def getXSDataInputBest(self, _xsDataInputStrategy):
xsDataBeam = _xsDataInputStrategy.getExperimentalCondition().getBeam()
xsDataSample = _xsDataInputStrategy.getSample()
xsDataDetector = _xsDataInputStrategy.getExperimentalCondition(
).getDetector()
xsDataGoniostat = _xsDataInputStrategy.getExperimentalCondition(
).getGoniostat()
xsDataDiffractionPlan = _xsDataInputStrategy.getDiffractionPlan()
xsDataStringBestFileContentDat = _xsDataInputStrategy.getBestFileContentDat(
)
xsDataStringBestFileContentPar = _xsDataInputStrategy.getBestFileContentPar(
)
xsDataFileXdsBackgroundImage = _xsDataInputStrategy.getXdsBackgroundImage(
)
listXSDataStringBestFileContentHKL = _xsDataInputStrategy.getBestFileContentHKL(
)
xsDataInputBest = XSDataInputBest()
# Sample
xsDataAbsorbedDose = None
xsDataSusceptibility = None
# Could be None if sample has not been set
# It could be not None in case Raddose has calculated an absorbed dose with default sample values
if (xsDataSample is not None):
xsDataAbsorbedDose = xsDataSample.getAbsorbedDoseRate()
xsDataSusceptibility = xsDataSample.getSusceptibility()
# crystalShape
# Default value is 1 (We assume that Xtal is smaller than beam)
if xsDataSample.size is not None and xsDataSample.omegaMin is not None:
xsDataInputBest.crystalSize = XSDataSize().parseString(
xsDataSample.size.marshal())
xsDataInputBest.omegaMin = xsDataSample.omegaMin
else:
xsDataDoubleCrystalShape = xsDataSample.getShape()
if (xsDataDoubleCrystalShape is None):
if (xsDataSample.getSize() is
None) or (xsDataBeam.getSize() is None):
xsDataDoubleCrystalShape = XSDataDouble(1)
else:
fCrystalSizeY = xsDataSample.getSize().getY().getValue(
)
fCrystalSizeZ = xsDataSample.getSize().getZ().getValue(
)
fDiagonal = math.sqrt(fCrystalSizeY**2 +
fCrystalSizeZ**2)
fBeamSizeY = xsDataBeam.getSize().getY().getValue()
fCrystalShape = None
if fBeamSizeY > fDiagonal:
fCrystalShape = 1.0
else:
fCrystalShape = int(
10 * fDiagonal / fBeamSizeY) / 10.0
xsDataDoubleCrystalShape = XSDataDouble(fCrystalShape)
xsDataInputBest.setCrystalShape(xsDataDoubleCrystalShape)
# Radiation damage model parameters
xsDataInputBest.setRadiationDamageModelBeta(
xsDataSample.getRadiationDamageModelBeta())
xsDataInputBest.setRadiationDamageModelGamma(
xsDataSample.getRadiationDamageModelGamma())
# Could be None if Raddose failed to calculate the absorbed dose
if (xsDataAbsorbedDose is not None):
xsDataInputBest.setCrystalAbsorbedDoseRate(
xsDataSample.getAbsorbedDoseRate())
xsDataInputBest.setCrystalSusceptibility(xsDataSusceptibility)
# Detector
xsDataInputBest.setDetectorType(xsDataDetector.getType())
# Minimum exposure time per image
xsDataTimeMinExposureTimePerImage = None
if xsDataBeam:
xsDataTimeMinExposureTimePerImage = xsDataBeam.getMinExposureTimePerImage(
)
if xsDataTimeMinExposureTimePerImage == None:
xsDataTimeMinExposureTimePerImage = xsDataDiffractionPlan.getMinExposureTimePerImage(
)
xsDataInputBest.setBeamMinExposureTime(
xsDataTimeMinExposureTimePerImage)
# Max rotation speed
xsDataAngularSpeedMax = None
