def getTestExperimentalCondition(self):
strPathToTestExperimentalCondition = os.path.join(
self.getPluginTestsDataHome(),
"XSDataExperimentalCondition_test.xml")
strXMLInput = self.readAndParseFile(strPathToTestExperimentalCondition)
xsDataExperimentalCondition = XSDataExperimentalCondition.parseString(
strXMLInput)
return xsDataExperimentalCondition
def generateXSDataIndexingResult(_xsDataResultXDSIndexing, _xsDataExperimentalCondition=None):
xsDataIndexingResult = XSDataIndexingResult()
xsDataIndexingSolutionSelected = XSDataIndexingSolutionSelected()
xsDataCrystalSelected = XSDataCrystal()
# xsDataIndexingSolutionSelected.setNumber(XSDataInteger(iIndex))
# xsDataCellSelected = xsDataLabelitSolution.getUnitCell()
spaceGroupName = EDUtilsSymmetry.getMinimumSymmetrySpaceGroupFromBravaisLattice(_xsDataResultXDSIndexing.bravaisLattice.value)
xsDataCrystalSelected = XSDataCrystal()
xsDataSpaceGroupSelected = XSDataSpaceGroup()
xsDataSpaceGroupSelected.setName(XSDataString(spaceGroupName))
xsDataCrystalSelected.setSpaceGroup(xsDataSpaceGroupSelected)
# xsDataCrystalSelected.setCell(xsDataCellSelected)
xsDataCrystalSelected.setMosaicity(XSDataDouble(_xsDataResultXDSIndexing.mosaicity.value))
xsDataCrystalSelected.setCell(XSDataCell.parseString(_xsDataResultXDSIndexing.unitCell.marshal()))
xsDataIndexingSolutionSelected.setCrystal(xsDataCrystalSelected)
xsDataOrientation = XSDataOrientation()
xsDataOrientation.setMatrixA(_xsDataResultXDSIndexing.getAMatrix())
xsDataOrientation.setMatrixU(_xsDataResultXDSIndexing.getUMatrix())
xsDataIndexingSolutionSelected.setOrientation(xsDataOrientation)
xsDataStatisticsIndexing = XSDataStatisticsIndexing()
if (_xsDataExperimentalCondition is not None):
fBeamPositionXOrig = _xsDataExperimentalCondition.getDetector().getBeamPositionX().getValue()
fBeamPositionYOrig = _xsDataExperimentalCondition.getDetector().getBeamPositionY().getValue()
fBeamPositionXNew = _xsDataResultXDSIndexing.getBeamCentreX().getValue()
fBeamPositionYNew = _xsDataResultXDSIndexing.getBeamCentreY().getValue()
xsDataStatisticsIndexing.setBeamPositionShiftX(XSDataLength(fBeamPositionXOrig - fBeamPositionXNew))
xsDataStatisticsIndexing.setBeamPositionShiftY(XSDataLength(fBeamPositionYOrig - fBeamPositionYNew))
xsDataExperimentalConditionRefined = None
if (_xsDataExperimentalCondition is None):
xsDataExperimentalConditionRefined = XSDataExperimentalCondition()
else:
# Copy the incoming experimental condition
xmlExperimentalCondition = _xsDataExperimentalCondition.marshal()
xsDataExperimentalConditionRefined = XSDataExperimentalCondition.parseString(xmlExperimentalCondition)
xsDataDetector = xsDataExperimentalConditionRefined.getDetector()
if (xsDataDetector is None):
xsDataDetector = XSDataDetector()
xsDataDetector.setBeamPositionX(XSDataLength(_xsDataResultXDSIndexing.getBeamCentreX().value))
xsDataDetector.setBeamPositionY(XSDataLength(_xsDataResultXDSIndexing.getBeamCentreY().value))
xsDataDetector.setDistance(_xsDataResultXDSIndexing.getDistance())
xsDataExperimentalConditionRefined.setDetector(xsDataDetector)
xsDataIndexingSolutionSelected.setExperimentalConditionRefined(xsDataExperimentalConditionRefined)
xsDataIndexingResult.setSelectedSolution(xsDataIndexingSolutionSelected)
return xsDataIndexingResult
def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
self.DEBUG("EDPluginControlGeneratePredictionv10.preProcess...")
xsDataGeneratePredictionInput = self.getDataInput()
xsDataSelectedIndexingSolution = xsDataGeneratePredictionInput.getSelectedIndexingSolution()
xsDataExperimentalConditionRefined = xsDataSelectedIndexingSolution.getExperimentalConditionRefined()
xsDataCollection = xsDataGeneratePredictionInput.getDataCollection()
xsDataSubWedgeList = xsDataCollection.getSubWedge()
# List containing instances of all the generate prediction plugins
self.__listPluginGeneratePrediction = []
# Loop through all subwedges
iIndex = 0
for xsDataSubWedge in xsDataSubWedgeList:
xsDataImageList = xsDataSubWedge.getImage()
# First find the lowest image number
iLowestImageNumber = None
for xsDataImage in xsDataImageList:
iImageNumber = xsDataImage.getNumber().getValue()
if (iLowestImageNumber is None):
iLowestImageNumber = iImageNumber
elif (iImageNumber < iLowestImageNumber):
iLowestImageNumber = iImageNumber
# Then loop through all images in a sub wedge
for xsDataImage in xsDataImageList:
iIndex += 1
edPluginGeneratePrediction = self.loadPlugin(self.__strPluginGeneratePredictionName,
"%s-%02d" % (self.__strPluginGeneratePredictionName, iIndex))
xsDataGeneratePredictionInput = XSDataGeneratePredictionInput()
xsDataGeneratePredictionInput.setSelectedIndexingSolution(XSDataIndexingSolutionSelected.parseString(xsDataSelectedIndexingSolution.marshal()))
xsDataCollectionNew = XSDataCollection()
xsDataSubWedgeNew = XSDataSubWedge()
xsDataSubWedgeNew.addImage(XSDataImage.parseString(xsDataImage.marshal()))
xsDataSubWedgeNew.setExperimentalCondition(XSDataExperimentalCondition.parseString(xsDataSubWedge.getExperimentalCondition().marshal()))
# We must modify the rotationOscillationStart for the new subwedge
xsDataGoniostatNew = xsDataSubWedgeNew.getExperimentalCondition().getGoniostat()
fGoniostatRotationAxisStart = xsDataGoniostatNew.getRotationAxisStart().getValue()
fGonioStatOscillationRange = xsDataGoniostatNew.getOscillationWidth().getValue()
iImageNumber = xsDataImage.getNumber().getValue()
fGoniostatRotationAxisStartNew = fGoniostatRotationAxisStart + (iImageNumber - iLowestImageNumber) * fGonioStatOscillationRange
xsDataGoniostatNew.setRotationAxisStart(XSDataAngle(fGoniostatRotationAxisStartNew))
#
xsDataCollectionNew.addSubWedge(xsDataSubWedgeNew)
xsDataGeneratePredictionInput.setDataCollection(xsDataCollectionNew)
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
xsDataMOSFLMInputGeneratePrediction = EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputGeneratePrediction(xsDataGeneratePredictionInput)
edPluginGeneratePrediction.setDataInput(xsDataMOSFLMInputGeneratePrediction)
self.__listPluginGeneratePrediction.append(edPluginGeneratePrediction)
def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
self.DEBUG("EDPluginControlIntegrationv10.preProcess...")
