def doIntegrationToStrategyTransition(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlInducedRadiationProcessv10.doIntegrationToStrategyTransition")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlInducedRadiationProcessv10.doIntegrationToStrategyTransition")
xsDataIntegrationOutput = self.__edPluginIntegration.getDataOutput()
self.__xsDataResultCharacterisation.setIntegrationResult(xsDataIntegrationOutput)
#EDVerbose.DEBUG( self.__xsDataExperimentCharacterisation.marshal() )
xsDataInputStrategy = XSDataInputStrategy()
xsDataSolutionSelected = self.__xsDataResultCharacterisation.getIndexingResult().getSelectedSolution()
xsDataInputStrategy.setCrystalRefined(xsDataSolutionSelected.getCrystal())
xsDataInputStrategy.setSample(self.__xsDataResultCharacterisation.getDataCollection().getSample())
xsDataIntegrationSubWedgeResultList = xsDataIntegrationOutput.getIntegrationSubWedgeResult()
xsDataInputStrategy.setBestFileContentDat(xsDataIntegrationSubWedgeResultList[0].getBestfileDat())
xsDataInputStrategy.setBestFileContentPar(xsDataIntegrationSubWedgeResultList[0].getBestfilePar())
xsDataInputStrategy.setExperimentalCondition(xsDataIntegrationSubWedgeResultList[0].getExperimentalConditionRefined())
xsDataInputStrategy.setDataCollection(self.getDataInput().getDataCollection())
for xsDataIntegrationSubWedgeResult in xsDataIntegrationSubWedgeResultList:
xsDataInputStrategy.addBestFileContentHKL(xsDataIntegrationSubWedgeResult.getBestfileHKL())
xsDataInputStrategy.setDiffractionPlan(self.__xsDataResultCharacterisation.getDataCollection().getDiffractionPlan())
#print xsDataInputStrategy.marshal()
self.__edPluginStrategy.setDataInput(xsDataInputStrategy)
self.__edPluginStrategy.executeSynchronous()
def doIntegrationToStrategyTransition(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv2_0.doIntegrationToStrategyTransition")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv2_0.doIntegrationToStrategyTransition")
xsDataIntegrationOutput = self.edPluginIntegration.getDataOutput()
self.xsDataResultCharacterisation.setIntegrationResult(xsDataIntegrationOutput)
#self.DEBUG( self.xsDataExperimentCharacterisation.marshal() )
from XSDataMXv1 import XSDataInputStrategy
xsDataInputStrategyOLD = XSDataInputStrategy()
xsDataSolutionSelected = self.xsDataResultCharacterisation.getIndexingResult().getSelectedSolution()
xsDataInputStrategyOLD.setCrystalRefined(xsDataSolutionSelected.getCrystal())
xsDataInputStrategyOLD.setSample(self.xsDataResultCharacterisation.getDataCollection().getSample())
xsDataIntegrationSubWedgeResultList = xsDataIntegrationOutput.getIntegrationSubWedgeResult()
xsDataInputStrategyOLD.setBestFileContentDat(xsDataIntegrationSubWedgeResultList[0].getBestfileDat())
xsDataInputStrategyOLD.setBestFileContentPar(xsDataIntegrationSubWedgeResultList[0].getBestfilePar())
xsDataInputStrategyOLD.setExperimentalCondition(xsDataIntegrationSubWedgeResultList[0].getExperimentalConditionRefined())
for xsDataIntegrationSubWedgeResult in xsDataIntegrationSubWedgeResultList:
xsDataInputStrategyOLD.addBestFileContentHKL(xsDataIntegrationSubWedgeResult.getBestfileHKL())
xsDataInputStrategyOLD.setDiffractionPlan(self.xsDataResultCharacterisation.getDataCollection().getDiffractionPlan())
xsDataInputStrategyOLD.setXdsBackgroundImage(self.xsDataResultCharacterisation.getXdsBackgroundImage())
#print xsDataInputStrategy.marshal()
self.edPluginStrategy.setDataInput(xsDataInputStrategyOLD, "mxv1InputStrategy")
if self.hasDataInput("mxv2DataCollection"):
self.edPluginStrategy.setDataInput(self.getDataInput("mxv2DataCollection")[0], "mxv2DataCollection")
self.edPluginStrategy.setDataInput(self.xsDataResultCharacterisation.getIndexingResult(), "mxv1IndexingResult")
self.edPluginStrategy.executeSynchronous()
def doCharacterisationSuccess(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlCharForReorientationv2_0.doCharacterisationSuccess")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv2_0.doCharacterisationSuccess")