if xsDataGoniostat:
xsDataAngularSpeedMax = xsDataGoniostat.getMaxOscillationSpeed()
if xsDataDiffractionPlan and xsDataAngularSpeedMax == None:
xsDataAngularSpeedMax = xsDataDiffractionPlan.getGoniostatMaxOscillationSpeed(
)
xsDataInputBest.setGoniostatMaxRotationSpeed(xsDataAngularSpeedMax)
# Min rotation width
xsDataAngleMin = None
if xsDataGoniostat:
xsDataAngleMin = xsDataGoniostat.getMinOscillationWidth()
if xsDataDiffractionPlan and xsDataAngleMin == None:
xsDataAngleMin = xsDataDiffractionPlan.getGoniostatMinOscillationWidth(
)
xsDataInputBest.setGoniostatMinRotationWidth(xsDataAngleMin)
# Other beam parameters
if xsDataBeam:
xsDataInputBest.setBeamExposureTime(xsDataBeam.getExposureTime())
if xsDataBeam.getTransmission():
# Fix for bug 741: if the transmission is zero don't set it and warn the user
fTransmission = xsDataBeam.getTransmission().getValue()
if (abs(fTransmission) < 0.1):
EDVerbose.warning(
"Input transmission to BEST ignored because it is zero or close to zero: %f"
% fTransmission)
else:
xsDataInputBest.setTransmission(
xsDataBeam.getTransmission())
if xsDataBeam.getApertureSize():
xsDataInputBest.setApertureSize(xsDataBeam.getApertureSize())
if xsDataBeam.size:
xsDataInputBest.setBeamSize(xsDataBeam.size)
if xsDataBeam.flux:
xsDataInputBest.setBeamFlux(xsDataBeam.flux)
# Other diffraction plan parameters
if xsDataDiffractionPlan:
xsDataInputBest.setAimedResolution(
xsDataDiffractionPlan.getAimedResolution())
xsDataInputBest.setAimedRedundancy(
xsDataDiffractionPlan.getAimedMultiplicity())
xsDataInputBest.setAimedCompleteness(
xsDataDiffractionPlan.getAimedCompleteness())
xsDataInputBest.setAimedIOverSigma(
xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution())
xsDataInputBest.setBeamMaxExposureTime(
xsDataDiffractionPlan.getMaxExposureTimePerDataCollection())
xsDataInputBest.setComplexity(
xsDataDiffractionPlan.getComplexity())
xsDataInputBest.setAnomalousData(
xsDataDiffractionPlan.getAnomalousData())
xsDataInputBest.setStrategyOption(
xsDataDiffractionPlan.getStrategyOption())
xsDataInputBest.setMinTransmission(
xsDataDiffractionPlan.getMinTransmission())
xsDataInputBest.setNumberOfCrystalPositions(
xsDataDiffractionPlan.getNumberOfPositions())
xsDataInputBest.setDetectorDistanceMin(
xsDataDiffractionPlan.getDetectorDistanceMin())
xsDataInputBest.setDetectorDistanceMax(
xsDataDiffractionPlan.getDetectorDistanceMax())
xsDataInputBest.setUserDefinedRotationStart(
xsDataDiffractionPlan.getUserDefinedRotationStart())
xsDataInputBest.setUserDefinedRotationRange(
xsDataDiffractionPlan.getUserDefinedRotationRange())
xsDataInputBest.doseLimit = xsDataDiffractionPlan.doseLimit
xsDataInputBest.rFriedel = xsDataDiffractionPlan.rFriedel
# Best Files
xsDataInputBest.setBestFileContentDat(xsDataStringBestFileContentDat)
xsDataInputBest.setBestFileContentPar(xsDataStringBestFileContentPar)
xsDataInputBest.setBestFileContentHKL(
listXSDataStringBestFileContentHKL)
xsDataInputBest.setXdsBackgroundImage(xsDataFileXdsBackgroundImage)