xsDataIntegrationInput = self.getDataInput()
xsDataSelectedIndexingSolution = xsDataIntegrationInput.getSelectedIndexingSolution()
self.__xsDataExperimentalConditionRefined = xsDataIntegrationInput.getExperimentalConditionRefined()
# To be changed (see bug #40)
if (self.__xsDataExperimentalConditionRefined is None):
self.__xsDataExperimentalConditionRefined = xsDataSelectedIndexingSolution.getExperimentalConditionRefined()
xsDataCollection = xsDataIntegrationInput.getDataCollection()
xsDataSubWedgeList = xsDataCollection.getSubWedge()
self.__edPluginIntegrationList = []
iIndex = 0
for xsDataSubWedge in xsDataSubWedgeList:
iSubWedgeNumber = iIndex
if (xsDataSubWedge.getSubWedgeNumber() is not None):
# Use the incoming subwedge number if it exists
iSubWedgeNumber = xsDataSubWedge.getSubWedgeNumber().getValue()
edPluginIntegration = self.loadPlugin(self.__strPluginIntegrationName)
if (not edPluginIntegration is None):
iIndex += 1
xsDataIntegrationInputSubWedge = XSDataIntegrationInput()
xsDataIntegrationInputSubWedge.setSelectedIndexingSolution(XSDataIndexingSolutionSelected.parseString(xsDataSelectedIndexingSolution.marshal()))
xsDataIntegrationInputSubWedge.setExperimentalConditionRefined(XSDataExperimentalCondition.parseString(self.__xsDataExperimentalConditionRefined.marshal()))
xsDataCollection = XSDataCollection()
xsDataCollection.addSubWedge(xsDataSubWedge)
xsDataIntegrationInputSubWedge.setDataCollection(xsDataCollection)
try:
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
xsDataMOSFLMInputIntegration = EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputIntegration(xsDataIntegrationInputSubWedge)
edPluginIntegration.setDataInput(xsDataMOSFLMInputIntegration)
edPluginIntegration.setBaseName("%s-%02d" % (self.__strPluginIntegrationName, iIndex))
edPluginIntegration.connectSUCCESS(self.doSuccessActionIntegration)
edPluginIntegration.connectFAILURE(self.doFailureActionIntegration)
# Here we store the sub wedge number for use in the results
self.__edPluginIntegrationList.append([iSubWedgeNumber, edPluginIntegration])
except Exception as strErrorMessage:
self.addErrorMessage(strErrorMessage)
self.ERROR(strErrorMessage)
self.setFailure()
else:
strErrorMessage = "EDPluginControlIntegrationv10.preProcess: could not load plugin %s" % self.__strPluginIntegrationName
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
def getXSDataResultStrategy(self, _xsDataResultBest, _xsDataExperimentalCondition, _xsDataSample):
xsDataResultStrategy = XSDataResultStrategy()
#xsDataCollectionRunsBest = _xsDataResultBest.getCollectionRun()
xsDataCollectionPlansBest = _xsDataResultBest.getCollectionPlan()
for xsDataCollectionPlanBest in xsDataCollectionPlansBest:
xsDataCollectionPlan = XSDataCollectionPlan()
xsDataCollectionStrategy = XSDataCollection()
xsDataDoubleTransmission = xsDataCollectionPlanBest.getStrategySummary().getAttenuation()
for xsDataCollectionRunBest in xsDataCollectionPlanBest.getCollectionRun():
xsDataSubWedge = XSDataSubWedge()
strXmlStringDataExperimentalCondition = _xsDataExperimentalCondition.marshal()
xsDataExperimentalCondition = XSDataExperimentalCondition.parseString(strXmlStringDataExperimentalCondition)
xsDataExperimentalCondition.getBeam().setExposureTime(xsDataCollectionRunBest.getExposureTime())
xsDataExperimentalCondition.getBeam().setTransmission(xsDataDoubleTransmission)
xsDataExperimentalCondition.getDetector().setDistance(xsDataCollectionRunBest.getDistance())
xsDataExperimentalCondition.getGoniostat().setRotationAxisStart(xsDataCollectionRunBest.getPhiStart())
xsDataExperimentalCondition.getGoniostat().setOscillationWidth(xsDataCollectionRunBest.getPhiWidth())
fRotationAxisEnd = xsDataCollectionRunBest.getPhiStart().getValue() + xsDataCollectionRunBest.getNumberOfImages().getValue() * xsDataCollectionRunBest.getPhiWidth().getValue()
xsDataExperimentalCondition.getGoniostat().setRotationAxisEnd(XSDataAngle(fRotationAxisEnd))
xsDataSubWedge.setExperimentalCondition(xsDataExperimentalCondition)
xsDataSubWedge.setSubWedgeNumber(xsDataCollectionRunBest.getCollectionRunNumber())
xsDataCollectionStrategy.addSubWedge(xsDataSubWedge)
xsDataCollectionStrategy.setSample(_xsDataSample)
xsDataCollectionPlan.setCollectionStrategy(xsDataCollectionStrategy)
xsDataStrategySummary = xsDataCollectionPlanBest.getStrategySummary()
xsDataCollectionPlan.setStrategySummary(xsDataStrategySummary)
xsDataStatistics = xsDataCollectionPlanBest.getStatisticalPrediction()
xsDataCollectionPlan.setStatistics(xsDataStatistics)
xsDataCollectionPlan.setCollectionPlanNumber(xsDataCollectionPlanBest.getCollectionPlanNumber())
xsDataResultStrategy.addCollectionPlan(xsDataCollectionPlan)
return xsDataResultStrategy
def getXSDataStrategyResult(self, _xsDataBestOutput, _xsDataExperimentalCondition, _xsDataSample):
xsDataStrategyResult = XSDataStrategyResult()
#xsDataCollectionRunsBest = _xsDataBestOutput.getCollectionRun()
xsDataCollectionPlansBest = _xsDataBestOutput.getCollectionPlan()
for xsDataCollectionPlanBest in xsDataCollectionPlansBest:
xsDataCollectionPlan = XSDataCollectionPlan()
xsDataCollectionStrategy = XSDataCollection()
for xsDataCollectionRunBest in xsDataCollectionPlanBest.getCollectionRun():
xsDataSubWedge = XSDataSubWedge()
strXmlStringDataExperimentalCondition = _xsDataExperimentalCondition.marshal()
xsDataExperimentalCondition = XSDataExperimentalCondition.parseString(strXmlStringDataExperimentalCondition)
xsDataExperimentalCondition.getBeam().setExposureTime(xsDataCollectionRunBest.getExposureTime())
xsDataExperimentalCondition.getDetector().setDistance(xsDataCollectionRunBest.getDistance())
xsDataExperimentalCondition.getGoniostat().setRotationAxisStart(xsDataCollectionRunBest.getPhiStart())
xsDataExperimentalCondition.getGoniostat().setOscillationWidth(xsDataCollectionRunBest.getPhiWidth())
fRotationAxisEnd = xsDataCollectionRunBest.getPhiStart().getValue() + xsDataCollectionRunBest.getNumberOfImages().getValue() * xsDataCollectionRunBest.getPhiWidth().getValue()
xsDataExperimentalCondition.getGoniostat().setRotationAxisEnd(XSDataAngle(fRotationAxisEnd))
xsDataSubWedge.setExperimentalCondition(xsDataExperimentalCondition)
xsDataCollectionStrategy.addSubWedge(xsDataSubWedge)
xsDataCollectionStrategy.setSample(_xsDataSample)
xsDataCollectionPlan.setCollectionStrategy(xsDataCollectionStrategy)
xsDataStrategySummary = xsDataCollectionPlanBest.getStrategySummary()
xsDataCollectionPlan.setStrategySummary(xsDataStrategySummary)
xsDataStatistics = xsDataCollectionPlanBest.getStatisticalPrediction()
xsDataCollectionPlan.setStatistics(xsDataStatistics)
xsDataStrategyResult.addCollectionPlan(xsDataCollectionPlan)
return xsDataStrategyResult
def generateXSDataIntegrationSubWedgeResult(
_xsDataMOSFLMOutputIntegration, _xsDataExperimentalCondition=None):
"""
Translation from XSDataMOSFLMOutputIntegration to XSDataIntegrationSubWedgeResult.
"""
EDVerbose.DEBUG(
"EDHandlerXSDataMOSFLMv10.generateXSDataIntegrationInput")
EDFactoryPluginStatic.loadModule("XSDataMOSFLMv10")
xsDataIntegrationSubWedgeResult = XSDataIntegrationSubWedgeResult()
xsDataExperimentalConditionRefined = None
if (_xsDataExperimentalCondition is None):
xsDataExperimentalConditionRefined = XSDataExperimentalCondition()
else:
# Copy the incoming experimental condition
xmlExperimentalCondition = _xsDataExperimentalCondition.marshal()
xsDataExperimentalConditionRefined = XSDataExperimentalCondition.parseString(
xmlExperimentalCondition)
xsDataDetector = xsDataExperimentalConditionRefined.getDetector()
if (xsDataDetector is None):
xsDataDetector = XSDataDetector()
if _xsDataMOSFLMOutputIntegration.getBestfilePar() is not None:
xsDataIntegrationSubWedgeResult.setBestfilePar(
XSDataString(_xsDataMOSFLMOutputIntegration.getBestfilePar().
getValue()))
xsDataIntegrationSubWedgeResult.setBestfileDat(
XSDataString(_xsDataMOSFLMOutputIntegration.getBestfileDat().
getValue()))
xsDataIntegrationSubWedgeResult.setBestfileHKL(
XSDataString(_xsDataMOSFLMOutputIntegration.getBestfileHKL().
