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 generateXSDataISPyBImage(_xsDataInputControlISPyB):
"""
"""
EDFactoryPluginStatic.loadModule("XSDataISPyBv1_2")
from XSDataISPyBv1_2 import XSDataString
from XSDataISPyBv1_2 import XSDataISPyBImage
xsDataResultCharacterisationv2_0 = _xsDataInputControlISPyB.getCharacterisationResult()
xsDataResultCharacterisation = xsDataResultCharacterisationv2_0.getMxv1ResultCharacterisation()
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 configure(self):
EDPluginExecProcessScript.configure(self)
self.DEBUG("EDPluginBestv1_3.configure")
self.setRequireCCP4(True)
strScriptExecutable = self.getScriptExecutable()
self.DEBUG("EDPluginBestv1_3.configure: Script Executable: " + strScriptExecutable)
strBestScriptHome = EDUtilsPath.getFolderName(strScriptExecutable)
strBestHome = self.config.get(self.strCONF_BEST_HOME_LABEL, strBestScriptHome)
self.setBestHome(strBestHome)
self.DEBUG("EDPluginBestv1_3.configure: Best Home: " + strBestHome)
self.setCommandBestHome("export besthome=" + self.getBestHome())
strVersion = self.config.get(self.CONF_EXEC_PROCESS_SCRIPT_VERSION_STRING, "Unknown")
def configure(self):
EDPluginExecProcessScript.configure(self)
self.DEBUG("EDPluginBestv1_3.configure")
self.setRequireCCP4(True)
strScriptExecutable = self.getScriptExecutable()
self.DEBUG("EDPluginBestv1_3.configure: Script Executable: " +
strScriptExecutable)
strBestScriptHome = EDUtilsPath.getFolderName(strScriptExecutable)
strBestHome = self.config.get(self.strCONF_BEST_HOME_LABEL,
strBestScriptHome)
self.setBestHome(strBestHome)
self.DEBUG("EDPluginBestv1_3.configure: Best Home: " + strBestHome)
self.setCommandBestHome("export besthome=" + self.getBestHome())
strVersion = self.config.get(
self.CONF_EXEC_PROCESS_SCRIPT_VERSION_STRING, "Unknown")
def configure(self):
EDPluginExecProcessScript.configure(self)
self.DEBUG("EDPluginBestv1_2.configure")
self.setRequireCCP4(True)
strScriptExecutable = self.getScriptExecutable()
self.DEBUG("EDPluginBestv1_2.configure: Script Executable: " + strScriptExecutable)
strBestScriptHome = EDUtilsPath.getFolderName(strScriptExecutable)
strBestHome = self.config.get(self.strCONF_BEST_HOME_LABEL, strBestScriptHome)
self.setBestHome(strBestHome)
self.DEBUG("EDPluginBestv1_2.configure: Best Home: " + strBestHome)
self.setCommandBestHome("export besthome=" + self.getBestHome())
strVersion = self.config.get(self.CONF_EXEC_PROCESS_SCRIPT_VERSION_STRING, "Unknown")
# Check if version is higher than 4.1:
try:
if float(strVersion[8:11]) > 4.0:
self.bVersionHigherThan4_0 = True
except Exception, e:
pass
def configure(self):
EDPluginExecProcessScript.configure(self)
self.DEBUG("EDPluginBestv1_2.configure")
self.setRequireCCP4(True)
strScriptExecutable = self.getScriptExecutable()
self.DEBUG("EDPluginBestv1_2.configure: Script Executable: " +
strScriptExecutable)
strBestScriptHome = EDUtilsPath.getFolderName(strScriptExecutable)
strBestHome = self.config.get(self.strCONF_BEST_HOME_LABEL,
strBestScriptHome)
