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)
class EDPluginControlGridScreeningv1_0(EDPluginControl):
"""
This plugin is a "light-weight" characterisation to be used for processing
images from grid scans.
"""
def __init__(self):
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputGridScreening)
self.strControlReadImageHeaderPluginName = "EDPluginControlReadImageHeaderv10"
self.edPluginControlReadImageHeader = None
self.strControlledIndicatorsPluginName = "EDPluginControlImageQualityIndicatorsv1_4"
self.edPluginControlIndicators = None
self.strISPyBStoreImageQualityIndicatorsPluginName = "EDPluginISPyBStoreImageQualityIndicatorsv1_4"
self.edPluginISPyBStoreImageQualityIndicators = None
self.strIndexingMOSFLMPluginName = "EDPluginMOSFLMIndexingv10"
self.edPluginMOSFLMIndexing = None
self.strPluginControlIntegration = "EDPluginControlIntegrationv10"
self.edPluginControlIntegration = None
self.strPluginControlStrategy = "EDPluginControlStrategyv1_2"
self.edPluginControlStrategy = None
self.strPluginExecMtz2Various = "EDPluginExecMtz2Variousv1_0"
self.edPluginExecMtz2Various = None
self.strImageFile = None
self.xsDataIndexingResultMOSFLM = None
self.xsDataCrystal = None
self.strCharacterisationShortSummary = ""
self.strStatusMessage = ""
self.xsDataDiffractionPlan = None
self.xsDataCollection = None
self.xsDataIndexingResult = None
self.xsDataStrategyResult = None
self.xsDataImageQualityIndicators = None
self.bStoreImageQualityIndicatorsInISPyB = False
self.bDoOnlyImageQualityIndicators = False
self.bDoOnlyIntegrationWithXMLOutput = False
self.iImageQualityIndicatorsId = None
self.xsDataGridScreeningResultIntegration = None
def checkParameters(self):
"""
Checks the mandatory parameters.
"""
self.DEBUG("EDPluginControlGridScreeningv1_0.checkParameters")
self.checkMandatoryParameters(self.getDataInput(), "Data Input is None")
self.checkMandatoryParameters(self.getDataInput().getImageFile(), "imageFile")
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginControlGridScreeningv1_0.preProcess")
# Load the plugins
self.edPluginControlReadImageHeader = self.loadPlugin(self.strControlReadImageHeaderPluginName, \
"ReadImageHeader")
self.edPluginControlIndicators = self.loadPlugin(self.strControlledIndicatorsPluginName, \
"ControlIndicators")
self.edPluginMOSFLMIndexing = self.loadPlugin(self.strIndexingMOSFLMPluginName, \
"IndexingMOSFLM")
self.edPluginControlIntegration = self.loadPlugin(self.strPluginControlIntegration, \
"Integration")
self.edPluginControlStrategy = self.loadPlugin(self.strPluginControlStrategy, \
"Strategy")
self.edPluginExecMtz2Various = self.loadPlugin(self.strPluginExecMtz2Various, \
"Mtz2Various")
# Input data
self.strImageFile = self.getDataInput().getImageFile().getPath().getValue()
self.xsDataGridScreeningFileNameParameters = self.getFileNameParameters(self.strImageFile)
self.xsDataDiffractionPlan = self.getDataInput().getDiffractionPlan()
if self.xsDataDiffractionPlan is None:
self.xsDataDiffractionPlan = XSDataDiffractionPlan()
if self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection() is None:
# Default max esposure time: 10000s
self.xsDataDiffractionPlan.setMaxExposureTimePerDataCollection(XSDataTime(10000))
self.xsDataDiffractionPlan.setEstimateRadiationDamage(XSDataBoolean(False))
# Image quality indicators
if self.getDataInput().getStoreImageQualityIndicatorsInISPyB():
self.bStoreImageQualityIndicatorsInISPyB = self.getDataInput().getStoreImageQualityIndicatorsInISPyB().getValue()
