def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
EDVerbose.DEBUG("EDPluginControlStrategyv10.preProcess...")
self.__edPluginRaddose = None
xsDataSampleCrystalMM = self.getDataInput().getSample()
if(xsDataSampleCrystalMM is None):
self.__xsDataSampleCopy = XSDataSampleCrystalMM()
else:
strXmlStringDataSample = xsDataSampleCrystalMM.marshal()
self.__xsDataSampleCopy = XSDataSampleCrystalMM.parseString(strXmlStringDataSample)
xsDataCrystal = self.getDataInput().getCrystalRefined()
if(xsDataCrystal is not None):
self.__xsDataSampleCopy.setCrystal(xsDataCrystal)
# Raddose is enabled only if the beam flux is set
if(self.getDataInput().getExperimentalCondition().getBeam().getFlux() is None):
warningMessage = EDMessage.WARNING_CANNOT_USE_PLUGIN_03 % ('EDPluginControlStrategyv10.preProcess', self.__strPluginRaddoseName, "Beam Flux not set")
EDVerbose.warning(warningMessage)
self.addWarningMessage(warningMessage)
else:
self.__edPluginRaddose = self.loadPlugin(self.__strPluginRaddoseName)
if (self.__edPluginRaddose is not None):
EDVerbose.DEBUG("EDPluginControlStrategyv10.preProcess: " + self.__strPluginRaddoseName + " Found... setting Data Input")
strFileSymop = os.path.join(self.getSymopHome(), "symop.lib")
xsDataStringSpaceGroup = self.getDataInput().getDiffractionPlan().getForcedSpaceGroup()
# Space Group has been forced
# Prepare chemical composition calculation with the forced Space Group (Space Group Name)
if(xsDataStringSpaceGroup is not None):
strSpaceGroup = xsDataStringSpaceGroup.getValue()
EDVerbose.DEBUG("EDPluginControlStrategyv10.preProcess: Forced Space Group Found: " + strSpaceGroup)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(strSpaceGroup, strFileSymop)
except Exception, detail:
errorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginControlStrategyv10.preProcess', "Problem to calculate Number of symmetry operators", detail)
EDVerbose.error(errorMessage)
self.addErrorMessage(errorMessage)
raise RuntimeError, errorMessage
# Space Group has NOT been forced
else:
xsDataStringSpaceGroup = self.__xsDataSampleCopy.getCrystal().getSpaceGroup().getName()
if (xsDataStringSpaceGroup is not None):
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group Name)
strSpaceGroupName = self.__xsDataSampleCopy.getCrystal().getSpaceGroup().getName().getValue()
EDVerbose.DEBUG("EDPluginControlStrategyv10.preProcess: Space Group IT Name found by indexing: " + strSpaceGroupName)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(strSpaceGroupName, strFileSymop)
except Exception, detail:
errorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginControlStrategyv10.preProcess', "Problem to calculate Number of symmetry operators", detail)
EDVerbose.error(errorMessage)
self.addErrorMessage(errorMessage)
raise RuntimeError, errorMessage
else:
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group IT number)
strSpaceGroupITNumber = str(self.__xsDataSampleCopy.getCrystal().getSpaceGroup().getITNumber().getValue())
def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
EDVerbose.DEBUG("EDPluginControlStrategyv1_2.preProcess...")
