def getOutputDataFromDNATableFile(self, _strFileName):
"""Parses the result 'DNA'-type XML file"""
xsDataResultRdfit = XSDataResultRdfit()
strDnaTablesXML = self.readProcessFile(_strFileName)
xsDataDnaTables = dna_tables.parseString(strDnaTablesXML)
# Loop through all the tables and fill in the relevant parts of xsDataResultBest
xsDataRDFIT_Results = EDUtilsTable.getTableListFromTables(xsDataDnaTables, "RDFIT_Results")[0]
xsDataListGeneral = EDUtilsTable.getListsFromTable(xsDataRDFIT_Results, "general")[0]
xsDataItemBeta = EDUtilsTable.getItemFromList(xsDataListGeneral, "beta")
if xsDataItemBeta is not None:
beta = xsDataItemBeta.getValueOf_()
xsDataResultRdfit.setBeta(XSDataDouble(beta))
xsDataItemGama = EDUtilsTable.getItemFromList(xsDataListGeneral, "gama")
if xsDataItemGama is not None:
gama = xsDataItemGama.getValueOf_()
xsDataResultRdfit.setGama(XSDataDouble(gama))
xsDataItemDose_half_th = EDUtilsTable.getItemFromList(xsDataListGeneral, "Dose_1/2_th")
if xsDataItemDose_half_th is not None:
dose_half_th = xsDataItemDose_half_th.getValueOf_()
xsDataResultRdfit.setDose_half_th(XSDataDouble(dose_half_th))
xsDataItemDose_half = EDUtilsTable.getItemFromList(xsDataListGeneral, "Dose_1/2")
if xsDataItemDose_half is not None:
dose_half = xsDataItemDose_half.getValueOf_()
xsDataResultRdfit.setDose_half(XSDataDouble(dose_half))
xsDataItemRelative_radiation_sensitivity = EDUtilsTable.getItemFromList(xsDataListGeneral, "Relative_Radiation_Sensitivity")
if xsDataItemRelative_radiation_sensitivity is not None:
relative_radiation_sensitivity = xsDataItemRelative_radiation_sensitivity.getValueOf_()
xsDataResultRdfit.setRelative_radiation_sensitivity(XSDataDouble(relative_radiation_sensitivity))
return xsDataResultRdfit
def testListOfTables(self):
xsItem = None
xsItem2 = None
strDnaTablesXML = EDUtilsFile.readFile(self.__strFilePath2)
xsDataDnaTables = dna_tables.parseString(strDnaTablesXML)
listTable = EDUtilsTable.getTableListFromTables(
xsDataDnaTables, "data_collection_strategy")
EDAssert.equal(2, len(listTable))
bFoundPlan1 = False
bFoundPlan2 = False
for xsTable in listTable:
xsItem = None
xsLists = EDUtilsTable.getListsFromTable(xsTable, "summary")
for xsList in xsLists:
xsItem = EDUtilsTable.getItemFromList(xsList,
"resolution_reasoning")
if (xsItem.getValueOf_() == "Low-resolution pass, no overloads"):
bFoundPlan1 = True
if (xsItem.getValueOf_() ==
"Resolution limit is set by the initial image resolution"):
bFoundPlan2 = True
EDAssert.equal(True, bFoundPlan1)
EDAssert.equal(True, bFoundPlan2)
def testListOfTables(self):
xsItem = None
xsItem2 = None
strDnaTablesXML = EDUtilsFile.readFile(self.__strFilePath2)
xsDataDnaTables = dna_tables.parseString(strDnaTablesXML)
listTable = EDUtilsTable.getTableListFromTables(xsDataDnaTables, "data_collection_strategy")
EDAssert.equal(2, len(listTable))
bFoundPlan1 = False
bFoundPlan2 = False
for xsTable in listTable:
xsItem = None
xsLists = EDUtilsTable.getListsFromTable(xsTable, "summary")
for xsList in xsLists:
xsItem = EDUtilsTable.getItemFromList(xsList, "resolution_reasoning")
if(xsItem.getValueOf_() == "Low-resolution pass, no overloads"):
bFoundPlan1 = True
if(xsItem.getValueOf_() == "Resolution limit is set by the initial image resolution"):
bFoundPlan2 = True
EDAssert.equal(True, bFoundPlan1)
EDAssert.equal(True, bFoundPlan2)
def testTableListItem(self):
xsItem = None
xsItem2 = None
strDnaTablesXML = EDUtilsFile.readFile(self.__strFilePath)
xsDataDnaTables = dna_tables.parseString(strDnaTablesXML)
xsTable = EDUtilsTable.getTableFromTables(xsDataDnaTables, "input")
xsLists = EDUtilsTable.getListsFromTable(xsTable, "select_task")
for xsList in xsLists:
xsItem = EDUtilsTable.getItemFromList(xsList, "task")
xsItem2 = EDUtilsTable.getItemFromList(xsList, "tata")
EDAssert.equal("optimize", xsItem.getValueOf_())
EDAssert.equal(None, xsItem2)
xsLists = EDUtilsTable.getListsFromTable(xsTable, "select_tata")
EDAssert.equal([], xsLists)
xsTable = EDUtilsTable.getTableFromTables(xsDataDnaTables, "toto")
EDAssert.equal(None, xsTable)
EDVerbose.DEBUG("Test done...")