if self.getDataInput().getDoOnlyImageQualityIndicators():
self.bDoOnlyImageQualityIndicators = self.getDataInput().getDoOnlyImageQualityIndicators().getValue()
if self.getDataInput().getDoOnlyIntegrationWithXMLOutput():
self.bDoOnlyIntegrationWithXMLOutput = self.getDataInput().getDoOnlyIntegrationWithXMLOutput().getValue()
if self.bStoreImageQualityIndicatorsInISPyB:
self.edPluginISPyBStoreImageQualityIndicators = self.loadPlugin(self.strISPyBStoreImageQualityIndicatorsPluginName, \
"ISPyBStoreImageQualityIndicators")
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlGridScreeningv1_0.process")
xsDataInputReadImageHeader = XSDataInputReadImageHeader()
xsDataInputReadImageHeader.setImage(image=XSDataFile(path=XSDataString(self.strImageFile)))
self.edPluginControlReadImageHeader.setDataInput(xsDataInputReadImageHeader)
self.edPluginControlReadImageHeader.connectSUCCESS(self.doSuccessReadImageHeader)
self.edPluginControlReadImageHeader.connectFAILURE(self.doFailureReadImageHeader)
self.executePluginSynchronous(self.edPluginControlReadImageHeader)
def finallyProcess(self, _edObject=None):
EDPluginControl.finallyProcess(self)
self.DEBUG("EDPluginControlGridScreeningv1_0.finallyProcess")
# Synchronise if necessary
if self.edPluginISPyBStoreImageQualityIndicators is not None:
self.edPluginISPyBStoreImageQualityIndicators.synchronize()
# Build up the output object
strComment = ""
xsDataResultGridScreening = XSDataResultGridScreening()
if self.xsDataGridScreeningFileNameParameters is not None:
xsDataResultGridScreening.setFileNameParameters(self.xsDataGridScreeningFileNameParameters)
if self.xsDataImageQualityIndicators is None:
strComment = "No image quality indicators"
else:
xsDataResultGridScreening.setImageQualityIndicators(self.xsDataImageQualityIndicators)
if self.xsDataImageQualityIndicators.getIceRings() is not None:
if self.xsDataImageQualityIndicators.getIceRings().getValue() > 1:
strComment = "Ice rings detected"
if self.xsDataIndexingResult is None:
if strComment == "":
strComment = "No indexing result"
else:
strComment += ", no indexing result"
else:
xsDataSelectedSolution = self.xsDataIndexingResult.getSelectedSolution()
xsDataResultGridScreening.setMosaicity(xsDataSelectedSolution.getCrystal().getMosaicity())
if self.xsDataStrategyResult is None:
if strComment == "":
strComment = "No strategy result"
else:
strComment += ", no strategy result"
else:
xsDataCollectionPlan = self.xsDataStrategyResult.getCollectionPlan()[0]
xsDataStrategySummary = xsDataCollectionPlan.getStrategySummary()
xsDataResultGridScreening.setRankingResolution(xsDataStrategySummary.getRankingResolution())
xsDataResultGridScreening.setResultIntegration(self.xsDataGridScreeningResultIntegration)
xsDataResultGridScreening.setComment(XSDataString(strComment))
if self.iImageQualityIndicatorsId is not None:
xsDataResultGridScreening.setImageQualityIndicatorsId(XSDataInteger(self.iImageQualityIndicatorsId))
# print xsDataResultGridScreening.marshal()
self.setDataOutput(xsDataResultGridScreening)
def doSuccessReadImageHeader(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doSuccessReadImageHeader")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlGridScreeningv1_0.doSuccessReadImageHeader")
xsDataResultReadImageHeader = self.edPluginControlReadImageHeader.getDataOutput()
if xsDataResultReadImageHeader is not None:
xsDataSubWedge = xsDataResultReadImageHeader.getSubWedge()
self.xsDataCollection = XSDataCollection()
self.xsDataCollection.addSubWedge(xsDataSubWedge)