self._edPluginRaddose = None
xsDataSampleCrystalMM = self.getDataInput().getSample()
if(xsDataSampleCrystalMM is None):
self._xsDataSampleCopy = XSDataSampleCrystalMM()
else:
strXmlStringDataSample = xsDataSampleCrystalMM.marshal()
self._xsDataSampleCopy = XSDataSampleCrystalMM.parseString(strXmlStringDataSample)
xsDataCrystal = self.getDataInput().getCrystalRefined()
if(xsDataCrystal is not None):
self._xsDataSampleCopy.setCrystal(xsDataCrystal)
# Load the Best plugin
self._edPluginBest = self.loadPlugin(self._strPluginBestName)
self._edPluginBest.setBaseDirectory(self.getWorkingDirectory())
self._edPluginBest.setBaseName(self._strPluginBestName)
# Load the plot gle plugin
self._edPluginPlotGle = self.loadPlugin(self._strPluginPlotGleName)
# Check if radiation damage estimation is required or not in the diffraction plan
xsDataDiffractionPlan = self.getDataInput().getDiffractionPlan()
if xsDataDiffractionPlan is not None:
if xsDataDiffractionPlan.getEstimateRadiationDamage():
if xsDataDiffractionPlan.getEstimateRadiationDamage().getValue():
# Yes, is requested
self._bEstimateRadiationDamage = True
else:
# No, is explicitly not requested
self._bEstimateRadiationDamage = False
elif xsDataDiffractionPlan.getStrategyOption() is not None:
if xsDataDiffractionPlan.getStrategyOption().getValue().find("-DamPar") != -1:
# The "-DamPar" option requires estimation of radiation damage
self._bEstimateRadiationDamage = True
# Check if we know what to do with radiation damage
if self._bEstimateRadiationDamage is None:
# "Force" the estimation of radiation damage if the flux is present
if self.getDataInput().getExperimentalCondition().getBeam().getFlux() is None:
strWarningMessage = "EDPluginControlStrategyv1_2: Missing flux input - cannot estimate radiation damage."
EDVerbose.WARNING(strWarningMessage)
self.addWarningMessage(strWarningMessage)
self._bEstimateRadiationDamage = False
else:
self._bEstimateRadiationDamage = True
if self._bEstimateRadiationDamage:
if self.getDataInput().getExperimentalCondition().getBeam().getFlux() is None:
strErrorMessage = "EDPluginControlStrategyv1_2: Missing flux input. Cannot estimate radiation damage"
EDVerbose.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
if not self.isFailure():
self._edPluginRaddose = self.loadPlugin(self._strPluginRaddoseName)
if (self._edPluginRaddose is not None):
EDVerbose.DEBUG("EDPluginControlStrategyv1_2.preProcess: " + self._strPluginRaddoseName + " Found... setting Data Input")
strFileSymop = os.path.join(self.getSymopHome(), "symop.lib")
xsDataStringSpaceGroup = self.getDataInput().getDiffractionPlan().getForcedSpaceGroup()
# Space Group has been forced
# Prepare chemical composition calculation with the forced Space Group (Space Group Name)
if(xsDataStringSpaceGroup is not None):
strSpaceGroup = xsDataStringSpaceGroup.getValue().upper()
EDVerbose.DEBUG("EDPluginControlStrategyv1_2.preProcess: Forced Space Group Found: " + strSpaceGroup)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(strSpaceGroup, strFileSymop)
except Exception, detail:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginControlStrategyv1_2.preProcess', "Problem to calculate Number of symmetry operators", detail)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
# Space Group has NOT been forced
else:
xsDataStringSpaceGroup = self._xsDataSampleCopy.getCrystal().getSpaceGroup().getName()
if (xsDataStringSpaceGroup is not None):
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group Name)
strSpaceGroupName = self._xsDataSampleCopy.getCrystal().getSpaceGroup().getName().getValue()
EDVerbose.DEBUG("EDPluginControlStrategyv1_2.preProcess: Space Group IT Name found by indexing: " + strSpaceGroupName)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(strSpaceGroupName, strFileSymop)
except Exception, detail:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginControlStrategyv1_2.preProcess', "Problem to calculate Number of symmetry operators", detail)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
else:
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group IT number)
iSpaceGroupITNumber = self._xsDataSampleCopy.getCrystal().getSpaceGroup().getITNumber().getValue()
EDVerbose.DEBUG("EDPluginControlStrategyv1_2.preProcess: Space Group IT Number Found by indexing: %d" % iSpaceGroupITNumber)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupITNumber(str(iSpaceGroupITNumber), strFileSymop)
except Exception, detail:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginControlStrategyv1_2.preProcess', "Problem to calculate Number of symmetry operators", detail)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
EDVerbose.DEBUG("EDPluginControlKappaStrategyv2_0.preProcess...")
