def doSuccessMOSFLMIndexing(self, _edPlugin=None):
self.DEBUG("EDPluginControlIndexingIndicatorsv10.doSuccessMOSFLMIndexing")
self.synchronizeOn()
xsDataMOSFLMIndexingOutput = self.__edPluginMOSFLMIndexing.getDataOutput()
xsDataExperimentalConditionRefined = None
if self.hasDataInput("refinedExperimentalCondition"):
xsDataExperimentalConditionRefined = self.getDataInput("refinedExperimentalCondition")[0]
else:
# Use the experimental condition from the xsDataCollection
xsDataCollection = self.getDataInput("dataCollection")[0]
xsDataExperimentalConditionRefined = xsDataCollection.getSubWedge()[0].getExperimentalCondition()
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
xsDataIndexingResult = EDHandlerXSDataMOSFLMv10.generateXSDataIndexingResult(xsDataMOSFLMIndexingOutput, xsDataExperimentalConditionRefined)
xsDataCollection = self.getDataInput("dataCollection")[0]
xsDataListImage = self.generateImageList(xsDataCollection)
xsDataIndexingResult.setImage(xsDataListImage)
xsDataIndexingResult.setLabelitIndexing(XSDataBoolean(False))
self.setDataOutput(xsDataIndexingResult, "indexingResult")
# self.generateExecutiveSummaryMOSFLM(_edPlugin)
self.addExecutiveSummarySeparator()
self.addExecutiveSummaryLine("Summary of indexing with %s :" % self.__strMOSFLMIndexingPluginName)
self.addExecutiveSummaryLine("")
self.appendExecutiveSummary(self.__edPluginMOSFLMIndexing, "MOSFLM : ", _bAddSeparator=False)
# Short summary:
self.generateIndexingShortSummary(xsDataIndexingResult)
self.synchronizeOff()
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginControlIndexingIndicatorsv10.preProcess")
# Load and prepare the execution plugin
self.__edPluginMOSFLMIndexing = self.loadPlugin(self.__strMOSFLMIndexingPluginName)
self.__edPluginMOSFLMIndexing.setUseWarningInsteadOfError(True)
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.setDataCollection(self.getDataInput("dataCollection")[0])
if self.hasDataInput("crystal"):
xsDataIndexingInput.setCrystal(self.getDataInput("crystal")[0])
if self.hasDataInput("refinedExperimentalCondition"):
xsDataIndexingInput.setExperimentalCondition(self.getDataInput("refinedExperimentalCondition")[0])
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
xsDataMOSFLMIndexingInput = EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputIndexing(xsDataIndexingInput)
self.__edPluginMOSFLMIndexing.setDataInput(xsDataMOSFLMIndexingInput)
if (self.getControlledPluginName("indicatorsPlugin") is not None):
self.__strControlledIndicatorsPluginName = self.getControlledPluginName("indicatorsPlugin")
self.__edPluginControlIndicators = self.loadPlugin(self.__strControlledIndicatorsPluginName)
# Extract the images from the data collections
xsDataSubWedgeList = self.getDataInput("dataCollection")[0].getSubWedge()
xsDataInputControlImageQualityIndicators = XSDataInputControlImageQualityIndicators()
for xsDataSubWedge in xsDataSubWedgeList:
xsDataImageList = xsDataSubWedge.getImage()
for xsDataImage in xsDataImageList:
xsDataInputControlImageQualityIndicators.addImage(xsDataImage)
self.__edPluginControlIndicators.setDataInput(xsDataInputControlImageQualityIndicators)
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 doSuccessMOSFLMIndexing(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlIndexingIndicatorsv10.doSuccessMOSFLMIndexing")
self.synchronizeOn()
xsDataMOSFLMIndexingOutput = self.__edPluginMOSFLMIndexing.getDataOutput(
)
xsDataExperimentalConditionRefined = None
if self.hasDataInput("refinedExperimentalCondition"):
xsDataExperimentalConditionRefined = self.getDataInput(
"refinedExperimentalCondition")[0]
else:
# Use the experimental condition from the xsDataCollection
xsDataCollection = self.getDataInput("dataCollection")[0]
xsDataExperimentalConditionRefined = xsDataCollection.getSubWedge(
)[0].getExperimentalCondition()
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
xsDataIndexingResult = EDHandlerXSDataMOSFLMv10.generateXSDataIndexingResult(
xsDataMOSFLMIndexingOutput, xsDataExperimentalConditionRefined)
xsDataCollection = self.getDataInput("dataCollection")[0]
xsDataListImage = self.generateImageList(xsDataCollection)
xsDataIndexingResult.setImage(xsDataListImage)
xsDataIndexingResult.setLabelitIndexing(XSDataBoolean(False))
self.setDataOutput(xsDataIndexingResult, "indexingResult")
# self.generateExecutiveSummaryMOSFLM(_edPlugin)
self.addExecutiveSummarySeparator()
self.addExecutiveSummaryLine("Summary of indexing with %s :" %
self.__strMOSFLMIndexingPluginName)
self.addExecutiveSummaryLine("")
self.appendExecutiveSummary(self.__edPluginMOSFLMIndexing,
"MOSFLM : ",
_bAddSeparator=False)
# Short summary:
self.generateIndexingShortSummary(xsDataIndexingResult)
self.synchronizeOff()
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginControlIndexingIndicatorsv10.preProcess")
# Load and prepare the execution plugin
self.__edPluginMOSFLMIndexing = self.loadPlugin(
self.__strMOSFLMIndexingPluginName)
self.__edPluginMOSFLMIndexing.setUseWarningInsteadOfError(True)
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.setDataCollection(
self.getDataInput("dataCollection")[0])
if self.hasDataInput("crystal"):
xsDataIndexingInput.setCrystal(self.getDataInput("crystal")[0])
if self.hasDataInput("refinedExperimentalCondition"):
xsDataIndexingInput.setExperimentalCondition(
self.getDataInput("refinedExperimentalCondition")[0])
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
xsDataMOSFLMIndexingInput = EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputIndexing(
xsDataIndexingInput)
self.__edPluginMOSFLMIndexing.setDataInput(xsDataMOSFLMIndexingInput)
self.__edPluginControlIndicators = self.loadPlugin(
self.__strControlledIndicatorsPluginName)
# Extract the images from the data collections
xsDataSubWedgeList = self.getDataInput(
"dataCollection")[0].getSubWedge()
xsDataInputControlImageQualityIndicators = XSDataInputControlImageQualityIndicators(
)
for xsDataSubWedge in xsDataSubWedgeList:
xsDataImageList = xsDataSubWedge.getImage()
for xsDataImage in xsDataImageList:
xsDataInputControlImageQualityIndicators.addImage(xsDataImage)
self.__edPluginControlIndicators.setDataInput(
xsDataInputControlImageQualityIndicators)
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 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 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 getDataIndexingResult(self, _edPlugin):
"""
This method retrieves the indexing results from a MOSFLM indexing plugin.
"""
self.verboseDebug("EDPluginControlIndexingv10.getDataIndexingResultFromMOSFLM")
xsDataMOSFLMOutputIndexing = _edPlugin.getDataOutput()
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
xsDataIndexingResult = EDHandlerXSDataMOSFLMv10.generateXSDataIndexingResult(xsDataMOSFLMOutputIndexing, self.getExperimentalCondition())
return xsDataIndexingResult
def finallyProcess(self, _edObject=None):
EDPluginControl.finallyProcess(self, _edObject)
self.DEBUG("EDPluginControlIntegrationv10.finallyProcess")
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
for (iSubWedgeNumber, edPluginIntegration) in self.__edPluginIntegrationList:
xsDataMOSFLMOutputIntegration = edPluginIntegration.getDataOutput()
if (xsDataMOSFLMOutputIntegration is None):
strWarning = "MOSFLM integration error : no integration results obtained."
self.addExecutiveSummaryLine(strWarning)
self.WARNING(strWarning)
# self.setFailure()
else:
xsDataIntegrationSubWedgeResult = None
try:
xsDataIntegrationSubWedgeResult = EDHandlerXSDataMOSFLMv10.generateXSDataIntegrationSubWedgeResult(xsDataMOSFLMOutputIntegration, self.__xsDataExperimentalConditionRefined)
except Exception as error:
strWarningMessage = str(error)
self.addWarningMessage(strWarningMessage)
self.WARNING(strWarningMessage)
# self.setFailure()
if (xsDataIntegrationSubWedgeResult is None):
strWarning = "MOSFLM integration error : no integration results obtained."
self.addExecutiveSummaryLine(strWarning)
self.WARNING(strWarning)
# self.setFailure()
else:
xsDataIntegrationSubWedgeResult.setSubWedgeNumber(XSDataInteger(iSubWedgeNumber))
xsDataStatisticsIntegration = xsDataIntegrationSubWedgeResult.getStatistics()
if xsDataStatisticsIntegration.getRMSSpotDeviation() is not None:
fRMSSpotDeviation = xsDataStatisticsIntegration.getRMSSpotDeviation().getValue()
if (self.__fMaxRMSSpotDeviation is not None):
if (self.__fMaxRMSSpotDeviation < fRMSSpotDeviation):
iImageStart = edPluginIntegration.getDataInput().getImageStart().getValue()
iImageEnd = edPluginIntegration.getDataInput().getImageEnd().getValue()
errorMessage = EDMessage.ERROR_DATA_HANDLER_02 % ("EDPluginControlIntegrationv10.postProcess", \
"MOSFLM Integration : RMS spot deviation (%.3f [mm]) larger than max value from configuration (%.3f [mm]) for images %d to %d" % \
(fRMSSpotDeviation, self.__fMaxRMSSpotDeviation, iImageStart, iImageEnd))
self.error(errorMessage)
self.addErrorMessage(errorMessage)
if (xsDataIntegrationSubWedgeResult is not None):
if (self.__xsDataIntegrationResult is None):
self.__xsDataIntegrationResult = XSDataIntegrationResult()
self.__xsDataIntegrationResult.addIntegrationSubWedgeResult(xsDataIntegrationSubWedgeResult)
bSuccess = False
for integrationSubWedgeResult in self.__xsDataIntegrationResult.integrationSubWedgeResult:
if integrationSubWedgeResult.statistics.iOverSigmaOverall is not None:
bSuccess = True
break
if not bSuccess:
strErrorMessage = "MOSFLM integration failed for all images"
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
self.setDataOutput(self.__xsDataIntegrationResult)
if self.__xsDataIntegrationResult is not None:
self.generateIntegrationShortSummary(self.__xsDataIntegrationResult)
def setDataInput(self, _dataInput):
"""
Sets the Plugin input data. A part from using the EDPlugin.setDataInput method,
this method also converts the input data to the MOSFLM specific data model indexing input.
"""
self.verboseDebug("EDPluginControlIndexingMOSFLMv10.setDataInput")
EDPluginControlIndexingv10.setDataInput(self, _dataInput)
# Convert the input data to MOSFLM specific input data
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
self.__xsDataMOSFLMIndexingInput = EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputIndexing(self.getDataInput())
def getDataIndexingResult(self, _edPlugin):
"""
This method retrieves the indexing results from a MOSFLM indexing plugin.
"""
self.verboseDebug("EDPluginControlIndexingv10.getDataIndexingResultFromMOSFLM")
xsDataMOSFLMOutputIndexing = _edPlugin.getDataOutput()
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
xsDataIndexingResult = EDHandlerXSDataMOSFLMv10.generateXSDataIndexingResult(xsDataMOSFLMOutputIndexing, self.getExperimentalCondition())
xsDataIndexingResult.setLabelitIndexing(XSDataBoolean(False))
return xsDataIndexingResult
def setDataInput(self, _dataInput):
"""
Sets the Plugin input data. A part from using the EDPlugin.setDataInput method,
this method also converts the input data to the MOSFLM specific data model indexing input.
