def buildChildren(self, child_, nodeName_): if child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'characterisationResult': obj_ = XSDataResultCharacterisation() obj_.build(child_) self.setCharacterisationResult(obj_) XSDataInput.buildChildren(self, child_, nodeName_)
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginControlCharacterisationv1_2.preProcess")
# Load the plugins
self.__edPluginControlIndexingIndicators = self.loadPlugin(self.__strPluginControlIndexingIndicators, \
"Indexing")
self.__edPluginControlIndexingLabelit = self.loadPlugin(self.__strPluginControlIndexingLabelit, \
"IndexingLabelit")
self.__edPluginExecEvaluationIndexingMOSFLM = self.loadPlugin(self.__strPluginExecEvaluationIndexing, \
"IndexingEvalualtionMOSFLM")
self.__edPluginExecEvaluationIndexingLABELIT = self.loadPlugin(self.__strPluginExecEvaluationIndexing, \
"IndexingEvalualtionLABELIT")
self.__edPluginControlGeneratePrediction = self.loadPlugin(self.__strPluginControlGeneratePrediction, \
"GeneratePrediction")
self.__edPluginControlIntegration = self.loadPlugin(self.__strPluginControlIntegration, \
"Integration")
self.__edPluginControlStrategy = self.loadPlugin(self.__strPluginControlStrategy, \
"Strategy")
if (self.__edPluginControlIndexingIndicators is not None):
self.DEBUG("EDPluginControlCharacterisationv1_2.preProcess: " + self.__strPluginControlIndexingIndicators + " Found... setting Data Input")
# create Data Input for indexing
xsDataInputCharacterisation = self.getDataInput()
self.__xsDataCollection = xsDataInputCharacterisation.getDataCollection()
xsDataCrystal = None
xsDataSubWedgeList = self.__xsDataCollection.getSubWedge()
if ((xsDataSubWedgeList is None) or (xsDataSubWedgeList == [])):
strError = "EDPluginControlCharacterisationv1_2.preProcess: No subwedges in input data."
self.ERROR(strError)
self.setFailure()
else:
xsDataExperimentalCondition = xsDataSubWedgeList[0].getExperimentalCondition()
# Fix for bug 431: if the flux is zero raise an error
xsDataDoubleFlux = xsDataExperimentalCondition.getBeam().getFlux()
if (xsDataDoubleFlux is not None):
if (xsDataDoubleFlux.getValue() < 0.1):
strErrorMessage = "Input flux is negative or close to zero. Execution of characterisation aborted."
self.ERROR(strErrorMessage)
self.addErrorMessage("EDPluginControlCharacterisationv1_2.preProcess ERROR: " + strErrorMessage)
#self.addComment(strErrorMessage)
self.setFailure()
xsDataDiffractionPlan = self.__xsDataCollection.getDiffractionPlan()
xsDataStringForcedSpaceGroup = xsDataDiffractionPlan.getForcedSpaceGroup()
if (xsDataStringForcedSpaceGroup is not None):
self.__xsDataCrystal = XSDataCrystal()
xsDataSpaceGroup = XSDataSpaceGroup()
xsDataSpaceGroup.setName(xsDataStringForcedSpaceGroup)
self.__xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
self.__edPluginControlIndexingIndicators.setDataInput(self.__xsDataCollection, "dataCollection")
if self.__xsDataCrystal is not None:
self.__edPluginControlIndexingIndicators.setDataInput(self.__xsDataCrystal, "crystal")
# Populate characterisation object
self.__xsDataResultCharacterisation = XSDataResultCharacterisation()
self.__xsDataResultCharacterisation.setDataCollection(XSDataCollection.parseString(self.__xsDataCollection.marshal()))
def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
EDVerbose.DEBUG("EDPluginControlCharacterisationv2_0.preProcess...")
self.edPluginIndexing = self.loadPlugin(self.strPluginIndexingName,
"Indexing")
self.edPluginIntegration = self.loadPlugin(
self.strPluginIntegrationName, "Integration")
self.edPluginStrategy = self.loadPlugin(self.strPluginStrategyName,
"Strategy")
if (self.edPluginIndexing is not None):
EDVerbose.DEBUG(
"EDPluginControlCharacterisationv2_0.preProcess: " +
self.strPluginIndexingName + " Found... setting Data Input")
# create Data Input for indexing
xsDataInputStrategy = self.getDataInput(
"mxv1InputCharacterisation")[0]
xsDataCollection = xsDataInputStrategy.getDataCollection()
#xsDataSample = xsDataCollection.getSample()
xsDataSubWedgeList = xsDataCollection.getSubWedge()
xsDataExperimentalCondition = xsDataSubWedgeList[
0].getExperimentalCondition()
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.setDataCollection(xsDataCollection)
xsDataIndexingInput.setExperimentalCondition(
xsDataExperimentalCondition)
xsDataDiffractionPlan = xsDataCollection.getDiffractionPlan()
xsDataStringForcedSpaceGroup = xsDataDiffractionPlan.getForcedSpaceGroup(
)
if (xsDataStringForcedSpaceGroup is not None):
xsDataCrystal = XSDataCrystal()
xsDataSpaceGroup = XSDataSpaceGroup()
xsDataSpaceGroup.setName(xsDataStringForcedSpaceGroup)
xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
xsDataIndexingInput.setCrystal(xsDataCrystal)
self.edPluginIndexing.setDataInput(xsDataIndexingInput)
# Populate characterisation object
self.xsDataResultCharacterisationv2_0 = XSDataResultCharacterisationv2_0(
)
self.xsDataResultCharacterisation = XSDataResultCharacterisation()
self.xsDataResultCharacterisationv2_0.setMxv1ResultCharacterisation(
self.xsDataResultCharacterisation)
self.xsDataResultCharacterisation.setDataCollection(
XSDataCollection.parseString(xsDataCollection.marshal()))
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_3.preProcess")
# Load the plugins
self._edPluginControlIndexingIndicators = self.loadPlugin(self._strPluginControlIndexingIndicators, \
"Indexing")
self._edPluginControlIndexingLabelit = self.loadPlugin(self._strPluginControlIndexingLabelit, \
"IndexingLabelit")
self._edPluginExecEvaluationIndexingMOSFLM = self.loadPlugin(self._strPluginExecEvaluationIndexing, \
"IndexingEvalualtionMOSFLM")
self._edPluginExecEvaluationIndexingLABELIT = self.loadPlugin(self._strPluginExecEvaluationIndexing, \
"IndexingEvalualtionLABELIT")
self._edPluginControlGeneratePrediction = self.loadPlugin(self._strPluginControlGeneratePrediction, \
"GeneratePrediction")
self._edPluginControlIntegration = self.loadPlugin(self._strPluginControlIntegration, \
"Integration")
self._edPluginControlXDSGenerateBackgroundImage = self.loadPlugin(self._strPluginControlXDSGenerateBackgroundImage, \
"ControlXDSGenerateBackgroundImage")
self._edPluginControlStrategy = self.loadPlugin(self._strPluginControlStrategy, \
"Strategy")
if (self._edPluginControlIndexingIndicators is not None):
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_3.preProcess: " + self._strPluginControlIndexingIndicators + " Found... setting Data Input")
# create Data Input for indexing
xsDataInputCharacterisation = self.getDataInput()
self._xsDataCollection = xsDataInputCharacterisation.getDataCollection()
xsDataCrystal = None
xsDataSubWedgeList = self._xsDataCollection.getSubWedge()
if ((xsDataSubWedgeList is None) or (xsDataSubWedgeList == [])):
strError = "EDPluginControlCharacterisationv1_3.preProcess: No subwedges in input data."
EDVerbose.ERROR(strError)
self.setFailure()
else:
xsDataExperimentalCondition = xsDataSubWedgeList[0].getExperimentalCondition()
# Fix for bug 431: if the flux is zero raise an error
xsDataDoubleFlux = xsDataExperimentalCondition.getBeam().getFlux()
if (xsDataDoubleFlux is not None):
if (xsDataDoubleFlux.getValue() < 0.1):
strErrorMessage = "Input flux is negative or close to zero. Execution of characterisation aborted."
EDVerbose.ERROR(strErrorMessage)
self.addErrorMessage("EDPluginControlCharacterisationv1_3.preProcess ERROR: " + strErrorMessage)
#self.addComment(strErrorMessage)
self.setFailure()
xsDataDiffractionPlan = self._xsDataCollection.getDiffractionPlan()
xsDataStringForcedSpaceGroup = xsDataDiffractionPlan.getForcedSpaceGroup()
if (xsDataStringForcedSpaceGroup is not None):
self._xsDataCrystal = XSDataCrystal()
xsDataSpaceGroup = XSDataSpaceGroup()
xsDataSpaceGroup.setName(xsDataStringForcedSpaceGroup)
self._xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
self._edPluginControlIndexingIndicators.setDataInput(self._xsDataCollection, "dataCollection")
if self._xsDataCrystal is not None:
self._edPluginControlIndexingIndicators.setDataInput(self._xsDataCrystal, "crystal")
# Populate characterisation object
self._xsDataResultCharacterisation = XSDataResultCharacterisation()
self._xsDataResultCharacterisation.setDataCollection(XSDataCollection.parseString(self._xsDataCollection.marshal()))
def testCheckParameters(self):
xsDataInputControlISPyB = XSDataInputControlISPyB()
xsDataResultCharacterisation = XSDataResultCharacterisation()
xsDataInputControlISPyB.setCharacterisationResult(
xsDataResultCharacterisation)
edPluginControlISPyB = self.createPlugin()
edPluginControlISPyB.setDataInput(xsDataInputControlISPyB)
edPluginControlISPyB.checkParameters()
def buildChildren(self, child_, nodeName_):
if child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'characterisationResult':
obj_ = XSDataResultCharacterisation()
obj_.build(child_)
self.setCharacterisationResult(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'characterisationResultv2_0':
obj_ = XSDataResultCharacterisationv2_0()
obj_.build(child_)
self.setCharacterisationResultv2_0(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'fileGraph':
obj_ = XSDataFile()
obj_.build(child_)
self.fileGraph.append(obj_)
XSDataInput.buildChildren(self, child_, nodeName_)
def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_1.preProcess...")
self.__edPluginIndexing = self.loadPlugin(self.__strPluginIndexingName , "Indexing")
self.__edPluginIntegration = self.loadPlugin(self.__strPluginIntegrationName, "Integration")
self.__edPluginStrategy = self.loadPlugin(self.__strPluginStrategyName , "Strategy")
if (self.__edPluginIndexing is not None):
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_1.preProcess: " + self.__strPluginIndexingName + " Found... setting Data Input")
# create Data Input for indexing
xsDataInputStrategy = self.getDataInput()
xsDataCollection = xsDataInputStrategy.getDataCollection()
xsDataSample = xsDataCollection.getSample()
xsDataSubWedgeList = xsDataCollection.getSubWedge()
if ((xsDataSubWedgeList is None) or (xsDataSubWedgeList == [])):
strError = "EDPluginControlCharacterisationv1_1.preProcess: No subwedges in input data."
EDVerbose.ERROR(strError)
self.setFailure()
else:
xsDataExperimentalCondition = xsDataSubWedgeList[0].getExperimentalCondition()
# Fix for bug 431: if the flux is zero raise an error
xsDataDoubleFlux = xsDataExperimentalCondition.getBeam().getFlux()
if (xsDataDoubleFlux is not None):
if (xsDataDoubleFlux.getValue() < 0.1):
pyStrErrorMessage = "EDPluginControlCharacterisationv1_1.preProcess ERROR: Input flux is negative or close to zero. Execution of characterisation aborted."
EDVerbose.ERROR(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
self.setFailure()
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.setDataCollection(xsDataCollection)
xsDataIndexingInput.setExperimentalCondition(xsDataExperimentalCondition)
xsDataDiffractionPlan = xsDataCollection.getDiffractionPlan()
xsDataStringForcedSpaceGroup = xsDataDiffractionPlan.getForcedSpaceGroup()
if (xsDataStringForcedSpaceGroup is not None):
xsDataCrystal = XSDataCrystal()
xsDataSpaceGroup = XSDataSpaceGroup()
xsDataSpaceGroup.setName(xsDataStringForcedSpaceGroup)
xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
xsDataIndexingInput.setCrystal(xsDataCrystal)
self.__edPluginIndexing.setDataInput(xsDataIndexingInput)
# Populate characterisation object
self.__xsDataResultCharacterisation = XSDataResultCharacterisation()
self.__xsDataResultCharacterisation.setDataCollection(XSDataCollection.parseString(xsDataCollection.marshal()))
def buildChildren(self, child_, nodeName_):
if child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'resultCharacterisation':
obj_ = XSDataResultCharacterisation()
obj_.build(child_)
self.setResultCharacterisation(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'resultControlISPyB':
obj_ = XSDataResultControlISPyB()
obj_.build(child_)
self.setResultControlISPyB(obj_)
def buildChildren(self, child_, nodeName_):
if child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'characterisationResult':
obj_ = XSDataResultCharacterisation()
obj_.build(child_)
self.setCharacterisationResult(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'characterisationResultv2_0':
obj_ = XSDataResultCharacterisationv2_0()
obj_.build(child_)
self.setCharacterisationResultv2_0(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'fileGraph':
obj_ = XSDataFile()
obj_.build(child_)
self.fileGraph.append(obj_)
XSDataInput.buildChildren(self, child_, nodeName_)
def buildChildren(self, child_, nodeName_): if child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'resultCharacterisation': obj_ = XSDataResultCharacterisation() obj_.build(child_) self.setResultCharacterisation(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'resultControlISPyB': obj_ = XSDataResultControlISPyB() obj_.build(child_) self.setResultControlISPyB(obj_)
def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
EDVerbose.DEBUG("EDPluginControlCharacterisationv2_0.preProcess...")
self.edPluginIndexing = self.loadPlugin(self.strPluginIndexingName, "Indexing")
self.edPluginIntegration = self.loadPlugin(self.strPluginIntegrationName, "Integration")
self.edPluginStrategy = self.loadPlugin(self.strPluginStrategyName, "Strategy")
if self.edPluginIndexing is not None:
EDVerbose.DEBUG(
"EDPluginControlCharacterisationv2_0.preProcess: "
+ self.strPluginIndexingName
+ " Found... setting Data Input"
)
# create Data Input for indexing
xsDataInputStrategy = self.getDataInput("mxv1InputCharacterisation")[0]
xsDataCollection = xsDataInputStrategy.getDataCollection()
# xsDataSample = xsDataCollection.getSample()
xsDataSubWedgeList = xsDataCollection.getSubWedge()
xsDataExperimentalCondition = xsDataSubWedgeList[0].getExperimentalCondition()
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.setDataCollection(xsDataCollection)
xsDataIndexingInput.setExperimentalCondition(xsDataExperimentalCondition)
xsDataDiffractionPlan = xsDataCollection.getDiffractionPlan()
xsDataStringForcedSpaceGroup = xsDataDiffractionPlan.getForcedSpaceGroup()
if xsDataStringForcedSpaceGroup is not None:
xsDataCrystal = XSDataCrystal()
xsDataSpaceGroup = XSDataSpaceGroup()
xsDataSpaceGroup.setName(xsDataStringForcedSpaceGroup)
xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
xsDataIndexingInput.setCrystal(xsDataCrystal)
self.edPluginIndexing.setDataInput(xsDataIndexingInput)
# Populate characterisation object
self.xsDataResultCharacterisationv2_0 = XSDataResultCharacterisationv2_0()
self.xsDataResultCharacterisation = XSDataResultCharacterisation()
self.xsDataResultCharacterisationv2_0.setMxv1ResultCharacterisation(self.xsDataResultCharacterisation)
self.xsDataResultCharacterisation.setDataCollection(
XSDataCollection.parseString(xsDataCollection.marshal())
)
def buildChildren(self, child_, nodeName_):
if child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'mxv1InputCharacterisation':
obj_ = XSDataInputCharacterisation()
obj_.build(child_)
self.setMxv1InputCharacterisation(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'mxv1ResultCharacterisation_Reference':
obj_ = XSDataResultCharacterisation()
obj_.build(child_)
self.setMxv1ResultCharacterisation_Reference(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'mxv2DataCollection':
obj_ = XSDataCollection()
obj_.build(child_)
self.setMxv2DataCollection(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'mxv2DataCollection_Reference':
obj_ = XSDataCollection()
obj_.build(child_)
self.setMxv2DataCollection_Reference(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'possibleOrientations':
obj_ = kappa_alignment_response()
obj_.build(child_)
self.setPossibleOrientations(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'omega':
obj_ = XSDataAngle()
obj_.build(child_)
self.setOmega(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'kappa':
obj_ = XSDataAngle()
obj_.build(child_)
self.setKappa(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'phi':
obj_ = XSDataAngle()
obj_.build(child_)
self.setPhi(obj_)
XSDataInputInterface.buildChildren(self, child_, nodeName_)
class EDPluginControlCharacterisationv1_1(EDPluginControl):
"""
The Plugin that controls the whole characterisation.
"""
def __init__(self):
"""
"""
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputCharacterisation)
self.__strPluginIndexingName = "EDPluginControlIndexingv10"
self.__edPluginIndexing = None
self.__strPluginIntegrationName = "EDPluginControlIntegrationv10"
self.__edPluginIntegration = None
self.__strPluginStrategyName = "EDPluginControlStrategyv1_1"
self.__edPluginStrategy = None
self.__xsDataResultCharacterisation = None
self.__strPluginKappaStrategyName = "EDPluginControlKappaStrategyv1_1"
self.__strPluginIntegrationPointlessName = "EDPluginControlIntegrationPointlessv10"
def checkParameters(self):
"""
Checks the mandatory parameters
"""
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_1.checkParameters")
self.checkMandatoryParameters(self.getDataInput(),
"Data Input is None")
self.checkMandatoryParameters(self.getDataInput().getDataCollection(),
"dataCollection")
self.checkMandatoryParameters(
self.getDataInput().getDataCollection().getDiffractionPlan(),
"diffractionPlan")
def configure(self):
"""
Gets the configuration parameters (if any).
"""
EDPluginControl.configure(self)
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_1.configure")
pluginConfiguration = self.getConfiguration()
if (pluginConfiguration is None):
EDVerbose.DEBUG(
"No plugin configuration found for EDPluginControlCharacterisationv1_1."
)
else:
if (self.getControlledPluginName("indexingPlugin") is not None):
self.__strPluginIndexingName = self.getControlledPluginName(
"indexingPlugin")
if (self.getControlledPluginName("integrationPlugin") is not None):
self.__strPluginIntegrationName = self.getControlledPluginName(
"integrationPlugin")
if (self.getControlledPluginName("strategyPlugin") is not None):
self.__strPluginStrategyName = self.getControlledPluginName(
"strategyPlugin")
if (self.getControlledPluginName("kappaStrategyPlugin")
is not None):
self.__strPluginKappaStrategyName = self.getControlledPluginName(
"kappaStrategyPlugin")
if (self.getControlledPluginName("integrationPointlessPlugin")
is not None):
self.__strPluginIntegrationPoitlessName = self.getControlledPluginName(
"integrationPointlessPlugin")
pyStrKappa = EDConfiguration.getStringParamValue(
pluginConfiguration, "KAPPA")
if (pyStrKappa == "ON"):
self.__strPluginStrategyName = self.__strPluginKappaStrategyName
pyStrPointless = EDConfiguration.getStringParamValue(
pluginConfiguration, "POINTLESS")
if (pyStrPointless == "ON"):
self.__strPluginIntegrationName = self.__strPluginIntegrationPointlessName
def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_1.preProcess...")
self.__edPluginIndexing = self.loadPlugin(self.__strPluginIndexingName,
"Indexing")
self.__edPluginIntegration = self.loadPlugin(
self.__strPluginIntegrationName, "Integration")
self.__edPluginStrategy = self.loadPlugin(self.__strPluginStrategyName,
"Strategy")
if (self.__edPluginIndexing is not None):
EDVerbose.DEBUG(
"EDPluginControlCharacterisationv1_1.preProcess: " +
self.__strPluginIndexingName + " Found... setting Data Input")
# create Data Input for indexing
xsDataInputStrategy = self.getDataInput()
xsDataCollection = xsDataInputStrategy.getDataCollection()
xsDataSample = xsDataCollection.getSample()
xsDataSubWedgeList = xsDataCollection.getSubWedge()
if ((xsDataSubWedgeList is None) or (xsDataSubWedgeList == [])):
strError = "EDPluginControlCharacterisationv1_1.preProcess: No subwedges in input data."
EDVerbose.ERROR(strError)
self.setFailure()
else:
xsDataExperimentalCondition = xsDataSubWedgeList[
0].getExperimentalCondition()
# Fix for bug 431: if the flux is zero raise an error
xsDataDoubleFlux = xsDataExperimentalCondition.getBeam(
).getFlux()
if (xsDataDoubleFlux is not None):
if (xsDataDoubleFlux.getValue() < 0.1):
pyStrErrorMessage = "EDPluginControlCharacterisationv1_1.preProcess ERROR: Input flux is negative or close to zero. Execution of characterisation aborted."
EDVerbose.ERROR(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
self.setFailure()
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.setDataCollection(xsDataCollection)
xsDataIndexingInput.setExperimentalCondition(
xsDataExperimentalCondition)
xsDataDiffractionPlan = xsDataCollection.getDiffractionPlan()
xsDataStringForcedSpaceGroup = xsDataDiffractionPlan.getForcedSpaceGroup(
)
if (xsDataStringForcedSpaceGroup is not None):
xsDataCrystal = XSDataCrystal()
xsDataSpaceGroup = XSDataSpaceGroup()
xsDataSpaceGroup.setName(xsDataStringForcedSpaceGroup)
xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
xsDataIndexingInput.setCrystal(xsDataCrystal)
self.__edPluginIndexing.setDataInput(xsDataIndexingInput)
# Populate characterisation object
self.__xsDataResultCharacterisation = XSDataResultCharacterisation(
)
self.__xsDataResultCharacterisation.setDataCollection(
XSDataCollection.parseString(xsDataCollection.marshal()))
def process(self, _edObject=None):
EDPluginControl.process(self, _edObject)
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_1.process")
self.connectProcess(self.__edPluginIndexing.executeSynchronous)
self.__edPluginIndexing.connectSUCCESS(
self.doIndexingToIntegrationTransition)
self.__edPluginIndexing.connectFAILURE(self.doFailureActionIndexing)
self.__edPluginIntegration.connectSUCCESS(
self.doIntegrationToStrategyTransition)
self.__edPluginIntegration.connectFAILURE(
self.doFailureActionIntegration)
self.__edPluginStrategy.connectFAILURE(self.doFailureActionStrategy)
self.__edPluginStrategy.connectSUCCESS(self.doSuccessActionStrategy)
def postProcess(self, _edObject=None):
EDPluginControl.postProcess(self, _edObject)
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_1.postProcess")
if (self.__xsDataResultCharacterisation is not None):
self.setDataOutput(self.__xsDataResultCharacterisation)
def doIndexingToIntegrationTransition(self, _edPlugin=None):
EDVerbose.DEBUG(
"EDPluginControlCharacterisationv1_1.doIndexingToIntegrationTransition"
)
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlCharacterisationv1_1.doIntegrationToStrategyTransition"
)
xsDataIndexingResult = self.__edPluginIndexing.getDataOutput()
self.__xsDataResultCharacterisation.setIndexingResult(
xsDataIndexingResult)
xsDataIntegrationInput = XSDataIntegrationInput()
xsDataIntegrationInput.setDataCollection(
self.__xsDataResultCharacterisation.getDataCollection())
xsDataIntegrationInput.setExperimentalConditionRefined(
xsDataIndexingResult.getSelectedSolution(
).getExperimentalConditionRefined())
xsDataIntegrationInput.setSelectedIndexingSolution(
xsDataIndexingResult.getSelectedSolution())
self.__edPluginIntegration.setDataInput(xsDataIntegrationInput)
self.__edPluginIntegration.executeSynchronous()
def doIntegrationToStrategyTransition(self, _edPlugin=None):
EDVerbose.DEBUG(
"EDPluginControlCharacterisationv1_1.doIntegrationToStrategyTransition"
)
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlCharacterisationv1_1.doIntegrationToStrategyTransition"
)
xsDataIntegrationOutput = self.__edPluginIntegration.getDataOutput()
self.__xsDataResultCharacterisation.setIntegrationResult(
xsDataIntegrationOutput)
#EDVerbose.DEBUG( self.__xsDataExperimentCharacterisation.marshal() )
xsDataInputStrategy = XSDataInputStrategy()
xsDataSolutionSelected = self.__xsDataResultCharacterisation.getIndexingResult(
).getSelectedSolution()
xsDataInputStrategy.setCrystalRefined(
xsDataSolutionSelected.getCrystal())
xsDataInputStrategy.setSample(self.__xsDataResultCharacterisation.
getDataCollection().getSample())
xsDataIntegrationSubWedgeResultList = xsDataIntegrationOutput.getIntegrationSubWedgeResult(
)
xsDataInputStrategy.setBestFileContentDat(
xsDataIntegrationSubWedgeResultList[0].getBestfileDat())
xsDataInputStrategy.setBestFileContentPar(
xsDataIntegrationSubWedgeResultList[0].getBestfilePar())
xsDataInputStrategy.setExperimentalCondition(
xsDataIntegrationSubWedgeResultList[0].
getExperimentalConditionRefined())
for xsDataIntegrationSubWedgeResult in xsDataIntegrationSubWedgeResultList:
xsDataInputStrategy.addBestFileContentHKL(
xsDataIntegrationSubWedgeResult.getBestfileHKL())
xsDataInputStrategy.setDiffractionPlan(
self.__xsDataResultCharacterisation.getDataCollection(
).getDiffractionPlan())
#print xsDataInputStrategy.marshal()
self.__edPluginStrategy.setDataInput(xsDataInputStrategy)
self.__edPluginStrategy.executeSynchronous()
def doFailureActionIndexing(self, _edPlugin=None):
EDVerbose.DEBUG(
"EDPluginControlCharacterisationv1_1.doFailureActionIndexing")
self.retrieveFailureMessages(
_edPlugin,
"EDPluginControlCharacterisationv1_1.doFailureActionIndexing")
# If indexing fails all processing should stop
self.generateExecutiveSummary(self)
self.setFailure()
def doFailureActionIntegration(self, _edPlugin=None):
EDVerbose.DEBUG(
"EDPluginControlCharacterisationv1_1.doFailureActionIntegration")
self.retrieveFailureMessages(
_edPlugin,
"EDPluginControlCharacterisationv1_1.doFailureActionIntegration")
def doFailureActionStrategy(self, _edPlugin=None):
EDVerbose.DEBUG(
"EDPluginControlCharacterisationv1_1.doFailureActionStrategy")
self.retrieveFailureMessages(
_edPlugin,
"EDPluginControlCharacterisationv1_1.doFailureActionStrategy")
def doSuccessActionStrategy(self, _edPlugin):
"""
retrieve the potential warning messages
"""
EDVerbose.DEBUG(
"EDPluginControlCharacterisationv1_1.doSuccessActionStrategy")
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlCharacterisationv1_1.doSuccessActionStrategy")
xsDataResultStrategy = self.__edPluginStrategy.getDataOutput()
self.__xsDataResultCharacterisation.setStrategyResult(
xsDataResultStrategy)
def generateExecutiveSummary(self, _edPlugin):
"""
Generates a summary of the execution of the plugin.
"""
EDVerbose.DEBUG(
"EDPluginControlCharacterisationv1_1.generateExecutiveSummary")
self.addExecutiveSummaryLine("Summary of characterisation:")
self.addErrorWarningMessagesToExecutiveSummary(
"Characterisation failure! Error messages: ")
self.addExecutiveSummarySeparator()
xsDataInputStrategy = self.getDataInput()
xsDataCollection = xsDataInputStrategy.getDataCollection()
xsDataDiffractionPlan = xsDataCollection.getDiffractionPlan()
self.addExecutiveSummaryLine("Diffraction plan:")
if (xsDataDiffractionPlan.getComplexity() is not None):
self.addExecutiveSummaryLine(
"BEST complexity : %s" %
xsDataDiffractionPlan.getComplexity().getValue())
if (xsDataDiffractionPlan.getAimedCompleteness() is not None):
self.addExecutiveSummaryLine(
"Aimed completeness : %6.1f [%%]" %
(100.0 *
xsDataDiffractionPlan.getAimedCompleteness().getValue()))
if (xsDataDiffractionPlan.getRequiredCompleteness() is not None):
self.addExecutiveSummaryLine(
"Required completeness : %6.1f [%%]" %
(100.0 *
xsDataDiffractionPlan.getRequiredCompleteness().getValue()))
if (xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution()
is not None):
self.addExecutiveSummaryLine(
"Aimed I/sigma at highest resolution : %6.1f" %
xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution(
).getValue())
if (xsDataDiffractionPlan.getAimedResolution() is not None):
self.addExecutiveSummaryLine(
"Aimed resolution : %6.1f [A]" %
xsDataDiffractionPlan.getAimedResolution().getValue())
if (xsDataDiffractionPlan.getRequiredResolution() is not None):
self.addExecutiveSummaryLine(
"Required resolution : %6.1f [A]" %
xsDataDiffractionPlan.getRequiredResolution().getValue())
if (xsDataDiffractionPlan.getAimedMultiplicity() is not None):
self.addExecutiveSummaryLine(
"Aimed multiplicity : %6.1f" %
xsDataDiffractionPlan.getAimedMultiplicity().getValue())
if (xsDataDiffractionPlan.getRequiredMultiplicity() is not None):
self.addExecutiveSummaryLine(
"Required multiplicity : %6.1f" %
xsDataDiffractionPlan.getRequiredMultiplicity().getValue())
if (xsDataDiffractionPlan.getForcedSpaceGroup() is not None):
self.addExecutiveSummaryLine(
"Forced space group : %6s" %
xsDataDiffractionPlan.getForcedSpaceGroup().getValue())
if (xsDataDiffractionPlan.getMaxExposureTimePerDataCollection()
is not None):
self.addExecutiveSummaryLine(
"Max exposure time per data collection : %6.1f [s]" %
xsDataDiffractionPlan.getMaxExposureTimePerDataCollection(
).getValue())
self.addExecutiveSummarySeparator()
if (self.__edPluginIndexing is not None):
self.appendExecutiveSummary(self.__edPluginIndexing, "Indexing : ")
if (self.__edPluginIntegration is not None):
self.appendExecutiveSummary(self.__edPluginIntegration,
"Integration : ")
if (self.__edPluginStrategy is not None):
self.appendExecutiveSummary(self.__edPluginStrategy, "Strategy : ")
def getPluginStrategyName(self):
return self.__strPluginStrategyName
def dna_execute_collection3(
dna_start,
dna_range,
dna_number_of_images,
dna_exptime,
dna_directory,
prefix,
start_image_number,
overlap,
dna_run_num,
charRequest,
):
global collect_and_characterize_success, dna_have_strategy_results, dna_have_index_results, picture_taken
global dna_strategy_exptime, dna_strategy_start, dna_strategy_range, dna_strategy_end, dna_strat_dist
global screeningoutputid
characterizationParams = charRequest["request_obj"]["characterizationParams"]
dna_res = float(characterizationParams["aimed_resolution"])
print "dna_res = " + str(dna_res)
dna_filename_list = []
print "number of images " + str(dna_number_of_images) + " overlap = " + str(overlap) + " dna_start " + str(
dna_start
) + " dna_range " + str(dna_range) + " prefix " + prefix + " start number " + str(start_image_number) + "\n"
collect_and_characterize_success = 0
dna_have_strategy_results = 0
dna_have_index_results = 0
dg2rd = 3.14159265 / 180.0
if daq_utils.detector_id == "ADSC-Q315":
det_radius = 157.5
elif daq_utils.detector_id == "ADSC-Q210":
det_radius = 105.0
elif daq_utils.detector_id == "PILATUS-6":
det_radius = 212.0
else: # default Pilatus
det_radius = 212.0
##### theta_radians = daq_lib.get_field("theta") * dg2rd
theta_radians = 0.0
wave = 12398.5 / beamline_lib.get_mono_energy() # for now
dx = det_radius / (tan(2.0 * (asin(wave / (2.0 * dna_res))) - theta_radians))
print "distance = ", dx
# skinner - could move distance and wave and scan axis here, leave wave alone for now
print "skinner about to take reference images."
for i in range(0, int(dna_number_of_images)):
print "skinner prefix7 = " + prefix[0:7] + " " + str(start_image_number) + "\n"
if len(prefix) > 8:
if (prefix[0:7] == "postref") and (start_image_number == 1):
print "skinner postref bail\n"
time.sleep(float(dna_number_of_images * float(dna_exptime)))
