def getTestExperimentalCondition(self): strPathToTestExperimentalCondition = os.path.join( self.getPluginTestsDataHome(), "XSDataExperimentalCondition_test.xml") strXMLInput = self.readAndParseFile(strPathToTestExperimentalCondition) xsDataExperimentalCondition = XSDataExperimentalCondition.parseString( strXMLInput) return xsDataExperimentalCondition
def preProcess(self, _edObject=None): """ Gets the Configuration Parameters, if found, overrides default parameters """ EDPluginControl.preProcess(self, _edObject) self.DEBUG("EDPluginControlGeneratePredictionv10.preProcess...") xsDataGeneratePredictionInput = self.getDataInput() xsDataSelectedIndexingSolution = xsDataGeneratePredictionInput.getSelectedIndexingSolution() xsDataExperimentalConditionRefined = xsDataSelectedIndexingSolution.getExperimentalConditionRefined() xsDataCollection = xsDataGeneratePredictionInput.getDataCollection() xsDataSubWedgeList = xsDataCollection.getSubWedge() # List containing instances of all the generate prediction plugins self.__listPluginGeneratePrediction = [] # Loop through all subwedges iIndex = 0 for xsDataSubWedge in xsDataSubWedgeList: xsDataImageList = xsDataSubWedge.getImage() # First find the lowest image number iLowestImageNumber = None for xsDataImage in xsDataImageList: iImageNumber = xsDataImage.getNumber().getValue() if (iLowestImageNumber is None): iLowestImageNumber = iImageNumber elif (iImageNumber < iLowestImageNumber): iLowestImageNumber = iImageNumber # Then loop through all images in a sub wedge for xsDataImage in xsDataImageList: iIndex += 1 edPluginGeneratePrediction = self.loadPlugin(self.__strPluginGeneratePredictionName, "%s-%02d" % (self.__strPluginGeneratePredictionName, iIndex)) xsDataGeneratePredictionInput = XSDataGeneratePredictionInput() xsDataGeneratePredictionInput.setSelectedIndexingSolution(XSDataIndexingSolutionSelected.parseString(xsDataSelectedIndexingSolution.marshal())) xsDataCollectionNew = XSDataCollection() xsDataSubWedgeNew = XSDataSubWedge() xsDataSubWedgeNew.addImage(XSDataImage.parseString(xsDataImage.marshal())) xsDataSubWedgeNew.setExperimentalCondition(XSDataExperimentalCondition.parseString(xsDataSubWedge.getExperimentalCondition().marshal())) # We must modify the rotationOscillationStart for the new subwedge xsDataGoniostatNew = xsDataSubWedgeNew.getExperimentalCondition().getGoniostat() fGoniostatRotationAxisStart = xsDataGoniostatNew.getRotationAxisStart().getValue() fGonioStatOscillationRange = xsDataGoniostatNew.getOscillationWidth().getValue() iImageNumber = xsDataImage.getNumber().getValue() fGoniostatRotationAxisStartNew = fGoniostatRotationAxisStart + (iImageNumber - iLowestImageNumber) * fGonioStatOscillationRange xsDataGoniostatNew.setRotationAxisStart(XSDataAngle(fGoniostatRotationAxisStartNew)) # xsDataCollectionNew.addSubWedge(xsDataSubWedgeNew) xsDataGeneratePredictionInput.setDataCollection(xsDataCollectionNew) from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10 xsDataMOSFLMInputGeneratePrediction = EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputGeneratePrediction(xsDataGeneratePredictionInput) edPluginGeneratePrediction.setDataInput(xsDataMOSFLMInputGeneratePrediction) self.__listPluginGeneratePrediction.append(edPluginGeneratePrediction)
def preProcess(self, _edObject=None): """ Gets the Configuration Parameters, if found, overrides default parameters """ EDPluginControl.preProcess(self, _edObject) self.DEBUG("EDPluginControlIntegrationv10.preProcess...") xsDataIntegrationInput = self.getDataInput() xsDataSelectedIndexingSolution = xsDataIntegrationInput.getSelectedIndexingSolution() self.__xsDataExperimentalConditionRefined = xsDataIntegrationInput.getExperimentalConditionRefined() # To be changed (see bug #40) if (self.__xsDataExperimentalConditionRefined is None): self.__xsDataExperimentalConditionRefined = xsDataSelectedIndexingSolution.getExperimentalConditionRefined() xsDataCollection = xsDataIntegrationInput.getDataCollection() xsDataSubWedgeList = xsDataCollection.getSubWedge() self.__edPluginIntegrationList = [] iIndex = 0 for xsDataSubWedge in xsDataSubWedgeList: iSubWedgeNumber = iIndex if (xsDataSubWedge.getSubWedgeNumber() is not None): # Use the incoming subwedge number if it exists iSubWedgeNumber = xsDataSubWedge.getSubWedgeNumber().getValue() edPluginIntegration = self.loadPlugin(self.__strPluginIntegrationName) if (not edPluginIntegration is None): iIndex += 1 xsDataIntegrationInputSubWedge = XSDataIntegrationInput() xsDataIntegrationInputSubWedge.setSelectedIndexingSolution(XSDataIndexingSolutionSelected.parseString(xsDataSelectedIndexingSolution.marshal())) xsDataIntegrationInputSubWedge.setExperimentalConditionRefined(XSDataExperimentalCondition.parseString(self.__xsDataExperimentalConditionRefined.marshal())) xsDataCollection = XSDataCollection() xsDataCollection.addSubWedge(xsDataSubWedge) xsDataIntegrationInputSubWedge.setDataCollection(xsDataCollection) try: from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10 xsDataMOSFLMInputIntegration = EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputIntegration(xsDataIntegrationInputSubWedge) edPluginIntegration.setDataInput(xsDataMOSFLMInputIntegration) edPluginIntegration.setBaseName("%s-%02d" % (self.__strPluginIntegrationName, iIndex)) edPluginIntegration.connectSUCCESS(self.doSuccessActionIntegration) edPluginIntegration.connectFAILURE(self.doFailureActionIntegration) # Here we store the sub wedge number for use in the results self.__edPluginIntegrationList.append([iSubWedgeNumber, edPluginIntegration]) except Exception as strErrorMessage: self.addErrorMessage(strErrorMessage) self.ERROR(strErrorMessage) self.setFailure() else: strErrorMessage = "EDPluginControlIntegrationv10.preProcess: could not load plugin %s" % self.__strPluginIntegrationName self.error(strErrorMessage) self.addErrorMessage(strErrorMessage) self.setFailure()
def generateXSDataIndexingResult(_xsDataResultXDSIndexing, _xsDataExperimentalCondition=None): xsDataIndexingResult = XSDataIndexingResult() xsDataIndexingSolutionSelected = XSDataIndexingSolutionSelected() xsDataCrystalSelected = XSDataCrystal() # xsDataIndexingSolutionSelected.setNumber(XSDataInteger(iIndex)) # xsDataCellSelected = xsDataLabelitSolution.getUnitCell() spaceGroupName = EDUtilsSymmetry.getMinimumSymmetrySpaceGroupFromBravaisLattice(_xsDataResultXDSIndexing.bravaisLattice.value) xsDataCrystalSelected = XSDataCrystal() xsDataSpaceGroupSelected = XSDataSpaceGroup() xsDataSpaceGroupSelected.setName(XSDataString(spaceGroupName)) xsDataCrystalSelected.setSpaceGroup(xsDataSpaceGroupSelected) # xsDataCrystalSelected.setCell(xsDataCellSelected) xsDataCrystalSelected.setMosaicity(XSDataDouble(_xsDataResultXDSIndexing.mosaicity.value)) xsDataCrystalSelected.setCell(XSDataCell.parseString(_xsDataResultXDSIndexing.unitCell.marshal())) xsDataIndexingSolutionSelected.setCrystal(xsDataCrystalSelected) xsDataOrientation = XSDataOrientation() xsDataOrientation.setMatrixA(_xsDataResultXDSIndexing.getAMatrix()) xsDataOrientation.setMatrixU(_xsDataResultXDSIndexing.getUMatrix()) xsDataIndexingSolutionSelected.setOrientation(xsDataOrientation) xsDataStatisticsIndexing = XSDataStatisticsIndexing() if (_xsDataExperimentalCondition is not None): fBeamPositionXOrig = _xsDataExperimentalCondition.getDetector().getBeamPositionX().getValue() fBeamPositionYOrig = _xsDataExperimentalCondition.getDetector().getBeamPositionY().getValue() fBeamPositionXNew = _xsDataResultXDSIndexing.getBeamCentreX().getValue() fBeamPositionYNew = _xsDataResultXDSIndexing.getBeamCentreY().getValue() xsDataStatisticsIndexing.setBeamPositionShiftX(XSDataLength(fBeamPositionXOrig - fBeamPositionXNew)) xsDataStatisticsIndexing.setBeamPositionShiftY(XSDataLength(fBeamPositionYOrig - fBeamPositionYNew)) xsDataExperimentalConditionRefined = None if (_xsDataExperimentalCondition is None): xsDataExperimentalConditionRefined = XSDataExperimentalCondition() else: # Copy the incoming experimental condition xmlExperimentalCondition = _xsDataExperimentalCondition.marshal() xsDataExperimentalConditionRefined = XSDataExperimentalCondition.parseString(xmlExperimentalCondition) xsDataDetector = xsDataExperimentalConditionRefined.getDetector() if (xsDataDetector is None): xsDataDetector = XSDataDetector() xsDataDetector.setBeamPositionX(XSDataLength(_xsDataResultXDSIndexing.getBeamCentreX().value)) xsDataDetector.setBeamPositionY(XSDataLength(_xsDataResultXDSIndexing.getBeamCentreY().value)) xsDataDetector.setDistance(_xsDataResultXDSIndexing.getDistance()) xsDataExperimentalConditionRefined.setDetector(xsDataDetector) xsDataIndexingSolutionSelected.setExperimentalConditionRefined(xsDataExperimentalConditionRefined) xsDataIndexingResult.setSelectedSolution(xsDataIndexingSolutionSelected) return xsDataIndexingResult
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 testSetDataModelInput(self): edPluginStrategy = self.createPlugin() strPathToTestConfigFile = os.path.join(self.getPluginTestsDataHome(), "XSConfiguration_ESRF.xml") edConfiguration = EDConfiguration(strPathToTestConfigFile) dictItem = edConfiguration.get(edPluginStrategy.getPluginName()) edPluginStrategy.setConfig(dictItem) edPluginStrategy.configure() xsDataStrategy = XSDataInputStrategy() # Beam xsExperimentalCondition = XSDataExperimentalCondition() xsBeam = XSDataBeam() xsBeam.setFlux(XSDataFlux(1e+12)) xsBeam.setWavelength(XSDataWavelength(2.41)) xsBeam.setSize(XSDataSize(x=XSDataLength(0.1), y=XSDataLength(0.1))) xsBeam.setExposureTime(XSDataTime(1)) xsExperimentalCondition.setBeam(xsBeam) # Detector and Exposure Time xsDataDetector = XSDataDetector() xsDataDetector.setType(XSDataString("q210-2x")) xsExperimentalCondition.setDetector(xsDataDetector) xsDataGoniostat = XSDataGoniostat() xsDataGoniostat.setRotationAxis(XSDataString("phi")) xsExperimentalCondition.setGoniostat(xsDataGoniostat) xsDataStrategy.setExperimentalCondition(xsExperimentalCondition) # Best Files bestFileContentDat = EDUtilsFile.readFile(os.path.join(self.strDataPath, "bestfile.dat")) xsDataStrategy.setBestFileContentDat(XSDataString(bestFileContentDat)) bestFileContentPar = EDUtilsFile.readFile(os.path.join(self.strDataPath, "bestfile.par")) xsDataStrategy.setBestFileContentPar(XSDataString(bestFileContentPar)) bestFileContentHKL = EDUtilsFile.readFile(os.path.join(self.strDataPath, "bestfile1.hkl")) xsDataStrategy.addBestFileContentHKL(XSDataString(bestFileContentHKL)) # Crystal xsDataSampleCrystalMM = XSDataSampleCrystalMM() xsDataStructure = XSDataStructure() xsDataComposition = XSDataChemicalCompositionMM() xsDataChain = XSDataChain() xsDataChain.setType(XSDataString("protein")) xsDataChain.setNumberOfCopies(XSDataDouble(2)) xsDataAtomicComposition = XSDataAtomicComposition() xsDataAtom1 = XSDataAtom() xsDataAtom1.setSymbol(XSDataString("Se")) xsDataAtom1.setNumberOf(XSDataDouble(4)) xsDataAtomicComposition.addAtom(xsDataAtom1) xsDataChain.setHeavyAtoms(xsDataAtomicComposition) xsDataChain.setNumberOfMonomers(XSDataDouble(100)) xsDataStructure.addChain(xsDataChain) xsDataChain2 = XSDataChain() xsDataChain2.setType(XSDataString("rna")) xsDataChain2.setNumberOfCopies(XSDataDouble(1)) xsDataChain2.setNumberOfMonomers(XSDataDouble(60)) xsDataStructure.addChain(xsDataChain2) xsDataLigand = XSDataLigand() xsDataLigand.setNumberOfCopies(XSDataDouble(2)) xsDataLigand.setNumberOfLightAtoms(XSDataDouble(42)) xsDataAtomicComposition = XSDataAtomicComposition() xsDataAtom2 = XSDataAtom() xsDataAtom2.setSymbol(XSDataString("Fe")) xsDataAtom2.setNumberOf(XSDataDouble(1)) xsDataAtomicComposition.addAtom(xsDataAtom2) xsDataLigand.setHeavyAtoms(xsDataAtomicComposition) xsDataStructure.addLigand(xsDataLigand) xsDataStructure.setNumberOfCopiesInAsymmetricUnit(XSDataDouble(0.25)) xsDataSolvent = XSDataSolvent() xsDataAtomicComposition = XSDataAtomicComposition() xsDataAtom3 = XSDataAtom() xsDataAtom3.setSymbol(XSDataString("Na")) xsDataAtom3.setConcentration(XSDataDouble(1000)) xsDataAtom4 = XSDataAtom() xsDataAtom4.setSymbol(XSDataString("Cl")) xsDataAtom4.setConcentration(XSDataDouble(1000)) xsDataAtomicComposition.addAtom(xsDataAtom3) xsDataAtomicComposition.addAtom(xsDataAtom4) xsDataSolvent.setAtoms(xsDataAtomicComposition) xsDataComposition.setStructure(xsDataStructure) xsDataComposition.setSolvent(xsDataSolvent) xsDataSampleCrystalMM.setChemicalComposition(xsDataComposition) xsDataSampleCrystalMM.setSize(XSDataSize(XSDataLength(0.1), XSDataLength(0.1), XSDataLength(0.1))) xsDataCrystal = XSDataCrystal() xsDataCell = XSDataCell(angle_alpha=XSDataAngle(90.0), angle_beta=XSDataAngle(90.0), angle_gamma=XSDataAngle(90.0), length_a=XSDataLength(78.9), length_b=XSDataLength(95.162), length_c=XSDataLength(104.087)) xsDataCrystal.setCell(xsDataCell) xsDataSpaceGroup = XSDataSpaceGroup() xsDataSpaceGroup.setITNumber(XSDataInteger(16)) xsDataCrystal.setSpaceGroup(xsDataSpaceGroup) xsDataSampleCrystalMM.setSusceptibility(XSDataDouble(1.5)) xsDataStrategy.setCrystalRefined(xsDataCrystal) xsDataStrategy.setSample(xsDataSampleCrystalMM) xsDataStrategy.exportToFile(self.strObtainedInputFile) pyStrExpectedInput = self.readAndParseFile (self.strReferenceInputFile) pyStrObtainedInput = self.readAndParseFile (self.strObtainedInputFile) xsDataInputExpected = XSDataInputStrategy.parseString(pyStrExpectedInput) xsDataInputObtained = XSDataInputStrategy.parseString(pyStrObtainedInput) EDAssert.equal(xsDataInputExpected.marshal(), xsDataInputObtained.marshal())
def generateXSDataIndexingResult(_xsDataResultLabelitIndexing, _xsDataExperimentalCondition=None): EDVerbose.DEBUG("EDHandlerXSDataLabelitv1_1.generateXSDataIndexingOutput") xsDataLabelitScreenOutput = _xsDataResultLabelitIndexing.screenOutput xsDataLabelitMosflmScriptsOutput = _xsDataResultLabelitIndexing.mosflmScriptsOutput iSelectedSolutionNumber = xsDataLabelitScreenOutput.getSelectedSolutionNumber().getValue() xsDataIndexingResult = XSDataIndexingResult() xsDataIndexingSolutionSelected = None for xsDataLabelitSolution in xsDataLabelitScreenOutput.getLabelitScreenSolution(): xsDataCrystal = XSDataCrystal() xsDataSpaceGroup = XSDataSpaceGroup() edStringSpaceGroupName = EDUtilsSymmetry.getMinimumSymmetrySpaceGroupFromBravaisLattice(xsDataLabelitSolution.getBravaisLattice().getValue()) xsDataSpaceGroup.setName(XSDataString(edStringSpaceGroupName)) xsDataCrystal.setSpaceGroup(xsDataSpaceGroup) xsDataCrystal.setCell(xsDataLabelitSolution.getUnitCell()) xsDataIndexingSolution = XSDataIndexingSolution() xsDataIndexingSolution.setCrystal(xsDataCrystal) iIndex = xsDataLabelitSolution.getSolutionNumber().getValue() xsDataIndexingSolution.setNumber(XSDataInteger(iIndex)) xsDataIndexingResult.addSolution(xsDataIndexingSolution) if (iIndex == iSelectedSolutionNumber): xsDataIndexingSolutionSelected = XSDataIndexingSolutionSelected() xsDataIndexingSolutionSelected.setNumber(XSDataInteger(iIndex)) edStringSelectedSpaceGroupName = edStringSpaceGroupName xsDataCellSelected = xsDataLabelitSolution.getUnitCell() fRmsdSelected = xsDataLabelitSolution.getRmsd().getValue() iNumberOfSpotsSelected = xsDataLabelitSolution.getNumberOfSpots().getValue() xsDataCrystalSelected = XSDataCrystal() xsDataSpaceGroupSelected = XSDataSpaceGroup() xsDataSpaceGroupSelected.setName(XSDataString(edStringSelectedSpaceGroupName)) xsDataSpaceGroupSelected.setITNumber(XSDataInteger(EDUtilsSymmetry.getITNumberFromSpaceGroupName(edStringSelectedSpaceGroupName))) xsDataCrystalSelected.setSpaceGroup(xsDataSpaceGroupSelected) xsDataCrystalSelected.setCell(xsDataCellSelected) xsDataCrystalSelected.setMosaicity(XSDataDouble(xsDataLabelitScreenOutput.getMosaicity().getValue())) xsDataIndexingSolutionSelected.setCrystal(xsDataCrystalSelected) xsDataOrientation = XSDataOrientation() xsDataOrientation.setMatrixA(xsDataLabelitMosflmScriptsOutput.getAMatrix()) xsDataOrientation.setMatrixU(xsDataLabelitMosflmScriptsOutput.getUMatrix()) xsDataIndexingSolutionSelected.setOrientation(xsDataOrientation) xsDataStatisticsIndexing = XSDataStatisticsIndexing() if (_xsDataExperimentalCondition is not None): fBeamPositionXOrig = _xsDataExperimentalCondition.getDetector().getBeamPositionX().getValue() fBeamPositionYOrig = _xsDataExperimentalCondition.getDetector().getBeamPositionY().getValue() fBeamPositionXNew = xsDataLabelitScreenOutput.getBeamCentreX().getValue() fBeamPositionYNew = xsDataLabelitScreenOutput.getBeamCentreY().getValue() xsDataStatisticsIndexing.setBeamPositionShiftX(XSDataLength(fBeamPositionXOrig - fBeamPositionXNew)) xsDataStatisticsIndexing.setBeamPositionShiftY(XSDataLength(fBeamPositionYOrig - fBeamPositionYNew)) # xsDataStatisticsIndexing.setSpotDeviXSDataLength( dDistanceRefinedationAngular( XSDataAngle( dDeviationAngular ) ) xsDataStatisticsIndexing.setSpotDeviationPositional(XSDataLength(fRmsdSelected)) xsDataStatisticsIndexing.setSpotsUsed(XSDataInteger(iNumberOfSpotsSelected)) xsDataStatisticsIndexing.setSpotsTotal(XSDataInteger(iNumberOfSpotsSelected)) xsDataIndexingSolutionSelected.setStatistics(xsDataStatisticsIndexing) xsDataExperimentalConditionRefined = None if (_xsDataExperimentalCondition is None): xsDataExperimentalConditionRefined = XSDataExperimentalCondition() else: # Copy the incoming experimental condition xmlExperimentalCondition = _xsDataExperimentalCondition.marshal() xsDataExperimentalConditionRefined = XSDataExperimentalCondition.parseString(xmlExperimentalCondition) xsDataDetector = xsDataExperimentalConditionRefined.getDetector() if (xsDataDetector is None): xsDataDetector = XSDataDetector() xsDataDetector.setBeamPositionX(xsDataLabelitScreenOutput.getBeamCentreX()) xsDataDetector.setBeamPositionY(xsDataLabelitScreenOutput.getBeamCentreY()) xsDataDetector.setDistance(xsDataLabelitScreenOutput.getDistance()) xsDataExperimentalConditionRefined.setDetector(xsDataDetector) xsDataIndexingSolutionSelected.setExperimentalConditionRefined(xsDataExperimentalConditionRefined) xsDataIndexingResult.setSelectedSolution(xsDataIndexingSolutionSelected) xsDataIndexingResult.setIndexingLogFile(xsDataLabelitScreenOutput.getPathToLogFile()) return xsDataIndexingResult
def process(self, _edObject=None): EDPluginExec.process(self) EDVerbose.DEBUG("EDPluginExecReadImageHeaderMARCCDv10.process") xsDataInputReadImageHeader = self.getDataInput() xsDataFile = xsDataInputReadImageHeader.getImage() strPath = xsDataFile.getPath().getValue() dictMARCCDHeader = self.readHeaderMarccd(strPath) if (dictMARCCDHeader is None): strErrorMessage = "EDPluginExecReadImageHeaderMARCCDv10.process : Cannot read header : %s" % strPath EDVerbose.error(strErrorMessage) self.addErrorMessage(strErrorMessage) self.setFailure() else: xsDataExperimentalCondition = XSDataExperimentalCondition() xsDataDetector = XSDataDetector() iNoPixelsX = int(dictMARCCDHeader["nslow"]) iNoPixelsY = int(dictMARCCDHeader["nfast"]) xsDataDetector.setNumberPixelX(XSDataInteger(iNoPixelsX)) xsDataDetector.setNumberPixelY(XSDataInteger(iNoPixelsY)) fPixelSizeX = float(dictMARCCDHeader["pixelsize_x"]) / 1000.0 xsDataDetector.setPixelSizeX(XSDataLength(fPixelSizeX)) fPixelSizeY = float(dictMARCCDHeader["pixelsize_y"]) / 1000.0 xsDataDetector.setPixelSizeY(XSDataLength(fPixelSizeY)) fBeamPositionX = float(dictMARCCDHeader["beam_x"]) / 1000.0 fBeamPositionY = float(dictMARCCDHeader["beam_y"]) / 1000.0 # Fix for bug 397 - check if the beam position is close to the centre of the image fTwoTheta = float(dictMARCCDHeader["end_twotheta"]) / 1000.0 xsDataDetector.setTwoTheta(XSDataAngle(fTwoTheta)) if (abs(fTwoTheta) < 0.1): if (abs(fBeamPositionX / (fPixelSizeX / 1000.0) - iNoPixelsX / 2.0) > (2 * iNoPixelsX)): fBeamPositionX = fBeamPositionX * fPixelSizeX / 1000.0 fBeamPositionY = fBeamPositionY * fPixelSizeY / 1000.0 xsDataDetector.setBeamPositionX(XSDataLength(fBeamPositionX)) xsDataDetector.setBeamPositionY(XSDataLength(fBeamPositionY)) fDistance = float(dictMARCCDHeader["xtal_to_detector"]) / 1000.0 if (abs(fDistance) < 0.1): fDistanceStart = float( dictMARCCDHeader["start_xtal_to_detector"]) / 1000.0 fDistanceEnd = float( dictMARCCDHeader["end_xtal_to_detector"]) / 1000.0 if (abs(fDistanceStart - fDistanceEnd) < 0.1): fDistance = fDistanceStart else: # Somethings very wrong with the distances... strErrorMessage = "EDPluginExecReadImageHeaderMARCCDv10.process : Inconsistency in MAR CCD image header: start_xtal_to_detector = %d, end_xtal_to_detector = %d" % \ (fDistanceStart, fDistanceEnd) EDVerbose.error(strErrorMessage) self.addErrorMessage(strErrorMessage) self.setFailure() xsDataDetector.setDistance(XSDataLength(fDistance)) xsDataDetector.setNumberBytesInHeader( XSDataInteger(float(dictMARCCDHeader["header_size"]))) #xsDataDetector.setSerialNumber( XSDataInteger( dictMARCCDHeader[ "DETECTOR_SN" ] ) ) ) #xsDataDetector.setBin( XSDataString( dictMARCCDHeader[ "BIN" ] ) ) ) #xsDataDetector.setDataType( XSDataString( dictMARCCDHeader[ "TYPE" ] ) ) ) #xsDataDetector.setByteOrder( XSDataString( dictMARCCDHeader[ "BYTE_ORDER" ] ) ) ) xsDataDetector.setImageSaturation( XSDataInteger(int(dictMARCCDHeader["saturation_level"]))) # Determine type of detector... if (iNoPixelsX == 2048 and iNoPixelsY == 2048): xsDataDetector.setName(XSDataString("MAR CCD 165")) xsDataDetector.setType(XSDataString("mar165")) elif (iNoPixelsX == 3072 and iNoPixelsY == 3072): xsDataDetector.setName(XSDataString("MAR CCD 225")) xsDataDetector.setType(XSDataString("mar225")) elif (iNoPixelsX == 4096 and iNoPixelsY == 4096): xsDataDetector.setName(XSDataString("MAR CCD 325")) xsDataDetector.setType(XSDataString("mar325")) else: strErrorMessage = EDMessage.ERROR_DATA_HANDLER_02 % ( "EDPluginExecReadImageHeaderMARCCDv10.process", "Unknown detector type") EDVerbose.error(strErrorMessage) self.addErrorMessage(strErrorMessage) raise RuntimeError, strErrorMessage xsDataExperimentalCondition.setDetector(xsDataDetector) # Beam object xsDataBeam = XSDataBeam() xsDataBeam.setWavelength( XSDataWavelength( float(dictMARCCDHeader["source_wavelength"]) / 100000.0)) xsDataBeam.setExposureTime( XSDataTime(float(dictMARCCDHeader["exposure_time"]) / 1000.0)) xsDataExperimentalCondition.setBeam(xsDataBeam) # Goniostat object xsDataGoniostat = XSDataGoniostat() fRotationAxisStart = float(dictMARCCDHeader["start_phi"]) / 1000.0 fOscillationWidth = float( dictMARCCDHeader["rotation_range"]) / 1000.0 xsDataGoniostat.setRotationAxisStart( XSDataAngle(fRotationAxisStart)) xsDataGoniostat.setRotationAxisEnd( XSDataAngle(fRotationAxisStart + fOscillationWidth)) xsDataGoniostat.setOscillationWidth(XSDataAngle(fOscillationWidth)) xsDataExperimentalCondition.setGoniostat(xsDataGoniostat) # Create the image object xsDataImage = XSDataImage() xsDataImage.setPath(XSDataString(strPath)) strTimeStamp = dictMARCCDHeader["acquire_timestamp"] xsDataImage.setDate(XSDataString(strTimeStamp)) iImageNumber = EDUtilsImage.getImageNumber(strPath) xsDataImage.setNumber(XSDataInteger(iImageNumber)) xsDataSubWedge = XSDataSubWedge() xsDataSubWedge.setExperimentalCondition( xsDataExperimentalCondition) xsDataSubWedge.addImage(xsDataImage) self.__xsDataResultReadImageHeader = XSDataResultReadImageHeader() self.__xsDataResultReadImageHeader.setSubWedge(xsDataSubWedge)