getValue()))
xsDataLengthRefinedDistance = _xsDataMOSFLMOutputIntegration.getRefinedDistance(
)
if (xsDataLengthRefinedDistance is not None):
xsDataDetector.setDistance(xsDataLengthRefinedDistance)
xsDataMOSFLMBeamPositionRefined = _xsDataMOSFLMOutputIntegration.getRefinedBeam(
)
if (xsDataMOSFLMBeamPositionRefined is not None):
xsDataDetector.setBeamPositionX(
XSDataLength(
xsDataMOSFLMBeamPositionRefined.getX().getValue()))
xsDataDetector.setBeamPositionY(
XSDataLength(
xsDataMOSFLMBeamPositionRefined.getY().getValue()))
xsDataExperimentalConditionRefined.setDetector(xsDataDetector)
xsDataIntegrationSubWedgeResult.setExperimentalConditionRefined(
xsDataExperimentalConditionRefined)
if (_xsDataMOSFLMOutputIntegration.getGeneratedMTZFile() is not None):
xsDataIntegrationSubWedgeResult.setGeneratedMTZFile(
_xsDataMOSFLMOutputIntegration.getGeneratedMTZFile())
xsDataStatisticsIntegration = XSDataStatisticsIntegration()
if (_xsDataMOSFLMOutputIntegration.getOverallIOverSigma() is not None):
xsDataStatisticsIntegration.setIOverSigmaOverall(
XSDataDouble(_xsDataMOSFLMOutputIntegration.
getOverallIOverSigma().getValue()))
if (_xsDataMOSFLMOutputIntegration.getHighestResolutionIOverSigma()
is not None):
xsDataStatisticsIntegration.setIOverSigmaAtHighestResolution(
XSDataDouble(_xsDataMOSFLMOutputIntegration.
getHighestResolutionIOverSigma().getValue()))
if (_xsDataMOSFLMOutputIntegration.getRMSSpotDeviation() is not None):
xsDataStatisticsIntegration.setRMSSpotDeviation(
XSDataLength(_xsDataMOSFLMOutputIntegration.
getRMSSpotDeviation().getValue()))
if (_xsDataMOSFLMOutputIntegration.getNumberOfBadReflections()
is not None):
xsDataStatisticsIntegration.setNumberOfBadReflections(
XSDataInteger(_xsDataMOSFLMOutputIntegration.
getNumberOfBadReflections().getValue()))
if (_xsDataMOSFLMOutputIntegration.getNumberOfFullyRecordedReflections(
) is not None):
xsDataStatisticsIntegration.setNumberOfFullyRecordedReflections(
XSDataInteger(
_xsDataMOSFLMOutputIntegration.
getNumberOfFullyRecordedReflections().getValue()))
if (_xsDataMOSFLMOutputIntegration.getNumberOfNegativeReflections()
is not None):
xsDataStatisticsIntegration.setNumberOfNegativeReflections(
XSDataInteger(_xsDataMOSFLMOutputIntegration.
getNumberOfNegativeReflections().getValue()))
if (_xsDataMOSFLMOutputIntegration.getNumberOfOverlappedReflections()
is not None):
xsDataStatisticsIntegration.setNumberOfOverlappedReflections(
XSDataInteger(_xsDataMOSFLMOutputIntegration.
getNumberOfOverlappedReflections().getValue()))
if (_xsDataMOSFLMOutputIntegration.getNumberOfPartialReflections()
is not None):
xsDataStatisticsIntegration.setNumberOfPartialReflections(
XSDataInteger(_xsDataMOSFLMOutputIntegration.
getNumberOfPartialReflections().getValue()))
if (_xsDataMOSFLMOutputIntegration.getNumberOfReflectionsGenerated()
is not None):
xsDataStatisticsIntegration.setNumberOfReflectionsGenerated(
XSDataInteger(_xsDataMOSFLMOutputIntegration.
getNumberOfReflectionsGenerated().getValue()))
xsDataIntegrationSubWedgeResult.setStatistics(
xsDataStatisticsIntegration)
xsDataIntegrationSubWedgeResult.setExperimentalConditionRefined(
xsDataExperimentalConditionRefined)
for xsDataMOSFLMIntegrationStatisticsPerResolutionBin in _xsDataMOSFLMOutputIntegration.getStatisticsPerResolutionBin(
):
xsDataStatisticsIntegrationPerResolutionBin = XSDataStatisticsIntegrationPerResolutionBin(
)
if (xsDataMOSFLMIntegrationStatisticsPerResolutionBin.
getMaxResolution() is not None):
xsDataStatisticsIntegrationPerResolutionBin.setMaxResolution(
XSDataDouble(
xsDataMOSFLMIntegrationStatisticsPerResolutionBin.
getMaxResolution().getValue()))
if (xsDataMOSFLMIntegrationStatisticsPerResolutionBin.
getMinResolution() is not None):
xsDataStatisticsIntegrationPerResolutionBin.setMinResolution(
XSDataDouble(
xsDataMOSFLMIntegrationStatisticsPerResolutionBin.
getMinResolution().getValue()))
xsDataStatisticsIntegrationPerResolutionBin.setProfileFitted(
EDHandlerXSDataMOSFLMv10.
generateXSDataIntegrationStatisticsPerReflectionType(
xsDataMOSFLMIntegrationStatisticsPerResolutionBin.
getProfileFitted()))
xsDataStatisticsIntegrationPerResolutionBin.setSummation(
EDHandlerXSDataMOSFLMv10.
generateXSDataIntegrationStatisticsPerReflectionType(
xsDataMOSFLMIntegrationStatisticsPerResolutionBin.
getSummation()))
xsDataIntegrationSubWedgeResult.addStatisticsPerResolutionBin(
xsDataStatisticsIntegrationPerResolutionBin)
xsDataIntegrationSubWedgeResult.setIntegrationLogFile(
_xsDataMOSFLMOutputIntegration.getPathToLogFile())
return xsDataIntegrationSubWedgeResult
def generateXSDataIndexingResult(_xsDataMOSFLMIndexingOutput,
_xsDataExperimentalCondition=None):
"""
Translation from XSDataMOSFLMIndexingOutput to XSDataIndexingResult.
"""
EDVerbose.DEBUG(
"EDHandlerXSDataMOSFLMv10.generateXSDataIndexingOutput")
xsDataMOSFLMBeamPositionRefined = _xsDataMOSFLMIndexingOutput.getRefinedBeam(
)
xsDataMOSFLMBeamPositionShift = _xsDataMOSFLMIndexingOutput.getBeamShift(
)
dDeviationAngular = _xsDataMOSFLMIndexingOutput.getDeviationAngular(
).getValue()
dDeviationPositional = _xsDataMOSFLMIndexingOutput.getDeviationPositional(
).getValue()
dMosaicityEstimation = _xsDataMOSFLMIndexingOutput.getMosaicityEstimation(
).getValue()
dDistanceRefined = _xsDataMOSFLMIndexingOutput.getRefinedDistance(
).getValue()
iSelectedSolution = _xsDataMOSFLMIndexingOutput.getSelectedSolutionNumber(
).getValue()
iSpotsTotal = _xsDataMOSFLMIndexingOutput.getSpotsTotal().getValue()
iSpotsUsed = _xsDataMOSFLMIndexingOutput.getSpotsUsed().getValue()
xsDataCellRefined = _xsDataMOSFLMIndexingOutput.getRefinedNewmat(
).getRefinedCell()
xsDataMatrixA = _xsDataMOSFLMIndexingOutput.getRefinedNewmat(
).getAMatrix()
xsDataMatrixU = _xsDataMOSFLMIndexingOutput.getRefinedNewmat(
).getUMatrix()
strSelectedSpaceGroupName = _xsDataMOSFLMIndexingOutput.getSelectedSolutionSpaceGroup(
).getValue()
iSelectedSpaceGroupNumber = _xsDataMOSFLMIndexingOutput.getSelectedSolutionSpaceGroupNumber(
).getValue()
xsDataIndexingResult = XSDataIndexingResult()
xsDataIndexingSolutionSelected = None
for possibleSolutions in _xsDataMOSFLMIndexingOutput.getPossibleSolutions(
):
xsDataCrystal = XSDataCrystal()
xsDataSpaceGroup = XSDataSpaceGroup()
xsDataSpaceGroup.setName(
XSDataString(possibleSolutions.getLattice().getValue()))
xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
xsDataCrystal.setCell(possibleSolutions.getCell())
xsDataIndexingSolution = XSDataIndexingSolution()
xsDataIndexingSolution.setCrystal(xsDataCrystal)
iIndex = possibleSolutions.getIndex().getValue()
xsDataIndexingSolution.setNumber(XSDataInteger(iIndex))
xsDataIndexingSolution.setPenalty(
XSDataFloat(possibleSolutions.getPenalty().getValue()))
xsDataIndexingResult.addSolution(xsDataIndexingSolution)
if (iIndex == iSelectedSolution):
xsDataIndexingSolutionSelected = XSDataIndexingSolutionSelected(
)
xsDataIndexingSolutionSelected.setNumber(XSDataInteger(iIndex))
xsDataIndexingSolutionSelected.setPenalty(
XSDataFloat(possibleSolutions.getPenalty().getValue()))
xsDataCrystalSelected = XSDataCrystal()
xsDataSpaceGroupSelected = XSDataSpaceGroup()
xsDataSpaceGroupSelected.setName(
XSDataString(strSelectedSpaceGroupName))
xsDataSpaceGroupSelected.setITNumber(
XSDataInteger(iSelectedSpaceGroupNumber))
xsDataCrystalSelected.setSpaceGroup(xsDataSpaceGroupSelected)
xsDataCrystalSelected.setCell(xsDataCellRefined)
xsDataCrystalSelected.setMosaicity(XSDataDouble(dMosaicityEstimation))
xsDataIndexingSolutionSelected.setCrystal(xsDataCrystalSelected)