break
# skinner roi - maybe I can measure and use that for dna_start so that first image is face on.
dna_start = daq_lib.get_field("datum_omega")
colstart = float(dna_start) + (i * (abs(overlap) + float(dna_range)))
dna_prefix = "ref-" + prefix + "_" + str(dna_run_num)
image_number = start_image_number + i
dna_prefix_long = dna_directory + "/" + dna_prefix
filename = daq_utils.create_filename(dna_prefix_long, image_number)
beamline_lib.mva("Omega", float(colstart))
##### daq_lib.move_axis_absolute(daq_lib.get_field("scan_axis"),colstart)
##### daq_lib.take_image(colstart,dna_range,dna_exptime,filename,daq_lib.get_field("scan_axis"),0,1)
daq_utils.take_crystal_picture(reqID=charRequest["request_id"])
######### BECAUSE I FAKE IT imagesAttempted = collect_detector_seq(dna_range,dna_range,dna_exptime,dna_prefix,dna_directory,image_number)
if i == 0:
commFake = "ln -sf /h/pxuser/skinner/testdata/B1GGTApo_9_00001.cbf " + filename
else:
commFake = "ln -sf /h/pxuser/skinner/testdata/B1GGTApo_9_00181.cbf " + filename
os.system(commFake)
dna_filename_list.append(filename)
diffImgJpegData = daq_utils.diff2jpeg(filename, reqID=charRequest["request_id"]) # returns a dictionary
# diffImgJpegData["timestamp"] = time.time()
# imgRef = db_lib.addFile(diffImgJpegData["data"])
# diffImgJpegData["data"] = imgRef
# imgRef = db_lib.addFile(diffImgJpegData["thumbData"])
# diffImgJpegData["thumbData"] = imgRef
picture_taken = 1
# xml_from_file_list(flux,x_beamsize,y_beamsize,max_exptime_per_dc,aimed_completeness,file_list):
edna_energy_ev = (12.3985 / wave) * 1000.0
##### xbeam_size = beamline_lib.get_motor_pos("slitHum")
##### ybeam_size = beamline_lib.get_motor_pos("slitVum")
# if (xbeam_size == 0.0 or ybeam_size == 0.0): #don't know where to get these from yet
if 1:
xbeam_size = 0.1
ybeam_size = 0.16
else:
xbeam_size = xbeam_size / 1000
ybeam_size = ybeam_size / 1000
aimed_completeness = characterizationParams["aimed_completeness"]
aimed_multiplicity = characterizationParams["aimed_multiplicity"]
aimed_resolution = characterizationParams["aimed_resolution"]
aimed_ISig = characterizationParams["aimed_ISig"]
timeout_check = 0
##### while(not os.path.exists(dna_filename_list[len(dna_filename_list)-1])): #this waits for edna images
if 0:
timeout_check = timeout_check + 1
time.sleep(1.0)
if timeout_check > 10:
break
print "generating edna input\n"
# edna_input_filename = edna_input_xml.xml_from_file_list(edna_energy_ev,xbeam_size,ybeam_size,1000000,aimed_completness,aimed_ISig,aimed_multiplicity,aimed_resolution,dna_filename_list)
##### flux = 10000000000 * beamline_lib.get_epics_pv("flux","VAL")
flux = 600000000.0 # for now
edna_input_filename = dna_directory + "/adsc1_in.xml"
edna_input_xml_command = (
"/h/data/backed-up/pxsys/skinner/edna_header_code/makeAnEDNAXML-bnl.sh 1232 %s %s none %f %f 4000 0.01 0.01 0 xh1223_2_ %f %f %f > %s"
% (dna_directory, dna_prefix, 3, aimed_ISig, flux, xbeam_size, ybeam_size, edna_input_filename)
)
##### edna_input_xml_command = "ssh swill \"/h/data/backed-up/pxsys/skinner/edna_header_code/makeAnEDNAXML-bnl.sh 1232 %s %s none %f %f 4000 0.01 0.01 0 xh1223_2_ %f %f %f\" > %s" % (daq_lib.data_directory_name,dna_prefix,3,aimed_ISig,flux,xbeam_size,ybeam_size,edna_input_filename)
print edna_input_xml_command
comm_sss = "echo " + edna_input_xml_command + "> edna_comm.txt"
os.system(comm_sss)
os.system(edna_input_xml_command)
print "done generating edna input\n"
# command_string = "cd %s; /usr/local/crys/edna-mx/mxv1/bin/edna-mxv1-characterisation.py --verbose --data %s" % (dna_directory,edna_input_filename)
command_string = "/usr/local/crys/edna-mx/mxv1/bin/edna-mxv1-characterisation.py --verbose --data %s" % (
edna_input_filename
)
# command_string = "/usr/local/crys/edna-mx/mxv1/bin/edna-mxv1-characterisation.py --verbose --data /img11/data1/pxuser/staff/skinner/edna_run/adsc1_in.xml"
# old command_string = "$EDNA_HOME/mxv1/bin/edna-mxv1-characterisation --data " + edna_input_filename
print command_string
# for i in range (0,len(dna_filename_list)):
# command_string = command_string + " " + dna_filename_list[i]
broadcast_output("\nProcessing with EDNA. Please stand by.\n")
if os.path.exists("edna.log"):
os.remove("edna.log")
if os.path.exists("edna.err"):
os.remove("edna.err")
edna_execution_status = os.system("%s > edna.log 2> edna.err" % command_string)
##### fEdnaLogFile = open(daq_lib.get_misc_dir_name() + "/edna.log", "r" )
fEdnaLogFile = open("./edna.log", "r")
ednaLogLines = fEdnaLogFile.readlines()
fEdnaLogFile.close()
for outline in ednaLogLines:
# for outline in os.popen(command_string,'r',0).readlines():
####skinner6/11 seg faults? broadcast_output(outline)
if string.find(outline, "EdnaDir") != -1:
(param, dirname) = string.split(outline, "=")
strXMLFileName = (
dirname[0 : len(dirname) - 1]
+ "/ControlInterfacev1_2/Characterisation/ControlCharacterisationv1_3_dataOutput.xml"
)
##### strXMLFileName = dirname[0:len(dirname)-1]+"/ControlInterfacev1_2/Characterisation/ControlCharacterisationv1_1_dataOutput.xml"
if string.find(outline, "characterisation successful!") != -1:
collect_and_characterize_success = 1
if not collect_and_characterize_success:
dna_comment = "Indexing Failure"
##### pxdb_lib.update_sweep(2,daq_lib.sweep_seq_id,dna_comment)
return 0
xsDataCharacterisation = XSDataResultCharacterisation.parseFile(strXMLFileName)
xsDataIndexingResult = xsDataCharacterisation.getIndexingResult()
xsDataIndexingSolutionSelected = xsDataIndexingResult.getSelectedSolution()
xsDataStatisticsIndexing = xsDataIndexingSolutionSelected.getStatistics()
numSpotsFound = xsDataStatisticsIndexing.getSpotsTotal().getValue()
numSpotsUsed = xsDataStatisticsIndexing.getSpotsUsed().getValue()
numSpotsRejected = numSpotsFound - numSpotsUsed
beamShiftX = xsDataStatisticsIndexing.getBeamPositionShiftX().getValue()
beamShiftY = xsDataStatisticsIndexing.getBeamPositionShiftY().getValue()
spotDeviationR = xsDataStatisticsIndexing.getSpotDeviationPositional().getValue()
try:
spotDeviationTheta = xsDataStatisticsIndexing.getSpotDeviationAngular().getValue()
except AttributeError:
spotDeviationTheta = 0.0
diffractionRings = 0 # for now, don't see this in xml except message string
reflections_used = 0 # for now
reflections_used_in_indexing = 0 # for now
rejectedReflections = 0 # for now
xsDataOrientation = xsDataIndexingSolutionSelected.getOrientation()
xsDataMatrixA = xsDataOrientation.getMatrixA()
rawOrientationMatrix_a_x = xsDataMatrixA.getM11()
rawOrientationMatrix_a_y = xsDataMatrixA.getM12()
rawOrientationMatrix_a_z = xsDataMatrixA.getM13()
rawOrientationMatrix_b_x = xsDataMatrixA.getM21()
rawOrientationMatrix_b_y = xsDataMatrixA.getM22()
rawOrientationMatrix_b_z = xsDataMatrixA.getM23()
rawOrientationMatrix_c_x = xsDataMatrixA.getM31()
rawOrientationMatrix_c_y = xsDataMatrixA.getM32()
rawOrientationMatrix_c_z = xsDataMatrixA.getM33()
xsDataCrystal = xsDataIndexingSolutionSelected.getCrystal()
xsDataCell = xsDataCrystal.getCell()
unitCell_alpha = xsDataCell.getAngle_alpha().getValue()
unitCell_beta = xsDataCell.getAngle_beta().getValue()
unitCell_gamma = xsDataCell.getAngle_gamma().getValue()
unitCell_a = xsDataCell.getLength_a().getValue()
unitCell_b = xsDataCell.getLength_b().getValue()
unitCell_c = xsDataCell.getLength_c().getValue()
mosaicity = xsDataCrystal.getMosaicity().getValue()
xsSpaceGroup = xsDataCrystal.getSpaceGroup()
spacegroup_name = xsSpaceGroup.getName().getValue()
pointGroup = spacegroup_name # for now
bravaisLattice = pointGroup # for now
statusDescription = "ok" # for now
try:
spacegroup_number = xsSpaceGroup.getITNumber().getValue()
except AttributeError:
spacegroup_number = 0
xsStrategyResult = xsDataCharacterisation.getStrategyResult()
resolutionObtained = -999
if xsStrategyResult != None:
dna_have_strategy_results = 1
xsCollectionPlan = xsStrategyResult.getCollectionPlan()
xsStrategySummary = xsCollectionPlan[0].getStrategySummary()
resolutionObtained = xsStrategySummary.getRankingResolution().getValue()
xsCollectionStrategy = xsCollectionPlan[0].getCollectionStrategy()
xsSubWedge = xsCollectionStrategy.getSubWedge()
for i in range(0, len(xsSubWedge)):
xsExperimentalCondition = xsSubWedge[i].getExperimentalCondition()
xsGoniostat = xsExperimentalCondition.getGoniostat()
xsDetector = xsExperimentalCondition.getDetector()
xsBeam = xsExperimentalCondition.getBeam()
dna_strategy_start = xsGoniostat.getRotationAxisStart().getValue()
dna_strategy_start = dna_strategy_start - (dna_strategy_start % 0.1)
dna_strategy_range = xsGoniostat.getOscillationWidth().getValue()
dna_strategy_range = dna_strategy_range - (dna_strategy_range % 0.1)
dna_strategy_end = xsGoniostat.getRotationAxisEnd().getValue()
dna_strategy_end = (dna_strategy_end - (dna_strategy_end % 0.1)) + dna_strategy_range
dna_strat_dist = xsDetector.getDistance().getValue()
dna_strat_dist = dna_strat_dist - (dna_strat_dist % 1)
dna_strategy_exptime = xsBeam.getExposureTime().getValue()
# wtf? dna_strategy_exptime = dna_strategy_exptime-(dna_strategy_exptime%.2)
program = "edna-1.0" # for now
##### screeningoutputid = pxdb_lib.insert_dna_index_results(daq_lib.sweep_seq_id,daq_lib.get_field("xtal_id"),program,statusDescription,rejectedReflections,resolutionObtained,spotDeviationR,spotDeviationTheta,beamShiftX,beamShiftY,numSpotsFound,numSpotsUsed,numSpotsRejected,mosaicity,diffractionRings,spacegroup_name,pointGroup,bravaisLattice,rawOrientationMatrix_a_x,rawOrientationMatrix_a_y,rawOrientationMatrix_a_z,rawOrientationMatrix_b_x,rawOrientationMatrix_b_y,rawOrientationMatrix_b_z,rawOrientationMatrix_c_x,rawOrientationMatrix_c_y,rawOrientationMatrix_c_z,unitCell_a,unitCell_b,unitCell_c,unitCell_alpha,unitCell_beta,unitCell_gamma)
dna_comment = (
"spacegroup = "
+ str(spacegroup_name)
+ " mosaicity = "
+ str(mosaicity)
+ " resolutionHigh = "
+ str(resolutionObtained)
+ " cell_a = "
+ str(unitCell_a)
+ " cell_b = "
+ str(unitCell_b)
+ " cell_c = "
+ str(unitCell_c)
+ " cell_alpha = "
+ str(unitCell_alpha)
+ " cell_beta = "
+ str(unitCell_beta)
+ " cell_gamma = "
+ str(unitCell_gamma)
+ " status = "
+ str(statusDescription)
)
##### print "\n\n skinner " + dna_comment + "\n" +str(daq_lib.sweep_seq_id) + "\n"
print "\n\n skinner " + dna_comment + "\n"
##### pxdb_lib.update_sweep(2,daq_lib.sweep_seq_id,dna_comment)
if dna_have_strategy_results:
##### pxdb_lib.insert_to_screening_strategy_table(screeningoutputid,dna_strategy_start,dna_strategy_end,dna_strategy_range,dna_strategy_exptime,resolutionObtained,program)
dna_strat_comment = (
"\ndna Strategy results: Start="
+ str(dna_strategy_start)
+ " End="
+ str(dna_strategy_end)
+ " Width="
+ str(dna_strategy_range)
+ " Time="
+ str(dna_strategy_exptime)
+ " Dist="
+ str(dna_strat_dist)
)
# characterizationResult = {}
characterizationResultObj = {}
# characterizationResult["type"] = "characterizationStrategy"
# characterizationResult["timestamp"] = time.time()
characterizationResultObj = {
"strategy": {
"start": dna_strategy_start,
"end": dna_strategy_end,
"width": dna_strategy_range,
"exptime": dna_strategy_exptime,
"detDist": dna_strat_dist,
}
}
# characterizationResult["resultObj"] = characterizationResultObj
db_lib.addResultforRequest("characterizationStrategy", charRequest["request_id"], characterizationResultObj)
##### pxdb_lib.update_sweep(2,daq_lib.sweep_seq_id,dna_strat_comment)
xsStrategyStatistics = xsCollectionPlan[0].getStatistics()
xsStrategyResolutionBins = xsStrategyStatistics.getResolutionBin()
now = time.time()
# edna_isig_plot_filename = dirname[0:len(dirname)-1] + "/edna_isig_res_" + str(now) + ".txt"
edna_isig_plot_filename = dirname[0 : len(dirname) - 1] + "/edna_isig_res.txt"
isig_plot_file = open(edna_isig_plot_filename, "w")
for i in range(0, len(xsStrategyResolutionBins) - 1):
i_over_sigma_bin = xsStrategyResolutionBins[i].getIOverSigma().getValue()
maxResolution_bin = xsStrategyResolutionBins[i].getMaxResolution().getValue()
print str(maxResolution_bin) + " " + str(i_over_sigma_bin)
isig_plot_file.write(str(maxResolution_bin) + " " + str(i_over_sigma_bin) + "\n")
isig_plot_file.close()
if dna_have_strategy_results:
broadcast_output(dna_strat_comment)
return 1
class EDPluginControlCharacterisationv2_0(EDPluginControl):
"""
The Plugin that controls the whole characterisation: Indexing-Integration-(Kappa)Strategy
Indexing-Integration is the same as mxv1 characterisation.
KappaStrategy:
Preferred Strategy is given at the initial orientation, but if KAPPA features are enabled,
strategies are calculated to some alignments.
"""
def __init__(self):
"""
"""
EDPluginControl.__init__(self)
#self.setXSDataInputClass( XSDataInputCharacterisation )
#self.setXSDataInputClass(EDList)
#self.strPluginIndexingName = "EDPluginControlIndexingv2_0"
self.strPluginIndexingName = "EDPluginControlIndexingv10"
self.edPluginIndexing = None
self.strPluginIntegrationName = "EDPluginControlIntegrationv10"
self.edPluginIntegration = None
self.xsDataResultCharacterisationv2_0 = None
self.xsDataResultCharacterisation = None
self.xsDataInputStrategy = None
self.setXSDataInputClass(XSDataInputCharacterisationv2_0)
EDFactoryPluginStatic.loadModule("XSDataMXv1")
import XSDataMXv1
self.setXSDataInputClass(XSDataMXv1.XSDataInputCharacterisation,
"mxv1InputCharacterisation")
EDFactoryPluginStatic.loadModule("XSDataMXv2")
import XSDataMXv2
self.setXSDataInputClass(XSDataMXv2.XSDataCollection,
"mxv2DataCollection")
def checkParameters(self):
"""
Checks the mandatory parameters
"""
EDVerbose.DEBUG("EDPluginControlCharacterisationv2_0.checkParameters")
# Check for mxv1InputCharacterisation:
if self.hasDataInput():
if self.hasDataInput("mxv1InputCharacterisation"
) or self.hasDataInput("mxv2DataCollection"):
EDVerbose.WARNING(
"Ambiguous input! Both XSDataInputCharacterisatiov2_0 input, and mxv1InputCharacterisation or mxv2DataCollection input(s), are given"
)
self.setDataInput(
self.getDataInput().getMxv1InputCharacterisation().marshal(),
"mxv1InputCharacterisation")
self.setDataInput(
self.getDataInput().getMxv2DataCollection().marshal(),
"mxv2DataCollection")
# Check for mxv1InputCharacterisation
self.checkMandatoryParameters(
self.getDataInput("mxv1InputCharacterisation"),
"Data Input is None")
self.checkMandatoryParameters(
self.getDataInput("mxv1InputCharacterisation")
[0].getDataCollection(), "dataCollection")
self.checkMandatoryParameters(
self.getDataInput("mxv1InputCharacterisation")
[0].getDataCollection().getDiffractionPlan(), "diffractionPlan")
def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
EDVerbose.DEBUG("EDPluginControlCharacterisationv2_0.preProcess...")
self.edPluginIndexing = self.loadPlugin(self.strPluginIndexingName,
"Indexing")
self.edPluginIntegration = self.loadPlugin(
self.strPluginIntegrationName, "Integration")
self.edPluginStrategy = self.loadPlugin(self.strPluginStrategyName,
"Strategy")
if (self.edPluginIndexing is not None):
EDVerbose.DEBUG(
"EDPluginControlCharacterisationv2_0.preProcess: " +
self.strPluginIndexingName + " Found... setting Data Input")
# create Data Input for indexing
xsDataInputStrategy = self.getDataInput(
"mxv1InputCharacterisation")[0]
xsDataCollection = xsDataInputStrategy.getDataCollection()
#xsDataSample = xsDataCollection.getSample()
xsDataSubWedgeList = xsDataCollection.getSubWedge()
xsDataExperimentalCondition = xsDataSubWedgeList[
0].getExperimentalCondition()
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.setDataCollection(xsDataCollection)
xsDataIndexingInput.setExperimentalCondition(
xsDataExperimentalCondition)
xsDataDiffractionPlan = xsDataCollection.getDiffractionPlan()
xsDataStringForcedSpaceGroup = xsDataDiffractionPlan.getForcedSpaceGroup(
)
if (xsDataStringForcedSpaceGroup is not None):
xsDataCrystal = XSDataCrystal()
xsDataSpaceGroup = XSDataSpaceGroup()
xsDataSpaceGroup.setName(xsDataStringForcedSpaceGroup)
xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
xsDataIndexingInput.setCrystal(xsDataCrystal)
self.edPluginIndexing.setDataInput(xsDataIndexingInput)
# Populate characterisation object
self.xsDataResultCharacterisationv2_0 = XSDataResultCharacterisationv2_0(
)
self.xsDataResultCharacterisation = XSDataResultCharacterisation()
self.xsDataResultCharacterisationv2_0.setMxv1ResultCharacterisation(
self.xsDataResultCharacterisation)
self.xsDataResultCharacterisation.setDataCollection(
XSDataCollection.parseString(xsDataCollection.marshal()))
def process(self, _edObject=None):
EDPluginControl.process(self, _edObject)
EDVerbose.DEBUG("EDPluginControlCharacterisationv2_0.process")
self.connectProcess(self.edPluginIndexing.executeSynchronous)
self.edPluginIndexing.connectSUCCESS(
self.doIndexingToIntegrationTransition)
self.edPluginIndexing.connectFAILURE(self.doFailureActionIndexing)
self.edPluginIntegration.connectSUCCESS(
self.doIntegrationToStrategyTransition)
self.edPluginIntegration.connectFAILURE(
self.doFailureActionIntegration)
self.edPluginStrategy.connectFAILURE(self.doFailureActionStrategy)
self.edPluginStrategy.connectSUCCESS(self.doSuccessActionStrategy)
def postProcess(self, _edObject=None):
"""
"""
EDPluginControl.postProcess(self, _edObject)
EDVerbose.DEBUG("EDPluginControlCharacterisationv2_0.postProcess")
if (self.xsDataResultCharacterisationv2_0 is not None):
self.setDataOutput(self.xsDataResultCharacterisationv2_0)
def doIndexingToIntegrationTransition(self, _edPlugin=None):
EDVerbose.DEBUG(
"EDPluginControlCharacterisationv2_0.doIndexingToIntegrationTransition"
)
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlCharacterisationv2_0.doIntegrationToStrategyTransition"
)
xsDataIndexingResult = self.edPluginIndexing.getDataOutput()
self.xsDataResultCharacterisation.setIndexingResult(
xsDataIndexingResult)
from XSDataMXv1 import XSDataIntegrationInput
xsDataIntegrationInput = XSDataIntegrationInput()
xsDataIntegrationInput.setDataCollection(
self.xsDataResultCharacterisation.getDataCollection())
xsDataIntegrationInput.setExperimentalConditionRefined(
xsDataIndexingResult.getSelectedSolution(
).getExperimentalConditionRefined())
xsDataIntegrationInput.setSelectedIndexingSolution(
xsDataIndexingResult.getSelectedSolution())
self.edPluginIntegration.setDataInput(xsDataIntegrationInput)
self.edPluginIntegration.executeSynchronous()
def doIntegrationToStrategyTransition(self, _edPlugin=None):
EDVerbose.DEBUG(
"EDPluginControlCharacterisationv2_0.doIntegrationToStrategyTransition"
)
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlCharacterisationv2_0.doIntegrationToStrategyTransition"
)
xsDataIntegrationOutput = self.edPluginIntegration.getDataOutput()
self.xsDataResultCharacterisation.setIntegrationResult(
xsDataIntegrationOutput)
#EDVerbose.DEBUG( self.xsDataExperimentCharacterisation.marshal() )
from XSDataMXv1 import XSDataInputStrategy
xsDataInputStrategyOLD = XSDataInputStrategy()
xsDataSolutionSelected = self.xsDataResultCharacterisation.getIndexingResult(
).getSelectedSolution()
xsDataInputStrategyOLD.setCrystalRefined(
xsDataSolutionSelected.getCrystal())
xsDataInputStrategyOLD.setSample(
self.xsDataResultCharacterisation.getDataCollection().getSample())
xsDataIntegrationSubWedgeResultList = xsDataIntegrationOutput.getIntegrationSubWedgeResult(
)
xsDataInputStrategyOLD.setBestFileContentDat(
xsDataIntegrationSubWedgeResultList[0].getBestfileDat())
xsDataInputStrategyOLD.setBestFileContentPar(
xsDataIntegrationSubWedgeResultList[0].getBestfilePar())
xsDataInputStrategyOLD.setExperimentalCondition(
xsDataIntegrationSubWedgeResultList[0].
getExperimentalConditionRefined())
for xsDataIntegrationSubWedgeResult in xsDataIntegrationSubWedgeResultList:
xsDataInputStrategyOLD.addBestFileContentHKL(
xsDataIntegrationSubWedgeResult.getBestfileHKL())
xsDataInputStrategyOLD.setDiffractionPlan(
self.xsDataResultCharacterisation.getDataCollection(
).getDiffractionPlan())
xsDataInputStrategyOLD.setXdsBackgroundImage(
self.xsDataResultCharacterisation.getXdsBackgroundImage())
#print xsDataInputStrategy.marshal()
self.edPluginStrategy.setDataInput(xsDataInputStrategyOLD,
"mxv1InputStrategy")
if self.hasDataInput("mxv2DataCollection"):
self.edPluginStrategy.setDataInput(
self.getDataInput("mxv2DataCollection")[0],
"mxv2DataCollection")
self.edPluginStrategy.setDataInput(
self.xsDataResultCharacterisation.getIndexingResult(),
"mxv1IndexingResult")
# xsDataInputStrategy= EDList()
# xsDataInputStrategy.add(xsDataInputStrategyOLD)
# xsDataInputStrategy.add(self.getDataInput()[1])
# xsDataInputStrategy.add(self.xsDataResultCharacterisationv2_0.getIndexingResult())
# self.edPluginStrategy.setDataInput( xsDataInputStrategy )
self.edPluginStrategy.executeSynchronous()
def doFailureActionIndexing(self, _edPlugin=None):
EDVerbose.DEBUG(
"EDPluginControlCharacterisationv2_0.doFailureActionIndexing")
self.retrieveFailureMessages(
_edPlugin,
"EDPluginControlCharacterisationv2_0.doFailureActionIndexing")
def doFailureActionIntegration(self, _edPlugin=None):
EDVerbose.DEBUG(
"EDPluginControlCharacterisationv2_0.doFailureActionIntegration")
self.retrieveFailureMessages(
_edPlugin,
"EDPluginControlCharacterisationv2_0.doFailureActionIntegration")
def doFailureActionStrategy(self, _edPlugin=None):
EDVerbose.DEBUG(
"EDPluginControlCharacterisationv2_0.doFailureActionStrategy")
self.retrieveFailureMessages(
_edPlugin,
"EDPluginControlCharacterisationv2_0.doFailureActionStrategy")
def doSuccessActionStrategy(self, _edPlugin):
"""
retrieve the potential warning messages
"""
EDVerbose.DEBUG(
"EDPluginControlCharacterisationv2_0.doSuccessActionStrategy")
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlCharacterisationv2_0.doSuccessActionStrategy")
xsDataResultStrategy = self.edPluginStrategy.getDataOutput()
self.xsDataResultCharacterisation.setStrategyResult(
xsDataResultStrategy)
def configure(self):
EDPluginControl.configure(self)
EDVerbose.DEBUG("EDPluginControlCharacterisationv2_0.configure")
pluginConfiguration = self.getConfiguration()
if (pluginConfiguration != None):
strPointlessOn = EDConfiguration.getStringParamValue(
pluginConfiguration, "POINTLESS")
if (strPointlessOn == None or strPointlessOn != "True"):
self.strPluginIntegrationName = "EDPluginControlIntegrationv10"
else:
self.strPluginIntegrationName = "EDPluginControlIntegrationPointlessv10"
def generateExecutiveSummary(self, _edPlugin):
"""
Generates a summary of the execution of the plugin.
"""
EDVerbose.DEBUG(
"EDPluginControlCharacterisationv2_0.generateExecutiveSummary")
self.addExecutiveSummaryLine("Summary of characterisation:")
self.addErrorWarningMessagesToExecutiveSummary(
"Characterisation failure! Error messages: ")
self.addExecutiveSummarySeparator()
xsDataInputStrategy = self.getDataInput("mxv1InputCharacterisation")[0]
xsDataCollection = xsDataInputStrategy.getDataCollection()
xsDataDiffractionPlan = xsDataCollection.getDiffractionPlan()
self.addExecutiveSummaryLine("Diffraction plan:")
if (xsDataDiffractionPlan.getComplexity() is not None):
self.addExecutiveSummaryLine(
"BEST complexity : %s" %
xsDataDiffractionPlan.getComplexity().getValue())
if (xsDataDiffractionPlan.getAimedCompleteness() is not None):
self.addExecutiveSummaryLine(
"Aimed completeness : %6.1f [%%]" %
(100.0 *
xsDataDiffractionPlan.getAimedCompleteness().getValue()))
if (xsDataDiffractionPlan.getRequiredCompleteness() is not None):
self.addExecutiveSummaryLine(
"Required completeness : %6.1f [%%]" %
(100.0 *
xsDataDiffractionPlan.getRequiredCompleteness().getValue()))
if (xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution()
is not None):
self.addExecutiveSummaryLine(
"Aimed I/sigma at highest resolution : %6.1f" %
xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution(
).getValue())
if (xsDataDiffractionPlan.getAimedResolution() is not None):
self.addExecutiveSummaryLine(
"Aimed resolution : %6.1f [A]" %
xsDataDiffractionPlan.getAimedResolution().getValue())
if (xsDataDiffractionPlan.getRequiredResolution() is not None):
self.addExecutiveSummaryLine(
"Required resolution : %6.1f [A]" %
xsDataDiffractionPlan.getRequiredResolution().getValue())
if (xsDataDiffractionPlan.getAimedMultiplicity() is not None):
self.addExecutiveSummaryLine(
"Aimed multiplicity : %6.1f" %
xsDataDiffractionPlan.getAimedMultiplicity().getValue())
if (xsDataDiffractionPlan.getRequiredMultiplicity() is not None):
self.addExecutiveSummaryLine(
"Required multiplicity : %6.1f" %
xsDataDiffractionPlan.getRequiredMultiplicity().getValue())
if (xsDataDiffractionPlan.getForcedSpaceGroup() is not None):
self.addExecutiveSummaryLine(
"Forced space group : %6s" %
xsDataDiffractionPlan.getForcedSpaceGroup().getValue())
if (xsDataDiffractionPlan.getMaxExposureTimePerDataCollection()
is not None):
self.addExecutiveSummaryLine(
"Max exposure time per data collection : %6.1f [s]" %
xsDataDiffractionPlan.getMaxExposureTimePerDataCollection(
).getValue())
self.addExecutiveSummarySeparator()
if (self.edPluginIndexing is not None):
self.appendExecutiveSummary(self.edPluginIndexing, "Indexing : ")
if (self.edPluginIntegration is not None):
self.appendExecutiveSummary(self.edPluginIntegration,
"Integration : ")
if (self.edPluginStrategy is not None):
self.appendExecutiveSummary(self.edPluginStrategy, "Strategy : ")
class EDPluginControlCharacterisationv1_1(EDPluginControl):
"""
The Plugin that controls the whole characterisation.
"""
def __init__ (self):
"""
"""
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputCharacterisation)
self.__strPluginIndexingName = "EDPluginControlIndexingv10"
self.__edPluginIndexing = None
self.__strPluginIntegrationName = "EDPluginControlIntegrationv10"
self.__edPluginIntegration = None
self.__strPluginStrategyName = "EDPluginControlStrategyv1_1"
self.__edPluginStrategy = None
self.__xsDataResultCharacterisation = None
self.__strPluginKappaStrategyName = "EDPluginControlKappaStrategyv1_1"
self.__strPluginIntegrationPointlessName = "EDPluginControlIntegrationPointlessv10"
def checkParameters(self):
"""
Checks the mandatory parameters
"""
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_1.checkParameters")
self.checkMandatoryParameters(self.getDataInput(), "Data Input is None")
self.checkMandatoryParameters(self.getDataInput().getDataCollection(), "dataCollection")
self.checkMandatoryParameters(self.getDataInput().getDataCollection().getDiffractionPlan(), "diffractionPlan")
def configure(self):
"""
Gets the configuration parameters (if any).
"""
EDPluginControl.configure(self)
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_1.configure")
pluginConfiguration = self.getConfiguration()
if(pluginConfiguration is None):
EDVerbose.DEBUG("No plugin configuration found for EDPluginControlCharacterisationv1_1.")
else:
if (self.getControlledPluginName("indexingPlugin") is not None):
self.__strPluginIndexingName = self.getControlledPluginName("indexingPlugin")
if (self.getControlledPluginName("integrationPlugin") is not None):
self.__strPluginIntegrationName = self.getControlledPluginName("integrationPlugin")
if (self.getControlledPluginName("strategyPlugin") is not None):
self.__strPluginStrategyName = self.getControlledPluginName("strategyPlugin")
if (self.getControlledPluginName("kappaStrategyPlugin") is not None):
self.__strPluginKappaStrategyName = self.getControlledPluginName("kappaStrategyPlugin")
if (self.getControlledPluginName("integrationPointlessPlugin") is not None):
self.__strPluginIntegrationPoitlessName = self.getControlledPluginName("integrationPointlessPlugin")
pyStrKappa = EDConfiguration.getStringParamValue(pluginConfiguration, "KAPPA")
if(pyStrKappa == "ON"):
self.__strPluginStrategyName = self.__strPluginKappaStrategyName
pyStrPointless = EDConfiguration.getStringParamValue(pluginConfiguration, "POINTLESS")
if(pyStrPointless == "ON"):
self.__strPluginIntegrationName = self.__strPluginIntegrationPointlessName
def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_1.preProcess...")
self.__edPluginIndexing = self.loadPlugin(self.__strPluginIndexingName , "Indexing")
self.__edPluginIntegration = self.loadPlugin(self.__strPluginIntegrationName, "Integration")
self.__edPluginStrategy = self.loadPlugin(self.__strPluginStrategyName , "Strategy")
if (self.__edPluginIndexing is not None):
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_1.preProcess: " + self.__strPluginIndexingName + " Found... setting Data Input")
# create Data Input for indexing
xsDataInputStrategy = self.getDataInput()
xsDataCollection = xsDataInputStrategy.getDataCollection()
xsDataSample = xsDataCollection.getSample()
xsDataSubWedgeList = xsDataCollection.getSubWedge()
if ((xsDataSubWedgeList is None) or (xsDataSubWedgeList == [])):
strError = "EDPluginControlCharacterisationv1_1.preProcess: No subwedges in input data."
EDVerbose.ERROR(strError)
self.setFailure()
else:
xsDataExperimentalCondition = xsDataSubWedgeList[0].getExperimentalCondition()
# Fix for bug 431: if the flux is zero raise an error
xsDataDoubleFlux = xsDataExperimentalCondition.getBeam().getFlux()
if (xsDataDoubleFlux is not None):
if (xsDataDoubleFlux.getValue() < 0.1):
pyStrErrorMessage = "EDPluginControlCharacterisationv1_1.preProcess ERROR: Input flux is negative or close to zero. Execution of characterisation aborted."
EDVerbose.ERROR(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
self.setFailure()
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.setDataCollection(xsDataCollection)
xsDataIndexingInput.setExperimentalCondition(xsDataExperimentalCondition)
xsDataDiffractionPlan = xsDataCollection.getDiffractionPlan()
xsDataStringForcedSpaceGroup = xsDataDiffractionPlan.getForcedSpaceGroup()
if (xsDataStringForcedSpaceGroup is not None):
xsDataCrystal = XSDataCrystal()
xsDataSpaceGroup = XSDataSpaceGroup()
xsDataSpaceGroup.setName(xsDataStringForcedSpaceGroup)
xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
xsDataIndexingInput.setCrystal(xsDataCrystal)
self.__edPluginIndexing.setDataInput(xsDataIndexingInput)
# Populate characterisation object
self.__xsDataResultCharacterisation = XSDataResultCharacterisation()
self.__xsDataResultCharacterisation.setDataCollection(XSDataCollection.parseString(xsDataCollection.marshal()))
def process(self, _edObject=None):
EDPluginControl.process(self, _edObject)
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_1.process")
self.connectProcess(self.__edPluginIndexing.executeSynchronous)
self.__edPluginIndexing.connectSUCCESS(self.doIndexingToIntegrationTransition)
self.__edPluginIndexing.connectFAILURE(self.doFailureActionIndexing)
self.__edPluginIntegration.connectSUCCESS(self.doIntegrationToStrategyTransition)
self.__edPluginIntegration.connectFAILURE(self.doFailureActionIntegration)
self.__edPluginStrategy.connectFAILURE(self.doFailureActionStrategy)
self.__edPluginStrategy.connectSUCCESS(self.doSuccessActionStrategy)
def postProcess(self, _edObject=None):
EDPluginControl.postProcess(self, _edObject)
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_1.postProcess")
if (self.__xsDataResultCharacterisation is not None):
self.setDataOutput(self.__xsDataResultCharacterisation)
def doIndexingToIntegrationTransition(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_1.doIndexingToIntegrationTransition")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv1_1.doIntegrationToStrategyTransition")
xsDataIndexingResult = self.__edPluginIndexing.getDataOutput()
self.__xsDataResultCharacterisation.setIndexingResult(xsDataIndexingResult)
xsDataIntegrationInput = XSDataIntegrationInput()
xsDataIntegrationInput.setDataCollection(self.__xsDataResultCharacterisation.getDataCollection())
xsDataIntegrationInput.setExperimentalConditionRefined(xsDataIndexingResult.getSelectedSolution().getExperimentalConditionRefined())
xsDataIntegrationInput.setSelectedIndexingSolution(xsDataIndexingResult.getSelectedSolution())
self.__edPluginIntegration.setDataInput(xsDataIntegrationInput)
self.__edPluginIntegration.executeSynchronous()
def doIntegrationToStrategyTransition(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_1.doIntegrationToStrategyTransition")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv1_1.doIntegrationToStrategyTransition")
xsDataIntegrationOutput = self.__edPluginIntegration.getDataOutput()
self.__xsDataResultCharacterisation.setIntegrationResult(xsDataIntegrationOutput)
#EDVerbose.DEBUG( self.__xsDataExperimentCharacterisation.marshal() )
xsDataInputStrategy = XSDataInputStrategy()
xsDataSolutionSelected = self.__xsDataResultCharacterisation.getIndexingResult().getSelectedSolution()
xsDataInputStrategy.setCrystalRefined(xsDataSolutionSelected.getCrystal())
xsDataInputStrategy.setSample(self.__xsDataResultCharacterisation.getDataCollection().getSample())
xsDataIntegrationSubWedgeResultList = xsDataIntegrationOutput.getIntegrationSubWedgeResult()
xsDataInputStrategy.setBestFileContentDat(xsDataIntegrationSubWedgeResultList[0].getBestfileDat())
xsDataInputStrategy.setBestFileContentPar(xsDataIntegrationSubWedgeResultList[0].getBestfilePar())
xsDataInputStrategy.setExperimentalCondition(xsDataIntegrationSubWedgeResultList[0].getExperimentalConditionRefined())
for xsDataIntegrationSubWedgeResult in xsDataIntegrationSubWedgeResultList:
xsDataInputStrategy.addBestFileContentHKL(xsDataIntegrationSubWedgeResult.getBestfileHKL())
xsDataInputStrategy.setDiffractionPlan(self.__xsDataResultCharacterisation.getDataCollection().getDiffractionPlan())
#print xsDataInputStrategy.marshal()
self.__edPluginStrategy.setDataInput(xsDataInputStrategy)
self.__edPluginStrategy.executeSynchronous()
def doFailureActionIndexing(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_1.doFailureActionIndexing")
self.retrieveFailureMessages(_edPlugin, "EDPluginControlCharacterisationv1_1.doFailureActionIndexing")
# If indexing fails all processing should stop
self.generateExecutiveSummary(self)
self.setFailure()
def doFailureActionIntegration(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_1.doFailureActionIntegration")
self.retrieveFailureMessages(_edPlugin, "EDPluginControlCharacterisationv1_1.doFailureActionIntegration")
def doFailureActionStrategy(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_1.doFailureActionStrategy")
self.retrieveFailureMessages(_edPlugin, "EDPluginControlCharacterisationv1_1.doFailureActionStrategy")
def doSuccessActionStrategy(self, _edPlugin):
"""
retrieve the potential warning messages
"""
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_1.doSuccessActionStrategy")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv1_1.doSuccessActionStrategy")
xsDataResultStrategy = self.__edPluginStrategy.getDataOutput()
self.__xsDataResultCharacterisation.setStrategyResult(xsDataResultStrategy)
def generateExecutiveSummary(self, _edPlugin):
"""
Generates a summary of the execution of the plugin.
"""
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_1.generateExecutiveSummary")
self.addExecutiveSummaryLine("Summary of characterisation:")
self.addErrorWarningMessagesToExecutiveSummary("Characterisation failure! Error messages: ")
self.addExecutiveSummarySeparator()
xsDataInputStrategy = self.getDataInput()
xsDataCollection = xsDataInputStrategy.getDataCollection()
xsDataDiffractionPlan = xsDataCollection.getDiffractionPlan()
self.addExecutiveSummaryLine("Diffraction plan:")
if (xsDataDiffractionPlan.getComplexity() is not None):
self.addExecutiveSummaryLine("BEST complexity : %s" % xsDataDiffractionPlan.getComplexity().getValue())
if (xsDataDiffractionPlan.getAimedCompleteness() is not None):
self.addExecutiveSummaryLine("Aimed completeness : %6.1f [%%]" % (100.0 * xsDataDiffractionPlan.getAimedCompleteness().getValue()))
if (xsDataDiffractionPlan.getRequiredCompleteness() is not None):
self.addExecutiveSummaryLine("Required completeness : %6.1f [%%]" % (100.0 * xsDataDiffractionPlan.getRequiredCompleteness().getValue()))
if (xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution() is not None):
self.addExecutiveSummaryLine("Aimed I/sigma at highest resolution : %6.1f" % xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution().getValue())
if (xsDataDiffractionPlan.getAimedResolution() is not None):
self.addExecutiveSummaryLine("Aimed resolution : %6.1f [A]" % xsDataDiffractionPlan.getAimedResolution().getValue())
if (xsDataDiffractionPlan.getRequiredResolution() is not None):
self.addExecutiveSummaryLine("Required resolution : %6.1f [A]" % xsDataDiffractionPlan.getRequiredResolution().getValue())
if (xsDataDiffractionPlan.getAimedMultiplicity() is not None):
self.addExecutiveSummaryLine("Aimed multiplicity : %6.1f" % xsDataDiffractionPlan.getAimedMultiplicity().getValue())
if (xsDataDiffractionPlan.getRequiredMultiplicity() is not None):
self.addExecutiveSummaryLine("Required multiplicity : %6.1f" % xsDataDiffractionPlan.getRequiredMultiplicity().getValue())
if (xsDataDiffractionPlan.getForcedSpaceGroup() is not None):
self.addExecutiveSummaryLine("Forced space group : %6s" % xsDataDiffractionPlan.getForcedSpaceGroup().getValue())
if (xsDataDiffractionPlan.getMaxExposureTimePerDataCollection() is not None):
self.addExecutiveSummaryLine("Max exposure time per data collection : %6.1f [s]" % xsDataDiffractionPlan.getMaxExposureTimePerDataCollection().getValue())
self.addExecutiveSummarySeparator()
if (self.__edPluginIndexing is not None):
self.appendExecutiveSummary(self.__edPluginIndexing, "Indexing : ")
if (self.__edPluginIntegration is not None):
self.appendExecutiveSummary(self.__edPluginIntegration, "Integration : ")
if (self.__edPluginStrategy is not None):
self.appendExecutiveSummary(self.__edPluginStrategy, "Strategy : ")
def getPluginStrategyName(self):
return self.__strPluginStrategyName
class EDPluginControlCharacterisationv1_3(EDPluginControl):
"""
[To be replaced with a description of EDPluginControlTemplatev10]
"""
def __init__(self):
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputCharacterisation)
self._strPluginControlIndexingIndicators = "EDPluginControlIndexingIndicatorsv10"
self._strPluginControlIndexingLabelit = "EDPluginControlIndexingLabelitv10"
self._strPluginExecEvaluationIndexing = "EDPluginExecEvaluationIndexingv10"
self._strPluginControlGeneratePrediction = "EDPluginControlGeneratePredictionv10"
self._strPluginControlIntegration = "EDPluginControlIntegrationv10"
self._strPluginControlXDSGenerateBackgroundImage = "EDPluginControlXDSGenerateBackgroundImagev1_0"
self._strPluginControlStrategy = "EDPluginControlStrategyv1_2"
self._edPluginControlIndexingIndicators = None
self._edPluginControlIndexingLabelit = None
self._edPluginExecEvaluationIndexingMOSFLM = None
self._edPluginExecEvaluationIndexingLABELIT = None
self._edPluginControlGeneratePrediction = None
self._edPluginControlIntegration = None
self._edPluginControlXDSGenerateBackgroundImage = None
self._edPluginControlStrategy = None
self._xsDataCollection = None
self._xsDataResultCharacterisation = None
self._xsDataIndexingResultMOSFLM = None
self._xsDataCrystal = None
self._strCharacterisationShortSummary = ""
self._strStatusMessage = ""
self._xsDataFileXdsBackgroundImage = None
self._bDoStrategyCalculation = True
def checkParameters(self):
"""
Checks the mandatory parameters.
