Python XSDataDiffractionPlan.getGoniostatMinOscillationWidth 예제들

예제 #1

파일: EDPluginControlInterfacev1_3.py 프로젝트: IvarsKarpics/edna-mx

class EDPluginControlInterfacev1_3(EDPluginControl):
    """
    This is the common class to all plugins managing user interfaces
    """

    def __init__ (self):
        """
        """
        EDPluginControl.__init__(self)

        self.setXSDataInputClass(XSDataInputInterface)

        self.setXSDataInputClass(XSDataExperimentalCondition, "experimentalCondition")
        self.setXSDataInputClass(XSDataDiffractionPlan, "diffractionPlan")
        self.setXSDataInputClass(XSDataSampleCrystalMM, "sample")
        self.setXSDataInputClass(XSDataString, "imagePaths")
        self.setXSDataInputClass(XSDataFloat, "flux")
        self.setXSDataInputClass(XSDataFloat, "minExposureTimePerImage")
        self.setXSDataInputClass(XSDataFloat, "beamSize")
        self.setXSDataInputClass(XSDataFloat, "beamSizeX")
        self.setXSDataInputClass(XSDataFloat, "beamSizeY")
        self.setXSDataInputClass(XSDataBoolean, "templateMode")
        self.setXSDataInputClass(XSDataString, "generatedTemplateFile")
        self.setXSDataInputClass(XSDataString, "resultsFilePath")
        self.setXSDataInputClass(XSDataFloat, "beamPosX")
        self.setXSDataInputClass(XSDataFloat, "beamPosY")
        self.setXSDataInputClass(XSDataDouble, "wavelength")
        self.setXSDataInputClass(XSDataDouble, "transmission")
        self.setXSDataInputClass(XSDataInteger, "dataCollectionId")
        self.setXSDataInputClass(XSDataString, "shortComments")
        self.setXSDataInputClass(XSDataString, "comments")
        self.setXSDataInputClass(XSDataInputCharacterisation, "inputCharacterisation")

        self.strEDPluginControlSubWedgeAssembleName = "EDPluginControlSubWedgeAssemblev1_1"
        self.strEDPluginControlCharacterisationName = "EDPluginControlCharacterisationv1_5"
        self.strEDPluginControlISPyBName = "EDPluginControlISPyBv1_1"

        self.edPluginControlSubWedgeAssemble = None
        self.edPluginControlCharacterisation = None
        self.edPluginControlISPyB = None

        self.pyListImagePaths = None
        self.xsDataInputCharacterisation = None
        self.strComplexity = "none"

        self.listImagePaths = []
        self.fFlux = None
        self.fMaxExposureTimePerDataCollection = 10000 # s, default prototype value
        self.fMinExposureTimePerImage = None
        self.fBeamSizeX = None
        self.fBeamSizeY = None
        self.fApertureSize = None
        self.bTemplateMode = False
        self.strGeneratedTemplateFile = None
        self.strResultsFilePath = None
        self.strForcedSpaceGroup = None
        self.bAnomalousData = False
        self.fBeamPosX = None
        self.fBeamPosY = None
        self.fMinOscillationWidth = None
        self.fMaxOscillationSpeed = None
        self.fWavelength = None
        self.fTransmission = None
        self.strStrategyOption = None
        self.iDataCollectionId = None
        self.strShortComments = None
        self.strComments = None
        self.strStatusMessage = None

        self.xsDataExperimentalCodition = None
        self.xsDataSample = None
        self.xsDataDiffractionPlan = None


    def configure(self):
        """
        Gets the configuration parameters (if any).
        """
        EDPluginControl.configure(self)
        self.DEBUG("EDPluginControlInterfacev1_3.configure")
        if (self.getControlledPluginName("subWedgeAssemblePlugin") is not None):
            self.strEDPluginControlSubWedgeAssembleName = self.getControlledPluginName("subWedgeAssemblePlugin")
        if (self.getControlledPluginName("characterisationPlugin") is not None):
            self.strEDPluginControlCharacterisationName = self.getControlledPluginName("characterisationPlugin")
        if (self.getControlledPluginName("ispybPlugin") is not None):
            self.strEDPluginControlISPyBName = self.getControlledPluginName("ispybPlugin")

        bUseISPyBPlugin = self.config.get("useISPyBPlugin")
        if not bUseISPyBPlugin:
            self.DEBUG("EDPluginControlInterfacev1_3 configured to not use ISPyB")
            self.strEDPluginControlISPyBName = None


    def preProcess(self, _edPlugin=None):
        """
        Gets the Configuration Parameters, if found, overrides default parameters
        """
        EDPluginControl.preProcess(self, _edPlugin)
        self.DEBUG("EDPluginControlInterfacev1_3.preProcess...")

        self.listImagePaths = []

        # Check if XSDataInputInterface is given as input
        if self.hasDataInput():
            xsDataInputInterface = self.getDataInput()

            if xsDataInputInterface.getExperimentalCondition():
                self.xsDataExperimentalCodition = xsDataInputInterface.getExperimentalCondition()
                if self.xsDataExperimentalCodition.getGoniostat():
                    if self.xsDataExperimentalCodition.getGoniostat().getMinOscillationWidth():
                        self.fMinOscillationWidth = self.xsDataExperimentalCodition.getGoniostat().getMinOscillationWidth().getValue()
                    if self.xsDataExperimentalCodition.getGoniostat().getMaxOscillationSpeed():
                        self.fMaxOscillationSpeed = self.xsDataExperimentalCodition.getGoniostat().getMaxOscillationSpeed().getValue()


            self.xsDataSample = xsDataInputInterface.getSample()

            self.xsDataDiffractionPlan = self.getDataInput().getDiffractionPlan()
            if self.xsDataDiffractionPlan:
                if self.xsDataDiffractionPlan.getForcedSpaceGroup():
                    self.strForcedSpaceGroup = self.xsDataDiffractionPlan.getForcedSpaceGroup().getValue()
                if self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection():
                    self.fMaxExposureTimePerDataCollection = self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection().getValue()
                if self.xsDataDiffractionPlan.getAnomalousData():
                    self.bAnomalousData = self.xsDataDiffractionPlan.getAnomalousData().getValue()
                if self.xsDataDiffractionPlan.getStrategyOption():
                    self.strStrategyOption = self.xsDataDiffractionPlan.getStrategyOption().getValue()
                if self.xsDataDiffractionPlan.getComplexity():
                    self.strComplexity = self.xsDataDiffractionPlan.getComplexity().getValue()
                if self.fMinOscillationWidth == None:
                    if self.xsDataDiffractionPlan.getGoniostatMinOscillationWidth():
                        self.fMinOscillationWidth = self.xsDataDiffractionPlan.getGoniostatMinOscillationWidth().getValue()
                if self.fMaxOscillationSpeed == None:
                    if self.xsDataDiffractionPlan.getGoniostatMaxOscillationSpeed():
                        self.fMaxOscillationSpeed = self.xsDataDiffractionPlan.getGoniostatMaxOscillationSpeed().getValue()


            self.xsDataSample = xsDataInputInterface.getSample()

            if xsDataInputInterface.getImagePath():
                for xsDataFile in xsDataInputInterface.getImagePath():
                    self.listImagePaths.append(xsDataFile.getPath())

            if xsDataInputInterface.getFlux():
                self.fFlux = xsDataInputInterface.getFlux().getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getBeam() != None:
                    if self.xsDataExperimentalCodition.getBeam().getFlux() != None:
                        self.fFlux = self.xsDataExperimentalCodition.getBeam().getFlux().getValue()

            if xsDataInputInterface.getMinExposureTimePerImage():
                self.fMinExposureTimePerImage = xsDataInputInterface.getMinExposureTimePerImage().getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getBeam() != None:
                    if self.xsDataExperimentalCodition.getBeam().getMinExposureTimePerImage() != None:
                        self.fMinExposureTimePerImage = self.xsDataExperimentalCodition.getBeam().getMinExposureTimePerImage().getValue()
            if self.fMinExposureTimePerImage == None and xsDataInputInterface.getDiffractionPlan():
                if xsDataInputInterface.getDiffractionPlan().getMinExposureTimePerImage() != None:
                    self.fMinExposureTimePerImage = xsDataInputInterface.getDiffractionPlan().getMinExposureTimePerImage().getValue()

            if self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getBeam() != None:
                    if self.xsDataExperimentalCodition.getBeam().getSize() != None:
                        self.fBeamSizeX = self.xsDataExperimentalCodition.getBeam().getSize().getX().getValue()
                        self.fBeamSizeY = self.xsDataExperimentalCodition.getBeam().getSize().getY().getValue()
                    if self.xsDataExperimentalCodition.getBeam().getApertureSize() != None:
                        self.fApertureSize = self.xsDataExperimentalCodition.getBeam().getApertureSize().getValue()

            if xsDataInputInterface.getBeamSize():
                self.fBeamSizeX = xsDataInputInterface.getBeamSize().getValue()
                self.fBeamSizeY = xsDataInputInterface.getBeamSize().getValue()

            if xsDataInputInterface.getApertureSize():
                self.fApertureSize = xsDataInputInterface.getApertureSize().getValue()
                
            if xsDataInputInterface.getBeamSizeX():
                self.fBeamSizeX = xsDataInputInterface.getBeamSizeX().getValue()

            if xsDataInputInterface.getBeamSizeY():
                self.fBeamSizeY = xsDataInputInterface.getBeamSizeY().getValue()

            if xsDataInputInterface.getApertureSize():
                self.fApertureSize = xsDataInputInterface.getApertureSize().getValue()

            if xsDataInputInterface.getTemplateMode():
                self.bTemplateMode = xsDataInputInterface.getTemplateMode().getValue()

            if xsDataInputInterface.getBeamPosX():
                self.fBeamPosX = xsDataInputInterface.getBeamPosX().getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getDetector() != None:
                    if self.xsDataExperimentalCodition.getDetector().getBeamPositionX() != None:
                        self.fBeamPosX = self.xsDataExperimentalCodition.getDetector().getBeamPositionX().getValue()

            if xsDataInputInterface.getBeamPosY():
                self.fBeamPosY = xsDataInputInterface.getBeamPosY().getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getDetector() != None:
                    if self.xsDataExperimentalCodition.getDetector().getBeamPositionY() != None:
                        self.fBeamPosY = self.xsDataExperimentalCodition.getDetector().getBeamPositionY().getValue()

            if xsDataInputInterface.getWavelength():
                self.fWavelength = xsDataInputInterface.getWavelength().getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getBeam() != None:
                    if self.xsDataExperimentalCodition.getBeam().getWavelength() != None:
                        self.fWavelength = self.xsDataExperimentalCodition.getBeam().getWavelength().getValue()

            if xsDataInputInterface.getTransmission():
                self.fTransmission = xsDataInputInterface.getTransmission().getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getBeam() != None:
                    if self.xsDataExperimentalCodition.getBeam().getTransmission() != None:
                        self.fTransmission = self.xsDataExperimentalCodition.getBeam().getTransmission().getValue()

            if xsDataInputInterface.getGeneratedTemplateFile():
                self.strGeneratedTemplateFile = xsDataInputInterface.getGeneratedTemplateFile().getPath().getValue()

            if xsDataInputInterface.getResultsFilePath():
                self.strResultsFilePath = xsDataInputInterface.getResultsFilePath().getPath().getValue()

            if xsDataInputInterface.getDataCollectionId():
                self.iDataCollectionId = xsDataInputInterface.getDataCollectionId().getValue()

            if xsDataInputInterface.getShortComments():
                self.strShortComments = xsDataInputInterface.getShortComments().getValue()

            if xsDataInputInterface.getComments():
                self.strComments = xsDataInputInterface.getComments().getValue()

            if xsDataInputInterface.getInputCharacterisation():
                self.xsDataInputCharacterisation = xsDataInputInterface.getInputCharacterisation()

            if xsDataInputInterface.getDataCollectionId():
                self.iDataCollectionId = xsDataInputInterface.getDataCollectionId().getValue()

        else:

            if self.hasDataInput("experimentalCondition"):
                self.xsDataExperimentalCodition = self.getDataInput("experimentalCondition")[0]
                if self.xsDataExperimentalCodition.getGoniostat():
                    if self.xsDataExperimentalCodition.getGoniostat().getMinOscillationWidth():
                        self.fMinOscillationWidth = self.xsDataExperimentalCodition.getGoniostat().getMinOscillationWidth().getValue()
                    if self.xsDataExperimentalCodition.getGoniostat().getMaxOscillationSpeed():
                        self.fMaxOscillationSpeed = self.xsDataExperimentalCodition.getGoniostat().getMaxOscillationSpeed().getValue()


            if self.hasDataInput("sample"):
                self.xsDataSample = self.getDataInput("sample")[0]

            if (self.hasDataInput("diffractionPlan")):
                if self.xsDataDiffractionPlan is None:
                    self.xsDataDiffractionPlan = XSDataDiffractionPlan()
                xsDataDiffractionPlans = self.getDataInput("diffractionPlan")
                if (not xsDataDiffractionPlans[0] is None):
                    self.xsDataDiffractionPlan = xsDataDiffractionPlans[0]
                    if self.xsDataDiffractionPlan.getForcedSpaceGroup():
                        self.strForcedSpaceGroup = self.xsDataDiffractionPlan.getForcedSpaceGroup().getValue()
                    if self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection():
                        self.fMaxExposureTimePerDataCollection = self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection().getValue()
                    if self.xsDataDiffractionPlan.getAnomalousData():
                        self.bAnomalousData = self.xsDataDiffractionPlan.getAnomalousData().getValue()
                    if self.xsDataDiffractionPlan.getStrategyOption():
                        self.strStrategyOption = self.xsDataDiffractionPlan.getStrategyOption().getValue()
                    if self.xsDataDiffractionPlan.getComplexity():
                        self.strComplexity = self.xsDataDiffractionPlan.getComplexity().getValue()
                    if self.fMinOscillationWidth == None:
                        if self.xsDataDiffractionPlan.getGoniostatMinOscillationWidth():
                            self.fMinOscillationWidth = self.xsDataDiffractionPlan.getGoniostatMinOscillationWidth().getValue()
                    if self.fMaxOscillationSpeed == None:
                        if self.xsDataDiffractionPlan.getGoniostatMaxOscillationSpeed():
                            self.fMaxOscillationSpeed = self.xsDataDiffractionPlan.getGoniostatMaxOscillationSpeed().getValue()


            if self.hasDataInput("sample"):
                self.xsDataSample = self.getDataInput("sample")[0]

            if self.hasDataInput("imagePaths"):
                for strImagePath in self.getDataInput("imagePaths"):
                    self.listImagePaths.append(strImagePath)