def testTableListItem(self):
xsItem = None
xsItem2 = None
strDnaTablesXML = EDUtilsFile.readFile(self.__strFilePath)
xsDataDnaTables = dna_tables.parseString(strDnaTablesXML)
xsTable = EDUtilsTable.getTableFromTables(xsDataDnaTables, "input")
xsLists = EDUtilsTable.getListsFromTable(xsTable, "select_task")
for xsList in xsLists:
xsItem = EDUtilsTable.getItemFromList(xsList, "task")
xsItem2 = EDUtilsTable.getItemFromList(xsList, "tata")
EDAssert.equal("optimize", xsItem.getValueOf_())
EDAssert.equal(None, xsItem2)
xsLists = EDUtilsTable.getListsFromTable(xsTable, "select_tata")
EDAssert.equal([], xsLists)
xsTable = EDUtilsTable.getTableFromTables(xsDataDnaTables, "toto")
EDAssert.equal(None, xsTable)
EDVerbose.DEBUG("Test done...")
def getOutputDataFromDNATableFile(self, _strFileName):
"""Parses the result 'DNA'-type XML file"""
xsDataResultRdfit = XSDataResultRdfit()
strDnaTablesXML = self.readProcessFile(_strFileName)
xsDataDnaTables = dna_tables.parseString(strDnaTablesXML)
# Loop through all the tables and fill in the relevant parts of xsDataResultBest
xsDataRDFIT_Results = EDUtilsTable.getTableListFromTables(
xsDataDnaTables, "RDFIT_Results")[0]
xsDataListGeneral = EDUtilsTable.getListsFromTable(
xsDataRDFIT_Results, "general")[0]
xsDataItemBeta = EDUtilsTable.getItemFromList(xsDataListGeneral,
"beta")
if xsDataItemBeta is not None:
beta = xsDataItemBeta.getValueOf_()
xsDataResultRdfit.setBeta(XSDataDouble(beta))
xsDataItemGama = EDUtilsTable.getItemFromList(xsDataListGeneral,
"gama")
if xsDataItemGama is not None:
gama = xsDataItemGama.getValueOf_()
xsDataResultRdfit.setGama(XSDataDouble(gama))
xsDataItemDose_half_th = EDUtilsTable.getItemFromList(
xsDataListGeneral, "Dose_1/2_th")
if xsDataItemDose_half_th is not None:
dose_half_th = xsDataItemDose_half_th.getValueOf_()
xsDataResultRdfit.setDose_half_th(XSDataDouble(dose_half_th))
xsDataItemDose_half = EDUtilsTable.getItemFromList(
xsDataListGeneral, "Dose_1/2")
if xsDataItemDose_half is not None:
dose_half = xsDataItemDose_half.getValueOf_()
xsDataResultRdfit.setDose_half(XSDataDouble(dose_half))
xsDataItemRelative_radiation_sensitivity = EDUtilsTable.getItemFromList(
xsDataListGeneral, "Relative_Radiation_Sensitivity")
if xsDataItemRelative_radiation_sensitivity is not None:
relative_radiation_sensitivity = xsDataItemRelative_radiation_sensitivity.getValueOf_(
)
xsDataResultRdfit.setRelative_radiation_sensitivity(
XSDataDouble(relative_radiation_sensitivity))
return xsDataResultRdfit
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 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 createDataMOSFLMOutputIndexing(self):
EDVerbose.DEBUG("EDPluginMOSFLMIndexingv10.createDataMOSFLMOutputIndexing")
xsDataMOSFLMOutputIndexing = XSDataMOSFLMOutputIndexing()
# Read Newmat file
xsDataMOSFLMNewmat = self.getDataMOSFLMNewmat()
if (xsDataMOSFLMNewmat is None):
strError = "MOSFLM indexing error : No solution was obtained!"