def process(self, _edObject=None): EDPluginExec.process(self) self.DEBUG("EDPluginExecReadImageHeaderEiger4Mv10.process") xsDataInputReadImageHeader = self.getDataInput() xsDataFile = xsDataInputReadImageHeader.getImage() strPath = xsDataFile.getPath().getValue() dictEiger4MHeader = self.readHeaderEiger4M(strPath) if (dictEiger4MHeader is None): strErrorMessage = "EDPluginExecReadImageHeaderEiger4Mv10.process : Cannot read header : %s" % strPath self.error(strErrorMessage) self.addErrorMessage(strErrorMessage) self.setFailure() else: xsDataExperimentalCondition = XSDataExperimentalCondition() xsDataDetector = XSDataDetector() iNoPixelsX = 2070 iNoPixelsY = 2167 xsDataDetector.setNumberPixelX(XSDataInteger(iNoPixelsX)) xsDataDetector.setNumberPixelY(XSDataInteger(iNoPixelsY)) # Pixel size listPixelSizeXY = dictEiger4MHeader[ "Pixel_size" ].split(" ") fPixelSizeX = float(listPixelSizeXY[0]) * 1000 xsDataDetector.setPixelSizeX(XSDataLength(fPixelSizeX)) fPixelSizeY = float(listPixelSizeXY[3]) * 1000 xsDataDetector.setPixelSizeY(XSDataLength(fPixelSizeY)) # Beam position listBeamPosition = dictEiger4MHeader["Beam_xy"].replace("(", " ").replace(")", " ").replace(",", " ").split() fBeamPositionX = float(listBeamPosition[1]) * fPixelSizeX fBeamPositionY = float(listBeamPosition[0]) * fPixelSizeY xsDataDetector.setBeamPositionX(XSDataLength(fBeamPositionX)) xsDataDetector.setBeamPositionY(XSDataLength(fBeamPositionY)) fDistance = float(dictEiger4MHeader[ "Detector_distance" ].split(" ")[0]) * 1000 xsDataDetector.setDistance(XSDataLength(fDistance)) # xsDataDetector.setNumberBytesInHeader(XSDataInteger(float(dictEiger4MHeader[ "header_size" ]))) xsDataDetector.setSerialNumber(XSDataString(dictEiger4MHeader[ "Detector:" ])) # #xsDataDetector.setBin( XSDataString( dictEiger4MHeader[ "BIN" ] ) ) ) # #xsDataDetector.setDataType( XSDataString( dictEiger4MHeader[ "TYPE" ] ) ) ) # #xsDataDetector.setByteOrder( XSDataString( dictEiger4MHeader[ "BYTE_ORDER" ] ) ) ) # xsDataDetector.setImageSaturation(XSDataInteger(int(dictEiger4MHeader[ "saturation_level" ]))) xsDataDetector.setName(XSDataString("EIGER 4M")) xsDataDetector.setType(XSDataString("eiger4m")) xsDataExperimentalCondition.setDetector(xsDataDetector) # Beam object xsDataBeam = XSDataBeam() xsDataBeam.setWavelength(XSDataWavelength(float(dictEiger4MHeader[ "Wavelength" ].split(" ")[0]))) xsDataBeam.setExposureTime(XSDataTime(float(dictEiger4MHeader[ "Exposure_time" ].split(" ")[0]))) xsDataExperimentalCondition.setBeam(xsDataBeam) # Goniostat object xsDataGoniostat = XSDataGoniostat() fRotationAxisStart = float(dictEiger4MHeader[ "Start_angle" ].split(" ")[0]) fOscillationWidth = float(dictEiger4MHeader[ "Angle_increment" ].split(" ")[0]) xsDataGoniostat.setRotationAxisStart(XSDataAngle(fRotationAxisStart)) xsDataGoniostat.setRotationAxisEnd(XSDataAngle(fRotationAxisStart + fOscillationWidth)) xsDataGoniostat.setOscillationWidth(XSDataAngle(fOscillationWidth)) xsDataExperimentalCondition.setGoniostat(xsDataGoniostat) # # Create the image object xsDataImage = XSDataImage() xsDataImage.setPath(XSDataString(strPath)) if "DateTime" in dictEiger4MHeader: strTimeStamp = dictEiger4MHeader[ "DateTime" ] xsDataImage.setDate(XSDataString(strTimeStamp)) iImageNumber = EDUtilsImage.getImageNumber(strPath) xsDataImage.setNumber(XSDataInteger(iImageNumber)) xsDataSubWedge = XSDataSubWedge() xsDataSubWedge.setExperimentalCondition(xsDataExperimentalCondition) xsDataSubWedge.addImage(xsDataImage) self.__xsDataResultReadImageHeader = XSDataResultReadImageHeader() self.__xsDataResultReadImageHeader.setSubWedge(xsDataSubWedge)
def process(self, _edObject=None): EDPluginExec.process(self) EDVerbose.DEBUG("*** EDPluginExecReadImageHeaderADSCv10.process") xsDataInputReadImageHeader = self.getDataInput() xsDataFile = xsDataInputReadImageHeader.getImage() strPath = xsDataFile.getPath().getValue() strAbsolutePath = os.path.abspath(strPath) dictHeader = self.readHeaderADSC(strPath) if (dictHeader is None): strErrorMessage = "EDPluginExecReadImageHeaderADSCv10.process : error when reading header from %s" % strAbsolutePath EDVerbose.error(strErrorMessage) self.addErrorMessage(strErrorMessage) self.setFailure() else: xsDataExperimentalCondition = XSDataExperimentalCondition() xsDataDetector = XSDataDetector() xsDataDetector.setBeamPositionX(XSDataLength(float(dictHeader[ "BEAM_CENTER_X" ]))) xsDataDetector.setBeamPositionY(XSDataLength(float(dictHeader[ "BEAM_CENTER_Y" ]))) xsDataDetector.setDistance(XSDataLength(float(dictHeader[ "DISTANCE" ]))) fPixelSize = float(dictHeader[ "PIXEL_SIZE" ]) xsDataDetector.setPixelSizeX(XSDataLength(fPixelSize)) xsDataDetector.setPixelSizeY(XSDataLength(fPixelSize)) if "TWOTHETA" in dictHeader.keys(): xsDataDetector.setTwoTheta(XSDataAngle(float(dictHeader[ "TWOTHETA" ]))) xsDataDetector.setNumberBytesInHeader(XSDataInteger(float(dictHeader[ "HEADER_BYTES" ]))) xsDataDetector.setSerialNumber(XSDataString(dictHeader[ "DETECTOR_SN" ])) xsDataDetector.setNumberPixelX(XSDataInteger(int(dictHeader[ "SIZE1" ]))) xsDataDetector.setNumberPixelY(XSDataInteger(int(dictHeader[ "SIZE2" ]))) xsDataDetector.setBin(XSDataString(dictHeader[ "BIN" ])) xsDataDetector.setDataType(XSDataString(dictHeader[ "TYPE" ])) xsDataDetector.setByteOrder(XSDataString(dictHeader[ "BYTE_ORDER" ])) if "CCD_IMAGE_SATURATION" in dictHeader.keys(): xsDataDetector.setImageSaturation(XSDataInteger(int(dictHeader[ "CCD_IMAGE_SATURATION" ]))) # Determine type of detector... iNoPixelsX = xsDataDetector.getNumberPixelX().getValue() iNoPixelsY = xsDataDetector.getNumberPixelY().getValue() if (iNoPixelsX == 2304 and iNoPixelsY == 2304): xsDataDetector.setName(XSDataString("ADSC Q4")) xsDataDetector.setType(XSDataString("q4")) elif (iNoPixelsX == 1152 and iNoPixelsY == 1152): xsDataDetector.setName(XSDataString("ADSC Q4 bin 2x2")) xsDataDetector.setType(XSDataString("q4-2x")) elif (iNoPixelsX == 4096 and iNoPixelsY == 4096): xsDataDetector.setName(XSDataString("ADSC Q210")) xsDataDetector.setType(XSDataString("q210")) elif (iNoPixelsX == 2048 and iNoPixelsY == 2048): xsDataDetector.setName(XSDataString("ADSC Q210 bin 2x2")) xsDataDetector.setType(XSDataString("q210-2x")) elif (iNoPixelsX == 6144 and iNoPixelsY == 6144): xsDataDetector.setName(XSDataString("ADSC Q315")) xsDataDetector.setType(XSDataString("q315")) elif (iNoPixelsX == 3072 and iNoPixelsY == 3072): xsDataDetector.setName(XSDataString("ADSC Q315 bin 2x2")) xsDataDetector.setType(XSDataString("q315-2x")) else: strErrorMessage = EDMessage.ERROR_DATA_HANDLER_02 % ("EDPluginExecReadImageHeaderADSCv10.process", "Unknown detector type") EDVerbose.error(strErrorMessage) self.addErrorMessage(strErrorMessage) raise RuntimeError, strErrorMessage xsDataExperimentalCondition.setDetector(xsDataDetector) # Beam object xsDataBeam = XSDataBeam() xsDataBeam.setWavelength(XSDataWavelength(float(dictHeader[ "WAVELENGTH" ]))) xsDataBeam.setExposureTime(XSDataTime(float(dictHeader[ "TIME" ]))) xsDataExperimentalCondition.setBeam(xsDataBeam) # Goniostat object xsDataGoniostat = XSDataGoniostat() fRotationAxisStart = float(dictHeader[ "OSC_START" ]) fOscillationWidth = float(dictHeader[ "OSC_RANGE" ]) xsDataGoniostat.setRotationAxisStart(XSDataAngle(fRotationAxisStart)) xsDataGoniostat.setRotationAxisEnd(XSDataAngle(fRotationAxisStart + fOscillationWidth)) xsDataGoniostat.setOscillationWidth(XSDataAngle(fOscillationWidth)) strRotationAxis = None if ("AXIS" in dictHeader.keys()): strRotationAxis = dictHeader[ "AXIS" ] elif ("OSC_AXIS" in dictHeader.keys()): strRotationAxis = dictHeader[ "OSC_AXIS" ] else: strErrorMessage = "EDPluginExecReadImageHeaderADSCv10.process : Neither AXIS nor OSC_AXIS header item found." EDVerbose.error(strErrorMessage) self.addErrorMessage(strErrorMessage) self.setFailure() xsDataGoniostat.setRotationAxis(XSDataString(strRotationAxis)) xsDataExperimentalCondition.setGoniostat(xsDataGoniostat) # Create the image object xsDataImage = XSDataImage() xsDataImage.setPath(XSDataString(strAbsolutePath)) xsDataImage.setDate(XSDataString(dictHeader[ "DATE" ])) strFileName = os.path.basename(strPath) iImageNumber = EDUtilsImage.getImageNumber(strFileName) xsDataImage.setNumber(XSDataInteger(iImageNumber)) xsDataSubWedge = XSDataSubWedge() xsDataSubWedge.setExperimentalCondition(xsDataExperimentalCondition) xsDataSubWedge.addImage(xsDataImage) self.__xsDataResultReadImageHeader = XSDataResultReadImageHeader() self.__xsDataResultReadImageHeader.setSubWedge(xsDataSubWedge)