            if self.hasDataInput("flux"):
                self.fFlux = self.getDataInput("flux")[0].getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getBeam() != None:
                    if self.xsDataExperimentalCodition.getBeam().getFlux() != None:
                        self.fFlux = self.xsDataExperimentalCodition.getBeam().getFlux().getValue()

            if self.hasDataInput("minExposureTimePerImage"):
                self.fMinExposureTimePerImage = self.getDataInput("minExposureTimePerImage")[0].getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getBeam() != None:
                    if self.xsDataExperimentalCodition.getBeam().getMinExposureTimePerImage() != None:
                        self.fMinExposureTimePerImage = self.xsDataExperimentalCodition.getBeam().getMinExposureTimePerImage().getValue()
            if self.fMinExposureTimePerImage == None and self.hasDataInput("diffractionPlan"):
                if self.getDataInput("diffractionPlan")[0].getMinExposureTimePerImage() != None:
                    self.fMinExposureTimePerImage = self.getDataInput("diffractionPlan")[0].getMinExposureTimePerImage().getValue()

            if self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getBeam() != None:
                    if self.xsDataExperimentalCodition.getBeam().getSize() != None:
                        self.fBeamSizeX = self.xsDataExperimentalCodition.getBeam().getSize().getX().getValue()
                        self.fBeamSizeY = self.xsDataExperimentalCodition.getBeam().getSize().getY().getValue()
                    if self.xsDataExperimentalCodition.getBeam().getApertureSize() != None:
                        self.fApertureSize = self.xsDataExperimentalCodition.getBeam().getApertureSize().getValue()

            if self.hasDataInput("beamSize"):
                self.fBeamSizeX = self.getDataInput("beamSize")[0].getValue()
                self.fBeamSizeY = self.getDataInput("beamSize")[0].getValue()

            if self.hasDataInput("apertureSize"):
                self.fApertureSize = self.getDataInput("apertureSize")[0].getValue()

            if self.hasDataInput("beamSizeX"):
                self.fBeamSizeX = self.getDataInput("beamSizeX")[0].getValue()

            if self.hasDataInput("beamSizeY"):
                self.fBeamSizeY = self.getDataInput("beamSizeY")[0].getValue()

            if self.hasDataInput("templateMode"):
                self.bTemplateMode = self.getDataInput("templateMode")[0].getValue()

            if (self.hasDataInput("beamPosX")):
                self.fBeamPosX = self.getDataInput("beamPosX")[0].getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getDetector() != None:
                    if self.xsDataExperimentalCodition.getDetector().getBeamPositionX() != None:
                        self.fBeamPosX = self.xsDataExperimentalCodition.getDetector().getBeamPositionX().getValue()

            if (self.hasDataInput("beamPosY")):
                self.fBeamPosY = self.getDataInput("beamPosY")[0].getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getDetector() != None:
                    if self.xsDataExperimentalCodition.getDetector().getBeamPositionY() != None:
                        self.fBeamPosY = self.xsDataExperimentalCodition.getDetector().getBeamPositionY().getValue()

            if (self.hasDataInput("wavelength")):
                self.fWavelength = self.getDataInput("wavelength")[0].getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getBeam() != None:
                    if self.xsDataExperimentalCodition.getBeam().getWavelength() != None:
                        self.fWavelength = self.xsDataExperimentalCodition.getBeam().getWavelength().getValue()

            if (self.hasDataInput("transmission")):
                self.fTransmission = self.getDataInput("transmission")[0].getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getBeam() != None:
                    if self.xsDataExperimentalCodition.getBeam().getTransmission() != None:
                        self.fTransmission = self.xsDataExperimentalCodition.getBeam().getTransmission().getValue()

            if self.hasDataInput("generatedTemplateFile"):
                self.strGeneratedTemplateFile = self.getDataInput("generatedTemplateFile")[0].getValue()

            if self.hasDataInput("resultsFilePath"):
                self.strResultsFilePath = self.getDataInput("resultsFilePath")[0].getValue()

            if self.hasDataInput("dataCollectionId"):
                self.iDataCollectionId = self.getDataInput("dataCollectionId")[0].getValue()

            if self.hasDataInput("shortComments"):
                self.strShortComments = self.getDataInput("shortComments")[0].getValue()

            if self.hasDataInput("comments"):
                self.strComments = self.getDataInput("comments")[0].getValue()

            if self.hasDataInput("inputCharacterisation"):
                self.xsDataInputCharacterisation = self.getDataInput("inputCharacterisation")[0]

        # Check if XML data is given as input :
        if (self.xsDataInputCharacterisation is None):
            self.edPluginControlSubWedgeAssemble = self.loadPlugin(self.strEDPluginControlSubWedgeAssembleName, "SubWedgeAssemble")

        self.edPluginControlCharacterisation = self.loadPlugin(self.strEDPluginControlCharacterisationName, "Characterisation")

        if (self.strEDPluginControlISPyBName is not None):
            self.edPluginControlISPyB = self.loadPlugin(self.strEDPluginControlISPyBName, "ISPyB")
            


    def process(self, _edPlugin=None):
        EDPluginControl.process(self, _edPlugin)
        self.DEBUG("EDPluginControlInterfacev1_3.process...")

        if (self.edPluginControlSubWedgeAssemble is not None):
            if(self.bTemplateMode == True):
                self.edPluginControlSubWedgeAssemble.connectSUCCESS(self.generateTemplateFile)
            else:
                self.edPluginControlSubWedgeAssemble.connectSUCCESS(self.doSubWedgeAssembleSUCCESS)
            self.edPluginControlSubWedgeAssemble.connectFAILURE(self.doSubWedgeAssembleFAILURE)

        if(self.edPluginControlCharacterisation is not None):
            self.edPluginControlCharacterisation.connectSUCCESS(self.doSuccessActionCharacterisation)
            self.edPluginControlCharacterisation.connectFAILURE(self.doFailureActionCharacterisation)

        if (self.edPluginControlISPyB is not None):
            self.edPluginControlISPyB.connectSUCCESS(self.doSuccessActionISPyB)
            self.edPluginControlISPyB.connectFAILURE(self.doFailureActionISPyB)

        if (self.xsDataInputCharacterisation is None):
            self.createInputCharacterisationFromImageHeaders(self.edPluginControlSubWedgeAssemble)
        else:
            self.runCharacterisationPlugin(self.edPluginControlCharacterisation)


    def finallyProcess(self, _edPlugin=None):
        EDPluginControl.finallyProcess(self, _edPlugin)
        self.DEBUG("EDPluginControlInterfacev1_3.finallyProcess...")

        if (not self.edPluginControlCharacterisation is None):
            if (self.edPluginControlCharacterisation.hasDataOutput()):
                self.setDataOutput(self.edPluginControlCharacterisation.getDataOutput(), "characterisation")
        if (not self.edPluginControlISPyB is None):
            if (self.edPluginControlISPyB.hasDataOutput()):
                self.setDataOutput(self.edPluginControlISPyB.getDataOutput(), "ISPyB")
        if self.hasDataInput():
            xsDataResultInterface = XSDataResultInterface()
            if self.edPluginControlCharacterisation:
                xsDataResultInterface.setResultCharacterisation(self.edPluginControlCharacterisation.getDataOutput())
            if self.edPluginControlISPyB:
                xsDataResultInterface.setResultControlISPyB(self.edPluginControlISPyB.getDataOutput())
            self.setDataOutput(xsDataResultInterface)


    def createInputCharacterisationFromImageHeaders(self, _edPlugin):
        self.DEBUG("EDPluginControlInterfacev1_3.createInputCharacterisationFromImageHeaders")
        xsDataInputSubWedgeAssemble = XSDataInputSubWedgeAssemble()
        for xsDataStringImagePath in self.listImagePaths:
            xsDataFile = XSDataFile()
            xsDataFile.setPath(xsDataStringImagePath)
            xsDataInputSubWedgeAssemble.addFile(xsDataFile)
        _edPlugin.setDataInput(xsDataInputSubWedgeAssemble)
        _edPlugin.executeSynchronous()


    def runCharacterisationPlugin(self, _edPlugin=None):
        self.DEBUG("EDPluginControlInterfacev1_3.runCharacterisationPlugin")
        self.edPluginControlCharacterisation.setDataInput(self.xsDataInputCharacterisation)
        self.edPluginControlCharacterisation.executeSynchronous()


    def storeResultsInISPyB(self, _edPlugin=None):
        self.DEBUG("EDPluginControlInterfacev1_3.storeResultsInISPyB")
        if (self.edPluginControlISPyB is not None):
            # Execute the ISPyB control plugin
            xsDataInputControlISPyB = XSDataInputControlISPyB()
            xsDataInputControlISPyB.setCharacterisationResult(self.edPluginControlCharacterisation.getDataOutput())
            if (not self.iDataCollectionId is None):
                dataCollectionGroupId = self.getDataCollectionGroupId(self.iDataCollectionId)
                xsDataInputControlISPyB.setDataCollectionGroupId(XSDataInteger(dataCollectionGroupId))
            if (not self.strShortComments is None):
                self.edPluginControlISPyB.setDataInput(XSDataString(self.strShortComments), "shortComments")
            if (not self.strComments is None):
                self.edPluginControlISPyB.setDataInput(XSDataString(self.strComments), "comments")
            if (not self.strStatusMessage is None):
                self.edPluginControlISPyB.setDataInput(XSDataString(self.strStatusMessage), "statusMessage")
            self.edPluginControlISPyB.setDataInput(xsDataInputControlISPyB)
            self.edPluginControlISPyB.executeSynchronous()
            self.checkDozorScores(self.edPluginControlCharacterisation.getDataOutput())


    def createInputCharacterisationFromSubWedges(self):
        self.DEBUG("EDPluginControlInterfacev1_3.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)
        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.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):
        """
        retrieve the potential warning messages
        retrieve the potential error messages
        """
        self.DEBUG("EDPluginControlInterfacev1_3.doFailureActionCharacterisation")
        self.retrieveFailureMessages(self.edPluginControlCharacterisation, "EDPluginControlInterfacev1_3.doSuccessActionISPyB")
        if _edPlugin.hasDataOutput("statusMessage"):
            self.strStatusMessage = _edPlugin.getDataOutput("statusMessage")[0].getValue()
        self.generateExecutiveSummary(self)
        self.storeResultsInISPyB(_edPlugin)
        self.setFailure()

    def doSuccessActionCharacterisation(self, _edPlugin=None):
        """
        retrieve the potential warning messages
        """
        self.DEBUG("EDPluginControlInterfacev1_3.doSuccessActionCharacterisation")
        # Store the results if requested
        if (self.strResultsFilePath is not None):
            xsDataCharacterisationResult = _edPlugin.getDataOutput()
            if (xsDataCharacterisationResult is not None):
                xsDataCharacterisationResult.exportToFile(self.strResultsFilePath)
        if _edPlugin.hasDataOutput("statusMessage"):
            self.strStatusMessage = _edPlugin.getDataOutput("statusMessage")[0].getValue()
        self.storeResultsInISPyB(_edPlugin)

    def doSuccessActionISPyB(self, _edPlugin):
        self.DEBUG("EDPluginControlInterfacev1_3.doSuccessActionISPyB...")
        self.retrieveSuccessMessages(self.edPluginControlISPyB, "EDPluginControlInterfacev1_3.doSuccessActionISPyB")

    def doFailureActionISPyB(self, _edPlugin=None):
        self.DEBUG("EDPluginControlInterfacev1_3.doFailureActionISpyB...")
        self.generateExecutiveSummary(self)
        self.setFailure()

    def generateExecutiveSummary(self, _edPlugin=None):
        """
        Prints the executive summary from the plugin
        """
        self.DEBUG("EDPluginControlInterfacev1_3.generateExecutiveSummary")
        if (self.edPluginControlSubWedgeAssemble is not None):
            if self.edPluginControlSubWedgeAssemble.getListExecutiveSummaryLines() != []:
                self.addExecutiveSummaryLine("Summary of plugin %s:" % self.strEDPluginControlSubWedgeAssembleName)
                self.appendExecutiveSummary(self.edPluginControlSubWedgeAssemble)
        if (self.edPluginControlCharacterisation is not None):
            self.addExecutiveSummaryLine("Summary of plugin %s:" % self.strEDPluginControlCharacterisationName)
            self.appendExecutiveSummary(self.edPluginControlCharacterisation)
        if (self.edPluginControlISPyB is not None):
            self.addExecutiveSummaryLine("Summary of plugin %s:" % self.strEDPluginControlISPyBName)
            self.appendExecutiveSummary(self.edPluginControlISPyB)
        self.verboseScreenExecutiveSummary()


    def checkDozorScores(self, _xsDataResultCharacterisation):
        # Check Dozor scores
        listImageQualityIndicators = _xsDataResultCharacterisation.imageQualityIndicators
        noWeakDiffraction = 0
        noTotal = 0
        newComment = None
        referenceImagePath = None
        listImageNoWithNoDiffraction = []
        for imageQualityIndicators in listImageQualityIndicators:
            if referenceImagePath is None:
                referenceImagePath = imageQualityIndicators.image.path.value
            if imageQualityIndicators.dozor_score is not None:
                noTotal += 1
                dozorScore = imageQualityIndicators.dozor_score.value
                if dozorScore <= 0.001:
                    listImageNoWithNoDiffraction.append(imageQualityIndicators.image.number.value)
                elif dozorScore < 1.0:
                    noWeakDiffraction += 1
        if noTotal > 0:
            if len(listImageNoWithNoDiffraction) == noTotal:
                newComment = "No diffraction."
            elif noWeakDiffraction + len(listImageNoWithNoDiffraction) == noTotal:
                newComment = "Very weak diffraction."
            else:
                subComment = None
                if len(listImageNoWithNoDiffraction) == 1:
                    subComment = "image {0}".format(listImageNoWithNoDiffraction[0])
                elif len(listImageNoWithNoDiffraction) == 2:
                    subComment = "images {0} and {1}".format(listImageNoWithNoDiffraction[0], listImageNoWithNoDiffraction[1])                    
                elif len(listImageNoWithNoDiffraction) > 2:
                    subComment = "images {0}".format(listImageNoWithNoDiffraction[0])
                    for imageNo in listImageNoWithNoDiffraction[1:-1]:
                        subComment += ", {0}".format(imageNo)
                    subComment += " and {0}".format(listImageNoWithNoDiffraction[-1])
                if subComment is not None:
                    newComment = "No diffraction detected in {0} - hint: sample might not be accurately centred.".format(subComment)
            
            if newComment is not None and self.iDataCollectionId is not None:
                xsDataInput = XSDataInputISPyBUpdateDataCollectionGroupComment()
                xsDataInput.newComment = XSDataString(newComment)
                xsDataInput.dataCollectionId = XSDataInteger(self.iDataCollectionId)
                edPluginISPyBUpdateDataCollectionGroupComment = self.loadPlugin("EDPluginISPyBUpdateDataCollectionGroupCommentv1_4")
                edPluginISPyBUpdateDataCollectionGroupComment.dataInput = xsDataInput
                self.executePluginSynchronous(edPluginISPyBUpdateDataCollectionGroupComment)

    def getDataCollectionGroupId(self, _dataCollectionId):
        self.DEBUG("EDPluginControlInterfacev1_2.getDataCollectionGroupId")
        self.DEBUG("dataCollectionId = {0}".format(_dataCollectionId))
        dataCollectionGroupId = None
        xsDataInputRetrieveDataCollection = XSDataInputRetrieveDataCollection()
        xsDataInputRetrieveDataCollection.dataCollectionId = XSDataInteger(_dataCollectionId)
        edPluginISPyBRetrieveDataCollection = self.loadPlugin("EDPluginISPyBRetrieveDataCollectionv1_4")
        edPluginISPyBRetrieveDataCollection.dataInput = xsDataInputRetrieveDataCollection
        edPluginISPyBRetrieveDataCollection.executeSynchronous()
        xsDataResultRetrieveDataCollection = edPluginISPyBRetrieveDataCollection.dataOutput
        if xsDataResultRetrieveDataCollection is not None:
            dataCollection = xsDataResultRetrieveDataCollection.dataCollection
            if dataCollection is not None:
                dataCollectionGroupId = dataCollection.dataCollectionGroupId
        self.DEBUG("dataCollectionGroupId = {0}".format(dataCollectionGroupId))
        return dataCollectionGroupId