xsDataOrientation = XSDataOrientation()
xsDataOrientation.setMatrixA(xsDataMatrixA)
xsDataOrientation.setMatrixU(xsDataMatrixU)
xsDataIndexingSolutionSelected.setOrientation(xsDataOrientation)
xsDataStatisticsIndexing = XSDataStatisticsIndexing()
xsDataStatisticsIndexing.setBeamPositionShiftX(
XSDataLength(xsDataMOSFLMBeamPositionShift.getX().getValue()))
xsDataStatisticsIndexing.setBeamPositionShiftY(
XSDataLength(xsDataMOSFLMBeamPositionShift.getY().getValue()))
xsDataStatisticsIndexing.setSpotDeviationAngular(
XSDataAngle(dDeviationAngular))
xsDataStatisticsIndexing.setSpotDeviationPositional(
XSDataLength(dDeviationPositional))
xsDataStatisticsIndexing.setSpotsUsed(XSDataInteger(iSpotsUsed))
xsDataStatisticsIndexing.setSpotsTotal(XSDataInteger(iSpotsTotal))
xsDataIndexingSolutionSelected.setStatistics(xsDataStatisticsIndexing)
xsDataExperimentalConditionRefined = None
if (_xsDataExperimentalCondition is None):
xsDataExperimentalConditionRefined = XSDataExperimentalCondition()
else:
# Copy the incoming experimental condition
xmlExperimentalCondition = _xsDataExperimentalCondition.marshal()
xsDataExperimentalConditionRefined = XSDataExperimentalCondition.parseString(
xmlExperimentalCondition)
xsDataDetector = xsDataExperimentalConditionRefined.getDetector()
if (xsDataDetector is None):
xsDataDetector = XSDataDetector()
xsDataDetector.setBeamPositionX(
XSDataLength(xsDataMOSFLMBeamPositionRefined.getX().getValue()))
xsDataDetector.setBeamPositionY(
XSDataLength(xsDataMOSFLMBeamPositionRefined.getY().getValue()))
xsDataDetector.setDistance(XSDataLength(dDistanceRefined))
xsDataExperimentalConditionRefined.setDetector(xsDataDetector)
xsDataIndexingSolutionSelected.setExperimentalConditionRefined(
xsDataExperimentalConditionRefined)
xsDataIndexingResult.setSelectedSolution(
xsDataIndexingSolutionSelected)
xsDataIndexingResult.setIndexingLogFile(
_xsDataMOSFLMIndexingOutput.getPathToLogFile())
return xsDataIndexingResult
def getXSDataResultStrategy(self, _xsDataResultBest,
_xsDataExperimentalCondition, _xsDataSample):
xsDataResultStrategy = XSDataResultStrategy()
listXSDataBestCollectionPlan = _xsDataResultBest.getCollectionPlan()
for xsDataBestCollectionPlan in listXSDataBestCollectionPlan:
xsDataCollectionPlan = XSDataCollectionPlan()
xsDataCollectionStrategy = XSDataCollection()
xsDataBestStrategySummary = xsDataBestCollectionPlan.getStrategySummary(
)
xsDataDoubleTransmission = xsDataBestStrategySummary.getTransmission(
)
for xsDataBestCollectionRun in xsDataBestCollectionPlan.getCollectionRun(
):
xsDataSubWedge = XSDataSubWedge()
strXmlStringDataExperimentalCondition = _xsDataExperimentalCondition.marshal(
)
xsDataExperimentalCondition = XSDataExperimentalCondition.parseString(
strXmlStringDataExperimentalCondition)
xsDataExperimentalCondition.getBeam().setExposureTime(
xsDataBestCollectionRun.getExposureTime())
if (xsDataBestCollectionRun.getTransmission() is None):
xsDataExperimentalCondition.getBeam().setTransmission(
xsDataDoubleTransmission)
else:
xsDataExperimentalCondition.getBeam().setTransmission(
xsDataBestCollectionRun.getTransmission())
xsDataExperimentalCondition.getDetector().setDistance(
xsDataBestStrategySummary.getDistance())
xsDataExperimentalCondition.getGoniostat(
).setRotationAxisStart(xsDataBestCollectionRun.getPhiStart())
xsDataExperimentalCondition.getGoniostat().setOscillationWidth(
xsDataBestCollectionRun.getPhiWidth())
fRotationAxisEnd = xsDataBestCollectionRun.getPhiStart(
).getValue(
) + xsDataBestCollectionRun.getNumberOfImages().getValue(
) * xsDataBestCollectionRun.getPhiWidth().getValue()
xsDataExperimentalCondition.getGoniostat().setRotationAxisEnd(
XSDataAngle(fRotationAxisEnd))
xsDataSubWedge.setExperimentalCondition(
xsDataExperimentalCondition)
xsDataSubWedge.setSubWedgeNumber(
xsDataBestCollectionRun.getCollectionRunNumber())
if xsDataBestCollectionRun.getCrystalPosition():
xsDataSubWedge.setAction(
XSDataString("Crystal position: %d" %
xsDataBestCollectionRun.
getCrystalPosition().getValue()))
else:
xsDataSubWedge.setAction(
xsDataBestCollectionRun.getAction())
xsDataCollectionStrategy.addSubWedge(xsDataSubWedge)
xsDataCollectionStrategy.setSample(_xsDataSample)
xsDataCollectionPlan.setCollectionStrategy(
xsDataCollectionStrategy)
xsDataStrategySummary = XSDataStrategySummary()
xsDataStrategySummary.setCompleteness(
xsDataBestStrategySummary.getCompleteness())
xsDataStrategySummary.setISigma(
xsDataBestStrategySummary.getISigma())
xsDataStrategySummary.setRankingResolution(
xsDataBestStrategySummary.getRankingResolution())
xsDataStrategySummary.setRedundancy(
xsDataBestStrategySummary.getRedundancy())
xsDataStrategySummary.setResolution(
xsDataBestStrategySummary.getResolution())
xsDataStrategySummary.setResolutionReasoning(
xsDataBestStrategySummary.getResolutionReasoning())
xsDataStrategySummary.setTotalDataCollectionTime(
xsDataBestStrategySummary.getTotalDataCollectionTime())
xsDataStrategySummary.setTotalExposureTime(
xsDataBestStrategySummary.getTotalExposureTime())
xsDataCollectionPlan.setStrategySummary(xsDataStrategySummary)
if xsDataBestCollectionPlan.getStatisticalPrediction() is not None:
xsDataStatisticsStrategy = XSDataStatisticsStrategy.parseString(
xsDataBestCollectionPlan.getStatisticalPrediction(
).marshal())
xsDataCollectionPlan.setStatistics(xsDataStatisticsStrategy)
xsDataCollectionPlan.setCollectionPlanNumber(
xsDataBestCollectionPlan.getCollectionPlanNumber())
xsDataResultStrategy.addCollectionPlan(xsDataCollectionPlan)
if _xsDataResultBest.getPathToLogFile() != None:
xsDataResultStrategy.setBestLogFile(
_xsDataResultBest.getPathToLogFile())
return xsDataResultStrategy
def generateXSDataIndexingResult(_xsDataLabelitScreenOutput, _xsDataLabelitMosflmScriptsOutput, \
_xsDataExperimentalCondition=None):
EDVerbose.DEBUG(
"EDHandlerXSDataLabelitv1_1.generateXSDataIndexingOutput")
iSelectedSolutionNumber = _xsDataLabelitScreenOutput.getSelectedSolutionNumber(
).getValue()
xsDataIndexingResult = XSDataIndexingResult()
xsDataIndexingSolutionSelected = None
for xsDataLabelitSolution in _xsDataLabelitScreenOutput.getLabelitScreenSolution(
):
xsDataCrystal = XSDataCrystal()
xsDataSpaceGroup = XSDataSpaceGroup()
edStringSpaceGroupName = EDUtilsSymmetry.getMinimumSymmetrySpaceGroupFromBravaisLattice(
xsDataLabelitSolution.getBravaisLattice().getValue())
xsDataSpaceGroup.setName(XSDataString(edStringSpaceGroupName))
xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
xsDataCrystal.setCell(xsDataLabelitSolution.getUnitCell())
xsDataIndexingSolution = XSDataIndexingSolution()
xsDataIndexingSolution.setCrystal(xsDataCrystal)
iIndex = xsDataLabelitSolution.getSolutionNumber().getValue()
xsDataIndexingSolution.setNumber(XSDataInteger(iIndex))
xsDataIndexingResult.addSolution(xsDataIndexingSolution)
if (iIndex == iSelectedSolutionNumber):
xsDataIndexingSolutionSelected = XSDataIndexingSolutionSelected(
)
xsDataIndexingSolutionSelected.setNumber(XSDataInteger(iIndex))
edStringSelectedSpaceGroupName = edStringSpaceGroupName
xsDataCellSelected = xsDataLabelitSolution.getUnitCell()
fRmsdSelected = xsDataLabelitSolution.getRmsd().getValue()
iNumberOfSpotsSelected = xsDataLabelitSolution.getNumberOfSpots(
).getValue()
xsDataCrystalSelected = XSDataCrystal()
xsDataSpaceGroupSelected = XSDataSpaceGroup()
xsDataSpaceGroupSelected.setName(
XSDataString(edStringSelectedSpaceGroupName))
#xsDataSpaceGroupSelected.setITNumber( XSDataInteger( iSelectedSpaceGroupNumber ) )
