def testDefaultChemicalComposition(self):
edPluginStrategy = self.createPlugin()
from XSDataCommon import XSDataAngle
from XSDataCommon import XSDataLength
from XSDataMXv1 import XSDataSampleCrystalMM
from XSDataMXv1 import XSDataCrystal
from XSDataMXv1 import XSDataCell
xsDataSampleCrystalMM = XSDataSampleCrystalMM()
xsDataCrystal = XSDataCrystal()
xsDataCell = XSDataCell(XSDataAngle(90.0),
XSDataAngle(90.0),
XSDataAngle(90.0),
XSDataLength(78.9),
XSDataLength(95.162),
XSDataLength(104.087))
xsDataCrystal.setCell(xsDataCell)
xsDataSampleCrystalMM.setCrystal(xsDataCrystal)
inumOperators = 4
xsDataSample2 = edPluginStrategy.getDefaultChemicalComposition(xsDataSampleCrystalMM, inumOperators)
strChainType = xsDataSample2.getStructure().getChain()[0].getType()
EDAssert.equal("protein", strChainType.getValue())
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 generateXSDataIndexingResult(_xsDataResultXDSIndexing, _xsDataExperimentalCondition=None):
xsDataIndexingResult = XSDataIndexingResult()
xsDataIndexingSolutionSelected = XSDataIndexingSolutionSelected()
xsDataCrystalSelected = XSDataCrystal()
# xsDataIndexingSolutionSelected.setNumber(XSDataInteger(iIndex))
# xsDataCellSelected = xsDataLabelitSolution.getUnitCell()
spaceGroupName = EDUtilsSymmetry.getMinimumSymmetrySpaceGroupFromBravaisLattice(_xsDataResultXDSIndexing.bravaisLattice.value)
xsDataCrystalSelected = XSDataCrystal()
xsDataSpaceGroupSelected = XSDataSpaceGroup()
xsDataSpaceGroupSelected.setName(XSDataString(spaceGroupName))
xsDataCrystalSelected.setSpaceGroup(xsDataSpaceGroupSelected)
# xsDataCrystalSelected.setCell(xsDataCellSelected)
xsDataCrystalSelected.setMosaicity(XSDataDouble(_xsDataResultXDSIndexing.mosaicity.value))
xsDataCrystalSelected.setCell(XSDataCell.parseString(_xsDataResultXDSIndexing.unitCell.marshal()))
xsDataIndexingSolutionSelected.setCrystal(xsDataCrystalSelected)
xsDataOrientation = XSDataOrientation()
xsDataOrientation.setMatrixA(_xsDataResultXDSIndexing.getAMatrix())
xsDataOrientation.setMatrixU(_xsDataResultXDSIndexing.getUMatrix())
xsDataIndexingSolutionSelected.setOrientation(xsDataOrientation)
xsDataStatisticsIndexing = XSDataStatisticsIndexing()
if (_xsDataExperimentalCondition is not None):
fBeamPositionXOrig = _xsDataExperimentalCondition.getDetector().getBeamPositionX().getValue()
fBeamPositionYOrig = _xsDataExperimentalCondition.getDetector().getBeamPositionY().getValue()
fBeamPositionXNew = _xsDataResultXDSIndexing.getBeamCentreX().getValue()
fBeamPositionYNew = _xsDataResultXDSIndexing.getBeamCentreY().getValue()
xsDataStatisticsIndexing.setBeamPositionShiftX(XSDataLength(fBeamPositionXOrig - fBeamPositionXNew))
xsDataStatisticsIndexing.setBeamPositionShiftY(XSDataLength(fBeamPositionYOrig - fBeamPositionYNew))
xsDataExperimentalConditionRefined = None
if (_xsDataExperimentalCondition is None):
xsDataExperimentalConditionRefined = XSDataExperimentalCondition()
else:
# Copy the incoming experimental condition
xmlExperimentalCondition = _xsDataExperimentalCondition.marshal()
xsDataExperimentalConditionRefined = XSDataExperimentalCondition.parseString(xmlExperimentalCondition)
xsDataDetector = xsDataExperimentalConditionRefined.getDetector()
if (xsDataDetector is None):
xsDataDetector = XSDataDetector()
xsDataDetector.setBeamPositionX(XSDataLength(_xsDataResultXDSIndexing.getBeamCentreX().value))
xsDataDetector.setBeamPositionY(XSDataLength(_xsDataResultXDSIndexing.getBeamCentreY().value))
xsDataDetector.setDistance(_xsDataResultXDSIndexing.getDistance())
xsDataExperimentalConditionRefined.setDetector(xsDataDetector)
xsDataIndexingSolutionSelected.setExperimentalConditionRefined(xsDataExperimentalConditionRefined)
xsDataIndexingResult.setSelectedSolution(xsDataIndexingSolutionSelected)
return xsDataIndexingResult
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 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 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 testDefaultChemicalComposition(self):
edPluginStrategy = self.createPlugin()
xsDataSampleCrystalMM = XSDataSampleCrystalMM()
xsDataCrystal = XSDataCrystal()
xsDataCell = XSDataCell(angle_alpha=XSDataAngle(90.0),
angle_beta=XSDataAngle(90.0),
angle_gamma=XSDataAngle(90.0),
length_a=XSDataLength(78.9),
length_b=XSDataLength(95.162),
length_c=XSDataLength(104.087))
xsDataCrystal.setCell(xsDataCell)
xsDataSampleCrystalMM.setCrystal(xsDataCrystal)
inumOperators = 4
xsDataSample2 = edPluginStrategy.getDefaultChemicalComposition(xsDataSampleCrystalMM, inumOperators)
pyStrChainType = xsDataSample2.getStructure().getChain()[0].getType()
EDAssert.equal("protein", pyStrChainType.getValue())
def testDefaultChemicalComposition(self):
edPluginStrategy = self.createPlugin()
xsDataSampleCrystalMM = XSDataSampleCrystalMM()
xsDataCrystal = XSDataCrystal()
xsDataCell = XSDataCell(angle_alpha=XSDataAngle(90.0),
angle_beta=XSDataAngle(90.0),
angle_gamma=XSDataAngle(90.0),
length_a=XSDataLength(78.9),
length_b=XSDataLength(95.162),
length_c=XSDataLength(104.087))
xsDataCrystal.setCell(xsDataCell)
xsDataSampleCrystalMM.setCrystal(xsDataCrystal)
inumOperators = 4