"""
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_3.checkParameters")
self.checkMandatoryParameters(self.getDataInput(),
"Data Input is None")
self.checkMandatoryParameters(self.getDataInput().getDataCollection(),
"dataCollection")
self.checkMandatoryParameters(
self.getDataInput().getDataCollection().getDiffractionPlan(),
"diffractionPlan")
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_3.preProcess")
# Load the plugins
self._edPluginControlIndexingIndicators = self.loadPlugin(self._strPluginControlIndexingIndicators, \
"Indexing")
self._edPluginControlIndexingLabelit = self.loadPlugin(self._strPluginControlIndexingLabelit, \
"IndexingLabelit")
self._edPluginExecEvaluationIndexingMOSFLM = self.loadPlugin(self._strPluginExecEvaluationIndexing, \
"IndexingEvalualtionMOSFLM")
self._edPluginExecEvaluationIndexingLABELIT = self.loadPlugin(self._strPluginExecEvaluationIndexing, \
"IndexingEvalualtionLABELIT")
self._edPluginControlGeneratePrediction = self.loadPlugin(self._strPluginControlGeneratePrediction, \
"GeneratePrediction")
self._edPluginControlIntegration = self.loadPlugin(self._strPluginControlIntegration, \
"Integration")
self._edPluginControlXDSGenerateBackgroundImage = self.loadPlugin(self._strPluginControlXDSGenerateBackgroundImage, \
"ControlXDSGenerateBackgroundImage")
self._edPluginControlStrategy = self.loadPlugin(self._strPluginControlStrategy, \
"Strategy")
if (self._edPluginControlIndexingIndicators is not None):
EDVerbose.DEBUG(
"EDPluginControlCharacterisationv1_3.preProcess: " +
self._strPluginControlIndexingIndicators +
" Found... setting Data Input")
# create Data Input for indexing
xsDataInputCharacterisation = self.getDataInput()
self._xsDataCollection = xsDataInputCharacterisation.getDataCollection(
)
xsDataCrystal = None
xsDataSubWedgeList = self._xsDataCollection.getSubWedge()
if ((xsDataSubWedgeList is None) or (xsDataSubWedgeList == [])):
strError = "EDPluginControlCharacterisationv1_3.preProcess: No subwedges in input data."
EDVerbose.ERROR(strError)
self.setFailure()
else:
xsDataExperimentalCondition = xsDataSubWedgeList[
0].getExperimentalCondition()
# Fix for bug 431: if the flux is zero raise an error
xsDataDoubleFlux = xsDataExperimentalCondition.getBeam(
).getFlux()
if (xsDataDoubleFlux is not None):
if (xsDataDoubleFlux.getValue() < 0.1):
strErrorMessage = "Input flux is negative or close to zero. Execution of characterisation aborted."
EDVerbose.ERROR(strErrorMessage)
self.addErrorMessage(
"EDPluginControlCharacterisationv1_3.preProcess ERROR: "
+ strErrorMessage)
#self.addComment(strErrorMessage)
self.setFailure()
xsDataDiffractionPlan = self._xsDataCollection.getDiffractionPlan(
)
xsDataStringForcedSpaceGroup = xsDataDiffractionPlan.getForcedSpaceGroup(
)
if (xsDataStringForcedSpaceGroup is not None):
self._xsDataCrystal = XSDataCrystal()
xsDataSpaceGroup = XSDataSpaceGroup()
xsDataSpaceGroup.setName(xsDataStringForcedSpaceGroup)
self._xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
self._edPluginControlIndexingIndicators.setDataInput(
self._xsDataCollection, "dataCollection")
if self._xsDataCrystal is not None:
self._edPluginControlIndexingIndicators.setDataInput(
self._xsDataCrystal, "crystal")
# Populate characterisation object
self._xsDataResultCharacterisation = XSDataResultCharacterisation(
)
self._xsDataResultCharacterisation.setDataCollection(
XSDataCollection.parseString(
self._xsDataCollection.marshal()))
def process(self, _edObject=None):
EDPluginControl.process(self)
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_3.process")
self._edPluginControlIndexingIndicators.connectSUCCESS(
self.doSuccessIndexingIndicators)
self._edPluginControlIndexingIndicators.connectFAILURE(
self.doFailureIndexingIndicators)
self._edPluginControlIndexingLabelit.connectSUCCESS(
self.doSuccessIndexingLabelit)
self._edPluginControlIndexingLabelit.connectFAILURE(
self.doFailureIndexingLabelit)
self._edPluginExecEvaluationIndexingMOSFLM.connectSUCCESS(
self.doSuccessEvaluationIndexingMOSFLM)
self._edPluginExecEvaluationIndexingMOSFLM.connectFAILURE(
self.doFailureEvaluationIndexingMOSFLM)
self._edPluginExecEvaluationIndexingLABELIT.connectSUCCESS(
self.doSuccessEvaluationIndexingLABELIT)
self._edPluginExecEvaluationIndexingLABELIT.connectFAILURE(
self.doFailureEvaluationIndexingLABELIT)
self._edPluginControlGeneratePrediction.connectSUCCESS(
self.doSuccessGeneratePrediction)
self._edPluginControlGeneratePrediction.connectFAILURE(
self.doFailureGeneratePrediction)
self._edPluginControlIntegration.connectSUCCESS(
self.doSuccessIntegration)
self._edPluginControlIntegration.connectFAILURE(
self.doFailureIntegration)
self._edPluginControlXDSGenerateBackgroundImage.connectSUCCESS(
self.doSuccessXDSGenerateBackgroundImage)
self._edPluginControlXDSGenerateBackgroundImage.connectFAILURE(
self.doFailureXDSGenerateBackgroundImage)
self._edPluginControlStrategy.connectSUCCESS(self.doSuccessStrategy)
self._edPluginControlStrategy.connectFAILURE(self.doFailureStrategy)
self.executePluginSynchronous(self._edPluginControlIndexingIndicators)
def finallyProcess(self, _edObject=None):
EDPluginControl.finallyProcess(self)
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_3.finallyProcess")
if self._edPluginControlGeneratePrediction.isRunning():
self._edPluginControlGeneratePrediction.synchronize()
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage),
"statusMessage")
self._xsDataResultCharacterisation.setStatusMessage(
XSDataString(self._strStatusMessage))
if self._strCharacterisationShortSummary != None:
self.setDataOutput(
XSDataString(self._strCharacterisationShortSummary),
"shortSummary")
self._xsDataResultCharacterisation.setShortSummary(
XSDataString(self._strCharacterisationShortSummary))
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
def doSuccessIndexingIndicators(self, _edPlugin=None):
EDVerbose.DEBUG(
"EDPluginControlCharacterisationv1_3.doSuccessIndexingIndicators")
#self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv1_3.doSuccessIndexingIndicators")
if self._edPluginControlIndexingIndicators.hasDataOutput(
"indexingResult"):
xsDataIndexingResult = self._edPluginControlIndexingIndicators.getDataOutput(
"indexingResult")[0]
#self._xsDataResultCharacterisation.setIndexingResult(xsDataIndexingResult)
self._edPluginExecEvaluationIndexingMOSFLM.setDataInput(
xsDataIndexingResult, "indexingResult")
if self._edPluginControlIndexingIndicators.hasDataOutput(
"imageQualityIndicators"):
listXSDataImageQualityIndicators = self._edPluginControlIndexingIndicators.getDataOutput(
"imageQualityIndicators")
for xsDataImageQualityIndicators in listXSDataImageQualityIndicators:
self._xsDataResultCharacterisation.addImageQualityIndicators(
xsDataImageQualityIndicators)
self._edPluginExecEvaluationIndexingMOSFLM.setDataInput(
xsDataImageQualityIndicators, "imageQualityIndicators")
if self._edPluginControlIndexingIndicators.hasDataOutput(
"indicatorsShortSummary"):
self._strCharacterisationShortSummary += self._edPluginControlIndexingIndicators.getDataOutput(
"indicatorsShortSummary")[0].getValue()
self.executePluginSynchronous(
self._edPluginExecEvaluationIndexingMOSFLM)
def doFailureIndexingIndicators(self, _edPlugin=None):
EDVerbose.DEBUG(
"EDPluginControlCharacterisationv1_3.doFailureIndexingIndicators")
strErrorMessage = "Execution of Indexing and Indicators plugin failed. Execution of characterisation aborted."
EDVerbose.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
self.setFailure()
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage),
"statusMessage")
self.writeDataOutput()
# def doSuccessIndexingLabelit(self, _edPlugin=None):
# EDVerbose.DEBUG("EDPluginControlCharacterisationv1_3.doSuccessIndexingLabelit")
# self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv1_3.doSuccessIndexingLabelit")
# # Retrieve the indexing result
# xsDataIndexingResult = self._edPluginControlIndexingLabelit.getDataOutput()
# self._xsDataResultCharacterisation.setIndexingResult(xsDataIndexingResult)
# if self._edPluginControlIndexingLabelit.hasDataOutput("indexingShortSummary"):
# self._strCharacterisationShortSummary += self._edPluginControlIndexingLabelit.getDataOutput("indexingShortSummary")[0].getValue()
# # Then start the integration of the reference images
# self.indexingToIntegration()
def doSuccessIndexingLabelit(self, _edPlugin=None):
EDVerbose.DEBUG(
"EDPluginControlCharacterisationv1_3.doSuccessIndexingLabelit")
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlCharacterisationv1_3.doSuccessIndexingLabelit")
if self._edPluginControlIndexingLabelit.hasDataOutput(
"indexingShortSummary"):
self._strCharacterisationShortSummary += self._edPluginControlIndexingLabelit.getDataOutput(
"indexingShortSummary")[0].getValue()
# Check the indexing results
xsDataIndexingResult = self._edPluginControlIndexingLabelit.getDataOutput(
)
self._edPluginExecEvaluationIndexingLABELIT.setDataInput(
xsDataIndexingResult, "indexingResult")
xsDataImageQualityIndicators = self._xsDataResultCharacterisation.getImageQualityIndicators(
)[0]
self._edPluginExecEvaluationIndexingLABELIT.setDataInput(
xsDataImageQualityIndicators, "imageQualityIndicators")
self.executePluginSynchronous(
self._edPluginExecEvaluationIndexingLABELIT)
def doFailureIndexingLabelit(self, _edPlugin=None):
EDVerbose.DEBUG(
"EDPluginControlCharacterisationv1_3.doFailureIndexingLabelit")
self.addStatusMessage("Labelit: Indexing FAILURE.")
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
if self._xsDataIndexingResultMOSFLM == None:
strErrorMessage = "Execution of indexing with both MOSFLM and Labelit failed. Execution of characterisation aborted."
EDVerbose.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.generateExecutiveSummary(self)
self.setFailure()
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage),
"statusMessage")
self.writeDataOutput()
else:
# Use the MOSFLM indexing results - even if it's P1
self._xsDataResultCharacterisation.setIndexingResult(
self._xsDataIndexingResultMOSFLM)
xsDataCollection = self._xsDataResultCharacterisation.getDataCollection(
)
xsDataGeneratePredictionInput = XSDataGeneratePredictionInput()
xsDataGeneratePredictionInput.setDataCollection(
XSDataCollection.parseString(xsDataCollection.marshal()))
xsDataGeneratePredictionInput.setSelectedIndexingSolution(
XSDataIndexingSolutionSelected.parseString(
self._xsDataIndexingResultMOSFLM.getSelectedSolution(
).marshal()))
self._edPluginControlGeneratePrediction.setDataInput(
xsDataGeneratePredictionInput)
if self._edPluginControlIndexingIndicators.hasDataOutput(
"indexingShortSummary"):
self._strCharacterisationShortSummary += self._edPluginControlIndexingIndicators.getDataOutput(
"indexingShortSummary")[0].getValue()
# Start the generation of prediction images - we synchronize in the post-process
self._edPluginControlGeneratePrediction.execute()
# Then start the integration of the reference images
self.indexingToIntegration()
def doSuccessEvaluationIndexingMOSFLM(self, _edPlugin=None):
EDVerbose.DEBUG(
"EDPluginControlCharacterisationv1_3.doSuccessEvaluationIndexingMOSFLM"
)
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlCharacterisationv1_3.doSuccessEvaluationIndexing")
# Retrieve status messages (if any)
if self._edPluginExecEvaluationIndexingMOSFLM.hasDataOutput(
"statusMessageImageQualityIndicators"):
self.addStatusMessage(
self._edPluginExecEvaluationIndexingMOSFLM.getDataOutput(
"statusMessageImageQualityIndicators")[0].getValue())
if self._edPluginExecEvaluationIndexingMOSFLM.hasDataOutput(
"statusMessageIndexing"):
self.addStatusMessage(
"MOSFLM: " +
self._edPluginExecEvaluationIndexingMOSFLM.getDataOutput(
"statusMessageIndexing")[0].getValue())
# Check if indexing was successful
bIndexWithLabelit = False
bIndexingSuccess = self._edPluginExecEvaluationIndexingMOSFLM.getDataOutput(
"indexingSuccess")[0].getValue()
if bIndexingSuccess:
xsDataIndexingResult = self._edPluginExecEvaluationIndexingMOSFLM.getDataOutput(
"indexingResult")[0]
self._xsDataIndexingResultMOSFLM = xsDataIndexingResult
# Check if space group is P1 - if yes run Labelit indexing
xsDataIndexingSolutionSelected = xsDataIndexingResult.getSelectedSolution(
)
xsDataCrystal = xsDataIndexingSolutionSelected.getCrystal()
xsDataSpaceGroup = xsDataCrystal.getSpaceGroup()
strSpaceGroupName = xsDataSpaceGroup.getName().getValue().upper()
# Check if MOSFLM has indexed in P1
if strSpaceGroupName == "P1":
# Check if the user maybe asked for P1!
bIndexWithLabelit = True
if self._xsDataCollection.getDiffractionPlan() is not None:
if self._xsDataCollection.getDiffractionPlan(
).getForcedSpaceGroup() is not None:
if self._xsDataCollection.getDiffractionPlan(
).getForcedSpaceGroup().getValue().upper() == "P1":
EDVerbose.screen(
"P1 space forced by diffraction plan")
bIndexWithLabelit = False
if bIndexWithLabelit:
EDVerbose.screen(
"P1 space group choosed - reindexing with Labelit")
else:
EDVerbose.screen("MOSFLM indexing successful!")
if self._edPluginControlIndexingIndicators.hasDataOutput(
"indexingShortSummary"):
self._strCharacterisationShortSummary += self._edPluginControlIndexingIndicators.getDataOutput(
"indexingShortSummary")[0].getValue()
# Generate prediction images
xsDataCollection = self._xsDataResultCharacterisation.getDataCollection(
)
self._xsDataResultCharacterisation.setIndexingResult(
xsDataIndexingResult)
xsDataGeneratePredictionInput = XSDataGeneratePredictionInput()
xsDataGeneratePredictionInput.setDataCollection(
XSDataCollection.parseString(xsDataCollection.marshal()))
xsDataGeneratePredictionInput.setSelectedIndexingSolution(
XSDataIndexingSolutionSelected.parseString(
xsDataIndexingResult.getSelectedSolution().marshal()))
self._edPluginControlGeneratePrediction.setDataInput(
xsDataGeneratePredictionInput)
# Start the generation of prediction images - we synchronize in the post-process
self._edPluginControlGeneratePrediction.execute()
# Then start the integration of the reference images
self.indexingToIntegration()
else:
EDVerbose.screen("Indexing with MOSFLM failed!")
bIndexWithLabelit = True
if bIndexWithLabelit:
# Execute Labelit indexing
EDVerbose.screen(
"Now trying to index with Labelit - please be patient...")
xsDataIndexingInput = XSDataIndexingInput()
xsDataSubWedgeList = self._xsDataCollection.getSubWedge()
xsDataExperimentalCondition = xsDataSubWedgeList[
0].getExperimentalCondition()
xsDataIndexingInput.setDataCollection(self._xsDataCollection)
xsDataIndexingInput.setExperimentalCondition(
xsDataExperimentalCondition)
if self._xsDataCrystal != None:
xsDataIndexingInput.setCrystal(self._xsDataCrystal)
self._edPluginControlIndexingLabelit.setDataInput(
xsDataIndexingInput)
self.executePluginSynchronous(self._edPluginControlIndexingLabelit)
def doSuccessEvaluationIndexingLABELIT(self, _edPlugin=None):
EDVerbose.DEBUG(
"EDPluginControlCharacterisationv1_3.doSuccessEvaluationIndexingLABELIT"
)
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlCharacterisationv1_3.doSuccessEvaluationIndexingLABELIT"
)
# Retrieve status messages (if any)
if self._edPluginExecEvaluationIndexingLABELIT.hasDataOutput(
"statusMessageIndexing"):
self.addStatusMessage(
"Labelit: " +
self._edPluginExecEvaluationIndexingLABELIT.getDataOutput(
"statusMessageIndexing")[0].getValue())
# Check if indexing was successful
bIndexingSuccess = self._edPluginExecEvaluationIndexingLABELIT.getDataOutput(
"indexingSuccess")[0].getValue()
if bIndexingSuccess:
xsDataIndexingResult = self._edPluginExecEvaluationIndexingLABELIT.getDataOutput(
"indexingResult")[0]
self._xsDataResultCharacterisation.setIndexingResult(
xsDataIndexingResult)
# Then start the integration of the reference images
self.indexingToIntegration()
else:
EDVerbose.screen("Indexing with LABELIT failed!")
self.setFailure()
def indexingToIntegration(self, _edPlugin=None):
# Create the XDS background image
xsDataInputControlXDSGenerateBackgroundImage = XSDataInputControlXDSGenerateBackgroundImage(
)
xsDataInputControlXDSGenerateBackgroundImage.setDataCollection(
self._xsDataCollection)
self._edPluginControlXDSGenerateBackgroundImage.setDataInput(
xsDataInputControlXDSGenerateBackgroundImage)
self._edPluginControlXDSGenerateBackgroundImage.execute()
# Integrate the reference images
xsDataIntegrationInput = XSDataIntegrationInput()
xsDataIntegrationInput.setDataCollection(
self._xsDataResultCharacterisation.getDataCollection())
xsDataIndexingResult = self._xsDataResultCharacterisation.getIndexingResult(
)
xsDataExperimentalConditionRefinded = xsDataIndexingResult.getSelectedSolution(
).getExperimentalConditionRefined()
xsDataIntegrationInput.setExperimentalConditionRefined(
xsDataExperimentalConditionRefinded)
xsDataIntegrationInput.setSelectedIndexingSolution(
xsDataIndexingResult.getSelectedSolution())
self._edPluginControlIntegration.setDataInput(xsDataIntegrationInput)
self.executePluginSynchronous(self._edPluginControlIntegration)
def doFailureEvaluationIndexingMOSFLM(self, _edPlugin=None):
EDVerbose.DEBUG(
"EDPluginControlCharacterisationv1_3.doFailureEvaluationIndexing")
strWarningMessage = "Execution of indexing evaluation plugin failed."
EDVerbose.WARNING(strWarningMessage)
self.addWarningMessage(strWarningMessage)
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
def doFailureEvaluationIndexingLABELIT(self, _edPlugin=None):
EDVerbose.DEBUG(
"EDPluginControlCharacterisationv1_3.doFailureEvaluationIndexing")
strWarningMessage = "Execution of indexing evaluation plugin failed."
EDVerbose.WARNING(strWarningMessage)
self.addWarningMessage(strWarningMessage)
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
def doSuccessGeneratePrediction(self, _edPlugin=None):
EDVerbose.DEBUG(
"EDPluginControlCharacterisationv1_3.doSuccessGeneratePrediction")
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlCharacterisationv1_3.doSuccessGeneratePrediction")
xsDataGeneratePredictionResult = _edPlugin.getDataOutput()
xsDataIndexingResult = self._xsDataResultCharacterisation.getIndexingResult(
)
xsDataIndexingResult.setPredictionResult(
xsDataGeneratePredictionResult)
def doFailureGeneratePrediction(self, _edPlugin=None):
EDVerbose.DEBUG(
"EDPluginControlCharacterisationv1_3.doFailureGeneratePrediction")
strWarningMessage = "Execution of generate prediction plugin failed."
EDVerbose.WARNING(strWarningMessage)
self.addWarningMessage(strWarningMessage)
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
#self.addComment("warning: no prediction images")
def doSuccessIntegration(self, _edPlugin=None):
EDVerbose.DEBUG(
"EDPluginControlCharacterisationv1_3.doSuccessIntegration")
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlCharacterisationv1_3.doSuccessIntegration")
# Wait for XDS plugin if necessary
self._edPluginControlXDSGenerateBackgroundImage.synchronize()
self.addStatusMessage("Integration successful.")
xsDataIntegrationOutput = self._edPluginControlIntegration.getDataOutput(
)
self._xsDataResultCharacterisation.setIntegrationResult(
xsDataIntegrationOutput)
# Integration short summary
if self._edPluginControlIntegration.hasDataOutput(
"integrationShortSummary"):
self._strCharacterisationShortSummary += self._edPluginControlIntegration.getDataOutput(
"integrationShortSummary")[0].getValue()
#EDVerbose.DEBUG( self._xsDataExperimentCharacterisation.marshal() )
if self._bDoStrategyCalculation:
xsDataInputStrategy = XSDataInputStrategy()
xsDataSolutionSelected = self._xsDataResultCharacterisation.getIndexingResult(
).getSelectedSolution()
xsDataInputStrategy.setCrystalRefined(
xsDataSolutionSelected.getCrystal())
xsDataInputStrategy.setSample(self._xsDataResultCharacterisation.
getDataCollection().getSample())
xsDataIntegrationSubWedgeResultList = xsDataIntegrationOutput.getIntegrationSubWedgeResult(
)
xsDataInputStrategy.setBestFileContentDat(
xsDataIntegrationSubWedgeResultList[0].getBestfileDat())
xsDataInputStrategy.setBestFileContentPar(
xsDataIntegrationSubWedgeResultList[0].getBestfilePar())
xsDataInputStrategy.setExperimentalCondition(
xsDataIntegrationSubWedgeResultList[0].
getExperimentalConditionRefined())
xsDataInputStrategy.setXdsBackgroundImage(
self._xsDataFileXdsBackgroundImage)
for xsDataIntegrationSubWedgeResult in xsDataIntegrationSubWedgeResultList:
xsDataInputStrategy.addBestFileContentHKL(
xsDataIntegrationSubWedgeResult.getBestfileHKL())
xsDataInputStrategy.setDiffractionPlan(
self._xsDataResultCharacterisation.getDataCollection(
).getDiffractionPlan())
self._edPluginControlStrategy.setDataInput(xsDataInputStrategy)
self.executePluginSynchronous(self._edPluginControlStrategy)
def doFailureIntegration(self, _edPlugin=None):
EDVerbose.DEBUG(
"EDPluginControlCharacterisationv1_3.doFailureIntegration")
strErrorMessage = "Execution of integration plugin failed."
self.addStatusMessage("Integration FAILURE.")
EDVerbose.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
#self.addComment("integration failure")
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
self.generateExecutiveSummary(self)
self.setFailure()
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage),
"statusMessage")
self.writeDataOutput()
def doSuccessXDSGenerateBackgroundImage(self, _edPlugin=None):
EDVerbose.DEBUG(
"EDPluginControlCharacterisationv1_3.doSuccessXDSGenerateBackgroundImage"
)
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlCharacterisationv1_3.doSuccessXDSGenerateBackgroundImage"
)
self._xsDataFileXdsBackgroundImage = self._edPluginControlXDSGenerateBackgroundImage.getDataOutput(
).getXdsBackgroundImage()
self._xsDataResultCharacterisation.setXdsBackgroundImage(
self._xsDataFileXdsBackgroundImage)
def doFailureXDSGenerateBackgroundImage(self, _edPlugin=None):
EDVerbose.DEBUG(
"EDPluginControlCharacterisationv1_3.doFailureXDSGenerateBackgroundImage"
)
def doSuccessStrategy(self, _edPlugin=None):
EDVerbose.DEBUG(
"EDPluginControlCharacterisationv1_3.doSuccessStrategy")
self.retrieveSuccessMessages(
self._edPluginControlStrategy,
"EDPluginControlCharacterisationv1_3.doSuccessStrategy")
xsDataStrategyResult = self._edPluginControlStrategy.getDataOutput()
self._xsDataResultCharacterisation.setStrategyResult(
xsDataStrategyResult)
if self._edPluginControlStrategy.hasDataOutput("strategyShortSummary"):
self._strCharacterisationShortSummary += self._edPluginControlStrategy.getDataOutput(
"strategyShortSummary")[0].getValue()
self.addStatusMessage("Strategy calculation successful.")
def doFailureStrategy(self, _edPlugin=None):
EDVerbose.DEBUG(
"EDPluginControlCharacterisationv1_3.doFailureStrategy")
strErrorMessage = "Execution of strategy plugin failed."
EDVerbose.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
self.addStatusMessage("Strategy calculation FAILURE.")
self.generateExecutiveSummary(self)
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage),
"statusMessage")
self.writeDataOutput()
self.setFailure()
def generateExecutiveSummary(self, _edPlugin):
"""
Generates a summary of the execution of the plugin.
"""
EDVerbose.DEBUG(
"EDPluginControlCharacterisationv1_3.generateExecutiveSummary")
self.addExecutiveSummaryLine("Summary of characterisation:")
xsDataInputStrategy = self.getDataInput()
xsDataCollection = xsDataInputStrategy.getDataCollection()
xsDataDiffractionPlan = xsDataCollection.getDiffractionPlan()
self.addExecutiveSummaryLine("Diffraction plan:")
if (xsDataDiffractionPlan.getComplexity() is not None):
self.addExecutiveSummaryLine(
"BEST complexity : %s" %
xsDataDiffractionPlan.getComplexity().getValue())
if (xsDataDiffractionPlan.getAimedCompleteness() is not None):
self.addExecutiveSummaryLine(
"Aimed completeness : %6.1f [%%]" %
(100.0 *
xsDataDiffractionPlan.getAimedCompleteness().getValue()))
if (xsDataDiffractionPlan.getRequiredCompleteness() is not None):
self.addExecutiveSummaryLine(
"Required completeness : %6.1f [%%]" %
(100.0 *
xsDataDiffractionPlan.getRequiredCompleteness().getValue()))
if (xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution()
is not None):
self.addExecutiveSummaryLine(
"Aimed I/sigma at highest resolution : %6.1f" %
xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution(
).getValue())
if (xsDataDiffractionPlan.getAimedResolution() is not None):
self.addExecutiveSummaryLine(
"Aimed resolution : %6.1f [A]" %
xsDataDiffractionPlan.getAimedResolution().getValue())
if (xsDataDiffractionPlan.getRequiredResolution() is not None):
self.addExecutiveSummaryLine(
"Required resolution : %6.1f [A]" %
xsDataDiffractionPlan.getRequiredResolution().getValue())
if (xsDataDiffractionPlan.getAimedMultiplicity() is not None):
self.addExecutiveSummaryLine(
"Aimed multiplicity : %6.1f" %
xsDataDiffractionPlan.getAimedMultiplicity().getValue())
if (xsDataDiffractionPlan.getRequiredMultiplicity() is not None):
self.addExecutiveSummaryLine(
"Required multiplicity : %6.1f" %
xsDataDiffractionPlan.getRequiredMultiplicity().getValue())
if (xsDataDiffractionPlan.getForcedSpaceGroup() is not None):
self.addExecutiveSummaryLine(
"Forced space group : %6s" %
xsDataDiffractionPlan.getForcedSpaceGroup().getValue())
if (xsDataDiffractionPlan.getMaxExposureTimePerDataCollection()
is not None):
self.addExecutiveSummaryLine(
"Max exposure time per data collection : %6.1f [s]" %
xsDataDiffractionPlan.getMaxExposureTimePerDataCollection(
).getValue())
self.addExecutiveSummarySeparator()
if self._edPluginControlIndexingIndicators is not None:
self.appendExecutiveSummary(
self._edPluginControlIndexingIndicators, "")
if self._edPluginControlIndexingLabelit is not None:
self.appendExecutiveSummary(self._edPluginControlIndexingLabelit,
"")
if self._edPluginControlIntegration is not None:
self.appendExecutiveSummary(self._edPluginControlIntegration, "")
if self._edPluginControlStrategy is not None:
self.appendExecutiveSummary(self._edPluginControlStrategy, "")
self.addExecutiveSummarySeparator()
if self._strCharacterisationShortSummary is not None:
self.addExecutiveSummaryLine("Characterisation short summary:")
self.addExecutiveSummaryLine("")
if self._strStatusMessage != None:
for strLine in self._strStatusMessage.split(". "):
if strLine.endswith("."):
self.addExecutiveSummaryLine(strLine)
else:
self.addExecutiveSummaryLine(strLine + ".")
self.addExecutiveSummaryLine("")
for strLine in self._strCharacterisationShortSummary.split("\n"):
if strLine != "\n":
self.addExecutiveSummaryLine(strLine)
self.addErrorWarningMessagesToExecutiveSummary(
"Characterisation error and warning messages: ")
self.addExecutiveSummarySeparator()
def getPluginStrategyName(self):
return self._strPluginControlStrategy
def addStatusMessage(self, _strStatusMessage):
if self._strStatusMessage != "":
self._strStatusMessage += " "
self._strStatusMessage += _strStatusMessage
def doStrategyCalculation(self, _bValue):
self._bDoStrategyCalculation = _bValue
class EDPluginControlCharacterisationv1_6(EDPluginControl):
"""
Characterisation based on XDS
"""
def __init__(self):
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputCharacterisation)
self._strPluginControlIndexingIndicators = "EDPluginControlIndexingIndicatorsv1_1"
self._fMinTransmission = 10 # %
self._listPluginGenerateThumbnail = []
self._strCharacterisationShortSummary = ""
self._strStatusMessage = ""
self._strIndexingPluginName = "EDPluginXDSIndexingv1_0"
self._strIntegrationPluginName = "EDPluginXDSIntegrationv1_0"
self._edPluginIndexing = None
def checkParameters(self):
"""
Checks the mandatory parameters.
"""
self.DEBUG("EDPluginControlCharacterisationv1_6.checkParameters")
self.checkMandatoryParameters(self.getDataInput(),
"Data Input is None")
self.checkMandatoryParameters(self.getDataInput().getDataCollection(),
"dataCollection")
self.checkMandatoryParameters(
self.getDataInput().getDataCollection().getDiffractionPlan(),
"diffractionPlan")
def configure(self):
"""
Gets the configuration parameters (if any).
"""
EDPluginControl.configure(self)
self.DEBUG("EDPluginControlCharacterisationv1_6.configure")
self._strMxCuBE_URI = self.config.get("mxCuBE_URI", None)
if self._strMxCuBE_URI is not None and "mxCuBE_XMLRPC_log" in os.environ.keys(
):
self.DEBUG(
"Enabling sending messages to mxCuBE via URI {0}".format(
self._strMxCuBE_URI))
self._oServerProxy = xmlrpclib.ServerProxy(self._strMxCuBE_URI)
self._runKappa = self.config.get("runKappa", False)
self._fMinTransmission = self.config.get("minTransmissionWarning",
self._fMinTransmission)
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginControlCharacterisationv1_6.preProcess")
self._xsDataResultCharacterisation = XSDataResultCharacterisation()
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlCharacterisationv1_6.process")
self.doXdsIndexingIntegration(self.dataInput.dataCollection)
def finallyProcess(self, _edObject=None):
EDPluginControl.finallyProcess(self)
self.DEBUG("EDPluginControlCharacterisationv1_6.finallyProcess")
# Synchronize thumbnail plugins
for tuplePlugin in self._listPluginGenerateThumbnail:
image = tuplePlugin[0]
tuplePlugin[1].synchronize()
jpegImage = image.copy()
jpegImage.path = tuplePlugin[1].dataOutput.thumbnail.path
self._xsDataResultCharacterisation.addJpegImage(jpegImage)
tuplePlugin[2].synchronize()
thumbnailImage = image.copy()
thumbnailImage.path = tuplePlugin[2].dataOutput.thumbnail.path
self._xsDataResultCharacterisation.addThumbnailImage(
thumbnailImage)
# if self._edPluginControlGeneratePrediction.isRunning():
# self._edPluginControlGeneratePrediction.synchronize()
# if self._strStatusMessage != None:
# self.setDataOutput(XSDataString(self._strStatusMessage), "statusMessage")
# self._xsDataResultCharacterisation.setStatusMessage(XSDataString(self._strStatusMessage))
# if self._strCharacterisationShortSummary != None:
# self.setDataOutput(XSDataString(self._strCharacterisationShortSummary), "shortSummary")
# self._xsDataResultCharacterisation.setShortSummary(XSDataString(self._strCharacterisationShortSummary))
# if self._xsDataResultCharacterisation is not None:
# self.setDataOutput(self._xsDataResultCharacterisation)
if self.isFailure():
self.sendMessageToMXCuBE("Ended with error messages", "error")
def doXdsIndexingIntegration(self, _xsDataCollection):
# Load the plugin
self._edPluginIndexing = self.loadPlugin(self._strIndexingPluginName,
"Indexing")
# XDS Indexing
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.setDataCollection(_xsDataCollection)
self._edPluginIndexing.dataInput = EDHandlerXSDataXDSv1_0.generateXSDataInputXDSIndexing(
xsDataIndexingInput)
self._edPluginIndexing.executeSynchronous()
xsDataResultXDSIndexing = self._edPluginIndexing.dataOutput
if xsDataResultXDSIndexing.spaceGroupNumber is not None:
spaceGroupNumber = xsDataResultXDSIndexing.spaceGroupNumber.value
unitCell = xsDataResultXDSIndexing.unitCell
filePaths = xsDataResultXDSIndexing.filePaths
index = 1
for subWedge in _xsDataCollection.subWedge:
xsDataCollection = XSDataCollection()
xsDataCollection.addSubWedge(subWedge)
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.setDataCollection(xsDataCollection)
xsDataInputXDSIntegration = EDHandlerXSDataXDSv1_0.generateXSDataInputXDSIntegration(
xsDataIndexingInput, spaceGroupNumber, unitCell, filePaths)
edPluginIntegration = self.loadPlugin(
self._strIntegrationPluginName,
"Integration_{0}".format(index))
edPluginIntegration.dataInput = xsDataInputXDSIntegration
edPluginIntegration.executeSynchronous()
# self._edPluginIntegration.dataInput = xsDataInputXDSIntegration
index += 1
def generateExecutiveSummary(self, _edPlugin):
"""
Generates a summary of the execution of the plugin.
"""
self.DEBUG(
"EDPluginControlCharacterisationv1_6.generateExecutiveSummary")
self.addExecutiveSummaryLine("Summary of characterisation:")
xsDataInputStrategy = self.getDataInput()
xsDataCollection = xsDataInputStrategy.getDataCollection()
# MXSUP-1445: Check if transmission is less than 10% and warn if it's the case
xsDataFirstSubWedge = xsDataCollection.getSubWedge()[0]
xsDataBeam = xsDataFirstSubWedge.getExperimentalCondition().getBeam()
if xsDataBeam.getTransmission() is not None:
fTransmission = xsDataBeam.getTransmission().getValue()
if fTransmission < self._fMinTransmission:
self.addExecutiveSummaryLine("^" * 80)
self.addExecutiveSummaryLine("^" * 80)
self.addExecutiveSummaryLine("")
self.addExecutiveSummaryLine(
"WARNING! Transmission for characterisation set to %.1f %%"
% fTransmission)
self.addExecutiveSummaryLine(
"Please consider re-characterising with transmission set to 100 %"
)
self.addExecutiveSummaryLine("")
self.addExecutiveSummaryLine("^" * 80)
self.addExecutiveSummaryLine("^" * 80)
xsDataDiffractionPlan = xsDataCollection.getDiffractionPlan()
self.addExecutiveSummaryLine("Diffraction plan:")
if (xsDataDiffractionPlan.getComplexity() is not None):
self.addExecutiveSummaryLine(
"BEST complexity : %s" %
xsDataDiffractionPlan.getComplexity().getValue())
if (xsDataDiffractionPlan.getAimedCompleteness() is not None):
self.addExecutiveSummaryLine(
"Aimed completeness : %6.1f [%%]" %
(100.0 *
xsDataDiffractionPlan.getAimedCompleteness().getValue()))
if (xsDataDiffractionPlan.getRequiredCompleteness() is not None):
self.addExecutiveSummaryLine(
"Required completeness : %6.1f [%%]" %
(100.0 *
xsDataDiffractionPlan.getRequiredCompleteness().getValue()))
if (xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution()
is not None):
self.addExecutiveSummaryLine(
"Aimed I/sigma at highest resolution : %6.1f" %
xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution(
).getValue())
if (xsDataDiffractionPlan.getAimedResolution() is not None):
self.addExecutiveSummaryLine(
"Aimed resolution : %6.1f [A]" %
xsDataDiffractionPlan.getAimedResolution().getValue())
if (xsDataDiffractionPlan.getRequiredResolution() is not None):
self.addExecutiveSummaryLine(
"Required resolution : %6.1f [A]" %
xsDataDiffractionPlan.getRequiredResolution().getValue())
if (xsDataDiffractionPlan.getAimedMultiplicity() is not None):
self.addExecutiveSummaryLine(
"Aimed multiplicity : %6.1f" %
xsDataDiffractionPlan.getAimedMultiplicity().getValue())
if (xsDataDiffractionPlan.getRequiredMultiplicity() is not None):
self.addExecutiveSummaryLine(
"Required multiplicity : %6.1f" %
xsDataDiffractionPlan.getRequiredMultiplicity().getValue())
if (xsDataDiffractionPlan.getForcedSpaceGroup() is not None):
self.addExecutiveSummaryLine(
"Forced space group : %6s" %
xsDataDiffractionPlan.getForcedSpaceGroup().getValue())
if (xsDataDiffractionPlan.getMaxExposureTimePerDataCollection()
is not None):
self.addExecutiveSummaryLine(
"Max exposure time per data collection : %6.1f [s]" %
xsDataDiffractionPlan.getMaxExposureTimePerDataCollection(
).getValue())
self.addExecutiveSummarySeparator()
# if self._edPluginControlIndexingIndicators is not None:
# self.appendExecutiveSummary(self._edPluginControlIndexingIndicators, "")
# if self._edPluginControlIntegration is not None:
# self.appendExecutiveSummary(self._edPluginControlIntegration, "")
# if self._edPluginControlStrategy is not None:
# self.appendExecutiveSummary(self._edPluginControlStrategy, "")
self.addExecutiveSummarySeparator()
if self._strCharacterisationShortSummary is not None:
self.addExecutiveSummaryLine("Characterisation short summary:")
self.addExecutiveSummaryLine("")
if self._strStatusMessage != None:
for strLine in self._strStatusMessage.split(". "):
if strLine.endswith("."):
self.addExecutiveSummaryLine(strLine)
else:
self.addExecutiveSummaryLine(strLine + ".")
self.addExecutiveSummaryLine("")
for strLine in self._strCharacterisationShortSummary.split("\n"):
if strLine != "\n":
self.addExecutiveSummaryLine(strLine)
self.addErrorWarningMessagesToExecutiveSummary(
"Characterisation error and warning messages: ")
self.addExecutiveSummarySeparator()
def getPluginStrategyName(self):
return self._strPluginControlStrategy
def addStatusMessage(self, _strStatusMessage):
if self._strStatusMessage != "":
self._strStatusMessage += " "
self._strStatusMessage += _strStatusMessage
self.sendMessageToMXCuBE(_strStatusMessage)
def doStrategyCalculation(self, _bValue):
self._bDoStrategyCalculation = _bValue
def sendMessageToMXCuBE(self, _strMessage, level="info"):
# Only for mxCuBE
if self._strMxCuBE_URI is not None:
self.DEBUG("Sending message to mxCuBE: {0}".format(_strMessage))
try:
for strMessage in _strMessage.split("\n"):
if strMessage != "":
self._oServerProxy.log_message(
"Characterisation: " + strMessage, level)
except:
self.DEBUG("Sending message to mxCuBE failed!")
