def generateXSDataInputISPyB(_xsDataInputControlISPyB, _strStatusMessage=None):
"""
"""
EDFactoryPluginStatic.loadModule("XSDataISPyBv1_1")
from XSDataISPyBv1_1 import XSDataString
from XSDataISPyBv1_1 import XSDataBoolean
from XSDataISPyBv1_1 import XSDataDouble
from XSDataISPyBv1_1 import XSDataInteger
from XSDataISPyBv1_1 import XSDataInputISPyB
from XSDataISPyBv1_1 import XSDataISPyBScreening
from XSDataISPyBv1_1 import XSDataISPyBScreeningInput
from XSDataISPyBv1_1 import XSDataISPyBScreeningOutput
from XSDataISPyBv1_1 import XSDataISPyBScreeningRank
from XSDataISPyBv1_1 import XSDataISPyBScreeningRankSet
from XSDataISPyBv1_1 import XSDatadbstatus
from XSDataISPyBv1_1 import XSDataISPyBScreeningOutputContainer
from XSDataISPyBv1_1 import XSDataISPyBScreeningOutputLattice
from XSDataISPyBv1_1 import XSDataISPyBScreeningStrategy
from XSDataISPyBv1_1 import XSDataISPyBDataCollection
from XSDataISPyBv1_1 import XSDataISPyBImage
from XSDataISPyBv1_1 import XSDataResultStatus
xsDataInputISPyB = XSDataInputISPyB()
xsDataISPyBScreeningInput = XSDataISPyBScreeningInput()
xsDataIPSyBScreeningOutput = XSDataISPyBScreeningOutput()
xsDataISPyBScreeningOutputContainer = XSDataISPyBScreeningOutputContainer()
xsDataISPyBScreeningOutputLattice = XSDataISPyBScreeningOutputLattice()
xsDataResultCharacterisation = _xsDataInputControlISPyB.getCharacterisationResult()
xsDataIntegerDataCollectionId = _xsDataInputControlISPyB.getDataCollectionId()
# General information
xsDataISPyBScreening = XSDataISPyBScreening()
xsDataISPyBScreening.setProgramVersion(XSDataString("EDNA MXv1"))
pyStrTimeStamp = PyTime.strftime("%Y-%m-%d %H:%M:%S")
xsDataISPyBScreening.setTimeStamp(XSDataString(pyStrTimeStamp))
# Data collection information
bAnomalousData = None
pyStrPathToFirstImage = None
xsDataCollection = xsDataResultCharacterisation.getDataCollection()
if (xsDataCollection is not None):
xsDataSubWedgeList = xsDataCollection.getSubWedge()
if (xsDataSubWedgeList is not None):
xsDataSubWedgeFirst = xsDataSubWedgeList[0]
xsDataExperimentalCondition = xsDataSubWedgeFirst.getExperimentalCondition()
if (xsDataExperimentalCondition is not None):
xsDataDetector = xsDataExperimentalCondition.getDetector()
if (xsDataDetector is not None):
fBeamPositionX = xsDataDetector.getBeamPositionX().getValue()
fBeamPositionY = xsDataDetector.getBeamPositionY().getValue()
xsDataISPyBScreeningInput.setBeamX(XSDataDouble(fBeamPositionX))
xsDataISPyBScreeningInput.setBeamY(XSDataDouble(fBeamPositionY))
pyListXSDataImage = xsDataSubWedgeFirst.getImage()
if (pyListXSDataImage is not None):
xsDataImageFirst = pyListXSDataImage[ 0 ]
pyStrPathToFirstImage = xsDataImageFirst.getPath().getValue()
xsDataDiffractionPlan = xsDataCollection.getDiffractionPlan()
if (xsDataDiffractionPlan is not None):
if (xsDataDiffractionPlan.getAnomalousData() is not None):
bAnomalousData = xsDataDiffractionPlan.getAnomalousData().getValue()
# Use dataCollectionId if provided in the input
if (xsDataIntegerDataCollectionId is not None):
xsDataISPyBScreening.setDataCollectionId(xsDataIntegerDataCollectionId)
else:
# Add an image path if the dataCollectionId is not present...
if (pyStrPathToFirstImage is not None):
xsDataISPyBImage = XSDataISPyBImage()
pyStrImageBaseName = EDUtilsFile.getBaseName(pyStrPathToFirstImage)
pyStrDirectoryName = EDUtilsPath.getFolderName(pyStrPathToFirstImage)
xsDataISPyBImage.setFileName(XSDataString(pyStrImageBaseName))
xsDataISPyBImage.setFileLocation(XSDataString(pyStrDirectoryName))
xsDataInputISPyB.setImage(xsDataISPyBImage)
# Indexing information
bSuccessfulIndexing = False
xsDataIndexingResult = xsDataResultCharacterisation.getIndexingResult()
if (xsDataIndexingResult is not None):
xsDataIndexingSolutionSelected = xsDataIndexingResult.getSelectedSolution()
if (xsDataIndexingSolutionSelected is not None):
bSuccessfulIndexing = True
xsDataStatisticsIndexing = xsDataIndexingSolutionSelected.getStatistics()
if (xsDataStatisticsIndexing is not None):
fBeamPositionShiftX = xsDataStatisticsIndexing.getBeamPositionShiftX().getValue()
fBeamPositionShiftY = xsDataStatisticsIndexing.getBeamPositionShiftY().getValue()
xsDataIPSyBScreeningOutput.setBeamShiftX(XSDataDouble(fBeamPositionShiftX))
xsDataIPSyBScreeningOutput.setBeamShiftY(XSDataDouble(fBeamPositionShiftY))
fSpotDeviationAngular = None
if xsDataStatisticsIndexing.getSpotDeviationAngular() is not None:
fSpotDeviationAngular = xsDataStatisticsIndexing.getSpotDeviationAngular().getValue()
fSpotDeviationPositional = xsDataStatisticsIndexing.getSpotDeviationPositional().getValue()
xsDataIPSyBScreeningOutput.setSpotDeviationR(XSDataDouble(fSpotDeviationPositional))
if fSpotDeviationAngular is not None:
xsDataIPSyBScreeningOutput.setSpotDeviationTheta(XSDataDouble(fSpotDeviationAngular))
if ((xsDataStatisticsIndexing.getSpotsTotal() is not None) and (xsDataStatisticsIndexing.getSpotsUsed is not None)):
iSpotsTotal = xsDataStatisticsIndexing.getSpotsTotal().getValue()
iSpotsUsed = xsDataStatisticsIndexing.getSpotsUsed().getValue()
xsDataIPSyBScreeningOutput.setNumSpotsFound(XSDataInteger(iSpotsTotal))
xsDataIPSyBScreeningOutput.setNumSpotsUsed(XSDataInteger(iSpotsUsed))
xsDataIPSyBScreeningOutput.setNumSpotsRejected(XSDataInteger(iSpotsTotal - iSpotsUsed))
xsDataCrystal = xsDataIndexingSolutionSelected.getCrystal()
xsDataIPSyBScreeningOutput.setMosaicityEstimated(XSDataBoolean(False))
if (xsDataCrystal is not None):
if (xsDataCrystal.getMosaicity() is not None):
fMosaicity = xsDataCrystal.getMosaicity().getValue()
xsDataIPSyBScreeningOutput.setMosaicity(XSDataDouble(fMosaicity))
xsDataIPSyBScreeningOutput.setMosaicityEstimated(XSDataBoolean(True))
xsDataCell = xsDataCrystal.getCell()
if (xsDataCell is not None):
fLength_a = xsDataCell.getLength_a().getValue()
fLength_b = xsDataCell.getLength_b().getValue()
fLength_c = xsDataCell.getLength_c().getValue()
fAngle_alpha = xsDataCell.getAngle_alpha().getValue()
fAngle_beta = xsDataCell.getAngle_beta().getValue()
fAngle_gamma = xsDataCell.getAngle_gamma().getValue()
xsDataISPyBScreeningOutputLattice.setUnitCell_a(XSDataDouble(fLength_a))
xsDataISPyBScreeningOutputLattice.setUnitCell_b(XSDataDouble(fLength_b))
xsDataISPyBScreeningOutputLattice.setUnitCell_c(XSDataDouble(fLength_c))
