class EDPluginControlCharacterisationv1_6(EDPluginControl):
"""
Characterisation based on XDS
"""
def __init__(self):
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputCharacterisation)
self._strPluginControlIndexingIndicators = "EDPluginControlIndexingIndicatorsv1_1"
self._fMinTransmission = 10 # %
self._listPluginGenerateThumbnail = []
self._strCharacterisationShortSummary = ""
self._strStatusMessage = ""
self._strIndexingPluginName = "EDPluginXDSIndexingv1_0"
self._strIntegrationPluginName = "EDPluginXDSIntegrationv1_0"
self._edPluginIndexing = None
def checkParameters(self):
"""
Checks the mandatory parameters.
"""
self.DEBUG("EDPluginControlCharacterisationv1_6.checkParameters")
self.checkMandatoryParameters(self.getDataInput(), "Data Input is None")
self.checkMandatoryParameters(self.getDataInput().getDataCollection(), "dataCollection")
self.checkMandatoryParameters(self.getDataInput().getDataCollection().getDiffractionPlan(), "diffractionPlan")
def configure(self):
"""
Gets the configuration parameters (if any).
"""
EDPluginControl.configure(self)
self.DEBUG("EDPluginControlCharacterisationv1_6.configure")
self._strMxCuBE_URI = self.config.get("mxCuBE_URI", None)
if self._strMxCuBE_URI is not None and "mxCuBE_XMLRPC_log" in os.environ.keys():
self.DEBUG("Enabling sending messages to mxCuBE via URI {0}".format(self._strMxCuBE_URI))
self._oServerProxy = xmlrpclib.ServerProxy(self._strMxCuBE_URI)
self._runKappa = self.config.get("runKappa", False)
self._fMinTransmission = self.config.get("minTransmissionWarning", self._fMinTransmission)
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginControlCharacterisationv1_6.preProcess")
self._xsDataResultCharacterisation = XSDataResultCharacterisation()
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlCharacterisationv1_6.process")
self.doXdsIndexingIntegration(self.dataInput.dataCollection)
def finallyProcess(self, _edObject=None):
EDPluginControl.finallyProcess(self)
self.DEBUG("EDPluginControlCharacterisationv1_6.finallyProcess")
# Synchronize thumbnail plugins
for tuplePlugin in self._listPluginGenerateThumbnail:
image = tuplePlugin[0]
tuplePlugin[1].synchronize()
jpegImage = image.copy()
jpegImage.path = tuplePlugin[1].dataOutput.thumbnail.path
self._xsDataResultCharacterisation.addJpegImage(jpegImage)
tuplePlugin[2].synchronize()
thumbnailImage = image.copy()
thumbnailImage.path = tuplePlugin[2].dataOutput.thumbnail.path
self._xsDataResultCharacterisation.addThumbnailImage(thumbnailImage)
# if self._edPluginControlGeneratePrediction.isRunning():
# self._edPluginControlGeneratePrediction.synchronize()
# if self._strStatusMessage != None:
# self.setDataOutput(XSDataString(self._strStatusMessage), "statusMessage")
# self._xsDataResultCharacterisation.setStatusMessage(XSDataString(self._strStatusMessage))
# if self._strCharacterisationShortSummary != None:
# self.setDataOutput(XSDataString(self._strCharacterisationShortSummary), "shortSummary")
# self._xsDataResultCharacterisation.setShortSummary(XSDataString(self._strCharacterisationShortSummary))
# if self._xsDataResultCharacterisation is not None:
# self.setDataOutput(self._xsDataResultCharacterisation)
if self.isFailure():
self.sendMessageToMXCuBE("Ended with error messages", "error")
def doXdsIndexingIntegration(self, _xsDataCollection):
# Load the plugin
self._edPluginIndexing = self.loadPlugin(self._strIndexingPluginName, "Indexing")
# XDS Indexing
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.setDataCollection(_xsDataCollection)
self._edPluginIndexing.dataInput = EDHandlerXSDataXDSv1_0.generateXSDataInputXDSIndexing(xsDataIndexingInput)
self._edPluginIndexing.executeSynchronous()
xsDataResultXDSIndexing = self._edPluginIndexing.dataOutput
if xsDataResultXDSIndexing.spaceGroupNumber is not None:
spaceGroupNumber = xsDataResultXDSIndexing.spaceGroupNumber.value
unitCell = xsDataResultXDSIndexing.unitCell
filePaths = xsDataResultXDSIndexing.filePaths
index = 1
for subWedge in _xsDataCollection.subWedge:
xsDataCollection = XSDataCollection()
xsDataCollection.addSubWedge(subWedge)
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.setDataCollection(xsDataCollection)
xsDataInputXDSIntegration = EDHandlerXSDataXDSv1_0.generateXSDataInputXDSIntegration(xsDataIndexingInput,
spaceGroupNumber,
unitCell,
filePaths)
edPluginIntegration = self.loadPlugin(self._strIntegrationPluginName, "Integration_{0}".format(index))
edPluginIntegration.dataInput = xsDataInputXDSIntegration
edPluginIntegration.executeSynchronous()
# self._edPluginIntegration.dataInput = xsDataInputXDSIntegration
index += 1
def generateExecutiveSummary(self, _edPlugin):
"""
Generates a summary of the execution of the plugin.
"""
self.DEBUG("EDPluginControlCharacterisationv1_6.generateExecutiveSummary")
self.addExecutiveSummaryLine("Summary of characterisation:")
xsDataInputStrategy = self.getDataInput()
xsDataCollection = xsDataInputStrategy.getDataCollection()
# MXSUP-1445: Check if transmission is less than 10% and warn if it's the case
xsDataFirstSubWedge = xsDataCollection.getSubWedge()[0]
xsDataBeam = xsDataFirstSubWedge.getExperimentalCondition().getBeam()
if xsDataBeam.getTransmission() is not None:
fTransmission = xsDataBeam.getTransmission().getValue()
if fTransmission < self._fMinTransmission:
self.addExecutiveSummaryLine("^"*80)
self.addExecutiveSummaryLine("^"*80)
self.addExecutiveSummaryLine("")
self.addExecutiveSummaryLine("WARNING! Transmission for characterisation set to %.1f %%" % fTransmission)
self.addExecutiveSummaryLine("Please consider re-characterising with transmission set to 100 %")
self.addExecutiveSummaryLine("")
self.addExecutiveSummaryLine("^"*80)
self.addExecutiveSummaryLine("^"*80)
xsDataDiffractionPlan = xsDataCollection.getDiffractionPlan()
self.addExecutiveSummaryLine("Diffraction plan:")
if (xsDataDiffractionPlan.getComplexity() is not None):
self.addExecutiveSummaryLine("BEST complexity : %s" % xsDataDiffractionPlan.getComplexity().getValue())
if (xsDataDiffractionPlan.getAimedCompleteness() is not None):
self.addExecutiveSummaryLine("Aimed completeness : %6.1f [%%]" % (100.0 * xsDataDiffractionPlan.getAimedCompleteness().getValue()))
if (xsDataDiffractionPlan.getRequiredCompleteness() is not None):
self.addExecutiveSummaryLine("Required completeness : %6.1f [%%]" % (100.0 * xsDataDiffractionPlan.getRequiredCompleteness().getValue()))
if (xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution() is not None):
self.addExecutiveSummaryLine("Aimed I/sigma at highest resolution : %6.1f" % xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution().getValue())
if (xsDataDiffractionPlan.getAimedResolution() is not None):
self.addExecutiveSummaryLine("Aimed resolution : %6.1f [A]" % xsDataDiffractionPlan.getAimedResolution().getValue())
if (xsDataDiffractionPlan.getRequiredResolution() is not None):
self.addExecutiveSummaryLine("Required resolution : %6.1f [A]" % xsDataDiffractionPlan.getRequiredResolution().getValue())
if (xsDataDiffractionPlan.getAimedMultiplicity() is not None):
self.addExecutiveSummaryLine("Aimed multiplicity : %6.1f" % xsDataDiffractionPlan.getAimedMultiplicity().getValue())
if (xsDataDiffractionPlan.getRequiredMultiplicity() is not None):
self.addExecutiveSummaryLine("Required multiplicity : %6.1f" % xsDataDiffractionPlan.getRequiredMultiplicity().getValue())
if (xsDataDiffractionPlan.getForcedSpaceGroup() is not None):
self.addExecutiveSummaryLine("Forced space group : %6s" % xsDataDiffractionPlan.getForcedSpaceGroup().getValue())
if (xsDataDiffractionPlan.getMaxExposureTimePerDataCollection() is not None):
self.addExecutiveSummaryLine("Max exposure time per data collection : %6.1f [s]" % xsDataDiffractionPlan.getMaxExposureTimePerDataCollection().getValue())
self.addExecutiveSummarySeparator()
# if self._edPluginControlIndexingIndicators is not None:
# self.appendExecutiveSummary(self._edPluginControlIndexingIndicators, "")
# if self._edPluginControlIntegration is not None:
# self.appendExecutiveSummary(self._edPluginControlIntegration, "")
# if self._edPluginControlStrategy is not None:
# self.appendExecutiveSummary(self._edPluginControlStrategy, "")
self.addExecutiveSummarySeparator()
if self._strCharacterisationShortSummary is not None:
self.addExecutiveSummaryLine("Characterisation short summary:")
self.addExecutiveSummaryLine("")
if self._strStatusMessage != None:
for strLine in self._strStatusMessage.split(". "):
if strLine.endswith("."):
self.addExecutiveSummaryLine(strLine)
else:
self.addExecutiveSummaryLine(strLine + ".")
self.addExecutiveSummaryLine("")
for strLine in self._strCharacterisationShortSummary.split("\n"):
if strLine != "\n":
self.addExecutiveSummaryLine(strLine)
self.addErrorWarningMessagesToExecutiveSummary("Characterisation error and warning messages: ")
self.addExecutiveSummarySeparator()
def getPluginStrategyName(self):
return self._strPluginControlStrategy
def addStatusMessage(self, _strStatusMessage):
if self._strStatusMessage != "":
self._strStatusMessage += " "
self._strStatusMessage += _strStatusMessage
self.sendMessageToMXCuBE(_strStatusMessage)
def doStrategyCalculation(self, _bValue):
self._bDoStrategyCalculation = _bValue
def sendMessageToMXCuBE(self, _strMessage, level="info"):
# Only for mxCuBE
if self._strMxCuBE_URI is not None:
self.DEBUG("Sending message to mxCuBE: {0}".format(_strMessage))
try:
for strMessage in _strMessage.split("\n"):
if strMessage != "":
self._oServerProxy.log_message("Characterisation: " + strMessage, level)
except:
self.DEBUG("Sending message to mxCuBE failed!")
class EDPluginControlCharacterisationv1_4(EDPluginControl):
"""
[To be replaced with a description of EDPluginControlTemplatev10]
"""
def __init__(self):
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputCharacterisation)
self._strPluginControlIndexingIndicators = "EDPluginControlIndexingIndicatorsv1_1"
self._strPluginExecEvaluationIndexing = "EDPluginExecEvaluationIndexingv10"
self._strPluginControlIndexingMOSFLM = "EDPluginControlIndexingMOSFLMv10"
self._strPluginControlGeneratePrediction = "EDPluginControlGeneratePredictionv10"
self._strPluginControlIntegration = "EDPluginControlIntegrationv10"
self._strPluginControlXDSGenerateBackgroundImage = "EDPluginControlXDSGenerateBackgroundImagev1_0"
self._strPluginControlStrategy = "EDPluginControlStrategyv1_2"
self._strPluginGenerateThumbnailName = "EDPluginMXThumbnailv1_1"
self._strPluginControlKappaName = "EDPluginControlKappav1_0"
self._listPluginGenerateThumbnail = []
self._edPluginControlIndexingIndicators = None
self._edPluginExecEvaluationIndexingMOSFLM = None
self._edPluginExecEvaluationIndexingLABELIT = None
self._edPluginControlGeneratePrediction = None
self._edPluginControlIntegration = None
self._edPluginControlXDSGenerateBackgroundImage = None
self._edPluginControlStrategy = None
self._edPluginControlKappa = None
self._xsDataCollection = None
self._xsDataResultCharacterisation = None
self._xsDataIndexingResultMOSFLM = None
self._xsDataCrystal = None
self._strCharacterisationShortSummary = ""
self._strStatusMessage = ""
self._xsDataFileXdsBackgroundImage = None
self._bDoStrategyCalculation = True
self._fMinTransmission = 10 # %
self._iNoReferenceImages = None
self._iNoImagesWithDozorScore = None
self._strMxCuBE_URI = None
self._oServerProxy = None
self._runKappa = False
self._bDoOnlyMoslmfIndexing = False
def checkParameters(self):
"""
Checks the mandatory parameters.
"""
self.DEBUG("EDPluginControlCharacterisationv1_4.checkParameters")
self.checkMandatoryParameters(self.getDataInput(),
"Data Input is None")
self.checkMandatoryParameters(self.getDataInput().getDataCollection(),
"dataCollection")
self.checkMandatoryParameters(
self.getDataInput().getDataCollection().getDiffractionPlan(),
"diffractionPlan")
def configure(self):
"""
Gets the configuration parameters (if any).
"""
EDPluginControl.configure(self)
self.DEBUG("EDPluginControlCharacterisationv1_4.configure")
self._strMxCuBE_URI = self.config.get("mxCuBE_URI", None)
if self._strMxCuBE_URI is not None and "mxCuBE_XMLRPC_log" in os.environ.keys(
):
self.DEBUG(
"Enabling sending messages to mxCuBE via URI {0}".format(
self._strMxCuBE_URI))
self._oServerProxy = ServerProxy(self._strMxCuBE_URI)
self._runKappa = self.config.get("runKappa", False)
self._fMinTransmission = self.config.get("minTransmissionWarning",
self._fMinTransmission)
self._bDoOnlyMoslmfIndexing = self.config.get("doOnlyMosflmIndexing",
False)
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginControlCharacterisationv1_4.preProcess")
self._xsDataResultCharacterisation = XSDataResultCharacterisation()
# Load the plugins
self._edPluginControlIndexingIndicators = self.loadPlugin(self._strPluginControlIndexingIndicators, \
"Indexing")
self._edPluginExecEvaluationIndexingLABELIT = self.loadPlugin(self._strPluginExecEvaluationIndexing, \
"IndexingEvalualtionLABELIT")
self._edPluginControlIndexingMOSFLM = self.loadPlugin(self._strPluginControlIndexingMOSFLM, \
"IndexingMOSFLM")
self._edPluginExecEvaluationIndexingMOSFLM = self.loadPlugin(self._strPluginExecEvaluationIndexing, \
"IndexingEvalualtionMOSFLM")
self._edPluginControlGeneratePrediction = self.loadPlugin(self._strPluginControlGeneratePrediction, \
"GeneratePrediction")
self._edPluginControlIntegration = self.loadPlugin(self._strPluginControlIntegration, \
"Integration")
self._edPluginControlXDSGenerateBackgroundImage = self.loadPlugin(self._strPluginControlXDSGenerateBackgroundImage, \
"ControlXDSGenerateBackgroundImage")
self._edPluginControlStrategy = self.loadPlugin(self._strPluginControlStrategy, \
"Strategy")
if self._runKappa:
self._edPluginControlKappa = self.loadPlugin(
self._strPluginControlKappaName, "Kappa")
if (self._edPluginControlIndexingIndicators is not None):
self.DEBUG("EDPluginControlCharacterisationv1_4.preProcess: " +
self._strPluginControlIndexingIndicators +
" Found... setting Data Input")
# create Data Input for indexing
xsDataInputCharacterisation = self.getDataInput()
self._xsDataCollection = xsDataInputCharacterisation.getDataCollection(
)
# MXSUP-1445: Check if transmission is less than 10% and warn if it's the case
xsDataFirstSubWedge = self._xsDataCollection.getSubWedge()[0]
xsDataBeam = xsDataFirstSubWedge.getExperimentalCondition(
).getBeam()
if xsDataBeam.getTransmission() is not None:
fTransmission = xsDataBeam.getTransmission().getValue()
if fTransmission < self._fMinTransmission:
strWarningMessageBanner = "^" * 80
strWarningMessage1 = "WARNING! Transmission for characterisation set to %.1f %%" % fTransmission
strWarningMessage2 = "Please consider re-characterising with transmission set to 100 %"
self.warning(strWarningMessageBanner)
self.warning(strWarningMessage1)
self.warning(strWarningMessage2)
self.warning(strWarningMessageBanner)
self.addWarningMessage(strWarningMessageBanner)
self.addWarningMessage(strWarningMessage1)
self.addWarningMessage(strWarningMessage2)
self.addWarningMessage(strWarningMessageBanner)
self.sendMessageToMXCuBE(strWarningMessage1, "warning")
self.sendMessageToMXCuBE(strWarningMessage2, "warning")
xsDataCrystal = None
xsDataSubWedgeList = self._xsDataCollection.getSubWedge()
if ((xsDataSubWedgeList is None) or (xsDataSubWedgeList == [])):
strError = "EDPluginControlCharacterisationv1_4.preProcess: No subwedges in input data."
self.ERROR(strError)
self.setFailure()
else:
# Load the thumbnail plugins
self._iNoReferenceImages = 0
for subWedge in xsDataInputCharacterisation.dataCollection.subWedge:
for image in subWedge.image:
self._iNoReferenceImages += 1
edPluginJpeg = self.loadPlugin(
self._strPluginGenerateThumbnailName)
xsDataInputMXThumbnail = XSDataInputMXThumbnail()
xsDataInputMXThumbnail.image = XSDataFile(image.path)
xsDataInputMXThumbnail.height = XSDataInteger(1024)
xsDataInputMXThumbnail.width = XSDataInteger(1024)
jpegFilename = os.path.splitext(
os.path.basename(image.path.value))[0] + ".jpg"
xsDataInputMXThumbnail.outputPath = XSDataFile(
XSDataString(
os.path.join(self.getWorkingDirectory(),
jpegFilename)))
edPluginJpeg.dataInput = xsDataInputMXThumbnail
edPluginThumnail = self.loadPlugin(
self._strPluginGenerateThumbnailName)
xsDataInputMXThumbnail = XSDataInputMXThumbnail()
xsDataInputMXThumbnail.image = XSDataFile(image.path)
xsDataInputMXThumbnail.height = XSDataInteger(256)
xsDataInputMXThumbnail.width = XSDataInteger(256)
thumbnailFilename = os.path.splitext(
os.path.basename(
image.path.value))[0] + ".thumbnail.jpg"
xsDataInputMXThumbnail.outputPath = XSDataFile(
XSDataString(
os.path.join(self.getWorkingDirectory(),
thumbnailFilename)))
edPluginThumnail.dataInput = xsDataInputMXThumbnail
self._listPluginGenerateThumbnail.append(
(image, edPluginJpeg, edPluginThumnail))
edPluginJpeg.execute()
edPluginThumnail.execute()
xsDataExperimentalCondition = xsDataSubWedgeList[
0].getExperimentalCondition()
# Fix for bug 431: if the flux is zero raise an error
xsDataDoubleFlux = xsDataExperimentalCondition.getBeam(
).getFlux()
if (xsDataDoubleFlux is not None):
if (xsDataDoubleFlux.getValue() < 0.1):
strErrorMessage = "Input flux is negative or close to zero. Execution of characterisation aborted."