self.setBestHome(strBestHome)
self.DEBUG("EDPluginBestv1_2.configure: Best Home: " + strBestHome)
self.setCommandBestHome("export besthome=" + self.getBestHome())
strVersion = self.config.get(
self.CONF_EXEC_PROCESS_SCRIPT_VERSION_STRING, "Unknown")
# Check if version is higher than 4.1:
try:
if float(strVersion[8:11]) > 4.0:
self.bVersionHigherThan4_0 = True
except Exception, e:
pass
def configure(self):
EDPluginExecProcessScript.configure(self)
EDVerbose.DEBUG("EDPluginBestv1_2.configure")
self.setRequireCCP4(True)
strScriptExecutable = self.getScriptExecutable()
EDVerbose.DEBUG("EDPluginBestv1_2.configure: Script Executable: " + strScriptExecutable)
strBestScriptHome = EDUtilsPath.getFolderName(strScriptExecutable)
strBestHome = None
pluginConfiguration = self.getConfiguration()
if(pluginConfiguration == None):
strBestHome = strBestScriptHome
else:
strBestHome = EDConfiguration.getStringParamValue(pluginConfiguration, self.__strCONF_BEST_HOME_LABEL)
if(strBestHome == None):
strBestHome = strBestScriptHome
self.setBestHome(strBestHome)
EDVerbose.DEBUG("EDPluginBestv1_2.configure: Best Home: " + strBestHome)
self.setCommandBestHome("export besthome=" + self.getBestHome())
def configure(self):
EDPluginExecProcessScript.configure(self)
self.DEBUG("EDPluginBestv1_2.configure")
self.setRequireCCP4(True)
strScriptExecutable = self.getScriptExecutable()
self.DEBUG("EDPluginBestv1_2.configure: Script Executable: " +
strScriptExecutable)
strBestScriptHome = EDUtilsPath.getFolderName(strScriptExecutable)
strBestHome = None
pluginConfiguration = self.getConfiguration()
if (pluginConfiguration == None):
strBestHome = strBestScriptHome
else:
strBestHome = EDConfiguration.getStringParamValue(
pluginConfiguration, self.__strCONF_BEST_HOME_LABEL)
if (strBestHome == None):
strBestHome = strBestScriptHome
self.setBestHome(strBestHome)
self.DEBUG("EDPluginBestv1_2.configure: Best Home: " + strBestHome)
self.setCommandBestHome("export besthome=" + self.getBestHome())
def generateXSDataInputXDS(_xsDataCollection):
xsDataCollection = _xsDataCollection
xsDataExperimentalCondition = _xsDataCollection.getSubWedge()[0].getExperimentalCondition()
xsDataSubWedgeList = xsDataCollection.getSubWedge()
xsDataInputXDS = XSDataInputXDSGenerateBackgroundImage()
xsDataBeam = xsDataExperimentalCondition.getBeam()
xsDataDetector = xsDataExperimentalCondition.getDetector()
xsDataGoniostat = xsDataExperimentalCondition.getGoniostat()
dWavelength = xsDataBeam.getWavelength().getValue()
dDistance = xsDataDetector.getDistance().getValue()
dBeamPositionX = xsDataDetector.getBeamPositionX().getValue()
dBeamPositionY = xsDataDetector.getBeamPositionY().getValue()
# Start with the detector
xsDataXDSDetector = EDHandlerXSDataXDSv1_0.getXSDataXDSDetector(xsDataDetector)
xsDataInputXDS.setDetector(xsDataXDSDetector)
# Then the beam
xsDataXDSBeam = XSDataXDSBeam()
xsDataVectorDoubleIncidentBeam = XSDataVectorDouble()
xsDataVectorDoubleIncidentBeam.setV1(0.0)
xsDataVectorDoubleIncidentBeam.setV2(0.0)
xsDataVectorDoubleIncidentBeam.setV3(1.0)
