Python XSDataCrystal.setSpaceGroup方法代码示例

# 需要导入模块: from XSDataMXv1 import XSDataCrystal [as 别名]
# 或者: from XSDataMXv1.XSDataCrystal import setSpaceGroup [as 别名]
    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

# 需要导入模块: from XSDataMXv1 import XSDataCrystal [as 别名]
# 或者: from XSDataMXv1.XSDataCrystal import setSpaceGroup [as 别名]
    def preProcess(self, _edObject=None):
        """
        Gets the Configuration Parameters, if found, overrides default parameters
        """
        EDPluginControl.preProcess(self, _edObject)
        EDVerbose.DEBUG("EDPluginControlCharacterisationv1_1.preProcess...")

        self.__edPluginIndexing = self.loadPlugin(self.__strPluginIndexingName   , "Indexing")
        self.__edPluginIntegration = self.loadPlugin(self.__strPluginIntegrationName, "Integration")
        self.__edPluginStrategy = self.loadPlugin(self.__strPluginStrategyName   , "Strategy")

        if (self.__edPluginIndexing is not None):
            EDVerbose.DEBUG("EDPluginControlCharacterisationv1_1.preProcess: " + self.__strPluginIndexingName + " Found... setting Data Input")
            # create Data Input for indexing
            xsDataInputStrategy = self.getDataInput()
            xsDataCollection = xsDataInputStrategy.getDataCollection()
            xsDataSample = xsDataCollection.getSample()
            xsDataSubWedgeList = xsDataCollection.getSubWedge()
            if ((xsDataSubWedgeList is None) or (xsDataSubWedgeList == [])):
            	strError = "EDPluginControlCharacterisationv1_1.preProcess: No subwedges in input data."
            	EDVerbose.ERROR(strError)
                self.setFailure()
            else:
                xsDataExperimentalCondition = xsDataSubWedgeList[0].getExperimentalCondition()

                # Fix for bug 431: if the flux is zero raise an error
                xsDataDoubleFlux = xsDataExperimentalCondition.getBeam().getFlux()
                if (xsDataDoubleFlux is not None):
                    if (xsDataDoubleFlux.getValue() < 0.1):
                        pyStrErrorMessage = "EDPluginControlCharacterisationv1_1.preProcess ERROR: Input flux is negative or close to zero. Execution of characterisation aborted."
                        EDVerbose.ERROR(pyStrErrorMessage)
                        self.addErrorMessage(pyStrErrorMessage)
                        self.setFailure()

                xsDataIndexingInput = XSDataIndexingInput()
                xsDataIndexingInput.setDataCollection(xsDataCollection)
                xsDataIndexingInput.setExperimentalCondition(xsDataExperimentalCondition)

                xsDataDiffractionPlan = xsDataCollection.getDiffractionPlan()
                xsDataStringForcedSpaceGroup = xsDataDiffractionPlan.getForcedSpaceGroup()
                if (xsDataStringForcedSpaceGroup is not None):
                    xsDataCrystal = XSDataCrystal()
                    xsDataSpaceGroup = XSDataSpaceGroup()
                    xsDataSpaceGroup.setName(xsDataStringForcedSpaceGroup)
                    xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
                    xsDataIndexingInput.setCrystal(xsDataCrystal)

                self.__edPluginIndexing.setDataInput(xsDataIndexingInput)

                # Populate characterisation object
                self.__xsDataResultCharacterisation = XSDataResultCharacterisation()
                self.__xsDataResultCharacterisation.setDataCollection(XSDataCollection.parseString(xsDataCollection.marshal()))

# 需要导入模块: from XSDataMXv1 import XSDataCrystal [as 别名]
# 或者: from XSDataMXv1.XSDataCrystal import setSpaceGroup [as 别名]
    def preProcess(self, _edObject=None):
        """
        Gets the Configuration Parameters, if found, overrides default parameters
        """
        EDPluginControl.preProcess(self, _edObject)
        EDVerbose.DEBUG("EDPluginControlCharacterisationv2_0.preProcess...")