EDVerbose.ERROR(strError)
self.setFailure()
else:
xsDataMOSFLMOutputIndexing.setRefinedNewmat(xsDataMOSFLMNewmat)
# Then read the XML file
strDnaTablesXML = self.readProcessFile(self.getScriptBaseName() + "_dnaTables.xml")
xsDataDnaTables = dna_tables.parseString(strDnaTablesXML)
listXSTableMosaicityEstimation = EDUtilsTable.getTableListFromTables(xsDataDnaTables, "mosaicity_estimation")
dMosaicityValueSum = 0.0
nValues = 0
for xsTableMosaicityEstimation in listXSTableMosaicityEstimation:
for xsListMosaicity in EDUtilsTable.getListsFromTable(xsTableMosaicityEstimation, "mosaicity"):
dMosaicityValue = float(EDUtilsTable.getItemFromList(xsListMosaicity, "value").getValueOf_())
dMosaicityValueSum += dMosaicityValue
nValues += 1
xsDataFloatMosaicityEstimation = XSDataFloat()
xsDataFloatMosaicityEstimation.setValue(dMosaicityValueSum / nValues)
xsDataMOSFLMOutputIndexing.setMosaicityEstimation(xsDataFloatMosaicityEstimation)
xsTableRefinement = EDUtilsTable.getTableFromTables(xsDataDnaTables, "refinement")
if (xsTableRefinement is None):
strError = "MOSFLM indexing error : No solution was refined!"
EDVerbose.ERROR(strError)
self.setFailure()
else:
xsListDeviations = EDUtilsTable.getListsFromTable(xsTableRefinement, "deviations")[0]
dDeviationAngular = float(EDUtilsTable.getItemFromList(xsListDeviations, "angular").getValueOf_())
dDeviationPositional = float(EDUtilsTable.getItemFromList(xsListDeviations, "positional").getValueOf_())
xsDataMOSFLMOutputIndexing.setDeviationAngular(XSDataAngle(dDeviationAngular))
xsDataMOSFLMOutputIndexing.setDeviationPositional(XSDataLength(dDeviationPositional))
xsListResults = EDUtilsTable.getListsFromTable(xsTableRefinement, "results")[0]
dDetectorDistance = float(EDUtilsTable.getItemFromList(xsListResults, "detector_distance").getValueOf_())
xsDataMOSFLMOutputIndexing.setRefinedDistance(XSDataLength(dDetectorDistance))
xsListParameters = EDUtilsTable.getListsFromTable(xsTableRefinement, "parameters")[0]
iSpotsUsed = int(EDUtilsTable.getItemFromList(xsListParameters, "used").getValueOf_())
iSpotsTotal = int(EDUtilsTable.getItemFromList(xsListParameters, "out_of").getValueOf_())
xsDataMOSFLMOutputIndexing.setSpotsUsed(XSDataInteger(iSpotsUsed))
xsDataMOSFLMOutputIndexing.setSpotsTotal(XSDataInteger(iSpotsTotal))
xsTableSolutionRefinement = EDUtilsTable.getTableFromTables(xsDataDnaTables, "solution_refinement")
xsListParameters = EDUtilsTable.getListsFromTable(xsTableSolutionRefinement, "selection")[0]
iSelectedSolutionNumber = int(EDUtilsTable.getItemFromList(xsListParameters, "number").getValueOf_())
xsDataMOSFLMOutputIndexing.setSelectedSolutionNumber(XSDataInteger(iSelectedSolutionNumber))
strSelectedSolutionSpaceGroup = (EDUtilsTable.getItemFromList(xsListParameters, "spacegroup").getValueOf_())
xsDataMOSFLMOutputIndexing.setSelectedSolutionSpaceGroup(XSDataString(strSelectedSolutionSpaceGroup))
iSelectedSolutionSpaceGroupNumber = int(EDUtilsTable.getItemFromList(xsListParameters, "spacegroup_number").getValueOf_())
xsDataMOSFLMOutputIndexing.setSelectedSolutionSpaceGroupNumber(XSDataInteger(iSelectedSolutionSpaceGroupNumber))
xsTableAutoIndexSolutions = EDUtilsTable.getTableFromTables(xsDataDnaTables, "autoindex_solutions")