xsDataCrystalSelected.setSpaceGroup(xsDataSpaceGroupSelected)
xsDataCrystalSelected.setCell(xsDataCellSelected)
xsDataCrystalSelected.setMosaicity(
XSDataDouble(_xsDataLabelitScreenOutput.getMosaicity().getValue()))
xsDataIndexingSolutionSelected.setCrystal(xsDataCrystalSelected)
xsDataOrientation = XSDataOrientation()
xsDataOrientation.setMatrixA(
_xsDataLabelitMosflmScriptsOutput.getAMatrix())
xsDataOrientation.setMatrixU(
_xsDataLabelitMosflmScriptsOutput.getUMatrix())
xsDataIndexingSolutionSelected.setOrientation(xsDataOrientation)
xsDataStatisticsIndexing = XSDataStatisticsIndexing()
if (_xsDataExperimentalCondition is not None):
fBeamPositionXOrig = _xsDataExperimentalCondition.getDetector(
).getBeamPositionX().getValue()
fBeamPositionYOrig = _xsDataExperimentalCondition.getDetector(
).getBeamPositionY().getValue()
fBeamPositionXNew = _xsDataLabelitScreenOutput.getBeamCentreX(
).getValue()
fBeamPositionYNew = _xsDataLabelitScreenOutput.getBeamCentreY(
).getValue()
xsDataStatisticsIndexing.setBeamPositionShiftX(
XSDataLength(fBeamPositionXOrig - fBeamPositionXNew))
xsDataStatisticsIndexing.setBeamPositionShiftY(
XSDataLength(fBeamPositionYOrig - fBeamPositionYNew))
#xsDataStatisticsIndexing.setSpotDeviXSDataLength( dDistanceRefinedationAngular( XSDataAngle( dDeviationAngular ) )
xsDataStatisticsIndexing.setSpotDeviationPositional(
XSDataLength(fRmsdSelected))
xsDataStatisticsIndexing.setSpotsUsed(
XSDataInteger(iNumberOfSpotsSelected))
xsDataStatisticsIndexing.setSpotsTotal(
XSDataInteger(iNumberOfSpotsSelected))
xsDataIndexingSolutionSelected.setStatistics(xsDataStatisticsIndexing)
xsDataExperimentalConditionRefined = None
if (_xsDataExperimentalCondition is None):
xsDataExperimentalConditionRefined = XSDataExperimentalCondition()
else:
# Copy the incoming experimental condition
xmlExperimentalCondition = _xsDataExperimentalCondition.marshal()
xsDataExperimentalConditionRefined = XSDataExperimentalCondition.parseString(
xmlExperimentalCondition)
xsDataDetector = xsDataExperimentalConditionRefined.getDetector()
if (xsDataDetector is None):
xsDataDetector = XSDataDetector()
xsDataDetector.setBeamPositionX(
_xsDataLabelitScreenOutput.getBeamCentreX())
xsDataDetector.setBeamPositionY(
_xsDataLabelitScreenOutput.getBeamCentreY())
xsDataDetector.setDistance(_xsDataLabelitScreenOutput.getDistance())
xsDataExperimentalConditionRefined.setDetector(xsDataDetector)
xsDataIndexingSolutionSelected.setExperimentalConditionRefined(
xsDataExperimentalConditionRefined)
xsDataIndexingResult.setSelectedSolution(
xsDataIndexingSolutionSelected)
xsDataIndexingResult.setIndexingLogFile(
_xsDataLabelitScreenOutput.getPathToLogFile())
return xsDataIndexingResult
def generateXSDataIndexingResult(_xsDataResultLabelitIndexing, _xsDataExperimentalCondition=None):
EDVerbose.DEBUG("EDHandlerXSDataLabelitv1_1.generateXSDataIndexingOutput")
xsDataLabelitScreenOutput = _xsDataResultLabelitIndexing.screenOutput
xsDataLabelitMosflmScriptsOutput = _xsDataResultLabelitIndexing.mosflmScriptsOutput
iSelectedSolutionNumber = xsDataLabelitScreenOutput.getSelectedSolutionNumber().getValue()
xsDataIndexingResult = XSDataIndexingResult()
xsDataIndexingSolutionSelected = None
for xsDataLabelitSolution in xsDataLabelitScreenOutput.getLabelitScreenSolution():
xsDataCrystal = XSDataCrystal()
xsDataSpaceGroup = XSDataSpaceGroup()
edStringSpaceGroupName = EDUtilsSymmetry.getMinimumSymmetrySpaceGroupFromBravaisLattice(xsDataLabelitSolution.getBravaisLattice().getValue())
xsDataSpaceGroup.setName(XSDataString(edStringSpaceGroupName))
xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
xsDataCrystal.setCell(xsDataLabelitSolution.getUnitCell())
xsDataIndexingSolution = XSDataIndexingSolution()
xsDataIndexingSolution.setCrystal(xsDataCrystal)
iIndex = xsDataLabelitSolution.getSolutionNumber().getValue()
xsDataIndexingSolution.setNumber(XSDataInteger(iIndex))
xsDataIndexingResult.addSolution(xsDataIndexingSolution)
if (iIndex == iSelectedSolutionNumber):
xsDataIndexingSolutionSelected = XSDataIndexingSolutionSelected()
xsDataIndexingSolutionSelected.setNumber(XSDataInteger(iIndex))
edStringSelectedSpaceGroupName = edStringSpaceGroupName
xsDataCellSelected = xsDataLabelitSolution.getUnitCell()
fRmsdSelected = xsDataLabelitSolution.getRmsd().getValue()
iNumberOfSpotsSelected = xsDataLabelitSolution.getNumberOfSpots().getValue()
xsDataCrystalSelected = XSDataCrystal()
xsDataSpaceGroupSelected = XSDataSpaceGroup()
xsDataSpaceGroupSelected.setName(XSDataString(edStringSelectedSpaceGroupName))
xsDataSpaceGroupSelected.setITNumber(XSDataInteger(EDUtilsSymmetry.getITNumberFromSpaceGroupName(edStringSelectedSpaceGroupName)))
xsDataCrystalSelected.setSpaceGroup(xsDataSpaceGroupSelected)
xsDataCrystalSelected.setCell(xsDataCellSelected)
xsDataCrystalSelected.setMosaicity(XSDataDouble(xsDataLabelitScreenOutput.getMosaicity().getValue()))
xsDataIndexingSolutionSelected.setCrystal(xsDataCrystalSelected)
xsDataOrientation = XSDataOrientation()
xsDataOrientation.setMatrixA(xsDataLabelitMosflmScriptsOutput.getAMatrix())
xsDataOrientation.setMatrixU(xsDataLabelitMosflmScriptsOutput.getUMatrix())
xsDataIndexingSolutionSelected.setOrientation(xsDataOrientation)
xsDataStatisticsIndexing = XSDataStatisticsIndexing()
if (_xsDataExperimentalCondition is not None):
fBeamPositionXOrig = _xsDataExperimentalCondition.getDetector().getBeamPositionX().getValue()
fBeamPositionYOrig = _xsDataExperimentalCondition.getDetector().getBeamPositionY().getValue()
fBeamPositionXNew = xsDataLabelitScreenOutput.getBeamCentreX().getValue()
fBeamPositionYNew = xsDataLabelitScreenOutput.getBeamCentreY().getValue()
xsDataStatisticsIndexing.setBeamPositionShiftX(XSDataLength(fBeamPositionXOrig - fBeamPositionXNew))
xsDataStatisticsIndexing.setBeamPositionShiftY(XSDataLength(fBeamPositionYOrig - fBeamPositionYNew))
# xsDataStatisticsIndexing.setSpotDeviXSDataLength( dDistanceRefinedationAngular( XSDataAngle( dDeviationAngular ) )
xsDataStatisticsIndexing.setSpotDeviationPositional(XSDataLength(fRmsdSelected))
xsDataStatisticsIndexing.setSpotsUsed(XSDataInteger(iNumberOfSpotsSelected))
xsDataStatisticsIndexing.setSpotsTotal(XSDataInteger(iNumberOfSpotsSelected))
xsDataIndexingSolutionSelected.setStatistics(xsDataStatisticsIndexing)
xsDataExperimentalConditionRefined = None
if (_xsDataExperimentalCondition is None):
xsDataExperimentalConditionRefined = XSDataExperimentalCondition()
else:
# Copy the incoming experimental condition
xmlExperimentalCondition = _xsDataExperimentalCondition.marshal()
xsDataExperimentalConditionRefined = XSDataExperimentalCondition.parseString(xmlExperimentalCondition)
xsDataDetector = xsDataExperimentalConditionRefined.getDetector()
if (xsDataDetector is None):
xsDataDetector = XSDataDetector()
xsDataDetector.setBeamPositionX(xsDataLabelitScreenOutput.getBeamCentreX())
xsDataDetector.setBeamPositionY(xsDataLabelitScreenOutput.getBeamCentreY())
xsDataDetector.setDistance(xsDataLabelitScreenOutput.getDistance())
xsDataExperimentalConditionRefined.setDetector(xsDataDetector)
xsDataIndexingSolutionSelected.setExperimentalConditionRefined(xsDataExperimentalConditionRefined)
xsDataIndexingResult.setSelectedSolution(xsDataIndexingSolutionSelected)
xsDataIndexingResult.setIndexingLogFile(xsDataLabelitScreenOutput.getPathToLogFile())
return xsDataIndexingResult
def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
self.DEBUG("EDPluginControlIntegrationv10.preProcess...")