예제 #2

파일: EDPluginControlInterfacev1_2.py 프로젝트: kif/edna

class EDPluginControlInterfacev1_2(EDPluginControl):
    """
    This is the common class to all plugins managing user interfaces
    """
    def __init__(self):
        """
        """
        EDPluginControl.__init__(self)

        self.setXSDataInputClass(XSDataInputInterface)

        self.setXSDataInputClass(XSDataExperimentalCondition,
                                 "experimentalCondition")
        self.setXSDataInputClass(XSDataDiffractionPlan, "diffractionPlan")
        self.setXSDataInputClass(XSDataSampleCrystalMM, "sample")
        self.setXSDataInputClass(XSDataString, "imagePaths")
        self.setXSDataInputClass(XSDataFloat, "flux")
        self.setXSDataInputClass(XSDataFloat, "minExposureTimePerImage")
        self.setXSDataInputClass(XSDataFloat, "beamSize")
        self.setXSDataInputClass(XSDataFloat, "beamSizeX")
        self.setXSDataInputClass(XSDataFloat, "beamSizeY")
        self.setXSDataInputClass(XSDataBoolean, "templateMode")
        self.setXSDataInputClass(XSDataString, "generatedTemplateFile")
        self.setXSDataInputClass(XSDataString, "resultsFilePath")
        self.setXSDataInputClass(XSDataFloat, "beamPosX")
        self.setXSDataInputClass(XSDataFloat, "beamPosY")
        self.setXSDataInputClass(XSDataDouble, "wavelength")
        self.setXSDataInputClass(XSDataDouble, "transmission")
        self.setXSDataInputClass(XSDataInteger, "dataCollectionId")
        self.setXSDataInputClass(XSDataString, "shortComments")
        self.setXSDataInputClass(XSDataString, "comments")
        self.setXSDataInputClass(XSDataInputCharacterisation,
                                 "inputCharacterisation")

        self.strEDPluginControlSubWedgeAssembleName = "EDPluginControlSubWedgeAssemblev1_1"
        self.strEDPluginControlCharacterisationName = "EDPluginControlCharacterisationv1_1"
        self.strEDPluginControlISPyBName = "EDPluginControlISPyBv1_1"

        self.edPluginControlSubWedgeAssemble = None
        self.edPluginControlCharacterisation = None
        self.edPluginControlISPyB = None

        self.pyListImagePaths = None
        self.xsDataInputCharacterisation = None
        self.strComplexity = "none"

        self.listImagePaths = []
        self.fFlux = None
        self.fMaxExposureTimePerDataCollection = 10000  # s, default prototype value
        self.fMinExposureTimePerImage = None
        self.fBeamSizeX = None
        self.fBeamSizeY = None
        self.bTemplateMode = False
        self.strGeneratedTemplateFile = None
        self.strResultsFilePath = None
        self.strForcedSpaceGroup = None
        self.bAnomalousData = False
        self.fBeamPosX = None
        self.fBeamPosY = None
        self.fMinOscillationWidth = None
        self.fMaxOscillationSpeed = None
        self.fWavelength = None
        self.fTransmission = None
        self.strStrategyOption = None
        self.iDataCollectionId = None
        self.strShortComments = None
        self.strComments = None
        self.strStatusMessage = None

        self.xsDataExperimentalCodition = None
        self.xsDataSample = None
        self.xsDataDiffractionPlan = None

    def configure(self):
        """
        Gets the configuration parameters (if any).
        """
        EDPluginControl.configure(self)
        EDVerbose.DEBUG("EDPluginControlInterfacev1_2.configure")
        pluginConfiguration = self.getConfiguration()

        if (pluginConfiguration is None):
            EDVerbose.DEBUG(
                "No plugin configuration found for EDPluginControlInterfacev1_2."
            )
        else:
            if (self.getControlledPluginName("subWedgeAssemblePlugin")
                    is not None):
                self.strEDPluginControlSubWedgeAssembleName = self.getControlledPluginName(
                    "subWedgeAssemblePlugin")
            if (self.getControlledPluginName("characterisationPlugin")
                    is not None):
                self.strEDPluginControlCharacterisationName = self.getControlledPluginName(
                    "characterisationPlugin")
            if (self.getControlledPluginName("ispybPlugin") is not None):
                self.strEDPluginControlISPyBName = self.getControlledPluginName(
                    "ispybPlugin")

            bUseISPyBPlugin = EDConfiguration.getStringParamValue(
                pluginConfiguration, "useISPyBPlugin")
            if (bUseISPyBPlugin.lower() != "true"):
                self.strEDPluginControlISPyBName = None

    def preProcess(self, _edPlugin=None):
        """
        Gets the Configuration Parameters, if found, overrides default parameters
        """
        EDPluginControl.preProcess(self, _edPlugin)
        EDVerbose.DEBUG("EDPluginControlInterfacev1_2.preProcess...")

        self.listImagePaths = []

        # Check if XSDataInputInterface is given as input
        if self.hasDataInput():
            xsDataInputInterface = self.getDataInput()

            if xsDataInputInterface.getExperimentalCondition():
                self.xsDataExperimentalCodition = xsDataInputInterface.getExperimentalCondition(
                )
                if self.xsDataExperimentalCodition.getGoniostat():
                    if self.xsDataExperimentalCodition.getGoniostat(
                    ).getMinOscillationWidth():
                        self.fMinOscillationWidth = self.xsDataExperimentalCodition.getGoniostat(
                        ).getMinOscillationWidth().getValue()
                    if self.xsDataExperimentalCodition.getGoniostat(
                    ).getMaxOscillationSpeed():
                        self.fMaxOscillationSpeed = self.xsDataExperimentalCodition.getGoniostat(
                        ).getMaxOscillationSpeed().getValue()

            self.xsDataSample = xsDataInputInterface.getSample()

            self.xsDataDiffractionPlan = self.getDataInput(
            ).getDiffractionPlan()
            if self.xsDataDiffractionPlan:
                if self.xsDataDiffractionPlan.getForcedSpaceGroup():
                    self.strForcedSpaceGroup = self.xsDataDiffractionPlan.getForcedSpaceGroup(
                    ).getValue()
                if self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection(
                ):
                    self.fMaxExposureTimePerDataCollection = self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection(
                    ).getValue()
                if self.xsDataDiffractionPlan.getAnomalousData():
                    self.bAnomalousData = self.xsDataDiffractionPlan.getAnomalousData(
                    ).getValue()
                if self.xsDataDiffractionPlan.getStrategyOption():
                    self.strStrategyOption = self.xsDataDiffractionPlan.getStrategyOption(
                    ).getValue()
                if self.xsDataDiffractionPlan.getComplexity():
                    self.strComplexity = self.xsDataDiffractionPlan.getComplexity(
                    ).getValue()
                if self.fMinOscillationWidth == None:
                    if self.xsDataDiffractionPlan.getGoniostatMinOscillationWidth(
                    ):
                        self.fMinOscillationWidth = self.xsDataDiffractionPlan.getGoniostatMinOscillationWidth(
                        ).getValue()
                if self.fMaxOscillationSpeed == None:
                    if self.xsDataDiffractionPlan.getGoniostatMaxOscillationSpeed(
                    ):
                        self.fMaxOscillationSpeed = self.xsDataDiffractionPlan.getGoniostatMaxOscillationSpeed(
                        ).getValue()

            self.xsDataSample = xsDataInputInterface.getSample()

            if xsDataInputInterface.getImagePath():
                for xsDataFile in xsDataInputInterface.getImagePath():
                    self.listImagePaths.append(xsDataFile.getPath())

            if xsDataInputInterface.getFlux():
                self.fFlux = xsDataInputInterface.getFlux().getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getBeam() != None:
                    if self.xsDataExperimentalCodition.getBeam().getFlux(
                    ) != None:
                        self.fFlux = self.xsDataExperimentalCodition.getBeam(
                        ).getFlux().getValue()

            if xsDataInputInterface.getMinExposureTimePerImage():
                self.fMinExposureTimePerImage = xsDataInputInterface.getMinExposureTimePerImage(
                ).getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getBeam() != None:
                    if self.xsDataExperimentalCodition.getBeam(
                    ).getMinExposureTimePerImage() != None:
                        self.fMinExposureTimePerImage = self.xsDataExperimentalCodition.getBeam(
                        ).getMinExposureTimePerImage().getValue()
            if self.fMinExposureTimePerImage == None and xsDataInputInterface.getDiffractionPlan(
            ):
                if xsDataInputInterface.getDiffractionPlan(
                ).getMinExposureTimePerImage() != None:
                    self.fMinExposureTimePerImage = xsDataInputInterface.getdiffractionPlan(
                    ).getMinExposureTimePerImage().getValue()

            if self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getBeam() != None:
                    if self.xsDataExperimentalCodition.getBeam().getSize(
                    ) != None:
                        self.fBeamSizeX = self.xsDataExperimentalCodition.getBeam(
                        ).getSize().getX().getValue()
                        self.fBeamSizeY = self.xsDataExperimentalCodition.getBeam(
                        ).getSize().getY().getValue()

            if xsDataInputInterface.getBeamSize():
                self.fBeamSizeX = xsDataInputInterface.getBeamSize().getValue()
                self.fBeamSizeY = xsDataInputInterface.getBeamSize().getValue()

            if xsDataInputInterface.getBeamSizeX():
                self.fBeamSizeX = xsDataInputInterface.getBeamSizeX().getValue(
                )

            if xsDataInputInterface.getBeamSizeY():
                self.fBeamSizeY = xsDataInputInterface.getBeamSizeY().getValue(
                )

            if xsDataInputInterface.getTemplateMode():
                self.bTemplateMode = xsDataInputInterface.getTemplateMode(
                ).getValue()

            if xsDataInputInterface.getBeamPosX():
                self.fBeamPosX = xsDataInputInterface.getBeamPosX().getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getDetector() != None:
                    if self.xsDataExperimentalCodition.getDetector(
                    ).getBeamPositionX() != None:
                        self.fBeamPosX = self.xsDataExperimentalCodition.getDetector(
                        ).getBeamPositionX().getValue()

            if xsDataInputInterface.getBeamPosY():
                self.fBeamPosY = xsDataInputInterface.getBeamPosY().getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getDetector() != None:
                    if self.xsDataExperimentalCodition.getDetector(
                    ).getBeamPositionY() != None:
                        self.fBeamPosY = self.xsDataExperimentalCodition.getDetector(
                        ).getBeamPositionY().getValue()

            if xsDataInputInterface.getWavelength():
                self.fWavelength = xsDataInputInterface.getWavelength(
                ).getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getBeam() != None:
                    if self.xsDataExperimentalCodition.getBeam().getWavelength(
                    ) != None:
                        self.fWavelength = self.xsDataExperimentalCodition.getBeam(
                        ).getWavelength().getValue()

            if xsDataInputInterface.getTransmission():
                self.fTransmission = xsDataInputInterface.getTransmission(
                ).getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getBeam() != None:
                    if self.xsDataExperimentalCodition.getBeam(
                    ).getTransmission() != None:
                        self.fTransmission = self.xsDataExperimentalCodition.getBeam(
                        ).getTransmission().getValue()

            if xsDataInputInterface.getGeneratedTemplateFile():
                self.strGeneratedTemplateFile = xsDataInputInterface.getGeneratedTemplateFile(
                ).getPath().getValue()

            if xsDataInputInterface.getResultsFilePath():
                self.strResultsFilePath = xsDataInputInterface.getResultsFilePath(
                ).getPath().getValue()

            if xsDataInputInterface.getDataCollectionId():
                self.iDataCollectionId = xsDataInputInterface.getDataCollectionId(
                ).getValue()

            if xsDataInputInterface.getShortComments():
                self.strShortComments = xsDataInputInterface.getShortComments(
                ).getValue()

            if xsDataInputInterface.getComments():
                self.strComments = xsDataInputInterface.getComments().getValue(
                )

            if xsDataInputInterface.getInputCharacterisation():
                self.xsDataInputCharacterisation = xsDataInputInterface.getInputCharacterisation(
                )

            if xsDataInputInterface.getDataCollectionId():
                self.iDataCollectionId = xsDataInputInterface.getDataCollectionId(
                ).getValue()

        else:

            if self.hasDataInput("experimentalCondition"):
                self.xsDataExperimentalCodition = self.getDataInput(
                    "experimentalCondition")[0]
                if self.xsDataExperimentalCodition.getGoniostat():
                    if self.xsDataExperimentalCodition.getGoniostat(
                    ).getMinOscillationWidth():
                        self.fMinOscillationWidth = self.xsDataExperimentalCodition.getGoniostat(
                        ).getMinOscillationWidth().getValue()
                    if self.xsDataExperimentalCodition.getGoniostat(
                    ).getMaxOscillationSpeed():
                        self.fMaxOscillationSpeed = self.xsDataExperimentalCodition.getGoniostat(
                        ).getMaxOscillationSpeed().getValue()

            if self.hasDataInput("sample"):
                self.xsDataSample = self.getDataInput("sample")[0]

