def preProcess(self, _edObject=None):
        EDPluginControl.preProcess(self)
        EDVerbose.DEBUG("EDPluginControlCharacterisationv1_3.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._edPluginControlXDSGenerateBackgroundImage = self.loadPlugin(self._strPluginControlXDSGenerateBackgroundImage, \
                                                            "ControlXDSGenerateBackgroundImage")
        self._edPluginControlStrategy = self.loadPlugin(self._strPluginControlStrategy, \
                                                         "Strategy")
        if (self._edPluginControlIndexingIndicators is not None):
            EDVerbose.DEBUG("EDPluginControlCharacterisationv1_3.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_3.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_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()))
    def preProcess(self, _edObject=None):
        EDPluginControl.preProcess(self)
        self.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):
            self.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."
                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_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()))
Example #3
0
    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)
        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()))
Example #5
0
    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()))
    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())
            )
Example #7
0
    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 testSetDataModelInput(self):
        edPluginStrategy = self.createPlugin()
        strPathToTestConfigFile = os.path.join(self.getPluginTestsDataHome(), "XSConfiguration_ESRF.xml")
        edConfiguration = EDConfiguration(strPathToTestConfigFile)
        dictItem = edConfiguration.get(edPluginStrategy.getPluginName())
        edPluginStrategy.setConfig(dictItem)
        edPluginStrategy.configure()

        xsDataStrategy = XSDataInputStrategy()

        # Beam

        xsExperimentalCondition = XSDataExperimentalCondition()

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

        xsExperimentalCondition.setBeam(xsBeam)

        # Detector and Exposure Time

        xsDataDetector = XSDataDetector()
        xsDataDetector.setType(XSDataString("q210-2x"))
        xsExperimentalCondition.setDetector(xsDataDetector)

        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())
    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
Example #10
0
    def preProcess(self, _edObject=None):
        EDPluginControl.preProcess(self)
        self.DEBUG("EDPluginControlCharacterisationv1_4.preProcess")
        self._xsDataResultCharacterisation = XSDataResultCharacterisation()
        # Load the plugins
        self._edPluginControlIndexingIndicators = self.loadPlugin(self._strPluginControlIndexingIndicators, \
                                                                   "Indexing")
        self._edPluginExecEvaluationIndexingLABELIT = self.loadPlugin(self._strPluginExecEvaluationIndexing, \
                                                                   "IndexingEvalualtionLABELIT")
        self._edPluginControlIndexingMOSFLM = self.loadPlugin(self._strPluginControlIndexingMOSFLM, \
                                                                   "IndexingMOSFLM")
        self._edPluginExecEvaluationIndexingMOSFLM = self.loadPlugin(self._strPluginExecEvaluationIndexing, \
                                                                   "IndexingEvalualtionMOSFLM")
        self._edPluginControlGeneratePrediction = self.loadPlugin(self._strPluginControlGeneratePrediction, \
                                                                   "GeneratePrediction")
        self._edPluginControlIntegration = self.loadPlugin(self._strPluginControlIntegration, \
                                                            "Integration")
        self._edPluginControlXDSGenerateBackgroundImage = self.loadPlugin(self._strPluginControlXDSGenerateBackgroundImage, \
                                                            "ControlXDSGenerateBackgroundImage")
        self._edPluginControlStrategy = self.loadPlugin(self._strPluginControlStrategy, \
                                                         "Strategy")
        if self._runKappa:
            self._edPluginControlKappa = self.loadPlugin(
                self._strPluginControlKappaName, "Kappa")
        if (self._edPluginControlIndexingIndicators is not None):
            self.DEBUG("EDPluginControlCharacterisationv1_4.preProcess: " +
                       self._strPluginControlIndexingIndicators +
                       " Found... setting Data Input")
            # create Data Input for indexing
            xsDataInputCharacterisation = self.getDataInput()
            self._xsDataCollection = xsDataInputCharacterisation.getDataCollection(
            )
            # MXSUP-1445: Check if transmission is less than 10% and warn if it's the case
            xsDataFirstSubWedge = self._xsDataCollection.getSubWedge()[0]
            xsDataBeam = xsDataFirstSubWedge.getExperimentalCondition(
            ).getBeam()
            if xsDataBeam.getTransmission() is not None:
                fTransmission = xsDataBeam.getTransmission().getValue()
                if fTransmission < self._fMinTransmission:
                    strWarningMessageBanner = "^" * 80
                    strWarningMessage1 = "WARNING! Transmission for characterisation set to %.1f %%" % fTransmission
                    strWarningMessage2 = "Please consider re-characterising with transmission set to 100 %"
                    self.warning(strWarningMessageBanner)
                    self.warning(strWarningMessage1)
                    self.warning(strWarningMessage2)
                    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_4.preProcess: No subwedges in input data."
                self.ERROR(strError)
                self.setFailure()
            else:
                # Load the thumbnail plugins
                self._iNoReferenceImages = 0
                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))
                        edPluginJpeg.execute()
                        edPluginThumnail.execute()
                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_4.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()))
    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 testGetXSDataRaddoseInput(self):
        """
        """
        from XSDataCommon import XSDataLength
        from XSDataCommon import XSDataWavelength
        from XSDataCommon import XSDataFlux
        from XSDataCommon import XSDataSize
        from XSDataCommon import XSDataDouble
        from XSDataCommon import XSDataString
        from XSDataCommon import XSDataAngle
        from XSDataCommon import XSDataTime
        from XSDataCommon import XSDataInteger