xsDataXDSBeam.setIncident_beam_direction(xsDataVectorDoubleIncidentBeam)
xsDataVectorDoublePolarizationPlaneNormal = XSDataVectorDouble()
xsDataVectorDoublePolarizationPlaneNormal.setV1(0.0)
xsDataVectorDoublePolarizationPlaneNormal.setV2(1.0)
xsDataVectorDoublePolarizationPlaneNormal.setV3(0.0)
xsDataXDSBeam.setPolarization_plane_normal(xsDataVectorDoublePolarizationPlaneNormal)
xsDataXDSBeam.setX_ray_wavelength(XSDataWavelength(dWavelength))
xsDataInputXDS.setBeam(xsDataXDSBeam)
# Then the goniostat
xsDataXDSGoniostat = XSDataXDSGoniostat()
xsDataVectorDoubleRotationAxis = XSDataVectorDouble()
xsDataVectorDoubleRotationAxis.setV1(1.0)
xsDataVectorDoubleRotationAxis.setV2(0.0)
xsDataVectorDoubleRotationAxis.setV3(0.0)
xsDataXDSGoniostat.setRotation_axis(xsDataVectorDoubleRotationAxis)
xsDataXDSGoniostat.setOscillation_range(xsDataGoniostat.getOscillationWidth())
xsDataXDSGoniostat.setStarting_angle(xsDataGoniostat.getRotationAxisStart())
xsDataInputXDS.setGoniostat(xsDataXDSGoniostat)
# # Then the Crystal
#
# xsDataXDSCrystal = XSDataXDSCrystal()
#
# xsDataXDSCrystal.setFriedels_law(XSDataString("FALSE"))
#
# # if ( xsDataCrystal is not None ):
# # xsDataSpaceGroup = xsDataCrystal.getSpaceGroup()
# # if ( xsDataSpaceGroup is not None ):
# # xsDataStringName = xsDataSpaceGroup.getName()
# # if ( xsDataStringName is not None ):
# # xsDataInputXDS.setSymmetry( XSDataString( xsDataStringName.getValue() ) )
# xsDataXDSCrystal.setSpace_group_number(XSDataInteger(0))
#
# xsDataXDSCrystal.setStrong_pixel(XSDataInteger(8))
#
# xsDataCell = XSDataCell()
# xsDataCell.setLength_a(XSDataLength(0.0))
# xsDataCell.setLength_b(XSDataLength(0.0))
# xsDataCell.setLength_c(XSDataLength(0.0))
# xsDataCell.setAngle_alpha(XSDataAngle(0.0))
# xsDataCell.setAngle_beta(XSDataAngle(0.0))
# xsDataCell.setAngle_gamma(XSDataAngle(0.0))
# xsDataXDSCrystal.setUnit_cell_constants(xsDataCell)
#
# xsDataInputXDS.setCrystal(xsDataXDSCrystal)
# Finaly the images
xsDataXDSImage = XSDataXDSImage()
xsDataSubWedgeFirst = xsDataSubWedgeList[0]
xsDataImageFirst = xsDataSubWedgeFirst.getImage()[0]
pyStrPath = xsDataImageFirst.getPath().getValue()
pyStrFileName = EDUtilsFile.getBaseName(pyStrPath)
pyStrDirectory = EDUtilsPath.getFolderName(pyStrPath)
pyStrPrefix = EDUtilsImage.getPrefix(pyStrFileName)
pyStrSuffix = EDUtilsImage.getSuffix(pyStrFileName)
pyStrXDSTemplate = "%s_xdslink_?????.%s" % (pyStrPrefix, pyStrSuffix)
xsDataXDSImage.setName_template_of_data_frames(XSDataString(pyStrXDSTemplate))
iXDSLowestImageNumberGlobal = 1
xsDataXDSImage.setStarting_frame(XSDataInteger(iXDSLowestImageNumberGlobal))
# First we have to find the smallest goniostat rotation axis start:
fGonioStatOscillationStartMin = None
for xsDataSubWedge in xsDataSubWedgeList:
xsDataGoniostat = xsDataSubWedge.getExperimentalCondition().getGoniostat()
fGonioStatOscillationStart = xsDataGoniostat.getRotationAxisStart().getValue()
if (fGonioStatOscillationStartMin is None):
fGonioStatOscillationStartMin = fGonioStatOscillationStart
