root.set('version', '5')
for element in root.find('detectors'):
if element.tag == '{http://pymontecarlo.sf.net}phiRhoZDetector':
element.tag = '{http://pymontecarlo.sf.net}photonDepthDetector'
with open(filepath, 'wb') as fp:
fp.write(xmlutil.tostring(root, pretty_print=True))
return self._update_version5(filepath)
def _update_version3(self, filepath):
logging.debug('Updating from "version 3"')
root = xmlutil.parse(filepath)
root.set('version', '4')
elements = list(list(root.find('geometry'))[0].find('materials'))
for element in elements:
element.set('absorptionEnergyPositron', '50.0')
with open(filepath, 'wb') as fp:
fp.write(xmlutil.tostring(root, pretty_print=True))
return self._update_version4(filepath)
def _load_time(zipfile, key):
element = xmlutil.parse(zipfile.open(key + '.xml', 'r'))
child = element.find('time')
if child is not None:
simulation_time = float(child.get('val', 0.0))
else:
simulation_time = 0.0
child = element.find('speed')
if child is not None:
simulation_speed = \
float(child.get('val', 0.0)), float(child.get('unc', 0.0))
else:
simulation_speed = (0.0, 0.0)
return TimeResult(simulation_time, simulation_speed)
def _update_version2(self, filepath):
logging.debug('Updating from "version 2"')
root = xmlutil.parse(filepath)
root.set('version', '3')
# Update beam
element = list(root.find('beam'))[0]
element.set('particle', 'electron')
# Update interaction forcings
_PARTICLES_REF = {1: ELECTRON, 2: PHOTON, 3: POSITRON}
_COLLISIONS_REF = {ELECTRON: {2: HARD_ELASTIC,
3: HARD_INELASTIC,
4: HARD_BREMSSTRAHLUNG_EMISSION,
5: INNERSHELL_IMPACT_IONISATION,
7: DELTA},
PHOTON: {1: COHERENT_RAYLEIGH_SCATTERING,
2: INCOHERENT_COMPTON_SCATTERING,
3: PHOTOELECTRIC_ABSORPTION,
4: ELECTRON_POSITRON_PAIR_PRODUCTION,
7: DELTA},
POSITRON: {2: HARD_ELASTIC,
3: HARD_INELASTIC,
4: HARD_BREMSSTRAHLUNG_EMISSION,
5: INNERSHELL_IMPACT_IONISATION,
6: ANNIHILATION,
7: DELTA}}
geometry_element = root.find('geometry')[0]
bodies_element = geometry_element.find('bodies')[0]
intforcings_element = bodies_element.find('interactionForcings')
if intforcings_element is not None:
for element in list(intforcings_element):
particle = _PARTICLES_REF[int(element.get('particle'))]
element.set('particle', str(particle))
collision = _COLLISIONS_REF[particle][int(element.get('collision'))]
element.set('collision', str(collision))
with open(filepath, 'wb') as fp:
fp.write(xmlutil.tostring(root, pretty_print=True))
return self._update_version3(filepath)
def _update_noversion(self, filepath):
logging.debug('Updating from "no version"')
root = xmlutil.parse(filepath)
if not root.tag.startswith("{") and \
root.tag.startswith('pymontecarlo.'):
with open(filepath, 'r') as fp:
content = fp.read()
lookup = {'<pymontecarlo.input.base.options.Options': '<mc:options xmlns:mc="http://pymontecarlo.sf.net" xmlns:mc-pen="http://pymontecarlo.sf.net/penelope" version="2"',
'pymontecarlo.input.base.options.Options>': 'mc:options>',
'pymontecarlo.input.base.beam.PencilBeam': 'mc:pencilBeam',
'pymontecarlo.input.base.beam.GaussianBeam': 'mc:gaussianBeam',
'pymontecarlo.input.base.body.Body': 'mc:body',
'pymontecarlo.input.base.body.Layer': 'mc:layer',
'pymontecarlo.input.base.detector.BackscatteredElectronEnergyDetector': 'mc:backscatteredElectronEnergyDetector',
'pymontecarlo.input.base.detector.TransmittedElectronEnergyDetector': 'mc:transmittedElectronEnergyDetector',
'pymontecarlo.input.base.detector.BackscatteredElectronPolarAngularDetector': 'mc:backscatteredElectronPolarAngularDetector',
'pymontecarlo.input.base.detector.TransmittedElectronPolarAngularDetector': 'mc:transmittedElectronPolarAngularDetector',
