def getReferenceDataMOSFLMNewmat(self):
xsDataMOSFLMNewmat = XSDataMOSFLMNewmat()
XSDataMatrixDoubleA = XSDataMatrixDouble()
XSDataMatrixDoubleA.setM11(-0.00826416)
XSDataMatrixDoubleA.setM12(0.00885073)
XSDataMatrixDoubleA.setM13(0.00937013)
XSDataMatrixDoubleA.setM21(0.00126554)
XSDataMatrixDoubleA.setM22(0.01251971)
XSDataMatrixDoubleA.setM23(-0.00845341)
XSDataMatrixDoubleA.setM31(-0.01484956)
XSDataMatrixDoubleA.setM32(-0.00385867)
XSDataMatrixDoubleA.setM33(-0.00593515)
xsDataMOSFLMNewmat.setAMatrix(XSDataMatrixDoubleA)
xsDataMOSFLMMissettingsAngles = XSDataMOSFLMMissettingsAngles()
xsDataMOSFLMMissettingsAngles.setPhix(XSDataAngle(1.000))
xsDataMOSFLMMissettingsAngles.setPhiy(XSDataAngle(2.000))
xsDataMOSFLMMissettingsAngles.setPhiz(XSDataAngle(3.000))
xsDataMOSFLMNewmat.setMissettingAngles(xsDataMOSFLMMissettingsAngles)
XSDataMatrixDoubleU = XSDataMatrixDouble()
XSDataMatrixDoubleU.setM11(-0.4849475)
XSDataMatrixDoubleU.setM12(0.5598049)
XSDataMatrixDoubleU.setM13(0.6718960)
XSDataMatrixDoubleU.setM21(0.0742629)
XSDataMatrixDoubleU.setM22(0.7918670)
XSDataMatrixDoubleU.setM23(-0.6061614)
XSDataMatrixDoubleU.setM31(-0.8713845)
XSDataMatrixDoubleU.setM32(-0.2440595)
XSDataMatrixDoubleU.setM33(-0.4255866)
xsDataMOSFLMNewmat.setUMatrix(XSDataMatrixDoubleU)
xsDataCellRefined = XSDataCell()
xsDataCellRefined.setLength_a(XSDataLength(54.8079))
xsDataCellRefined.setLength_b(XSDataLength(59.0751))
xsDataCellRefined.setLength_c(XSDataLength(66.9736))
xsDataCellRefined.setAngle_alpha(XSDataAngle(91.0000))
xsDataCellRefined.setAngle_beta(XSDataAngle(92.0000))
xsDataCellRefined.setAngle_gamma(XSDataAngle(93.0000))
xsDataMOSFLMNewmat.setRefinedCell(xsDataCellRefined)
return xsDataMOSFLMNewmat
def getReferenceDataMOSFLMNewmat(self):
xsDataMOSFLMNewmat = XSDataMOSFLMNewmat()
XSDataMatrixDoubleA = XSDataMatrixDouble()
XSDataMatrixDoubleA.setM11(-0.00826416)
XSDataMatrixDoubleA.setM12(0.00885073)
XSDataMatrixDoubleA.setM13(0.00937013)
XSDataMatrixDoubleA.setM21(0.00126554)
XSDataMatrixDoubleA.setM22(0.01251971)
XSDataMatrixDoubleA.setM23(-0.00845341)
XSDataMatrixDoubleA.setM31(-0.01484956)
XSDataMatrixDoubleA.setM32(-0.00385867)
XSDataMatrixDoubleA.setM33(-0.00593515)
xsDataMOSFLMNewmat.setAMatrix(XSDataMatrixDoubleA)
xsDataMOSFLMMissettingsAngles = XSDataMOSFLMMissettingsAngles()
xsDataMOSFLMMissettingsAngles.setPhix(XSDataAngle(1.000))
xsDataMOSFLMMissettingsAngles.setPhiy(XSDataAngle(2.000))
xsDataMOSFLMMissettingsAngles.setPhiz(XSDataAngle(3.000))
xsDataMOSFLMNewmat.setMissettingAngles(xsDataMOSFLMMissettingsAngles)
XSDataMatrixDoubleU = XSDataMatrixDouble()
XSDataMatrixDoubleU.setM11(-0.4849475)
XSDataMatrixDoubleU.setM12(0.5598049)
XSDataMatrixDoubleU.setM13(0.6718960)
XSDataMatrixDoubleU.setM21(0.0742629)
XSDataMatrixDoubleU.setM22(0.7918670)
XSDataMatrixDoubleU.setM23(-0.6061614)
XSDataMatrixDoubleU.setM31(-0.8713845)
XSDataMatrixDoubleU.setM32(-0.2440595)
XSDataMatrixDoubleU.setM33(-0.4255866)
xsDataMOSFLMNewmat.setUMatrix(XSDataMatrixDoubleU)
xsDataCellRefined = XSDataCell()
xsDataCellRefined.setLength_a(XSDataLength(54.8079))
xsDataCellRefined.setLength_b(XSDataLength(59.0751))
xsDataCellRefined.setLength_c(XSDataLength(66.9736))
xsDataCellRefined.setAngle_alpha(XSDataAngle(91.0000))