self.ERROR(strErrorMessage)
self.sendMessageToMXCuBE(strErrorMessage, "error")
self.addErrorMessage(
"EDPluginControlCharacterisationv1_4.preProcess ERROR: "
+ strErrorMessage)
# self.addComment(strErrorMessage)
self.setFailure()
xsDataDiffractionPlan = self._xsDataCollection.getDiffractionPlan(
)
xsDataStringForcedSpaceGroup = xsDataDiffractionPlan.getForcedSpaceGroup(
)
if (xsDataStringForcedSpaceGroup is not None):
self._xsDataCrystal = XSDataCrystal()
xsDataSpaceGroup = XSDataSpaceGroup()
xsDataSpaceGroup.setName(xsDataStringForcedSpaceGroup)
self._xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
self._edPluginControlIndexingIndicators.setDataInput(
self._xsDataCollection, "dataCollection")
if self._xsDataCrystal is not None:
self._edPluginControlIndexingIndicators.setDataInput(
self._xsDataCrystal, "crystal")
# Populate characterisation object
self._xsDataResultCharacterisation.setDataCollection(
XSDataCollection.parseString(
self._xsDataCollection.marshal()))
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlCharacterisationv1_4.process")
self._edPluginControlIndexingIndicators.connectSUCCESS(
self.doSuccessIndexingIndicators)
self._edPluginControlIndexingIndicators.connectFAILURE(
self.doFailureIndexingIndicators)
self._edPluginExecEvaluationIndexingLABELIT.connectSUCCESS(
self.doSuccessEvaluationIndexingLABELIT)
self._edPluginExecEvaluationIndexingLABELIT.connectFAILURE(
self.doFailureEvaluationIndexingLABELIT)
self._edPluginControlIndexingMOSFLM.connectSUCCESS(
self.doSuccessIndexingMOSFLM)
self._edPluginControlIndexingMOSFLM.connectFAILURE(
self.doFailureIndexingMOSFLM)
self._edPluginExecEvaluationIndexingMOSFLM.connectSUCCESS(
self.doSuccessEvaluationIndexingMOSFLM)
self._edPluginExecEvaluationIndexingMOSFLM.connectFAILURE(
self.doFailureEvaluationIndexingMOSFLM)
self._edPluginControlGeneratePrediction.connectSUCCESS(
self.doSuccessGeneratePrediction)
self._edPluginControlGeneratePrediction.connectFAILURE(
self.doFailureGeneratePrediction)
self._edPluginControlIntegration.connectSUCCESS(
self.doSuccessIntegration)
self._edPluginControlIntegration.connectFAILURE(
self.doFailureIntegration)
self._edPluginControlXDSGenerateBackgroundImage.connectSUCCESS(
self.doSuccessXDSGenerateBackgroundImage)
self._edPluginControlXDSGenerateBackgroundImage.connectFAILURE(
self.doFailureXDSGenerateBackgroundImage)
self._edPluginControlStrategy.connectSUCCESS(self.doSuccessStrategy)
self._edPluginControlStrategy.connectFAILURE(self.doFailureStrategy)
self.executePluginSynchronous(self._edPluginControlIndexingIndicators)
def finallyProcess(self, _edObject=None):
EDPluginControl.finallyProcess(self)
self.DEBUG("EDPluginControlCharacterisationv1_4.finallyProcess")
# Synchronize thumbnail plugins
for tuplePlugin in self._listPluginGenerateThumbnail:
image = tuplePlugin[0]
tuplePlugin[1].synchronize()
jpegImage = image.copy()
jpegImage.path = tuplePlugin[1].dataOutput.thumbnail.path
self._xsDataResultCharacterisation.addJpegImage(jpegImage)
tuplePlugin[2].synchronize()
thumbnailImage = image.copy()
thumbnailImage.path = tuplePlugin[2].dataOutput.thumbnail.path
self._xsDataResultCharacterisation.addThumbnailImage(
thumbnailImage)
if self._edPluginControlGeneratePrediction.isRunning():
self._edPluginControlGeneratePrediction.synchronize()
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage),
"statusMessage")
self._xsDataResultCharacterisation.setStatusMessage(
XSDataString(self._strStatusMessage))
if self._strCharacterisationShortSummary != None:
self.setDataOutput(
XSDataString(self._strCharacterisationShortSummary),
"shortSummary")
self._xsDataResultCharacterisation.setShortSummary(
XSDataString(self._strCharacterisationShortSummary))
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
if self.isFailure():
self.sendMessageToMXCuBE("Ended with error messages", "error")
def doSuccessIndexingIndicators(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlCharacterisationv1_4.doSuccessIndexingIndicators")
# self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv1_4.doSuccessIndexingIndicators")
if self._edPluginControlIndexingIndicators.hasDataOutput(
"indexingResult"):
xsDataIndexingResult = self._edPluginControlIndexingIndicators.getDataOutput(
"indexingResult")[0]
# self._xsDataResultCharacterisation.setIndexingResult(xsDataIndexingResult)
self._edPluginExecEvaluationIndexingLABELIT.setDataInput(
xsDataIndexingResult, "indexingResult")
if self._edPluginControlIndexingIndicators.hasDataOutput(
"imageQualityIndicators"):
listXSDataImageQualityIndicators = self._edPluginControlIndexingIndicators.getDataOutput(
"imageQualityIndicators")
for xsDataImageQualityIndicators in listXSDataImageQualityIndicators:
if xsDataImageQualityIndicators.dozor_score:
if self._iNoImagesWithDozorScore is None:
self._iNoImagesWithDozorScore = 0
if xsDataImageQualityIndicators.dozor_score.value > 0.001:
self._iNoImagesWithDozorScore += 1
self._xsDataResultCharacterisation.addImageQualityIndicators(
xsDataImageQualityIndicators)
self._edPluginExecEvaluationIndexingLABELIT.setDataInput(
xsDataImageQualityIndicators, "imageQualityIndicators")
if self._edPluginControlIndexingIndicators.hasDataOutput(
"indicatorsShortSummary"):
indicatorsShortSummary = self._edPluginControlIndexingIndicators.getDataOutput(
"indicatorsShortSummary")[0].getValue()
self._strCharacterisationShortSummary += indicatorsShortSummary
self.sendMessageToMXCuBE(indicatorsShortSummary)
self.executePluginSynchronous(
self._edPluginExecEvaluationIndexingLABELIT)
def doFailureIndexingIndicators(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlCharacterisationv1_4.doFailureIndexingIndicators")
# If more than two reference images try to index with MOSFLM:
if self._edPluginControlIndexingIndicators.hasDataOutput(
"indicatorsShortSummary"):
indicatorsShortSummary = self._edPluginControlIndexingIndicators.getDataOutput(
"indicatorsShortSummary")[0].getValue()
self._strCharacterisationShortSummary += indicatorsShortSummary
self.sendMessageToMXCuBE(indicatorsShortSummary)
if self._iNoImagesWithDozorScore > 0:
if not self._bDoOnlyMoslmfIndexing:
strWarningMessage = "Execution of Indexing and Indicators plugin failed - trying to index with MOSFLM."
self.WARNING(strWarningMessage)
self.sendMessageToMXCuBE(strWarningMessage, "warning")
self.addWarningMessage(strWarningMessage)
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.dataCollection = self._xsDataCollection
xsDataIndexingInput.experimentalCondition = self._xsDataCollection.subWedge[
0].experimentalCondition
xsDataIndexingInput.crystal = self._xsDataCrystal
self._edPluginControlIndexingMOSFLM.dataInput = xsDataIndexingInput
self.executePluginSynchronous(self._edPluginControlIndexingMOSFLM)
else:
strErrorMessage = "Execution of Indexing and Indicators plugin failed. Execution of characterisation aborted."
self.ERROR(strErrorMessage)
self.sendMessageToMXCuBE(strErrorMessage, "error")
self.addErrorMessage(strErrorMessage)
self.generateExecutiveSummary(self)
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
self.setFailure()
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage),
"statusMessage")
self.writeDataOutput()
def doSuccessIndexingMOSFLM(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlCharacterisationv1_4.doSuccessIndexingMOSFLM")
xsDataIndexingResult = self._edPluginControlIndexingMOSFLM.dataOutput
self._edPluginExecEvaluationIndexingMOSFLM.setDataInput(
xsDataIndexingResult, "indexingResult")
self.executePluginSynchronous(
self._edPluginExecEvaluationIndexingMOSFLM)
def doFailureIndexingMOSFLM(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlCharacterisationv1_4.doFailureIndexingMOSFLM")
strErrorMessage = "Indexing with MOSFLM failed."
self.ERROR(strErrorMessage)
self.sendMessageToMXCuBE(strErrorMessage, "error")
self.executePluginSynchronous(
self._edPluginExecEvaluationIndexingMOSFLM)
def doSuccessEvaluationIndexingLABELIT(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlCharacterisationv1_4.doSuccessEvaluationIndexingLABELIT"
)
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlCharacterisationv1_4.doSuccessEvaluationIndexingLABELIT"
)
# Retrieve status messages (if any)
if self._edPluginExecEvaluationIndexingLABELIT.hasDataOutput(
"statusMessageIndexing"):
self.addStatusMessage(
"Labelit: " +
self._edPluginExecEvaluationIndexingLABELIT.getDataOutput(
"statusMessageIndexing")[0].getValue())
# Check if indexing was successful
bIndexingSuccess = self._edPluginExecEvaluationIndexingLABELIT.getDataOutput(
"indexingSuccess")[0].getValue()
if bIndexingSuccess:
xsDataIndexingResult = self._edPluginExecEvaluationIndexingLABELIT.getDataOutput(
"indexingResult")[0]
self._xsDataResultCharacterisation.setIndexingResult(
xsDataIndexingResult)
xsDataCollection = self._xsDataResultCharacterisation.getDataCollection(
)
xsDataGeneratePredictionInput = XSDataGeneratePredictionInput()
xsDataGeneratePredictionInput.setDataCollection(
XSDataCollection.parseString(xsDataCollection.marshal()))
xsDataGeneratePredictionInput.setSelectedIndexingSolution(
XSDataIndexingSolutionSelected.parseString(
xsDataIndexingResult.getSelectedSolution().marshal()))
self._edPluginControlGeneratePrediction.setDataInput(
xsDataGeneratePredictionInput)
if self._edPluginControlIndexingIndicators.hasDataOutput(
"indexingShortSummary"):
indexingShortSummary = self._edPluginControlIndexingIndicators.getDataOutput(
"indexingShortSummary")[0].getValue()
self._strCharacterisationShortSummary += indexingShortSummary
self.sendMessageToMXCuBE(indexingShortSummary)
# Start the generation of prediction images - we synchronize in the post-process
self._edPluginControlGeneratePrediction.execute()
# Then start the integration of the reference images
self.indexingToIntegration()
else:
if self._iNoImagesWithDozorScore > 0:
if not self._bDoOnlyMoslmfIndexing:
strWarningMessage = "Execution of Indexing and Indicators plugin failed - trying to index with MOSFLM."
self.WARNING(strWarningMessage)
self.sendMessageToMXCuBE(strWarningMessage, "warning")
self.addWarningMessage(strWarningMessage)
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.dataCollection = self._xsDataCollection
xsDataIndexingInput.experimentalCondition = self._xsDataCollection.subWedge[
0].experimentalCondition
xsDataIndexingInput.crystal = self._xsDataCrystal
self._edPluginControlIndexingMOSFLM.setDataInput(
xsDataIndexingInput)
self.executePluginSynchronous(
self._edPluginControlIndexingMOSFLM)
else:
strErrorMessage = "Execution of indexing with Labelit failed."
self.ERROR(strErrorMessage)
self.sendMessageToMXCuBE(strErrorMessage, "error")
self.addErrorMessage(strErrorMessage)
self.setFailure()
self.generateExecutiveSummary(self)
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage),
"statusMessage")
self.writeDataOutput()
def doSuccessEvaluationIndexingMOSFLM(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlCharacterisationv1_4.doSuccessEvaluationIndexingMOSFLM"
)
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlCharacterisationv1_4.doSuccessEvaluationIndexingMOSFLM"
)
# Retrieve status messages (if any)
if self._edPluginExecEvaluationIndexingMOSFLM.hasDataOutput(
"statusMessageIndexing"):
self.addStatusMessage(
"MOSFLM: " +
self._edPluginExecEvaluationIndexingMOSFLM.getDataOutput(
"statusMessageIndexing")[0].getValue())
# Check if indexing was successful
bIndexingSuccess = self._edPluginExecEvaluationIndexingMOSFLM.getDataOutput(
"indexingSuccess")[0].getValue()
if bIndexingSuccess:
xsDataIndexingResult = self._edPluginExecEvaluationIndexingMOSFLM.getDataOutput(
"indexingResult")[0]
self._xsDataResultCharacterisation.setIndexingResult(
xsDataIndexingResult)
self._strCharacterisationShortSummary += self.generateIndexingShortSummary(
xsDataIndexingResult)
xsDataCollection = self._xsDataResultCharacterisation.getDataCollection(
)
xsDataGeneratePredictionInput = XSDataGeneratePredictionInput()
xsDataGeneratePredictionInput.setDataCollection(
XSDataCollection.parseString(xsDataCollection.marshal()))
xsDataGeneratePredictionInput.setSelectedIndexingSolution(
XSDataIndexingSolutionSelected.parseString(
xsDataIndexingResult.getSelectedSolution().marshal()))
self._edPluginControlGeneratePrediction.setDataInput(
xsDataGeneratePredictionInput)
if self._edPluginControlIndexingIndicators.hasDataOutput(
"indexingShortSummary"):
self._strCharacterisationShortSummary += self._edPluginControlIndexingIndicators.getDataOutput(
"indexingShortSummary")[0].getValue()
# Start the generation of prediction images - we synchronize in the post-process
self._edPluginControlGeneratePrediction.execute()
# Then start the integration of the reference images
self.indexingToIntegration()
else:
strErrorMessage = "Execution of indexing with MOSFLM failed."
self.ERROR(strErrorMessage)
self.sendMessageToMXCuBE(strErrorMessage, "error")
self.addErrorMessage(strErrorMessage)
self.setFailure()
self.generateExecutiveSummary(self)
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage),
"statusMessage")
self.writeDataOutput()
def generateIndexingShortSummary(self, _xsDataIndexingResult):
"""
Generates a very short summary of the indexing
"""
strIndexingShortSummary = ""
if self.hasDataInput("crystal"):
xsDataCrystal = self.getDataInput("crystal")[0]
if xsDataCrystal.getSpaceGroup() is not None:
strForcedSpaceGroup = xsDataCrystal.getSpaceGroup().getName(
).getValue().upper()
if xsDataCrystal.getSpaceGroup().getName().getValue() != "":
strIndexingShortSummary += "Forced space group: %s\n" % strForcedSpaceGroup
if _xsDataIndexingResult is not None:
# Indexing solution
xsDataSelectedSolution = _xsDataIndexingResult.getSelectedSolution(
)
xsDataCrystal = xsDataSelectedSolution.getCrystal()
# Refined cell parameters
xsDataCell = xsDataCrystal.getCell()
fA = xsDataCell.getLength_a().getValue()
fB = xsDataCell.getLength_b().getValue()
fC = xsDataCell.getLength_c().getValue()
fAlpha = xsDataCell.getAngle_alpha().getValue()
fBeta = xsDataCell.getAngle_beta().getValue()
fGamma = xsDataCell.getAngle_gamma().getValue()
# Estimated mosaicity
fEstimatedMosaicity = xsDataCrystal.getMosaicity().getValue()
# Space group
strSpaceGroup = xsDataCrystal.getSpaceGroup().getName().getValue()
# Spot deviation
xsDataStatisticsIndexing = xsDataSelectedSolution.getStatistics()
fSpotDeviationPositional = xsDataStatisticsIndexing.getSpotDeviationPositional(
).getValue()
strIndexingShortSummary += "Indexing: laue/space group %s, mosaicity %.2f [degree], " % (
strSpaceGroup, fEstimatedMosaicity)
strIndexingShortSummary += "RMS dev pos %.2f [mm]" % fSpotDeviationPositional
if xsDataStatisticsIndexing.getSpotDeviationAngular() is not None:
fSpotDeviationAngular = xsDataStatisticsIndexing.getSpotDeviationAngular(
).getValue()
strIndexingShortSummary += " ang %.2f [degree]" % fSpotDeviationAngular
strIndexingShortSummary += "\n"
strIndexingShortSummary += "Indexing: refined Cell: %7.2f %7.2f %7.2f %7.2f %7.2f %7.2f\n" % (
fA, fB, fC, fAlpha, fBeta, fGamma)
else:
strIndexingShortSummary += "Indexing failed."
return strIndexingShortSummary
def indexingToIntegration(self, _edPlugin=None):
# Run Kappa if configured
if self._runKappa:
xsDataInputControlKappa = XSDataInputControlKappa()
xsDataInputControlKappa.dataCollection = self._xsDataCollection
xsDataInputControlKappa.selectedSolution = self._xsDataResultCharacterisation.indexingResult.selectedSolution
self._edPluginControlKappa.dataInput = xsDataInputControlKappa
self.executePluginSynchronous(self._edPluginControlKappa)
if not self._edPluginControlKappa.isFailure():
self._xsDataResultCharacterisation.kappaReorientation = self._edPluginControlKappa.dataOutput
# Create the XDS background image
xsDataInputControlXDSGenerateBackgroundImage = XSDataInputControlXDSGenerateBackgroundImage(
)
xsDataInputControlXDSGenerateBackgroundImage.setDataCollection(
self._xsDataCollection)
self._edPluginControlXDSGenerateBackgroundImage.setDataInput(
xsDataInputControlXDSGenerateBackgroundImage)
self._edPluginControlXDSGenerateBackgroundImage.execute()
# Integrate the reference images
xsDataIntegrationInput = XSDataIntegrationInput()
xsDataIntegrationInput.setDataCollection(
self._xsDataResultCharacterisation.getDataCollection())
xsDataIndexingResult = self._xsDataResultCharacterisation.getIndexingResult(
)
xsDataExperimentalConditionRefinded = xsDataIndexingResult.getSelectedSolution(
).getExperimentalConditionRefined()
xsDataIntegrationInput.setExperimentalConditionRefined(
xsDataExperimentalConditionRefinded)
xsDataIntegrationInput.setSelectedIndexingSolution(
xsDataIndexingResult.getSelectedSolution())
self._edPluginControlIntegration.setDataInput(xsDataIntegrationInput)
self.executePluginSynchronous(self._edPluginControlIntegration)
def doFailureEvaluationIndexingLABELIT(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlCharacterisationv1_4.doFailureEvaluationIndexing")
strErrorMessage = "Execution of indexing evaluation plugin failed."
self.ERROR(strErrorMessage)
self.sendMessageToMXCuBE(strErrorMessage, "error")
self.addErrorMessage(strErrorMessage)
self.generateExecutiveSummary(self)
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
self.setFailure()
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage),
"statusMessage")
self.writeDataOutput()
def doFailureEvaluationIndexingMOSFLM(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlCharacterisationv1_4.doFailureEvaluationIndexingMOSFLM"
)
strErrorMessage = "Execution of indexing evaluation plugin failed."
self.ERROR(strErrorMessage)
self.sendMessageToMXCuBE(strErrorMessage, "error")
self.addErrorMessage(strErrorMessage)
self.generateExecutiveSummary(self)
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
self.setFailure()
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage),
"statusMessage")
self.writeDataOutput()
def doSuccessGeneratePrediction(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlCharacterisationv1_4.doSuccessGeneratePrediction")
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlCharacterisationv1_4.doSuccessGeneratePrediction")
xsDataGeneratePredictionResult = _edPlugin.getDataOutput()
xsDataIndexingResult = self._xsDataResultCharacterisation.getIndexingResult(
)
xsDataIndexingResult.setPredictionResult(
xsDataGeneratePredictionResult)
def doFailureGeneratePrediction(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlCharacterisationv1_4.doFailureGeneratePrediction")
strWarningMessage = "Execution of generate prediction plugin failed."
self.WARNING(strWarningMessage)
self.addWarningMessage(strWarningMessage)
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
# self.addComment("warning: no prediction images")
def doSuccessIntegration(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_4.doSuccessIntegration")
self.retrieveSuccessMessages(
self._edPluginControlIntegration,
"EDPluginControlCharacterisationv1_4.doSuccessIntegration")
# Wait for XDS plugin if necessary
self._edPluginControlXDSGenerateBackgroundImage.synchronize()
self.addStatusMessage("Integration successful.")
xsDataIntegrationOutput = self._edPluginControlIntegration.getDataOutput(
)
self._xsDataResultCharacterisation.setIntegrationResult(
xsDataIntegrationOutput)
# Integration short summary
if self._edPluginControlIntegration.hasDataOutput(
"integrationShortSummary"):
integrationShortSummary = self._edPluginControlIntegration.getDataOutput(
"integrationShortSummary")[0].getValue()
self._strCharacterisationShortSummary += integrationShortSummary
self.sendMessageToMXCuBE(integrationShortSummary)
# self.DEBUG( self._xsDataExperimentCharacterisation.marshal() )
if self._bDoStrategyCalculation:
xsDataInputStrategy = XSDataInputStrategy()
xsDataSolutionSelected = self._xsDataResultCharacterisation.getIndexingResult(
).getSelectedSolution()
xsDataInputStrategy.setCrystalRefined(
xsDataSolutionSelected.getCrystal())
xsDataInputStrategy.setSample(self._xsDataResultCharacterisation.
getDataCollection().getSample())
xsDataIntegrationSubWedgeResultList = xsDataIntegrationOutput.getIntegrationSubWedgeResult(
)
bFirst = True
for xsDataIntegrationSubWedgeResult in xsDataIntegrationSubWedgeResultList:
if xsDataIntegrationSubWedgeResult.getBestfileHKL(
) is not None:
xsDataInputStrategy.addBestFileContentHKL(
xsDataIntegrationSubWedgeResult.getBestfileHKL())
if bFirst:
xsDataInputStrategy.setBestFileContentDat(
xsDataIntegrationSubWedgeResult.getBestfileDat())
xsDataInputStrategy.setBestFileContentPar(
xsDataIntegrationSubWedgeResult.getBestfilePar())
xsDataInputStrategy.setExperimentalCondition(
xsDataIntegrationSubWedgeResult.
getExperimentalConditionRefined())
bFirst = False
xsDataInputStrategy.setXdsBackgroundImage(
self._xsDataFileXdsBackgroundImage)
xsDataInputStrategy.setDataCollection(self._xsDataCollection)
xsDataInputStrategy.setDiffractionPlan(
self._xsDataResultCharacterisation.getDataCollection(
).getDiffractionPlan())
self._edPluginControlStrategy.setDataInput(xsDataInputStrategy)
self.executePluginSynchronous(self._edPluginControlStrategy)
def doFailureIntegration(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_4.doFailureIntegration")
strErrorMessage = "Execution of integration failed."
self.addStatusMessage("Integration FAILURE.")