xsListsSolution = xsTableAutoIndexSolutions.getList()
for xsListSolution in xsListsSolution:
xsDataMOSFLMIndexingSolution = XSDataMOSFLMIndexingSolution()
xsDataCell = XSDataCell()
iSolutionNumber = int(EDUtilsTable.getItemFromList(xsListSolution, "index").getValueOf_())
xsDataMOSFLMIndexingSolution.setIndex(XSDataInteger(iSolutionNumber))
iPenalty = int(EDUtilsTable.getItemFromList(xsListSolution, "penalty").getValueOf_())
xsDataMOSFLMIndexingSolution.setPenalty(XSDataInteger(iPenalty))
strLattice = (EDUtilsTable.getItemFromList(xsListSolution, "lattice").getValueOf_())
xsDataMOSFLMIndexingSolution.setLattice(XSDataString(strLattice))
dA = float(EDUtilsTable.getItemFromList(xsListSolution, "a").getValueOf_())
xsDataCell.setLength_a(XSDataLength(dA))
dB = float(EDUtilsTable.getItemFromList(xsListSolution, "b").getValueOf_())
xsDataCell.setLength_b(XSDataLength(dB))
dC = float(EDUtilsTable.getItemFromList(xsListSolution, "c").getValueOf_())
xsDataCell.setLength_c(XSDataLength(dC))
dAlpha = float(EDUtilsTable.getItemFromList(xsListSolution, "alpha").getValueOf_())
xsDataCell.setAngle_alpha(XSDataAngle(dAlpha))
dBeta = float(EDUtilsTable.getItemFromList(xsListSolution, "beta").getValueOf_())
xsDataCell.setAngle_beta(XSDataAngle(dBeta))
dGamma = float(EDUtilsTable.getItemFromList(xsListSolution, "gamma").getValueOf_())
xsDataCell.setAngle_gamma(XSDataAngle(dGamma))
xsDataMOSFLMIndexingSolution.setCell(xsDataCell)
xsDataMOSFLMOutputIndexing.addPossibleSolutions(xsDataMOSFLMIndexingSolution)
xsTableBeamRefinement = EDUtilsTable.getTableFromTables(xsDataDnaTables, "beam_refinement")
xsDataMOSFLMBeamPositionRefined = XSDataMOSFLMBeamPosition()
xsDataMOSFLMBeamPositionShift = XSDataMOSFLMBeamPosition()
dInitialBeamX = 0.0
dInitialBeamY = 0.0
dRefinedBeamX = 0.0
dRefinedBeamY = 0.0
xsListInitialBeam = EDUtilsTable.getListsFromTable(xsTableBeamRefinement, "initial_beam")[0]
fInitialBeamPositionX = float(EDUtilsTable.getItemFromList(xsListInitialBeam, "x").getValueOf_())
fInitialBeamPositionY = float(EDUtilsTable.getItemFromList(xsListInitialBeam, "y").getValueOf_())
xsListRefinedBeam = EDUtilsTable.getListsFromTable(xsTableBeamRefinement, "refined_beam")[0]
fRefinedBeamPositionX = float(EDUtilsTable.getItemFromList(xsListRefinedBeam, "x").getValueOf_())
fRefinedBeamPositionY = float(EDUtilsTable.getItemFromList(xsListRefinedBeam, "y").getValueOf_())
xsDataMOSFLMBeamPositionRefined.setX(XSDataLength(fRefinedBeamPositionX))
xsDataMOSFLMBeamPositionRefined.setY(XSDataLength(fRefinedBeamPositionY))
xsDataMOSFLMBeamPositionShift.setX(XSDataLength(fInitialBeamPositionX - fRefinedBeamPositionX))
xsDataMOSFLMBeamPositionShift.setY(XSDataLength(fInitialBeamPositionY - fRefinedBeamPositionY))
xsDataMOSFLMOutputIndexing.setRefinedBeam(xsDataMOSFLMBeamPositionRefined)
xsDataMOSFLMOutputIndexing.setBeamShift(xsDataMOSFLMBeamPositionShift)
return xsDataMOSFLMOutputIndexing
def createDataMOSFLMOutputIndexing(self):
self.DEBUG("EDPluginMOSFLMIndexingv10.createDataMOSFLMOutputIndexing")
xsDataMOSFLMOutputIndexing = XSDataMOSFLMOutputIndexing()
# Read Newmat file
xsDataMOSFLMNewmat = self.getDataMOSFLMNewmat()
if (xsDataMOSFLMNewmat is None):
strError = "MOSFLM indexing error : No solution was obtained!"