            if (self.hasDataInput("diffractionPlan")):
                if self.xsDataDiffractionPlan is None:
                    self.xsDataDiffractionPlan = XSDataDiffractionPlan()
                xsDataDiffractionPlans = self.getDataInput("diffractionPlan")
                if (not xsDataDiffractionPlans[0] is None):
                    self.xsDataDiffractionPlan = xsDataDiffractionPlans[0]
                    if self.xsDataDiffractionPlan.getForcedSpaceGroup():
                        self.strForcedSpaceGroup = self.xsDataDiffractionPlan.getForcedSpaceGroup(
                        ).getValue()
                    if self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection(
                    ):
                        self.fMaxExposureTimePerDataCollection = self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection(
                        ).getValue()
                    if self.xsDataDiffractionPlan.getAnomalousData():
                        self.bAnomalousData = self.xsDataDiffractionPlan.getAnomalousData(
                        ).getValue()
                    if self.xsDataDiffractionPlan.getStrategyOption():
                        self.strStrategyOption = self.xsDataDiffractionPlan.getStrategyOption(
                        ).getValue()
                    if self.xsDataDiffractionPlan.getComplexity():
                        self.strComplexity = self.xsDataDiffractionPlan.getComplexity(
                        ).getValue()
                    if self.fMinOscillationWidth == None:
                        if self.xsDataDiffractionPlan.getGoniostatMinOscillationWidth(
                        ):
                            self.fMinOscillationWidth = self.xsDataDiffractionPlan.getGoniostatMinOscillationWidth(
                            ).getValue()
                    if self.fMaxOscillationSpeed == None:
                        if self.xsDataDiffractionPlan.getGoniostatMaxOscillationSpeed(
                        ):
                            self.fMaxOscillationSpeed = self.xsDataDiffractionPlan.getGoniostatMaxOscillationSpeed(
                            ).getValue()

            if self.hasDataInput("sample"):
                self.xsDataSample = self.getDataInput("sample")[0]

            if self.hasDataInput("imagePaths"):
                for strImagePath in self.getDataInput("imagePaths"):
                    self.listImagePaths.append(strImagePath)

            if self.hasDataInput("flux"):
                self.fFlux = self.getDataInput("flux")[0].getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getBeam() != None:
                    if self.xsDataExperimentalCodition.getBeam().getFlux(
                    ) != None:
                        self.fFlux = self.xsDataExperimentalCodition.getBeam(
                        ).getFlux().getValue()

            if self.hasDataInput("minExposureTimePerImage"):
                self.fMinExposureTimePerImage = self.getDataInput(
                    "minExposureTimePerImage")[0].getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getBeam() != None:
                    if self.xsDataExperimentalCodition.getBeam(
                    ).getMinExposureTimePerImage() != None:
                        self.fMinExposureTimePerImage = self.xsDataExperimentalCodition.getBeam(
                        ).getMinExposureTimePerImage().getValue()
            if self.fMinExposureTimePerImage == None and self.hasDataInput(
                    "diffractionPlan"):
                if self.getDataInput("diffractionPlan"
                                     )[0].getMinExposureTimePerImage() != None:
                    self.fMinExposureTimePerImage = self.getDataInput(
                        "diffractionPlan")[0].getMinExposureTimePerImage(
                        ).getValue()

            if self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getBeam() != None:
                    if self.xsDataExperimentalCodition.getBeam().getSize(
                    ) != None:
                        self.fBeamSizeX = self.xsDataExperimentalCodition.getBeam(
                        ).getSize().getX().getValue()
                        self.fBeamSizeY = self.xsDataExperimentalCodition.getBeam(
                        ).getSize().getY().getValue()

            if self.hasDataInput("beamSize"):
                self.fBeamSizeX = self.getDataInput("beamSize")[0].getValue()
                self.fBeamSizeY = self.getDataInput("beamSize")[0].getValue()

            if self.hasDataInput("beamSizeX"):
                self.fBeamSizeX = self.getDataInput("beamSizeX")[0].getValue()

            if self.hasDataInput("beamSizeY"):
                self.fBeamSizeY = self.getDataInput("beamSizeY")[0].getValue()

            if self.hasDataInput("templateMode"):
                self.bTemplateMode = self.getDataInput(
                    "templateMode")[0].getValue()

            if (self.hasDataInput("beamPosX")):
                self.fBeamPosX = self.getDataInput("beamPosX")[0].getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getDetector() != None:
                    if self.xsDataExperimentalCodition.getDetector(
                    ).getBeamPositionX() != None:
                        self.fBeamPosX = self.xsDataExperimentalCodition.getDetector(
                        ).getBeamPositionX().getValue()

            if (self.hasDataInput("beamPosY")):
                self.fBeamPosY = self.getDataInput("beamPosY")[0].getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getDetector() != None:
                    if self.xsDataExperimentalCodition.getDetector(
                    ).getBeamPositionY() != None:
                        self.fBeamPosY = self.xsDataExperimentalCodition.getDetector(
                        ).getBeamPositionY().getValue()

            if (self.hasDataInput("wavelength")):
                self.fWavelength = self.getDataInput(
                    "wavelength")[0].getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getBeam() != None:
                    if self.xsDataExperimentalCodition.getBeam().getWavelength(
                    ) != None:
                        self.fWavelength = self.xsDataExperimentalCodition.getBeam(
                        ).getWavelength().getValue()

            if (self.hasDataInput("transmission")):
                self.fTransmission = self.getDataInput(
                    "transmission")[0].getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getBeam() != None:
                    if self.xsDataExperimentalCodition.getBeam(
                    ).getTransmission() != None:
                        self.fTransmission = self.xsDataExperimentalCodition.getBeam(
                        ).getTransmission().getValue()

            if self.hasDataInput("generatedTemplateFile"):
                self.strGeneratedTemplateFile = self.getDataInput(
                    "generatedTemplateFile")[0].getValue()

            if self.hasDataInput("resultsFilePath"):
                self.strResultsFilePath = self.getDataInput(
                    "resultsFilePath")[0].getValue()

            if self.hasDataInput("dataCollectionId"):
                self.iDataCollectionId = self.getDataInput(
                    "dataCollectionId")[0].getValue()

            if self.hasDataInput("shortComments"):
                self.strShortComments = self.getDataInput(
                    "shortComments")[0].getValue()

            if self.hasDataInput("comments"):
                self.strComments = self.getDataInput("comments")[0].getValue()

            if self.hasDataInput("inputCharacterisation"):
                self.xsDataInputCharacterisation = self.getDataInput(
                    "inputCharacterisation")[0]

        # Check if XML data is given as input :
        if (self.xsDataInputCharacterisation is None):
            self.edPluginControlSubWedgeAssemble = self.loadPlugin(
                self.strEDPluginControlSubWedgeAssembleName,
                "SubWedgeAssemble")

        self.edPluginControlCharacterisation = self.loadPlugin(
            self.strEDPluginControlCharacterisationName, "Characterisation")

        if (self.strEDPluginControlISPyBName is not None):
            self.edPluginControlISPyB = self.loadPlugin(
                self.strEDPluginControlISPyBName, "ISPyB")

    def process(self, _edPlugin=None):
        EDPluginControl.process(self, _edPlugin)
        EDVerbose.DEBUG("EDPluginControlInterfacev1_2.process...")

        if (self.edPluginControlSubWedgeAssemble is not None):
            if (self.bTemplateMode == True):
                self.edPluginControlSubWedgeAssemble.connectSUCCESS(
                    self.generateTemplateFile)
            else:
                self.edPluginControlSubWedgeAssemble.connectSUCCESS(
                    self.doSubWedgeAssembleSUCCESS)
            self.edPluginControlSubWedgeAssemble.connectFAILURE(
                self.doSubWedgeAssembleFAILURE)

        if (self.edPluginControlCharacterisation is not None):
            self.edPluginControlCharacterisation.connectSUCCESS(
                self.doSuccessActionCharacterisation)
            self.edPluginControlCharacterisation.connectFAILURE(
                self.doFailureActionCharacterisation)

        if (self.edPluginControlISPyB is not None):
            self.edPluginControlISPyB.connectSUCCESS(self.doSuccessActionISPyB)
            self.edPluginControlISPyB.connectFAILURE(self.doFailureActionISPyB)

        if (self.xsDataInputCharacterisation is None):
            self.createInputCharacterisationFromImageHeaders(
                self.edPluginControlSubWedgeAssemble)
        else:
            self.runCharacterisationPlugin(
                self.edPluginControlCharacterisation)

    def finallyProcess(self, _edPlugin=None):
        EDPluginControl.finallyProcess(self, _edPlugin)
        EDVerbose.DEBUG("EDPluginControlInterfacev1_2.finallyProcess...")

        if (not self.edPluginControlCharacterisation is None):
            if (self.edPluginControlCharacterisation.hasDataOutput()):
                self.setDataOutput(
                    self.edPluginControlCharacterisation.getDataOutput(),
                    "characterisation")
        if (not self.edPluginControlISPyB is None):
            if (self.edPluginControlISPyB.hasDataOutput()):
                self.setDataOutput(self.edPluginControlISPyB.getDataOutput(),
                                   "ISPyB")
        if self.hasDataInput():
            xsDataResultInterface = XSDataResultInterface()
            if self.edPluginControlCharacterisation:
                xsDataResultInterface.setResultCharacterisation(
                    self.edPluginControlCharacterisation.getDataOutput())
            if self.edPluginControlISPyB:
                xsDataResultInterface.setResultControlISPyB(
                    self.edPluginControlISPyB.getDataOutput())
            self.setDataOutput(xsDataResultInterface)

    def createInputCharacterisationFromImageHeaders(self, _edPlugin):
        EDVerbose.DEBUG(
            "EDPluginControlInterfacev1_2.createInputCharacterisationFromImageHeaders"
        )
        xsDataInputSubWedgeAssemble = XSDataInputSubWedgeAssemble()
        for xsDataStringImagePath in self.listImagePaths:
            xsDataFile = XSDataFile()
            xsDataFile.setPath(xsDataStringImagePath)
            xsDataInputSubWedgeAssemble.addFile(xsDataFile)
        _edPlugin.setDataInput(xsDataInputSubWedgeAssemble)
        _edPlugin.executeSynchronous()

    def runCharacterisationPlugin(self, _edPlugin=None):
        EDVerbose.DEBUG(
            "EDPluginControlInterfacev1_2.runCharacterisationPlugin")
        self.edPluginControlCharacterisation.setDataInput(
            self.xsDataInputCharacterisation)
        self.edPluginControlCharacterisation.executeSynchronous()

    def storeResultsInISPyB(self, _edPlugin=None):
        EDVerbose.DEBUG("EDPluginControlInterfacev1_2.storeResultsInISPyB")
        if (self.edPluginControlISPyB is not None):
            # Execute the ISPyB control plugin
            xsDataInputControlISPyB = XSDataInputControlISPyB()
            xsDataInputControlISPyB.setCharacterisationResult(
                self.edPluginControlCharacterisation.getDataOutput())
            if (not self.iDataCollectionId is None):
                xsDataInputControlISPyB.setDataCollectionId(
                    XSDataInteger(self.iDataCollectionId))
            if (not self.strShortComments is None):
                self.edPluginControlISPyB.setDataInput(
                    XSDataString(self.strShortComments), "shortComments")
            if (not self.strComments is None):
                self.edPluginControlISPyB.setDataInput(
                    XSDataString(self.strComments), "comments")
            if (not self.strStatusMessage is None):
                self.edPluginControlISPyB.setDataInput(
                    XSDataString(self.strStatusMessage), "statusMessage")
            self.edPluginControlISPyB.setDataInput(xsDataInputControlISPyB)
            self.edPluginControlISPyB.executeSynchronous()

    def createInputCharacterisationFromSubWedges(self):
        EDVerbose.DEBUG(
            "EDPluginControlInterfacev1_2.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)
        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):
        """
        retrieve the potential warning messages
        retrieve the potential error messages
        """
        EDVerbose.DEBUG(
            "EDPluginControlInterfacev1_2.doFailureActionCharacterisation")
        self.retrieveFailureMessages(
            self.edPluginControlCharacterisation,
            "EDPluginControlInterfacev1_2.doSuccessActionISPyB")
        if _edPlugin.hasDataOutput("statusMessage"):
            self.strStatusMessage = _edPlugin.getDataOutput(
                "statusMessage")[0].getValue()
        self.generateExecutiveSummary(self)
        self.storeResultsInISPyB(_edPlugin)
        self.setFailure()

    def doSuccessActionCharacterisation(self, _edPlugin=None):
        """
        retrieve the potential warning messages
        """
        EDVerbose.DEBUG(
            "EDPluginControlInterfacev1_2.doSuccessActionCharacterisation")
        # Store the results if requested
        if (self.strResultsFilePath is not None):
            xsDataCharacterisationResult = _edPlugin.getDataOutput()
            if (xsDataCharacterisationResult is not None):
                xsDataCharacterisationResult.exportToFile(
                    self.strResultsFilePath)
        if _edPlugin.hasDataOutput("statusMessage"):
            self.strStatusMessage = _edPlugin.getDataOutput(
                "statusMessage")[0].getValue()
        self.storeResultsInISPyB(_edPlugin)

    def doSuccessActionISPyB(self, _edPlugin):
        EDVerbose.DEBUG("EDPluginControlInterfacev1_2.doSuccessActionISPyB...")
        self.retrieveSuccessMessages(
            self.edPluginControlISPyB,
            "EDPluginControlInterfacev1_2.doSuccessActionISPyB")

    def doFailureActionISPyB(self, _edPlugin=None):
        EDVerbose.DEBUG("EDPluginControlInterfacev1_2.doFailureActionISpyB...")
        self.generateExecutiveSummary(self)
        self.setFailure()

    def generateExecutiveSummary(self, _edPlugin=None):
        """
        Prints the executive summary from the plugin
        """
        EDVerbose.DEBUG(
            "EDPluginControlInterfacev1_2.generateExecutiveSummary")
        if (self.edPluginControlSubWedgeAssemble is not None):
            if self.edPluginControlSubWedgeAssemble.getListExecutiveSummaryLines(
            ) != []:
                self.addExecutiveSummaryLine(
                    "Summary of plugin %s:" %
                    self.strEDPluginControlSubWedgeAssembleName)
                self.appendExecutiveSummary(
                    self.edPluginControlSubWedgeAssemble)
        if (self.edPluginControlCharacterisation is not None):
            self.addExecutiveSummaryLine(
                "Summary of plugin %s:" %
                self.strEDPluginControlCharacterisationName)
            self.appendExecutiveSummary(self.edPluginControlCharacterisation)
        if (self.edPluginControlISPyB is not None):
            self.addExecutiveSummaryLine("Summary of plugin %s:" %
                                         self.strEDPluginControlISPyBName)
            self.appendExecutiveSummary(self.edPluginControlISPyB)
        self.verboseScreenExecutiveSummary()