xsDataSample2 = edPluginStrategy.getDefaultChemicalComposition(xsDataSampleCrystalMM, inumOperators)
pyStrChainType = xsDataSample2.getStructure().getChain()[0].getType()
EDAssert.equal("protein", pyStrChainType.getValue())
def generateXSDataIndexingResult(_xsDataResultLabelitIndexing, _xsDataExperimentalCondition=None):
EDVerbose.DEBUG("EDHandlerXSDataLabelitv1_1.generateXSDataIndexingOutput")
xsDataLabelitScreenOutput = _xsDataResultLabelitIndexing.screenOutput
xsDataLabelitMosflmScriptsOutput = _xsDataResultLabelitIndexing.mosflmScriptsOutput
iSelectedSolutionNumber = xsDataLabelitScreenOutput.getSelectedSolutionNumber().getValue()
xsDataIndexingResult = XSDataIndexingResult()
xsDataIndexingSolutionSelected = None
for xsDataLabelitSolution in xsDataLabelitScreenOutput.getLabelitScreenSolution():
xsDataCrystal = XSDataCrystal()
xsDataSpaceGroup = XSDataSpaceGroup()
edStringSpaceGroupName = EDUtilsSymmetry.getMinimumSymmetrySpaceGroupFromBravaisLattice(xsDataLabelitSolution.getBravaisLattice().getValue())
xsDataSpaceGroup.setName(XSDataString(edStringSpaceGroupName))
xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
xsDataCrystal.setCell(xsDataLabelitSolution.getUnitCell())
xsDataIndexingSolution = XSDataIndexingSolution()
xsDataIndexingSolution.setCrystal(xsDataCrystal)
iIndex = xsDataLabelitSolution.getSolutionNumber().getValue()
xsDataIndexingSolution.setNumber(XSDataInteger(iIndex))
xsDataIndexingResult.addSolution(xsDataIndexingSolution)
if (iIndex == iSelectedSolutionNumber):
xsDataIndexingSolutionSelected = XSDataIndexingSolutionSelected()
xsDataIndexingSolutionSelected.setNumber(XSDataInteger(iIndex))
edStringSelectedSpaceGroupName = edStringSpaceGroupName
xsDataCellSelected = xsDataLabelitSolution.getUnitCell()
fRmsdSelected = xsDataLabelitSolution.getRmsd().getValue()
iNumberOfSpotsSelected = xsDataLabelitSolution.getNumberOfSpots().getValue()
xsDataCrystalSelected = XSDataCrystal()
xsDataSpaceGroupSelected = XSDataSpaceGroup()
xsDataSpaceGroupSelected.setName(XSDataString(edStringSelectedSpaceGroupName))
xsDataSpaceGroupSelected.setITNumber(XSDataInteger(EDUtilsSymmetry.getITNumberFromSpaceGroupName(edStringSelectedSpaceGroupName)))
xsDataCrystalSelected.setSpaceGroup(xsDataSpaceGroupSelected)
xsDataCrystalSelected.setCell(xsDataCellSelected)
xsDataCrystalSelected.setMosaicity(XSDataDouble(xsDataLabelitScreenOutput.getMosaicity().getValue()))
xsDataIndexingSolutionSelected.setCrystal(xsDataCrystalSelected)
xsDataOrientation = XSDataOrientation()
xsDataOrientation.setMatrixA(xsDataLabelitMosflmScriptsOutput.getAMatrix())
xsDataOrientation.setMatrixU(xsDataLabelitMosflmScriptsOutput.getUMatrix())
xsDataIndexingSolutionSelected.setOrientation(xsDataOrientation)
xsDataStatisticsIndexing = XSDataStatisticsIndexing()
if (_xsDataExperimentalCondition is not None):
fBeamPositionXOrig = _xsDataExperimentalCondition.getDetector().getBeamPositionX().getValue()
fBeamPositionYOrig = _xsDataExperimentalCondition.getDetector().getBeamPositionY().getValue()
fBeamPositionXNew = xsDataLabelitScreenOutput.getBeamCentreX().getValue()
fBeamPositionYNew = xsDataLabelitScreenOutput.getBeamCentreY().getValue()
xsDataStatisticsIndexing.setBeamPositionShiftX(XSDataLength(fBeamPositionXOrig - fBeamPositionXNew))
xsDataStatisticsIndexing.setBeamPositionShiftY(XSDataLength(fBeamPositionYOrig - fBeamPositionYNew))
# xsDataStatisticsIndexing.setSpotDeviXSDataLength( dDistanceRefinedationAngular( XSDataAngle( dDeviationAngular ) )
xsDataStatisticsIndexing.setSpotDeviationPositional(XSDataLength(fRmsdSelected))
xsDataStatisticsIndexing.setSpotsUsed(XSDataInteger(iNumberOfSpotsSelected))
xsDataStatisticsIndexing.setSpotsTotal(XSDataInteger(iNumberOfSpotsSelected))
xsDataIndexingSolutionSelected.setStatistics(xsDataStatisticsIndexing)
xsDataExperimentalConditionRefined = None
if (_xsDataExperimentalCondition is None):
xsDataExperimentalConditionRefined = XSDataExperimentalCondition()
else:
# Copy the incoming experimental condition
xmlExperimentalCondition = _xsDataExperimentalCondition.marshal()
xsDataExperimentalConditionRefined = XSDataExperimentalCondition.parseString(xmlExperimentalCondition)
xsDataDetector = xsDataExperimentalConditionRefined.getDetector()
if (xsDataDetector is None):
xsDataDetector = XSDataDetector()
xsDataDetector.setBeamPositionX(xsDataLabelitScreenOutput.getBeamCentreX())
xsDataDetector.setBeamPositionY(xsDataLabelitScreenOutput.getBeamCentreY())
xsDataDetector.setDistance(xsDataLabelitScreenOutput.getDistance())
xsDataExperimentalConditionRefined.setDetector(xsDataDetector)
xsDataIndexingSolutionSelected.setExperimentalConditionRefined(xsDataExperimentalConditionRefined)
xsDataIndexingResult.setSelectedSolution(xsDataIndexingSolutionSelected)
xsDataIndexingResult.setIndexingLogFile(xsDataLabelitScreenOutput.getPathToLogFile())
return xsDataIndexingResult
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!")
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 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()))
def generateXSDataIndexingResult(_xsDataMOSFLMIndexingOutput,
_xsDataExperimentalCondition=None):
"""
Translation from XSDataMOSFLMIndexingOutput to XSDataIndexingResult.