self.ERROR(strError)
self.setFailure()
else:
xsDataMOSFLMOutputIndexing.setRefinedNewmat(xsDataMOSFLMNewmat)
# Then read the XML file
strDnaTablesXML = self.readProcessFile(self.getScriptBaseName() +
"_dnaTables.xml")
xsDataDnaTables = dna_tables.parseString(strDnaTablesXML)
listXSTableMosaicityEstimation = EDUtilsTable.getTableListFromTables(
xsDataDnaTables, "mosaicity_estimation")
dMosaicityValueSum = 0.0
nValues = 0
for xsTableMosaicityEstimation in listXSTableMosaicityEstimation:
for xsListMosaicity in EDUtilsTable.getListsFromTable(
xsTableMosaicityEstimation, "mosaicity"):
dMosaicityValue = float(
EDUtilsTable.getItemFromList(xsListMosaicity,
"value").getValueOf_())
dMosaicityValueSum += dMosaicityValue
nValues += 1
xsDataFloatMosaicityEstimation = XSDataFloat()
xsDataFloatMosaicityEstimation.setValue(dMosaicityValueSum /
nValues)
xsDataMOSFLMOutputIndexing.setMosaicityEstimation(
xsDataFloatMosaicityEstimation)
xsTableRefinement = EDUtilsTable.getTableFromTables(
xsDataDnaTables, "refinement")
if (xsTableRefinement is None):
strError = "MOSFLM indexing error : No solution was refined!"
self.ERROR(strError)
self.setFailure()
else:
xsListDeviations = EDUtilsTable.getListsFromTable(
xsTableRefinement, "deviations")[0]
dDeviationAngular = float(
EDUtilsTable.getItemFromList(xsListDeviations,
"angular").getValueOf_())
dDeviationPositional = float(
EDUtilsTable.getItemFromList(xsListDeviations,
"positional").getValueOf_())
xsDataMOSFLMOutputIndexing.setDeviationAngular(
XSDataAngle(dDeviationAngular))
xsDataMOSFLMOutputIndexing.setDeviationPositional(
XSDataLength(dDeviationPositional))
xsListResults = EDUtilsTable.getListsFromTable(
xsTableRefinement, "results")[0]
dDetectorDistance = float(
EDUtilsTable.getItemFromList(
xsListResults, "detector_distance").getValueOf_())
xsDataMOSFLMOutputIndexing.setRefinedDistance(
XSDataLength(dDetectorDistance))
xsListParameters = EDUtilsTable.getListsFromTable(
xsTableRefinement, "parameters")[0]
iSpotsUsed = int(
EDUtilsTable.getItemFromList(xsListParameters,
"used").getValueOf_())
iSpotsTotal = int(
EDUtilsTable.getItemFromList(xsListParameters,
"out_of").getValueOf_())
xsDataMOSFLMOutputIndexing.setSpotsUsed(
XSDataInteger(iSpotsUsed))
xsDataMOSFLMOutputIndexing.setSpotsTotal(
XSDataInteger(iSpotsTotal))
xsTableSolutionRefinement = EDUtilsTable.getTableFromTables(
xsDataDnaTables, "solution_refinement")
xsListParameters = EDUtilsTable.getListsFromTable(
xsTableSolutionRefinement, "selection")[0]
iSelectedSolutionNumber = int(
EDUtilsTable.getItemFromList(xsListParameters,
"number").getValueOf_())
xsDataMOSFLMOutputIndexing.setSelectedSolutionNumber(
XSDataInteger(iSelectedSolutionNumber))
strSelectedSolutionSpaceGroup = (EDUtilsTable.getItemFromList(
xsListParameters, "spacegroup").getValueOf_())
xsDataMOSFLMOutputIndexing.setSelectedSolutionSpaceGroup(
XSDataString(strSelectedSolutionSpaceGroup))
iSelectedSolutionSpaceGroupNumber = int(
EDUtilsTable.getItemFromList(
xsListParameters, "spacegroup_number").getValueOf_())
xsDataMOSFLMOutputIndexing.setSelectedSolutionSpaceGroupNumber(
XSDataInteger(iSelectedSolutionSpaceGroupNumber))
