def createInputCharacterisationFromSubWedges(self):
self.DEBUG("EDPluginControlInterfacev1_3.createInputCharacterisationFromSubWedges")
xsDataResultSubWedgeAssemble = self.edPluginControlSubWedgeAssemble.getDataOutput()
self.xsDataInputCharacterisation = XSDataInputCharacterisation()
xsDataCollection = XSDataCollection()
# Default exposure time (for the moment, this value should be
# possible to read from the command line)
if self.xsDataDiffractionPlan is None:
self.xsDataDiffractionPlan = XSDataDiffractionPlan()
if (not xsDataResultSubWedgeAssemble is None):
pyListSubWedge = xsDataResultSubWedgeAssemble.getSubWedge()
xsDataCollection.setSubWedge(pyListSubWedge)
for xsDataSubWedge in pyListSubWedge:
if (self.strComplexity is not None):
self.xsDataDiffractionPlan.setComplexity(XSDataString(self.strComplexity))
if (self.fFlux is not None):
xsDataSubWedge.getExperimentalCondition().getBeam().setFlux(XSDataFlux(self.fFlux))
if (self.fBeamSizeX is not None) and (self.fBeamSizeY is not None):
xsDataSize = XSDataSize()
xsDataSize.setX(XSDataLength(self.fBeamSizeX))
xsDataSize.setY(XSDataLength(self.fBeamSizeY))
xsDataSubWedge.getExperimentalCondition().getBeam().setSize(xsDataSize)
if (self.fApertureSize is not None):
xsDataSubWedge.getExperimentalCondition().getBeam().setApertureSize(XSDataLength(self.fApertureSize))
if (self.fBeamPosX is not None):
xsDataSubWedge.getExperimentalCondition().getDetector().setBeamPositionX(XSDataLength(self.fBeamPosX))
if (self.fBeamPosY is not None):
xsDataSubWedge.getExperimentalCondition().getDetector().setBeamPositionY(XSDataLength(self.fBeamPosY))
if (self.fMinExposureTimePerImage is not None):
xsDataSubWedge.getExperimentalCondition().getBeam().setMinExposureTimePerImage(XSDataTime(self.fMinExposureTimePerImage))
if (self.fTransmission is not None):
xsDataSubWedge.getExperimentalCondition().getBeam().setTransmission(XSDataDouble(self.fTransmission))
if (self.fWavelength is not None):
xsDataSubWedge.getExperimentalCondition().getBeam().setWavelength(XSDataWavelength(self.fWavelength))
if self.fMinOscillationWidth != None:
xsDataSubWedge.getExperimentalCondition().getGoniostat().setMinOscillationWidth(XSDataAngle(self.fMinOscillationWidth))
if self.fMaxOscillationSpeed != None:
xsDataSubWedge.getExperimentalCondition().getGoniostat().setMaxOscillationSpeed(XSDataAngularSpeed(self.fMaxOscillationSpeed))
if (self.strForcedSpaceGroup is not None):
self.xsDataDiffractionPlan.setForcedSpaceGroup(XSDataString(self.strForcedSpaceGroup))
self.xsDataDiffractionPlan.setAnomalousData(XSDataBoolean(self.bAnomalousData))
self.xsDataDiffractionPlan.setMaxExposureTimePerDataCollection(XSDataTime(self.fMaxExposureTimePerDataCollection))
if (self.strStrategyOption is not None):
self.xsDataDiffractionPlan.setStrategyOption(XSDataString(self.strStrategyOption))
xsDataCollection.setDiffractionPlan(self.xsDataDiffractionPlan)
if self.xsDataSample is not None:
xsDataCollection.setSample(XSDataSampleCrystalMM.parseString(self.xsDataSample.marshal()))
self.xsDataInputCharacterisation.setDataCollection(xsDataCollection)
def createInputCharacterisationFromSubWedges(self):
self.DEBUG("EDPluginControlInterfacev1_2.createInputCharacterisationFromSubWedges")
xsDataResultSubWedgeAssemble = self.edPluginControlSubWedgeAssemble.getDataOutput()
self.xsDataInputCharacterisation = XSDataInputCharacterisation()
xsDataCollection = XSDataCollection()
# Default exposure time (for the moment, this value should be
# possible to read from the command line)
if self.xsDataDiffractionPlan is None:
self.xsDataDiffractionPlan = XSDataDiffractionPlan()
if (not xsDataResultSubWedgeAssemble is None):
pyListSubWedge = xsDataResultSubWedgeAssemble.getSubWedge()
xsDataCollection.setSubWedge(pyListSubWedge)
for xsDataSubWedge in pyListSubWedge:
if (self.strComplexity is not None):
self.xsDataDiffractionPlan.setComplexity(XSDataString(self.strComplexity))
if (self.fFlux is not None):
xsDataSubWedge.getExperimentalCondition().getBeam().setFlux(XSDataFlux(self.fFlux))
if (self.fBeamSizeX is not None) and (self.fBeamSizeY is not None):
xsDataSize = XSDataSize()
xsDataSize.setX(XSDataLength(self.fBeamSizeX))
xsDataSize.setY(XSDataLength(self.fBeamSizeY))
xsDataSubWedge.getExperimentalCondition().getBeam().setSize(xsDataSize)
if (self.fBeamPosX is not None):
xsDataSubWedge.getExperimentalCondition().getDetector().setBeamPositionX(XSDataLength(self.fBeamPosX))
if (self.fBeamPosY is not None):
xsDataSubWedge.getExperimentalCondition().getDetector().setBeamPositionY(XSDataLength(self.fBeamPosY))
if (self.fMinExposureTimePerImage is not None):
xsDataSubWedge.getExperimentalCondition().getBeam().setMinExposureTimePerImage(XSDataTime(self.fMinExposureTimePerImage))
if (self.fTransmission is not None):
xsDataSubWedge.getExperimentalCondition().getBeam().setTransmission(XSDataDouble(self.fTransmission))
if (self.fWavelength is not None):
xsDataSubWedge.getExperimentalCondition().getBeam().setWavelength(XSDataWavelength(self.fWavelength))
if self.fMinOscillationWidth != None:
xsDataSubWedge.getExperimentalCondition().getGoniostat().setMinOscillationWidth(XSDataAngle(self.fMinOscillationWidth))
if self.fMaxOscillationSpeed != None:
xsDataSubWedge.getExperimentalCondition().getGoniostat().setMaxOscillationSpeed(XSDataAngularSpeed(self.fMaxOscillationSpeed))
if (self.strForcedSpaceGroup is not None):
self.xsDataDiffractionPlan.setForcedSpaceGroup(XSDataString(self.strForcedSpaceGroup))
self.xsDataDiffractionPlan.setAnomalousData(XSDataBoolean(self.bAnomalousData))
self.xsDataDiffractionPlan.setMaxExposureTimePerDataCollection(XSDataTime(self.fMaxExposureTimePerDataCollection))
if (self.strStrategyOption is not None):
self.xsDataDiffractionPlan.setStrategyOption(XSDataString(self.strStrategyOption))
xsDataCollection.setDiffractionPlan(self.xsDataDiffractionPlan)
if self.xsDataSample is not None:
xsDataCollection.setSample(XSDataSampleCrystalMM.parseString(self.xsDataSample.marshal()))
self.xsDataInputCharacterisation.setDataCollection(xsDataCollection)
self.xsDataInputCharacterisation.setToken(self.xsDataToken)
def getXSDataResultStrategy(self, _xsDataResultBest, _xsDataExperimentalCondition, _xsDataSample):
xsDataResultStrategy = XSDataResultStrategy()
#xsDataCollectionRunsBest = _xsDataResultBest.getCollectionRun()
xsDataCollectionPlansBest = _xsDataResultBest.getCollectionPlan()
for xsDataCollectionPlanBest in xsDataCollectionPlansBest:
xsDataCollectionPlan = XSDataCollectionPlan()
xsDataCollectionStrategy = XSDataCollection()
xsDataDoubleTransmission = xsDataCollectionPlanBest.getStrategySummary().getAttenuation()
for xsDataCollectionRunBest in xsDataCollectionPlanBest.getCollectionRun():
xsDataSubWedge = XSDataSubWedge()
strXmlStringDataExperimentalCondition = _xsDataExperimentalCondition.marshal()
xsDataExperimentalCondition = XSDataExperimentalCondition.parseString(strXmlStringDataExperimentalCondition)
xsDataExperimentalCondition.getBeam().setExposureTime(xsDataCollectionRunBest.getExposureTime())
xsDataExperimentalCondition.getBeam().setTransmission(xsDataDoubleTransmission)