        from XSDataMXv1 import XSDataBeam
        from XSDataMXv1 import XSDataStructure
        from XSDataMXv1 import XSDataChain
        from XSDataMXv1 import XSDataAtom
        from XSDataMXv1 import XSDataLigand
        from XSDataMXv1 import XSDataCrystal
        from XSDataMXv1 import XSDataSpaceGroup
        from XSDataMXv1 import XSDataSampleCrystalMM
        from XSDataMXv1 import XSDataChemicalCompositionMM
        from XSDataMXv1 import XSDataAtomicComposition
        from XSDataMXv1 import XSDataSolvent
        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))
        xsDataBeam.setExposureTime(XSDataTime(0.037))

        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
        iNumberOfImages = 2

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

        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())
    def preProcess(self, _edObject=None):
        EDPluginControl.preProcess(self)
        EDVerbose.DEBUG("EDPluginControlCharacterisationv1_3.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._edPluginControlXDSGenerateBackgroundImage = self.loadPlugin(self._strPluginControlXDSGenerateBackgroundImage, \
                                                            "ControlXDSGenerateBackgroundImage")
        self._edPluginControlStrategy = self.loadPlugin(self._strPluginControlStrategy, \
                                                         "Strategy")
        if (self._edPluginControlIndexingIndicators is not None):
            EDVerbose.DEBUG("EDPluginControlCharacterisationv1_3.preProcess: " + self._strPluginControlIndexingIndicators + " Found... setting Data Input")
            # create Data Input for indexing
            xsDataInputCharacterisation = self.getDataInput()
            self._xsDataCollection = xsDataInputCharacterisation.getDataCollection()
            # MXSUP-1445: Check if transmission is less than 10% and warn if it's the case
            xsDataFirstSubWedge = self._xsDataCollection.getSubWedge()[0]
            xsDataBeam = xsDataFirstSubWedge.getExperimentalCondition().getBeam()
            if xsDataBeam.getTransmission() is not None:
                fTransmission = xsDataBeam.getTransmission().getValue()
                if fTransmission < self._fMinTransmission:
                    strWarningMessageBanner = "^"*80 
                    strWarningMessage1 = "WARNING! Transmission for characterisation set to %.1f %%" % fTransmission
                    strWarningMessage2 = "Please consider re-characterising with transmission set to 100 %" 
                    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."
                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_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()))
Example #14
0
    def preProcess(self, _edObject=None):
        EDPluginControl.preProcess(self)
        EDVerbose.DEBUG("EDPluginControlCharacterisationv1_3.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._edPluginControlXDSGenerateBackgroundImage = self.loadPlugin(self._strPluginControlXDSGenerateBackgroundImage, \
                                                            "ControlXDSGenerateBackgroundImage")
        self._edPluginControlStrategy = self.loadPlugin(self._strPluginControlStrategy, \
                                                         "Strategy")
        if (self._edPluginControlIndexingIndicators is not None):
            EDVerbose.DEBUG(
                "EDPluginControlCharacterisationv1_3.preProcess: " +
                self._strPluginControlIndexingIndicators +
                " Found... setting Data Input")
            # create Data Input for indexing
            xsDataInputCharacterisation = self.getDataInput()
            self._xsDataCollection = xsDataInputCharacterisation.getDataCollection(
            )
            # MXSUP-1445: Check if transmission is less than 10% and warn if it's the case
            xsDataFirstSubWedge = self._xsDataCollection.getSubWedge()[0]
            xsDataBeam = xsDataFirstSubWedge.getExperimentalCondition(
            ).getBeam()
            if xsDataBeam.getTransmission() is not None:
                fTransmission = xsDataBeam.getTransmission().getValue()
                if fTransmission < self._fMinTransmission:
                    strWarningMessageBanner = "^" * 80
                    strWarningMessage1 = "WARNING! Transmission for characterisation set to %.1f %%" % fTransmission
                    strWarningMessage2 = "Please consider re-characterising with transmission set to 100 %"
                    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."
                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_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()))
    def testSetDataModelInput(self):
        edPluginStrategy = self.createPlugin()
        strPathToTestConfigFile = os.path.join(self.getPluginTestsDataHome(),
                                               "XSConfiguration_ESRF.xml")
        edConfiguration = EDConfiguration(strPathToTestConfigFile)
        dictItem = edConfiguration.get(edPluginStrategy.getPluginName())
        edPluginStrategy.setConfig(dictItem)
        edPluginStrategy.configure()

        xsDataStrategy = XSDataInputStrategy()