'pymontecarlo.input.base.detector.BackscatteredElectronAzimuthalAngularDetector': 'mc:backscatteredElectronAzimuthalAngularDetector',
'pymontecarlo.input.base.detector.TransmittedElectronAzimuthalAngularDetector': 'mc:transmittedElectronAzimuthalAngularDetector',
'pymontecarlo.input.base.detector.PhotonPolarAngularDetector': 'mc:photonPolarAngularDetector',
'pymontecarlo.input.base.detector.PhotonAzimuthalAngularDetector': 'mc:photonAzimuthalAngularDetector',
'pymontecarlo.input.base.detector.EnergyDepositedSpatialDetector': 'mc:energyDepositedSpatialDetector',
'pymontecarlo.input.base.detector.PhotonSpectrumDetector': 'mc:photonSpectrumDetector',
'pymontecarlo.input.base.detector.PhiRhoZDetector': 'mc:phiRhoZDetector',
'pymontecarlo.input.base.detector.PhotonIntensityDetector': 'mc:photonIntensityDetector',
'pymontecarlo.input.base.detector.TimeDetector': 'mc:timeDetector',
'pymontecarlo.input.base.detector.ElectronFractionDetector': 'mc:electronFractionDetector',
'pymontecarlo.input.base.geometry.Substrate': 'mc:substrate',
'pymontecarlo.input.base.geometry.Inclusion': 'mc:inclusion',
'pymontecarlo.input.base.geometry.MultiLayers': 'mc:multiLayers',
'pymontecarlo.input.base.geometry.GrainBoundaries': 'mc:grainBoundaries',
'pymontecarlo.input.base.limit.TimeLimit': 'mc:timeLimit',
'pymontecarlo.input.base.limit.ShowersLimit': 'mc:showersLimit',
'pymontecarlo.input.base.limit.UncertaintyLimit': 'mc:uncertaintyLimit',
'pymontecarlo.input.base.material.Material': 'mc:material',
'pymontecarlo.input.base.model.Model': 'mc:model',
'pymontecarlo.input.penelope.body.Body': 'mc-pen:body',
'pymontecarlo.input.penelope.body.Layer': 'mc-pen:layer',
'pymontecarlo.input.penelope.interactionforcing.InteractionForcing': 'mc-pen:interactionForcing',
'pymontecarlo.input.penelope.material.Material': 'mc-pen:material',
}
for oldvalue, newvalue in lookup.items():
content = content.replace(oldvalue, newvalue)
with open(filepath, 'w') as fp:
fp.write(content)
else:
root.set('version', '2')
with open(filepath, 'wb') as fp:
fp.write(xmlutil.tostring(root, pretty_print=True))
return self._update_version2(filepath)
def _get_version(self, filepath):
root = xmlutil.parse(filepath)
return int(root.get('version', 0))
def _update_version5(self, filepath):
logging.debug('Updating from "version 5"')
root = xmlutil.parse(filepath)
# Header
root.set('version', '6')
if 'uuid' not in root.attrib:
root.set('uuid', uuid.uuid4().hex)
# Beam
element = root.find('beam/*/direction')
element.set('u', element.attrib.pop('x'))
element.set('v', element.attrib.pop('y'))
element.set('w', element.attrib.pop('z'))
# Geometry
element = root.find('geometry/')
materials_lookup = {}
for subelement in element.findall('bodies/*'):
materials_lookup[subelement.get('index')] = subelement.get('material')
if element.tag == '{http://pymontecarlo.sf.net}substrate':
material = materials_lookup[element.attrib.pop('substrate')]
etree.SubElement(element, 'body', {'material': material})
elif element.tag == '{http://pymontecarlo.sf.net}inclusion':
material = materials_lookup[element.attrib.pop('substrate')]
etree.SubElement(element, 'substrate', {'material': material})
material = materials_lookup[element.attrib.pop('inclusion')]
diameter = element.attrib.pop('diameter')
etree.SubElement(element, 'inclusion',
{'material': material, 'diameter': diameter})
elif element.tag == '{http://pymontecarlo.sf.net}multiLayers':
element.tag = '{http://pymontecarlo.sf.net}horizontalLayers'
if 'substrate' in element.attrib:
material = materials_lookup[element.attrib.pop('substrate')]
etree.SubElement(element, 'substrate', {'material': material})
