def testGenerateXSDataInputBestv1_2(
self, _strFileNameXSDataInputStrategy_reference,
_strFileNameXSDataInputBest_reference):
"""
This method is testing the generation of the XSDataInputBest object given a XSDataIndexingStrategy object.
"""
strReferenceInputFile = os.path.join(
self.strDataPath, _strFileNameXSDataInputStrategy_reference)
strPath = os.path.join(self.strDataPath, strReferenceInputFile)
from XSDataMXv1 import XSDataInputStrategy
xsDataInputStrategy = XSDataInputStrategy.parseFile(strPath)
from EDHandlerXSDataBestv1_2 import EDHandlerXSDataBestv1_2
edHandlerXSDataBestv1_2 = EDHandlerXSDataBestv1_2()
xsDataInputBestv1_2 = edHandlerXSDataBestv1_2.getXSDataInputBest(
xsDataInputStrategy)
strReferencePath = os.path.join(self.strDataPath,
_strFileNameXSDataInputBest_reference)
strXMLInputBestReference = EDUtilsTest.readAndParseFile(
strReferencePath)
EDFactoryPluginStatic.loadModule("XSDataBestv1_2")
from XSDataBestv1_2 import XSDataInputBest
xsDataInputBestReference = XSDataInputBest.parseString(
strXMLInputBestReference)
EDAssert.equal(xsDataInputBestReference.marshal(),
xsDataInputBestv1_2.marshal())
def testGenerateExecutiveSummary(self):
pyStrInputBest = self.readAndParseFile (self.m_edReferenceInputFile)
pyStrResultBest = self.readAndParseFile (self.m_edReferenceResultFile)
from XSDataBestv1_2 import XSDataInputBest
from XSDataBestv1_2 import XSDataResultBest
xsDataInputBest = XSDataInputBest.parseString(pyStrInputBest)
xsDataResultBest = XSDataResultBest.parseString(pyStrResultBest)
edPluginBest = self.createPlugin()
edPluginBest.setDataInput(xsDataInputBest)
edPluginBest.setDataOutput(xsDataResultBest)
edPluginBest.generateExecutiveSummary(edPluginBest)
def testGenerateExecutiveSummary(self):
pyStrInputBest = self.readAndParseFile(self.m_edReferenceInputFile)
pyStrResultBest = self.readAndParseFile(self.m_edReferenceResultFile)
from XSDataBestv1_2 import XSDataInputBest
from XSDataBestv1_2 import XSDataResultBest
xsDataInputBest = XSDataInputBest.parseString(pyStrInputBest)
xsDataResultBest = XSDataResultBest.parseString(pyStrResultBest)
edPluginBest = self.createPlugin()
edPluginBest.setDataInput(xsDataInputBest)
edPluginBest.setDataOutput(xsDataResultBest)
edPluginBest.generateExecutiveSummary(edPluginBest)
def testGenerateXSDataInputBestv1_2(self, _strFileNameXSDataInputStrategy_reference, _strFileNameXSDataInputBest_reference):
"""
This method is testing the generation of the XSDataInputBest object given a XSDataIndexingStrategy object.