xsDataISPyBScreeningOutputLattice.setUnitCell_alpha(XSDataDouble(fAngle_alpha))
xsDataISPyBScreeningOutputLattice.setUnitCell_beta(XSDataDouble(fAngle_beta))
xsDataISPyBScreeningOutputLattice.setUnitCell_gamma(XSDataDouble(fAngle_gamma))
xsDataSpaceGroup = xsDataCrystal.getSpaceGroup()
if (xsDataSpaceGroup is not None):
pyStrSpaceGroupName = xsDataSpaceGroup.getName().getValue()
xsDataISPyBScreeningOutputLattice.setSpaceGroup(XSDataString(pyStrSpaceGroupName))
if (bSuccessfulIndexing):
xsDataIPSyBScreeningOutput.setScreeningSuccess(XSDataBoolean(True))
if _strStatusMessage:
xsDataIPSyBScreeningOutput.setStatusDescription(XSDataString(_strStatusMessage))
else:
xsDataIPSyBScreeningOutput.setStatusDescription(XSDataString("Indexing successful"))
else:
xsDataIPSyBScreeningOutput.setScreeningSuccess(XSDataBoolean(False))
if _strStatusMessage:
xsDataIPSyBScreeningOutput.setStatusDescription(XSDataString(_strStatusMessage))
else:
xsDataIPSyBScreeningOutput.setStatusDescription(XSDataString("Indexing failed"))
# Strategy information
xsDataResultStrategy = xsDataResultCharacterisation.getStrategyResult()
if (xsDataResultStrategy is not None):
pyListXSDataCollectionPlan = xsDataResultStrategy.getCollectionPlan()
if (pyListXSDataCollectionPlan is not None):
for xsDataCollectionPlan in pyListXSDataCollectionPlan:
iCollectionPlanNumber = xsDataCollectionPlan.getCollectionPlanNumber().getValue()
pyStrCollectionPlanComment = None
if (xsDataCollectionPlan.getComment() is not None):
pyStrCollectionPlanComment = xsDataCollectionPlan.getComment().getValue()
fCompleteness = None
fMultiplicity = None
fResolution = None
fRankingResolution = None
fTransmission = None
xsDataStrategySummary = xsDataCollectionPlan.getStrategySummary()
if (xsDataStrategySummary is not None):
if (xsDataStrategySummary.getCompleteness() is not None):
fCompleteness = xsDataStrategySummary.getCompleteness().getValue()
if (xsDataStrategySummary.getRedundancy() is not None):
fMultiplicity = xsDataStrategySummary.getRedundancy().getValue()
if (xsDataStrategySummary.getResolution() is not None):
fResolution = xsDataStrategySummary.getResolution().getValue()
if (xsDataStrategySummary.getRankingResolution() is not None):
fRankingResolution = xsDataStrategySummary.getRankingResolution().getValue()
xsDataCollectionStrategy = xsDataCollectionPlan.getCollectionStrategy()
if (xsDataCollectionStrategy is not None):
pyListXSDataSubWedge = xsDataCollectionStrategy.getSubWedge()
if (pyListXSDataSubWedge is not None):
for xsDataSubWedge in pyListXSDataSubWedge:
iSubWedgeNumber = xsDataSubWedge.getSubWedgeNumber().getValue()
xsDataISPyBScreeningStrategy = XSDataISPyBScreeningStrategy()
fPhiStart = xsDataSubWedge.getExperimentalCondition().getGoniostat().getRotationAxisStart().getValue()
fPhiEnd = xsDataSubWedge.getExperimentalCondition().getGoniostat().getRotationAxisEnd().getValue()
fRotation = xsDataSubWedge.getExperimentalCondition().getGoniostat().getOscillationWidth().getValue()
fExposureTime = xsDataSubWedge.getExperimentalCondition().getBeam().getExposureTime().getValue()