"""
self.verboseDebug("EDPluginControlIndexingMOSFLMv10.setDataInput")
EDPluginControlIndexingv10.setDataInput(self, _dataInput)
# Convert the input data to MOSFLM specific input data
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
self.__xsDataMOSFLMIndexingInput = EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputIndexing(self.getDataInput())
def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
self.DEBUG("EDPluginControlGeneratePredictionv10.preProcess...")
xsDataGeneratePredictionInput = self.getDataInput()
xsDataSelectedIndexingSolution = xsDataGeneratePredictionInput.getSelectedIndexingSolution()
xsDataExperimentalConditionRefined = xsDataSelectedIndexingSolution.getExperimentalConditionRefined()
xsDataCollection = xsDataGeneratePredictionInput.getDataCollection()
xsDataSubWedgeList = xsDataCollection.getSubWedge()
# List containing instances of all the generate prediction plugins
self.__listPluginGeneratePrediction = []
# Loop through all subwedges
iIndex = 0
for xsDataSubWedge in xsDataSubWedgeList:
xsDataImageList = xsDataSubWedge.getImage()
# First find the lowest image number
iLowestImageNumber = None
for xsDataImage in xsDataImageList:
iImageNumber = xsDataImage.getNumber().getValue()
if (iLowestImageNumber is None):
iLowestImageNumber = iImageNumber
elif (iImageNumber < iLowestImageNumber):
iLowestImageNumber = iImageNumber
# Then loop through all images in a sub wedge
for xsDataImage in xsDataImageList:
iIndex += 1
edPluginGeneratePrediction = self.loadPlugin(self.__strPluginGeneratePredictionName,
"%s-%02d" % (self.__strPluginGeneratePredictionName, iIndex))
xsDataGeneratePredictionInput = XSDataGeneratePredictionInput()
xsDataGeneratePredictionInput.setSelectedIndexingSolution(XSDataIndexingSolutionSelected.parseString(xsDataSelectedIndexingSolution.marshal()))
xsDataCollectionNew = XSDataCollection()
xsDataSubWedgeNew = XSDataSubWedge()
xsDataSubWedgeNew.addImage(XSDataImage.parseString(xsDataImage.marshal()))
xsDataSubWedgeNew.setExperimentalCondition(XSDataExperimentalCondition.parseString(xsDataSubWedge.getExperimentalCondition().marshal()))
# We must modify the rotationOscillationStart for the new subwedge
xsDataGoniostatNew = xsDataSubWedgeNew.getExperimentalCondition().getGoniostat()
fGoniostatRotationAxisStart = xsDataGoniostatNew.getRotationAxisStart().getValue()
fGonioStatOscillationRange = xsDataGoniostatNew.getOscillationWidth().getValue()
iImageNumber = xsDataImage.getNumber().getValue()
fGoniostatRotationAxisStartNew = fGoniostatRotationAxisStart + (iImageNumber - iLowestImageNumber) * fGonioStatOscillationRange
xsDataGoniostatNew.setRotationAxisStart(XSDataAngle(fGoniostatRotationAxisStartNew))
#
xsDataCollectionNew.addSubWedge(xsDataSubWedgeNew)
xsDataGeneratePredictionInput.setDataCollection(xsDataCollectionNew)
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
xsDataMOSFLMInputGeneratePrediction = EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputGeneratePrediction(xsDataGeneratePredictionInput)
edPluginGeneratePrediction.setDataInput(xsDataMOSFLMInputGeneratePrediction)
self.__listPluginGeneratePrediction.append(edPluginGeneratePrediction)
def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
self.DEBUG("EDPluginControlIntegrationv10.preProcess...")
xsDataIntegrationInput = self.getDataInput()
xsDataSelectedIndexingSolution = xsDataIntegrationInput.getSelectedIndexingSolution()
self.__xsDataExperimentalConditionRefined = xsDataIntegrationInput.getExperimentalConditionRefined()
# To be changed (see bug #40)
if (self.__xsDataExperimentalConditionRefined is None):
self.__xsDataExperimentalConditionRefined = xsDataSelectedIndexingSolution.getExperimentalConditionRefined()
xsDataCollection = xsDataIntegrationInput.getDataCollection()
xsDataSubWedgeList = xsDataCollection.getSubWedge()
self.__edPluginIntegrationList = []
iIndex = 0
for xsDataSubWedge in xsDataSubWedgeList:
iSubWedgeNumber = iIndex
if (xsDataSubWedge.getSubWedgeNumber() is not None):
# Use the incoming subwedge number if it exists
iSubWedgeNumber = xsDataSubWedge.getSubWedgeNumber().getValue()
edPluginIntegration = self.loadPlugin(self.__strPluginIntegrationName)
if (not edPluginIntegration is None):
iIndex += 1
xsDataIntegrationInputSubWedge = XSDataIntegrationInput()
xsDataIntegrationInputSubWedge.setSelectedIndexingSolution(XSDataIndexingSolutionSelected.parseString(xsDataSelectedIndexingSolution.marshal()))
xsDataIntegrationInputSubWedge.setExperimentalConditionRefined(XSDataExperimentalCondition.parseString(self.__xsDataExperimentalConditionRefined.marshal()))
xsDataCollection = XSDataCollection()
xsDataCollection.addSubWedge(xsDataSubWedge)
xsDataIntegrationInputSubWedge.setDataCollection(xsDataCollection)
try:
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
xsDataMOSFLMInputIntegration = EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputIntegration(xsDataIntegrationInputSubWedge)
edPluginIntegration.setDataInput(xsDataMOSFLMInputIntegration)
edPluginIntegration.setBaseName("%s-%02d" % (self.__strPluginIntegrationName, iIndex))
edPluginIntegration.connectSUCCESS(self.doSuccessActionIntegration)
edPluginIntegration.connectFAILURE(self.doFailureActionIntegration)
# Here we store the sub wedge number for use in the results
self.__edPluginIntegrationList.append([iSubWedgeNumber, edPluginIntegration])
except Exception as strErrorMessage:
self.addErrorMessage(strErrorMessage)
self.ERROR(strErrorMessage)
self.setFailure()
else:
strErrorMessage = "EDPluginControlIntegrationv10.preProcess: could not load plugin %s" % self.__strPluginIntegrationName
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
def testGenerateXSDataIndexingResult(self):
strFilename = "XSDataMOSFLMOutputIndexing_reference.xml"
strPath = os.path.join(self.m_strDataPath, strFilename)
strXMLMOSFLMOutputIndexing = EDUtilsTest.readAndParseFile(strPath)
from XSDataMOSFLMv10 import XSDataMOSFLMOutputIndexing
xsDataMOSFLMOutputIndexing = XSDataMOSFLMOutputIndexing.parseString(strXMLMOSFLMOutputIndexing)
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
xsDataIndexingResult = EDHandlerXSDataMOSFLMv10.generateXSDataIndexingResult(xsDataMOSFLMOutputIndexing)
strReferenceFilename = "XSDataIndexingResult_reference.xml"
strReferencePath = os.path.join(self.m_strDataPath, strReferenceFilename)
strXMLIndexingOutputReference = EDUtilsTest.readAndParseFile(strReferencePath)
from XSDataMXv1 import XSDataIndexingResult
xsdataIndexingResultReference = XSDataIndexingResult.parseString(strXMLIndexingOutputReference)
EDAssert.equal(xsdataIndexingResultReference.marshal(), xsDataIndexingResult.marshal())
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 testGenerateXSDataMOSFLMInputIntegration(self):
strFilename = "XSDataIntegrationInput_reference.xml"
strPath = os.path.join(self.m_strDataPath, strFilename)
strXMLIntegrationInput = EDUtilsTest.readAndParseFile(strPath)
from XSDataMXv1 import XSDataIntegrationInput
xsDataIntegrationInput = XSDataIntegrationInput.parseString(strXMLIntegrationInput)
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
xsDataMOSFLMInputIntegration = EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputIntegration(xsDataIntegrationInput)
strReferenceFilename = "XSDataMOSFLMInputIntegration_reference.xml"
strReferencePath = os.path.join(self.m_strDataPath, strReferenceFilename)
strXMLIntegrationInputReference = EDUtilsTest.readAndParseFile(strReferencePath)
EDFactoryPluginStatic.loadModule("XSDataMOSFLMv10")
from XSDataMOSFLMv10 import XSDataMOSFLMInputIntegration
xsDataMOSFLMInputIntegrationReference = XSDataMOSFLMInputIntegration.parseString(strXMLIntegrationInputReference)
EDAssert.equal(xsDataMOSFLMInputIntegrationReference.marshal(), xsDataMOSFLMInputIntegration.marshal())
def testGenerateXSDataIndexingResult(self):
strFilename = "XSDataMOSFLMOutputIndexing_reference.xml"
strPath = os.path.join(self.m_strDataPath, strFilename)
strXMLMOSFLMOutputIndexing = EDUtilsTest.readAndParseFile(strPath)
from XSDataMOSFLMv10 import XSDataMOSFLMOutputIndexing
xsDataMOSFLMOutputIndexing = XSDataMOSFLMOutputIndexing.parseString(
strXMLMOSFLMOutputIndexing)
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
xsDataIndexingResult = EDHandlerXSDataMOSFLMv10.generateXSDataIndexingResult(
xsDataMOSFLMOutputIndexing)
strReferenceFilename = "XSDataIndexingResult_reference.xml"
strReferencePath = os.path.join(self.m_strDataPath,
strReferenceFilename)
strXMLIndexingOutputReference = EDUtilsTest.readAndParseFile(
strReferencePath)
from XSDataMXv1 import XSDataIndexingResult
xsdataIndexingResultReference = XSDataIndexingResult.parseString(
strXMLIndexingOutputReference)
EDAssert.equal(xsdataIndexingResultReference.marshal(),
xsDataIndexingResult.marshal())
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 testGenerateXSDataMOSFLMInputIntegration(self):
strFilename = "XSDataIntegrationInput_reference.xml"
strPath = os.path.join(self.m_strDataPath, strFilename)
strXMLIntegrationInput = EDUtilsTest.readAndParseFile(strPath)
from XSDataMXv1 import XSDataIntegrationInput
xsDataIntegrationInput = XSDataIntegrationInput.parseString(
strXMLIntegrationInput)
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
xsDataMOSFLMInputIntegration = EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputIntegration(
xsDataIntegrationInput)
strReferenceFilename = "XSDataMOSFLMInputIntegration_reference.xml"
strReferencePath = os.path.join(self.m_strDataPath,
strReferenceFilename)
strXMLIntegrationInputReference = EDUtilsTest.readAndParseFile(
strReferencePath)
EDFactoryPluginStatic.loadModule("XSDataMOSFLMv10")
from XSDataMOSFLMv10 import XSDataMOSFLMInputIntegration
xsDataMOSFLMInputIntegrationReference = XSDataMOSFLMInputIntegration.parseString(
strXMLIntegrationInputReference)
EDAssert.equal(xsDataMOSFLMInputIntegrationReference.marshal(),
xsDataMOSFLMInputIntegration.marshal())
def process(self, _edPlugin=None):
"""
Executes the execution plugins
"""
EDPluginControl.process(self, _edPlugin)
self.DEBUG("EDPluginControlImageQualityIndicatorsv1_3.process")
EDUtilsParallel.initializeNbThread()
# Check if we should do indexing:
bDoIndexing = False
if self.dataInput.doIndexing is not None:
if self.dataInput.doIndexing.value:
bDoIndexing = True
# Loop through all the incoming reference images
listXSDataImage = self.dataInput.image
xsDataInputMXWaitFile = XSDataInputMXWaitFile()
self.xsDataResultControlImageQualityIndicators = XSDataResultControlImageQualityIndicators(
)
listPlugin = []
for xsDataImage in listXSDataImage:
self.edPluginMXWaitFile = self.loadPlugin(
self.strPluginMXWaitFileName)
xsDataInputMXWaitFile.file = XSDataFile(xsDataImage.path)
xsDataInputMXWaitFile.setSize(XSDataInteger(self.minImageSize))
xsDataInputMXWaitFile.setTimeOut(
XSDataTime(self.fMXWaitFileTimeOut))
self.DEBUG("Wait file timeOut set to %f" % self.fMXWaitFileTimeOut)
self.edPluginMXWaitFile.setDataInput(xsDataInputMXWaitFile)
self.edPluginMXWaitFile.executeSynchronous()
