Python XSDataDiffractionPlan.setMaxExposureTimePerDataCollection方法代碼示例

# 需要導入模塊: from XSDataMXv1 import XSDataDiffractionPlan [as 別名]
# 或者: from XSDataMXv1.XSDataDiffractionPlan import setMaxExposureTimePerDataCollection [as 別名]
def functionXMLin(_strFilename):
    """Here we create the XML string to be passed to the EDNA plugin from the input strFilename
    This can / should be modified by the final user
    
    @param _strFilename: full path of the input file
    @type _strFilename: python string representing the path
    @return: string  
    """
    EDVerbose.screen("Starting processing of image %s" % (_strFilename))
    # First check if the filename end with .img or .mccd:
    strXML = None
    if _strFilename.endswith(".img") or _strFilename.endswith(".mccd") or _strFilename.endswith(".cbf"):
        xsDataInputGridScreening = XSDataInputGridScreening()
        xsDataDiffractionPlan = XSDataDiffractionPlan()
        xsDataDiffractionPlan.setMaxExposureTimePerDataCollection(
            XSDataTime(EDParallelExecuteGridScreening.fMaxExposureTime)
        )
        xsDataInputGridScreening.setDiffractionPlan(xsDataDiffractionPlan)
        xsDataFile = XSDataFile()
        xsDataFile.setPath(XSDataString(_strFilename))
        xsDataInputGridScreening.setImageFile(xsDataFile)
        if EDParallelExecuteGridScreening.bOnlyImageQualityIndicators:
            xsDataInputGridScreening.setDoOnlyImageQualityIndicators(XSDataBoolean(True))
        if EDParallelExecuteGridScreening.bStoreInISPyB:
            xsDataInputGridScreening.setStoreImageQualityIndicatorsInISPyB(XSDataBoolean(True))
        if EDParallelExecuteGridScreening.bDoOnlyIntegrationWithXMLOutput:
            xsDataInputGridScreening.setDoOnlyIntegrationWithXMLOutput(XSDataBoolean(True))
        strXML = xsDataInputGridScreening.marshal()
    else:
        EDVerbose.screen("File name not ending with .img or .mccd - ignored : %s" % _strFilename)
    return strXML

# 需要導入模塊: from XSDataMXv1 import XSDataDiffractionPlan [as 別名]
# 或者: from XSDataMXv1.XSDataDiffractionPlan import setMaxExposureTimePerDataCollection [as 別名]
    def setPluginInput(self, _edPlugin):
        xsDataDiffractionPlan = XSDataDiffractionPlan()
        if (not self.__fMaxExposureTimePerDataCollection is None):
            xsDataDiffractionPlan.setMaxExposureTimePerDataCollection(XSDataTime(self.__fMaxExposureTimePerDataCollection))
        if (not self.__strForcedSpaceGroup is None):
            xsDataDiffractionPlan.setForcedSpaceGroup(XSDataString(self.__strForcedSpaceGroup))
        if (not self.__bAnomalousData is None):
            xsDataDiffractionPlan.setAnomalousData(XSDataBoolean(self.__bAnomalousData))
        if (not self.__strStrategyOption is None):
            xsDataDiffractionPlan.setStrategyOption(XSDataString(self.__strStrategyOption))
        if (not self.__strComplexity is None):
            xsDataDiffractionPlan.setComplexity(XSDataString(self.__strComplexity))
        _edPlugin.setDataInput(xsDataDiffractionPlan, "diffractionPlan")

        if (not self.__listImagePaths is None):
            for strImagePath in self.__listImagePaths:
                _edPlugin.setDataInput(XSDataString(strImagePath), "imagePaths")

