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()))
Esempio n. 3
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    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()))
Esempio n. 5
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    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())
            )
    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
Esempio n. 8
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    def generateXSDataIndexingResult(_xsDataLabelitScreenOutput, _xsDataLabelitMosflmScriptsOutput, \
                                     _xsDataExperimentalCondition=None):
        EDVerbose.DEBUG(
            "EDHandlerXSDataLabelitv1_1.generateXSDataIndexingOutput")

        iSelectedSolutionNumber = _xsDataLabelitScreenOutput.getSelectedSolutionNumber(
        ).getValue()

        xsDataIndexingResult = XSDataIndexingResult()
        xsDataIndexingSolutionSelected = None

        for xsDataLabelitSolution in _xsDataLabelitScreenOutput.getLabelitScreenSolution(
        ):
            xsDataCrystal = XSDataCrystal()
            xsDataSpaceGroup = XSDataSpaceGroup()
            edStringSpaceGroupName = EDUtilsSymmetry.getMinimumSymmetrySpaceGroupFromBravaisLattice(
                xsDataLabelitSolution.getBravaisLattice().getValue())
            xsDataSpaceGroup.setName(XSDataString(edStringSpaceGroupName))
            xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
            xsDataCrystal.setCell(xsDataLabelitSolution.getUnitCell())
            xsDataIndexingSolution = XSDataIndexingSolution()
            xsDataIndexingSolution.setCrystal(xsDataCrystal)
            iIndex = xsDataLabelitSolution.getSolutionNumber().getValue()
            xsDataIndexingSolution.setNumber(XSDataInteger(iIndex))
            xsDataIndexingResult.addSolution(xsDataIndexingSolution)
            if (iIndex == iSelectedSolutionNumber):
                xsDataIndexingSolutionSelected = XSDataIndexingSolutionSelected(
                )
                xsDataIndexingSolutionSelected.setNumber(XSDataInteger(iIndex))
                edStringSelectedSpaceGroupName = edStringSpaceGroupName
                xsDataCellSelected = xsDataLabelitSolution.getUnitCell()
                fRmsdSelected = xsDataLabelitSolution.getRmsd().getValue()
                iNumberOfSpotsSelected = xsDataLabelitSolution.getNumberOfSpots(
                ).getValue()

        xsDataCrystalSelected = XSDataCrystal()
        xsDataSpaceGroupSelected = XSDataSpaceGroup()
        xsDataSpaceGroupSelected.setName(
            XSDataString(edStringSelectedSpaceGroupName))
        #xsDataSpaceGroupSelected.setITNumber( XSDataInteger( iSelectedSpaceGroupNumber ) )
        xsDataCrystalSelected.setSpaceGroup(xsDataSpaceGroupSelected)
        xsDataCrystalSelected.setCell(xsDataCellSelected)
        xsDataCrystalSelected.setMosaicity(
            XSDataDouble(_xsDataLabelitScreenOutput.getMosaicity().getValue()))
        xsDataIndexingSolutionSelected.setCrystal(xsDataCrystalSelected)

        xsDataOrientation = XSDataOrientation()
        xsDataOrientation.setMatrixA(
            _xsDataLabelitMosflmScriptsOutput.getAMatrix())
        xsDataOrientation.setMatrixU(
            _xsDataLabelitMosflmScriptsOutput.getUMatrix())
        xsDataIndexingSolutionSelected.setOrientation(xsDataOrientation)

        xsDataStatisticsIndexing = XSDataStatisticsIndexing()

        if (_xsDataExperimentalCondition is not None):
            fBeamPositionXOrig = _xsDataExperimentalCondition.getDetector(
            ).getBeamPositionX().getValue()
            fBeamPositionYOrig = _xsDataExperimentalCondition.getDetector(
            ).getBeamPositionY().getValue()
            fBeamPositionXNew = _xsDataLabelitScreenOutput.getBeamCentreX(
            ).getValue()
            fBeamPositionYNew = _xsDataLabelitScreenOutput.getBeamCentreY(
            ).getValue()
            xsDataStatisticsIndexing.setBeamPositionShiftX(
                XSDataLength(fBeamPositionXOrig - fBeamPositionXNew))
            xsDataStatisticsIndexing.setBeamPositionShiftY(
                XSDataLength(fBeamPositionYOrig - fBeamPositionYNew))