self.xsDataCollection.setDiffractionPlan(self.xsDataDiffractionPlan)
if not self.bDoOnlyIntegrationWithXMLOutput:
xsDataInputControlImageQualityIndicators = XSDataInputControlImageQualityIndicators()
if self.bStoreImageQualityIndicatorsInISPyB:
xsDataInputControlImageQualityIndicators.doUploadToIspyb = XSDataBoolean(True)
else:
xsDataInputControlImageQualityIndicators.doUploadToIspyb = XSDataBoolean(False)
xsDataInputControlImageQualityIndicators.addImage(XSDataImage(path=XSDataString(self.strImageFile)))
self.edPluginControlIndicators.setDataInput(xsDataInputControlImageQualityIndicators)
self.edPluginControlIndicators.connectSUCCESS(self.doSuccessIndicators)
self.edPluginControlIndicators.connectFAILURE(self.doFailureIndicators)
self.executePluginSynchronous(self.edPluginControlIndicators)
else:
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.setDataCollection(self.xsDataCollection)
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
xsDataMOSFLMIndexingInput = EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputIndexing(xsDataIndexingInput)
self.edPluginMOSFLMIndexing.connectSUCCESS(self.doSuccessIndexingMOSFLM)
self.edPluginMOSFLMIndexing.connectFAILURE(self.doFailureIndexingMOSFLM)
self.edPluginMOSFLMIndexing.setDataInput(xsDataMOSFLMIndexingInput)
self.edPluginMOSFLMIndexing.executeSynchronous()
def doFailureReadImageHeader(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doFailureReadImageHeader")
self.retrieveFailureMessages(_edPlugin, "EDPluginControlGridScreeningv1_0.doSuccessReadImageHeader")
def doSuccessIndicators(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doSuccessIndicators")
# self.retrieveSuccessMessages(_edPlugin, "EDPluginControlGridScreeningv1_0.doSuccessIndexingIndicators")
if self.edPluginControlIndicators.hasDataOutput():
self.xsDataImageQualityIndicators = self.edPluginControlIndicators.getDataOutput().getImageQualityIndicators()[0]
# Continue only if requested
if not self.bDoOnlyImageQualityIndicators:
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.setDataCollection(self.xsDataCollection)
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
xsDataMOSFLMIndexingInput = EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputIndexing(xsDataIndexingInput)
self.edPluginMOSFLMIndexing.connectSUCCESS(self.doSuccessIndexingMOSFLM)
self.edPluginMOSFLMIndexing.connectFAILURE(self.doFailureIndexingMOSFLM)
self.edPluginMOSFLMIndexing.setDataInput(xsDataMOSFLMIndexingInput)
self.edPluginMOSFLMIndexing.executeSynchronous()
def doFailureIndicators(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doFailureIndicators")
strErrorMessage = "Execution of Indexing and Indicators plugin failed. Execution of characterisation aborted."
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
def doSuccessISPyBStoreImageQualityIndicators(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doSuccessISPyBStoreImageQualityIndicators")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlGridScreeningv1_0.doSuccessISPyBStoreImageQualityIndicators")
self.iImageQualityIndicatorsId = self.edPluginISPyBStoreImageQualityIndicators.getDataOutput().getImageQualityIndicatorsId().getValue()
if self.iImageQualityIndicatorsId is None:
self.WARNING("Image quality indicators result not stored in ISPyB!")
def doFailureISPyBStoreImageQualityIndicators(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doFailureISPyBStoreImageQualityIndicators")
strErrorMessage = "Execution of store ISPyB image quality indicators plugin failed."