        if (not self.__xsDataInputCharacterisation is None):
            _edPlugin.setDataInput(self.__xsDataInputCharacterisation, "inputCharacterisation")
        if (not self.__fFlux is None):
            _edPlugin.setDataInput(XSDataFloat(self.__fFlux), "flux")
        if (not self.__fMinExposureTimePerImage is None):
            _edPlugin.setDataInput(XSDataFloat(self.__fMinExposureTimePerImage), "minExposureTimePerImage")
        if (not self.__fBeamSize is None):
            _edPlugin.setDataInput(XSDataFloat(self.__fBeamSize), "beamSize")
        if (not self.__bTemplateMode is None):
            _edPlugin.setDataInput(XSDataBoolean(self.__bTemplateMode), "templateMode")
        if (not self.__strGeneratedTemplateFile is None):
            _edPlugin.setDataInput(XSDataString(self.__strGeneratedTemplateFile), "generatedTemplateFile")
        if (not self.__strResultsFilePath is None):
            _edPlugin.setDataInput(XSDataString(self.__strResultsFilePath), "resultsFilePath")
        if (not self.__fBeamPosX is None):
            _edPlugin.setDataInput(XSDataFloat(self.__fBeamPosX), "beamPosX")
        if (not self.__fBeamPosY is None):
            _edPlugin.setDataInput(XSDataFloat(self.__fBeamPosY), "beamPosY")
        if (not self.__iDataCollectionId is None):
            _edPlugin.setDataInput(XSDataInteger(self.__iDataCollectionId), "dataCollectionId")
        if (not self.__strShortComments is None):
            _edPlugin.setDataInput(XSDataString(self.__strShortComments), "shortComments")
        if (not self.__strComments is None):
            _edPlugin.setDataInput(XSDataString(self.__strComments), "comments")
        if (not self.__fTransmission is None):
            _edPlugin.setDataInput(XSDataDouble(self.__fTransmission), "transmission")

# 需要導入模塊: from XSDataMXv1 import XSDataDiffractionPlan [as 別名]
# 或者: from XSDataMXv1.XSDataDiffractionPlan import setMaxExposureTimePerDataCollection [as 別名]
def functionXMLin(_strFilename):
    """Here we create the XML string to be passed to the EDNA plugin from the input strFilename
    This can / should be modified by the final user
    
    @param _strFilename: full path of the input file
    @type _strFilename: python string representing the path
    @return: string  
    """
    EDVerbose.screen("Starting processing of image %s" % (_strFilename))
    # First check if the filename end with .img or .mccd:
    strXML = None
    if (_strFilename.endswith(".img") or _strFilename.endswith(".mccd") or _strFilename.endswith(".cbf")):
        xsDataInputInterface = XSDataInputInterface()
        xsDataDiffractionPlan = XSDataDiffractionPlan()
        xsDataDiffractionPlan.setMaxExposureTimePerDataCollection(XSDataTime(EDParallelExecuteMXv1Characterisation.m_fMaxExposureTime))
        xsDataInputInterface.setDiffractionPlan(xsDataDiffractionPlan)
        xsDataFile = XSDataFile()
        xsDataFile.setPath(XSDataString(_strFilename))
        xsDataInputInterface.addImagePath(xsDataFile)
        strXML = xsDataInputInterface.marshal()
    else:
        EDVerbose.screen("File name not ending with .img or .mccd - ignored : %s" % _strFilename)
    return strXML