"""
EDVerbose.DEBUG(
"EDHandlerXSDataMOSFLMv10.generateXSDataIndexingOutput")
xsDataMOSFLMBeamPositionRefined = _xsDataMOSFLMIndexingOutput.getRefinedBeam(
)
xsDataMOSFLMBeamPositionShift = _xsDataMOSFLMIndexingOutput.getBeamShift(
)
dDeviationAngular = _xsDataMOSFLMIndexingOutput.getDeviationAngular(
).getValue()
dDeviationPositional = _xsDataMOSFLMIndexingOutput.getDeviationPositional(
).getValue()
dMosaicityEstimation = _xsDataMOSFLMIndexingOutput.getMosaicityEstimation(
).getValue()
dDistanceRefined = _xsDataMOSFLMIndexingOutput.getRefinedDistance(
).getValue()
iSelectedSolution = _xsDataMOSFLMIndexingOutput.getSelectedSolutionNumber(
).getValue()
iSpotsTotal = _xsDataMOSFLMIndexingOutput.getSpotsTotal().getValue()
iSpotsUsed = _xsDataMOSFLMIndexingOutput.getSpotsUsed().getValue()
xsDataCellRefined = _xsDataMOSFLMIndexingOutput.getRefinedNewmat(
).getRefinedCell()
xsDataMatrixA = _xsDataMOSFLMIndexingOutput.getRefinedNewmat(
).getAMatrix()
xsDataMatrixU = _xsDataMOSFLMIndexingOutput.getRefinedNewmat(
).getUMatrix()
strSelectedSpaceGroupName = _xsDataMOSFLMIndexingOutput.getSelectedSolutionSpaceGroup(
).getValue()
iSelectedSpaceGroupNumber = _xsDataMOSFLMIndexingOutput.getSelectedSolutionSpaceGroupNumber(
).getValue()
xsDataIndexingResult = XSDataIndexingResult()
xsDataIndexingSolutionSelected = None
for possibleSolutions in _xsDataMOSFLMIndexingOutput.getPossibleSolutions(
):
xsDataCrystal = XSDataCrystal()
xsDataSpaceGroup = XSDataSpaceGroup()
xsDataSpaceGroup.setName(
XSDataString(possibleSolutions.getLattice().getValue()))
xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
xsDataCrystal.setCell(possibleSolutions.getCell())
xsDataIndexingSolution = XSDataIndexingSolution()
xsDataIndexingSolution.setCrystal(xsDataCrystal)
iIndex = possibleSolutions.getIndex().getValue()
xsDataIndexingSolution.setNumber(XSDataInteger(iIndex))
xsDataIndexingSolution.setPenalty(
XSDataFloat(possibleSolutions.getPenalty().getValue()))
xsDataIndexingResult.addSolution(xsDataIndexingSolution)
if (iIndex == iSelectedSolution):
xsDataIndexingSolutionSelected = XSDataIndexingSolutionSelected(
)
xsDataIndexingSolutionSelected.setNumber(XSDataInteger(iIndex))
xsDataIndexingSolutionSelected.setPenalty(
XSDataFloat(possibleSolutions.getPenalty().getValue()))
xsDataCrystalSelected = XSDataCrystal()
xsDataSpaceGroupSelected = XSDataSpaceGroup()
xsDataSpaceGroupSelected.setName(
XSDataString(strSelectedSpaceGroupName))
xsDataSpaceGroupSelected.setITNumber(
XSDataInteger(iSelectedSpaceGroupNumber))
xsDataCrystalSelected.setSpaceGroup(xsDataSpaceGroupSelected)
xsDataCrystalSelected.setCell(xsDataCellRefined)
xsDataCrystalSelected.setMosaicity(XSDataDouble(dMosaicityEstimation))
xsDataIndexingSolutionSelected.setCrystal(xsDataCrystalSelected)
xsDataOrientation = XSDataOrientation()
xsDataOrientation.setMatrixA(xsDataMatrixA)
xsDataOrientation.setMatrixU(xsDataMatrixU)
xsDataIndexingSolutionSelected.setOrientation(xsDataOrientation)
xsDataStatisticsIndexing = XSDataStatisticsIndexing()
xsDataStatisticsIndexing.setBeamPositionShiftX(
XSDataLength(xsDataMOSFLMBeamPositionShift.getX().getValue()))
xsDataStatisticsIndexing.setBeamPositionShiftY(
XSDataLength(xsDataMOSFLMBeamPositionShift.getY().getValue()))
xsDataStatisticsIndexing.setSpotDeviationAngular(
XSDataAngle(dDeviationAngular))
xsDataStatisticsIndexing.setSpotDeviationPositional(
XSDataLength(dDeviationPositional))
xsDataStatisticsIndexing.setSpotsUsed(XSDataInteger(iSpotsUsed))
xsDataStatisticsIndexing.setSpotsTotal(XSDataInteger(iSpotsTotal))
xsDataIndexingSolutionSelected.setStatistics(xsDataStatisticsIndexing)
xsDataExperimentalConditionRefined = None
if (_xsDataExperimentalCondition is None):
xsDataExperimentalConditionRefined = XSDataExperimentalCondition()
else:
# Copy the incoming experimental condition
xmlExperimentalCondition = _xsDataExperimentalCondition.marshal()
xsDataExperimentalConditionRefined = XSDataExperimentalCondition.parseString(
xmlExperimentalCondition)
xsDataDetector = xsDataExperimentalConditionRefined.getDetector()
if (xsDataDetector is None):
xsDataDetector = XSDataDetector()
xsDataDetector.setBeamPositionX(
XSDataLength(xsDataMOSFLMBeamPositionRefined.getX().getValue()))
xsDataDetector.setBeamPositionY(
XSDataLength(xsDataMOSFLMBeamPositionRefined.getY().getValue()))
xsDataDetector.setDistance(XSDataLength(dDistanceRefined))
xsDataExperimentalConditionRefined.setDetector(xsDataDetector)
xsDataIndexingSolutionSelected.setExperimentalConditionRefined(
xsDataExperimentalConditionRefined)
xsDataIndexingResult.setSelectedSolution(
xsDataIndexingSolutionSelected)
xsDataIndexingResult.setIndexingLogFile(
_xsDataMOSFLMIndexingOutput.getPathToLogFile())
return xsDataIndexingResult
def generateXSDataIndexingResult(_xsDataLabelitScreenOutput, _xsDataLabelitMosflmScriptsOutput, \
_xsDataExperimentalCondition=None):
EDVerbose.DEBUG(
"EDHandlerXSDataLabelitv1_1.generateXSDataIndexingOutput")
iSelectedSolutionNumber = _xsDataLabelitScreenOutput.getSelectedSolutionNumber(
).getValue()
xsDataIndexingResult = XSDataIndexingResult()
xsDataIndexingSolutionSelected = None
for xsDataLabelitSolution in _xsDataLabelitScreenOutput.getLabelitScreenSolution(
):
xsDataCrystal = XSDataCrystal()
xsDataSpaceGroup = XSDataSpaceGroup()
edStringSpaceGroupName = EDUtilsSymmetry.getMinimumSymmetrySpaceGroupFromBravaisLattice(
xsDataLabelitSolution.getBravaisLattice().getValue())