if not os.path.exists(xsDataImage.path.value):
self.edPluginMXWaitFile = self.loadPlugin(
self.strPluginMXWaitFileName)
xsDataInputMXWaitFile.file = XSDataFile(xsDataImage.path)
xsDataInputMXWaitFile.setSize(XSDataInteger(5000000))
xsDataInputMXWaitFile.setTimeOut(
XSDataTime(self.fMXWaitFileTimeOut))
self.DEBUG("Wait file timeOut set to %f" %
self.fMXWaitFileTimeOut)
self.edPluginMXWaitFile.setDataInput(xsDataInputMXWaitFile)
self.edPluginMXWaitFile.executeSynchronous()
if not os.path.exists(xsDataImage.path.value):
strError = "Time-out while waiting for image %s" % xsDataImage.path.value
self.error(strError)
self.addErrorMessage(strError)
self.setFailure()
else:
if self.bUseThinClient:
strPluginName = self.strPluginNameThinClient
else:
strPluginName = self.strPluginName
edPluginPluginExecImageQualityIndicator = self.loadPlugin(
strPluginName)
self.listPluginExecImageQualityIndicator.append(
edPluginPluginExecImageQualityIndicator)
xsDataInputDistlSignalStrength = XSDataInputDistlSignalStrength(
)
xsDataInputDistlSignalStrength.setReferenceImage(xsDataImage)
edPluginPluginExecImageQualityIndicator.setDataInput(
xsDataInputDistlSignalStrength)
edPluginPluginExecImageQualityIndicator.execute()
edPluginControlBackground3D = self.loadPlugin(
self.strPluginNameControlBackground3D)
listPlugin.append([
edPluginPluginExecImageQualityIndicator,
edPluginControlBackground3D
])
xsDataInputControlBackground3D = XSDataInputControlBackground3D(
)
xsDataInputControlBackground3D.addImage(
XSDataFile(xsDataImage.path))
edPluginControlBackground3D.dataInput = xsDataInputControlBackground3D
edPluginControlBackground3D.execute()
listIndexing = []
# Synchronize all image quality indicator plugins and upload to ISPyB
xsDataInputStoreListOfImageQualityIndicators = XSDataInputStoreListOfImageQualityIndicators(
)
for pluginPair in listPlugin:
edPluginPluginExecImageQualityIndicator = pluginPair[0]
edPluginControlBackground3D = pluginPair[1]
edPluginPluginExecImageQualityIndicator.synchronize()
edPluginControlBackground3D.synchronize()
xsDataImageQualityIndicators = XSDataImageQualityIndicators.parseString(\
edPluginPluginExecImageQualityIndicator.dataOutput.imageQualityIndicators.marshal())
if edPluginControlBackground3D.dataOutput.imageBackground != []:
xsDataImageQualityIndicators.background3D_estimate = edPluginControlBackground3D.dataOutput.imageBackground[
0].estimate
self.xsDataResultControlImageQualityIndicators.addImageQualityIndicators(
xsDataImageQualityIndicators)
xsDataISPyBImageQualityIndicators = \
XSDataISPyBImageQualityIndicators.parseString(xsDataImageQualityIndicators.marshal())
xsDataInputStoreListOfImageQualityIndicators.addImageQualityIndicators(
xsDataISPyBImageQualityIndicators)
# print xsDataInputStoreListOfImageQualityIndicators.marshal()
if self.dataInput.doUploadToIspyb is not None and self.dataInput.doUploadToIspyb.value:
self.edPluginISPyB = self.loadPlugin(self.strISPyBPluginName)
self.edPluginISPyB.dataInput = xsDataInputStoreListOfImageQualityIndicators
self.edPluginISPyB.execute()
#
if bDoIndexing:
# Find the 5 most intensive images (TIS):
listImage = []
# Check that we have background3D_estimate from all images:
has_background3D_estimate = True
for imageQualityIndicators in self.xsDataResultControlImageQualityIndicators.imageQualityIndicators:
if imageQualityIndicators.background3D_estimate is None:
has_background3D_estimate = False
if has_background3D_estimate:
listSorted = sorted(
self.xsDataResultControlImageQualityIndicators.
imageQualityIndicators,
key=lambda imageQualityIndicators: imageQualityIndicators.
background3D_estimate.value)
else:
listSorted = sorted(
self.xsDataResultControlImageQualityIndicators.
imageQualityIndicators,
key=lambda imageQualityIndicators: imageQualityIndicators.
totalIntegratedSignal.value)
for xsDataResultControlImageQualityIndicator in listSorted[-5:]:
if xsDataResultControlImageQualityIndicator.goodBraggCandidates.value > 30:
xsDataInputReadImageHeader = XSDataInputReadImageHeader()
xsDataInputReadImageHeader.image = XSDataFile(
xsDataResultControlImageQualityIndicator.image.path)
self.edPluginReadImageHeader = self.loadPlugin(
self.strPluginReadImageHeaderName)
self.edPluginReadImageHeader.dataInput = xsDataInputReadImageHeader
self.edPluginReadImageHeader.executeSynchronous()
xsDataResultReadImageHeader = self.edPluginReadImageHeader.dataOutput
if xsDataResultReadImageHeader is not None:
xsDataSubWedge = xsDataResultReadImageHeader.subWedge
self.xsDataCollection = XSDataCollection()
self.xsDataCollection.addSubWedge(xsDataSubWedge)
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.setDataCollection(
self.xsDataCollection)
xsDataMOSFLMIndexingInput = EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputIndexing(
xsDataIndexingInput)
edPluginMOSFLMIndexing = self.loadPlugin(
self.strIndexingMOSFLMPluginName)
self.listPluginMOSFLM.append([
edPluginMOSFLMIndexing,
xsDataResultControlImageQualityIndicator
])
edPluginMOSFLMIndexing.setDataInput(
xsDataMOSFLMIndexingInput)
edPluginMOSFLMIndexing.execute()
for tupleMOSFLM in self.listPluginMOSFLM:
edPluginMOSFLMIndexing = tupleMOSFLM[0]
xsDataResultControlImageQualityIndicator = tupleMOSFLM[1]
edPluginMOSFLMIndexing.synchronize()
if not edPluginMOSFLMIndexing.isFailure():
xsDataMOSFLMOutput = edPluginMOSFLMIndexing.dataOutput
xsDataIndexingResult = EDHandlerXSDataMOSFLMv10.generateXSDataIndexingResult(
xsDataMOSFLMOutput)
selectedSolution = xsDataIndexingResult.selectedSolution
if selectedSolution is not None:
xsDataResultControlImageQualityIndicator.selectedIndexingSolution = selectedSolution
def finallyProcess(self, _edObject=None):
EDPluginControl.finallyProcess(self, _edObject)
self.DEBUG("EDPluginControlIntegrationv10.finallyProcess")
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
for (iSubWedgeNumber,
edPluginIntegration) in self.__edPluginIntegrationList:
xsDataMOSFLMOutputIntegration = edPluginIntegration.getDataOutput()
if (xsDataMOSFLMOutputIntegration is None):
strWarning = "MOSFLM integration error : no integration results obtained."
self.addExecutiveSummaryLine(strWarning)
self.WARNING(strWarning)
# self.setFailure()
else:
xsDataIntegrationSubWedgeResult = None
try:
xsDataIntegrationSubWedgeResult = EDHandlerXSDataMOSFLMv10.generateXSDataIntegrationSubWedgeResult(
xsDataMOSFLMOutputIntegration,
self.__xsDataExperimentalConditionRefined)
except Exception as error:
strWarningMessage = str(error)
self.addWarningMessage(strWarningMessage)
self.WARNING(strWarningMessage)
# self.setFailure()
if (xsDataIntegrationSubWedgeResult is None):
strWarning = "MOSFLM integration error : no integration results obtained."
self.addExecutiveSummaryLine(strWarning)
self.WARNING(strWarning)
# self.setFailure()
else:
xsDataIntegrationSubWedgeResult.setSubWedgeNumber(
XSDataInteger(iSubWedgeNumber))
xsDataStatisticsIntegration = xsDataIntegrationSubWedgeResult.getStatistics(
)
if xsDataStatisticsIntegration.getRMSSpotDeviation(
) is not None:
fRMSSpotDeviation = xsDataStatisticsIntegration.getRMSSpotDeviation(
).getValue()
if (self.__fMaxRMSSpotDeviation is not None):
if (self.__fMaxRMSSpotDeviation <
fRMSSpotDeviation):
iImageStart = edPluginIntegration.getDataInput(
).getImageStart().getValue()
iImageEnd = edPluginIntegration.getDataInput(
).getImageEnd().getValue()
errorMessage = EDMessage.ERROR_DATA_HANDLER_02 % ("EDPluginControlIntegrationv10.postProcess", \
"MOSFLM Integration : RMS spot deviation (%.3f [mm]) larger than max value from configuration (%.3f [mm]) for images %d to %d" % \
(fRMSSpotDeviation, self.__fMaxRMSSpotDeviation, iImageStart, iImageEnd))
self.error(errorMessage)
self.addErrorMessage(errorMessage)
if (xsDataIntegrationSubWedgeResult is not None):
if (self.__xsDataIntegrationResult is None):
self.__xsDataIntegrationResult = XSDataIntegrationResult(
)
self.__xsDataIntegrationResult.addIntegrationSubWedgeResult(
xsDataIntegrationSubWedgeResult)
bSuccess = False
for integrationSubWedgeResult in self.__xsDataIntegrationResult.integrationSubWedgeResult:
if integrationSubWedgeResult.statistics.iOverSigmaOverall is not None:
bSuccess = True
break
if not bSuccess:
strErrorMessage = "MOSFLM integration failed for all images"
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
self.setDataOutput(self.__xsDataIntegrationResult)
if self.__xsDataIntegrationResult is not None:
self.generateIntegrationShortSummary(
self.__xsDataIntegrationResult)
def process(self, _edPlugin=None):
"""
Executes the execution plugins
"""
EDPluginControl.process(self, _edPlugin)
self.DEBUG("EDPluginControlImageQualityIndicatorsv1_4.process")
EDUtilsParallel.initializeNbThread()
# Check batch size
if self.dataInput.batchSize is None:
batchSize = 1
else:
batchSize = self.dataInput.batchSize.value
self.screen("Image quality indicators batch size: {0}".format(batchSize))
# Check if we should do distlSignalStrength:
bDoDistlSignalStrength = True
if self.dataInput.doDistlSignalStrength is not None:
if not self.dataInput.doDistlSignalStrength.value:
bDoDistlSignalStrength = False
# Check if we should do indexing:
bDoIndexing = False
if self.dataInput.doIndexing is not None:
if self.dataInput.doIndexing.value:
bDoIndexing = True
# Check if fast mesh (for HDF5)
isFastMesh = False
if self.dataInput.fastMesh:
isFastMesh = self.dataInput.fastMesh.value
# Loop through all the incoming reference images
if len(self.dataInput.image) == 0:
directory = self.dataInput.directory.path.value
template = self.dataInput.template.value
startNo = self.dataInput.startNo.value
endNo = self.dataInput.endNo.value
listXSDataImage = []
for index in range(startNo, endNo + 1):
imageName = template.replace("####", "{0:04d}".format(index))
imagePath = os.path.join(directory, imageName)
xsDataImage = XSDataImage(path=XSDataString(imagePath), number=XSDataInteger(index))
listXSDataImage.append(xsDataImage)
else:
listXSDataImage = self.dataInput.image
xsDataInputMXWaitFile = XSDataInputMXWaitFile()
self.xsDataResultControlImageQualityIndicators = XSDataResultControlImageQualityIndicators()
listPluginDistl = []
listPluginDozor = []
listOfImagesInBatch = []
listOfAllBatches = []
indexBatch = 0
listH5FilePath = []
# Process data in batches
for xsDataImage in listXSDataImage:
listOfImagesInBatch.append(xsDataImage.copy())
if len(listOfImagesInBatch) == batchSize:
listOfAllBatches.append(listOfImagesInBatch)
listOfImagesInBatch = []
if len(listOfImagesInBatch) > 0:
listOfAllBatches.append(listOfImagesInBatch)
listOfImagesInBatch = []
# Loop over batches
for listOfImagesInBatch in listOfAllBatches:
# First wait for images
for image in listOfImagesInBatch:
strPathToImage = image.path.value
# If Eiger, just wait for the h5 file
if strPathToImage.endswith(".h5"):
h5MasterFilePath, h5DataFilePath, hdf5ImageNumber = self.getH5FilePath(strPathToImage,
batchSize=batchSize,
isFastMesh=isFastMesh)
# print(h5FilePath)
# print(hdf5ImageNumber)
if not h5DataFilePath in listH5FilePath:
self.screen("ID30a3 Eiger data, waiting for master and data files...")
