def functionXMLin(_strFilename):
"""Here we create the XML string to be passed to the EDNA plugin from the input strFilename
This can / should be modified by the final user
@param _strFilename: full path of the input file
@type _strFilename: python string representing the path
@return: string
"""
EDVerbose.screen("Starting processing of image %s" % (_strFilename))
# First check if the filename end with .img or .mccd:
strXML = None
if _strFilename.endswith(".img") or _strFilename.endswith(".mccd") or _strFilename.endswith(".cbf"):
xsDataInputGridScreening = XSDataInputGridScreening()
xsDataDiffractionPlan = XSDataDiffractionPlan()
xsDataDiffractionPlan.setMaxExposureTimePerDataCollection(
XSDataTime(EDParallelExecuteGridScreening.fMaxExposureTime)
)
xsDataInputGridScreening.setDiffractionPlan(xsDataDiffractionPlan)
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(_strFilename))
xsDataInputGridScreening.setImageFile(xsDataFile)
if EDParallelExecuteGridScreening.bOnlyImageQualityIndicators:
xsDataInputGridScreening.setDoOnlyImageQualityIndicators(XSDataBoolean(True))
if EDParallelExecuteGridScreening.bStoreInISPyB:
xsDataInputGridScreening.setStoreImageQualityIndicatorsInISPyB(XSDataBoolean(True))
if EDParallelExecuteGridScreening.bDoOnlyIntegrationWithXMLOutput:
xsDataInputGridScreening.setDoOnlyIntegrationWithXMLOutput(XSDataBoolean(True))
strXML = xsDataInputGridScreening.marshal()
else:
EDVerbose.screen("File name not ending with .img or .mccd - ignored : %s" % _strFilename)
return strXML
def functionXMLin(_strFilename):
"""Here we create the XML string to be passed to the EDNA plugin from the input strFilename
This can / should be modified by the final user
@param _strFilename: full path of the input file
@type _strFilename: python string representing the path
@return: string
"""
EDVerbose.screen("Starting processing of image %s" % (_strFilename))
# First check if the filename end with .img or .mccd:
strXML = None
if (_strFilename.endswith(".img") or _strFilename.endswith(".mccd") or _strFilename.endswith(".cbf")):
xsDataInputGridScreening = XSDataInputGridScreening()
xsDataDiffractionPlan = XSDataDiffractionPlan()
xsDataDiffractionPlan.setMaxExposureTimePerDataCollection(XSDataTime(EDParallelExecuteGridScreening.fMaxExposureTime))
xsDataInputGridScreening.setDiffractionPlan(xsDataDiffractionPlan)
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(_strFilename))
xsDataInputGridScreening.setImageFile(xsDataFile)
if EDParallelExecuteGridScreening.bOnlyImageQualityIndicators:
xsDataInputGridScreening.setDoOnlyImageQualityIndicators(XSDataBoolean(True))
if EDParallelExecuteGridScreening.bStoreInISPyB:
xsDataInputGridScreening.setStoreImageQualityIndicatorsInISPyB(XSDataBoolean(True))
if EDParallelExecuteGridScreening.bDoOnlyIntegrationWithXMLOutput:
xsDataInputGridScreening.setDoOnlyIntegrationWithXMLOutput(XSDataBoolean(True))
strXML = xsDataInputGridScreening.marshal()
else:
EDVerbose.screen("File name not ending with .img or .mccd - ignored : %s" % _strFilename)
return strXML
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginControlGridScreeningv1_0.preProcess")
# Load the plugins
self.edPluginControlReadImageHeader = self.loadPlugin(self.strControlReadImageHeaderPluginName, \
"ReadImageHeader")
self.edPluginControlIndicators = self.loadPlugin(self.strControlledIndicatorsPluginName, \
"ControlIndicators")
self.edPluginMOSFLMIndexing = self.loadPlugin(self.strIndexingMOSFLMPluginName, \
"IndexingMOSFLM")
self.edPluginControlIntegration = self.loadPlugin(self.strPluginControlIntegration, \
"Integration")
self.edPluginControlStrategy = self.loadPlugin(self.strPluginControlStrategy, \
"Strategy")
# Input data
self.strImageFile = self.getDataInput().getImageFile().getPath().getValue()
self.xsDataGridScreeningFileNameParameters = self.getFileNameParameters(self.strImageFile)
self.xsDataDiffractionPlan = self.getDataInput().getDiffractionPlan()
if self.xsDataDiffractionPlan is None:
self.xsDataDiffractionPlan = XSDataDiffractionPlan()
if self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection() is None:
# Default max esposure time: 10000s
self.xsDataDiffractionPlan.setMaxExposureTimePerDataCollection(XSDataTime(10000))
self.xsDataDiffractionPlan.setEstimateRadiationDamage(XSDataBoolean(False))
# Image quality indicators
if self.getDataInput().getStoreImageQualityIndicatorsInISPyB():
self.bStoreImageQualityIndicatorsInISPyB = self.getDataInput().getStoreImageQualityIndicatorsInISPyB().getValue()
if self.getDataInput().getDoOnlyImageQualityIndicators():
self.bDoOnlyImageQualityIndicators = self.getDataInput().getDoOnlyImageQualityIndicators().getValue()
if self.bStoreImageQualityIndicatorsInISPyB:
self.edPluginISPyBStoreImageQualityIndicators = self.loadPlugin(self.strISPyBStoreImageQualityIndicatorsPluginName, \
"ISPyBStoreImageQualityIndicators")
def buildChildren(self, child_, nodeName_):
if child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'imageFile':
obj_ = XSDataFile()
obj_.build(child_)
self.setImageFile(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'diffractionPlan':
obj_ = XSDataDiffractionPlan()
obj_.build(child_)
self.setDiffractionPlan(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'storeImageQualityIndicatorsInISPyB':
obj_ = XSDataBoolean()
obj_.build(child_)
self.setStoreImageQualityIndicatorsInISPyB(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'doOnlyImageQualityIndicators':
obj_ = XSDataBoolean()
obj_.build(child_)
self.setDoOnlyImageQualityIndicators(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'doOnlyIntegrationWithXMLOutput':
obj_ = XSDataBoolean()
obj_.build(child_)
self.setDoOnlyIntegrationWithXMLOutput(obj_)
XSDataInput.buildChildren(self, child_, nodeName_)
def createInputCharacterisationFromSubWedges(self):
self.DEBUG("EDPluginControlInterfacev1_2.createInputCharacterisationFromSubWedges")
xsDataResultSubWedgeAssemble = self.edPluginControlSubWedgeAssemble.getDataOutput()
self.xsDataInputCharacterisation = XSDataInputCharacterisation()
xsDataCollection = XSDataCollection()
# Default exposure time (for the moment, this value should be
# possible to read from the command line)
if self.xsDataDiffractionPlan is None:
self.xsDataDiffractionPlan = XSDataDiffractionPlan()
if (not xsDataResultSubWedgeAssemble is None):
pyListSubWedge = xsDataResultSubWedgeAssemble.getSubWedge()
xsDataCollection.setSubWedge(pyListSubWedge)
for xsDataSubWedge in pyListSubWedge:
if (self.strComplexity is not None):
self.xsDataDiffractionPlan.setComplexity(XSDataString(self.strComplexity))
if (self.fFlux is not None):
xsDataSubWedge.getExperimentalCondition().getBeam().setFlux(XSDataFlux(self.fFlux))
if (self.fBeamSizeX is not None) and (self.fBeamSizeY is not None):
xsDataSize = XSDataSize()
xsDataSize.setX(XSDataLength(self.fBeamSizeX))
xsDataSize.setY(XSDataLength(self.fBeamSizeY))
xsDataSubWedge.getExperimentalCondition().getBeam().setSize(xsDataSize)
if (self.fBeamPosX is not None):
xsDataSubWedge.getExperimentalCondition().getDetector().setBeamPositionX(XSDataLength(self.fBeamPosX))
if (self.fBeamPosY is not None):
xsDataSubWedge.getExperimentalCondition().getDetector().setBeamPositionY(XSDataLength(self.fBeamPosY))
if (self.fMinExposureTimePerImage is not None):
xsDataSubWedge.getExperimentalCondition().getBeam().setMinExposureTimePerImage(XSDataTime(self.fMinExposureTimePerImage))
if (self.fTransmission is not None):
xsDataSubWedge.getExperimentalCondition().getBeam().setTransmission(XSDataDouble(self.fTransmission))
if (self.fWavelength is not None):
xsDataSubWedge.getExperimentalCondition().getBeam().setWavelength(XSDataWavelength(self.fWavelength))
if self.fMinOscillationWidth != None:
xsDataSubWedge.getExperimentalCondition().getGoniostat().setMinOscillationWidth(XSDataAngle(self.fMinOscillationWidth))
if self.fMaxOscillationSpeed != None:
xsDataSubWedge.getExperimentalCondition().getGoniostat().setMaxOscillationSpeed(XSDataAngularSpeed(self.fMaxOscillationSpeed))
if (self.strForcedSpaceGroup is not None):
self.xsDataDiffractionPlan.setForcedSpaceGroup(XSDataString(self.strForcedSpaceGroup))
self.xsDataDiffractionPlan.setAnomalousData(XSDataBoolean(self.bAnomalousData))
self.xsDataDiffractionPlan.setMaxExposureTimePerDataCollection(XSDataTime(self.fMaxExposureTimePerDataCollection))
if (self.strStrategyOption is not None):
self.xsDataDiffractionPlan.setStrategyOption(XSDataString(self.strStrategyOption))
xsDataCollection.setDiffractionPlan(self.xsDataDiffractionPlan)
if self.xsDataSample is not None:
xsDataCollection.setSample(XSDataSampleCrystalMM.parseString(self.xsDataSample.marshal()))
self.xsDataInputCharacterisation.setDataCollection(xsDataCollection)
self.xsDataInputCharacterisation.setToken(self.xsDataToken)
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginControlGridScreeningv1_0.preProcess")
# Load the plugins
self.edPluginControlReadImageHeader = self.loadPlugin(self.strControlReadImageHeaderPluginName, \
"ReadImageHeader")
self.edPluginControlIndicators = self.loadPlugin(self.strControlledIndicatorsPluginName, \
"ControlIndicators")
self.edPluginMOSFLMIndexing = self.loadPlugin(self.strIndexingMOSFLMPluginName, \
"IndexingMOSFLM")
self.edPluginControlIntegration = self.loadPlugin(self.strPluginControlIntegration, \
"Integration")
self.edPluginControlStrategy = self.loadPlugin(self.strPluginControlStrategy, \
"Strategy")
self.edPluginExecMtz2Various = self.loadPlugin(self.strPluginExecMtz2Various, \
"Mtz2Various")
# Input data
self.strImageFile = self.getDataInput().getImageFile().getPath(
).getValue()
self.xsDataGridScreeningFileNameParameters = self.getFileNameParameters(
self.strImageFile)
self.xsDataDiffractionPlan = self.getDataInput().getDiffractionPlan()
if self.xsDataDiffractionPlan is None:
self.xsDataDiffractionPlan = XSDataDiffractionPlan()
if self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection(
) is None:
# Default max esposure time: 10000s
self.xsDataDiffractionPlan.setMaxExposureTimePerDataCollection(
XSDataTime(10000))
self.xsDataDiffractionPlan.setEstimateRadiationDamage(
XSDataBoolean(False))
# Image quality indicators
if self.getDataInput().getStoreImageQualityIndicatorsInISPyB():
self.bStoreImageQualityIndicatorsInISPyB = self.getDataInput(
).getStoreImageQualityIndicatorsInISPyB().getValue()
if self.getDataInput().getDoOnlyImageQualityIndicators():
self.bDoOnlyImageQualityIndicators = self.getDataInput(
).getDoOnlyImageQualityIndicators().getValue()
if self.getDataInput().getDoOnlyIntegrationWithXMLOutput():
self.bDoOnlyIntegrationWithXMLOutput = self.getDataInput(
).getDoOnlyIntegrationWithXMLOutput().getValue()
if self.bStoreImageQualityIndicatorsInISPyB:
self.edPluginISPyBStoreImageQualityIndicators = self.loadPlugin(self.strISPyBStoreImageQualityIndicatorsPluginName, \
"ISPyBStoreImageQualityIndicators")
def functionXMLin(_strFilename):
"""Here we create the XML string to be passed to the EDNA plugin from the input strFilename
This can / should be modified by the final user
@param _strFilename: full path of the input file
@type _strFilename: python string representing the path
@return: string
"""
EDVerbose.screen("Starting processing of image %s" % (_strFilename))
# First check if the filename end with .img or .mccd:
strXML = None
if (_strFilename.endswith(".img") or _strFilename.endswith(".mccd") or _strFilename.endswith(".cbf")):
xsDataInputInterface = XSDataInputInterface()
xsDataDiffractionPlan = XSDataDiffractionPlan()
xsDataDiffractionPlan.setMaxExposureTimePerDataCollection(XSDataTime(EDParallelExecuteMXv1Characterisation.m_fMaxExposureTime))
xsDataInputInterface.setDiffractionPlan(xsDataDiffractionPlan)
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(_strFilename))
xsDataInputInterface.addImagePath(xsDataFile)
strXML = xsDataInputInterface.marshal()
else:
EDVerbose.screen("File name not ending with .img or .mccd - ignored : %s" % _strFilename)
return strXML
def createInputCharacterisationFromSubWedges(self):
self.DEBUG("EDPluginControlInterfacev1_3.createInputCharacterisationFromSubWedges")
xsDataResultSubWedgeAssemble = self.edPluginControlSubWedgeAssemble.getDataOutput()
self.xsDataInputCharacterisation = XSDataInputCharacterisation()
xsDataCollection = XSDataCollection()
# Default exposure time (for the moment, this value should be
# possible to read from the command line)
if self.xsDataDiffractionPlan is None:
self.xsDataDiffractionPlan = XSDataDiffractionPlan()
if (not xsDataResultSubWedgeAssemble is None):
pyListSubWedge = xsDataResultSubWedgeAssemble.getSubWedge()
xsDataCollection.setSubWedge(pyListSubWedge)
for xsDataSubWedge in pyListSubWedge:
if (self.strComplexity is not None):
self.xsDataDiffractionPlan.setComplexity(XSDataString(self.strComplexity))
if (self.fFlux is not None):
xsDataSubWedge.getExperimentalCondition().getBeam().setFlux(XSDataFlux(self.fFlux))
if (self.fBeamSizeX is not None) and (self.fBeamSizeY is not None):
xsDataSize = XSDataSize()
xsDataSize.setX(XSDataLength(self.fBeamSizeX))
xsDataSize.setY(XSDataLength(self.fBeamSizeY))
xsDataSubWedge.getExperimentalCondition().getBeam().setSize(xsDataSize)
if (self.fApertureSize is not None):
xsDataSubWedge.getExperimentalCondition().getBeam().setApertureSize(XSDataLength(self.fApertureSize))
if (self.fBeamPosX is not None):
xsDataSubWedge.getExperimentalCondition().getDetector().setBeamPositionX(XSDataLength(self.fBeamPosX))
if (self.fBeamPosY is not None):
xsDataSubWedge.getExperimentalCondition().getDetector().setBeamPositionY(XSDataLength(self.fBeamPosY))
if (self.fMinExposureTimePerImage is not None):
xsDataSubWedge.getExperimentalCondition().getBeam().setMinExposureTimePerImage(XSDataTime(self.fMinExposureTimePerImage))
if (self.fTransmission is not None):
xsDataSubWedge.getExperimentalCondition().getBeam().setTransmission(XSDataDouble(self.fTransmission))
if (self.fWavelength is not None):
xsDataSubWedge.getExperimentalCondition().getBeam().setWavelength(XSDataWavelength(self.fWavelength))
if self.fMinOscillationWidth != None:
xsDataSubWedge.getExperimentalCondition().getGoniostat().setMinOscillationWidth(XSDataAngle(self.fMinOscillationWidth))
if self.fMaxOscillationSpeed != None:
xsDataSubWedge.getExperimentalCondition().getGoniostat().setMaxOscillationSpeed(XSDataAngularSpeed(self.fMaxOscillationSpeed))
if (self.strForcedSpaceGroup is not None):
self.xsDataDiffractionPlan.setForcedSpaceGroup(XSDataString(self.strForcedSpaceGroup))
self.xsDataDiffractionPlan.setAnomalousData(XSDataBoolean(self.bAnomalousData))
self.xsDataDiffractionPlan.setMaxExposureTimePerDataCollection(XSDataTime(self.fMaxExposureTimePerDataCollection))
if (self.strStrategyOption is not None):
self.xsDataDiffractionPlan.setStrategyOption(XSDataString(self.strStrategyOption))
xsDataCollection.setDiffractionPlan(self.xsDataDiffractionPlan)
if self.xsDataSample is not None:
xsDataCollection.setSample(XSDataSampleCrystalMM.parseString(self.xsDataSample.marshal()))
self.xsDataInputCharacterisation.setDataCollection(xsDataCollection)
class EDPluginControlGridScreeningv1_0(EDPluginControl):
"""
This plugin is a "light-weight" characterisation to be used for processing
images from grid scans.