def generateXSDataIntegrationSubWedgeResult( _xsDataMOSFLMOutputIntegration, _xsDataExperimentalCondition=None): """ Translation from XSDataMOSFLMOutputIntegration to XSDataIntegrationSubWedgeResult. """ EDVerbose.DEBUG( "EDHandlerXSDataMOSFLMv10.generateXSDataIntegrationInput") EDFactoryPluginStatic.loadModule("XSDataMOSFLMv10") xsDataIntegrationSubWedgeResult = XSDataIntegrationSubWedgeResult() xsDataExperimentalConditionRefined = None if (_xsDataExperimentalCondition is None): xsDataExperimentalConditionRefined = XSDataExperimentalCondition() else: # Copy the incoming experimental condition xmlExperimentalCondition = _xsDataExperimentalCondition.marshal() xsDataExperimentalConditionRefined = XSDataExperimentalCondition.parseString( xmlExperimentalCondition) xsDataDetector = xsDataExperimentalConditionRefined.getDetector() if (xsDataDetector is None): xsDataDetector = XSDataDetector() if _xsDataMOSFLMOutputIntegration.getBestfilePar() is not None: xsDataIntegrationSubWedgeResult.setBestfilePar( XSDataString(_xsDataMOSFLMOutputIntegration.getBestfilePar(). getValue())) xsDataIntegrationSubWedgeResult.setBestfileDat( XSDataString(_xsDataMOSFLMOutputIntegration.getBestfileDat(). getValue())) xsDataIntegrationSubWedgeResult.setBestfileHKL( XSDataString(_xsDataMOSFLMOutputIntegration.getBestfileHKL(). getValue())) xsDataLengthRefinedDistance = _xsDataMOSFLMOutputIntegration.getRefinedDistance( ) if (xsDataLengthRefinedDistance is not None): xsDataDetector.setDistance(xsDataLengthRefinedDistance) xsDataMOSFLMBeamPositionRefined = _xsDataMOSFLMOutputIntegration.getRefinedBeam( ) if (xsDataMOSFLMBeamPositionRefined is not None): xsDataDetector.setBeamPositionX( XSDataLength( xsDataMOSFLMBeamPositionRefined.getX().getValue())) xsDataDetector.setBeamPositionY( XSDataLength( xsDataMOSFLMBeamPositionRefined.getY().getValue())) xsDataExperimentalConditionRefined.setDetector(xsDataDetector) xsDataIntegrationSubWedgeResult.setExperimentalConditionRefined( xsDataExperimentalConditionRefined) if (_xsDataMOSFLMOutputIntegration.getGeneratedMTZFile() is not None): xsDataIntegrationSubWedgeResult.setGeneratedMTZFile( _xsDataMOSFLMOutputIntegration.getGeneratedMTZFile()) xsDataStatisticsIntegration = XSDataStatisticsIntegration() if (_xsDataMOSFLMOutputIntegration.getOverallIOverSigma() is not None): xsDataStatisticsIntegration.setIOverSigmaOverall( XSDataDouble(_xsDataMOSFLMOutputIntegration. getOverallIOverSigma().getValue())) if (_xsDataMOSFLMOutputIntegration.getHighestResolutionIOverSigma() is not None): xsDataStatisticsIntegration.setIOverSigmaAtHighestResolution( XSDataDouble(_xsDataMOSFLMOutputIntegration. getHighestResolutionIOverSigma().getValue())) if (_xsDataMOSFLMOutputIntegration.getRMSSpotDeviation() is not None): xsDataStatisticsIntegration.setRMSSpotDeviation( XSDataLength(_xsDataMOSFLMOutputIntegration. getRMSSpotDeviation().getValue())) if (_xsDataMOSFLMOutputIntegration.getNumberOfBadReflections() is not None): xsDataStatisticsIntegration.setNumberOfBadReflections( XSDataInteger(_xsDataMOSFLMOutputIntegration. getNumberOfBadReflections().getValue())) if (_xsDataMOSFLMOutputIntegration.getNumberOfFullyRecordedReflections( ) is not None): xsDataStatisticsIntegration.setNumberOfFullyRecordedReflections( XSDataInteger( _xsDataMOSFLMOutputIntegration. getNumberOfFullyRecordedReflections().getValue())) if (_xsDataMOSFLMOutputIntegration.getNumberOfNegativeReflections() is not None): xsDataStatisticsIntegration.setNumberOfNegativeReflections( XSDataInteger(_xsDataMOSFLMOutputIntegration. getNumberOfNegativeReflections().getValue())) if (_xsDataMOSFLMOutputIntegration.getNumberOfOverlappedReflections() is not None): xsDataStatisticsIntegration.setNumberOfOverlappedReflections( XSDataInteger(_xsDataMOSFLMOutputIntegration. getNumberOfOverlappedReflections().getValue())) if (_xsDataMOSFLMOutputIntegration.getNumberOfPartialReflections() is not None): xsDataStatisticsIntegration.setNumberOfPartialReflections( XSDataInteger(_xsDataMOSFLMOutputIntegration. getNumberOfPartialReflections().getValue())) if (_xsDataMOSFLMOutputIntegration.getNumberOfReflectionsGenerated() is not None): xsDataStatisticsIntegration.setNumberOfReflectionsGenerated( XSDataInteger(_xsDataMOSFLMOutputIntegration. getNumberOfReflectionsGenerated().getValue())) xsDataIntegrationSubWedgeResult.setStatistics( xsDataStatisticsIntegration) xsDataIntegrationSubWedgeResult.setExperimentalConditionRefined( xsDataExperimentalConditionRefined) for xsDataMOSFLMIntegrationStatisticsPerResolutionBin in _xsDataMOSFLMOutputIntegration.getStatisticsPerResolutionBin( ): xsDataStatisticsIntegrationPerResolutionBin = XSDataStatisticsIntegrationPerResolutionBin( ) if (xsDataMOSFLMIntegrationStatisticsPerResolutionBin. getMaxResolution() is not None): xsDataStatisticsIntegrationPerResolutionBin.setMaxResolution( XSDataDouble( xsDataMOSFLMIntegrationStatisticsPerResolutionBin. getMaxResolution().getValue())) if (xsDataMOSFLMIntegrationStatisticsPerResolutionBin. getMinResolution() is not None): xsDataStatisticsIntegrationPerResolutionBin.setMinResolution( XSDataDouble( xsDataMOSFLMIntegrationStatisticsPerResolutionBin. getMinResolution().getValue())) xsDataStatisticsIntegrationPerResolutionBin.setProfileFitted( EDHandlerXSDataMOSFLMv10. generateXSDataIntegrationStatisticsPerReflectionType( xsDataMOSFLMIntegrationStatisticsPerResolutionBin. getProfileFitted())) xsDataStatisticsIntegrationPerResolutionBin.setSummation( EDHandlerXSDataMOSFLMv10. generateXSDataIntegrationStatisticsPerReflectionType( xsDataMOSFLMIntegrationStatisticsPerResolutionBin. getSummation())) xsDataIntegrationSubWedgeResult.addStatisticsPerResolutionBin( xsDataStatisticsIntegrationPerResolutionBin) xsDataIntegrationSubWedgeResult.setIntegrationLogFile( _xsDataMOSFLMOutputIntegration.getPathToLogFile()) return xsDataIntegrationSubWedgeResult
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 generateXSDataIndexingResult(_xsDataLabelitScreenOutput, _xsDataLabelitMosflmScriptsOutput, \ _xsDataExperimentalCondition=None): EDVerbose.DEBUG( "EDHandlerXSDataLabelitv1_1.generateXSDataIndexingOutput") iSelectedSolutionNumber = _xsDataLabelitScreenOutput.getSelectedSolutionNumber( ).getValue() xsDataIndexingResult = XSDataIndexingResult() xsDataIndexingSolutionSelected = None for xsDataLabelitSolution in _xsDataLabelitScreenOutput.getLabelitScreenSolution( ): xsDataCrystal = XSDataCrystal() xsDataSpaceGroup = XSDataSpaceGroup() edStringSpaceGroupName = EDUtilsSymmetry.getMinimumSymmetrySpaceGroupFromBravaisLattice( xsDataLabelitSolution.getBravaisLattice().getValue()) xsDataSpaceGroup.setName(XSDataString(edStringSpaceGroupName)) xsDataCrystal.setSpaceGroup(xsDataSpaceGroup) xsDataCrystal.setCell(xsDataLabelitSolution.getUnitCell()) xsDataIndexingSolution = XSDataIndexingSolution() xsDataIndexingSolution.setCrystal(xsDataCrystal) iIndex = xsDataLabelitSolution.getSolutionNumber().getValue() xsDataIndexingSolution.setNumber(XSDataInteger(iIndex)) xsDataIndexingResult.addSolution(xsDataIndexingSolution) if (iIndex == iSelectedSolutionNumber): xsDataIndexingSolutionSelected = XSDataIndexingSolutionSelected( ) xsDataIndexingSolutionSelected.setNumber(XSDataInteger(iIndex)) edStringSelectedSpaceGroupName = edStringSpaceGroupName xsDataCellSelected = xsDataLabelitSolution.getUnitCell() fRmsdSelected = xsDataLabelitSolution.getRmsd().getValue() iNumberOfSpotsSelected = xsDataLabelitSolution.getNumberOfSpots( ).getValue() xsDataCrystalSelected = XSDataCrystal() xsDataSpaceGroupSelected = XSDataSpaceGroup() xsDataSpaceGroupSelected.setName( XSDataString(edStringSelectedSpaceGroupName)) #xsDataSpaceGroupSelected.setITNumber( XSDataInteger( iSelectedSpaceGroupNumber ) ) xsDataCrystalSelected.setSpaceGroup(xsDataSpaceGroupSelected) xsDataCrystalSelected.setCell(xsDataCellSelected) xsDataCrystalSelected.setMosaicity( XSDataDouble(_xsDataLabelitScreenOutput.getMosaicity().getValue())) xsDataIndexingSolutionSelected.setCrystal(xsDataCrystalSelected) xsDataOrientation = XSDataOrientation() xsDataOrientation.setMatrixA( _xsDataLabelitMosflmScriptsOutput.getAMatrix()) xsDataOrientation.setMatrixU( _xsDataLabelitMosflmScriptsOutput.getUMatrix()) xsDataIndexingSolutionSelected.setOrientation(xsDataOrientation) xsDataStatisticsIndexing = XSDataStatisticsIndexing() if (_xsDataExperimentalCondition is not None): fBeamPositionXOrig = _xsDataExperimentalCondition.getDetector( ).getBeamPositionX().getValue() fBeamPositionYOrig = _xsDataExperimentalCondition.getDetector( ).getBeamPositionY().getValue() fBeamPositionXNew = _xsDataLabelitScreenOutput.getBeamCentreX( ).getValue() fBeamPositionYNew = _xsDataLabelitScreenOutput.getBeamCentreY( ).getValue() xsDataStatisticsIndexing.setBeamPositionShiftX( XSDataLength(fBeamPositionXOrig - fBeamPositionXNew)) xsDataStatisticsIndexing.setBeamPositionShiftY( XSDataLength(fBeamPositionYOrig - fBeamPositionYNew)) #xsDataStatisticsIndexing.setSpotDeviXSDataLength( dDistanceRefinedationAngular( XSDataAngle( dDeviationAngular ) ) xsDataStatisticsIndexing.setSpotDeviationPositional( XSDataLength(fRmsdSelected)) xsDataStatisticsIndexing.setSpotsUsed( XSDataInteger(iNumberOfSpotsSelected)) xsDataStatisticsIndexing.setSpotsTotal( XSDataInteger(iNumberOfSpotsSelected)) xsDataIndexingSolutionSelected.setStatistics(xsDataStatisticsIndexing) xsDataExperimentalConditionRefined = None if (_xsDataExperimentalCondition is None): xsDataExperimentalConditionRefined = XSDataExperimentalCondition() else: # Copy the incoming experimental condition xmlExperimentalCondition = _xsDataExperimentalCondition.marshal() xsDataExperimentalConditionRefined = XSDataExperimentalCondition.parseString( xmlExperimentalCondition) xsDataDetector = xsDataExperimentalConditionRefined.getDetector() if (xsDataDetector is None): xsDataDetector = XSDataDetector() xsDataDetector.setBeamPositionX( _xsDataLabelitScreenOutput.getBeamCentreX()) xsDataDetector.setBeamPositionY( _xsDataLabelitScreenOutput.getBeamCentreY()) xsDataDetector.setDistance(_xsDataLabelitScreenOutput.getDistance()) xsDataExperimentalConditionRefined.setDetector(xsDataDetector) xsDataIndexingSolutionSelected.setExperimentalConditionRefined( xsDataExperimentalConditionRefined) xsDataIndexingResult.setSelectedSolution( xsDataIndexingSolutionSelected) xsDataIndexingResult.setIndexingLogFile( _xsDataLabelitScreenOutput.getPathToLogFile()) return xsDataIndexingResult
