def testGenerateExecutiveSummary(self):
"""
This method tests the generateExecutiveSummary of the Labelit plugin.
It contains no assert call so the contents of the executive summary is not tested.
"""
edPluginLabelitIndexingv1_1 = self.createPlugin()
xmlInput1 = self.readAndParseFile(self.__strReferenceInputFile1)
edPluginLabelitIndexingv1_1.setDataInput(xmlInput1, "referenceImage")
xmlInput2 = self.readAndParseFile(self.__strReferenceInputFile1)
edPluginLabelitIndexingv1_1.setDataInput(xmlInput2, "referenceImage")
strLabelitScreenOutputFile = os.path.join(
self.getPluginTestsDataHome(),
"XSDataLabelitScreenOutput_reference.xml")
strLabelitScreenOutputXML = self.readAndParseFile(
strLabelitScreenOutputFile)
from XSDataLabelitv1_1 import XSDataLabelitScreenOutput
xsDataLabelitScreenOutputReference = XSDataLabelitScreenOutput.parseString(
strLabelitScreenOutputXML)
edPluginLabelitIndexingv1_1.setDataOutput(
xsDataLabelitScreenOutputReference, "labelitScreenOutput")
strLabelitMosflmScriptsOutputFile = os.path.join(
self.getPluginTestsDataHome(),
"XSDataLabelitMosflmScriptsOutput_reference.xml")
strLabelitMosflmScriptsOutputXML = self.readAndParseFile(
strLabelitMosflmScriptsOutputFile)
from XSDataLabelitv1_1 import XSDataLabelitMosflmScriptsOutput
xsDataLabelitMosflmScriptsOutputReference = XSDataLabelitMosflmScriptsOutput.parseString(
strLabelitMosflmScriptsOutputXML)
edPluginLabelitIndexingv1_1.setDataOutput(
xsDataLabelitMosflmScriptsOutputReference, "mosflmScriptOutput")
edPluginLabelitIndexingv1_1.generateExecutiveSummary(
edPluginLabelitIndexingv1_1)
def testParseLabelitScreenOutput(self):
"""
This method test the parsing of the Labelit results in the log file.
"""
edPluginLabelitIndexingv1_1 = self.createPlugin()
strPathToLabelitLogText = os.path.join(self.getPluginTestsDataHome(), "labelit_v1000rc11.log")
strLabelitLogText = self.readAndParseFile(strPathToLabelitLogText)
xsDataLabelitScreenOutput = edPluginLabelitIndexingv1_1.parseLabelitScreenOutput(strLabelitLogText)
strLabelitScreenOutputFile = os.path.join(self.getPluginTestsDataHome(), "XSDataLabelitScreenOutput_reference.xml")
strLabelitScreenOutputXML = self.readAndParseFile(strLabelitScreenOutputFile)
from XSDataLabelitv1_1 import XSDataLabelitScreenOutput
xsDataLabelitScreenOutputReference = XSDataLabelitScreenOutput.parseString(strLabelitScreenOutputXML)
EDAssert.equal(xsDataLabelitScreenOutputReference.marshal(), xsDataLabelitScreenOutput.marshal())
def testParseLabelitScreenOutput(self):
"""
This method test the parsing of the Labelit results in the log file.
"""
edPluginLabelitIndexingv1_1 = self.createPlugin()
strPathToLabelitLogText = os.path.join(self.getPluginTestsDataHome(),
"labelit_v1000rc11.log")
strLabelitLogText = self.readAndParseFile(strPathToLabelitLogText)
xsDataLabelitScreenOutput = edPluginLabelitIndexingv1_1.parseLabelitScreenOutput(
strLabelitLogText)
strLabelitScreenOutputFile = os.path.join(
self.getPluginTestsDataHome(),
"XSDataLabelitScreenOutput_reference.xml")
strLabelitScreenOutputXML = self.readAndParseFile(
strLabelitScreenOutputFile)
from XSDataLabelitv1_1 import XSDataLabelitScreenOutput
xsDataLabelitScreenOutputReference = XSDataLabelitScreenOutput.parseString(
strLabelitScreenOutputXML)
EDAssert.equal(xsDataLabelitScreenOutputReference.marshal(),
xsDataLabelitScreenOutput.marshal())
def testGenerateExecutiveSummary(self):
"""
This method tests the generateExecutiveSummary of the Labelit plugin.
It contains no assert call so the contents of the executive summary is not tested.