        # Beam

        xsExperimentalCondition = XSDataExperimentalCondition()

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

        xsExperimentalCondition.setBeam(xsBeam)

        # Detector and Exposure Time

        xsDataDetector = XSDataDetector()
        xsDataDetector.setType(XSDataString("q210-2x"))
        xsExperimentalCondition.setDetector(xsDataDetector)

        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())
    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 preProcess(self, _edObject=None):
        EDPluginControl.preProcess(self)
        self.DEBUG("EDPluginControlCharacterisationv1_5.preProcess")
        self._xsDataResultCharacterisation = XSDataResultCharacterisation()
        # Load the plugins
        self._edPluginControlIndexingIndicators = self.loadPlugin(self._strPluginControlIndexingIndicators, \
                                                                   "Indexing")
        self._edPluginExecEvaluationIndexingLABELIT = self.loadPlugin(self._strPluginExecEvaluationIndexing, \
                                                                   "IndexingEvalualtionLABELIT")
        self._edPluginControlIndexingMOSFLM = self.loadPlugin(self._strPluginControlIndexingMOSFLM, \
                                                                   "IndexingMOSFLM")
        self._edPluginExecEvaluationIndexingMOSFLM = self.loadPlugin(self._strPluginExecEvaluationIndexing, \
                                                                   "IndexingEvalualtionMOSFLM")
        self._edPluginControlGeneratePrediction = self.loadPlugin(self._strPluginControlGeneratePrediction, \
                                                                   "GeneratePrediction")
        self._edPluginControlIntegration = self.loadPlugin(self._strPluginControlIntegration, \
                                                            "Integration")
        self._edPluginControlXDSGenerateBackgroundImage = self.loadPlugin(self._strPluginControlXDSGenerateBackgroundImage, \
                                                            "ControlXDSGenerateBackgroundImage")
        self._edPluginControlStrategy = self.loadPlugin(self._strPluginControlStrategy, \
                                                         "Strategy")
        if self._runKappa:
            self._edPluginControlKappa = self.loadPlugin(self._strPluginControlKappaName, "Kappa")
        if (self._edPluginControlIndexingIndicators is not None):
            self.DEBUG("EDPluginControlCharacterisationv1_5.preProcess: " + self._strPluginControlIndexingIndicators + " Found... setting Data Input")
            # create Data Input for indexing
            xsDataInputCharacterisation = self.getDataInput()
            self._xsDataCollection = xsDataInputCharacterisation.getDataCollection()
            # MXSUP-1445: Check if transmission is less than 10% and warn if it's the case
            xsDataFirstSubWedge = self._xsDataCollection.getSubWedge()[0]
            xsDataBeam = xsDataFirstSubWedge.getExperimentalCondition().getBeam()
            if xsDataBeam.getTransmission() is not None:
                fTransmission = xsDataBeam.getTransmission().getValue()
                if fTransmission < self._fMinTransmission:
                    strWarningMessageBanner = "^"*80
                    strWarningMessage1 = "WARNING! Transmission for characterisation set to %.1f %%" % fTransmission
                    strWarningMessage2 = "Please consider re-characterising with transmission set to 100 %"
                    self.warning(strWarningMessageBanner)
                    self.warning(strWarningMessage1)
                    self.warning(strWarningMessage2)
                    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))
    def testGetXSDataRaddoseInput(self):
        """
        """
        from XSDataCommon import XSDataLength
        from XSDataCommon import XSDataWavelength
        from XSDataCommon import XSDataFlux
        from XSDataCommon import XSDataSize
        from XSDataCommon import XSDataDouble
        from XSDataCommon import XSDataString
        from XSDataCommon import XSDataAngle
        from XSDataCommon import XSDataTime
        from XSDataCommon import XSDataInteger

        from XSDataMXv1   import XSDataBeam
        from XSDataMXv1   import XSDataStructure
        from XSDataMXv1   import XSDataChain
        from XSDataMXv1   import XSDataAtom
        from XSDataMXv1   import XSDataLigand
        from XSDataMXv1   import XSDataCrystal
        from XSDataMXv1   import XSDataSpaceGroup
        from XSDataMXv1   import XSDataSampleCrystalMM
        from XSDataMXv1   import XSDataChemicalCompositionMM
        from XSDataMXv1   import XSDataAtomicComposition
        from XSDataMXv1   import XSDataSolvent
        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())
    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()))