listH5FilePath.append(h5DataFilePath)
self.edPluginMXWaitFile = self.loadPlugin(self.strPluginMXWaitFileName)
xsDataInputMXWaitFile.file = XSDataFile(XSDataString(h5DataFilePath))
xsDataInputMXWaitFile.setSize(XSDataInteger(self.minImageSize))
xsDataInputMXWaitFile.setTimeOut(XSDataTime(self.fMXWaitFileTimeOut))
self.screen("Waiting for file {0}".format(h5DataFilePath))
self.DEBUG("Wait file timeOut set to %f" % self.fMXWaitFileTimeOut)
self.edPluginMXWaitFile.setDataInput(xsDataInputMXWaitFile)
self.edPluginMXWaitFile.executeSynchronous()
# hdf5FilePath = strPathToImage.replace(".cbf", ".h5")
time.sleep(1)
if not os.path.exists(h5DataFilePath):
strError = "Time-out while waiting for image %s" % h5DataFilePath
self.error(strError)
self.addErrorMessage(strError)
self.setFailure()
else:
if not os.path.exists(strPathToImage):
# self.screen("Waiting for file {0}".format(strPathToImage))
self.edPluginMXWaitFile = self.loadPlugin(self.strPluginMXWaitFileName)
xsDataInputMXWaitFile.file = XSDataFile(XSDataString(strPathToImage))
xsDataInputMXWaitFile.setSize(XSDataInteger(self.minImageSize))
xsDataInputMXWaitFile.setTimeOut(XSDataTime(self.fMXWaitFileTimeOut))
self.screen("Wait file timeOut set to %.0f s" % self.fMXWaitFileTimeOut)
self.edPluginMXWaitFile.setDataInput(xsDataInputMXWaitFile)
self.edPluginMXWaitFile.executeSynchronous()
if not os.path.exists(strPathToImage):
strError = "Time-out while waiting for image %s" % strPathToImage
self.error(strError)
self.addErrorMessage(strError)
self.setFailure()
if not self.isFailure():
strPathToFirstImage = listOfImagesInBatch[0].path.value
if strPathToImage.endswith(".h5"):
indexLoop = 1
continueLoop = True
while continueLoop:
directory = os.path.dirname(strPathToFirstImage)
firstImage = EDUtilsImage.getImageNumber(listOfImagesInBatch[0].path.value)
lastImage = EDUtilsImage.getImageNumber(listOfImagesInBatch[-1].path.value)
xsDataInputH5ToCBF = XSDataInputH5ToCBF()
xsDataInputH5ToCBF.hdf5File = XSDataFile(listOfImagesInBatch[0].path)
xsDataInputH5ToCBF.hdf5ImageNumber = XSDataInteger(1)
xsDataInputH5ToCBF.startImageNumber = XSDataInteger(firstImage)
xsDataInputH5ToCBF.endImageNumber = XSDataInteger(lastImage)
xsDataInputH5ToCBF.forcedOutputDirectory = XSDataFile(XSDataString(directory))
edPluginH5ToCBF = self.loadPlugin("EDPluginH5ToCBFv1_1")
edPluginH5ToCBF.dataInput = xsDataInputH5ToCBF
edPluginH5ToCBF.execute()
edPluginH5ToCBF.synchronize()
outputCBFFileTemplate = edPluginH5ToCBF.dataOutput.outputCBFFileTemplate
if outputCBFFileTemplate is not None:
lastCbfFile = outputCBFFileTemplate.path.value.replace("######", "{0:06d}".format(EDUtilsImage.getImageNumber(listOfImagesInBatch[-1].path.value)))
strPathToImage = os.path.join(directory, lastCbfFile)
# print(cbfFile.path.value)
if os.path.exists(strPathToImage):
# Rename all images
for image in listOfImagesInBatch:
image.path.value = image.path.value.replace(".h5", ".cbf")
imageNumber = EDUtilsImage.getImageNumber(image.path.value)
oldPath = os.path.join(directory, outputCBFFileTemplate.path.value.replace("######", "{0:06d}".format(imageNumber)))
newPath = os.path.join(directory, outputCBFFileTemplate.path.value.replace("######", "{0:04d}".format(imageNumber)))
os.rename(oldPath, newPath)
lastCbfFile = outputCBFFileTemplate.path.value.replace("######", "{0:04d}".format(EDUtilsImage.getImageNumber(listOfImagesInBatch[-1].path.value)))
strPathToImage = os.path.join(directory, lastCbfFile)
self.screen("Image has been converted to CBF file: {0}".format(strPathToImage))
continueLoop = False
# print(continueLoop)
if continueLoop:
self.screen("Still waiting for converting to CBF file: {0}".format(strPathToImage))
indexLoop += 1
time.sleep(5)
if indexLoop > 10:
continueLoop = False
for image in listOfImagesInBatch:
strPathToImage = image.path.value
# Check if we should run distl.signalStrength
xsDataImageNew = XSDataImage(XSDataString(strPathToImage))
xsDataImageNew.number = XSDataInteger(EDUtilsImage.getImageNumber(image.path.value))
edPluginPluginExecImageQualityIndicator = None
if bDoDistlSignalStrength:
if self.bUseThinClient:
strPluginName = self.strPluginNameThinClient
else:
strPluginName = self.strPluginName
edPluginPluginExecImageQualityIndicator = self.loadPlugin(strPluginName)
self.listPluginExecImageQualityIndicator.append(edPluginPluginExecImageQualityIndicator)
xsDataInputDistlSignalStrength = XSDataInputDistlSignalStrength()
xsDataInputDistlSignalStrength.setReferenceImage(xsDataImageNew)
edPluginPluginExecImageQualityIndicator.setDataInput(xsDataInputDistlSignalStrength)
edPluginPluginExecImageQualityIndicator.execute()
listPluginDistl.append((xsDataImageNew.copy(), edPluginPluginExecImageQualityIndicator))
edPluginControlDozor = self.loadPlugin(self.strPluginNameControlDozor,
"ControlDozor_{0}".format(os.path.splitext(os.path.basename(strPathToFirstImage))[0]))
xsDataInputControlDozor = XSDataInputControlDozor()
for image in listOfImagesInBatch:
xsDataInputControlDozor.addImage(XSDataFile(image.path))
xsDataInputControlDozor.batchSize = XSDataInteger(len(listOfImagesInBatch))
edPluginControlDozor.dataInput = xsDataInputControlDozor
edPluginControlDozor.execute()
listPluginDozor.append((edPluginControlDozor, list(listOfImagesInBatch)))
if not self.isFailure():
listIndexing = []
# Synchronize all image quality indicator plugins and upload to ISPyB
xsDataInputStoreListOfImageQualityIndicators = XSDataInputStoreListOfImageQualityIndicators()
for (xsDataImage, edPluginPluginExecImageQualityIndicator) in listPluginDistl:
xsDataImageQualityIndicators = XSDataImageQualityIndicators()
xsDataImageQualityIndicators.image = xsDataImage.copy()
if edPluginPluginExecImageQualityIndicator is not None:
edPluginPluginExecImageQualityIndicator.synchronize()
if edPluginPluginExecImageQualityIndicator.dataOutput is not None:
if edPluginPluginExecImageQualityIndicator.dataOutput.imageQualityIndicators is not None:
xsDataImageQualityIndicators = XSDataImageQualityIndicators.parseString(\
edPluginPluginExecImageQualityIndicator.dataOutput.imageQualityIndicators.marshal())
self.xsDataResultControlImageQualityIndicators.addImageQualityIndicators(xsDataImageQualityIndicators)
for (edPluginControlDozor, listBatch) in listPluginDozor:
edPluginControlDozor.synchronize()
# Check that we got at least one result
if len(edPluginControlDozor.dataOutput.imageDozor) == 0:
# Run the dozor plugin again, this time synchronously
firstImage = os.path.basename(listBatch[0].path.value)
lastImage = os.path.basename(listBatch[-1].path.value)
self.screen("No dozor results! Re-executing Dozor for images {0} to {1}".format(firstImage, lastImage))
time.sleep(5)
edPluginControlDozor = self.loadPlugin(self.strPluginNameControlDozor, "ControlDozor_reexecution_{0}".format(os.path.splitext(firstImage)[0]))
xsDataInputControlDozor = XSDataInputControlDozor()
for image in listBatch:
xsDataInputControlDozor.addImage(XSDataFile(image.path))
xsDataInputControlDozor.batchSize = XSDataInteger(batchSize)
edPluginControlDozor.dataInput = xsDataInputControlDozor
edPluginControlDozor.executeSynchronous()
for imageDozor in edPluginControlDozor.dataOutput.imageDozor:
for xsDataImageQualityIndicators in self.xsDataResultControlImageQualityIndicators.imageQualityIndicators:
if xsDataImageQualityIndicators.image.path.value == imageDozor.image.path.value:
xsDataImageQualityIndicators.dozor_score = imageDozor.mainScore
xsDataImageQualityIndicators.dozorSpotFile = imageDozor.spotFile
if imageDozor.spotFile is not None:
if os.path.exists(imageDozor.spotFile.path.value):
numpyArray = numpy.loadtxt(imageDozor.spotFile.path.value, skiprows=3)
xsDataImageQualityIndicators.dozorSpotList = XSDataString(base64.b64encode(numpyArray.tostring()))
xsDataImageQualityIndicators.addDozorSpotListShape(XSDataInteger(numpyArray.shape[0]))
if len(numpyArray.shape) > 1:
xsDataImageQualityIndicators.addDozorSpotListShape(XSDataInteger(numpyArray.shape[1]))
xsDataImageQualityIndicators.dozorSpotsIntAver = imageDozor.spotsIntAver
xsDataImageQualityIndicators.dozorSpotsResolution = imageDozor.spotsResolution
xsDataImageQualityIndicators.dozorVisibleResolution = imageDozor.visibleResolution
if self.xsDataResultControlImageQualityIndicators.inputDozor is None:
if edPluginControlDozor.dataOutput.inputDozor is not None:
self.xsDataResultControlImageQualityIndicators.inputDozor = XSDataDozorInput().parseString(
edPluginControlDozor.dataOutput.inputDozor.marshal())
if self.dataInput.doUploadToIspyb is not None and self.dataInput.doUploadToIspyb.value:
xsDataISPyBImageQualityIndicators = \
XSDataISPyBImageQualityIndicators.parseString(xsDataImageQualityIndicators.marshal())