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
# self.addComment("integration failure")
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
self.generateExecutiveSummary(self)
self.setFailure()
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage),
"statusMessage")
self.writeDataOutput()
def doSuccessXDSGenerateBackgroundImage(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlCharacterisationv1_4.doSuccessXDSGenerateBackgroundImage"
)
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlCharacterisationv1_4.doSuccessXDSGenerateBackgroundImage"
)
self._xsDataFileXdsBackgroundImage = self._edPluginControlXDSGenerateBackgroundImage.getDataOutput(
).getXdsBackgroundImage()
self._xsDataResultCharacterisation.setXdsBackgroundImage(
self._xsDataFileXdsBackgroundImage)
def doFailureXDSGenerateBackgroundImage(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlCharacterisationv1_4.doFailureXDSGenerateBackgroundImage"
)
def doSuccessStrategy(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_4.doSuccessStrategy")
self.retrieveSuccessMessages(
self._edPluginControlStrategy,
"EDPluginControlCharacterisationv1_4.doSuccessStrategy")
xsDataStrategyResult = self._edPluginControlStrategy.getDataOutput()
self._xsDataResultCharacterisation.setStrategyResult(
xsDataStrategyResult)
if self._edPluginControlStrategy.hasDataOutput("strategyShortSummary"):
strategyShortSummary = self._edPluginControlStrategy.getDataOutput(
"strategyShortSummary")[0].getValue()
self._strCharacterisationShortSummary += strategyShortSummary
self.sendMessageToMXCuBE(strategyShortSummary)
self.addStatusMessage("Strategy calculation successful.")
def doFailureStrategy(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_4.doFailureStrategy")
strErrorMessage = "Strategy calculation FAILURE."
self.ERROR(strErrorMessage)
self.sendMessageToMXCuBE(strErrorMessage, "error")
self.addErrorMessage(strErrorMessage)
xsDataStrategyResult = self._edPluginControlStrategy.getDataOutput()
self._xsDataResultCharacterisation.setStrategyResult(
xsDataStrategyResult)
if self._edPluginControlStrategy.hasDataOutput("strategyShortSummary"):
strategyShortSummary = self._edPluginControlStrategy.getDataOutput(
"strategyShortSummary")[0].getValue()
self._strCharacterisationShortSummary += strategyShortSummary
self.sendMessageToMXCuBE(strategyShortSummary)
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
self.addStatusMessage("Strategy calculation FAILURE.")
self.generateExecutiveSummary(self)
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage),
"statusMessage")
self.writeDataOutput()
self.setFailure()
def generateExecutiveSummary(self, _edPlugin):
"""
Generates a summary of the execution of the plugin.
"""
self.DEBUG(
"EDPluginControlCharacterisationv1_4.generateExecutiveSummary")
self.addExecutiveSummaryLine("Summary of characterisation:")
xsDataInputStrategy = self.getDataInput()
xsDataCollection = xsDataInputStrategy.getDataCollection()
# MXSUP-1445: Check if transmission is less than 10% and warn if it's the case
xsDataFirstSubWedge = xsDataCollection.getSubWedge()[0]
xsDataBeam = xsDataFirstSubWedge.getExperimentalCondition().getBeam()
if xsDataBeam.getTransmission() is not None:
fTransmission = xsDataBeam.getTransmission().getValue()
if fTransmission < self._fMinTransmission:
self.addExecutiveSummaryLine("^" * 80)
self.addExecutiveSummaryLine("^" * 80)
self.addExecutiveSummaryLine("")
self.addExecutiveSummaryLine(
"WARNING! Transmission for characterisation set to %.1f %%"
% fTransmission)
self.addExecutiveSummaryLine(
"Please consider re-characterising with transmission set to 100 %"
)
self.addExecutiveSummaryLine("")
self.addExecutiveSummaryLine("^" * 80)
self.addExecutiveSummaryLine("^" * 80)
xsDataDiffractionPlan = xsDataCollection.getDiffractionPlan()
self.addExecutiveSummaryLine("Diffraction plan:")
if (xsDataDiffractionPlan.getComplexity() is not None):
self.addExecutiveSummaryLine(
"BEST complexity : %s" %
xsDataDiffractionPlan.getComplexity().getValue())
if (xsDataDiffractionPlan.getAimedCompleteness() is not None):
self.addExecutiveSummaryLine(
"Aimed completeness : %6.1f [%%]" %
(100.0 *
xsDataDiffractionPlan.getAimedCompleteness().getValue()))
if (xsDataDiffractionPlan.getRequiredCompleteness() is not None):
self.addExecutiveSummaryLine(
"Required completeness : %6.1f [%%]" %
(100.0 *
xsDataDiffractionPlan.getRequiredCompleteness().getValue()))
if (xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution()
is not None):
self.addExecutiveSummaryLine(
"Aimed I/sigma at highest resolution : %6.1f" %
xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution(
).getValue())
if (xsDataDiffractionPlan.getAimedResolution() is not None):
self.addExecutiveSummaryLine(
"Aimed resolution : %6.1f [A]" %
xsDataDiffractionPlan.getAimedResolution().getValue())
if (xsDataDiffractionPlan.getRequiredResolution() is not None):
self.addExecutiveSummaryLine(
"Required resolution : %6.1f [A]" %
xsDataDiffractionPlan.getRequiredResolution().getValue())
if (xsDataDiffractionPlan.getAimedMultiplicity() is not None):
self.addExecutiveSummaryLine(
"Aimed multiplicity : %6.1f" %
xsDataDiffractionPlan.getAimedMultiplicity().getValue())
if (xsDataDiffractionPlan.getRequiredMultiplicity() is not None):
self.addExecutiveSummaryLine(
"Required multiplicity : %6.1f" %
xsDataDiffractionPlan.getRequiredMultiplicity().getValue())
if (xsDataDiffractionPlan.getForcedSpaceGroup() is not None):
self.addExecutiveSummaryLine(
"Forced space group : %6s" %
xsDataDiffractionPlan.getForcedSpaceGroup().getValue())
if (xsDataDiffractionPlan.getMaxExposureTimePerDataCollection()
is not None):
self.addExecutiveSummaryLine(
"Max exposure time per data collection : %6.1f [s]" %
xsDataDiffractionPlan.getMaxExposureTimePerDataCollection(
).getValue())
self.addExecutiveSummarySeparator()
if self._edPluginControlIndexingIndicators is not None:
self.appendExecutiveSummary(
self._edPluginControlIndexingIndicators, "")
if self._edPluginControlIntegration is not None:
self.appendExecutiveSummary(self._edPluginControlIntegration, "")
if self._edPluginControlStrategy is not None:
self.appendExecutiveSummary(self._edPluginControlStrategy, "")
self.addExecutiveSummarySeparator()
if self._strCharacterisationShortSummary is not None:
self.addExecutiveSummaryLine("Characterisation short summary:")
self.addExecutiveSummaryLine("")
if self._strStatusMessage != None:
for strLine in self._strStatusMessage.split(". "):
if strLine.endswith("."):
self.addExecutiveSummaryLine(strLine)
else:
self.addExecutiveSummaryLine(strLine + ".")
self.addExecutiveSummaryLine("")
for strLine in self._strCharacterisationShortSummary.split("\n"):
if strLine != "\n":
self.addExecutiveSummaryLine(strLine)
self.addErrorWarningMessagesToExecutiveSummary(
"Characterisation error and warning messages: ")
self.addExecutiveSummarySeparator()
def getPluginStrategyName(self):
return self._strPluginControlStrategy
def addStatusMessage(self, _strStatusMessage):
if self._strStatusMessage != "":
self._strStatusMessage += " "
self._strStatusMessage += _strStatusMessage
self.sendMessageToMXCuBE(_strStatusMessage)
def doStrategyCalculation(self, _bValue):
self._bDoStrategyCalculation = _bValue
def sendMessageToMXCuBE(self, _strMessage, level="info"):
# Only for mxCuBE
if self._strMxCuBE_URI is not None:
self.DEBUG("Sending message to mxCuBE: {0}".format(_strMessage))
try:
for strMessage in _strMessage.split("\n"):
if strMessage != "":
self._oServerProxy.log_message(
"Characterisation: " + strMessage, level)
except:
self.DEBUG("Sending message to mxCuBE failed!")
class EDPluginControlCharacterisationv1_5(EDPluginControl):
"""
[To be replaced with a description of EDPluginControlTemplatev10]
"""
def __init__(self):
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputCharacterisation)
self._strPluginControlIndexingIndicators = "EDPluginControlIndexingIndicatorsv1_1"
self._strPluginExecEvaluationIndexing = "EDPluginExecEvaluationIndexingv10"
self._strPluginControlIndexingMOSFLM = "EDPluginControlIndexingMOSFLMv10"
self._strPluginControlGeneratePrediction = "EDPluginControlGeneratePredictionv10"
self._strPluginControlIntegration = "EDPluginControlIntegrationv10"
self._strPluginControlXDSGenerateBackgroundImage = "EDPluginControlXDSGenerateBackgroundImagev1_0"
self._strPluginControlStrategy = "EDPluginControlStrategyv1_3"
self._strPluginGenerateThumbnailName = "EDPluginMXThumbnailv1_1"
self._strPluginControlKappaName = "EDPluginControlKappav1_0"
self._listPluginGenerateThumbnail = []
self._edPluginControlIndexingIndicators = None
self._edPluginExecEvaluationIndexingMOSFLM = None
self._edPluginExecEvaluationIndexingLABELIT = None
self._edPluginControlGeneratePrediction = None
self._edPluginControlIntegration = None
self._edPluginControlXDSGenerateBackgroundImage = None
self._edPluginControlStrategy = None
self._edPluginControlKappa = None
self._xsDataCollection = None
self._xsDataResultCharacterisation = None
self._xsDataIndexingResultMOSFLM = None
self._xsDataCrystal = None
self._strCharacterisationShortSummary = ""
self._strStatusMessage = ""
self._xsDataFileXdsBackgroundImage = None
self._bDoStrategyCalculation = True
self._fMinTransmission = 10 # %
self._iNoReferenceImages = None
self._iNoImagesWithDozorScore = None
self._strMxCuBE_URI = None
self._oServerProxy = None
self._runKappa = False
def checkParameters(self):
"""
Checks the mandatory parameters.
"""
self.DEBUG("EDPluginControlCharacterisationv1_5.checkParameters")
self.checkMandatoryParameters(self.getDataInput(), "Data Input is None")
self.checkMandatoryParameters(self.getDataInput().getDataCollection(), "dataCollection")
self.checkMandatoryParameters(self.getDataInput().getDataCollection().getDiffractionPlan(), "diffractionPlan")
def configure(self):
"""
Gets the configuration parameters (if any).
"""
EDPluginControl.configure(self)
self.DEBUG("EDPluginControlCharacterisationv1_5.configure")
self._strMxCuBE_URI = self.config.get("mxCuBE_URI", None)
if self._strMxCuBE_URI is not None and "mxCuBE_XMLRPC_log" in os.environ.keys():
self.DEBUG("Enabling sending messages to mxCuBE via URI {0}".format(self._strMxCuBE_URI))
self._oServerProxy = xmlrpclib.ServerProxy(self._strMxCuBE_URI)
self._runKappa = self.config.get("runKappa", False)
self._fMinTransmission = self.config.get("minTransmissionWarning", self._fMinTransmission)
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginControlCharacterisationv1_5.preProcess")
self._xsDataResultCharacterisation = XSDataResultCharacterisation()
# Load the plugins
self._edPluginControlIndexingIndicators = self.loadPlugin(self._strPluginControlIndexingIndicators, \
"Indexing")
self._edPluginExecEvaluationIndexingLABELIT = self.loadPlugin(self._strPluginExecEvaluationIndexing, \
"IndexingEvalualtionLABELIT")
self._edPluginControlIndexingMOSFLM = self.loadPlugin(self._strPluginControlIndexingMOSFLM, \
"IndexingMOSFLM")
self._edPluginExecEvaluationIndexingMOSFLM = self.loadPlugin(self._strPluginExecEvaluationIndexing, \
"IndexingEvalualtionMOSFLM")
self._edPluginControlGeneratePrediction = self.loadPlugin(self._strPluginControlGeneratePrediction, \
"GeneratePrediction")
self._edPluginControlIntegration = self.loadPlugin(self._strPluginControlIntegration, \
"Integration")
self._edPluginControlXDSGenerateBackgroundImage = self.loadPlugin(self._strPluginControlXDSGenerateBackgroundImage, \
"ControlXDSGenerateBackgroundImage")
self._edPluginControlStrategy = self.loadPlugin(self._strPluginControlStrategy, \
"Strategy")
if self._runKappa:
self._edPluginControlKappa = self.loadPlugin(self._strPluginControlKappaName, "Kappa")
if (self._edPluginControlIndexingIndicators is not None):
self.DEBUG("EDPluginControlCharacterisationv1_5.preProcess: " + self._strPluginControlIndexingIndicators + " Found... setting Data Input")
# create Data Input for indexing
xsDataInputCharacterisation = self.getDataInput()
self._xsDataCollection = xsDataInputCharacterisation.getDataCollection()
# MXSUP-1445: Check if transmission is less than 10% and warn if it's the case
xsDataFirstSubWedge = self._xsDataCollection.getSubWedge()[0]
xsDataBeam = xsDataFirstSubWedge.getExperimentalCondition().getBeam()
if xsDataBeam.getTransmission() is not None:
fTransmission = xsDataBeam.getTransmission().getValue()
if fTransmission < self._fMinTransmission:
strWarningMessageBanner = "^"*80
strWarningMessage1 = "WARNING! Transmission for characterisation set to %.1f %%" % fTransmission
strWarningMessage2 = "Please consider re-characterising with transmission set to 100 %"
self.warning(strWarningMessageBanner)
self.warning(strWarningMessage1)
self.warning(strWarningMessage2)
self.warning(strWarningMessageBanner)
self.addWarningMessage(strWarningMessageBanner)
self.addWarningMessage(strWarningMessage1)
self.addWarningMessage(strWarningMessage2)
self.addWarningMessage(strWarningMessageBanner)
self.sendMessageToMXCuBE(strWarningMessage1, "warning")
self.sendMessageToMXCuBE(strWarningMessage2, "warning")
xsDataCrystal = None
xsDataSubWedgeList = self._xsDataCollection.getSubWedge()
if ((xsDataSubWedgeList is None) or (xsDataSubWedgeList == [])):
strError = "EDPluginControlCharacterisationv1_5.preProcess: No subwedges in input data."
self.ERROR(strError)
self.setFailure()
else:
xsDataExperimentalCondition = xsDataSubWedgeList[0].getExperimentalCondition()
# Fix for bug 431: if the flux is zero raise an error
xsDataDoubleFlux = xsDataExperimentalCondition.getBeam().getFlux()
if (xsDataDoubleFlux is not None):
if (xsDataDoubleFlux.getValue() < 0.1):
strErrorMessage = "Input flux is negative or close to zero. Execution of characterisation aborted."
self.ERROR(strErrorMessage)
self.sendMessageToMXCuBE(strErrorMessage, "error")
self.addErrorMessage("EDPluginControlCharacterisationv1_5.preProcess ERROR: " + strErrorMessage)
# self.addComment(strErrorMessage)
self.setFailure()
xsDataDiffractionPlan = self._xsDataCollection.getDiffractionPlan()
xsDataStringForcedSpaceGroup = xsDataDiffractionPlan.getForcedSpaceGroup()
if (xsDataStringForcedSpaceGroup is not None):
self._xsDataCrystal = XSDataCrystal()
xsDataSpaceGroup = XSDataSpaceGroup()
xsDataSpaceGroup.setName(xsDataStringForcedSpaceGroup)
self._xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
self._edPluginControlIndexingIndicators.setDataInput(self._xsDataCollection, "dataCollection")
if self._xsDataCrystal is not None:
self._edPluginControlIndexingIndicators.setDataInput(self._xsDataCrystal, "crystal")
# Populate characterisation object
self._xsDataResultCharacterisation.setDataCollection(XSDataCollection.parseString(self._xsDataCollection.marshal()))
# Load the thumbnail plugins
self._iNoReferenceImages = 0
if not self.isFailure():
for subWedge in xsDataInputCharacterisation.dataCollection.subWedge:
for image in subWedge.image:
self._iNoReferenceImages += 1
edPluginJpeg = self.loadPlugin(self._strPluginGenerateThumbnailName)
xsDataInputMXThumbnail = XSDataInputMXThumbnail()
xsDataInputMXThumbnail.image = XSDataFile(image.path)
xsDataInputMXThumbnail.height = XSDataInteger(1024)
xsDataInputMXThumbnail.width = XSDataInteger(1024)
jpegFilename = os.path.splitext(os.path.basename(image.path.value))[0] + ".jpg"
xsDataInputMXThumbnail.outputPath = XSDataFile(XSDataString(os.path.join(self.getWorkingDirectory(), jpegFilename)))
edPluginJpeg.dataInput = xsDataInputMXThumbnail
edPluginThumnail = self.loadPlugin(self._strPluginGenerateThumbnailName)
xsDataInputMXThumbnail = XSDataInputMXThumbnail()
xsDataInputMXThumbnail.image = XSDataFile(image.path)
xsDataInputMXThumbnail.height = XSDataInteger(256)
xsDataInputMXThumbnail.width = XSDataInteger(256)
thumbnailFilename = os.path.splitext(os.path.basename(image.path.value))[0] + ".thumbnail.jpg"
xsDataInputMXThumbnail.outputPath = XSDataFile(XSDataString(os.path.join(self.getWorkingDirectory(), thumbnailFilename)))
edPluginThumnail.dataInput = xsDataInputMXThumbnail
self._listPluginGenerateThumbnail.append((image, edPluginJpeg, edPluginThumnail))
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlCharacterisationv1_5.process")
self._edPluginControlIndexingIndicators.connectSUCCESS(self.doSuccessIndexingIndicators)
self._edPluginControlIndexingIndicators.connectFAILURE(self.doFailureIndexingIndicators)
self._edPluginExecEvaluationIndexingLABELIT.connectSUCCESS(self.doSuccessEvaluationIndexingLABELIT)
self._edPluginExecEvaluationIndexingLABELIT.connectFAILURE(self.doFailureEvaluationIndexingLABELIT)
self._edPluginControlIndexingMOSFLM.connectSUCCESS(self.doSuccessIndexingMOSFLM)
self._edPluginControlIndexingMOSFLM.connectFAILURE(self.doFailureIndexingMOSFLM)
self._edPluginExecEvaluationIndexingMOSFLM.connectSUCCESS(self.doSuccessEvaluationIndexingMOSFLM)
self._edPluginExecEvaluationIndexingMOSFLM.connectFAILURE(self.doFailureEvaluationIndexingMOSFLM)
self._edPluginControlGeneratePrediction.connectSUCCESS(self.doSuccessGeneratePrediction)
self._edPluginControlGeneratePrediction.connectFAILURE(self.doFailureGeneratePrediction)
self._edPluginControlIntegration.connectSUCCESS(self.doSuccessIntegration)
self._edPluginControlIntegration.connectFAILURE(self.doFailureIntegration)
self._edPluginControlXDSGenerateBackgroundImage.connectSUCCESS(self.doSuccessXDSGenerateBackgroundImage)
self._edPluginControlXDSGenerateBackgroundImage.connectFAILURE(self.doFailureXDSGenerateBackgroundImage)
self._edPluginControlStrategy.connectSUCCESS(self.doSuccessStrategy)
self._edPluginControlStrategy.connectFAILURE(self.doFailureStrategy)
self.executePluginSynchronous(self._edPluginControlIndexingIndicators)
def finallyProcess(self, _edObject=None):
EDPluginControl.finallyProcess(self)
self.DEBUG("EDPluginControlCharacterisationv1_5.finallyProcess")
# Synchronize thumbnail plugins
for tuplePlugin in self._listPluginGenerateThumbnail:
image = tuplePlugin[0]
tuplePlugin[1].synchronize()
jpegImage = image.copy()
jpegImage.path = tuplePlugin[1].dataOutput.thumbnail.path
self._xsDataResultCharacterisation.addJpegImage(jpegImage)
tuplePlugin[2].synchronize()
thumbnailImage = image.copy()
thumbnailImage.path = tuplePlugin[2].dataOutput.thumbnail.path
self._xsDataResultCharacterisation.addThumbnailImage(thumbnailImage)
if self._edPluginControlGeneratePrediction.isRunning():
self._edPluginControlGeneratePrediction.synchronize()
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage), "statusMessage")
self._xsDataResultCharacterisation.setStatusMessage(XSDataString(self._strStatusMessage))
if self._strCharacterisationShortSummary != None:
self.setDataOutput(XSDataString(self._strCharacterisationShortSummary), "shortSummary")
self._xsDataResultCharacterisation.setShortSummary(XSDataString(self._strCharacterisationShortSummary))
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
if self.isFailure():
self.sendMessageToMXCuBE("Ended with error messages", "error")
def doSuccessIndexingIndicators(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_5.doSuccessIndexingIndicators")
# self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv1_5.doSuccessIndexingIndicators")
if self._edPluginControlIndexingIndicators.hasDataOutput("indexingResult"):
xsDataIndexingResult = self._edPluginControlIndexingIndicators.getDataOutput("indexingResult")[0]
# self._xsDataResultCharacterisation.setIndexingResult(xsDataIndexingResult)
self._edPluginExecEvaluationIndexingLABELIT.setDataInput(xsDataIndexingResult, "indexingResult")
if self._edPluginControlIndexingIndicators.hasDataOutput("imageQualityIndicators"):
listXSDataImageQualityIndicators = self._edPluginControlIndexingIndicators.getDataOutput("imageQualityIndicators")
for xsDataImageQualityIndicators in listXSDataImageQualityIndicators:
if xsDataImageQualityIndicators.dozor_score:
if self._iNoImagesWithDozorScore is None:
self._iNoImagesWithDozorScore = 0
if xsDataImageQualityIndicators.dozor_score.value > 0.001:
self._iNoImagesWithDozorScore += 1
self._xsDataResultCharacterisation.addImageQualityIndicators(xsDataImageQualityIndicators)
self._edPluginExecEvaluationIndexingLABELIT.setDataInput(xsDataImageQualityIndicators, "imageQualityIndicators")
if self._edPluginControlIndexingIndicators.hasDataOutput("indicatorsShortSummary"):
indicatorsShortSummary = self._edPluginControlIndexingIndicators.getDataOutput("indicatorsShortSummary")[0].getValue()
self._strCharacterisationShortSummary += indicatorsShortSummary
self.sendMessageToMXCuBE(indicatorsShortSummary)
for tuplePlugin in self._listPluginGenerateThumbnail:
tuplePlugin[1].execute()
tuplePlugin[2].execute()
self.executePluginSynchronous(self._edPluginExecEvaluationIndexingLABELIT)
def doFailureIndexingIndicators(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_5.doFailureIndexingIndicators")
# If more than two reference images try to index with MOSFLM:
if self._edPluginControlIndexingIndicators.hasDataOutput("indicatorsShortSummary"):
indicatorsShortSummary = self._edPluginControlIndexingIndicators.getDataOutput("indicatorsShortSummary")[0].getValue()
self._strCharacterisationShortSummary += indicatorsShortSummary
self.sendMessageToMXCuBE(indicatorsShortSummary)
if self._iNoImagesWithDozorScore > 0:
strWarningMessage = "Execution of Indexing and Indicators plugin failed - trying to index with MOSFLM."