xsDataSpaceGroup.setName(XSDataString(edStringSpaceGroupName))
xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
xsDataCrystal.setCell(xsDataLabelitSolution.getUnitCell())
xsDataIndexingSolution = XSDataIndexingSolution()
xsDataIndexingSolution.setCrystal(xsDataCrystal)
iIndex = xsDataLabelitSolution.getSolutionNumber().getValue()
xsDataIndexingSolution.setNumber(XSDataInteger(iIndex))
xsDataIndexingResult.addSolution(xsDataIndexingSolution)
if (iIndex == iSelectedSolutionNumber):
xsDataIndexingSolutionSelected = XSDataIndexingSolutionSelected(
)
xsDataIndexingSolutionSelected.setNumber(XSDataInteger(iIndex))
edStringSelectedSpaceGroupName = edStringSpaceGroupName
xsDataCellSelected = xsDataLabelitSolution.getUnitCell()
fRmsdSelected = xsDataLabelitSolution.getRmsd().getValue()
iNumberOfSpotsSelected = xsDataLabelitSolution.getNumberOfSpots(
).getValue()
xsDataCrystalSelected = XSDataCrystal()
xsDataSpaceGroupSelected = XSDataSpaceGroup()
xsDataSpaceGroupSelected.setName(
XSDataString(edStringSelectedSpaceGroupName))
#xsDataSpaceGroupSelected.setITNumber( XSDataInteger( iSelectedSpaceGroupNumber ) )
xsDataCrystalSelected.setSpaceGroup(xsDataSpaceGroupSelected)
xsDataCrystalSelected.setCell(xsDataCellSelected)
xsDataCrystalSelected.setMosaicity(
XSDataDouble(_xsDataLabelitScreenOutput.getMosaicity().getValue()))
xsDataIndexingSolutionSelected.setCrystal(xsDataCrystalSelected)
xsDataOrientation = XSDataOrientation()
xsDataOrientation.setMatrixA(
_xsDataLabelitMosflmScriptsOutput.getAMatrix())
xsDataOrientation.setMatrixU(
_xsDataLabelitMosflmScriptsOutput.getUMatrix())
xsDataIndexingSolutionSelected.setOrientation(xsDataOrientation)
xsDataStatisticsIndexing = XSDataStatisticsIndexing()
if (_xsDataExperimentalCondition is not None):
fBeamPositionXOrig = _xsDataExperimentalCondition.getDetector(
).getBeamPositionX().getValue()
fBeamPositionYOrig = _xsDataExperimentalCondition.getDetector(
).getBeamPositionY().getValue()
fBeamPositionXNew = _xsDataLabelitScreenOutput.getBeamCentreX(
).getValue()
fBeamPositionYNew = _xsDataLabelitScreenOutput.getBeamCentreY(
).getValue()
xsDataStatisticsIndexing.setBeamPositionShiftX(
XSDataLength(fBeamPositionXOrig - fBeamPositionXNew))
xsDataStatisticsIndexing.setBeamPositionShiftY(
XSDataLength(fBeamPositionYOrig - fBeamPositionYNew))
#xsDataStatisticsIndexing.setSpotDeviXSDataLength( dDistanceRefinedationAngular( XSDataAngle( dDeviationAngular ) )
xsDataStatisticsIndexing.setSpotDeviationPositional(
XSDataLength(fRmsdSelected))
xsDataStatisticsIndexing.setSpotsUsed(
XSDataInteger(iNumberOfSpotsSelected))
xsDataStatisticsIndexing.setSpotsTotal(
XSDataInteger(iNumberOfSpotsSelected))
xsDataIndexingSolutionSelected.setStatistics(xsDataStatisticsIndexing)
xsDataExperimentalConditionRefined = None
if (_xsDataExperimentalCondition is None):
xsDataExperimentalConditionRefined = XSDataExperimentalCondition()
else:
# Copy the incoming experimental condition
xmlExperimentalCondition = _xsDataExperimentalCondition.marshal()
xsDataExperimentalConditionRefined = XSDataExperimentalCondition.parseString(
xmlExperimentalCondition)
xsDataDetector = xsDataExperimentalConditionRefined.getDetector()
if (xsDataDetector is None):
xsDataDetector = XSDataDetector()
xsDataDetector.setBeamPositionX(
_xsDataLabelitScreenOutput.getBeamCentreX())
xsDataDetector.setBeamPositionY(
_xsDataLabelitScreenOutput.getBeamCentreY())
xsDataDetector.setDistance(_xsDataLabelitScreenOutput.getDistance())
xsDataExperimentalConditionRefined.setDetector(xsDataDetector)
xsDataIndexingSolutionSelected.setExperimentalConditionRefined(
xsDataExperimentalConditionRefined)
xsDataIndexingResult.setSelectedSolution(
xsDataIndexingSolutionSelected)
xsDataIndexingResult.setIndexingLogFile(
_xsDataLabelitScreenOutput.getPathToLogFile())
return xsDataIndexingResult
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()))
def testGetXSDataRaddoseInput(self):
"""
"""
from XSDataCommon import XSDataLength
from XSDataCommon import XSDataWavelength
from XSDataCommon import XSDataFlux
from XSDataCommon import XSDataSize
from XSDataCommon import XSDataDouble
from XSDataCommon import XSDataString
from XSDataCommon import XSDataAngle
from XSDataCommon import XSDataTime
from XSDataCommon import XSDataInteger
from XSDataMXv1 import XSDataBeam
from XSDataMXv1 import XSDataStructure
from XSDataMXv1 import XSDataChain
from XSDataMXv1 import XSDataAtom
from XSDataMXv1 import XSDataLigand
from XSDataMXv1 import XSDataCrystal
from XSDataMXv1 import XSDataSpaceGroup
from XSDataMXv1 import XSDataSampleCrystalMM
from XSDataMXv1 import XSDataChemicalCompositionMM
from XSDataMXv1 import XSDataAtomicComposition
from XSDataMXv1 import XSDataSolvent
from XSDataMXv1 import XSDataCell
from EDHandlerXSDataRaddosev10 import EDHandlerXSDataRaddosev10
EDFactoryPluginStatic.loadModule("XSDataRaddosev10")
from XSDataRaddosev10 import XSDataRaddoseInput
xsDataBeam = XSDataBeam()
xsDataBeam.setSize(XSDataSize(x=XSDataLength(0.1),
y=XSDataLength(0.1)))
xsDataBeam.setWavelength(XSDataWavelength(2.41))
xsDataBeam.setFlux(XSDataFlux(1e+12))
xsDataBeam.setExposureTime(XSDataTime(0.037))
xsDataSample = XSDataSampleCrystalMM()
xsDataStructure = XSDataStructure()
xsDataComposition = XSDataChemicalCompositionMM()
xsDataChain = XSDataChain()
xsDataChain.setType(XSDataString("protein"))
xsDataChain.setNumberOfCopies(XSDataDouble(2))