self.xsDataResultCharacterisation = self.edPluginControlCharacterisation.getDataOutput()
# Check if kappa strategy is requested:
if self.strPluginStrategyName is not None:
self.edPluginControlStrategy = self.loadPlugin(self.strPluginStrategyName, \
"MXv2KappaStrategy")
xsDataInputStrategy = XSDataInputStrategy()
xsDataSolutionSelected = self.xsDataResultCharacterisation.getIndexingResult().getSelectedSolution()
xsDataInputStrategy.setCrystalRefined(xsDataSolutionSelected.getCrystal())
xsDataInputStrategy.setSample(self.xsDataResultCharacterisation.getDataCollection().getSample())
xsDataIntegrationSubWedgeResultList = self.xsDataResultCharacterisation.getIntegrationResult().getIntegrationSubWedgeResult()
xsDataInputStrategy.setBestFileContentDat(xsDataIntegrationSubWedgeResultList[0].getBestfileDat())
xsDataInputStrategy.setBestFileContentPar(xsDataIntegrationSubWedgeResultList[0].getBestfilePar())
xsDataInputStrategy.setExperimentalCondition(xsDataIntegrationSubWedgeResultList[0].getExperimentalConditionRefined())
xsDataInputStrategy.setDataCollection(self.mxv1InputCharacterisation.getDataCollection())
xsDataInputStrategy.setXdsBackgroundImage(self.xsDataResultCharacterisation.getXdsBackgroundImage())
for xsDataIntegrationSubWedgeResult in xsDataIntegrationSubWedgeResultList:
xsDataInputStrategy.addBestFileContentHKL(xsDataIntegrationSubWedgeResult.getBestfileHKL())
xsDataInputStrategy.setDiffractionPlan(self.xsDataResultCharacterisation.getDataCollection().getDiffractionPlan())
self.edPluginControlStrategy.setDataInput(xsDataInputStrategy, "mxv1InputStrategy")
self.edPluginControlStrategy.setDataInput(self.mxv2DataCollection, "mxv2DataCollection")
self.edPluginControlStrategy.setDataInput(self.xsDataResultCharacterisation.getIndexingResult(), "mxv1IndexingResult")
self.edPluginControlStrategy.connectSUCCESS(self.doStrategySuccess)
self.edPluginControlStrategy.connectFAILURE(self.doStrategyFailure)
self.executePluginSynchronous(self.edPluginControlStrategy)
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 doIntegrationToStrategyTransition(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlInducedRadiationProcessv10.doIntegrationToStrategyTransition")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlInducedRadiationProcessv10.doIntegrationToStrategyTransition")
xsDataIntegrationOutput = self.__edPluginIntegration.getDataOutput()
self.__xsDataResultCharacterisation.setIntegrationResult(xsDataIntegrationOutput)
#EDVerbose.DEBUG( self.__xsDataExperimentCharacterisation.marshal() )
xsDataInputStrategy = XSDataInputStrategy()
xsDataSolutionSelected = self.__xsDataResultCharacterisation.getIndexingResult().getSelectedSolution()
xsDataInputStrategy.setCrystalRefined(xsDataSolutionSelected.getCrystal())
xsDataInputStrategy.setSample(self.__xsDataResultCharacterisation.getDataCollection().getSample())
xsDataIntegrationSubWedgeResultList = xsDataIntegrationOutput.getIntegrationSubWedgeResult()
xsDataInputStrategy.setBestFileContentDat(xsDataIntegrationSubWedgeResultList[0].getBestfileDat())
xsDataInputStrategy.setBestFileContentPar(xsDataIntegrationSubWedgeResultList[0].getBestfilePar())
xsDataInputStrategy.setExperimentalCondition(xsDataIntegrationSubWedgeResultList[0].getExperimentalConditionRefined())
for xsDataIntegrationSubWedgeResult in xsDataIntegrationSubWedgeResultList:
xsDataInputStrategy.addBestFileContentHKL(xsDataIntegrationSubWedgeResult.getBestfileHKL())
xsDataInputStrategy.setDiffractionPlan(self.__xsDataResultCharacterisation.getDataCollection().getDiffractionPlan())
#print xsDataInputStrategy.marshal()
self.__edPluginStrategy.setDataInput(xsDataInputStrategy)
self.__edPluginStrategy.executeSynchronous()