return xsDataInputBest
def getXSDataInputBest(self, _xsDataInputStrategy):
xsDataBeam = _xsDataInputStrategy.getExperimentalCondition().getBeam()
xsDataSample = _xsDataInputStrategy.getSample()
xsDataDetector = _xsDataInputStrategy.getExperimentalCondition().getDetector()
xsDataGoniostat = _xsDataInputStrategy.getExperimentalCondition().getGoniostat()
xsDataDiffractionPlan = _xsDataInputStrategy.getDiffractionPlan()
xsDataStringBestFileContentDat = _xsDataInputStrategy.getBestFileContentDat()
xsDataStringBestFileContentPar = _xsDataInputStrategy.getBestFileContentPar()
xsDataFileXdsBackgroundImage = _xsDataInputStrategy.getXdsBackgroundImage()
listXSDataStringBestFileContentHKL = _xsDataInputStrategy.getBestFileContentHKL()
xsDataInputBest = XSDataInputBest()
# Sample
xsDataAbsorbedDose = None
xsDataSusceptibility = None
# Could be None if sample has not been set
# It could be not None in case Raddose has calculated an absorbed dose with default sample values
if xsDataSample is not None:
xsDataAbsorbedDose = xsDataSample.getAbsorbedDoseRate()
xsDataSusceptibility = xsDataSample.getSusceptibility()
# crystalShape
# Default value is 1 (We assume that Xtal is smaller than beam)
if xsDataSample.size is not None and xsDataSample.omegaMin is not None:
xsDataInputBest.crystalSize = XSDataSize().parseString(xsDataSample.size.marshal())
xsDataInputBest.omegaMin = xsDataSample.omegaMin
else:
xsDataDoubleCrystalShape = xsDataSample.getShape()
if xsDataDoubleCrystalShape is None:
if (xsDataSample.getSize() is None) or (xsDataBeam.getSize() is None):
xsDataDoubleCrystalShape = XSDataDouble(1)
else:
fCrystalSizeY = xsDataSample.getSize().getY().getValue()
fCrystalSizeZ = xsDataSample.getSize().getZ().getValue()
fDiagonal = math.sqrt(fCrystalSizeY ** 2 + fCrystalSizeZ ** 2)
fBeamSizeY = xsDataBeam.getSize().getY().getValue()
fCrystalShape = None
if fBeamSizeY > fDiagonal:
fCrystalShape = 1.0
else:
fCrystalShape = int(10 * fDiagonal / fBeamSizeY) / 10.0
xsDataDoubleCrystalShape = XSDataDouble(fCrystalShape)
xsDataInputBest.setCrystalShape(xsDataDoubleCrystalShape)
# Radiation damage model parameters
xsDataInputBest.setRadiationDamageModelBeta(xsDataSample.getRadiationDamageModelBeta())
xsDataInputBest.setRadiationDamageModelGamma(xsDataSample.getRadiationDamageModelGamma())
# Could be None if Raddose failed to calculate the absorbed dose
if xsDataAbsorbedDose is not None:
xsDataInputBest.setCrystalAbsorbedDoseRate(xsDataSample.getAbsorbedDoseRate())
xsDataInputBest.setCrystalSusceptibility(xsDataSusceptibility)
# Detector
xsDataInputBest.setDetectorType(xsDataDetector.getType())
# Minimum exposure time per image
xsDataTimeMinExposureTimePerImage = None
if xsDataBeam:
xsDataTimeMinExposureTimePerImage = xsDataBeam.getMinExposureTimePerImage()
if xsDataTimeMinExposureTimePerImage == None:
xsDataTimeMinExposureTimePerImage = xsDataDiffractionPlan.getMinExposureTimePerImage()
xsDataInputBest.setBeamMinExposureTime(xsDataTimeMinExposureTimePerImage)
# Max rotation speed
xsDataAngularSpeedMax = None