        self.edPluginIndexing = self.loadPlugin(self.strPluginIndexingName, "Indexing")
        self.edPluginIntegration = self.loadPlugin(self.strPluginIntegrationName, "Integration")
        self.edPluginStrategy = self.loadPlugin(self.strPluginStrategyName, "Strategy")

        if self.edPluginIndexing is not None:
            EDVerbose.DEBUG(
                "EDPluginControlCharacterisationv2_0.preProcess: "
                + self.strPluginIndexingName
                + " Found... setting Data Input"
            )
            # create Data Input for indexing
            xsDataInputStrategy = self.getDataInput("mxv1InputCharacterisation")[0]
            xsDataCollection = xsDataInputStrategy.getDataCollection()
            # xsDataSample = xsDataCollection.getSample()
            xsDataSubWedgeList = xsDataCollection.getSubWedge()
            xsDataExperimentalCondition = xsDataSubWedgeList[0].getExperimentalCondition()

            xsDataIndexingInput = XSDataIndexingInput()
            xsDataIndexingInput.setDataCollection(xsDataCollection)
            xsDataIndexingInput.setExperimentalCondition(xsDataExperimentalCondition)

            xsDataDiffractionPlan = xsDataCollection.getDiffractionPlan()
            xsDataStringForcedSpaceGroup = xsDataDiffractionPlan.getForcedSpaceGroup()
            if xsDataStringForcedSpaceGroup is not None:
                xsDataCrystal = XSDataCrystal()
                xsDataSpaceGroup = XSDataSpaceGroup()
                xsDataSpaceGroup.setName(xsDataStringForcedSpaceGroup)
                xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
                xsDataIndexingInput.setCrystal(xsDataCrystal)

            self.edPluginIndexing.setDataInput(xsDataIndexingInput)

            # Populate characterisation object
            self.xsDataResultCharacterisationv2_0 = XSDataResultCharacterisationv2_0()
            self.xsDataResultCharacterisation = XSDataResultCharacterisation()
            self.xsDataResultCharacterisationv2_0.setMxv1ResultCharacterisation(self.xsDataResultCharacterisation)
            self.xsDataResultCharacterisation.setDataCollection(
                XSDataCollection.parseString(xsDataCollection.marshal())
            )

# 需要导入模块: from XSDataMXv1 import XSDataCrystal [as 别名]
# 或者: from XSDataMXv1.XSDataCrystal import setSpaceGroup [as 别名]
class EDPluginControlCharacterisationv1_2(EDPluginControl):
    """
    [To be replaced with a description of EDPluginControlTemplatev10]
    """


    def __init__(self):
        EDPluginControl.__init__(self)
        self.setXSDataInputClass(XSDataInputCharacterisation)
        self.__strPluginControlIndexingIndicators = "EDPluginControlIndexingIndicatorsv10"
        self.__strPluginControlIndexingLabelit = "EDPluginControlIndexingLabelitv10"
        self.__strPluginExecEvaluationIndexing = "EDPluginExecEvaluationIndexingv10"
        self.__strPluginControlGeneratePrediction = "EDPluginControlGeneratePredictionv10"
        self.__strPluginControlIntegration = "EDPluginControlIntegrationv10"
        self.__strPluginControlStrategy = "EDPluginControlStrategyv1_2"
        self.__edPluginControlIndexingIndicators = None
        self.__edPluginControlIndexingLabelit = None
        self.__edPluginExecEvaluationIndexingMOSFLM = None
        self.__edPluginExecEvaluationIndexingLABELIT = None
        self.__edPluginControlGeneratePrediction = None
        self.__edPluginControlIntegration = None
        self.__edPluginControlStrategy = None
        self.__xsDataCollection = None
        self.__xsDataResultCharacterisation = None
        self.__xsDataIndexingResultMOSFLM = None
        self.__xsDataCrystal = None
        self.__strCharacterisationShortSummary = ""
        self.__strStatusMessage = ""
        self.__bDoStrategyCalculation = True



