def generateMOSFLMCommands(self):
"""
This method creates a list of MOSFLM indexing commands given a valid
XSDataMOSFLMIndexingingInput as self.getDataInput()
"""
EDPluginMOSFLMv10.generateMOSFLMCommands(self)
EDVerbose.DEBUG("EDPluginMOSFLMIndexingv10.generateMOSFLMCommands")
xsDataMOSFLMIndexingInput = self.getDataInput()
if (xsDataMOSFLMIndexingInput != None):
self.addListCommandExecution("NEWMAT " + self.getNewmatFileName())
xsDataMOSFLMImageList = xsDataMOSFLMIndexingInput.getImage()
for xsDataMOSFLMImage in xsDataMOSFLMImageList:
iImageNumber = xsDataMOSFLMImage.getNumber().getValue()
fRotationAxisStart = xsDataMOSFLMImage.getRotationAxisStart().getValue()
fRotationAxisEnd = xsDataMOSFLMImage.getRotationAxisEnd().getValue()
self.addListCommandExecution("AUTOINDEX DPS REFINE IMAGE " + str(iImageNumber) + " " \
"PHI " + str(fRotationAxisStart) + " " + str(fRotationAxisEnd))
self.addListCommandExecution("GO")
for xsDataImage in xsDataMOSFLMImageList:
self.addListCommandExecution("MOSAIC ESTIMATE %d" % xsDataImage.getNumber().getValue())
self.addListCommandExecution("GO")
# strPrefix = strTemplate.split("#")[0][:-1]
# strGenFileName = strPrefix + ".gen"
# strSptFileName = strPrefix + ".spt"
EDVerbose.DEBUG("Finished EDPluginMOSFLMIndexingv10.generateMOSFLMIndexingCommands")
def generateMOSFLMCommands(self):
"""
This method creates a list of MOSFLM integration commands given a valid
XSDataMOSFLMIntegrationingInput as self.getDataInput()
"""
EDPluginMOSFLMv10.generateMOSFLMCommands(self)
EDVerbose.DEBUG("EDPluginMOSFLMIntegrationv10.generateMOSFLMCommands")
xsDataMOSFLMInputIntegration = self.getDataInput()
if xsDataMOSFLMInputIntegration is not None:
iImageStart = xsDataMOSFLMInputIntegration.getImageStart().getValue()
iImageEnd = xsDataMOSFLMInputIntegration.getImageEnd().getValue()
fRotationAxisStart = xsDataMOSFLMInputIntegration.getRotationAxisStart().getValue()
fOscillationWidth = xsDataMOSFLMInputIntegration.getOscillationWidth().getValue()
self.addListCommandExecution("HKLOUT process_%d_%d.mtz" % (iImageStart, iImageEnd))
self.addListCommandExecution(
"PROCESS %d TO %d START %f ANGLE %f" % (iImageStart, iImageEnd, fRotationAxisStart, fOscillationWidth)
)
self.addListCommandExecution("BEST ON")
self.addListCommandExecution("GO")
self.addListCommandExecution("BEST OFF")
EDVerbose.DEBUG("Finished EDPluginMOSFLMIntegrationv10.generateMOSFLMCommands")
def generateMOSFLMCommands(self):
"""
This method creates a list of MOSFLM integration commands given a valid
XSDataMOSFLMInputGeneratePrediction as input to the plugin.
"""
EDPluginMOSFLMv10.generateMOSFLMCommands(self)
EDVerbose.DEBUG("EDPluginMOSFLMGeneratePredictionv10.generateMOSFLMCommands")
xsDataMOSFLMInputGeneratePrediction = self.getDataInput()
if (xsDataMOSFLMInputGeneratePrediction is not None):
pyStrTemplate = xsDataMOSFLMInputGeneratePrediction.getTemplate().getValue()
xsDataMOSFLMImage = xsDataMOSFLMInputGeneratePrediction.getImage()
iImageNumber = xsDataMOSFLMImage.getNumber().getValue()
pyStrImageFileName = self.getImageFileNameFromTemplate(pyStrTemplate, iImageNumber)
if (pyStrImageFileName is not None):
self.setPredictionImageFileName(pyStrImageFileName + "_pred.jpg")
fRotationAxisStart = xsDataMOSFLMImage.getRotationAxisStart().getValue()
fRotationAxisEnd = xsDataMOSFLMImage.getRotationAxisEnd().getValue()
self.addListCommandExecution("XGUI ON")
self.addListCommandExecution("IMAGE %d PHI %f TO %f" % (iImageNumber, fRotationAxisStart, fRotationAxisEnd))
self.addListCommandExecution("GO")
self.addListCommandExecution("PREDICT_SPOTS")
self.addListCommandExecution("CREATE_IMAGE PREDICTION ON BINARY TRUE FILENAME %s" % (self.getPredictionImageFileName()))
self.addListCommandExecution("RETURN")
self.addListCommandExecution("EXIT")