self.WARNING(strWarningMessage)
self.sendMessageToMXCuBE(strWarningMessage, "warning")
self.addWarningMessage(strWarningMessage)
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.dataCollection = self._xsDataCollection
xsDataIndexingInput.experimentalCondition = self._xsDataCollection.subWedge[0].experimentalCondition
xsDataIndexingInput.crystal = self._xsDataCrystal
self._edPluginControlIndexingMOSFLM.dataInput = xsDataIndexingInput
self.executePluginSynchronous(self._edPluginControlIndexingMOSFLM)
else:
strErrorMessage = "Execution of Indexing and Indicators plugin failed. Execution of characterisation aborted."
self.ERROR(strErrorMessage)
self.sendMessageToMXCuBE(strErrorMessage, "error")
self.addErrorMessage(strErrorMessage)
self.generateExecutiveSummary(self)
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
self.setFailure()
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage), "statusMessage")
self.writeDataOutput()
def doSuccessIndexingMOSFLM(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_5.doSuccessIndexingMOSFLM")
xsDataIndexingResult = self._edPluginControlIndexingMOSFLM.dataOutput
self._edPluginExecEvaluationIndexingMOSFLM.setDataInput(xsDataIndexingResult, "indexingResult")
self.executePluginSynchronous(self._edPluginExecEvaluationIndexingMOSFLM)
def doFailureIndexingMOSFLM(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_5.doFailureIndexingMOSFLM")
strErrorMessage = "Indexing with MOSFLM failed."
self.ERROR(strErrorMessage)
self.sendMessageToMXCuBE(strErrorMessage, "error")
self.executePluginSynchronous(self._edPluginExecEvaluationIndexingMOSFLM)
def doSuccessEvaluationIndexingLABELIT(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_5.doSuccessEvaluationIndexingLABELIT")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv1_5.doSuccessEvaluationIndexingLABELIT")
# Retrieve status messages (if any)
if self._edPluginExecEvaluationIndexingLABELIT.hasDataOutput("statusMessageIndexing"):
self.addStatusMessage("Labelit: " + self._edPluginExecEvaluationIndexingLABELIT.getDataOutput("statusMessageIndexing")[0].getValue())
# Check if indexing was successful
bIndexingSuccess = self._edPluginExecEvaluationIndexingLABELIT.getDataOutput("indexingSuccess")[0].getValue()
if bIndexingSuccess:
xsDataIndexingResult = self._edPluginExecEvaluationIndexingLABELIT.getDataOutput("indexingResult")[0]
self._xsDataResultCharacterisation.setIndexingResult(xsDataIndexingResult)
if self._edPluginControlIndexingIndicators.hasDataOutput("indexingShortSummary"):
self._strCharacterisationShortSummary += self._edPluginControlIndexingIndicators.getDataOutput("indexingShortSummary")[0].getValue()
xsDataCollection = self._xsDataResultCharacterisation.getDataCollection()
xsDataGeneratePredictionInput = XSDataGeneratePredictionInput()
xsDataGeneratePredictionInput.setDataCollection(XSDataCollection.parseString(xsDataCollection.marshal()))
xsDataGeneratePredictionInput.setSelectedIndexingSolution(XSDataIndexingSolutionSelected.parseString(xsDataIndexingResult.getSelectedSolution().marshal()))
self._edPluginControlGeneratePrediction.setDataInput(xsDataGeneratePredictionInput)
if self._edPluginControlIndexingIndicators.hasDataOutput("indexingShortSummary"):
indexingShortSummary = self._edPluginControlIndexingIndicators.getDataOutput("indexingShortSummary")[0].getValue()
self._strCharacterisationShortSummary += indexingShortSummary
self.sendMessageToMXCuBE(indexingShortSummary)
# Start the generation of prediction images - we synchronize in the post-process
self._edPluginControlGeneratePrediction.execute()
# Then start the integration of the reference images
self.indexingToIntegration()
else:
if self._iNoImagesWithDozorScore > 0:
strWarningMessage = "Execution of Indexing and Indicators plugin failed - trying to index with MOSFLM."
self.WARNING(strWarningMessage)
self.sendMessageToMXCuBE(strWarningMessage, "warning")
self.addWarningMessage(strWarningMessage)
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.dataCollection = self._xsDataCollection
xsDataIndexingInput.experimentalCondition = self._xsDataCollection.subWedge[0].experimentalCondition
xsDataIndexingInput.crystal = self._xsDataCrystal
self._edPluginControlIndexingMOSFLM.setDataInput(xsDataIndexingInput)
self.executePluginSynchronous(self._edPluginControlIndexingMOSFLM)
else:
strErrorMessage = "Execution of indexing with Labelit failed."
self.ERROR(strErrorMessage)
self.sendMessageToMXCuBE(strErrorMessage, "error")
self.addErrorMessage(strErrorMessage)
self.setFailure()
self.generateExecutiveSummary(self)
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage), "statusMessage")
self.writeDataOutput()
def doSuccessEvaluationIndexingMOSFLM(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_5.doSuccessEvaluationIndexingMOSFLM")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv1_5.doSuccessEvaluationIndexingMOSFLM")
# Retrieve status messages (if any)
if self._edPluginExecEvaluationIndexingMOSFLM.hasDataOutput("statusMessageIndexing"):
self.addStatusMessage("MOSFLM: " + self._edPluginExecEvaluationIndexingMOSFLM.getDataOutput("statusMessageIndexing")[0].getValue())
# Check if indexing was successful
bIndexingSuccess = self._edPluginExecEvaluationIndexingMOSFLM.getDataOutput("indexingSuccess")[0].getValue()
if bIndexingSuccess:
xsDataIndexingResult = self._edPluginExecEvaluationIndexingMOSFLM.getDataOutput("indexingResult")[0]
self._xsDataResultCharacterisation.setIndexingResult(xsDataIndexingResult)
self._strCharacterisationShortSummary += self.generateIndexingShortSummary(xsDataIndexingResult)
xsDataCollection = self._xsDataResultCharacterisation.getDataCollection()
xsDataGeneratePredictionInput = XSDataGeneratePredictionInput()
xsDataGeneratePredictionInput.setDataCollection(XSDataCollection.parseString(xsDataCollection.marshal()))
xsDataGeneratePredictionInput.setSelectedIndexingSolution(XSDataIndexingSolutionSelected.parseString(xsDataIndexingResult.getSelectedSolution().marshal()))
self._edPluginControlGeneratePrediction.setDataInput(xsDataGeneratePredictionInput)
if self._edPluginControlIndexingIndicators.hasDataOutput("indexingShortSummary"):
self._strCharacterisationShortSummary += self._edPluginControlIndexingIndicators.getDataOutput("indexingShortSummary")[0].getValue()
# Start the generation of prediction images - we synchronize in the post-process
self._edPluginControlGeneratePrediction.execute()
# Then start the integration of the reference images
self.indexingToIntegration()
else:
strErrorMessage = "Execution of indexing with MOSFLM failed."
self.ERROR(strErrorMessage)
self.sendMessageToMXCuBE(strErrorMessage, "error")
self.addErrorMessage(strErrorMessage)
self.setFailure()
self.generateExecutiveSummary(self)
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage), "statusMessage")
self.writeDataOutput()
def generateIndexingShortSummary(self, _xsDataIndexingResult):
"""
Generates a very short summary of the indexing
"""
strIndexingShortSummary = ""
if self.hasDataInput("crystal"):
xsDataCrystal = self.getDataInput("crystal")[0]
if xsDataCrystal.getSpaceGroup() is not None:
strForcedSpaceGroup = xsDataCrystal.getSpaceGroup().getName().getValue().upper()
if xsDataCrystal.getSpaceGroup().getName().getValue() != "":
strIndexingShortSummary += "Forced space group: %s\n" % strForcedSpaceGroup
if _xsDataIndexingResult is not None:
# Indexing solution
xsDataSelectedSolution = _xsDataIndexingResult.getSelectedSolution()
xsDataCrystal = xsDataSelectedSolution.getCrystal()
# Refined cell parameters
xsDataCell = xsDataCrystal.getCell()
fA = xsDataCell.getLength_a().getValue()
fB = xsDataCell.getLength_b().getValue()
fC = xsDataCell.getLength_c().getValue()
fAlpha = xsDataCell.getAngle_alpha().getValue()
fBeta = xsDataCell.getAngle_beta().getValue()
fGamma = xsDataCell.getAngle_gamma().getValue()
# Estimated mosaicity
fEstimatedMosaicity = xsDataCrystal.getMosaicity().getValue()
# Space group
strSpaceGroup = xsDataCrystal.getSpaceGroup().getName().getValue()
# Spot deviation
xsDataStatisticsIndexing = xsDataSelectedSolution.getStatistics()
fSpotDeviationPositional = xsDataStatisticsIndexing.getSpotDeviationPositional().getValue()
strIndexingShortSummary += "Indexing: laue/space group %s, mosaicity %.2f [degree], " % (strSpaceGroup, fEstimatedMosaicity)
strIndexingShortSummary += "RMS dev pos %.2f [mm]" % fSpotDeviationPositional
if xsDataStatisticsIndexing.getSpotDeviationAngular() is not None:
fSpotDeviationAngular = xsDataStatisticsIndexing.getSpotDeviationAngular().getValue()
strIndexingShortSummary += " ang %.2f [degree]" % fSpotDeviationAngular
strIndexingShortSummary += "\n"
strIndexingShortSummary += "Indexing: refined Cell: %7.2f %7.2f %7.2f %7.2f %7.2f %7.2f\n" % (fA, fB, fC, fAlpha, fBeta, fGamma)
else:
strIndexingShortSummary += "Indexing failed."
return strIndexingShortSummary
def indexingToIntegration(self, _edPlugin=None):
# Run Kappa if configured
if self._runKappa:
xsDataInputControlKappa = XSDataInputControlKappa()
xsDataInputControlKappa.dataCollection = self._xsDataCollection
xsDataInputControlKappa.selectedSolution = self._xsDataResultCharacterisation.indexingResult.selectedSolution
self._edPluginControlKappa.dataInput = xsDataInputControlKappa
self.executePluginSynchronous(self._edPluginControlKappa)
if not self._edPluginControlKappa.isFailure():
self._xsDataResultCharacterisation.kappaReorientation = self._edPluginControlKappa.dataOutput
# Create the XDS background image
xsDataInputControlXDSGenerateBackgroundImage = XSDataInputControlXDSGenerateBackgroundImage()
xsDataInputControlXDSGenerateBackgroundImage.setDataCollection(self._xsDataCollection)
self._edPluginControlXDSGenerateBackgroundImage.setDataInput(xsDataInputControlXDSGenerateBackgroundImage)
self._edPluginControlXDSGenerateBackgroundImage.execute()
# Integrate the reference images
xsDataIntegrationInput = XSDataIntegrationInput()
xsDataIntegrationInput.setDataCollection(self._xsDataResultCharacterisation.getDataCollection())
xsDataIndexingResult = self._xsDataResultCharacterisation.getIndexingResult()
xsDataExperimentalConditionRefinded = xsDataIndexingResult.getSelectedSolution().getExperimentalConditionRefined()
xsDataIntegrationInput.setExperimentalConditionRefined(xsDataExperimentalConditionRefinded)
xsDataIntegrationInput.setSelectedIndexingSolution(xsDataIndexingResult.getSelectedSolution())
self._edPluginControlIntegration.setDataInput(xsDataIntegrationInput)
self.executePluginSynchronous(self._edPluginControlIntegration)
def doFailureEvaluationIndexingLABELIT(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_5.doFailureEvaluationIndexing")
strErrorMessage = "Execution of indexing evaluation plugin failed."
self.ERROR(strErrorMessage)
self.sendMessageToMXCuBE(strErrorMessage, "error")
self.addErrorMessage(strErrorMessage)
self.generateExecutiveSummary(self)
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
self.setFailure()
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage), "statusMessage")
self.writeDataOutput()
def doFailureEvaluationIndexingMOSFLM(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_5.doFailureEvaluationIndexingMOSFLM")
strErrorMessage = "Execution of indexing evaluation plugin failed."
self.ERROR(strErrorMessage)
self.sendMessageToMXCuBE(strErrorMessage, "error")
self.addErrorMessage(strErrorMessage)
self.generateExecutiveSummary(self)
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
self.setFailure()
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage), "statusMessage")
self.writeDataOutput()
def doSuccessGeneratePrediction(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_5.doSuccessGeneratePrediction")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv1_5.doSuccessGeneratePrediction")
xsDataGeneratePredictionResult = _edPlugin.getDataOutput()
xsDataIndexingResult = self._xsDataResultCharacterisation.getIndexingResult()
xsDataIndexingResult.setPredictionResult(xsDataGeneratePredictionResult)
def doFailureGeneratePrediction(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_5.doFailureGeneratePrediction")
strWarningMessage = "Execution of generate prediction plugin failed."
self.WARNING(strWarningMessage)
self.addWarningMessage(strWarningMessage)
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
# self.addComment("warning: no prediction images")
def doSuccessIntegration(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_5.doSuccessIntegration")
self.retrieveSuccessMessages(self._edPluginControlIntegration, "EDPluginControlCharacterisationv1_5.doSuccessIntegration")
# Wait for XDS plugin if necessary
self._edPluginControlXDSGenerateBackgroundImage.synchronize()
self.addStatusMessage("Integration successful.")
xsDataIntegrationOutput = self._edPluginControlIntegration.getDataOutput()
self._xsDataResultCharacterisation.setIntegrationResult(xsDataIntegrationOutput)
# Integration short summary
if self._edPluginControlIntegration.hasDataOutput("integrationShortSummary"):
integrationShortSummary = self._edPluginControlIntegration.getDataOutput("integrationShortSummary")[0].getValue()
self._strCharacterisationShortSummary += integrationShortSummary
self.sendMessageToMXCuBE(integrationShortSummary)
# self.DEBUG( self._xsDataExperimentCharacterisation.marshal() )
if self._bDoStrategyCalculation:
xsDataInputStrategy = XSDataInputStrategy()
xsDataSolutionSelected = self._xsDataResultCharacterisation.getIndexingResult().getSelectedSolution()
xsDataInputStrategy.setCrystalRefined(xsDataSolutionSelected.getCrystal())
xsDataInputStrategy.setSample(self._xsDataResultCharacterisation.getDataCollection().getSample())
xsDataIntegrationSubWedgeResultList = xsDataIntegrationOutput.getIntegrationSubWedgeResult()
bFirst = True
for xsDataIntegrationSubWedgeResult in xsDataIntegrationSubWedgeResultList:
if xsDataIntegrationSubWedgeResult.getBestfileHKL() is not None:
xsDataInputStrategy.addBestFileContentHKL(xsDataIntegrationSubWedgeResult.getBestfileHKL())
if bFirst:
xsDataInputStrategy.setBestFileContentDat(xsDataIntegrationSubWedgeResult.getBestfileDat())
xsDataInputStrategy.setBestFileContentPar(xsDataIntegrationSubWedgeResult.getBestfilePar())
xsDataInputStrategy.setExperimentalCondition(xsDataIntegrationSubWedgeResult.getExperimentalConditionRefined())
bFirst = False
xsDataInputStrategy.setXdsBackgroundImage(self._xsDataFileXdsBackgroundImage)
xsDataInputStrategy.setDataCollection(self._xsDataCollection)
xsDataInputStrategy.setDiffractionPlan(self._xsDataResultCharacterisation.getDataCollection().getDiffractionPlan())
self._edPluginControlStrategy.setDataInput(xsDataInputStrategy)
self.executePluginSynchronous(self._edPluginControlStrategy)
def doFailureIntegration(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_5.doFailureIntegration")
strErrorMessage = "Execution of integration failed."
self.addStatusMessage("Integration FAILURE.")
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
# self.addComment("integration failure")
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
self.generateExecutiveSummary(self)
self.setFailure()
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage), "statusMessage")
self.writeDataOutput()
def doSuccessXDSGenerateBackgroundImage(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_5.doSuccessXDSGenerateBackgroundImage")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv1_5.doSuccessXDSGenerateBackgroundImage")
self._xsDataFileXdsBackgroundImage = self._edPluginControlXDSGenerateBackgroundImage.getDataOutput().getXdsBackgroundImage()
self._xsDataResultCharacterisation.setXdsBackgroundImage(self._xsDataFileXdsBackgroundImage)
def doFailureXDSGenerateBackgroundImage(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_5.doFailureXDSGenerateBackgroundImage")
def doSuccessStrategy(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_5.doSuccessStrategy")
self.retrieveSuccessMessages(self._edPluginControlStrategy, "EDPluginControlCharacterisationv1_5.doSuccessStrategy")
xsDataStrategyResult = self._edPluginControlStrategy.getDataOutput()
self._xsDataResultCharacterisation.setStrategyResult(xsDataStrategyResult)
if self._edPluginControlStrategy.hasDataOutput("strategyShortSummary"):
strategyShortSummary = self._edPluginControlStrategy.getDataOutput("strategyShortSummary")[0].getValue()
self._strCharacterisationShortSummary += strategyShortSummary
self.sendMessageToMXCuBE(strategyShortSummary)
self.addStatusMessage("Strategy calculation successful.")
def doFailureStrategy(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_5.doFailureStrategy")
strErrorMessage = "Strategy calculation FAILURE."
self.ERROR(strErrorMessage)
self.sendMessageToMXCuBE(strErrorMessage, "error")
self.addErrorMessage(strErrorMessage)
xsDataStrategyResult = self._edPluginControlStrategy.getDataOutput()
self._xsDataResultCharacterisation.setStrategyResult(xsDataStrategyResult)
if self._edPluginControlStrategy.hasDataOutput("strategyShortSummary"):
strategyShortSummary = self._edPluginControlStrategy.getDataOutput("strategyShortSummary")[0].getValue()
self._strCharacterisationShortSummary += strategyShortSummary
self.sendMessageToMXCuBE(strategyShortSummary)
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
self.addStatusMessage("Strategy calculation FAILURE.")
self.generateExecutiveSummary(self)
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage), "statusMessage")
self.writeDataOutput()
self.setFailure()
def generateExecutiveSummary(self, _edPlugin):
"""
Generates a summary of the execution of the plugin.
