def generateXSDataISPyBScreening(_xsDataInputControlISPyB,
_strShortComments=None,
_strComments=None):
"""
"""
EDFactoryPluginStatic.loadModule("XSDataISPyBv1_2")
from XSDataISPyBv1_2 import XSDataString
from XSDataISPyBv1_2 import XSDataISPyBScreening
xsDataIntegerDataCollectionId = _xsDataInputControlISPyB.getDataCollectionId(
)
# General information
xsDataISPyBScreening = XSDataISPyBScreening()
xsDataISPyBScreening.setProgramVersion(XSDataString("EDNA MXv1"))
pyStrTimeStamp = time.strftime("%Y-%m-%d %H:%M:%S")
xsDataISPyBScreening.setTimeStamp(XSDataString(pyStrTimeStamp))
if (not _strShortComments is None):
xsDataISPyBScreening.setShortComments(
XSDataString(_strShortComments))
if (not _strComments is None):
xsDataISPyBScreening.setComments(XSDataString(_strComments))
# Use dataCollectionId if provided in the input
if (xsDataIntegerDataCollectionId is not None):
xsDataISPyBScreening.setDataCollectionId(
xsDataIntegerDataCollectionId)
return xsDataISPyBScreening
def generateXSDataISPyBImage(_xsDataInputControlISPyB):
"""
"""
EDFactoryPluginStatic.loadModule("XSDataISPyBv1_2")
from XSDataISPyBv1_2 import XSDataString
from XSDataISPyBv1_2 import XSDataISPyBImage
xsDataResultCharacterisation = _xsDataInputControlISPyB.getCharacterisationResult(
)
xsDataISPyBImage = None
# Find path to first image from data collection information
strPathToFirstImage = None
xsDataCollection = xsDataResultCharacterisation.getDataCollection()
if (xsDataCollection is not None):
lXSDataSubWedge = xsDataCollection.getSubWedge()
if (lXSDataSubWedge is not None):
xsDataSubWedgeFirst = lXSDataSubWedge[0]
lXSDataImage = xsDataSubWedgeFirst.getImage()
if (lXSDataImage is not None):
xsDataImageFirst = lXSDataImage[0]
strPathToFirstImage = xsDataImageFirst.getPath().getValue()
# Add an image path if the dataCollectionId is not present...
if (strPathToFirstImage is not None):
xsDataISPyBImage = XSDataISPyBImage()
strImageBaseName = EDUtilsFile.getBaseName(strPathToFirstImage)
strDirectoryName = EDUtilsPath.getFolderName(
strPathToFirstImage)
xsDataISPyBImage.setFileName(XSDataString(strImageBaseName))
xsDataISPyBImage.setFileLocation(
XSDataString(strDirectoryName))
return xsDataISPyBImage
def generateXSDataISPyBScreeningOutputContainer(_xsDataInputControlISPyB,
_strStatusMessage=None):
"""
"""
EDFactoryPluginStatic.loadModule("XSDataISPyBv1_2")
from XSDataISPyBv1_2 import XSDataISPyBScreeningOutputContainer
from XSDataISPyBv1_2 import XSDataISPyBScreeningOutput
from XSDataISPyBv1_2 import XSDataISPyBScreeningOutputLattice
from XSDataISPyBv1_2 import XSDataISPyBScreeningStrategyContainer
from XSDataISPyBv1_2 import XSDataISPyBScreeningStrategyWedgeContainer
from XSDataISPyBv1_2 import XSDataISPyBScreeningStrategy
from XSDataISPyBv1_2 import XSDataISPyBScreeningStrategyWedge
from XSDataISPyBv1_2 import XSDataISPyBScreeningStrategySubWedge
from XSDataISPyBv1_2 import XSDataDouble
from XSDataISPyBv1_2 import XSDataInteger
from XSDataISPyBv1_2 import XSDataBoolean
from XSDataISPyBv1_2 import XSDataString
import math
xsDataISPyBScreeningOutputContainer = XSDataISPyBScreeningOutputContainer(
)
xsDataISPyBScreeningOutput = XSDataISPyBScreeningOutput()
xsDataISPyBScreeningOutputContainer.setScreeningOutput(
xsDataISPyBScreeningOutput)
xsDataResultCharacterisation = _xsDataInputControlISPyB.getCharacterisationResult(
)
# Determine whether anomalous data:
bAnomalousData = None
xsDataCollection = xsDataResultCharacterisation.getDataCollection()
if (xsDataCollection is not None):
xsDataDiffractionPlan = xsDataCollection.getDiffractionPlan()
if (xsDataDiffractionPlan is not None):
if (xsDataDiffractionPlan.getAnomalousData() is not None):
bAnomalousData = xsDataDiffractionPlan.getAnomalousData(
).getValue()