self.addListCommandPostExecution("chmod 644 %s" % self.getPredictionImageFileName())
EDVerbose.DEBUG("Finished EDPluginMOSFLMGeneratePredictionv10.generateMOSFLMCommands")
def configure(self):
EDPluginMOSFLMv10.configure(self)
EDVerbose.DEBUG("EDPluginMOSFLMGeneratePredictionv10.configure")
xsPluginItem = self.getConfiguration()
if (xsPluginItem == None):
EDVerbose.DEBUG("EDPluginMOSFLMGeneratePredictionv10.configure: xsPluginItem is None")
self.createPredictionImageFileName()
def checkParameters(self):
"""
Checks the mandatory parameters for MOSLFM indexing
"""
EDPluginMOSFLMv10.checkParameters(self)
EDVerbose.DEBUG("EDPluginMOSFLMGeneratePredictionv10.checkParameters")
self.checkMandatoryParameters(self.getDataInput().getImage(), "image")
def checkParameters(self):
"""
Checks the mandatory parameters for MOSLFM indexing
"""
EDPluginMOSFLMv10.checkParameters(self)
self.DEBUG("EDPluginMOSFLMIndexingv10.checkParameters")
self.checkMandatoryParameters(self.getDataInput().getImage(), "image")
def generateMOSFLMCommands(self):
"""
This method creates a list of MOSFLM integration commands given a valid
XSDataMOSFLMIntegrationingInput as self.getDataInput()
"""
EDPluginMOSFLMv10.generateMOSFLMCommands(self)
self.DEBUG("EDPluginMOSFLMIntegrationv10.generateMOSFLMCommands")
xsDataMOSFLMInputIntegration = self.getDataInput()
if (xsDataMOSFLMInputIntegration is not None):
iImageStart = xsDataMOSFLMInputIntegration.getImageStart().getValue()
iImageEnd = xsDataMOSFLMInputIntegration.getImageEnd().getValue()
fRotationAxisStart = xsDataMOSFLMInputIntegration.getRotationAxisStart().getValue()
fOscillationWidth = xsDataMOSFLMInputIntegration.getOscillationWidth().getValue()
self.addListCommandExecution("HKLOUT process_%d_%d.mtz" %
(iImageStart, iImageEnd))
self.addListCommandExecution("PROCESS %d TO %d START %f ANGLE %f" %
(iImageStart, iImageEnd, fRotationAxisStart, fOscillationWidth))
self.addListCommandExecution("BEST ON")
self.addListCommandExecution("GO")
self.addListCommandExecution("BEST OFF")
# Force name of log file
self.setScriptLogFileName(self.compactPluginName(self.getClassName())+".log")
self.DEBUG("Finished EDPluginMOSFLMIntegrationv10.generateMOSFLMCommands")
def checkParameters(self):
"""
Checks the mandatory parameters for MOSLFM indexing
"""
EDPluginMOSFLMv10.checkParameters(self)
self.DEBUG("EDPluginMOSFLMIntegrationv10.checkParameters")
self.checkMandatoryParameters(self.getDataInput().getImageEnd(), "imageEnd")
self.checkMandatoryParameters(self.getDataInput().getImageStart(), "imageStart")
self.checkMandatoryParameters(self.getDataInput().getOscillationWidth(), "oscillationWidth")
self.checkMandatoryParameters(self.getDataInput().getRotationAxisStart(), "rotationAxisStart")
def postProcess(self, _edObject=None):
EDPluginMOSFLMv10.postProcess(self)
self.DEBUG("EDPluginMOSFLMIntegrationv10.postProcess")
xsDataMOSFLMOutputIntegration = self.createDataMOSFLMOutputIntegration()
if (xsDataMOSFLMOutputIntegration is None):
strError = "MOSFLM integration error : no integration results obtained."
self.addExecutiveSummaryLine(strError)
self.ERROR(strError)
self.setFailure()
else:
self.setDataOutput(xsDataMOSFLMOutputIntegration)
def __init__(self):
EDPluginMOSFLMv10.__init__(self)
self.setXSDataInputClass(XSDataMOSFLMInputIntegration)
def generateExecutiveSummary(self, _edPlugin):
"""
Generates a summary of the execution of the plugin.
"""
EDPluginMOSFLMv10.generateExecutiveSummary(self, _edPlugin)
self.DEBUG(
"EDPluginMOSFLMIntegrationv10.createDataMOSFLMOutputIndexing")
xsDataMOSFLMInputIntegration = self.getDataInput()
xsDataMOSFLMOutputIntegration = self.getDataOutput()
if (xsDataMOSFLMOutputIntegration is not None):
self.addExecutiveSummaryLine(
"Execution of MOSFLM integration successful.")