def process(self, _edObject=None): EDPluginExec.process(self) EDVerbose.DEBUG("EDPluginExecReadImageHeaderMARCCDv10.process") xsDataInputReadImageHeader = self.getDataInput() xsDataFile = xsDataInputReadImageHeader.getImage() strPath = xsDataFile.getPath().getValue() dictMARCCDHeader = self.readHeaderMarccd(strPath) if (dictMARCCDHeader is None): strErrorMessage = "EDPluginExecReadImageHeaderMARCCDv10.process : Cannot read header : %s" % strPath EDVerbose.error(strErrorMessage) self.addErrorMessage(strErrorMessage) self.setFailure() else: xsDataExperimentalCondition = XSDataExperimentalCondition() xsDataDetector = XSDataDetector() iNoPixelsX = int(dictMARCCDHeader[ "nslow" ]) iNoPixelsY = int(dictMARCCDHeader[ "nfast" ]) xsDataDetector.setNumberPixelX(XSDataInteger(iNoPixelsX)) xsDataDetector.setNumberPixelY(XSDataInteger(iNoPixelsY)) fPixelSizeX = float(dictMARCCDHeader[ "pixelsize_x" ]) / 1000.0 xsDataDetector.setPixelSizeX(XSDataLength(fPixelSizeX)) fPixelSizeY = float(dictMARCCDHeader[ "pixelsize_y" ]) / 1000.0 xsDataDetector.setPixelSizeY(XSDataLength(fPixelSizeY)) fBeamPositionX = float(dictMARCCDHeader[ "beam_x" ]) / 1000.0 fBeamPositionY = float(dictMARCCDHeader[ "beam_y" ]) / 1000.0 # Fix for bug 397 - check if the beam position is close to the centre of the image fTwoTheta = float(dictMARCCDHeader[ "end_twotheta" ]) / 1000.0 xsDataDetector.setTwoTheta(XSDataAngle(fTwoTheta)) if (abs(fTwoTheta) < 0.1): if (abs(fBeamPositionX / (fPixelSizeX / 1000.0) - iNoPixelsX / 2.0) > (2 * iNoPixelsX)): fBeamPositionX = fBeamPositionX * fPixelSizeX / 1000.0 fBeamPositionY = fBeamPositionY * fPixelSizeY / 1000.0 xsDataDetector.setBeamPositionX(XSDataLength(fBeamPositionX)) xsDataDetector.setBeamPositionY(XSDataLength(fBeamPositionY)) fDistance = float(dictMARCCDHeader[ "xtal_to_detector" ]) / 1000.0 if (abs(fDistance) < 0.1): fDistanceStart = float(dictMARCCDHeader[ "start_xtal_to_detector" ]) / 1000.0 fDistanceEnd = float(dictMARCCDHeader[ "end_xtal_to_detector" ]) / 1000.0 if (abs(fDistanceStart - fDistanceEnd) < 0.1): fDistance = fDistanceStart else: # Somethings very wrong with the distances... strErrorMessage = "EDPluginExecReadImageHeaderMARCCDv10.process : Inconsistency in MAR CCD image header: start_xtal_to_detector = %d, end_xtal_to_detector = %d" % \ (fDistanceStart, fDistanceEnd) EDVerbose.error(strErrorMessage) self.addErrorMessage(strErrorMessage) self.setFailure() xsDataDetector.setDistance(XSDataLength(fDistance)) xsDataDetector.setNumberBytesInHeader(XSDataInteger(float(dictMARCCDHeader[ "header_size" ]))) # xsDataDetector.setSerialNumber( XSDataInteger( dictMARCCDHeader[ "DETECTOR_SN" ] ) ) ) # xsDataDetector.setBin( XSDataString( dictMARCCDHeader[ "BIN" ] ) ) ) # xsDataDetector.setDataType( XSDataString( dictMARCCDHeader[ "TYPE" ] ) ) ) # xsDataDetector.setByteOrder( XSDataString( dictMARCCDHeader[ "BYTE_ORDER" ] ) ) ) xsDataDetector.setImageSaturation(XSDataInteger(int(dictMARCCDHeader[ "saturation_level" ]))) # Determine type of detector... if (iNoPixelsX == 2048 and iNoPixelsY == 2048): xsDataDetector.setName(XSDataString("MAR CCD 165")) xsDataDetector.setType(XSDataString("mar165")) elif (iNoPixelsX == 3072 and iNoPixelsY == 3072): xsDataDetector.setName(XSDataString("MAR CCD 225")) xsDataDetector.setType(XSDataString("mar225")) elif (iNoPixelsX == 4096 and iNoPixelsY == 4096): xsDataDetector.setName(XSDataString("MAR CCD 325")) xsDataDetector.setType(XSDataString("mar325")) else: strErrorMessage = EDMessage.ERROR_DATA_HANDLER_02 % ("EDPluginExecReadImageHeaderMARCCDv10.process", "Unknown detector type") EDVerbose.error(strErrorMessage) self.addErrorMessage(strErrorMessage) raise RuntimeError, strErrorMessage xsDataExperimentalCondition.setDetector(xsDataDetector) # Beam object xsDataBeam = XSDataBeam() xsDataBeam.setWavelength(XSDataWavelength(float(dictMARCCDHeader[ "source_wavelength" ]) / 100000.0)) xsDataBeam.setExposureTime(XSDataTime(float(dictMARCCDHeader[ "exposure_time" ]) / 1000.0)) xsDataExperimentalCondition.setBeam(xsDataBeam) # Goniostat object xsDataGoniostat = XSDataGoniostat() fRotationAxisStart = float(dictMARCCDHeader[ "start_phi" ]) / 1000.0 fOscillationWidth = float(dictMARCCDHeader[ "rotation_range" ]) / 1000.0 xsDataGoniostat.setRotationAxisStart(XSDataAngle(fRotationAxisStart)) xsDataGoniostat.setRotationAxisEnd(XSDataAngle(fRotationAxisStart + fOscillationWidth)) xsDataGoniostat.setOscillationWidth(XSDataAngle(fOscillationWidth)) xsDataExperimentalCondition.setGoniostat(xsDataGoniostat) # Create the image object xsDataImage = XSDataImage() xsDataImage.setPath(XSDataString(strPath)) strTimeStamp = dictMARCCDHeader[ "acquire_timestamp" ] xsDataImage.setDate(XSDataString(strTimeStamp)) iImageNumber = EDUtilsImage.getImageNumber(strPath) xsDataImage.setNumber(XSDataInteger(iImageNumber)) xsDataSubWedge = XSDataSubWedge() xsDataSubWedge.setExperimentalCondition(xsDataExperimentalCondition) xsDataSubWedge.addImage(xsDataImage) self.__xsDataResultReadImageHeader = XSDataResultReadImageHeader() self.__xsDataResultReadImageHeader.setSubWedge(xsDataSubWedge)
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 preProcess(self, _edObject=None): """ Gets the Configuration Parameters, if found, overrides default parameters """ EDPluginControl.preProcess(self, _edObject) self.DEBUG("EDPluginControlIntegrationv10.preProcess...") xsDataIntegrationInput = self.getDataInput() xsDataSelectedIndexingSolution = xsDataIntegrationInput.getSelectedIndexingSolution( ) self.__xsDataExperimentalConditionRefined = xsDataIntegrationInput.getExperimentalConditionRefined( ) # To be changed (see bug #40) if (self.__xsDataExperimentalConditionRefined is None): self.__xsDataExperimentalConditionRefined = xsDataSelectedIndexingSolution.getExperimentalConditionRefined( ) xsDataCollection = xsDataIntegrationInput.getDataCollection() xsDataSubWedgeList = xsDataCollection.getSubWedge() self.__edPluginIntegrationList = [] iIndex = 0 for xsDataSubWedge in xsDataSubWedgeList: iSubWedgeNumber = iIndex if (xsDataSubWedge.getSubWedgeNumber() is not None): # Use the incoming subwedge number if it exists iSubWedgeNumber = xsDataSubWedge.getSubWedgeNumber().getValue() edPluginIntegration = self.loadPlugin( self.__strPluginIntegrationName) if (not edPluginIntegration is None): iIndex += 1 xsDataIntegrationInputSubWedge = XSDataIntegrationInput() xsDataIntegrationInputSubWedge.setSelectedIndexingSolution( XSDataIndexingSolutionSelected.parseString( xsDataSelectedIndexingSolution.marshal())) xsDataIntegrationInputSubWedge.setExperimentalConditionRefined( XSDataExperimentalCondition.parseString( self.__xsDataExperimentalConditionRefined.marshal())) xsDataCollection = XSDataCollection() xsDataCollection.addSubWedge(xsDataSubWedge) xsDataIntegrationInputSubWedge.setDataCollection( xsDataCollection) try: from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10 xsDataMOSFLMInputIntegration = EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputIntegration( xsDataIntegrationInputSubWedge) edPluginIntegration.setDataInput( xsDataMOSFLMInputIntegration) edPluginIntegration.setBaseName( "%s-%02d" % (self.__strPluginIntegrationName, iIndex)) edPluginIntegration.connectSUCCESS( self.doSuccessActionIntegration) edPluginIntegration.connectFAILURE( self.doFailureActionIntegration) # Here we store the sub wedge number for use in the results self.__edPluginIntegrationList.append( [iSubWedgeNumber, edPluginIntegration]) except Exception as strErrorMessage: self.addErrorMessage(strErrorMessage) self.ERROR(strErrorMessage) self.setFailure() else: strErrorMessage = "EDPluginControlIntegrationv10.preProcess: could not load plugin %s" % self.__strPluginIntegrationName self.error(strErrorMessage) self.addErrorMessage(strErrorMessage) self.setFailure()
def testSetDataModelInput(self): edPluginStrategy = self.createPlugin() strPathToTestConfigFile = os.path.join(self.getPluginTestsDataHome(), "XSConfiguration_ESRF.xml") edConfiguration = EDConfiguration(strPathToTestConfigFile) dictItem = edConfiguration.get(edPluginStrategy.getPluginName()) edPluginStrategy.setConfig(dictItem) edPluginStrategy.configure() xsDataStrategy = XSDataInputStrategy() # Beam xsExperimentalCondition = XSDataExperimentalCondition() xsBeam = XSDataBeam() xsBeam.setFlux(XSDataFlux(1e+12)) xsBeam.setWavelength(XSDataWavelength(2.41)) xsBeam.setSize(XSDataSize(x=XSDataLength(0.1), y=XSDataLength(0.1))) xsBeam.setExposureTime(XSDataTime(1)) xsExperimentalCondition.setBeam(xsBeam) # Detector and Exposure Time xsDataDetector = XSDataDetector() xsDataDetector.setType(XSDataString("q210-2x")) xsExperimentalCondition.setDetector(xsDataDetector) xsDataGoniostat = XSDataGoniostat() xsDataGoniostat.setRotationAxis(XSDataString("phi")) xsExperimentalCondition.setGoniostat(xsDataGoniostat) xsDataStrategy.setExperimentalCondition(xsExperimentalCondition) # Best Files bestFileContentDat = EDUtilsFile.readFile( os.path.join(self.strDataPath, "bestfile.dat")) xsDataStrategy.setBestFileContentDat(XSDataString(bestFileContentDat)) bestFileContentPar = EDUtilsFile.readFile( os.path.join(self.strDataPath, "bestfile.par")) xsDataStrategy.setBestFileContentPar(XSDataString(bestFileContentPar)) bestFileContentHKL = EDUtilsFile.readFile( os.path.join(self.strDataPath, "bestfile1.hkl")) xsDataStrategy.addBestFileContentHKL(XSDataString(bestFileContentHKL)) # Crystal xsDataSampleCrystalMM = XSDataSampleCrystalMM() xsDataStructure = XSDataStructure() xsDataComposition = XSDataChemicalCompositionMM() xsDataChain = XSDataChain() xsDataChain.setType(XSDataString("protein")) xsDataChain.setNumberOfCopies(XSDataDouble(2)) xsDataAtomicComposition = XSDataAtomicComposition() xsDataAtom1 = XSDataAtom() xsDataAtom1.setSymbol(XSDataString("Se")) xsDataAtom1.setNumberOf(XSDataDouble(4)) xsDataAtomicComposition.addAtom(xsDataAtom1) xsDataChain.setHeavyAtoms(xsDataAtomicComposition) xsDataChain.setNumberOfMonomers(XSDataDouble(100)) xsDataStructure.addChain(xsDataChain) xsDataChain2 = XSDataChain() xsDataChain2.setType(XSDataString("rna")) xsDataChain2.setNumberOfCopies(XSDataDouble(1)) xsDataChain2.setNumberOfMonomers(XSDataDouble(60)) xsDataStructure.addChain(xsDataChain2) xsDataLigand = XSDataLigand() xsDataLigand.setNumberOfCopies(XSDataDouble(2)) xsDataLigand.setNumberOfLightAtoms(XSDataDouble(42)) xsDataAtomicComposition = XSDataAtomicComposition() xsDataAtom2 = XSDataAtom() xsDataAtom2.setSymbol(XSDataString("Fe")) xsDataAtom2.setNumberOf(XSDataDouble(1)) xsDataAtomicComposition.addAtom(xsDataAtom2) xsDataLigand.setHeavyAtoms(xsDataAtomicComposition) xsDataStructure.addLigand(xsDataLigand) xsDataStructure.setNumberOfCopiesInAsymmetricUnit(XSDataDouble(0.25)) xsDataSolvent = XSDataSolvent() xsDataAtomicComposition = XSDataAtomicComposition() xsDataAtom3 = XSDataAtom() xsDataAtom3.setSymbol(XSDataString("Na")) xsDataAtom3.setConcentration(XSDataDouble(1000)) xsDataAtom4 = XSDataAtom() xsDataAtom4.setSymbol(XSDataString("Cl")) xsDataAtom4.setConcentration(XSDataDouble(1000)) xsDataAtomicComposition.addAtom(xsDataAtom3) xsDataAtomicComposition.addAtom(xsDataAtom4) xsDataSolvent.setAtoms(xsDataAtomicComposition) xsDataComposition.setStructure(xsDataStructure) xsDataComposition.setSolvent(xsDataSolvent) xsDataSampleCrystalMM.setChemicalComposition(xsDataComposition) xsDataSampleCrystalMM.setSize( XSDataSize(XSDataLength(0.1), XSDataLength(0.1), XSDataLength(0.1))) xsDataCrystal = XSDataCrystal() xsDataCell = XSDataCell(angle_alpha=XSDataAngle(90.0), angle_beta=XSDataAngle(90.0), angle_gamma=XSDataAngle(90.0), length_a=XSDataLength(78.9), length_b=XSDataLength(95.162), length_c=XSDataLength(104.087)) xsDataCrystal.setCell(xsDataCell) xsDataSpaceGroup = XSDataSpaceGroup() xsDataSpaceGroup.setITNumber(XSDataInteger(16)) xsDataCrystal.setSpaceGroup(xsDataSpaceGroup) xsDataSampleCrystalMM.setSusceptibility(XSDataDouble(1.5)) xsDataStrategy.setCrystalRefined(xsDataCrystal) xsDataStrategy.setSample(xsDataSampleCrystalMM) xsDataStrategy.exportToFile(self.strObtainedInputFile) pyStrExpectedInput = self.readAndParseFile(self.strReferenceInputFile) pyStrObtainedInput = self.readAndParseFile(self.strObtainedInputFile) xsDataInputExpected = XSDataInputStrategy.parseString( pyStrExpectedInput) xsDataInputObtained = XSDataInputStrategy.parseString( pyStrObtainedInput) EDAssert.equal(xsDataInputExpected.marshal(), xsDataInputObtained.marshal())