xsDataIntegrationInput = self.getDataInput()
xsDataSelectedIndexingSolution = xsDataIntegrationInput.getSelectedIndexingSolution(
)
self.__xsDataExperimentalConditionRefined = xsDataIntegrationInput.getExperimentalConditionRefined(
)
# To be changed (see bug #40)
if (self.__xsDataExperimentalConditionRefined is None):
self.__xsDataExperimentalConditionRefined = xsDataSelectedIndexingSolution.getExperimentalConditionRefined(
)
xsDataCollection = xsDataIntegrationInput.getDataCollection()
xsDataSubWedgeList = xsDataCollection.getSubWedge()
self.__edPluginIntegrationList = []
iIndex = 0
for xsDataSubWedge in xsDataSubWedgeList:
iSubWedgeNumber = iIndex
if (xsDataSubWedge.getSubWedgeNumber() is not None):
# Use the incoming subwedge number if it exists
iSubWedgeNumber = xsDataSubWedge.getSubWedgeNumber().getValue()
edPluginIntegration = self.loadPlugin(
self.__strPluginIntegrationName)
if (not edPluginIntegration is None):
iIndex += 1
xsDataIntegrationInputSubWedge = XSDataIntegrationInput()
xsDataIntegrationInputSubWedge.setSelectedIndexingSolution(
XSDataIndexingSolutionSelected.parseString(
xsDataSelectedIndexingSolution.marshal()))
xsDataIntegrationInputSubWedge.setExperimentalConditionRefined(
XSDataExperimentalCondition.parseString(
self.__xsDataExperimentalConditionRefined.marshal()))
xsDataCollection = XSDataCollection()
xsDataCollection.addSubWedge(xsDataSubWedge)
xsDataIntegrationInputSubWedge.setDataCollection(
xsDataCollection)
try:
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
xsDataMOSFLMInputIntegration = EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputIntegration(
xsDataIntegrationInputSubWedge)
edPluginIntegration.setDataInput(
xsDataMOSFLMInputIntegration)
edPluginIntegration.setBaseName(
"%s-%02d" % (self.__strPluginIntegrationName, iIndex))
edPluginIntegration.connectSUCCESS(
self.doSuccessActionIntegration)
edPluginIntegration.connectFAILURE(
self.doFailureActionIntegration)
# Here we store the sub wedge number for use in the results
self.__edPluginIntegrationList.append(
[iSubWedgeNumber, edPluginIntegration])
except Exception as strErrorMessage:
self.addErrorMessage(strErrorMessage)
self.ERROR(strErrorMessage)
self.setFailure()
else:
strErrorMessage = "EDPluginControlIntegrationv10.preProcess: could not load plugin %s" % self.__strPluginIntegrationName
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
def generateXSDataIndexingResult(_xsDataMOSFLMIndexingOutput, _xsDataExperimentalCondition=None):
"""
Translation from XSDataMOSFLMIndexingOutput to XSDataIndexingResult.
"""
EDVerbose.DEBUG("EDHandlerXSDataMOSFLMv10.generateXSDataIndexingOutput")
xsDataMOSFLMBeamPositionRefined = _xsDataMOSFLMIndexingOutput.getRefinedBeam()
xsDataMOSFLMBeamPositionShift = _xsDataMOSFLMIndexingOutput.getBeamShift()
dDeviationAngular = _xsDataMOSFLMIndexingOutput.getDeviationAngular().getValue()
dDeviationPositional = _xsDataMOSFLMIndexingOutput.getDeviationPositional().getValue()
dMosaicityEstimation = _xsDataMOSFLMIndexingOutput.getMosaicityEstimation().getValue()
dDistanceRefined = _xsDataMOSFLMIndexingOutput.getRefinedDistance().getValue()
iSelectedSolution = _xsDataMOSFLMIndexingOutput.getSelectedSolutionNumber().getValue()
iSpotsTotal = _xsDataMOSFLMIndexingOutput.getSpotsTotal().getValue()
iSpotsUsed = _xsDataMOSFLMIndexingOutput.getSpotsUsed().getValue()
xsDataCellRefined = _xsDataMOSFLMIndexingOutput.getRefinedNewmat().getRefinedCell()
xsDataMatrixA = _xsDataMOSFLMIndexingOutput.getRefinedNewmat().getAMatrix()
xsDataMatrixU = _xsDataMOSFLMIndexingOutput.getRefinedNewmat().getUMatrix()
strSelectedSpaceGroupName = _xsDataMOSFLMIndexingOutput.getSelectedSolutionSpaceGroup().getValue()
iSelectedSpaceGroupNumber = _xsDataMOSFLMIndexingOutput.getSelectedSolutionSpaceGroupNumber().getValue()
xsDataIndexingResult = XSDataIndexingResult()
xsDataIndexingSolutionSelected = None
for possibleSolutions in _xsDataMOSFLMIndexingOutput.getPossibleSolutions():
xsDataCrystal = XSDataCrystal()
xsDataSpaceGroup = XSDataSpaceGroup()
xsDataSpaceGroup.setName(XSDataString(possibleSolutions.getLattice().getValue()))
xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
xsDataCrystal.setCell(possibleSolutions.getCell())
xsDataIndexingSolution = XSDataIndexingSolution()
xsDataIndexingSolution.setCrystal(xsDataCrystal)
iIndex = possibleSolutions.getIndex().getValue()
xsDataIndexingSolution.setNumber(XSDataInteger(iIndex))
xsDataIndexingSolution.setPenalty(XSDataFloat(possibleSolutions.getPenalty().getValue()))
xsDataIndexingResult.addSolution(xsDataIndexingSolution)
if (iIndex == iSelectedSolution):
xsDataIndexingSolutionSelected = XSDataIndexingSolutionSelected()
xsDataIndexingSolutionSelected.setNumber(XSDataInteger(iIndex))
xsDataIndexingSolutionSelected.setPenalty(XSDataFloat(possibleSolutions.getPenalty().getValue()))
xsDataCrystalSelected = XSDataCrystal()
xsDataSpaceGroupSelected = XSDataSpaceGroup()
xsDataSpaceGroupSelected.setName(XSDataString(strSelectedSpaceGroupName))
xsDataSpaceGroupSelected.setITNumber(XSDataInteger(iSelectedSpaceGroupNumber))
xsDataCrystalSelected.setSpaceGroup(xsDataSpaceGroupSelected)
xsDataCrystalSelected.setCell(xsDataCellRefined)
xsDataCrystalSelected.setMosaicity(XSDataDouble(dMosaicityEstimation))
xsDataIndexingSolutionSelected.setCrystal(xsDataCrystalSelected)
xsDataOrientation = XSDataOrientation()
xsDataOrientation.setMatrixA(xsDataMatrixA)
xsDataOrientation.setMatrixU(xsDataMatrixU)
xsDataIndexingSolutionSelected.setOrientation(xsDataOrientation)
xsDataStatisticsIndexing = XSDataStatisticsIndexing()
xsDataStatisticsIndexing.setBeamPositionShiftX(XSDataLength(xsDataMOSFLMBeamPositionShift.getX().getValue()))