예제 #3

class EDPluginControlInterfacev1_3(EDPluginControl):
    """
    This is the common class to all plugins managing user interfaces
    """
    def __init__(self):
        """
        """
        EDPluginControl.__init__(self)

        self.setXSDataInputClass(XSDataInputInterface)

        self.setXSDataInputClass(XSDataExperimentalCondition,
                                 "experimentalCondition")
        self.setXSDataInputClass(XSDataDiffractionPlan, "diffractionPlan")
        self.setXSDataInputClass(XSDataSampleCrystalMM, "sample")
        self.setXSDataInputClass(XSDataString, "imagePaths")
        self.setXSDataInputClass(XSDataFloat, "flux")
        self.setXSDataInputClass(XSDataFloat, "minExposureTimePerImage")
        self.setXSDataInputClass(XSDataFloat, "beamSize")
        self.setXSDataInputClass(XSDataFloat, "beamSizeX")
        self.setXSDataInputClass(XSDataFloat, "beamSizeY")
        self.setXSDataInputClass(XSDataBoolean, "templateMode")
        self.setXSDataInputClass(XSDataString, "generatedTemplateFile")
        self.setXSDataInputClass(XSDataString, "resultsFilePath")
        self.setXSDataInputClass(XSDataFloat, "beamPosX")
        self.setXSDataInputClass(XSDataFloat, "beamPosY")
        self.setXSDataInputClass(XSDataDouble, "wavelength")
        self.setXSDataInputClass(XSDataDouble, "transmission")
        self.setXSDataInputClass(XSDataInteger, "dataCollectionId")
        self.setXSDataInputClass(XSDataString, "shortComments")
        self.setXSDataInputClass(XSDataString, "comments")
        self.setXSDataInputClass(XSDataInputCharacterisation,
                                 "inputCharacterisation")

        self.strEDPluginControlSubWedgeAssembleName = "EDPluginControlSubWedgeAssemblev1_1"
        self.strEDPluginControlCharacterisationName = "EDPluginControlCharacterisationv1_5"
        self.strEDPluginControlISPyBName = "EDPluginControlISPyBv1_1"

        self.edPluginControlSubWedgeAssemble = None
        self.edPluginControlCharacterisation = None
        self.edPluginControlISPyB = None

        self.pyListImagePaths = None
        self.xsDataInputCharacterisation = None
        self.strComplexity = "none"

        self.listImagePaths = []
        self.fFlux = None
        self.fMaxExposureTimePerDataCollection = 10000  # s, default prototype value
        self.fMinExposureTimePerImage = None
        self.fBeamSizeX = None
        self.fBeamSizeY = None
        self.fApertureSize = None
        self.bTemplateMode = False
        self.strGeneratedTemplateFile = None
        self.strResultsFilePath = None
        self.strForcedSpaceGroup = None
        self.bAnomalousData = False
        self.fBeamPosX = None
        self.fBeamPosY = None
        self.fMinOscillationWidth = None
        self.fMaxOscillationSpeed = None
        self.fWavelength = None
        self.fTransmission = None
        self.strStrategyOption = None
        self.iDataCollectionId = None
        self.strShortComments = None
        self.strComments = None
        self.strStatusMessage = None

        self.xsDataExperimentalCodition = None
        self.xsDataSample = None
        self.xsDataDiffractionPlan = None

    def configure(self):
        """
        Gets the configuration parameters (if any).
        """
        EDPluginControl.configure(self)
        self.DEBUG("EDPluginControlInterfacev1_3.configure")
        if (self.getControlledPluginName("subWedgeAssemblePlugin")
                is not None):
            self.strEDPluginControlSubWedgeAssembleName = self.getControlledPluginName(
                "subWedgeAssemblePlugin")
        if (self.getControlledPluginName("characterisationPlugin")
                is not None):
            self.strEDPluginControlCharacterisationName = self.getControlledPluginName(
                "characterisationPlugin")
        if (self.getControlledPluginName("ispybPlugin") is not None):
            self.strEDPluginControlISPyBName = self.getControlledPluginName(
                "ispybPlugin")

        bUseISPyBPlugin = self.config.get("useISPyBPlugin")
        if not bUseISPyBPlugin:
            self.DEBUG(
                "EDPluginControlInterfacev1_3 configured to not use ISPyB")
            self.strEDPluginControlISPyBName = None

    def preProcess(self, _edPlugin=None):
        """
        Gets the Configuration Parameters, if found, overrides default parameters
        """
        EDPluginControl.preProcess(self, _edPlugin)
        self.DEBUG("EDPluginControlInterfacev1_3.preProcess...")

        self.listImagePaths = []

        # Check if XSDataInputInterface is given as input
        if self.hasDataInput():
            xsDataInputInterface = self.getDataInput()

            if xsDataInputInterface.getExperimentalCondition():
                self.xsDataExperimentalCodition = xsDataInputInterface.getExperimentalCondition(
                )
                if self.xsDataExperimentalCodition.getGoniostat():
                    if self.xsDataExperimentalCodition.getGoniostat(
                    ).getMinOscillationWidth():
                        self.fMinOscillationWidth = self.xsDataExperimentalCodition.getGoniostat(
                        ).getMinOscillationWidth().getValue()
                    if self.xsDataExperimentalCodition.getGoniostat(
                    ).getMaxOscillationSpeed():
                        self.fMaxOscillationSpeed = self.xsDataExperimentalCodition.getGoniostat(
                        ).getMaxOscillationSpeed().getValue()

            self.xsDataSample = xsDataInputInterface.getSample()

            self.xsDataDiffractionPlan = self.getDataInput(
            ).getDiffractionPlan()
            if self.xsDataDiffractionPlan:
                if self.xsDataDiffractionPlan.getForcedSpaceGroup():
                    self.strForcedSpaceGroup = self.xsDataDiffractionPlan.getForcedSpaceGroup(
                    ).getValue()
                if self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection(
                ):
                    self.fMaxExposureTimePerDataCollection = self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection(
                    ).getValue()
                if self.xsDataDiffractionPlan.getAnomalousData():
                    self.bAnomalousData = self.xsDataDiffractionPlan.getAnomalousData(
                    ).getValue()
                if self.xsDataDiffractionPlan.getStrategyOption():
                    self.strStrategyOption = self.xsDataDiffractionPlan.getStrategyOption(
                    ).getValue()
                if self.xsDataDiffractionPlan.getComplexity():
                    self.strComplexity = self.xsDataDiffractionPlan.getComplexity(
                    ).getValue()
                if self.fMinOscillationWidth == None:
                    if self.xsDataDiffractionPlan.getGoniostatMinOscillationWidth(
                    ):
                        self.fMinOscillationWidth = self.xsDataDiffractionPlan.getGoniostatMinOscillationWidth(
                        ).getValue()
                if self.fMaxOscillationSpeed == None:
                    if self.xsDataDiffractionPlan.getGoniostatMaxOscillationSpeed(
                    ):
                        self.fMaxOscillationSpeed = self.xsDataDiffractionPlan.getGoniostatMaxOscillationSpeed(
                        ).getValue()

            self.xsDataSample = xsDataInputInterface.getSample()

            if xsDataInputInterface.getImagePath():
                for xsDataFile in xsDataInputInterface.getImagePath():
                    self.listImagePaths.append(xsDataFile.getPath())

            if xsDataInputInterface.getFlux():
                self.fFlux = xsDataInputInterface.getFlux().getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getBeam() != None:
                    if self.xsDataExperimentalCodition.getBeam().getFlux(
                    ) != None:
                        self.fFlux = self.xsDataExperimentalCodition.getBeam(
                        ).getFlux().getValue()

            if xsDataInputInterface.getMinExposureTimePerImage():
                self.fMinExposureTimePerImage = xsDataInputInterface.getMinExposureTimePerImage(
                ).getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getBeam() != None:
                    if self.xsDataExperimentalCodition.getBeam(
                    ).getMinExposureTimePerImage() != None:
                        self.fMinExposureTimePerImage = self.xsDataExperimentalCodition.getBeam(
                        ).getMinExposureTimePerImage().getValue()
            if self.fMinExposureTimePerImage == None and xsDataInputInterface.getDiffractionPlan(
            ):
                if xsDataInputInterface.getDiffractionPlan(
                ).getMinExposureTimePerImage() != None:
                    self.fMinExposureTimePerImage = xsDataInputInterface.getDiffractionPlan(
                    ).getMinExposureTimePerImage().getValue()

            if self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getBeam() != None:
                    if self.xsDataExperimentalCodition.getBeam().getSize(
                    ) != None:
                        self.fBeamSizeX = self.xsDataExperimentalCodition.getBeam(
                        ).getSize().getX().getValue()
                        self.fBeamSizeY = self.xsDataExperimentalCodition.getBeam(
                        ).getSize().getY().getValue()
                    if self.xsDataExperimentalCodition.getBeam(
                    ).getApertureSize() != None:
                        self.fApertureSize = self.xsDataExperimentalCodition.getBeam(
                        ).getApertureSize().getValue()

            if xsDataInputInterface.getBeamSize():
                self.fBeamSizeX = xsDataInputInterface.getBeamSize().getValue()
                self.fBeamSizeY = xsDataInputInterface.getBeamSize().getValue()

            if xsDataInputInterface.getApertureSize():
                self.fApertureSize = xsDataInputInterface.getApertureSize(
                ).getValue()

            if xsDataInputInterface.getBeamSizeX():
                self.fBeamSizeX = xsDataInputInterface.getBeamSizeX().getValue(
                )

            if xsDataInputInterface.getBeamSizeY():
                self.fBeamSizeY = xsDataInputInterface.getBeamSizeY().getValue(
                )

            if xsDataInputInterface.getApertureSize():
                self.fApertureSize = xsDataInputInterface.getApertureSize(
                ).getValue()

            if xsDataInputInterface.getTemplateMode():
                self.bTemplateMode = xsDataInputInterface.getTemplateMode(
                ).getValue()

            if xsDataInputInterface.getBeamPosX():
                self.fBeamPosX = xsDataInputInterface.getBeamPosX().getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getDetector() != None:
                    if self.xsDataExperimentalCodition.getDetector(
                    ).getBeamPositionX() != None:
                        self.fBeamPosX = self.xsDataExperimentalCodition.getDetector(
                        ).getBeamPositionX().getValue()

            if xsDataInputInterface.getBeamPosY():
                self.fBeamPosY = xsDataInputInterface.getBeamPosY().getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getDetector() != None:
                    if self.xsDataExperimentalCodition.getDetector(
                    ).getBeamPositionY() != None:
                        self.fBeamPosY = self.xsDataExperimentalCodition.getDetector(
                        ).getBeamPositionY().getValue()

            if xsDataInputInterface.getWavelength():
                self.fWavelength = xsDataInputInterface.getWavelength(
                ).getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getBeam() != None:
                    if self.xsDataExperimentalCodition.getBeam().getWavelength(
                    ) != None:
                        self.fWavelength = self.xsDataExperimentalCodition.getBeam(
                        ).getWavelength().getValue()

            if xsDataInputInterface.getTransmission():
                self.fTransmission = xsDataInputInterface.getTransmission(
                ).getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getBeam() != None:
                    if self.xsDataExperimentalCodition.getBeam(
                    ).getTransmission() != None:
                        self.fTransmission = self.xsDataExperimentalCodition.getBeam(
                        ).getTransmission().getValue()

            if xsDataInputInterface.getGeneratedTemplateFile():
                self.strGeneratedTemplateFile = xsDataInputInterface.getGeneratedTemplateFile(
                ).getPath().getValue()

            if xsDataInputInterface.getResultsFilePath():
                self.strResultsFilePath = xsDataInputInterface.getResultsFilePath(
                ).getPath().getValue()

            if xsDataInputInterface.getDataCollectionId():
                self.iDataCollectionId = xsDataInputInterface.getDataCollectionId(
                ).getValue()

            if xsDataInputInterface.getShortComments():
                self.strShortComments = xsDataInputInterface.getShortComments(
                ).getValue()

            if xsDataInputInterface.getComments():
                self.strComments = xsDataInputInterface.getComments().getValue(
                )

            if xsDataInputInterface.getInputCharacterisation():
                self.xsDataInputCharacterisation = xsDataInputInterface.getInputCharacterisation(
                )

            if xsDataInputInterface.getDataCollectionId():
                self.iDataCollectionId = xsDataInputInterface.getDataCollectionId(
                ).getValue()

        else:

            if self.hasDataInput("experimentalCondition"):
                self.xsDataExperimentalCodition = self.getDataInput(
                    "experimentalCondition")[0]
                if self.xsDataExperimentalCodition.getGoniostat():
                    if self.xsDataExperimentalCodition.getGoniostat(
                    ).getMinOscillationWidth():
                        self.fMinOscillationWidth = self.xsDataExperimentalCodition.getGoniostat(
                        ).getMinOscillationWidth().getValue()
                    if self.xsDataExperimentalCodition.getGoniostat(
                    ).getMaxOscillationSpeed():
                        self.fMaxOscillationSpeed = self.xsDataExperimentalCodition.getGoniostat(
                        ).getMaxOscillationSpeed().getValue()

            if self.hasDataInput("sample"):
                self.xsDataSample = self.getDataInput("sample")[0]

            if (self.hasDataInput("diffractionPlan")):
                if self.xsDataDiffractionPlan is None:
                    self.xsDataDiffractionPlan = XSDataDiffractionPlan()
                xsDataDiffractionPlans = self.getDataInput("diffractionPlan")
                if (not xsDataDiffractionPlans[0] is None):
                    self.xsDataDiffractionPlan = xsDataDiffractionPlans[0]
                    if self.xsDataDiffractionPlan.getForcedSpaceGroup():
                        self.strForcedSpaceGroup = self.xsDataDiffractionPlan.getForcedSpaceGroup(
                        ).getValue()
                    if self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection(
                    ):
                        self.fMaxExposureTimePerDataCollection = self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection(
                        ).getValue()
                    if self.xsDataDiffractionPlan.getAnomalousData():
                        self.bAnomalousData = self.xsDataDiffractionPlan.getAnomalousData(
                        ).getValue()
                    if self.xsDataDiffractionPlan.getStrategyOption():
                        self.strStrategyOption = self.xsDataDiffractionPlan.getStrategyOption(
                        ).getValue()
                    if self.xsDataDiffractionPlan.getComplexity():
                        self.strComplexity = self.xsDataDiffractionPlan.getComplexity(
                        ).getValue()
                    if self.fMinOscillationWidth == None:
                        if self.xsDataDiffractionPlan.getGoniostatMinOscillationWidth(
                        ):
                            self.fMinOscillationWidth = self.xsDataDiffractionPlan.getGoniostatMinOscillationWidth(
                            ).getValue()
                    if self.fMaxOscillationSpeed == None:
                        if self.xsDataDiffractionPlan.getGoniostatMaxOscillationSpeed(
                        ):
                            self.fMaxOscillationSpeed = self.xsDataDiffractionPlan.getGoniostatMaxOscillationSpeed(
                            ).getValue()