"""
def __init__(self):
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputGridScreening)
self.strControlReadImageHeaderPluginName = "EDPluginControlReadImageHeaderv10"
self.edPluginControlReadImageHeader = None
self.strControlledIndicatorsPluginName = "EDPluginControlImageQualityIndicatorsv1_4"
self.edPluginControlIndicators = None
self.strISPyBStoreImageQualityIndicatorsPluginName = "EDPluginISPyBStoreImageQualityIndicatorsv1_4"
self.edPluginISPyBStoreImageQualityIndicators = None
self.strIndexingMOSFLMPluginName = "EDPluginMOSFLMIndexingv10"
self.edPluginMOSFLMIndexing = None
self.strPluginControlIntegration = "EDPluginControlIntegrationv10"
self.edPluginControlIntegration = None
self.strPluginControlStrategy = "EDPluginControlStrategyv1_2"
self.edPluginControlStrategy = None
self.strPluginExecMtz2Various = "EDPluginExecMtz2Variousv1_0"
self.edPluginExecMtz2Various = None
self.strImageFile = None
self.xsDataIndexingResultMOSFLM = None
self.xsDataCrystal = None
self.strCharacterisationShortSummary = ""
self.strStatusMessage = ""
self.xsDataDiffractionPlan = None
self.xsDataCollection = None
self.xsDataIndexingResult = None
self.xsDataStrategyResult = None
self.xsDataImageQualityIndicators = None
self.bStoreImageQualityIndicatorsInISPyB = False
self.bDoOnlyImageQualityIndicators = False
self.bDoOnlyIntegrationWithXMLOutput = False
self.iImageQualityIndicatorsId = None
self.xsDataGridScreeningResultIntegration = None
def checkParameters(self):
"""
Checks the mandatory parameters.
"""
self.DEBUG("EDPluginControlGridScreeningv1_0.checkParameters")
self.checkMandatoryParameters(self.getDataInput(), "Data Input is None")
self.checkMandatoryParameters(self.getDataInput().getImageFile(), "imageFile")
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginControlGridScreeningv1_0.preProcess")
# Load the plugins
self.edPluginControlReadImageHeader = self.loadPlugin(self.strControlReadImageHeaderPluginName, \
"ReadImageHeader")
self.edPluginControlIndicators = self.loadPlugin(self.strControlledIndicatorsPluginName, \
"ControlIndicators")
self.edPluginMOSFLMIndexing = self.loadPlugin(self.strIndexingMOSFLMPluginName, \
"IndexingMOSFLM")
self.edPluginControlIntegration = self.loadPlugin(self.strPluginControlIntegration, \
"Integration")
self.edPluginControlStrategy = self.loadPlugin(self.strPluginControlStrategy, \
"Strategy")
self.edPluginExecMtz2Various = self.loadPlugin(self.strPluginExecMtz2Various, \
"Mtz2Various")
# Input data
self.strImageFile = self.getDataInput().getImageFile().getPath().getValue()
self.xsDataGridScreeningFileNameParameters = self.getFileNameParameters(self.strImageFile)
self.xsDataDiffractionPlan = self.getDataInput().getDiffractionPlan()
if self.xsDataDiffractionPlan is None:
self.xsDataDiffractionPlan = XSDataDiffractionPlan()
if self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection() is None:
# Default max esposure time: 10000s
self.xsDataDiffractionPlan.setMaxExposureTimePerDataCollection(XSDataTime(10000))
self.xsDataDiffractionPlan.setEstimateRadiationDamage(XSDataBoolean(False))
# Image quality indicators
if self.getDataInput().getStoreImageQualityIndicatorsInISPyB():
self.bStoreImageQualityIndicatorsInISPyB = self.getDataInput().getStoreImageQualityIndicatorsInISPyB().getValue()
if self.getDataInput().getDoOnlyImageQualityIndicators():
self.bDoOnlyImageQualityIndicators = self.getDataInput().getDoOnlyImageQualityIndicators().getValue()
if self.getDataInput().getDoOnlyIntegrationWithXMLOutput():
self.bDoOnlyIntegrationWithXMLOutput = self.getDataInput().getDoOnlyIntegrationWithXMLOutput().getValue()
if self.bStoreImageQualityIndicatorsInISPyB:
self.edPluginISPyBStoreImageQualityIndicators = self.loadPlugin(self.strISPyBStoreImageQualityIndicatorsPluginName, \
"ISPyBStoreImageQualityIndicators")
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlGridScreeningv1_0.process")
xsDataInputReadImageHeader = XSDataInputReadImageHeader()
xsDataInputReadImageHeader.setImage(image=XSDataFile(path=XSDataString(self.strImageFile)))
self.edPluginControlReadImageHeader.setDataInput(xsDataInputReadImageHeader)
self.edPluginControlReadImageHeader.connectSUCCESS(self.doSuccessReadImageHeader)
self.edPluginControlReadImageHeader.connectFAILURE(self.doFailureReadImageHeader)
self.executePluginSynchronous(self.edPluginControlReadImageHeader)
def finallyProcess(self, _edObject=None):
EDPluginControl.finallyProcess(self)
self.DEBUG("EDPluginControlGridScreeningv1_0.finallyProcess")
# Synchronise if necessary
if self.edPluginISPyBStoreImageQualityIndicators is not None:
self.edPluginISPyBStoreImageQualityIndicators.synchronize()
# Build up the output object
strComment = ""
xsDataResultGridScreening = XSDataResultGridScreening()
if self.xsDataGridScreeningFileNameParameters is not None:
xsDataResultGridScreening.setFileNameParameters(self.xsDataGridScreeningFileNameParameters)
if self.xsDataImageQualityIndicators is None:
strComment = "No image quality indicators"
else:
xsDataResultGridScreening.setImageQualityIndicators(self.xsDataImageQualityIndicators)
if self.xsDataImageQualityIndicators.getIceRings() is not None:
if self.xsDataImageQualityIndicators.getIceRings().getValue() > 1:
strComment = "Ice rings detected"
if self.xsDataIndexingResult is None:
if strComment == "":
strComment = "No indexing result"
else:
strComment += ", no indexing result"
else:
xsDataSelectedSolution = self.xsDataIndexingResult.getSelectedSolution()
xsDataResultGridScreening.setMosaicity(xsDataSelectedSolution.getCrystal().getMosaicity())
if self.xsDataStrategyResult is None:
if strComment == "":
strComment = "No strategy result"
else:
strComment += ", no strategy result"
else:
xsDataCollectionPlan = self.xsDataStrategyResult.getCollectionPlan()[0]
xsDataStrategySummary = xsDataCollectionPlan.getStrategySummary()
xsDataResultGridScreening.setRankingResolution(xsDataStrategySummary.getRankingResolution())
xsDataResultGridScreening.setResultIntegration(self.xsDataGridScreeningResultIntegration)
xsDataResultGridScreening.setComment(XSDataString(strComment))
if self.iImageQualityIndicatorsId is not None:
xsDataResultGridScreening.setImageQualityIndicatorsId(XSDataInteger(self.iImageQualityIndicatorsId))
# print xsDataResultGridScreening.marshal()
self.setDataOutput(xsDataResultGridScreening)
def doSuccessReadImageHeader(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doSuccessReadImageHeader")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlGridScreeningv1_0.doSuccessReadImageHeader")
xsDataResultReadImageHeader = self.edPluginControlReadImageHeader.getDataOutput()
if xsDataResultReadImageHeader is not None:
xsDataSubWedge = xsDataResultReadImageHeader.getSubWedge()
self.xsDataCollection = XSDataCollection()
self.xsDataCollection.addSubWedge(xsDataSubWedge)
self.xsDataCollection.setDiffractionPlan(self.xsDataDiffractionPlan)
if not self.bDoOnlyIntegrationWithXMLOutput:
xsDataInputControlImageQualityIndicators = XSDataInputControlImageQualityIndicators()
if self.bStoreImageQualityIndicatorsInISPyB:
xsDataInputControlImageQualityIndicators.doUploadToIspyb = XSDataBoolean(True)
else:
xsDataInputControlImageQualityIndicators.doUploadToIspyb = XSDataBoolean(False)
xsDataInputControlImageQualityIndicators.addImage(XSDataImage(path=XSDataString(self.strImageFile)))
self.edPluginControlIndicators.setDataInput(xsDataInputControlImageQualityIndicators)
self.edPluginControlIndicators.connectSUCCESS(self.doSuccessIndicators)
self.edPluginControlIndicators.connectFAILURE(self.doFailureIndicators)
self.executePluginSynchronous(self.edPluginControlIndicators)
else:
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.setDataCollection(self.xsDataCollection)
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
xsDataMOSFLMIndexingInput = EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputIndexing(xsDataIndexingInput)
self.edPluginMOSFLMIndexing.connectSUCCESS(self.doSuccessIndexingMOSFLM)
self.edPluginMOSFLMIndexing.connectFAILURE(self.doFailureIndexingMOSFLM)
self.edPluginMOSFLMIndexing.setDataInput(xsDataMOSFLMIndexingInput)
self.edPluginMOSFLMIndexing.executeSynchronous()
def doFailureReadImageHeader(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doFailureReadImageHeader")
self.retrieveFailureMessages(_edPlugin, "EDPluginControlGridScreeningv1_0.doSuccessReadImageHeader")
def doSuccessIndicators(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doSuccessIndicators")
# self.retrieveSuccessMessages(_edPlugin, "EDPluginControlGridScreeningv1_0.doSuccessIndexingIndicators")
if self.edPluginControlIndicators.hasDataOutput():
self.xsDataImageQualityIndicators = self.edPluginControlIndicators.getDataOutput().getImageQualityIndicators()[0]
# Continue only if requested
if not self.bDoOnlyImageQualityIndicators:
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.setDataCollection(self.xsDataCollection)
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
xsDataMOSFLMIndexingInput = EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputIndexing(xsDataIndexingInput)
self.edPluginMOSFLMIndexing.connectSUCCESS(self.doSuccessIndexingMOSFLM)
self.edPluginMOSFLMIndexing.connectFAILURE(self.doFailureIndexingMOSFLM)
self.edPluginMOSFLMIndexing.setDataInput(xsDataMOSFLMIndexingInput)
self.edPluginMOSFLMIndexing.executeSynchronous()
def doFailureIndicators(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doFailureIndicators")
strErrorMessage = "Execution of Indexing and Indicators plugin failed. Execution of characterisation aborted."
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
def doSuccessISPyBStoreImageQualityIndicators(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doSuccessISPyBStoreImageQualityIndicators")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlGridScreeningv1_0.doSuccessISPyBStoreImageQualityIndicators")
self.iImageQualityIndicatorsId = self.edPluginISPyBStoreImageQualityIndicators.getDataOutput().getImageQualityIndicatorsId().getValue()
if self.iImageQualityIndicatorsId is None:
self.WARNING("Image quality indicators result not stored in ISPyB!")
def doFailureISPyBStoreImageQualityIndicators(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doFailureISPyBStoreImageQualityIndicators")
strErrorMessage = "Execution of store ISPyB image quality indicators plugin failed."
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
def doSuccessIndexingMOSFLM(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doSuccessIndexingMOSFLM")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlGridScreeningv1_0.doIntegrationToStrategyTransition")
xsDataMOSFLMIndexingOutput = self.edPluginMOSFLMIndexing.getDataOutput()
xsDataExperimentalConditionRefined = None
if self.hasDataInput("refinedExperimentalCondition"):
xsDataExperimentalConditionRefined = self.getDataInput("refinedExperimentalCondition")[0]
else:
# Use the experimental condition from the xsDataCollection
xsDataExperimentalConditionRefined = self.xsDataCollection.getSubWedge()[0].getExperimentalCondition()
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
self.xsDataIndexingResult = EDHandlerXSDataMOSFLMv10.generateXSDataIndexingResult(xsDataMOSFLMIndexingOutput, xsDataExperimentalConditionRefined)
xsDataIntegrationInput = XSDataIntegrationInput()
xsDataIntegrationInput.setDataCollection(self.xsDataCollection)
xsDataIntegrationInput.setExperimentalConditionRefined(self.xsDataIndexingResult.getSelectedSolution().getExperimentalConditionRefined())
xsDataIntegrationInput.setSelectedIndexingSolution(self.xsDataIndexingResult.getSelectedSolution())
self.edPluginControlIntegration.connectSUCCESS(self.doSuccessIntegration)
self.edPluginControlIntegration.connectFAILURE(self.doFailureIntegration)
self.edPluginControlIntegration.setDataInput(xsDataIntegrationInput)
self.executePluginSynchronous(self.edPluginControlIntegration)
def doFailureIndexingMOSFLM(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doFailureActionIndexing")
self.retrieveFailureMessages(_edPlugin, "EDPluginControlCharacterisationv1_1.doFailureActionIndexing")
def doSuccessIntegration(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doSuccessIntegration")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlGridScreeningv1_0.doSuccessIntegration")
self.addStatusMessage("Integration successful.")
self.xsDataIntegrationOutput = self.edPluginControlIntegration.getDataOutput()
# Integration short summary
if self.edPluginControlIntegration.hasDataOutput("integrationShortSummary"):
self.strCharacterisationShortSummary += self.edPluginControlIntegration.getDataOutput("integrationShortSummary")[0].getValue()
# self.DEBUG( self.xsDataExperimentCharacterisation.marshal() )
if self.bDoOnlyIntegrationWithXMLOutput:
# Run mtz2various
xsDataInputMtz2Various = XSDataInputMtz2Various()
xsDataInputMtz2Various.setMtzfile(self.edPluginControlIntegration.getDataOutput().getIntegrationSubWedgeResult()[0].getGeneratedMTZFile())
xsDataInputMtz2Various.addLabin(XSDataString("I=I"))
xsDataInputMtz2Various.addLabin(XSDataString("SIGI=SIGI"))
xsDataInputMtz2Various.setOutput(XSDataString("USER '(3I4,2F10.1)'"))
self.edPluginExecMtz2Various.setDataInput(xsDataInputMtz2Various)
self.edPluginExecMtz2Various.executeSynchronous()
strHklFilePath = self.edPluginExecMtz2Various.getDataOutput().getHklfile().getPath().getValue()
strIntegration = EDUtilsFile.readFile(strHklFilePath)
# Output the result in XML format
self.xsDataGridScreeningResultIntegration = XSDataGridScreeningResultIntegration()
self.xsDataGridScreeningResultIntegration.setFileName(os.path.basename(self.strImageFile))
self.xsDataGridScreeningResultIntegration.setFileDirectory(os.path.dirname(self.strImageFile))
self.xsDataGridScreeningResultIntegration.setIntegratedData(strIntegration)
else:
# We continue with the strategy calculation
xsDataInputStrategy = XSDataInputStrategy()
xsDataSolutionSelected = self.xsDataIndexingResult.getSelectedSolution()
xsDataInputStrategy.setCrystalRefined(xsDataSolutionSelected.getCrystal())
xsDataInputStrategy.setSample(self.xsDataCollection.getSample())
xsDataIntegrationSubWedgeResultList = self.xsDataIntegrationOutput.getIntegrationSubWedgeResult()
xsDataInputStrategy.setBestFileContentDat(xsDataIntegrationSubWedgeResultList[0].getBestfileDat())
xsDataInputStrategy.setBestFileContentPar(xsDataIntegrationSubWedgeResultList[0].getBestfilePar())
xsDataInputStrategy.setExperimentalCondition(xsDataIntegrationSubWedgeResultList[0].getExperimentalConditionRefined())
xsDataInputStrategy.setDataCollection(self.xsDataCollection)
for xsDataIntegrationSubWedgeResult in xsDataIntegrationSubWedgeResultList:
xsDataInputStrategy.addBestFileContentHKL(xsDataIntegrationSubWedgeResult.getBestfileHKL())
xsDataInputStrategy.setDiffractionPlan(self.xsDataDiffractionPlan)
self.edPluginControlStrategy.connectSUCCESS(self.doSuccessStrategy)
self.edPluginControlStrategy.connectFAILURE(self.doFailureStrategy)
self.edPluginControlStrategy.setDataInput(xsDataInputStrategy)
self.executePluginSynchronous(self.edPluginControlStrategy)
def doFailureIntegration(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doFailureIntegration")
strErrorMessage = "Execution of integration plugin failed."
self.addStatusMessage("Integration FAILURE.")
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
def doSuccessStrategy(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doSuccessStrategy")
self.retrieveSuccessMessages(self.edPluginControlStrategy, "EDPluginControlGridScreeningv1_0.doSuccessStrategy")
self.xsDataStrategyResult = self.edPluginControlStrategy.getDataOutput()
def doFailureStrategy(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doFailureStrategy")
self.retrieveFailureMessages(self.edPluginControlStrategy, "EDPluginControlGridScreeningv1_0.doFailureStrategy")
strErrorMessage = "Strategy calculation FAILURE."