    def checkParameters(self):
        """
        Checks the mandatory parameters.
        """
        EDVerbose.DEBUG("EDPluginControlCharacterisationv1_2.checkParameters")
        self.checkMandatoryParameters(self.getDataInput(), "Data Input is None")
        self.checkMandatoryParameters(self.getDataInput().getDataCollection(), "dataCollection")
        self.checkMandatoryParameters(self.getDataInput().getDataCollection().getDiffractionPlan(), "diffractionPlan")


    def preProcess(self, _edObject=None):
        EDPluginControl.preProcess(self)
        EDVerbose.DEBUG("EDPluginControlCharacterisationv1_2.preProcess")
        # Load the plugins
        self.__edPluginControlIndexingIndicators = self.loadPlugin(self.__strPluginControlIndexingIndicators, \
                                                                   "Indexing")
        self.__edPluginControlIndexingLabelit = self.loadPlugin(self.__strPluginControlIndexingLabelit, \
                                                                   "IndexingLabelit")
        self.__edPluginExecEvaluationIndexingMOSFLM = self.loadPlugin(self.__strPluginExecEvaluationIndexing, \
                                                                   "IndexingEvalualtionMOSFLM")
        self.__edPluginExecEvaluationIndexingLABELIT = self.loadPlugin(self.__strPluginExecEvaluationIndexing, \
                                                                   "IndexingEvalualtionLABELIT")
        self.__edPluginControlGeneratePrediction = self.loadPlugin(self.__strPluginControlGeneratePrediction, \
                                                                   "GeneratePrediction")
        self.__edPluginControlIntegration = self.loadPlugin(self.__strPluginControlIntegration, \
                                                            "Integration")
        self.__edPluginControlStrategy = self.loadPlugin(self.__strPluginControlStrategy, \
                                                         "Strategy")
        if (self.__edPluginControlIndexingIndicators is not None):
            EDVerbose.DEBUG("EDPluginControlCharacterisationv1_2.preProcess: " + self.__strPluginControlIndexingIndicators + " Found... setting Data Input")
            # create Data Input for indexing
            xsDataInputCharacterisation = self.getDataInput()
            self.__xsDataCollection = xsDataInputCharacterisation.getDataCollection()
            xsDataCrystal = None
            xsDataSubWedgeList = self.__xsDataCollection.getSubWedge()
            if ((xsDataSubWedgeList is None) or (xsDataSubWedgeList == [])):
                strError = "EDPluginControlCharacterisationv1_2.preProcess: No subwedges in input data."
                EDVerbose.ERROR(strError)
                self.setFailure()
            else:
                xsDataExperimentalCondition = xsDataSubWedgeList[0].getExperimentalCondition()

                # Fix for bug 431: if the flux is zero raise an error
                xsDataDoubleFlux = xsDataExperimentalCondition.getBeam().getFlux()
                if (xsDataDoubleFlux is not None):
                    if (xsDataDoubleFlux.getValue() < 0.1):
                        strErrorMessage = "Input flux is negative or close to zero. Execution of characterisation aborted."
                        EDVerbose.ERROR(strErrorMessage)
                        self.addErrorMessage("EDPluginControlCharacterisationv1_2.preProcess ERROR: " + strErrorMessage)
                        #self.addComment(strErrorMessage)
                        self.setFailure()

                xsDataDiffractionPlan = self.__xsDataCollection.getDiffractionPlan()
                xsDataStringForcedSpaceGroup = xsDataDiffractionPlan.getForcedSpaceGroup()
                if (xsDataStringForcedSpaceGroup is not None):
                    self.__xsDataCrystal = XSDataCrystal()
                    xsDataSpaceGroup = XSDataSpaceGroup()
                    xsDataSpaceGroup.setName(xsDataStringForcedSpaceGroup)
                    self.__xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)

                self.__edPluginControlIndexingIndicators.setDataInput(self.__xsDataCollection, "dataCollection")
                if self.__xsDataCrystal is not None:
                    self.__edPluginControlIndexingIndicators.setDataInput(self.__xsDataCrystal, "crystal")

                # Populate characterisation object
                self.__xsDataResultCharacterisation = XSDataResultCharacterisation()
                self.__xsDataResultCharacterisation.setDataCollection(XSDataCollection.parseString(self.__xsDataCollection.marshal()))

#.........这里部分代码省略.........