xsDataExperimentalCondition.getDetector().setDistance(xsDataCollectionRunBest.getDistance())
xsDataExperimentalCondition.getGoniostat().setRotationAxisStart(xsDataCollectionRunBest.getPhiStart())
xsDataExperimentalCondition.getGoniostat().setOscillationWidth(xsDataCollectionRunBest.getPhiWidth())
fRotationAxisEnd = xsDataCollectionRunBest.getPhiStart().getValue() + xsDataCollectionRunBest.getNumberOfImages().getValue() * xsDataCollectionRunBest.getPhiWidth().getValue()
xsDataExperimentalCondition.getGoniostat().setRotationAxisEnd(XSDataAngle(fRotationAxisEnd))
xsDataSubWedge.setExperimentalCondition(xsDataExperimentalCondition)
xsDataSubWedge.setSubWedgeNumber(xsDataCollectionRunBest.getCollectionRunNumber())
xsDataCollectionStrategy.addSubWedge(xsDataSubWedge)
xsDataCollectionStrategy.setSample(_xsDataSample)
xsDataCollectionPlan.setCollectionStrategy(xsDataCollectionStrategy)
xsDataStrategySummary = xsDataCollectionPlanBest.getStrategySummary()
xsDataCollectionPlan.setStrategySummary(xsDataStrategySummary)
xsDataStatistics = xsDataCollectionPlanBest.getStatisticalPrediction()
xsDataCollectionPlan.setStatistics(xsDataStatistics)
xsDataCollectionPlan.setCollectionPlanNumber(xsDataCollectionPlanBest.getCollectionPlanNumber())
xsDataResultStrategy.addCollectionPlan(xsDataCollectionPlan)
return xsDataResultStrategy
def getXSDataStrategyResult(self, _xsDataBestOutput, _xsDataExperimentalCondition, _xsDataSample):
xsDataStrategyResult = XSDataStrategyResult()
#xsDataCollectionRunsBest = _xsDataBestOutput.getCollectionRun()
xsDataCollectionPlansBest = _xsDataBestOutput.getCollectionPlan()
for xsDataCollectionPlanBest in xsDataCollectionPlansBest:
xsDataCollectionPlan = XSDataCollectionPlan()
xsDataCollectionStrategy = XSDataCollection()
for xsDataCollectionRunBest in xsDataCollectionPlanBest.getCollectionRun():
xsDataSubWedge = XSDataSubWedge()
strXmlStringDataExperimentalCondition = _xsDataExperimentalCondition.marshal()
xsDataExperimentalCondition = XSDataExperimentalCondition.parseString(strXmlStringDataExperimentalCondition)
xsDataExperimentalCondition.getBeam().setExposureTime(xsDataCollectionRunBest.getExposureTime())
xsDataExperimentalCondition.getDetector().setDistance(xsDataCollectionRunBest.getDistance())
xsDataExperimentalCondition.getGoniostat().setRotationAxisStart(xsDataCollectionRunBest.getPhiStart())
xsDataExperimentalCondition.getGoniostat().setOscillationWidth(xsDataCollectionRunBest.getPhiWidth())
fRotationAxisEnd = xsDataCollectionRunBest.getPhiStart().getValue() + xsDataCollectionRunBest.getNumberOfImages().getValue() * xsDataCollectionRunBest.getPhiWidth().getValue()
xsDataExperimentalCondition.getGoniostat().setRotationAxisEnd(XSDataAngle(fRotationAxisEnd))
xsDataSubWedge.setExperimentalCondition(xsDataExperimentalCondition)
xsDataCollectionStrategy.addSubWedge(xsDataSubWedge)
xsDataCollectionStrategy.setSample(_xsDataSample)
xsDataCollectionPlan.setCollectionStrategy(xsDataCollectionStrategy)
xsDataStrategySummary = xsDataCollectionPlanBest.getStrategySummary()
xsDataCollectionPlan.setStrategySummary(xsDataStrategySummary)
xsDataStatistics = xsDataCollectionPlanBest.getStatisticalPrediction()
xsDataCollectionPlan.setStatistics(xsDataStatistics)
xsDataStrategyResult.addCollectionPlan(xsDataCollectionPlan)
return xsDataStrategyResult
def getXSDataResultStrategy(self, _xsDataResultBest,
_xsDataExperimentalCondition, _xsDataSample):
xsDataResultStrategy = XSDataResultStrategy()
listXSDataBestCollectionPlan = _xsDataResultBest.getCollectionPlan()
for xsDataBestCollectionPlan in listXSDataBestCollectionPlan:
xsDataCollectionPlan = XSDataCollectionPlan()
xsDataCollectionStrategy = XSDataCollection()
xsDataBestStrategySummary = xsDataBestCollectionPlan.getStrategySummary(
)
xsDataDoubleTransmission = xsDataBestStrategySummary.getTransmission(
)
for xsDataBestCollectionRun in xsDataBestCollectionPlan.getCollectionRun(
):
xsDataSubWedge = XSDataSubWedge()
strXmlStringDataExperimentalCondition = _xsDataExperimentalCondition.marshal(
)
xsDataExperimentalCondition = XSDataExperimentalCondition.parseString(
strXmlStringDataExperimentalCondition)
xsDataExperimentalCondition.getBeam().setExposureTime(
xsDataBestCollectionRun.getExposureTime())
if (xsDataBestCollectionRun.getTransmission() is None):
xsDataExperimentalCondition.getBeam().setTransmission(
xsDataDoubleTransmission)
else:
xsDataExperimentalCondition.getBeam().setTransmission(
xsDataBestCollectionRun.getTransmission())
xsDataExperimentalCondition.getDetector().setDistance(
xsDataBestStrategySummary.getDistance())
xsDataExperimentalCondition.getGoniostat(
).setRotationAxisStart(xsDataBestCollectionRun.getPhiStart())
xsDataExperimentalCondition.getGoniostat().setOscillationWidth(
xsDataBestCollectionRun.getPhiWidth())
fRotationAxisEnd = xsDataBestCollectionRun.getPhiStart(
).getValue(
) + xsDataBestCollectionRun.getNumberOfImages().getValue(
) * xsDataBestCollectionRun.getPhiWidth().getValue()
xsDataExperimentalCondition.getGoniostat().setRotationAxisEnd(
XSDataAngle(fRotationAxisEnd))
xsDataSubWedge.setExperimentalCondition(
xsDataExperimentalCondition)
xsDataSubWedge.setSubWedgeNumber(
xsDataBestCollectionRun.getCollectionRunNumber())
if xsDataBestCollectionRun.getCrystalPosition():
xsDataSubWedge.setAction(
XSDataString("Crystal position: %d" %
xsDataBestCollectionRun.
getCrystalPosition().getValue()))
else:
xsDataSubWedge.setAction(
xsDataBestCollectionRun.getAction())
xsDataCollectionStrategy.addSubWedge(xsDataSubWedge)
xsDataCollectionStrategy.setSample(_xsDataSample)
xsDataCollectionPlan.setCollectionStrategy(
xsDataCollectionStrategy)
xsDataStrategySummary = XSDataStrategySummary()
xsDataStrategySummary.setCompleteness(
xsDataBestStrategySummary.getCompleteness())
xsDataStrategySummary.setISigma(
xsDataBestStrategySummary.getISigma())
xsDataStrategySummary.setRankingResolution(
xsDataBestStrategySummary.getRankingResolution())
xsDataStrategySummary.setRedundancy(
xsDataBestStrategySummary.getRedundancy())
xsDataStrategySummary.setResolution(
xsDataBestStrategySummary.getResolution())
xsDataStrategySummary.setResolutionReasoning(
xsDataBestStrategySummary.getResolutionReasoning())
xsDataStrategySummary.setTotalDataCollectionTime(
xsDataBestStrategySummary.getTotalDataCollectionTime())
xsDataStrategySummary.setTotalExposureTime(
xsDataBestStrategySummary.getTotalExposureTime())
xsDataCollectionPlan.setStrategySummary(xsDataStrategySummary)
if xsDataBestCollectionPlan.getStatisticalPrediction() is not None:
xsDataStatisticsStrategy = XSDataStatisticsStrategy.parseString(
xsDataBestCollectionPlan.getStatisticalPrediction(
).marshal())
xsDataCollectionPlan.setStatistics(xsDataStatisticsStrategy)
xsDataCollectionPlan.setCollectionPlanNumber(
xsDataBestCollectionPlan.getCollectionPlanNumber())
xsDataResultStrategy.addCollectionPlan(xsDataCollectionPlan)
if _xsDataResultBest.getPathToLogFile() != None:
xsDataResultStrategy.setBestLogFile(
_xsDataResultBest.getPathToLogFile())
return xsDataResultStrategy
def getXSDataResultStrategy(self, _xsDataResultBest, _xsDataExperimentalCondition, _xsDataSample):