# 需要導入模塊: from XSDataMXv1 import XSDataDiffractionPlan [as 別名]
# 或者: from XSDataMXv1.XSDataDiffractionPlan import setMaxExposureTimePerDataCollection [as 別名]
 def createInputCharacterisationFromSubWedges(self):
     self.DEBUG("EDPluginControlInterfacev2_0.createInputCharacterisationFromSubWedges")
     xsDataResultSubWedgeAssemble = self.edPluginControlSubWedgeAssemble.getDataOutput()
     self.xsDataInputCharacterisation = XSDataInputCharacterisation()
     xsDataCollection = XSDataCollection()
     # Default exposure time (for the moment, this value should be
     # possible to read from the command line)
     xsDataDiffractionPlan = XSDataDiffractionPlan()
     if (not xsDataResultSubWedgeAssemble is None):
         pyListSubWedge = xsDataResultSubWedgeAssemble.getSubWedge()
         xsDataCollection.setSubWedge(pyListSubWedge)
         for xsDataSubWedge in pyListSubWedge:
             if (self.strComplexity is not None):
                 xsDataDiffractionPlan.setComplexity(XSDataString(self.strComplexity))
             if (self.fFlux is not None):
                 xsDataSubWedge.getExperimentalCondition().getBeam().setFlux(XSDataFloat(self.fFlux))
             if (self.fBeamSize is not None):
                 xsDataSize = XSDataSize()
                 xsDataSize.setX(XSDataLength(self.fBeamSize))
                 xsDataSize.setY(XSDataLength(self.fBeamSize))
                 xsDataSubWedge.getExperimentalCondition().getBeam().setSize(xsDataSize)
             if (self.fBeamPosX is not None):
                 xsDataSubWedge.getExperimentalCondition().getDetector().setBeamPositionX(XSDataLength(self.fBeamPosX))
             if (self.fBeamPosY is not None):
                 xsDataSubWedge.getExperimentalCondition().getDetector().setBeamPositionY(XSDataLength(self.fBeamPosY))
             if (self.fMinExposureTimePerImage is not None):
                 xsDataSubWedge.getExperimentalCondition().getBeam().setMinExposureTimePerImage(XSDataFloat(self.fMinExposureTimePerImage))
             if (self.fTransmission is not None):
                 xsDataSubWedge.getExperimentalCondition().getBeam().setTransmission(XSDataDouble(self.fTransmission))
     if (self.strForcedSpaceGroup is not None):
         xsDataDiffractionPlan.setForcedSpaceGroup(XSDataString(self.strForcedSpaceGroup))
     xsDataDiffractionPlan.setAnomalousData(XSDataBoolean(self.bAnomalousData))
     xsDataDiffractionPlan.setMaxExposureTimePerDataCollection(XSDataTime(self.fMaxExposureTimePerDataCollection))
     if (self.strStrategyOption is not None):
         xsDataDiffractionPlan.setStrategyOption(XSDataString(self.strStrategyOption))
     xsDataCollection.setDiffractionPlan(xsDataDiffractionPlan)
     self.xsDataInputCharacterisation.setDataCollection(xsDataCollection)

# 需要導入模塊: from XSDataMXv1 import XSDataDiffractionPlan [as 別名]
# 或者: from XSDataMXv1.XSDataDiffractionPlan import setMaxExposureTimePerDataCollection [as 別名]

#.........這裏部分代碼省略.........
            self.xsDataDiffractionPlan = XSDataDiffractionPlan()
        if (not xsDataResultSubWedgeAssemble is None):
            pyListSubWedge = xsDataResultSubWedgeAssemble.getSubWedge()
            xsDataCollection.setSubWedge(pyListSubWedge)
            for xsDataSubWedge in pyListSubWedge:
                if (self.strComplexity is not None):
                    self.xsDataDiffractionPlan.setComplexity(XSDataString(self.strComplexity))
                if (self.fFlux is not None):
                    xsDataSubWedge.getExperimentalCondition().getBeam().setFlux(XSDataFlux(self.fFlux))
                if (self.fBeamSizeX is not None) and (self.fBeamSizeY is not None):
                    xsDataSize = XSDataSize()
                    xsDataSize.setX(XSDataLength(self.fBeamSizeX))
                    xsDataSize.setY(XSDataLength(self.fBeamSizeY))
                    xsDataSubWedge.getExperimentalCondition().getBeam().setSize(xsDataSize)
                if (self.fApertureSize is not None):
                    xsDataSubWedge.getExperimentalCondition().getBeam().setApertureSize(XSDataLength(self.fApertureSize))
                if (self.fBeamPosX is not None):
                    xsDataSubWedge.getExperimentalCondition().getDetector().setBeamPositionX(XSDataLength(self.fBeamPosX))
                if (self.fBeamPosY is not None):
                    xsDataSubWedge.getExperimentalCondition().getDetector().setBeamPositionY(XSDataLength(self.fBeamPosY))
                if (self.fMinExposureTimePerImage is not None):
                    xsDataSubWedge.getExperimentalCondition().getBeam().setMinExposureTimePerImage(XSDataTime(self.fMinExposureTimePerImage))
                if (self.fTransmission is not None):
                    xsDataSubWedge.getExperimentalCondition().getBeam().setTransmission(XSDataDouble(self.fTransmission))
                if (self.fWavelength is not None):
                    xsDataSubWedge.getExperimentalCondition().getBeam().setWavelength(XSDataWavelength(self.fWavelength))
                if self.fMinOscillationWidth != None:
                    xsDataSubWedge.getExperimentalCondition().getGoniostat().setMinOscillationWidth(XSDataAngle(self.fMinOscillationWidth))
                if self.fMaxOscillationSpeed != None:
                    xsDataSubWedge.getExperimentalCondition().getGoniostat().setMaxOscillationSpeed(XSDataAngularSpeed(self.fMaxOscillationSpeed))
        if (self.strForcedSpaceGroup is not None):
            self.xsDataDiffractionPlan.setForcedSpaceGroup(XSDataString(self.strForcedSpaceGroup))
        self.xsDataDiffractionPlan.setAnomalousData(XSDataBoolean(self.bAnomalousData))
        self.xsDataDiffractionPlan.setMaxExposureTimePerDataCollection(XSDataTime(self.fMaxExposureTimePerDataCollection))
        if (self.strStrategyOption is not None):
            self.xsDataDiffractionPlan.setStrategyOption(XSDataString(self.strStrategyOption))
        xsDataCollection.setDiffractionPlan(self.xsDataDiffractionPlan)
        if self.xsDataSample is not None:
            xsDataCollection.setSample(XSDataSampleCrystalMM.parseString(self.xsDataSample.marshal()))
        self.xsDataInputCharacterisation.setDataCollection(xsDataCollection)