# 需要导入模块: from XSDataMXv1 import XSDataCrystal [as 别名]
# 或者: from XSDataMXv1.XSDataCrystal import setSpaceGroup [as 别名]

#.........这里部分代码省略.........
        xsDataGoniostat = XSDataGoniostat()
        xsDataGoniostat.setRotationAxis(XSDataString("phi"))
        xsExperimentalCondition.setGoniostat(xsDataGoniostat)

        xsDataStrategy.setExperimentalCondition(xsExperimentalCondition)


        # Best Files
        bestFileContentDat = EDUtilsFile.readFile(os.path.join(self.strDataPath, "bestfile.dat"))
        xsDataStrategy.setBestFileContentDat(XSDataString(bestFileContentDat))
        bestFileContentPar = EDUtilsFile.readFile(os.path.join(self.strDataPath, "bestfile.par"))
        xsDataStrategy.setBestFileContentPar(XSDataString(bestFileContentPar))
        bestFileContentHKL = EDUtilsFile.readFile(os.path.join(self.strDataPath, "bestfile1.hkl"))
        xsDataStrategy.addBestFileContentHKL(XSDataString(bestFileContentHKL))

        # Crystal

        xsDataSampleCrystalMM = XSDataSampleCrystalMM()
        xsDataStructure = XSDataStructure()
        xsDataComposition = XSDataChemicalCompositionMM()

        xsDataChain = XSDataChain()
        xsDataChain.setType(XSDataString("protein"))
        xsDataChain.setNumberOfCopies(XSDataDouble(2))
        xsDataAtomicComposition = XSDataAtomicComposition()
        xsDataAtom1 = XSDataAtom()
        xsDataAtom1.setSymbol(XSDataString("Se"))
        xsDataAtom1.setNumberOf(XSDataDouble(4))
        xsDataAtomicComposition.addAtom(xsDataAtom1)

        xsDataChain.setHeavyAtoms(xsDataAtomicComposition)
        xsDataChain.setNumberOfMonomers(XSDataDouble(100))
        xsDataStructure.addChain(xsDataChain)

        xsDataChain2 = XSDataChain()
        xsDataChain2.setType(XSDataString("rna"))
        xsDataChain2.setNumberOfCopies(XSDataDouble(1))
        xsDataChain2.setNumberOfMonomers(XSDataDouble(60))
        xsDataStructure.addChain(xsDataChain2)

        xsDataLigand = XSDataLigand()
        xsDataLigand.setNumberOfCopies(XSDataDouble(2))
        xsDataLigand.setNumberOfLightAtoms(XSDataDouble(42))
        xsDataAtomicComposition = XSDataAtomicComposition()
        xsDataAtom2 = XSDataAtom()
        xsDataAtom2.setSymbol(XSDataString("Fe"))
        xsDataAtom2.setNumberOf(XSDataDouble(1))
        xsDataAtomicComposition.addAtom(xsDataAtom2)
        xsDataLigand.setHeavyAtoms(xsDataAtomicComposition)
        xsDataStructure.addLigand(xsDataLigand)
        xsDataStructure.setNumberOfCopiesInAsymmetricUnit(XSDataDouble(0.25))

        xsDataSolvent = XSDataSolvent()
        xsDataAtomicComposition = XSDataAtomicComposition()

        xsDataAtom3 = XSDataAtom()
        xsDataAtom3.setSymbol(XSDataString("Na"))
        xsDataAtom3.setConcentration(XSDataDouble(1000))
        xsDataAtom4 = XSDataAtom()
        xsDataAtom4.setSymbol(XSDataString("Cl"))
        xsDataAtom4.setConcentration(XSDataDouble(1000))

        xsDataAtomicComposition.addAtom(xsDataAtom3)
        xsDataAtomicComposition.addAtom(xsDataAtom4)
        xsDataSolvent.setAtoms(xsDataAtomicComposition)

        xsDataComposition.setStructure(xsDataStructure)
        xsDataComposition.setSolvent(xsDataSolvent)
        xsDataSampleCrystalMM.setChemicalComposition(xsDataComposition)