xsDataResultStrategy = XSDataResultStrategy()
listXSDataBestCollectionPlan = _xsDataResultBest.getCollectionPlan()
for xsDataBestCollectionPlan in listXSDataBestCollectionPlan:
xsDataCollectionPlan = XSDataCollectionPlan()
xsDataCollectionStrategy = XSDataCollection()
xsDataBestStrategySummary = xsDataBestCollectionPlan.getStrategySummary()
xsDataDoubleTransmission = xsDataBestStrategySummary.getTransmission()
for xsDataBestCollectionRun in xsDataBestCollectionPlan.getCollectionRun():
xsDataSubWedge = XSDataSubWedge()
strXmlStringDataExperimentalCondition = _xsDataExperimentalCondition.marshal()
xsDataExperimentalCondition = XSDataExperimentalCondition.parseString(
strXmlStringDataExperimentalCondition
)
xsDataExperimentalCondition.getBeam().setExposureTime(xsDataBestCollectionRun.getExposureTime())
if xsDataBestCollectionRun.getTransmission() is None:
xsDataExperimentalCondition.getBeam().setTransmission(xsDataDoubleTransmission)
else:
xsDataExperimentalCondition.getBeam().setTransmission(xsDataBestCollectionRun.getTransmission())
xsDataExperimentalCondition.getDetector().setDistance(xsDataBestStrategySummary.getDistance())
xsDataExperimentalCondition.getGoniostat().setRotationAxisStart(xsDataBestCollectionRun.getPhiStart())
xsDataExperimentalCondition.getGoniostat().setOscillationWidth(xsDataBestCollectionRun.getPhiWidth())
fRotationAxisEnd = (
xsDataBestCollectionRun.getPhiStart().getValue()
+ xsDataBestCollectionRun.getNumberOfImages().getValue()
* xsDataBestCollectionRun.getPhiWidth().getValue()
)
xsDataExperimentalCondition.getGoniostat().setRotationAxisEnd(XSDataAngle(fRotationAxisEnd))
xsDataSubWedge.setExperimentalCondition(xsDataExperimentalCondition)
xsDataSubWedge.setSubWedgeNumber(xsDataBestCollectionRun.getCollectionRunNumber())
if xsDataBestCollectionRun.getCrystalPosition():
xsDataSubWedge.setAction(
XSDataString("Crystal position: %d" % xsDataBestCollectionRun.getCrystalPosition().getValue())
)
else:
xsDataSubWedge.setAction(xsDataBestCollectionRun.getAction())
xsDataCollectionStrategy.addSubWedge(xsDataSubWedge)
xsDataCollectionStrategy.setSample(_xsDataSample)
xsDataCollectionPlan.setCollectionStrategy(xsDataCollectionStrategy)
xsDataStrategySummary = XSDataStrategySummary()
xsDataStrategySummary.setCompleteness(xsDataBestStrategySummary.getCompleteness())
xsDataStrategySummary.setISigma(xsDataBestStrategySummary.getISigma())
xsDataStrategySummary.setRankingResolution(xsDataBestStrategySummary.getRankingResolution())
xsDataStrategySummary.setRedundancy(xsDataBestStrategySummary.getRedundancy())
xsDataStrategySummary.setResolution(xsDataBestStrategySummary.getResolution())
xsDataStrategySummary.setResolutionReasoning(xsDataBestStrategySummary.getResolutionReasoning())
xsDataStrategySummary.setTotalDataCollectionTime(xsDataBestStrategySummary.getTotalDataCollectionTime())
xsDataStrategySummary.setTotalExposureTime(xsDataBestStrategySummary.getTotalExposureTime())
xsDataCollectionPlan.setStrategySummary(xsDataStrategySummary)
if xsDataBestCollectionPlan.getStatisticalPrediction() is not None:
xsDataStatisticsStrategy = XSDataStatisticsStrategy.parseString(
xsDataBestCollectionPlan.getStatisticalPrediction().marshal()
)
xsDataCollectionPlan.setStatistics(xsDataStatisticsStrategy)
xsDataCollectionPlan.setCollectionPlanNumber(xsDataBestCollectionPlan.getCollectionPlanNumber())
xsDataResultStrategy.addCollectionPlan(xsDataCollectionPlan)
if _xsDataResultBest.getPathToLogFile() != None:
xsDataResultStrategy.setBestLogFile(_xsDataResultBest.getPathToLogFile())
return xsDataResultStrategy