            if self.hasDataInput("sample"):
                self.xsDataSample = self.getDataInput("sample")[0]

            if self.hasDataInput("imagePaths"):
                for strImagePath in self.getDataInput("imagePaths"):
                    self.listImagePaths.append(strImagePath)

            if self.hasDataInput("flux"):
                self.fFlux = self.getDataInput("flux")[0].getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getBeam() != None:
                    if self.xsDataExperimentalCodition.getBeam().getFlux(
                    ) != None:
                        self.fFlux = self.xsDataExperimentalCodition.getBeam(
                        ).getFlux().getValue()

            if self.hasDataInput("minExposureTimePerImage"):
                self.fMinExposureTimePerImage = self.getDataInput(
                    "minExposureTimePerImage")[0].getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getBeam() != None:
                    if self.xsDataExperimentalCodition.getBeam(
                    ).getMinExposureTimePerImage() != None:
                        self.fMinExposureTimePerImage = self.xsDataExperimentalCodition.getBeam(
                        ).getMinExposureTimePerImage().getValue()
            if self.fMinExposureTimePerImage == None and self.hasDataInput(
                    "diffractionPlan"):
                if self.getDataInput("diffractionPlan"
                                     )[0].getMinExposureTimePerImage() != None:
                    self.fMinExposureTimePerImage = self.getDataInput(
                        "diffractionPlan")[0].getMinExposureTimePerImage(
                        ).getValue()

            if self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getBeam() != None:
                    if self.xsDataExperimentalCodition.getBeam().getSize(
                    ) != None:
                        self.fBeamSizeX = self.xsDataExperimentalCodition.getBeam(
                        ).getSize().getX().getValue()
                        self.fBeamSizeY = self.xsDataExperimentalCodition.getBeam(
                        ).getSize().getY().getValue()
                    if self.xsDataExperimentalCodition.getBeam(
                    ).getApertureSize() != None:
                        self.fApertureSize = self.xsDataExperimentalCodition.getBeam(
                        ).getApertureSize().getValue()

            if self.hasDataInput("beamSize"):
                self.fBeamSizeX = self.getDataInput("beamSize")[0].getValue()
                self.fBeamSizeY = self.getDataInput("beamSize")[0].getValue()

            if self.hasDataInput("apertureSize"):
                self.fApertureSize = self.getDataInput(
                    "apertureSize")[0].getValue()

            if self.hasDataInput("beamSizeX"):
                self.fBeamSizeX = self.getDataInput("beamSizeX")[0].getValue()

            if self.hasDataInput("beamSizeY"):
                self.fBeamSizeY = self.getDataInput("beamSizeY")[0].getValue()

            if self.hasDataInput("templateMode"):
                self.bTemplateMode = self.getDataInput(
                    "templateMode")[0].getValue()

            if (self.hasDataInput("beamPosX")):
                self.fBeamPosX = self.getDataInput("beamPosX")[0].getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getDetector() != None:
                    if self.xsDataExperimentalCodition.getDetector(
                    ).getBeamPositionX() != None:
                        self.fBeamPosX = self.xsDataExperimentalCodition.getDetector(
                        ).getBeamPositionX().getValue()

            if (self.hasDataInput("beamPosY")):
                self.fBeamPosY = self.getDataInput("beamPosY")[0].getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getDetector() != None:
                    if self.xsDataExperimentalCodition.getDetector(
                    ).getBeamPositionY() != None:
                        self.fBeamPosY = self.xsDataExperimentalCodition.getDetector(
                        ).getBeamPositionY().getValue()

            if (self.hasDataInput("wavelength")):
                self.fWavelength = self.getDataInput(
                    "wavelength")[0].getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getBeam() != None:
                    if self.xsDataExperimentalCodition.getBeam().getWavelength(
                    ) != None:
                        self.fWavelength = self.xsDataExperimentalCodition.getBeam(
                        ).getWavelength().getValue()

            if (self.hasDataInput("transmission")):
                self.fTransmission = self.getDataInput(
                    "transmission")[0].getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getBeam() != None:
                    if self.xsDataExperimentalCodition.getBeam(
                    ).getTransmission() != None:
                        self.fTransmission = self.xsDataExperimentalCodition.getBeam(
                        ).getTransmission().getValue()

            if self.hasDataInput("generatedTemplateFile"):
                self.strGeneratedTemplateFile = self.getDataInput(
                    "generatedTemplateFile")[0].getValue()

            if self.hasDataInput("resultsFilePath"):
                self.strResultsFilePath = self.getDataInput(
                    "resultsFilePath")[0].getValue()

            if self.hasDataInput("dataCollectionId"):
                self.iDataCollectionId = self.getDataInput(
                    "dataCollectionId")[0].getValue()

            if self.hasDataInput("shortComments"):
                self.strShortComments = self.getDataInput(
                    "shortComments")[0].getValue()

            if self.hasDataInput("comments"):
                self.strComments = self.getDataInput("comments")[0].getValue()

            if self.hasDataInput("inputCharacterisation"):
                self.xsDataInputCharacterisation = self.getDataInput(
                    "inputCharacterisation")[0]

        # Check if XML data is given as input :
        if (self.xsDataInputCharacterisation is None):
            self.edPluginControlSubWedgeAssemble = self.loadPlugin(
                self.strEDPluginControlSubWedgeAssembleName,
                "SubWedgeAssemble")

        self.edPluginControlCharacterisation = self.loadPlugin(
            self.strEDPluginControlCharacterisationName, "Characterisation")

        if (self.strEDPluginControlISPyBName is not None):
            self.edPluginControlISPyB = self.loadPlugin(
                self.strEDPluginControlISPyBName, "ISPyB")

    def process(self, _edPlugin=None):
        EDPluginControl.process(self, _edPlugin)
        self.DEBUG("EDPluginControlInterfacev1_3.process...")

        if (self.edPluginControlSubWedgeAssemble is not None):
            if (self.bTemplateMode == True):
                self.edPluginControlSubWedgeAssemble.connectSUCCESS(
                    self.generateTemplateFile)
            else:
                self.edPluginControlSubWedgeAssemble.connectSUCCESS(
                    self.doSubWedgeAssembleSUCCESS)
            self.edPluginControlSubWedgeAssemble.connectFAILURE(
                self.doSubWedgeAssembleFAILURE)

        if (self.edPluginControlCharacterisation is not None):
            self.edPluginControlCharacterisation.connectSUCCESS(
                self.doSuccessActionCharacterisation)
            self.edPluginControlCharacterisation.connectFAILURE(
                self.doFailureActionCharacterisation)

        if (self.edPluginControlISPyB is not None):
            self.edPluginControlISPyB.connectSUCCESS(self.doSuccessActionISPyB)
            self.edPluginControlISPyB.connectFAILURE(self.doFailureActionISPyB)

        if (self.xsDataInputCharacterisation is None):
            self.createInputCharacterisationFromImageHeaders(
                self.edPluginControlSubWedgeAssemble)
        else:
            self.runCharacterisationPlugin(
                self.edPluginControlCharacterisation)

    def finallyProcess(self, _edPlugin=None):
        EDPluginControl.finallyProcess(self, _edPlugin)
        self.DEBUG("EDPluginControlInterfacev1_3.finallyProcess...")

        if (not self.edPluginControlCharacterisation is None):
            if (self.edPluginControlCharacterisation.hasDataOutput()):
                self.setDataOutput(
                    self.edPluginControlCharacterisation.getDataOutput(),
                    "characterisation")
        if (not self.edPluginControlISPyB is None):
            if (self.edPluginControlISPyB.hasDataOutput()):
                self.setDataOutput(self.edPluginControlISPyB.getDataOutput(),
                                   "ISPyB")
        if self.hasDataInput():
            xsDataResultInterface = XSDataResultInterface()
            if self.edPluginControlCharacterisation:
                xsDataResultInterface.setResultCharacterisation(
                    self.edPluginControlCharacterisation.getDataOutput())
            if self.edPluginControlISPyB:
                xsDataResultInterface.setResultControlISPyB(
                    self.edPluginControlISPyB.getDataOutput())
            self.setDataOutput(xsDataResultInterface)

    def createInputCharacterisationFromImageHeaders(self, _edPlugin):
        self.DEBUG(
            "EDPluginControlInterfacev1_3.createInputCharacterisationFromImageHeaders"
        )
        xsDataInputSubWedgeAssemble = XSDataInputSubWedgeAssemble()
        for xsDataStringImagePath in self.listImagePaths:
            xsDataFile = XSDataFile()
            xsDataFile.setPath(xsDataStringImagePath)
            xsDataInputSubWedgeAssemble.addFile(xsDataFile)
        _edPlugin.setDataInput(xsDataInputSubWedgeAssemble)
        _edPlugin.executeSynchronous()

    def runCharacterisationPlugin(self, _edPlugin=None):
        self.DEBUG("EDPluginControlInterfacev1_3.runCharacterisationPlugin")
        self.edPluginControlCharacterisation.setDataInput(
            self.xsDataInputCharacterisation)
        self.edPluginControlCharacterisation.executeSynchronous()

    def storeResultsInISPyB(self, _edPlugin=None):
        self.DEBUG("EDPluginControlInterfacev1_3.storeResultsInISPyB")
        if (self.edPluginControlISPyB is not None):
            # Execute the ISPyB control plugin
            xsDataInputControlISPyB = XSDataInputControlISPyB()
            xsDataInputControlISPyB.setCharacterisationResult(
                self.edPluginControlCharacterisation.getDataOutput())
            if (not self.iDataCollectionId is None):
                dataCollectionGroupId = self.getDataCollectionGroupId(
                    self.iDataCollectionId)
                xsDataInputControlISPyB.setDataCollectionGroupId(
                    XSDataInteger(dataCollectionGroupId))
            if (not self.strShortComments is None):
                self.edPluginControlISPyB.setDataInput(
                    XSDataString(self.strShortComments), "shortComments")
            if (not self.strComments is None):
                self.edPluginControlISPyB.setDataInput(
                    XSDataString(self.strComments), "comments")
            if (not self.strStatusMessage is None):
                self.edPluginControlISPyB.setDataInput(
                    XSDataString(self.strStatusMessage), "statusMessage")
            self.edPluginControlISPyB.setDataInput(xsDataInputControlISPyB)
            self.edPluginControlISPyB.executeSynchronous()
            self.checkDozorScores(
                self.edPluginControlCharacterisation.getDataOutput())

    def createInputCharacterisationFromSubWedges(self):
        self.DEBUG(
            "EDPluginControlInterfacev1_3.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)
        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.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):
        """
        retrieve the potential warning messages
        retrieve the potential error messages
        """
        self.DEBUG(
            "EDPluginControlInterfacev1_3.doFailureActionCharacterisation")
        self.retrieveFailureMessages(
            self.edPluginControlCharacterisation,
            "EDPluginControlInterfacev1_3.doSuccessActionISPyB")
        if _edPlugin.hasDataOutput("statusMessage"):
            self.strStatusMessage = _edPlugin.getDataOutput(
                "statusMessage")[0].getValue()
        self.generateExecutiveSummary(self)
        self.storeResultsInISPyB(_edPlugin)
        self.setFailure()

    def doSuccessActionCharacterisation(self, _edPlugin=None):
        """
        retrieve the potential warning messages
        """
        self.DEBUG(
            "EDPluginControlInterfacev1_3.doSuccessActionCharacterisation")
        # Store the results if requested
        if (self.strResultsFilePath is not None):
            xsDataCharacterisationResult = _edPlugin.getDataOutput()
            if (xsDataCharacterisationResult is not None):
                xsDataCharacterisationResult.exportToFile(
                    self.strResultsFilePath)
        if _edPlugin.hasDataOutput("statusMessage"):
            self.strStatusMessage = _edPlugin.getDataOutput(
                "statusMessage")[0].getValue()
        self.storeResultsInISPyB(_edPlugin)

    def doSuccessActionISPyB(self, _edPlugin):
        self.DEBUG("EDPluginControlInterfacev1_3.doSuccessActionISPyB...")
        self.retrieveSuccessMessages(
            self.edPluginControlISPyB,
            "EDPluginControlInterfacev1_3.doSuccessActionISPyB")

    def doFailureActionISPyB(self, _edPlugin=None):
        self.DEBUG("EDPluginControlInterfacev1_3.doFailureActionISpyB...")
        self.generateExecutiveSummary(self)
        self.setFailure()

    def generateExecutiveSummary(self, _edPlugin=None):
        """
        Prints the executive summary from the plugin
        """
        self.DEBUG("EDPluginControlInterfacev1_3.generateExecutiveSummary")
        if (self.edPluginControlSubWedgeAssemble is not None):
            if self.edPluginControlSubWedgeAssemble.getListExecutiveSummaryLines(
            ) != []:
                self.addExecutiveSummaryLine(
                    "Summary of plugin %s:" %
                    self.strEDPluginControlSubWedgeAssembleName)
                self.appendExecutiveSummary(
                    self.edPluginControlSubWedgeAssemble)
        if (self.edPluginControlCharacterisation is not None):
            self.addExecutiveSummaryLine(
                "Summary of plugin %s:" %
                self.strEDPluginControlCharacterisationName)
            self.appendExecutiveSummary(self.edPluginControlCharacterisation)
        if (self.edPluginControlISPyB is not None):
            self.addExecutiveSummaryLine("Summary of plugin %s:" %
                                         self.strEDPluginControlISPyBName)
            self.appendExecutiveSummary(self.edPluginControlISPyB)
        self.verboseScreenExecutiveSummary()

    def checkDozorScores(self, _xsDataResultCharacterisation):
        # Check Dozor scores
        listImageQualityIndicators = _xsDataResultCharacterisation.imageQualityIndicators
        noWeakDiffraction = 0
        noTotal = 0
        newComment = None
        referenceImagePath = None
        listImageNoWithNoDiffraction = []
        for imageQualityIndicators in listImageQualityIndicators:
            if referenceImagePath is None:
                referenceImagePath = imageQualityIndicators.image.path.value
            if imageQualityIndicators.dozor_score is not None:
                noTotal += 1
                dozorScore = imageQualityIndicators.dozor_score.value
                if dozorScore <= 0.001:
                    listImageNoWithNoDiffraction.append(
                        imageQualityIndicators.image.number.value)
                elif dozorScore < 1.0:
                    noWeakDiffraction += 1
        if noTotal > 0:
            if len(listImageNoWithNoDiffraction) == noTotal:
                newComment = "No diffraction."
            elif noWeakDiffraction + len(
                    listImageNoWithNoDiffraction) == noTotal:
                newComment = "Very weak diffraction."
            else:
                subComment = None
                if len(listImageNoWithNoDiffraction) == 1:
                    subComment = "image {0}".format(
                        listImageNoWithNoDiffraction[0])
                elif len(listImageNoWithNoDiffraction) == 2:
                    subComment = "images {0} and {1}".format(
                        listImageNoWithNoDiffraction[0],
                        listImageNoWithNoDiffraction[1])
                elif len(listImageNoWithNoDiffraction) > 2:
                    subComment = "images {0}".format(
                        listImageNoWithNoDiffraction[0])
                    for imageNo in listImageNoWithNoDiffraction[1:-1]:
                        subComment += ", {0}".format(imageNo)
                    subComment += " and {0}".format(
                        listImageNoWithNoDiffraction[-1])
                if subComment is not None:
                    newComment = "No diffraction detected in {0} - hint: sample might not be accurately centred.".format(
                        subComment)