"""
strReferenceInputFile = os.path.join(self.strDataPath, _strFileNameXSDataInputStrategy_reference)
strPath = os.path.join(self.strDataPath, strReferenceInputFile)
from XSDataMXv1 import XSDataInputStrategy
xsDataInputStrategy = XSDataInputStrategy.parseFile(strPath)
from EDHandlerXSDataBestv1_2 import EDHandlerXSDataBestv1_2
edHandlerXSDataBestv1_2 = EDHandlerXSDataBestv1_2()
xsDataInputBestv1_2 = edHandlerXSDataBestv1_2.getXSDataInputBest(xsDataInputStrategy)
strReferencePath = os.path.join(self.strDataPath, _strFileNameXSDataInputBest_reference)
strXMLInputBestReference = EDUtilsTest.readAndParseFile(strReferencePath)
EDFactoryPluginStatic.loadModule("XSDataBestv1_2")
from XSDataBestv1_2 import XSDataInputBest
xsDataInputBestReference = XSDataInputBest.parseString(strXMLInputBestReference)
EDAssert.equal(xsDataInputBestReference.marshal(), xsDataInputBestv1_2.marshal())
def testSetDataModelInput(self):
edPluginBest = self.createPlugin()
xsPluginItemGood01 = self.getPluginConfiguration(os.path.join(self.m_pyStrDataPath, "XSConfiguration.xml"))
edPluginBest.setConfiguration(xsPluginItemGood01)
edPluginBest.setScriptExecutable("cat")
edPluginBest.configure()
from XSDataBestv1_2 import XSDataInputBest
xsDataInputBest = XSDataInputBest()
from XSDataCommon import XSDataAbsorbedDoseRate
from XSDataCommon import XSDataDouble
from XSDataCommon import XSDataString
from XSDataCommon import XSDataTime
from XSDataCommon import XSDataFile
from XSDataCommon import XSDataSpeed
from XSDataCommon import XSDataString
from XSDataCommon import XSDataAngle
from XSDataCommon import XSDataBoolean
xsDataInputBest.setCrystalAbsorbedDoseRate(XSDataAbsorbedDoseRate(0.22E+06))
xsDataInputBest.setCrystalShape(XSDataDouble(1))
xsDataInputBest.setCrystalSusceptibility(XSDataDouble(1.5))
xsDataInputBest.setDetectorType(XSDataString("q210-2x"))
xsDataInputBest.setBeamExposureTime(XSDataTime(1))
xsDataInputBest.setBeamMaxExposureTime(XSDataTime(10000))
xsDataInputBest.setBeamMinExposureTime(XSDataTime(0.1))
xsDataInputBest.setGoniostatMinRotationWidth(XSDataAngle(0.1))
xsDataInputBest.setGoniostatMaxRotationSpeed(XSDataSpeed(10))
xsDataInputBest.setAimedResolution(XSDataDouble(2))
xsDataInputBest.setAimedRedundancy(XSDataDouble(6.5))
xsDataInputBest.setAimedCompleteness(XSDataDouble(0.9))
xsDataInputBest.setAimedIOverSigma(XSDataDouble(3))
xsDataInputBest.setComplexity(XSDataString("min"))
xsDataInputBest.setAnomalousData(XSDataBoolean(False))
fileDirectory = edPluginBest.getWorkingDirectory()
bestFileContentDat = EDUtilsFile.readFile(os.path.join(self.m_pyStrDataPath, "bestfile.dat"))
xsDataInputBest.setBestFileContentDat(XSDataString(bestFileContentDat))
bestFileContentPar = EDUtilsFile.readFile(os.path.join(self.m_pyStrDataPath, "bestfile.par"))
xsDataInputBest.setBestFileContentPar(XSDataString(bestFileContentPar))
bestFileContentHKL = EDUtilsFile.readFile(os.path.join(self.m_pyStrDataPath, "bestfile1.hkl"))
xsDataInputBest.addBestFileContentHKL(XSDataString(bestFileContentHKL))
xsDataInputBest.exportToFile(self.m_edObtainedInputFile)
pyStrExpectedInput = self.readAndParseFile (self.m_edReferenceInputFile)
pyStrObtainedInput = self.readAndParseFile (self.m_edObtainedInputFile)
xsDataInputExpected = XSDataInputBest.parseString(pyStrExpectedInput)
xsDataInputObtained = XSDataInputBest.parseString(pyStrObtainedInput)
EDAssert.equal(xsDataInputExpected.marshal(), xsDataInputObtained.marshal())
EDUtilsFile.deleteFile(self.m_edObtainedInputFile)
self.cleanUp(edPluginBest)
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
xdDataAbsorbedDose = 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):
xdDataAbsorbedDose = xsDataSample.getAbsorbedDoseRate()
xsDataSusceptibility = xsDataSample.getSusceptibility()
# crystalShape
# Default value is 1 (We assume that Xtal is smaller than beam)
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)
fBeamSizeX = xsDataBeam.getSize().getX().getValue()
fCrystalShape = None
if fBeamSizeX > fDiagonal:
fCrystalShape = 1.0
else:
fCrystalShape = int(10 * fDiagonal / fBeamSizeX) / 10.0
xsDataDoubleCrystalShape = XSDataDouble(fCrystalShape)
xsDataInputBest.setCrystalShape(xsDataDoubleCrystalShape)
# Could be None if Raddose failed to calculate the absorbed dose
if(xdDataAbsorbedDose 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())
# 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())
# Best Files
xsDataInputBest.setBestFileContentDat(xsDataStringBestFileContentDat)
xsDataInputBest.setBestFileContentPar(xsDataStringBestFileContentPar)
xsDataInputBest.setBestFileContentHKL(listXSDataStringBestFileContentHKL)
xsDataInputBest.setXdsBackgroundImage(xsDataFileXdsBackgroundImage)
return xsDataInputBest
def testSetDataModelInput(self):
edPluginBest = self.createPlugin()
xsPluginItemGood01 = self.getPluginConfiguration(
os.path.join(self.m_pyStrDataPath, "XSConfiguration.xml"))
edPluginBest.setConfiguration(xsPluginItemGood01)
edPluginBest.setScriptExecutable("cat")
edPluginBest.configure()
from XSDataBestv1_2 import XSDataInputBest
xsDataInputBest = XSDataInputBest()
from XSDataCommon import XSDataAbsorbedDoseRate
from XSDataCommon import XSDataDouble
from XSDataCommon import XSDataString
from XSDataCommon import XSDataTime
from XSDataCommon import XSDataFile
from XSDataCommon import XSDataSpeed
from XSDataCommon import XSDataString
from XSDataCommon import XSDataAngle
from XSDataCommon import XSDataBoolean
xsDataInputBest.setCrystalAbsorbedDoseRate(
XSDataAbsorbedDoseRate(0.22E+06))
xsDataInputBest.setCrystalShape(XSDataDouble(1))
xsDataInputBest.setCrystalSusceptibility(XSDataDouble(1.5))
xsDataInputBest.setDetectorType(XSDataString("q210-2x"))
xsDataInputBest.setBeamExposureTime(XSDataTime(1))
xsDataInputBest.setBeamMaxExposureTime(XSDataTime(10000))
xsDataInputBest.setBeamMinExposureTime(XSDataTime(0.1))
xsDataInputBest.setGoniostatMinRotationWidth(XSDataAngle(0.1))
xsDataInputBest.setGoniostatMaxRotationSpeed(XSDataSpeed(10))
xsDataInputBest.setAimedResolution(XSDataDouble(2))
xsDataInputBest.setAimedRedundancy(XSDataDouble(6.5))
xsDataInputBest.setAimedCompleteness(XSDataDouble(0.9))
xsDataInputBest.setAimedIOverSigma(XSDataDouble(3))
xsDataInputBest.setComplexity(XSDataString("min"))
xsDataInputBest.setAnomalousData(XSDataBoolean(False))
fileDirectory = edPluginBest.getWorkingDirectory()
bestFileContentDat = EDUtilsFile.readFile(
os.path.join(self.m_pyStrDataPath, "bestfile.dat"))
xsDataInputBest.setBestFileContentDat(XSDataString(bestFileContentDat))
bestFileContentPar = EDUtilsFile.readFile(
os.path.join(self.m_pyStrDataPath, "bestfile.par"))
xsDataInputBest.setBestFileContentPar(XSDataString(bestFileContentPar))
bestFileContentHKL = EDUtilsFile.readFile(
os.path.join(self.m_pyStrDataPath, "bestfile1.hkl"))
xsDataInputBest.addBestFileContentHKL(XSDataString(bestFileContentHKL))
xsDataInputBest.exportToFile(self.m_edObtainedInputFile)
pyStrExpectedInput = self.readAndParseFile(self.m_edReferenceInputFile)
pyStrObtainedInput = self.readAndParseFile(self.m_edObtainedInputFile)
xsDataInputExpected = XSDataInputBest.parseString(pyStrExpectedInput)
xsDataInputObtained = XSDataInputBest.parseString(pyStrObtainedInput)
EDAssert.equal(xsDataInputExpected.marshal(),
xsDataInputObtained.marshal())
EDUtilsFile.deleteFile(self.m_edObtainedInputFile)
self.cleanUp(edPluginBest)
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)
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)
fBeamSizeX = xsDataBeam.getSize().getX().getValue()
fCrystalShape = None
if fBeamSizeX > fDiagonal:
fCrystalShape = 1.0
else:
fCrystalShape = int(10 * fDiagonal / fBeamSizeX) / 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())
# 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())
# Best Files
xsDataInputBest.setBestFileContentDat(xsDataStringBestFileContentDat)
xsDataInputBest.setBestFileContentPar(xsDataStringBestFileContentPar)
xsDataInputBest.setBestFileContentHKL(listXSDataStringBestFileContentHKL)
xsDataInputBest.setXdsBackgroundImage(xsDataFileXdsBackgroundImage)
return xsDataInputBest