def generateXSDataIndexingResult(_xsDataMOSFLMIndexingOutput, _xsDataExperimentalCondition=None): """ Translation from XSDataMOSFLMIndexingOutput to XSDataIndexingResult. """ EDVerbose.DEBUG("EDHandlerXSDataMOSFLMv10.generateXSDataIndexingOutput") xsDataMOSFLMBeamPositionRefined = _xsDataMOSFLMIndexingOutput.getRefinedBeam() xsDataMOSFLMBeamPositionShift = _xsDataMOSFLMIndexingOutput.getBeamShift() dDeviationAngular = _xsDataMOSFLMIndexingOutput.getDeviationAngular().getValue() dDeviationPositional = _xsDataMOSFLMIndexingOutput.getDeviationPositional().getValue() dMosaicityEstimation = _xsDataMOSFLMIndexingOutput.getMosaicityEstimation().getValue() dDistanceRefined = _xsDataMOSFLMIndexingOutput.getRefinedDistance().getValue() iSelectedSolution = _xsDataMOSFLMIndexingOutput.getSelectedSolutionNumber().getValue() iSpotsTotal = _xsDataMOSFLMIndexingOutput.getSpotsTotal().getValue() iSpotsUsed = _xsDataMOSFLMIndexingOutput.getSpotsUsed().getValue() xsDataCellRefined = _xsDataMOSFLMIndexingOutput.getRefinedNewmat().getRefinedCell() xsDataMatrixA = _xsDataMOSFLMIndexingOutput.getRefinedNewmat().getAMatrix() xsDataMatrixU = _xsDataMOSFLMIndexingOutput.getRefinedNewmat().getUMatrix() strSelectedSpaceGroupName = _xsDataMOSFLMIndexingOutput.getSelectedSolutionSpaceGroup().getValue() iSelectedSpaceGroupNumber = _xsDataMOSFLMIndexingOutput.getSelectedSolutionSpaceGroupNumber().getValue() xsDataIndexingResult = XSDataIndexingResult() xsDataIndexingSolutionSelected = None for possibleSolutions in _xsDataMOSFLMIndexingOutput.getPossibleSolutions(): xsDataCrystal = XSDataCrystal() xsDataSpaceGroup = XSDataSpaceGroup() xsDataSpaceGroup.setName(XSDataString(possibleSolutions.getLattice().getValue())) xsDataCrystal.setSpaceGroup(xsDataSpaceGroup) xsDataCrystal.setCell(possibleSolutions.getCell()) xsDataIndexingSolution = XSDataIndexingSolution() xsDataIndexingSolution.setCrystal(xsDataCrystal) iIndex = possibleSolutions.getIndex().getValue() xsDataIndexingSolution.setNumber(XSDataInteger(iIndex)) xsDataIndexingSolution.setPenalty(XSDataFloat(possibleSolutions.getPenalty().getValue())) xsDataIndexingResult.addSolution(xsDataIndexingSolution) if (iIndex == iSelectedSolution): xsDataIndexingSolutionSelected = XSDataIndexingSolutionSelected() xsDataIndexingSolutionSelected.setNumber(XSDataInteger(iIndex)) xsDataIndexingSolutionSelected.setPenalty(XSDataFloat(possibleSolutions.getPenalty().getValue())) xsDataCrystalSelected = XSDataCrystal() xsDataSpaceGroupSelected = XSDataSpaceGroup() xsDataSpaceGroupSelected.setName(XSDataString(strSelectedSpaceGroupName)) xsDataSpaceGroupSelected.setITNumber(XSDataInteger(iSelectedSpaceGroupNumber)) xsDataCrystalSelected.setSpaceGroup(xsDataSpaceGroupSelected) xsDataCrystalSelected.setCell(xsDataCellRefined) xsDataCrystalSelected.setMosaicity(XSDataDouble(dMosaicityEstimation)) xsDataIndexingSolutionSelected.setCrystal(xsDataCrystalSelected) xsDataOrientation = XSDataOrientation() xsDataOrientation.setMatrixA(xsDataMatrixA) xsDataOrientation.setMatrixU(xsDataMatrixU) xsDataIndexingSolutionSelected.setOrientation(xsDataOrientation) xsDataStatisticsIndexing = XSDataStatisticsIndexing() xsDataStatisticsIndexing.setBeamPositionShiftX(XSDataLength(xsDataMOSFLMBeamPositionShift.getX().getValue())) xsDataStatisticsIndexing.setBeamPositionShiftY(XSDataLength(xsDataMOSFLMBeamPositionShift.getY().getValue())) xsDataStatisticsIndexing.setSpotDeviationAngular(XSDataAngle(dDeviationAngular)) xsDataStatisticsIndexing.setSpotDeviationPositional(XSDataLength(dDeviationPositional)) xsDataStatisticsIndexing.setSpotsUsed(XSDataInteger(iSpotsUsed)) xsDataStatisticsIndexing.setSpotsTotal(XSDataInteger(iSpotsTotal)) xsDataIndexingSolutionSelected.setStatistics(xsDataStatisticsIndexing) xsDataExperimentalConditionRefined = None if (_xsDataExperimentalCondition is None): xsDataExperimentalConditionRefined = XSDataExperimentalCondition() else: # Copy the incoming experimental condition xmlExperimentalCondition = _xsDataExperimentalCondition.marshal() xsDataExperimentalConditionRefined = XSDataExperimentalCondition.parseString(xmlExperimentalCondition) xsDataDetector = xsDataExperimentalConditionRefined.getDetector() if (xsDataDetector is None): xsDataDetector = XSDataDetector() xsDataDetector.setBeamPositionX(XSDataLength(xsDataMOSFLMBeamPositionRefined.getX().getValue())) xsDataDetector.setBeamPositionY(XSDataLength(xsDataMOSFLMBeamPositionRefined.getY().getValue())) xsDataDetector.setDistance(XSDataLength(dDistanceRefined)) xsDataExperimentalConditionRefined.setDetector(xsDataDetector) xsDataIndexingSolutionSelected.setExperimentalConditionRefined(xsDataExperimentalConditionRefined) xsDataIndexingResult.setSelectedSolution(xsDataIndexingSolutionSelected) return xsDataIndexingResult
def generateXSDataIndexingResult(_xsDataMOSFLMIndexingOutput, _xsDataExperimentalCondition=None): """ Translation from XSDataMOSFLMIndexingOutput to XSDataIndexingResult. """ EDVerbose.DEBUG( "EDHandlerXSDataMOSFLMv10.generateXSDataIndexingOutput") xsDataMOSFLMBeamPositionRefined = _xsDataMOSFLMIndexingOutput.getRefinedBeam( ) xsDataMOSFLMBeamPositionShift = _xsDataMOSFLMIndexingOutput.getBeamShift( ) dDeviationAngular = _xsDataMOSFLMIndexingOutput.getDeviationAngular( ).getValue() dDeviationPositional = _xsDataMOSFLMIndexingOutput.getDeviationPositional( ).getValue() dMosaicityEstimation = _xsDataMOSFLMIndexingOutput.getMosaicityEstimation( ).getValue() dDistanceRefined = _xsDataMOSFLMIndexingOutput.getRefinedDistance( ).getValue() iSelectedSolution = _xsDataMOSFLMIndexingOutput.getSelectedSolutionNumber( ).getValue() iSpotsTotal = _xsDataMOSFLMIndexingOutput.getSpotsTotal().getValue() iSpotsUsed = _xsDataMOSFLMIndexingOutput.getSpotsUsed().getValue() xsDataCellRefined = _xsDataMOSFLMIndexingOutput.getRefinedNewmat( ).getRefinedCell() xsDataMatrixA = _xsDataMOSFLMIndexingOutput.getRefinedNewmat( ).getAMatrix() xsDataMatrixU = _xsDataMOSFLMIndexingOutput.getRefinedNewmat( ).getUMatrix() strSelectedSpaceGroupName = _xsDataMOSFLMIndexingOutput.getSelectedSolutionSpaceGroup( ).getValue() iSelectedSpaceGroupNumber = _xsDataMOSFLMIndexingOutput.getSelectedSolutionSpaceGroupNumber( ).getValue() xsDataIndexingResult = XSDataIndexingResult() xsDataIndexingSolutionSelected = None for possibleSolutions in _xsDataMOSFLMIndexingOutput.getPossibleSolutions( ): xsDataCrystal = XSDataCrystal() xsDataSpaceGroup = XSDataSpaceGroup() xsDataSpaceGroup.setName( XSDataString(possibleSolutions.getLattice().getValue())) xsDataCrystal.setSpaceGroup(xsDataSpaceGroup) xsDataCrystal.setCell(possibleSolutions.getCell()) xsDataIndexingSolution = XSDataIndexingSolution() xsDataIndexingSolution.setCrystal(xsDataCrystal) iIndex = possibleSolutions.getIndex().getValue() xsDataIndexingSolution.setNumber(XSDataInteger(iIndex)) xsDataIndexingSolution.setPenalty( XSDataFloat(possibleSolutions.getPenalty().getValue())) xsDataIndexingResult.addSolution(xsDataIndexingSolution) if (iIndex == iSelectedSolution): xsDataIndexingSolutionSelected = XSDataIndexingSolutionSelected( ) xsDataIndexingSolutionSelected.setNumber(XSDataInteger(iIndex)) xsDataIndexingSolutionSelected.setPenalty( XSDataFloat(possibleSolutions.getPenalty().getValue())) xsDataCrystalSelected = XSDataCrystal() xsDataSpaceGroupSelected = XSDataSpaceGroup() xsDataSpaceGroupSelected.setName( XSDataString(strSelectedSpaceGroupName)) xsDataSpaceGroupSelected.setITNumber( XSDataInteger(iSelectedSpaceGroupNumber)) xsDataCrystalSelected.setSpaceGroup(xsDataSpaceGroupSelected) xsDataCrystalSelected.setCell(xsDataCellRefined) xsDataCrystalSelected.setMosaicity(XSDataDouble(dMosaicityEstimation)) xsDataIndexingSolutionSelected.setCrystal(xsDataCrystalSelected) xsDataOrientation = XSDataOrientation() xsDataOrientation.setMatrixA(xsDataMatrixA) xsDataOrientation.setMatrixU(xsDataMatrixU) xsDataIndexingSolutionSelected.setOrientation(xsDataOrientation) xsDataStatisticsIndexing = XSDataStatisticsIndexing() xsDataStatisticsIndexing.setBeamPositionShiftX( XSDataLength(xsDataMOSFLMBeamPositionShift.getX().getValue())) xsDataStatisticsIndexing.setBeamPositionShiftY( XSDataLength(xsDataMOSFLMBeamPositionShift.getY().getValue())) xsDataStatisticsIndexing.setSpotDeviationAngular( XSDataAngle(dDeviationAngular)) xsDataStatisticsIndexing.setSpotDeviationPositional( XSDataLength(dDeviationPositional)) xsDataStatisticsIndexing.setSpotsUsed(XSDataInteger(iSpotsUsed)) xsDataStatisticsIndexing.setSpotsTotal(XSDataInteger(iSpotsTotal)) xsDataIndexingSolutionSelected.setStatistics(xsDataStatisticsIndexing) xsDataExperimentalConditionRefined = None if (_xsDataExperimentalCondition is None): xsDataExperimentalConditionRefined = XSDataExperimentalCondition() else: # Copy the incoming experimental condition xmlExperimentalCondition = _xsDataExperimentalCondition.marshal() xsDataExperimentalConditionRefined = XSDataExperimentalCondition.parseString( xmlExperimentalCondition) xsDataDetector = xsDataExperimentalConditionRefined.getDetector() if (xsDataDetector is None): xsDataDetector = XSDataDetector() xsDataDetector.setBeamPositionX( XSDataLength(xsDataMOSFLMBeamPositionRefined.getX().getValue())) xsDataDetector.setBeamPositionY( XSDataLength(xsDataMOSFLMBeamPositionRefined.getY().getValue())) xsDataDetector.setDistance(XSDataLength(dDistanceRefined)) xsDataExperimentalConditionRefined.setDetector(xsDataDetector) xsDataIndexingSolutionSelected.setExperimentalConditionRefined( xsDataExperimentalConditionRefined) xsDataIndexingResult.setSelectedSolution( xsDataIndexingSolutionSelected) xsDataIndexingResult.setIndexingLogFile( _xsDataMOSFLMIndexingOutput.getPathToLogFile()) return xsDataIndexingResult