xsTableAutoIndexSolutions = EDUtilsTable.getTableFromTables(
xsDataDnaTables, "autoindex_solutions")
xsListsSolution = xsTableAutoIndexSolutions.getList()
for xsListSolution in xsListsSolution:
xsDataMOSFLMIndexingSolution = XSDataMOSFLMIndexingSolution(
)
xsDataCell = XSDataCell()
iSolutionNumber = int(
EDUtilsTable.getItemFromList(xsListSolution,
"index").getValueOf_())
xsDataMOSFLMIndexingSolution.setIndex(
XSDataInteger(iSolutionNumber))
iPenalty = int(
EDUtilsTable.getItemFromList(xsListSolution,
"penalty").getValueOf_())
xsDataMOSFLMIndexingSolution.setPenalty(
XSDataInteger(iPenalty))
strLattice = (EDUtilsTable.getItemFromList(
xsListSolution, "lattice").getValueOf_())
xsDataMOSFLMIndexingSolution.setLattice(
XSDataString(strLattice))
dA = float(
EDUtilsTable.getItemFromList(xsListSolution,
"a").getValueOf_())
xsDataCell.setLength_a(XSDataLength(dA))
dB = float(
EDUtilsTable.getItemFromList(xsListSolution,
"b").getValueOf_())
xsDataCell.setLength_b(XSDataLength(dB))
dC = float(
EDUtilsTable.getItemFromList(xsListSolution,
"c").getValueOf_())
xsDataCell.setLength_c(XSDataLength(dC))
dAlpha = float(
EDUtilsTable.getItemFromList(xsListSolution,
"alpha").getValueOf_())
xsDataCell.setAngle_alpha(XSDataAngle(dAlpha))
dBeta = float(
EDUtilsTable.getItemFromList(xsListSolution,
"beta").getValueOf_())
xsDataCell.setAngle_beta(XSDataAngle(dBeta))
dGamma = float(
EDUtilsTable.getItemFromList(xsListSolution,
"gamma").getValueOf_())
xsDataCell.setAngle_gamma(XSDataAngle(dGamma))
xsDataMOSFLMIndexingSolution.setCell(xsDataCell)
xsDataMOSFLMOutputIndexing.addPossibleSolutions(
xsDataMOSFLMIndexingSolution)
xsTableBeamRefinement = EDUtilsTable.getTableFromTables(
xsDataDnaTables, "beam_refinement")
xsDataMOSFLMBeamPositionRefined = XSDataMOSFLMBeamPosition()
xsDataMOSFLMBeamPositionShift = XSDataMOSFLMBeamPosition()
dInitialBeamX = 0.0
dInitialBeamY = 0.0
dRefinedBeamX = 0.0
dRefinedBeamY = 0.0
xsListInitialBeam = EDUtilsTable.getListsFromTable(
xsTableBeamRefinement, "initial_beam")[0]
fInitialBeamPositionX = float(
EDUtilsTable.getItemFromList(xsListInitialBeam,
"x").getValueOf_())
fInitialBeamPositionY = float(
EDUtilsTable.getItemFromList(xsListInitialBeam,
"y").getValueOf_())
xsListRefinedBeam = EDUtilsTable.getListsFromTable(
xsTableBeamRefinement, "refined_beam")[0]
fRefinedBeamPositionX = float(
EDUtilsTable.getItemFromList(xsListRefinedBeam,
"x").getValueOf_())
fRefinedBeamPositionY = float(
EDUtilsTable.getItemFromList(xsListRefinedBeam,
"y").getValueOf_())
xsDataMOSFLMBeamPositionRefined.setX(
XSDataLength(fRefinedBeamPositionX))
xsDataMOSFLMBeamPositionRefined.setY(
XSDataLength(fRefinedBeamPositionY))
xsDataMOSFLMBeamPositionShift.setX(
XSDataLength(fInitialBeamPositionX -
fRefinedBeamPositionX))
xsDataMOSFLMBeamPositionShift.setY(
XSDataLength(fInitialBeamPositionY -
fRefinedBeamPositionY))
xsDataMOSFLMOutputIndexing.setRefinedBeam(
xsDataMOSFLMBeamPositionRefined)
xsDataMOSFLMOutputIndexing.setBeamShift(
xsDataMOSFLMBeamPositionShift)
# Path to log file
xsDataMOSFLMOutputIndexing.setPathToLogFile(
XSDataFile(
XSDataString(
os.path.join(self.getWorkingDirectory(),
self.getScriptLogFileName()))))
return xsDataMOSFLMOutputIndexing