fTransmission = xsDataSubWedge.getExperimentalCondition().getBeam().getTransmission().getValue()
pyStrProgram = "BEST: Wedge no %d," % iCollectionPlanNumber
if (pyStrCollectionPlanComment is not None):
pyStrProgram += " ( %s )" % pyStrCollectionPlanComment
pyStrProgram += " sub wedge no %d" % iSubWedgeNumber
xsDataISPyBScreeningStrategy.setPhiStart(XSDataDouble(fPhiStart))
xsDataISPyBScreeningStrategy.setPhiEnd(XSDataDouble(fPhiEnd))
xsDataISPyBScreeningStrategy.setRotation(XSDataDouble(fRotation))
xsDataISPyBScreeningStrategy.setExposureTime(XSDataDouble(fExposureTime))
xsDataISPyBScreeningStrategy.setTransmission(XSDataDouble(fTransmission))
if (fCompleteness is not None):
xsDataISPyBScreeningStrategy.setCompleteness(XSDataDouble(fCompleteness))
if (fMultiplicity is not None):
xsDataISPyBScreeningStrategy.setMultiplicity(XSDataDouble(fMultiplicity))
if (fResolution is not None):
xsDataISPyBScreeningStrategy.setResolution(XSDataDouble(fResolution))
if (fRankingResolution is not None):
xsDataISPyBScreeningStrategy.setRankingResolution(XSDataDouble(fRankingResolution))
if (bAnomalousData is not None):
xsDataISPyBScreeningStrategy.setAnomalous(XSDataBoolean(bAnomalousData))
else:
xsDataISPyBScreeningStrategy.setAnomalous(XSDataBoolean(False))
xsDataISPyBScreeningStrategy.setProgram(XSDataString(pyStrProgram))
xsDataISPyBScreeningOutputContainer.addScreeningStrategy(xsDataISPyBScreeningStrategy)
xsDataInputISPyB.setScreening(xsDataISPyBScreening)
xsDataInputISPyB.addScreeningInput(xsDataISPyBScreeningInput)
xsDataISPyBScreeningOutputContainer.setScreeningOutput(xsDataIPSyBScreeningOutput)
xsDataISPyBScreeningOutputContainer.addScreeningOutputLattice(xsDataISPyBScreeningOutputLattice)
xsDataInputISPyB.addScreeningOutputContainer(xsDataISPyBScreeningOutputContainer)
return xsDataInputISPyB
def testSetDataModelInput(self):
"""
A test for whether we can obtain the expected XML by setting a certain input for the plugin.
"""
edPluginISPyB = self.createPlugin()
xsPluginItemISPyB = self.getPluginConfiguration(
os.path.join(self.getPluginTestsDataHome(), "XSConfiguration.xml"))
edPluginISPyB.setConfiguration(xsPluginItemISPyB)
edPluginISPyB.configure()
xsDataInputISPyB = XSDataInputISPyB()
xsDataISPyBImage = XSDataISPyBImage()
xsDataISPyBImage.setFileName(XSDataString("test.img"))
xsDataISPyBImage.setFileLocation(XSDataString("/tmp"))
xsDataISPyBScreening = XSDataISPyBScreening()
# xsDataISPyBScreening.setDataCollectionId( XSDataInteger ( 1 ) )
xsDataISPyBScreening.setProgramVersion(XSDataString("EDNA Prototype"))
xsDataISPyBScreeningInput = XSDataISPyBScreeningInput()
xsDataISPyBScreeningInput.setBeamX(XSDataDouble(10.4))
xsDataISPyBScreeningInput.setBeamY(XSDataDouble(2.31))
xsDataISPyBScreeningInput.setRmsErrorLimits(XSDataDouble(0.8))
xsDataISPyBScreeningInput.setMinimumFractionIndexed(XSDataDouble(0.4))
xsDataISPyBScreeningInput.setMaximumFractionRejected(
XSDataDouble(0.45))
xsDataISPyBScreeningInput.setMinimumSignalToNoise(XSDataDouble(0.56))
xsDataISPyBScreeningOutput = XSDataISPyBScreeningOutput()
xsDataISPyBScreeningOutput.setStatusDescription(
XSDataString("It's just fine."))