def generateXSDataIntegrationSubWedgeResult(_xsDataMOSFLMOutputIntegration, _xsDataExperimentalCondition=None): """ Translation from XSDataMOSFLMOutputIntegration to XSDataIntegrationSubWedgeResult. """ EDVerbose.DEBUG("EDHandlerXSDataMOSFLMv10.generateXSDataIntegrationInput") EDFactoryPluginStatic.loadModule("XSDataMOSFLMv10") xsDataIntegrationSubWedgeResult = XSDataIntegrationSubWedgeResult() xsDataExperimentalConditionRefined = None if (_xsDataExperimentalCondition is None): xsDataExperimentalConditionRefined = XSDataExperimentalCondition() else: # Copy the incoming experimental condition xmlExperimentalCondition = _xsDataExperimentalCondition.marshal() xsDataExperimentalConditionRefined = XSDataExperimentalCondition.parseString(xmlExperimentalCondition) xsDataDetector = xsDataExperimentalConditionRefined.getDetector() if (xsDataDetector is None): xsDataDetector = XSDataDetector() xsDataIntegrationSubWedgeResult.setBestfilePar(XSDataString(_xsDataMOSFLMOutputIntegration.getBestfilePar().getValue())) xsDataIntegrationSubWedgeResult.setBestfileDat(XSDataString(_xsDataMOSFLMOutputIntegration.getBestfileDat().getValue())) xsDataIntegrationSubWedgeResult.setBestfileHKL(XSDataString(_xsDataMOSFLMOutputIntegration.getBestfileHKL().getValue())) xsDataLengthRefinedDistance = _xsDataMOSFLMOutputIntegration.getRefinedDistance() if (xsDataLengthRefinedDistance is not None): xsDataDetector.setDistance(xsDataLengthRefinedDistance) xsDataMOSFLMBeamPositionRefined = _xsDataMOSFLMOutputIntegration.getRefinedBeam() if (xsDataMOSFLMBeamPositionRefined is not None): xsDataDetector.setBeamPositionX(XSDataLength(xsDataMOSFLMBeamPositionRefined.getX().getValue())) xsDataDetector.setBeamPositionY(XSDataLength(xsDataMOSFLMBeamPositionRefined.getY().getValue())) xsDataExperimentalConditionRefined.setDetector(xsDataDetector) xsDataIntegrationSubWedgeResult.setExperimentalConditionRefined(xsDataExperimentalConditionRefined) if (_xsDataMOSFLMOutputIntegration.getGeneratedMTZFile() is not None): xsDataIntegrationSubWedgeResult.setGeneratedMTZFile(_xsDataMOSFLMOutputIntegration.getGeneratedMTZFile()) xsDataStatisticsIntegration = XSDataStatisticsIntegration() if (_xsDataMOSFLMOutputIntegration.getOverallIOverSigma() is not None): xsDataStatisticsIntegration.setIOverSigmaOverall(XSDataDouble(_xsDataMOSFLMOutputIntegration.getOverallIOverSigma().getValue())) if (_xsDataMOSFLMOutputIntegration.getHighestResolutionIOverSigma() is not None): xsDataStatisticsIntegration.setIOverSigmaAtHighestResolution(XSDataDouble(_xsDataMOSFLMOutputIntegration.getHighestResolutionIOverSigma().getValue())) if (_xsDataMOSFLMOutputIntegration.getRMSSpotDeviation() is not None): xsDataStatisticsIntegration.setRMSSpotDeviation(XSDataLength(_xsDataMOSFLMOutputIntegration.getRMSSpotDeviation().getValue())) if (_xsDataMOSFLMOutputIntegration.getNumberOfBadReflections() is not None): xsDataStatisticsIntegration.setNumberOfBadReflections(XSDataInteger(_xsDataMOSFLMOutputIntegration.getNumberOfBadReflections().getValue())) if (_xsDataMOSFLMOutputIntegration.getNumberOfFullyRecordedReflections() is not None): xsDataStatisticsIntegration.setNumberOfFullyRecordedReflections(XSDataInteger(_xsDataMOSFLMOutputIntegration.getNumberOfFullyRecordedReflections().getValue())) if (_xsDataMOSFLMOutputIntegration.getNumberOfNegativeReflections() is not None): xsDataStatisticsIntegration.setNumberOfNegativeReflections(XSDataInteger(_xsDataMOSFLMOutputIntegration.getNumberOfNegativeReflections().getValue())) if (_xsDataMOSFLMOutputIntegration.getNumberOfOverlappedReflections() is not None): xsDataStatisticsIntegration.setNumberOfOverlappedReflections(XSDataInteger(_xsDataMOSFLMOutputIntegration.getNumberOfOverlappedReflections().getValue())) if (_xsDataMOSFLMOutputIntegration.getNumberOfPartialReflections() is not None): xsDataStatisticsIntegration.setNumberOfPartialReflections(XSDataInteger(_xsDataMOSFLMOutputIntegration.getNumberOfPartialReflections().getValue())) if (_xsDataMOSFLMOutputIntegration.getNumberOfReflectionsGenerated() is not None): xsDataStatisticsIntegration.setNumberOfReflectionsGenerated(XSDataInteger(_xsDataMOSFLMOutputIntegration.getNumberOfReflectionsGenerated().getValue())) xsDataIntegrationSubWedgeResult.setStatistics(xsDataStatisticsIntegration) xsDataIntegrationSubWedgeResult.setExperimentalConditionRefined(xsDataExperimentalConditionRefined) for xsDataMOSFLMIntegrationStatisticsPerResolutionBin in _xsDataMOSFLMOutputIntegration.getStatisticsPerResolutionBin(): xsDataStatisticsIntegrationPerResolutionBin = XSDataStatisticsIntegrationPerResolutionBin() if (xsDataMOSFLMIntegrationStatisticsPerResolutionBin.getMaxResolution() is not None): xsDataStatisticsIntegrationPerResolutionBin.setMaxResolution(XSDataDouble(xsDataMOSFLMIntegrationStatisticsPerResolutionBin.getMaxResolution().getValue())) if (xsDataMOSFLMIntegrationStatisticsPerResolutionBin.getMinResolution() is not None): xsDataStatisticsIntegrationPerResolutionBin.setMinResolution(XSDataDouble(xsDataMOSFLMIntegrationStatisticsPerResolutionBin.getMinResolution().getValue())) xsDataStatisticsIntegrationPerResolutionBin.setProfileFitted(EDHandlerXSDataMOSFLMv10.generateXSDataIntegrationStatisticsPerReflectionType(xsDataMOSFLMIntegrationStatisticsPerResolutionBin.getProfileFitted())) xsDataStatisticsIntegrationPerResolutionBin.setSummation(EDHandlerXSDataMOSFLMv10.generateXSDataIntegrationStatisticsPerReflectionType(xsDataMOSFLMIntegrationStatisticsPerResolutionBin.getSummation())) xsDataIntegrationSubWedgeResult.addStatisticsPerResolutionBin(xsDataStatisticsIntegrationPerResolutionBin) return xsDataIntegrationSubWedgeResult
def getTestExperimentalCondition(self): strPathToTestExperimentalCondition = os.path.join(self.getPluginTestsDataHome(), "XSDataExperimentalCondition_test.xml") strXMLInput = self.readAndParseFile(strPathToTestExperimentalCondition) xsDataExperimentalCondition = XSDataExperimentalCondition.parseString(strXMLInput) return xsDataExperimentalCondition
def buildChildren(self, child_, nodeName_): if child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'experimentalCondition': obj_ = XSDataExperimentalCondition() obj_.build(child_) self.setExperimentalCondition(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'diffractionPlan': obj_ = XSDataDiffractionPlan() obj_.build(child_) self.setDiffractionPlan(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'sample': obj_ = XSDataSampleCrystalMM() obj_.build(child_) self.setSample(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'imagePath': obj_ = XSDataFile() obj_.build(child_) self.imagePath.append(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'flux': obj_ = XSDataFloat() obj_.build(child_) self.setFlux(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'minExposureTimePerImage': obj_ = XSDataTime() obj_.build(child_) self.setMinExposureTimePerImage(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'beamSize': obj_ = XSDataLength() obj_.build(child_) self.setBeamSize(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'beamSizeX': obj_ = XSDataLength() obj_.build(child_) self.setBeamSizeX(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'beamSizeY': obj_ = XSDataLength() obj_.build(child_) self.setBeamSizeY(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'templateMode': obj_ = XSDataBoolean() obj_.build(child_) self.setTemplateMode(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'generatedTemplateFile': obj_ = XSDataFile() obj_.build(child_) self.setGeneratedTemplateFile(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'resultsFilePath': obj_ = XSDataFile() obj_.build(child_) self.setResultsFilePath(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'beamPosX': obj_ = XSDataFloat() obj_.build(child_) self.setBeamPosX(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'beamPosY': obj_ = XSDataFloat() obj_.build(child_) self.setBeamPosY(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'wavelength': obj_ = XSDataWavelength() obj_.build(child_) self.setWavelength(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'transmission': obj_ = XSDataDouble() obj_.build(child_) self.setTransmission(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'dataCollectionId': obj_ = XSDataInteger() obj_.build(child_) self.setDataCollectionId(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'shortComments': obj_ = XSDataString() obj_.build(child_) self.setShortComments(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'comments': obj_ = XSDataString() obj_.build(child_) self.setComments(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'inputCharacterisation': obj_ = XSDataInputCharacterisation() obj_.build(child_) self.setInputCharacterisation(obj_)
def preProcess(self, _edObject=None): """ Gets the Configuration Parameters, if found, overrides default parameters """ EDPluginControl.preProcess(self, _edObject) EDVerbose.DEBUG("EDPluginControlGeneratePredictionv10.preProcess...") xsDataGeneratePredictionInput = self.getDataInput() xsDataSelectedIndexingSolution = xsDataGeneratePredictionInput.getSelectedIndexingSolution( ) xsDataExperimentalConditionRefined = xsDataSelectedIndexingSolution.getExperimentalConditionRefined( ) xsDataCollection = xsDataGeneratePredictionInput.getDataCollection() xsDataSubWedgeList = xsDataCollection.getSubWedge() # List containing instances of all the generate prediction plugins self.__listPluginGeneratePrediction = [] # Loop through all subwedges iIndex = 0 for xsDataSubWedge in xsDataSubWedgeList: xsDataImageList = xsDataSubWedge.getImage() # First find the lowest image number iLowestImageNumber = None for xsDataImage in xsDataImageList: iImageNumber = xsDataImage.getNumber().getValue() if (iLowestImageNumber is None): iLowestImageNumber = iImageNumber elif (iImageNumber < iLowestImageNumber): iLowestImageNumber = iImageNumber # Then loop through all images in a sub wedge for xsDataImage in xsDataImageList: iIndex += 1 edPluginGeneratePrediction = self.loadPlugin( self.__strPluginGeneratePredictionName, "%s-%02d" % (self.__strPluginGeneratePredictionName, iIndex)) xsDataGeneratePredictionInput = XSDataGeneratePredictionInput() xsDataGeneratePredictionInput.setSelectedIndexingSolution( XSDataIndexingSolutionSelected.parseString( xsDataSelectedIndexingSolution.marshal())) xsDataCollectionNew = XSDataCollection() xsDataSubWedgeNew = XSDataSubWedge() xsDataSubWedgeNew.addImage( XSDataImage.parseString(xsDataImage.marshal())) xsDataSubWedgeNew.setExperimentalCondition( XSDataExperimentalCondition.parseString( xsDataSubWedge.getExperimentalCondition().marshal())) # We must modify the rotationOscillationStart for the new subwedge xsDataGoniostatNew = xsDataSubWedgeNew.getExperimentalCondition( ).getGoniostat() fGoniostatRotationAxisStart = xsDataGoniostatNew.getRotationAxisStart( ).getValue() fGonioStatOscillationRange = xsDataGoniostatNew.getOscillationWidth( ).getValue() iImageNumber = xsDataImage.getNumber().getValue() fGoniostatRotationAxisStartNew = fGoniostatRotationAxisStart + ( iImageNumber - iLowestImageNumber) * fGonioStatOscillationRange xsDataGoniostatNew.setRotationAxisStart( XSDataAngle(fGoniostatRotationAxisStartNew)) # xsDataCollectionNew.addSubWedge(xsDataSubWedgeNew) xsDataGeneratePredictionInput.setDataCollection( xsDataCollectionNew) from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10 xsDataMOSFLMInputGeneratePrediction = EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputGeneratePrediction( xsDataGeneratePredictionInput) edPluginGeneratePrediction.setDataInput( xsDataMOSFLMInputGeneratePrediction) self.__listPluginGeneratePrediction.append( edPluginGeneratePrediction)