        xsDataSampleCrystalMM.setSize(XSDataSize(XSDataLength(0.1), XSDataLength(0.1), XSDataLength(0.1)))

        xsDataCrystal = XSDataCrystal()
        xsDataCell = XSDataCell(angle_alpha=XSDataAngle(90.0),
                                angle_beta=XSDataAngle(90.0),
                                angle_gamma=XSDataAngle(90.0),
                                length_a=XSDataLength(78.9),
                                length_b=XSDataLength(95.162),
                                length_c=XSDataLength(104.087))
        xsDataCrystal.setCell(xsDataCell)

        xsDataSpaceGroup = XSDataSpaceGroup()
        xsDataSpaceGroup.setITNumber(XSDataInteger(16))
        xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)

        xsDataSampleCrystalMM.setSusceptibility(XSDataDouble(1.5))

        xsDataStrategy.setCrystalRefined(xsDataCrystal)

        xsDataStrategy.setSample(xsDataSampleCrystalMM)

        xsDataStrategy.exportToFile(self.strObtainedInputFile)

        pyStrExpectedInput = self.readAndParseFile (self.strReferenceInputFile)
        pyStrObtainedInput = self.readAndParseFile (self.strObtainedInputFile)

        xsDataInputExpected = XSDataInputStrategy.parseString(pyStrExpectedInput)
        xsDataInputObtained = XSDataInputStrategy.parseString(pyStrObtainedInput)

        EDAssert.equal(xsDataInputExpected.marshal(), xsDataInputObtained.marshal())

# 需要导入模块: from XSDataMXv1 import XSDataCrystal [as 别名]
# 或者: from XSDataMXv1.XSDataCrystal import setSpaceGroup [as 别名]
    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

# 需要导入模块: from XSDataMXv1 import XSDataCrystal [as 别名]
# 或者: from XSDataMXv1.XSDataCrystal import setSpaceGroup [as 别名]

#.........这里部分代码省略.........
        from XSDataMXv1   import XSDataCell

        from EDHandlerXSDataRaddosev10 import EDHandlerXSDataRaddosev10

        EDFactoryPluginStatic.loadModule("XSDataRaddosev10")
        from XSDataRaddosev10 import XSDataRaddoseInput

        xsDataBeam = XSDataBeam()
        xsDataBeam.setSize(XSDataSize(x=XSDataLength(0.1), y=XSDataLength(0.1)))
        xsDataBeam.setWavelength(XSDataWavelength(2.41))
        xsDataBeam.setFlux(XSDataFlux(1e+12))

        xsDataSample = XSDataSampleCrystalMM()
        xsDataStructure = XSDataStructure()
        xsDataComposition = XSDataChemicalCompositionMM()

        xsDataChain = XSDataChain()
        xsDataChain.setType(XSDataString("protein"))
        xsDataChain.setNumberOfCopies(XSDataDouble(2))
        xsDataAtomicComposition = XSDataAtomicComposition()
        xsDataAtom1 = XSDataAtom()
        xsDataAtom1.setSymbol(XSDataString("Se"))
        xsDataAtom1.setNumberOf(XSDataDouble(4))
        xsDataAtomicComposition.addAtom(xsDataAtom1)
        xsDataAtom2 = XSDataAtom()
        xsDataAtom2.setSymbol(XSDataString("S"))
        xsDataAtom2.setNumberOf(XSDataDouble(5))
        xsDataAtomicComposition.addAtom(xsDataAtom2)
        xsDataChain.setHeavyAtoms(xsDataAtomicComposition)
        xsDataChain.setNumberOfMonomers(XSDataDouble(100))
        xsDataStructure.addChain(xsDataChain)

        xsDataChain2 = XSDataChain()
        xsDataChain2.setType(XSDataString("rna"))
        xsDataChain2.setNumberOfCopies(XSDataDouble(1))
        xsDataChain2.setNumberOfMonomers(XSDataDouble(60))
        xsDataStructure.addChain(xsDataChain2)