self.addExecutiveSummaryLine(
"Image directory : %s" %
xsDataMOSFLMInputIntegration.getDirectory().getValue())
self.addExecutiveSummaryLine(
"Image template : %s" %
xsDataMOSFLMInputIntegration.getTemplate().getValue())
self.addExecutiveSummaryLine(
"Image start : %4d" %
xsDataMOSFLMInputIntegration.getImageStart().getValue())
self.addExecutiveSummaryLine(
"Image end : %4d" %
xsDataMOSFLMInputIntegration.getImageEnd().getValue())
fRotationAxisStart = xsDataMOSFLMInputIntegration.getRotationAxisStart(
).getValue()
fOscillationWidth = xsDataMOSFLMInputIntegration.getOscillationWidth(
).getValue()
self.addExecutiveSummaryLine(
"Rotation axis start : %4.1f [degrees]" % fRotationAxisStart)
self.addExecutiveSummaryLine(
"Rotation axis end : %4.1f [degrees]" %
(fRotationAxisStart + fOscillationWidth))
self.addExecutiveSummaryLine("")
iNumberOfFullyRecordedReflections = xsDataMOSFLMOutputIntegration.getNumberOfFullyRecordedReflections(
).getValue()
self.addExecutiveSummaryLine(
"Number of fully recorded reflections : %5d" %
iNumberOfFullyRecordedReflections)
self.addExecutiveSummaryLine(
"Number of partials : %5d" %
xsDataMOSFLMOutputIntegration.getNumberOfPartialReflections(
).getValue())
self.addExecutiveSummaryLine(
"Number of overlapped reflections : %5d" %
xsDataMOSFLMOutputIntegration.getNumberOfOverlappedReflections(
).getValue())
self.addExecutiveSummaryLine(
"Number of reflections with negative intensity : %5d" %
xsDataMOSFLMOutputIntegration.getNumberOfNegativeReflections(
).getValue())
self.addExecutiveSummaryLine(
"Number of bad reflections : %5d" %
xsDataMOSFLMOutputIntegration.getNumberOfBadReflections(
).getValue())
self.addExecutiveSummaryLine("")
self.addExecutiveSummaryLine(
"RMS spot deviation : %5.3f [mm]" %
xsDataMOSFLMOutputIntegration.getRMSSpotDeviation().getValue())
self.addExecutiveSummaryLine(
"Average I/sigma overall : %5.1f" %
xsDataMOSFLMOutputIntegration.getOverallIOverSigma().getValue(
))
self.addExecutiveSummaryLine(
"Average I/sigma at highest resolution : %5.1f" %
xsDataMOSFLMOutputIntegration.getHighestResolutionIOverSigma(
).getValue())
self.addExecutiveSummaryLine("")
self.addExecutiveSummaryLine(
"Analysis as a function of resolution:")
strResolution = "Res (Ang) "
strNumberProfileFittedFullyRecorded = "Number "
strAverageIntensityProfileFittedFullyRecorded = " <I> "
strAverageIOverSigmaProfileFittedFullyRecorded = " <I/sigma>"
strNumberProfileFittedPartials = "Number "
strAverageIntensityProfileFittedPartials = " <I> "
strAverageIOverSigmaProfileFittedPartials = " <I/sigma>"
for xsDataMOSFLMIntegrationStatisticsPerResolutionBin in xsDataMOSFLMOutputIntegration.getStatisticsPerResolutionBin(
):
fMaxResolution = xsDataMOSFLMIntegrationStatisticsPerResolutionBin.getMaxResolution(
).getValue()
strResolution += "%7.2f" % fMaxResolution
xsDataMOSFLMIntegrationStatisticsProfileFitted = xsDataMOSFLMIntegrationStatisticsPerResolutionBin.getProfileFitted(
)
xsDataMOSFLMIntegrationStatisticsProfileFittedFullyRecorded = xsDataMOSFLMIntegrationStatisticsProfileFitted.getFullyRecorded(
)
strNumberProfileFittedFullyRecorded += "%7d" % xsDataMOSFLMIntegrationStatisticsProfileFittedFullyRecorded.getNumberOfReflections(
).getValue()
strAverageIntensityProfileFittedFullyRecorded += "%7.0f" % xsDataMOSFLMIntegrationStatisticsProfileFittedFullyRecorded.getAverageIntensity(
).getValue()
strAverageIOverSigmaProfileFittedFullyRecorded += "%7.1f" % xsDataMOSFLMIntegrationStatisticsProfileFittedFullyRecorded.getAverageIOverSigma(
).getValue()
xsDataMOSFLMIntegrationStatisticsProfileFittedPartials = xsDataMOSFLMIntegrationStatisticsProfileFitted.getPartials(
)
strNumberProfileFittedPartials += "%7d" % xsDataMOSFLMIntegrationStatisticsProfileFittedPartials.getNumberOfReflections(
).getValue()
strAverageIntensityProfileFittedPartials += "%7.0f" % xsDataMOSFLMIntegrationStatisticsProfileFittedPartials.getAverageIntensity(
).getValue()