elif (fGonioStatOscillationStartMin > fGonioStatOscillationStart):
fGonioStatOscillationStartMin = fGonioStatOscillationStart
# Loop through the list of sub wedges
for xsDataSubWedge in xsDataSubWedgeList:
xsDataImageList = xsDataSubWedge.getImage()
xsDataGoniostat = xsDataSubWedge.getExperimentalCondition().getGoniostat()
fGonioStatOscillationStart = xsDataGoniostat.getRotationAxisStart().getValue()
fGonioStatOscillationRange = xsDataGoniostat.getOscillationWidth().getValue()
# First find the lowest and highest image numbers
iLowestImageNumber = None
for xsDataImage in xsDataImageList:
iImageNumber = xsDataImage.getNumber().getValue()
if (iLowestImageNumber is None):
iLowestImageNumber = iImageNumber
elif (iImageNumber < iLowestImageNumber):
iLowestImageNumber = iImageNumber
# Loop through the list of images
iLowestXDSImageNumber = None
iHighestXDSImageNumber = None
for xsDataImage in xsDataImageList:
iImageNumber = xsDataImage.getNumber().getValue()
fImageOscillationStart = fGonioStatOscillationStart + (iImageNumber - iLowestImageNumber) * fGonioStatOscillationRange
iXDSImageNumber = iXDSLowestImageNumberGlobal + int((fImageOscillationStart - fGonioStatOscillationStartMin) / fGonioStatOscillationRange)
# print iXDSImageNumber, fImageOscillationStart, fGonioStatOscillationStartMin, fGonioStatOscillationRange
pyStrSourcePath = xsDataImage.getPath()
pyStrTarget = "%s_xdslink_%05d.%s" % (pyStrPrefix, iXDSImageNumber, pyStrSuffix)
xsDataXDSImageLink = XSDataXDSImageLink()
xsDataFileSource = XSDataFile()
xsDataFileSource.setPath(pyStrSourcePath)
xsDataXDSImageLink.setSource(xsDataFileSource)
xsDataXDSImageLink.setTarget(XSDataString(pyStrTarget))
xsDataInputXDS.addImage_link(xsDataXDSImageLink)
if (iLowestXDSImageNumber is None):
iLowestXDSImageNumber = iXDSImageNumber
elif (iLowestXDSImageNumber > iXDSImageNumber):
iLowestXDSImageNumber = iXDSImageNumber
if (iHighestXDSImageNumber is None):
iHighestXDSImageNumber = iXDSImageNumber
elif (iHighestXDSImageNumber < iXDSImageNumber):
iHighestXDSImageNumber = iXDSImageNumber
xsDataXDSIntegerRange = XSDataXDSIntegerRange()
xsDataXDSIntegerRange.setLower(XSDataInteger(iLowestXDSImageNumber))
xsDataXDSIntegerRange.setUpper(XSDataInteger(iHighestXDSImageNumber))
xsDataXDSImage.addBackground_range(xsDataXDSIntegerRange)
xsDataXDSImage.addData_range(xsDataXDSIntegerRange)
xsDataXDSImage.addSpot_range(xsDataXDSIntegerRange)
xsDataInputXDS.setImage(xsDataXDSImage)
return xsDataInputXDS
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 generateXSDataInputXDS(_xsDataCollection):
xsDataCollection = _xsDataCollection
xsDataExperimentalCondition = _xsDataCollection.getSubWedge(
)[0].getExperimentalCondition()
xsDataSubWedgeList = xsDataCollection.getSubWedge()
xsDataInputXDS = XSDataInputXDSGenerateBackgroundImage()
xsDataBeam = xsDataExperimentalCondition.getBeam()
xsDataDetector = xsDataExperimentalCondition.getDetector()
xsDataGoniostat = xsDataExperimentalCondition.getGoniostat()
dWavelength = xsDataBeam.getWavelength().getValue()