self.edPluginRaddose = None
xsDataSampleCrystalMM = self.getDataInput(
"mxv1InputStrategy")[0].getSample()
if (xsDataSampleCrystalMM is None):
self.xsDataSampleCopy = XSDataSampleCrystalMM()
else:
strXmlStringDataSample = xsDataSampleCrystalMM.marshal()
self.xsDataSampleCopy = XSDataSampleCrystalMM.parseString(
strXmlStringDataSample)
xsDataCrystal = self.getDataInput(
"mxv1InputStrategy")[0].getCrystalRefined()
if (xsDataCrystal is not None):
self.xsDataSampleCopy.setCrystal(xsDataCrystal)
# Raddose is enabled only if the beam flux is set
if (self.getDataInput("mxv1InputStrategy")
[0].getExperimentalCondition().getBeam().getFlux() is None):
strWarningMessage = EDMessage.WARNING_CANNOT_USE_PLUGIN_03 % (
'EDPluginControlKappaStrategyv2_0.preProcess',
self.strPluginRaddoseName, "Beam Flux not set")
EDVerbose.warning(strWarningMessage)
self.addWarningMessage(strWarningMessage)
else:
self.edPluginRaddose = self.loadPlugin(self.strPluginRaddoseName)
if (self.edPluginRaddose is not None):
EDVerbose.DEBUG(
"EDPluginControlKappaStrategyv2_0.preProcess: " +
self.strPluginRaddoseName + " Found... setting Data Input")
strFileSymop = os.path.join(self.getSymopHome(), "symop.lib")
xsDataStringSpaceGroup = self.getDataInput(
"mxv1InputStrategy")[0].getDiffractionPlan(
).getForcedSpaceGroup()
# Space Group has been forced
# Prepare chemical composition calculation with the forced Space Group (Space Group Name)
strNumOperators = None
strSpaceGroup = None
if (xsDataStringSpaceGroup is not None):
strSpaceGroup = xsDataStringSpaceGroup.getValue()
EDVerbose.DEBUG(
"EDPluginControlKappaStrategyv2_0.preProcess: Forced Space Group Found: "
+ strSpaceGroup)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(
strSpaceGroup, strFileSymop)
except Exception, detail:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginControlKappaStrategyv2_0.preProcess',
"Problem to calculate Number of symmetry operators",
detail)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
# Space Group has NOT been forced
else:
xsDataStringSpaceGroup = self.xsDataSampleCopy.getCrystal(
).getSpaceGroup().getName()
if (xsDataStringSpaceGroup is not None):
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group Name)
strSpaceGroup = self.xsDataSampleCopy.getCrystal(
).getSpaceGroup().getName().getValue()
EDVerbose.DEBUG(
"EDPluginControlKappaStrategyv2_0.preProcess: Space Group IT Name found by indexing: "
+ strSpaceGroup)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(
strSpaceGroup, strFileSymop)
except Exception, detail:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginControlKappaStrategyv2_0.preProcess',
"Problem to calculate Number of symmetry operators",
detail)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
else:
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group IT number)
dSpaceGroupITNumber = self.xsDataSampleCopy.getCrystal(
def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
self.DEBUG("EDPluginControlStrategyv1_2.preProcess...")