strAverageIOverSigmaProfileFittedPartials += "%7.1f" % xsDataMOSFLMIntegrationStatisticsProfileFittedPartials.getAverageIOverSigma(
).getValue()
strResolution += " Overall"
self.addExecutiveSummaryLine(strResolution)
strNumberProfileFittedFullyRecorded += "%8d" % xsDataMOSFLMOutputIntegration.getOverallStatistics(
).getProfileFitted().getFullyRecorded().getNumberOfReflections(
).getValue()
strAverageIntensityProfileFittedFullyRecorded += "%8.0f" % xsDataMOSFLMOutputIntegration.getOverallStatistics(
).getProfileFitted().getFullyRecorded().getAverageIntensity(
).getValue()
strAverageIOverSigmaProfileFittedFullyRecorded += "%8.1f" % xsDataMOSFLMOutputIntegration.getOverallStatistics(
).getProfileFitted().getFullyRecorded().getAverageIOverSigma(
).getValue()
strNumberProfileFittedPartials += "%8d" % xsDataMOSFLMOutputIntegration.getOverallStatistics(
).getProfileFitted().getPartials().getNumberOfReflections(
).getValue()
strAverageIntensityProfileFittedPartials += "%8.0f" % xsDataMOSFLMOutputIntegration.getOverallStatistics(
).getProfileFitted().getPartials().getAverageIntensity().getValue(
)
strAverageIOverSigmaProfileFittedPartials += "%8.1f" % xsDataMOSFLMOutputIntegration.getOverallStatistics(
).getProfileFitted().getPartials().getAverageIOverSigma().getValue(
)
if (iNumberOfFullyRecordedReflections > 0):
self.addExecutiveSummaryLine("Profile fitted fully recorded:")
self.addExecutiveSummaryLine(
strNumberProfileFittedFullyRecorded)
self.addExecutiveSummaryLine(
strAverageIntensityProfileFittedFullyRecorded)
self.addExecutiveSummaryLine(
strAverageIOverSigmaProfileFittedFullyRecorded)
self.addExecutiveSummaryLine("Profile fitted partials:")
self.addExecutiveSummaryLine(strNumberProfileFittedPartials)
self.addExecutiveSummaryLine(
strAverageIntensityProfileFittedPartials)
#self.addExecutiveSummaryLine( strAverageSigmaProfileFittedPartials )
self.addExecutiveSummaryLine(
strAverageIOverSigmaProfileFittedPartials)
self.addExecutiveSummaryLine("")
self.addExecutiveSummaryLine(
"Path to MTZ file : %s" % xsDataMOSFLMOutputIntegration.
getGeneratedMTZFile().getPath().getValue())
def preProcess(self, _edObject=None):
EDPluginMOSFLMv10.preProcess(self)
EDVerbose.DEBUG("EDPluginMOSFLMGeneratePredictionv10.preProcess")
self.generateMOSFLMCommands()
def postProcess(self, _edObject=None):
EDPluginMOSFLMv10.postProcess(self)
EDVerbose.DEBUG("EDPluginMOSFLMGeneratePredictionv10.postProcess")
xsDataMOSFLMOutputGeneratePrediction = self.createDataMOSFLMOutputGeneratePrediction()
self.setDataOutput(xsDataMOSFLMOutputGeneratePrediction)
def preProcess(self, _edObject=None):
EDPluginMOSFLMv10.preProcess(self)
self.DEBUG("EDPluginMOSFLMIndexingv10.preProcess")
self.generateMOSFLMCommands()
def __init__(self):
EDPluginMOSFLMv10.__init__(self)
self.setXSDataInputClass(XSDataMOSFLMInputGeneratePrediction)
self.__strPredictionImageFileName = "EDPluginMOSFLMGeneratePredictionv10.jpg"
def preProcess(self, _edObject=None):
EDPluginMOSFLMv10.preProcess(self)
self.DEBUG("EDPluginMOSFLMGeneratePredictionv10.preProcess")
self.generateMOSFLMCommands()
def preProcess(self, _edObject=None):
EDPluginMOSFLMv10.preProcess(self)
self.DEBUG("EDPluginMOSFLMIntegrationv10.preProcess")
self.generateMOSFLMCommands()
def finallyProcess(self, _edObject=None):
EDPluginMOSFLMv10.finallyProcess(self)
self.DEBUG("EDPluginMOSFLMIndexingv10.finallyProcess")
xsDataMOSFLMOutputIndexing = self.createDataMOSFLMOutputIndexing()
self.setDataOutput(xsDataMOSFLMOutputIndexing)
def postProcess(self, _edObject=None):
EDPluginMOSFLMv10.postProcess(self)
self.DEBUG("EDPluginMOSFLMGeneratePredictionv10.postProcess")
xsDataMOSFLMOutputGeneratePrediction = self.createDataMOSFLMOutputGeneratePrediction(
)
self.setDataOutput(xsDataMOSFLMOutputGeneratePrediction)
def __init__(self):
EDPluginMOSFLMv10.__init__(self)
self.setXSDataInputClass(XSDataMOSFLMInputIndexing)
def generateExecutiveSummary(self, _edPlugin):
"""
Generates a summary of the execution of the plugin.