dDistance = xsDataDetector.getDistance().getValue()
dBeamPositionX = xsDataDetector.getBeamPositionX().getValue()
dBeamPositionY = xsDataDetector.getBeamPositionY().getValue()
# Start with the detector
xsDataXDSDetector = EDHandlerXSDataXDSv1_0.getXSDataXDSDetector(
xsDataDetector)
xsDataInputXDS.setDetector(xsDataXDSDetector)
# Then the beam
xsDataXDSBeam = XSDataXDSBeam()
xsDataVectorDoubleIncidentBeam = XSDataVectorDouble()
xsDataVectorDoubleIncidentBeam.setV1(0.0)
xsDataVectorDoubleIncidentBeam.setV2(0.0)
xsDataVectorDoubleIncidentBeam.setV3(1.0)
xsDataXDSBeam.setIncident_beam_direction(
xsDataVectorDoubleIncidentBeam)
xsDataVectorDoublePolarizationPlaneNormal = XSDataVectorDouble()
xsDataVectorDoublePolarizationPlaneNormal.setV1(0.0)
xsDataVectorDoublePolarizationPlaneNormal.setV2(1.0)
xsDataVectorDoublePolarizationPlaneNormal.setV3(0.0)
xsDataXDSBeam.setPolarization_plane_normal(
xsDataVectorDoublePolarizationPlaneNormal)
xsDataXDSBeam.setX_ray_wavelength(XSDataWavelength(dWavelength))
xsDataInputXDS.setBeam(xsDataXDSBeam)
# Then the goniostat
xsDataXDSGoniostat = XSDataXDSGoniostat()
xsDataVectorDoubleRotationAxis = XSDataVectorDouble()
xsDataVectorDoubleRotationAxis.setV1(1.0)
xsDataVectorDoubleRotationAxis.setV2(0.0)
xsDataVectorDoubleRotationAxis.setV3(0.0)
xsDataXDSGoniostat.setRotation_axis(xsDataVectorDoubleRotationAxis)
xsDataXDSGoniostat.setOscillation_range(
xsDataGoniostat.getOscillationWidth())
xsDataXDSGoniostat.setStarting_angle(
xsDataGoniostat.getRotationAxisStart())
xsDataInputXDS.setGoniostat(xsDataXDSGoniostat)
# # Then the Crystal
#
# xsDataXDSCrystal = XSDataXDSCrystal()
#
# xsDataXDSCrystal.setFriedels_law(XSDataString("FALSE"))
#
## if ( xsDataCrystal is not None ):
## xsDataSpaceGroup = xsDataCrystal.getSpaceGroup()
## if ( xsDataSpaceGroup is not None ):
## xsDataStringName = xsDataSpaceGroup.getName()
## if ( xsDataStringName is not None ):
## xsDataInputXDS.setSymmetry( XSDataString( xsDataStringName.getValue() ) )
# xsDataXDSCrystal.setSpace_group_number(XSDataInteger(0))
#
# xsDataXDSCrystal.setStrong_pixel(XSDataInteger(8))
#
# xsDataCell = XSDataCell()
# xsDataCell.setLength_a(XSDataLength(0.0))
# xsDataCell.setLength_b(XSDataLength(0.0))
# xsDataCell.setLength_c(XSDataLength(0.0))
# xsDataCell.setAngle_alpha(XSDataAngle(0.0))
# xsDataCell.setAngle_beta(XSDataAngle(0.0))
# xsDataCell.setAngle_gamma(XSDataAngle(0.0))
# xsDataXDSCrystal.setUnit_cell_constants(xsDataCell)
#
# xsDataInputXDS.setCrystal(xsDataXDSCrystal)
# Finaly the images
xsDataXDSImage = XSDataXDSImage()
xsDataSubWedgeFirst = xsDataSubWedgeList[0]
xsDataImageFirst = xsDataSubWedgeFirst.getImage()[0]
pyStrPath = xsDataImageFirst.getPath().getValue()
pyStrFileName = EDUtilsFile.getBaseName(pyStrPath)
pyStrDirectory = EDUtilsPath.getFolderName(pyStrPath)
pyStrPrefix = EDUtilsImage.getPrefix(pyStrFileName)
pyStrSuffix = EDUtilsImage.getSuffix(pyStrFileName)
pyStrXDSTemplate = "%s_xdslink_?????.%s" % (pyStrPrefix, pyStrSuffix)
xsDataXDSImage.setName_template_of_data_frames(