self._edPluginRaddose = None
xsDataSampleCrystalMM = self.getDataInput().getSample()
if xsDataSampleCrystalMM is None:
self._xsDataSampleCopy = XSDataSampleCrystalMM()
else:
strXmlStringDataSample = xsDataSampleCrystalMM.marshal()
self._xsDataSampleCopy = XSDataSampleCrystalMM.parseString(strXmlStringDataSample)
xsDataCrystal = self.getDataInput().getCrystalRefined()
if xsDataCrystal is not None:
self._xsDataSampleCopy.setCrystal(xsDataCrystal)
# Load the Best plugin
self._edPluginBest = self.loadPlugin(self._strPluginBestName)
self._edPluginBest.setBaseDirectory(self.getWorkingDirectory())
self._edPluginBest.setBaseName(self._strPluginBestName)
# Load the plot gle plugin
self._edPluginPlotGle = self.loadPlugin(self._strPluginPlotGleName)
# Check if radiation damage estimation is required or not in the diffraction plan
xsDataDiffractionPlan = self.getDataInput().getDiffractionPlan()
if xsDataDiffractionPlan is not None:
if xsDataDiffractionPlan.getEstimateRadiationDamage():
if xsDataDiffractionPlan.getEstimateRadiationDamage().getValue():
# Yes, is requested
self._bEstimateRadiationDamage = True
else:
# No, is explicitly not requested
self._bEstimateRadiationDamage = False
elif xsDataDiffractionPlan.getStrategyOption() is not None:
if xsDataDiffractionPlan.getStrategyOption().getValue().find("-DamPar") != -1:
# The "-DamPar" option requires estimation of radiation damage
self._bEstimateRadiationDamage = True
# Check if we know what to do with radiation damage
if self._bEstimateRadiationDamage is None:
# "Force" the estimation of radiation damage if the flux is present
if self.getDataInput().getExperimentalCondition().getBeam().getFlux() is None:
strWarningMessage = (
"EDPluginControlStrategyv1_2: Missing flux input - cannot estimate radiation damage."
)
self.WARNING(strWarningMessage)
self.addWarningMessage(strWarningMessage)
self._bEstimateRadiationDamage = False
else:
self._bEstimateRadiationDamage = True
if self._bEstimateRadiationDamage:
if self.getDataInput().getExperimentalCondition().getBeam().getFlux() is None:
strErrorMessage = "EDPluginControlStrategyv1_2: Missing flux input. Cannot estimate radiation damage"
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
if not self.isFailure():
self._edPluginRaddose = self.loadPlugin(self._strPluginRaddoseName)
if self._edPluginRaddose is not None:
self.DEBUG(
"EDPluginControlStrategyv1_2.preProcess: "
+ self._strPluginRaddoseName
+ " Found... setting Data Input"
)
strFileSymop = os.path.join(self.getSymopHome(), "symop.lib")
xsDataStringSpaceGroup = self.getDataInput().getDiffractionPlan().getForcedSpaceGroup()
# Space Group has been forced
# Prepare chemical composition calculation with the forced Space Group (Space Group Name)
bSpaceGroupForced = False
if xsDataStringSpaceGroup is not None:
strSpaceGroup = xsDataStringSpaceGroup.getValue().upper().replace(" ", "")
if strSpaceGroup != "":
self.DEBUG("EDPluginControlStrategyv1_2.preProcess: Forced Space Group Found: " + strSpaceGroup)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(
strSpaceGroup, strFileSymop
)
bSpaceGroupForced = True
except Exception as detail:
strErrorMessage = "EDPluginControlStrategyv1_2: Problem to calculate Number of symmetry operators: {0}".format(
detail
)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError(strErrorMessage)
if not bSpaceGroupForced:
# Space Group has NOT been forced
xsDataStringSpaceGroup = self._xsDataSampleCopy.getCrystal().getSpaceGroup().getName()