"""
EDPluginMOSFLMv10.generateExecutiveSummary(self, _edPlugin)
EDVerbose.DEBUG("EDPluginMOSFLMIndexingv10.createDataMOSFLMOutputIndexing")
xsDataMOSFLMInputIndexing = self.getDataInput()
xsDataMOSFLMOutputIndexing = self.getDataOutput()
if not self.isFailure():
self.addExecutiveSummaryLine("Execution of MOSFLM indexing successful.")
self.addExecutiveSummaryLine("Image directory : %s" % xsDataMOSFLMInputIndexing.getDirectory().getValue())
self.addExecutiveSummaryLine("Image template : %s" % xsDataMOSFLMInputIndexing.getTemplate().getValue())
strImagesUsed = "Images used in indexing : "
for xsDataMOSFLMImage in xsDataMOSFLMInputIndexing.getImage():
strImagesUsed += "%3d" % xsDataMOSFLMImage.getNumber().getValue()
self.addExecutiveSummaryLine(strImagesUsed)
if (xsDataMOSFLMInputIndexing.getSymmetry() is not None):
self.addExecutiveSummaryLine("Target symmetry : %s" % xsDataMOSFLMInputIndexing.getSymmetry().getValue())
self.addExecutiveSummaryLine("")
if (xsDataMOSFLMOutputIndexing is not None):
self.addExecutiveSummaryLine("")
self.addExecutiveSummaryLine("List of possible solutions (index, penalty, lattice and cell):")
iSelectedSolutionNumber = xsDataMOSFLMOutputIndexing.getSelectedSolutionNumber().getValue()
# Add all solutions with penalty < 100 + 1 solution with penalty > 100
bAddSolution = False
listMOSFLMOutputIndexing = xsDataMOSFLMOutputIndexing.getPossibleSolutions()
iNumberOfSolutions = len(listMOSFLMOutputIndexing)
for i in range(iNumberOfSolutions):
iPenalty = listMOSFLMOutputIndexing[i].getPenalty().getValue()
if (i < (iNumberOfSolutions - 1)):
iPenaltyNext = listMOSFLMOutputIndexing[i + 1].getPenalty().getValue()
if ((iPenalty >= 100) and (iPenaltyNext <= 100)):
bAddSolution = True
if (bAddSolution):
iIndex = listMOSFLMOutputIndexing[i].getIndex().getValue()
xsDataCell = listMOSFLMOutputIndexing[i].getCell()
strLattice = listMOSFLMOutputIndexing[i].getLattice().getValue()
strPossibleSolution = "%3d %4d %2s %6.2f %6.2f %6.2f %6.2f %6.2f %6.2f" % \
(iIndex, iPenalty, strLattice, \
xsDataCell.getLength_a().getValue(),
xsDataCell.getLength_b().getValue(),
xsDataCell.getLength_c().getValue(),
xsDataCell.getAngle_alpha().getValue(),
xsDataCell.getAngle_beta().getValue(),
xsDataCell.getAngle_gamma().getValue(),
)
self.addExecutiveSummaryLine(strPossibleSolution)
iPenaltyOld = iPenalty
self.addExecutiveSummaryLine("")
self.addExecutiveSummaryLine("Choosen solution number : %14d" % iSelectedSolutionNumber)
strSelectedSpaceGroup = xsDataMOSFLMOutputIndexing.getSelectedSolutionSpaceGroup().getValue()
self.addExecutiveSummaryLine("Selected space group : %14s" % (strSelectedSpaceGroup))
xsDataCellRefined = xsDataMOSFLMOutputIndexing.getRefinedNewmat().getRefinedCell()
self.addExecutiveSummaryLine("Refined cell : %6.2f %7.2f %7.2f %5.1f %5.1f %5.1f" % (\
xsDataCellRefined.getLength_a().getValue(),
xsDataCellRefined.getLength_b().getValue(),
xsDataCellRefined.getLength_c().getValue(),
xsDataCellRefined.getAngle_alpha().getValue(),
xsDataCellRefined.getAngle_beta().getValue(),
xsDataCellRefined.getAngle_gamma().getValue()
))
iSpotsTotal = xsDataMOSFLMOutputIndexing.getSpotsTotal().getValue()
iSpotsUsed = xsDataMOSFLMOutputIndexing.getSpotsUsed().getValue()
self.addExecutiveSummaryLine("Number of spots used : %14d " % (iSpotsUsed))
self.addExecutiveSummaryLine("Number of spots total : %14d " % (iSpotsTotal))
fDeviationPositional = xsDataMOSFLMOutputIndexing.getDeviationPositional().getValue()
fDeviationAngular = xsDataMOSFLMOutputIndexing.getDeviationAngular().getValue()
self.addExecutiveSummaryLine("Spot deviation positional : %14.2f [mm]" % (fDeviationPositional))
self.addExecutiveSummaryLine("Spot deviation angular : %14.2f [degrees]" % (fDeviationAngular))
fBeamshiftX = xsDataMOSFLMOutputIndexing.getBeamShift().getX().getValue()
fBeamshiftY = xsDataMOSFLMOutputIndexing.getBeamShift().getY().getValue()
self.addExecutiveSummaryLine("Beam shift (X, Y) : %6.3f, %6.3f [mm]" % \
(fBeamshiftX, fBeamshiftY))
fMosaicityEstimated = xsDataMOSFLMOutputIndexing.getMosaicityEstimation().getValue()
self.addExecutiveSummaryLine("Estimated mosaicity : %14.2f [degrees]" % fMosaicityEstimated)
def generateExecutiveSummary(self, _edPlugin):
"""
Generates a summary of the execution of the plugin.