    def generateTemplateFile(self, _edPlugin):
        self.DEBUG("EDPluginControlInterfacev1_3.generateTemplateFile")
        self.createInputCharacterisationFromSubWedges()
        if(self.strGeneratedTemplateFile is None):
            self.screen("No argument for command line --generateTemplate key word found!")
        elif (self.xsDataInputCharacterisation is None):
            self.screen("ERROR! Cannot generate template file %s, please check the log files." % self.strGeneratedTemplateFile)
        else:
            self.screen("Generating xml template input file for edna: " + self.strGeneratedTemplateFile + "...")
            self.xsDataInputCharacterisation.exportToFile(self.strGeneratedTemplateFile)


    def doSubWedgeAssembleSUCCESS(self, _edPlugin):
        self.DEBUG("EDPluginControlInterfacev1_3.doSubWedgeAssembleSUCCESS")
        self.createInputCharacterisationFromSubWedges()
        self.runCharacterisationPlugin(_edPlugin)

    def doSubWedgeAssembleFAILURE(self, _edPlugin):
        self.DEBUG("EDPluginControlInterfacev1_3.doSubWedgeAssembleFAILURE")
        self.screen("Execution of " + self.strEDPluginControlSubWedgeAssembleName + "  failed.")
        self.screen("Please inspect the log file for further information.")
        self.setFailure()

    def doFailureActionCharacterisation(self, _edPlugin=None):

# 需要導入模塊: from XSDataMXv1 import XSDataDiffractionPlan [as 別名]
# 或者: from XSDataMXv1.XSDataDiffractionPlan import setMaxExposureTimePerDataCollection [as 別名]
class EDPluginControlGridScreeningv1_0(EDPluginControl):
    """
    This plugin is a "light-weight" characterisation to be used for processing
    images from grid scans.
    """


    def __init__(self):
        EDPluginControl.__init__(self)
        self.setXSDataInputClass(XSDataInputGridScreening)
        self.strControlReadImageHeaderPluginName = "EDPluginControlReadImageHeaderv10"
        self.edPluginControlReadImageHeader = None
        self.strControlledIndicatorsPluginName = "EDPluginControlImageQualityIndicatorsv1_4"
        self.edPluginControlIndicators = None
        self.strISPyBStoreImageQualityIndicatorsPluginName = "EDPluginISPyBStoreImageQualityIndicatorsv1_4"
        self.edPluginISPyBStoreImageQualityIndicators = None
        self.strIndexingMOSFLMPluginName = "EDPluginMOSFLMIndexingv10"
        self.edPluginMOSFLMIndexing = None
        self.strPluginControlIntegration = "EDPluginControlIntegrationv10"
        self.edPluginControlIntegration = None
        self.strPluginControlStrategy = "EDPluginControlStrategyv1_2"
        self.edPluginControlStrategy = None
        self.strPluginExecMtz2Various = "EDPluginExecMtz2Variousv1_0"
        self.edPluginExecMtz2Various = None
        self.strImageFile = None
        self.xsDataIndexingResultMOSFLM = None
        self.xsDataCrystal = None
        self.strCharacterisationShortSummary = ""
        self.strStatusMessage = ""
        self.xsDataDiffractionPlan = None
        self.xsDataCollection = None
        self.xsDataIndexingResult = None
        self.xsDataStrategyResult = None
        self.xsDataImageQualityIndicators = None
        self.bStoreImageQualityIndicatorsInISPyB = False
        self.bDoOnlyImageQualityIndicators = False
        self.bDoOnlyIntegrationWithXMLOutput = False
        self.iImageQualityIndicatorsId = None
        self.xsDataGridScreeningResultIntegration = None