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_3.preProcess")
# Load the plugins
self._edPluginControlIndexingIndicators = self.loadPlugin(self._strPluginControlIndexingIndicators, \
"Indexing")
self._edPluginControlIndexingLabelit = self.loadPlugin(self._strPluginControlIndexingLabelit, \
"IndexingLabelit")
self._edPluginExecEvaluationIndexingMOSFLM = self.loadPlugin(self._strPluginExecEvaluationIndexing, \
"IndexingEvalualtionMOSFLM")
self._edPluginExecEvaluationIndexingLABELIT = self.loadPlugin(self._strPluginExecEvaluationIndexing, \
"IndexingEvalualtionLABELIT")
self._edPluginControlGeneratePrediction = self.loadPlugin(self._strPluginControlGeneratePrediction, \
"GeneratePrediction")
self._edPluginControlIntegration = self.loadPlugin(self._strPluginControlIntegration, \
"Integration")
self._edPluginControlXDSGenerateBackgroundImage = self.loadPlugin(self._strPluginControlXDSGenerateBackgroundImage, \
"ControlXDSGenerateBackgroundImage")
self._edPluginControlStrategy = self.loadPlugin(self._strPluginControlStrategy, \
"Strategy")
if (self._edPluginControlIndexingIndicators is not None):
EDVerbose.DEBUG(
"EDPluginControlCharacterisationv1_3.preProcess: " +
self._strPluginControlIndexingIndicators +
" Found... setting Data Input")
# create Data Input for indexing
xsDataInputCharacterisation = self.getDataInput()
self._xsDataCollection = xsDataInputCharacterisation.getDataCollection(
)
# MXSUP-1445: Check if transmission is less than 10% and warn if it's the case
xsDataFirstSubWedge = self._xsDataCollection.getSubWedge()[0]
xsDataBeam = xsDataFirstSubWedge.getExperimentalCondition(
).getBeam()
if xsDataBeam.getTransmission() is not None:
fTransmission = xsDataBeam.getTransmission().getValue()
if fTransmission < self._fMinTransmission:
strWarningMessageBanner = "^" * 80
strWarningMessage1 = "WARNING! Transmission for characterisation set to %.1f %%" % fTransmission
strWarningMessage2 = "Please consider re-characterising with transmission set to 100 %"
self.warning(strWarningMessageBanner)
self.warning(strWarningMessage1)
self.warning(strWarningMessage2)
self.warning(strWarningMessageBanner)
self.addWarningMessage(strWarningMessageBanner)
self.addWarningMessage(strWarningMessage1)
self.addWarningMessage(strWarningMessage2)
self.addWarningMessage(strWarningMessageBanner)
xsDataCrystal = None
xsDataSubWedgeList = self._xsDataCollection.getSubWedge()
if ((xsDataSubWedgeList is None) or (xsDataSubWedgeList == [])):
strError = "EDPluginControlCharacterisationv1_3.preProcess: No subwedges in input data."
EDVerbose.ERROR(strError)
self.setFailure()
else:
xsDataExperimentalCondition = xsDataSubWedgeList[
0].getExperimentalCondition()
# Fix for bug 431: if the flux is zero raise an error
xsDataDoubleFlux = xsDataExperimentalCondition.getBeam(
).getFlux()
if (xsDataDoubleFlux is not None):
if (xsDataDoubleFlux.getValue() < 0.1):
strErrorMessage = "Input flux is negative or close to zero. Execution of characterisation aborted."
EDVerbose.ERROR(strErrorMessage)
self.addErrorMessage(
"EDPluginControlCharacterisationv1_3.preProcess ERROR: "
+ strErrorMessage)
#self.addComment(strErrorMessage)
self.setFailure()
xsDataDiffractionPlan = self._xsDataCollection.getDiffractionPlan(
)
xsDataStringForcedSpaceGroup = xsDataDiffractionPlan.getForcedSpaceGroup(
)
if (xsDataStringForcedSpaceGroup is not None):
self._xsDataCrystal = XSDataCrystal()
xsDataSpaceGroup = XSDataSpaceGroup()
xsDataSpaceGroup.setName(xsDataStringForcedSpaceGroup)
self._xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
self._edPluginControlIndexingIndicators.setDataInput(
self._xsDataCollection, "dataCollection")
if self._xsDataCrystal is not None:
self._edPluginControlIndexingIndicators.setDataInput(
self._xsDataCrystal, "crystal")
# Populate characterisation object
self._xsDataResultCharacterisation = XSDataResultCharacterisation(
)
self._xsDataResultCharacterisation.setDataCollection(
XSDataCollection.parseString(
self._xsDataCollection.marshal()))
class EDPluginControlCharacterisationv1_3(EDPluginControl):
"""
[To be replaced with a description of EDPluginControlTemplatev10]
"""
def __init__(self):
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputCharacterisation)
self._strPluginControlIndexingIndicators = "EDPluginControlIndexingIndicatorsv10"
self._strPluginControlIndexingLabelit = "EDPluginControlIndexingLabelitv10"
self._strPluginExecEvaluationIndexing = "EDPluginExecEvaluationIndexingv10"
self._strPluginControlGeneratePrediction = "EDPluginControlGeneratePredictionv10"
self._strPluginControlIntegration = "EDPluginControlIntegrationv10"
self._strPluginControlXDSGenerateBackgroundImage = "EDPluginControlXDSGenerateBackgroundImagev1_0"
self._strPluginControlStrategy = "EDPluginControlStrategyv1_2"
self._strPluginGenerateThumbnailName = "EDPluginMXThumbnailv1_1"
self._listPluginGenerateThumbnail = []
self._edPluginControlIndexingIndicators = None
self._edPluginControlIndexingLabelit = None
self._edPluginExecEvaluationIndexingMOSFLM = None
self._edPluginExecEvaluationIndexingLABELIT = None
self._edPluginControlGeneratePrediction = None
self._edPluginControlIntegration = None
self._edPluginControlXDSGenerateBackgroundImage = None
self._edPluginControlStrategy = None
self._xsDataCollection = None
self._xsDataResultCharacterisation = None
self._xsDataIndexingResultMOSFLM = None
self._xsDataCrystal = None
self._strCharacterisationShortSummary = ""
self._strStatusMessage = ""
self._xsDataFileXdsBackgroundImage = None
self._bDoStrategyCalculation = True
self._fMinTransmission = 10 # %
def checkParameters(self):
"""
Checks the mandatory parameters.
"""
self.DEBUG("EDPluginControlCharacterisationv1_3.checkParameters")
self.checkMandatoryParameters(self.getDataInput(), "Data Input is None")
self.checkMandatoryParameters(self.getDataInput().getDataCollection(), "dataCollection")
self.checkMandatoryParameters(self.getDataInput().getDataCollection().getDiffractionPlan(), "diffractionPlan")
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginControlCharacterisationv1_3.preProcess")
# Load the plugins
self._edPluginControlIndexingIndicators = self.loadPlugin(self._strPluginControlIndexingIndicators, \
"Indexing")
self._edPluginControlIndexingLabelit = self.loadPlugin(self._strPluginControlIndexingLabelit, \
"IndexingLabelit")
self._edPluginExecEvaluationIndexingMOSFLM = self.loadPlugin(self._strPluginExecEvaluationIndexing, \
"IndexingEvalualtionMOSFLM")
self._edPluginExecEvaluationIndexingLABELIT = self.loadPlugin(self._strPluginExecEvaluationIndexing, \
"IndexingEvalualtionLABELIT")
self._edPluginControlGeneratePrediction = self.loadPlugin(self._strPluginControlGeneratePrediction, \
"GeneratePrediction")
self._edPluginControlIntegration = self.loadPlugin(self._strPluginControlIntegration, \
"Integration")
self._edPluginControlXDSGenerateBackgroundImage = self.loadPlugin(self._strPluginControlXDSGenerateBackgroundImage, \
"ControlXDSGenerateBackgroundImage")
self._edPluginControlStrategy = self.loadPlugin(self._strPluginControlStrategy, \
"Strategy")
if (self._edPluginControlIndexingIndicators is not None):
self.DEBUG("EDPluginControlCharacterisationv1_3.preProcess: " + self._strPluginControlIndexingIndicators + " Found... setting Data Input")
# create Data Input for indexing
xsDataInputCharacterisation = self.getDataInput()
self._xsDataCollection = xsDataInputCharacterisation.getDataCollection()
# MXSUP-1445: Check if transmission is less than 10% and warn if it's the case
xsDataFirstSubWedge = self._xsDataCollection.getSubWedge()[0]
xsDataBeam = xsDataFirstSubWedge.getExperimentalCondition().getBeam()
if xsDataBeam.getTransmission() is not None:
fTransmission = xsDataBeam.getTransmission().getValue()
if fTransmission < self._fMinTransmission:
strWarningMessageBanner = "^"*80
strWarningMessage1 = "WARNING! Transmission for characterisation set to %.1f %%" % fTransmission
strWarningMessage2 = "Please consider re-characterising with transmission set to 100 %"
self.warning(strWarningMessageBanner)
self.warning(strWarningMessage1)
self.warning(strWarningMessage2)
self.warning(strWarningMessageBanner)
self.addWarningMessage(strWarningMessageBanner)
self.addWarningMessage(strWarningMessage1)
self.addWarningMessage(strWarningMessage2)
self.addWarningMessage(strWarningMessageBanner)
xsDataCrystal = None
xsDataSubWedgeList = self._xsDataCollection.getSubWedge()
if ((xsDataSubWedgeList is None) or (xsDataSubWedgeList == [])):
strError = "EDPluginControlCharacterisationv1_3.preProcess: No subwedges in input data."
self.ERROR(strError)
self.setFailure()
else:
xsDataExperimentalCondition = xsDataSubWedgeList[0].getExperimentalCondition()
# Fix for bug 431: if the flux is zero raise an error
xsDataDoubleFlux = xsDataExperimentalCondition.getBeam().getFlux()
if (xsDataDoubleFlux is not None):
if (xsDataDoubleFlux.getValue() < 0.1):
strErrorMessage = "Input flux is negative or close to zero. Execution of characterisation aborted."
self.ERROR(strErrorMessage)
self.addErrorMessage("EDPluginControlCharacterisationv1_3.preProcess ERROR: " + strErrorMessage)
#self.addComment(strErrorMessage)
self.setFailure()
xsDataDiffractionPlan = self._xsDataCollection.getDiffractionPlan()
xsDataStringForcedSpaceGroup = xsDataDiffractionPlan.getForcedSpaceGroup()
if (xsDataStringForcedSpaceGroup is not None):
self._xsDataCrystal = XSDataCrystal()
xsDataSpaceGroup = XSDataSpaceGroup()
xsDataSpaceGroup.setName(xsDataStringForcedSpaceGroup)
self._xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
self._edPluginControlIndexingIndicators.setDataInput(self._xsDataCollection, "dataCollection")
if self._xsDataCrystal is not None:
self._edPluginControlIndexingIndicators.setDataInput(self._xsDataCrystal, "crystal")
# Populate characterisation object
self._xsDataResultCharacterisation = XSDataResultCharacterisation()
self._xsDataResultCharacterisation.setDataCollection(XSDataCollection.parseString(self._xsDataCollection.marshal()))
# Load the thumbnail plugins
for subWedge in xsDataInputCharacterisation.dataCollection.subWedge:
for image in subWedge.image:
edPluginJpeg = self.loadPlugin(self._strPluginGenerateThumbnailName)
xsDataInputMXThumbnail = XSDataInputMXThumbnail()
xsDataInputMXThumbnail.image = XSDataFile(image.path)
xsDataInputMXThumbnail.height = XSDataInteger(1024)
xsDataInputMXThumbnail.width = XSDataInteger(1024)
jpegFilename = os.path.splitext(os.path.basename(image.path.value))[0]+".jpg"
xsDataInputMXThumbnail.outputPath = XSDataFile(XSDataString(os.path.join(self.getWorkingDirectory(), jpegFilename)))
edPluginJpeg.dataInput = xsDataInputMXThumbnail
edPluginThumnail = self.loadPlugin(self._strPluginGenerateThumbnailName)
xsDataInputMXThumbnail = XSDataInputMXThumbnail()
xsDataInputMXThumbnail.image = XSDataFile(image.path)
xsDataInputMXThumbnail.height = XSDataInteger(256)
xsDataInputMXThumbnail.width = XSDataInteger(256)
thumbnailFilename = os.path.splitext(os.path.basename(image.path.value))[0]+".thumbnail.jpg"
xsDataInputMXThumbnail.outputPath = XSDataFile(XSDataString(os.path.join(self.getWorkingDirectory(), thumbnailFilename)))
edPluginThumnail.dataInput = xsDataInputMXThumbnail
self._listPluginGenerateThumbnail.append((image, edPluginJpeg, edPluginThumnail))
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlCharacterisationv1_3.process")
self._edPluginControlIndexingIndicators.connectSUCCESS(self.doSuccessIndexingIndicators)
self._edPluginControlIndexingIndicators.connectFAILURE(self.doFailureIndexingIndicators)
self._edPluginControlIndexingLabelit.connectSUCCESS(self.doSuccessIndexingLabelit)
self._edPluginControlIndexingLabelit.connectFAILURE(self.doFailureIndexingLabelit)
self._edPluginExecEvaluationIndexingMOSFLM.connectSUCCESS(self.doSuccessEvaluationIndexingMOSFLM)
self._edPluginExecEvaluationIndexingMOSFLM.connectFAILURE(self.doFailureEvaluationIndexingMOSFLM)
self._edPluginExecEvaluationIndexingLABELIT.connectSUCCESS(self.doSuccessEvaluationIndexingLABELIT)
self._edPluginExecEvaluationIndexingLABELIT.connectFAILURE(self.doFailureEvaluationIndexingLABELIT)
self._edPluginControlGeneratePrediction.connectSUCCESS(self.doSuccessGeneratePrediction)
self._edPluginControlGeneratePrediction.connectFAILURE(self.doFailureGeneratePrediction)
self._edPluginControlIntegration.connectSUCCESS(self.doSuccessIntegration)
self._edPluginControlIntegration.connectFAILURE(self.doFailureIntegration)
self._edPluginControlXDSGenerateBackgroundImage.connectSUCCESS(self.doSuccessXDSGenerateBackgroundImage)
self._edPluginControlXDSGenerateBackgroundImage.connectFAILURE(self.doFailureXDSGenerateBackgroundImage)
self._edPluginControlStrategy.connectSUCCESS(self.doSuccessStrategy)
self._edPluginControlStrategy.connectFAILURE(self.doFailureStrategy)
self.executePluginSynchronous(self._edPluginControlIndexingIndicators)
def finallyProcess(self, _edObject=None):
EDPluginControl.finallyProcess(self)
self.DEBUG("EDPluginControlCharacterisationv1_3.finallyProcess")
# Synchronize thumbnail plugins
for tuplePlugin in self._listPluginGenerateThumbnail:
image = tuplePlugin[0]
tuplePlugin[1].synchronize()
jpegImage = image.copy()
jpegImage.path = tuplePlugin[1].dataOutput.thumbnail.path
self._xsDataResultCharacterisation.addJpegImage(jpegImage)
tuplePlugin[2].synchronize()
thumbnailImage = image.copy()
thumbnailImage.path = tuplePlugin[2].dataOutput.thumbnail.path
self._xsDataResultCharacterisation.addThumbnailImage(thumbnailImage)
if self._edPluginControlGeneratePrediction.isRunning():
self._edPluginControlGeneratePrediction.synchronize()
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage), "statusMessage")
self._xsDataResultCharacterisation.setStatusMessage(XSDataString(self._strStatusMessage))
if self._strCharacterisationShortSummary != None:
self.setDataOutput(XSDataString(self._strCharacterisationShortSummary), "shortSummary")
self._xsDataResultCharacterisation.setShortSummary(XSDataString(self._strCharacterisationShortSummary))
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
def doSuccessIndexingIndicators(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_3.doSuccessIndexingIndicators")
#self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv1_3.doSuccessIndexingIndicators")
if self._edPluginControlIndexingIndicators.hasDataOutput("indexingResult"):
xsDataIndexingResult = self._edPluginControlIndexingIndicators.getDataOutput("indexingResult")[0]
#self._xsDataResultCharacterisation.setIndexingResult(xsDataIndexingResult)
self._edPluginExecEvaluationIndexingMOSFLM.setDataInput(xsDataIndexingResult, "indexingResult")
if self._edPluginControlIndexingIndicators.hasDataOutput("imageQualityIndicators"):
listXSDataImageQualityIndicators = self._edPluginControlIndexingIndicators.getDataOutput("imageQualityIndicators")
for xsDataImageQualityIndicators in listXSDataImageQualityIndicators:
self._xsDataResultCharacterisation.addImageQualityIndicators(xsDataImageQualityIndicators)
self._edPluginExecEvaluationIndexingMOSFLM.setDataInput(xsDataImageQualityIndicators, "imageQualityIndicators")
if self._edPluginControlIndexingIndicators.hasDataOutput("indicatorsShortSummary"):
self._strCharacterisationShortSummary += self._edPluginControlIndexingIndicators.getDataOutput("indicatorsShortSummary")[0].getValue()
for tuplePlugin in self._listPluginGenerateThumbnail:
tuplePlugin[1].execute()
tuplePlugin[2].execute()
self.executePluginSynchronous(self._edPluginExecEvaluationIndexingMOSFLM)
def doFailureIndexingIndicators(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_3.doFailureIndexingIndicators")
strErrorMessage = "Execution of Indexing and Indicators plugin failed. Execution of characterisation aborted."
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
self.setFailure()
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage), "statusMessage")
self.writeDataOutput()
# def doSuccessIndexingLabelit(self, _edPlugin=None):
# self.DEBUG("EDPluginControlCharacterisationv1_3.doSuccessIndexingLabelit")
# self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv1_3.doSuccessIndexingLabelit")
# # Retrieve the indexing result
# xsDataIndexingResult = self._edPluginControlIndexingLabelit.getDataOutput()
# self._xsDataResultCharacterisation.setIndexingResult(xsDataIndexingResult)
# if self._edPluginControlIndexingLabelit.hasDataOutput("indexingShortSummary"):
# self._strCharacterisationShortSummary += self._edPluginControlIndexingLabelit.getDataOutput("indexingShortSummary")[0].getValue()
# # Then start the integration of the reference images
# self.indexingToIntegration()
def doSuccessIndexingLabelit(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_3.doSuccessIndexingLabelit")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv1_3.doSuccessIndexingLabelit")
if self._edPluginControlIndexingLabelit.hasDataOutput("indexingShortSummary"):
self._strCharacterisationShortSummary += self._edPluginControlIndexingLabelit.getDataOutput("indexingShortSummary")[0].getValue()
# Check the indexing results
xsDataIndexingResult = self._edPluginControlIndexingLabelit.getDataOutput()
self._edPluginExecEvaluationIndexingLABELIT.setDataInput(xsDataIndexingResult, "indexingResult")
xsDataImageQualityIndicators = self._xsDataResultCharacterisation.getImageQualityIndicators()[0]
self._edPluginExecEvaluationIndexingLABELIT.setDataInput(xsDataImageQualityIndicators, "imageQualityIndicators")
self.executePluginSynchronous(self._edPluginExecEvaluationIndexingLABELIT)
def doFailureIndexingLabelit(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_3.doFailureIndexingLabelit")
self.addStatusMessage("Labelit: Indexing FAILURE.")
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
if self._xsDataIndexingResultMOSFLM == None:
strErrorMessage = "Execution of indexing with both MOSFLM and Labelit failed. Execution of characterisation aborted."
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.generateExecutiveSummary(self)
self.setFailure()
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage), "statusMessage")
self.writeDataOutput()
else:
# Use the MOSFLM indexing results - even if it's P1
self._xsDataResultCharacterisation.setIndexingResult(self._xsDataIndexingResultMOSFLM)
xsDataCollection = self._xsDataResultCharacterisation.getDataCollection()
xsDataGeneratePredictionInput = XSDataGeneratePredictionInput()
xsDataGeneratePredictionInput.setDataCollection(XSDataCollection.parseString(xsDataCollection.marshal()))
xsDataGeneratePredictionInput.setSelectedIndexingSolution(XSDataIndexingSolutionSelected.parseString(self._xsDataIndexingResultMOSFLM.getSelectedSolution().marshal()))
self._edPluginControlGeneratePrediction.setDataInput(xsDataGeneratePredictionInput)
if self._edPluginControlIndexingIndicators.hasDataOutput("indexingShortSummary"):
self._strCharacterisationShortSummary += self._edPluginControlIndexingIndicators.getDataOutput("indexingShortSummary")[0].getValue()
# Start the generation of prediction images - we synchronize in the post-process
self._edPluginControlGeneratePrediction.execute()
# Then start the integration of the reference images
self.indexingToIntegration()
def doSuccessEvaluationIndexingMOSFLM(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_3.doSuccessEvaluationIndexingMOSFLM")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv1_3.doSuccessEvaluationIndexing")
# Retrieve status messages (if any)
if self._edPluginExecEvaluationIndexingMOSFLM.hasDataOutput("statusMessageImageQualityIndicators"):
self.addStatusMessage(self._edPluginExecEvaluationIndexingMOSFLM.getDataOutput("statusMessageImageQualityIndicators")[0].getValue())
if self._edPluginExecEvaluationIndexingMOSFLM.hasDataOutput("statusMessageIndexing"):
self.addStatusMessage("MOSFLM: " + self._edPluginExecEvaluationIndexingMOSFLM.getDataOutput("statusMessageIndexing")[0].getValue())
# Check if indexing was successful
bIndexWithLabelit = False
bIndexingSuccess = self._edPluginExecEvaluationIndexingMOSFLM.getDataOutput("indexingSuccess")[0].getValue()
if bIndexingSuccess:
xsDataIndexingResult = self._edPluginExecEvaluationIndexingMOSFLM.getDataOutput("indexingResult")[0]
self._xsDataIndexingResultMOSFLM = xsDataIndexingResult
# Check if space group is P1 - if yes run Labelit indexing
xsDataIndexingSolutionSelected = xsDataIndexingResult.getSelectedSolution()
xsDataCrystal = xsDataIndexingSolutionSelected.getCrystal()
xsDataSpaceGroup = xsDataCrystal.getSpaceGroup()
strSpaceGroupName = xsDataSpaceGroup.getName().getValue().upper()
# Check if MOSFLM has indexed in P1
if strSpaceGroupName == "P1":
# Check if the user maybe asked for P1!
bIndexWithLabelit = True
if self._xsDataCollection.getDiffractionPlan() is not None:
if self._xsDataCollection.getDiffractionPlan().getForcedSpaceGroup() is not None:
if self._xsDataCollection.getDiffractionPlan().getForcedSpaceGroup().getValue().upper() == "P1":
self.screen("P1 space forced by diffraction plan")
bIndexWithLabelit = False
if bIndexWithLabelit:
self.screen("P1 space group choosed - reindexing with Labelit")
else:
self.screen("MOSFLM indexing successful!")
if self._edPluginControlIndexingIndicators.hasDataOutput("indexingShortSummary"):
self._strCharacterisationShortSummary += self._edPluginControlIndexingIndicators.getDataOutput("indexingShortSummary")[0].getValue()
# Generate prediction images
xsDataCollection = self._xsDataResultCharacterisation.getDataCollection()
self._xsDataResultCharacterisation.setIndexingResult(xsDataIndexingResult)
xsDataGeneratePredictionInput = XSDataGeneratePredictionInput()
xsDataGeneratePredictionInput.setDataCollection(XSDataCollection.parseString(xsDataCollection.marshal()))
xsDataGeneratePredictionInput.setSelectedIndexingSolution(XSDataIndexingSolutionSelected.parseString(xsDataIndexingResult.getSelectedSolution().marshal()))
self._edPluginControlGeneratePrediction.setDataInput(xsDataGeneratePredictionInput)
# Start the generation of prediction images - we synchronize in the post-process
self._edPluginControlGeneratePrediction.execute()
# Then start the integration of the reference images
self.indexingToIntegration()
else:
self.screen("Indexing with MOSFLM failed!")
bIndexWithLabelit = True
if bIndexWithLabelit:
# Execute Labelit indexing
self.screen("Now trying to index with Labelit - please be patient...")
xsDataIndexingInput = XSDataIndexingInput()
xsDataSubWedgeList = self._xsDataCollection.getSubWedge()
xsDataExperimentalCondition = xsDataSubWedgeList[0].getExperimentalCondition()
xsDataIndexingInput.setDataCollection(self._xsDataCollection)
xsDataIndexingInput.setExperimentalCondition(xsDataExperimentalCondition)
if self._xsDataCrystal != None:
xsDataIndexingInput.setCrystal(self._xsDataCrystal)
self._edPluginControlIndexingLabelit.setDataInput(xsDataIndexingInput)
self.executePluginSynchronous(self._edPluginControlIndexingLabelit)
def doSuccessEvaluationIndexingLABELIT(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_3.doSuccessEvaluationIndexingLABELIT")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv1_3.doSuccessEvaluationIndexingLABELIT")
# Retrieve status messages (if any)
if self._edPluginExecEvaluationIndexingLABELIT.hasDataOutput("statusMessageIndexing"):
self.addStatusMessage("Labelit: " + self._edPluginExecEvaluationIndexingLABELIT.getDataOutput("statusMessageIndexing")[0].getValue())
# Check if indexing was successful
bIndexingSuccess = self._edPluginExecEvaluationIndexingLABELIT.getDataOutput("indexingSuccess")[0].getValue()
if bIndexingSuccess:
xsDataIndexingResult = self._edPluginExecEvaluationIndexingLABELIT.getDataOutput("indexingResult")[0]
self._xsDataResultCharacterisation.setIndexingResult(xsDataIndexingResult)
# Then start the integration of the reference images
self.indexingToIntegration()
else:
self.screen("Indexing with LABELIT failed!")
self.setFailure()
def indexingToIntegration(self, _edPlugin=None):
# Create the XDS background image
xsDataInputControlXDSGenerateBackgroundImage = XSDataInputControlXDSGenerateBackgroundImage()
xsDataInputControlXDSGenerateBackgroundImage.setDataCollection(self._xsDataCollection)
self._edPluginControlXDSGenerateBackgroundImage.setDataInput(xsDataInputControlXDSGenerateBackgroundImage)
self._edPluginControlXDSGenerateBackgroundImage.execute()
# Integrate the reference images
xsDataIntegrationInput = XSDataIntegrationInput()
xsDataIntegrationInput.setDataCollection(self._xsDataResultCharacterisation.getDataCollection())
xsDataIndexingResult = self._xsDataResultCharacterisation.getIndexingResult()
xsDataExperimentalConditionRefinded = xsDataIndexingResult.getSelectedSolution().getExperimentalConditionRefined()
xsDataIntegrationInput.setExperimentalConditionRefined(xsDataExperimentalConditionRefinded)
xsDataIntegrationInput.setSelectedIndexingSolution(xsDataIndexingResult.getSelectedSolution())
self._edPluginControlIntegration.setDataInput(xsDataIntegrationInput)
self.executePluginSynchronous(self._edPluginControlIntegration)
def doFailureEvaluationIndexingMOSFLM(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_3.doFailureEvaluationIndexing")
strWarningMessage = "Execution of indexing evaluation plugin failed."
self.WARNING(strWarningMessage)
self.addWarningMessage(strWarningMessage)
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
def doFailureEvaluationIndexingLABELIT(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_3.doFailureEvaluationIndexing")
strWarningMessage = "Execution of indexing evaluation plugin failed."
self.WARNING(strWarningMessage)
self.addWarningMessage(strWarningMessage)
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
def doSuccessGeneratePrediction(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_3.doSuccessGeneratePrediction")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv1_3.doSuccessGeneratePrediction")
xsDataGeneratePredictionResult = _edPlugin.getDataOutput()
xsDataIndexingResult = self._xsDataResultCharacterisation.getIndexingResult()
xsDataIndexingResult.setPredictionResult(xsDataGeneratePredictionResult)
def doFailureGeneratePrediction(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_3.doFailureGeneratePrediction")
strWarningMessage = "Execution of generate prediction plugin failed."
self.WARNING(strWarningMessage)
self.addWarningMessage(strWarningMessage)
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
#self.addComment("warning: no prediction images")
def doSuccessIntegration(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_3.doSuccessIntegration")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv1_3.doSuccessIntegration")
# Wait for XDS plugin if necessary
self._edPluginControlXDSGenerateBackgroundImage.synchronize()
self.addStatusMessage("Integration successful.")
xsDataIntegrationOutput = self._edPluginControlIntegration.getDataOutput()
self._xsDataResultCharacterisation.setIntegrationResult(xsDataIntegrationOutput)
# Integration short summary
if self._edPluginControlIntegration.hasDataOutput("integrationShortSummary"):
self._strCharacterisationShortSummary += self._edPluginControlIntegration.getDataOutput("integrationShortSummary")[0].getValue()
#self.DEBUG( self._xsDataExperimentCharacterisation.marshal() )
if self._bDoStrategyCalculation:
xsDataInputStrategy = XSDataInputStrategy()
xsDataSolutionSelected = self._xsDataResultCharacterisation.getIndexingResult().getSelectedSolution()
xsDataInputStrategy.setCrystalRefined(xsDataSolutionSelected.getCrystal())
xsDataInputStrategy.setSample(self._xsDataResultCharacterisation.getDataCollection().getSample())
xsDataIntegrationSubWedgeResultList = xsDataIntegrationOutput.getIntegrationSubWedgeResult()
xsDataInputStrategy.setBestFileContentDat(xsDataIntegrationSubWedgeResultList[0].getBestfileDat())
xsDataInputStrategy.setBestFileContentPar(xsDataIntegrationSubWedgeResultList[0].getBestfilePar())
xsDataInputStrategy.setExperimentalCondition(xsDataIntegrationSubWedgeResultList[0].getExperimentalConditionRefined())
xsDataInputStrategy.setXdsBackgroundImage(self._xsDataFileXdsBackgroundImage)
xsDataInputStrategy.setDataCollection(self._xsDataCollection)
for xsDataIntegrationSubWedgeResult in xsDataIntegrationSubWedgeResultList:
xsDataInputStrategy.addBestFileContentHKL(xsDataIntegrationSubWedgeResult.getBestfileHKL())
xsDataInputStrategy.setDiffractionPlan(self._xsDataResultCharacterisation.getDataCollection().getDiffractionPlan())
self._edPluginControlStrategy.setDataInput(xsDataInputStrategy)
self.executePluginSynchronous(self._edPluginControlStrategy)
def doFailureIntegration(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_3.doFailureIntegration")
strErrorMessage = "Execution of integration plugin failed."
self.addStatusMessage("Integration FAILURE.")
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
#self.addComment("integration failure")
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
self.generateExecutiveSummary(self)
self.setFailure()
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage), "statusMessage")
self.writeDataOutput()
def doSuccessXDSGenerateBackgroundImage(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_3.doSuccessXDSGenerateBackgroundImage")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv1_3.doSuccessXDSGenerateBackgroundImage")
self._xsDataFileXdsBackgroundImage = self._edPluginControlXDSGenerateBackgroundImage.getDataOutput().getXdsBackgroundImage()
self._xsDataResultCharacterisation.setXdsBackgroundImage(self._xsDataFileXdsBackgroundImage)
def doFailureXDSGenerateBackgroundImage(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_3.doFailureXDSGenerateBackgroundImage")
def doSuccessStrategy(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_3.doSuccessStrategy")
self.retrieveSuccessMessages(self._edPluginControlStrategy, "EDPluginControlCharacterisationv1_3.doSuccessStrategy")
xsDataStrategyResult = self._edPluginControlStrategy.getDataOutput()
self._xsDataResultCharacterisation.setStrategyResult(xsDataStrategyResult)
if self._edPluginControlStrategy.hasDataOutput("strategyShortSummary"):
self._strCharacterisationShortSummary += self._edPluginControlStrategy.getDataOutput("strategyShortSummary")[0].getValue()
self.addStatusMessage("Strategy calculation successful.")
def doFailureStrategy(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_3.doFailureStrategy")
strErrorMessage = "Strategy calculation FAILURE."
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
xsDataStrategyResult = self._edPluginControlStrategy.getDataOutput()
self._xsDataResultCharacterisation.setStrategyResult(xsDataStrategyResult)
if self._edPluginControlStrategy.hasDataOutput("strategyShortSummary"):
self._strCharacterisationShortSummary += self._edPluginControlStrategy.getDataOutput("strategyShortSummary")[0].getValue()
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
self.addStatusMessage("Strategy calculation FAILURE.")
self.generateExecutiveSummary(self)
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage), "statusMessage")
self.writeDataOutput()
self.setFailure()
def generateExecutiveSummary(self, _edPlugin):
"""
Generates a summary of the execution of the plugin.
"""
self.DEBUG("EDPluginControlCharacterisationv1_3.generateExecutiveSummary")
self.addExecutiveSummaryLine("Summary of characterisation:")
xsDataInputStrategy = self.getDataInput()
xsDataCollection = xsDataInputStrategy.getDataCollection()
# MXSUP-1445: Check if transmission is less than 10% and warn if it's the case
xsDataFirstSubWedge = xsDataCollection.getSubWedge()[0]
xsDataBeam = xsDataFirstSubWedge.getExperimentalCondition().getBeam()
if xsDataBeam.getTransmission() is not None:
fTransmission = xsDataBeam.getTransmission().getValue()
if fTransmission < self._fMinTransmission:
self.addExecutiveSummaryLine("^"*80)
self.addExecutiveSummaryLine("^"*80)
self.addExecutiveSummaryLine("")
self.addExecutiveSummaryLine("WARNING! Transmission for characterisation set to %.1f %%" % fTransmission)
self.addExecutiveSummaryLine("Please consider re-characterising with transmission set to 100 %")
self.addExecutiveSummaryLine("")
self.addExecutiveSummaryLine("^"*80)
self.addExecutiveSummaryLine("^"*80)
xsDataDiffractionPlan = xsDataCollection.getDiffractionPlan()
self.addExecutiveSummaryLine("Diffraction plan:")
if (xsDataDiffractionPlan.getComplexity() is not None):
self.addExecutiveSummaryLine("BEST complexity : %s" % xsDataDiffractionPlan.getComplexity().getValue())
if (xsDataDiffractionPlan.getAimedCompleteness() is not None):
self.addExecutiveSummaryLine("Aimed completeness : %6.1f [%%]" % (100.0 * xsDataDiffractionPlan.getAimedCompleteness().getValue()))
if (xsDataDiffractionPlan.getRequiredCompleteness() is not None):
self.addExecutiveSummaryLine("Required completeness : %6.1f [%%]" % (100.0 * xsDataDiffractionPlan.getRequiredCompleteness().getValue()))
if (xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution() is not None):
self.addExecutiveSummaryLine("Aimed I/sigma at highest resolution : %6.1f" % xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution().getValue())
if (xsDataDiffractionPlan.getAimedResolution() is not None):
self.addExecutiveSummaryLine("Aimed resolution : %6.1f [A]" % xsDataDiffractionPlan.getAimedResolution().getValue())
if (xsDataDiffractionPlan.getRequiredResolution() is not None):
self.addExecutiveSummaryLine("Required resolution : %6.1f [A]" % xsDataDiffractionPlan.getRequiredResolution().getValue())
if (xsDataDiffractionPlan.getAimedMultiplicity() is not None):
self.addExecutiveSummaryLine("Aimed multiplicity : %6.1f" % xsDataDiffractionPlan.getAimedMultiplicity().getValue())
if (xsDataDiffractionPlan.getRequiredMultiplicity() is not None):
self.addExecutiveSummaryLine("Required multiplicity : %6.1f" % xsDataDiffractionPlan.getRequiredMultiplicity().getValue())
if (xsDataDiffractionPlan.getForcedSpaceGroup() is not None):
self.addExecutiveSummaryLine("Forced space group : %6s" % xsDataDiffractionPlan.getForcedSpaceGroup().getValue())
if (xsDataDiffractionPlan.getMaxExposureTimePerDataCollection() is not None):
self.addExecutiveSummaryLine("Max exposure time per data collection : %6.1f [s]" % xsDataDiffractionPlan.getMaxExposureTimePerDataCollection().getValue())
self.addExecutiveSummarySeparator()
if self._edPluginControlIndexingIndicators is not None:
self.appendExecutiveSummary(self._edPluginControlIndexingIndicators, "")
if self._edPluginControlIndexingLabelit is not None:
self.appendExecutiveSummary(self._edPluginControlIndexingLabelit, "")
if self._edPluginControlIntegration is not None:
self.appendExecutiveSummary(self._edPluginControlIntegration, "")
if self._edPluginControlStrategy is not None:
self.appendExecutiveSummary(self._edPluginControlStrategy, "")
self.addExecutiveSummarySeparator()
if self._strCharacterisationShortSummary is not None:
self.addExecutiveSummaryLine("Characterisation short summary:")
self.addExecutiveSummaryLine("")
if self._strStatusMessage != None:
for strLine in self._strStatusMessage.split(". "):
if strLine.endswith("."):
self.addExecutiveSummaryLine(strLine)
else:
self.addExecutiveSummaryLine(strLine + ".")
self.addExecutiveSummaryLine("")
for strLine in self._strCharacterisationShortSummary.split("\n"):
if strLine != "\n":
self.addExecutiveSummaryLine(strLine)
self.addErrorWarningMessagesToExecutiveSummary("Characterisation error and warning messages: ")
self.addExecutiveSummarySeparator()
def getPluginStrategyName(self):
return self._strPluginControlStrategy
def addStatusMessage(self, _strStatusMessage):
if self._strStatusMessage != "":
self._strStatusMessage += " "
self._strStatusMessage += _strStatusMessage
def doStrategyCalculation(self, _bValue):
self._bDoStrategyCalculation = _bValue
def buildChildren(self, child_, nodeName_):
if child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'mxv1ResultCharacterisation':
obj_ = XSDataResultCharacterisation()
obj_.build(child_)
self.setMxv1ResultCharacterisation(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'mxv1ResultCharacterisation_Reference':
obj_ = XSDataResultCharacterisation()
obj_.build(child_)
self.setMxv1ResultCharacterisation_Reference(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'mxv2DataCollection':
obj_ = XSDataCollection()
obj_.build(child_)
self.setMxv2DataCollection(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'mxv2DataCollection_Reference':
obj_ = XSDataCollection()
obj_.build(child_)
self.setMxv2DataCollection_Reference(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'suggestedStrategy':
obj_ = XSDataResultStrategy()
obj_.build(child_)
self.setSuggestedStrategy(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'possibleOrientations':
obj_ = kappa_alignment_response()
obj_.build(child_)
self.setPossibleOrientations(obj_)
XSDataResultInterface.buildChildren(self, child_, nodeName_)
def buildChildren(self, child_, nodeName_):
if child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'characterisationResult':
obj_ = XSDataResultCharacterisation()
obj_.build(child_)
self.setCharacterisationResult(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'fileGraph':
obj_ = XSDataFile()
obj_.build(child_)
self.fileGraph.append(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'helicalDistance':
obj_ = XSDataDouble()
obj_.build(child_)
self.setHelicalDistance(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'logFile':
obj_ = XSDataFile()
obj_.build(child_)
self.setLogFile(obj_)
XSDataInput.buildChildren(self, child_, nodeName_)
def buildChildren(self, child_, nodeName_):
if child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'characterisationResult':
obj_ = XSDataResultCharacterisation()
obj_.build(child_)
self.setCharacterisationResult(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'fileGraph':
obj_ = XSDataFile()
obj_.build(child_)
self.fileGraph.append(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'helicalDistance':
obj_ = XSDataDouble()
obj_.build(child_)
self.setHelicalDistance(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'logFile':
obj_ = XSDataFile()
obj_.build(child_)
self.setLogFile(obj_)
XSDataInput.buildChildren(self, child_, nodeName_)
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginControlCharacterisationv1_6.preProcess")
self._xsDataResultCharacterisation = XSDataResultCharacterisation()
class EDPluginControlCharacterisationv1_4(EDPluginControl):
"""
[To be replaced with a description of EDPluginControlTemplatev10]
"""
def __init__(self):
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputCharacterisation)
self._strPluginControlIndexingIndicators = "EDPluginControlIndexingIndicatorsv1_1"
self._strPluginExecEvaluationIndexing = "EDPluginExecEvaluationIndexingv10"
self._strPluginControlIndexingMOSFLM = "EDPluginControlIndexingMOSFLMv10"
self._strPluginControlGeneratePrediction = "EDPluginControlGeneratePredictionv10"
self._strPluginControlIntegration = "EDPluginControlIntegrationv10"
self._strPluginControlXDSGenerateBackgroundImage = "EDPluginControlXDSGenerateBackgroundImagev1_0"
self._strPluginControlStrategy = "EDPluginControlStrategyv1_2"
self._strPluginGenerateThumbnailName = "EDPluginMXThumbnailv1_1"
self._strPluginControlKappaName = "EDPluginControlKappav1_0"
self._listPluginGenerateThumbnail = []
self._edPluginControlIndexingIndicators = None
self._edPluginExecEvaluationIndexingMOSFLM = None
self._edPluginExecEvaluationIndexingLABELIT = None
self._edPluginControlGeneratePrediction = None
self._edPluginControlIntegration = None
self._edPluginControlXDSGenerateBackgroundImage = None
self._edPluginControlStrategy = None
self._edPluginControlKappa = None
self._xsDataCollection = None
self._xsDataResultCharacterisation = None
self._xsDataIndexingResultMOSFLM = None
self._xsDataCrystal = None
self._strCharacterisationShortSummary = ""
self._strStatusMessage = ""
self._xsDataFileXdsBackgroundImage = None
self._bDoStrategyCalculation = True
self._fMinTransmission = 10 # %
self._iNoReferenceImages = None
self._iNoImagesWithDozorScore = None
self._strMxCuBE_URI = None
self._oServerProxy = None
self._runKappa = False
self._bDoOnlyMoslmfIndexing = False
def checkParameters(self):
"""
Checks the mandatory parameters.