if xsDataStringSpaceGroup is not None:
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group Name)
strSpaceGroupName = self._xsDataSampleCopy.getCrystal().getSpaceGroup().getName().getValue()
self.DEBUG(
"EDPluginControlStrategyv1_2.preProcess: Space Group IT Name found by indexing: "
+ strSpaceGroupName
)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(
strSpaceGroupName, strFileSymop
)
except Exception as detail:
strErrorMessage = "EDPluginControlStrategyv1_2: Problem to calculate Number of symmetry operators: {0}".format(
detail
)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError(strErrorMessage)
else:
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group IT number)
iSpaceGroupITNumber = (
self._xsDataSampleCopy.getCrystal().getSpaceGroup().getITNumber().getValue()
)
self.DEBUG(
"EDPluginControlStrategyv1_2.preProcess: Space Group IT Number Found by indexing: %d"
% iSpaceGroupITNumber
)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupITNumber(
str(iSpaceGroupITNumber), strFileSymop
)
except Exception as detail:
strErrorMessage = "EDPluginControlStrategyv1_2: Problem to calculate Number of symmetry operators: {0}".format(
detail
)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError(strErrorMessage)
if strNumOperators is not None:
iNumOperators = int(strNumOperators)
else:
strErrorMessage = "EDPluginControlStrategyv1_2: No symmetry operators found for Space Group: {0}".format(
strNumOperators
)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError(strErrorMessage)
xsDataChemicalComposition = self._xsDataSampleCopy.getChemicalComposition()
if xsDataChemicalComposition is None:
# create a default chemical composition and assign it to the sample
xsDataDefaultChemicalComposition = self.getDefaultChemicalComposition(
self._xsDataSampleCopy, iNumOperators
)
self._xsDataSampleCopy.setChemicalComposition(xsDataDefaultChemicalComposition)
else:
# Check for Sulfur atoms, if none, add native sulfur atoms
xsDataUpdatedChemicalComposition = self.updateChemicalComposition(xsDataChemicalComposition)
self._xsDataSampleCopy.setChemicalComposition(xsDataUpdatedChemicalComposition)
# create Data Input for Raddose
from EDHandlerXSDataRaddosev10 import EDHandlerXSDataRaddosev10
self._edHandlerXSDataRaddose = EDHandlerXSDataRaddosev10()
xsDataBeam = self.getDataInput().getExperimentalCondition().getBeam()
# Calculate number of images (MXSUP-1616):
iNumberOfImages = None
xsDataCollection = self.dataInput.dataCollection
if xsDataCollection is not None:
iNumberOfImages = 0
for xsDataSubWedge in xsDataCollection.subWedge:
xsDataGoniostat = xsDataSubWedge.experimentalCondition.goniostat
iOscStart = xsDataGoniostat.rotationAxisStart.value
iOscEnd = xsDataGoniostat.rotationAxisEnd.value
iOscWidth = xsDataGoniostat.oscillationWidth.value
iNumberOfImages += int(round((iOscEnd - iOscStart) / iOscWidth, 0))
if iNumberOfImages is None:
iNumberOfImages = 1
self.WARNING("No goniostat information, number of images for RADDOSE set to 1")
xsDataRaddoseInput = self._edHandlerXSDataRaddose.getXSDataRaddoseInput(
xsDataBeam, self._xsDataSampleCopy, iNumOperators, iNumberOfImages
)
if xsDataRaddoseInput is not None:
self._edPluginRaddose.setDataInput(xsDataRaddoseInput)
self._edPluginRaddose.setBaseDirectory(self.getWorkingDirectory())
self._edPluginRaddose.setBaseName(self._strPluginRaddoseName)
def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
EDVerbose.DEBUG("EDPluginControlStrategyv1_2.preProcess...")