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
def doSuccessIndexingMOSFLM(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doSuccessIndexingMOSFLM")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlGridScreeningv1_0.doIntegrationToStrategyTransition")
xsDataMOSFLMIndexingOutput = self.edPluginMOSFLMIndexing.getDataOutput()
xsDataExperimentalConditionRefined = None
if self.hasDataInput("refinedExperimentalCondition"):
xsDataExperimentalConditionRefined = self.getDataInput("refinedExperimentalCondition")[0]
else:
# Use the experimental condition from the xsDataCollection
xsDataExperimentalConditionRefined = self.xsDataCollection.getSubWedge()[0].getExperimentalCondition()
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
self.xsDataIndexingResult = EDHandlerXSDataMOSFLMv10.generateXSDataIndexingResult(xsDataMOSFLMIndexingOutput, xsDataExperimentalConditionRefined)
xsDataIntegrationInput = XSDataIntegrationInput()
xsDataIntegrationInput.setDataCollection(self.xsDataCollection)
xsDataIntegrationInput.setExperimentalConditionRefined(self.xsDataIndexingResult.getSelectedSolution().getExperimentalConditionRefined())
xsDataIntegrationInput.setSelectedIndexingSolution(self.xsDataIndexingResult.getSelectedSolution())
self.edPluginControlIntegration.connectSUCCESS(self.doSuccessIntegration)
self.edPluginControlIntegration.connectFAILURE(self.doFailureIntegration)
self.edPluginControlIntegration.setDataInput(xsDataIntegrationInput)
self.executePluginSynchronous(self.edPluginControlIntegration)
def doFailureIndexingMOSFLM(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doFailureActionIndexing")
self.retrieveFailureMessages(_edPlugin, "EDPluginControlCharacterisationv1_1.doFailureActionIndexing")
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 doFailureIntegration(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doFailureIntegration")
strErrorMessage = "Execution of integration plugin failed."
self.addStatusMessage("Integration FAILURE.")
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
def doSuccessStrategy(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doSuccessStrategy")
self.retrieveSuccessMessages(self.edPluginControlStrategy, "EDPluginControlGridScreeningv1_0.doSuccessStrategy")
self.xsDataStrategyResult = self.edPluginControlStrategy.getDataOutput()
def doFailureStrategy(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doFailureStrategy")
self.retrieveFailureMessages(self.edPluginControlStrategy, "EDPluginControlGridScreeningv1_0.doFailureStrategy")
strErrorMessage = "Strategy calculation FAILURE."
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
# def generateExecutiveSummary(self, _edPlugin):
# """
# Generates a summary of the execution of the plugin.
# """
# self.DEBUG("EDPluginControlGridScreeningv1_0.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 addStatusMessage(self, _strStatusMessage):
if self.strStatusMessage != "":
self.strStatusMessage += " "
self.strStatusMessage += _strStatusMessage
def getFileNameParameters(self, _strFileName):
"""Method for extracting the rotation start angle, the two motor positions and the grid scan image no from the file name"""
# Typical file name: mesh_0_21.676_-0.051_22_001.mccd
listParts = os.path.basename(_strFileName).split("_")
xsDataGridScreeningFileNameParameters = XSDataGridScreeningFileNameParameters()
try:
strScanId1 = listParts[1]
xsDataGridScreeningFileNameParameters.setScanId1(XSDataString(strScanId1))
strMotorPosition1 = listParts[2]
xsDataGridScreeningFileNameParameters.setMotorPosition1(XSDataString(strMotorPosition1))
strMotorPosition2 = listParts[3]
xsDataGridScreeningFileNameParameters.setMotorPosition2(XSDataString(strMotorPosition2))
strScanId2 = listParts[4]
xsDataGridScreeningFileNameParameters.setScanId2(XSDataString(strScanId2))
except:
xsDataGridScreeningFileNameParameters = None
return xsDataGridScreeningFileNameParameters
class EDPluginControlGridScreeningv1_0(EDPluginControl):
"""
This plugin is a "light-weight" characterisation to be used for processing
images from grid scans.