        xsDataLigand = XSDataLigand()
        xsDataLigand.setNumberOfCopies(XSDataDouble(2))
        xsDataLigand.setNumberOfLightAtoms(XSDataDouble(42))
        xsDataAtomicComposition = XSDataAtomicComposition()
        xsDataAtom3 = XSDataAtom()
        xsDataAtom3.setSymbol(XSDataString("Fe"))
        xsDataAtom3.setNumberOf(XSDataDouble(1))
        xsDataAtomicComposition.addAtom(xsDataAtom3)
        xsDataLigand.setHeavyAtoms(xsDataAtomicComposition)
        xsDataStructure.addLigand(xsDataLigand)
        xsDataStructure.setNumberOfCopiesInAsymmetricUnit(XSDataDouble(0.25))

        xsDataSolvent = XSDataSolvent()
        xsDataAtomicComposition = XSDataAtomicComposition()
        xsDataAtomNa = XSDataAtom()
        xsDataAtomNa.setSymbol(XSDataString("Na"))
        xsDataAtomNa.setConcentration(XSDataDouble(1000))
        xsDataAtomicComposition.addAtom(xsDataAtomNa)
        xsDataAtomCl = XSDataAtom()
        xsDataAtomCl.setSymbol(XSDataString("Cl"))
        xsDataAtomCl.setConcentration(XSDataDouble(1000))
        xsDataAtomicComposition.addAtom(xsDataAtomCl)
        xsDataSolvent.setAtoms(xsDataAtomicComposition)

        xsDataComposition.setStructure(xsDataStructure)
        xsDataComposition.setSolvent(xsDataSolvent)
        xsDataSample.setChemicalComposition(xsDataComposition)

        xsDataSample.setSize(XSDataSize(XSDataLength(0.1), XSDataLength(0.1), XSDataLength(0.1)))
        xsDataCell = XSDataCell(angle_alpha=XSDataAngle(90.0),
                                angle_beta=XSDataAngle(90.0),
                                angle_gamma=XSDataAngle(90.0),
                                length_a=XSDataLength(78.9),
                                length_b=XSDataLength(95.162),
                                length_c=XSDataLength(104.087))

        xsDataCrystal = XSDataCrystal()
        xsDataSpaceGroup = XSDataSpaceGroup()

        xsDataCrystal.setCell(xsDataCell)

        xsDataSpaceGroup.setITNumber(XSDataInteger(16))
        xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)

        xsDataSample.setCrystal(xsDataCrystal)

        iNumSymOperators = 4


        xsDataRaddosev01Input = EDHandlerXSDataRaddosev10().getXSDataRaddoseInput(xsDataBeam,
                                                                                      xsDataSample,
                                                                                      iNumSymOperators)


        xsDataRaddosev01Input.exportToFile(self.strObtainedInputFile2)
        strExpectedInput = EDUtilsTest.readAndParseFile (self.strReferenceInputFile2)
        strObtainedInput = EDUtilsTest.readAndParseFile (self.strObtainedInputFile2)

        xsDataInputExpected = XSDataRaddoseInput.parseString(strExpectedInput)
        xsDataInputObtained = XSDataRaddoseInput.parseString(strObtainedInput)

        EDAssert.equal(xsDataInputExpected.marshal(), xsDataInputObtained.marshal())

# 需要导入模块: from XSDataMXv1 import XSDataCrystal [as 别名]
# 或者: from XSDataMXv1.XSDataCrystal import setSpaceGroup [as 别名]

#.........这里部分代码省略.........
                    self.warning(strWarningMessageBanner)
                    self.addWarningMessage(strWarningMessageBanner)
                    self.addWarningMessage(strWarningMessage1)
                    self.addWarningMessage(strWarningMessage2)
                    self.addWarningMessage(strWarningMessageBanner)
                    self.sendMessageToMXCuBE(strWarningMessage1, "warning")
                    self.sendMessageToMXCuBE(strWarningMessage2, "warning")
            xsDataCrystal = None
            xsDataSubWedgeList = self._xsDataCollection.getSubWedge()
            if ((xsDataSubWedgeList is None) or (xsDataSubWedgeList == [])):
                strError = "EDPluginControlCharacterisationv1_5.preProcess: No subwedges in input data."
                self.ERROR(strError)
                self.setFailure()
            else:
                xsDataExperimentalCondition = xsDataSubWedgeList[0].getExperimentalCondition()