# Indexing information (populate xsDataISPyBScreeningOutputContainer, xsDataIPSyBScreeningOutput and xsDataISPyBScreeningOutputLattice)
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()
xsDataISPyBScreeningOutput.setBeamShiftX(
XSDataDouble(fBeamPositionShiftX))
xsDataISPyBScreeningOutput.setBeamShiftY(
XSDataDouble(fBeamPositionShiftY))
if xsDataStatisticsIndexing.getSpotDeviationAngular(
) is not None:
fSpotDeviationAngular = xsDataStatisticsIndexing.getSpotDeviationAngular(
).getValue()
xsDataISPyBScreeningOutput.setSpotDeviationTheta(
XSDataDouble(fSpotDeviationAngular))
if xsDataStatisticsIndexing.getSpotDeviationPositional(
) is not None:
fSpotDeviationPositional = xsDataStatisticsIndexing.getSpotDeviationPositional(
).getValue()
xsDataISPyBScreeningOutput.setSpotDeviationR(
XSDataDouble(fSpotDeviationPositional))
if ((xsDataStatisticsIndexing.getSpotsTotal() is not None)
and
(xsDataStatisticsIndexing.getSpotsUsed is not None)):
iSpotsTotal = xsDataStatisticsIndexing.getSpotsTotal(
).getValue()
iSpotsUsed = xsDataStatisticsIndexing.getSpotsUsed(
).getValue()
xsDataISPyBScreeningOutput.setNumSpotsFound(
XSDataInteger(iSpotsTotal))
xsDataISPyBScreeningOutput.setNumSpotsUsed(
XSDataInteger(iSpotsUsed))
xsDataISPyBScreeningOutput.setNumSpotsRejected(
XSDataInteger(iSpotsTotal - iSpotsUsed))
xsDataCrystal = xsDataIndexingSolutionSelected.getCrystal()
xsDataISPyBScreeningOutput.setMosaicityEstimated(
XSDataBoolean(False))
if (xsDataCrystal is not None):
if (xsDataCrystal.getMosaicity() is not None):
fMosaicity = xsDataCrystal.getMosaicity().getValue()
xsDataISPyBScreeningOutput.setMosaicity(
XSDataDouble(fMosaicity))
xsDataISPyBScreeningOutput.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 = XSDataISPyBScreeningOutputLattice(
)
xsDataISPyBScreeningOutputContainer.getScreeningOutputLattice(
).append(xsDataISPyBScreeningOutputLattice)
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):
if _strStatusMessage == None:
xsDataISPyBScreeningOutput.setStatusDescription(
XSDataString("Indexing successful"))
else:
xsDataISPyBScreeningOutput.setStatusDescription(
XSDataString(_strStatusMessage))
xsDataISPyBScreeningOutput.setScreeningSuccess(XSDataBoolean(True))
else:
if _strStatusMessage == None:
xsDataISPyBScreeningOutput.setStatusDescription(
XSDataString("Indexing failed"))
else:
xsDataISPyBScreeningOutput.setStatusDescription(
XSDataString(_strStatusMessage))
xsDataISPyBScreeningOutput.setScreeningSuccess(
XSDataBoolean(False))
# Strategy information (populate xsDataISPyBScreeningStrategyContainer, xsDataISPyBScreeningStrategyWedge, xsDataISPyBScreeningStrategySubWedge)
xsDataResultStrategy = xsDataResultCharacterisation.getStrategyResult()
xsDataISPyBScreeningStrategyContainer = XSDataISPyBScreeningStrategyContainer(
)
xsDataISPyBScreeningStrategy = XSDataISPyBScreeningStrategy()
xsDataISPyBScreeningStrategyContainer.setScreeningStrategy(
xsDataISPyBScreeningStrategy)
xsDataISPyBScreeningOutputContainer.getScreeningStrategyContainer(
).append(xsDataISPyBScreeningStrategyContainer)
fAccumulatedExposureTime = 0.0
if (bAnomalousData is not None):
xsDataISPyBScreeningStrategy.setAnomalous(
XSDataBoolean(bAnomalousData))
else:
xsDataISPyBScreeningStrategy.setAnomalous(XSDataBoolean(False))
xsDataISPyBScreeningStrategy.setProgram(XSDataString("BEST"))
if (xsDataResultStrategy is not None):
lXSDataCollectionPlan = xsDataResultStrategy.getCollectionPlan()
if (lXSDataCollectionPlan is not None):
for xsDataCollectionPlan in lXSDataCollectionPlan:
iCollectionPlanNumber = xsDataCollectionPlan.getCollectionPlanNumber(
).getValue()
#strCollectionPlanComment = None
#if (xsDataCollectionPlan.getComment() is not None):
# strCollectionPlanComment = xsDataCollectionPlan.getComment().getValue()
fCompleteness = None