if xsDataGoniostat:
xsDataAngularSpeedMax = xsDataGoniostat.getMaxOscillationSpeed()
if xsDataDiffractionPlan and xsDataAngularSpeedMax == None:
xsDataAngularSpeedMax = xsDataDiffractionPlan.getGoniostatMaxOscillationSpeed()
xsDataInputBest.setGoniostatMaxRotationSpeed(xsDataAngularSpeedMax)
# Min rotation width
xsDataAngleMin = None
if xsDataGoniostat:
xsDataAngleMin = xsDataGoniostat.getMinOscillationWidth()
if xsDataDiffractionPlan and xsDataAngleMin == None:
xsDataAngleMin = xsDataDiffractionPlan.getGoniostatMinOscillationWidth()
xsDataInputBest.setGoniostatMinRotationWidth(xsDataAngleMin)
# Other beam parameters
if xsDataBeam:
xsDataInputBest.setBeamExposureTime(xsDataBeam.getExposureTime())
if xsDataBeam.getTransmission():
# Fix for bug 741: if the transmission is zero don't set it and warn the user
fTransmission = xsDataBeam.getTransmission().getValue()
if abs(fTransmission) < 0.1:
EDVerbose.warning(
"Input transmission to BEST ignored because it is zero or close to zero: %f" % fTransmission
)
else:
xsDataInputBest.setTransmission(xsDataBeam.getTransmission())
if xsDataBeam.getApertureSize():
xsDataInputBest.setApertureSize(xsDataBeam.getApertureSize())
if xsDataBeam.size:
xsDataInputBest.setBeamSize(xsDataBeam.size)
if xsDataBeam.flux:
xsDataInputBest.setBeamFlux(xsDataBeam.flux)
# Other diffraction plan parameters
if xsDataDiffractionPlan:
xsDataInputBest.setAimedResolution(xsDataDiffractionPlan.getAimedResolution())
xsDataInputBest.setAimedRedundancy(xsDataDiffractionPlan.getAimedMultiplicity())
xsDataInputBest.setAimedCompleteness(xsDataDiffractionPlan.getAimedCompleteness())
xsDataInputBest.setAimedIOverSigma(xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution())
xsDataInputBest.setBeamMaxExposureTime(xsDataDiffractionPlan.getMaxExposureTimePerDataCollection())
xsDataInputBest.setComplexity(xsDataDiffractionPlan.getComplexity())
xsDataInputBest.setAnomalousData(xsDataDiffractionPlan.getAnomalousData())
xsDataInputBest.setStrategyOption(xsDataDiffractionPlan.getStrategyOption())
xsDataInputBest.setMinTransmission(xsDataDiffractionPlan.getMinTransmission())
xsDataInputBest.setNumberOfCrystalPositions(xsDataDiffractionPlan.getNumberOfPositions())
xsDataInputBest.setDetectorDistanceMin(xsDataDiffractionPlan.getDetectorDistanceMin())
xsDataInputBest.setDetectorDistanceMax(xsDataDiffractionPlan.getDetectorDistanceMax())
xsDataInputBest.setUserDefinedRotationStart(xsDataDiffractionPlan.getUserDefinedRotationStart())
xsDataInputBest.setUserDefinedRotationRange(xsDataDiffractionPlan.getUserDefinedRotationRange())
xsDataInputBest.doseLimit = xsDataDiffractionPlan.doseLimit
xsDataInputBest.rFriedel = xsDataDiffractionPlan.rFriedel
# Best Files
xsDataInputBest.setBestFileContentDat(xsDataStringBestFileContentDat)
xsDataInputBest.setBestFileContentPar(xsDataStringBestFileContentPar)
xsDataInputBest.setBestFileContentHKL(listXSDataStringBestFileContentHKL)
xsDataInputBest.setXdsBackgroundImage(xsDataFileXdsBackgroundImage)
return xsDataInputBest