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtom1 = XSDataAtom()
xsDataAtom1.setSymbol(XSDataString("Se"))
xsDataAtom1.setNumberOf(XSDataDouble(4))
xsDataAtomicComposition.addAtom(xsDataAtom1)
xsDataAtom2 = XSDataAtom()
xsDataAtom2.setSymbol(XSDataString("S"))
xsDataAtom2.setNumberOf(XSDataDouble(5))
xsDataAtomicComposition.addAtom(xsDataAtom2)
xsDataChain.setHeavyAtoms(xsDataAtomicComposition)
xsDataChain.setNumberOfMonomers(XSDataDouble(100))
xsDataStructure.addChain(xsDataChain)
xsDataChain2 = XSDataChain()
xsDataChain2.setType(XSDataString("rna"))
xsDataChain2.setNumberOfCopies(XSDataDouble(1))
xsDataChain2.setNumberOfMonomers(XSDataDouble(60))
xsDataStructure.addChain(xsDataChain2)
xsDataLigand = XSDataLigand()
xsDataLigand.setNumberOfCopies(XSDataDouble(2))
xsDataLigand.setNumberOfLightAtoms(XSDataDouble(42))
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtom3 = XSDataAtom()
xsDataAtom3.setSymbol(XSDataString("Fe"))
xsDataAtom3.setNumberOf(XSDataDouble(1))
xsDataAtomicComposition.addAtom(xsDataAtom3)
xsDataLigand.setHeavyAtoms(xsDataAtomicComposition)
xsDataStructure.addLigand(xsDataLigand)
xsDataStructure.setNumberOfCopiesInAsymmetricUnit(XSDataDouble(0.25))
xsDataSolvent = XSDataSolvent()
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtomNa = XSDataAtom()
xsDataAtomNa.setSymbol(XSDataString("Na"))
xsDataAtomNa.setConcentration(XSDataDouble(1000))
xsDataAtomicComposition.addAtom(xsDataAtomNa)
xsDataAtomCl = XSDataAtom()
xsDataAtomCl.setSymbol(XSDataString("Cl"))
xsDataAtomCl.setConcentration(XSDataDouble(1000))
xsDataAtomicComposition.addAtom(xsDataAtomCl)
xsDataSolvent.setAtoms(xsDataAtomicComposition)
xsDataComposition.setStructure(xsDataStructure)
xsDataComposition.setSolvent(xsDataSolvent)
xsDataSample.setChemicalComposition(xsDataComposition)
xsDataSample.setSize(
XSDataSize(XSDataLength(0.1), XSDataLength(0.1),
XSDataLength(0.1)))
xsDataCell = XSDataCell(angle_alpha=XSDataAngle(90.0),
angle_beta=XSDataAngle(90.0),
angle_gamma=XSDataAngle(90.0),
length_a=XSDataLength(78.9),
length_b=XSDataLength(95.162),
length_c=XSDataLength(104.087))
xsDataCrystal = XSDataCrystal()
xsDataSpaceGroup = XSDataSpaceGroup()
xsDataCrystal.setCell(xsDataCell)
xsDataSpaceGroup.setITNumber(XSDataInteger(16))
xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
xsDataSample.setCrystal(xsDataCrystal)
iNumSymOperators = 4
iNumberOfImages = 2
xsDataRaddosev01Input = EDHandlerXSDataRaddosev10(
).getXSDataRaddoseInput(xsDataBeam, xsDataSample, iNumSymOperators,
iNumberOfImages)
xsDataRaddosev01Input.exportToFile(self.strObtainedInputFile2)
strExpectedInput = EDUtilsTest.readAndParseFile(
self.strReferenceInputFile2)
strObtainedInput = EDUtilsTest.readAndParseFile(
self.strObtainedInputFile2)
xsDataInputExpected = XSDataRaddoseInput.parseString(strExpectedInput)
xsDataInputObtained = XSDataRaddoseInput.parseString(strObtainedInput)
EDAssert.equal(xsDataInputExpected.marshal(),
xsDataInputObtained.marshal())
def testSetDataModelInput(self):
edPluginStrategy = self.createPlugin()
strPathToTestConfigFile = os.path.join(self.getPluginTestsDataHome(), "XSConfiguration_ESRF.xml")
edConfiguration = EDConfiguration(strPathToTestConfigFile)
dictItem = edConfiguration.get(edPluginStrategy.getPluginName())
edPluginStrategy.setConfig(dictItem)
edPluginStrategy.configure()
xsDataStrategy = XSDataInputStrategy()
# Beam
xsExperimentalCondition = XSDataExperimentalCondition()
xsBeam = XSDataBeam()
xsBeam.setFlux(XSDataFlux(1e+12))
xsBeam.setWavelength(XSDataWavelength(2.41))
xsBeam.setSize(XSDataSize(x=XSDataLength(0.1), y=XSDataLength(0.1)))
xsBeam.setExposureTime(XSDataTime(1))
xsExperimentalCondition.setBeam(xsBeam)
# Detector and Exposure Time
xsDataDetector = XSDataDetector()
xsDataDetector.setType(XSDataString("q210-2x"))
xsExperimentalCondition.setDetector(xsDataDetector)
xsDataGoniostat = XSDataGoniostat()
xsDataGoniostat.setRotationAxis(XSDataString("phi"))
xsExperimentalCondition.setGoniostat(xsDataGoniostat)
xsDataStrategy.setExperimentalCondition(xsExperimentalCondition)
# Best Files
bestFileContentDat = EDUtilsFile.readFile(os.path.join(self.strDataPath, "bestfile.dat"))
xsDataStrategy.setBestFileContentDat(XSDataString(bestFileContentDat))
bestFileContentPar = EDUtilsFile.readFile(os.path.join(self.strDataPath, "bestfile.par"))
xsDataStrategy.setBestFileContentPar(XSDataString(bestFileContentPar))
bestFileContentHKL = EDUtilsFile.readFile(os.path.join(self.strDataPath, "bestfile1.hkl"))
xsDataStrategy.addBestFileContentHKL(XSDataString(bestFileContentHKL))
# Crystal
xsDataSampleCrystalMM = XSDataSampleCrystalMM()
xsDataStructure = XSDataStructure()
xsDataComposition = XSDataChemicalCompositionMM()
xsDataChain = XSDataChain()
xsDataChain.setType(XSDataString("protein"))
xsDataChain.setNumberOfCopies(XSDataDouble(2))
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtom1 = XSDataAtom()
xsDataAtom1.setSymbol(XSDataString("Se"))
xsDataAtom1.setNumberOf(XSDataDouble(4))
xsDataAtomicComposition.addAtom(xsDataAtom1)
xsDataChain.setHeavyAtoms(xsDataAtomicComposition)
xsDataChain.setNumberOfMonomers(XSDataDouble(100))
xsDataStructure.addChain(xsDataChain)
xsDataChain2 = XSDataChain()
xsDataChain2.setType(XSDataString("rna"))
xsDataChain2.setNumberOfCopies(XSDataDouble(1))
xsDataChain2.setNumberOfMonomers(XSDataDouble(60))
xsDataStructure.addChain(xsDataChain2)
xsDataLigand = XSDataLigand()