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
# def generateExecutiveSummary(self, _edPlugin):
# """
# Generates a summary of the execution of the plugin.
# """
# self.DEBUG("EDPluginControlGridScreeningv1_0.generateExecutiveSummary")
# self.addExecutiveSummaryLine("Summary of characterisation:")
# xsDataInputStrategy = self.getDataInput()
# xsDataCollection = xsDataInputStrategy.getDataCollection()
# xsDataDiffractionPlan = xsDataCollection.getDiffractionPlan()
# self.addExecutiveSummaryLine("Diffraction plan:")
# if (xsDataDiffractionPlan.getComplexity() is not None):
# self.addExecutiveSummaryLine("BEST complexity : %s" % xsDataDiffractionPlan.getComplexity().getValue())
# if (xsDataDiffractionPlan.getAimedCompleteness() is not None):
# self.addExecutiveSummaryLine("Aimed completeness : %6.1f [%%]" % (100.0 * xsDataDiffractionPlan.getAimedCompleteness().getValue()))
# if (xsDataDiffractionPlan.getRequiredCompleteness() is not None):
# self.addExecutiveSummaryLine("Required completeness : %6.1f [%%]" % (100.0 * xsDataDiffractionPlan.getRequiredCompleteness().getValue()))
# if (xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution() is not None):
# self.addExecutiveSummaryLine("Aimed I/sigma at highest resolution : %6.1f" % xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution().getValue())
# if (xsDataDiffractionPlan.getAimedResolution() is not None):
# self.addExecutiveSummaryLine("Aimed resolution : %6.1f [A]" % xsDataDiffractionPlan.getAimedResolution().getValue())
# if (xsDataDiffractionPlan.getRequiredResolution() is not None):
# self.addExecutiveSummaryLine("Required resolution : %6.1f [A]" % xsDataDiffractionPlan.getRequiredResolution().getValue())
# if (xsDataDiffractionPlan.getAimedMultiplicity() is not None):
# self.addExecutiveSummaryLine("Aimed multiplicity : %6.1f" % xsDataDiffractionPlan.getAimedMultiplicity().getValue())
# if (xsDataDiffractionPlan.getRequiredMultiplicity() is not None):
# self.addExecutiveSummaryLine("Required multiplicity : %6.1f" % xsDataDiffractionPlan.getRequiredMultiplicity().getValue())
# if (xsDataDiffractionPlan.getForcedSpaceGroup() is not None):
# self.addExecutiveSummaryLine("Forced space group : %6s" % xsDataDiffractionPlan.getForcedSpaceGroup().getValue())
# if (xsDataDiffractionPlan.getMaxExposureTimePerDataCollection() is not None):
# self.addExecutiveSummaryLine("Max exposure time per data collection : %6.1f [s]" % xsDataDiffractionPlan.getMaxExposureTimePerDataCollection().getValue())
# self.addExecutiveSummarySeparator()
# if self.edPluginControlIndexingIndicators is not None:
# self.appendExecutiveSummary(self.edPluginControlIndexingIndicators, "")
# if self.edPluginControlIndexingLabelit is not None:
# self.appendExecutiveSummary(self.edPluginControlIndexingLabelit, "")
# if self.edPluginControlIntegration is not None:
# self.appendExecutiveSummary(self.edPluginControlIntegration, "")
# if self.edPluginControlStrategy is not None:
# self.appendExecutiveSummary(self.edPluginControlStrategy, "")
# self.addExecutiveSummarySeparator()
# if self.strCharacterisationShortSummary is not None:
# self.addExecutiveSummaryLine("Characterisation short summary:")
# self.addExecutiveSummaryLine("")
# if self.strStatusMessage != None:
# for strLine in self.strStatusMessage.split(". "):
# if strLine.endswith("."):
# self.addExecutiveSummaryLine(strLine)
# else:
# self.addExecutiveSummaryLine(strLine + ".")
# self.addExecutiveSummaryLine("")
# for strLine in self.strCharacterisationShortSummary.split("\n"):
# if strLine != "\n":
# self.addExecutiveSummaryLine(strLine)
# self.addErrorWarningMessagesToExecutiveSummary("Characterisation error and warning messages: ")
# self.addExecutiveSummarySeparator()
def addStatusMessage(self, _strStatusMessage):
if self.strStatusMessage != "":
self.strStatusMessage += " "
self.strStatusMessage += _strStatusMessage
def getFileNameParameters(self, _strFileName):
"""Method for extracting the rotation start angle, the two motor positions and the grid scan image no from the file name"""
# Typical file name: mesh_0_21.676_-0.051_22_001.mccd
listParts = os.path.basename(_strFileName).split("_")
xsDataGridScreeningFileNameParameters = XSDataGridScreeningFileNameParameters()
try:
strScanId1 = listParts[1]
xsDataGridScreeningFileNameParameters.setScanId1(XSDataString(strScanId1))
strMotorPosition1 = listParts[2]
xsDataGridScreeningFileNameParameters.setMotorPosition1(XSDataString(strMotorPosition1))
strMotorPosition2 = listParts[3]
xsDataGridScreeningFileNameParameters.setMotorPosition2(XSDataString(strMotorPosition2))
strScanId2 = listParts[4]
xsDataGridScreeningFileNameParameters.setScanId2(XSDataString(strScanId2))
except:
xsDataGridScreeningFileNameParameters = None
return xsDataGridScreeningFileNameParameters
def diffractionPlan(self):
# Do we have a diffracionPlan?
xsDataDiffractionPlan = self.xsDataResultCharacterisation.getDataCollection(
).getDiffractionPlan()
if xsDataDiffractionPlan is None:
xsDataDiffractionPlan = XSDataDiffractionPlan()
strTitle = "Diffraction Plan"
strExtraColumnTitle = None
strExtraColumnValue = None
if xsDataDiffractionPlan.strategyOption is not None:
strStrategyOption = xsDataDiffractionPlan.strategyOption.value
if strStrategyOption.find("-helic") != -1:
strTitle = "Helical Diffraction Plan"
self.bIsHelical = True
strExtraColumnTitle = "Helical\ndistance (mm)"
if self.dataInput.helicalDistance is not None:
fHelicalDistance = self.dataInput.helicalDistance.value
strExtraColumnValue = "%.3f" % fHelicalDistance
else:
strExtraColumnValue = "Unknown"
elif strStrategyOption.find("-Npos") != -1:
strTitle = "Multi-positional Diffraction Plan"
self.bIsMultiPositional = True
dictTable = {
"type": "table",
"title": "Diffraction Plan",
"columns": [],
"data": []
}
dictTable["columns"].append("Forced\nspace group")
dictTable["columns"].append("Anomalous\ndata")
dictTable["columns"].append("Aimed\nmultiplicity")
dictTable["columns"].append("Aimed\ncompleteness")
dictTable["columns"].append("Aimed I/sigma\nat highest res.")
dictTable["columns"].append("Aimed\nresolution (Å)")
dictTable["columns"].append("Min osc.\nwidth")
if strExtraColumnTitle is not None:
dictTable["columns"].append(strExtraColumnTitle)
listRow = []
# Forced space group
if xsDataDiffractionPlan.getForcedSpaceGroup() is None:
strForcedSpaceGroup = "None"
else:
strForcedSpaceGroup = xsDataDiffractionPlan.getForcedSpaceGroup(
).getValue()
listRow.append(strForcedSpaceGroup)
# Anomalous data
if xsDataDiffractionPlan.getAnomalousData(
) is None or xsDataDiffractionPlan.getAnomalousData().getValue(
) == False:
strAnomalousData = "False"
else:
strAnomalousData = "True"
listRow.append(strAnomalousData)
# Aimed multiplicity
if xsDataDiffractionPlan.getAimedMultiplicity() is None:
strAimedMultiplicity = "Default\n(optimized)"
else:
strAimedMultiplicity = "%.2f" % xsDataDiffractionPlan.getAimedMultiplicity(
).getValue()
listRow.append(strAimedMultiplicity)
# Aimed completeness
if xsDataDiffractionPlan.getAimedCompleteness() is None:
strAimedCompleteness = "Default\n(>= 0.99)"
else:
strAimedCompleteness = "%.2f" % xsDataDiffractionPlan.getAimedCompleteness(
).getValue()
listRow.append(strAimedCompleteness)
# Aimed aimedIOverSigmaAtHighestResolution
if xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution(
) is None:
strAimedIOverSigmaAtHighestResolution = "BEST Default"
else:
strAimedIOverSigmaAtHighestResolution = "%.2f" % xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution(
).getValue()
listRow.append(strAimedIOverSigmaAtHighestResolution)
# Aimed resolution
if xsDataDiffractionPlan.getAimedResolution() is None:
strAimedResolution = "Default\n(highest possible)"
else:
strAimedResolution = "%0.2f" % xsDataDiffractionPlan.getAimedResolution(
).getValue()
listRow.append(strAimedResolution)
# Min osc width
if xsDataDiffractionPlan.goniostatMinOscillationWidth is None:
strMinOscWidth = "Default"
else:
strMinOscWidth = "%0.2f" % xsDataDiffractionPlan.goniostatMinOscillationWidth.value
listRow.append(strMinOscWidth)
if strExtraColumnValue is not None:
listRow.append(strExtraColumnValue)
#
dictTable["data"].append(listRow)
self.workflowStepReport.addTable(strTitle, dictTable["columns"],
dictTable["data"])
def createInputCharacterisationFromSubWedges(self):
self.DEBUG("EDPluginControlInterfacev2_0.createInputCharacterisationFromSubWedges")
xsDataResultSubWedgeAssemble = self.edPluginControlSubWedgeAssemble.getDataOutput()
self.xsDataInputCharacterisation = XSDataInputCharacterisation()
xsDataCollection = XSDataCollection()
# Default exposure time (for the moment, this value should be
# possible to read from the command line)
xsDataDiffractionPlan = XSDataDiffractionPlan()
if (not xsDataResultSubWedgeAssemble is None):
pyListSubWedge = xsDataResultSubWedgeAssemble.getSubWedge()
xsDataCollection.setSubWedge(pyListSubWedge)
for xsDataSubWedge in pyListSubWedge:
if (self.strComplexity is not None):
xsDataDiffractionPlan.setComplexity(XSDataString(self.strComplexity))
if (self.fFlux is not None):
xsDataSubWedge.getExperimentalCondition().getBeam().setFlux(XSDataFloat(self.fFlux))
if (self.fBeamSize is not None):
xsDataSize = XSDataSize()
xsDataSize.setX(XSDataLength(self.fBeamSize))
xsDataSize.setY(XSDataLength(self.fBeamSize))
xsDataSubWedge.getExperimentalCondition().getBeam().setSize(xsDataSize)
if (self.fBeamPosX is not None):
xsDataSubWedge.getExperimentalCondition().getDetector().setBeamPositionX(XSDataLength(self.fBeamPosX))
if (self.fBeamPosY is not None):
xsDataSubWedge.getExperimentalCondition().getDetector().setBeamPositionY(XSDataLength(self.fBeamPosY))
if (self.fMinExposureTimePerImage is not None):
xsDataSubWedge.getExperimentalCondition().getBeam().setMinExposureTimePerImage(XSDataFloat(self.fMinExposureTimePerImage))
if (self.fTransmission is not None):
xsDataSubWedge.getExperimentalCondition().getBeam().setTransmission(XSDataDouble(self.fTransmission))
if (self.strForcedSpaceGroup is not None):
xsDataDiffractionPlan.setForcedSpaceGroup(XSDataString(self.strForcedSpaceGroup))
xsDataDiffractionPlan.setAnomalousData(XSDataBoolean(self.bAnomalousData))
xsDataDiffractionPlan.setMaxExposureTimePerDataCollection(XSDataTime(self.fMaxExposureTimePerDataCollection))
if (self.strStrategyOption is not None):
xsDataDiffractionPlan.setStrategyOption(XSDataString(self.strStrategyOption))
xsDataCollection.setDiffractionPlan(xsDataDiffractionPlan)
self.xsDataInputCharacterisation.setDataCollection(xsDataCollection)
def preProcess(self, _edPlugin=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edPlugin)
self.DEBUG("EDPluginControlInterfacev2_0.preProcess...")
self.listImagePaths = []
if (self.hasDataInput("diffractionPlan")):
xsDataDiffractionPlan = XSDataDiffractionPlan()
xsDataDiffractionPlans = self.getDataInput("diffractionPlan")
if (not xsDataDiffractionPlans[0] is None):
xsDataDiffractionPlan = xsDataDiffractionPlans[0]
if (not xsDataDiffractionPlan.getForcedSpaceGroup() is None):
self.strForcedSpaceGroup = xsDataDiffractionPlan.getForcedSpaceGroup().getValue()
if (not xsDataDiffractionPlan.getMaxExposureTimePerDataCollection() is None):
self.fMaxExposureTimePerDataCollection = xsDataDiffractionPlan.getMaxExposureTimePerDataCollection().getValue()
if (not xsDataDiffractionPlan.getAnomalousData() is None):
self.bAnomalousData = xsDataDiffractionPlan.getAnomalousData().getValue()
if (not xsDataDiffractionPlan.getStrategyOption() is None):
self.strStrategyOption = xsDataDiffractionPlan.getStrategyOption().getValue()
if (not xsDataDiffractionPlan.getComplexity() is None):
self.strComplexity = xsDataDiffractionPlan.getComplexity().getValue()
if (self.hasDataInput("imagePaths")):
for strImagePath in self.getDataInput("imagePaths"):
self.listImagePaths.append(strImagePath)
if (self.hasDataInput("flux")):
self.fFlux = self.getDataInput("flux")[0].getValue()
if (self.hasDataInput("minExposureTimePerImage")):
self.fMinExposureTimePerImage = self.getDataInput("minExposureTimePerImage")[0].getValue()
if (self.hasDataInput("beamSize")):
self.fBeamSize = self.getDataInput("beamSize")[0].getValue()
if (self.hasDataInput("templateMode")):
self.bTemplateMode = self.getDataInput("templateMode")[0].getValue()
if (self.hasDataInput("generatedTemplateFile")):
self.strGeneratedTemplateFile = self.getDataInput("generatedTemplateFile")[0].getValue()
if (self.hasDataInput("generatedTemplateFileMXv2")):
self.strGeneratedTemplateFileMXv2 = self.getDataInput("generatedTemplateFileMXv2")[0].getValue()
if (self.hasDataInput("resultsFilePath")):
self.strResultsFilePath = self.getDataInput("resultsFilePath")[0].getValue()
if (self.hasDataInput("beamPosX")):
self.fBeamPosX = self.getDataInput("beamPosX")[0].getValue()
if (self.hasDataInput("beamPosY")):
self.fBeamPosY = self.getDataInput("beamPosY")[0].getValue()
if (self.hasDataInput("transmission")):
self.fTransmission = self.getDataInput("transmission")[0].getValue()
if (self.hasDataInput("dataCollectionId")):
self.iDataCollectionId = self.getDataInput("dataCollectionId")[0].getValue()
if (self.hasDataInput("shortComments")):
self.strShortComments = self.getDataInput("shortComments")[0].getValue()
if (self.hasDataInput("comments")):
self.strComments = self.getDataInput("comments")[0].getValue()
if (self.hasDataInput("inputCharacterisation")):
self.xsDataInputCharacterisation = self.getDataInput("inputCharacterisation")[0]
if (self.hasDataInput("mxv2DataCollection")):
self.xsDataCollectionMXv2 = self.getDataInput("mxv2DataCollection")[0]
# Check if XML data is given as input :
if (self.xsDataInputCharacterisation is None):
self.edPluginControlSubWedgeAssemble = self.loadPlugin(self.strEDPluginControlSubWedgeAssembleName, "SubWedgeAssemble")
self.edPluginControlCharacterisation = self.loadPlugin(self.strEDPluginControlCharacterisationName, "Characterisation")
if (self.strEDPluginControlISPyBName is not None):
self.edPluginControlISPyB = self.loadPlugin(self.strEDPluginControlISPyBName, "ISPyB")
def createInputCharacterisationFromSubWedges(self):
EDVerbose.DEBUG(
"EDPluginControlInterfacev2_0.createInputCharacterisationFromSubWedges"
)
xsDataResultSubWedgeAssemble = self.edPluginControlSubWedgeAssemble.getDataOutput(
)
self.xsDataInputCharacterisation = XSDataInputCharacterisation()
xsDataCollection = XSDataCollection()
# Default exposure time (for the moment, this value should be
# possible to read from the command line)
xsDataDiffractionPlan = XSDataDiffractionPlan()
if (not xsDataResultSubWedgeAssemble is None):
pyListSubWedge = xsDataResultSubWedgeAssemble.getSubWedge()
xsDataCollection.setSubWedge(pyListSubWedge)
for xsDataSubWedge in pyListSubWedge:
if (self.strComplexity is not None):
xsDataDiffractionPlan.setComplexity(
XSDataString(self.strComplexity))
if (self.fFlux is not None):
xsDataSubWedge.getExperimentalCondition().getBeam(
).setFlux(XSDataFloat(self.fFlux))
if (self.fBeamSize is not None):
xsDataSize = XSDataSize()
xsDataSize.setX(XSDataLength(self.fBeamSize))
xsDataSize.setY(XSDataLength(self.fBeamSize))
xsDataSubWedge.getExperimentalCondition().getBeam(
).setSize(xsDataSize)
if (self.fBeamPosX is not None):
xsDataSubWedge.getExperimentalCondition().getDetector(
).setBeamPositionX(XSDataLength(self.fBeamPosX))
if (self.fBeamPosY is not None):
xsDataSubWedge.getExperimentalCondition().getDetector(
).setBeamPositionY(XSDataLength(self.fBeamPosY))
if (self.fMinExposureTimePerImage is not None):
xsDataSubWedge.getExperimentalCondition().getBeam(
).setMinExposureTimePerImage(
XSDataFloat(self.fMinExposureTimePerImage))
if (self.fTransmission is not None):
xsDataSubWedge.getExperimentalCondition().getBeam(
).setTransmission(XSDataDouble(self.fTransmission))
if (self.strForcedSpaceGroup is not None):
xsDataDiffractionPlan.setForcedSpaceGroup(
XSDataString(self.strForcedSpaceGroup))
xsDataDiffractionPlan.setAnomalousData(
XSDataBoolean(self.bAnomalousData))
xsDataDiffractionPlan.setMaxExposureTimePerDataCollection(
XSDataTime(self.fMaxExposureTimePerDataCollection))
if (self.strStrategyOption is not None):
xsDataDiffractionPlan.setStrategyOption(
XSDataString(self.strStrategyOption))
xsDataCollection.setDiffractionPlan(xsDataDiffractionPlan)
self.xsDataInputCharacterisation.setDataCollection(xsDataCollection)
def diffractionPlan(self):
# Do we have a diffracionPlan?
xsDataDiffractionPlan = self.xsDataResultCharacterisation.getDataCollection().getDiffractionPlan()
if xsDataDiffractionPlan is None:
xsDataDiffractionPlan = XSDataDiffractionPlan()
strTitle = "Diffraction Plan"
strExtraColumnTitle = None
strExtraColumnValue = None
if xsDataDiffractionPlan.strategyOption is not None:
strStrategyOption = xsDataDiffractionPlan.strategyOption.value
if strStrategyOption.find("-helic") != -1:
strTitle = "Helical Diffraction Plan"
self.bIsHelical = True
strExtraColumnTitle = "Helical<br>distance (mm)"
if self.dataInput.helicalDistance is not None:
fHelicalDistance = self.dataInput.helicalDistance.value
strExtraColumnValue = "%.3f" % fHelicalDistance
else:
strExtraColumnValue = "Unknown"
elif strStrategyOption.find("-Npos") != -1:
strTitle = "Multi-positional Diffraction Plan"
self.bIsMultiPositional = True
dictTable = {"type": "table",
"title": "Diffraction Plan",
"columns": [],
"data": []}
dictTable["columns"].append("Forced\nspace group")
dictTable["columns"].append("Anomalous\ndata")
dictTable["columns"].append("Aimed\nmultiplicity")
dictTable["columns"].append("Aimed\ncompleteness")
dictTable["columns"].append("Aimed I/sigma\nat highest res.")