xsDataISPyBScreeningOutput.setMosaicity(XSDataDouble(0.25))
xsDataISPyBScreeningOutput.setBeamShiftX(XSDataDouble(0.141))
xsDataISPyBScreeningOutput.setBeamShiftY(XSDataDouble(0.156))
xsDataISPyBScreeningOutputLattice = XSDataISPyBScreeningOutputLattice()
xsDataISPyBScreeningOutputLattice.setSpaceGroup(XSDataString("P222"))
xsDataISPyBScreeningStrategy = XSDataISPyBScreeningStrategy()
xsDataISPyBScreeningStrategy.setPhiStart(XSDataDouble(0))
xsDataISPyBScreeningStrategy.setPhiEnd(XSDataDouble(20))
xsDataISPyBScreeningStrategy.setRotation(XSDataDouble(1))
xsDataISPyBScreeningStrategy.setProgram(XSDataString("EDNA"))
xsDataISPyBScreeningStrategy.setAnomalous(XSDataBoolean(1))
xsDataISPyBScreeningOutputContainer = XSDataISPyBScreeningOutputContainer(
)
xsDataISPyBScreeningOutputContainer.setScreeningOutput(
xsDataISPyBScreeningOutput)
xsDataISPyBScreeningOutputContainer.getScreeningOutputLattice().append(
xsDataISPyBScreeningOutputLattice)
xsDataISPyBScreeningOutputContainer.getScreeningStrategy().append(
xsDataISPyBScreeningStrategy)
xsDataISPyBScreeningRank = XSDataISPyBScreeningRank()
xsDataISPyBScreeningRank.setRankValue(XSDataDouble(1.4))
xsDataISPyBScreeningRank.setRankInformation(
XSDataString("This is the only one"))
xsDataISPyBScreeningRankSet = XSDataISPyBScreeningRankSet()
xsDataISPyBScreeningRankSet.setRankEngine(XSDataString("ISPyB"))
xsDataInputISPyB.setImage(xsDataISPyBImage)
xsDataInputISPyB.setScreening(xsDataISPyBScreening)
xsDataInputISPyB.getScreeningInput().append(xsDataISPyBScreeningInput)
xsDataInputISPyB.getScreeningOutputContainer().append(
xsDataISPyBScreeningOutputContainer)
xsDataInputISPyB.getScreeningRank().append(xsDataISPyBScreeningRank)
xsDataInputISPyB.setScreeningRankSet(xsDataISPyBScreeningRankSet)
xsDataInputISPyB.outputFile(self.m_edObtainedInputFile)
pyStrExpectedInput = self.readAndParseFile(self.m_edReferenceInputFile)
xsDataScreeningExpected = XSDataInputISPyB.parseString(
pyStrExpectedInput)
pyStrExpectedXML = xsDataScreeningExpected.marshal()
pyStrObtainedInput = self.readAndParseFile(self.m_edObtainedInputFile)
xsDataScreeningObtained = XSDataInputISPyB.parseString(
pyStrObtainedInput)
pyStrObtainedXML = xsDataScreeningObtained.marshal()
EDAssert.equal(pyStrExpectedXML, pyStrObtainedXML)
self.cleanUp(edPluginISPyB)
def testSetDataModelInput(self):
"""
A test for whether we can obtain the expected XML by setting a certain input for the plugin.