    def checkParameters(self):
        """
        Checks the mandatory parameters.
        """
        self.DEBUG("EDPluginControlGridScreeningv1_0.checkParameters")
        self.checkMandatoryParameters(self.getDataInput(), "Data Input is None")
        self.checkMandatoryParameters(self.getDataInput().getImageFile(), "imageFile")


    def preProcess(self, _edObject=None):
        EDPluginControl.preProcess(self)
        self.DEBUG("EDPluginControlGridScreeningv1_0.preProcess")
        # Load the plugins
        self.edPluginControlReadImageHeader = self.loadPlugin(self.strControlReadImageHeaderPluginName, \
                                                                   "ReadImageHeader")
        self.edPluginControlIndicators = self.loadPlugin(self.strControlledIndicatorsPluginName, \
                                                                   "ControlIndicators")
        self.edPluginMOSFLMIndexing = self.loadPlugin(self.strIndexingMOSFLMPluginName, \
                                                                   "IndexingMOSFLM")
        self.edPluginControlIntegration = self.loadPlugin(self.strPluginControlIntegration, \
                                                            "Integration")
        self.edPluginControlStrategy = self.loadPlugin(self.strPluginControlStrategy, \
                                                         "Strategy")
        self.edPluginExecMtz2Various = self.loadPlugin(self.strPluginExecMtz2Various, \
                                                         "Mtz2Various")
        # Input data
        self.strImageFile = self.getDataInput().getImageFile().getPath().getValue()
        self.xsDataGridScreeningFileNameParameters = self.getFileNameParameters(self.strImageFile)
        self.xsDataDiffractionPlan = self.getDataInput().getDiffractionPlan()
        if self.xsDataDiffractionPlan is None:
            self.xsDataDiffractionPlan = XSDataDiffractionPlan()
        if self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection() is None:
            # Default max esposure time: 10000s
            self.xsDataDiffractionPlan.setMaxExposureTimePerDataCollection(XSDataTime(10000))
        self.xsDataDiffractionPlan.setEstimateRadiationDamage(XSDataBoolean(False))
        # Image quality indicators
        if self.getDataInput().getStoreImageQualityIndicatorsInISPyB():
            self.bStoreImageQualityIndicatorsInISPyB = self.getDataInput().getStoreImageQualityIndicatorsInISPyB().getValue()
        if self.getDataInput().getDoOnlyImageQualityIndicators():
            self.bDoOnlyImageQualityIndicators = self.getDataInput().getDoOnlyImageQualityIndicators().getValue()
        if self.getDataInput().getDoOnlyIntegrationWithXMLOutput():
            self.bDoOnlyIntegrationWithXMLOutput = self.getDataInput().getDoOnlyIntegrationWithXMLOutput().getValue()
        if self.bStoreImageQualityIndicatorsInISPyB:
            self.edPluginISPyBStoreImageQualityIndicators = self.loadPlugin(self.strISPyBStoreImageQualityIndicatorsPluginName, \
                                                         "ISPyBStoreImageQualityIndicators")



    def process(self, _edObject=None):
        EDPluginControl.process(self)
        self.DEBUG("EDPluginControlGridScreeningv1_0.process")
        xsDataInputReadImageHeader = XSDataInputReadImageHeader()
        xsDataInputReadImageHeader.setImage(image=XSDataFile(path=XSDataString(self.strImageFile)))
        self.edPluginControlReadImageHeader.setDataInput(xsDataInputReadImageHeader)
        self.edPluginControlReadImageHeader.connectSUCCESS(self.doSuccessReadImageHeader)
        self.edPluginControlReadImageHeader.connectFAILURE(self.doFailureReadImageHeader)
        self.executePluginSynchronous(self.edPluginControlReadImageHeader)


#.........這裏部分代碼省略.........