dictTable["columns"].append("Aimed\nresolution (Å)")
dictTable["columns"].append("Min osc.\nwidth")
if strExtraColumnTitle is not None:
dictTable["columns"].append(strExtraColumnTitle)
listRow = []
# Forced space group
if xsDataDiffractionPlan.getForcedSpaceGroup() is None:
strForcedSpaceGroup = "None"
else:
strForcedSpaceGroup = xsDataDiffractionPlan.getForcedSpaceGroup().getValue()
listRow.append(strForcedSpaceGroup)
# Anomalous data
if xsDataDiffractionPlan.getAnomalousData() is None or xsDataDiffractionPlan.getAnomalousData().getValue() == False:
strAnomalousData = "False"
else:
strAnomalousData = "True"
listRow.append(strAnomalousData)
# Aimed multiplicity
if xsDataDiffractionPlan.getAimedMultiplicity() is None:
strAimedMultiplicity = "Default<br>(optimized)"
else:
strAimedMultiplicity = "%.2f" % xsDataDiffractionPlan.getAimedMultiplicity().getValue()
listRow.append(strAimedMultiplicity)
# Aimed completeness
if xsDataDiffractionPlan.getAimedCompleteness() is None:
strAimedCompleteness = "Default<br>(>= 0.99)"
else:
strAimedCompleteness = "%.2f" % xsDataDiffractionPlan.getAimedCompleteness().getValue()
listRow.append(strAimedCompleteness)
# Aimed aimedIOverSigmaAtHighestResolution
if xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution() is None:
strAimedIOverSigmaAtHighestResolution = "BEST Default"
else:
strAimedIOverSigmaAtHighestResolution = "%.2f" % xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution().getValue()
listRow.append(strAimedIOverSigmaAtHighestResolution)
# Aimed resolution
if xsDataDiffractionPlan.getAimedResolution() is None:
strAimedResolution = "Default<br>(highest possible)"
else:
strAimedResolution = "%0.2f" % xsDataDiffractionPlan.getAimedResolution().getValue()
listRow.append(strAimedResolution)
# Min osc width
if xsDataDiffractionPlan.goniostatMinOscillationWidth is None:
strMinOscWidth = "Default"
else:
strMinOscWidth = "%0.2f" % xsDataDiffractionPlan.goniostatMinOscillationWidth.value
listRow.append(strMinOscWidth)
if strExtraColumnValue is not None:
listRow.append(strExtraColumnValue)
#
dictTable["data"].append(listRow)
self.workflowStepReport.addTable(strTitle,
dictTable["columns"],
dictTable["data"])
class EDPluginControlInterfacev1_2(EDPluginControl):
"""
This is the common class to all plugins managing user interfaces
"""
def __init__ (self):
"""
"""
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputInterface)
self.setXSDataInputClass(XSDataExperimentalCondition, "experimentalCondition")
self.setXSDataInputClass(XSDataDiffractionPlan, "diffractionPlan")
self.setXSDataInputClass(XSDataSampleCrystalMM, "sample")
self.setXSDataInputClass(XSDataString, "imagePaths")
self.setXSDataInputClass(XSDataFloat, "flux")
self.setXSDataInputClass(XSDataFloat, "minExposureTimePerImage")
self.setXSDataInputClass(XSDataFloat, "beamSize")
self.setXSDataInputClass(XSDataFloat, "beamSizeX")
self.setXSDataInputClass(XSDataFloat, "beamSizeY")
self.setXSDataInputClass(XSDataBoolean, "templateMode")
self.setXSDataInputClass(XSDataString, "generatedTemplateFile")
self.setXSDataInputClass(XSDataString, "resultsFilePath")
self.setXSDataInputClass(XSDataFloat, "beamPosX")
self.setXSDataInputClass(XSDataFloat, "beamPosY")
self.setXSDataInputClass(XSDataDouble, "wavelength")
self.setXSDataInputClass(XSDataDouble, "transmission")
self.setXSDataInputClass(XSDataInteger, "dataCollectionId")
self.setXSDataInputClass(XSDataString, "shortComments")
self.setXSDataInputClass(XSDataString, "comments")
self.setXSDataInputClass(XSDataInputCharacterisation, "inputCharacterisation")
self.strEDPluginControlSubWedgeAssembleName = "EDPluginControlSubWedgeAssemblev1_1"
self.strEDPluginControlCharacterisationName = "EDPluginControlCharacterisationv1_1"
self.strEDPluginControlISPyBName = "EDPluginControlISPyBv1_1"
self.edPluginControlSubWedgeAssemble = None
self.edPluginControlCharacterisation = None
self.edPluginControlISPyB = None
self.pyListImagePaths = None
self.xsDataInputCharacterisation = None
self.strComplexity = "none"
self.listImagePaths = []
self.fFlux = None
self.fMaxExposureTimePerDataCollection = 10000 # s, default prototype value
self.fMinExposureTimePerImage = None
self.fBeamSizeX = None
self.fBeamSizeY = None
self.bTemplateMode = False
self.strGeneratedTemplateFile = None
self.strResultsFilePath = None
self.strForcedSpaceGroup = None
self.bAnomalousData = False
self.fBeamPosX = None
self.fBeamPosY = None
self.fMinOscillationWidth = None
self.fMaxOscillationSpeed = None
self.fWavelength = None
self.fTransmission = None
self.strStrategyOption = None
self.iDataCollectionId = None
self.strShortComments = None
self.strComments = None
self.strStatusMessage = None
self.xsDataExperimentalCodition = None
self.xsDataSample = None
self.xsDataDiffractionPlan = None
def configure(self):
"""
Gets the configuration parameters (if any).
"""
EDPluginControl.configure(self)
EDVerbose.DEBUG("EDPluginControlInterfacev1_2.configure")
pluginConfiguration = self.getConfiguration()
if (pluginConfiguration is None):
EDVerbose.DEBUG("No plugin configuration found for EDPluginControlInterfacev1_2.")
else:
if (self.getControlledPluginName("subWedgeAssemblePlugin") is not None):
self.strEDPluginControlSubWedgeAssembleName = self.getControlledPluginName("subWedgeAssemblePlugin")
if (self.getControlledPluginName("characterisationPlugin") is not None):
self.strEDPluginControlCharacterisationName = self.getControlledPluginName("characterisationPlugin")
if (self.getControlledPluginName("ispybPlugin") is not None):
self.strEDPluginControlISPyBName = self.getControlledPluginName("ispybPlugin")
bUseISPyBPlugin = EDConfiguration.getStringParamValue(pluginConfiguration, "useISPyBPlugin")
if (bUseISPyBPlugin.lower() != "true"):
self.strEDPluginControlISPyBName = None
def preProcess(self, _edPlugin=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edPlugin)
EDVerbose.DEBUG("EDPluginControlInterfacev1_2.preProcess...")
self.listImagePaths = []
# Check if XSDataInputInterface is given as input
if self.hasDataInput():
xsDataInputInterface = self.getDataInput()
if xsDataInputInterface.getExperimentalCondition():
self.xsDataExperimentalCodition = xsDataInputInterface.getExperimentalCondition()
if self.xsDataExperimentalCodition.getGoniostat():
if self.xsDataExperimentalCodition.getGoniostat().getMinOscillationWidth():
self.fMinOscillationWidth = self.xsDataExperimentalCodition.getGoniostat().getMinOscillationWidth().getValue()
if self.xsDataExperimentalCodition.getGoniostat().getMaxOscillationSpeed():
self.fMaxOscillationSpeed = self.xsDataExperimentalCodition.getGoniostat().getMaxOscillationSpeed().getValue()
self.xsDataSample = xsDataInputInterface.getSample()
self.xsDataDiffractionPlan = self.getDataInput().getDiffractionPlan()
if self.xsDataDiffractionPlan:
if self.xsDataDiffractionPlan.getForcedSpaceGroup():
self.strForcedSpaceGroup = self.xsDataDiffractionPlan.getForcedSpaceGroup().getValue()
if self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection():
self.fMaxExposureTimePerDataCollection = self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection().getValue()
if self.xsDataDiffractionPlan.getAnomalousData():
self.bAnomalousData = self.xsDataDiffractionPlan.getAnomalousData().getValue()
if self.xsDataDiffractionPlan.getStrategyOption():
self.strStrategyOption = self.xsDataDiffractionPlan.getStrategyOption().getValue()
if self.xsDataDiffractionPlan.getComplexity():
self.strComplexity = self.xsDataDiffractionPlan.getComplexity().getValue()
if self.fMinOscillationWidth == None:
if self.xsDataDiffractionPlan.getGoniostatMinOscillationWidth():
self.fMinOscillationWidth = self.xsDataDiffractionPlan.getGoniostatMinOscillationWidth().getValue()
if self.fMaxOscillationSpeed == None:
if self.xsDataDiffractionPlan.getGoniostatMaxOscillationSpeed():
self.fMaxOscillationSpeed = self.xsDataDiffractionPlan.getGoniostatMaxOscillationSpeed().getValue()
self.xsDataSample = xsDataInputInterface.getSample()
if xsDataInputInterface.getImagePath():
for xsDataFile in xsDataInputInterface.getImagePath():
self.listImagePaths.append(xsDataFile.getPath())
if xsDataInputInterface.getFlux():
self.fFlux = xsDataInputInterface.getFlux().getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getFlux() != None:
self.fFlux = self.xsDataExperimentalCodition.getBeam().getFlux().getValue()
if xsDataInputInterface.getMinExposureTimePerImage():
self.fMinExposureTimePerImage = xsDataInputInterface.getMinExposureTimePerImage().getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getMinExposureTimePerImage() != None:
self.fMinExposureTimePerImage = self.xsDataExperimentalCodition.getBeam().getMinExposureTimePerImage().getValue()
if self.fMinExposureTimePerImage == None and xsDataInputInterface.getDiffractionPlan():
if xsDataInputInterface.getDiffractionPlan().getMinExposureTimePerImage() != None:
self.fMinExposureTimePerImage = xsDataInputInterface.getdiffractionPlan().getMinExposureTimePerImage().getValue()
if self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getSize() != None:
self.fBeamSizeX = self.xsDataExperimentalCodition.getBeam().getSize().getX().getValue()
self.fBeamSizeY = self.xsDataExperimentalCodition.getBeam().getSize().getY().getValue()
if xsDataInputInterface.getBeamSize():
self.fBeamSizeX = xsDataInputInterface.getBeamSize().getValue()
self.fBeamSizeY = xsDataInputInterface.getBeamSize().getValue()
if xsDataInputInterface.getBeamSizeX():
self.fBeamSizeX = xsDataInputInterface.getBeamSizeX().getValue()
if xsDataInputInterface.getBeamSizeY():
self.fBeamSizeY = xsDataInputInterface.getBeamSizeY().getValue()
if xsDataInputInterface.getTemplateMode():
self.bTemplateMode = xsDataInputInterface.getTemplateMode().getValue()
if xsDataInputInterface.getBeamPosX():
self.fBeamPosX = xsDataInputInterface.getBeamPosX().getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getDetector() != None:
if self.xsDataExperimentalCodition.getDetector().getBeamPositionX() != None:
self.fBeamPosX = self.xsDataExperimentalCodition.getDetector().getBeamPositionX().getValue()
if xsDataInputInterface.getBeamPosY():
self.fBeamPosY = xsDataInputInterface.getBeamPosY().getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getDetector() != None:
if self.xsDataExperimentalCodition.getDetector().getBeamPositionY() != None:
self.fBeamPosY = self.xsDataExperimentalCodition.getDetector().getBeamPositionY().getValue()
if xsDataInputInterface.getWavelength():
self.fWavelength = xsDataInputInterface.getWavelength().getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getWavelength() != None:
self.fWavelength = self.xsDataExperimentalCodition.getBeam().getWavelength().getValue()
if xsDataInputInterface.getTransmission():
self.fTransmission = xsDataInputInterface.getTransmission().getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getTransmission() != None:
self.fTransmission = self.xsDataExperimentalCodition.getBeam().getTransmission().getValue()
if xsDataInputInterface.getGeneratedTemplateFile():
self.strGeneratedTemplateFile = xsDataInputInterface.getGeneratedTemplateFile().getPath().getValue()
if xsDataInputInterface.getResultsFilePath():
self.strResultsFilePath = xsDataInputInterface.getResultsFilePath().getPath().getValue()
if xsDataInputInterface.getDataCollectionId():
self.iDataCollectionId = xsDataInputInterface.getDataCollectionId().getValue()
if xsDataInputInterface.getShortComments():
self.strShortComments = xsDataInputInterface.getShortComments().getValue()
if xsDataInputInterface.getComments():
self.strComments = xsDataInputInterface.getComments().getValue()
if xsDataInputInterface.getInputCharacterisation():
self.xsDataInputCharacterisation = xsDataInputInterface.getInputCharacterisation()
if xsDataInputInterface.getDataCollectionId():
self.iDataCollectionId = xsDataInputInterface.getDataCollectionId().getValue()
else:
if self.hasDataInput("experimentalCondition"):
self.xsDataExperimentalCodition = self.getDataInput("experimentalCondition")[0]
if self.xsDataExperimentalCodition.getGoniostat():
if self.xsDataExperimentalCodition.getGoniostat().getMinOscillationWidth():
self.fMinOscillationWidth = self.xsDataExperimentalCodition.getGoniostat().getMinOscillationWidth().getValue()
if self.xsDataExperimentalCodition.getGoniostat().getMaxOscillationSpeed():
self.fMaxOscillationSpeed = self.xsDataExperimentalCodition.getGoniostat().getMaxOscillationSpeed().getValue()
if self.hasDataInput("sample"):
self.xsDataSample = self.getDataInput("sample")[0]
if (self.hasDataInput("diffractionPlan")):
if self.xsDataDiffractionPlan is None:
self.xsDataDiffractionPlan = XSDataDiffractionPlan()
xsDataDiffractionPlans = self.getDataInput("diffractionPlan")
if (not xsDataDiffractionPlans[0] is None):
self.xsDataDiffractionPlan = xsDataDiffractionPlans[0]
if self.xsDataDiffractionPlan.getForcedSpaceGroup():
self.strForcedSpaceGroup = self.xsDataDiffractionPlan.getForcedSpaceGroup().getValue()
if self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection():
self.fMaxExposureTimePerDataCollection = self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection().getValue()
if self.xsDataDiffractionPlan.getAnomalousData():
self.bAnomalousData = self.xsDataDiffractionPlan.getAnomalousData().getValue()
if self.xsDataDiffractionPlan.getStrategyOption():
self.strStrategyOption = self.xsDataDiffractionPlan.getStrategyOption().getValue()
if self.xsDataDiffractionPlan.getComplexity():
self.strComplexity = self.xsDataDiffractionPlan.getComplexity().getValue()
if self.fMinOscillationWidth == None:
if self.xsDataDiffractionPlan.getGoniostatMinOscillationWidth():
self.fMinOscillationWidth = self.xsDataDiffractionPlan.getGoniostatMinOscillationWidth().getValue()
if self.fMaxOscillationSpeed == None:
if self.xsDataDiffractionPlan.getGoniostatMaxOscillationSpeed():
self.fMaxOscillationSpeed = self.xsDataDiffractionPlan.getGoniostatMaxOscillationSpeed().getValue()
if self.hasDataInput("sample"):
self.xsDataSample = self.getDataInput("sample")[0]
if self.hasDataInput("imagePaths"):
for strImagePath in self.getDataInput("imagePaths"):
self.listImagePaths.append(strImagePath)
if self.hasDataInput("flux"):
self.fFlux = self.getDataInput("flux")[0].getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getFlux() != None:
self.fFlux = self.xsDataExperimentalCodition.getBeam().getFlux().getValue()
if self.hasDataInput("minExposureTimePerImage"):
self.fMinExposureTimePerImage = self.getDataInput("minExposureTimePerImage")[0].getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getMinExposureTimePerImage() != None:
self.fMinExposureTimePerImage = self.xsDataExperimentalCodition.getBeam().getMinExposureTimePerImage().getValue()
if self.fMinExposureTimePerImage == None and self.hasDataInput("diffractionPlan"):
if self.getDataInput("diffractionPlan")[0].getMinExposureTimePerImage() != None:
self.fMinExposureTimePerImage = self.getDataInput("diffractionPlan")[0].getMinExposureTimePerImage().getValue()
if self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getSize() != None:
self.fBeamSizeX = self.xsDataExperimentalCodition.getBeam().getSize().getX().getValue()
self.fBeamSizeY = self.xsDataExperimentalCodition.getBeam().getSize().getY().getValue()
if self.hasDataInput("beamSize"):
self.fBeamSizeX = self.getDataInput("beamSize")[0].getValue()
self.fBeamSizeY = self.getDataInput("beamSize")[0].getValue()
if self.hasDataInput("beamSizeX"):
self.fBeamSizeX = self.getDataInput("beamSizeX")[0].getValue()
if self.hasDataInput("beamSizeY"):
self.fBeamSizeY = self.getDataInput("beamSizeY")[0].getValue()
if self.hasDataInput("templateMode"):
self.bTemplateMode = self.getDataInput("templateMode")[0].getValue()
if (self.hasDataInput("beamPosX")):
self.fBeamPosX = self.getDataInput("beamPosX")[0].getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getDetector() != None:
if self.xsDataExperimentalCodition.getDetector().getBeamPositionX() != None:
self.fBeamPosX = self.xsDataExperimentalCodition.getDetector().getBeamPositionX().getValue()
if (self.hasDataInput("beamPosY")):
self.fBeamPosY = self.getDataInput("beamPosY")[0].getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getDetector() != None:
if self.xsDataExperimentalCodition.getDetector().getBeamPositionY() != None:
self.fBeamPosY = self.xsDataExperimentalCodition.getDetector().getBeamPositionY().getValue()
if (self.hasDataInput("wavelength")):
self.fWavelength = self.getDataInput("wavelength")[0].getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getWavelength() != None:
self.fWavelength = self.xsDataExperimentalCodition.getBeam().getWavelength().getValue()
if (self.hasDataInput("transmission")):
self.fTransmission = self.getDataInput("transmission")[0].getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getTransmission() != None:
self.fTransmission = self.xsDataExperimentalCodition.getBeam().getTransmission().getValue()
if self.hasDataInput("generatedTemplateFile"):
self.strGeneratedTemplateFile = self.getDataInput("generatedTemplateFile")[0].getValue()
if self.hasDataInput("resultsFilePath"):
self.strResultsFilePath = self.getDataInput("resultsFilePath")[0].getValue()
if self.hasDataInput("dataCollectionId"):
self.iDataCollectionId = self.getDataInput("dataCollectionId")[0].getValue()
if self.hasDataInput("shortComments"):
self.strShortComments = self.getDataInput("shortComments")[0].getValue()
if self.hasDataInput("comments"):
self.strComments = self.getDataInput("comments")[0].getValue()
if self.hasDataInput("inputCharacterisation"):
self.xsDataInputCharacterisation = self.getDataInput("inputCharacterisation")[0]
# Check if XML data is given as input :
if (self.xsDataInputCharacterisation is None):
self.edPluginControlSubWedgeAssemble = self.loadPlugin(self.strEDPluginControlSubWedgeAssembleName, "SubWedgeAssemble")
self.edPluginControlCharacterisation = self.loadPlugin(self.strEDPluginControlCharacterisationName, "Characterisation")
if (self.strEDPluginControlISPyBName is not None):
self.edPluginControlISPyB = self.loadPlugin(self.strEDPluginControlISPyBName, "ISPyB")
def process(self, _edPlugin=None):
EDPluginControl.process(self, _edPlugin)
EDVerbose.DEBUG("EDPluginControlInterfacev1_2.process...")