xsDataInputStoreListOfImageQualityIndicators.addImageQualityIndicators(xsDataISPyBImageQualityIndicators)
# print xsDataInputStoreListOfImageQualityIndicators.marshal()
if self.dataInput.doUploadToIspyb is not None and self.dataInput.doUploadToIspyb.value:
self.edPluginISPyB = self.loadPlugin(self.strISPyBPluginName)
self.edPluginISPyB.dataInput = xsDataInputStoreListOfImageQualityIndicators
self.edPluginISPyB.execute()
#
if bDoIndexing:
# Find the 5 most intensive images (TIS):
listImage = []
# Check that we have dozor_score from all images:
has_dozor_score = True
for imageQualityIndicators in self.xsDataResultControlImageQualityIndicators.imageQualityIndicators:
if imageQualityIndicators.dozor_score is None:
has_dozor_score = False
if has_dozor_score:
listSorted = sorted(self.xsDataResultControlImageQualityIndicators.imageQualityIndicators,
key=lambda imageQualityIndicators: imageQualityIndicators.dozor_score.value)
else:
listSorted = sorted(self.xsDataResultControlImageQualityIndicators.imageQualityIndicators,
key=lambda imageQualityIndicators: imageQualityIndicators.totalIntegratedSignal.value)
for xsDataResultControlImageQualityIndicator in listSorted[-5:]:
if xsDataResultControlImageQualityIndicator.dozor_score.value > 1:
xsDataInputReadImageHeader = XSDataInputReadImageHeader()
xsDataInputReadImageHeader.image = XSDataFile(xsDataResultControlImageQualityIndicator.image.path)
self.edPluginReadImageHeader = self.loadPlugin(self.strPluginReadImageHeaderName)
self.edPluginReadImageHeader.dataInput = xsDataInputReadImageHeader
self.edPluginReadImageHeader.executeSynchronous()
xsDataResultReadImageHeader = self.edPluginReadImageHeader.dataOutput
if xsDataResultReadImageHeader is not None:
xsDataSubWedge = xsDataResultReadImageHeader.subWedge
self.xsDataCollection = XSDataCollection()
self.xsDataCollection.addSubWedge(xsDataSubWedge)
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.setDataCollection(self.xsDataCollection)
xsDataMOSFLMIndexingInput = EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputIndexing(xsDataIndexingInput)
edPluginMOSFLMIndexing = self.loadPlugin(self.strIndexingMOSFLMPluginName)
self.listPluginMOSFLM.append([edPluginMOSFLMIndexing, xsDataResultControlImageQualityIndicator])
edPluginMOSFLMIndexing.setDataInput(xsDataMOSFLMIndexingInput)
edPluginMOSFLMIndexing.execute()
for tupleMOSFLM in self.listPluginMOSFLM:
edPluginMOSFLMIndexing = tupleMOSFLM[0]
xsDataResultControlImageQualityIndicator = tupleMOSFLM[1]
edPluginMOSFLMIndexing.synchronize()
if not edPluginMOSFLMIndexing.isFailure():
xsDataMOSFLMOutput = edPluginMOSFLMIndexing.dataOutput
xsDataIndexingResult = EDHandlerXSDataMOSFLMv10.generateXSDataIndexingResult(xsDataMOSFLMOutput)
selectedSolution = xsDataIndexingResult.selectedSolution
if selectedSolution is not None:
xsDataResultControlImageQualityIndicator.selectedIndexingSolution = selectedSolution
def process(self, _edPlugin=None):
"""
Executes the execution plugins
"""
EDPluginControl.process(self, _edPlugin)
self.DEBUG("EDPluginControlImageQualityIndicatorsv1_4.process")
EDUtilsParallel.initializeNbThread()
# Check batch size
if self.dataInput.batchSize is None:
batchSize = 1
else:
batchSize = self.dataInput.batchSize.value
self.screen(
"Image quality indicators batch size: {0}".format(batchSize))
# Check if we should do distlSignalStrength:
bDoDistlSignalStrength = True
if self.dataInput.doDistlSignalStrength is not None:
if not self.dataInput.doDistlSignalStrength.value:
bDoDistlSignalStrength = False
# Check if we should do indexing:
bDoIndexing = False
if self.dataInput.doIndexing is not None:
if self.dataInput.doIndexing.value:
bDoIndexing = True
# Check if fast mesh (for HDF5)
isFastMesh = False
if self.dataInput.fastMesh:
isFastMesh = self.dataInput.fastMesh.value
# Loop through all the incoming reference images
if len(self.dataInput.image) == 0:
directory = self.dataInput.directory.path.value
template = self.dataInput.template.value
startNo = self.dataInput.startNo.value
endNo = self.dataInput.endNo.value
listXSDataImage = []
for index in range(startNo, endNo + 1):
imageName = template.replace("####", "{0:04d}".format(index))
imagePath = os.path.join(directory, imageName)
xsDataImage = XSDataImage(path=XSDataString(imagePath),
number=XSDataInteger(index))
listXSDataImage.append(xsDataImage)
else:
listXSDataImage = self.dataInput.image
xsDataInputMXWaitFile = XSDataInputMXWaitFile()
self.xsDataResultControlImageQualityIndicators = XSDataResultControlImageQualityIndicators(
)
listPluginDistl = []
listPluginDozor = []
listOfImagesInBatch = []
listOfAllBatches = []
indexBatch = 0
listH5FilePath = []
# Process data in batches
for xsDataImage in listXSDataImage:
listOfImagesInBatch.append(xsDataImage.copy())
if len(listOfImagesInBatch) == batchSize:
listOfAllBatches.append(listOfImagesInBatch)
listOfImagesInBatch = []
if len(listOfImagesInBatch) > 0:
listOfAllBatches.append(listOfImagesInBatch)
listOfImagesInBatch = []
# Loop over batches
for listOfImagesInBatch in listOfAllBatches:
# First wait for images
for image in listOfImagesInBatch:
strPathToImage = image.path.value
# If Eiger, just wait for the h5 file
if strPathToImage.endswith(".h5"):
h5MasterFilePath, h5DataFilePath, hdf5ImageNumber = self.getH5FilePath(
strPathToImage,
batchSize=batchSize,
isFastMesh=isFastMesh)
# print(h5FilePath)
# print(hdf5ImageNumber)
if not h5DataFilePath in listH5FilePath:
self.screen(
"ID30a3 Eiger data, waiting for master and data files..."
)
listH5FilePath.append(h5DataFilePath)
self.edPluginMXWaitFile = self.loadPlugin(
self.strPluginMXWaitFileName)
xsDataInputMXWaitFile.file = XSDataFile(
XSDataString(h5DataFilePath))
xsDataInputMXWaitFile.setSize(
XSDataInteger(self.minImageSize))
xsDataInputMXWaitFile.setTimeOut(
XSDataTime(self.fMXWaitFileTimeOut))
self.screen(
"Waiting for file {0}".format(h5DataFilePath))
self.DEBUG("Wait file timeOut set to %f" %
self.fMXWaitFileTimeOut)
self.edPluginMXWaitFile.setDataInput(
xsDataInputMXWaitFile)
self.edPluginMXWaitFile.executeSynchronous()
# hdf5FilePath = strPathToImage.replace(".cbf", ".h5")
time.sleep(1)
if not os.path.exists(h5DataFilePath):
strError = "Time-out while waiting for image %s" % h5DataFilePath
self.error(strError)
self.addErrorMessage(strError)
self.setFailure()
else:
if not os.path.exists(strPathToImage):
# self.screen("Waiting for file {0}".format(strPathToImage))
self.edPluginMXWaitFile = self.loadPlugin(
self.strPluginMXWaitFileName)
xsDataInputMXWaitFile.file = XSDataFile(
XSDataString(strPathToImage))
xsDataInputMXWaitFile.setSize(
XSDataInteger(self.minImageSize))
xsDataInputMXWaitFile.setTimeOut(
XSDataTime(self.fMXWaitFileTimeOut))
self.screen("Wait file timeOut set to %.0f s" %
self.fMXWaitFileTimeOut)
self.edPluginMXWaitFile.setDataInput(
xsDataInputMXWaitFile)
self.edPluginMXWaitFile.executeSynchronous()
if not os.path.exists(strPathToImage):
strError = "Time-out while waiting for image %s" % strPathToImage
self.error(strError)
self.addErrorMessage(strError)
self.setFailure()
if not self.isFailure():
strPathToFirstImage = listOfImagesInBatch[0].path.value
if strPathToImage.endswith(".h5"):
indexLoop = 1
continueLoop = True
while continueLoop:
directory = os.path.dirname(strPathToFirstImage)
firstImage = EDUtilsImage.getImageNumber(
listOfImagesInBatch[0].path.value)
lastImage = EDUtilsImage.getImageNumber(
listOfImagesInBatch[-1].path.value)
xsDataInputH5ToCBF = XSDataInputH5ToCBF()
xsDataInputH5ToCBF.hdf5File = XSDataFile(
listOfImagesInBatch[0].path)
xsDataInputH5ToCBF.hdf5ImageNumber = XSDataInteger(1)
xsDataInputH5ToCBF.startImageNumber = XSDataInteger(
firstImage)
xsDataInputH5ToCBF.endImageNumber = XSDataInteger(
lastImage)
xsDataInputH5ToCBF.forcedOutputDirectory = XSDataFile(
XSDataString(directory))
edPluginH5ToCBF = self.loadPlugin(
"EDPluginH5ToCBFv1_1")
edPluginH5ToCBF.dataInput = xsDataInputH5ToCBF
edPluginH5ToCBF.execute()
edPluginH5ToCBF.synchronize()
outputCBFFileTemplate = edPluginH5ToCBF.dataOutput.outputCBFFileTemplate
if outputCBFFileTemplate is not None:
lastCbfFile = outputCBFFileTemplate.path.value.replace(
"######", "{0:06d}".format(
EDUtilsImage.getImageNumber(
listOfImagesInBatch[-1].path.value)))
strPathToImage = os.path.join(
directory, lastCbfFile)
# print(cbfFile.path.value)
if os.path.exists(strPathToImage):
# Rename all images
for image in listOfImagesInBatch:
image.path.value = image.path.value.replace(
".h5", ".cbf")
imageNumber = EDUtilsImage.getImageNumber(
image.path.value)
oldPath = os.path.join(
directory,
outputCBFFileTemplate.path.value.
replace("######",
"{0:06d}".format(imageNumber)))
newPath = os.path.join(
directory,
outputCBFFileTemplate.path.value.