xsDataLigand.setNumberOfCopies(XSDataDouble(2))
xsDataLigand.setNumberOfLightAtoms(XSDataDouble(42))
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtom2 = XSDataAtom()
xsDataAtom2.setSymbol(XSDataString("Fe"))
xsDataAtom2.setNumberOf(XSDataDouble(1))
xsDataAtomicComposition.addAtom(xsDataAtom2)
xsDataLigand.setHeavyAtoms(xsDataAtomicComposition)
xsDataStructure.addLigand(xsDataLigand)
xsDataStructure.setNumberOfCopiesInAsymmetricUnit(XSDataDouble(0.25))
xsDataSolvent = XSDataSolvent()
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtom3 = XSDataAtom()
xsDataAtom3.setSymbol(XSDataString("Na"))
xsDataAtom3.setConcentration(XSDataDouble(1000))
xsDataAtom4 = XSDataAtom()
xsDataAtom4.setSymbol(XSDataString("Cl"))
xsDataAtom4.setConcentration(XSDataDouble(1000))
xsDataAtomicComposition.addAtom(xsDataAtom3)
xsDataAtomicComposition.addAtom(xsDataAtom4)
xsDataSolvent.setAtoms(xsDataAtomicComposition)
xsDataComposition.setStructure(xsDataStructure)
xsDataComposition.setSolvent(xsDataSolvent)
xsDataSampleCrystalMM.setChemicalComposition(xsDataComposition)
xsDataSampleCrystalMM.setSize(XSDataSize(XSDataLength(0.1), XSDataLength(0.1), XSDataLength(0.1)))
xsDataCrystal = XSDataCrystal()
xsDataCell = XSDataCell(angle_alpha=XSDataAngle(90.0),
angle_beta=XSDataAngle(90.0),
angle_gamma=XSDataAngle(90.0),
length_a=XSDataLength(78.9),
length_b=XSDataLength(95.162),
length_c=XSDataLength(104.087))
xsDataCrystal.setCell(xsDataCell)
xsDataSpaceGroup = XSDataSpaceGroup()
xsDataSpaceGroup.setITNumber(XSDataInteger(16))
xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
xsDataSampleCrystalMM.setSusceptibility(XSDataDouble(1.5))
xsDataStrategy.setCrystalRefined(xsDataCrystal)
xsDataStrategy.setSample(xsDataSampleCrystalMM)
xsDataStrategy.exportToFile(self.strObtainedInputFile)
pyStrExpectedInput = self.readAndParseFile (self.strReferenceInputFile)
pyStrObtainedInput = self.readAndParseFile (self.strObtainedInputFile)
xsDataInputExpected = XSDataInputStrategy.parseString(pyStrExpectedInput)
xsDataInputObtained = XSDataInputStrategy.parseString(pyStrObtainedInput)
EDAssert.equal(xsDataInputExpected.marshal(), xsDataInputObtained.marshal())
def generateXSDataIndexingResult(_xsDataMOSFLMIndexingOutput, _xsDataExperimentalCondition=None):
"""
Translation from XSDataMOSFLMIndexingOutput to XSDataIndexingResult.
"""
EDVerbose.DEBUG("EDHandlerXSDataMOSFLMv10.generateXSDataIndexingOutput")
xsDataMOSFLMBeamPositionRefined = _xsDataMOSFLMIndexingOutput.getRefinedBeam()
xsDataMOSFLMBeamPositionShift = _xsDataMOSFLMIndexingOutput.getBeamShift()
dDeviationAngular = _xsDataMOSFLMIndexingOutput.getDeviationAngular().getValue()
dDeviationPositional = _xsDataMOSFLMIndexingOutput.getDeviationPositional().getValue()
dMosaicityEstimation = _xsDataMOSFLMIndexingOutput.getMosaicityEstimation().getValue()
dDistanceRefined = _xsDataMOSFLMIndexingOutput.getRefinedDistance().getValue()
iSelectedSolution = _xsDataMOSFLMIndexingOutput.getSelectedSolutionNumber().getValue()
iSpotsTotal = _xsDataMOSFLMIndexingOutput.getSpotsTotal().getValue()
iSpotsUsed = _xsDataMOSFLMIndexingOutput.getSpotsUsed().getValue()
xsDataCellRefined = _xsDataMOSFLMIndexingOutput.getRefinedNewmat().getRefinedCell()
xsDataMatrixA = _xsDataMOSFLMIndexingOutput.getRefinedNewmat().getAMatrix()
xsDataMatrixU = _xsDataMOSFLMIndexingOutput.getRefinedNewmat().getUMatrix()
strSelectedSpaceGroupName = _xsDataMOSFLMIndexingOutput.getSelectedSolutionSpaceGroup().getValue()
iSelectedSpaceGroupNumber = _xsDataMOSFLMIndexingOutput.getSelectedSolutionSpaceGroupNumber().getValue()
xsDataIndexingResult = XSDataIndexingResult()
xsDataIndexingSolutionSelected = None
for possibleSolutions in _xsDataMOSFLMIndexingOutput.getPossibleSolutions():
xsDataCrystal = XSDataCrystal()
xsDataSpaceGroup = XSDataSpaceGroup()
xsDataSpaceGroup.setName(XSDataString(possibleSolutions.getLattice().getValue()))
xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
xsDataCrystal.setCell(possibleSolutions.getCell())
xsDataIndexingSolution = XSDataIndexingSolution()
xsDataIndexingSolution.setCrystal(xsDataCrystal)
iIndex = possibleSolutions.getIndex().getValue()
xsDataIndexingSolution.setNumber(XSDataInteger(iIndex))
xsDataIndexingSolution.setPenalty(XSDataFloat(possibleSolutions.getPenalty().getValue()))
xsDataIndexingResult.addSolution(xsDataIndexingSolution)
if (iIndex == iSelectedSolution):
xsDataIndexingSolutionSelected = XSDataIndexingSolutionSelected()
xsDataIndexingSolutionSelected.setNumber(XSDataInteger(iIndex))
xsDataIndexingSolutionSelected.setPenalty(XSDataFloat(possibleSolutions.getPenalty().getValue()))
xsDataCrystalSelected = XSDataCrystal()
xsDataSpaceGroupSelected = XSDataSpaceGroup()
xsDataSpaceGroupSelected.setName(XSDataString(strSelectedSpaceGroupName))
xsDataSpaceGroupSelected.setITNumber(XSDataInteger(iSelectedSpaceGroupNumber))
xsDataCrystalSelected.setSpaceGroup(xsDataSpaceGroupSelected)
xsDataCrystalSelected.setCell(xsDataCellRefined)
xsDataCrystalSelected.setMosaicity(XSDataDouble(dMosaicityEstimation))
xsDataIndexingSolutionSelected.setCrystal(xsDataCrystalSelected)
xsDataOrientation = XSDataOrientation()
xsDataOrientation.setMatrixA(xsDataMatrixA)
xsDataOrientation.setMatrixU(xsDataMatrixU)
xsDataIndexingSolutionSelected.setOrientation(xsDataOrientation)
xsDataStatisticsIndexing = XSDataStatisticsIndexing()
xsDataStatisticsIndexing.setBeamPositionShiftX(XSDataLength(xsDataMOSFLMBeamPositionShift.getX().getValue()))