"""
self.DEBUG("EDPluginControlCharacterisationv1_4.checkParameters")
self.checkMandatoryParameters(self.getDataInput(),
"Data Input is None")
self.checkMandatoryParameters(self.getDataInput().getDataCollection(),
"dataCollection")
self.checkMandatoryParameters(
self.getDataInput().getDataCollection().getDiffractionPlan(),
"diffractionPlan")
def configure(self):
"""
Gets the configuration parameters (if any).
"""
EDPluginControl.configure(self)
self.DEBUG("EDPluginControlCharacterisationv1_4.configure")
self._strMxCuBE_URI = self.config.get("mxCuBE_URI", None)
if self._strMxCuBE_URI is not None and "mxCuBE_XMLRPC_log" in os.environ.keys(
):
self.DEBUG(
"Enabling sending messages to mxCuBE via URI {0}".format(
self._strMxCuBE_URI))
self._oServerProxy = ServerProxy(self._strMxCuBE_URI)
self._runKappa = self.config.get("runKappa", False)
self._fMinTransmission = self.config.get("minTransmissionWarning",
self._fMinTransmission)
self._bDoOnlyMoslmfIndexing = self.config.get("doOnlyMosflmIndexing",
False)
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginControlCharacterisationv1_4.preProcess")
self._xsDataResultCharacterisation = XSDataResultCharacterisation()
# Load the plugins
self._edPluginControlIndexingIndicators = self.loadPlugin(self._strPluginControlIndexingIndicators, \
"Indexing")
self._edPluginExecEvaluationIndexingLABELIT = self.loadPlugin(self._strPluginExecEvaluationIndexing, \
"IndexingEvalualtionLABELIT")
self._edPluginControlIndexingMOSFLM = self.loadPlugin(self._strPluginControlIndexingMOSFLM, \
"IndexingMOSFLM")
self._edPluginExecEvaluationIndexingMOSFLM = self.loadPlugin(self._strPluginExecEvaluationIndexing, \
"IndexingEvalualtionMOSFLM")
self._edPluginControlGeneratePrediction = self.loadPlugin(self._strPluginControlGeneratePrediction, \
"GeneratePrediction")
self._edPluginControlIntegration = self.loadPlugin(self._strPluginControlIntegration, \
"Integration")
self._edPluginControlXDSGenerateBackgroundImage = self.loadPlugin(self._strPluginControlXDSGenerateBackgroundImage, \
"ControlXDSGenerateBackgroundImage")
self._edPluginControlStrategy = self.loadPlugin(self._strPluginControlStrategy, \
"Strategy")
if self._runKappa:
self._edPluginControlKappa = self.loadPlugin(
self._strPluginControlKappaName, "Kappa")
if (self._edPluginControlIndexingIndicators is not None):
self.DEBUG("EDPluginControlCharacterisationv1_4.preProcess: " +
self._strPluginControlIndexingIndicators +
" Found... setting Data Input")
# create Data Input for indexing
xsDataInputCharacterisation = self.getDataInput()
self._xsDataCollection = xsDataInputCharacterisation.getDataCollection(
)
# MXSUP-1445: Check if transmission is less than 10% and warn if it's the case
xsDataFirstSubWedge = self._xsDataCollection.getSubWedge()[0]
xsDataBeam = xsDataFirstSubWedge.getExperimentalCondition(
).getBeam()
if xsDataBeam.getTransmission() is not None:
fTransmission = xsDataBeam.getTransmission().getValue()
if fTransmission < self._fMinTransmission:
strWarningMessageBanner = "^" * 80
strWarningMessage1 = "WARNING! Transmission for characterisation set to %.1f %%" % fTransmission
strWarningMessage2 = "Please consider re-characterising with transmission set to 100 %"
self.warning(strWarningMessageBanner)
self.warning(strWarningMessage1)
self.warning(strWarningMessage2)
self.warning(strWarningMessageBanner)
self.addWarningMessage(strWarningMessageBanner)
self.addWarningMessage(strWarningMessage1)
self.addWarningMessage(strWarningMessage2)
self.addWarningMessage(strWarningMessageBanner)
self.sendMessageToMXCuBE(strWarningMessage1, "warning")
self.sendMessageToMXCuBE(strWarningMessage2, "warning")
xsDataCrystal = None
xsDataSubWedgeList = self._xsDataCollection.getSubWedge()
if ((xsDataSubWedgeList is None) or (xsDataSubWedgeList == [])):
strError = "EDPluginControlCharacterisationv1_4.preProcess: No subwedges in input data."
self.ERROR(strError)
self.setFailure()
else:
# Load the thumbnail plugins
self._iNoReferenceImages = 0
for subWedge in xsDataInputCharacterisation.dataCollection.subWedge:
for image in subWedge.image:
self._iNoReferenceImages += 1
edPluginJpeg = self.loadPlugin(
self._strPluginGenerateThumbnailName)
xsDataInputMXThumbnail = XSDataInputMXThumbnail()
xsDataInputMXThumbnail.image = XSDataFile(image.path)
xsDataInputMXThumbnail.height = XSDataInteger(1024)
xsDataInputMXThumbnail.width = XSDataInteger(1024)
jpegFilename = os.path.splitext(
os.path.basename(image.path.value))[0] + ".jpg"
xsDataInputMXThumbnail.outputPath = XSDataFile(
XSDataString(
os.path.join(self.getWorkingDirectory(),
jpegFilename)))
edPluginJpeg.dataInput = xsDataInputMXThumbnail
edPluginThumnail = self.loadPlugin(
self._strPluginGenerateThumbnailName)
xsDataInputMXThumbnail = XSDataInputMXThumbnail()
xsDataInputMXThumbnail.image = XSDataFile(image.path)
xsDataInputMXThumbnail.height = XSDataInteger(256)
xsDataInputMXThumbnail.width = XSDataInteger(256)
thumbnailFilename = os.path.splitext(
os.path.basename(
image.path.value))[0] + ".thumbnail.jpg"
xsDataInputMXThumbnail.outputPath = XSDataFile(
XSDataString(
os.path.join(self.getWorkingDirectory(),
thumbnailFilename)))
edPluginThumnail.dataInput = xsDataInputMXThumbnail
self._listPluginGenerateThumbnail.append(
(image, edPluginJpeg, edPluginThumnail))
edPluginJpeg.execute()
edPluginThumnail.execute()
xsDataExperimentalCondition = xsDataSubWedgeList[
0].getExperimentalCondition()
# Fix for bug 431: if the flux is zero raise an error
xsDataDoubleFlux = xsDataExperimentalCondition.getBeam(
).getFlux()
if (xsDataDoubleFlux is not None):
if (xsDataDoubleFlux.getValue() < 0.1):
strErrorMessage = "Input flux is negative or close to zero. Execution of characterisation aborted."
self.ERROR(strErrorMessage)
self.sendMessageToMXCuBE(strErrorMessage, "error")
self.addErrorMessage(
"EDPluginControlCharacterisationv1_4.preProcess ERROR: "
+ strErrorMessage)
# self.addComment(strErrorMessage)
self.setFailure()
xsDataDiffractionPlan = self._xsDataCollection.getDiffractionPlan(
)
xsDataStringForcedSpaceGroup = xsDataDiffractionPlan.getForcedSpaceGroup(
)
if (xsDataStringForcedSpaceGroup is not None):
self._xsDataCrystal = XSDataCrystal()
xsDataSpaceGroup = XSDataSpaceGroup()
xsDataSpaceGroup.setName(xsDataStringForcedSpaceGroup)
self._xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
self._edPluginControlIndexingIndicators.setDataInput(
self._xsDataCollection, "dataCollection")
if self._xsDataCrystal is not None:
self._edPluginControlIndexingIndicators.setDataInput(
self._xsDataCrystal, "crystal")
# Populate characterisation object
self._xsDataResultCharacterisation.setDataCollection(
XSDataCollection.parseString(
self._xsDataCollection.marshal()))
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlCharacterisationv1_4.process")
self._edPluginControlIndexingIndicators.connectSUCCESS(
self.doSuccessIndexingIndicators)
self._edPluginControlIndexingIndicators.connectFAILURE(
self.doFailureIndexingIndicators)
self._edPluginExecEvaluationIndexingLABELIT.connectSUCCESS(
self.doSuccessEvaluationIndexingLABELIT)
self._edPluginExecEvaluationIndexingLABELIT.connectFAILURE(
self.doFailureEvaluationIndexingLABELIT)
self._edPluginControlIndexingMOSFLM.connectSUCCESS(
self.doSuccessIndexingMOSFLM)
self._edPluginControlIndexingMOSFLM.connectFAILURE(
self.doFailureIndexingMOSFLM)
self._edPluginExecEvaluationIndexingMOSFLM.connectSUCCESS(
self.doSuccessEvaluationIndexingMOSFLM)
self._edPluginExecEvaluationIndexingMOSFLM.connectFAILURE(
self.doFailureEvaluationIndexingMOSFLM)
self._edPluginControlGeneratePrediction.connectSUCCESS(
self.doSuccessGeneratePrediction)
self._edPluginControlGeneratePrediction.connectFAILURE(
self.doFailureGeneratePrediction)
self._edPluginControlIntegration.connectSUCCESS(
self.doSuccessIntegration)
self._edPluginControlIntegration.connectFAILURE(
self.doFailureIntegration)
self._edPluginControlXDSGenerateBackgroundImage.connectSUCCESS(
self.doSuccessXDSGenerateBackgroundImage)
self._edPluginControlXDSGenerateBackgroundImage.connectFAILURE(
self.doFailureXDSGenerateBackgroundImage)
self._edPluginControlStrategy.connectSUCCESS(self.doSuccessStrategy)
self._edPluginControlStrategy.connectFAILURE(self.doFailureStrategy)
self.executePluginSynchronous(self._edPluginControlIndexingIndicators)
def finallyProcess(self, _edObject=None):
EDPluginControl.finallyProcess(self)
self.DEBUG("EDPluginControlCharacterisationv1_4.finallyProcess")
# Synchronize thumbnail plugins
for tuplePlugin in self._listPluginGenerateThumbnail:
image = tuplePlugin[0]
tuplePlugin[1].synchronize()
jpegImage = image.copy()
jpegImage.path = tuplePlugin[1].dataOutput.thumbnail.path
self._xsDataResultCharacterisation.addJpegImage(jpegImage)
tuplePlugin[2].synchronize()
thumbnailImage = image.copy()
thumbnailImage.path = tuplePlugin[2].dataOutput.thumbnail.path
self._xsDataResultCharacterisation.addThumbnailImage(
thumbnailImage)
if self._edPluginControlGeneratePrediction.isRunning():
self._edPluginControlGeneratePrediction.synchronize()
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage),
"statusMessage")
self._xsDataResultCharacterisation.setStatusMessage(
XSDataString(self._strStatusMessage))
if self._strCharacterisationShortSummary != None:
self.setDataOutput(
XSDataString(self._strCharacterisationShortSummary),
"shortSummary")
self._xsDataResultCharacterisation.setShortSummary(
XSDataString(self._strCharacterisationShortSummary))
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
if self.isFailure():
self.sendMessageToMXCuBE("Ended with error messages", "error")
def doSuccessIndexingIndicators(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlCharacterisationv1_4.doSuccessIndexingIndicators")
# self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv1_4.doSuccessIndexingIndicators")
if self._edPluginControlIndexingIndicators.hasDataOutput(
"indexingResult"):
xsDataIndexingResult = self._edPluginControlIndexingIndicators.getDataOutput(
"indexingResult")[0]
# self._xsDataResultCharacterisation.setIndexingResult(xsDataIndexingResult)
self._edPluginExecEvaluationIndexingLABELIT.setDataInput(
xsDataIndexingResult, "indexingResult")
if self._edPluginControlIndexingIndicators.hasDataOutput(
"imageQualityIndicators"):
listXSDataImageQualityIndicators = self._edPluginControlIndexingIndicators.getDataOutput(
"imageQualityIndicators")
for xsDataImageQualityIndicators in listXSDataImageQualityIndicators:
if xsDataImageQualityIndicators.dozor_score:
if self._iNoImagesWithDozorScore is None:
self._iNoImagesWithDozorScore = 0
if xsDataImageQualityIndicators.dozor_score.value > 0.001:
self._iNoImagesWithDozorScore += 1
self._xsDataResultCharacterisation.addImageQualityIndicators(
xsDataImageQualityIndicators)
self._edPluginExecEvaluationIndexingLABELIT.setDataInput(
xsDataImageQualityIndicators, "imageQualityIndicators")
if self._edPluginControlIndexingIndicators.hasDataOutput(
"indicatorsShortSummary"):
indicatorsShortSummary = self._edPluginControlIndexingIndicators.getDataOutput(
"indicatorsShortSummary")[0].getValue()
self._strCharacterisationShortSummary += indicatorsShortSummary
self.sendMessageToMXCuBE(indicatorsShortSummary)
self.executePluginSynchronous(
self._edPluginExecEvaluationIndexingLABELIT)
def doFailureIndexingIndicators(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlCharacterisationv1_4.doFailureIndexingIndicators")
# If more than two reference images try to index with MOSFLM:
if self._edPluginControlIndexingIndicators.hasDataOutput(
"indicatorsShortSummary"):
indicatorsShortSummary = self._edPluginControlIndexingIndicators.getDataOutput(
"indicatorsShortSummary")[0].getValue()
self._strCharacterisationShortSummary += indicatorsShortSummary
self.sendMessageToMXCuBE(indicatorsShortSummary)
if self._iNoImagesWithDozorScore > 0:
if not self._bDoOnlyMoslmfIndexing:
strWarningMessage = "Execution of Indexing and Indicators plugin failed - trying to index with MOSFLM."
self.WARNING(strWarningMessage)
self.sendMessageToMXCuBE(strWarningMessage, "warning")
self.addWarningMessage(strWarningMessage)
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.dataCollection = self._xsDataCollection
xsDataIndexingInput.experimentalCondition = self._xsDataCollection.subWedge[
0].experimentalCondition
xsDataIndexingInput.crystal = self._xsDataCrystal
self._edPluginControlIndexingMOSFLM.dataInput = xsDataIndexingInput
self.executePluginSynchronous(self._edPluginControlIndexingMOSFLM)
else:
strErrorMessage = "Execution of Indexing and Indicators plugin failed. Execution of characterisation aborted."
self.ERROR(strErrorMessage)
self.sendMessageToMXCuBE(strErrorMessage, "error")
self.addErrorMessage(strErrorMessage)
self.generateExecutiveSummary(self)
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
self.setFailure()
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage),
"statusMessage")
self.writeDataOutput()
def doSuccessIndexingMOSFLM(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlCharacterisationv1_4.doSuccessIndexingMOSFLM")
xsDataIndexingResult = self._edPluginControlIndexingMOSFLM.dataOutput
self._edPluginExecEvaluationIndexingMOSFLM.setDataInput(
xsDataIndexingResult, "indexingResult")
self.executePluginSynchronous(
self._edPluginExecEvaluationIndexingMOSFLM)
def doFailureIndexingMOSFLM(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlCharacterisationv1_4.doFailureIndexingMOSFLM")
strErrorMessage = "Indexing with MOSFLM failed."
self.ERROR(strErrorMessage)
self.sendMessageToMXCuBE(strErrorMessage, "error")
self.executePluginSynchronous(
self._edPluginExecEvaluationIndexingMOSFLM)
def doSuccessEvaluationIndexingLABELIT(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlCharacterisationv1_4.doSuccessEvaluationIndexingLABELIT"
)
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlCharacterisationv1_4.doSuccessEvaluationIndexingLABELIT"
)
# Retrieve status messages (if any)
if self._edPluginExecEvaluationIndexingLABELIT.hasDataOutput(
"statusMessageIndexing"):
self.addStatusMessage(
"Labelit: " +
self._edPluginExecEvaluationIndexingLABELIT.getDataOutput(
"statusMessageIndexing")[0].getValue())
# Check if indexing was successful
bIndexingSuccess = self._edPluginExecEvaluationIndexingLABELIT.getDataOutput(
"indexingSuccess")[0].getValue()
if bIndexingSuccess:
xsDataIndexingResult = self._edPluginExecEvaluationIndexingLABELIT.getDataOutput(
"indexingResult")[0]
self._xsDataResultCharacterisation.setIndexingResult(
xsDataIndexingResult)
xsDataCollection = self._xsDataResultCharacterisation.getDataCollection(
)
xsDataGeneratePredictionInput = XSDataGeneratePredictionInput()
xsDataGeneratePredictionInput.setDataCollection(
XSDataCollection.parseString(xsDataCollection.marshal()))
xsDataGeneratePredictionInput.setSelectedIndexingSolution(
XSDataIndexingSolutionSelected.parseString(
xsDataIndexingResult.getSelectedSolution().marshal()))
self._edPluginControlGeneratePrediction.setDataInput(
xsDataGeneratePredictionInput)
if self._edPluginControlIndexingIndicators.hasDataOutput(
"indexingShortSummary"):
indexingShortSummary = self._edPluginControlIndexingIndicators.getDataOutput(
"indexingShortSummary")[0].getValue()
self._strCharacterisationShortSummary += indexingShortSummary
self.sendMessageToMXCuBE(indexingShortSummary)
# Start the generation of prediction images - we synchronize in the post-process
self._edPluginControlGeneratePrediction.execute()
# Then start the integration of the reference images
self.indexingToIntegration()
else:
if self._iNoImagesWithDozorScore > 0:
if not self._bDoOnlyMoslmfIndexing:
strWarningMessage = "Execution of Indexing and Indicators plugin failed - trying to index with MOSFLM."
self.WARNING(strWarningMessage)
self.sendMessageToMXCuBE(strWarningMessage, "warning")
self.addWarningMessage(strWarningMessage)
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.dataCollection = self._xsDataCollection
xsDataIndexingInput.experimentalCondition = self._xsDataCollection.subWedge[
0].experimentalCondition
xsDataIndexingInput.crystal = self._xsDataCrystal
self._edPluginControlIndexingMOSFLM.setDataInput(
xsDataIndexingInput)
self.executePluginSynchronous(
self._edPluginControlIndexingMOSFLM)
else:
strErrorMessage = "Execution of indexing with Labelit failed."
self.ERROR(strErrorMessage)
self.sendMessageToMXCuBE(strErrorMessage, "error")
self.addErrorMessage(strErrorMessage)
self.setFailure()
self.generateExecutiveSummary(self)
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage),
"statusMessage")
self.writeDataOutput()
def doSuccessEvaluationIndexingMOSFLM(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlCharacterisationv1_4.doSuccessEvaluationIndexingMOSFLM"
)
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlCharacterisationv1_4.doSuccessEvaluationIndexingMOSFLM"
)
# Retrieve status messages (if any)
if self._edPluginExecEvaluationIndexingMOSFLM.hasDataOutput(
"statusMessageIndexing"):
self.addStatusMessage(
"MOSFLM: " +
self._edPluginExecEvaluationIndexingMOSFLM.getDataOutput(
"statusMessageIndexing")[0].getValue())
# Check if indexing was successful
bIndexingSuccess = self._edPluginExecEvaluationIndexingMOSFLM.getDataOutput(
"indexingSuccess")[0].getValue()
if bIndexingSuccess:
xsDataIndexingResult = self._edPluginExecEvaluationIndexingMOSFLM.getDataOutput(
"indexingResult")[0]
self._xsDataResultCharacterisation.setIndexingResult(
xsDataIndexingResult)
self._strCharacterisationShortSummary += self.generateIndexingShortSummary(
xsDataIndexingResult)
xsDataCollection = self._xsDataResultCharacterisation.getDataCollection(
)
xsDataGeneratePredictionInput = XSDataGeneratePredictionInput()
xsDataGeneratePredictionInput.setDataCollection(
XSDataCollection.parseString(xsDataCollection.marshal()))
xsDataGeneratePredictionInput.setSelectedIndexingSolution(
XSDataIndexingSolutionSelected.parseString(
xsDataIndexingResult.getSelectedSolution().marshal()))
self._edPluginControlGeneratePrediction.setDataInput(
xsDataGeneratePredictionInput)
if self._edPluginControlIndexingIndicators.hasDataOutput(
"indexingShortSummary"):
self._strCharacterisationShortSummary += self._edPluginControlIndexingIndicators.getDataOutput(
"indexingShortSummary")[0].getValue()
# Start the generation of prediction images - we synchronize in the post-process
self._edPluginControlGeneratePrediction.execute()
# Then start the integration of the reference images
self.indexingToIntegration()
else:
strErrorMessage = "Execution of indexing with MOSFLM failed."
self.ERROR(strErrorMessage)
self.sendMessageToMXCuBE(strErrorMessage, "error")
self.addErrorMessage(strErrorMessage)
self.setFailure()
self.generateExecutiveSummary(self)
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage),
"statusMessage")
self.writeDataOutput()
def generateIndexingShortSummary(self, _xsDataIndexingResult):
"""
Generates a very short summary of the indexing
"""
strIndexingShortSummary = ""
if self.hasDataInput("crystal"):
xsDataCrystal = self.getDataInput("crystal")[0]
if xsDataCrystal.getSpaceGroup() is not None:
strForcedSpaceGroup = xsDataCrystal.getSpaceGroup().getName(
).getValue().upper()
if xsDataCrystal.getSpaceGroup().getName().getValue() != "":
strIndexingShortSummary += "Forced space group: %s\n" % strForcedSpaceGroup
if _xsDataIndexingResult is not None:
# Indexing solution
xsDataSelectedSolution = _xsDataIndexingResult.getSelectedSolution(
)
xsDataCrystal = xsDataSelectedSolution.getCrystal()
# Refined cell parameters
xsDataCell = xsDataCrystal.getCell()
fA = xsDataCell.getLength_a().getValue()
fB = xsDataCell.getLength_b().getValue()
fC = xsDataCell.getLength_c().getValue()
fAlpha = xsDataCell.getAngle_alpha().getValue()
fBeta = xsDataCell.getAngle_beta().getValue()
fGamma = xsDataCell.getAngle_gamma().getValue()
# Estimated mosaicity
fEstimatedMosaicity = xsDataCrystal.getMosaicity().getValue()
# Space group
strSpaceGroup = xsDataCrystal.getSpaceGroup().getName().getValue()
# Spot deviation
xsDataStatisticsIndexing = xsDataSelectedSolution.getStatistics()
fSpotDeviationPositional = xsDataStatisticsIndexing.getSpotDeviationPositional(
).getValue()
strIndexingShortSummary += "Indexing: laue/space group %s, mosaicity %.2f [degree], " % (
strSpaceGroup, fEstimatedMosaicity)
strIndexingShortSummary += "RMS dev pos %.2f [mm]" % fSpotDeviationPositional
if xsDataStatisticsIndexing.getSpotDeviationAngular() is not None:
fSpotDeviationAngular = xsDataStatisticsIndexing.getSpotDeviationAngular(
).getValue()
strIndexingShortSummary += " ang %.2f [degree]" % fSpotDeviationAngular
strIndexingShortSummary += "\n"
strIndexingShortSummary += "Indexing: refined Cell: %7.2f %7.2f %7.2f %7.2f %7.2f %7.2f\n" % (
fA, fB, fC, fAlpha, fBeta, fGamma)
else:
strIndexingShortSummary += "Indexing failed."
return strIndexingShortSummary
def indexingToIntegration(self, _edPlugin=None):
# Run Kappa if configured
if self._runKappa:
xsDataInputControlKappa = XSDataInputControlKappa()
xsDataInputControlKappa.dataCollection = self._xsDataCollection
xsDataInputControlKappa.selectedSolution = self._xsDataResultCharacterisation.indexingResult.selectedSolution
self._edPluginControlKappa.dataInput = xsDataInputControlKappa
self.executePluginSynchronous(self._edPluginControlKappa)
if not self._edPluginControlKappa.isFailure():
self._xsDataResultCharacterisation.kappaReorientation = self._edPluginControlKappa.dataOutput
# Create the XDS background image
xsDataInputControlXDSGenerateBackgroundImage = XSDataInputControlXDSGenerateBackgroundImage(
)
xsDataInputControlXDSGenerateBackgroundImage.setDataCollection(
self._xsDataCollection)
self._edPluginControlXDSGenerateBackgroundImage.setDataInput(
xsDataInputControlXDSGenerateBackgroundImage)
self._edPluginControlXDSGenerateBackgroundImage.execute()
# Integrate the reference images
xsDataIntegrationInput = XSDataIntegrationInput()
xsDataIntegrationInput.setDataCollection(
self._xsDataResultCharacterisation.getDataCollection())
xsDataIndexingResult = self._xsDataResultCharacterisation.getIndexingResult(
)
xsDataExperimentalConditionRefinded = xsDataIndexingResult.getSelectedSolution(
).getExperimentalConditionRefined()
xsDataIntegrationInput.setExperimentalConditionRefined(
xsDataExperimentalConditionRefinded)
xsDataIntegrationInput.setSelectedIndexingSolution(
xsDataIndexingResult.getSelectedSolution())
self._edPluginControlIntegration.setDataInput(xsDataIntegrationInput)
self.executePluginSynchronous(self._edPluginControlIntegration)
def doFailureEvaluationIndexingLABELIT(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlCharacterisationv1_4.doFailureEvaluationIndexing")
strErrorMessage = "Execution of indexing evaluation plugin failed."
self.ERROR(strErrorMessage)
self.sendMessageToMXCuBE(strErrorMessage, "error")
self.addErrorMessage(strErrorMessage)
self.generateExecutiveSummary(self)
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
self.setFailure()
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage),
"statusMessage")
self.writeDataOutput()
def doFailureEvaluationIndexingMOSFLM(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlCharacterisationv1_4.doFailureEvaluationIndexingMOSFLM"
)
strErrorMessage = "Execution of indexing evaluation plugin failed."
self.ERROR(strErrorMessage)
self.sendMessageToMXCuBE(strErrorMessage, "error")
self.addErrorMessage(strErrorMessage)
self.generateExecutiveSummary(self)
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
self.setFailure()
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage),
"statusMessage")
self.writeDataOutput()
def doSuccessGeneratePrediction(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlCharacterisationv1_4.doSuccessGeneratePrediction")
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlCharacterisationv1_4.doSuccessGeneratePrediction")
xsDataGeneratePredictionResult = _edPlugin.getDataOutput()
xsDataIndexingResult = self._xsDataResultCharacterisation.getIndexingResult(
)
xsDataIndexingResult.setPredictionResult(
xsDataGeneratePredictionResult)
def doFailureGeneratePrediction(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlCharacterisationv1_4.doFailureGeneratePrediction")
strWarningMessage = "Execution of generate prediction plugin failed."
self.WARNING(strWarningMessage)
self.addWarningMessage(strWarningMessage)
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
# self.addComment("warning: no prediction images")
def doSuccessIntegration(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_4.doSuccessIntegration")
self.retrieveSuccessMessages(
self._edPluginControlIntegration,
"EDPluginControlCharacterisationv1_4.doSuccessIntegration")
# Wait for XDS plugin if necessary
self._edPluginControlXDSGenerateBackgroundImage.synchronize()
self.addStatusMessage("Integration successful.")
xsDataIntegrationOutput = self._edPluginControlIntegration.getDataOutput(
)
self._xsDataResultCharacterisation.setIntegrationResult(
xsDataIntegrationOutput)
# Integration short summary
if self._edPluginControlIntegration.hasDataOutput(
"integrationShortSummary"):
integrationShortSummary = self._edPluginControlIntegration.getDataOutput(
"integrationShortSummary")[0].getValue()
self._strCharacterisationShortSummary += integrationShortSummary
self.sendMessageToMXCuBE(integrationShortSummary)
# self.DEBUG( self._xsDataExperimentCharacterisation.marshal() )
if self._bDoStrategyCalculation:
xsDataInputStrategy = XSDataInputStrategy()
xsDataSolutionSelected = self._xsDataResultCharacterisation.getIndexingResult(
).getSelectedSolution()
xsDataInputStrategy.setCrystalRefined(
xsDataSolutionSelected.getCrystal())
xsDataInputStrategy.setSample(self._xsDataResultCharacterisation.
getDataCollection().getSample())
xsDataIntegrationSubWedgeResultList = xsDataIntegrationOutput.getIntegrationSubWedgeResult(
)
bFirst = True
for xsDataIntegrationSubWedgeResult in xsDataIntegrationSubWedgeResultList:
if xsDataIntegrationSubWedgeResult.getBestfileHKL(
) is not None:
xsDataInputStrategy.addBestFileContentHKL(
xsDataIntegrationSubWedgeResult.getBestfileHKL())
if bFirst:
xsDataInputStrategy.setBestFileContentDat(
xsDataIntegrationSubWedgeResult.getBestfileDat())
xsDataInputStrategy.setBestFileContentPar(
xsDataIntegrationSubWedgeResult.getBestfilePar())
xsDataInputStrategy.setExperimentalCondition(
xsDataIntegrationSubWedgeResult.
getExperimentalConditionRefined())
bFirst = False
xsDataInputStrategy.setXdsBackgroundImage(
self._xsDataFileXdsBackgroundImage)
xsDataInputStrategy.setDataCollection(self._xsDataCollection)
xsDataInputStrategy.setDiffractionPlan(
self._xsDataResultCharacterisation.getDataCollection(
).getDiffractionPlan())
self._edPluginControlStrategy.setDataInput(xsDataInputStrategy)
self.executePluginSynchronous(self._edPluginControlStrategy)
def doFailureIntegration(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_4.doFailureIntegration")
strErrorMessage = "Execution of integration failed."
self.addStatusMessage("Integration FAILURE.")
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
# self.addComment("integration failure")
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
self.generateExecutiveSummary(self)
self.setFailure()
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage),
"statusMessage")
self.writeDataOutput()
def doSuccessXDSGenerateBackgroundImage(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlCharacterisationv1_4.doSuccessXDSGenerateBackgroundImage"
)
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlCharacterisationv1_4.doSuccessXDSGenerateBackgroundImage"
)
self._xsDataFileXdsBackgroundImage = self._edPluginControlXDSGenerateBackgroundImage.getDataOutput(
).getXdsBackgroundImage()
self._xsDataResultCharacterisation.setXdsBackgroundImage(
self._xsDataFileXdsBackgroundImage)
def doFailureXDSGenerateBackgroundImage(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlCharacterisationv1_4.doFailureXDSGenerateBackgroundImage"
)
def doSuccessStrategy(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_4.doSuccessStrategy")
self.retrieveSuccessMessages(
self._edPluginControlStrategy,
"EDPluginControlCharacterisationv1_4.doSuccessStrategy")
xsDataStrategyResult = self._edPluginControlStrategy.getDataOutput()
self._xsDataResultCharacterisation.setStrategyResult(
xsDataStrategyResult)
if self._edPluginControlStrategy.hasDataOutput("strategyShortSummary"):
strategyShortSummary = self._edPluginControlStrategy.getDataOutput(
"strategyShortSummary")[0].getValue()
self._strCharacterisationShortSummary += strategyShortSummary
self.sendMessageToMXCuBE(strategyShortSummary)
self.addStatusMessage("Strategy calculation successful.")
def doFailureStrategy(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_4.doFailureStrategy")
strErrorMessage = "Strategy calculation FAILURE."
self.ERROR(strErrorMessage)
self.sendMessageToMXCuBE(strErrorMessage, "error")
self.addErrorMessage(strErrorMessage)
xsDataStrategyResult = self._edPluginControlStrategy.getDataOutput()
self._xsDataResultCharacterisation.setStrategyResult(
xsDataStrategyResult)
if self._edPluginControlStrategy.hasDataOutput("strategyShortSummary"):
strategyShortSummary = self._edPluginControlStrategy.getDataOutput(
"strategyShortSummary")[0].getValue()
self._strCharacterisationShortSummary += strategyShortSummary
self.sendMessageToMXCuBE(strategyShortSummary)
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
self.addStatusMessage("Strategy calculation FAILURE.")
self.generateExecutiveSummary(self)
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage),
"statusMessage")
self.writeDataOutput()
self.setFailure()
def generateExecutiveSummary(self, _edPlugin):
"""
Generates a summary of the execution of the plugin.
"""
self.DEBUG(
"EDPluginControlCharacterisationv1_4.generateExecutiveSummary")
self.addExecutiveSummaryLine("Summary of characterisation:")
xsDataInputStrategy = self.getDataInput()
xsDataCollection = xsDataInputStrategy.getDataCollection()
# MXSUP-1445: Check if transmission is less than 10% and warn if it's the case
xsDataFirstSubWedge = xsDataCollection.getSubWedge()[0]
xsDataBeam = xsDataFirstSubWedge.getExperimentalCondition().getBeam()
if xsDataBeam.getTransmission() is not None:
fTransmission = xsDataBeam.getTransmission().getValue()
if fTransmission < self._fMinTransmission:
self.addExecutiveSummaryLine("^" * 80)
self.addExecutiveSummaryLine("^" * 80)
self.addExecutiveSummaryLine("")
self.addExecutiveSummaryLine(
"WARNING! Transmission for characterisation set to %.1f %%"
% fTransmission)
self.addExecutiveSummaryLine(
"Please consider re-characterising with transmission set to 100 %"
)
self.addExecutiveSummaryLine("")
self.addExecutiveSummaryLine("^" * 80)
self.addExecutiveSummaryLine("^" * 80)
xsDataDiffractionPlan = xsDataCollection.getDiffractionPlan()
self.addExecutiveSummaryLine("Diffraction plan:")
if (xsDataDiffractionPlan.getComplexity() is not None):
self.addExecutiveSummaryLine(
"BEST complexity : %s" %
xsDataDiffractionPlan.getComplexity().getValue())
if (xsDataDiffractionPlan.getAimedCompleteness() is not None):
self.addExecutiveSummaryLine(
"Aimed completeness : %6.1f [%%]" %
(100.0 *
xsDataDiffractionPlan.getAimedCompleteness().getValue()))
if (xsDataDiffractionPlan.getRequiredCompleteness() is not None):
self.addExecutiveSummaryLine(
"Required completeness : %6.1f [%%]" %
(100.0 *
xsDataDiffractionPlan.getRequiredCompleteness().getValue()))
if (xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution()
is not None):
self.addExecutiveSummaryLine(
"Aimed I/sigma at highest resolution : %6.1f" %
xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution(
).getValue())
if (xsDataDiffractionPlan.getAimedResolution() is not None):
self.addExecutiveSummaryLine(
"Aimed resolution : %6.1f [A]" %
xsDataDiffractionPlan.getAimedResolution().getValue())
if (xsDataDiffractionPlan.getRequiredResolution() is not None):
self.addExecutiveSummaryLine(
"Required resolution : %6.1f [A]" %
xsDataDiffractionPlan.getRequiredResolution().getValue())
if (xsDataDiffractionPlan.getAimedMultiplicity() is not None):
self.addExecutiveSummaryLine(
"Aimed multiplicity : %6.1f" %
xsDataDiffractionPlan.getAimedMultiplicity().getValue())
if (xsDataDiffractionPlan.getRequiredMultiplicity() is not None):
self.addExecutiveSummaryLine(
"Required multiplicity : %6.1f" %
xsDataDiffractionPlan.getRequiredMultiplicity().getValue())
if (xsDataDiffractionPlan.getForcedSpaceGroup() is not None):
self.addExecutiveSummaryLine(
"Forced space group : %6s" %
xsDataDiffractionPlan.getForcedSpaceGroup().getValue())
if (xsDataDiffractionPlan.getMaxExposureTimePerDataCollection()
is not None):
self.addExecutiveSummaryLine(
"Max exposure time per data collection : %6.1f [s]" %
xsDataDiffractionPlan.getMaxExposureTimePerDataCollection(
).getValue())
self.addExecutiveSummarySeparator()
if self._edPluginControlIndexingIndicators is not None:
self.appendExecutiveSummary(
self._edPluginControlIndexingIndicators, "")
if self._edPluginControlIntegration is not None:
self.appendExecutiveSummary(self._edPluginControlIntegration, "")
if self._edPluginControlStrategy is not None:
self.appendExecutiveSummary(self._edPluginControlStrategy, "")
self.addExecutiveSummarySeparator()
if self._strCharacterisationShortSummary is not None:
self.addExecutiveSummaryLine("Characterisation short summary:")
self.addExecutiveSummaryLine("")
if self._strStatusMessage != None:
for strLine in self._strStatusMessage.split(". "):
if strLine.endswith("."):
self.addExecutiveSummaryLine(strLine)
else:
self.addExecutiveSummaryLine(strLine + ".")
self.addExecutiveSummaryLine("")
for strLine in self._strCharacterisationShortSummary.split("\n"):
if strLine != "\n":
self.addExecutiveSummaryLine(strLine)
self.addErrorWarningMessagesToExecutiveSummary(
"Characterisation error and warning messages: ")
self.addExecutiveSummarySeparator()
def getPluginStrategyName(self):
return self._strPluginControlStrategy
def addStatusMessage(self, _strStatusMessage):
if self._strStatusMessage != "":
self._strStatusMessage += " "
self._strStatusMessage += _strStatusMessage
self.sendMessageToMXCuBE(_strStatusMessage)
def doStrategyCalculation(self, _bValue):
self._bDoStrategyCalculation = _bValue
def sendMessageToMXCuBE(self, _strMessage, level="info"):
# Only for mxCuBE
if self._strMxCuBE_URI is not None:
self.DEBUG("Sending message to mxCuBE: {0}".format(_strMessage))
try:
for strMessage in _strMessage.split("\n"):
if strMessage != "":
self._oServerProxy.log_message(
"Characterisation: " + strMessage, level)
except:
self.DEBUG("Sending message to mxCuBE failed!")