if (self.edPluginControlSubWedgeAssemble is not None):
if(self.bTemplateMode == True):
self.edPluginControlSubWedgeAssemble.connectSUCCESS(self.generateTemplateFile)
else:
self.edPluginControlSubWedgeAssemble.connectSUCCESS(self.doSubWedgeAssembleSUCCESS)
self.edPluginControlSubWedgeAssemble.connectFAILURE(self.doSubWedgeAssembleFAILURE)
if(self.edPluginControlCharacterisation is not None):
self.edPluginControlCharacterisation.connectSUCCESS(self.doSuccessActionCharacterisation)
self.edPluginControlCharacterisation.connectFAILURE(self.doFailureActionCharacterisation)
if (self.edPluginControlISPyB is not None):
self.edPluginControlISPyB.connectSUCCESS(self.doSuccessActionISPyB)
self.edPluginControlISPyB.connectFAILURE(self.doFailureActionISPyB)
if (self.xsDataInputCharacterisation is None):
self.createInputCharacterisationFromImageHeaders(self.edPluginControlSubWedgeAssemble)
else:
self.runCharacterisationPlugin(self.edPluginControlCharacterisation)
def finallyProcess(self, _edPlugin=None):
EDPluginControl.finallyProcess(self, _edPlugin)
EDVerbose.DEBUG("EDPluginControlInterfacev1_2.finallyProcess...")
if (not self.edPluginControlCharacterisation is None):
if (self.edPluginControlCharacterisation.hasDataOutput()):
self.setDataOutput(self.edPluginControlCharacterisation.getDataOutput(), "characterisation")
if (not self.edPluginControlISPyB is None):
if (self.edPluginControlISPyB.hasDataOutput()):
self.setDataOutput(self.edPluginControlISPyB.getDataOutput(), "ISPyB")
if self.hasDataInput():
xsDataResultInterface = XSDataResultInterface()
if self.edPluginControlCharacterisation:
xsDataResultInterface.setResultCharacterisation(self.edPluginControlCharacterisation.getDataOutput())
if self.edPluginControlISPyB:
xsDataResultInterface.setResultControlISPyB(self.edPluginControlISPyB.getDataOutput())
self.setDataOutput(xsDataResultInterface)
def createInputCharacterisationFromImageHeaders(self, _edPlugin):
EDVerbose.DEBUG("EDPluginControlInterfacev1_2.createInputCharacterisationFromImageHeaders")
xsDataInputSubWedgeAssemble = XSDataInputSubWedgeAssemble()
for xsDataStringImagePath in self.listImagePaths:
xsDataFile = XSDataFile()
xsDataFile.setPath(xsDataStringImagePath)
xsDataInputSubWedgeAssemble.addFile(xsDataFile)
_edPlugin.setDataInput(xsDataInputSubWedgeAssemble)
_edPlugin.executeSynchronous()
def runCharacterisationPlugin(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlInterfacev1_2.runCharacterisationPlugin")
self.edPluginControlCharacterisation.setDataInput(self.xsDataInputCharacterisation)
self.edPluginControlCharacterisation.executeSynchronous()
def storeResultsInISPyB(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlInterfacev1_2.storeResultsInISPyB")
if (self.edPluginControlISPyB is not None):
# Execute the ISPyB control plugin
xsDataInputControlISPyB = XSDataInputControlISPyB()
xsDataInputControlISPyB.setCharacterisationResult(self.edPluginControlCharacterisation.getDataOutput())
if (not self.iDataCollectionId is None):
xsDataInputControlISPyB.setDataCollectionId(XSDataInteger(self.iDataCollectionId))
if (not self.strShortComments is None):
self.edPluginControlISPyB.setDataInput(XSDataString(self.strShortComments), "shortComments")
if (not self.strComments is None):
self.edPluginControlISPyB.setDataInput(XSDataString(self.strComments), "comments")
if (not self.strStatusMessage is None):
self.edPluginControlISPyB.setDataInput(XSDataString(self.strStatusMessage), "statusMessage")
self.edPluginControlISPyB.setDataInput(xsDataInputControlISPyB)
self.edPluginControlISPyB.executeSynchronous()
def createInputCharacterisationFromSubWedges(self):
EDVerbose.DEBUG("EDPluginControlInterfacev1_2.createInputCharacterisationFromSubWedges")
xsDataResultSubWedgeAssemble = self.edPluginControlSubWedgeAssemble.getDataOutput()
self.xsDataInputCharacterisation = XSDataInputCharacterisation()
xsDataCollection = XSDataCollection()
# Default exposure time (for the moment, this value should be
# possible to read from the command line)
if self.xsDataDiffractionPlan is None:
self.xsDataDiffractionPlan = XSDataDiffractionPlan()
if (not xsDataResultSubWedgeAssemble is None):
pyListSubWedge = xsDataResultSubWedgeAssemble.getSubWedge()
xsDataCollection.setSubWedge(pyListSubWedge)
for xsDataSubWedge in pyListSubWedge:
if (self.strComplexity is not None):
self.xsDataDiffractionPlan.setComplexity(XSDataString(self.strComplexity))
if (self.fFlux is not None):
xsDataSubWedge.getExperimentalCondition().getBeam().setFlux(XSDataFlux(self.fFlux))
if (self.fBeamSizeX is not None) and (self.fBeamSizeY is not None):
xsDataSize = XSDataSize()
xsDataSize.setX(XSDataLength(self.fBeamSizeX))
xsDataSize.setY(XSDataLength(self.fBeamSizeY))
xsDataSubWedge.getExperimentalCondition().getBeam().setSize(xsDataSize)
if (self.fBeamPosX is not None):
xsDataSubWedge.getExperimentalCondition().getDetector().setBeamPositionX(XSDataLength(self.fBeamPosX))
if (self.fBeamPosY is not None):
xsDataSubWedge.getExperimentalCondition().getDetector().setBeamPositionY(XSDataLength(self.fBeamPosY))
if (self.fMinExposureTimePerImage is not None):
xsDataSubWedge.getExperimentalCondition().getBeam().setMinExposureTimePerImage(XSDataTime(self.fMinExposureTimePerImage))
if (self.fTransmission is not None):
xsDataSubWedge.getExperimentalCondition().getBeam().setTransmission(XSDataDouble(self.fTransmission))
if (self.fWavelength is not None):
xsDataSubWedge.getExperimentalCondition().getBeam().setWavelength(XSDataWavelength(self.fWavelength))
if self.fMinOscillationWidth != None:
xsDataSubWedge.getExperimentalCondition().getGoniostat().setMinOscillationWidth(XSDataAngle(self.fMinOscillationWidth))
if self.fMaxOscillationSpeed != None:
xsDataSubWedge.getExperimentalCondition().getGoniostat().setMaxOscillationSpeed(XSDataAngularSpeed(self.fMaxOscillationSpeed))
if (self.strForcedSpaceGroup is not None):
self.xsDataDiffractionPlan.setForcedSpaceGroup(XSDataString(self.strForcedSpaceGroup))
self.xsDataDiffractionPlan.setAnomalousData(XSDataBoolean(self.bAnomalousData))
self.xsDataDiffractionPlan.setMaxExposureTimePerDataCollection(XSDataTime(self.fMaxExposureTimePerDataCollection))
if (self.strStrategyOption is not None):
self.xsDataDiffractionPlan.setStrategyOption(XSDataString(self.strStrategyOption))
xsDataCollection.setDiffractionPlan(self.xsDataDiffractionPlan)
if self.xsDataSample is not None:
xsDataCollection.setSample(XSDataSampleCrystalMM.parseString(self.xsDataSample.marshal()))
self.xsDataInputCharacterisation.setDataCollection(xsDataCollection)
def generateTemplateFile(self, _edPlugin):
EDVerbose.DEBUG("EDPluginControlInterfacev1_2.generateTemplateFile")
self.createInputCharacterisationFromSubWedges()
if(self.strGeneratedTemplateFile is None):
EDVerbose.screen("No argument for command line --generateTemplate key word found!")
elif (self.xsDataInputCharacterisation is None):
EDVerbose.screen("ERROR! Cannot generate template file %s, please check the log files." % self.strGeneratedTemplateFile)
else:
EDVerbose.screen("Generating xml template input file for edna: " + self.strGeneratedTemplateFile + "...")
self.xsDataInputCharacterisation.exportToFile(self.strGeneratedTemplateFile)
def doSubWedgeAssembleSUCCESS(self, _edPlugin):
EDVerbose.DEBUG("EDPluginControlInterfacev1_2.doSubWedgeAssembleSUCCESS")
self.createInputCharacterisationFromSubWedges()
self.runCharacterisationPlugin(_edPlugin)
def doSubWedgeAssembleFAILURE(self, _edPlugin):
EDVerbose.DEBUG("EDPluginControlInterfacev1_2.doSubWedgeAssembleFAILURE")
EDVerbose.screen("Execution of " + self.strEDPluginControlSubWedgeAssembleName + " failed.")
EDVerbose.screen("Please inspect the log file for further information.")
self.setFailure()
def doFailureActionCharacterisation(self, _edPlugin=None):
"""
retrieve the potential warning messages
retrieve the potential error messages
"""
EDVerbose.DEBUG("EDPluginControlInterfacev1_2.doFailureActionCharacterisation")
self.retrieveFailureMessages(self.edPluginControlCharacterisation, "EDPluginControlInterfacev1_2.doSuccessActionISPyB")
if _edPlugin.hasDataOutput("statusMessage"):
self.strStatusMessage = _edPlugin.getDataOutput("statusMessage")[0].getValue()
self.generateExecutiveSummary(self)
self.storeResultsInISPyB(_edPlugin)
self.setFailure()
def doSuccessActionCharacterisation(self, _edPlugin=None):
"""
retrieve the potential warning messages
"""
EDVerbose.DEBUG("EDPluginControlInterfacev1_2.doSuccessActionCharacterisation")
# Store the results if requested
if (self.strResultsFilePath is not None):
xsDataCharacterisationResult = _edPlugin.getDataOutput()
if (xsDataCharacterisationResult is not None):
xsDataCharacterisationResult.exportToFile(self.strResultsFilePath)
if _edPlugin.hasDataOutput("statusMessage"):
self.strStatusMessage = _edPlugin.getDataOutput("statusMessage")[0].getValue()
self.storeResultsInISPyB(_edPlugin)
def doSuccessActionISPyB(self, _edPlugin):
EDVerbose.DEBUG("EDPluginControlInterfacev1_2.doSuccessActionISPyB...")
self.retrieveSuccessMessages(self.edPluginControlISPyB, "EDPluginControlInterfacev1_2.doSuccessActionISPyB")
def doFailureActionISPyB(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlInterfacev1_2.doFailureActionISpyB...")
self.generateExecutiveSummary(self)
self.setFailure()
def generateExecutiveSummary(self, _edPlugin=None):
"""
Prints the executive summary from the plugin
"""
EDVerbose.DEBUG("EDPluginControlInterfacev1_2.generateExecutiveSummary")
if (self.edPluginControlSubWedgeAssemble is not None):
if self.edPluginControlSubWedgeAssemble.getListExecutiveSummaryLines() != []:
self.addExecutiveSummaryLine("Summary of plugin %s:" % self.strEDPluginControlSubWedgeAssembleName)
self.appendExecutiveSummary(self.edPluginControlSubWedgeAssemble)
if (self.edPluginControlCharacterisation is not None):
self.addExecutiveSummaryLine("Summary of plugin %s:" % self.strEDPluginControlCharacterisationName)
self.appendExecutiveSummary(self.edPluginControlCharacterisation)
if (self.edPluginControlISPyB is not None):
self.addExecutiveSummaryLine("Summary of plugin %s:" % self.strEDPluginControlISPyBName)
self.appendExecutiveSummary(self.edPluginControlISPyB)
self.verboseScreenExecutiveSummary()
class EDPluginControlInterfacev1_3(EDPluginControl):
"""
This is the common class to all plugins managing user interfaces
"""
def __init__(self):
"""
"""
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputInterface)
self.setXSDataInputClass(XSDataExperimentalCondition,
"experimentalCondition")
self.setXSDataInputClass(XSDataDiffractionPlan, "diffractionPlan")
self.setXSDataInputClass(XSDataSampleCrystalMM, "sample")
self.setXSDataInputClass(XSDataString, "imagePaths")
self.setXSDataInputClass(XSDataFloat, "flux")
self.setXSDataInputClass(XSDataFloat, "minExposureTimePerImage")
self.setXSDataInputClass(XSDataFloat, "beamSize")
self.setXSDataInputClass(XSDataFloat, "beamSizeX")
self.setXSDataInputClass(XSDataFloat, "beamSizeY")
self.setXSDataInputClass(XSDataBoolean, "templateMode")
self.setXSDataInputClass(XSDataString, "generatedTemplateFile")
self.setXSDataInputClass(XSDataString, "resultsFilePath")
self.setXSDataInputClass(XSDataFloat, "beamPosX")
self.setXSDataInputClass(XSDataFloat, "beamPosY")
self.setXSDataInputClass(XSDataDouble, "wavelength")
self.setXSDataInputClass(XSDataDouble, "transmission")
self.setXSDataInputClass(XSDataInteger, "dataCollectionId")
self.setXSDataInputClass(XSDataString, "shortComments")
self.setXSDataInputClass(XSDataString, "comments")
self.setXSDataInputClass(XSDataInputCharacterisation,
"inputCharacterisation")
self.strEDPluginControlSubWedgeAssembleName = "EDPluginControlSubWedgeAssemblev1_1"
self.strEDPluginControlCharacterisationName = "EDPluginControlCharacterisationv1_5"
self.strEDPluginControlISPyBName = "EDPluginControlISPyBv1_1"
self.edPluginControlSubWedgeAssemble = None
self.edPluginControlCharacterisation = None
self.edPluginControlISPyB = None
self.pyListImagePaths = None
self.xsDataInputCharacterisation = None
self.strComplexity = "none"
self.listImagePaths = []
self.fFlux = None
self.fMaxExposureTimePerDataCollection = 10000 # s, default prototype value
self.fMinExposureTimePerImage = None
self.fBeamSizeX = None
self.fBeamSizeY = None
self.fApertureSize = None
self.bTemplateMode = False
self.strGeneratedTemplateFile = None
self.strResultsFilePath = None
self.strForcedSpaceGroup = None
self.bAnomalousData = False
self.fBeamPosX = None
self.fBeamPosY = None
self.fMinOscillationWidth = None
self.fMaxOscillationSpeed = None
self.fWavelength = None
self.fTransmission = None
self.strStrategyOption = None
self.iDataCollectionId = None
self.strShortComments = None
self.strComments = None
self.strStatusMessage = None
self.xsDataExperimentalCodition = None
self.xsDataSample = None
self.xsDataDiffractionPlan = None
def configure(self):
"""
Gets the configuration parameters (if any).