"""
self.DEBUG("EDPluginControlCharacterisationv1_5.generateExecutiveSummary")
self.addExecutiveSummaryLine("Summary of characterisation:")
xsDataInputStrategy = self.getDataInput()
xsDataCollection = xsDataInputStrategy.getDataCollection()
# MXSUP-1445: Check if transmission is less than 10% and warn if it's the case
xsDataFirstSubWedge = xsDataCollection.getSubWedge()[0]
xsDataBeam = xsDataFirstSubWedge.getExperimentalCondition().getBeam()
if xsDataBeam.getTransmission() is not None:
fTransmission = xsDataBeam.getTransmission().getValue()
if fTransmission < self._fMinTransmission:
self.addExecutiveSummaryLine("^"*80)
self.addExecutiveSummaryLine("^"*80)
self.addExecutiveSummaryLine("")
self.addExecutiveSummaryLine("WARNING! Transmission for characterisation set to %.1f %%" % fTransmission)
self.addExecutiveSummaryLine("Please consider re-characterising with transmission set to 100 %")
self.addExecutiveSummaryLine("")
self.addExecutiveSummaryLine("^"*80)
self.addExecutiveSummaryLine("^"*80)
xsDataDiffractionPlan = xsDataCollection.getDiffractionPlan()
self.addExecutiveSummaryLine("Diffraction plan:")
if (xsDataDiffractionPlan.getComplexity() is not None):
self.addExecutiveSummaryLine("BEST complexity : %s" % xsDataDiffractionPlan.getComplexity().getValue())
if (xsDataDiffractionPlan.getAimedCompleteness() is not None):
self.addExecutiveSummaryLine("Aimed completeness : %6.1f [%%]" % (100.0 * xsDataDiffractionPlan.getAimedCompleteness().getValue()))
if (xsDataDiffractionPlan.getRequiredCompleteness() is not None):
self.addExecutiveSummaryLine("Required completeness : %6.1f [%%]" % (100.0 * xsDataDiffractionPlan.getRequiredCompleteness().getValue()))
if (xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution() is not None):
self.addExecutiveSummaryLine("Aimed I/sigma at highest resolution : %6.1f" % xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution().getValue())
if (xsDataDiffractionPlan.getAimedResolution() is not None):
self.addExecutiveSummaryLine("Aimed resolution : %6.1f [A]" % xsDataDiffractionPlan.getAimedResolution().getValue())
if (xsDataDiffractionPlan.getRequiredResolution() is not None):
self.addExecutiveSummaryLine("Required resolution : %6.1f [A]" % xsDataDiffractionPlan.getRequiredResolution().getValue())
if (xsDataDiffractionPlan.getAimedMultiplicity() is not None):
self.addExecutiveSummaryLine("Aimed multiplicity : %6.1f" % xsDataDiffractionPlan.getAimedMultiplicity().getValue())
if (xsDataDiffractionPlan.getRequiredMultiplicity() is not None):
self.addExecutiveSummaryLine("Required multiplicity : %6.1f" % xsDataDiffractionPlan.getRequiredMultiplicity().getValue())
if (xsDataDiffractionPlan.getForcedSpaceGroup() is not None):
self.addExecutiveSummaryLine("Forced space group : %6s" % xsDataDiffractionPlan.getForcedSpaceGroup().getValue())
if (xsDataDiffractionPlan.getMaxExposureTimePerDataCollection() is not None):
self.addExecutiveSummaryLine("Max exposure time per data collection : %6.1f [s]" % xsDataDiffractionPlan.getMaxExposureTimePerDataCollection().getValue())
self.addExecutiveSummarySeparator()
if self._edPluginControlIndexingIndicators is not None:
self.appendExecutiveSummary(self._edPluginControlIndexingIndicators, "")
if self._edPluginControlIntegration is not None:
self.appendExecutiveSummary(self._edPluginControlIntegration, "")
if self._edPluginControlStrategy is not None:
self.appendExecutiveSummary(self._edPluginControlStrategy, "")
self.addExecutiveSummarySeparator()
if self._strCharacterisationShortSummary is not None:
self.addExecutiveSummaryLine("Characterisation short summary:")
self.addExecutiveSummaryLine("")
if self._strStatusMessage != None:
for strLine in self._strStatusMessage.split(". "):
if strLine.endswith("."):
self.addExecutiveSummaryLine(strLine)
else:
self.addExecutiveSummaryLine(strLine + ".")
self.addExecutiveSummaryLine("")
for strLine in self._strCharacterisationShortSummary.split("\n"):
if strLine != "\n":
self.addExecutiveSummaryLine(strLine)
self.addErrorWarningMessagesToExecutiveSummary("Characterisation error and warning messages: ")
self.addExecutiveSummarySeparator()
def getPluginStrategyName(self):
return self._strPluginControlStrategy
def addStatusMessage(self, _strStatusMessage):
if self._strStatusMessage != "":
self._strStatusMessage += " "
self._strStatusMessage += _strStatusMessage
self.sendMessageToMXCuBE(_strStatusMessage)
def doStrategyCalculation(self, _bValue):
self._bDoStrategyCalculation = _bValue
def sendMessageToMXCuBE(self, _strMessage, level="info"):
# Only for mxCuBE
if self._strMxCuBE_URI is not None:
self.DEBUG("Sending message to mxCuBE: {0}".format(_strMessage))
try:
for strMessage in _strMessage.split("\n"):
if strMessage != "":
self._oServerProxy.log_message("Characterisation: " + strMessage, level)
except:
self.DEBUG("Sending message to mxCuBE failed!")
class EDPluginControlCharacterisationv1_3(EDPluginControl):
"""
[To be replaced with a description of EDPluginControlTemplatev10]
"""
def __init__(self):
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputCharacterisation)
self._strPluginControlIndexingIndicators = "EDPluginControlIndexingIndicatorsv10"
self._strPluginControlIndexingLabelit = "EDPluginControlIndexingLabelitv10"
self._strPluginExecEvaluationIndexing = "EDPluginExecEvaluationIndexingv10"
self._strPluginControlGeneratePrediction = "EDPluginControlGeneratePredictionv10"
self._strPluginControlIntegration = "EDPluginControlIntegrationv10"
self._strPluginControlXDSGenerateBackgroundImage = "EDPluginControlXDSGenerateBackgroundImagev1_0"
self._strPluginControlStrategy = "EDPluginControlStrategyv1_2"
self._strPluginGenerateThumbnailName = "EDPluginMXThumbnailv1_1"
self._listPluginGenerateThumbnail = []
self._edPluginControlIndexingIndicators = None
self._edPluginControlIndexingLabelit = None
self._edPluginExecEvaluationIndexingMOSFLM = None
self._edPluginExecEvaluationIndexingLABELIT = None
self._edPluginControlGeneratePrediction = None
self._edPluginControlIntegration = None
self._edPluginControlXDSGenerateBackgroundImage = None
self._edPluginControlStrategy = None
self._xsDataCollection = None
self._xsDataResultCharacterisation = None
self._xsDataIndexingResultMOSFLM = None
self._xsDataCrystal = None
self._strCharacterisationShortSummary = ""
self._strStatusMessage = ""
self._xsDataFileXdsBackgroundImage = None
self._bDoStrategyCalculation = True
self._fMinTransmission = 10 # %
def checkParameters(self):
"""
Checks the mandatory parameters.
"""
self.DEBUG("EDPluginControlCharacterisationv1_3.checkParameters")
self.checkMandatoryParameters(self.getDataInput(),
"Data Input is None")
self.checkMandatoryParameters(self.getDataInput().getDataCollection(),
"dataCollection")
self.checkMandatoryParameters(
self.getDataInput().getDataCollection().getDiffractionPlan(),
"diffractionPlan")
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginControlCharacterisationv1_3.preProcess")
# Load the plugins
self._edPluginControlIndexingIndicators = self.loadPlugin(self._strPluginControlIndexingIndicators, \
"Indexing")
self._edPluginControlIndexingLabelit = self.loadPlugin(self._strPluginControlIndexingLabelit, \
"IndexingLabelit")
self._edPluginExecEvaluationIndexingMOSFLM = self.loadPlugin(self._strPluginExecEvaluationIndexing, \
"IndexingEvalualtionMOSFLM")
self._edPluginExecEvaluationIndexingLABELIT = self.loadPlugin(self._strPluginExecEvaluationIndexing, \
"IndexingEvalualtionLABELIT")
self._edPluginControlGeneratePrediction = self.loadPlugin(self._strPluginControlGeneratePrediction, \
"GeneratePrediction")
self._edPluginControlIntegration = self.loadPlugin(self._strPluginControlIntegration, \
"Integration")
self._edPluginControlXDSGenerateBackgroundImage = self.loadPlugin(self._strPluginControlXDSGenerateBackgroundImage, \
"ControlXDSGenerateBackgroundImage")
self._edPluginControlStrategy = self.loadPlugin(self._strPluginControlStrategy, \
"Strategy")
if (self._edPluginControlIndexingIndicators is not None):
self.DEBUG("EDPluginControlCharacterisationv1_3.preProcess: " +
self._strPluginControlIndexingIndicators +
" Found... setting Data Input")
# create Data Input for indexing
xsDataInputCharacterisation = self.getDataInput()
self._xsDataCollection = xsDataInputCharacterisation.getDataCollection(
)
# MXSUP-1445: Check if transmission is less than 10% and warn if it's the case
xsDataFirstSubWedge = self._xsDataCollection.getSubWedge()[0]
xsDataBeam = xsDataFirstSubWedge.getExperimentalCondition(
).getBeam()
if xsDataBeam.getTransmission() is not None:
fTransmission = xsDataBeam.getTransmission().getValue()
if fTransmission < self._fMinTransmission:
strWarningMessageBanner = "^" * 80
strWarningMessage1 = "WARNING! Transmission for characterisation set to %.1f %%" % fTransmission
strWarningMessage2 = "Please consider re-characterising with transmission set to 100 %"
self.warning(strWarningMessageBanner)
self.warning(strWarningMessage1)
self.warning(strWarningMessage2)
self.warning(strWarningMessageBanner)
self.addWarningMessage(strWarningMessageBanner)
self.addWarningMessage(strWarningMessage1)
self.addWarningMessage(strWarningMessage2)
self.addWarningMessage(strWarningMessageBanner)
xsDataCrystal = None
xsDataSubWedgeList = self._xsDataCollection.getSubWedge()
if ((xsDataSubWedgeList is None) or (xsDataSubWedgeList == [])):
strError = "EDPluginControlCharacterisationv1_3.preProcess: No subwedges in input data."
self.ERROR(strError)
self.setFailure()
else:
xsDataExperimentalCondition = xsDataSubWedgeList[
0].getExperimentalCondition()
# Fix for bug 431: if the flux is zero raise an error
xsDataDoubleFlux = xsDataExperimentalCondition.getBeam(
).getFlux()
if (xsDataDoubleFlux is not None):
if (xsDataDoubleFlux.getValue() < 0.1):
strErrorMessage = "Input flux is negative or close to zero. Execution of characterisation aborted."
self.ERROR(strErrorMessage)
self.addErrorMessage(
"EDPluginControlCharacterisationv1_3.preProcess ERROR: "
+ strErrorMessage)
#self.addComment(strErrorMessage)
self.setFailure()
xsDataDiffractionPlan = self._xsDataCollection.getDiffractionPlan(
)
xsDataStringForcedSpaceGroup = xsDataDiffractionPlan.getForcedSpaceGroup(
)
if (xsDataStringForcedSpaceGroup is not None):
self._xsDataCrystal = XSDataCrystal()
xsDataSpaceGroup = XSDataSpaceGroup()
xsDataSpaceGroup.setName(xsDataStringForcedSpaceGroup)
self._xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
self._edPluginControlIndexingIndicators.setDataInput(
self._xsDataCollection, "dataCollection")
if self._xsDataCrystal is not None:
self._edPluginControlIndexingIndicators.setDataInput(
self._xsDataCrystal, "crystal")
# Populate characterisation object
self._xsDataResultCharacterisation = XSDataResultCharacterisation(
)
self._xsDataResultCharacterisation.setDataCollection(
XSDataCollection.parseString(
self._xsDataCollection.marshal()))
# Load the thumbnail plugins
for subWedge in xsDataInputCharacterisation.dataCollection.subWedge:
for image in subWedge.image:
edPluginJpeg = self.loadPlugin(
self._strPluginGenerateThumbnailName)
xsDataInputMXThumbnail = XSDataInputMXThumbnail()
xsDataInputMXThumbnail.image = XSDataFile(image.path)
xsDataInputMXThumbnail.height = XSDataInteger(1024)
xsDataInputMXThumbnail.width = XSDataInteger(1024)
jpegFilename = os.path.splitext(
os.path.basename(image.path.value))[0] + ".jpg"
xsDataInputMXThumbnail.outputPath = XSDataFile(
XSDataString(
os.path.join(self.getWorkingDirectory(),
jpegFilename)))
edPluginJpeg.dataInput = xsDataInputMXThumbnail
edPluginThumnail = self.loadPlugin(
self._strPluginGenerateThumbnailName)
xsDataInputMXThumbnail = XSDataInputMXThumbnail()
xsDataInputMXThumbnail.image = XSDataFile(image.path)
xsDataInputMXThumbnail.height = XSDataInteger(256)
xsDataInputMXThumbnail.width = XSDataInteger(256)
thumbnailFilename = os.path.splitext(
os.path.basename(
image.path.value))[0] + ".thumbnail.jpg"
xsDataInputMXThumbnail.outputPath = XSDataFile(
XSDataString(
os.path.join(self.getWorkingDirectory(),
thumbnailFilename)))
edPluginThumnail.dataInput = xsDataInputMXThumbnail
self._listPluginGenerateThumbnail.append(
(image, edPluginJpeg, edPluginThumnail))
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlCharacterisationv1_3.process")
self._edPluginControlIndexingIndicators.connectSUCCESS(
self.doSuccessIndexingIndicators)
self._edPluginControlIndexingIndicators.connectFAILURE(
self.doFailureIndexingIndicators)
self._edPluginControlIndexingLabelit.connectSUCCESS(
self.doSuccessIndexingLabelit)
self._edPluginControlIndexingLabelit.connectFAILURE(
self.doFailureIndexingLabelit)
self._edPluginExecEvaluationIndexingMOSFLM.connectSUCCESS(
self.doSuccessEvaluationIndexingMOSFLM)
self._edPluginExecEvaluationIndexingMOSFLM.connectFAILURE(
self.doFailureEvaluationIndexingMOSFLM)
self._edPluginExecEvaluationIndexingLABELIT.connectSUCCESS(
self.doSuccessEvaluationIndexingLABELIT)
self._edPluginExecEvaluationIndexingLABELIT.connectFAILURE(
self.doFailureEvaluationIndexingLABELIT)
self._edPluginControlGeneratePrediction.connectSUCCESS(
self.doSuccessGeneratePrediction)
self._edPluginControlGeneratePrediction.connectFAILURE(
self.doFailureGeneratePrediction)
self._edPluginControlIntegration.connectSUCCESS(
self.doSuccessIntegration)
self._edPluginControlIntegration.connectFAILURE(
self.doFailureIntegration)
self._edPluginControlXDSGenerateBackgroundImage.connectSUCCESS(
self.doSuccessXDSGenerateBackgroundImage)
self._edPluginControlXDSGenerateBackgroundImage.connectFAILURE(
self.doFailureXDSGenerateBackgroundImage)
self._edPluginControlStrategy.connectSUCCESS(self.doSuccessStrategy)
self._edPluginControlStrategy.connectFAILURE(self.doFailureStrategy)
self.executePluginSynchronous(self._edPluginControlIndexingIndicators)
def finallyProcess(self, _edObject=None):
EDPluginControl.finallyProcess(self)
self.DEBUG("EDPluginControlCharacterisationv1_3.finallyProcess")
# Synchronize thumbnail plugins
for tuplePlugin in self._listPluginGenerateThumbnail:
image = tuplePlugin[0]
tuplePlugin[1].synchronize()
jpegImage = image.copy()
jpegImage.path = tuplePlugin[1].dataOutput.thumbnail.path
self._xsDataResultCharacterisation.addJpegImage(jpegImage)
tuplePlugin[2].synchronize()
thumbnailImage = image.copy()
thumbnailImage.path = tuplePlugin[2].dataOutput.thumbnail.path
self._xsDataResultCharacterisation.addThumbnailImage(
thumbnailImage)
if self._edPluginControlGeneratePrediction.isRunning():
self._edPluginControlGeneratePrediction.synchronize()
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage),
"statusMessage")
self._xsDataResultCharacterisation.setStatusMessage(
XSDataString(self._strStatusMessage))
if self._strCharacterisationShortSummary != None:
self.setDataOutput(
XSDataString(self._strCharacterisationShortSummary),
"shortSummary")
self._xsDataResultCharacterisation.setShortSummary(
XSDataString(self._strCharacterisationShortSummary))
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
def doSuccessIndexingIndicators(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlCharacterisationv1_3.doSuccessIndexingIndicators")
#self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv1_3.doSuccessIndexingIndicators")
if self._edPluginControlIndexingIndicators.hasDataOutput(
"indexingResult"):
xsDataIndexingResult = self._edPluginControlIndexingIndicators.getDataOutput(
"indexingResult")[0]
#self._xsDataResultCharacterisation.setIndexingResult(xsDataIndexingResult)
self._edPluginExecEvaluationIndexingMOSFLM.setDataInput(
xsDataIndexingResult, "indexingResult")
if self._edPluginControlIndexingIndicators.hasDataOutput(
"imageQualityIndicators"):
listXSDataImageQualityIndicators = self._edPluginControlIndexingIndicators.getDataOutput(
"imageQualityIndicators")
for xsDataImageQualityIndicators in listXSDataImageQualityIndicators:
self._xsDataResultCharacterisation.addImageQualityIndicators(
xsDataImageQualityIndicators)
self._edPluginExecEvaluationIndexingMOSFLM.setDataInput(
xsDataImageQualityIndicators, "imageQualityIndicators")
if self._edPluginControlIndexingIndicators.hasDataOutput(
"indicatorsShortSummary"):
self._strCharacterisationShortSummary += self._edPluginControlIndexingIndicators.getDataOutput(
"indicatorsShortSummary")[0].getValue()
for tuplePlugin in self._listPluginGenerateThumbnail:
tuplePlugin[1].execute()
tuplePlugin[2].execute()
self.executePluginSynchronous(
self._edPluginExecEvaluationIndexingMOSFLM)
def doFailureIndexingIndicators(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlCharacterisationv1_3.doFailureIndexingIndicators")
strErrorMessage = "Execution of Indexing and Indicators plugin failed. Execution of characterisation aborted."
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
self.setFailure()
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage),
"statusMessage")
self.writeDataOutput()
# def doSuccessIndexingLabelit(self, _edPlugin=None):
# self.DEBUG("EDPluginControlCharacterisationv1_3.doSuccessIndexingLabelit")
# self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv1_3.doSuccessIndexingLabelit")
# # Retrieve the indexing result
# xsDataIndexingResult = self._edPluginControlIndexingLabelit.getDataOutput()
# self._xsDataResultCharacterisation.setIndexingResult(xsDataIndexingResult)
# if self._edPluginControlIndexingLabelit.hasDataOutput("indexingShortSummary"):
# self._strCharacterisationShortSummary += self._edPluginControlIndexingLabelit.getDataOutput("indexingShortSummary")[0].getValue()
# # Then start the integration of the reference images
# self.indexingToIntegration()
def doSuccessIndexingLabelit(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlCharacterisationv1_3.doSuccessIndexingLabelit")
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlCharacterisationv1_3.doSuccessIndexingLabelit")
if self._edPluginControlIndexingLabelit.hasDataOutput(
"indexingShortSummary"):
self._strCharacterisationShortSummary += self._edPluginControlIndexingLabelit.getDataOutput(
"indexingShortSummary")[0].getValue()
# Check the indexing results
xsDataIndexingResult = self._edPluginControlIndexingLabelit.getDataOutput(
)
self._edPluginExecEvaluationIndexingLABELIT.setDataInput(
xsDataIndexingResult, "indexingResult")
xsDataImageQualityIndicators = self._xsDataResultCharacterisation.getImageQualityIndicators(
)[0]
self._edPluginExecEvaluationIndexingLABELIT.setDataInput(
xsDataImageQualityIndicators, "imageQualityIndicators")
self.executePluginSynchronous(
self._edPluginExecEvaluationIndexingLABELIT)
def doFailureIndexingLabelit(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlCharacterisationv1_3.doFailureIndexingLabelit")
self.addStatusMessage("Labelit: Indexing FAILURE.")
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
if self._xsDataIndexingResultMOSFLM == None:
strErrorMessage = "Execution of indexing with both MOSFLM and Labelit failed. Execution of characterisation aborted."