XSDataString(pyStrXDSTemplate))
iXDSLowestImageNumberGlobal = 1
xsDataXDSImage.setStarting_frame(
XSDataInteger(iXDSLowestImageNumberGlobal))
# First we have to find the smallest goniostat rotation axis start:
fGonioStatOscillationStartMin = None
for xsDataSubWedge in xsDataSubWedgeList:
xsDataGoniostat = xsDataSubWedge.getExperimentalCondition(
).getGoniostat()
fGonioStatOscillationStart = xsDataGoniostat.getRotationAxisStart(
).getValue()
if (fGonioStatOscillationStartMin is None):
fGonioStatOscillationStartMin = fGonioStatOscillationStart
elif (fGonioStatOscillationStartMin > fGonioStatOscillationStart):
fGonioStatOscillationStartMin = fGonioStatOscillationStart
# Loop through the list of sub wedges
for xsDataSubWedge in xsDataSubWedgeList:
xsDataImageList = xsDataSubWedge.getImage()
xsDataGoniostat = xsDataSubWedge.getExperimentalCondition(
).getGoniostat()
fGonioStatOscillationStart = xsDataGoniostat.getRotationAxisStart(
).getValue()
fGonioStatOscillationRange = xsDataGoniostat.getOscillationWidth(
).getValue()
# First find the lowest and highest image numbers
iLowestImageNumber = None
for xsDataImage in xsDataImageList:
iImageNumber = xsDataImage.getNumber().getValue()
if (iLowestImageNumber is None):
iLowestImageNumber = iImageNumber
elif (iImageNumber < iLowestImageNumber):
iLowestImageNumber = iImageNumber
# Loop through the list of images
iLowestXDSImageNumber = None
iHighestXDSImageNumber = None
for xsDataImage in xsDataImageList:
iImageNumber = xsDataImage.getNumber().getValue()
fImageOscillationStart = fGonioStatOscillationStart + (
iImageNumber -
iLowestImageNumber) * fGonioStatOscillationRange
iXDSImageNumber = iXDSLowestImageNumberGlobal + int(
(fImageOscillationStart - fGonioStatOscillationStartMin) /
fGonioStatOscillationRange)
#print iXDSImageNumber, fImageOscillationStart, fGonioStatOscillationStartMin, fGonioStatOscillationRange
pyStrSourcePath = xsDataImage.getPath()
pyStrTarget = "%s_xdslink_%05d.%s" % (
pyStrPrefix, iXDSImageNumber, pyStrSuffix)
xsDataXDSImageLink = XSDataXDSImageLink()
xsDataFileSource = XSDataFile()
xsDataFileSource.setPath(pyStrSourcePath)
xsDataXDSImageLink.setSource(xsDataFileSource)
xsDataXDSImageLink.setTarget(XSDataString(pyStrTarget))
xsDataInputXDS.addImage_link(xsDataXDSImageLink)
if (iLowestXDSImageNumber is None):
iLowestXDSImageNumber = iXDSImageNumber
elif (iLowestXDSImageNumber > iXDSImageNumber):
iLowestXDSImageNumber = iXDSImageNumber
if (iHighestXDSImageNumber is None):
iHighestXDSImageNumber = iXDSImageNumber
elif (iHighestXDSImageNumber < iXDSImageNumber):
iHighestXDSImageNumber = iXDSImageNumber
xsDataXDSIntegerRange = XSDataXDSIntegerRange()
xsDataXDSIntegerRange.setLower(
XSDataInteger(iLowestXDSImageNumber))
xsDataXDSIntegerRange.setUpper(
XSDataInteger(iHighestXDSImageNumber))
xsDataXDSImage.addBackground_range(xsDataXDSIntegerRange)
xsDataXDSImage.addData_range(xsDataXDSIntegerRange)
xsDataXDSImage.addSpot_range(xsDataXDSIntegerRange)
xsDataInputXDS.setImage(xsDataXDSImage)
return xsDataInputXDS