"""
EDPluginControl.configure(self)
self.DEBUG("EDPluginControlInterfacev1_3.configure")
if (self.getControlledPluginName("subWedgeAssemblePlugin")
is not None):
self.strEDPluginControlSubWedgeAssembleName = self.getControlledPluginName(
"subWedgeAssemblePlugin")
if (self.getControlledPluginName("characterisationPlugin")
is not None):
self.strEDPluginControlCharacterisationName = self.getControlledPluginName(
"characterisationPlugin")
if (self.getControlledPluginName("ispybPlugin") is not None):
self.strEDPluginControlISPyBName = self.getControlledPluginName(
"ispybPlugin")
bUseISPyBPlugin = self.config.get("useISPyBPlugin")
if not bUseISPyBPlugin:
self.DEBUG(
"EDPluginControlInterfacev1_3 configured to not use ISPyB")
self.strEDPluginControlISPyBName = None
def preProcess(self, _edPlugin=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edPlugin)
self.DEBUG("EDPluginControlInterfacev1_3.preProcess...")
self.listImagePaths = []
# Check if XSDataInputInterface is given as input
if self.hasDataInput():
xsDataInputInterface = self.getDataInput()
if xsDataInputInterface.getExperimentalCondition():
self.xsDataExperimentalCodition = xsDataInputInterface.getExperimentalCondition(
)
if self.xsDataExperimentalCodition.getGoniostat():
if self.xsDataExperimentalCodition.getGoniostat(
).getMinOscillationWidth():
self.fMinOscillationWidth = self.xsDataExperimentalCodition.getGoniostat(
).getMinOscillationWidth().getValue()
if self.xsDataExperimentalCodition.getGoniostat(
).getMaxOscillationSpeed():
self.fMaxOscillationSpeed = self.xsDataExperimentalCodition.getGoniostat(
).getMaxOscillationSpeed().getValue()
self.xsDataSample = xsDataInputInterface.getSample()
self.xsDataDiffractionPlan = self.getDataInput(
).getDiffractionPlan()
if self.xsDataDiffractionPlan:
if self.xsDataDiffractionPlan.getForcedSpaceGroup():
self.strForcedSpaceGroup = self.xsDataDiffractionPlan.getForcedSpaceGroup(
).getValue()
if self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection(
):
self.fMaxExposureTimePerDataCollection = self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection(
).getValue()
if self.xsDataDiffractionPlan.getAnomalousData():
self.bAnomalousData = self.xsDataDiffractionPlan.getAnomalousData(
).getValue()
if self.xsDataDiffractionPlan.getStrategyOption():
self.strStrategyOption = self.xsDataDiffractionPlan.getStrategyOption(
).getValue()
if self.xsDataDiffractionPlan.getComplexity():
self.strComplexity = self.xsDataDiffractionPlan.getComplexity(
).getValue()
if self.fMinOscillationWidth == None:
if self.xsDataDiffractionPlan.getGoniostatMinOscillationWidth(
):
self.fMinOscillationWidth = self.xsDataDiffractionPlan.getGoniostatMinOscillationWidth(
).getValue()
if self.fMaxOscillationSpeed == None:
if self.xsDataDiffractionPlan.getGoniostatMaxOscillationSpeed(
):
self.fMaxOscillationSpeed = self.xsDataDiffractionPlan.getGoniostatMaxOscillationSpeed(
).getValue()
self.xsDataSample = xsDataInputInterface.getSample()
if xsDataInputInterface.getImagePath():
for xsDataFile in xsDataInputInterface.getImagePath():
self.listImagePaths.append(xsDataFile.getPath())
if xsDataInputInterface.getFlux():
self.fFlux = xsDataInputInterface.getFlux().getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getFlux(
) != None:
self.fFlux = self.xsDataExperimentalCodition.getBeam(
).getFlux().getValue()
if xsDataInputInterface.getMinExposureTimePerImage():
self.fMinExposureTimePerImage = xsDataInputInterface.getMinExposureTimePerImage(
).getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam(
).getMinExposureTimePerImage() != None:
self.fMinExposureTimePerImage = self.xsDataExperimentalCodition.getBeam(
).getMinExposureTimePerImage().getValue()
if self.fMinExposureTimePerImage == None and xsDataInputInterface.getDiffractionPlan(
):
if xsDataInputInterface.getDiffractionPlan(
).getMinExposureTimePerImage() != None:
self.fMinExposureTimePerImage = xsDataInputInterface.getDiffractionPlan(
).getMinExposureTimePerImage().getValue()
if self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getSize(
) != None:
self.fBeamSizeX = self.xsDataExperimentalCodition.getBeam(
).getSize().getX().getValue()
self.fBeamSizeY = self.xsDataExperimentalCodition.getBeam(
).getSize().getY().getValue()
if self.xsDataExperimentalCodition.getBeam(
).getApertureSize() != None:
self.fApertureSize = self.xsDataExperimentalCodition.getBeam(
).getApertureSize().getValue()
if xsDataInputInterface.getBeamSize():
self.fBeamSizeX = xsDataInputInterface.getBeamSize().getValue()
self.fBeamSizeY = xsDataInputInterface.getBeamSize().getValue()
if xsDataInputInterface.getApertureSize():
self.fApertureSize = xsDataInputInterface.getApertureSize(
).getValue()
if xsDataInputInterface.getBeamSizeX():
self.fBeamSizeX = xsDataInputInterface.getBeamSizeX().getValue(
)
if xsDataInputInterface.getBeamSizeY():
self.fBeamSizeY = xsDataInputInterface.getBeamSizeY().getValue(
)
if xsDataInputInterface.getApertureSize():
self.fApertureSize = xsDataInputInterface.getApertureSize(
).getValue()
if xsDataInputInterface.getTemplateMode():
self.bTemplateMode = xsDataInputInterface.getTemplateMode(
).getValue()
if xsDataInputInterface.getBeamPosX():
self.fBeamPosX = xsDataInputInterface.getBeamPosX().getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getDetector() != None:
if self.xsDataExperimentalCodition.getDetector(
).getBeamPositionX() != None:
self.fBeamPosX = self.xsDataExperimentalCodition.getDetector(
).getBeamPositionX().getValue()
if xsDataInputInterface.getBeamPosY():
self.fBeamPosY = xsDataInputInterface.getBeamPosY().getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getDetector() != None:
if self.xsDataExperimentalCodition.getDetector(
).getBeamPositionY() != None:
self.fBeamPosY = self.xsDataExperimentalCodition.getDetector(
).getBeamPositionY().getValue()
if xsDataInputInterface.getWavelength():
self.fWavelength = xsDataInputInterface.getWavelength(
).getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getWavelength(
) != None:
self.fWavelength = self.xsDataExperimentalCodition.getBeam(
).getWavelength().getValue()
if xsDataInputInterface.getTransmission():
self.fTransmission = xsDataInputInterface.getTransmission(
).getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam(
).getTransmission() != None:
self.fTransmission = self.xsDataExperimentalCodition.getBeam(
).getTransmission().getValue()
if xsDataInputInterface.getGeneratedTemplateFile():
self.strGeneratedTemplateFile = xsDataInputInterface.getGeneratedTemplateFile(
).getPath().getValue()
if xsDataInputInterface.getResultsFilePath():
self.strResultsFilePath = xsDataInputInterface.getResultsFilePath(
).getPath().getValue()
if xsDataInputInterface.getDataCollectionId():
self.iDataCollectionId = xsDataInputInterface.getDataCollectionId(
).getValue()
if xsDataInputInterface.getShortComments():
self.strShortComments = xsDataInputInterface.getShortComments(
).getValue()
if xsDataInputInterface.getComments():
self.strComments = xsDataInputInterface.getComments().getValue(
)
if xsDataInputInterface.getInputCharacterisation():
self.xsDataInputCharacterisation = xsDataInputInterface.getInputCharacterisation(
)
if xsDataInputInterface.getDataCollectionId():
self.iDataCollectionId = xsDataInputInterface.getDataCollectionId(
).getValue()
else:
if self.hasDataInput("experimentalCondition"):
self.xsDataExperimentalCodition = self.getDataInput(
"experimentalCondition")[0]
if self.xsDataExperimentalCodition.getGoniostat():
if self.xsDataExperimentalCodition.getGoniostat(
).getMinOscillationWidth():
self.fMinOscillationWidth = self.xsDataExperimentalCodition.getGoniostat(
).getMinOscillationWidth().getValue()
if self.xsDataExperimentalCodition.getGoniostat(
).getMaxOscillationSpeed():
self.fMaxOscillationSpeed = self.xsDataExperimentalCodition.getGoniostat(
).getMaxOscillationSpeed().getValue()
if self.hasDataInput("sample"):
self.xsDataSample = self.getDataInput("sample")[0]
if (self.hasDataInput("diffractionPlan")):
if self.xsDataDiffractionPlan is None:
self.xsDataDiffractionPlan = XSDataDiffractionPlan()
xsDataDiffractionPlans = self.getDataInput("diffractionPlan")
if (not xsDataDiffractionPlans[0] is None):
self.xsDataDiffractionPlan = xsDataDiffractionPlans[0]
if self.xsDataDiffractionPlan.getForcedSpaceGroup():
self.strForcedSpaceGroup = self.xsDataDiffractionPlan.getForcedSpaceGroup(
).getValue()
if self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection(
):
self.fMaxExposureTimePerDataCollection = self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection(
).getValue()
if self.xsDataDiffractionPlan.getAnomalousData():
self.bAnomalousData = self.xsDataDiffractionPlan.getAnomalousData(
).getValue()
if self.xsDataDiffractionPlan.getStrategyOption():
self.strStrategyOption = self.xsDataDiffractionPlan.getStrategyOption(
).getValue()
if self.xsDataDiffractionPlan.getComplexity():
self.strComplexity = self.xsDataDiffractionPlan.getComplexity(
).getValue()
if self.fMinOscillationWidth == None:
if self.xsDataDiffractionPlan.getGoniostatMinOscillationWidth(
):
self.fMinOscillationWidth = self.xsDataDiffractionPlan.getGoniostatMinOscillationWidth(
).getValue()
if self.fMaxOscillationSpeed == None:
if self.xsDataDiffractionPlan.getGoniostatMaxOscillationSpeed(
):
self.fMaxOscillationSpeed = self.xsDataDiffractionPlan.getGoniostatMaxOscillationSpeed(
).getValue()
if self.hasDataInput("sample"):
self.xsDataSample = self.getDataInput("sample")[0]
if self.hasDataInput("imagePaths"):
for strImagePath in self.getDataInput("imagePaths"):
self.listImagePaths.append(strImagePath)
if self.hasDataInput("flux"):
self.fFlux = self.getDataInput("flux")[0].getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getFlux(
) != None:
self.fFlux = self.xsDataExperimentalCodition.getBeam(
).getFlux().getValue()
if self.hasDataInput("minExposureTimePerImage"):
self.fMinExposureTimePerImage = self.getDataInput(
"minExposureTimePerImage")[0].getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam(
).getMinExposureTimePerImage() != None:
self.fMinExposureTimePerImage = self.xsDataExperimentalCodition.getBeam(
).getMinExposureTimePerImage().getValue()
if self.fMinExposureTimePerImage == None and self.hasDataInput(
"diffractionPlan"):
if self.getDataInput("diffractionPlan"
)[0].getMinExposureTimePerImage() != None:
self.fMinExposureTimePerImage = self.getDataInput(
"diffractionPlan")[0].getMinExposureTimePerImage(
).getValue()
if self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getSize(
) != None:
self.fBeamSizeX = self.xsDataExperimentalCodition.getBeam(
).getSize().getX().getValue()
self.fBeamSizeY = self.xsDataExperimentalCodition.getBeam(
).getSize().getY().getValue()
if self.xsDataExperimentalCodition.getBeam(
).getApertureSize() != None:
self.fApertureSize = self.xsDataExperimentalCodition.getBeam(
).getApertureSize().getValue()
if self.hasDataInput("beamSize"):
self.fBeamSizeX = self.getDataInput("beamSize")[0].getValue()
self.fBeamSizeY = self.getDataInput("beamSize")[0].getValue()
if self.hasDataInput("apertureSize"):
self.fApertureSize = self.getDataInput(
"apertureSize")[0].getValue()
if self.hasDataInput("beamSizeX"):
self.fBeamSizeX = self.getDataInput("beamSizeX")[0].getValue()
if self.hasDataInput("beamSizeY"):
self.fBeamSizeY = self.getDataInput("beamSizeY")[0].getValue()
if self.hasDataInput("templateMode"):
self.bTemplateMode = self.getDataInput(
"templateMode")[0].getValue()
if (self.hasDataInput("beamPosX")):
self.fBeamPosX = self.getDataInput("beamPosX")[0].getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getDetector() != None:
if self.xsDataExperimentalCodition.getDetector(
).getBeamPositionX() != None:
self.fBeamPosX = self.xsDataExperimentalCodition.getDetector(
).getBeamPositionX().getValue()
if (self.hasDataInput("beamPosY")):
self.fBeamPosY = self.getDataInput("beamPosY")[0].getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getDetector() != None:
if self.xsDataExperimentalCodition.getDetector(
).getBeamPositionY() != None:
self.fBeamPosY = self.xsDataExperimentalCodition.getDetector(
).getBeamPositionY().getValue()
if (self.hasDataInput("wavelength")):
self.fWavelength = self.getDataInput(
"wavelength")[0].getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getWavelength(
) != None:
self.fWavelength = self.xsDataExperimentalCodition.getBeam(
).getWavelength().getValue()
if (self.hasDataInput("transmission")):
self.fTransmission = self.getDataInput(
"transmission")[0].getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam(
).getTransmission() != None:
self.fTransmission = self.xsDataExperimentalCodition.getBeam(
).getTransmission().getValue()
if self.hasDataInput("generatedTemplateFile"):
self.strGeneratedTemplateFile = self.getDataInput(
"generatedTemplateFile")[0].getValue()
if self.hasDataInput("resultsFilePath"):
self.strResultsFilePath = self.getDataInput(
"resultsFilePath")[0].getValue()
if self.hasDataInput("dataCollectionId"):
self.iDataCollectionId = self.getDataInput(
"dataCollectionId")[0].getValue()
if self.hasDataInput("shortComments"):
self.strShortComments = self.getDataInput(
"shortComments")[0].getValue()
if self.hasDataInput("comments"):
self.strComments = self.getDataInput("comments")[0].getValue()
if self.hasDataInput("inputCharacterisation"):
self.xsDataInputCharacterisation = self.getDataInput(
"inputCharacterisation")[0]
# Check if XML data is given as input :
if (self.xsDataInputCharacterisation is None):
self.edPluginControlSubWedgeAssemble = self.loadPlugin(
self.strEDPluginControlSubWedgeAssembleName,
"SubWedgeAssemble")
self.edPluginControlCharacterisation = self.loadPlugin(
self.strEDPluginControlCharacterisationName, "Characterisation")
if (self.strEDPluginControlISPyBName is not None):
self.edPluginControlISPyB = self.loadPlugin(
self.strEDPluginControlISPyBName, "ISPyB")
def process(self, _edPlugin=None):
EDPluginControl.process(self, _edPlugin)
self.DEBUG("EDPluginControlInterfacev1_3.process...")
if (self.edPluginControlSubWedgeAssemble is not None):
if (self.bTemplateMode == True):
self.edPluginControlSubWedgeAssemble.connectSUCCESS(
self.generateTemplateFile)
else:
self.edPluginControlSubWedgeAssemble.connectSUCCESS(
self.doSubWedgeAssembleSUCCESS)
self.edPluginControlSubWedgeAssemble.connectFAILURE(
self.doSubWedgeAssembleFAILURE)
if (self.edPluginControlCharacterisation is not None):
self.edPluginControlCharacterisation.connectSUCCESS(
self.doSuccessActionCharacterisation)
self.edPluginControlCharacterisation.connectFAILURE(
self.doFailureActionCharacterisation)
if (self.edPluginControlISPyB is not None):
self.edPluginControlISPyB.connectSUCCESS(self.doSuccessActionISPyB)
self.edPluginControlISPyB.connectFAILURE(self.doFailureActionISPyB)
if (self.xsDataInputCharacterisation is None):
self.createInputCharacterisationFromImageHeaders(
self.edPluginControlSubWedgeAssemble)
else:
self.runCharacterisationPlugin(
self.edPluginControlCharacterisation)
def finallyProcess(self, _edPlugin=None):
EDPluginControl.finallyProcess(self, _edPlugin)
self.DEBUG("EDPluginControlInterfacev1_3.finallyProcess...")