"""
EDPluginMOSFLMv10.generateExecutiveSummary(self, _edPlugin)
self.DEBUG("EDPluginMOSFLMIndexingv10.createDataMOSFLMOutputIndexing")
xsDataMOSFLMInputIndexing = self.getDataInput()
xsDataMOSFLMOutputIndexing = self.getDataOutput()
if not self.isFailure():
self.addExecutiveSummaryLine(
"Execution of MOSFLM indexing successful.")
self.addExecutiveSummaryLine(
"Image directory : %s" %
xsDataMOSFLMInputIndexing.getDirectory().getValue())
self.addExecutiveSummaryLine(
"Image template : %s" %
xsDataMOSFLMInputIndexing.getTemplate().getValue())
strImagesUsed = "Images used in indexing : "
for xsDataMOSFLMImage in xsDataMOSFLMInputIndexing.getImage():
strImagesUsed += "%3d" % xsDataMOSFLMImage.getNumber().getValue()
self.addExecutiveSummaryLine(strImagesUsed)
if (xsDataMOSFLMInputIndexing.getSymmetry() is not None):
self.addExecutiveSummaryLine(
"Target symmetry : %s" %
xsDataMOSFLMInputIndexing.getSymmetry().getValue())
self.addExecutiveSummaryLine("")
if (xsDataMOSFLMOutputIndexing is not None):
self.addExecutiveSummaryLine("")
self.addExecutiveSummaryLine(
"List of possible solutions (index, penalty, lattice and cell):"
)
iSelectedSolutionNumber = xsDataMOSFLMOutputIndexing.getSelectedSolutionNumber(
).getValue()
# Add all solutions with penalty < 100 + 1 solution with penalty > 100
bAddSolution = False
listMOSFLMOutputIndexing = xsDataMOSFLMOutputIndexing.getPossibleSolutions(
)
iNumberOfSolutions = len(listMOSFLMOutputIndexing)
for i in range(iNumberOfSolutions):
iPenalty = listMOSFLMOutputIndexing[i].getPenalty().getValue()
if (i < (iNumberOfSolutions - 1)):
iPenaltyNext = listMOSFLMOutputIndexing[
i + 1].getPenalty().getValue()
if ((iPenalty >= 100) and (iPenaltyNext <= 100)):
bAddSolution = True
if (bAddSolution):
iIndex = listMOSFLMOutputIndexing[i].getIndex().getValue()
xsDataCell = listMOSFLMOutputIndexing[i].getCell()
strLattice = listMOSFLMOutputIndexing[i].getLattice(
).getValue()
strPossibleSolution = "%3d %4d %2s %6.2f %6.2f %6.2f %6.2f %6.2f %6.2f" % \
(iIndex, iPenalty, strLattice, \
xsDataCell.getLength_a().getValue(),
xsDataCell.getLength_b().getValue(),
xsDataCell.getLength_c().getValue(),
xsDataCell.getAngle_alpha().getValue(),
xsDataCell.getAngle_beta().getValue(),
xsDataCell.getAngle_gamma().getValue(),
)
self.addExecutiveSummaryLine(strPossibleSolution)
iPenaltyOld = iPenalty
self.addExecutiveSummaryLine("")
self.addExecutiveSummaryLine("Choosen solution number : %14d" %
iSelectedSolutionNumber)
strSelectedSpaceGroup = xsDataMOSFLMOutputIndexing.getSelectedSolutionSpaceGroup(
).getValue()
self.addExecutiveSummaryLine("Selected space group : %14s" %
(strSelectedSpaceGroup))
xsDataCellRefined = xsDataMOSFLMOutputIndexing.getRefinedNewmat(
).getRefinedCell()
self.addExecutiveSummaryLine("Refined cell : %6.2f %7.2f %7.2f %5.1f %5.1f %5.1f" % (\
xsDataCellRefined.getLength_a().getValue(),
xsDataCellRefined.getLength_b().getValue(),
xsDataCellRefined.getLength_c().getValue(),
xsDataCellRefined.getAngle_alpha().getValue(),
xsDataCellRefined.getAngle_beta().getValue(),
xsDataCellRefined.getAngle_gamma().getValue()
))
iSpotsTotal = xsDataMOSFLMOutputIndexing.getSpotsTotal().getValue()
iSpotsUsed = xsDataMOSFLMOutputIndexing.getSpotsUsed().getValue()
self.addExecutiveSummaryLine("Number of spots used : %14d " %
(iSpotsUsed))
self.addExecutiveSummaryLine("Number of spots total : %14d " %
(iSpotsTotal))
fDeviationPositional = xsDataMOSFLMOutputIndexing.getDeviationPositional(
).getValue()
fDeviationAngular = xsDataMOSFLMOutputIndexing.getDeviationAngular(
).getValue()
self.addExecutiveSummaryLine(
"Spot deviation positional : %14.2f [mm]" %
(fDeviationPositional))
self.addExecutiveSummaryLine(
"Spot deviation angular : %14.2f [degrees]" %
(fDeviationAngular))
fBeamshiftX = xsDataMOSFLMOutputIndexing.getBeamShift().getX(
).getValue()
fBeamshiftY = xsDataMOSFLMOutputIndexing.getBeamShift().getY(
).getValue()
self.addExecutiveSummaryLine("Beam shift (X, Y) : %6.3f, %6.3f [mm]" % \
(fBeamshiftX, fBeamshiftY))
fMosaicityEstimated = xsDataMOSFLMOutputIndexing.getMosaicityEstimation(
).getValue()
self.addExecutiveSummaryLine(
"Estimated mosaicity : %14.2f [degrees]" %
fMosaicityEstimated)
def generateExecutiveSummary(self, _edPlugin):
"""
Generates a summary of the execution of the plugin.