"""
def __init__(self):
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputGridScreening)
self.strControlReadImageHeaderPluginName = "EDPluginControlReadImageHeaderv10"
self.edPluginControlReadImageHeader = None
self.strControlledIndicatorsPluginName = "EDPluginControlImageQualityIndicatorsv1_1"
self.edPluginControlIndicators = None
self.strISPyBStoreImageQualityIndicatorsPluginName = "EDPluginISPyBStoreImageQualityIndicatorsv1_3"
self.edPluginISPyBStoreImageQualityIndicators = None
self.strIndexingMOSFLMPluginName = "EDPluginMOSFLMIndexingv10"
self.edPluginMOSFLMIndexing = None
self.strPluginControlIntegration = "EDPluginControlIntegrationv10"
self.edPluginControlIntegration = None
self.strPluginControlStrategy = "EDPluginControlStrategyv1_2"
self.edPluginControlStrategy = None
self.strPluginExecMtz2Various = "EDPluginExecMtz2Variousv1_0"
self.edPluginExecMtz2Various = None
self.strImageFile = None
self.xsDataIndexingResultMOSFLM = None
self.xsDataCrystal = None
self.strCharacterisationShortSummary = ""
self.strStatusMessage = ""
self.xsDataDiffractionPlan = None
self.xsDataCollection = None
self.xsDataIndexingResult = None
self.xsDataStrategyResult = None
self.xsDataImageQualityIndicators = None
self.bStoreImageQualityIndicatorsInISPyB = False
self.bDoOnlyImageQualityIndicators = False
self.bDoOnlyIntegrationWithXMLOutput = False
self.iImageQualityIndicatorsId = None
self.xsDataGridScreeningResultIntegration = None
def checkParameters(self):
"""
Checks the mandatory parameters.
"""
self.DEBUG("EDPluginControlGridScreeningv1_0.checkParameters")
self.checkMandatoryParameters(self.getDataInput(),
"Data Input is None")
self.checkMandatoryParameters(self.getDataInput().getImageFile(),
"imageFile")
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginControlGridScreeningv1_0.preProcess")
# Load the plugins
self.edPluginControlReadImageHeader = self.loadPlugin(self.strControlReadImageHeaderPluginName, \
"ReadImageHeader")
self.edPluginControlIndicators = self.loadPlugin(self.strControlledIndicatorsPluginName, \
"ControlIndicators")
self.edPluginMOSFLMIndexing = self.loadPlugin(self.strIndexingMOSFLMPluginName, \
"IndexingMOSFLM")
self.edPluginControlIntegration = self.loadPlugin(self.strPluginControlIntegration, \
"Integration")
self.edPluginControlStrategy = self.loadPlugin(self.strPluginControlStrategy, \
"Strategy")
self.edPluginExecMtz2Various = self.loadPlugin(self.strPluginExecMtz2Various, \
"Mtz2Various")
# Input data
self.strImageFile = self.getDataInput().getImageFile().getPath(
).getValue()
self.xsDataGridScreeningFileNameParameters = self.getFileNameParameters(
self.strImageFile)
self.xsDataDiffractionPlan = self.getDataInput().getDiffractionPlan()
if self.xsDataDiffractionPlan is None:
self.xsDataDiffractionPlan = XSDataDiffractionPlan()
if self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection(
) is None:
# Default max esposure time: 10000s
self.xsDataDiffractionPlan.setMaxExposureTimePerDataCollection(
XSDataTime(10000))
self.xsDataDiffractionPlan.setEstimateRadiationDamage(
XSDataBoolean(False))
# Image quality indicators
if self.getDataInput().getStoreImageQualityIndicatorsInISPyB():
self.bStoreImageQualityIndicatorsInISPyB = self.getDataInput(
).getStoreImageQualityIndicatorsInISPyB().getValue()
if self.getDataInput().getDoOnlyImageQualityIndicators():
self.bDoOnlyImageQualityIndicators = self.getDataInput(
).getDoOnlyImageQualityIndicators().getValue()
if self.getDataInput().getDoOnlyIntegrationWithXMLOutput():
self.bDoOnlyIntegrationWithXMLOutput = self.getDataInput(
).getDoOnlyIntegrationWithXMLOutput().getValue()