        #xsDataStatisticsIndexing.setSpotDeviXSDataLength( dDistanceRefinedationAngular( XSDataAngle( dDeviationAngular ) )
        xsDataStatisticsIndexing.setSpotDeviationPositional(
            XSDataLength(fRmsdSelected))
        xsDataStatisticsIndexing.setSpotsUsed(
            XSDataInteger(iNumberOfSpotsSelected))
        xsDataStatisticsIndexing.setSpotsTotal(
            XSDataInteger(iNumberOfSpotsSelected))
        xsDataIndexingSolutionSelected.setStatistics(xsDataStatisticsIndexing)

        xsDataExperimentalConditionRefined = None
        if (_xsDataExperimentalCondition is None):
            xsDataExperimentalConditionRefined = XSDataExperimentalCondition()
        else:
            # Copy the incoming experimental condition
            xmlExperimentalCondition = _xsDataExperimentalCondition.marshal()
            xsDataExperimentalConditionRefined = XSDataExperimentalCondition.parseString(
                xmlExperimentalCondition)

        xsDataDetector = xsDataExperimentalConditionRefined.getDetector()
        if (xsDataDetector is None):
            xsDataDetector = XSDataDetector()

        xsDataDetector.setBeamPositionX(
            _xsDataLabelitScreenOutput.getBeamCentreX())
        xsDataDetector.setBeamPositionY(
            _xsDataLabelitScreenOutput.getBeamCentreY())
        xsDataDetector.setDistance(_xsDataLabelitScreenOutput.getDistance())

        xsDataExperimentalConditionRefined.setDetector(xsDataDetector)
        xsDataIndexingSolutionSelected.setExperimentalConditionRefined(
            xsDataExperimentalConditionRefined)

        xsDataIndexingResult.setSelectedSolution(
            xsDataIndexingSolutionSelected)

        xsDataIndexingResult.setIndexingLogFile(
            _xsDataLabelitScreenOutput.getPathToLogFile())

        return xsDataIndexingResult
    def generateXSDataIndexingResult(_xsDataResultLabelitIndexing, _xsDataExperimentalCondition=None):
        EDVerbose.DEBUG("EDHandlerXSDataLabelitv1_1.generateXSDataIndexingOutput")

        xsDataLabelitScreenOutput = _xsDataResultLabelitIndexing.screenOutput
        xsDataLabelitMosflmScriptsOutput = _xsDataResultLabelitIndexing.mosflmScriptsOutput

        iSelectedSolutionNumber = xsDataLabelitScreenOutput.getSelectedSolutionNumber().getValue()

        xsDataIndexingResult = XSDataIndexingResult()
        xsDataIndexingSolutionSelected = None

        for xsDataLabelitSolution in xsDataLabelitScreenOutput.getLabelitScreenSolution():
            xsDataCrystal = XSDataCrystal()
            xsDataSpaceGroup = XSDataSpaceGroup()
            edStringSpaceGroupName = EDUtilsSymmetry.getMinimumSymmetrySpaceGroupFromBravaisLattice(xsDataLabelitSolution.getBravaisLattice().getValue())
            xsDataSpaceGroup.setName(XSDataString(edStringSpaceGroupName))
            xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
            xsDataCrystal.setCell(xsDataLabelitSolution.getUnitCell())
            xsDataIndexingSolution = XSDataIndexingSolution()
            xsDataIndexingSolution.setCrystal(xsDataCrystal)
            iIndex = xsDataLabelitSolution.getSolutionNumber().getValue()
            xsDataIndexingSolution.setNumber(XSDataInteger(iIndex))
            xsDataIndexingResult.addSolution(xsDataIndexingSolution)
            if (iIndex == iSelectedSolutionNumber):
                xsDataIndexingSolutionSelected = XSDataIndexingSolutionSelected()
                xsDataIndexingSolutionSelected.setNumber(XSDataInteger(iIndex))
                edStringSelectedSpaceGroupName = edStringSpaceGroupName
                xsDataCellSelected = xsDataLabelitSolution.getUnitCell()
                fRmsdSelected = xsDataLabelitSolution.getRmsd().getValue()
                iNumberOfSpotsSelected = xsDataLabelitSolution.getNumberOfSpots().getValue()