"""
EDPluginMOSFLMv10.generateExecutiveSummary(self, _edPlugin)
self.DEBUG("EDPluginMOSFLMIntegrationv10.createDataMOSFLMOutputIndexing")
xsDataMOSFLMInputIntegration = self.getDataInput()
xsDataMOSFLMOutputIntegration = self.getDataOutput()
if xsDataMOSFLMOutputIntegration.getNumberOfFullyRecordedReflections() is not None:
self.addExecutiveSummaryLine("Execution of MOSFLM integration successful.")
self.addExecutiveSummaryLine("Image directory : %s" % xsDataMOSFLMInputIntegration.getDirectory().getValue())
self.addExecutiveSummaryLine("Image template : %s" % xsDataMOSFLMInputIntegration.getTemplate().getValue())
self.addExecutiveSummaryLine("Image start : %4d" % xsDataMOSFLMInputIntegration.getImageStart().getValue())
self.addExecutiveSummaryLine("Image end : %4d" % xsDataMOSFLMInputIntegration.getImageEnd().getValue())
fRotationAxisStart = xsDataMOSFLMInputIntegration.getRotationAxisStart().getValue()
fOscillationWidth = xsDataMOSFLMInputIntegration.getOscillationWidth().getValue()
self.addExecutiveSummaryLine("Rotation axis start : %4.1f [degrees]" % fRotationAxisStart)
self.addExecutiveSummaryLine("Rotation axis end : %4.1f [degrees]" % (fRotationAxisStart + fOscillationWidth))
self.addExecutiveSummaryLine("")
iNumberOfFullyRecordedReflections = xsDataMOSFLMOutputIntegration.getNumberOfFullyRecordedReflections().getValue()
self.addExecutiveSummaryLine("Number of fully recorded reflections : %5d" % iNumberOfFullyRecordedReflections)
self.addExecutiveSummaryLine("Number of partials : %5d" % xsDataMOSFLMOutputIntegration.getNumberOfPartialReflections().getValue())
self.addExecutiveSummaryLine("Number of overlapped reflections : %5d" % xsDataMOSFLMOutputIntegration.getNumberOfOverlappedReflections().getValue())
self.addExecutiveSummaryLine("Number of reflections with negative intensity : %5d" % xsDataMOSFLMOutputIntegration.getNumberOfNegativeReflections().getValue())
self.addExecutiveSummaryLine("Number of bad reflections : %5d" % xsDataMOSFLMOutputIntegration.getNumberOfBadReflections().getValue())
self.addExecutiveSummaryLine("")
self.addExecutiveSummaryLine("RMS spot deviation : %5.3f [mm]" % xsDataMOSFLMOutputIntegration.getRMSSpotDeviation().getValue())
self.addExecutiveSummaryLine("Average I/sigma overall : %5.1f" % xsDataMOSFLMOutputIntegration.getOverallIOverSigma().getValue())
self.addExecutiveSummaryLine("Average I/sigma at highest resolution : %5.1f" % xsDataMOSFLMOutputIntegration.getHighestResolutionIOverSigma().getValue())
self.addExecutiveSummaryLine("")
self.addExecutiveSummaryLine("Analysis as a function of resolution:")
strResolution = "Res (Ang) "
strNumberProfileFittedFullyRecorded = "Number "
strAverageIntensityProfileFittedFullyRecorded = " <I> "
strAverageIOverSigmaProfileFittedFullyRecorded = " <I/sigma>"
strNumberProfileFittedPartials = "Number "
strAverageIntensityProfileFittedPartials = " <I> "
strAverageIOverSigmaProfileFittedPartials = " <I/sigma>"
for xsDataMOSFLMIntegrationStatisticsPerResolutionBin in xsDataMOSFLMOutputIntegration.getStatisticsPerResolutionBin():
fMaxResolution = xsDataMOSFLMIntegrationStatisticsPerResolutionBin.getMaxResolution().getValue()
strResolution += "%7.2f" % fMaxResolution
xsDataMOSFLMIntegrationStatisticsProfileFitted = xsDataMOSFLMIntegrationStatisticsPerResolutionBin.getProfileFitted()
xsDataMOSFLMIntegrationStatisticsProfileFittedFullyRecorded = xsDataMOSFLMIntegrationStatisticsProfileFitted.getFullyRecorded()
strNumberProfileFittedFullyRecorded += "%7d" % xsDataMOSFLMIntegrationStatisticsProfileFittedFullyRecorded.getNumberOfReflections().getValue()
strAverageIntensityProfileFittedFullyRecorded += "%7.0f" % xsDataMOSFLMIntegrationStatisticsProfileFittedFullyRecorded.getAverageIntensity().getValue()
strAverageIOverSigmaProfileFittedFullyRecorded += "%7.1f" % xsDataMOSFLMIntegrationStatisticsProfileFittedFullyRecorded.getAverageIOverSigma().getValue()