if (not self.edPluginControlCharacterisation is None):
if (self.edPluginControlCharacterisation.hasDataOutput()):
self.setDataOutput(
self.edPluginControlCharacterisation.getDataOutput(),
"characterisation")
if (not self.edPluginControlISPyB is None):
if (self.edPluginControlISPyB.hasDataOutput()):
self.setDataOutput(self.edPluginControlISPyB.getDataOutput(),
"ISPyB")
if self.hasDataInput():
xsDataResultInterface = XSDataResultInterface()
if self.edPluginControlCharacterisation:
xsDataResultInterface.setResultCharacterisation(
self.edPluginControlCharacterisation.getDataOutput())
if self.edPluginControlISPyB:
xsDataResultInterface.setResultControlISPyB(
self.edPluginControlISPyB.getDataOutput())
self.setDataOutput(xsDataResultInterface)
def createInputCharacterisationFromImageHeaders(self, _edPlugin):
self.DEBUG(
"EDPluginControlInterfacev1_3.createInputCharacterisationFromImageHeaders"
)
xsDataInputSubWedgeAssemble = XSDataInputSubWedgeAssemble()
for xsDataStringImagePath in self.listImagePaths:
xsDataFile = XSDataFile()
xsDataFile.setPath(xsDataStringImagePath)
xsDataInputSubWedgeAssemble.addFile(xsDataFile)
_edPlugin.setDataInput(xsDataInputSubWedgeAssemble)
_edPlugin.executeSynchronous()
def runCharacterisationPlugin(self, _edPlugin=None):
self.DEBUG("EDPluginControlInterfacev1_3.runCharacterisationPlugin")
self.edPluginControlCharacterisation.setDataInput(
self.xsDataInputCharacterisation)
self.edPluginControlCharacterisation.executeSynchronous()
def storeResultsInISPyB(self, _edPlugin=None):
self.DEBUG("EDPluginControlInterfacev1_3.storeResultsInISPyB")
if (self.edPluginControlISPyB is not None):
# Execute the ISPyB control plugin
xsDataInputControlISPyB = XSDataInputControlISPyB()
xsDataInputControlISPyB.setCharacterisationResult(
self.edPluginControlCharacterisation.getDataOutput())
if (not self.iDataCollectionId is None):
dataCollectionGroupId = self.getDataCollectionGroupId(
self.iDataCollectionId)
xsDataInputControlISPyB.setDataCollectionGroupId(
XSDataInteger(dataCollectionGroupId))
if (not self.strShortComments is None):
self.edPluginControlISPyB.setDataInput(
XSDataString(self.strShortComments), "shortComments")
if (not self.strComments is None):
self.edPluginControlISPyB.setDataInput(
XSDataString(self.strComments), "comments")
if (not self.strStatusMessage is None):
self.edPluginControlISPyB.setDataInput(
XSDataString(self.strStatusMessage), "statusMessage")
self.edPluginControlISPyB.setDataInput(xsDataInputControlISPyB)
self.edPluginControlISPyB.executeSynchronous()
self.checkDozorScores(
self.edPluginControlCharacterisation.getDataOutput())
def createInputCharacterisationFromSubWedges(self):
self.DEBUG(
"EDPluginControlInterfacev1_3.createInputCharacterisationFromSubWedges"
)
xsDataResultSubWedgeAssemble = self.edPluginControlSubWedgeAssemble.getDataOutput(
)
self.xsDataInputCharacterisation = XSDataInputCharacterisation()
xsDataCollection = XSDataCollection()
# Default exposure time (for the moment, this value should be
# possible to read from the command line)
if self.xsDataDiffractionPlan is None:
self.xsDataDiffractionPlan = XSDataDiffractionPlan()
if (not xsDataResultSubWedgeAssemble is None):
pyListSubWedge = xsDataResultSubWedgeAssemble.getSubWedge()
xsDataCollection.setSubWedge(pyListSubWedge)
for xsDataSubWedge in pyListSubWedge:
if (self.strComplexity is not None):
self.xsDataDiffractionPlan.setComplexity(
XSDataString(self.strComplexity))
if (self.fFlux is not None):
xsDataSubWedge.getExperimentalCondition().getBeam(
).setFlux(XSDataFlux(self.fFlux))
if (self.fBeamSizeX is not None) and (self.fBeamSizeY
is not None):
xsDataSize = XSDataSize()
xsDataSize.setX(XSDataLength(self.fBeamSizeX))
xsDataSize.setY(XSDataLength(self.fBeamSizeY))
xsDataSubWedge.getExperimentalCondition().getBeam(
).setSize(xsDataSize)
if (self.fApertureSize is not None):
xsDataSubWedge.getExperimentalCondition().getBeam(
).setApertureSize(XSDataLength(self.fApertureSize))
if (self.fBeamPosX is not None):
xsDataSubWedge.getExperimentalCondition().getDetector(
).setBeamPositionX(XSDataLength(self.fBeamPosX))
if (self.fBeamPosY is not None):
xsDataSubWedge.getExperimentalCondition().getDetector(
).setBeamPositionY(XSDataLength(self.fBeamPosY))
if (self.fMinExposureTimePerImage is not None):
xsDataSubWedge.getExperimentalCondition().getBeam(
).setMinExposureTimePerImage(
XSDataTime(self.fMinExposureTimePerImage))
if (self.fTransmission is not None):
xsDataSubWedge.getExperimentalCondition().getBeam(
).setTransmission(XSDataDouble(self.fTransmission))
if (self.fWavelength is not None):
xsDataSubWedge.getExperimentalCondition().getBeam(
).setWavelength(XSDataWavelength(self.fWavelength))
if self.fMinOscillationWidth != None:
xsDataSubWedge.getExperimentalCondition().getGoniostat(
).setMinOscillationWidth(
XSDataAngle(self.fMinOscillationWidth))
if self.fMaxOscillationSpeed != None:
xsDataSubWedge.getExperimentalCondition().getGoniostat(
).setMaxOscillationSpeed(
XSDataAngularSpeed(self.fMaxOscillationSpeed))
if (self.strForcedSpaceGroup is not None):
self.xsDataDiffractionPlan.setForcedSpaceGroup(
XSDataString(self.strForcedSpaceGroup))
self.xsDataDiffractionPlan.setAnomalousData(
XSDataBoolean(self.bAnomalousData))
self.xsDataDiffractionPlan.setMaxExposureTimePerDataCollection(
XSDataTime(self.fMaxExposureTimePerDataCollection))
if (self.strStrategyOption is not None):
self.xsDataDiffractionPlan.setStrategyOption(
XSDataString(self.strStrategyOption))
xsDataCollection.setDiffractionPlan(self.xsDataDiffractionPlan)
if self.xsDataSample is not None:
xsDataCollection.setSample(
XSDataSampleCrystalMM.parseString(self.xsDataSample.marshal()))
self.xsDataInputCharacterisation.setDataCollection(xsDataCollection)
def generateTemplateFile(self, _edPlugin):
self.DEBUG("EDPluginControlInterfacev1_3.generateTemplateFile")
self.createInputCharacterisationFromSubWedges()
if (self.strGeneratedTemplateFile is None):
self.screen(
"No argument for command line --generateTemplate key word found!"
)
elif (self.xsDataInputCharacterisation is None):
self.screen(
"ERROR! Cannot generate template file %s, please check the log files."
% self.strGeneratedTemplateFile)
else:
self.screen("Generating xml template input file for edna: " +
self.strGeneratedTemplateFile + "...")
self.xsDataInputCharacterisation.exportToFile(
self.strGeneratedTemplateFile)
def doSubWedgeAssembleSUCCESS(self, _edPlugin):
self.DEBUG("EDPluginControlInterfacev1_3.doSubWedgeAssembleSUCCESS")
self.createInputCharacterisationFromSubWedges()
self.runCharacterisationPlugin(_edPlugin)
def doSubWedgeAssembleFAILURE(self, _edPlugin):
self.DEBUG("EDPluginControlInterfacev1_3.doSubWedgeAssembleFAILURE")
self.screen("Execution of " +
self.strEDPluginControlSubWedgeAssembleName + " failed.")
self.screen("Please inspect the log file for further information.")
self.setFailure()
def doFailureActionCharacterisation(self, _edPlugin=None):
"""
retrieve the potential warning messages
retrieve the potential error messages
"""
self.DEBUG(
"EDPluginControlInterfacev1_3.doFailureActionCharacterisation")
self.retrieveFailureMessages(
self.edPluginControlCharacterisation,
"EDPluginControlInterfacev1_3.doSuccessActionISPyB")
if _edPlugin.hasDataOutput("statusMessage"):
self.strStatusMessage = _edPlugin.getDataOutput(
"statusMessage")[0].getValue()
self.generateExecutiveSummary(self)
self.storeResultsInISPyB(_edPlugin)
self.setFailure()
def doSuccessActionCharacterisation(self, _edPlugin=None):
"""
retrieve the potential warning messages
"""
self.DEBUG(
"EDPluginControlInterfacev1_3.doSuccessActionCharacterisation")
# Store the results if requested
if (self.strResultsFilePath is not None):
xsDataCharacterisationResult = _edPlugin.getDataOutput()
if (xsDataCharacterisationResult is not None):
xsDataCharacterisationResult.exportToFile(
self.strResultsFilePath)
if _edPlugin.hasDataOutput("statusMessage"):
self.strStatusMessage = _edPlugin.getDataOutput(
"statusMessage")[0].getValue()
self.storeResultsInISPyB(_edPlugin)
def doSuccessActionISPyB(self, _edPlugin):
self.DEBUG("EDPluginControlInterfacev1_3.doSuccessActionISPyB...")
self.retrieveSuccessMessages(
self.edPluginControlISPyB,
"EDPluginControlInterfacev1_3.doSuccessActionISPyB")
def doFailureActionISPyB(self, _edPlugin=None):
self.DEBUG("EDPluginControlInterfacev1_3.doFailureActionISpyB...")
self.generateExecutiveSummary(self)
self.setFailure()
def generateExecutiveSummary(self, _edPlugin=None):
"""
Prints the executive summary from the plugin
"""
self.DEBUG("EDPluginControlInterfacev1_3.generateExecutiveSummary")
if (self.edPluginControlSubWedgeAssemble is not None):
if self.edPluginControlSubWedgeAssemble.getListExecutiveSummaryLines(
) != []:
self.addExecutiveSummaryLine(
"Summary of plugin %s:" %
self.strEDPluginControlSubWedgeAssembleName)
self.appendExecutiveSummary(
self.edPluginControlSubWedgeAssemble)
if (self.edPluginControlCharacterisation is not None):
self.addExecutiveSummaryLine(
"Summary of plugin %s:" %
self.strEDPluginControlCharacterisationName)
self.appendExecutiveSummary(self.edPluginControlCharacterisation)
if (self.edPluginControlISPyB is not None):
self.addExecutiveSummaryLine("Summary of plugin %s:" %
self.strEDPluginControlISPyBName)
self.appendExecutiveSummary(self.edPluginControlISPyB)
self.verboseScreenExecutiveSummary()
def checkDozorScores(self, _xsDataResultCharacterisation):
# Check Dozor scores
listImageQualityIndicators = _xsDataResultCharacterisation.imageQualityIndicators
noWeakDiffraction = 0
noTotal = 0
newComment = None
referenceImagePath = None
listImageNoWithNoDiffraction = []
for imageQualityIndicators in listImageQualityIndicators:
if referenceImagePath is None:
referenceImagePath = imageQualityIndicators.image.path.value
if imageQualityIndicators.dozor_score is not None:
noTotal += 1
dozorScore = imageQualityIndicators.dozor_score.value
if dozorScore <= 0.001:
listImageNoWithNoDiffraction.append(
imageQualityIndicators.image.number.value)
elif dozorScore < 1.0:
noWeakDiffraction += 1
if noTotal > 0:
if len(listImageNoWithNoDiffraction) == noTotal:
newComment = "No diffraction."
elif noWeakDiffraction + len(
listImageNoWithNoDiffraction) == noTotal:
newComment = "Very weak diffraction."
else:
subComment = None
if len(listImageNoWithNoDiffraction) == 1:
subComment = "image {0}".format(
listImageNoWithNoDiffraction[0])
elif len(listImageNoWithNoDiffraction) == 2:
subComment = "images {0} and {1}".format(
listImageNoWithNoDiffraction[0],
listImageNoWithNoDiffraction[1])
elif len(listImageNoWithNoDiffraction) > 2:
subComment = "images {0}".format(
listImageNoWithNoDiffraction[0])
for imageNo in listImageNoWithNoDiffraction[1:-1]:
subComment += ", {0}".format(imageNo)
subComment += " and {0}".format(
listImageNoWithNoDiffraction[-1])
if subComment is not None:
newComment = "No diffraction detected in {0} - hint: sample might not be accurately centred.".format(
subComment)
if newComment is not None and self.iDataCollectionId is not None:
xsDataInput = XSDataInputISPyBUpdateDataCollectionGroupComment(
)
xsDataInput.newComment = XSDataString(newComment)
xsDataInput.dataCollectionId = XSDataInteger(
self.iDataCollectionId)
edPluginISPyBUpdateDataCollectionGroupComment = self.loadPlugin(
"EDPluginISPyBUpdateDataCollectionGroupCommentv1_4")
edPluginISPyBUpdateDataCollectionGroupComment.dataInput = xsDataInput
self.executePluginSynchronous(
edPluginISPyBUpdateDataCollectionGroupComment)
def getDataCollectionGroupId(self, _dataCollectionId):
self.DEBUG("EDPluginControlInterfacev1_2.getDataCollectionGroupId")
self.DEBUG("dataCollectionId = {0}".format(_dataCollectionId))
dataCollectionGroupId = None
xsDataInputRetrieveDataCollection = XSDataInputRetrieveDataCollection()
xsDataInputRetrieveDataCollection.dataCollectionId = XSDataInteger(
_dataCollectionId)
edPluginISPyBRetrieveDataCollection = self.loadPlugin(
"EDPluginISPyBRetrieveDataCollectionv1_4")
edPluginISPyBRetrieveDataCollection.dataInput = xsDataInputRetrieveDataCollection
edPluginISPyBRetrieveDataCollection.executeSynchronous()
xsDataResultRetrieveDataCollection = edPluginISPyBRetrieveDataCollection.dataOutput
if xsDataResultRetrieveDataCollection is not None:
dataCollection = xsDataResultRetrieveDataCollection.dataCollection
if dataCollection is not None:
dataCollectionGroupId = dataCollection.dataCollectionGroupId
self.DEBUG("dataCollectionGroupId = {0}".format(dataCollectionGroupId))
return dataCollectionGroupId
def diffractionPlan(self):
# Do we have a diffracionPlan?
xsDataDiffractionPlan = self.xsDataResultCharacterisation.getDataCollection().getDiffractionPlan()
if xsDataDiffractionPlan is None:
xsDataDiffractionPlan = XSDataDiffractionPlan()
self.page.h2( "Diffraction Plan" )
self.page.table( class_='diffractionPlan', border_="1", cellpadding_="0")
self.page.tr( align_="CENTER", bgcolor_=self.strTableColourTitle2)
self.page.th("Forced<br>space group")
self.page.th("Anomalous<br>data")
self.page.th("Aimed<br>multiplicity")
self.page.th("Aimed<br>completeness")
self.page.th("Aimed I/sigma<br>at highest res.")
self.page.th("Aimed<br>resolution (Å)")
self.page.tr.close()
self.page.tr( align_="CENTER", bgcolor_=self.strTableColourRows)
# Forced space group
if xsDataDiffractionPlan.getForcedSpaceGroup() is None:
strForcedSpaceGroup = "None"
else:
strForcedSpaceGroup = xsDataDiffractionPlan.getForcedSpaceGroup().getValue()
self.page.th(strForcedSpaceGroup)
# Anomalous data
if xsDataDiffractionPlan.getAnomalousData() is None or xsDataDiffractionPlan.getAnomalousData().getValue() == False:
strAnomalousData = "False"
else:
strAnomalousData = "True"
self.page.th(strAnomalousData)
# Aimed multiplicity
if xsDataDiffractionPlan.getAimedMultiplicity() is None:
strAimedMultiplicity = "Default<br>(optimized)"
else:
strAimedMultiplicity = "%.2f" % xsDataDiffractionPlan.getAimedMultiplicity().getValue()
self.page.th(strAimedMultiplicity)
# Aimed completeness
if xsDataDiffractionPlan.getAimedCompleteness() is None:
strAimedCompleteness = "Default<br>(>= 0.99)"
else:
strAimedCompleteness = "%.2f" % xsDataDiffractionPlan.getAimedCompleteness().getValue()
self.page.th(strAimedCompleteness)
# Aimed aimedIOverSigmaAtHighestResolution
if xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution() is None:
strAimedIOverSigmaAtHighestResolution = "BEST Default"
else:
strAimedIOverSigmaAtHighestResolution = "%.2f" % xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution().getValue()
self.page.th(strAimedIOverSigmaAtHighestResolution)
# Aimed resolution
if xsDataDiffractionPlan.getAimedResolution() is None:
strAimedResolution = "Default<br>(highest possible)"
else:
strAimedResolution = "%0.2f" % xsDataDiffractionPlan.getAimedResolution().getValue()
self.page.th(strAimedResolution)
# Close the table
self.page.tr.close()
self.page.table.close()
class EDPluginControlInterfacev1_2(EDPluginControl):
"""
This is the common class to all plugins managing user interfaces
"""
def __init__(self):
"""
"""
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputInterface)
self.setXSDataInputClass(XSDataExperimentalCondition,
"experimentalCondition")
self.setXSDataInputClass(XSDataDiffractionPlan, "diffractionPlan")
self.setXSDataInputClass(XSDataSampleCrystalMM, "sample")
self.setXSDataInputClass(XSDataString, "imagePaths")
self.setXSDataInputClass(XSDataFloat, "flux")
self.setXSDataInputClass(XSDataFloat, "minExposureTimePerImage")
self.setXSDataInputClass(XSDataFloat, "beamSize")
self.setXSDataInputClass(XSDataFloat, "beamSizeX")
self.setXSDataInputClass(XSDataFloat, "beamSizeY")
self.setXSDataInputClass(XSDataBoolean, "templateMode")
self.setXSDataInputClass(XSDataString, "generatedTemplateFile")
self.setXSDataInputClass(XSDataString, "resultsFilePath")
self.setXSDataInputClass(XSDataFloat, "beamPosX")
self.setXSDataInputClass(XSDataFloat, "beamPosY")
self.setXSDataInputClass(XSDataDouble, "wavelength")
self.setXSDataInputClass(XSDataDouble, "transmission")
self.setXSDataInputClass(XSDataInteger, "dataCollectionId")
self.setXSDataInputClass(XSDataString, "shortComments")
self.setXSDataInputClass(XSDataString, "comments")
self.setXSDataInputClass(XSDataInputCharacterisation,
"inputCharacterisation")
self.strEDPluginControlSubWedgeAssembleName = "EDPluginControlSubWedgeAssemblev1_1"
self.strEDPluginControlCharacterisationName = "EDPluginControlCharacterisationv1_1"
self.strEDPluginControlISPyBName = "EDPluginControlISPyBv1_1"
self.edPluginControlSubWedgeAssemble = None
self.edPluginControlCharacterisation = None
self.edPluginControlISPyB = None
self.pyListImagePaths = None
self.xsDataInputCharacterisation = None
self.strComplexity = "none"
self.listImagePaths = []
self.fFlux = None
self.fMaxExposureTimePerDataCollection = 10000 # s, default prototype value
self.fMinExposureTimePerImage = None
self.fBeamSizeX = None
self.fBeamSizeY = None
self.bTemplateMode = False
self.strGeneratedTemplateFile = None
self.strResultsFilePath = None
self.strForcedSpaceGroup = None
self.bAnomalousData = False
self.fBeamPosX = None
self.fBeamPosY = None
self.fMinOscillationWidth = None
self.fMaxOscillationSpeed = None
self.fWavelength = None
self.fTransmission = None
self.strStrategyOption = None
self.iDataCollectionId = None
self.strShortComments = None
self.strComments = None
self.strStatusMessage = None
self.xsDataExperimentalCodition = None
self.xsDataSample = None
self.xsDataDiffractionPlan = None
def configure(self):
"""
Gets the configuration parameters (if any).