def doIntegrationToStrategyTransition(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv2_0.doIntegrationToStrategyTransition")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv2_0.doIntegrationToStrategyTransition")
xsDataIntegrationOutput = self.edPluginIntegration.getDataOutput()
self.xsDataResultCharacterisation.setIntegrationResult(xsDataIntegrationOutput)
# self.DEBUG( self.xsDataExperimentCharacterisation.marshal() )
from XSDataMXv1 import XSDataInputStrategy
xsDataInputStrategyOLD = XSDataInputStrategy()
xsDataSolutionSelected = self.xsDataResultCharacterisation.getIndexingResult().getSelectedSolution()
xsDataInputStrategyOLD.setCrystalRefined(xsDataSolutionSelected.getCrystal())
xsDataInputStrategyOLD.setSample(self.xsDataResultCharacterisation.getDataCollection().getSample())
xsDataIntegrationSubWedgeResultList = xsDataIntegrationOutput.getIntegrationSubWedgeResult()
xsDataInputStrategyOLD.setBestFileContentDat(xsDataIntegrationSubWedgeResultList[0].getBestfileDat())
xsDataInputStrategyOLD.setBestFileContentPar(xsDataIntegrationSubWedgeResultList[0].getBestfilePar())
xsDataInputStrategyOLD.setExperimentalCondition(xsDataIntegrationSubWedgeResultList[0].getExperimentalConditionRefined())
for xsDataIntegrationSubWedgeResult in xsDataIntegrationSubWedgeResultList:
xsDataInputStrategyOLD.addBestFileContentHKL(xsDataIntegrationSubWedgeResult.getBestfileHKL())
xsDataInputStrategyOLD.setDiffractionPlan(self.xsDataResultCharacterisation.getDataCollection().getDiffractionPlan())
xsDataInputStrategyOLD.setXdsBackgroundImage(self.xsDataResultCharacterisation.getXdsBackgroundImage())
# print xsDataInputStrategy.marshal()
self.edPluginStrategy.setDataInput(xsDataInputStrategyOLD, "mxv1InputStrategy")
if self.hasDataInput("mxv2DataCollection"):
self.edPluginStrategy.setDataInput(self.getDataInput("mxv2DataCollection")[0], "mxv2DataCollection")
self.edPluginStrategy.setDataInput(self.xsDataResultCharacterisation.getIndexingResult(), "mxv1IndexingResult")
self.edPluginStrategy.executeSynchronous()
def doSuccessIntegration(self, _edPlugin=None):
self.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()
#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.setDataCollection(self.getDataInput().getDataCollection())
for xsDataIntegrationSubWedgeResult in xsDataIntegrationSubWedgeResultList:
xsDataInputStrategy.addBestFileContentHKL(xsDataIntegrationSubWedgeResult.getBestfileHKL())
xsDataInputStrategy.setDiffractionPlan(self.__xsDataResultCharacterisation.getDataCollection().getDiffractionPlan())
self.__edPluginControlStrategy.setDataInput(xsDataInputStrategy)
self.__edPluginControlStrategy.executeSynchronous()
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 doCharacterisationSuccess(self, _edPlugin=None):
EDVerbose.DEBUG(
"EDPluginControlCharForReorientationv2_0.doCharacterisationSuccess"
)
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlCharacterisationv2_0.doCharacterisationSuccess")
self.xsDataResultCharacterisation = self.edPluginControlCharacterisation.getDataOutput(
)
# Check if kappa strategy is requested:
if self.strPluginStrategyName is not None:
self.edPluginControlStrategy = self.loadPlugin(self.strPluginStrategyName, \
"MXv2KappaStrategy")
xsDataInputStrategy = XSDataInputStrategy()
xsDataSolutionSelected = self.xsDataResultCharacterisation.getIndexingResult(
).getSelectedSolution()
xsDataInputStrategy.setCrystalRefined(
xsDataSolutionSelected.getCrystal())
xsDataInputStrategy.setSample(self.xsDataResultCharacterisation.
getDataCollection().getSample())
xsDataIntegrationSubWedgeResultList = self.xsDataResultCharacterisation.getIntegrationResult(
).getIntegrationSubWedgeResult()
xsDataInputStrategy.setBestFileContentDat(
xsDataIntegrationSubWedgeResultList[0].getBestfileDat())
xsDataInputStrategy.setBestFileContentPar(
xsDataIntegrationSubWedgeResultList[0].getBestfilePar())
xsDataInputStrategy.setExperimentalCondition(
xsDataIntegrationSubWedgeResultList[0].
