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Python XSDataMXv1.XSDataCrystal类代码示例

本文整理汇总了Python中XSDataMXv1.XSDataCrystal的典型用法代码示例。如果您正苦于以下问题:Python XSDataCrystal类的具体用法?Python XSDataCrystal怎么用?Python XSDataCrystal使用的例子?那么, 这里精选的类代码示例或许可以为您提供帮助。


在下文中一共展示了XSDataCrystal类的15个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于系统推荐出更棒的Python代码示例。

示例1: testDefaultChemicalComposition

    def testDefaultChemicalComposition(self):
        edPluginStrategy = self.createPlugin()

        from XSDataCommon import XSDataAngle
        from XSDataCommon import XSDataLength
        from XSDataMXv1 import XSDataSampleCrystalMM
        from XSDataMXv1 import XSDataCrystal
        from XSDataMXv1 import XSDataCell


        xsDataSampleCrystalMM = XSDataSampleCrystalMM()
        xsDataCrystal = XSDataCrystal()
        xsDataCell = XSDataCell(XSDataAngle(90.0),
                                 XSDataAngle(90.0),
                                 XSDataAngle(90.0),
                                 XSDataLength(78.9),
                                 XSDataLength(95.162),
                                 XSDataLength(104.087))
        xsDataCrystal.setCell(xsDataCell)
        xsDataSampleCrystalMM.setCrystal(xsDataCrystal)
        inumOperators = 4

        xsDataSample2 = edPluginStrategy.getDefaultChemicalComposition(xsDataSampleCrystalMM, inumOperators)
        strChainType = xsDataSample2.getStructure().getChain()[0].getType()
        EDAssert.equal("protein", strChainType.getValue())
开发者ID:antolinos,项目名称:edna,代码行数:25,代码来源:EDTestCasePluginUnitControlStrategyv1_1.py

示例2: preProcess

    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()))
开发者ID:antolinos,项目名称:edna,代码行数:52,代码来源:EDPluginControlCharacterisationv1_1.py

示例3: preProcess

    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()))
开发者ID:antolinos,项目名称:edna,代码行数:59,代码来源:EDPluginControlCharacterisationv1_3.py

示例4: preProcess

    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())
            )
开发者ID:gbourgh,项目名称:edna,代码行数:46,代码来源:EDPluginControlCharacterisationv2_0.py

示例5: generateXSDataIndexingResult

    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
开发者ID:IvarsKarpics,项目名称:edna-mx,代码行数:56,代码来源:EDHandlerXSDataXDSv1_0.py

示例6: testDefaultChemicalComposition

    def testDefaultChemicalComposition(self):
        edPluginStrategy = self.createPlugin()

        xsDataSampleCrystalMM = XSDataSampleCrystalMM()
        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)
        xsDataSampleCrystalMM.setCrystal(xsDataCrystal)
        inumOperators = 4

        xsDataSample2 = edPluginStrategy.getDefaultChemicalComposition(xsDataSampleCrystalMM, inumOperators)
        pyStrChainType = xsDataSample2.getStructure().getChain()[0].getType()
        EDAssert.equal("protein", pyStrChainType.getValue())
开发者ID:IvarsKarpics,项目名称:edna-mx,代码行数:18,代码来源:EDTestCasePluginUnitControlStrategyv1_3.py

示例7: EDPluginControlCharacterisationv1_2

class EDPluginControlCharacterisationv1_2(EDPluginControl):
    """
    [To be replaced with a description of EDPluginControlTemplatev10]
    """


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



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


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

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

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

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

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

#.........这里部分代码省略.........
开发者ID:antolinos,项目名称:edna,代码行数:101,代码来源:EDPluginControlCharacterisationv1_2.py

示例8: testSetDataModelInput


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

        xsDataStrategy.setExperimentalCondition(xsExperimentalCondition)


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

        # Crystal

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

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

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

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

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

        xsDataSolvent = XSDataSolvent()
        xsDataAtomicComposition = XSDataAtomicComposition()

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

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

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

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

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

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

        xsDataSampleCrystalMM.setSusceptibility(XSDataDouble(1.5))

        xsDataStrategy.setCrystalRefined(xsDataCrystal)

        xsDataStrategy.setSample(xsDataSampleCrystalMM)

        xsDataStrategy.exportToFile(self.strObtainedInputFile)

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

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

        EDAssert.equal(xsDataInputExpected.marshal(), xsDataInputObtained.marshal())
开发者ID:IvarsKarpics,项目名称:edna-mx,代码行数:101,代码来源:EDTestCasePluginUnitControlStrategyv1_3.py