# 需要導入模塊: from XSDataMXv1 import XSDataDiffractionPlan [as 別名]
# 或者: from XSDataMXv1.XSDataDiffractionPlan import setMaxExposureTimePerDataCollection [as 別名]

#.........這裏部分代碼省略.........

        xsDataGoniostat = XSDataGoniostat()
        xsDataGoniostat.setMaxOscillationSpeed(XSDataSpeed(0.2))
        xsDataGoniostat.setMinOscillationWidth(XSDataAngle(0.1))
        xsExperimentalCondition.setGoniostat(xsDataGoniostat)
        xsDataInputCCP4i.setExperimentalCondition(xsExperimentalCondition)

        # Sample
        from XSDataCommon import XSDataString
        from XSDataCommon import XSDataFloat
        from XSDataCommon import XSDataString

        from XSDataMXv1 import XSDataStructure
        from XSDataMXv1 import XSDataChain
        from XSDataMXv1 import XSDataAtom
        from XSDataMXv1 import XSDataLigand
        from XSDataMXv1 import XSDataSampleCrystalMM
        from XSDataMXv1 import XSDataChemicalCompositionMM
        from XSDataMXv1 import XSDataAtomicComposition
        from XSDataMXv1 import XSDataSolvent

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

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

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

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

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

        xsDataSolvent = XSDataSolvent()
        xsDataAtomicComposition = XSDataAtomicComposition()

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

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

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

        xsDataSampleCrystalMM.setSize(XSDataSize(XSDataLength(0.2), XSDataLength(0.2), XSDataLength(0.2)))
        xsDataSampleCrystalMM.setSusceptibility(XSDataFloat(1.5))
        xsDataSampleCrystalMM.setShape(XSDataFloat(2))

        xsDataInputCCP4i.setSample(xsDataSampleCrystalMM)

        from XSDataMXv1 import XSDataDiffractionPlan

        xsDataDiffractionPlan = XSDataDiffractionPlan()

        xsDataDiffractionPlan.setAimedCompleteness(XSDataFloat(95.5))
        xsDataDiffractionPlan.setAimedIOverSigmaAtHighestResolution(XSDataFloat(2.5))
        xsDataDiffractionPlan.setAimedMultiplicity(XSDataFloat(95.5))
        xsDataDiffractionPlan.setAimedResolution(XSDataFloat(3))
        xsDataDiffractionPlan.setComplexity(XSDataString("full"))
        xsDataDiffractionPlan.setForcedSpaceGroup(XSDataString("P222"))
        xsDataDiffractionPlan.setMaxExposureTimePerDataCollection(XSDataFloat(10000))

        xsDataInputCCP4i.setDiffractionPlan(xsDataDiffractionPlan)

        from XSDataCommon import XSDataFile

        listInputDataFile = []
        xsDataFile = XSDataFile(XSDataString(self.strXSDataGenerateTemplateFile))
        listInputDataFile.append(xsDataFile)
        xsDataInputCCP4i.setDataFile(listInputDataFile)

# 需要導入模塊: from XSDataMXv1 import XSDataDiffractionPlan [as 別名]
# 或者: from XSDataMXv1.XSDataDiffractionPlan import setMaxExposureTimePerDataCollection [as 別名]