if self.bStoreImageQualityIndicatorsInISPyB:
self.edPluginISPyBStoreImageQualityIndicators = self.loadPlugin(self.strISPyBStoreImageQualityIndicatorsPluginName, \
"ISPyBStoreImageQualityIndicators")
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlGridScreeningv1_0.process")
xsDataInputReadImageHeader = XSDataInputReadImageHeader()
xsDataInputReadImageHeader.setImage(image=XSDataFile(
path=XSDataString(self.strImageFile)))
self.edPluginControlReadImageHeader.setDataInput(
xsDataInputReadImageHeader)
self.edPluginControlReadImageHeader.connectSUCCESS(
self.doSuccessReadImageHeader)
self.edPluginControlReadImageHeader.connectFAILURE(
self.doFailureReadImageHeader)
self.executePluginSynchronous(self.edPluginControlReadImageHeader)
def finallyProcess(self, _edObject=None):
EDPluginControl.finallyProcess(self)
self.DEBUG("EDPluginControlGridScreeningv1_0.finallyProcess")
# Synchronise if necessary
if self.edPluginISPyBStoreImageQualityIndicators is not None:
self.edPluginISPyBStoreImageQualityIndicators.synchronize()
# Build up the output object
strComment = ""
xsDataResultGridScreening = XSDataResultGridScreening()
if self.xsDataGridScreeningFileNameParameters is not None:
xsDataResultGridScreening.setFileNameParameters(
self.xsDataGridScreeningFileNameParameters)
if self.xsDataImageQualityIndicators is None:
strComment = "No image quality indicators"
else:
xsDataResultGridScreening.setImageQualityIndicators(
self.xsDataImageQualityIndicators)
if self.xsDataImageQualityIndicators.getIceRings().getValue() > 1:
strComment = "Ice rings detected"
if self.xsDataIndexingResult is None:
if strComment == "":
strComment = "No indexing result"
else:
strComment += ", no indexing result"
else:
xsDataSelectedSolution = self.xsDataIndexingResult.getSelectedSolution(
)
xsDataResultGridScreening.setMosaicity(
xsDataSelectedSolution.getCrystal().getMosaicity())
if self.xsDataStrategyResult is None:
if strComment == "":
strComment = "No strategy result"
else:
strComment += ", no strategy result"
else:
xsDataCollectionPlan = self.xsDataStrategyResult.getCollectionPlan(
)[0]
xsDataStrategySummary = xsDataCollectionPlan.getStrategySummary(
)
xsDataResultGridScreening.setRankingResolution(
xsDataStrategySummary.getRankingResolution())
xsDataResultGridScreening.setResultIntegration(
self.xsDataGridScreeningResultIntegration)
xsDataResultGridScreening.setComment(XSDataString(strComment))
if self.iImageQualityIndicatorsId is not None:
xsDataResultGridScreening.setImageQualityIndicatorsId(
XSDataInteger(self.iImageQualityIndicatorsId))
#print xsDataResultGridScreening.marshal()
self.setDataOutput(xsDataResultGridScreening)
def doSuccessReadImageHeader(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doSuccessReadImageHeader")
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlGridScreeningv1_0.doSuccessReadImageHeader")
xsDataResultReadImageHeader = self.edPluginControlReadImageHeader.getDataOutput(
)
if xsDataResultReadImageHeader is not None:
xsDataSubWedge = xsDataResultReadImageHeader.getSubWedge()
self.xsDataCollection = XSDataCollection()
self.xsDataCollection.addSubWedge(xsDataSubWedge)
self.xsDataCollection.setDiffractionPlan(
self.xsDataDiffractionPlan)
if not self.bDoOnlyIntegrationWithXMLOutput:
xsDataInputControlImageQualityIndicators = XSDataInputControlImageQualityIndicators(
)
xsDataInputControlImageQualityIndicators.addImage(
XSDataImage(path=XSDataString(self.strImageFile)))
self.edPluginControlIndicators.setDataInput(
xsDataInputControlImageQualityIndicators)
self.edPluginControlIndicators.connectSUCCESS(
self.doSuccessIndicators)
self.edPluginControlIndicators.connectFAILURE(