                # Fix for bug 431: if the flux is zero raise an error
                xsDataDoubleFlux = xsDataExperimentalCondition.getBeam().getFlux()
                if (xsDataDoubleFlux is not None):
                    if (xsDataDoubleFlux.getValue() < 0.1):
                        strErrorMessage = "Input flux is negative or close to zero. Execution of characterisation aborted."
                        self.ERROR(strErrorMessage)
                        self.sendMessageToMXCuBE(strErrorMessage, "error")
                        self.addErrorMessage("EDPluginControlCharacterisationv1_5.preProcess ERROR: " + strErrorMessage)
                        # self.addComment(strErrorMessage)
                        self.setFailure()

                xsDataDiffractionPlan = self._xsDataCollection.getDiffractionPlan()
                xsDataStringForcedSpaceGroup = xsDataDiffractionPlan.getForcedSpaceGroup()
                if (xsDataStringForcedSpaceGroup is not None):
                    self._xsDataCrystal = XSDataCrystal()
                    xsDataSpaceGroup = XSDataSpaceGroup()
                    xsDataSpaceGroup.setName(xsDataStringForcedSpaceGroup)
                    self._xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)

                self._edPluginControlIndexingIndicators.setDataInput(self._xsDataCollection, "dataCollection")
                if self._xsDataCrystal is not None:
                    self._edPluginControlIndexingIndicators.setDataInput(self._xsDataCrystal, "crystal")

                # Populate characterisation object
                self._xsDataResultCharacterisation.setDataCollection(XSDataCollection.parseString(self._xsDataCollection.marshal()))
            # Load the thumbnail plugins
            self._iNoReferenceImages = 0
            if not self.isFailure():
                for subWedge in xsDataInputCharacterisation.dataCollection.subWedge:
                    for image in subWedge.image:
                        self._iNoReferenceImages += 1
                        edPluginJpeg = self.loadPlugin(self._strPluginGenerateThumbnailName)
                        xsDataInputMXThumbnail = XSDataInputMXThumbnail()
                        xsDataInputMXThumbnail.image = XSDataFile(image.path)
                        xsDataInputMXThumbnail.height = XSDataInteger(1024)
                        xsDataInputMXThumbnail.width = XSDataInteger(1024)
                        jpegFilename = os.path.splitext(os.path.basename(image.path.value))[0] + ".jpg"
                        xsDataInputMXThumbnail.outputPath = XSDataFile(XSDataString(os.path.join(self.getWorkingDirectory(), jpegFilename)))
                        edPluginJpeg.dataInput = xsDataInputMXThumbnail
                        edPluginThumnail = self.loadPlugin(self._strPluginGenerateThumbnailName)
                        xsDataInputMXThumbnail = XSDataInputMXThumbnail()
                        xsDataInputMXThumbnail.image = XSDataFile(image.path)
                        xsDataInputMXThumbnail.height = XSDataInteger(256)
                        xsDataInputMXThumbnail.width = XSDataInteger(256)
                        thumbnailFilename = os.path.splitext(os.path.basename(image.path.value))[0] + ".thumbnail.jpg"
                        xsDataInputMXThumbnail.outputPath = XSDataFile(XSDataString(os.path.join(self.getWorkingDirectory(), thumbnailFilename)))
                        edPluginThumnail.dataInput = xsDataInputMXThumbnail
                        self._listPluginGenerateThumbnail.append((image, edPluginJpeg, edPluginThumnail))

# 需要导入模块: from XSDataMXv1 import XSDataCrystal [as 别名]
# 或者: from XSDataMXv1.XSDataCrystal import setSpaceGroup [as 别名]
    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