#.........這裏部分代碼省略.........
        # possible to read from the command line)
        if self.xsDataDiffractionPlan is None:
            self.xsDataDiffractionPlan = XSDataDiffractionPlan()
        if (not xsDataResultSubWedgeAssemble is None):
            pyListSubWedge = xsDataResultSubWedgeAssemble.getSubWedge()
            xsDataCollection.setSubWedge(pyListSubWedge)
            for xsDataSubWedge in pyListSubWedge:
                if (self.strComplexity is not None):
                    self.xsDataDiffractionPlan.setComplexity(XSDataString(self.strComplexity))
                if (self.fFlux is not None):
                    xsDataSubWedge.getExperimentalCondition().getBeam().setFlux(XSDataFlux(self.fFlux))
                if (self.fBeamSizeX is not None) and (self.fBeamSizeY is not None):
                    xsDataSize = XSDataSize()
                    xsDataSize.setX(XSDataLength(self.fBeamSizeX))
                    xsDataSize.setY(XSDataLength(self.fBeamSizeY))
                    xsDataSubWedge.getExperimentalCondition().getBeam().setSize(xsDataSize)
                if (self.fBeamPosX is not None):
                    xsDataSubWedge.getExperimentalCondition().getDetector().setBeamPositionX(XSDataLength(self.fBeamPosX))
                if (self.fBeamPosY is not None):
                    xsDataSubWedge.getExperimentalCondition().getDetector().setBeamPositionY(XSDataLength(self.fBeamPosY))
                if (self.fMinExposureTimePerImage is not None):
                    xsDataSubWedge.getExperimentalCondition().getBeam().setMinExposureTimePerImage(XSDataTime(self.fMinExposureTimePerImage))
                if (self.fTransmission is not None):
                    xsDataSubWedge.getExperimentalCondition().getBeam().setTransmission(XSDataDouble(self.fTransmission))
                if (self.fWavelength is not None):
                    xsDataSubWedge.getExperimentalCondition().getBeam().setWavelength(XSDataWavelength(self.fWavelength))
                if self.fMinOscillationWidth != None:
                    xsDataSubWedge.getExperimentalCondition().getGoniostat().setMinOscillationWidth(XSDataAngle(self.fMinOscillationWidth))
                if self.fMaxOscillationSpeed != None:
                    xsDataSubWedge.getExperimentalCondition().getGoniostat().setMaxOscillationSpeed(XSDataAngularSpeed(self.fMaxOscillationSpeed))
        if (self.strForcedSpaceGroup is not None):
            self.xsDataDiffractionPlan.setForcedSpaceGroup(XSDataString(self.strForcedSpaceGroup))
        self.xsDataDiffractionPlan.setAnomalousData(XSDataBoolean(self.bAnomalousData))
        self.xsDataDiffractionPlan.setMaxExposureTimePerDataCollection(XSDataTime(self.fMaxExposureTimePerDataCollection))
        if (self.strStrategyOption is not None):
            self.xsDataDiffractionPlan.setStrategyOption(XSDataString(self.strStrategyOption))
        xsDataCollection.setDiffractionPlan(self.xsDataDiffractionPlan)
        if self.xsDataSample is not None:
            xsDataCollection.setSample(XSDataSampleCrystalMM.parseString(self.xsDataSample.marshal()))
        self.xsDataInputCharacterisation.setDataCollection(xsDataCollection)


    def generateTemplateFile(self, _edPlugin):
        EDVerbose.DEBUG("EDPluginControlInterfacev1_2.generateTemplateFile")
        self.createInputCharacterisationFromSubWedges()
        if(self.strGeneratedTemplateFile is None):
            EDVerbose.screen("No argument for command line --generateTemplate key word found!")
        elif (self.xsDataInputCharacterisation is None):
            EDVerbose.screen("ERROR! Cannot generate template file %s, please check the log files." % self.strGeneratedTemplateFile)
        else:
            EDVerbose.screen("Generating xml template input file for edna: " + self.strGeneratedTemplateFile + "...")
            self.xsDataInputCharacterisation.exportToFile(self.strGeneratedTemplateFile)


    def doSubWedgeAssembleSUCCESS(self, _edPlugin):
        EDVerbose.DEBUG("EDPluginControlInterfacev1_2.doSubWedgeAssembleSUCCESS")
        self.createInputCharacterisationFromSubWedges()
        self.runCharacterisationPlugin(_edPlugin)

    def doSubWedgeAssembleFAILURE(self, _edPlugin):
        EDVerbose.DEBUG("EDPluginControlInterfacev1_2.doSubWedgeAssembleFAILURE")
        EDVerbose.screen("Execution of " + self.strEDPluginControlSubWedgeAssembleName + "  failed.")
        EDVerbose.screen("Please inspect the log file for further information.")
        self.setFailure()

    def doFailureActionCharacterisation(self, _edPlugin=None):