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginControlCharacterisationv1_4.preProcess")
self._xsDataResultCharacterisation = XSDataResultCharacterisation()
# Load the plugins
self._edPluginControlIndexingIndicators = self.loadPlugin(self._strPluginControlIndexingIndicators, \
"Indexing")
self._edPluginExecEvaluationIndexingLABELIT = self.loadPlugin(self._strPluginExecEvaluationIndexing, \
"IndexingEvalualtionLABELIT")
self._edPluginControlIndexingMOSFLM = self.loadPlugin(self._strPluginControlIndexingMOSFLM, \
"IndexingMOSFLM")
self._edPluginExecEvaluationIndexingMOSFLM = self.loadPlugin(self._strPluginExecEvaluationIndexing, \
"IndexingEvalualtionMOSFLM")
self._edPluginControlGeneratePrediction = self.loadPlugin(self._strPluginControlGeneratePrediction, \
"GeneratePrediction")
self._edPluginControlIntegration = self.loadPlugin(self._strPluginControlIntegration, \
"Integration")
self._edPluginControlXDSGenerateBackgroundImage = self.loadPlugin(self._strPluginControlXDSGenerateBackgroundImage, \
"ControlXDSGenerateBackgroundImage")
self._edPluginControlStrategy = self.loadPlugin(self._strPluginControlStrategy, \
"Strategy")
if self._runKappa:
self._edPluginControlKappa = self.loadPlugin(
self._strPluginControlKappaName, "Kappa")
if (self._edPluginControlIndexingIndicators is not None):
self.DEBUG("EDPluginControlCharacterisationv1_4.preProcess: " +
self._strPluginControlIndexingIndicators +
" Found... setting Data Input")
# create Data Input for indexing
xsDataInputCharacterisation = self.getDataInput()
self._xsDataCollection = xsDataInputCharacterisation.getDataCollection(
)
# MXSUP-1445: Check if transmission is less than 10% and warn if it's the case
xsDataFirstSubWedge = self._xsDataCollection.getSubWedge()[0]
xsDataBeam = xsDataFirstSubWedge.getExperimentalCondition(
).getBeam()
if xsDataBeam.getTransmission() is not None:
fTransmission = xsDataBeam.getTransmission().getValue()
if fTransmission < self._fMinTransmission:
strWarningMessageBanner = "^" * 80
strWarningMessage1 = "WARNING! Transmission for characterisation set to %.1f %%" % fTransmission
strWarningMessage2 = "Please consider re-characterising with transmission set to 100 %"
self.warning(strWarningMessageBanner)
self.warning(strWarningMessage1)
self.warning(strWarningMessage2)
self.warning(strWarningMessageBanner)
self.addWarningMessage(strWarningMessageBanner)
self.addWarningMessage(strWarningMessage1)
self.addWarningMessage(strWarningMessage2)
self.addWarningMessage(strWarningMessageBanner)
self.sendMessageToMXCuBE(strWarningMessage1, "warning")
self.sendMessageToMXCuBE(strWarningMessage2, "warning")
xsDataCrystal = None
xsDataSubWedgeList = self._xsDataCollection.getSubWedge()
if ((xsDataSubWedgeList is None) or (xsDataSubWedgeList == [])):
strError = "EDPluginControlCharacterisationv1_4.preProcess: No subwedges in input data."
self.ERROR(strError)
self.setFailure()
else:
# Load the thumbnail plugins
self._iNoReferenceImages = 0
for subWedge in xsDataInputCharacterisation.dataCollection.subWedge:
for image in subWedge.image:
self._iNoReferenceImages += 1
edPluginJpeg = self.loadPlugin(
self._strPluginGenerateThumbnailName)
xsDataInputMXThumbnail = XSDataInputMXThumbnail()
xsDataInputMXThumbnail.image = XSDataFile(image.path)
xsDataInputMXThumbnail.height = XSDataInteger(1024)
xsDataInputMXThumbnail.width = XSDataInteger(1024)
jpegFilename = os.path.splitext(
os.path.basename(image.path.value))[0] + ".jpg"
xsDataInputMXThumbnail.outputPath = XSDataFile(
XSDataString(
os.path.join(self.getWorkingDirectory(),
jpegFilename)))
edPluginJpeg.dataInput = xsDataInputMXThumbnail
edPluginThumnail = self.loadPlugin(
self._strPluginGenerateThumbnailName)
xsDataInputMXThumbnail = XSDataInputMXThumbnail()
xsDataInputMXThumbnail.image = XSDataFile(image.path)
xsDataInputMXThumbnail.height = XSDataInteger(256)
xsDataInputMXThumbnail.width = XSDataInteger(256)
thumbnailFilename = os.path.splitext(
os.path.basename(
image.path.value))[0] + ".thumbnail.jpg"
xsDataInputMXThumbnail.outputPath = XSDataFile(
XSDataString(
os.path.join(self.getWorkingDirectory(),
thumbnailFilename)))
edPluginThumnail.dataInput = xsDataInputMXThumbnail
self._listPluginGenerateThumbnail.append(
(image, edPluginJpeg, edPluginThumnail))
edPluginJpeg.execute()
edPluginThumnail.execute()
xsDataExperimentalCondition = xsDataSubWedgeList[
0].getExperimentalCondition()
# Fix for bug 431: if the flux is zero raise an error
xsDataDoubleFlux = xsDataExperimentalCondition.getBeam(
).getFlux()
if (xsDataDoubleFlux is not None):
if (xsDataDoubleFlux.getValue() < 0.1):
strErrorMessage = "Input flux is negative or close to zero. Execution of characterisation aborted."
self.ERROR(strErrorMessage)
self.sendMessageToMXCuBE(strErrorMessage, "error")
self.addErrorMessage(
"EDPluginControlCharacterisationv1_4.preProcess ERROR: "
+ strErrorMessage)
# self.addComment(strErrorMessage)
self.setFailure()
xsDataDiffractionPlan = self._xsDataCollection.getDiffractionPlan(
)
xsDataStringForcedSpaceGroup = xsDataDiffractionPlan.getForcedSpaceGroup(
)
if (xsDataStringForcedSpaceGroup is not None):
self._xsDataCrystal = XSDataCrystal()
xsDataSpaceGroup = XSDataSpaceGroup()
xsDataSpaceGroup.setName(xsDataStringForcedSpaceGroup)
self._xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
self._edPluginControlIndexingIndicators.setDataInput(
self._xsDataCollection, "dataCollection")
if self._xsDataCrystal is not None:
self._edPluginControlIndexingIndicators.setDataInput(
self._xsDataCrystal, "crystal")
# Populate characterisation object
self._xsDataResultCharacterisation.setDataCollection(
XSDataCollection.parseString(
self._xsDataCollection.marshal()))
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginControlCharacterisationv1_5.preProcess")
self._xsDataResultCharacterisation = XSDataResultCharacterisation()
# Load the plugins
self._edPluginControlIndexingIndicators = self.loadPlugin(self._strPluginControlIndexingIndicators, \
"Indexing")
self._edPluginExecEvaluationIndexingLABELIT = self.loadPlugin(self._strPluginExecEvaluationIndexing, \
"IndexingEvalualtionLABELIT")
self._edPluginControlIndexingMOSFLM = self.loadPlugin(self._strPluginControlIndexingMOSFLM, \
"IndexingMOSFLM")
self._edPluginExecEvaluationIndexingMOSFLM = self.loadPlugin(self._strPluginExecEvaluationIndexing, \
"IndexingEvalualtionMOSFLM")
self._edPluginControlGeneratePrediction = self.loadPlugin(self._strPluginControlGeneratePrediction, \
"GeneratePrediction")
self._edPluginControlIntegration = self.loadPlugin(self._strPluginControlIntegration, \
"Integration")
self._edPluginControlXDSGenerateBackgroundImage = self.loadPlugin(self._strPluginControlXDSGenerateBackgroundImage, \
"ControlXDSGenerateBackgroundImage")
self._edPluginControlStrategy = self.loadPlugin(self._strPluginControlStrategy, \
"Strategy")
if self._runKappa:
self._edPluginControlKappa = self.loadPlugin(self._strPluginControlKappaName, "Kappa")
if (self._edPluginControlIndexingIndicators is not None):
self.DEBUG("EDPluginControlCharacterisationv1_5.preProcess: " + self._strPluginControlIndexingIndicators + " Found... setting Data Input")
# create Data Input for indexing
xsDataInputCharacterisation = self.getDataInput()
self._xsDataCollection = xsDataInputCharacterisation.getDataCollection()
# MXSUP-1445: Check if transmission is less than 10% and warn if it's the case
xsDataFirstSubWedge = self._xsDataCollection.getSubWedge()[0]
xsDataBeam = xsDataFirstSubWedge.getExperimentalCondition().getBeam()
if xsDataBeam.getTransmission() is not None:
fTransmission = xsDataBeam.getTransmission().getValue()
if fTransmission < self._fMinTransmission:
strWarningMessageBanner = "^"*80
strWarningMessage1 = "WARNING! Transmission for characterisation set to %.1f %%" % fTransmission
strWarningMessage2 = "Please consider re-characterising with transmission set to 100 %"
self.warning(strWarningMessageBanner)
self.warning(strWarningMessage1)
self.warning(strWarningMessage2)
self.warning(strWarningMessageBanner)
self.addWarningMessage(strWarningMessageBanner)
self.addWarningMessage(strWarningMessage1)
self.addWarningMessage(strWarningMessage2)
self.addWarningMessage(strWarningMessageBanner)
self.sendMessageToMXCuBE(strWarningMessage1, "warning")
self.sendMessageToMXCuBE(strWarningMessage2, "warning")
xsDataCrystal = None
xsDataSubWedgeList = self._xsDataCollection.getSubWedge()
if ((xsDataSubWedgeList is None) or (xsDataSubWedgeList == [])):
strError = "EDPluginControlCharacterisationv1_5.preProcess: No subwedges in input data."
self.ERROR(strError)
self.setFailure()
else:
xsDataExperimentalCondition = xsDataSubWedgeList[0].getExperimentalCondition()
# Fix for bug 431: if the flux is zero raise an error
xsDataDoubleFlux = xsDataExperimentalCondition.getBeam().getFlux()
if (xsDataDoubleFlux is not None):
if (xsDataDoubleFlux.getValue() < 0.1):
strErrorMessage = "Input flux is negative or close to zero. Execution of characterisation aborted."
self.ERROR(strErrorMessage)
self.sendMessageToMXCuBE(strErrorMessage, "error")
self.addErrorMessage("EDPluginControlCharacterisationv1_5.preProcess ERROR: " + strErrorMessage)
# self.addComment(strErrorMessage)
self.setFailure()
xsDataDiffractionPlan = self._xsDataCollection.getDiffractionPlan()
xsDataStringForcedSpaceGroup = xsDataDiffractionPlan.getForcedSpaceGroup()
if (xsDataStringForcedSpaceGroup is not None):
self._xsDataCrystal = XSDataCrystal()
xsDataSpaceGroup = XSDataSpaceGroup()
xsDataSpaceGroup.setName(xsDataStringForcedSpaceGroup)
self._xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
self._edPluginControlIndexingIndicators.setDataInput(self._xsDataCollection, "dataCollection")
if self._xsDataCrystal is not None:
self._edPluginControlIndexingIndicators.setDataInput(self._xsDataCrystal, "crystal")
# Populate characterisation object
self._xsDataResultCharacterisation.setDataCollection(XSDataCollection.parseString(self._xsDataCollection.marshal()))
# Load the thumbnail plugins
self._iNoReferenceImages = 0
if not self.isFailure():
for subWedge in xsDataInputCharacterisation.dataCollection.subWedge:
for image in subWedge.image:
self._iNoReferenceImages += 1
edPluginJpeg = self.loadPlugin(self._strPluginGenerateThumbnailName)
xsDataInputMXThumbnail = XSDataInputMXThumbnail()
xsDataInputMXThumbnail.image = XSDataFile(image.path)
xsDataInputMXThumbnail.height = XSDataInteger(1024)
xsDataInputMXThumbnail.width = XSDataInteger(1024)
jpegFilename = os.path.splitext(os.path.basename(image.path.value))[0] + ".jpg"
xsDataInputMXThumbnail.outputPath = XSDataFile(XSDataString(os.path.join(self.getWorkingDirectory(), jpegFilename)))
edPluginJpeg.dataInput = xsDataInputMXThumbnail
edPluginThumnail = self.loadPlugin(self._strPluginGenerateThumbnailName)
xsDataInputMXThumbnail = XSDataInputMXThumbnail()
xsDataInputMXThumbnail.image = XSDataFile(image.path)
xsDataInputMXThumbnail.height = XSDataInteger(256)
xsDataInputMXThumbnail.width = XSDataInteger(256)
thumbnailFilename = os.path.splitext(os.path.basename(image.path.value))[0] + ".thumbnail.jpg"
xsDataInputMXThumbnail.outputPath = XSDataFile(XSDataString(os.path.join(self.getWorkingDirectory(), thumbnailFilename)))
edPluginThumnail.dataInput = xsDataInputMXThumbnail
self._listPluginGenerateThumbnail.append((image, edPluginJpeg, edPluginThumnail))
class EDPluginControlCharacterisationv1_5(EDPluginControl):
"""
[To be replaced with a description of EDPluginControlTemplatev10]
"""
def __init__(self):
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputCharacterisation)
self._strPluginControlIndexingIndicators = "EDPluginControlIndexingIndicatorsv1_1"
self._strPluginExecEvaluationIndexing = "EDPluginExecEvaluationIndexingv10"
self._strPluginControlIndexingMOSFLM = "EDPluginControlIndexingMOSFLMv10"
self._strPluginControlGeneratePrediction = "EDPluginControlGeneratePredictionv10"
self._strPluginControlIntegration = "EDPluginControlIntegrationv10"
self._strPluginControlXDSGenerateBackgroundImage = "EDPluginControlXDSGenerateBackgroundImagev1_0"
self._strPluginControlStrategy = "EDPluginControlStrategyv1_3"
self._strPluginGenerateThumbnailName = "EDPluginMXThumbnailv1_1"
self._strPluginControlKappaName = "EDPluginControlKappav1_0"
self._listPluginGenerateThumbnail = []
self._edPluginControlIndexingIndicators = None
self._edPluginExecEvaluationIndexingMOSFLM = None
self._edPluginExecEvaluationIndexingLABELIT = None
self._edPluginControlGeneratePrediction = None
self._edPluginControlIntegration = None
self._edPluginControlXDSGenerateBackgroundImage = None
self._edPluginControlStrategy = None
self._edPluginControlKappa = None
self._xsDataCollection = None
self._xsDataResultCharacterisation = None
self._xsDataIndexingResultMOSFLM = None
self._xsDataCrystal = None
self._strCharacterisationShortSummary = ""
self._strStatusMessage = ""
self._xsDataFileXdsBackgroundImage = None
self._bDoStrategyCalculation = True
self._fMinTransmission = 10 # %
self._iNoReferenceImages = None
self._iNoImagesWithDozorScore = None
self._strMxCuBE_URI = None
self._oServerProxy = None
self._runKappa = False
def checkParameters(self):
"""
Checks the mandatory parameters.
"""
self.DEBUG("EDPluginControlCharacterisationv1_5.checkParameters")
self.checkMandatoryParameters(self.getDataInput(), "Data Input is None")
self.checkMandatoryParameters(self.getDataInput().getDataCollection(), "dataCollection")
self.checkMandatoryParameters(self.getDataInput().getDataCollection().getDiffractionPlan(), "diffractionPlan")
def configure(self):
"""
Gets the configuration parameters (if any).
"""
EDPluginControl.configure(self)
self.DEBUG("EDPluginControlCharacterisationv1_5.configure")
self._strMxCuBE_URI = self.config.get("mxCuBE_URI", None)
if self._strMxCuBE_URI is not None and "mxCuBE_XMLRPC_log" in os.environ.keys():
self.DEBUG("Enabling sending messages to mxCuBE via URI {0}".format(self._strMxCuBE_URI))
self._oServerProxy = xmlrpclib.ServerProxy(self._strMxCuBE_URI)
self._runKappa = self.config.get("runKappa", False)
self._fMinTransmission = self.config.get("minTransmissionWarning", self._fMinTransmission)
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginControlCharacterisationv1_5.preProcess")
self._xsDataResultCharacterisation = XSDataResultCharacterisation()
# Load the plugins
self._edPluginControlIndexingIndicators = self.loadPlugin(self._strPluginControlIndexingIndicators, \
"Indexing")
self._edPluginExecEvaluationIndexingLABELIT = self.loadPlugin(self._strPluginExecEvaluationIndexing, \
"IndexingEvalualtionLABELIT")
self._edPluginControlIndexingMOSFLM = self.loadPlugin(self._strPluginControlIndexingMOSFLM, \
"IndexingMOSFLM")
self._edPluginExecEvaluationIndexingMOSFLM = self.loadPlugin(self._strPluginExecEvaluationIndexing, \
"IndexingEvalualtionMOSFLM")
self._edPluginControlGeneratePrediction = self.loadPlugin(self._strPluginControlGeneratePrediction, \
"GeneratePrediction")
self._edPluginControlIntegration = self.loadPlugin(self._strPluginControlIntegration, \
"Integration")
self._edPluginControlXDSGenerateBackgroundImage = self.loadPlugin(self._strPluginControlXDSGenerateBackgroundImage, \
"ControlXDSGenerateBackgroundImage")
self._edPluginControlStrategy = self.loadPlugin(self._strPluginControlStrategy, \
"Strategy")
if self._runKappa:
self._edPluginControlKappa = self.loadPlugin(self._strPluginControlKappaName, "Kappa")
if (self._edPluginControlIndexingIndicators is not None):
self.DEBUG("EDPluginControlCharacterisationv1_5.preProcess: " + self._strPluginControlIndexingIndicators + " Found... setting Data Input")
# create Data Input for indexing
xsDataInputCharacterisation = self.getDataInput()
self._xsDataCollection = xsDataInputCharacterisation.getDataCollection()
# MXSUP-1445: Check if transmission is less than 10% and warn if it's the case
xsDataFirstSubWedge = self._xsDataCollection.getSubWedge()[0]
xsDataBeam = xsDataFirstSubWedge.getExperimentalCondition().getBeam()
if xsDataBeam.getTransmission() is not None:
fTransmission = xsDataBeam.getTransmission().getValue()
if fTransmission < self._fMinTransmission:
strWarningMessageBanner = "^"*80
strWarningMessage1 = "WARNING! Transmission for characterisation set to %.1f %%" % fTransmission
strWarningMessage2 = "Please consider re-characterising with transmission set to 100 %"
self.warning(strWarningMessageBanner)
self.warning(strWarningMessage1)
self.warning(strWarningMessage2)
self.warning(strWarningMessageBanner)
self.addWarningMessage(strWarningMessageBanner)
self.addWarningMessage(strWarningMessage1)
self.addWarningMessage(strWarningMessage2)
self.addWarningMessage(strWarningMessageBanner)
self.sendMessageToMXCuBE(strWarningMessage1, "warning")
self.sendMessageToMXCuBE(strWarningMessage2, "warning")
xsDataCrystal = None
xsDataSubWedgeList = self._xsDataCollection.getSubWedge()
if ((xsDataSubWedgeList is None) or (xsDataSubWedgeList == [])):
strError = "EDPluginControlCharacterisationv1_5.preProcess: No subwedges in input data."
self.ERROR(strError)
self.setFailure()
else:
xsDataExperimentalCondition = xsDataSubWedgeList[0].getExperimentalCondition()
# Fix for bug 431: if the flux is zero raise an error
xsDataDoubleFlux = xsDataExperimentalCondition.getBeam().getFlux()
if (xsDataDoubleFlux is not None):
if (xsDataDoubleFlux.getValue() < 0.1):
strErrorMessage = "Input flux is negative or close to zero. Execution of characterisation aborted."
self.ERROR(strErrorMessage)
self.sendMessageToMXCuBE(strErrorMessage, "error")
self.addErrorMessage("EDPluginControlCharacterisationv1_5.preProcess ERROR: " + strErrorMessage)
# self.addComment(strErrorMessage)
self.setFailure()
xsDataDiffractionPlan = self._xsDataCollection.getDiffractionPlan()
xsDataStringForcedSpaceGroup = xsDataDiffractionPlan.getForcedSpaceGroup()
if (xsDataStringForcedSpaceGroup is not None):
self._xsDataCrystal = XSDataCrystal()
xsDataSpaceGroup = XSDataSpaceGroup()
xsDataSpaceGroup.setName(xsDataStringForcedSpaceGroup)
self._xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
self._edPluginControlIndexingIndicators.setDataInput(self._xsDataCollection, "dataCollection")
if self._xsDataCrystal is not None:
self._edPluginControlIndexingIndicators.setDataInput(self._xsDataCrystal, "crystal")
# Populate characterisation object
self._xsDataResultCharacterisation.setDataCollection(XSDataCollection.parseString(self._xsDataCollection.marshal()))
# Load the thumbnail plugins
self._iNoReferenceImages = 0
if not self.isFailure():
for subWedge in xsDataInputCharacterisation.dataCollection.subWedge:
for image in subWedge.image:
self._iNoReferenceImages += 1
edPluginJpeg = self.loadPlugin(self._strPluginGenerateThumbnailName)
xsDataInputMXThumbnail = XSDataInputMXThumbnail()
xsDataInputMXThumbnail.image = XSDataFile(image.path)
xsDataInputMXThumbnail.height = XSDataInteger(1024)
xsDataInputMXThumbnail.width = XSDataInteger(1024)
jpegFilename = os.path.splitext(os.path.basename(image.path.value))[0] + ".jpg"
xsDataInputMXThumbnail.outputPath = XSDataFile(XSDataString(os.path.join(self.getWorkingDirectory(), jpegFilename)))
edPluginJpeg.dataInput = xsDataInputMXThumbnail
edPluginThumnail = self.loadPlugin(self._strPluginGenerateThumbnailName)
xsDataInputMXThumbnail = XSDataInputMXThumbnail()
xsDataInputMXThumbnail.image = XSDataFile(image.path)
xsDataInputMXThumbnail.height = XSDataInteger(256)
xsDataInputMXThumbnail.width = XSDataInteger(256)
thumbnailFilename = os.path.splitext(os.path.basename(image.path.value))[0] + ".thumbnail.jpg"
xsDataInputMXThumbnail.outputPath = XSDataFile(XSDataString(os.path.join(self.getWorkingDirectory(), thumbnailFilename)))
edPluginThumnail.dataInput = xsDataInputMXThumbnail
self._listPluginGenerateThumbnail.append((image, edPluginJpeg, edPluginThumnail))
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlCharacterisationv1_5.process")
self._edPluginControlIndexingIndicators.connectSUCCESS(self.doSuccessIndexingIndicators)
self._edPluginControlIndexingIndicators.connectFAILURE(self.doFailureIndexingIndicators)
self._edPluginExecEvaluationIndexingLABELIT.connectSUCCESS(self.doSuccessEvaluationIndexingLABELIT)
self._edPluginExecEvaluationIndexingLABELIT.connectFAILURE(self.doFailureEvaluationIndexingLABELIT)
self._edPluginControlIndexingMOSFLM.connectSUCCESS(self.doSuccessIndexingMOSFLM)
self._edPluginControlIndexingMOSFLM.connectFAILURE(self.doFailureIndexingMOSFLM)
self._edPluginExecEvaluationIndexingMOSFLM.connectSUCCESS(self.doSuccessEvaluationIndexingMOSFLM)
self._edPluginExecEvaluationIndexingMOSFLM.connectFAILURE(self.doFailureEvaluationIndexingMOSFLM)
self._edPluginControlGeneratePrediction.connectSUCCESS(self.doSuccessGeneratePrediction)
self._edPluginControlGeneratePrediction.connectFAILURE(self.doFailureGeneratePrediction)
self._edPluginControlIntegration.connectSUCCESS(self.doSuccessIntegration)
self._edPluginControlIntegration.connectFAILURE(self.doFailureIntegration)
self._edPluginControlXDSGenerateBackgroundImage.connectSUCCESS(self.doSuccessXDSGenerateBackgroundImage)
self._edPluginControlXDSGenerateBackgroundImage.connectFAILURE(self.doFailureXDSGenerateBackgroundImage)
self._edPluginControlStrategy.connectSUCCESS(self.doSuccessStrategy)
self._edPluginControlStrategy.connectFAILURE(self.doFailureStrategy)
self.executePluginSynchronous(self._edPluginControlIndexingIndicators)
def finallyProcess(self, _edObject=None):
EDPluginControl.finallyProcess(self)
self.DEBUG("EDPluginControlCharacterisationv1_5.finallyProcess")
# Synchronize thumbnail plugins
for tuplePlugin in self._listPluginGenerateThumbnail:
image = tuplePlugin[0]
tuplePlugin[1].synchronize()
jpegImage = image.copy()
jpegImage.path = tuplePlugin[1].dataOutput.thumbnail.path
self._xsDataResultCharacterisation.addJpegImage(jpegImage)
tuplePlugin[2].synchronize()
thumbnailImage = image.copy()
thumbnailImage.path = tuplePlugin[2].dataOutput.thumbnail.path
self._xsDataResultCharacterisation.addThumbnailImage(thumbnailImage)
if self._edPluginControlGeneratePrediction.isRunning():
self._edPluginControlGeneratePrediction.synchronize()
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage), "statusMessage")
self._xsDataResultCharacterisation.setStatusMessage(XSDataString(self._strStatusMessage))
if self._strCharacterisationShortSummary != None:
self.setDataOutput(XSDataString(self._strCharacterisationShortSummary), "shortSummary")
self._xsDataResultCharacterisation.setShortSummary(XSDataString(self._strCharacterisationShortSummary))
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
if self.isFailure():
self.sendMessageToMXCuBE("Ended with error messages", "error")
def doSuccessIndexingIndicators(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_5.doSuccessIndexingIndicators")
# self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv1_5.doSuccessIndexingIndicators")
if self._edPluginControlIndexingIndicators.hasDataOutput("indexingResult"):
xsDataIndexingResult = self._edPluginControlIndexingIndicators.getDataOutput("indexingResult")[0]
# self._xsDataResultCharacterisation.setIndexingResult(xsDataIndexingResult)
self._edPluginExecEvaluationIndexingLABELIT.setDataInput(xsDataIndexingResult, "indexingResult")
if self._edPluginControlIndexingIndicators.hasDataOutput("imageQualityIndicators"):
listXSDataImageQualityIndicators = self._edPluginControlIndexingIndicators.getDataOutput("imageQualityIndicators")
for xsDataImageQualityIndicators in listXSDataImageQualityIndicators:
if xsDataImageQualityIndicators.dozor_score:
if self._iNoImagesWithDozorScore is None:
self._iNoImagesWithDozorScore = 0
if xsDataImageQualityIndicators.dozor_score.value > 0.001:
self._iNoImagesWithDozorScore += 1
self._xsDataResultCharacterisation.addImageQualityIndicators(xsDataImageQualityIndicators)
self._edPluginExecEvaluationIndexingLABELIT.setDataInput(xsDataImageQualityIndicators, "imageQualityIndicators")
if self._edPluginControlIndexingIndicators.hasDataOutput("indicatorsShortSummary"):
indicatorsShortSummary = self._edPluginControlIndexingIndicators.getDataOutput("indicatorsShortSummary")[0].getValue()
self._strCharacterisationShortSummary += indicatorsShortSummary
self.sendMessageToMXCuBE(indicatorsShortSummary)
for tuplePlugin in self._listPluginGenerateThumbnail:
tuplePlugin[1].execute()
tuplePlugin[2].execute()
self.executePluginSynchronous(self._edPluginExecEvaluationIndexingLABELIT)
def doFailureIndexingIndicators(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_5.doFailureIndexingIndicators")
# If more than two reference images try to index with MOSFLM:
if self._edPluginControlIndexingIndicators.hasDataOutput("indicatorsShortSummary"):
indicatorsShortSummary = self._edPluginControlIndexingIndicators.getDataOutput("indicatorsShortSummary")[0].getValue()
self._strCharacterisationShortSummary += indicatorsShortSummary
self.sendMessageToMXCuBE(indicatorsShortSummary)
if self._iNoImagesWithDozorScore > 0:
strWarningMessage = "Execution of Indexing and Indicators plugin failed - trying to index with MOSFLM."
self.WARNING(strWarningMessage)
self.sendMessageToMXCuBE(strWarningMessage, "warning")
self.addWarningMessage(strWarningMessage)
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.dataCollection = self._xsDataCollection
xsDataIndexingInput.experimentalCondition = self._xsDataCollection.subWedge[0].experimentalCondition
xsDataIndexingInput.crystal = self._xsDataCrystal
self._edPluginControlIndexingMOSFLM.dataInput = xsDataIndexingInput
self.executePluginSynchronous(self._edPluginControlIndexingMOSFLM)
else:
strErrorMessage = "Execution of Indexing and Indicators plugin failed. Execution of characterisation aborted."
self.ERROR(strErrorMessage)
self.sendMessageToMXCuBE(strErrorMessage, "error")
self.addErrorMessage(strErrorMessage)
self.generateExecutiveSummary(self)
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
self.setFailure()
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage), "statusMessage")
self.writeDataOutput()
def doSuccessIndexingMOSFLM(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_5.doSuccessIndexingMOSFLM")
xsDataIndexingResult = self._edPluginControlIndexingMOSFLM.dataOutput
self._edPluginExecEvaluationIndexingMOSFLM.setDataInput(xsDataIndexingResult, "indexingResult")
self.executePluginSynchronous(self._edPluginExecEvaluationIndexingMOSFLM)
def doFailureIndexingMOSFLM(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_5.doFailureIndexingMOSFLM")
strErrorMessage = "Indexing with MOSFLM failed."
self.ERROR(strErrorMessage)
self.sendMessageToMXCuBE(strErrorMessage, "error")
self.executePluginSynchronous(self._edPluginExecEvaluationIndexingMOSFLM)
def doSuccessEvaluationIndexingLABELIT(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_5.doSuccessEvaluationIndexingLABELIT")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv1_5.doSuccessEvaluationIndexingLABELIT")
# Retrieve status messages (if any)
if self._edPluginExecEvaluationIndexingLABELIT.hasDataOutput("statusMessageIndexing"):
self.addStatusMessage("Labelit: " + self._edPluginExecEvaluationIndexingLABELIT.getDataOutput("statusMessageIndexing")[0].getValue())
# Check if indexing was successful
bIndexingSuccess = self._edPluginExecEvaluationIndexingLABELIT.getDataOutput("indexingSuccess")[0].getValue()
if bIndexingSuccess:
xsDataIndexingResult = self._edPluginExecEvaluationIndexingLABELIT.getDataOutput("indexingResult")[0]
self._xsDataResultCharacterisation.setIndexingResult(xsDataIndexingResult)
if self._edPluginControlIndexingIndicators.hasDataOutput("indexingShortSummary"):
self._strCharacterisationShortSummary += self._edPluginControlIndexingIndicators.getDataOutput("indexingShortSummary")[0].getValue()
xsDataCollection = self._xsDataResultCharacterisation.getDataCollection()
xsDataGeneratePredictionInput = XSDataGeneratePredictionInput()
xsDataGeneratePredictionInput.setDataCollection(XSDataCollection.parseString(xsDataCollection.marshal()))
xsDataGeneratePredictionInput.setSelectedIndexingSolution(XSDataIndexingSolutionSelected.parseString(xsDataIndexingResult.getSelectedSolution().marshal()))
self._edPluginControlGeneratePrediction.setDataInput(xsDataGeneratePredictionInput)
if self._edPluginControlIndexingIndicators.hasDataOutput("indexingShortSummary"):
indexingShortSummary = self._edPluginControlIndexingIndicators.getDataOutput("indexingShortSummary")[0].getValue()
self._strCharacterisationShortSummary += indexingShortSummary
self.sendMessageToMXCuBE(indexingShortSummary)
# Start the generation of prediction images - we synchronize in the post-process
self._edPluginControlGeneratePrediction.execute()
# Then start the integration of the reference images
self.indexingToIntegration()
else:
if self._iNoImagesWithDozorScore > 0:
strWarningMessage = "Execution of Indexing and Indicators plugin failed - trying to index with MOSFLM."
self.WARNING(strWarningMessage)
self.sendMessageToMXCuBE(strWarningMessage, "warning")
self.addWarningMessage(strWarningMessage)
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.dataCollection = self._xsDataCollection
xsDataIndexingInput.experimentalCondition = self._xsDataCollection.subWedge[0].experimentalCondition
xsDataIndexingInput.crystal = self._xsDataCrystal
self._edPluginControlIndexingMOSFLM.setDataInput(xsDataIndexingInput)
self.executePluginSynchronous(self._edPluginControlIndexingMOSFLM)
else:
strErrorMessage = "Execution of indexing with Labelit failed."
self.ERROR(strErrorMessage)
self.sendMessageToMXCuBE(strErrorMessage, "error")
self.addErrorMessage(strErrorMessage)
self.setFailure()
self.generateExecutiveSummary(self)
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage), "statusMessage")
self.writeDataOutput()
def doSuccessEvaluationIndexingMOSFLM(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_5.doSuccessEvaluationIndexingMOSFLM")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv1_5.doSuccessEvaluationIndexingMOSFLM")
# Retrieve status messages (if any)
if self._edPluginExecEvaluationIndexingMOSFLM.hasDataOutput("statusMessageIndexing"):
self.addStatusMessage("MOSFLM: " + self._edPluginExecEvaluationIndexingMOSFLM.getDataOutput("statusMessageIndexing")[0].getValue())
# Check if indexing was successful
bIndexingSuccess = self._edPluginExecEvaluationIndexingMOSFLM.getDataOutput("indexingSuccess")[0].getValue()
if bIndexingSuccess:
xsDataIndexingResult = self._edPluginExecEvaluationIndexingMOSFLM.getDataOutput("indexingResult")[0]
self._xsDataResultCharacterisation.setIndexingResult(xsDataIndexingResult)
self._strCharacterisationShortSummary += self.generateIndexingShortSummary(xsDataIndexingResult)
xsDataCollection = self._xsDataResultCharacterisation.getDataCollection()
xsDataGeneratePredictionInput = XSDataGeneratePredictionInput()
xsDataGeneratePredictionInput.setDataCollection(XSDataCollection.parseString(xsDataCollection.marshal()))
xsDataGeneratePredictionInput.setSelectedIndexingSolution(XSDataIndexingSolutionSelected.parseString(xsDataIndexingResult.getSelectedSolution().marshal()))
self._edPluginControlGeneratePrediction.setDataInput(xsDataGeneratePredictionInput)
if self._edPluginControlIndexingIndicators.hasDataOutput("indexingShortSummary"):
self._strCharacterisationShortSummary += self._edPluginControlIndexingIndicators.getDataOutput("indexingShortSummary")[0].getValue()
# Start the generation of prediction images - we synchronize in the post-process
self._edPluginControlGeneratePrediction.execute()
# Then start the integration of the reference images
self.indexingToIntegration()
else:
strErrorMessage = "Execution of indexing with MOSFLM failed."
self.ERROR(strErrorMessage)
self.sendMessageToMXCuBE(strErrorMessage, "error")
self.addErrorMessage(strErrorMessage)
self.setFailure()
self.generateExecutiveSummary(self)
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage), "statusMessage")
self.writeDataOutput()
def generateIndexingShortSummary(self, _xsDataIndexingResult):
"""
Generates a very short summary of the indexing
"""
strIndexingShortSummary = ""
if self.hasDataInput("crystal"):
xsDataCrystal = self.getDataInput("crystal")[0]
if xsDataCrystal.getSpaceGroup() is not None:
strForcedSpaceGroup = xsDataCrystal.getSpaceGroup().getName().getValue().upper()
if xsDataCrystal.getSpaceGroup().getName().getValue() != "":
strIndexingShortSummary += "Forced space group: %s\n" % strForcedSpaceGroup
if _xsDataIndexingResult is not None:
# Indexing solution
xsDataSelectedSolution = _xsDataIndexingResult.getSelectedSolution()
xsDataCrystal = xsDataSelectedSolution.getCrystal()
# Refined cell parameters
xsDataCell = xsDataCrystal.getCell()
fA = xsDataCell.getLength_a().getValue()
fB = xsDataCell.getLength_b().getValue()
fC = xsDataCell.getLength_c().getValue()
fAlpha = xsDataCell.getAngle_alpha().getValue()
fBeta = xsDataCell.getAngle_beta().getValue()
fGamma = xsDataCell.getAngle_gamma().getValue()
# Estimated mosaicity
fEstimatedMosaicity = xsDataCrystal.getMosaicity().getValue()
# Space group
strSpaceGroup = xsDataCrystal.getSpaceGroup().getName().getValue()
# Spot deviation
xsDataStatisticsIndexing = xsDataSelectedSolution.getStatistics()
fSpotDeviationPositional = xsDataStatisticsIndexing.getSpotDeviationPositional().getValue()
strIndexingShortSummary += "Indexing: laue/space group %s, mosaicity %.2f [degree], " % (strSpaceGroup, fEstimatedMosaicity)
strIndexingShortSummary += "RMS dev pos %.2f [mm]" % fSpotDeviationPositional
if xsDataStatisticsIndexing.getSpotDeviationAngular() is not None:
fSpotDeviationAngular = xsDataStatisticsIndexing.getSpotDeviationAngular().getValue()
strIndexingShortSummary += " ang %.2f [degree]" % fSpotDeviationAngular
strIndexingShortSummary += "\n"
strIndexingShortSummary += "Indexing: refined Cell: %7.2f %7.2f %7.2f %7.2f %7.2f %7.2f\n" % (fA, fB, fC, fAlpha, fBeta, fGamma)
else:
strIndexingShortSummary += "Indexing failed."