"""
edPluginISPyB = self.createPlugin()
xsPluginItemISPyB = self.getPluginConfiguration(os.path.join(self.getPluginTestsDataHome(), "XSConfiguration.xml"))
edPluginISPyB.setConfiguration(xsPluginItemISPyB)
edPluginISPyB.configure()
xsDataInputISPyB = XSDataInputISPyB()
xsDataISPyBImage = XSDataISPyBImage()
xsDataISPyBImage.setFileName(XSDataString("test.img"))
xsDataISPyBImage.setFileLocation(XSDataString("/tmp"))
xsDataISPyBScreening = XSDataISPyBScreening()
# xsDataISPyBScreening.setDataCollectionId( XSDataInteger ( 1 ) )
xsDataISPyBScreening.setProgramVersion(XSDataString("EDNA Prototype"))
xsDataISPyBScreeningInput = XSDataISPyBScreeningInput()
xsDataISPyBScreeningInput.setBeamX(XSDataDouble(10.4))
xsDataISPyBScreeningInput.setBeamY(XSDataDouble(2.31))
xsDataISPyBScreeningInput.setRmsErrorLimits(XSDataDouble(0.8))
xsDataISPyBScreeningInput.setMinimumFractionIndexed(XSDataDouble(0.4))
xsDataISPyBScreeningInput.setMaximumFractionRejected(XSDataDouble(0.45))
xsDataISPyBScreeningInput.setMinimumSignalToNoise(XSDataDouble(0.56))
xsDataISPyBScreeningOutput = XSDataISPyBScreeningOutput()
xsDataISPyBScreeningOutput.setStatusDescription(XSDataString("It's just fine."))
xsDataISPyBScreeningOutput.setMosaicity(XSDataDouble(0.25))
xsDataISPyBScreeningOutput.setBeamShiftX(XSDataDouble (0.141))
xsDataISPyBScreeningOutput.setBeamShiftY(XSDataDouble (0.156))
xsDataISPyBScreeningOutputLattice = XSDataISPyBScreeningOutputLattice()
xsDataISPyBScreeningOutputLattice.setSpaceGroup(XSDataString("P222"))
xsDataISPyBScreeningStrategy = XSDataISPyBScreeningStrategy()
xsDataISPyBScreeningStrategy.setPhiStart(XSDataDouble(0))
xsDataISPyBScreeningStrategy.setPhiEnd(XSDataDouble(20))
xsDataISPyBScreeningStrategy.setRotation(XSDataDouble(1))
xsDataISPyBScreeningStrategy.setProgram(XSDataString("EDNA"))
xsDataISPyBScreeningStrategy.setAnomalous(XSDataBoolean(1))
xsDataISPyBScreeningOutputContainer = XSDataISPyBScreeningOutputContainer()
xsDataISPyBScreeningOutputContainer.setScreeningOutput(xsDataISPyBScreeningOutput)
xsDataISPyBScreeningOutputContainer.getScreeningOutputLattice().append(xsDataISPyBScreeningOutputLattice)
xsDataISPyBScreeningOutputContainer.getScreeningStrategy().append(xsDataISPyBScreeningStrategy)
xsDataISPyBScreeningRank = XSDataISPyBScreeningRank()
xsDataISPyBScreeningRank.setRankValue(XSDataDouble(1.4))
xsDataISPyBScreeningRank.setRankInformation(XSDataString("This is the only one"))
xsDataISPyBScreeningRankSet = XSDataISPyBScreeningRankSet()
xsDataISPyBScreeningRankSet.setRankEngine(XSDataString("ISPyB"))
xsDataInputISPyB.setImage(xsDataISPyBImage)
xsDataInputISPyB.setScreening(xsDataISPyBScreening)
xsDataInputISPyB.getScreeningInput().append(xsDataISPyBScreeningInput)
xsDataInputISPyB.getScreeningOutputContainer().append(xsDataISPyBScreeningOutputContainer)
xsDataInputISPyB.getScreeningRank().append(xsDataISPyBScreeningRank)
xsDataInputISPyB.setScreeningRankSet(xsDataISPyBScreeningRankSet)
xsDataInputISPyB.outputFile(self.m_edObtainedInputFile)
pyStrExpectedInput = self.readAndParseFile (self.m_edReferenceInputFile)
xsDataScreeningExpected = XSDataInputISPyB.parseString(pyStrExpectedInput)
pyStrExpectedXML = xsDataScreeningExpected.marshal()
pyStrObtainedInput = self.readAndParseFile (self.m_edObtainedInputFile)
xsDataScreeningObtained = XSDataInputISPyB.parseString(pyStrObtainedInput)
pyStrObtainedXML = xsDataScreeningObtained.marshal()
EDAssert.equal(pyStrExpectedXML, pyStrObtainedXML)
self.cleanUp(edPluginISPyB)