示例9: generateXSDataIndexingResult

    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
开发者ID:IvarsKarpics,项目名称:edna-mx,代码行数:85,代码来源:EDHandlerXSDataPhenixv1_1.py

示例10: testGetXSDataRaddoseInput

    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()
#.........这里部分代码省略.........
开发者ID:antolinos,项目名称:edna,代码行数:101,代码来源:EDTestCaseEDHandlerRaddosev10.py

示例11: EDPluginControlCharacterisationv1_5


#.........这里部分代码省略.........
                    self.warning(strWarningMessageBanner)
                    self.warning(strWarningMessage1)
                    self.warning(strWarningMessage2)
                    self.warning(strWarningMessageBanner)
                    self.addWarningMessage(strWarningMessageBanner)
                    self.addWarningMessage(strWarningMessage1)
                    self.addWarningMessage(strWarningMessage2)
                    self.addWarningMessage(strWarningMessageBanner)
                    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
开发者ID:IvarsKarpics,项目名称:edna-mx,代码行数:67,代码来源:EDPluginControlCharacterisationv1_5.py

示例12: preProcess

    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)
#.........这里部分代码省略.........
开发者ID:IvarsKarpics,项目名称:edna-mx,代码行数:101,代码来源:EDPluginControlCharacterisationv1_5.py

示例13: generateXSDataIndexingResult

    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
开发者ID:olofsvensson,项目名称:edna-plugins-mx,代码行数:86,代码来源:EDHandlerXSDataMOSFLMv10.py

示例14: preProcess

    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()))
开发者ID:edna-site,项目名称:edna,代码行数:76,代码来源:EDPluginControlCharacterisationv1_3.py

示例15: EDPluginControlCharacterisationv1_3


#.........这里部分代码省略.........
                    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."
                self.ERROR(strError)
                self.setFailure()
            else:
                xsDataExperimentalCondition = xsDataSubWedgeList[0].getExperimentalCondition()

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

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

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

                # Populate characterisation object
                self._xsDataResultCharacterisation = XSDataResultCharacterisation()
                self._xsDataResultCharacterisation.setDataCollection(XSDataCollection.parseString(self._xsDataCollection.marshal()))
            # Load the thumbnail plugins
            for subWedge in xsDataInputCharacterisation.dataCollection.subWedge:
                for image in subWedge.image:
                    edPluginJpeg = self.loadPlugin(self._strPluginGenerateThumbnailName)
                    xsDataInputMXThumbnail = XSDataInputMXThumbnail()
                    xsDataInputMXThumbnail.image = XSDataFile(image.path)
                    xsDataInputMXThumbnail.height = XSDataInteger(1024)
                    xsDataInputMXThumbnail.width = XSDataInteger(1024)
                    jpegFilename = os.path.splitext(os.path.basename(image.path.value))[0]+".jpg"
                    xsDataInputMXThumbnail.outputPath = XSDataFile(XSDataString(os.path.join(self.getWorkingDirectory(), jpegFilename)))
                    edPluginJpeg.dataInput = xsDataInputMXThumbnail
                    edPluginThumnail = self.loadPlugin(self._strPluginGenerateThumbnailName)
                    xsDataInputMXThumbnail = XSDataInputMXThumbnail()
                    xsDataInputMXThumbnail.image = XSDataFile(image.path)
                    xsDataInputMXThumbnail.height = XSDataInteger(256)
                    xsDataInputMXThumbnail.width = XSDataInteger(256)
                    thumbnailFilename = os.path.splitext(os.path.basename(image.path.value))[0]+".thumbnail.jpg"
                    xsDataInputMXThumbnail.outputPath = XSDataFile(XSDataString(os.path.join(self.getWorkingDirectory(), thumbnailFilename)))
                    edPluginThumnail.dataInput = xsDataInputMXThumbnail
                    self._listPluginGenerateThumbnail.append((image, edPluginJpeg, edPluginThumnail))
开发者ID:IvarsKarpics,项目名称:edna-mx,代码行数:66,代码来源:EDPluginControlCharacterisationv1_3.py


注:本文中的XSDataMXv1.XSDataCrystal类示例由纯净天空整理自Github/MSDocs等开源代码及文档管理平台,相关代码片段筛选自各路编程大神贡献的开源项目,源码版权归原作者所有,传播和使用请参考对应项目的License;未经允许,请勿转载。