# 需要导入模块: from XSDataMXv1 import XSDataCrystal [as 别名]
# 或者: from XSDataMXv1.XSDataCrystal import setSpaceGroup [as 别名]

#.........这里部分代码省略.........
                    self.warning(strWarningMessageBanner)
                    self.warning(strWarningMessage1)
                    self.warning(strWarningMessage2)
                    self.warning(strWarningMessageBanner)
                    self.addWarningMessage(strWarningMessageBanner)
                    self.addWarningMessage(strWarningMessage1)
                    self.addWarningMessage(strWarningMessage2)
                    self.addWarningMessage(strWarningMessageBanner)
            xsDataCrystal = None
            xsDataSubWedgeList = self._xsDataCollection.getSubWedge()
            if ((xsDataSubWedgeList is None) or (xsDataSubWedgeList == [])):
                strError = "EDPluginControlCharacterisationv1_3.preProcess: No subwedges in input data."
                self.ERROR(strError)
                self.setFailure()
            else:
                xsDataExperimentalCondition = xsDataSubWedgeList[0].getExperimentalCondition()

                # Fix for bug 431: if the flux is zero raise an error
                xsDataDoubleFlux = xsDataExperimentalCondition.getBeam().getFlux()
                if (xsDataDoubleFlux is not None):
                    if (xsDataDoubleFlux.getValue() < 0.1):
                        strErrorMessage = "Input flux is negative or close to zero. Execution of characterisation aborted."
                        self.ERROR(strErrorMessage)
                        self.addErrorMessage("EDPluginControlCharacterisationv1_3.preProcess ERROR: " + strErrorMessage)
                        #self.addComment(strErrorMessage)
                        self.setFailure()

                xsDataDiffractionPlan = self._xsDataCollection.getDiffractionPlan()
                xsDataStringForcedSpaceGroup = xsDataDiffractionPlan.getForcedSpaceGroup()
                if (xsDataStringForcedSpaceGroup is not None):
                    self._xsDataCrystal = XSDataCrystal()
                    xsDataSpaceGroup = XSDataSpaceGroup()
                    xsDataSpaceGroup.setName(xsDataStringForcedSpaceGroup)
                    self._xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)

                self._edPluginControlIndexingIndicators.setDataInput(self._xsDataCollection, "dataCollection")
                if self._xsDataCrystal is not None:
                    self._edPluginControlIndexingIndicators.setDataInput(self._xsDataCrystal, "crystal")

                # Populate characterisation object
                self._xsDataResultCharacterisation = XSDataResultCharacterisation()
                self._xsDataResultCharacterisation.setDataCollection(XSDataCollection.parseString(self._xsDataCollection.marshal()))
            # Load the thumbnail plugins
            for subWedge in xsDataInputCharacterisation.dataCollection.subWedge:
                for image in subWedge.image:
                    edPluginJpeg = self.loadPlugin(self._strPluginGenerateThumbnailName)
                    xsDataInputMXThumbnail = XSDataInputMXThumbnail()
                    xsDataInputMXThumbnail.image = XSDataFile(image.path)
                    xsDataInputMXThumbnail.height = XSDataInteger(1024)
                    xsDataInputMXThumbnail.width = XSDataInteger(1024)
                    jpegFilename = os.path.splitext(os.path.basename(image.path.value))[0]+".jpg"
                    xsDataInputMXThumbnail.outputPath = XSDataFile(XSDataString(os.path.join(self.getWorkingDirectory(), jpegFilename)))
                    edPluginJpeg.dataInput = xsDataInputMXThumbnail
                    edPluginThumnail = self.loadPlugin(self._strPluginGenerateThumbnailName)
                    xsDataInputMXThumbnail = XSDataInputMXThumbnail()
                    xsDataInputMXThumbnail.image = XSDataFile(image.path)
                    xsDataInputMXThumbnail.height = XSDataInteger(256)
                    xsDataInputMXThumbnail.width = XSDataInteger(256)
                    thumbnailFilename = os.path.splitext(os.path.basename(image.path.value))[0]+".thumbnail.jpg"
                    xsDataInputMXThumbnail.outputPath = XSDataFile(XSDataString(os.path.join(self.getWorkingDirectory(), thumbnailFilename)))
                    edPluginThumnail.dataInput = xsDataInputMXThumbnail
                    self._listPluginGenerateThumbnail.append((image, edPluginJpeg, edPluginThumnail))


    def process(self, _edObject=None):
        EDPluginControl.process(self)