replace("######",
"{0:04d}".format(imageNumber)))
os.rename(oldPath, newPath)
lastCbfFile = outputCBFFileTemplate.path.value.replace(
"######", "{0:04d}".format(
EDUtilsImage.getImageNumber(
listOfImagesInBatch[-1].path.value)
))
strPathToImage = os.path.join(
directory, lastCbfFile)
self.screen(
"Image has been converted to CBF file: {0}"
.format(strPathToImage))
continueLoop = False
# print(continueLoop)
if continueLoop:
self.screen(
"Still waiting for converting to CBF file: {0}"
.format(strPathToImage))
indexLoop += 1
time.sleep(5)
if indexLoop > 10:
continueLoop = False
for image in listOfImagesInBatch:
strPathToImage = image.path.value
# Check if we should run distl.signalStrength
xsDataImageNew = XSDataImage(XSDataString(strPathToImage))
xsDataImageNew.number = XSDataInteger(
EDUtilsImage.getImageNumber(image.path.value))
edPluginPluginExecImageQualityIndicator = None
if bDoDistlSignalStrength:
if self.bUseThinClient:
strPluginName = self.strPluginNameThinClient
else:
strPluginName = self.strPluginName
edPluginPluginExecImageQualityIndicator = self.loadPlugin(
strPluginName)
self.listPluginExecImageQualityIndicator.append(
edPluginPluginExecImageQualityIndicator)
xsDataInputDistlSignalStrength = XSDataInputDistlSignalStrength(
)
xsDataInputDistlSignalStrength.setReferenceImage(
xsDataImageNew)
edPluginPluginExecImageQualityIndicator.setDataInput(
xsDataInputDistlSignalStrength)
edPluginPluginExecImageQualityIndicator.execute()
listPluginDistl.append(
(xsDataImageNew.copy(),
edPluginPluginExecImageQualityIndicator))
edPluginControlDozor = self.loadPlugin(
self.strPluginNameControlDozor, "ControlDozor_{0}".format(
os.path.splitext(
os.path.basename(strPathToFirstImage))[0]))
xsDataInputControlDozor = XSDataInputControlDozor()
for image in listOfImagesInBatch:
xsDataInputControlDozor.addImage(XSDataFile(image.path))
xsDataInputControlDozor.batchSize = XSDataInteger(
len(listOfImagesInBatch))
edPluginControlDozor.dataInput = xsDataInputControlDozor
edPluginControlDozor.execute()
listPluginDozor.append(
(edPluginControlDozor, list(listOfImagesInBatch)))
if not self.isFailure():
listIndexing = []
# Synchronize all image quality indicator plugins and upload to ISPyB
xsDataInputStoreListOfImageQualityIndicators = XSDataInputStoreListOfImageQualityIndicators(
)
for (xsDataImage,
edPluginPluginExecImageQualityIndicator) in listPluginDistl:
xsDataImageQualityIndicators = XSDataImageQualityIndicators()
xsDataImageQualityIndicators.image = xsDataImage.copy()
if edPluginPluginExecImageQualityIndicator is not None:
edPluginPluginExecImageQualityIndicator.synchronize()
if edPluginPluginExecImageQualityIndicator.dataOutput is not None:
if edPluginPluginExecImageQualityIndicator.dataOutput.imageQualityIndicators is not None:
xsDataImageQualityIndicators = XSDataImageQualityIndicators.parseString(\
edPluginPluginExecImageQualityIndicator.dataOutput.imageQualityIndicators.marshal())
self.xsDataResultControlImageQualityIndicators.addImageQualityIndicators(
xsDataImageQualityIndicators)
for (edPluginControlDozor, listBatch) in listPluginDozor:
edPluginControlDozor.synchronize()
# Check that we got at least one result
if len(edPluginControlDozor.dataOutput.imageDozor) == 0:
# Run the dozor plugin again, this time synchronously
firstImage = os.path.basename(listBatch[0].path.value)
lastImage = os.path.basename(listBatch[-1].path.value)
self.screen(
"No dozor results! Re-executing Dozor for images {0} to {1}"
.format(firstImage, lastImage))
time.sleep(5)
edPluginControlDozor = self.loadPlugin(
self.strPluginNameControlDozor,
"ControlDozor_reexecution_{0}".format(
os.path.splitext(firstImage)[0]))
xsDataInputControlDozor = XSDataInputControlDozor()
for image in listBatch:
xsDataInputControlDozor.addImage(XSDataFile(
image.path))
xsDataInputControlDozor.batchSize = XSDataInteger(
batchSize)
edPluginControlDozor.dataInput = xsDataInputControlDozor
edPluginControlDozor.executeSynchronous()
for imageDozor in edPluginControlDozor.dataOutput.imageDozor:
for xsDataImageQualityIndicators in self.xsDataResultControlImageQualityIndicators.imageQualityIndicators:
if xsDataImageQualityIndicators.image.path.value == imageDozor.image.path.value:
xsDataImageQualityIndicators.dozor_score = imageDozor.mainScore
xsDataImageQualityIndicators.dozorSpotFile = imageDozor.spotFile
if imageDozor.spotFile is not None:
if os.path.exists(
imageDozor.spotFile.path.value):
numpyArray = numpy.loadtxt(
imageDozor.spotFile.path.value,
skiprows=3)
xsDataImageQualityIndicators.dozorSpotList = XSDataString(
base64.b64encode(
numpyArray.tostring()))
xsDataImageQualityIndicators.addDozorSpotListShape(
XSDataInteger(numpyArray.shape[0]))
if len(numpyArray.shape) > 1:
xsDataImageQualityIndicators.addDozorSpotListShape(
XSDataInteger(numpyArray.shape[1]))
xsDataImageQualityIndicators.dozorSpotsIntAver = imageDozor.spotsIntAver
xsDataImageQualityIndicators.dozorSpotsResolution = imageDozor.spotsResolution
xsDataImageQualityIndicators.dozorVisibleResolution = imageDozor.visibleResolution
if self.xsDataResultControlImageQualityIndicators.inputDozor is None:
if edPluginControlDozor.dataOutput.inputDozor is not None:
self.xsDataResultControlImageQualityIndicators.inputDozor = XSDataDozorInput(
).parseString(
edPluginControlDozor.dataOutput.
inputDozor.marshal())
if self.dataInput.doUploadToIspyb is not None and self.dataInput.doUploadToIspyb.value:
xsDataISPyBImageQualityIndicators = \
XSDataISPyBImageQualityIndicators.parseString(xsDataImageQualityIndicators.marshal())
xsDataInputStoreListOfImageQualityIndicators.addImageQualityIndicators(
xsDataISPyBImageQualityIndicators)
# print xsDataInputStoreListOfImageQualityIndicators.marshal()
if self.dataInput.doUploadToIspyb is not None and self.dataInput.doUploadToIspyb.value:
self.edPluginISPyB = self.loadPlugin(self.strISPyBPluginName)
self.edPluginISPyB.dataInput = xsDataInputStoreListOfImageQualityIndicators
self.edPluginISPyB.execute()
#
if bDoIndexing:
# Find the 5 most intensive images (TIS):
listImage = []
# Check that we have dozor_score from all images:
has_dozor_score = True
for imageQualityIndicators in self.xsDataResultControlImageQualityIndicators.imageQualityIndicators:
if imageQualityIndicators.dozor_score is None:
has_dozor_score = False
if has_dozor_score:
listSorted = sorted(
self.xsDataResultControlImageQualityIndicators.
imageQualityIndicators,
key=lambda imageQualityIndicators:
imageQualityIndicators.dozor_score.value)
else:
listSorted = sorted(
self.xsDataResultControlImageQualityIndicators.
imageQualityIndicators,
key=lambda imageQualityIndicators:
imageQualityIndicators.totalIntegratedSignal.value)
for xsDataResultControlImageQualityIndicator in listSorted[
-5:]:
if xsDataResultControlImageQualityIndicator.dozor_score.value > 1:
xsDataInputReadImageHeader = XSDataInputReadImageHeader(
)
xsDataInputReadImageHeader.image = XSDataFile(
xsDataResultControlImageQualityIndicator.image.path
)
self.edPluginReadImageHeader = self.loadPlugin(
self.strPluginReadImageHeaderName)
self.edPluginReadImageHeader.dataInput = xsDataInputReadImageHeader
self.edPluginReadImageHeader.executeSynchronous()
xsDataResultReadImageHeader = self.edPluginReadImageHeader.dataOutput
if xsDataResultReadImageHeader is not None:
xsDataSubWedge = xsDataResultReadImageHeader.subWedge
self.xsDataCollection = XSDataCollection()
self.xsDataCollection.addSubWedge(xsDataSubWedge)
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.setDataCollection(
self.xsDataCollection)
xsDataMOSFLMIndexingInput = EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputIndexing(
xsDataIndexingInput)
edPluginMOSFLMIndexing = self.loadPlugin(
self.strIndexingMOSFLMPluginName)
self.listPluginMOSFLM.append([
edPluginMOSFLMIndexing,
xsDataResultControlImageQualityIndicator
])
edPluginMOSFLMIndexing.setDataInput(
xsDataMOSFLMIndexingInput)
edPluginMOSFLMIndexing.execute()
for tupleMOSFLM in self.listPluginMOSFLM:
edPluginMOSFLMIndexing = tupleMOSFLM[0]
xsDataResultControlImageQualityIndicator = tupleMOSFLM[1]
edPluginMOSFLMIndexing.synchronize()
if not edPluginMOSFLMIndexing.isFailure():
xsDataMOSFLMOutput = edPluginMOSFLMIndexing.dataOutput
xsDataIndexingResult = EDHandlerXSDataMOSFLMv10.generateXSDataIndexingResult(
xsDataMOSFLMOutput)
selectedSolution = xsDataIndexingResult.selectedSolution
if selectedSolution is not None:
xsDataResultControlImageQualityIndicator.selectedIndexingSolution = selectedSolution
def process(self, _edPlugin=None):
"""
Executes the execution plugins
"""
EDPluginControl.process(self, _edPlugin)
self.DEBUG("EDPluginControlImageQualityIndicatorsv1_2.process")
EDUtilsParallel.initializeNbThread()
# Check if we should do indexing:
bDoIndexing = False
if self.dataInput.doIndexing is not None:
if self.dataInput.doIndexing.value:
bDoIndexing = True
# Loop through all the incoming reference images
listXSDataImage = self.dataInput.image
xsDataInputMXWaitFile = XSDataInputMXWaitFile()
self.xsDataResultControlImageQualityIndicators = XSDataResultControlImageQualityIndicators(
)
listPlugin = []
for xsDataImage in listXSDataImage:
self.edPluginMXWaitFile = self.loadPlugin(
self.strPluginMXWaitFileName)
xsDataInputMXWaitFile.file = XSDataFile(xsDataImage.path)
xsDataInputMXWaitFile.setSize(XSDataInteger(self.minImageSize))
xsDataInputMXWaitFile.setTimeOut(
XSDataTime(self.fMXWaitFileTimeOut))
self.DEBUG("Wait file timeOut set to %f" % self.fMXWaitFileTimeOut)
self.edPluginMXWaitFile.setDataInput(xsDataInputMXWaitFile)
self.edPluginMXWaitFile.executeSynchronous()
if not os.path.exists(xsDataImage.path.value):
strError = "Time-out while waiting for image %s" % xsDataImage.path.value
self.error(strError)
self.addErrorMessage(strError)
self.setFailure()
else:
if self.bUseThinClient:
strPluginName = self.strPluginNameThinClient
else:
strPluginName = self.strPluginName
edPluginPluginExecImageQualityIndicator = self.loadPlugin(
strPluginName)
listPlugin.append(edPluginPluginExecImageQualityIndicator)
self.listPluginExecImageQualityIndicator.append(
edPluginPluginExecImageQualityIndicator)
xsDataInputDistlSignalStrength = XSDataInputDistlSignalStrength(
)
xsDataInputDistlSignalStrength.setReferenceImage(xsDataImage)
edPluginPluginExecImageQualityIndicator.setDataInput(
xsDataInputDistlSignalStrength)
edPluginPluginExecImageQualityIndicator.execute()
listIndexing = []
# Synchronize all image quality indicator plugins and upload to ISPyB
xsDataInputStoreListOfImageQualityIndicators = XSDataInputStoreListOfImageQualityIndicators(
)
for edPluginPluginExecImageQualityIndicator in listPlugin:
edPluginPluginExecImageQualityIndicator.synchronize()
xsDataImageQualityIndicators = XSDataImageQualityIndicators.parseString( \
edPluginPluginExecImageQualityIndicator.dataOutput.imageQualityIndicators.marshal())
self.xsDataResultControlImageQualityIndicators.addImageQualityIndicators(
xsDataImageQualityIndicators)
xsDataISPyBImageQualityIndicators = \
XSDataISPyBImageQualityIndicators.parseString(xsDataImageQualityIndicators.marshal())
xsDataInputStoreListOfImageQualityIndicators.addImageQualityIndicators(
xsDataISPyBImageQualityIndicators)
# print xsDataInputStoreListOfImageQualityIndicators.marshal()
if self.bDoISPyBUpload:
self.edPluginISPyB = self.loadPlugin(self.strISPyBPluginName)
self.edPluginISPyB.dataInput = xsDataInputStoreListOfImageQualityIndicators
self.edPluginISPyB.execute()
#
if bDoIndexing:
# Find the 5 most intensive images (TIS):
listImage = []
listSorted = sorted(
self.xsDataResultControlImageQualityIndicators.