fMultiplicity = None
fResolution = None
fRankingResolution = None
fTransmission = None
iWedgeNumberOfImages = 0
fWedgeDoseTotal = 0.0
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()
xsDataISPyBScreeningStrategy.setRankingResolution(
XSDataDouble(fRankingResolution))
xsDataISPyBScreeningStrategyWedgeContainer = XSDataISPyBScreeningStrategyWedgeContainer(
)
xsDataISPyBScreeningStrategyWedge = XSDataISPyBScreeningStrategyWedge(
)
xsDataISPyBScreeningStrategyWedgeContainer.setScreeningStrategyWedge(
xsDataISPyBScreeningStrategyWedge)
xsDataISPyBScreeningStrategyContainer.getScreeningStrategyWedgeContainer(
).append(xsDataISPyBScreeningStrategyWedgeContainer)
xsDataISPyBScreeningStrategyWedge.setWedgeNumber(
XSDataInteger(iCollectionPlanNumber))
xsDataISPyBScreeningStrategyWedge.setCompleteness(
XSDataDouble(fCompleteness))
xsDataISPyBScreeningStrategyWedge.setMultiplicity(
XSDataDouble(fMultiplicity))
xsDataISPyBScreeningStrategyWedge.setResolution(
XSDataDouble(fResolution))
xsDataCollectionStrategy = xsDataCollectionPlan.getCollectionStrategy(
)
if (xsDataCollectionStrategy is not None):
lXSDataSubWedge = xsDataCollectionStrategy.getSubWedge(
)
if (lXSDataSubWedge is not None):
for xsDataSubWedge in lXSDataSubWedge:
iSubWedgeNumber = xsDataSubWedge.getSubWedgeNumber(
).getValue()
fPhiStart = xsDataSubWedge.getExperimentalCondition(
).getGoniostat().getRotationAxisStart(
).getValue()
fPhiEnd = xsDataSubWedge.getExperimentalCondition(
).getGoniostat().getRotationAxisEnd().getValue(
)
fRotation = xsDataSubWedge.getExperimentalCondition(
).getGoniostat().getOscillationWidth(
).getValue()
fExposureTime = xsDataSubWedge.getExperimentalCondition(
).getBeam().getExposureTime().getValue()
fAccumulatedExposureTime += fExposureTime
fTransmission = xsDataSubWedge.getExperimentalCondition(
).getBeam().getTransmission().getValue()
if (not xsDataSubWedge.
getExperimentalCondition().getBeam(
).getFlux() is None):
fFlux = xsDataSubWedge.getExperimentalCondition(
).getBeam().getFlux().getValue()
else:
fFlux = None
iNumberOfImages = int(
math.ceil(
(fPhiEnd - fPhiStart) / fRotation))
xsDataISPyBScreeningStrategySubWedge = XSDataISPyBScreeningStrategySubWedge(
)
xsDataISPyBScreeningStrategyWedgeContainer.getScreeningStrategySubWedge(
).append(xsDataISPyBScreeningStrategySubWedge)
xsDataISPyBScreeningStrategySubWedge.setSubWedgeNumber(
XSDataInteger(iSubWedgeNumber))
xsDataISPyBScreeningStrategySubWedge.setAxisStart(
XSDataDouble(fPhiStart))
xsDataISPyBScreeningStrategySubWedge.setAxisEnd(
XSDataDouble(fPhiEnd))
xsDataISPyBScreeningStrategySubWedge.setRotationAxis(
XSDataString("Omega"))
xsDataISPyBScreeningStrategySubWedge.setOscillationRange(
XSDataDouble(fRotation))
xsDataISPyBScreeningStrategySubWedge.setExposureTime(
XSDataDouble(fExposureTime))
xsDataISPyBScreeningStrategySubWedge.setTransmission(
XSDataDouble(fTransmission))
xsDataISPyBScreeningStrategySubWedge.setNumberOfImages(
XSDataInteger(iNumberOfImages))
iWedgeNumberOfImages += iNumberOfImages
if (fFlux is not None):
xsDataISPyBScreeningStrategySubWedge.setDoseTotal(
XSDataDouble(fFlux))
fWedgeDoseTotal += fFlux
if (fCompleteness is not None):
xsDataISPyBScreeningStrategySubWedge.setCompleteness(
XSDataDouble(fCompleteness))
if (fMultiplicity is not None):
xsDataISPyBScreeningStrategySubWedge.setMultiplicity(
XSDataDouble(fMultiplicity))
if (fResolution is not None):
xsDataISPyBScreeningStrategySubWedge.setResolution(
XSDataDouble(fResolution))
xsDataISPyBScreeningStrategyWedge.setNumberOfImages(
XSDataInteger(iWedgeNumberOfImages))
xsDataISPyBScreeningStrategyWedge.setDoseTotal(
XSDataDouble(fWedgeDoseTotal))
xsDataISPyBScreeningStrategy.setExposureTime(
XSDataDouble(fAccumulatedExposureTime))
return xsDataISPyBScreeningOutputContainer