return strIndexingShortSummary
def indexingToIntegration(self, _edPlugin=None):
# Run Kappa if configured
if self._runKappa:
xsDataInputControlKappa = XSDataInputControlKappa()
xsDataInputControlKappa.dataCollection = self._xsDataCollection
xsDataInputControlKappa.selectedSolution = self._xsDataResultCharacterisation.indexingResult.selectedSolution
self._edPluginControlKappa.dataInput = xsDataInputControlKappa
self.executePluginSynchronous(self._edPluginControlKappa)
if not self._edPluginControlKappa.isFailure():
self._xsDataResultCharacterisation.kappaReorientation = self._edPluginControlKappa.dataOutput
# Create the XDS background image
xsDataInputControlXDSGenerateBackgroundImage = XSDataInputControlXDSGenerateBackgroundImage()
xsDataInputControlXDSGenerateBackgroundImage.setDataCollection(self._xsDataCollection)
self._edPluginControlXDSGenerateBackgroundImage.setDataInput(xsDataInputControlXDSGenerateBackgroundImage)
self._edPluginControlXDSGenerateBackgroundImage.execute()
# Integrate the reference images
xsDataIntegrationInput = XSDataIntegrationInput()
xsDataIntegrationInput.setDataCollection(self._xsDataResultCharacterisation.getDataCollection())
xsDataIndexingResult = self._xsDataResultCharacterisation.getIndexingResult()
xsDataExperimentalConditionRefinded = xsDataIndexingResult.getSelectedSolution().getExperimentalConditionRefined()
xsDataIntegrationInput.setExperimentalConditionRefined(xsDataExperimentalConditionRefinded)
xsDataIntegrationInput.setSelectedIndexingSolution(xsDataIndexingResult.getSelectedSolution())
self._edPluginControlIntegration.setDataInput(xsDataIntegrationInput)
self.executePluginSynchronous(self._edPluginControlIntegration)
def doFailureEvaluationIndexingLABELIT(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_5.doFailureEvaluationIndexing")
strErrorMessage = "Execution of indexing evaluation plugin failed."
self.ERROR(strErrorMessage)
self.sendMessageToMXCuBE(strErrorMessage, "error")
self.addErrorMessage(strErrorMessage)
self.generateExecutiveSummary(self)
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
self.setFailure()
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage), "statusMessage")
self.writeDataOutput()
def doFailureEvaluationIndexingMOSFLM(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_5.doFailureEvaluationIndexingMOSFLM")
strErrorMessage = "Execution of indexing evaluation plugin failed."
self.ERROR(strErrorMessage)
self.sendMessageToMXCuBE(strErrorMessage, "error")
self.addErrorMessage(strErrorMessage)
self.generateExecutiveSummary(self)
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
self.setFailure()
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage), "statusMessage")
self.writeDataOutput()
def doSuccessGeneratePrediction(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_5.doSuccessGeneratePrediction")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv1_5.doSuccessGeneratePrediction")
xsDataGeneratePredictionResult = _edPlugin.getDataOutput()
xsDataIndexingResult = self._xsDataResultCharacterisation.getIndexingResult()
xsDataIndexingResult.setPredictionResult(xsDataGeneratePredictionResult)
def doFailureGeneratePrediction(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_5.doFailureGeneratePrediction")
strWarningMessage = "Execution of generate prediction plugin failed."
self.WARNING(strWarningMessage)
self.addWarningMessage(strWarningMessage)
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
# self.addComment("warning: no prediction images")
def doSuccessIntegration(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_5.doSuccessIntegration")
self.retrieveSuccessMessages(self._edPluginControlIntegration, "EDPluginControlCharacterisationv1_5.doSuccessIntegration")
# Wait for XDS plugin if necessary
self._edPluginControlXDSGenerateBackgroundImage.synchronize()
self.addStatusMessage("Integration successful.")
xsDataIntegrationOutput = self._edPluginControlIntegration.getDataOutput()
self._xsDataResultCharacterisation.setIntegrationResult(xsDataIntegrationOutput)
# Integration short summary
if self._edPluginControlIntegration.hasDataOutput("integrationShortSummary"):
integrationShortSummary = self._edPluginControlIntegration.getDataOutput("integrationShortSummary")[0].getValue()
self._strCharacterisationShortSummary += integrationShortSummary
self.sendMessageToMXCuBE(integrationShortSummary)
# self.DEBUG( self._xsDataExperimentCharacterisation.marshal() )
if self._bDoStrategyCalculation:
xsDataInputStrategy = XSDataInputStrategy()
xsDataSolutionSelected = self._xsDataResultCharacterisation.getIndexingResult().getSelectedSolution()
xsDataInputStrategy.setCrystalRefined(xsDataSolutionSelected.getCrystal())
xsDataInputStrategy.setSample(self._xsDataResultCharacterisation.getDataCollection().getSample())
xsDataIntegrationSubWedgeResultList = xsDataIntegrationOutput.getIntegrationSubWedgeResult()
bFirst = True
for xsDataIntegrationSubWedgeResult in xsDataIntegrationSubWedgeResultList:
if xsDataIntegrationSubWedgeResult.getBestfileHKL() is not None:
xsDataInputStrategy.addBestFileContentHKL(xsDataIntegrationSubWedgeResult.getBestfileHKL())
if bFirst:
xsDataInputStrategy.setBestFileContentDat(xsDataIntegrationSubWedgeResult.getBestfileDat())
xsDataInputStrategy.setBestFileContentPar(xsDataIntegrationSubWedgeResult.getBestfilePar())
xsDataInputStrategy.setExperimentalCondition(xsDataIntegrationSubWedgeResult.getExperimentalConditionRefined())
bFirst = False
xsDataInputStrategy.setXdsBackgroundImage(self._xsDataFileXdsBackgroundImage)
xsDataInputStrategy.setDataCollection(self._xsDataCollection)
xsDataInputStrategy.setDiffractionPlan(self._xsDataResultCharacterisation.getDataCollection().getDiffractionPlan())
self._edPluginControlStrategy.setDataInput(xsDataInputStrategy)
self.executePluginSynchronous(self._edPluginControlStrategy)
def doFailureIntegration(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_5.doFailureIntegration")
strErrorMessage = "Execution of integration failed."
self.addStatusMessage("Integration FAILURE.")
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
# self.addComment("integration failure")
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
self.generateExecutiveSummary(self)
self.setFailure()
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage), "statusMessage")
self.writeDataOutput()
def doSuccessXDSGenerateBackgroundImage(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_5.doSuccessXDSGenerateBackgroundImage")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv1_5.doSuccessXDSGenerateBackgroundImage")
self._xsDataFileXdsBackgroundImage = self._edPluginControlXDSGenerateBackgroundImage.getDataOutput().getXdsBackgroundImage()
self._xsDataResultCharacterisation.setXdsBackgroundImage(self._xsDataFileXdsBackgroundImage)
def doFailureXDSGenerateBackgroundImage(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_5.doFailureXDSGenerateBackgroundImage")
def doSuccessStrategy(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_5.doSuccessStrategy")
self.retrieveSuccessMessages(self._edPluginControlStrategy, "EDPluginControlCharacterisationv1_5.doSuccessStrategy")
xsDataStrategyResult = self._edPluginControlStrategy.getDataOutput()
self._xsDataResultCharacterisation.setStrategyResult(xsDataStrategyResult)
if self._edPluginControlStrategy.hasDataOutput("strategyShortSummary"):
strategyShortSummary = self._edPluginControlStrategy.getDataOutput("strategyShortSummary")[0].getValue()
self._strCharacterisationShortSummary += strategyShortSummary
self.sendMessageToMXCuBE(strategyShortSummary)
self.addStatusMessage("Strategy calculation successful.")
def doFailureStrategy(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_5.doFailureStrategy")
strErrorMessage = "Strategy calculation FAILURE."
self.ERROR(strErrorMessage)
self.sendMessageToMXCuBE(strErrorMessage, "error")
self.addErrorMessage(strErrorMessage)
xsDataStrategyResult = self._edPluginControlStrategy.getDataOutput()
self._xsDataResultCharacterisation.setStrategyResult(xsDataStrategyResult)
if self._edPluginControlStrategy.hasDataOutput("strategyShortSummary"):
strategyShortSummary = self._edPluginControlStrategy.getDataOutput("strategyShortSummary")[0].getValue()
self._strCharacterisationShortSummary += strategyShortSummary
self.sendMessageToMXCuBE(strategyShortSummary)
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
self.addStatusMessage("Strategy calculation FAILURE.")
self.generateExecutiveSummary(self)
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage), "statusMessage")
self.writeDataOutput()
self.setFailure()
def generateExecutiveSummary(self, _edPlugin):
"""
Generates a summary of the execution of the plugin.
"""
self.DEBUG("EDPluginControlCharacterisationv1_5.generateExecutiveSummary")
self.addExecutiveSummaryLine("Summary of characterisation:")
xsDataInputStrategy = self.getDataInput()
xsDataCollection = xsDataInputStrategy.getDataCollection()
# MXSUP-1445: Check if transmission is less than 10% and warn if it's the case
xsDataFirstSubWedge = xsDataCollection.getSubWedge()[0]
xsDataBeam = xsDataFirstSubWedge.getExperimentalCondition().getBeam()
if xsDataBeam.getTransmission() is not None:
fTransmission = xsDataBeam.getTransmission().getValue()
if fTransmission < self._fMinTransmission:
self.addExecutiveSummaryLine("^"*80)
self.addExecutiveSummaryLine("^"*80)
self.addExecutiveSummaryLine("")
self.addExecutiveSummaryLine("WARNING! Transmission for characterisation set to %.1f %%" % fTransmission)
self.addExecutiveSummaryLine("Please consider re-characterising with transmission set to 100 %")
self.addExecutiveSummaryLine("")
self.addExecutiveSummaryLine("^"*80)
self.addExecutiveSummaryLine("^"*80)
xsDataDiffractionPlan = xsDataCollection.getDiffractionPlan()
self.addExecutiveSummaryLine("Diffraction plan:")
if (xsDataDiffractionPlan.getComplexity() is not None):
self.addExecutiveSummaryLine("BEST complexity : %s" % xsDataDiffractionPlan.getComplexity().getValue())
if (xsDataDiffractionPlan.getAimedCompleteness() is not None):
self.addExecutiveSummaryLine("Aimed completeness : %6.1f [%%]" % (100.0 * xsDataDiffractionPlan.getAimedCompleteness().getValue()))
if (xsDataDiffractionPlan.getRequiredCompleteness() is not None):
self.addExecutiveSummaryLine("Required completeness : %6.1f [%%]" % (100.0 * xsDataDiffractionPlan.getRequiredCompleteness().getValue()))
if (xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution() is not None):
self.addExecutiveSummaryLine("Aimed I/sigma at highest resolution : %6.1f" % xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution().getValue())
if (xsDataDiffractionPlan.getAimedResolution() is not None):
self.addExecutiveSummaryLine("Aimed resolution : %6.1f [A]" % xsDataDiffractionPlan.getAimedResolution().getValue())
if (xsDataDiffractionPlan.getRequiredResolution() is not None):
self.addExecutiveSummaryLine("Required resolution : %6.1f [A]" % xsDataDiffractionPlan.getRequiredResolution().getValue())
if (xsDataDiffractionPlan.getAimedMultiplicity() is not None):
self.addExecutiveSummaryLine("Aimed multiplicity : %6.1f" % xsDataDiffractionPlan.getAimedMultiplicity().getValue())
if (xsDataDiffractionPlan.getRequiredMultiplicity() is not None):
self.addExecutiveSummaryLine("Required multiplicity : %6.1f" % xsDataDiffractionPlan.getRequiredMultiplicity().getValue())
if (xsDataDiffractionPlan.getForcedSpaceGroup() is not None):
self.addExecutiveSummaryLine("Forced space group : %6s" % xsDataDiffractionPlan.getForcedSpaceGroup().getValue())
if (xsDataDiffractionPlan.getMaxExposureTimePerDataCollection() is not None):
self.addExecutiveSummaryLine("Max exposure time per data collection : %6.1f [s]" % xsDataDiffractionPlan.getMaxExposureTimePerDataCollection().getValue())
self.addExecutiveSummarySeparator()
if self._edPluginControlIndexingIndicators is not None:
self.appendExecutiveSummary(self._edPluginControlIndexingIndicators, "")
if self._edPluginControlIntegration is not None:
self.appendExecutiveSummary(self._edPluginControlIntegration, "")
if self._edPluginControlStrategy is not None:
self.appendExecutiveSummary(self._edPluginControlStrategy, "")
self.addExecutiveSummarySeparator()
if self._strCharacterisationShortSummary is not None:
self.addExecutiveSummaryLine("Characterisation short summary:")
self.addExecutiveSummaryLine("")
if self._strStatusMessage != None:
for strLine in self._strStatusMessage.split(". "):
if strLine.endswith("."):
self.addExecutiveSummaryLine(strLine)
else:
self.addExecutiveSummaryLine(strLine + ".")
self.addExecutiveSummaryLine("")
for strLine in self._strCharacterisationShortSummary.split("\n"):
if strLine != "\n":
self.addExecutiveSummaryLine(strLine)
self.addErrorWarningMessagesToExecutiveSummary("Characterisation error and warning messages: ")
self.addExecutiveSummarySeparator()
def getPluginStrategyName(self):
return self._strPluginControlStrategy
def addStatusMessage(self, _strStatusMessage):
if self._strStatusMessage != "":
self._strStatusMessage += " "
self._strStatusMessage += _strStatusMessage
self.sendMessageToMXCuBE(_strStatusMessage)
def doStrategyCalculation(self, _bValue):
self._bDoStrategyCalculation = _bValue
def sendMessageToMXCuBE(self, _strMessage, level="info"):
# Only for mxCuBE
if self._strMxCuBE_URI is not None:
self.DEBUG("Sending message to mxCuBE: {0}".format(_strMessage))
try:
for strMessage in _strMessage.split("\n"):
if strMessage != "":
self._oServerProxy.log_message("Characterisation: " + strMessage, level)
except:
self.DEBUG("Sending message to mxCuBE failed!")
def buildChildren(self, child_, nodeName_): if child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'mxv1ResultCharacterisation': obj_ = XSDataResultCharacterisation() obj_.build(child_) self.setMxv1ResultCharacterisation(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'mxv1ResultCharacterisation_Reference': obj_ = XSDataResultCharacterisation() obj_.build(child_) self.setMxv1ResultCharacterisation_Reference(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'mxv2DataCollection': obj_ = XSDataCollection() obj_.build(child_) self.setMxv2DataCollection(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'mxv2DataCollection_Reference': obj_ = XSDataCollection() obj_.build(child_) self.setMxv2DataCollection_Reference(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'suggestedStrategy': obj_ = XSDataResultStrategy() obj_.build(child_) self.setSuggestedStrategy(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'possibleOrientations': obj_ = kappa_alignment_response() obj_.build(child_) self.setPossibleOrientations(obj_) XSDataResultInterface.buildChildren(self, child_, nodeName_)
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginControlCharacterisationv1_6.preProcess")
self._xsDataResultCharacterisation = XSDataResultCharacterisation()
class EDPluginControlCharacterisationv1_6(EDPluginControl):
"""
Characterisation based on XDS
"""
def __init__(self):
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputCharacterisation)
self._strPluginControlIndexingIndicators = "EDPluginControlIndexingIndicatorsv1_1"
self._fMinTransmission = 10 # %
self._listPluginGenerateThumbnail = []
self._strCharacterisationShortSummary = ""
self._strStatusMessage = ""
self._strIndexingPluginName = "EDPluginXDSIndexingv1_0"
self._strIntegrationPluginName = "EDPluginXDSIntegrationv1_0"
self._edPluginIndexing = None
def checkParameters(self):
"""
Checks the mandatory parameters.
"""
self.DEBUG("EDPluginControlCharacterisationv1_6.checkParameters")
self.checkMandatoryParameters(self.getDataInput(), "Data Input is None")
self.checkMandatoryParameters(self.getDataInput().getDataCollection(), "dataCollection")
self.checkMandatoryParameters(self.getDataInput().getDataCollection().getDiffractionPlan(), "diffractionPlan")
def configure(self):
"""
Gets the configuration parameters (if any).
"""
EDPluginControl.configure(self)
self.DEBUG("EDPluginControlCharacterisationv1_6.configure")
self._strMxCuBE_URI = self.config.get("mxCuBE_URI", None)
if self._strMxCuBE_URI is not None and "mxCuBE_XMLRPC_log" in os.environ.keys():
self.DEBUG("Enabling sending messages to mxCuBE via URI {0}".format(self._strMxCuBE_URI))
self._oServerProxy = xmlrpclib.ServerProxy(self._strMxCuBE_URI)
self._runKappa = self.config.get("runKappa", False)
self._fMinTransmission = self.config.get("minTransmissionWarning", self._fMinTransmission)
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginControlCharacterisationv1_6.preProcess")
self._xsDataResultCharacterisation = XSDataResultCharacterisation()
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlCharacterisationv1_6.process")
self.doXdsIndexingIntegration(self.dataInput.dataCollection)
def finallyProcess(self, _edObject=None):
EDPluginControl.finallyProcess(self)
self.DEBUG("EDPluginControlCharacterisationv1_6.finallyProcess")
# Synchronize thumbnail plugins
for tuplePlugin in self._listPluginGenerateThumbnail:
image = tuplePlugin[0]
tuplePlugin[1].synchronize()
jpegImage = image.copy()
jpegImage.path = tuplePlugin[1].dataOutput.thumbnail.path
self._xsDataResultCharacterisation.addJpegImage(jpegImage)
tuplePlugin[2].synchronize()
thumbnailImage = image.copy()
thumbnailImage.path = tuplePlugin[2].dataOutput.thumbnail.path
self._xsDataResultCharacterisation.addThumbnailImage(thumbnailImage)
# if self._edPluginControlGeneratePrediction.isRunning():
# self._edPluginControlGeneratePrediction.synchronize()
# if self._strStatusMessage != None:
# self.setDataOutput(XSDataString(self._strStatusMessage), "statusMessage")
# self._xsDataResultCharacterisation.setStatusMessage(XSDataString(self._strStatusMessage))
# if self._strCharacterisationShortSummary != None:
# self.setDataOutput(XSDataString(self._strCharacterisationShortSummary), "shortSummary")
# self._xsDataResultCharacterisation.setShortSummary(XSDataString(self._strCharacterisationShortSummary))
# if self._xsDataResultCharacterisation is not None:
# self.setDataOutput(self._xsDataResultCharacterisation)
if self.isFailure():
self.sendMessageToMXCuBE("Ended with error messages", "error")
def doXdsIndexingIntegration(self, _xsDataCollection):
# Load the plugin
self._edPluginIndexing = self.loadPlugin(self._strIndexingPluginName, "Indexing")
# XDS Indexing
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.setDataCollection(_xsDataCollection)
self._edPluginIndexing.dataInput = EDHandlerXSDataXDSv1_0.generateXSDataInputXDSIndexing(xsDataIndexingInput)
self._edPluginIndexing.executeSynchronous()
xsDataResultXDSIndexing = self._edPluginIndexing.dataOutput
if xsDataResultXDSIndexing.spaceGroupNumber is not None:
spaceGroupNumber = xsDataResultXDSIndexing.spaceGroupNumber.value
unitCell = xsDataResultXDSIndexing.unitCell
filePaths = xsDataResultXDSIndexing.filePaths
index = 1
for subWedge in _xsDataCollection.subWedge:
xsDataCollection = XSDataCollection()
xsDataCollection.addSubWedge(subWedge)
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.setDataCollection(xsDataCollection)
xsDataInputXDSIntegration = EDHandlerXSDataXDSv1_0.generateXSDataInputXDSIntegration(xsDataIndexingInput,
spaceGroupNumber,
unitCell,
filePaths)
edPluginIntegration = self.loadPlugin(self._strIntegrationPluginName, "Integration_{0}".format(index))
edPluginIntegration.dataInput = xsDataInputXDSIntegration
edPluginIntegration.executeSynchronous()
# self._edPluginIntegration.dataInput = xsDataInputXDSIntegration
index += 1
def generateExecutiveSummary(self, _edPlugin):
"""
Generates a summary of the execution of the plugin.
"""
self.DEBUG("EDPluginControlCharacterisationv1_6.generateExecutiveSummary")
self.addExecutiveSummaryLine("Summary of characterisation:")
xsDataInputStrategy = self.getDataInput()
xsDataCollection = xsDataInputStrategy.getDataCollection()
# MXSUP-1445: Check if transmission is less than 10% and warn if it's the case
xsDataFirstSubWedge = xsDataCollection.getSubWedge()[0]
xsDataBeam = xsDataFirstSubWedge.getExperimentalCondition().getBeam()
if xsDataBeam.getTransmission() is not None:
fTransmission = xsDataBeam.getTransmission().getValue()
if fTransmission < self._fMinTransmission:
self.addExecutiveSummaryLine("^"*80)
self.addExecutiveSummaryLine("^"*80)
self.addExecutiveSummaryLine("")
self.addExecutiveSummaryLine("WARNING! Transmission for characterisation set to %.1f %%" % fTransmission)
self.addExecutiveSummaryLine("Please consider re-characterising with transmission set to 100 %")
self.addExecutiveSummaryLine("")
self.addExecutiveSummaryLine("^"*80)
self.addExecutiveSummaryLine("^"*80)
xsDataDiffractionPlan = xsDataCollection.getDiffractionPlan()
self.addExecutiveSummaryLine("Diffraction plan:")
if (xsDataDiffractionPlan.getComplexity() is not None):
self.addExecutiveSummaryLine("BEST complexity : %s" % xsDataDiffractionPlan.getComplexity().getValue())
if (xsDataDiffractionPlan.getAimedCompleteness() is not None):
self.addExecutiveSummaryLine("Aimed completeness : %6.1f [%%]" % (100.0 * xsDataDiffractionPlan.getAimedCompleteness().getValue()))
if (xsDataDiffractionPlan.getRequiredCompleteness() is not None):
self.addExecutiveSummaryLine("Required completeness : %6.1f [%%]" % (100.0 * xsDataDiffractionPlan.getRequiredCompleteness().getValue()))
if (xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution() is not None):
self.addExecutiveSummaryLine("Aimed I/sigma at highest resolution : %6.1f" % xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution().getValue())
if (xsDataDiffractionPlan.getAimedResolution() is not None):
self.addExecutiveSummaryLine("Aimed resolution : %6.1f [A]" % xsDataDiffractionPlan.getAimedResolution().getValue())
if (xsDataDiffractionPlan.getRequiredResolution() is not None):
self.addExecutiveSummaryLine("Required resolution : %6.1f [A]" % xsDataDiffractionPlan.getRequiredResolution().getValue())
if (xsDataDiffractionPlan.getAimedMultiplicity() is not None):
self.addExecutiveSummaryLine("Aimed multiplicity : %6.1f" % xsDataDiffractionPlan.getAimedMultiplicity().getValue())
if (xsDataDiffractionPlan.getRequiredMultiplicity() is not None):
self.addExecutiveSummaryLine("Required multiplicity : %6.1f" % xsDataDiffractionPlan.getRequiredMultiplicity().getValue())
if (xsDataDiffractionPlan.getForcedSpaceGroup() is not None):
self.addExecutiveSummaryLine("Forced space group : %6s" % xsDataDiffractionPlan.getForcedSpaceGroup().getValue())
if (xsDataDiffractionPlan.getMaxExposureTimePerDataCollection() is not None):
self.addExecutiveSummaryLine("Max exposure time per data collection : %6.1f [s]" % xsDataDiffractionPlan.getMaxExposureTimePerDataCollection().getValue())
self.addExecutiveSummarySeparator()
# if self._edPluginControlIndexingIndicators is not None:
# self.appendExecutiveSummary(self._edPluginControlIndexingIndicators, "")
# if self._edPluginControlIntegration is not None:
# self.appendExecutiveSummary(self._edPluginControlIntegration, "")
# if self._edPluginControlStrategy is not None:
# self.appendExecutiveSummary(self._edPluginControlStrategy, "")
self.addExecutiveSummarySeparator()
if self._strCharacterisationShortSummary is not None:
self.addExecutiveSummaryLine("Characterisation short summary:")
self.addExecutiveSummaryLine("")
if self._strStatusMessage != None:
for strLine in self._strStatusMessage.split(". "):
if strLine.endswith("."):
self.addExecutiveSummaryLine(strLine)
else:
self.addExecutiveSummaryLine(strLine + ".")
self.addExecutiveSummaryLine("")
for strLine in self._strCharacterisationShortSummary.split("\n"):
if strLine != "\n":
self.addExecutiveSummaryLine(strLine)
self.addErrorWarningMessagesToExecutiveSummary("Characterisation error and warning messages: ")
self.addExecutiveSummarySeparator()
def getPluginStrategyName(self):
return self._strPluginControlStrategy
def addStatusMessage(self, _strStatusMessage):
if self._strStatusMessage != "":
self._strStatusMessage += " "
self._strStatusMessage += _strStatusMessage
self.sendMessageToMXCuBE(_strStatusMessage)
def doStrategyCalculation(self, _bValue):
self._bDoStrategyCalculation = _bValue
def sendMessageToMXCuBE(self, _strMessage, level="info"):
# Only for mxCuBE
if self._strMxCuBE_URI is not None:
self.DEBUG("Sending message to mxCuBE: {0}".format(_strMessage))
try:
for strMessage in _strMessage.split("\n"):
if strMessage != "":
self._oServerProxy.log_message("Characterisation: " + strMessage, level)
except:
self.DEBUG("Sending message to mxCuBE failed!")
fEdnaLogFile = open("./edna.log", "r" )
ednaLogLines = fEdnaLogFile.readlines()
fEdnaLogFile.close()
for outline in ednaLogLines:
if (outline.find("EdnaDir")!= -1):
(param,dirname) = outline.split('=')
strXMLFileName = dirname[0:len(dirname)-1]+"/ControlInterfacev1_2/Characterisation/ControlCharacterisationv1_3_dataOutput.xml"
##### strXMLFileName = dirname[0:len(dirname)-1]+"/ControlInterfacev1_2/Characterisation/ControlCharacterisationv1_1_dataOutput.xml"
if (outline.find("characterisation successful!")!= -1):
collect_and_characterize_success = 1
if (not collect_and_characterize_success):
dna_comment = "Indexing Failure"
##### pxdb_lib.update_sweep(2,daq_lib.sweep_seq_id,dna_comment)
exit(0)
else:
xsDataCharacterisation = XSDataResultCharacterisation.parseFile( strXMLFileName )
xsDataIndexingResult = xsDataCharacterisation.getIndexingResult()
xsDataIndexingSolutionSelected = xsDataIndexingResult.getSelectedSolution()
xsDataStatisticsIndexing = xsDataIndexingSolutionSelected.getStatistics()
numSpotsFound = xsDataStatisticsIndexing.getSpotsTotal().getValue()
numSpotsUsed = xsDataStatisticsIndexing.getSpotsUsed().getValue()
numSpotsRejected = numSpotsFound-numSpotsUsed
beamShiftX = xsDataStatisticsIndexing.getBeamPositionShiftX().getValue()
beamShiftY = xsDataStatisticsIndexing.getBeamPositionShiftY().getValue()
spotDeviationR = xsDataStatisticsIndexing.getSpotDeviationPositional().getValue()
try:
spotDeviationTheta = xsDataStatisticsIndexing.getSpotDeviationAngular().getValue()
except AttributeError:
spotDeviationTheta = 0.0
diffractionRings = 0 #for now, don't see this in xml except message string
reflections_used = 0 #for now
class EDPluginControlCharacterisationv2_0(EDPluginControl):
"""
The Plugin that controls the whole characterisation: Indexing-Integration-(Kappa)Strategy
Indexing-Integration is the same as mxv1 characterisation.
KappaStrategy:
Preferred Strategy is given at the initial orientation, but if KAPPA features are enabled,
strategies are calculated to some alignments.
"""
def __init__ (self):
"""
"""
EDPluginControl.__init__(self)
#self.setXSDataInputClass( XSDataInputCharacterisation )
#self.setXSDataInputClass(EDList)
#self.strPluginIndexingName = "EDPluginControlIndexingv2_0"
self.strPluginIndexingName = "EDPluginControlIndexingv10"
self.edPluginIndexing = None
self.strPluginIntegrationName = "EDPluginControlIntegrationv10"
self.edPluginIntegration = None
self.xsDataResultCharacterisationv2_0 = None
self.xsDataResultCharacterisation = None
self.xsDataInputStrategy = None
self.setXSDataInputClass(XSDataInputCharacterisationv2_0)
EDFactoryPluginStatic.loadModule("XSDataMXv1")
import XSDataMXv1
self.setXSDataInputClass(XSDataMXv1.XSDataInputCharacterisation, "mxv1InputCharacterisation")
EDFactoryPluginStatic.loadModule("XSDataMXv2")
import XSDataMXv2
self.setXSDataInputClass(XSDataMXv2.XSDataCollection, "mxv2DataCollection")
def checkParameters(self):
"""
Checks the mandatory parameters
"""
EDVerbose.DEBUG("EDPluginControlCharacterisationv2_0.checkParameters")
# Check for mxv1InputCharacterisation:
if self.hasDataInput():
if self.hasDataInput("mxv1InputCharacterisation") or self.hasDataInput("mxv2DataCollection"):
EDVerbose.WARNING("Ambiguous input! Both XSDataInputCharacterisatiov2_0 input, and mxv1InputCharacterisation or mxv2DataCollection input(s), are given")
self.setDataInput(self.getDataInput().getMxv1InputCharacterisation().marshal(), "mxv1InputCharacterisation")
self.setDataInput(self.getDataInput().getMxv2DataCollection().marshal(), "mxv2DataCollection")
# Check for mxv1InputCharacterisation
self.checkMandatoryParameters(self.getDataInput("mxv1InputCharacterisation"), "Data Input is None")
self.checkMandatoryParameters(self.getDataInput("mxv1InputCharacterisation")[0].getDataCollection(), "dataCollection")
self.checkMandatoryParameters(self.getDataInput("mxv1InputCharacterisation")[0].getDataCollection().getDiffractionPlan(), "diffractionPlan")
def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
EDVerbose.DEBUG("EDPluginControlCharacterisationv2_0.preProcess...")
self.edPluginIndexing = self.loadPlugin(self.strPluginIndexingName , "Indexing")
self.edPluginIntegration = self.loadPlugin(self.strPluginIntegrationName, "Integration")
self.edPluginStrategy = self.loadPlugin(self.strPluginStrategyName , "Strategy")
if (self.edPluginIndexing is not None):
EDVerbose.DEBUG("EDPluginControlCharacterisationv2_0.preProcess: " + self.strPluginIndexingName + " Found... setting Data Input")
# create Data Input for indexing
xsDataInputStrategy = self.getDataInput("mxv1InputCharacterisation")[0]
xsDataCollection = xsDataInputStrategy.getDataCollection()
#xsDataSample = xsDataCollection.getSample()
xsDataSubWedgeList = xsDataCollection.getSubWedge()
xsDataExperimentalCondition = xsDataSubWedgeList[0].getExperimentalCondition()
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.setDataCollection(xsDataCollection)
xsDataIndexingInput.setExperimentalCondition(xsDataExperimentalCondition)
xsDataDiffractionPlan = xsDataCollection.getDiffractionPlan()
xsDataStringForcedSpaceGroup = xsDataDiffractionPlan.getForcedSpaceGroup()
if (xsDataStringForcedSpaceGroup is not None):
xsDataCrystal = XSDataCrystal()
xsDataSpaceGroup = XSDataSpaceGroup()
xsDataSpaceGroup.setName(xsDataStringForcedSpaceGroup)
xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
xsDataIndexingInput.setCrystal(xsDataCrystal)
self.edPluginIndexing.setDataInput(xsDataIndexingInput)
# Populate characterisation object
self.xsDataResultCharacterisationv2_0 = XSDataResultCharacterisationv2_0()
self.xsDataResultCharacterisation = XSDataResultCharacterisation()
self.xsDataResultCharacterisationv2_0.setMxv1ResultCharacterisation(self.xsDataResultCharacterisation)
self.xsDataResultCharacterisation.setDataCollection(XSDataCollection.parseString(xsDataCollection.marshal()))
def process(self, _edObject=None):
EDPluginControl.process(self, _edObject)
EDVerbose.DEBUG("EDPluginControlCharacterisationv2_0.process")
self.connectProcess(self.edPluginIndexing.executeSynchronous)
self.edPluginIndexing.connectSUCCESS(self.doIndexingToIntegrationTransition)
self.edPluginIndexing.connectFAILURE(self.doFailureActionIndexing)
self.edPluginIntegration.connectSUCCESS(self.doIntegrationToStrategyTransition)
self.edPluginIntegration.connectFAILURE(self.doFailureActionIntegration)
self.edPluginStrategy.connectFAILURE(self.doFailureActionStrategy)
self.edPluginStrategy.connectSUCCESS(self.doSuccessActionStrategy)
def postProcess(self, _edObject=None):
"""
"""
EDPluginControl.postProcess(self, _edObject)
EDVerbose.DEBUG("EDPluginControlCharacterisationv2_0.postProcess")
if (self.xsDataResultCharacterisationv2_0 is not None):
self.setDataOutput(self.xsDataResultCharacterisationv2_0)
def doIndexingToIntegrationTransition(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlCharacterisationv2_0.doIndexingToIntegrationTransition")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv2_0.doIntegrationToStrategyTransition")
xsDataIndexingResult = self.edPluginIndexing.getDataOutput()
self.xsDataResultCharacterisation.setIndexingResult(xsDataIndexingResult)
from XSDataMXv1 import XSDataIntegrationInput
xsDataIntegrationInput = XSDataIntegrationInput()
xsDataIntegrationInput.setDataCollection(self.xsDataResultCharacterisation.getDataCollection())
xsDataIntegrationInput.setExperimentalConditionRefined(xsDataIndexingResult.getSelectedSolution().getExperimentalConditionRefined())
xsDataIntegrationInput.setSelectedIndexingSolution(xsDataIndexingResult.getSelectedSolution())
self.edPluginIntegration.setDataInput(xsDataIntegrationInput)
self.edPluginIntegration.executeSynchronous()
def doIntegrationToStrategyTransition(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlCharacterisationv2_0.doIntegrationToStrategyTransition")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv2_0.doIntegrationToStrategyTransition")
xsDataIntegrationOutput = self.edPluginIntegration.getDataOutput()
self.xsDataResultCharacterisation.setIntegrationResult(xsDataIntegrationOutput)
#EDVerbose.DEBUG( self.xsDataExperimentCharacterisation.marshal() )
from XSDataMXv1 import XSDataInputStrategy
xsDataInputStrategyOLD = XSDataInputStrategy()
xsDataSolutionSelected = self.xsDataResultCharacterisation.getIndexingResult().getSelectedSolution()
xsDataInputStrategyOLD.setCrystalRefined(xsDataSolutionSelected.getCrystal())
xsDataInputStrategyOLD.setSample(self.xsDataResultCharacterisation.getDataCollection().getSample())
xsDataIntegrationSubWedgeResultList = xsDataIntegrationOutput.getIntegrationSubWedgeResult()
xsDataInputStrategyOLD.setBestFileContentDat(xsDataIntegrationSubWedgeResultList[0].getBestfileDat())
xsDataInputStrategyOLD.setBestFileContentPar(xsDataIntegrationSubWedgeResultList[0].getBestfilePar())
xsDataInputStrategyOLD.setExperimentalCondition(xsDataIntegrationSubWedgeResultList[0].getExperimentalConditionRefined())
for xsDataIntegrationSubWedgeResult in xsDataIntegrationSubWedgeResultList:
xsDataInputStrategyOLD.addBestFileContentHKL(xsDataIntegrationSubWedgeResult.getBestfileHKL())
xsDataInputStrategyOLD.setDiffractionPlan(self.xsDataResultCharacterisation.getDataCollection().getDiffractionPlan())
xsDataInputStrategyOLD.setXdsBackgroundImage(self.xsDataResultCharacterisation.getXdsBackgroundImage())
#print xsDataInputStrategy.marshal()
self.edPluginStrategy.setDataInput(xsDataInputStrategyOLD, "mxv1InputStrategy")
if self.hasDataInput("mxv2DataCollection"):
self.edPluginStrategy.setDataInput(self.getDataInput("mxv2DataCollection")[0], "mxv2DataCollection")
self.edPluginStrategy.setDataInput(self.xsDataResultCharacterisation.getIndexingResult(), "mxv1IndexingResult")
# xsDataInputStrategy= EDList()
# xsDataInputStrategy.add(xsDataInputStrategyOLD)
# xsDataInputStrategy.add(self.getDataInput()[1])
# xsDataInputStrategy.add(self.xsDataResultCharacterisationv2_0.getIndexingResult())
# self.edPluginStrategy.setDataInput( xsDataInputStrategy )
self.edPluginStrategy.executeSynchronous()
def doFailureActionIndexing(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlCharacterisationv2_0.doFailureActionIndexing")
self.retrieveFailureMessages(_edPlugin, "EDPluginControlCharacterisationv2_0.doFailureActionIndexing")
def doFailureActionIntegration(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlCharacterisationv2_0.doFailureActionIntegration")
self.retrieveFailureMessages(_edPlugin, "EDPluginControlCharacterisationv2_0.doFailureActionIntegration")
def doFailureActionStrategy(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlCharacterisationv2_0.doFailureActionStrategy")
self.retrieveFailureMessages(_edPlugin, "EDPluginControlCharacterisationv2_0.doFailureActionStrategy")
def doSuccessActionStrategy(self, _edPlugin):
"""
retrieve the potential warning messages
"""
EDVerbose.DEBUG("EDPluginControlCharacterisationv2_0.doSuccessActionStrategy")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv2_0.doSuccessActionStrategy")
xsDataResultStrategy = self.edPluginStrategy.getDataOutput()
self.xsDataResultCharacterisation.setStrategyResult(xsDataResultStrategy)
def configure(self):
EDPluginControl.configure(self)
EDVerbose.DEBUG("EDPluginControlCharacterisationv2_0.configure")
pluginConfiguration = self.getConfiguration()
if(pluginConfiguration != None):
strPointlessOn = EDConfiguration.getStringParamValue(pluginConfiguration, "POINTLESS")
if(strPointlessOn == None or strPointlessOn != "True"):
self.strPluginIntegrationName = "EDPluginControlIntegrationv10"
else:
self.strPluginIntegrationName = "EDPluginControlIntegrationPointlessv10"
def generateExecutiveSummary(self, _edPlugin):
"""
Generates a summary of the execution of the plugin.