xsDataCellRefined.setAngle_beta(XSDataAngle(92.0000))
xsDataCellRefined.setAngle_gamma(XSDataAngle(93.0000))
xsDataMOSFLMNewmat.setRefinedCell(xsDataCellRefined)
return xsDataMOSFLMNewmat
def getDataMOSFLMNewmat(self, _strNewmatFileName=None):
self.DEBUG("EDPluginMOSFLMv10.getDataMOSFLMNewmat")
xsDataMOSFLMNewmat = None
strNewmatFileName = None
listOfListOfFloat = []
if (_strNewmatFileName == None):
strNewmatFileName = self.getNewmatFileName()
else:
strNewmatFileName = _strNewmatFileName
strNewmat = None
try:
strNewmat = self.readProcessFile(strNewmatFileName)
except:
strError = self.readProcessErrorLogFile()
if (strError is not None) and (strError != ""):
strErrorMessage = "EDPluginMOSFLMv10.getDataMOSFLMNewmat: %s : error reading newmat file : %s" % \
(self.getClassName(), strError)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
else:
strErrorMessage = "EDPluginMOSFLMv10.getDataMOSFLMNewmat : Cannot read MOSFLM NEWMAT file : " + strNewmatFileName
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
#print strNewmat
if (strNewmat is not None):
listLine = strNewmat.split("\n")
# Convert into list of lists of float
for strLine in listLine:
if not strLine.startswith("SYMM"):
listOfListOfFloat.append(self.splitStringIntoListOfFloats(strLine))
# Fill in the data
xsDataMOSFLMNewmat = XSDataMOSFLMNewmat()
XSDataMatrixDoubleA = XSDataMatrixDouble()
XSDataMatrixDoubleA.setM11(listOfListOfFloat[0][0])
XSDataMatrixDoubleA.setM12(listOfListOfFloat[0][1])
XSDataMatrixDoubleA.setM13(listOfListOfFloat[0][2])
XSDataMatrixDoubleA.setM21(listOfListOfFloat[1][0])
XSDataMatrixDoubleA.setM22(listOfListOfFloat[1][1])
XSDataMatrixDoubleA.setM23(listOfListOfFloat[1][2])
XSDataMatrixDoubleA.setM31(listOfListOfFloat[2][0])
XSDataMatrixDoubleA.setM32(listOfListOfFloat[2][1])
XSDataMatrixDoubleA.setM33(listOfListOfFloat[2][2])
xsDataMOSFLMNewmat.setAMatrix(XSDataMatrixDoubleA)
xsDataMOSFLMMissettingsAngles = XSDataMOSFLMMissettingsAngles()
xsDataMOSFLMMissettingsAngles.setPhix(XSDataAngle(listOfListOfFloat[3][0]))
xsDataMOSFLMMissettingsAngles.setPhiy(XSDataAngle(listOfListOfFloat[3][1]))
xsDataMOSFLMMissettingsAngles.setPhiz(XSDataAngle(listOfListOfFloat[3][2]))
xsDataMOSFLMNewmat.setMissettingAngles(xsDataMOSFLMMissettingsAngles)
XSDataMatrixDoubleU = XSDataMatrixDouble()
XSDataMatrixDoubleU.setM11(listOfListOfFloat[4][0])
XSDataMatrixDoubleU.setM12(listOfListOfFloat[4][1])
XSDataMatrixDoubleU.setM13(listOfListOfFloat[4][2])
XSDataMatrixDoubleU.setM21(listOfListOfFloat[5][0])
XSDataMatrixDoubleU.setM22(listOfListOfFloat[5][1])
XSDataMatrixDoubleU.setM23(listOfListOfFloat[5][2])
XSDataMatrixDoubleU.setM31(listOfListOfFloat[6][0])
XSDataMatrixDoubleU.setM32(listOfListOfFloat[6][1])
XSDataMatrixDoubleU.setM33(listOfListOfFloat[6][2])
xsDataMOSFLMNewmat.setUMatrix(XSDataMatrixDoubleU)
xsDataCellRefined = XSDataCell()
xsDataCellRefined.setLength_a(XSDataLength(listOfListOfFloat[7][0]))
xsDataCellRefined.setLength_b(XSDataLength(listOfListOfFloat[7][1]))
xsDataCellRefined.setLength_c(XSDataLength(listOfListOfFloat[7][2]))
xsDataCellRefined.setAngle_alpha(XSDataAngle(listOfListOfFloat[7][3]))
xsDataCellRefined.setAngle_beta(XSDataAngle(listOfListOfFloat[7][4]))
xsDataCellRefined.setAngle_gamma(XSDataAngle(listOfListOfFloat[7][5]))
xsDataMOSFLMNewmat.setRefinedCell(xsDataCellRefined)