        xsDataCrystalSelected = XSDataCrystal()
        xsDataSpaceGroupSelected = XSDataSpaceGroup()
        xsDataSpaceGroupSelected.setName(XSDataString(edStringSelectedSpaceGroupName))
        xsDataSpaceGroupSelected.setITNumber(XSDataInteger(EDUtilsSymmetry.getITNumberFromSpaceGroupName(edStringSelectedSpaceGroupName)))
        xsDataCrystalSelected.setSpaceGroup(xsDataSpaceGroupSelected)
        xsDataCrystalSelected.setCell(xsDataCellSelected)
        xsDataCrystalSelected.setMosaicity(XSDataDouble(xsDataLabelitScreenOutput.getMosaicity().getValue()))
        xsDataIndexingSolutionSelected.setCrystal(xsDataCrystalSelected)

        xsDataOrientation = XSDataOrientation()
        xsDataOrientation.setMatrixA(xsDataLabelitMosflmScriptsOutput.getAMatrix())
        xsDataOrientation.setMatrixU(xsDataLabelitMosflmScriptsOutput.getUMatrix())
        xsDataIndexingSolutionSelected.setOrientation(xsDataOrientation)

        xsDataStatisticsIndexing = XSDataStatisticsIndexing()

        if (_xsDataExperimentalCondition is not None):
            fBeamPositionXOrig = _xsDataExperimentalCondition.getDetector().getBeamPositionX().getValue()
            fBeamPositionYOrig = _xsDataExperimentalCondition.getDetector().getBeamPositionY().getValue()
            fBeamPositionXNew = xsDataLabelitScreenOutput.getBeamCentreX().getValue()
            fBeamPositionYNew = xsDataLabelitScreenOutput.getBeamCentreY().getValue()
            xsDataStatisticsIndexing.setBeamPositionShiftX(XSDataLength(fBeamPositionXOrig - fBeamPositionXNew))
            xsDataStatisticsIndexing.setBeamPositionShiftY(XSDataLength(fBeamPositionYOrig - fBeamPositionYNew))

        # xsDataStatisticsIndexing.setSpotDeviXSDataLength( dDistanceRefinedationAngular( XSDataAngle( dDeviationAngular ) )
        xsDataStatisticsIndexing.setSpotDeviationPositional(XSDataLength(fRmsdSelected))
        xsDataStatisticsIndexing.setSpotsUsed(XSDataInteger(iNumberOfSpotsSelected))
        xsDataStatisticsIndexing.setSpotsTotal(XSDataInteger(iNumberOfSpotsSelected))
        xsDataIndexingSolutionSelected.setStatistics(xsDataStatisticsIndexing)

        xsDataExperimentalConditionRefined = None
        if (_xsDataExperimentalCondition is None):
            xsDataExperimentalConditionRefined = XSDataExperimentalCondition()
        else:
            # Copy the incoming experimental condition
            xmlExperimentalCondition = _xsDataExperimentalCondition.marshal()
            xsDataExperimentalConditionRefined = XSDataExperimentalCondition.parseString(xmlExperimentalCondition)

        xsDataDetector = xsDataExperimentalConditionRefined.getDetector()
        if (xsDataDetector is None):
            xsDataDetector = XSDataDetector()

        xsDataDetector.setBeamPositionX(xsDataLabelitScreenOutput.getBeamCentreX())
        xsDataDetector.setBeamPositionY(xsDataLabelitScreenOutput.getBeamCentreY())
        xsDataDetector.setDistance(xsDataLabelitScreenOutput.getDistance())

        xsDataExperimentalConditionRefined.setDetector(xsDataDetector)
        xsDataIndexingSolutionSelected.setExperimentalConditionRefined(xsDataExperimentalConditionRefined)

        xsDataIndexingResult.setSelectedSolution(xsDataIndexingSolutionSelected)

        xsDataIndexingResult.setIndexingLogFile(xsDataLabelitScreenOutput.getPathToLogFile())

        return xsDataIndexingResult
Esempio n. 10
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    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 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 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 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()))
Esempio n. 14
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    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 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()))