xsDataStatisticsIndexing.setBeamPositionShiftY(XSDataLength(xsDataMOSFLMBeamPositionShift.getY().getValue()))
xsDataStatisticsIndexing.setSpotDeviationAngular(XSDataAngle(dDeviationAngular))
xsDataStatisticsIndexing.setSpotDeviationPositional(XSDataLength(dDeviationPositional))
xsDataStatisticsIndexing.setSpotsUsed(XSDataInteger(iSpotsUsed))
xsDataStatisticsIndexing.setSpotsTotal(XSDataInteger(iSpotsTotal))
xsDataIndexingSolutionSelected.setStatistics(xsDataStatisticsIndexing)
xsDataExperimentalConditionRefined = None
if (_xsDataExperimentalCondition is None):
xsDataExperimentalConditionRefined = XSDataExperimentalCondition()
else:
# Copy the incoming experimental condition
xmlExperimentalCondition = _xsDataExperimentalCondition.marshal()
xsDataExperimentalConditionRefined = XSDataExperimentalCondition.parseString(xmlExperimentalCondition)
xsDataDetector = xsDataExperimentalConditionRefined.getDetector()
if (xsDataDetector is None):
xsDataDetector = XSDataDetector()
xsDataDetector.setBeamPositionX(XSDataLength(xsDataMOSFLMBeamPositionRefined.getX().getValue()))
xsDataDetector.setBeamPositionY(XSDataLength(xsDataMOSFLMBeamPositionRefined.getY().getValue()))
xsDataDetector.setDistance(XSDataLength(dDistanceRefined))
xsDataExperimentalConditionRefined.setDetector(xsDataDetector)
xsDataIndexingSolutionSelected.setExperimentalConditionRefined(xsDataExperimentalConditionRefined)
xsDataIndexingResult.setSelectedSolution(xsDataIndexingSolutionSelected)
return xsDataIndexingResult
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
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 testSetDataModelInput(self):
edPluginStrategy = self.createPlugin()
strPathToTestConfigFile = os.path.join(self.getPluginTestsDataHome(),
"XSConfiguration_ESRF.xml")
edConfiguration = EDConfiguration(strPathToTestConfigFile)
dictItem = edConfiguration.get(edPluginStrategy.getPluginName())
edPluginStrategy.setConfig(dictItem)
edPluginStrategy.configure()
xsDataStrategy = XSDataInputStrategy()
# Beam
xsExperimentalCondition = XSDataExperimentalCondition()
xsBeam = XSDataBeam()
xsBeam.setFlux(XSDataFlux(1e+12))
xsBeam.setWavelength(XSDataWavelength(2.41))
xsBeam.setSize(XSDataSize(x=XSDataLength(0.1), y=XSDataLength(0.1)))
xsBeam.setExposureTime(XSDataTime(1))
xsExperimentalCondition.setBeam(xsBeam)
# Detector and Exposure Time
xsDataDetector = XSDataDetector()
xsDataDetector.setType(XSDataString("q210-2x"))
xsExperimentalCondition.setDetector(xsDataDetector)
xsDataGoniostat = XSDataGoniostat()
xsDataGoniostat.setRotationAxis(XSDataString("phi"))
xsExperimentalCondition.setGoniostat(xsDataGoniostat)
xsDataStrategy.setExperimentalCondition(xsExperimentalCondition)
# Best Files
bestFileContentDat = EDUtilsFile.readFile(
os.path.join(self.strDataPath, "bestfile.dat"))
xsDataStrategy.setBestFileContentDat(XSDataString(bestFileContentDat))
bestFileContentPar = EDUtilsFile.readFile(
os.path.join(self.strDataPath, "bestfile.par"))
xsDataStrategy.setBestFileContentPar(XSDataString(bestFileContentPar))
bestFileContentHKL = EDUtilsFile.readFile(
os.path.join(self.strDataPath, "bestfile1.hkl"))
xsDataStrategy.addBestFileContentHKL(XSDataString(bestFileContentHKL))
# Crystal
xsDataSampleCrystalMM = XSDataSampleCrystalMM()
xsDataStructure = XSDataStructure()
xsDataComposition = XSDataChemicalCompositionMM()
xsDataChain = XSDataChain()
xsDataChain.setType(XSDataString("protein"))
xsDataChain.setNumberOfCopies(XSDataDouble(2))
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtom1 = XSDataAtom()
xsDataAtom1.setSymbol(XSDataString("Se"))
xsDataAtom1.setNumberOf(XSDataDouble(4))
xsDataAtomicComposition.addAtom(xsDataAtom1)
xsDataChain.setHeavyAtoms(xsDataAtomicComposition)
xsDataChain.setNumberOfMonomers(XSDataDouble(100))
xsDataStructure.addChain(xsDataChain)
xsDataChain2 = XSDataChain()
xsDataChain2.setType(XSDataString("rna"))
xsDataChain2.setNumberOfCopies(XSDataDouble(1))
xsDataChain2.setNumberOfMonomers(XSDataDouble(60))
xsDataStructure.addChain(xsDataChain2)
xsDataLigand = XSDataLigand()
xsDataLigand.setNumberOfCopies(XSDataDouble(2))
xsDataLigand.setNumberOfLightAtoms(XSDataDouble(42))
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtom2 = XSDataAtom()
xsDataAtom2.setSymbol(XSDataString("Fe"))
xsDataAtom2.setNumberOf(XSDataDouble(1))
xsDataAtomicComposition.addAtom(xsDataAtom2)
xsDataLigand.setHeavyAtoms(xsDataAtomicComposition)
xsDataStructure.addLigand(xsDataLigand)
xsDataStructure.setNumberOfCopiesInAsymmetricUnit(XSDataDouble(0.25))
xsDataSolvent = XSDataSolvent()
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtom3 = XSDataAtom()
xsDataAtom3.setSymbol(XSDataString("Na"))
xsDataAtom3.setConcentration(XSDataDouble(1000))
xsDataAtom4 = XSDataAtom()
xsDataAtom4.setSymbol(XSDataString("Cl"))
xsDataAtom4.setConcentration(XSDataDouble(1000))
xsDataAtomicComposition.addAtom(xsDataAtom3)
xsDataAtomicComposition.addAtom(xsDataAtom4)
xsDataSolvent.setAtoms(xsDataAtomicComposition)
xsDataComposition.setStructure(xsDataStructure)
xsDataComposition.setSolvent(xsDataSolvent)
xsDataSampleCrystalMM.setChemicalComposition(xsDataComposition)
xsDataSampleCrystalMM.setSize(
XSDataSize(XSDataLength(0.1), XSDataLength(0.1),
XSDataLength(0.1)))
xsDataCrystal = XSDataCrystal()
xsDataCell = XSDataCell(angle_alpha=XSDataAngle(90.0),
angle_beta=XSDataAngle(90.0),
angle_gamma=XSDataAngle(90.0),
