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
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()
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
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()