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.generateExecutiveSummary(self)
self.setFailure()
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage),
"statusMessage")
self.writeDataOutput()
else:
# Use the MOSFLM indexing results - even if it's P1
self._xsDataResultCharacterisation.setIndexingResult(
self._xsDataIndexingResultMOSFLM)
xsDataCollection = self._xsDataResultCharacterisation.getDataCollection(
)
xsDataGeneratePredictionInput = XSDataGeneratePredictionInput()
xsDataGeneratePredictionInput.setDataCollection(
XSDataCollection.parseString(xsDataCollection.marshal()))
xsDataGeneratePredictionInput.setSelectedIndexingSolution(
XSDataIndexingSolutionSelected.parseString(
self._xsDataIndexingResultMOSFLM.getSelectedSolution(
).marshal()))
self._edPluginControlGeneratePrediction.setDataInput(
xsDataGeneratePredictionInput)
if self._edPluginControlIndexingIndicators.hasDataOutput(
"indexingShortSummary"):
self._strCharacterisationShortSummary += self._edPluginControlIndexingIndicators.getDataOutput(
"indexingShortSummary")[0].getValue()
# Start the generation of prediction images - we synchronize in the post-process
self._edPluginControlGeneratePrediction.execute()
# Then start the integration of the reference images
self.indexingToIntegration()
def doSuccessEvaluationIndexingMOSFLM(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlCharacterisationv1_3.doSuccessEvaluationIndexingMOSFLM"
)
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlCharacterisationv1_3.doSuccessEvaluationIndexing")
# Retrieve status messages (if any)
if self._edPluginExecEvaluationIndexingMOSFLM.hasDataOutput(
"statusMessageImageQualityIndicators"):
self.addStatusMessage(
self._edPluginExecEvaluationIndexingMOSFLM.getDataOutput(
"statusMessageImageQualityIndicators")[0].getValue())
if self._edPluginExecEvaluationIndexingMOSFLM.hasDataOutput(
"statusMessageIndexing"):
self.addStatusMessage(
"MOSFLM: " +
self._edPluginExecEvaluationIndexingMOSFLM.getDataOutput(
"statusMessageIndexing")[0].getValue())
# Check if indexing was successful
bIndexWithLabelit = False
bIndexingSuccess = self._edPluginExecEvaluationIndexingMOSFLM.getDataOutput(
"indexingSuccess")[0].getValue()
if bIndexingSuccess:
xsDataIndexingResult = self._edPluginExecEvaluationIndexingMOSFLM.getDataOutput(
"indexingResult")[0]
self._xsDataIndexingResultMOSFLM = xsDataIndexingResult
# Check if space group is P1 - if yes run Labelit indexing
xsDataIndexingSolutionSelected = xsDataIndexingResult.getSelectedSolution(
)
xsDataCrystal = xsDataIndexingSolutionSelected.getCrystal()
xsDataSpaceGroup = xsDataCrystal.getSpaceGroup()
strSpaceGroupName = xsDataSpaceGroup.getName().getValue().upper()
# Check if MOSFLM has indexed in P1
if strSpaceGroupName == "P1":
# Check if the user maybe asked for P1!
bIndexWithLabelit = True
if self._xsDataCollection.getDiffractionPlan() is not None:
if self._xsDataCollection.getDiffractionPlan(
).getForcedSpaceGroup() is not None:
if self._xsDataCollection.getDiffractionPlan(
).getForcedSpaceGroup().getValue().upper() == "P1":
self.screen("P1 space forced by diffraction plan")
bIndexWithLabelit = False
if bIndexWithLabelit:
self.screen("P1 space group choosed - reindexing with Labelit")
else:
self.screen("MOSFLM indexing successful!")
if self._edPluginControlIndexingIndicators.hasDataOutput(
"indexingShortSummary"):
self._strCharacterisationShortSummary += self._edPluginControlIndexingIndicators.getDataOutput(
"indexingShortSummary")[0].getValue()
# Generate prediction images
xsDataCollection = self._xsDataResultCharacterisation.getDataCollection(
)
self._xsDataResultCharacterisation.setIndexingResult(
xsDataIndexingResult)
xsDataGeneratePredictionInput = XSDataGeneratePredictionInput()
xsDataGeneratePredictionInput.setDataCollection(
XSDataCollection.parseString(xsDataCollection.marshal()))
xsDataGeneratePredictionInput.setSelectedIndexingSolution(
XSDataIndexingSolutionSelected.parseString(
xsDataIndexingResult.getSelectedSolution().marshal()))
self._edPluginControlGeneratePrediction.setDataInput(
xsDataGeneratePredictionInput)
# Start the generation of prediction images - we synchronize in the post-process
self._edPluginControlGeneratePrediction.execute()
# Then start the integration of the reference images
self.indexingToIntegration()
else:
self.screen("Indexing with MOSFLM failed!")
bIndexWithLabelit = True
if bIndexWithLabelit:
# Execute Labelit indexing
self.screen(
"Now trying to index with Labelit - please be patient...")
xsDataIndexingInput = XSDataIndexingInput()
xsDataSubWedgeList = self._xsDataCollection.getSubWedge()
xsDataExperimentalCondition = xsDataSubWedgeList[
0].getExperimentalCondition()
xsDataIndexingInput.setDataCollection(self._xsDataCollection)
xsDataIndexingInput.setExperimentalCondition(
xsDataExperimentalCondition)
if self._xsDataCrystal != None:
xsDataIndexingInput.setCrystal(self._xsDataCrystal)
self._edPluginControlIndexingLabelit.setDataInput(
xsDataIndexingInput)
self.executePluginSynchronous(self._edPluginControlIndexingLabelit)
def doSuccessEvaluationIndexingLABELIT(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlCharacterisationv1_3.doSuccessEvaluationIndexingLABELIT"
)
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlCharacterisationv1_3.doSuccessEvaluationIndexingLABELIT"
)
# Retrieve status messages (if any)
if self._edPluginExecEvaluationIndexingLABELIT.hasDataOutput(
"statusMessageIndexing"):
self.addStatusMessage(
"Labelit: " +
self._edPluginExecEvaluationIndexingLABELIT.getDataOutput(
"statusMessageIndexing")[0].getValue())
# Check if indexing was successful
bIndexingSuccess = self._edPluginExecEvaluationIndexingLABELIT.getDataOutput(
"indexingSuccess")[0].getValue()
if bIndexingSuccess:
xsDataIndexingResult = self._edPluginExecEvaluationIndexingLABELIT.getDataOutput(
"indexingResult")[0]
self._xsDataResultCharacterisation.setIndexingResult(
xsDataIndexingResult)
# Then start the integration of the reference images
self.indexingToIntegration()
else:
self.screen("Indexing with LABELIT failed!")
self.setFailure()
def indexingToIntegration(self, _edPlugin=None):
# Create the XDS background image
xsDataInputControlXDSGenerateBackgroundImage = XSDataInputControlXDSGenerateBackgroundImage(
)
xsDataInputControlXDSGenerateBackgroundImage.setDataCollection(
self._xsDataCollection)
self._edPluginControlXDSGenerateBackgroundImage.setDataInput(
xsDataInputControlXDSGenerateBackgroundImage)
self._edPluginControlXDSGenerateBackgroundImage.execute()
# Integrate the reference images
xsDataIntegrationInput = XSDataIntegrationInput()
xsDataIntegrationInput.setDataCollection(
self._xsDataResultCharacterisation.getDataCollection())
xsDataIndexingResult = self._xsDataResultCharacterisation.getIndexingResult(
)
xsDataExperimentalConditionRefinded = xsDataIndexingResult.getSelectedSolution(
).getExperimentalConditionRefined()
xsDataIntegrationInput.setExperimentalConditionRefined(
xsDataExperimentalConditionRefinded)
xsDataIntegrationInput.setSelectedIndexingSolution(
xsDataIndexingResult.getSelectedSolution())
self._edPluginControlIntegration.setDataInput(xsDataIntegrationInput)
self.executePluginSynchronous(self._edPluginControlIntegration)
def doFailureEvaluationIndexingMOSFLM(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlCharacterisationv1_3.doFailureEvaluationIndexing")
strWarningMessage = "Execution of indexing evaluation plugin failed."
self.WARNING(strWarningMessage)
self.addWarningMessage(strWarningMessage)
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
def doFailureEvaluationIndexingLABELIT(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlCharacterisationv1_3.doFailureEvaluationIndexing")
strWarningMessage = "Execution of indexing evaluation plugin failed."
self.WARNING(strWarningMessage)
self.addWarningMessage(strWarningMessage)
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
def doSuccessGeneratePrediction(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlCharacterisationv1_3.doSuccessGeneratePrediction")
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlCharacterisationv1_3.doSuccessGeneratePrediction")
xsDataGeneratePredictionResult = _edPlugin.getDataOutput()
xsDataIndexingResult = self._xsDataResultCharacterisation.getIndexingResult(
)
xsDataIndexingResult.setPredictionResult(
xsDataGeneratePredictionResult)
def doFailureGeneratePrediction(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlCharacterisationv1_3.doFailureGeneratePrediction")
strWarningMessage = "Execution of generate prediction plugin failed."
self.WARNING(strWarningMessage)
self.addWarningMessage(strWarningMessage)
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
#self.addComment("warning: no prediction images")
def doSuccessIntegration(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_3.doSuccessIntegration")
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlCharacterisationv1_3.doSuccessIntegration")
# Wait for XDS plugin if necessary
self._edPluginControlXDSGenerateBackgroundImage.synchronize()
self.addStatusMessage("Integration successful.")
xsDataIntegrationOutput = self._edPluginControlIntegration.getDataOutput(
)
self._xsDataResultCharacterisation.setIntegrationResult(
xsDataIntegrationOutput)
# Integration short summary
if self._edPluginControlIntegration.hasDataOutput(
"integrationShortSummary"):
self._strCharacterisationShortSummary += self._edPluginControlIntegration.getDataOutput(
"integrationShortSummary")[0].getValue()
#self.DEBUG( self._xsDataExperimentCharacterisation.marshal() )
if self._bDoStrategyCalculation:
xsDataInputStrategy = XSDataInputStrategy()
xsDataSolutionSelected = self._xsDataResultCharacterisation.getIndexingResult(
).getSelectedSolution()
xsDataInputStrategy.setCrystalRefined(
xsDataSolutionSelected.getCrystal())
xsDataInputStrategy.setSample(self._xsDataResultCharacterisation.
getDataCollection().getSample())
xsDataIntegrationSubWedgeResultList = xsDataIntegrationOutput.getIntegrationSubWedgeResult(
)
xsDataInputStrategy.setBestFileContentDat(
xsDataIntegrationSubWedgeResultList[0].getBestfileDat())
xsDataInputStrategy.setBestFileContentPar(
xsDataIntegrationSubWedgeResultList[0].getBestfilePar())
xsDataInputStrategy.setExperimentalCondition(
xsDataIntegrationSubWedgeResultList[0].
getExperimentalConditionRefined())
xsDataInputStrategy.setXdsBackgroundImage(
self._xsDataFileXdsBackgroundImage)
xsDataInputStrategy.setDataCollection(self._xsDataCollection)
for xsDataIntegrationSubWedgeResult in xsDataIntegrationSubWedgeResultList:
xsDataInputStrategy.addBestFileContentHKL(
xsDataIntegrationSubWedgeResult.getBestfileHKL())
xsDataInputStrategy.setDiffractionPlan(
self._xsDataResultCharacterisation.getDataCollection(
).getDiffractionPlan())
self._edPluginControlStrategy.setDataInput(xsDataInputStrategy)
self.executePluginSynchronous(self._edPluginControlStrategy)
def doFailureIntegration(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_3.doFailureIntegration")
strErrorMessage = "Execution of integration plugin failed."
self.addStatusMessage("Integration FAILURE.")
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
#self.addComment("integration failure")
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
self.generateExecutiveSummary(self)
self.setFailure()
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage),
"statusMessage")
self.writeDataOutput()
def doSuccessXDSGenerateBackgroundImage(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlCharacterisationv1_3.doSuccessXDSGenerateBackgroundImage"
)
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlCharacterisationv1_3.doSuccessXDSGenerateBackgroundImage"
)
self._xsDataFileXdsBackgroundImage = self._edPluginControlXDSGenerateBackgroundImage.getDataOutput(
).getXdsBackgroundImage()
self._xsDataResultCharacterisation.setXdsBackgroundImage(
self._xsDataFileXdsBackgroundImage)
def doFailureXDSGenerateBackgroundImage(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlCharacterisationv1_3.doFailureXDSGenerateBackgroundImage"
)
def doSuccessStrategy(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_3.doSuccessStrategy")
self.retrieveSuccessMessages(
self._edPluginControlStrategy,
"EDPluginControlCharacterisationv1_3.doSuccessStrategy")
xsDataStrategyResult = self._edPluginControlStrategy.getDataOutput()
self._xsDataResultCharacterisation.setStrategyResult(
xsDataStrategyResult)
if self._edPluginControlStrategy.hasDataOutput("strategyShortSummary"):
self._strCharacterisationShortSummary += self._edPluginControlStrategy.getDataOutput(
"strategyShortSummary")[0].getValue()
self.addStatusMessage("Strategy calculation successful.")
def doFailureStrategy(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_3.doFailureStrategy")
strErrorMessage = "Strategy calculation FAILURE."
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
xsDataStrategyResult = self._edPluginControlStrategy.getDataOutput()
self._xsDataResultCharacterisation.setStrategyResult(
xsDataStrategyResult)
if self._edPluginControlStrategy.hasDataOutput("strategyShortSummary"):
self._strCharacterisationShortSummary += self._edPluginControlStrategy.getDataOutput(
"strategyShortSummary")[0].getValue()
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
self.addStatusMessage("Strategy calculation FAILURE.")
self.generateExecutiveSummary(self)
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage),
"statusMessage")
self.writeDataOutput()
self.setFailure()
def generateExecutiveSummary(self, _edPlugin):
"""
Generates a summary of the execution of the plugin.
"""
self.DEBUG(
"EDPluginControlCharacterisationv1_3.generateExecutiveSummary")
self.addExecutiveSummaryLine("Summary of characterisation:")
xsDataInputStrategy = self.getDataInput()
xsDataCollection = xsDataInputStrategy.getDataCollection()
# MXSUP-1445: Check if transmission is less than 10% and warn if it's the case
xsDataFirstSubWedge = xsDataCollection.getSubWedge()[0]
xsDataBeam = xsDataFirstSubWedge.getExperimentalCondition().getBeam()
if xsDataBeam.getTransmission() is not None:
fTransmission = xsDataBeam.getTransmission().getValue()
if fTransmission < self._fMinTransmission:
self.addExecutiveSummaryLine("^" * 80)
self.addExecutiveSummaryLine("^" * 80)
self.addExecutiveSummaryLine("")
self.addExecutiveSummaryLine(
"WARNING! Transmission for characterisation set to %.1f %%"
% fTransmission)
self.addExecutiveSummaryLine(
"Please consider re-characterising with transmission set to 100 %"
)
self.addExecutiveSummaryLine("")
self.addExecutiveSummaryLine("^" * 80)
self.addExecutiveSummaryLine("^" * 80)
xsDataDiffractionPlan = xsDataCollection.getDiffractionPlan()
self.addExecutiveSummaryLine("Diffraction plan:")
if (xsDataDiffractionPlan.getComplexity() is not None):
self.addExecutiveSummaryLine(
"BEST complexity : %s" %
xsDataDiffractionPlan.getComplexity().getValue())
if (xsDataDiffractionPlan.getAimedCompleteness() is not None):
self.addExecutiveSummaryLine(
"Aimed completeness : %6.1f [%%]" %
(100.0 *
xsDataDiffractionPlan.getAimedCompleteness().getValue()))
if (xsDataDiffractionPlan.getRequiredCompleteness() is not None):
self.addExecutiveSummaryLine(
"Required completeness : %6.1f [%%]" %
(100.0 *
xsDataDiffractionPlan.getRequiredCompleteness().getValue()))
if (xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution()
is not None):
self.addExecutiveSummaryLine(
"Aimed I/sigma at highest resolution : %6.1f" %
xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution(
).getValue())
if (xsDataDiffractionPlan.getAimedResolution() is not None):
self.addExecutiveSummaryLine(
"Aimed resolution : %6.1f [A]" %
xsDataDiffractionPlan.getAimedResolution().getValue())
if (xsDataDiffractionPlan.getRequiredResolution() is not None):
self.addExecutiveSummaryLine(
"Required resolution : %6.1f [A]" %
xsDataDiffractionPlan.getRequiredResolution().getValue())
if (xsDataDiffractionPlan.getAimedMultiplicity() is not None):
self.addExecutiveSummaryLine(
"Aimed multiplicity : %6.1f" %
xsDataDiffractionPlan.getAimedMultiplicity().getValue())
if (xsDataDiffractionPlan.getRequiredMultiplicity() is not None):
self.addExecutiveSummaryLine(
"Required multiplicity : %6.1f" %
xsDataDiffractionPlan.getRequiredMultiplicity().getValue())
if (xsDataDiffractionPlan.getForcedSpaceGroup() is not None):
self.addExecutiveSummaryLine(
"Forced space group : %6s" %
xsDataDiffractionPlan.getForcedSpaceGroup().getValue())
if (xsDataDiffractionPlan.getMaxExposureTimePerDataCollection()
is not None):
self.addExecutiveSummaryLine(
"Max exposure time per data collection : %6.1f [s]" %
xsDataDiffractionPlan.getMaxExposureTimePerDataCollection(
).getValue())
self.addExecutiveSummarySeparator()
if self._edPluginControlIndexingIndicators is not None:
self.appendExecutiveSummary(
self._edPluginControlIndexingIndicators, "")
if self._edPluginControlIndexingLabelit is not None:
self.appendExecutiveSummary(self._edPluginControlIndexingLabelit,
"")
if self._edPluginControlIntegration is not None:
self.appendExecutiveSummary(self._edPluginControlIntegration, "")
if self._edPluginControlStrategy is not None:
self.appendExecutiveSummary(self._edPluginControlStrategy, "")
self.addExecutiveSummarySeparator()
if self._strCharacterisationShortSummary is not None:
self.addExecutiveSummaryLine("Characterisation short summary:")
self.addExecutiveSummaryLine("")
if self._strStatusMessage != None:
for strLine in self._strStatusMessage.split(". "):
if strLine.endswith("."):
self.addExecutiveSummaryLine(strLine)
else:
self.addExecutiveSummaryLine(strLine + ".")
self.addExecutiveSummaryLine("")
for strLine in self._strCharacterisationShortSummary.split("\n"):
if strLine != "\n":
self.addExecutiveSummaryLine(strLine)
self.addErrorWarningMessagesToExecutiveSummary(
"Characterisation error and warning messages: ")
self.addExecutiveSummarySeparator()
def getPluginStrategyName(self):
return self._strPluginControlStrategy
def addStatusMessage(self, _strStatusMessage):
if self._strStatusMessage != "":
self._strStatusMessage += " "
self._strStatusMessage += _strStatusMessage
def doStrategyCalculation(self, _bValue):
self._bDoStrategyCalculation = _bValue
class EDPluginControlCharacterisationv1_6(EDPluginControl):
"""
Characterisation based on XDS
"""
def __init__(self):
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputCharacterisation)
self._strPluginControlIndexingIndicators = "EDPluginControlIndexingIndicatorsv1_1"
self._fMinTransmission = 10 # %
self._listPluginGenerateThumbnail = []
self._strCharacterisationShortSummary = ""
self._strStatusMessage = ""
self._strIndexingPluginName = "EDPluginXDSIndexingv1_0"
self._strIntegrationPluginName = "EDPluginXDSIntegrationv1_0"
self._edPluginIndexing = None
def checkParameters(self):
"""
Checks the mandatory parameters.
"""
self.DEBUG("EDPluginControlCharacterisationv1_6.checkParameters")
self.checkMandatoryParameters(self.getDataInput(),
"Data Input is None")
self.checkMandatoryParameters(self.getDataInput().getDataCollection(),
"dataCollection")
self.checkMandatoryParameters(
self.getDataInput().getDataCollection().getDiffractionPlan(),
"diffractionPlan")
def configure(self):
"""
Gets the configuration parameters (if any).