xsDataStatisticsIndexing.setBeamPositionShiftY(XSDataLength(xsDataMOSFLMBeamPositionShift.getY().getValue()))
xsDataStatisticsIndexing.setSpotDeviationAngular(XSDataAngle(dDeviationAngular))
xsDataStatisticsIndexing.setSpotDeviationPositional(XSDataLength(dDeviationPositional))
xsDataStatisticsIndexing.setSpotsUsed(XSDataInteger(iSpotsUsed))
xsDataStatisticsIndexing.setSpotsTotal(XSDataInteger(iSpotsTotal))
xsDataIndexingSolutionSelected.setStatistics(xsDataStatisticsIndexing)
xsDataExperimentalConditionRefined = None
if (_xsDataExperimentalCondition is None):
xsDataExperimentalConditionRefined = XSDataExperimentalCondition()
else:
# Copy the incoming experimental condition
xmlExperimentalCondition = _xsDataExperimentalCondition.marshal()
xsDataExperimentalConditionRefined = XSDataExperimentalCondition.parseString(xmlExperimentalCondition)
xsDataDetector = xsDataExperimentalConditionRefined.getDetector()
if (xsDataDetector is None):
xsDataDetector = XSDataDetector()
xsDataDetector.setBeamPositionX(XSDataLength(xsDataMOSFLMBeamPositionRefined.getX().getValue()))
xsDataDetector.setBeamPositionY(XSDataLength(xsDataMOSFLMBeamPositionRefined.getY().getValue()))
xsDataDetector.setDistance(XSDataLength(dDistanceRefined))
xsDataExperimentalConditionRefined.setDetector(xsDataDetector)
xsDataIndexingSolutionSelected.setExperimentalConditionRefined(xsDataExperimentalConditionRefined)
xsDataIndexingResult.setSelectedSolution(xsDataIndexingSolutionSelected)
return xsDataIndexingResult
def getXSDataResultStrategy(self, _xsDataResultBest, _xsDataExperimentalCondition, _xsDataSample):
xsDataResultStrategy = XSDataResultStrategy()
listXSDataBestCollectionPlan = _xsDataResultBest.getCollectionPlan()
for xsDataBestCollectionPlan in listXSDataBestCollectionPlan:
xsDataCollectionPlan = XSDataCollectionPlan()
xsDataCollectionStrategy = XSDataCollection()
xsDataBestStrategySummary = xsDataBestCollectionPlan.getStrategySummary()
xsDataDoubleTransmission = xsDataBestStrategySummary.getTransmission()
for xsDataBestCollectionRun in xsDataBestCollectionPlan.getCollectionRun():
xsDataSubWedge = XSDataSubWedge()
strXmlStringDataExperimentalCondition = _xsDataExperimentalCondition.marshal()
xsDataExperimentalCondition = XSDataExperimentalCondition.parseString(
strXmlStringDataExperimentalCondition
)
xsDataExperimentalCondition.getBeam().setExposureTime(xsDataBestCollectionRun.getExposureTime())
if xsDataBestCollectionRun.getTransmission() is None:
xsDataExperimentalCondition.getBeam().setTransmission(xsDataDoubleTransmission)
else:
xsDataExperimentalCondition.getBeam().setTransmission(xsDataBestCollectionRun.getTransmission())
xsDataExperimentalCondition.getDetector().setDistance(xsDataBestStrategySummary.getDistance())
xsDataExperimentalCondition.getGoniostat().setRotationAxisStart(xsDataBestCollectionRun.getPhiStart())
xsDataExperimentalCondition.getGoniostat().setOscillationWidth(xsDataBestCollectionRun.getPhiWidth())
fRotationAxisEnd = (
xsDataBestCollectionRun.getPhiStart().getValue()
+ xsDataBestCollectionRun.getNumberOfImages().getValue()
* xsDataBestCollectionRun.getPhiWidth().getValue()
)
xsDataExperimentalCondition.getGoniostat().setRotationAxisEnd(XSDataAngle(fRotationAxisEnd))
xsDataSubWedge.setExperimentalCondition(xsDataExperimentalCondition)
xsDataSubWedge.setSubWedgeNumber(xsDataBestCollectionRun.getCollectionRunNumber())
if xsDataBestCollectionRun.getCrystalPosition():
xsDataSubWedge.setAction(
XSDataString("Crystal position: %d" % xsDataBestCollectionRun.getCrystalPosition().getValue())
)
else:
xsDataSubWedge.setAction(xsDataBestCollectionRun.getAction())
xsDataCollectionStrategy.addSubWedge(xsDataSubWedge)
xsDataCollectionStrategy.setSample(_xsDataSample)
xsDataCollectionPlan.setCollectionStrategy(xsDataCollectionStrategy)
xsDataStrategySummary = XSDataStrategySummary()
xsDataStrategySummary.setCompleteness(xsDataBestStrategySummary.getCompleteness())
xsDataStrategySummary.setISigma(xsDataBestStrategySummary.getISigma())
xsDataStrategySummary.setRankingResolution(xsDataBestStrategySummary.getRankingResolution())
xsDataStrategySummary.setRedundancy(xsDataBestStrategySummary.getRedundancy())
xsDataStrategySummary.setResolution(xsDataBestStrategySummary.getResolution())
xsDataStrategySummary.setResolutionReasoning(xsDataBestStrategySummary.getResolutionReasoning())
xsDataStrategySummary.setTotalDataCollectionTime(xsDataBestStrategySummary.getTotalDataCollectionTime())
xsDataStrategySummary.setTotalExposureTime(xsDataBestStrategySummary.getTotalExposureTime())
xsDataCollectionPlan.setStrategySummary(xsDataStrategySummary)
if xsDataBestCollectionPlan.getStatisticalPrediction() is not None:
xsDataStatisticsStrategy = XSDataStatisticsStrategy.parseString(
xsDataBestCollectionPlan.getStatisticalPrediction().marshal()
)
xsDataCollectionPlan.setStatistics(xsDataStatisticsStrategy)
xsDataCollectionPlan.setCollectionPlanNumber(xsDataBestCollectionPlan.getCollectionPlanNumber())
xsDataResultStrategy.addCollectionPlan(xsDataCollectionPlan)
if _xsDataResultBest.getPathToLogFile() != None:
xsDataResultStrategy.setBestLogFile(_xsDataResultBest.getPathToLogFile())
return xsDataResultStrategy
def getTestExperimentalCondition(self):
strPathToTestExperimentalCondition = os.path.join(self.getPluginTestsDataHome(), "XSDataExperimentalCondition_test.xml")
strXMLInput = self.readAndParseFile(strPathToTestExperimentalCondition)
xsDataExperimentalCondition = XSDataExperimentalCondition.parseString(strXMLInput)
return xsDataExperimentalCondition
def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
EDVerbose.DEBUG("EDPluginControlGeneratePredictionv10.preProcess...")