"""
EDVerbose.DEBUG("EDPluginControlCharacterisationv2_0.generateExecutiveSummary")
self.addExecutiveSummaryLine("Summary of characterisation:")
self.addErrorWarningMessagesToExecutiveSummary("Characterisation failure! Error messages: ")
self.addExecutiveSummarySeparator()
xsDataInputStrategy = self.getDataInput("mxv1InputCharacterisation")[0]
xsDataCollection = xsDataInputStrategy.getDataCollection()
xsDataDiffractionPlan = xsDataCollection.getDiffractionPlan()
self.addExecutiveSummaryLine("Diffraction plan:")
if (xsDataDiffractionPlan.getComplexity() is not None):
self.addExecutiveSummaryLine("BEST complexity : %s" % xsDataDiffractionPlan.getComplexity().getValue())
if (xsDataDiffractionPlan.getAimedCompleteness() is not None):
self.addExecutiveSummaryLine("Aimed completeness : %6.1f [%%]" % (100.0 * xsDataDiffractionPlan.getAimedCompleteness().getValue()))
if (xsDataDiffractionPlan.getRequiredCompleteness() is not None):
self.addExecutiveSummaryLine("Required completeness : %6.1f [%%]" % (100.0 * xsDataDiffractionPlan.getRequiredCompleteness().getValue()))
if (xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution() is not None):
self.addExecutiveSummaryLine("Aimed I/sigma at highest resolution : %6.1f" % xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution().getValue())
if (xsDataDiffractionPlan.getAimedResolution() is not None):
self.addExecutiveSummaryLine("Aimed resolution : %6.1f [A]" % xsDataDiffractionPlan.getAimedResolution().getValue())
if (xsDataDiffractionPlan.getRequiredResolution() is not None):
self.addExecutiveSummaryLine("Required resolution : %6.1f [A]" % xsDataDiffractionPlan.getRequiredResolution().getValue())
if (xsDataDiffractionPlan.getAimedMultiplicity() is not None):
self.addExecutiveSummaryLine("Aimed multiplicity : %6.1f" % xsDataDiffractionPlan.getAimedMultiplicity().getValue())
if (xsDataDiffractionPlan.getRequiredMultiplicity() is not None):
self.addExecutiveSummaryLine("Required multiplicity : %6.1f" % xsDataDiffractionPlan.getRequiredMultiplicity().getValue())
if (xsDataDiffractionPlan.getForcedSpaceGroup() is not None):
self.addExecutiveSummaryLine("Forced space group : %6s" % xsDataDiffractionPlan.getForcedSpaceGroup().getValue())
if (xsDataDiffractionPlan.getMaxExposureTimePerDataCollection() is not None):
self.addExecutiveSummaryLine("Max exposure time per data collection : %6.1f [s]" % xsDataDiffractionPlan.getMaxExposureTimePerDataCollection().getValue())
self.addExecutiveSummarySeparator()
if (self.edPluginIndexing is not None):
self.appendExecutiveSummary(self.edPluginIndexing, "Indexing : ")
if (self.edPluginIntegration is not None):
self.appendExecutiveSummary(self.edPluginIntegration, "Integration : ")
if (self.edPluginStrategy is not None):
self.appendExecutiveSummary(self.edPluginStrategy, "Strategy : ")
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_3.preProcess")
# Load the plugins
self._edPluginControlIndexingIndicators = self.loadPlugin(self._strPluginControlIndexingIndicators, \
"Indexing")
self._edPluginControlIndexingLabelit = self.loadPlugin(self._strPluginControlIndexingLabelit, \
"IndexingLabelit")
self._edPluginExecEvaluationIndexingMOSFLM = self.loadPlugin(self._strPluginExecEvaluationIndexing, \
"IndexingEvalualtionMOSFLM")
self._edPluginExecEvaluationIndexingLABELIT = self.loadPlugin(self._strPluginExecEvaluationIndexing, \
"IndexingEvalualtionLABELIT")
self._edPluginControlGeneratePrediction = self.loadPlugin(self._strPluginControlGeneratePrediction, \
"GeneratePrediction")
self._edPluginControlIntegration = self.loadPlugin(self._strPluginControlIntegration, \
"Integration")
self._edPluginControlXDSGenerateBackgroundImage = self.loadPlugin(self._strPluginControlXDSGenerateBackgroundImage, \
"ControlXDSGenerateBackgroundImage")
self._edPluginControlStrategy = self.loadPlugin(self._strPluginControlStrategy, \
"Strategy")
if (self._edPluginControlIndexingIndicators is not None):
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_3.preProcess: " + self._strPluginControlIndexingIndicators + " Found... setting Data Input")
# create Data Input for indexing
xsDataInputCharacterisation = self.getDataInput()
self._xsDataCollection = xsDataInputCharacterisation.getDataCollection()
# MXSUP-1445: Check if transmission is less than 10% and warn if it's the case
xsDataFirstSubWedge = self._xsDataCollection.getSubWedge()[0]
xsDataBeam = xsDataFirstSubWedge.getExperimentalCondition().getBeam()
if xsDataBeam.getTransmission() is not None:
fTransmission = xsDataBeam.getTransmission().getValue()
if fTransmission < self._fMinTransmission:
strWarningMessageBanner = "^"*80
strWarningMessage1 = "WARNING! Transmission for characterisation set to %.1f %%" % fTransmission
strWarningMessage2 = "Please consider re-characterising with transmission set to 100 %"
self.warning(strWarningMessageBanner)
self.warning(strWarningMessage1)
self.warning(strWarningMessage2)
self.warning(strWarningMessageBanner)
self.addWarningMessage(strWarningMessageBanner)
self.addWarningMessage(strWarningMessage1)
self.addWarningMessage(strWarningMessage2)
self.addWarningMessage(strWarningMessageBanner)
xsDataCrystal = None
xsDataSubWedgeList = self._xsDataCollection.getSubWedge()
if ((xsDataSubWedgeList is None) or (xsDataSubWedgeList == [])):
strError = "EDPluginControlCharacterisationv1_3.preProcess: No subwedges in input data."
EDVerbose.ERROR(strError)
self.setFailure()
else:
xsDataExperimentalCondition = xsDataSubWedgeList[0].getExperimentalCondition()
# Fix for bug 431: if the flux is zero raise an error
xsDataDoubleFlux = xsDataExperimentalCondition.getBeam().getFlux()
if (xsDataDoubleFlux is not None):
if (xsDataDoubleFlux.getValue() < 0.1):
strErrorMessage = "Input flux is negative or close to zero. Execution of characterisation aborted."
EDVerbose.ERROR(strErrorMessage)
self.addErrorMessage("EDPluginControlCharacterisationv1_3.preProcess ERROR: " + strErrorMessage)
#self.addComment(strErrorMessage)
self.setFailure()
xsDataDiffractionPlan = self._xsDataCollection.getDiffractionPlan()
xsDataStringForcedSpaceGroup = xsDataDiffractionPlan.getForcedSpaceGroup()
if (xsDataStringForcedSpaceGroup is not None):
self._xsDataCrystal = XSDataCrystal()
xsDataSpaceGroup = XSDataSpaceGroup()
xsDataSpaceGroup.setName(xsDataStringForcedSpaceGroup)
self._xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
self._edPluginControlIndexingIndicators.setDataInput(self._xsDataCollection, "dataCollection")
if self._xsDataCrystal is not None:
self._edPluginControlIndexingIndicators.setDataInput(self._xsDataCrystal, "crystal")
# Populate characterisation object
self._xsDataResultCharacterisation = XSDataResultCharacterisation()
self._xsDataResultCharacterisation.setDataCollection(XSDataCollection.parseString(self._xsDataCollection.marshal()))
class EDPluginControlCharacterisationv1_2(EDPluginControl):
"""
[To be replaced with a description of EDPluginControlTemplatev10]
"""
def __init__(self):
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputCharacterisation)
self.__strPluginControlIndexingIndicators = "EDPluginControlIndexingIndicatorsv10"
self.__strPluginControlIndexingLabelit = "EDPluginControlIndexingLabelitv10"
self.__strPluginExecEvaluationIndexing = "EDPluginExecEvaluationIndexingv10"
self.__strPluginControlGeneratePrediction = "EDPluginControlGeneratePredictionv10"
self.__strPluginControlIntegration = "EDPluginControlIntegrationv10"
self.__strPluginControlStrategy = "EDPluginControlStrategyv1_2"
self.__edPluginControlIndexingIndicators = None
self.__edPluginControlIndexingLabelit = None
self.__edPluginExecEvaluationIndexingMOSFLM = None
self.__edPluginExecEvaluationIndexingLABELIT = None
self.__edPluginControlGeneratePrediction = None
self.__edPluginControlIntegration = None
self.__edPluginControlStrategy = None
self.__xsDataCollection = None
self.__xsDataResultCharacterisation = None
self.__xsDataIndexingResultMOSFLM = None
self.__xsDataCrystal = None
self.__strCharacterisationShortSummary = ""
self.__strStatusMessage = ""
self.__bDoStrategyCalculation = True
def checkParameters(self):
"""
Checks the mandatory parameters.
"""
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_2.checkParameters")
self.checkMandatoryParameters(self.getDataInput(), "Data Input is None")
self.checkMandatoryParameters(self.getDataInput().getDataCollection(), "dataCollection")
self.checkMandatoryParameters(self.getDataInput().getDataCollection().getDiffractionPlan(), "diffractionPlan")
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_2.preProcess")
# Load the plugins
self.__edPluginControlIndexingIndicators = self.loadPlugin(self.__strPluginControlIndexingIndicators, \
"Indexing")
self.__edPluginControlIndexingLabelit = self.loadPlugin(self.__strPluginControlIndexingLabelit, \
"IndexingLabelit")
self.__edPluginExecEvaluationIndexingMOSFLM = self.loadPlugin(self.__strPluginExecEvaluationIndexing, \
"IndexingEvalualtionMOSFLM")
self.__edPluginExecEvaluationIndexingLABELIT = self.loadPlugin(self.__strPluginExecEvaluationIndexing, \
"IndexingEvalualtionLABELIT")
self.__edPluginControlGeneratePrediction = self.loadPlugin(self.__strPluginControlGeneratePrediction, \
"GeneratePrediction")
self.__edPluginControlIntegration = self.loadPlugin(self.__strPluginControlIntegration, \
"Integration")
self.__edPluginControlStrategy = self.loadPlugin(self.__strPluginControlStrategy, \
"Strategy")
if (self.__edPluginControlIndexingIndicators is not None):
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_2.preProcess: " + self.__strPluginControlIndexingIndicators + " Found... setting Data Input")
# create Data Input for indexing
xsDataInputCharacterisation = self.getDataInput()
self.__xsDataCollection = xsDataInputCharacterisation.getDataCollection()
xsDataCrystal = None
xsDataSubWedgeList = self.__xsDataCollection.getSubWedge()
if ((xsDataSubWedgeList is None) or (xsDataSubWedgeList == [])):
strError = "EDPluginControlCharacterisationv1_2.preProcess: No subwedges in input data."
EDVerbose.ERROR(strError)
self.setFailure()
else:
xsDataExperimentalCondition = xsDataSubWedgeList[0].getExperimentalCondition()
# Fix for bug 431: if the flux is zero raise an error
xsDataDoubleFlux = xsDataExperimentalCondition.getBeam().getFlux()
if (xsDataDoubleFlux is not None):
if (xsDataDoubleFlux.getValue() < 0.1):
strErrorMessage = "Input flux is negative or close to zero. Execution of characterisation aborted."
EDVerbose.ERROR(strErrorMessage)
self.addErrorMessage("EDPluginControlCharacterisationv1_2.preProcess ERROR: " + strErrorMessage)
#self.addComment(strErrorMessage)
self.setFailure()
xsDataDiffractionPlan = self.__xsDataCollection.getDiffractionPlan()
xsDataStringForcedSpaceGroup = xsDataDiffractionPlan.getForcedSpaceGroup()
if (xsDataStringForcedSpaceGroup is not None):
self.__xsDataCrystal = XSDataCrystal()
xsDataSpaceGroup = XSDataSpaceGroup()
xsDataSpaceGroup.setName(xsDataStringForcedSpaceGroup)
self.__xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
self.__edPluginControlIndexingIndicators.setDataInput(self.__xsDataCollection, "dataCollection")
if self.__xsDataCrystal is not None:
self.__edPluginControlIndexingIndicators.setDataInput(self.__xsDataCrystal, "crystal")
# Populate characterisation object
self.__xsDataResultCharacterisation = XSDataResultCharacterisation()
self.__xsDataResultCharacterisation.setDataCollection(XSDataCollection.parseString(self.__xsDataCollection.marshal()))
def process(self, _edObject=None):
EDPluginControl.process(self)
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_2.process")
self.__edPluginControlIndexingIndicators.connectSUCCESS(self.doSuccessIndexingIndicators)
self.__edPluginControlIndexingIndicators.connectFAILURE(self.doFailureIndexingIndicators)
self.__edPluginControlIndexingLabelit.connectSUCCESS(self.doSuccessIndexingLabelit)
self.__edPluginControlIndexingLabelit.connectFAILURE(self.doFailureIndexingLabelit)
self.__edPluginExecEvaluationIndexingMOSFLM.connectSUCCESS(self.doSuccessEvaluationIndexingMOSFLM)
self.__edPluginExecEvaluationIndexingMOSFLM.connectFAILURE(self.doFailureEvaluationIndexingMOSFLM)
self.__edPluginExecEvaluationIndexingLABELIT.connectSUCCESS(self.doSuccessEvaluationIndexingLABELIT)
self.__edPluginExecEvaluationIndexingLABELIT.connectFAILURE(self.doFailureEvaluationIndexingLABELIT)
self.__edPluginControlGeneratePrediction.connectSUCCESS(self.doSuccessGeneratePrediction)
self.__edPluginControlGeneratePrediction.connectFAILURE(self.doFailureGeneratePrediction)
self.__edPluginControlIntegration.connectSUCCESS(self.doSuccessIntegration)
self.__edPluginControlIntegration.connectFAILURE(self.doFailureIntegration)
self.__edPluginControlStrategy.connectSUCCESS(self.doSuccessStrategy)
self.__edPluginControlStrategy.connectFAILURE(self.doFailureStrategy)
self.__edPluginControlIndexingIndicators.executeSynchronous()
def finallyProcess(self, _edObject=None):
EDPluginControl.finallyProcess(self)
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_2.finallyProcess")
if self.__edPluginControlGeneratePrediction.isRunning():
self.__edPluginControlGeneratePrediction.synchronize()
if self.__strStatusMessage != None:
self.setDataOutput(XSDataString(self.__strStatusMessage), "statusMessage")
self.__xsDataResultCharacterisation.setStatusMessage(XSDataString(self.__strStatusMessage))
if self.__strCharacterisationShortSummary != None:
self.setDataOutput(XSDataString(self.__strCharacterisationShortSummary), "shortSummary")
self.__xsDataResultCharacterisation.setShortSummary(XSDataString(self.__strCharacterisationShortSummary))
if self.__xsDataResultCharacterisation is not None:
self.setDataOutput(self.__xsDataResultCharacterisation)
def doSuccessIndexingIndicators(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_2.doSuccessIndexingIndicators")
#self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv1_2.doSuccessIndexingIndicators")
if self.__edPluginControlIndexingIndicators.hasDataOutput("indexingResult"):
xsDataIndexingResult = self.__edPluginControlIndexingIndicators.getDataOutput("indexingResult")[0]
#self.__xsDataResultCharacterisation.setIndexingResult(xsDataIndexingResult)
self.__edPluginExecEvaluationIndexingMOSFLM.setDataInput(xsDataIndexingResult, "indexingResult")
if self.__edPluginControlIndexingIndicators.hasDataOutput("imageQualityIndicators"):
listXSDataImageQualityIndicators = self.__edPluginControlIndexingIndicators.getDataOutput("imageQualityIndicators")
for xsDataImageQualityIndicators in listXSDataImageQualityIndicators:
self.__xsDataResultCharacterisation.addImageQualityIndicators(xsDataImageQualityIndicators)
self.__edPluginExecEvaluationIndexingMOSFLM.setDataInput(xsDataImageQualityIndicators, "imageQualityIndicators")
if self.__edPluginControlIndexingIndicators.hasDataOutput("indicatorsShortSummary"):
self.__strCharacterisationShortSummary += self.__edPluginControlIndexingIndicators.getDataOutput("indicatorsShortSummary")[0].getValue()
self.__edPluginExecEvaluationIndexingMOSFLM.executeSynchronous()
def doFailureIndexingIndicators(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_2.doFailureIndexingIndicators")
strErrorMessage = "Execution of Indexing and Indicators plugin failed. Execution of characterisation aborted."
EDVerbose.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
if self.__xsDataResultCharacterisation is not None:
self.setDataOutput(self.__xsDataResultCharacterisation)
self.setFailure()
if self.__strStatusMessage != None:
self.setDataOutput(XSDataString(self.__strStatusMessage), "statusMessage")
self.writeDataOutput()
# def doSuccessIndexingLabelit(self, _edPlugin=None):
# EDVerbose.DEBUG("EDPluginControlCharacterisationv1_2.doSuccessIndexingLabelit")
# self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv1_2.doSuccessIndexingLabelit")
# # Retrieve the indexing result
# xsDataIndexingResult = self.__edPluginControlIndexingLabelit.getDataOutput()
# self.__xsDataResultCharacterisation.setIndexingResult(xsDataIndexingResult)
# if self.__edPluginControlIndexingLabelit.hasDataOutput("indexingShortSummary"):
# self.__strCharacterisationShortSummary += self.__edPluginControlIndexingLabelit.getDataOutput("indexingShortSummary")[0].getValue()
# # Then start the integration of the reference images
# self.indexingToIntegration()
def doSuccessIndexingLabelit(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_2.doSuccessIndexingLabelit")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv1_2.doSuccessIndexingLabelit")
if self.__edPluginControlIndexingLabelit.hasDataOutput("indexingShortSummary"):
self.__strCharacterisationShortSummary += self.__edPluginControlIndexingLabelit.getDataOutput("indexingShortSummary")[0].getValue()
# Check the indexing results
xsDataIndexingResult = self.__edPluginControlIndexingLabelit.getDataOutput()
self.__edPluginExecEvaluationIndexingLABELIT.setDataInput(xsDataIndexingResult, "indexingResult")
xsDataImageQualityIndicators = self.__xsDataResultCharacterisation.getImageQualityIndicators()[0]
self.__edPluginExecEvaluationIndexingLABELIT.setDataInput(xsDataImageQualityIndicators, "imageQualityIndicators")
self.__edPluginExecEvaluationIndexingLABELIT.executeSynchronous()
def doFailureIndexingLabelit(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_2.doFailureIndexingLabelit")
self.addStatusMessage("Labelit: Indexing FAILURE.")
if self.__xsDataResultCharacterisation is not None:
self.setDataOutput(self.__xsDataResultCharacterisation)
if self.__xsDataIndexingResultMOSFLM == None:
strErrorMessage = "Execution of indexing with both MOSFLM and Labelit failed. Execution of characterisation aborted."
EDVerbose.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.generateExecutiveSummary(self)
self.setFailure()
if self.__strStatusMessage != None:
self.setDataOutput(XSDataString(self.__strStatusMessage), "statusMessage")
self.writeDataOutput()
else:
# Use the MOSFLM indexing results - even if it's P1
self.__xsDataResultCharacterisation.setIndexingResult(self.__xsDataIndexingResultMOSFLM)
xsDataCollection = self.__xsDataResultCharacterisation.getDataCollection()
xsDataGeneratePredictionInput = XSDataGeneratePredictionInput()
xsDataGeneratePredictionInput.setDataCollection(XSDataCollection.parseString(xsDataCollection.marshal()))
xsDataGeneratePredictionInput.setSelectedIndexingSolution(XSDataIndexingSolutionSelected.parseString(self.__xsDataIndexingResultMOSFLM.getSelectedSolution().marshal()))
self.__edPluginControlGeneratePrediction.setDataInput(xsDataGeneratePredictionInput)
if self.__edPluginControlIndexingIndicators.hasDataOutput("indexingShortSummary"):
self.__strCharacterisationShortSummary += self.__edPluginControlIndexingIndicators.getDataOutput("indexingShortSummary")[0].getValue()
# Start the generation of prediction images - we synchronize in the post-process
self.__edPluginControlGeneratePrediction.execute()
# Then start the integration of the reference images
self.indexingToIntegration()
def doSuccessEvaluationIndexingMOSFLM(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_2.doSuccessEvaluationIndexingMOSFLM")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv1_2.doSuccessEvaluationIndexing")
# Retrieve status messages (if any)
if self.__edPluginExecEvaluationIndexingMOSFLM.hasDataOutput("statusMessageImageQualityIndicators"):
self.addStatusMessage(self.__edPluginExecEvaluationIndexingMOSFLM.getDataOutput("statusMessageImageQualityIndicators")[0].getValue())
if self.__edPluginExecEvaluationIndexingMOSFLM.hasDataOutput("statusMessageIndexing"):
self.addStatusMessage("MOSFLM: " + self.__edPluginExecEvaluationIndexingMOSFLM.getDataOutput("statusMessageIndexing")[0].getValue())
# Check if indexing was successful
bIndexWithLabelit = False
bIndexingSuccess = self.__edPluginExecEvaluationIndexingMOSFLM.getDataOutput("indexingSuccess")[0].getValue()
if bIndexingSuccess:
xsDataIndexingResult = self.__edPluginExecEvaluationIndexingMOSFLM.getDataOutput("indexingResult")[0]
self.__xsDataIndexingResultMOSFLM = xsDataIndexingResult
# Check if space group is P1 - if yes run Labelit indexing
xsDataIndexingSolutionSelected = xsDataIndexingResult.getSelectedSolution()
xsDataCrystal = xsDataIndexingSolutionSelected.getCrystal()
xsDataSpaceGroup = xsDataCrystal.getSpaceGroup()
strSpaceGroupName = xsDataSpaceGroup.getName().getValue().upper()
# Check if MOSFLM has indexed in P1
if strSpaceGroupName == "P1":
# Check if the user maybe asked for P1!
bIndexWithLabelit = True
if self.__xsDataCollection.getDiffractionPlan() is not None:
if self.__xsDataCollection.getDiffractionPlan().getForcedSpaceGroup() is not None:
if self.__xsDataCollection.getDiffractionPlan().getForcedSpaceGroup().getValue().upper() == "P1":
EDVerbose.screen("P1 space forced by diffraction plan")
bIndexWithLabelit = False
if bIndexWithLabelit:
EDVerbose.screen("P1 space group choosed - reindexing with Labelit")
else:
EDVerbose.screen("MOSFLM indexing successful!")
if self.__edPluginControlIndexingIndicators.hasDataOutput("indexingShortSummary"):
self.__strCharacterisationShortSummary += self.__edPluginControlIndexingIndicators.getDataOutput("indexingShortSummary")[0].getValue()
# Generate prediction images
xsDataCollection = self.__xsDataResultCharacterisation.getDataCollection()
self.__xsDataResultCharacterisation.setIndexingResult(xsDataIndexingResult)
xsDataGeneratePredictionInput = XSDataGeneratePredictionInput()
xsDataGeneratePredictionInput.setDataCollection(XSDataCollection.parseString(xsDataCollection.marshal()))
xsDataGeneratePredictionInput.setSelectedIndexingSolution(XSDataIndexingSolutionSelected.parseString(xsDataIndexingResult.getSelectedSolution().marshal()))
self.__edPluginControlGeneratePrediction.setDataInput(xsDataGeneratePredictionInput)
# Start the generation of prediction images - we synchronize in the post-process
self.__edPluginControlGeneratePrediction.execute()
# Then start the integration of the reference images
self.indexingToIntegration()
else:
EDVerbose.screen("Indexing with MOSFLM failed!")
bIndexWithLabelit = True
if bIndexWithLabelit:
# Execute Labelit indexing
EDVerbose.screen("Now trying to index with Labelit - please be patient...")
xsDataIndexingInput = XSDataIndexingInput()
xsDataSubWedgeList = self.__xsDataCollection.getSubWedge()
xsDataExperimentalCondition = xsDataSubWedgeList[0].getExperimentalCondition()
xsDataIndexingInput.setDataCollection(self.__xsDataCollection)
xsDataIndexingInput.setExperimentalCondition(xsDataExperimentalCondition)
if self.__xsDataCrystal != None:
xsDataIndexingInput.setCrystal(self.__xsDataCrystal)
self.__edPluginControlIndexingLabelit.setDataInput(xsDataIndexingInput)
self.__edPluginControlIndexingLabelit.executeSynchronous()
def doSuccessEvaluationIndexingLABELIT(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_2.doSuccessEvaluationIndexingLABELIT")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv1_2.doSuccessEvaluationIndexingLABELIT")
# Retrieve status messages (if any)
if self.__edPluginExecEvaluationIndexingLABELIT.hasDataOutput("statusMessageIndexing"):
self.addStatusMessage("Labelit: " + self.__edPluginExecEvaluationIndexingLABELIT.getDataOutput("statusMessageIndexing")[0].getValue())
# Check if indexing was successful
bIndexingSuccess = self.__edPluginExecEvaluationIndexingLABELIT.getDataOutput("indexingSuccess")[0].getValue()
if bIndexingSuccess:
xsDataIndexingResult = self.__edPluginExecEvaluationIndexingLABELIT.getDataOutput("indexingResult")[0]
self.__xsDataResultCharacterisation.setIndexingResult(xsDataIndexingResult)
# Then start the integration of the reference images
self.indexingToIntegration()
else:
EDVerbose.screen("Indexing with LABELIT failed!")
self.setFailure()
def indexingToIntegration(self, _edPlugin=None):
# Integrate the reference images
xsDataIntegrationInput = XSDataIntegrationInput()
xsDataIntegrationInput.setDataCollection(self.__xsDataResultCharacterisation.getDataCollection())
xsDataIndexingResult = self.__xsDataResultCharacterisation.getIndexingResult()
xsDataExperimentalConditionRefinded = xsDataIndexingResult.getSelectedSolution().getExperimentalConditionRefined()
xsDataIntegrationInput.setExperimentalConditionRefined(xsDataExperimentalConditionRefinded)
xsDataIntegrationInput.setSelectedIndexingSolution(xsDataIndexingResult.getSelectedSolution())
self.__edPluginControlIntegration.setDataInput(xsDataIntegrationInput)
self.__edPluginControlIntegration.executeSynchronous()
def doFailureEvaluationIndexingMOSFLM(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_2.doFailureEvaluationIndexing")
strWarningMessage = "Execution of indexing evaluation plugin failed."
EDVerbose.WARNING(strWarningMessage)
self.addWarningMessage(strWarningMessage)
if self.__xsDataResultCharacterisation is not None:
self.setDataOutput(self.__xsDataResultCharacterisation)
def doFailureEvaluationIndexingLABELIT(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_2.doFailureEvaluationIndexing")
strWarningMessage = "Execution of indexing evaluation plugin failed."
EDVerbose.WARNING(strWarningMessage)
self.addWarningMessage(strWarningMessage)
if self.__xsDataResultCharacterisation is not None:
self.setDataOutput(self.__xsDataResultCharacterisation)
def doSuccessGeneratePrediction(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_2.doSuccessGeneratePrediction")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv1_2.doSuccessGeneratePrediction")
xsDataGeneratePredictionResult = _edPlugin.getDataOutput()
xsDataIndexingResult = self.__xsDataResultCharacterisation.getIndexingResult()
xsDataIndexingResult.setPredictionResult(xsDataGeneratePredictionResult)
def doFailureGeneratePrediction(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_2.doFailureGeneratePrediction")
strWarningMessage = "Execution of generate prediction plugin failed."
EDVerbose.WARNING(strWarningMessage)
self.addWarningMessage(strWarningMessage)
if self.__xsDataResultCharacterisation is not None:
self.setDataOutput(self.__xsDataResultCharacterisation)
#self.addComment("warning: no prediction images")
def doSuccessIntegration(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_2.doSuccessIntegration")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv1_2.doSuccessIntegration")
self.addStatusMessage("Integration successful.")
xsDataIntegrationOutput = self.__edPluginControlIntegration.getDataOutput()
self.__xsDataResultCharacterisation.setIntegrationResult(xsDataIntegrationOutput)
# Integration short summary
if self.__edPluginControlIntegration.hasDataOutput("integrationShortSummary"):
self.__strCharacterisationShortSummary += self.__edPluginControlIntegration.getDataOutput("integrationShortSummary")[0].getValue()
#EDVerbose.DEBUG( self.__xsDataExperimentCharacterisation.marshal() )
if self.__bDoStrategyCalculation:
xsDataInputStrategy = XSDataInputStrategy()
xsDataSolutionSelected = self.__xsDataResultCharacterisation.getIndexingResult().getSelectedSolution()
xsDataInputStrategy.setCrystalRefined(xsDataSolutionSelected.getCrystal())
xsDataInputStrategy.setSample(self.__xsDataResultCharacterisation.getDataCollection().getSample())
xsDataIntegrationSubWedgeResultList = xsDataIntegrationOutput.getIntegrationSubWedgeResult()
xsDataInputStrategy.setBestFileContentDat(xsDataIntegrationSubWedgeResultList[0].getBestfileDat())
xsDataInputStrategy.setBestFileContentPar(xsDataIntegrationSubWedgeResultList[0].getBestfilePar())
xsDataInputStrategy.setExperimentalCondition(xsDataIntegrationSubWedgeResultList[0].getExperimentalConditionRefined())
for xsDataIntegrationSubWedgeResult in xsDataIntegrationSubWedgeResultList:
xsDataInputStrategy.addBestFileContentHKL(xsDataIntegrationSubWedgeResult.getBestfileHKL())
xsDataInputStrategy.setDiffractionPlan(self.__xsDataResultCharacterisation.getDataCollection().getDiffractionPlan())
self.__edPluginControlStrategy.setDataInput(xsDataInputStrategy)
self.__edPluginControlStrategy.executeSynchronous()
def doFailureIntegration(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_2.doFailureIntegration")
strErrorMessage = "Execution of integration plugin failed."
self.addStatusMessage("Integration FAILURE.")
EDVerbose.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
#self.addComment("integration failure")
if self.__xsDataResultCharacterisation is not None:
self.setDataOutput(self.__xsDataResultCharacterisation)
self.generateExecutiveSummary(self)
self.setFailure()
if self.__strStatusMessage != None:
self.setDataOutput(XSDataString(self.__strStatusMessage), "statusMessage")
self.writeDataOutput()
def doSuccessStrategy(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_2.doSuccessStrategy")
self.retrieveSuccessMessages(self.__edPluginControlStrategy, "EDPluginControlCharacterisationv1_2.doSuccessStrategy")
xsDataStrategyResult = self.__edPluginControlStrategy.getDataOutput()
self.__xsDataResultCharacterisation.setStrategyResult(xsDataStrategyResult)
if self.__edPluginControlStrategy.hasDataOutput("strategyShortSummary"):
self.__strCharacterisationShortSummary += self.__edPluginControlStrategy.getDataOutput("strategyShortSummary")[0].getValue()
self.addStatusMessage("Strategy calculation successful.")
def doFailureStrategy(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_2.doFailureStrategy")
strErrorMessage = "Execution of strategy plugin failed."
EDVerbose.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
if self.__xsDataResultCharacterisation is not None:
self.setDataOutput(self.__xsDataResultCharacterisation)
self.addStatusMessage("Strategy calculation FAILURE.")
self.generateExecutiveSummary(self)
if self.__strStatusMessage != None:
self.setDataOutput(XSDataString(self.__strStatusMessage), "statusMessage")
self.writeDataOutput()
self.setFailure()
def generateExecutiveSummary(self, _edPlugin):
"""
Generates a summary of the execution of the plugin.
"""
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_2.generateExecutiveSummary")
self.addExecutiveSummaryLine("Summary of characterisation:")
xsDataInputStrategy = self.getDataInput()
xsDataCollection = xsDataInputStrategy.getDataCollection()
xsDataDiffractionPlan = xsDataCollection.getDiffractionPlan()
self.addExecutiveSummaryLine("Diffraction plan:")
if (xsDataDiffractionPlan.getComplexity() is not None):
self.addExecutiveSummaryLine("BEST complexity : %s" % xsDataDiffractionPlan.getComplexity().getValue())
if (xsDataDiffractionPlan.getAimedCompleteness() is not None):
self.addExecutiveSummaryLine("Aimed completeness : %6.1f [%%]" % (100.0 * xsDataDiffractionPlan.getAimedCompleteness().getValue()))
if (xsDataDiffractionPlan.getRequiredCompleteness() is not None):
self.addExecutiveSummaryLine("Required completeness : %6.1f [%%]" % (100.0 * xsDataDiffractionPlan.getRequiredCompleteness().getValue()))
if (xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution() is not None):
self.addExecutiveSummaryLine("Aimed I/sigma at highest resolution : %6.1f" % xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution().getValue())
if (xsDataDiffractionPlan.getAimedResolution() is not None):
self.addExecutiveSummaryLine("Aimed resolution : %6.1f [A]" % xsDataDiffractionPlan.getAimedResolution().getValue())
if (xsDataDiffractionPlan.getRequiredResolution() is not None):
self.addExecutiveSummaryLine("Required resolution : %6.1f [A]" % xsDataDiffractionPlan.getRequiredResolution().getValue())
if (xsDataDiffractionPlan.getAimedMultiplicity() is not None):
self.addExecutiveSummaryLine("Aimed multiplicity : %6.1f" % xsDataDiffractionPlan.getAimedMultiplicity().getValue())
if (xsDataDiffractionPlan.getRequiredMultiplicity() is not None):
self.addExecutiveSummaryLine("Required multiplicity : %6.1f" % xsDataDiffractionPlan.getRequiredMultiplicity().getValue())
if (xsDataDiffractionPlan.getForcedSpaceGroup() is not None):
self.addExecutiveSummaryLine("Forced space group : %6s" % xsDataDiffractionPlan.getForcedSpaceGroup().getValue())
if (xsDataDiffractionPlan.getMaxExposureTimePerDataCollection() is not None):
self.addExecutiveSummaryLine("Max exposure time per data collection : %6.1f [s]" % xsDataDiffractionPlan.getMaxExposureTimePerDataCollection().getValue())
self.addExecutiveSummarySeparator()
if self.__edPluginControlIndexingIndicators is not None:
self.appendExecutiveSummary(self.__edPluginControlIndexingIndicators, "")
if self.__edPluginControlIndexingLabelit is not None:
self.appendExecutiveSummary(self.__edPluginControlIndexingLabelit, "")
if self.__edPluginControlIntegration is not None:
self.appendExecutiveSummary(self.__edPluginControlIntegration, "")
if self.__edPluginControlStrategy is not None:
self.appendExecutiveSummary(self.__edPluginControlStrategy, "")
self.addExecutiveSummarySeparator()
if self.__strCharacterisationShortSummary is not None:
self.addExecutiveSummaryLine("Characterisation short summary:")
self.addExecutiveSummaryLine("")
if self.__strStatusMessage != None:
for strLine in self.__strStatusMessage.split(". "):
if strLine.endswith("."):
self.addExecutiveSummaryLine(strLine)
else:
self.addExecutiveSummaryLine(strLine+".")
self.addExecutiveSummaryLine("")
for strLine in self.__strCharacterisationShortSummary.split("\n"):
if strLine != "\n":
self.addExecutiveSummaryLine(strLine)
self.addErrorWarningMessagesToExecutiveSummary("Characterisation error and warning messages: ")
self.addExecutiveSummarySeparator()
def getPluginStrategyName(self):
return self.__strPluginControlStrategy
def addStatusMessage(self, _strStatusMessage):
if self.__strStatusMessage != "":
self.__strStatusMessage += " "
self.__strStatusMessage += _strStatusMessage
def doStrategyCalculation(self, _bValue):
self.__bDoStrategyCalculation = _bValue
def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
EDVerbose.DEBUG("EDPluginControlCharacterisationv1_1.preProcess...")
self.__edPluginIndexing = self.loadPlugin(self.__strPluginIndexingName,
"Indexing")
self.__edPluginIntegration = self.loadPlugin(
self.__strPluginIntegrationName, "Integration")
self.__edPluginStrategy = self.loadPlugin(self.__strPluginStrategyName,
"Strategy")
if (self.__edPluginIndexing is not None):
EDVerbose.DEBUG(
"EDPluginControlCharacterisationv1_1.preProcess: " +
self.__strPluginIndexingName + " Found... setting Data Input")
# create Data Input for indexing
xsDataInputStrategy = self.getDataInput()
xsDataCollection = xsDataInputStrategy.getDataCollection()
xsDataSample = xsDataCollection.getSample()
xsDataSubWedgeList = xsDataCollection.getSubWedge()
if ((xsDataSubWedgeList is None) or (xsDataSubWedgeList == [])):
strError = "EDPluginControlCharacterisationv1_1.preProcess: No subwedges in input data."
EDVerbose.ERROR(strError)
self.setFailure()
else:
xsDataExperimentalCondition = xsDataSubWedgeList[
0].getExperimentalCondition()
# Fix for bug 431: if the flux is zero raise an error
xsDataDoubleFlux = xsDataExperimentalCondition.getBeam(
).getFlux()
if (xsDataDoubleFlux is not None):
if (xsDataDoubleFlux.getValue() < 0.1):
pyStrErrorMessage = "EDPluginControlCharacterisationv1_1.preProcess ERROR: Input flux is negative or close to zero. Execution of characterisation aborted."
EDVerbose.ERROR(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
self.setFailure()
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.setDataCollection(xsDataCollection)
xsDataIndexingInput.setExperimentalCondition(
xsDataExperimentalCondition)
xsDataDiffractionPlan = xsDataCollection.getDiffractionPlan()
xsDataStringForcedSpaceGroup = xsDataDiffractionPlan.getForcedSpaceGroup(
)
if (xsDataStringForcedSpaceGroup is not None):
xsDataCrystal = XSDataCrystal()
xsDataSpaceGroup = XSDataSpaceGroup()
xsDataSpaceGroup.setName(xsDataStringForcedSpaceGroup)
xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
xsDataIndexingInput.setCrystal(xsDataCrystal)
self.__edPluginIndexing.setDataInput(xsDataIndexingInput)
# Populate characterisation object
self.__xsDataResultCharacterisation = XSDataResultCharacterisation(
)
self.__xsDataResultCharacterisation.setDataCollection(
XSDataCollection.parseString(xsDataCollection.marshal()))