"""
EDPluginControl.configure(self)
self.DEBUG("EDPluginControlCharacterisationv1_6.configure")
self._strMxCuBE_URI = self.config.get("mxCuBE_URI", None)
if self._strMxCuBE_URI is not None and "mxCuBE_XMLRPC_log" in os.environ.keys(
):
self.DEBUG(
"Enabling sending messages to mxCuBE via URI {0}".format(
self._strMxCuBE_URI))
self._oServerProxy = xmlrpclib.ServerProxy(self._strMxCuBE_URI)
self._runKappa = self.config.get("runKappa", False)
self._fMinTransmission = self.config.get("minTransmissionWarning",
self._fMinTransmission)
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginControlCharacterisationv1_6.preProcess")
self._xsDataResultCharacterisation = XSDataResultCharacterisation()
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlCharacterisationv1_6.process")
self.doXdsIndexingIntegration(self.dataInput.dataCollection)
def finallyProcess(self, _edObject=None):
EDPluginControl.finallyProcess(self)
self.DEBUG("EDPluginControlCharacterisationv1_6.finallyProcess")
# Synchronize thumbnail plugins
for tuplePlugin in self._listPluginGenerateThumbnail:
image = tuplePlugin[0]
tuplePlugin[1].synchronize()
jpegImage = image.copy()
jpegImage.path = tuplePlugin[1].dataOutput.thumbnail.path
self._xsDataResultCharacterisation.addJpegImage(jpegImage)
tuplePlugin[2].synchronize()
thumbnailImage = image.copy()
thumbnailImage.path = tuplePlugin[2].dataOutput.thumbnail.path
self._xsDataResultCharacterisation.addThumbnailImage(
thumbnailImage)
# if self._edPluginControlGeneratePrediction.isRunning():
# self._edPluginControlGeneratePrediction.synchronize()
# if self._strStatusMessage != None:
# self.setDataOutput(XSDataString(self._strStatusMessage), "statusMessage")
# self._xsDataResultCharacterisation.setStatusMessage(XSDataString(self._strStatusMessage))
# if self._strCharacterisationShortSummary != None:
# self.setDataOutput(XSDataString(self._strCharacterisationShortSummary), "shortSummary")
# self._xsDataResultCharacterisation.setShortSummary(XSDataString(self._strCharacterisationShortSummary))
# if self._xsDataResultCharacterisation is not None:
# self.setDataOutput(self._xsDataResultCharacterisation)
if self.isFailure():
self.sendMessageToMXCuBE("Ended with error messages", "error")
def doXdsIndexingIntegration(self, _xsDataCollection):
# Load the plugin
self._edPluginIndexing = self.loadPlugin(self._strIndexingPluginName,
"Indexing")
# XDS Indexing
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.setDataCollection(_xsDataCollection)
self._edPluginIndexing.dataInput = EDHandlerXSDataXDSv1_0.generateXSDataInputXDSIndexing(
xsDataIndexingInput)
self._edPluginIndexing.executeSynchronous()
xsDataResultXDSIndexing = self._edPluginIndexing.dataOutput
if xsDataResultXDSIndexing.spaceGroupNumber is not None:
spaceGroupNumber = xsDataResultXDSIndexing.spaceGroupNumber.value
unitCell = xsDataResultXDSIndexing.unitCell
filePaths = xsDataResultXDSIndexing.filePaths
index = 1
for subWedge in _xsDataCollection.subWedge:
xsDataCollection = XSDataCollection()
xsDataCollection.addSubWedge(subWedge)
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.setDataCollection(xsDataCollection)
xsDataInputXDSIntegration = EDHandlerXSDataXDSv1_0.generateXSDataInputXDSIntegration(
xsDataIndexingInput, spaceGroupNumber, unitCell, filePaths)
edPluginIntegration = self.loadPlugin(
self._strIntegrationPluginName,
"Integration_{0}".format(index))
edPluginIntegration.dataInput = xsDataInputXDSIntegration
edPluginIntegration.executeSynchronous()
# self._edPluginIntegration.dataInput = xsDataInputXDSIntegration
index += 1
def generateExecutiveSummary(self, _edPlugin):
"""
Generates a summary of the execution of the plugin.
"""
self.DEBUG(
"EDPluginControlCharacterisationv1_6.generateExecutiveSummary")
self.addExecutiveSummaryLine("Summary of characterisation:")
xsDataInputStrategy = self.getDataInput()
xsDataCollection = xsDataInputStrategy.getDataCollection()
# MXSUP-1445: Check if transmission is less than 10% and warn if it's the case
xsDataFirstSubWedge = xsDataCollection.getSubWedge()[0]
xsDataBeam = xsDataFirstSubWedge.getExperimentalCondition().getBeam()
if xsDataBeam.getTransmission() is not None:
fTransmission = xsDataBeam.getTransmission().getValue()
if fTransmission < self._fMinTransmission:
self.addExecutiveSummaryLine("^" * 80)
self.addExecutiveSummaryLine("^" * 80)
self.addExecutiveSummaryLine("")
self.addExecutiveSummaryLine(
"WARNING! Transmission for characterisation set to %.1f %%"
% fTransmission)
self.addExecutiveSummaryLine(
"Please consider re-characterising with transmission set to 100 %"
)
self.addExecutiveSummaryLine("")
self.addExecutiveSummaryLine("^" * 80)
self.addExecutiveSummaryLine("^" * 80)
xsDataDiffractionPlan = xsDataCollection.getDiffractionPlan()
self.addExecutiveSummaryLine("Diffraction plan:")
if (xsDataDiffractionPlan.getComplexity() is not None):
self.addExecutiveSummaryLine(
"BEST complexity : %s" %
xsDataDiffractionPlan.getComplexity().getValue())
if (xsDataDiffractionPlan.getAimedCompleteness() is not None):
self.addExecutiveSummaryLine(
"Aimed completeness : %6.1f [%%]" %
(100.0 *
xsDataDiffractionPlan.getAimedCompleteness().getValue()))
if (xsDataDiffractionPlan.getRequiredCompleteness() is not None):
self.addExecutiveSummaryLine(
"Required completeness : %6.1f [%%]" %
(100.0 *
xsDataDiffractionPlan.getRequiredCompleteness().getValue()))
if (xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution()
is not None):
self.addExecutiveSummaryLine(
"Aimed I/sigma at highest resolution : %6.1f" %
xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution(
).getValue())
if (xsDataDiffractionPlan.getAimedResolution() is not None):
self.addExecutiveSummaryLine(
"Aimed resolution : %6.1f [A]" %
xsDataDiffractionPlan.getAimedResolution().getValue())
if (xsDataDiffractionPlan.getRequiredResolution() is not None):
self.addExecutiveSummaryLine(
"Required resolution : %6.1f [A]" %
xsDataDiffractionPlan.getRequiredResolution().getValue())
if (xsDataDiffractionPlan.getAimedMultiplicity() is not None):
self.addExecutiveSummaryLine(
"Aimed multiplicity : %6.1f" %
xsDataDiffractionPlan.getAimedMultiplicity().getValue())
if (xsDataDiffractionPlan.getRequiredMultiplicity() is not None):
self.addExecutiveSummaryLine(
"Required multiplicity : %6.1f" %
xsDataDiffractionPlan.getRequiredMultiplicity().getValue())
if (xsDataDiffractionPlan.getForcedSpaceGroup() is not None):
self.addExecutiveSummaryLine(
"Forced space group : %6s" %
xsDataDiffractionPlan.getForcedSpaceGroup().getValue())
if (xsDataDiffractionPlan.getMaxExposureTimePerDataCollection()
is not None):
self.addExecutiveSummaryLine(
"Max exposure time per data collection : %6.1f [s]" %
xsDataDiffractionPlan.getMaxExposureTimePerDataCollection(
).getValue())
self.addExecutiveSummarySeparator()
# if self._edPluginControlIndexingIndicators is not None:
# self.appendExecutiveSummary(self._edPluginControlIndexingIndicators, "")
# if self._edPluginControlIntegration is not None:
# self.appendExecutiveSummary(self._edPluginControlIntegration, "")
# if self._edPluginControlStrategy is not None:
# self.appendExecutiveSummary(self._edPluginControlStrategy, "")
self.addExecutiveSummarySeparator()
if self._strCharacterisationShortSummary is not None:
self.addExecutiveSummaryLine("Characterisation short summary:")
self.addExecutiveSummaryLine("")
if self._strStatusMessage != None:
for strLine in self._strStatusMessage.split(". "):
if strLine.endswith("."):
self.addExecutiveSummaryLine(strLine)
else:
self.addExecutiveSummaryLine(strLine + ".")
self.addExecutiveSummaryLine("")
for strLine in self._strCharacterisationShortSummary.split("\n"):
if strLine != "\n":
self.addExecutiveSummaryLine(strLine)
self.addErrorWarningMessagesToExecutiveSummary(
"Characterisation error and warning messages: ")
self.addExecutiveSummarySeparator()
def getPluginStrategyName(self):
return self._strPluginControlStrategy
def addStatusMessage(self, _strStatusMessage):
if self._strStatusMessage != "":
self._strStatusMessage += " "
self._strStatusMessage += _strStatusMessage
self.sendMessageToMXCuBE(_strStatusMessage)
def doStrategyCalculation(self, _bValue):
self._bDoStrategyCalculation = _bValue
def sendMessageToMXCuBE(self, _strMessage, level="info"):
# Only for mxCuBE
if self._strMxCuBE_URI is not None:
self.DEBUG("Sending message to mxCuBE: {0}".format(_strMessage))
try:
for strMessage in _strMessage.split("\n"):
if strMessage != "":
self._oServerProxy.log_message(
"Characterisation: " + strMessage, level)
except:
self.DEBUG("Sending message to mxCuBE failed!")
class EDPluginControlCharacterisationv1_3(EDPluginControl):
"""
[To be replaced with a description of EDPluginControlTemplatev10]
"""
def __init__(self):
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputCharacterisation)
self._strPluginControlIndexingIndicators = "EDPluginControlIndexingIndicatorsv10"
self._strPluginControlIndexingLabelit = "EDPluginControlIndexingLabelitv10"
self._strPluginExecEvaluationIndexing = "EDPluginExecEvaluationIndexingv10"
self._strPluginControlGeneratePrediction = "EDPluginControlGeneratePredictionv10"
self._strPluginControlIntegration = "EDPluginControlIntegrationv10"
self._strPluginControlXDSGenerateBackgroundImage = "EDPluginControlXDSGenerateBackgroundImagev1_0"
self._strPluginControlStrategy = "EDPluginControlStrategyv1_2"
self._strPluginGenerateThumbnailName = "EDPluginMXThumbnailv1_1"
self._listPluginGenerateThumbnail = []
self._edPluginControlIndexingIndicators = None
self._edPluginControlIndexingLabelit = None
self._edPluginExecEvaluationIndexingMOSFLM = None
self._edPluginExecEvaluationIndexingLABELIT = None
self._edPluginControlGeneratePrediction = None
self._edPluginControlIntegration = None
self._edPluginControlXDSGenerateBackgroundImage = None
self._edPluginControlStrategy = None
self._xsDataCollection = None
self._xsDataResultCharacterisation = None
self._xsDataIndexingResultMOSFLM = None
self._xsDataCrystal = None
self._strCharacterisationShortSummary = ""
self._strStatusMessage = ""
self._xsDataFileXdsBackgroundImage = None
self._bDoStrategyCalculation = True
self._fMinTransmission = 10 # %
def checkParameters(self):
"""
Checks the mandatory parameters.
"""
self.DEBUG("EDPluginControlCharacterisationv1_3.checkParameters")
self.checkMandatoryParameters(self.getDataInput(), "Data Input is None")
self.checkMandatoryParameters(self.getDataInput().getDataCollection(), "dataCollection")
self.checkMandatoryParameters(self.getDataInput().getDataCollection().getDiffractionPlan(), "diffractionPlan")
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginControlCharacterisationv1_3.preProcess")
# Load the plugins
self._edPluginControlIndexingIndicators = self.loadPlugin(self._strPluginControlIndexingIndicators, \
"Indexing")
self._edPluginControlIndexingLabelit = self.loadPlugin(self._strPluginControlIndexingLabelit, \
"IndexingLabelit")
self._edPluginExecEvaluationIndexingMOSFLM = self.loadPlugin(self._strPluginExecEvaluationIndexing, \
"IndexingEvalualtionMOSFLM")
self._edPluginExecEvaluationIndexingLABELIT = self.loadPlugin(self._strPluginExecEvaluationIndexing, \
"IndexingEvalualtionLABELIT")
self._edPluginControlGeneratePrediction = self.loadPlugin(self._strPluginControlGeneratePrediction, \
"GeneratePrediction")
self._edPluginControlIntegration = self.loadPlugin(self._strPluginControlIntegration, \
"Integration")
self._edPluginControlXDSGenerateBackgroundImage = self.loadPlugin(self._strPluginControlXDSGenerateBackgroundImage, \
"ControlXDSGenerateBackgroundImage")
self._edPluginControlStrategy = self.loadPlugin(self._strPluginControlStrategy, \
"Strategy")
if (self._edPluginControlIndexingIndicators is not None):
self.DEBUG("EDPluginControlCharacterisationv1_3.preProcess: " + self._strPluginControlIndexingIndicators + " Found... setting Data Input")
# create Data Input for indexing
xsDataInputCharacterisation = self.getDataInput()
self._xsDataCollection = xsDataInputCharacterisation.getDataCollection()
# MXSUP-1445: Check if transmission is less than 10% and warn if it's the case
xsDataFirstSubWedge = self._xsDataCollection.getSubWedge()[0]
xsDataBeam = xsDataFirstSubWedge.getExperimentalCondition().getBeam()
if xsDataBeam.getTransmission() is not None:
fTransmission = xsDataBeam.getTransmission().getValue()
if fTransmission < self._fMinTransmission:
strWarningMessageBanner = "^"*80
strWarningMessage1 = "WARNING! Transmission for characterisation set to %.1f %%" % fTransmission
strWarningMessage2 = "Please consider re-characterising with transmission set to 100 %"
self.warning(strWarningMessageBanner)
self.warning(strWarningMessage1)
self.warning(strWarningMessage2)
self.warning(strWarningMessageBanner)
self.addWarningMessage(strWarningMessageBanner)
self.addWarningMessage(strWarningMessage1)
self.addWarningMessage(strWarningMessage2)
self.addWarningMessage(strWarningMessageBanner)
xsDataCrystal = None
xsDataSubWedgeList = self._xsDataCollection.getSubWedge()
if ((xsDataSubWedgeList is None) or (xsDataSubWedgeList == [])):
strError = "EDPluginControlCharacterisationv1_3.preProcess: No subwedges in input data."
self.ERROR(strError)
self.setFailure()
else:
xsDataExperimentalCondition = xsDataSubWedgeList[0].getExperimentalCondition()
# Fix for bug 431: if the flux is zero raise an error
xsDataDoubleFlux = xsDataExperimentalCondition.getBeam().getFlux()
if (xsDataDoubleFlux is not None):
if (xsDataDoubleFlux.getValue() < 0.1):
strErrorMessage = "Input flux is negative or close to zero. Execution of characterisation aborted."
self.ERROR(strErrorMessage)
self.addErrorMessage("EDPluginControlCharacterisationv1_3.preProcess ERROR: " + strErrorMessage)
#self.addComment(strErrorMessage)
self.setFailure()
xsDataDiffractionPlan = self._xsDataCollection.getDiffractionPlan()
xsDataStringForcedSpaceGroup = xsDataDiffractionPlan.getForcedSpaceGroup()
if (xsDataStringForcedSpaceGroup is not None):
self._xsDataCrystal = XSDataCrystal()
xsDataSpaceGroup = XSDataSpaceGroup()
xsDataSpaceGroup.setName(xsDataStringForcedSpaceGroup)
self._xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
self._edPluginControlIndexingIndicators.setDataInput(self._xsDataCollection, "dataCollection")
if self._xsDataCrystal is not None:
self._edPluginControlIndexingIndicators.setDataInput(self._xsDataCrystal, "crystal")
# Populate characterisation object
self._xsDataResultCharacterisation = XSDataResultCharacterisation()
self._xsDataResultCharacterisation.setDataCollection(XSDataCollection.parseString(self._xsDataCollection.marshal()))
# Load the thumbnail plugins
for subWedge in xsDataInputCharacterisation.dataCollection.subWedge:
for image in subWedge.image:
edPluginJpeg = self.loadPlugin(self._strPluginGenerateThumbnailName)
xsDataInputMXThumbnail = XSDataInputMXThumbnail()
xsDataInputMXThumbnail.image = XSDataFile(image.path)
xsDataInputMXThumbnail.height = XSDataInteger(1024)
xsDataInputMXThumbnail.width = XSDataInteger(1024)
jpegFilename = os.path.splitext(os.path.basename(image.path.value))[0]+".jpg"
xsDataInputMXThumbnail.outputPath = XSDataFile(XSDataString(os.path.join(self.getWorkingDirectory(), jpegFilename)))
edPluginJpeg.dataInput = xsDataInputMXThumbnail
edPluginThumnail = self.loadPlugin(self._strPluginGenerateThumbnailName)
xsDataInputMXThumbnail = XSDataInputMXThumbnail()
xsDataInputMXThumbnail.image = XSDataFile(image.path)
xsDataInputMXThumbnail.height = XSDataInteger(256)
xsDataInputMXThumbnail.width = XSDataInteger(256)
thumbnailFilename = os.path.splitext(os.path.basename(image.path.value))[0]+".thumbnail.jpg"
xsDataInputMXThumbnail.outputPath = XSDataFile(XSDataString(os.path.join(self.getWorkingDirectory(), thumbnailFilename)))
edPluginThumnail.dataInput = xsDataInputMXThumbnail
self._listPluginGenerateThumbnail.append((image, edPluginJpeg, edPluginThumnail))
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlCharacterisationv1_3.process")
self._edPluginControlIndexingIndicators.connectSUCCESS(self.doSuccessIndexingIndicators)
self._edPluginControlIndexingIndicators.connectFAILURE(self.doFailureIndexingIndicators)
self._edPluginControlIndexingLabelit.connectSUCCESS(self.doSuccessIndexingLabelit)
self._edPluginControlIndexingLabelit.connectFAILURE(self.doFailureIndexingLabelit)
self._edPluginExecEvaluationIndexingMOSFLM.connectSUCCESS(self.doSuccessEvaluationIndexingMOSFLM)
self._edPluginExecEvaluationIndexingMOSFLM.connectFAILURE(self.doFailureEvaluationIndexingMOSFLM)
self._edPluginExecEvaluationIndexingLABELIT.connectSUCCESS(self.doSuccessEvaluationIndexingLABELIT)
self._edPluginExecEvaluationIndexingLABELIT.connectFAILURE(self.doFailureEvaluationIndexingLABELIT)
self._edPluginControlGeneratePrediction.connectSUCCESS(self.doSuccessGeneratePrediction)
self._edPluginControlGeneratePrediction.connectFAILURE(self.doFailureGeneratePrediction)
self._edPluginControlIntegration.connectSUCCESS(self.doSuccessIntegration)
self._edPluginControlIntegration.connectFAILURE(self.doFailureIntegration)
self._edPluginControlXDSGenerateBackgroundImage.connectSUCCESS(self.doSuccessXDSGenerateBackgroundImage)
self._edPluginControlXDSGenerateBackgroundImage.connectFAILURE(self.doFailureXDSGenerateBackgroundImage)
self._edPluginControlStrategy.connectSUCCESS(self.doSuccessStrategy)
self._edPluginControlStrategy.connectFAILURE(self.doFailureStrategy)
self.executePluginSynchronous(self._edPluginControlIndexingIndicators)
def finallyProcess(self, _edObject=None):
EDPluginControl.finallyProcess(self)
self.DEBUG("EDPluginControlCharacterisationv1_3.finallyProcess")
# Synchronize thumbnail plugins
for tuplePlugin in self._listPluginGenerateThumbnail:
image = tuplePlugin[0]
tuplePlugin[1].synchronize()
jpegImage = image.copy()
jpegImage.path = tuplePlugin[1].dataOutput.thumbnail.path
self._xsDataResultCharacterisation.addJpegImage(jpegImage)
tuplePlugin[2].synchronize()
thumbnailImage = image.copy()
thumbnailImage.path = tuplePlugin[2].dataOutput.thumbnail.path
self._xsDataResultCharacterisation.addThumbnailImage(thumbnailImage)
if self._edPluginControlGeneratePrediction.isRunning():
self._edPluginControlGeneratePrediction.synchronize()
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage), "statusMessage")
self._xsDataResultCharacterisation.setStatusMessage(XSDataString(self._strStatusMessage))
if self._strCharacterisationShortSummary != None:
self.setDataOutput(XSDataString(self._strCharacterisationShortSummary), "shortSummary")
self._xsDataResultCharacterisation.setShortSummary(XSDataString(self._strCharacterisationShortSummary))
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
def doSuccessIndexingIndicators(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_3.doSuccessIndexingIndicators")
#self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv1_3.doSuccessIndexingIndicators")
if self._edPluginControlIndexingIndicators.hasDataOutput("indexingResult"):
xsDataIndexingResult = self._edPluginControlIndexingIndicators.getDataOutput("indexingResult")[0]
#self._xsDataResultCharacterisation.setIndexingResult(xsDataIndexingResult)
self._edPluginExecEvaluationIndexingMOSFLM.setDataInput(xsDataIndexingResult, "indexingResult")
if self._edPluginControlIndexingIndicators.hasDataOutput("imageQualityIndicators"):
listXSDataImageQualityIndicators = self._edPluginControlIndexingIndicators.getDataOutput("imageQualityIndicators")
for xsDataImageQualityIndicators in listXSDataImageQualityIndicators:
self._xsDataResultCharacterisation.addImageQualityIndicators(xsDataImageQualityIndicators)
self._edPluginExecEvaluationIndexingMOSFLM.setDataInput(xsDataImageQualityIndicators, "imageQualityIndicators")
if self._edPluginControlIndexingIndicators.hasDataOutput("indicatorsShortSummary"):
self._strCharacterisationShortSummary += self._edPluginControlIndexingIndicators.getDataOutput("indicatorsShortSummary")[0].getValue()
for tuplePlugin in self._listPluginGenerateThumbnail:
tuplePlugin[1].execute()
tuplePlugin[2].execute()
self.executePluginSynchronous(self._edPluginExecEvaluationIndexingMOSFLM)
def doFailureIndexingIndicators(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_3.doFailureIndexingIndicators")
strErrorMessage = "Execution of Indexing and Indicators plugin failed. Execution of characterisation aborted."