xsDataMOSFLMIntegrationStatisticsProfileFittedPartials = xsDataMOSFLMIntegrationStatisticsProfileFitted.getPartials()
strNumberProfileFittedPartials += "%7d" % xsDataMOSFLMIntegrationStatisticsProfileFittedPartials.getNumberOfReflections().getValue()
strAverageIntensityProfileFittedPartials += "%7.0f" % xsDataMOSFLMIntegrationStatisticsProfileFittedPartials.getAverageIntensity().getValue()
strAverageIOverSigmaProfileFittedPartials += "%7.1f" % xsDataMOSFLMIntegrationStatisticsProfileFittedPartials.getAverageIOverSigma().getValue()
strResolution += " Overall"
self.addExecutiveSummaryLine(strResolution)
strNumberProfileFittedFullyRecorded += "%8d" % xsDataMOSFLMOutputIntegration.getOverallStatistics().getProfileFitted().getFullyRecorded().getNumberOfReflections().getValue()
strAverageIntensityProfileFittedFullyRecorded += "%8.0f" % xsDataMOSFLMOutputIntegration.getOverallStatistics().getProfileFitted().getFullyRecorded().getAverageIntensity().getValue()
strAverageIOverSigmaProfileFittedFullyRecorded += "%8.1f" % xsDataMOSFLMOutputIntegration.getOverallStatistics().getProfileFitted().getFullyRecorded().getAverageIOverSigma().getValue()
strNumberProfileFittedPartials += "%8d" % xsDataMOSFLMOutputIntegration.getOverallStatistics().getProfileFitted().getPartials().getNumberOfReflections().getValue()
strAverageIntensityProfileFittedPartials += "%8.0f" % xsDataMOSFLMOutputIntegration.getOverallStatistics().getProfileFitted().getPartials().getAverageIntensity().getValue()
strAverageIOverSigmaProfileFittedPartials += "%8.1f" % xsDataMOSFLMOutputIntegration.getOverallStatistics().getProfileFitted().getPartials().getAverageIOverSigma().getValue()
if (iNumberOfFullyRecordedReflections > 0):
self.addExecutiveSummaryLine("Profile fitted fully recorded:")
self.addExecutiveSummaryLine(strNumberProfileFittedFullyRecorded)
self.addExecutiveSummaryLine(strAverageIntensityProfileFittedFullyRecorded)
self.addExecutiveSummaryLine(strAverageIOverSigmaProfileFittedFullyRecorded)
self.addExecutiveSummaryLine("Profile fitted partials:")
self.addExecutiveSummaryLine(strNumberProfileFittedPartials)
self.addExecutiveSummaryLine(strAverageIntensityProfileFittedPartials)
#self.addExecutiveSummaryLine( strAverageSigmaProfileFittedPartials )
self.addExecutiveSummaryLine(strAverageIOverSigmaProfileFittedPartials)
self.addExecutiveSummaryLine("")
self.addExecutiveSummaryLine("Path to MTZ file : %s" % xsDataMOSFLMOutputIntegration.getGeneratedMTZFile().getPath().getValue())
def configure(self):
EDPluginMOSFLMv10.configure(self)
self.DEBUG("EDPluginMOSFLMGeneratePredictionv10.configure")
self.createPredictionImageFileName()
def __init__(self):
EDPluginMOSFLMv10.__init__(self)
self.setXSDataInputClass(XSDataMOSFLMInputIntegration)
self.setDataOutput(XSDataMOSFLMOutputIntegration())
def __init__(self):
EDPluginMOSFLMv10.__init__(self)
self.setXSDataInputClass(XSDataMOSFLMInputGeneratePrediction)
self.__strPredictionImageFileName = "EDPluginMOSFLMGeneratePredictionv10.jpg"
def finallyProcess(self, _edObject=None):
EDPluginMOSFLMv10.postProcess(self)
EDVerbose.DEBUG("EDPluginMOSFLMIndexingv10.finallyProcess")
xsDataMOSFLMOutputIndexing = self.createDataMOSFLMOutputIndexing()
self.setDataOutput(xsDataMOSFLMOutputIndexing)
def __init__(self):
EDPluginMOSFLMv10.__init__(self)
self.setXSDataInputClass(XSDataMOSFLMInputIndexing)
def configure(self):
EDPluginMOSFLMv10.configure(self)
EDVerbose.DEBUG("EDPluginMOSFLMIndexingv10.configure")
xsPluginItem = self.getConfiguration()
if (xsPluginItem == None):
EDVerbose.DEBUG("EDPluginMOSFLMIndexingv10.configure: xsPluginItem is None")
def configure(self):
EDPluginMOSFLMv10.configure(self)
self.DEBUG("EDPluginMOSFLMIntegrationv10.configure")
xsPluginItem = self.getConfiguration()
if (xsPluginItem == None):
self.DEBUG("EDPluginMOSFLMIntegrationv10.configure: xsPluginItem is None")