return xsDataMOSFLMNewmat
def getDataMOSFLMNewmat(self, _strNewmatFileName=None):
self.DEBUG("EDPluginMOSFLMv10.getDataMOSFLMNewmat")
xsDataMOSFLMNewmat = None
strNewmatFileName = None
listOfListOfFloat = []
if (_strNewmatFileName == None):
strNewmatFileName = self.getNewmatFileName()
else:
strNewmatFileName = _strNewmatFileName
strNewmat = None
try:
strNewmat = self.readProcessFile(strNewmatFileName)
except:
strError = self.readProcessErrorLogFile()
if (strError is not None) and (strError != ""):
strErrorMessage = "EDPluginMOSFLMv10.getDataMOSFLMNewmat: %s : error reading newmat file : %s" % \
(self.getClassName(), strError)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
else:
strErrorMessage = "EDPluginMOSFLMv10.getDataMOSFLMNewmat : Cannot read MOSFLM NEWMAT file : " + strNewmatFileName
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
# print strNewmat
if (strNewmat is not None):
listLine = strNewmat.split("\n")
# Convert into list of lists of float
for strLine in listLine:
if not strLine.startswith("SYMM"):
listOfListOfFloat.append(
self.splitStringIntoListOfFloats(strLine))
# Fill in the data
xsDataMOSFLMNewmat = XSDataMOSFLMNewmat()
XSDataMatrixDoubleA = XSDataMatrixDouble()
XSDataMatrixDoubleA.setM11(listOfListOfFloat[0][0])
XSDataMatrixDoubleA.setM12(listOfListOfFloat[0][1])
XSDataMatrixDoubleA.setM13(listOfListOfFloat[0][2])
XSDataMatrixDoubleA.setM21(listOfListOfFloat[1][0])
XSDataMatrixDoubleA.setM22(listOfListOfFloat[1][1])
XSDataMatrixDoubleA.setM23(listOfListOfFloat[1][2])
XSDataMatrixDoubleA.setM31(listOfListOfFloat[2][0])
XSDataMatrixDoubleA.setM32(listOfListOfFloat[2][1])
XSDataMatrixDoubleA.setM33(listOfListOfFloat[2][2])
xsDataMOSFLMNewmat.setAMatrix(XSDataMatrixDoubleA)
xsDataMOSFLMMissettingsAngles = XSDataMOSFLMMissettingsAngles()
xsDataMOSFLMMissettingsAngles.setPhix(
XSDataAngle(listOfListOfFloat[3][0]))
xsDataMOSFLMMissettingsAngles.setPhiy(
XSDataAngle(listOfListOfFloat[3][1]))
xsDataMOSFLMMissettingsAngles.setPhiz(
XSDataAngle(listOfListOfFloat[3][2]))
xsDataMOSFLMNewmat.setMissettingAngles(
xsDataMOSFLMMissettingsAngles)
XSDataMatrixDoubleU = XSDataMatrixDouble()
XSDataMatrixDoubleU.setM11(listOfListOfFloat[4][0])
XSDataMatrixDoubleU.setM12(listOfListOfFloat[4][1])
XSDataMatrixDoubleU.setM13(listOfListOfFloat[4][2])
XSDataMatrixDoubleU.setM21(listOfListOfFloat[5][0])
XSDataMatrixDoubleU.setM22(listOfListOfFloat[5][1])
XSDataMatrixDoubleU.setM23(listOfListOfFloat[5][2])
XSDataMatrixDoubleU.setM31(listOfListOfFloat[6][0])
XSDataMatrixDoubleU.setM32(listOfListOfFloat[6][1])
XSDataMatrixDoubleU.setM33(listOfListOfFloat[6][2])
xsDataMOSFLMNewmat.setUMatrix(XSDataMatrixDoubleU)
xsDataCellRefined = XSDataCell()
xsDataCellRefined.setLength_a(XSDataLength(
listOfListOfFloat[7][0]))
xsDataCellRefined.setLength_b(XSDataLength(
listOfListOfFloat[7][1]))
xsDataCellRefined.setLength_c(XSDataLength(
listOfListOfFloat[7][2]))
xsDataCellRefined.setAngle_alpha(
XSDataAngle(listOfListOfFloat[7][3]))
xsDataCellRefined.setAngle_beta(
XSDataAngle(listOfListOfFloat[7][4]))
xsDataCellRefined.setAngle_gamma(
XSDataAngle(listOfListOfFloat[7][5]))
xsDataMOSFLMNewmat.setRefinedCell(xsDataCellRefined)
return xsDataMOSFLMNewmat
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