length_a=XSDataLength(78.9),
length_b=XSDataLength(95.162),
length_c=XSDataLength(104.087))
xsDataCrystal.setCell(xsDataCell)
xsDataSpaceGroup = XSDataSpaceGroup()
xsDataSpaceGroup.setITNumber(XSDataInteger(16))
xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
xsDataSampleCrystalMM.setSusceptibility(XSDataDouble(1.5))
xsDataStrategy.setCrystalRefined(xsDataCrystal)
xsDataStrategy.setSample(xsDataSampleCrystalMM)
xsDataStrategy.exportToFile(self.strObtainedInputFile)
pyStrExpectedInput = self.readAndParseFile(self.strReferenceInputFile)
pyStrObtainedInput = self.readAndParseFile(self.strObtainedInputFile)
xsDataInputExpected = XSDataInputStrategy.parseString(
pyStrExpectedInput)
xsDataInputObtained = XSDataInputStrategy.parseString(
pyStrObtainedInput)
EDAssert.equal(xsDataInputExpected.marshal(),
xsDataInputObtained.marshal())
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 testGetXSDataRaddoseInput(self):
"""
"""
from XSDataCommon import XSDataLength
from XSDataCommon import XSDataWavelength
from XSDataCommon import XSDataFlux
from XSDataCommon import XSDataSize
from XSDataCommon import XSDataDouble
from XSDataCommon import XSDataString
from XSDataCommon import XSDataAngle
from XSDataCommon import XSDataTime
from XSDataCommon import XSDataInteger
from XSDataMXv1 import XSDataBeam
from XSDataMXv1 import XSDataStructure
from XSDataMXv1 import XSDataChain
from XSDataMXv1 import XSDataAtom
from XSDataMXv1 import XSDataLigand
from XSDataMXv1 import XSDataCrystal
from XSDataMXv1 import XSDataSpaceGroup
from XSDataMXv1 import XSDataSampleCrystalMM
from XSDataMXv1 import XSDataChemicalCompositionMM
from XSDataMXv1 import XSDataAtomicComposition
from XSDataMXv1 import XSDataSolvent
from XSDataMXv1 import XSDataCell
from EDHandlerXSDataRaddosev10 import EDHandlerXSDataRaddosev10
EDFactoryPluginStatic.loadModule("XSDataRaddosev10")
from XSDataRaddosev10 import XSDataRaddoseInput
xsDataBeam = XSDataBeam()
xsDataBeam.setSize(XSDataSize(x=XSDataLength(0.1), y=XSDataLength(0.1)))
xsDataBeam.setWavelength(XSDataWavelength(2.41))
xsDataBeam.setFlux(XSDataFlux(1e+12))
xsDataSample = XSDataSampleCrystalMM()
xsDataStructure = XSDataStructure()
xsDataComposition = XSDataChemicalCompositionMM()
xsDataChain = XSDataChain()
xsDataChain.setType(XSDataString("protein"))
xsDataChain.setNumberOfCopies(XSDataDouble(2))
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtom1 = XSDataAtom()
xsDataAtom1.setSymbol(XSDataString("Se"))
xsDataAtom1.setNumberOf(XSDataDouble(4))
xsDataAtomicComposition.addAtom(xsDataAtom1)
xsDataAtom2 = XSDataAtom()
xsDataAtom2.setSymbol(XSDataString("S"))
xsDataAtom2.setNumberOf(XSDataDouble(5))
xsDataAtomicComposition.addAtom(xsDataAtom2)
xsDataChain.setHeavyAtoms(xsDataAtomicComposition)
xsDataChain.setNumberOfMonomers(XSDataDouble(100))
xsDataStructure.addChain(xsDataChain)
xsDataChain2 = XSDataChain()
xsDataChain2.setType(XSDataString("rna"))
xsDataChain2.setNumberOfCopies(XSDataDouble(1))
xsDataChain2.setNumberOfMonomers(XSDataDouble(60))
xsDataStructure.addChain(xsDataChain2)
xsDataLigand = XSDataLigand()
xsDataLigand.setNumberOfCopies(XSDataDouble(2))
xsDataLigand.setNumberOfLightAtoms(XSDataDouble(42))
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtom3 = XSDataAtom()
xsDataAtom3.setSymbol(XSDataString("Fe"))
xsDataAtom3.setNumberOf(XSDataDouble(1))
xsDataAtomicComposition.addAtom(xsDataAtom3)
xsDataLigand.setHeavyAtoms(xsDataAtomicComposition)
xsDataStructure.addLigand(xsDataLigand)
xsDataStructure.setNumberOfCopiesInAsymmetricUnit(XSDataDouble(0.25))
xsDataSolvent = XSDataSolvent()
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtomNa = XSDataAtom()
xsDataAtomNa.setSymbol(XSDataString("Na"))
xsDataAtomNa.setConcentration(XSDataDouble(1000))
xsDataAtomicComposition.addAtom(xsDataAtomNa)
xsDataAtomCl = XSDataAtom()
xsDataAtomCl.setSymbol(XSDataString("Cl"))
xsDataAtomCl.setConcentration(XSDataDouble(1000))
xsDataAtomicComposition.addAtom(xsDataAtomCl)
xsDataSolvent.setAtoms(xsDataAtomicComposition)
xsDataComposition.setStructure(xsDataStructure)
xsDataComposition.setSolvent(xsDataSolvent)
xsDataSample.setChemicalComposition(xsDataComposition)
xsDataSample.setSize(XSDataSize(XSDataLength(0.1), XSDataLength(0.1), XSDataLength(0.1)))
xsDataCell = XSDataCell(angle_alpha=XSDataAngle(90.0),
angle_beta=XSDataAngle(90.0),
angle_gamma=XSDataAngle(90.0),
length_a=XSDataLength(78.9),
length_b=XSDataLength(95.162),
length_c=XSDataLength(104.087))
xsDataCrystal = XSDataCrystal()
xsDataSpaceGroup = XSDataSpaceGroup()
xsDataCrystal.setCell(xsDataCell)
xsDataSpaceGroup.setITNumber(XSDataInteger(16))
xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
xsDataSample.setCrystal(xsDataCrystal)
iNumSymOperators = 4
xsDataRaddosev01Input = EDHandlerXSDataRaddosev10().getXSDataRaddoseInput(xsDataBeam,
xsDataSample,
iNumSymOperators)
xsDataRaddosev01Input.exportToFile(self.strObtainedInputFile2)
strExpectedInput = EDUtilsTest.readAndParseFile (self.strReferenceInputFile2)
strObtainedInput = EDUtilsTest.readAndParseFile (self.strObtainedInputFile2)
xsDataInputExpected = XSDataRaddoseInput.parseString(strExpectedInput)
xsDataInputObtained = XSDataRaddoseInput.parseString(strObtainedInput)
EDAssert.equal(xsDataInputExpected.marshal(), xsDataInputObtained.marshal())
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()))
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()))