getExperimentalConditionRefined())
xsDataInputStrategy.setDataCollection(
self.mxv1InputCharacterisation.getDataCollection())
xsDataInputStrategy.setXdsBackgroundImage(
self.xsDataResultCharacterisation.getXdsBackgroundImage())
for xsDataIntegrationSubWedgeResult in xsDataIntegrationSubWedgeResultList:
xsDataInputStrategy.addBestFileContentHKL(
xsDataIntegrationSubWedgeResult.getBestfileHKL())
xsDataInputStrategy.setDiffractionPlan(
self.xsDataResultCharacterisation.getDataCollection(
).getDiffractionPlan())
self.edPluginControlStrategy.setDataInput(xsDataInputStrategy,
"mxv1InputStrategy")
self.edPluginControlStrategy.setDataInput(self.mxv2DataCollection,
"mxv2DataCollection")
self.edPluginControlStrategy.setDataInput(
self.xsDataResultCharacterisation.getIndexingResult(),
"mxv1IndexingResult")
self.edPluginControlStrategy.connectSUCCESS(self.doStrategySuccess)
self.edPluginControlStrategy.connectFAILURE(self.doStrategyFailure)
self.executePluginSynchronous(self.edPluginControlStrategy)
def doSuccessIntegration(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doSuccessIntegration")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlGridScreeningv1_0.doSuccessIntegration")
self.addStatusMessage("Integration successful.")
self.xsDataIntegrationOutput = self.edPluginControlIntegration.getDataOutput()
# Integration short summary
if self.edPluginControlIntegration.hasDataOutput("integrationShortSummary"):
self.strCharacterisationShortSummary += self.edPluginControlIntegration.getDataOutput("integrationShortSummary")[0].getValue()
# self.DEBUG( self.xsDataExperimentCharacterisation.marshal() )
if self.bDoOnlyIntegrationWithXMLOutput:
# Run mtz2various
xsDataInputMtz2Various = XSDataInputMtz2Various()
xsDataInputMtz2Various.setMtzfile(self.edPluginControlIntegration.getDataOutput().getIntegrationSubWedgeResult()[0].getGeneratedMTZFile())
xsDataInputMtz2Various.addLabin(XSDataString("I=I"))
xsDataInputMtz2Various.addLabin(XSDataString("SIGI=SIGI"))
xsDataInputMtz2Various.setOutput(XSDataString("USER '(3I4,2F10.1)'"))
self.edPluginExecMtz2Various.setDataInput(xsDataInputMtz2Various)
self.edPluginExecMtz2Various.executeSynchronous()
strHklFilePath = self.edPluginExecMtz2Various.getDataOutput().getHklfile().getPath().getValue()
strIntegration = EDUtilsFile.readFile(strHklFilePath)
# Output the result in XML format
self.xsDataGridScreeningResultIntegration = XSDataGridScreeningResultIntegration()
self.xsDataGridScreeningResultIntegration.setFileName(os.path.basename(self.strImageFile))
self.xsDataGridScreeningResultIntegration.setFileDirectory(os.path.dirname(self.strImageFile))
self.xsDataGridScreeningResultIntegration.setIntegratedData(strIntegration)
else:
# We continue with the strategy calculation
xsDataInputStrategy = XSDataInputStrategy()
xsDataSolutionSelected = self.xsDataIndexingResult.getSelectedSolution()
xsDataInputStrategy.setCrystalRefined(xsDataSolutionSelected.getCrystal())
xsDataInputStrategy.setSample(self.xsDataCollection.getSample())
xsDataIntegrationSubWedgeResultList = self.xsDataIntegrationOutput.getIntegrationSubWedgeResult()
xsDataInputStrategy.setBestFileContentDat(xsDataIntegrationSubWedgeResultList[0].getBestfileDat())
xsDataInputStrategy.setBestFileContentPar(xsDataIntegrationSubWedgeResultList[0].getBestfilePar())
xsDataInputStrategy.setExperimentalCondition(xsDataIntegrationSubWedgeResultList[0].getExperimentalConditionRefined())
xsDataInputStrategy.setDataCollection(self.xsDataCollection)
for xsDataIntegrationSubWedgeResult in xsDataIntegrationSubWedgeResultList:
xsDataInputStrategy.addBestFileContentHKL(xsDataIntegrationSubWedgeResult.getBestfileHKL())
xsDataInputStrategy.setDiffractionPlan(self.xsDataDiffractionPlan)
self.edPluginControlStrategy.connectSUCCESS(self.doSuccessStrategy)
self.edPluginControlStrategy.connectFAILURE(self.doFailureStrategy)
self.edPluginControlStrategy.setDataInput(xsDataInputStrategy)
self.executePluginSynchronous(self.edPluginControlStrategy)
def doSuccessIntegration(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doSuccessIntegration")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlGridScreeningv1_0.doSuccessIntegration")
self.addStatusMessage("Integration successful.")