xsDataGeneratePredictionInput = self.getDataInput()
xsDataSelectedIndexingSolution = xsDataGeneratePredictionInput.getSelectedIndexingSolution(
)
xsDataExperimentalConditionRefined = xsDataSelectedIndexingSolution.getExperimentalConditionRefined(
)
xsDataCollection = xsDataGeneratePredictionInput.getDataCollection()
xsDataSubWedgeList = xsDataCollection.getSubWedge()
# List containing instances of all the generate prediction plugins
self.__listPluginGeneratePrediction = []
# Loop through all subwedges
iIndex = 0
for xsDataSubWedge in xsDataSubWedgeList:
xsDataImageList = xsDataSubWedge.getImage()
# First find the lowest image number
iLowestImageNumber = None
for xsDataImage in xsDataImageList:
iImageNumber = xsDataImage.getNumber().getValue()
if (iLowestImageNumber is None):
iLowestImageNumber = iImageNumber
elif (iImageNumber < iLowestImageNumber):
iLowestImageNumber = iImageNumber
# Then loop through all images in a sub wedge
for xsDataImage in xsDataImageList:
iIndex += 1
edPluginGeneratePrediction = self.loadPlugin(
self.__strPluginGeneratePredictionName, "%s-%02d" %
(self.__strPluginGeneratePredictionName, iIndex))
xsDataGeneratePredictionInput = XSDataGeneratePredictionInput()
xsDataGeneratePredictionInput.setSelectedIndexingSolution(
XSDataIndexingSolutionSelected.parseString(
xsDataSelectedIndexingSolution.marshal()))
xsDataCollectionNew = XSDataCollection()
xsDataSubWedgeNew = XSDataSubWedge()
xsDataSubWedgeNew.addImage(
XSDataImage.parseString(xsDataImage.marshal()))
xsDataSubWedgeNew.setExperimentalCondition(
XSDataExperimentalCondition.parseString(
xsDataSubWedge.getExperimentalCondition().marshal()))
# We must modify the rotationOscillationStart for the new subwedge
xsDataGoniostatNew = xsDataSubWedgeNew.getExperimentalCondition(
).getGoniostat()
fGoniostatRotationAxisStart = xsDataGoniostatNew.getRotationAxisStart(
).getValue()
fGonioStatOscillationRange = xsDataGoniostatNew.getOscillationWidth(
).getValue()
iImageNumber = xsDataImage.getNumber().getValue()
fGoniostatRotationAxisStartNew = fGoniostatRotationAxisStart + (
iImageNumber -
iLowestImageNumber) * fGonioStatOscillationRange
xsDataGoniostatNew.setRotationAxisStart(
XSDataAngle(fGoniostatRotationAxisStartNew))
#
xsDataCollectionNew.addSubWedge(xsDataSubWedgeNew)
xsDataGeneratePredictionInput.setDataCollection(
xsDataCollectionNew)
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
xsDataMOSFLMInputGeneratePrediction = EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputGeneratePrediction(
xsDataGeneratePredictionInput)
edPluginGeneratePrediction.setDataInput(
xsDataMOSFLMInputGeneratePrediction)
self.__listPluginGeneratePrediction.append(
edPluginGeneratePrediction)
def generateXSDataIntegrationSubWedgeResult(_xsDataMOSFLMOutputIntegration, _xsDataExperimentalCondition=None):
"""
Translation from XSDataMOSFLMOutputIntegration to XSDataIntegrationSubWedgeResult.
"""
EDVerbose.DEBUG("EDHandlerXSDataMOSFLMv10.generateXSDataIntegrationInput")
EDFactoryPluginStatic.loadModule("XSDataMOSFLMv10")
xsDataIntegrationSubWedgeResult = XSDataIntegrationSubWedgeResult()
xsDataExperimentalConditionRefined = None
if (_xsDataExperimentalCondition is None):
xsDataExperimentalConditionRefined = XSDataExperimentalCondition()
else:
# Copy the incoming experimental condition
xmlExperimentalCondition = _xsDataExperimentalCondition.marshal()
xsDataExperimentalConditionRefined = XSDataExperimentalCondition.parseString(xmlExperimentalCondition)
xsDataDetector = xsDataExperimentalConditionRefined.getDetector()
if (xsDataDetector is None):
xsDataDetector = XSDataDetector()
xsDataIntegrationSubWedgeResult.setBestfilePar(XSDataString(_xsDataMOSFLMOutputIntegration.getBestfilePar().getValue()))
xsDataIntegrationSubWedgeResult.setBestfileDat(XSDataString(_xsDataMOSFLMOutputIntegration.getBestfileDat().getValue()))
xsDataIntegrationSubWedgeResult.setBestfileHKL(XSDataString(_xsDataMOSFLMOutputIntegration.getBestfileHKL().getValue()))
xsDataLengthRefinedDistance = _xsDataMOSFLMOutputIntegration.getRefinedDistance()
if (xsDataLengthRefinedDistance is not None):
xsDataDetector.setDistance(xsDataLengthRefinedDistance)
xsDataMOSFLMBeamPositionRefined = _xsDataMOSFLMOutputIntegration.getRefinedBeam()
if (xsDataMOSFLMBeamPositionRefined is not None):
xsDataDetector.setBeamPositionX(XSDataLength(xsDataMOSFLMBeamPositionRefined.getX().getValue()))
xsDataDetector.setBeamPositionY(XSDataLength(xsDataMOSFLMBeamPositionRefined.getY().getValue()))
xsDataExperimentalConditionRefined.setDetector(xsDataDetector)
xsDataIntegrationSubWedgeResult.setExperimentalConditionRefined(xsDataExperimentalConditionRefined)
if (_xsDataMOSFLMOutputIntegration.getGeneratedMTZFile() is not None):
xsDataIntegrationSubWedgeResult.setGeneratedMTZFile(_xsDataMOSFLMOutputIntegration.getGeneratedMTZFile())
xsDataStatisticsIntegration = XSDataStatisticsIntegration()
if (_xsDataMOSFLMOutputIntegration.getOverallIOverSigma() is not None):
xsDataStatisticsIntegration.setIOverSigmaOverall(XSDataDouble(_xsDataMOSFLMOutputIntegration.getOverallIOverSigma().getValue()))
if (_xsDataMOSFLMOutputIntegration.getHighestResolutionIOverSigma() is not None):
xsDataStatisticsIntegration.setIOverSigmaAtHighestResolution(XSDataDouble(_xsDataMOSFLMOutputIntegration.getHighestResolutionIOverSigma().getValue()))
if (_xsDataMOSFLMOutputIntegration.getRMSSpotDeviation() is not None):
xsDataStatisticsIntegration.setRMSSpotDeviation(XSDataLength(_xsDataMOSFLMOutputIntegration.getRMSSpotDeviation().getValue()))
if (_xsDataMOSFLMOutputIntegration.getNumberOfBadReflections() is not None):
xsDataStatisticsIntegration.setNumberOfBadReflections(XSDataInteger(_xsDataMOSFLMOutputIntegration.getNumberOfBadReflections().getValue()))
if (_xsDataMOSFLMOutputIntegration.getNumberOfFullyRecordedReflections() is not None):
xsDataStatisticsIntegration.setNumberOfFullyRecordedReflections(XSDataInteger(_xsDataMOSFLMOutputIntegration.getNumberOfFullyRecordedReflections().getValue()))
if (_xsDataMOSFLMOutputIntegration.getNumberOfNegativeReflections() is not None):
xsDataStatisticsIntegration.setNumberOfNegativeReflections(XSDataInteger(_xsDataMOSFLMOutputIntegration.getNumberOfNegativeReflections().getValue()))
if (_xsDataMOSFLMOutputIntegration.getNumberOfOverlappedReflections() is not None):
xsDataStatisticsIntegration.setNumberOfOverlappedReflections(XSDataInteger(_xsDataMOSFLMOutputIntegration.getNumberOfOverlappedReflections().getValue()))
if (_xsDataMOSFLMOutputIntegration.getNumberOfPartialReflections() is not None):
xsDataStatisticsIntegration.setNumberOfPartialReflections(XSDataInteger(_xsDataMOSFLMOutputIntegration.getNumberOfPartialReflections().getValue()))
if (_xsDataMOSFLMOutputIntegration.getNumberOfReflectionsGenerated() is not None):
xsDataStatisticsIntegration.setNumberOfReflectionsGenerated(XSDataInteger(_xsDataMOSFLMOutputIntegration.getNumberOfReflectionsGenerated().getValue()))
xsDataIntegrationSubWedgeResult.setStatistics(xsDataStatisticsIntegration)
xsDataIntegrationSubWedgeResult.setExperimentalConditionRefined(xsDataExperimentalConditionRefined)
for xsDataMOSFLMIntegrationStatisticsPerResolutionBin in _xsDataMOSFLMOutputIntegration.getStatisticsPerResolutionBin():
xsDataStatisticsIntegrationPerResolutionBin = XSDataStatisticsIntegrationPerResolutionBin()
if (xsDataMOSFLMIntegrationStatisticsPerResolutionBin.getMaxResolution() is not None):
xsDataStatisticsIntegrationPerResolutionBin.setMaxResolution(XSDataDouble(xsDataMOSFLMIntegrationStatisticsPerResolutionBin.getMaxResolution().getValue()))
if (xsDataMOSFLMIntegrationStatisticsPerResolutionBin.getMinResolution() is not None):
xsDataStatisticsIntegrationPerResolutionBin.setMinResolution(XSDataDouble(xsDataMOSFLMIntegrationStatisticsPerResolutionBin.getMinResolution().getValue()))
xsDataStatisticsIntegrationPerResolutionBin.setProfileFitted(EDHandlerXSDataMOSFLMv10.generateXSDataIntegrationStatisticsPerReflectionType(xsDataMOSFLMIntegrationStatisticsPerResolutionBin.getProfileFitted()))
xsDataStatisticsIntegrationPerResolutionBin.setSummation(EDHandlerXSDataMOSFLMv10.generateXSDataIntegrationStatisticsPerReflectionType(xsDataMOSFLMIntegrationStatisticsPerResolutionBin.getSummation()))
xsDataIntegrationSubWedgeResult.addStatisticsPerResolutionBin(xsDataStatisticsIntegrationPerResolutionBin)
return xsDataIntegrationSubWedgeResult