def testSetDataModelInput(self): from XSDataCCP4iv1_1 import XSDataInputCCP4i xsDataInputCCP4i = XSDataInputCCP4i() # Beam from XSDataCommon import XSDataFlux from XSDataCommon import XSDataSize from XSDataCommon import XSDataLength from XSDataCommon import XSDataFloat from XSDataMXv1 import XSDataBeam from XSDataMXv1 import XSDataExperimentalCondition xsExperimentalCondition = XSDataExperimentalCondition() xsBeam = XSDataBeam() xsBeam.setFlux(XSDataFlux(1e+12)) xsBeam.setSize(XSDataSize(XSDataLength(0.1), XSDataLength(0.1))) xsBeam.setMinExposureTimePerImage(XSDataFloat(0.1)) xsExperimentalCondition.setBeam(xsBeam) # Goniostat from XSDataCommon import XSDataSpeed from XSDataCommon import XSDataAngle from XSDataMXv1 import XSDataGoniostat xsDataGoniostat = XSDataGoniostat() xsDataGoniostat.setMaxOscillationSpeed(XSDataSpeed(0.2)) xsDataGoniostat.setMinOscillationWidth(XSDataAngle(0.1)) xsExperimentalCondition.setGoniostat(xsDataGoniostat) xsDataInputCCP4i.setExperimentalCondition(xsExperimentalCondition) # Sample from XSDataCommon import XSDataString from XSDataCommon import XSDataFloat from XSDataCommon import XSDataString from XSDataMXv1 import XSDataStructure from XSDataMXv1 import XSDataChain from XSDataMXv1 import XSDataAtom from XSDataMXv1 import XSDataLigand from XSDataMXv1 import XSDataSampleCrystalMM from XSDataMXv1 import XSDataChemicalCompositionMM from XSDataMXv1 import XSDataAtomicComposition from XSDataMXv1 import XSDataSolvent xsDataSampleCrystalMM = XSDataSampleCrystalMM() xsDataStructure = XSDataStructure() xsDataComposition = XSDataChemicalCompositionMM() xsDataChain = XSDataChain() xsDataChain.setType(XSDataString("protein")) xsDataChain.setNumberOfCopies(XSDataFloat(2)) xsDataAtomicComposition = XSDataAtomicComposition() xsDataAtom1 = XSDataAtom() xsDataAtom1.setSymbol(XSDataString("Se")) xsDataAtom1.setNumberOf(XSDataFloat(4)) xsDataAtomicComposition.addAtom(xsDataAtom1) xsDataChain.setHeavyAtoms(xsDataAtomicComposition) xsDataChain.setNumberOfMonomers(XSDataFloat(100)) xsDataStructure.addChain(xsDataChain) xsDataChain2 = XSDataChain() xsDataChain2.setType(XSDataString("rna")) xsDataChain2.setNumberOfCopies(XSDataFloat(1)) xsDataChain2.setNumberOfMonomers(XSDataFloat(60)) xsDataStructure.addChain(xsDataChain2) xsDataLigand = XSDataLigand() xsDataLigand.setNumberOfCopies(XSDataFloat(2)) xsDataLigand.setNumberOfLightAtoms(XSDataFloat(42)) xsDataAtomicComposition = XSDataAtomicComposition() xsDataAtom2 = XSDataAtom() xsDataAtom2.setSymbol(XSDataString("Fe")) xsDataAtom2.setNumberOf(XSDataFloat(1)) xsDataAtomicComposition.addAtom(xsDataAtom2) xsDataLigand.setHeavyAtoms(xsDataAtomicComposition) xsDataStructure.addLigand(xsDataLigand) xsDataStructure.setNumberOfCopiesInAsymmetricUnit(XSDataFloat(0.25)) xsDataSolvent = XSDataSolvent() xsDataAtomicComposition = XSDataAtomicComposition() xsDataAtom3 = XSDataAtom() xsDataAtom3.setSymbol(XSDataString("Na")) xsDataAtom3.setConcentration(XSDataFloat(1000)) xsDataAtom4 = XSDataAtom() xsDataAtom4.setSymbol(XSDataString("Cl")) xsDataAtom4.setConcentration(XSDataFloat(1000)) xsDataAtomicComposition.addAtom(xsDataAtom3) xsDataAtomicComposition.addAtom(xsDataAtom4) xsDataSolvent.setAtoms(xsDataAtomicComposition) xsDataComposition.setStructure(xsDataStructure) xsDataComposition.setSolvent(xsDataSolvent) xsDataSampleCrystalMM.setChemicalComposition(xsDataComposition) xsDataSampleCrystalMM.setSize(XSDataSize(XSDataLength(0.2), XSDataLength(0.2), XSDataLength(0.2))) xsDataSampleCrystalMM.setSusceptibility(XSDataFloat(1.5)) xsDataSampleCrystalMM.setShape(XSDataFloat(2)) xsDataInputCCP4i.setSample(xsDataSampleCrystalMM) from XSDataMXv1 import XSDataDiffractionPlan xsDataDiffractionPlan = XSDataDiffractionPlan() xsDataDiffractionPlan.setAimedCompleteness(XSDataFloat(95.5)) xsDataDiffractionPlan.setAimedIOverSigmaAtHighestResolution(XSDataFloat(2.5)) xsDataDiffractionPlan.setAimedMultiplicity(XSDataFloat(95.5)) xsDataDiffractionPlan.setAimedResolution(XSDataFloat(3)) xsDataDiffractionPlan.setComplexity(XSDataString("full")) xsDataDiffractionPlan.setForcedSpaceGroup(XSDataString("P222")) xsDataDiffractionPlan.setMaxExposureTimePerDataCollection(XSDataFloat(10000)) xsDataInputCCP4i.setDiffractionPlan(xsDataDiffractionPlan) from XSDataCommon import XSDataFile listInputDataFile = [] xsDataFile = XSDataFile(XSDataString(self.strXSDataGenerateTemplateFile)) listInputDataFile.append(xsDataFile) xsDataInputCCP4i.setDataFile(listInputDataFile)
def process(self, _edObject=None): EDPluginExec.process(self) EDVerbose.DEBUG("EDPluginExecReadImageHeaderPilatus2Mv10.process") xsDataInputReadImageHeader = self.getDataInput() xsDataFile = xsDataInputReadImageHeader.getImage() strPath = xsDataFile.getPath().getValue() dictPilatus2MHeader = self.readHeaderPilatus2M(strPath) if (dictPilatus2MHeader is None): strErrorMessage = "EDPluginExecReadImageHeaderPilatus2Mv10.process : Cannot read header : %s" % strPath EDVerbose.error(strErrorMessage) self.addErrorMessage(strErrorMessage) self.setFailure() else: xsDataExperimentalCondition = XSDataExperimentalCondition() xsDataDetector = XSDataDetector() iNoPixelsX = 1475 iNoPixelsY = 1679 xsDataDetector.setNumberPixelX(XSDataInteger(iNoPixelsX)) xsDataDetector.setNumberPixelY(XSDataInteger(iNoPixelsY)) # Pixel size listPixelSizeXY = dictPilatus2MHeader[ "Pixel_size" ].split(" ") fPixelSizeX = float(listPixelSizeXY[0]) * 1000 xsDataDetector.setPixelSizeX(XSDataLength(fPixelSizeX)) fPixelSizeY = float(listPixelSizeXY[3]) * 1000 xsDataDetector.setPixelSizeY(XSDataLength(fPixelSizeY)) # Beam position listBeamPosition = dictPilatus2MHeader["Beam_xy"].replace("(", " ").replace(")", " ").replace(",", " ").split() fBeamPositionX = float(listBeamPosition[1]) * fPixelSizeX fBeamPositionY = float(listBeamPosition[0]) * fPixelSizeY xsDataDetector.setBeamPositionX(XSDataLength(fBeamPositionX)) xsDataDetector.setBeamPositionY(XSDataLength(fBeamPositionY)) fDistance = float(dictPilatus2MHeader[ "Detector_distance" ].split(" ")[0]) * 1000 xsDataDetector.setDistance(XSDataLength(fDistance)) # xsDataDetector.setNumberBytesInHeader(XSDataInteger(float(dictPilatus2MHeader[ "header_size" ]))) xsDataDetector.setSerialNumber(XSDataString(dictPilatus2MHeader[ "Detector:" ])) # #xsDataDetector.setBin( XSDataString( dictPilatus2MHeader[ "BIN" ] ) ) ) # #xsDataDetector.setDataType( XSDataString( dictPilatus2MHeader[ "TYPE" ] ) ) ) # #xsDataDetector.setByteOrder( XSDataString( dictPilatus2MHeader[ "BYTE_ORDER" ] ) ) ) # xsDataDetector.setImageSaturation(XSDataInteger(int(dictPilatus2MHeader[ "saturation_level" ]))) xsDataDetector.setName(XSDataString("PILATUS2 3M")) xsDataDetector.setType(XSDataString("pilatus2m")) xsDataExperimentalCondition.setDetector(xsDataDetector) # Beam object xsDataBeam = XSDataBeam() xsDataBeam.setWavelength(XSDataWavelength(float(dictPilatus2MHeader[ "Wavelength" ].split(" ")[0]))) xsDataBeam.setExposureTime(XSDataTime(float(dictPilatus2MHeader[ "Exposure_time" ].split(" ")[0]))) xsDataExperimentalCondition.setBeam(xsDataBeam) # Goniostat object xsDataGoniostat = XSDataGoniostat() fRotationAxisStart = float(dictPilatus2MHeader[ "Start_angle" ].split(" ")[0]) fOscillationWidth = float(dictPilatus2MHeader[ "Angle_increment" ].split(" ")[0]) xsDataGoniostat.setRotationAxisStart(XSDataAngle(fRotationAxisStart)) xsDataGoniostat.setRotationAxisEnd(XSDataAngle(fRotationAxisStart + fOscillationWidth)) xsDataGoniostat.setOscillationWidth(XSDataAngle(fOscillationWidth)) xsDataExperimentalCondition.setGoniostat(xsDataGoniostat) # # Create the image object xsDataImage = XSDataImage() xsDataImage.setPath(XSDataString(strPath)) if "DateTime" in dictPilatus2MHeader: strTimeStamp = dictPilatus2MHeader[ "DateTime" ] xsDataImage.setDate(XSDataString(strTimeStamp)) iImageNumber = EDUtilsImage.getImageNumber(strPath) xsDataImage.setNumber(XSDataInteger(iImageNumber)) xsDataSubWedge = XSDataSubWedge() xsDataSubWedge.setExperimentalCondition(xsDataExperimentalCondition) xsDataSubWedge.addImage(xsDataImage) self.__xsDataResultReadImageHeader = XSDataResultReadImageHeader() self.__xsDataResultReadImageHeader.setSubWedge(xsDataSubWedge)
def buildChildren(self, child_, nodeName_): if child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'experimentalCondition': obj_ = XSDataExperimentalCondition() obj_.build(child_) self.setExperimentalCondition(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'diffractionPlan': obj_ = XSDataDiffractionPlan() obj_.build(child_) self.setDiffractionPlan(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'sample': obj_ = XSDataSampleCrystalMM() obj_.build(child_) self.setSample(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'imagePath': obj_ = XSDataFile() obj_.build(child_) self.imagePath.append(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'flux': obj_ = XSDataFloat() obj_.build(child_) self.setFlux(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'minExposureTimePerImage': obj_ = XSDataTime() obj_.build(child_) self.setMinExposureTimePerImage(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'beamSize': obj_ = XSDataLength() obj_.build(child_) self.setBeamSize(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'beamSizeX': obj_ = XSDataLength() obj_.build(child_) self.setBeamSizeX(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'beamSizeY': obj_ = XSDataLength() obj_.build(child_) self.setBeamSizeY(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'apertureSize': obj_ = XSDataLength() obj_.build(child_) self.setApertureSize(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'templateMode': obj_ = XSDataBoolean() obj_.build(child_) self.setTemplateMode(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'generatedTemplateFile': obj_ = XSDataFile() obj_.build(child_) self.setGeneratedTemplateFile(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'resultsFilePath': obj_ = XSDataFile() obj_.build(child_) self.setResultsFilePath(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'beamPosX': obj_ = XSDataFloat() obj_.build(child_) self.setBeamPosX(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'beamPosY': obj_ = XSDataFloat() obj_.build(child_) self.setBeamPosY(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'wavelength': obj_ = XSDataWavelength() obj_.build(child_) self.setWavelength(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'transmission': obj_ = XSDataDouble() obj_.build(child_) self.setTransmission(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'dataCollectionId': obj_ = XSDataInteger() obj_.build(child_) self.setDataCollectionId(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'shortComments': obj_ = XSDataString() obj_.build(child_) self.setShortComments(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'comments': obj_ = XSDataString() obj_.build(child_) self.setComments(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'inputCharacterisation': obj_ = XSDataInputCharacterisation() obj_.build(child_) self.setInputCharacterisation(obj_)