thicknesses_lookup = {}
for subelement in element.findall('bodies/*'):
thicknesses_lookup[subelement.get('index')] = subelement.get('thickness')
subelement = etree.SubElement(element, 'layers')
for layer in element.get('layers').split(','):
etree.SubElement(subelement, layer,
{'material': materials_lookup[layer],
'thickness': thicknesses_lookup[layer]})
elif element.tag == '{http://pymontecarlo.sf.net}grainBoundaries' or \
element.tag == '':
element.tag = '{http://pymontecarlo.sf.net}verticalLayers'
depth = element.get('thickness', str(float('inf')))
material = materials_lookup[element.attrib.pop('left_substrate')]
etree.SubElement(element, 'leftSubstrate',
{'material': material, 'depth': depth})
material = materials_lookup[element.attrib.pop('right_substrate')]
etree.SubElement(element, 'rightSubstrate',
{'material': material, 'depth': depth})
thicknesses_lookup = {}
for subelement in element.findall('bodies/*'):
thicknesses_lookup[subelement.get('index')] = subelement.get('thickness')
subelement = etree.SubElement(element, 'layers')
for layer in element.get('layers').split(','):
etree.SubElement(subelement, layer,
{'material': materials_lookup[layer],
'thickness': thicknesses_lookup[layer],
'depth': depth})
elif element.tag == '{http://pymontecarlo.sf.net}sphere':
material = materials_lookup[element.attrib.pop('substrate')]
diameter = element.attrib.pop('diameter')
etree.SubElement(element, 'body',
{'material': material, 'diameter': diameter})
else:
raise ValueError('Unknown geometry to update: %s' % element.tag)
element.remove(element.find('bodies'))
# Detectors
for element in root.findall('detectors/*'):
if 'elevation_min' in element.attrib and \
'elevation_max' in element.attrib:
lower = element.attrib.pop('elevation_min')
upper = element.attrib.pop('elevation_max')
etree.SubElement(element, 'elevation',
{'lower': min(lower, upper),
'upper': max(lower, upper)})
if 'azimuth_min' in element.attrib and \
'azimuth_max' in element.attrib:
lower = element.attrib.pop('azimuth_min')
upper = element.attrib.pop('azimuth_max')
etree.SubElement(element, 'azimuth',
{'lower': min(lower, upper),
'upper': max(lower, upper)})
if 'channels' in element.attrib:
subelement = etree.SubElement(element, 'channels')
subelement.text = element.attrib.pop('channels')
if 'xlimit_min' in element.attrib and \
'xlimit_max' in element.attrib:
lower = element.attrib.pop('xlimit_min')
upper = element.attrib.pop('xlimit_max')
etree.SubElement(element, 'xlimits',
{'lower': min(lower, upper),
'upper': max(lower, upper)})
if 'ylimit_min' in element.attrib and \
'ylimit_max' in element.attrib:
lower = element.attrib.pop('ylimit_min')
upper = element.attrib.pop('ylimit_max')
etree.SubElement(element, 'ylimits',
{'lower': min(lower, upper),
'upper': max(lower, upper)})
if 'zlimit_min' in element.attrib and \
'zlimit_max' in element.attrib:
lower = element.attrib.pop('zlimit_min')
upper = element.attrib.pop('zlimit_max')
etree.SubElement(element, 'zlimits',
{'lower': min(lower, upper),
'upper': max(lower, upper)})
if 'limit_min' in element.attrib and \
'limit_max' in element.attrib:
lower = element.attrib.pop('limit_min')
upper = element.attrib.pop('limit_max')
etree.SubElement(element, 'limits',
{'lower': min(lower, upper),
'upper': max(lower, upper)})
if 'secondary' in element.attrib:
subelement = etree.SubElement(element, 'secondary')
subelement.text = element.attrib.pop('secondary')
with open(filepath, 'wb') as fp:
fp.write(xmlutil.tostring(root, pretty_print=True))
return self._update_version6(filepath)
def _run(self, source):
element = xmlutil.parse(source)
return _OptionsElementReaderThread._run(self, element)