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
self.setFailure()
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage), "statusMessage")
self.writeDataOutput()
# def doSuccessIndexingLabelit(self, _edPlugin=None):
# self.DEBUG("EDPluginControlCharacterisationv1_3.doSuccessIndexingLabelit")
# self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv1_3.doSuccessIndexingLabelit")
# # Retrieve the indexing result
# xsDataIndexingResult = self._edPluginControlIndexingLabelit.getDataOutput()
# self._xsDataResultCharacterisation.setIndexingResult(xsDataIndexingResult)
# if self._edPluginControlIndexingLabelit.hasDataOutput("indexingShortSummary"):
# self._strCharacterisationShortSummary += self._edPluginControlIndexingLabelit.getDataOutput("indexingShortSummary")[0].getValue()
# # Then start the integration of the reference images
# self.indexingToIntegration()
def doSuccessIndexingLabelit(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_3.doSuccessIndexingLabelit")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv1_3.doSuccessIndexingLabelit")
if self._edPluginControlIndexingLabelit.hasDataOutput("indexingShortSummary"):
self._strCharacterisationShortSummary += self._edPluginControlIndexingLabelit.getDataOutput("indexingShortSummary")[0].getValue()
# Check the indexing results
xsDataIndexingResult = self._edPluginControlIndexingLabelit.getDataOutput()
self._edPluginExecEvaluationIndexingLABELIT.setDataInput(xsDataIndexingResult, "indexingResult")
xsDataImageQualityIndicators = self._xsDataResultCharacterisation.getImageQualityIndicators()[0]
self._edPluginExecEvaluationIndexingLABELIT.setDataInput(xsDataImageQualityIndicators, "imageQualityIndicators")
self.executePluginSynchronous(self._edPluginExecEvaluationIndexingLABELIT)
def doFailureIndexingLabelit(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_3.doFailureIndexingLabelit")
self.addStatusMessage("Labelit: Indexing FAILURE.")
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
if self._xsDataIndexingResultMOSFLM == None:
strErrorMessage = "Execution of indexing with both MOSFLM and Labelit failed. Execution of characterisation aborted."
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.generateExecutiveSummary(self)
self.setFailure()
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage), "statusMessage")
self.writeDataOutput()
else:
# Use the MOSFLM indexing results - even if it's P1
self._xsDataResultCharacterisation.setIndexingResult(self._xsDataIndexingResultMOSFLM)
xsDataCollection = self._xsDataResultCharacterisation.getDataCollection()
xsDataGeneratePredictionInput = XSDataGeneratePredictionInput()
xsDataGeneratePredictionInput.setDataCollection(XSDataCollection.parseString(xsDataCollection.marshal()))
xsDataGeneratePredictionInput.setSelectedIndexingSolution(XSDataIndexingSolutionSelected.parseString(self._xsDataIndexingResultMOSFLM.getSelectedSolution().marshal()))
self._edPluginControlGeneratePrediction.setDataInput(xsDataGeneratePredictionInput)
if self._edPluginControlIndexingIndicators.hasDataOutput("indexingShortSummary"):
self._strCharacterisationShortSummary += self._edPluginControlIndexingIndicators.getDataOutput("indexingShortSummary")[0].getValue()
# Start the generation of prediction images - we synchronize in the post-process
self._edPluginControlGeneratePrediction.execute()
# Then start the integration of the reference images
self.indexingToIntegration()
def doSuccessEvaluationIndexingMOSFLM(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_3.doSuccessEvaluationIndexingMOSFLM")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv1_3.doSuccessEvaluationIndexing")
# Retrieve status messages (if any)
if self._edPluginExecEvaluationIndexingMOSFLM.hasDataOutput("statusMessageImageQualityIndicators"):
self.addStatusMessage(self._edPluginExecEvaluationIndexingMOSFLM.getDataOutput("statusMessageImageQualityIndicators")[0].getValue())
if self._edPluginExecEvaluationIndexingMOSFLM.hasDataOutput("statusMessageIndexing"):
self.addStatusMessage("MOSFLM: " + self._edPluginExecEvaluationIndexingMOSFLM.getDataOutput("statusMessageIndexing")[0].getValue())
# Check if indexing was successful
bIndexWithLabelit = False
bIndexingSuccess = self._edPluginExecEvaluationIndexingMOSFLM.getDataOutput("indexingSuccess")[0].getValue()
if bIndexingSuccess:
xsDataIndexingResult = self._edPluginExecEvaluationIndexingMOSFLM.getDataOutput("indexingResult")[0]
self._xsDataIndexingResultMOSFLM = xsDataIndexingResult
# Check if space group is P1 - if yes run Labelit indexing
xsDataIndexingSolutionSelected = xsDataIndexingResult.getSelectedSolution()
xsDataCrystal = xsDataIndexingSolutionSelected.getCrystal()
xsDataSpaceGroup = xsDataCrystal.getSpaceGroup()
strSpaceGroupName = xsDataSpaceGroup.getName().getValue().upper()
# Check if MOSFLM has indexed in P1
if strSpaceGroupName == "P1":
# Check if the user maybe asked for P1!
bIndexWithLabelit = True
if self._xsDataCollection.getDiffractionPlan() is not None:
if self._xsDataCollection.getDiffractionPlan().getForcedSpaceGroup() is not None:
if self._xsDataCollection.getDiffractionPlan().getForcedSpaceGroup().getValue().upper() == "P1":
self.screen("P1 space forced by diffraction plan")
bIndexWithLabelit = False
if bIndexWithLabelit:
self.screen("P1 space group choosed - reindexing with Labelit")
else:
self.screen("MOSFLM indexing successful!")
if self._edPluginControlIndexingIndicators.hasDataOutput("indexingShortSummary"):
self._strCharacterisationShortSummary += self._edPluginControlIndexingIndicators.getDataOutput("indexingShortSummary")[0].getValue()
# Generate prediction images
xsDataCollection = self._xsDataResultCharacterisation.getDataCollection()
self._xsDataResultCharacterisation.setIndexingResult(xsDataIndexingResult)
xsDataGeneratePredictionInput = XSDataGeneratePredictionInput()
xsDataGeneratePredictionInput.setDataCollection(XSDataCollection.parseString(xsDataCollection.marshal()))
xsDataGeneratePredictionInput.setSelectedIndexingSolution(XSDataIndexingSolutionSelected.parseString(xsDataIndexingResult.getSelectedSolution().marshal()))
self._edPluginControlGeneratePrediction.setDataInput(xsDataGeneratePredictionInput)
# Start the generation of prediction images - we synchronize in the post-process
self._edPluginControlGeneratePrediction.execute()
# Then start the integration of the reference images
self.indexingToIntegration()
else:
self.screen("Indexing with MOSFLM failed!")
bIndexWithLabelit = True
if bIndexWithLabelit:
# Execute Labelit indexing
self.screen("Now trying to index with Labelit - please be patient...")
xsDataIndexingInput = XSDataIndexingInput()
xsDataSubWedgeList = self._xsDataCollection.getSubWedge()
xsDataExperimentalCondition = xsDataSubWedgeList[0].getExperimentalCondition()
xsDataIndexingInput.setDataCollection(self._xsDataCollection)
xsDataIndexingInput.setExperimentalCondition(xsDataExperimentalCondition)
if self._xsDataCrystal != None:
xsDataIndexingInput.setCrystal(self._xsDataCrystal)
self._edPluginControlIndexingLabelit.setDataInput(xsDataIndexingInput)
self.executePluginSynchronous(self._edPluginControlIndexingLabelit)
def doSuccessEvaluationIndexingLABELIT(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_3.doSuccessEvaluationIndexingLABELIT")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv1_3.doSuccessEvaluationIndexingLABELIT")
# Retrieve status messages (if any)
if self._edPluginExecEvaluationIndexingLABELIT.hasDataOutput("statusMessageIndexing"):
self.addStatusMessage("Labelit: " + self._edPluginExecEvaluationIndexingLABELIT.getDataOutput("statusMessageIndexing")[0].getValue())
# Check if indexing was successful
bIndexingSuccess = self._edPluginExecEvaluationIndexingLABELIT.getDataOutput("indexingSuccess")[0].getValue()
if bIndexingSuccess:
xsDataIndexingResult = self._edPluginExecEvaluationIndexingLABELIT.getDataOutput("indexingResult")[0]
self._xsDataResultCharacterisation.setIndexingResult(xsDataIndexingResult)
# Then start the integration of the reference images
self.indexingToIntegration()
else:
self.screen("Indexing with LABELIT failed!")
self.setFailure()
def indexingToIntegration(self, _edPlugin=None):
# Create the XDS background image
xsDataInputControlXDSGenerateBackgroundImage = XSDataInputControlXDSGenerateBackgroundImage()
xsDataInputControlXDSGenerateBackgroundImage.setDataCollection(self._xsDataCollection)
self._edPluginControlXDSGenerateBackgroundImage.setDataInput(xsDataInputControlXDSGenerateBackgroundImage)
self._edPluginControlXDSGenerateBackgroundImage.execute()
# Integrate the reference images
xsDataIntegrationInput = XSDataIntegrationInput()
xsDataIntegrationInput.setDataCollection(self._xsDataResultCharacterisation.getDataCollection())
xsDataIndexingResult = self._xsDataResultCharacterisation.getIndexingResult()
xsDataExperimentalConditionRefinded = xsDataIndexingResult.getSelectedSolution().getExperimentalConditionRefined()
xsDataIntegrationInput.setExperimentalConditionRefined(xsDataExperimentalConditionRefinded)
xsDataIntegrationInput.setSelectedIndexingSolution(xsDataIndexingResult.getSelectedSolution())
self._edPluginControlIntegration.setDataInput(xsDataIntegrationInput)
self.executePluginSynchronous(self._edPluginControlIntegration)
def doFailureEvaluationIndexingMOSFLM(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_3.doFailureEvaluationIndexing")
strWarningMessage = "Execution of indexing evaluation plugin failed."
self.WARNING(strWarningMessage)
self.addWarningMessage(strWarningMessage)
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
def doFailureEvaluationIndexingLABELIT(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_3.doFailureEvaluationIndexing")
strWarningMessage = "Execution of indexing evaluation plugin failed."
self.WARNING(strWarningMessage)
self.addWarningMessage(strWarningMessage)
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
def doSuccessGeneratePrediction(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_3.doSuccessGeneratePrediction")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv1_3.doSuccessGeneratePrediction")
xsDataGeneratePredictionResult = _edPlugin.getDataOutput()
xsDataIndexingResult = self._xsDataResultCharacterisation.getIndexingResult()
xsDataIndexingResult.setPredictionResult(xsDataGeneratePredictionResult)
def doFailureGeneratePrediction(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_3.doFailureGeneratePrediction")
strWarningMessage = "Execution of generate prediction plugin failed."
self.WARNING(strWarningMessage)
self.addWarningMessage(strWarningMessage)
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
#self.addComment("warning: no prediction images")
def doSuccessIntegration(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_3.doSuccessIntegration")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv1_3.doSuccessIntegration")
# Wait for XDS plugin if necessary
self._edPluginControlXDSGenerateBackgroundImage.synchronize()
self.addStatusMessage("Integration successful.")
xsDataIntegrationOutput = self._edPluginControlIntegration.getDataOutput()
self._xsDataResultCharacterisation.setIntegrationResult(xsDataIntegrationOutput)
# Integration short summary
if self._edPluginControlIntegration.hasDataOutput("integrationShortSummary"):
self._strCharacterisationShortSummary += self._edPluginControlIntegration.getDataOutput("integrationShortSummary")[0].getValue()
#self.DEBUG( self._xsDataExperimentCharacterisation.marshal() )
if self._bDoStrategyCalculation:
xsDataInputStrategy = XSDataInputStrategy()
xsDataSolutionSelected = self._xsDataResultCharacterisation.getIndexingResult().getSelectedSolution()
xsDataInputStrategy.setCrystalRefined(xsDataSolutionSelected.getCrystal())
xsDataInputStrategy.setSample(self._xsDataResultCharacterisation.getDataCollection().getSample())
xsDataIntegrationSubWedgeResultList = xsDataIntegrationOutput.getIntegrationSubWedgeResult()
xsDataInputStrategy.setBestFileContentDat(xsDataIntegrationSubWedgeResultList[0].getBestfileDat())
xsDataInputStrategy.setBestFileContentPar(xsDataIntegrationSubWedgeResultList[0].getBestfilePar())
xsDataInputStrategy.setExperimentalCondition(xsDataIntegrationSubWedgeResultList[0].getExperimentalConditionRefined())
xsDataInputStrategy.setXdsBackgroundImage(self._xsDataFileXdsBackgroundImage)
xsDataInputStrategy.setDataCollection(self._xsDataCollection)
for xsDataIntegrationSubWedgeResult in xsDataIntegrationSubWedgeResultList:
xsDataInputStrategy.addBestFileContentHKL(xsDataIntegrationSubWedgeResult.getBestfileHKL())
xsDataInputStrategy.setDiffractionPlan(self._xsDataResultCharacterisation.getDataCollection().getDiffractionPlan())
self._edPluginControlStrategy.setDataInput(xsDataInputStrategy)
self.executePluginSynchronous(self._edPluginControlStrategy)
def doFailureIntegration(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_3.doFailureIntegration")
strErrorMessage = "Execution of integration plugin failed."
self.addStatusMessage("Integration FAILURE.")
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
#self.addComment("integration failure")
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
self.generateExecutiveSummary(self)
self.setFailure()
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage), "statusMessage")
self.writeDataOutput()
def doSuccessXDSGenerateBackgroundImage(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_3.doSuccessXDSGenerateBackgroundImage")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv1_3.doSuccessXDSGenerateBackgroundImage")
self._xsDataFileXdsBackgroundImage = self._edPluginControlXDSGenerateBackgroundImage.getDataOutput().getXdsBackgroundImage()
self._xsDataResultCharacterisation.setXdsBackgroundImage(self._xsDataFileXdsBackgroundImage)
def doFailureXDSGenerateBackgroundImage(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_3.doFailureXDSGenerateBackgroundImage")
def doSuccessStrategy(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_3.doSuccessStrategy")
self.retrieveSuccessMessages(self._edPluginControlStrategy, "EDPluginControlCharacterisationv1_3.doSuccessStrategy")
xsDataStrategyResult = self._edPluginControlStrategy.getDataOutput()
self._xsDataResultCharacterisation.setStrategyResult(xsDataStrategyResult)
if self._edPluginControlStrategy.hasDataOutput("strategyShortSummary"):
self._strCharacterisationShortSummary += self._edPluginControlStrategy.getDataOutput("strategyShortSummary")[0].getValue()
self.addStatusMessage("Strategy calculation successful.")
def doFailureStrategy(self, _edPlugin=None):
self.DEBUG("EDPluginControlCharacterisationv1_3.doFailureStrategy")
strErrorMessage = "Strategy calculation FAILURE."
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
xsDataStrategyResult = self._edPluginControlStrategy.getDataOutput()
self._xsDataResultCharacterisation.setStrategyResult(xsDataStrategyResult)
if self._edPluginControlStrategy.hasDataOutput("strategyShortSummary"):
self._strCharacterisationShortSummary += self._edPluginControlStrategy.getDataOutput("strategyShortSummary")[0].getValue()
if self._xsDataResultCharacterisation is not None:
self.setDataOutput(self._xsDataResultCharacterisation)
self.addStatusMessage("Strategy calculation FAILURE.")
self.generateExecutiveSummary(self)
if self._strStatusMessage != None:
self.setDataOutput(XSDataString(self._strStatusMessage), "statusMessage")
self.writeDataOutput()
self.setFailure()
def generateExecutiveSummary(self, _edPlugin):
"""
Generates a summary of the execution of the plugin.
"""
self.DEBUG("EDPluginControlCharacterisationv1_3.generateExecutiveSummary")
self.addExecutiveSummaryLine("Summary of characterisation:")
xsDataInputStrategy = self.getDataInput()
xsDataCollection = xsDataInputStrategy.getDataCollection()
# MXSUP-1445: Check if transmission is less than 10% and warn if it's the case
xsDataFirstSubWedge = xsDataCollection.getSubWedge()[0]
xsDataBeam = xsDataFirstSubWedge.getExperimentalCondition().getBeam()
if xsDataBeam.getTransmission() is not None:
fTransmission = xsDataBeam.getTransmission().getValue()
if fTransmission < self._fMinTransmission:
self.addExecutiveSummaryLine("^"*80)
self.addExecutiveSummaryLine("^"*80)
self.addExecutiveSummaryLine("")
self.addExecutiveSummaryLine("WARNING! Transmission for characterisation set to %.1f %%" % fTransmission)
self.addExecutiveSummaryLine("Please consider re-characterising with transmission set to 100 %")
self.addExecutiveSummaryLine("")
self.addExecutiveSummaryLine("^"*80)
self.addExecutiveSummaryLine("^"*80)
xsDataDiffractionPlan = xsDataCollection.getDiffractionPlan()
self.addExecutiveSummaryLine("Diffraction plan:")
if (xsDataDiffractionPlan.getComplexity() is not None):
self.addExecutiveSummaryLine("BEST complexity : %s" % xsDataDiffractionPlan.getComplexity().getValue())
if (xsDataDiffractionPlan.getAimedCompleteness() is not None):
self.addExecutiveSummaryLine("Aimed completeness : %6.1f [%%]" % (100.0 * xsDataDiffractionPlan.getAimedCompleteness().getValue()))
if (xsDataDiffractionPlan.getRequiredCompleteness() is not None):
self.addExecutiveSummaryLine("Required completeness : %6.1f [%%]" % (100.0 * xsDataDiffractionPlan.getRequiredCompleteness().getValue()))
if (xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution() is not None):
self.addExecutiveSummaryLine("Aimed I/sigma at highest resolution : %6.1f" % xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution().getValue())
if (xsDataDiffractionPlan.getAimedResolution() is not None):
self.addExecutiveSummaryLine("Aimed resolution : %6.1f [A]" % xsDataDiffractionPlan.getAimedResolution().getValue())
if (xsDataDiffractionPlan.getRequiredResolution() is not None):
self.addExecutiveSummaryLine("Required resolution : %6.1f [A]" % xsDataDiffractionPlan.getRequiredResolution().getValue())
if (xsDataDiffractionPlan.getAimedMultiplicity() is not None):
self.addExecutiveSummaryLine("Aimed multiplicity : %6.1f" % xsDataDiffractionPlan.getAimedMultiplicity().getValue())
if (xsDataDiffractionPlan.getRequiredMultiplicity() is not None):
self.addExecutiveSummaryLine("Required multiplicity : %6.1f" % xsDataDiffractionPlan.getRequiredMultiplicity().getValue())
if (xsDataDiffractionPlan.getForcedSpaceGroup() is not None):
self.addExecutiveSummaryLine("Forced space group : %6s" % xsDataDiffractionPlan.getForcedSpaceGroup().getValue())
if (xsDataDiffractionPlan.getMaxExposureTimePerDataCollection() is not None):
self.addExecutiveSummaryLine("Max exposure time per data collection : %6.1f [s]" % xsDataDiffractionPlan.getMaxExposureTimePerDataCollection().getValue())
self.addExecutiveSummarySeparator()
if self._edPluginControlIndexingIndicators is not None:
self.appendExecutiveSummary(self._edPluginControlIndexingIndicators, "")
if self._edPluginControlIndexingLabelit is not None:
self.appendExecutiveSummary(self._edPluginControlIndexingLabelit, "")
if self._edPluginControlIntegration is not None:
self.appendExecutiveSummary(self._edPluginControlIntegration, "")
if self._edPluginControlStrategy is not None:
self.appendExecutiveSummary(self._edPluginControlStrategy, "")
self.addExecutiveSummarySeparator()
if self._strCharacterisationShortSummary is not None:
self.addExecutiveSummaryLine("Characterisation short summary:")
self.addExecutiveSummaryLine("")
if self._strStatusMessage != None:
for strLine in self._strStatusMessage.split(". "):
if strLine.endswith("."):
self.addExecutiveSummaryLine(strLine)
else:
self.addExecutiveSummaryLine(strLine + ".")
self.addExecutiveSummaryLine("")
for strLine in self._strCharacterisationShortSummary.split("\n"):
if strLine != "\n":
self.addExecutiveSummaryLine(strLine)
self.addErrorWarningMessagesToExecutiveSummary("Characterisation error and warning messages: ")
self.addExecutiveSummarySeparator()
def getPluginStrategyName(self):
return self._strPluginControlStrategy
def addStatusMessage(self, _strStatusMessage):
if self._strStatusMessage != "":
self._strStatusMessage += " "
self._strStatusMessage += _strStatusMessage
def doStrategyCalculation(self, _bValue):
self._bDoStrategyCalculation = _bValue