self.xsDataIntegrationOutput = self.edPluginControlIntegration.getDataOutput()
# Integration short summary
if self.edPluginControlIntegration.hasDataOutput("integrationShortSummary"):
self.strCharacterisationShortSummary += self.edPluginControlIntegration.getDataOutput("integrationShortSummary")[0].getValue()
# self.DEBUG( self.xsDataExperimentCharacterisation.marshal() )
if self.bDoOnlyIntegrationWithXMLOutput:
# Run mtz2various
xsDataInputMtz2Various = XSDataInputMtz2Various()
xsDataInputMtz2Various.setMtzfile(self.edPluginControlIntegration.getDataOutput().getIntegrationSubWedgeResult()[0].getGeneratedMTZFile())
xsDataInputMtz2Various.addLabin(XSDataString("I=I"))
xsDataInputMtz2Various.addLabin(XSDataString("SIGI=SIGI"))
xsDataInputMtz2Various.setOutput(XSDataString("USER '(3I4,2F10.1)'"))
self.edPluginExecMtz2Various.setDataInput(xsDataInputMtz2Various)
self.edPluginExecMtz2Various.executeSynchronous()
strHklFilePath = self.edPluginExecMtz2Various.getDataOutput().getHklfile().getPath().getValue()
strIntegration = EDUtilsFile.readFile(strHklFilePath)
# Output the result in XML format
self.xsDataGridScreeningResultIntegration = XSDataGridScreeningResultIntegration()
self.xsDataGridScreeningResultIntegration.setFileName(os.path.basename(self.strImageFile))
self.xsDataGridScreeningResultIntegration.setFileDirectory(os.path.dirname(self.strImageFile))
self.xsDataGridScreeningResultIntegration.setIntegratedData(strIntegration)
else:
# We continue with the strategy calculation
xsDataInputStrategy = XSDataInputStrategy()
xsDataSolutionSelected = self.xsDataIndexingResult.getSelectedSolution()
xsDataInputStrategy.setCrystalRefined(xsDataSolutionSelected.getCrystal())
xsDataInputStrategy.setSample(self.xsDataCollection.getSample())
xsDataIntegrationSubWedgeResultList = self.xsDataIntegrationOutput.getIntegrationSubWedgeResult()
xsDataInputStrategy.setBestFileContentDat(xsDataIntegrationSubWedgeResultList[0].getBestfileDat())
xsDataInputStrategy.setBestFileContentPar(xsDataIntegrationSubWedgeResultList[0].getBestfilePar())
xsDataInputStrategy.setExperimentalCondition(xsDataIntegrationSubWedgeResultList[0].getExperimentalConditionRefined())
xsDataInputStrategy.setDataCollection(self.xsDataCollection)
for xsDataIntegrationSubWedgeResult in xsDataIntegrationSubWedgeResultList:
xsDataInputStrategy.addBestFileContentHKL(xsDataIntegrationSubWedgeResult.getBestfileHKL())
xsDataInputStrategy.setDiffractionPlan(self.xsDataDiffractionPlan)
self.edPluginControlStrategy.connectSUCCESS(self.doSuccessStrategy)
self.edPluginControlStrategy.connectFAILURE(self.doFailureStrategy)
self.edPluginControlStrategy.setDataInput(xsDataInputStrategy)
self.executePluginSynchronous(self.edPluginControlStrategy)
def doSuccessIntegration(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doSuccessIntegration")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlGridScreeningv1_0.doSuccessIntegration")
self.addStatusMessage("Integration successful.")
self.xsDataIntegrationOutput = self.edPluginControlIntegration.getDataOutput()
# Integration short summary
if self.edPluginControlIntegration.hasDataOutput("integrationShortSummary"):
self.strCharacterisationShortSummary += self.edPluginControlIntegration.getDataOutput("integrationShortSummary")[0].getValue()
#self.DEBUG( self.xsDataExperimentCharacterisation.marshal() )
xsDataInputStrategy = XSDataInputStrategy()
xsDataSolutionSelected = self.xsDataIndexingResult.getSelectedSolution()
xsDataInputStrategy.setCrystalRefined(xsDataSolutionSelected.getCrystal())
xsDataInputStrategy.setSample(self.xsDataCollection.getSample())
xsDataIntegrationSubWedgeResultList = self.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.xsDataDiffractionPlan)
self.edPluginControlStrategy.connectSUCCESS(self.doSuccessStrategy)
self.edPluginControlStrategy.connectFAILURE(self.doFailureStrategy)
self.edPluginControlStrategy.setDataInput(xsDataInputStrategy)
self.executePluginSynchronous(self.edPluginControlStrategy)
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 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())