            if newComment is not None and self.iDataCollectionId is not None:
                xsDataInput = XSDataInputISPyBUpdateDataCollectionGroupComment(
                )
                xsDataInput.newComment = XSDataString(newComment)
                xsDataInput.dataCollectionId = XSDataInteger(
                    self.iDataCollectionId)
                edPluginISPyBUpdateDataCollectionGroupComment = self.loadPlugin(
                    "EDPluginISPyBUpdateDataCollectionGroupCommentv1_4")
                edPluginISPyBUpdateDataCollectionGroupComment.dataInput = xsDataInput
                self.executePluginSynchronous(
                    edPluginISPyBUpdateDataCollectionGroupComment)

    def getDataCollectionGroupId(self, _dataCollectionId):
        self.DEBUG("EDPluginControlInterfacev1_2.getDataCollectionGroupId")
        self.DEBUG("dataCollectionId = {0}".format(_dataCollectionId))
        dataCollectionGroupId = None
        xsDataInputRetrieveDataCollection = XSDataInputRetrieveDataCollection()
        xsDataInputRetrieveDataCollection.dataCollectionId = XSDataInteger(
            _dataCollectionId)
        edPluginISPyBRetrieveDataCollection = self.loadPlugin(
            "EDPluginISPyBRetrieveDataCollectionv1_4")
        edPluginISPyBRetrieveDataCollection.dataInput = xsDataInputRetrieveDataCollection
        edPluginISPyBRetrieveDataCollection.executeSynchronous()
        xsDataResultRetrieveDataCollection = edPluginISPyBRetrieveDataCollection.dataOutput
        if xsDataResultRetrieveDataCollection is not None:
            dataCollection = xsDataResultRetrieveDataCollection.dataCollection
            if dataCollection is not None:
                dataCollectionGroupId = dataCollection.dataCollectionGroupId
        self.DEBUG("dataCollectionGroupId = {0}".format(dataCollectionGroupId))
        return dataCollectionGroupId

예제 #4

파일: EDPluginControlInterfacev1_2.py 프로젝트: antolinos/edna

class EDPluginControlInterfacev1_2(EDPluginControl):
    """
    This is the common class to all plugins managing user interfaces
    """

    def __init__ (self):
        """
        """
        EDPluginControl.__init__(self)

        self.setXSDataInputClass(XSDataInputInterface)

        self.setXSDataInputClass(XSDataExperimentalCondition, "experimentalCondition")
        self.setXSDataInputClass(XSDataDiffractionPlan, "diffractionPlan")
        self.setXSDataInputClass(XSDataSampleCrystalMM, "sample")
        self.setXSDataInputClass(XSDataString, "imagePaths")
        self.setXSDataInputClass(XSDataFloat, "flux")
        self.setXSDataInputClass(XSDataFloat, "minExposureTimePerImage")
        self.setXSDataInputClass(XSDataFloat, "beamSize")
        self.setXSDataInputClass(XSDataFloat, "beamSizeX")
        self.setXSDataInputClass(XSDataFloat, "beamSizeY")
        self.setXSDataInputClass(XSDataBoolean, "templateMode")
        self.setXSDataInputClass(XSDataString, "generatedTemplateFile")
        self.setXSDataInputClass(XSDataString, "resultsFilePath")
        self.setXSDataInputClass(XSDataFloat, "beamPosX")
        self.setXSDataInputClass(XSDataFloat, "beamPosY")
        self.setXSDataInputClass(XSDataDouble, "wavelength")
        self.setXSDataInputClass(XSDataDouble, "transmission")
        self.setXSDataInputClass(XSDataInteger, "dataCollectionId")
        self.setXSDataInputClass(XSDataString, "shortComments")
        self.setXSDataInputClass(XSDataString, "comments")
        self.setXSDataInputClass(XSDataInputCharacterisation, "inputCharacterisation")

        self.strEDPluginControlSubWedgeAssembleName = "EDPluginControlSubWedgeAssemblev1_1"
        self.strEDPluginControlCharacterisationName = "EDPluginControlCharacterisationv1_1"
        self.strEDPluginControlISPyBName = "EDPluginControlISPyBv1_1"

        self.edPluginControlSubWedgeAssemble = None
        self.edPluginControlCharacterisation = None
        self.edPluginControlISPyB = None

        self.pyListImagePaths = None
        self.xsDataInputCharacterisation = None
        self.strComplexity = "none"

        self.listImagePaths = []
        self.fFlux = None
        self.fMaxExposureTimePerDataCollection = 10000 # s, default prototype value
        self.fMinExposureTimePerImage = None
        self.fBeamSizeX = None
        self.fBeamSizeY = None
        self.bTemplateMode = False
        self.strGeneratedTemplateFile = None
        self.strResultsFilePath = None
        self.strForcedSpaceGroup = None
        self.bAnomalousData = False
        self.fBeamPosX = None
        self.fBeamPosY = None
        self.fMinOscillationWidth = None
        self.fMaxOscillationSpeed = None
        self.fWavelength = None
        self.fTransmission = None
        self.strStrategyOption = None
        self.iDataCollectionId = None
        self.strShortComments = None
        self.strComments = None
        self.strStatusMessage = None

        self.xsDataExperimentalCodition = None
        self.xsDataSample = None
        self.xsDataDiffractionPlan = None


    def configure(self):
        """
        Gets the configuration parameters (if any).
        """
        EDPluginControl.configure(self)
        EDVerbose.DEBUG("EDPluginControlInterfacev1_2.configure")
        pluginConfiguration = self.getConfiguration()

        if (pluginConfiguration is None):
            EDVerbose.DEBUG("No plugin configuration found for EDPluginControlInterfacev1_2.")
        else:
            if (self.getControlledPluginName("subWedgeAssemblePlugin") is not None):
                self.strEDPluginControlSubWedgeAssembleName = self.getControlledPluginName("subWedgeAssemblePlugin")
            if (self.getControlledPluginName("characterisationPlugin") is not None):
                self.strEDPluginControlCharacterisationName = self.getControlledPluginName("characterisationPlugin")
            if (self.getControlledPluginName("ispybPlugin") is not None):
                self.strEDPluginControlISPyBName = self.getControlledPluginName("ispybPlugin")

            bUseISPyBPlugin = EDConfiguration.getStringParamValue(pluginConfiguration, "useISPyBPlugin")
            if (bUseISPyBPlugin.lower() != "true"):
                self.strEDPluginControlISPyBName = None


    def preProcess(self, _edPlugin=None):
        """
        Gets the Configuration Parameters, if found, overrides default parameters
        """
        EDPluginControl.preProcess(self, _edPlugin)
        EDVerbose.DEBUG("EDPluginControlInterfacev1_2.preProcess...")

        self.listImagePaths = []

        # Check if XSDataInputInterface is given as input
        if self.hasDataInput():
            xsDataInputInterface = self.getDataInput()

            if xsDataInputInterface.getExperimentalCondition():
                self.xsDataExperimentalCodition = xsDataInputInterface.getExperimentalCondition()
                if self.xsDataExperimentalCodition.getGoniostat():
                    if self.xsDataExperimentalCodition.getGoniostat().getMinOscillationWidth():
                        self.fMinOscillationWidth = self.xsDataExperimentalCodition.getGoniostat().getMinOscillationWidth().getValue()
                    if self.xsDataExperimentalCodition.getGoniostat().getMaxOscillationSpeed():
                        self.fMaxOscillationSpeed = self.xsDataExperimentalCodition.getGoniostat().getMaxOscillationSpeed().getValue()


            self.xsDataSample = xsDataInputInterface.getSample()

            self.xsDataDiffractionPlan = self.getDataInput().getDiffractionPlan()
            if self.xsDataDiffractionPlan:
                if self.xsDataDiffractionPlan.getForcedSpaceGroup():
                    self.strForcedSpaceGroup = self.xsDataDiffractionPlan.getForcedSpaceGroup().getValue()
                if self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection():
                    self.fMaxExposureTimePerDataCollection = self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection().getValue()
                if self.xsDataDiffractionPlan.getAnomalousData():
                    self.bAnomalousData = self.xsDataDiffractionPlan.getAnomalousData().getValue()
                if self.xsDataDiffractionPlan.getStrategyOption():
                    self.strStrategyOption = self.xsDataDiffractionPlan.getStrategyOption().getValue()
                if self.xsDataDiffractionPlan.getComplexity():
                    self.strComplexity = self.xsDataDiffractionPlan.getComplexity().getValue()
                if self.fMinOscillationWidth == None:
                    if self.xsDataDiffractionPlan.getGoniostatMinOscillationWidth():
                        self.fMinOscillationWidth = self.xsDataDiffractionPlan.getGoniostatMinOscillationWidth().getValue()
                if self.fMaxOscillationSpeed == None:
                    if self.xsDataDiffractionPlan.getGoniostatMaxOscillationSpeed():
                        self.fMaxOscillationSpeed = self.xsDataDiffractionPlan.getGoniostatMaxOscillationSpeed().getValue()


            self.xsDataSample = xsDataInputInterface.getSample()

            if xsDataInputInterface.getImagePath():
                for xsDataFile in xsDataInputInterface.getImagePath():
                    self.listImagePaths.append(xsDataFile.getPath())

            if xsDataInputInterface.getFlux():
                self.fFlux = xsDataInputInterface.getFlux().getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getBeam() != None:
                    if self.xsDataExperimentalCodition.getBeam().getFlux() != None:
                        self.fFlux = self.xsDataExperimentalCodition.getBeam().getFlux().getValue()

            if xsDataInputInterface.getMinExposureTimePerImage():
                self.fMinExposureTimePerImage = xsDataInputInterface.getMinExposureTimePerImage().getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getBeam() != None:
                    if self.xsDataExperimentalCodition.getBeam().getMinExposureTimePerImage() != None:
                        self.fMinExposureTimePerImage = self.xsDataExperimentalCodition.getBeam().getMinExposureTimePerImage().getValue()
            if self.fMinExposureTimePerImage == None and xsDataInputInterface.getDiffractionPlan():
                if xsDataInputInterface.getDiffractionPlan().getMinExposureTimePerImage() != None:
                    self.fMinExposureTimePerImage = xsDataInputInterface.getdiffractionPlan().getMinExposureTimePerImage().getValue()

            if self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getBeam() != None:
                    if self.xsDataExperimentalCodition.getBeam().getSize() != None:
                        self.fBeamSizeX = self.xsDataExperimentalCodition.getBeam().getSize().getX().getValue()
                        self.fBeamSizeY = self.xsDataExperimentalCodition.getBeam().getSize().getY().getValue()

            if xsDataInputInterface.getBeamSize():
                self.fBeamSizeX = xsDataInputInterface.getBeamSize().getValue()
                self.fBeamSizeY = xsDataInputInterface.getBeamSize().getValue()

            if xsDataInputInterface.getBeamSizeX():
                self.fBeamSizeX = xsDataInputInterface.getBeamSizeX().getValue()

            if xsDataInputInterface.getBeamSizeY():
                self.fBeamSizeY = xsDataInputInterface.getBeamSizeY().getValue()

            if xsDataInputInterface.getTemplateMode():
                self.bTemplateMode = xsDataInputInterface.getTemplateMode().getValue()

            if xsDataInputInterface.getBeamPosX():
                self.fBeamPosX = xsDataInputInterface.getBeamPosX().getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getDetector() != None:
                    if self.xsDataExperimentalCodition.getDetector().getBeamPositionX() != None:
                        self.fBeamPosX = self.xsDataExperimentalCodition.getDetector().getBeamPositionX().getValue()

            if xsDataInputInterface.getBeamPosY():
                self.fBeamPosY = xsDataInputInterface.getBeamPosY().getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getDetector() != None:
                    if self.xsDataExperimentalCodition.getDetector().getBeamPositionY() != None:
                        self.fBeamPosY = self.xsDataExperimentalCodition.getDetector().getBeamPositionY().getValue()

            if xsDataInputInterface.getWavelength():
                self.fWavelength = xsDataInputInterface.getWavelength().getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getBeam() != None:
                    if self.xsDataExperimentalCodition.getBeam().getWavelength() != None:
                        self.fWavelength = self.xsDataExperimentalCodition.getBeam().getWavelength().getValue()

            if xsDataInputInterface.getTransmission():
                self.fTransmission = xsDataInputInterface.getTransmission().getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getBeam() != None:
                    if self.xsDataExperimentalCodition.getBeam().getTransmission() != None:
                        self.fTransmission = self.xsDataExperimentalCodition.getBeam().getTransmission().getValue()

            if xsDataInputInterface.getGeneratedTemplateFile():
                self.strGeneratedTemplateFile = xsDataInputInterface.getGeneratedTemplateFile().getPath().getValue()

            if xsDataInputInterface.getResultsFilePath():
                self.strResultsFilePath = xsDataInputInterface.getResultsFilePath().getPath().getValue()

            if xsDataInputInterface.getDataCollectionId():
                self.iDataCollectionId = xsDataInputInterface.getDataCollectionId().getValue()

            if xsDataInputInterface.getShortComments():
                self.strShortComments = xsDataInputInterface.getShortComments().getValue()

            if xsDataInputInterface.getComments():
                self.strComments = xsDataInputInterface.getComments().getValue()

            if xsDataInputInterface.getInputCharacterisation():
                self.xsDataInputCharacterisation = xsDataInputInterface.getInputCharacterisation()

            if xsDataInputInterface.getDataCollectionId():
                self.iDataCollectionId = xsDataInputInterface.getDataCollectionId().getValue()

        else:

            if self.hasDataInput("experimentalCondition"):
                self.xsDataExperimentalCodition = self.getDataInput("experimentalCondition")[0]
                if self.xsDataExperimentalCodition.getGoniostat():
                    if self.xsDataExperimentalCodition.getGoniostat().getMinOscillationWidth():
                        self.fMinOscillationWidth = self.xsDataExperimentalCodition.getGoniostat().getMinOscillationWidth().getValue()
                    if self.xsDataExperimentalCodition.getGoniostat().getMaxOscillationSpeed():
                        self.fMaxOscillationSpeed = self.xsDataExperimentalCodition.getGoniostat().getMaxOscillationSpeed().getValue()


            if self.hasDataInput("sample"):
                self.xsDataSample = self.getDataInput("sample")[0]

            if (self.hasDataInput("diffractionPlan")):
                if self.xsDataDiffractionPlan is None:
                    self.xsDataDiffractionPlan = XSDataDiffractionPlan()
                xsDataDiffractionPlans = self.getDataInput("diffractionPlan")
                if (not xsDataDiffractionPlans[0] is None):
                    self.xsDataDiffractionPlan = xsDataDiffractionPlans[0]
                    if self.xsDataDiffractionPlan.getForcedSpaceGroup():
                        self.strForcedSpaceGroup = self.xsDataDiffractionPlan.getForcedSpaceGroup().getValue()
                    if self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection():
                        self.fMaxExposureTimePerDataCollection = self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection().getValue()
                    if self.xsDataDiffractionPlan.getAnomalousData():
                        self.bAnomalousData = self.xsDataDiffractionPlan.getAnomalousData().getValue()
                    if self.xsDataDiffractionPlan.getStrategyOption():
                        self.strStrategyOption = self.xsDataDiffractionPlan.getStrategyOption().getValue()
                    if self.xsDataDiffractionPlan.getComplexity():
                        self.strComplexity = self.xsDataDiffractionPlan.getComplexity().getValue()
                    if self.fMinOscillationWidth == None:
                        if self.xsDataDiffractionPlan.getGoniostatMinOscillationWidth():
                            self.fMinOscillationWidth = self.xsDataDiffractionPlan.getGoniostatMinOscillationWidth().getValue()
                    if self.fMaxOscillationSpeed == None:
                        if self.xsDataDiffractionPlan.getGoniostatMaxOscillationSpeed():
                            self.fMaxOscillationSpeed = self.xsDataDiffractionPlan.getGoniostatMaxOscillationSpeed().getValue()


            if self.hasDataInput("sample"):
                self.xsDataSample = self.getDataInput("sample")[0]

            if self.hasDataInput("imagePaths"):
                for strImagePath in self.getDataInput("imagePaths"):
                    self.listImagePaths.append(strImagePath)

            if self.hasDataInput("flux"):
                self.fFlux = self.getDataInput("flux")[0].getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getBeam() != None:
                    if self.xsDataExperimentalCodition.getBeam().getFlux() != None:
                        self.fFlux = self.xsDataExperimentalCodition.getBeam().getFlux().getValue()

            if self.hasDataInput("minExposureTimePerImage"):
                self.fMinExposureTimePerImage = self.getDataInput("minExposureTimePerImage")[0].getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getBeam() != None:
                    if self.xsDataExperimentalCodition.getBeam().getMinExposureTimePerImage() != None:
                        self.fMinExposureTimePerImage = self.xsDataExperimentalCodition.getBeam().getMinExposureTimePerImage().getValue()
            if self.fMinExposureTimePerImage == None and self.hasDataInput("diffractionPlan"):
                if self.getDataInput("diffractionPlan")[0].getMinExposureTimePerImage() != None:
                    self.fMinExposureTimePerImage = self.getDataInput("diffractionPlan")[0].getMinExposureTimePerImage().getValue()

            if self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getBeam() != None:
                    if self.xsDataExperimentalCodition.getBeam().getSize() != None:
                        self.fBeamSizeX = self.xsDataExperimentalCodition.getBeam().getSize().getX().getValue()
                        self.fBeamSizeY = self.xsDataExperimentalCodition.getBeam().getSize().getY().getValue()

            if self.hasDataInput("beamSize"):
                self.fBeamSizeX = self.getDataInput("beamSize")[0].getValue()
                self.fBeamSizeY = self.getDataInput("beamSize")[0].getValue()

            if self.hasDataInput("beamSizeX"):
                self.fBeamSizeX = self.getDataInput("beamSizeX")[0].getValue()

            if self.hasDataInput("beamSizeY"):
                self.fBeamSizeY = self.getDataInput("beamSizeY")[0].getValue()

            if self.hasDataInput("templateMode"):
                self.bTemplateMode = self.getDataInput("templateMode")[0].getValue()

            if (self.hasDataInput("beamPosX")):
                self.fBeamPosX = self.getDataInput("beamPosX")[0].getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getDetector() != None:
                    if self.xsDataExperimentalCodition.getDetector().getBeamPositionX() != None:
                        self.fBeamPosX = self.xsDataExperimentalCodition.getDetector().getBeamPositionX().getValue()

            if (self.hasDataInput("beamPosY")):
                self.fBeamPosY = self.getDataInput("beamPosY")[0].getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getDetector() != None:
                    if self.xsDataExperimentalCodition.getDetector().getBeamPositionY() != None:
                        self.fBeamPosY = self.xsDataExperimentalCodition.getDetector().getBeamPositionY().getValue()

            if (self.hasDataInput("wavelength")):
                self.fWavelength = self.getDataInput("wavelength")[0].getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getBeam() != None:
                    if self.xsDataExperimentalCodition.getBeam().getWavelength() != None:
                        self.fWavelength = self.xsDataExperimentalCodition.getBeam().getWavelength().getValue()

            if (self.hasDataInput("transmission")):
                self.fTransmission = self.getDataInput("transmission")[0].getValue()
            elif self.xsDataExperimentalCodition != None:
                if self.xsDataExperimentalCodition.getBeam() != None:
                    if self.xsDataExperimentalCodition.getBeam().getTransmission() != None:
                        self.fTransmission = self.xsDataExperimentalCodition.getBeam().getTransmission().getValue()

            if self.hasDataInput("generatedTemplateFile"):
                self.strGeneratedTemplateFile = self.getDataInput("generatedTemplateFile")[0].getValue()

            if self.hasDataInput("resultsFilePath"):
                self.strResultsFilePath = self.getDataInput("resultsFilePath")[0].getValue()

            if self.hasDataInput("dataCollectionId"):
                self.iDataCollectionId = self.getDataInput("dataCollectionId")[0].getValue()

            if self.hasDataInput("shortComments"):
                self.strShortComments = self.getDataInput("shortComments")[0].getValue()

            if self.hasDataInput("comments"):
                self.strComments = self.getDataInput("comments")[0].getValue()

            if self.hasDataInput("inputCharacterisation"):
                self.xsDataInputCharacterisation = self.getDataInput("inputCharacterisation")[0]

        # Check if XML data is given as input :
        if (self.xsDataInputCharacterisation is None):
            self.edPluginControlSubWedgeAssemble = self.loadPlugin(self.strEDPluginControlSubWedgeAssembleName, "SubWedgeAssemble")

        self.edPluginControlCharacterisation = self.loadPlugin(self.strEDPluginControlCharacterisationName, "Characterisation")

        if (self.strEDPluginControlISPyBName is not None):
            self.edPluginControlISPyB = self.loadPlugin(self.strEDPluginControlISPyBName, "ISPyB")


    def process(self, _edPlugin=None):
        EDPluginControl.process(self, _edPlugin)
        EDVerbose.DEBUG("EDPluginControlInterfacev1_2.process...")

        if (self.edPluginControlSubWedgeAssemble is not None):
            if(self.bTemplateMode == True):
                self.edPluginControlSubWedgeAssemble.connectSUCCESS(self.generateTemplateFile)
            else:
                self.edPluginControlSubWedgeAssemble.connectSUCCESS(self.doSubWedgeAssembleSUCCESS)
            self.edPluginControlSubWedgeAssemble.connectFAILURE(self.doSubWedgeAssembleFAILURE)

        if(self.edPluginControlCharacterisation is not None):
            self.edPluginControlCharacterisation.connectSUCCESS(self.doSuccessActionCharacterisation)
            self.edPluginControlCharacterisation.connectFAILURE(self.doFailureActionCharacterisation)

        if (self.edPluginControlISPyB is not None):
            self.edPluginControlISPyB.connectSUCCESS(self.doSuccessActionISPyB)
            self.edPluginControlISPyB.connectFAILURE(self.doFailureActionISPyB)

        if (self.xsDataInputCharacterisation is None):
            self.createInputCharacterisationFromImageHeaders(self.edPluginControlSubWedgeAssemble)
        else:
            self.runCharacterisationPlugin(self.edPluginControlCharacterisation)


    def finallyProcess(self, _edPlugin=None):
        EDPluginControl.finallyProcess(self, _edPlugin)
        EDVerbose.DEBUG("EDPluginControlInterfacev1_2.finallyProcess...")

        if (not self.edPluginControlCharacterisation is None):
            if (self.edPluginControlCharacterisation.hasDataOutput()):
                self.setDataOutput(self.edPluginControlCharacterisation.getDataOutput(), "characterisation")
        if (not self.edPluginControlISPyB is None):
            if (self.edPluginControlISPyB.hasDataOutput()):
                self.setDataOutput(self.edPluginControlISPyB.getDataOutput(), "ISPyB")
        if self.hasDataInput():
            xsDataResultInterface = XSDataResultInterface()
            if self.edPluginControlCharacterisation:
                xsDataResultInterface.setResultCharacterisation(self.edPluginControlCharacterisation.getDataOutput())
            if self.edPluginControlISPyB:
                xsDataResultInterface.setResultControlISPyB(self.edPluginControlISPyB.getDataOutput())
            self.setDataOutput(xsDataResultInterface)


    def createInputCharacterisationFromImageHeaders(self, _edPlugin):
        EDVerbose.DEBUG("EDPluginControlInterfacev1_2.createInputCharacterisationFromImageHeaders")
        xsDataInputSubWedgeAssemble = XSDataInputSubWedgeAssemble()
        for xsDataStringImagePath in self.listImagePaths:
            xsDataFile = XSDataFile()
            xsDataFile.setPath(xsDataStringImagePath)
            xsDataInputSubWedgeAssemble.addFile(xsDataFile)
        _edPlugin.setDataInput(xsDataInputSubWedgeAssemble)
        _edPlugin.executeSynchronous()


    def runCharacterisationPlugin(self, _edPlugin=None):
        EDVerbose.DEBUG("EDPluginControlInterfacev1_2.runCharacterisationPlugin")
        self.edPluginControlCharacterisation.setDataInput(self.xsDataInputCharacterisation)
        self.edPluginControlCharacterisation.executeSynchronous()


    def storeResultsInISPyB(self, _edPlugin=None):
        EDVerbose.DEBUG("EDPluginControlInterfacev1_2.storeResultsInISPyB")
        if (self.edPluginControlISPyB is not None):
            # Execute the ISPyB control plugin
            xsDataInputControlISPyB = XSDataInputControlISPyB()
            xsDataInputControlISPyB.setCharacterisationResult(self.edPluginControlCharacterisation.getDataOutput())
            if (not self.iDataCollectionId is None):
                xsDataInputControlISPyB.setDataCollectionId(XSDataInteger(self.iDataCollectionId))
            if (not self.strShortComments is None):
                self.edPluginControlISPyB.setDataInput(XSDataString(self.strShortComments), "shortComments")
            if (not self.strComments is None):
                self.edPluginControlISPyB.setDataInput(XSDataString(self.strComments), "comments")
            if (not self.strStatusMessage is None):
                self.edPluginControlISPyB.setDataInput(XSDataString(self.strStatusMessage), "statusMessage")
            self.edPluginControlISPyB.setDataInput(xsDataInputControlISPyB)
            self.edPluginControlISPyB.executeSynchronous()


    def createInputCharacterisationFromSubWedges(self):
        EDVerbose.DEBUG("EDPluginControlInterfacev1_2.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)
        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):
        """
        retrieve the potential warning messages
        retrieve the potential error messages
        """
        EDVerbose.DEBUG("EDPluginControlInterfacev1_2.doFailureActionCharacterisation")
        self.retrieveFailureMessages(self.edPluginControlCharacterisation, "EDPluginControlInterfacev1_2.doSuccessActionISPyB")
        if _edPlugin.hasDataOutput("statusMessage"):
            self.strStatusMessage = _edPlugin.getDataOutput("statusMessage")[0].getValue()
        self.generateExecutiveSummary(self)
        self.storeResultsInISPyB(_edPlugin)
        self.setFailure()

    def doSuccessActionCharacterisation(self, _edPlugin=None):
        """
        retrieve the potential warning messages
        """
        EDVerbose.DEBUG("EDPluginControlInterfacev1_2.doSuccessActionCharacterisation")
        # Store the results if requested
        if (self.strResultsFilePath is not None):
            xsDataCharacterisationResult = _edPlugin.getDataOutput()
            if (xsDataCharacterisationResult is not None):
                xsDataCharacterisationResult.exportToFile(self.strResultsFilePath)
        if _edPlugin.hasDataOutput("statusMessage"):
            self.strStatusMessage = _edPlugin.getDataOutput("statusMessage")[0].getValue()
        self.storeResultsInISPyB(_edPlugin)

    def doSuccessActionISPyB(self, _edPlugin):
        EDVerbose.DEBUG("EDPluginControlInterfacev1_2.doSuccessActionISPyB...")
        self.retrieveSuccessMessages(self.edPluginControlISPyB, "EDPluginControlInterfacev1_2.doSuccessActionISPyB")

    def doFailureActionISPyB(self, _edPlugin=None):
        EDVerbose.DEBUG("EDPluginControlInterfacev1_2.doFailureActionISpyB...")
        self.generateExecutiveSummary(self)
        self.setFailure()

    def generateExecutiveSummary(self, _edPlugin=None):
        """
        Prints the executive summary from the plugin
        """
        EDVerbose.DEBUG("EDPluginControlInterfacev1_2.generateExecutiveSummary")
        if (self.edPluginControlSubWedgeAssemble is not None):
            if self.edPluginControlSubWedgeAssemble.getListExecutiveSummaryLines() != []:
                self.addExecutiveSummaryLine("Summary of plugin %s:" % self.strEDPluginControlSubWedgeAssembleName)
                self.appendExecutiveSummary(self.edPluginControlSubWedgeAssemble)
        if (self.edPluginControlCharacterisation is not None):
            self.addExecutiveSummaryLine("Summary of plugin %s:" % self.strEDPluginControlCharacterisationName)
            self.appendExecutiveSummary(self.edPluginControlCharacterisation)
        if (self.edPluginControlISPyB is not None):
            self.addExecutiveSummaryLine("Summary of plugin %s:" % self.strEDPluginControlISPyBName)
            self.appendExecutiveSummary(self.edPluginControlISPyB)
        self.verboseScreenExecutiveSummary()