"""
edPluginLabelitIndexingv1_1 = self.createPlugin()
xmlInput1 = self.readAndParseFile(self.__strReferenceInputFile1)
edPluginLabelitIndexingv1_1.setDataInput(xmlInput1, "referenceImage")
xmlInput2 = self.readAndParseFile(self.__strReferenceInputFile1)
edPluginLabelitIndexingv1_1.setDataInput(xmlInput2, "referenceImage")
strLabelitScreenOutputFile = os.path.join(self.getPluginTestsDataHome(), "XSDataLabelitScreenOutput_reference.xml")
strLabelitScreenOutputXML = self.readAndParseFile(strLabelitScreenOutputFile)
from XSDataLabelitv1_1 import XSDataLabelitScreenOutput
xsDataLabelitScreenOutputReference = XSDataLabelitScreenOutput.parseString(strLabelitScreenOutputXML)
edPluginLabelitIndexingv1_1.setDataOutput(xsDataLabelitScreenOutputReference, "labelitScreenOutput")
strLabelitMosflmScriptsOutputFile = os.path.join(self.getPluginTestsDataHome(), "XSDataLabelitMosflmScriptsOutput_reference.xml")
strLabelitMosflmScriptsOutputXML = self.readAndParseFile(strLabelitMosflmScriptsOutputFile)
from XSDataLabelitv1_1 import XSDataLabelitMosflmScriptsOutput
xsDataLabelitMosflmScriptsOutputReference = XSDataLabelitMosflmScriptsOutput.parseString(strLabelitMosflmScriptsOutputXML)
edPluginLabelitIndexingv1_1.setDataOutput(xsDataLabelitMosflmScriptsOutputReference, "mosflmScriptOutput")
edPluginLabelitIndexingv1_1.generateExecutiveSummary(edPluginLabelitIndexingv1_1)
def parseLabelitScreenOutput(self, _strLabelitLogText):
"""
This method parses the labelit.screen log and populates the relevant
parts of the XSDataLabelitScreenOutput object which is then returned.
"""
self.DEBUG("EDPluginLabelitIndexingv1_1.parseLabelitLogText")
xsDataLabelitScreenOutput = None
iIndex = 0
listLogLines = _strLabelitLogText.split('\n')
bFoundLabelitIndexingResults = False
bContinue = True
while (bContinue):
if (listLogLines[iIndex].find("LABELIT Indexing results:") != -1):
bFoundLabelitIndexingResults = True
bContinue = False
else:
if (iIndex < (len(listLogLines) - 2)):
iIndex += 1
else:
bContinue = False
if (bFoundLabelitIndexingResults == False):
strErrorMessage = "EDPluginLabelitIndexingv1_1.parseLabelitLogText : Labelit log message: %s" % _strLabelitLogText
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
else:
# We found some indexing results!
xsDataLabelitScreenOutput = XSDataLabelitScreenOutput()
iIndex += 1
strBeamDistanceMosaicity = listLogLines[iIndex]
strBeamDistanceMosaicity = strBeamDistanceMosaicity.replace(
',', '')
strBeamDistanceMosaicity = strBeamDistanceMosaicity.replace(
'mm', ' ')
strBeamDistanceMosaicity = strBeamDistanceMosaicity.replace(
'=', ' ')
listStringBeamDistanceMosaicity = strBeamDistanceMosaicity.split()
fBeamX = float(listStringBeamDistanceMosaicity[3])
fBeamY = float(listStringBeamDistanceMosaicity[5])
xsDataLabelitScreenOutput.setBeamCentreX(XSDataLength(fBeamX))
xsDataLabelitScreenOutput.setBeamCentreY(XSDataLength(fBeamY))
fDistance = float(listStringBeamDistanceMosaicity[7])
xsDataLabelitScreenOutput.setDistance(XSDataLength(fDistance))
fMosaicity = float(listStringBeamDistanceMosaicity[11])
xsDataLabelitScreenOutput.setMosaicity(XSDataAngle(fMosaicity))
iIndex += 3
bContinue = True
bFoundSelectedSolution = False
while (bContinue):
xsDataLabelitScreenSolution = XSDataLabelitScreenSolution()
strLabelitSolution = listLogLines[iIndex]
listStringLabelitSolution = strLabelitSolution.split()
if (listStringLabelitSolution[0] == ":)"):
xsDataLabelitScreenSolution.setHappy(XSDataBoolean(True))
elif (listStringLabelitSolution[0] == ":("):
xsDataLabelitScreenSolution.setHappy(XSDataBoolean(False))
elif (listStringLabelitSolution[0] == ";("):
xsDataLabelitScreenSolution.setHappy(XSDataBoolean(False))
else:
# We have an error...
strErrorMessage = "Indexing with labelit.screen failed! Log file:"
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.ERROR(_strLabelitLogText)
self.addErrorMessage(_strLabelitLogText)
self.setFailure()
bContinue = False
if bContinue:
iSolutionNumber = int(listStringLabelitSolution[1])
xsDataLabelitScreenSolution.setSolutionNumber(
XSDataInteger(iSolutionNumber))
fMetricFitValue = float(listStringLabelitSolution[2])
xsDataLabelitScreenSolution.setMetricFitValue(
XSDataDouble(fMetricFitValue))
strMetricFitCode = listStringLabelitSolution[3]
xsDataLabelitScreenSolution.setMetricFitCode(
XSDataString(strMetricFitCode))
fRMSD = float(listStringLabelitSolution[4])
xsDataLabelitScreenSolution.setRmsd(XSDataLength(fRMSD))
iNumberOfSpots = int(listStringLabelitSolution[5])
xsDataLabelitScreenSolution.setNumberOfSpots(
XSDataInteger(iNumberOfSpots))
strCrystalSystem = listStringLabelitSolution[6]
strBravaisLattice = listStringLabelitSolution[7]
xsDataLabelitScreenSolution.setCrystalSystem(
XSDataString(strCrystalSystem))
xsDataLabelitScreenSolution.setBravaisLattice(
XSDataString(strBravaisLattice))
xsDataCell = XSDataCell()
xsDataCell.setLength_a(
XSDataLength(float(listStringLabelitSolution[8])))
xsDataCell.setLength_b(
XSDataLength(float(listStringLabelitSolution[9])))
xsDataCell.setLength_c(
XSDataLength(float(listStringLabelitSolution[10])))
xsDataCell.setAngle_alpha(
XSDataAngle(float(listStringLabelitSolution[11])))
xsDataCell.setAngle_beta(
XSDataAngle(float(listStringLabelitSolution[12])))
xsDataCell.setAngle_gamma(
XSDataAngle(float(listStringLabelitSolution[13])))
xsDataLabelitScreenSolution.setUnitCell(xsDataCell)
iVolume = int(listStringLabelitSolution[14])
xsDataLabelitScreenSolution.setVolume(
XSDataInteger(iVolume))
# Find the selected solution
if (bFoundSelectedSolution == False):
if (xsDataLabelitScreenSolution.getHappy().getValue()
== True):
# Check if forced space group
if self.__strForcedSpaceGroup == None:
bFoundSelectedSolution = True
xsDataLabelitScreenOutput.setSelectedSolutionNumber(
XSDataInteger(iSolutionNumber))
else:
listBravaisLattice = self.getBravaisLatticeFromSpaceGroup(
self.__strForcedSpaceGroup)
for strPossibleBravaisLattice in listBravaisLattice:
if strBravaisLattice == strPossibleBravaisLattice:
bFoundSelectedSolution = True
xsDataLabelitScreenOutput.setSelectedSolutionNumber(
XSDataInteger(iSolutionNumber))
xsDataLabelitScreenOutput.addLabelitScreenSolution(
xsDataLabelitScreenSolution)
if (iIndex < (len(listLogLines) - 2)):
iIndex += 1
else:
bContinue = False
return xsDataLabelitScreenOutput
def parseLabelitScreenOutput(self, _strLabelitLogText):
"""
This method parses the labelit.screen log and populates the relevant
parts of the XSDataLabelitScreenOutput object which is then returned.
"""
self.DEBUG("EDPluginLabelitIndexingv1_1.parseLabelitLogText")
xsDataLabelitScreenOutput = None
iIndex = 0
listLogLines = _strLabelitLogText.split('\n')
bFoundLabelitIndexingResults = False
bContinue = True
while (bContinue) :
if (listLogLines[ iIndex ].find("LABELIT Indexing results:") != -1) :
bFoundLabelitIndexingResults = True
bContinue = False
else:
if (iIndex < (len(listLogLines) - 2)):
iIndex += 1
else:
bContinue = False
if (bFoundLabelitIndexingResults == False):
strErrorMessage = "EDPluginLabelitIndexingv1_1.parseLabelitLogText : Labelit log message: %s" % _strLabelitLogText
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
else:
# We found some indexing results!
xsDataLabelitScreenOutput = XSDataLabelitScreenOutput()
iIndex += 1
strBeamDistanceMosaicity = listLogLines[ iIndex ]
strBeamDistanceMosaicity = strBeamDistanceMosaicity.replace(',', '')
strBeamDistanceMosaicity = strBeamDistanceMosaicity.replace('mm', ' ')
strBeamDistanceMosaicity = strBeamDistanceMosaicity.replace('=', ' ')
listStringBeamDistanceMosaicity = strBeamDistanceMosaicity.split()
fBeamX = float(listStringBeamDistanceMosaicity[3])
fBeamY = float(listStringBeamDistanceMosaicity[5])
xsDataLabelitScreenOutput.setBeamCentreX(XSDataLength(fBeamX))
xsDataLabelitScreenOutput.setBeamCentreY(XSDataLength(fBeamY))
fDistance = float(listStringBeamDistanceMosaicity[7])
xsDataLabelitScreenOutput.setDistance(XSDataLength(fDistance))
fMosaicity = float(listStringBeamDistanceMosaicity[11])
xsDataLabelitScreenOutput.setMosaicity(XSDataAngle(fMosaicity))
iIndex += 3
bContinue = True
bFoundSelectedSolution = False
while (bContinue):
xsDataLabelitScreenSolution = XSDataLabelitScreenSolution()
strLabelitSolution = listLogLines[ iIndex ]
listStringLabelitSolution = strLabelitSolution.split()
if (listStringLabelitSolution[0] == ":)"):
xsDataLabelitScreenSolution.setHappy(XSDataBoolean(True))
elif (listStringLabelitSolution[0] == ":("):
xsDataLabelitScreenSolution.setHappy(XSDataBoolean(False))
elif (listStringLabelitSolution[0] == ";("):
xsDataLabelitScreenSolution.setHappy(XSDataBoolean(False))
else:
# We have an error...
strErrorMessage = "Indexing with labelit.screen failed! Log file:"
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.ERROR(_strLabelitLogText)
self.addErrorMessage(_strLabelitLogText)
self.setFailure()
bContinue = False
if bContinue:
iSolutionNumber = int(listStringLabelitSolution[1])
xsDataLabelitScreenSolution.setSolutionNumber(XSDataInteger(iSolutionNumber))
fMetricFitValue = float(listStringLabelitSolution[2])
xsDataLabelitScreenSolution.setMetricFitValue(XSDataDouble(fMetricFitValue))
strMetricFitCode = listStringLabelitSolution[3]
xsDataLabelitScreenSolution.setMetricFitCode(XSDataString(strMetricFitCode))
fRMSD = float(listStringLabelitSolution[4])
xsDataLabelitScreenSolution.setRmsd(XSDataLength(fRMSD))
iNumberOfSpots = int(listStringLabelitSolution[5])
xsDataLabelitScreenSolution.setNumberOfSpots(XSDataInteger(iNumberOfSpots))
strCrystalSystem = listStringLabelitSolution[6]
strBravaisLattice = listStringLabelitSolution[7]
xsDataLabelitScreenSolution.setCrystalSystem(XSDataString(strCrystalSystem))
xsDataLabelitScreenSolution.setBravaisLattice(XSDataString(strBravaisLattice))
xsDataCell = XSDataCell()
xsDataCell.setLength_a(XSDataLength(float(listStringLabelitSolution[ 8])))
xsDataCell.setLength_b(XSDataLength(float(listStringLabelitSolution[ 9])))
xsDataCell.setLength_c(XSDataLength(float(listStringLabelitSolution[10])))
xsDataCell.setAngle_alpha(XSDataAngle(float(listStringLabelitSolution[11])))
xsDataCell.setAngle_beta(XSDataAngle(float(listStringLabelitSolution[12])))
xsDataCell.setAngle_gamma(XSDataAngle(float(listStringLabelitSolution[13])))
xsDataLabelitScreenSolution.setUnitCell(xsDataCell)
iVolume = int(listStringLabelitSolution[14])
xsDataLabelitScreenSolution.setVolume(XSDataInteger(iVolume))
# Find the selected solution
if (bFoundSelectedSolution == False):
if (xsDataLabelitScreenSolution.getHappy().getValue() == True):
# Check if forced space group
if self.__strForcedSpaceGroup == None or self.__strForcedSpaceGroup == "":
bFoundSelectedSolution = True
xsDataLabelitScreenOutput.setSelectedSolutionNumber(XSDataInteger(iSolutionNumber))
else:
listBravaisLattice = self.getBravaisLatticeFromSpaceGroup(self.__strForcedSpaceGroup)
for strPossibleBravaisLattice in listBravaisLattice:
if strBravaisLattice == strPossibleBravaisLattice:
bFoundSelectedSolution = True
xsDataLabelitScreenOutput.setSelectedSolutionNumber(XSDataInteger(iSolutionNumber))
xsDataLabelitScreenOutput.addLabelitScreenSolution(xsDataLabelitScreenSolution)
if (iIndex < (len(listLogLines) - 2)):
iIndex += 1
else:
bContinue = False
return xsDataLabelitScreenOutput