self.doFailureIndicators)
self.executePluginSynchronous(self.edPluginControlIndicators)
else:
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.setDataCollection(self.xsDataCollection)
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
xsDataMOSFLMIndexingInput = EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputIndexing(
xsDataIndexingInput)
self.edPluginMOSFLMIndexing.connectSUCCESS(
self.doSuccessIndexingMOSFLM)
self.edPluginMOSFLMIndexing.connectFAILURE(
self.doFailureIndexingMOSFLM)
self.edPluginMOSFLMIndexing.setDataInput(
xsDataMOSFLMIndexingInput)
self.edPluginMOSFLMIndexing.executeSynchronous()
def doFailureReadImageHeader(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doFailureReadImageHeader")
self.retrieveFailureMessages(
_edPlugin,
"EDPluginControlGridScreeningv1_0.doSuccessReadImageHeader")
def doSuccessIndicators(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doSuccessIndicators")
#self.retrieveSuccessMessages(_edPlugin, "EDPluginControlGridScreeningv1_0.doSuccessIndexingIndicators")
if self.edPluginControlIndicators.hasDataOutput():
self.xsDataImageQualityIndicators = self.edPluginControlIndicators.getDataOutput(
).getImageQualityIndicators()[0]
# Store results in ISPyB if requested
if self.bStoreImageQualityIndicatorsInISPyB:
xsDataInputStoreImageQualityIndicators = XSDataInputStoreImageQualityIndicators(
)
xsDataISPyBImageQualityIndicators = XSDataISPyBImageQualityIndicators.parseString(
self.xsDataImageQualityIndicators.marshal())
xsDataInputStoreImageQualityIndicators.setImageQualityIndicators(
xsDataISPyBImageQualityIndicators)
self.edPluginISPyBStoreImageQualityIndicators.setDataInput(
xsDataInputStoreImageQualityIndicators)
self.edPluginISPyBStoreImageQualityIndicators.connectSUCCESS(
self.doSuccessISPyBStoreImageQualityIndicators)
self.edPluginISPyBStoreImageQualityIndicators.connectFAILURE(
self.doFailureISPyBStoreImageQualityIndicators)
self.edPluginISPyBStoreImageQualityIndicators.execute()
# Continue only if requested
if not self.bDoOnlyImageQualityIndicators:
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.setDataCollection(self.xsDataCollection)
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
xsDataMOSFLMIndexingInput = EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputIndexing(
xsDataIndexingInput)
self.edPluginMOSFLMIndexing.connectSUCCESS(
self.doSuccessIndexingMOSFLM)
self.edPluginMOSFLMIndexing.connectFAILURE(
self.doFailureIndexingMOSFLM)
self.edPluginMOSFLMIndexing.setDataInput(
xsDataMOSFLMIndexingInput)
self.edPluginMOSFLMIndexing.executeSynchronous()
def doFailureIndicators(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doFailureIndicators")
strErrorMessage = "Execution of Indexing and Indicators plugin failed. Execution of characterisation aborted."
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
def doSuccessISPyBStoreImageQualityIndicators(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlGridScreeningv1_0.doSuccessISPyBStoreImageQualityIndicators"
)
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlGridScreeningv1_0.doSuccessISPyBStoreImageQualityIndicators"
)
self.iImageQualityIndicatorsId = self.edPluginISPyBStoreImageQualityIndicators.getDataOutput(
).getImageQualityIndicatorsId().getValue()
if self.iImageQualityIndicatorsId is None:
self.WARNING(
"Image quality indicators result not stored in ISPyB!")
def doFailureISPyBStoreImageQualityIndicators(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlGridScreeningv1_0.doFailureISPyBStoreImageQualityIndicators"
)
strErrorMessage = "Execution of store ISPyB image quality indicators plugin failed."