self._edPluginRaddose = None
xsDataSampleCrystalMM = self.getDataInput().getSample()
if(xsDataSampleCrystalMM is None):
self._xsDataSampleCopy = XSDataSampleCrystalMM()
else:
strXmlStringDataSample = xsDataSampleCrystalMM.marshal()
self._xsDataSampleCopy = XSDataSampleCrystalMM.parseString(strXmlStringDataSample)
xsDataCrystal = self.getDataInput().getCrystalRefined()
if(xsDataCrystal is not None):
self._xsDataSampleCopy.setCrystal(xsDataCrystal)
# Load the Best plugin
self._edPluginBest = self.loadPlugin(self._strPluginBestName)
self._edPluginBest.setBaseDirectory(self.getWorkingDirectory())
self._edPluginBest.setBaseName(self._strPluginBestName)
# Load the plot gle plugin
self._edPluginPlotGle = self.loadPlugin(self._strPluginPlotGleName)
# Check if radiation damage estimation is required or not in the diffraction plan
xsDataDiffractionPlan = self.getDataInput().getDiffractionPlan()
if xsDataDiffractionPlan is not None:
if xsDataDiffractionPlan.getEstimateRadiationDamage():
if xsDataDiffractionPlan.getEstimateRadiationDamage().getValue():
# Yes, is requested
self._bEstimateRadiationDamage = True
else:
# No, is explicitly not requested
self._bEstimateRadiationDamage = False
elif xsDataDiffractionPlan.getStrategyOption() is not None:
if xsDataDiffractionPlan.getStrategyOption().getValue().find("-DamPar") != -1:
# The "-DamPar" option requires estimation of radiation damage
self._bEstimateRadiationDamage = True
# Check if we know what to do with radiation damage
if self._bEstimateRadiationDamage is None:
# "Force" the estimation of radiation damage if the flux is present
if self.getDataInput().getExperimentalCondition().getBeam().getFlux() is None:
strWarningMessage = "EDPluginControlStrategyv1_2: Missing flux input - cannot estimate radiation damage."
EDVerbose.WARNING(strWarningMessage)
self.addWarningMessage(strWarningMessage)
self._bEstimateRadiationDamage = False
else:
self._bEstimateRadiationDamage = True
if self._bEstimateRadiationDamage:
if self.getDataInput().getExperimentalCondition().getBeam().getFlux() is None:
strErrorMessage = "EDPluginControlStrategyv1_2: Missing flux input. Cannot estimate radiation damage"
EDVerbose.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
if not self.isFailure():
self._edPluginRaddose = self.loadPlugin(self._strPluginRaddoseName)
if (self._edPluginRaddose is not None):
EDVerbose.DEBUG("EDPluginControlStrategyv1_2.preProcess: " + self._strPluginRaddoseName + " Found... setting Data Input")
strFileSymop = os.path.join(self.getSymopHome(), "symop.lib")
xsDataStringSpaceGroup = self.getDataInput().getDiffractionPlan().getForcedSpaceGroup()
# Space Group has been forced
# Prepare chemical composition calculation with the forced Space Group (Space Group Name)
bSpaceGroupForced = False
if(xsDataStringSpaceGroup is not None):
strSpaceGroup = xsDataStringSpaceGroup.getValue().upper().replace(" ", "")
if strSpaceGroup != "":
EDVerbose.DEBUG("EDPluginControlStrategyv1_2.preProcess: Forced Space Group Found: " + strSpaceGroup)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(strSpaceGroup, strFileSymop)
bSpaceGroupForced = True
except Exception, detail:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginControlStrategyv1_2.preProcess', "Problem to calculate Number of symmetry operators", detail)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
if not bSpaceGroupForced:
# Space Group has NOT been forced
xsDataStringSpaceGroup = self._xsDataSampleCopy.getCrystal().getSpaceGroup().getName()
if (xsDataStringSpaceGroup is not None):
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group Name)
strSpaceGroupName = self._xsDataSampleCopy.getCrystal().getSpaceGroup().getName().getValue()
EDVerbose.DEBUG("EDPluginControlStrategyv1_2.preProcess: Space Group IT Name found by indexing: " + strSpaceGroupName)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(strSpaceGroupName, strFileSymop)
except Exception, detail:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginControlStrategyv1_2.preProcess', "Problem to calculate Number of symmetry operators", detail)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
else:
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group IT number)
iSpaceGroupITNumber = self._xsDataSampleCopy.getCrystal().getSpaceGroup().getITNumber().getValue()
EDVerbose.DEBUG("EDPluginControlStrategyv1_2.preProcess: Space Group IT Number Found by indexing: %d" % iSpaceGroupITNumber)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupITNumber(str(iSpaceGroupITNumber), strFileSymop)
except Exception, detail:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginControlStrategyv1_2.preProcess', "Problem to calculate Number of symmetry operators", detail)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
