def createDataMOSFLMOutputIntegration(self): self.DEBUG("EDPluginMOSFLMIntegrationv10.createDataMOSFLMOutputIntegration") xsDataMOSFLMOutputIntegration = XSDataMOSFLMOutputIntegration() # Read bestfile.par, bestfile.hkl and bestfile.dat strBestfilePar = self.readBestFile("bestfile.par") bContinue = True if (strBestfilePar is not None): xsDataMOSFLMOutputIntegration.setBestfilePar(XSDataString(strBestfilePar)) else: bContinue = False if bContinue: strBestfileHKL = self.readBestFile("bestfile.hkl") if (strBestfileHKL is not None): xsDataMOSFLMOutputIntegration.setBestfileHKL(XSDataString(strBestfileHKL)) else: bContinue = False if bContinue: strBestfileDat = self.readBestFile("bestfile.dat") if (strBestfileDat is not None): xsDataMOSFLMOutputIntegration.setBestfileDat(XSDataString(strBestfileDat)) else: bContinue = False if bContinue: strDnaTablesXML = self.readProcessFile(self.getBaseName() + "_dnaTables.xml") xsDataDnaTables = dna_tables.parseString(strDnaTablesXML) xsTableIntegrationResults = EDUtilsTable.getTableFromTables(xsDataDnaTables, "integration_results") xsListFinalResiduals = EDUtilsTable.getListsFromTable(xsTableIntegrationResults, "final_residuals")[0] strRMSSpotDeviation = EDUtilsTable.getItemFromList(xsListFinalResiduals, "rms").getValueOf_() xsDataMOSFLMOutputIntegration.setRMSSpotDeviation(XSDataLength(float(strRMSSpotDeviation))) strBeamPositionX = EDUtilsTable.getItemFromList(xsListFinalResiduals, "xcen").getValueOf_() strBeamPositionY = EDUtilsTable.getItemFromList(xsListFinalResiduals, "ycen").getValueOf_() xsDataMOSFLMBeamPosition = XSDataMOSFLMBeamPosition() xsDataMOSFLMBeamPosition.setX(XSDataLength(float(strBeamPositionX))) xsDataMOSFLMBeamPosition.setY(XSDataLength(float(strBeamPositionY))) xsDataMOSFLMOutputIntegration.setRefinedBeam(xsDataMOSFLMBeamPosition) xsDataMOSFLMNewmatMatrix = self.getDataMOSFLMMatrix() xsDataMOSFLMOutputIntegration.setRefinedNewmat(xsDataMOSFLMNewmatMatrix) # New results (described in bug #63) xsTableIntegrationOutput = EDUtilsTable.getTableFromTables(xsDataDnaTables, "integration_output") xsListOutputFiles = EDUtilsTable.getListsFromTable(xsTableIntegrationOutput, "output_files")[0] strMTZFilename = EDUtilsTable.getItemFromList(xsListOutputFiles, "hklout").getValueOf_() strMTZPath = os.path.join(self.getWorkingDirectory(), strMTZFilename) xsDataFile = XSDataFile() xsDataFile.setPath(XSDataString(strMTZPath)) xsDataMOSFLMOutputIntegration.setGeneratedMTZFile(xsDataFile) xsTableSummaryInformation = EDUtilsTable.getTableFromTables(xsDataDnaTables, "summary_information") xsListSummary = EDUtilsTable.getListsFromTable(xsTableSummaryInformation, "summary")[0] xsListSpots = EDUtilsTable.getListsFromTable(xsTableSummaryInformation, "spots")[0] strDistance = EDUtilsTable.getItemFromList(xsListSummary, "distance").getValueOf_() xsDataMOSFLMOutputIntegration.setRefinedDistance(XSDataLength(float(strDistance))) strYScale = EDUtilsTable.getItemFromList(xsListSummary, "yscale").getValueOf_() xsDataMOSFLMOutputIntegration.setRefinedYScale(XSDataFloat(float(strYScale))) strOverallIOverSigma = EDUtilsTable.getItemFromList(xsListSummary, "isigall").getValueOf_() xsDataMOSFLMOutputIntegration.setOverallIOverSigma(XSDataFloat(float(strOverallIOverSigma))) strHighestResolutionIOverSigma = EDUtilsTable.getItemFromList(xsListSummary, "isigout").getValueOf_() xsDataMOSFLMOutputIntegration.setHighestResolutionIOverSigma(XSDataFloat(float(strHighestResolutionIOverSigma))) strNumberOfBadReflections = EDUtilsTable.getItemFromList(xsListSpots, "bad_spots").getValueOf_() xsDataMOSFLMOutputIntegration.setNumberOfBadReflections(XSDataInteger(int(strNumberOfBadReflections))) strNumberOfFullyRecordedReflections = EDUtilsTable.getItemFromList(xsListSpots, "full").getValueOf_() xsDataMOSFLMOutputIntegration.setNumberOfFullyRecordedReflections(XSDataInteger(int(strNumberOfFullyRecordedReflections))) strNumberOfNegativeReflections = EDUtilsTable.getItemFromList(xsListSpots, "negative").getValueOf_() xsDataMOSFLMOutputIntegration.setNumberOfNegativeReflections(XSDataInteger(int(strNumberOfNegativeReflections))) strNumberOfOverlappedReflections = EDUtilsTable.getItemFromList(xsListSpots, "overlap").getValueOf_() xsDataMOSFLMOutputIntegration.setNumberOfOverlappedReflections(XSDataInteger(int(strNumberOfOverlappedReflections))) strNumberOfPartialReflections = EDUtilsTable.getItemFromList(xsListSpots, "partial").getValueOf_() xsDataMOSFLMOutputIntegration.setNumberOfPartialReflections(XSDataInteger(int(strNumberOfPartialReflections))) # Fill in the statistics xsDataMOSFLMOutputIntegration.setOverallStatistics(self.getMOSFLMIntegrationStatisticsPerResolutionBin(xsDataDnaTables, "bin_0")) iIndex = 1 bContinue = True fMinResolution = None while (bContinue == True): strBin = "bin_%d" % iIndex # I don't know how many intensity bins there are. Since the EDUtilsTable.getListsFromTable # method crashes if the list is not present, I had to wrap the calls to this method in # try - except: try: xsDataMOSFLMIntegrationStatisticsPerResolutionBin = self.getMOSFLMIntegrationStatisticsPerResolutionBin(xsDataDnaTables, strBin, fMinResolution) fMinResolution = xsDataMOSFLMIntegrationStatisticsPerResolutionBin.getMaxResolution().getValue() xsDataMOSFLMOutputIntegration.addStatisticsPerResolutionBin(xsDataMOSFLMIntegrationStatisticsPerResolutionBin) iIndex += 1 except: bContinue = False # Path to log file xsDataMOSFLMOutputIntegration.setPathToLogFile(XSDataFile(XSDataString(os.path.join(self.getWorkingDirectory(), self.getScriptLogFileName())))) return xsDataMOSFLMOutputIntegration
def __init__(self): EDPluginMOSFLMv10.__init__(self) self.setXSDataInputClass(XSDataMOSFLMInputIntegration) self.setDataOutput(XSDataMOSFLMOutputIntegration())