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
def doSuccessIndexingMOSFLM(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doSuccessIndexingMOSFLM")
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlGridScreeningv1_0.doIntegrationToStrategyTransition"
)
xsDataMOSFLMIndexingOutput = self.edPluginMOSFLMIndexing.getDataOutput(
)
xsDataExperimentalConditionRefined = None
if self.hasDataInput("refinedExperimentalCondition"):
xsDataExperimentalConditionRefined = self.getDataInput(
"refinedExperimentalCondition")[0]
else:
# Use the experimental condition from the xsDataCollection
xsDataExperimentalConditionRefined = self.xsDataCollection.getSubWedge(
)[0].getExperimentalCondition()
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
self.xsDataIndexingResult = EDHandlerXSDataMOSFLMv10.generateXSDataIndexingResult(
xsDataMOSFLMIndexingOutput, xsDataExperimentalConditionRefined)
xsDataIntegrationInput = XSDataIntegrationInput()
xsDataIntegrationInput.setDataCollection(self.xsDataCollection)
xsDataIntegrationInput.setExperimentalConditionRefined(
self.xsDataIndexingResult.getSelectedSolution(
).getExperimentalConditionRefined())
xsDataIntegrationInput.setSelectedIndexingSolution(
self.xsDataIndexingResult.getSelectedSolution())
self.edPluginControlIntegration.connectSUCCESS(
self.doSuccessIntegration)
self.edPluginControlIntegration.connectFAILURE(
self.doFailureIntegration)
self.edPluginControlIntegration.setDataInput(xsDataIntegrationInput)
self.executePluginSynchronous(self.edPluginControlIntegration)
def doFailureIndexingMOSFLM(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doFailureActionIndexing")
self.retrieveFailureMessages(
_edPlugin,
"EDPluginControlCharacterisationv1_1.doFailureActionIndexing")
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())
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 doFailureIntegration(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doFailureIntegration")
strErrorMessage = "Execution of integration plugin failed."
self.addStatusMessage("Integration FAILURE.")
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
def doSuccessStrategy(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doSuccessStrategy")
self.retrieveSuccessMessages(
self.edPluginControlStrategy,
"EDPluginControlGridScreeningv1_0.doSuccessStrategy")
self.xsDataStrategyResult = self.edPluginControlStrategy.getDataOutput(
)
def doFailureStrategy(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doFailureStrategy")
self.retrieveFailureMessages(
self.edPluginControlStrategy,
"EDPluginControlGridScreeningv1_0.doFailureStrategy")
strErrorMessage = "Execution of strategy plugin failed."
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
# def generateExecutiveSummary(self, _edPlugin):
# """
# Generates a summary of the execution of the plugin.
# """
# self.DEBUG("EDPluginControlGridScreeningv1_0.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 addStatusMessage(self, _strStatusMessage):
if self.strStatusMessage != "":
self.strStatusMessage += " "
self.strStatusMessage += _strStatusMessage
def getFileNameParameters(self, _strFileName):
"""Method for extracting the rotation start angle, the two motor positions and the grid scan image no from the file name"""
# Typical file name: mesh_0_21.676_-0.051_22_001.mccd
listParts = os.path.basename(_strFileName).split("_")
xsDataGridScreeningFileNameParameters = XSDataGridScreeningFileNameParameters(
)
try:
strScanId1 = listParts[1]
xsDataGridScreeningFileNameParameters.setScanId1(
XSDataString(strScanId1))
strMotorPosition1 = listParts[2]
xsDataGridScreeningFileNameParameters.setMotorPosition1(
XSDataString(strMotorPosition1))
strMotorPosition2 = listParts[3]
xsDataGridScreeningFileNameParameters.setMotorPosition2(
XSDataString(strMotorPosition2))
strScanId2 = listParts[4]
xsDataGridScreeningFileNameParameters.setScanId2(
XSDataString(strScanId2))
except:
xsDataGridScreeningFileNameParameters = None
return xsDataGridScreeningFileNameParameters