imageQualityIndicators,
key=
lambda imageQualityIndicators: imageQualityIndicators.totalIntegratedSignal.value
)
for xsDataResultControlImageQualityIndicator in listSorted[-5:]:
if xsDataResultControlImageQualityIndicator.goodBraggCandidates.value > 30:
xsDataInputReadImageHeader = XSDataInputReadImageHeader()
xsDataInputReadImageHeader.image = XSDataFile(
xsDataResultControlImageQualityIndicator.image.path)
self.edPluginReadImageHeader = self.loadPlugin(
self.strPluginReadImageHeaderName)
self.edPluginReadImageHeader.dataInput = xsDataInputReadImageHeader
self.edPluginReadImageHeader.executeSynchronous()
xsDataResultReadImageHeader = self.edPluginReadImageHeader.dataOutput
if xsDataResultReadImageHeader is not None:
xsDataSubWedge = xsDataResultReadImageHeader.subWedge
self.xsDataCollection = XSDataCollection()
self.xsDataCollection.addSubWedge(xsDataSubWedge)
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.setDataCollection(
self.xsDataCollection)
xsDataMOSFLMIndexingInput = EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputIndexing(
xsDataIndexingInput)
edPluginMOSFLMIndexing = self.loadPlugin(
self.strIndexingMOSFLMPluginName)
self.listPluginMOSFLM.append([
edPluginMOSFLMIndexing,
xsDataResultControlImageQualityIndicator
])
edPluginMOSFLMIndexing.setDataInput(
xsDataMOSFLMIndexingInput)
edPluginMOSFLMIndexing.execute()
for tupleMOSFLM in self.listPluginMOSFLM:
edPluginMOSFLMIndexing = tupleMOSFLM[0]
xsDataResultControlImageQualityIndicator = tupleMOSFLM[1]
edPluginMOSFLMIndexing.synchronize()
if not edPluginMOSFLMIndexing.isFailure():
xsDataMOSFLMOutput = edPluginMOSFLMIndexing.dataOutput
xsDataIndexingResult = EDHandlerXSDataMOSFLMv10.generateXSDataIndexingResult(
xsDataMOSFLMOutput)
selectedSolution = xsDataIndexingResult.selectedSolution
if selectedSolution is not None:
xsDataResultControlImageQualityIndicator.selectedIndexingSolution = selectedSolution
def process(self, _edPlugin=None):
"""
Executes the execution plugins
"""
EDPluginControl.process(self, _edPlugin)
self.DEBUG("EDPluginControlImageQualityIndicatorsv1_4.process")
EDUtilsParallel.initializeNbThread()
# Check batch size
if self.dataInput.batchSize is None:
batchSize = 1
else:
batchSize = self.dataInput.batchSize.value
self.screen("Batch size: {0}".format(batchSize))
# Check if we should do distlSignalStrength:
bDoDistlSignalStrength = True
if self.dataInput.doDistlSignalStrength is not None:
if not self.dataInput.doDistlSignalStrength.value:
bDoDistlSignalStrength = False
# Check if we should do indexing:
bDoIndexing = False
if self.dataInput.doIndexing is not None:
if self.dataInput.doIndexing.value:
bDoIndexing = True
# Loop through all the incoming reference images
listXSDataImage = self.dataInput.image
xsDataInputMXWaitFile = XSDataInputMXWaitFile()
self.xsDataResultControlImageQualityIndicators = XSDataResultControlImageQualityIndicators()
listPluginDistl = []
listPluginDozor = []
listBatch = []
indexBatch = 0
listH5FilePath = []
ispybDataCollection = None
for xsDataImage in listXSDataImage:
strPathToImage = xsDataImage.path.value
# If Eiger, just wait for the h5 file
if "id30a3" in strPathToImage:
h5MasterFilePath, h5DataFilePath, hdf5ImageNumber = self.getH5FilePath(strPathToImage, batchSize)
# print(h5FilePath)
# print(hdf5ImageNumber)
if not h5DataFilePath in listH5FilePath:
self.screen("ID30a3 Eiger data, waiting for master and data files...")
listH5FilePath.append(h5DataFilePath)
self.edPluginMXWaitFile = self.loadPlugin(self.strPluginMXWaitFileName)
xsDataInputMXWaitFile.file = XSDataFile(XSDataString(h5DataFilePath))
xsDataInputMXWaitFile.setSize(XSDataInteger(self.minImageSize))
xsDataInputMXWaitFile.setTimeOut(XSDataTime(self.fMXWaitFileTimeOut))
self.screen("Waiting for file {0}".format(h5DataFilePath))
self.DEBUG("Wait file timeOut set to %f" % self.fMXWaitFileTimeOut)
self.edPluginMXWaitFile.setDataInput(xsDataInputMXWaitFile)
self.edPluginMXWaitFile.executeSynchronous()
# hdf5FilePath = strPathToImage.replace(".cbf", ".h5")
ispybDataCollection = None
time.sleep(1)
indexLoop = 1
continueLoop = True
while continueLoop:
xsDataInputControlH5ToCBF = XSDataInputControlH5ToCBF()
xsDataInputControlH5ToCBF.hdf5File = XSDataFile(XSDataString(strPathToImage))
imageNumber = EDUtilsImage.getImageNumber(strPathToImage)
xsDataInputControlH5ToCBF.imageNumber = XSDataInteger(imageNumber)
xsDataInputControlH5ToCBF.hdf5ImageNumber = XSDataInteger(hdf5ImageNumber)
xsDataInputControlH5ToCBF.ispybDataCollection = ispybDataCollection
edPluginControlH5ToCBF = self.loadPlugin(self.strPluginControlH5ToCBF, "ControlH5ToCBF_%04d_%02d" % (imageNumber, indexLoop))
edPluginControlH5ToCBF.dataInput = xsDataInputControlH5ToCBF
edPluginControlH5ToCBF.executeSynchronous()
cbfFile = edPluginControlH5ToCBF.dataOutput.outputCBFFile
# print(cbfFile)
# print(indexLoop)
if cbfFile is not None:
strPathToImage = cbfFile.path.value
# print(cbfFile.path.value)
if os.path.exists(strPathToImage):
self.screen("Image has been converted to CBF file: {0}".format(strPathToImage))
continueLoop = False
# print(continueLoop)
if continueLoop:
self.screen("Still waiting for converting to CBF file: {0}".format(strPathToImage))
indexLoop += 1
time.sleep(5)
if indexLoop > 10:
continueLoop = False
ispybDataCollection = edPluginControlH5ToCBF.dataOutput.ispybDataCollection
elif not os.path.exists(strPathToImage):
self.screen("Waiting for file {0}".format(strPathToImage))
self.edPluginMXWaitFile = self.loadPlugin(self.strPluginMXWaitFileName)
xsDataInputMXWaitFile.file = XSDataFile(XSDataString(strPathToImage))
xsDataInputMXWaitFile.setSize(XSDataInteger(self.minImageSize))
xsDataInputMXWaitFile.setTimeOut(XSDataTime(self.fMXWaitFileTimeOut))
self.DEBUG("Wait file timeOut set to %f" % self.fMXWaitFileTimeOut)
self.edPluginMXWaitFile.setDataInput(xsDataInputMXWaitFile)
self.edPluginMXWaitFile.executeSynchronous()
if not os.path.exists(strPathToImage):
strError = "Time-out while waiting for image %s" % strPathToImage
self.error(strError)
self.addErrorMessage(strError)
self.setFailure()
else:
# Check if we should run distl.signalStrength
xsDataImageNew = XSDataImage(XSDataString(strPathToImage))
edPluginPluginExecImageQualityIndicator = None
if bDoDistlSignalStrength:
if self.bUseThinClient:
strPluginName = self.strPluginNameThinClient
else:
strPluginName = self.strPluginName
edPluginPluginExecImageQualityIndicator = self.loadPlugin(strPluginName)
self.listPluginExecImageQualityIndicator.append(edPluginPluginExecImageQualityIndicator)
xsDataInputDistlSignalStrength = XSDataInputDistlSignalStrength()
xsDataInputDistlSignalStrength.setReferenceImage(xsDataImageNew)
edPluginPluginExecImageQualityIndicator.setDataInput(xsDataInputDistlSignalStrength)
edPluginPluginExecImageQualityIndicator.execute()
listPluginDistl.append((xsDataImageNew.copy(), edPluginPluginExecImageQualityIndicator))
listBatch.append(xsDataImageNew.copy())
if len(listBatch) == batchSize:
edPluginControlDozor = self.loadPlugin(self.strPluginNameControlDozor)
xsDataInputControlDozor = XSDataInputControlDozor()
for image in listBatch:
xsDataInputControlDozor.addImage(XSDataFile(image.path))
xsDataInputControlDozor.batchSize = XSDataInteger(batchSize)
edPluginControlDozor.dataInput = xsDataInputControlDozor
edPluginControlDozor.execute()
listPluginDozor.append((edPluginControlDozor, listBatch))
listBatch = []
if len(listBatch) > 0:
# Process the remaining images...
edPluginControlDozor = self.loadPlugin(self.strPluginNameControlDozor)
xsDataInputControlDozor = XSDataInputControlDozor()
for image in listBatch:
xsDataInputControlDozor.addImage(XSDataFile(image.path))
xsDataInputControlDozor.batchSize = XSDataInteger(batchSize)
edPluginControlDozor.dataInput = xsDataInputControlDozor
edPluginControlDozor.execute()
listPluginDozor.append([edPluginControlDozor, listBatch])
listIndexing = []
# Synchronize all image quality indicator plugins and upload to ISPyB
xsDataInputStoreListOfImageQualityIndicators = XSDataInputStoreListOfImageQualityIndicators()
for (xsDataImage, edPluginPluginExecImageQualityIndicator) in listPluginDistl:
xsDataImageQualityIndicators = XSDataImageQualityIndicators()
xsDataImageQualityIndicators.image = xsDataImage.copy()
if edPluginPluginExecImageQualityIndicator is not None:
edPluginPluginExecImageQualityIndicator.synchronize()
if edPluginPluginExecImageQualityIndicator.dataOutput.imageQualityIndicators is not None:
xsDataImageQualityIndicators = XSDataImageQualityIndicators.parseString(\
edPluginPluginExecImageQualityIndicator.dataOutput.imageQualityIndicators.marshal())
self.xsDataResultControlImageQualityIndicators.addImageQualityIndicators(xsDataImageQualityIndicators)
for (edPluginControlDozor, listBatch) in listPluginDozor:
edPluginControlDozor.synchronize()
for imageDozor in edPluginControlDozor.dataOutput.imageDozor:
for xsDataImageQualityIndicators in self.xsDataResultControlImageQualityIndicators.imageQualityIndicators:
if xsDataImageQualityIndicators.image.path.value == imageDozor.image.path.value:
xsDataImageQualityIndicators.dozor_score = imageDozor.mainScore
xsDataImageQualityIndicators.dozorSpotFile = imageDozor.spotFile
if imageDozor.spotFile is not None:
if os.path.exists(imageDozor.spotFile.path.value):
numpyArray = numpy.loadtxt(imageDozor.spotFile.path.value, skiprows=3)
xsDataImageQualityIndicators.dozorSpotList = XSDataString(base64.b64encode(numpyArray.tostring()))
xsDataImageQualityIndicators.addDozorSpotListShape(XSDataInteger(numpyArray.shape[0]))
if len(numpyArray.shape) > 1:
xsDataImageQualityIndicators.addDozorSpotListShape(XSDataInteger(numpyArray.shape[1]))
xsDataImageQualityIndicators.dozorSpotsIntAver = imageDozor.spotsIntAver
xsDataImageQualityIndicators.dozorSpotsResolution = imageDozor.spotsResolution
if self.xsDataResultControlImageQualityIndicators.inputDozor is None:
if edPluginControlDozor.dataOutput.inputDozor is not None:
self.xsDataResultControlImageQualityIndicators.inputDozor = XSDataDozorInput().parseString(
edPluginControlDozor.dataOutput.inputDozor.marshal())
if self.dataInput.doUploadToIspyb is not None and self.dataInput.doUploadToIspyb.value:
xsDataISPyBImageQualityIndicators = \
XSDataISPyBImageQualityIndicators.parseString(xsDataImageQualityIndicators.marshal())
xsDataInputStoreListOfImageQualityIndicators.addImageQualityIndicators(xsDataISPyBImageQualityIndicators)
# print xsDataInputStoreListOfImageQualityIndicators.marshal()
if self.dataInput.doUploadToIspyb is not None and self.dataInput.doUploadToIspyb.value:
self.edPluginISPyB = self.loadPlugin(self.strISPyBPluginName)
self.edPluginISPyB.dataInput = xsDataInputStoreListOfImageQualityIndicators
self.edPluginISPyB.execute()
#
if bDoIndexing:
# Find the 5 most intensive images (TIS):
listImage = []
# Check that we have dozor_score from all images:
has_dozor_score = True
for imageQualityIndicators in self.xsDataResultControlImageQualityIndicators.imageQualityIndicators:
if imageQualityIndicators.dozor_score is None:
has_dozor_score = False
if has_dozor_score:
listSorted = sorted(self.xsDataResultControlImageQualityIndicators.imageQualityIndicators,
key=lambda imageQualityIndicators: imageQualityIndicators.dozor_score.value)
else:
listSorted = sorted(self.xsDataResultControlImageQualityIndicators.imageQualityIndicators,
key=lambda imageQualityIndicators: imageQualityIndicators.totalIntegratedSignal.value)
for xsDataResultControlImageQualityIndicator in listSorted[-5:]:
if xsDataResultControlImageQualityIndicator.goodBraggCandidates.value > 30:
xsDataInputReadImageHeader = XSDataInputReadImageHeader()
xsDataInputReadImageHeader.image = XSDataFile(xsDataResultControlImageQualityIndicator.image.path)
self.edPluginReadImageHeader = self.loadPlugin(self.strPluginReadImageHeaderName)
self.edPluginReadImageHeader.dataInput = xsDataInputReadImageHeader
self.edPluginReadImageHeader.executeSynchronous()
xsDataResultReadImageHeader = self.edPluginReadImageHeader.dataOutput
if xsDataResultReadImageHeader is not None:
xsDataSubWedge = xsDataResultReadImageHeader.subWedge
self.xsDataCollection = XSDataCollection()
self.xsDataCollection.addSubWedge(xsDataSubWedge)
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.setDataCollection(self.xsDataCollection)
xsDataMOSFLMIndexingInput = EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputIndexing(xsDataIndexingInput)
edPluginMOSFLMIndexing = self.loadPlugin(self.strIndexingMOSFLMPluginName)
self.listPluginMOSFLM.append([edPluginMOSFLMIndexing, xsDataResultControlImageQualityIndicator])
edPluginMOSFLMIndexing.setDataInput(xsDataMOSFLMIndexingInput)
edPluginMOSFLMIndexing.execute()
for tupleMOSFLM in self.listPluginMOSFLM:
edPluginMOSFLMIndexing = tupleMOSFLM[0]
xsDataResultControlImageQualityIndicator = tupleMOSFLM[1]
edPluginMOSFLMIndexing.synchronize()
if not edPluginMOSFLMIndexing.isFailure():
xsDataMOSFLMOutput = edPluginMOSFLMIndexing.dataOutput
xsDataIndexingResult = EDHandlerXSDataMOSFLMv10.generateXSDataIndexingResult(xsDataMOSFLMOutput)
selectedSolution = xsDataIndexingResult.selectedSolution
if selectedSolution is not None:
xsDataResultControlImageQualityIndicator.selectedIndexingSolution = selectedSolution
def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
EDVerbose.DEBUG("EDPluginControlGeneratePredictionv10.preProcess...")
xsDataGeneratePredictionInput = self.getDataInput()
xsDataSelectedIndexingSolution = xsDataGeneratePredictionInput.getSelectedIndexingSolution(
)
xsDataExperimentalConditionRefined = xsDataSelectedIndexingSolution.getExperimentalConditionRefined(
)
xsDataCollection = xsDataGeneratePredictionInput.getDataCollection()
xsDataSubWedgeList = xsDataCollection.getSubWedge()
# List containing instances of all the generate prediction plugins
self.__listPluginGeneratePrediction = []
# Loop through all subwedges
iIndex = 0
for xsDataSubWedge in xsDataSubWedgeList:
xsDataImageList = xsDataSubWedge.getImage()
# First find the lowest image number
iLowestImageNumber = None
for xsDataImage in xsDataImageList:
iImageNumber = xsDataImage.getNumber().getValue()
if (iLowestImageNumber is None):
iLowestImageNumber = iImageNumber
elif (iImageNumber < iLowestImageNumber):
iLowestImageNumber = iImageNumber
# Then loop through all images in a sub wedge
for xsDataImage in xsDataImageList:
iIndex += 1
edPluginGeneratePrediction = self.loadPlugin(
self.__strPluginGeneratePredictionName, "%s-%02d" %
(self.__strPluginGeneratePredictionName, iIndex))
xsDataGeneratePredictionInput = XSDataGeneratePredictionInput()
xsDataGeneratePredictionInput.setSelectedIndexingSolution(
XSDataIndexingSolutionSelected.parseString(
xsDataSelectedIndexingSolution.marshal()))
xsDataCollectionNew = XSDataCollection()
xsDataSubWedgeNew = XSDataSubWedge()
xsDataSubWedgeNew.addImage(
XSDataImage.parseString(xsDataImage.marshal()))
xsDataSubWedgeNew.setExperimentalCondition(
XSDataExperimentalCondition.parseString(
xsDataSubWedge.getExperimentalCondition().marshal()))
# We must modify the rotationOscillationStart for the new subwedge
xsDataGoniostatNew = xsDataSubWedgeNew.getExperimentalCondition(
).getGoniostat()
fGoniostatRotationAxisStart = xsDataGoniostatNew.getRotationAxisStart(
).getValue()
fGonioStatOscillationRange = xsDataGoniostatNew.getOscillationWidth(
).getValue()
iImageNumber = xsDataImage.getNumber().getValue()
fGoniostatRotationAxisStartNew = fGoniostatRotationAxisStart + (
iImageNumber -
iLowestImageNumber) * fGonioStatOscillationRange
xsDataGoniostatNew.setRotationAxisStart(
XSDataAngle(fGoniostatRotationAxisStartNew))
#
xsDataCollectionNew.addSubWedge(xsDataSubWedgeNew)
xsDataGeneratePredictionInput.setDataCollection(
xsDataCollectionNew)
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
xsDataMOSFLMInputGeneratePrediction = EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputGeneratePrediction(
xsDataGeneratePredictionInput)
edPluginGeneratePrediction.setDataInput(
xsDataMOSFLMInputGeneratePrediction)
self.__listPluginGeneratePrediction.append(
edPluginGeneratePrediction)
def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
self.DEBUG("EDPluginControlIntegrationv10.preProcess...")
xsDataIntegrationInput = self.getDataInput()
xsDataSelectedIndexingSolution = xsDataIntegrationInput.getSelectedIndexingSolution(
)
self.__xsDataExperimentalConditionRefined = xsDataIntegrationInput.getExperimentalConditionRefined(
)
# To be changed (see bug #40)
if (self.__xsDataExperimentalConditionRefined is None):
self.__xsDataExperimentalConditionRefined = xsDataSelectedIndexingSolution.getExperimentalConditionRefined(
)
xsDataCollection = xsDataIntegrationInput.getDataCollection()
xsDataSubWedgeList = xsDataCollection.getSubWedge()
self.__edPluginIntegrationList = []
iIndex = 0
for xsDataSubWedge in xsDataSubWedgeList:
iSubWedgeNumber = iIndex
if (xsDataSubWedge.getSubWedgeNumber() is not None):
# Use the incoming subwedge number if it exists
iSubWedgeNumber = xsDataSubWedge.getSubWedgeNumber().getValue()
edPluginIntegration = self.loadPlugin(
self.__strPluginIntegrationName)
if (not edPluginIntegration is None):
iIndex += 1
xsDataIntegrationInputSubWedge = XSDataIntegrationInput()
xsDataIntegrationInputSubWedge.setSelectedIndexingSolution(
XSDataIndexingSolutionSelected.parseString(
xsDataSelectedIndexingSolution.marshal()))
xsDataIntegrationInputSubWedge.setExperimentalConditionRefined(
XSDataExperimentalCondition.parseString(
self.__xsDataExperimentalConditionRefined.marshal()))
xsDataCollection = XSDataCollection()
xsDataCollection.addSubWedge(xsDataSubWedge)
xsDataIntegrationInputSubWedge.setDataCollection(
xsDataCollection)
try:
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
xsDataMOSFLMInputIntegration = EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputIntegration(
xsDataIntegrationInputSubWedge)
edPluginIntegration.setDataInput(
xsDataMOSFLMInputIntegration)
edPluginIntegration.setBaseName(
"%s-%02d" % (self.__strPluginIntegrationName, iIndex))
edPluginIntegration.connectSUCCESS(
self.doSuccessActionIntegration)
edPluginIntegration.connectFAILURE(
self.doFailureActionIntegration)
# Here we store the sub wedge number for use in the results
self.__edPluginIntegrationList.append(
[iSubWedgeNumber, edPluginIntegration])
except Exception as strErrorMessage:
self.addErrorMessage(strErrorMessage)
self.ERROR(strErrorMessage)
self.setFailure()
else:
strErrorMessage = "EDPluginControlIntegrationv10.preProcess: could not load plugin %s" % self.__strPluginIntegrationName
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()