"""
EDPluginControl.configure(self)
EDVerbose.DEBUG("EDPluginControlInterfacev1_2.configure")
pluginConfiguration = self.getConfiguration()
if (pluginConfiguration is None):
EDVerbose.DEBUG(
"No plugin configuration found for EDPluginControlInterfacev1_2."
)
else:
if (self.getControlledPluginName("subWedgeAssemblePlugin")
is not None):
self.strEDPluginControlSubWedgeAssembleName = self.getControlledPluginName(
"subWedgeAssemblePlugin")
if (self.getControlledPluginName("characterisationPlugin")
is not None):
self.strEDPluginControlCharacterisationName = self.getControlledPluginName(
"characterisationPlugin")
if (self.getControlledPluginName("ispybPlugin") is not None):
self.strEDPluginControlISPyBName = self.getControlledPluginName(
"ispybPlugin")
bUseISPyBPlugin = EDConfiguration.getStringParamValue(
pluginConfiguration, "useISPyBPlugin")
if (bUseISPyBPlugin.lower() != "true"):
self.strEDPluginControlISPyBName = None
def preProcess(self, _edPlugin=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edPlugin)
EDVerbose.DEBUG("EDPluginControlInterfacev1_2.preProcess...")
self.listImagePaths = []
# Check if XSDataInputInterface is given as input
if self.hasDataInput():
xsDataInputInterface = self.getDataInput()
if xsDataInputInterface.getExperimentalCondition():
self.xsDataExperimentalCodition = xsDataInputInterface.getExperimentalCondition(
)
if self.xsDataExperimentalCodition.getGoniostat():
if self.xsDataExperimentalCodition.getGoniostat(
).getMinOscillationWidth():
self.fMinOscillationWidth = self.xsDataExperimentalCodition.getGoniostat(
).getMinOscillationWidth().getValue()
if self.xsDataExperimentalCodition.getGoniostat(
).getMaxOscillationSpeed():
self.fMaxOscillationSpeed = self.xsDataExperimentalCodition.getGoniostat(
).getMaxOscillationSpeed().getValue()
self.xsDataSample = xsDataInputInterface.getSample()
self.xsDataDiffractionPlan = self.getDataInput(
).getDiffractionPlan()
if self.xsDataDiffractionPlan:
if self.xsDataDiffractionPlan.getForcedSpaceGroup():
self.strForcedSpaceGroup = self.xsDataDiffractionPlan.getForcedSpaceGroup(
).getValue()
if self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection(
):
self.fMaxExposureTimePerDataCollection = self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection(
).getValue()
if self.xsDataDiffractionPlan.getAnomalousData():
self.bAnomalousData = self.xsDataDiffractionPlan.getAnomalousData(
).getValue()
if self.xsDataDiffractionPlan.getStrategyOption():
self.strStrategyOption = self.xsDataDiffractionPlan.getStrategyOption(
).getValue()
if self.xsDataDiffractionPlan.getComplexity():
self.strComplexity = self.xsDataDiffractionPlan.getComplexity(
).getValue()
if self.fMinOscillationWidth == None:
if self.xsDataDiffractionPlan.getGoniostatMinOscillationWidth(
):
self.fMinOscillationWidth = self.xsDataDiffractionPlan.getGoniostatMinOscillationWidth(
).getValue()
if self.fMaxOscillationSpeed == None:
if self.xsDataDiffractionPlan.getGoniostatMaxOscillationSpeed(
):
self.fMaxOscillationSpeed = self.xsDataDiffractionPlan.getGoniostatMaxOscillationSpeed(
).getValue()
self.xsDataSample = xsDataInputInterface.getSample()
if xsDataInputInterface.getImagePath():
for xsDataFile in xsDataInputInterface.getImagePath():
self.listImagePaths.append(xsDataFile.getPath())
if xsDataInputInterface.getFlux():
self.fFlux = xsDataInputInterface.getFlux().getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getFlux(
) != None:
self.fFlux = self.xsDataExperimentalCodition.getBeam(
).getFlux().getValue()
if xsDataInputInterface.getMinExposureTimePerImage():
self.fMinExposureTimePerImage = xsDataInputInterface.getMinExposureTimePerImage(
).getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam(
).getMinExposureTimePerImage() != None:
self.fMinExposureTimePerImage = self.xsDataExperimentalCodition.getBeam(
).getMinExposureTimePerImage().getValue()
if self.fMinExposureTimePerImage == None and xsDataInputInterface.getDiffractionPlan(
):
if xsDataInputInterface.getDiffractionPlan(
).getMinExposureTimePerImage() != None:
self.fMinExposureTimePerImage = xsDataInputInterface.getdiffractionPlan(
).getMinExposureTimePerImage().getValue()
if self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getSize(
) != None:
self.fBeamSizeX = self.xsDataExperimentalCodition.getBeam(
).getSize().getX().getValue()
self.fBeamSizeY = self.xsDataExperimentalCodition.getBeam(
).getSize().getY().getValue()
if xsDataInputInterface.getBeamSize():
self.fBeamSizeX = xsDataInputInterface.getBeamSize().getValue()
self.fBeamSizeY = xsDataInputInterface.getBeamSize().getValue()
if xsDataInputInterface.getBeamSizeX():
self.fBeamSizeX = xsDataInputInterface.getBeamSizeX().getValue(
)
if xsDataInputInterface.getBeamSizeY():
self.fBeamSizeY = xsDataInputInterface.getBeamSizeY().getValue(
)
if xsDataInputInterface.getTemplateMode():
self.bTemplateMode = xsDataInputInterface.getTemplateMode(
).getValue()
if xsDataInputInterface.getBeamPosX():
self.fBeamPosX = xsDataInputInterface.getBeamPosX().getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getDetector() != None:
if self.xsDataExperimentalCodition.getDetector(
).getBeamPositionX() != None:
self.fBeamPosX = self.xsDataExperimentalCodition.getDetector(
).getBeamPositionX().getValue()
if xsDataInputInterface.getBeamPosY():
self.fBeamPosY = xsDataInputInterface.getBeamPosY().getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getDetector() != None:
if self.xsDataExperimentalCodition.getDetector(
).getBeamPositionY() != None:
self.fBeamPosY = self.xsDataExperimentalCodition.getDetector(
).getBeamPositionY().getValue()
if xsDataInputInterface.getWavelength():
self.fWavelength = xsDataInputInterface.getWavelength(
).getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getWavelength(
) != None:
self.fWavelength = self.xsDataExperimentalCodition.getBeam(
).getWavelength().getValue()
if xsDataInputInterface.getTransmission():
self.fTransmission = xsDataInputInterface.getTransmission(
).getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam(
).getTransmission() != None:
self.fTransmission = self.xsDataExperimentalCodition.getBeam(
).getTransmission().getValue()
if xsDataInputInterface.getGeneratedTemplateFile():
self.strGeneratedTemplateFile = xsDataInputInterface.getGeneratedTemplateFile(
).getPath().getValue()
if xsDataInputInterface.getResultsFilePath():
self.strResultsFilePath = xsDataInputInterface.getResultsFilePath(
).getPath().getValue()
if xsDataInputInterface.getDataCollectionId():
self.iDataCollectionId = xsDataInputInterface.getDataCollectionId(
).getValue()
if xsDataInputInterface.getShortComments():
self.strShortComments = xsDataInputInterface.getShortComments(
).getValue()
if xsDataInputInterface.getComments():
self.strComments = xsDataInputInterface.getComments().getValue(
)
if xsDataInputInterface.getInputCharacterisation():
self.xsDataInputCharacterisation = xsDataInputInterface.getInputCharacterisation(
)
if xsDataInputInterface.getDataCollectionId():
self.iDataCollectionId = xsDataInputInterface.getDataCollectionId(
).getValue()
else:
if self.hasDataInput("experimentalCondition"):
self.xsDataExperimentalCodition = self.getDataInput(
"experimentalCondition")[0]
if self.xsDataExperimentalCodition.getGoniostat():
if self.xsDataExperimentalCodition.getGoniostat(
).getMinOscillationWidth():
self.fMinOscillationWidth = self.xsDataExperimentalCodition.getGoniostat(
).getMinOscillationWidth().getValue()
if self.xsDataExperimentalCodition.getGoniostat(
).getMaxOscillationSpeed():
self.fMaxOscillationSpeed = self.xsDataExperimentalCodition.getGoniostat(
).getMaxOscillationSpeed().getValue()
if self.hasDataInput("sample"):
self.xsDataSample = self.getDataInput("sample")[0]
if (self.hasDataInput("diffractionPlan")):
if self.xsDataDiffractionPlan is None:
self.xsDataDiffractionPlan = XSDataDiffractionPlan()
xsDataDiffractionPlans = self.getDataInput("diffractionPlan")
if (not xsDataDiffractionPlans[0] is None):
self.xsDataDiffractionPlan = xsDataDiffractionPlans[0]
if self.xsDataDiffractionPlan.getForcedSpaceGroup():
self.strForcedSpaceGroup = self.xsDataDiffractionPlan.getForcedSpaceGroup(
).getValue()
if self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection(
):
self.fMaxExposureTimePerDataCollection = self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection(
).getValue()
if self.xsDataDiffractionPlan.getAnomalousData():
self.bAnomalousData = self.xsDataDiffractionPlan.getAnomalousData(
).getValue()
if self.xsDataDiffractionPlan.getStrategyOption():
self.strStrategyOption = self.xsDataDiffractionPlan.getStrategyOption(
).getValue()
if self.xsDataDiffractionPlan.getComplexity():
self.strComplexity = self.xsDataDiffractionPlan.getComplexity(
).getValue()
if self.fMinOscillationWidth == None:
if self.xsDataDiffractionPlan.getGoniostatMinOscillationWidth(
):
self.fMinOscillationWidth = self.xsDataDiffractionPlan.getGoniostatMinOscillationWidth(
).getValue()
if self.fMaxOscillationSpeed == None:
if self.xsDataDiffractionPlan.getGoniostatMaxOscillationSpeed(
):
self.fMaxOscillationSpeed = self.xsDataDiffractionPlan.getGoniostatMaxOscillationSpeed(
).getValue()
if self.hasDataInput("sample"):
self.xsDataSample = self.getDataInput("sample")[0]
if self.hasDataInput("imagePaths"):
for strImagePath in self.getDataInput("imagePaths"):
self.listImagePaths.append(strImagePath)
if self.hasDataInput("flux"):
self.fFlux = self.getDataInput("flux")[0].getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getFlux(
) != None:
self.fFlux = self.xsDataExperimentalCodition.getBeam(
).getFlux().getValue()
if self.hasDataInput("minExposureTimePerImage"):
self.fMinExposureTimePerImage = self.getDataInput(
"minExposureTimePerImage")[0].getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam(
).getMinExposureTimePerImage() != None:
self.fMinExposureTimePerImage = self.xsDataExperimentalCodition.getBeam(
).getMinExposureTimePerImage().getValue()
if self.fMinExposureTimePerImage == None and self.hasDataInput(
"diffractionPlan"):
if self.getDataInput("diffractionPlan"
)[0].getMinExposureTimePerImage() != None:
self.fMinExposureTimePerImage = self.getDataInput(
"diffractionPlan")[0].getMinExposureTimePerImage(
).getValue()
if self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getSize(
) != None:
self.fBeamSizeX = self.xsDataExperimentalCodition.getBeam(
).getSize().getX().getValue()
self.fBeamSizeY = self.xsDataExperimentalCodition.getBeam(
).getSize().getY().getValue()
if self.hasDataInput("beamSize"):
self.fBeamSizeX = self.getDataInput("beamSize")[0].getValue()
self.fBeamSizeY = self.getDataInput("beamSize")[0].getValue()
if self.hasDataInput("beamSizeX"):
self.fBeamSizeX = self.getDataInput("beamSizeX")[0].getValue()
if self.hasDataInput("beamSizeY"):
self.fBeamSizeY = self.getDataInput("beamSizeY")[0].getValue()
if self.hasDataInput("templateMode"):
self.bTemplateMode = self.getDataInput(
"templateMode")[0].getValue()
if (self.hasDataInput("beamPosX")):
self.fBeamPosX = self.getDataInput("beamPosX")[0].getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getDetector() != None:
if self.xsDataExperimentalCodition.getDetector(
).getBeamPositionX() != None:
self.fBeamPosX = self.xsDataExperimentalCodition.getDetector(
).getBeamPositionX().getValue()
if (self.hasDataInput("beamPosY")):
self.fBeamPosY = self.getDataInput("beamPosY")[0].getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getDetector() != None:
if self.xsDataExperimentalCodition.getDetector(
).getBeamPositionY() != None:
self.fBeamPosY = self.xsDataExperimentalCodition.getDetector(
).getBeamPositionY().getValue()
if (self.hasDataInput("wavelength")):
self.fWavelength = self.getDataInput(
"wavelength")[0].getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getWavelength(
) != None:
self.fWavelength = self.xsDataExperimentalCodition.getBeam(
).getWavelength().getValue()
if (self.hasDataInput("transmission")):
self.fTransmission = self.getDataInput(
"transmission")[0].getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam(
).getTransmission() != None:
self.fTransmission = self.xsDataExperimentalCodition.getBeam(
).getTransmission().getValue()
if self.hasDataInput("generatedTemplateFile"):
self.strGeneratedTemplateFile = self.getDataInput(
"generatedTemplateFile")[0].getValue()
if self.hasDataInput("resultsFilePath"):
self.strResultsFilePath = self.getDataInput(
"resultsFilePath")[0].getValue()
if self.hasDataInput("dataCollectionId"):
self.iDataCollectionId = self.getDataInput(
"dataCollectionId")[0].getValue()
if self.hasDataInput("shortComments"):
self.strShortComments = self.getDataInput(
"shortComments")[0].getValue()
if self.hasDataInput("comments"):
self.strComments = self.getDataInput("comments")[0].getValue()
if self.hasDataInput("inputCharacterisation"):
self.xsDataInputCharacterisation = self.getDataInput(
"inputCharacterisation")[0]
# Check if XML data is given as input :
if (self.xsDataInputCharacterisation is None):
self.edPluginControlSubWedgeAssemble = self.loadPlugin(
self.strEDPluginControlSubWedgeAssembleName,
"SubWedgeAssemble")
self.edPluginControlCharacterisation = self.loadPlugin(
self.strEDPluginControlCharacterisationName, "Characterisation")
if (self.strEDPluginControlISPyBName is not None):
self.edPluginControlISPyB = self.loadPlugin(
self.strEDPluginControlISPyBName, "ISPyB")
def process(self, _edPlugin=None):
EDPluginControl.process(self, _edPlugin)
EDVerbose.DEBUG("EDPluginControlInterfacev1_2.process...")
if (self.edPluginControlSubWedgeAssemble is not None):
if (self.bTemplateMode == True):
self.edPluginControlSubWedgeAssemble.connectSUCCESS(
self.generateTemplateFile)
else:
self.edPluginControlSubWedgeAssemble.connectSUCCESS(
self.doSubWedgeAssembleSUCCESS)
self.edPluginControlSubWedgeAssemble.connectFAILURE(
self.doSubWedgeAssembleFAILURE)
if (self.edPluginControlCharacterisation is not None):
self.edPluginControlCharacterisation.connectSUCCESS(
self.doSuccessActionCharacterisation)
self.edPluginControlCharacterisation.connectFAILURE(
self.doFailureActionCharacterisation)
if (self.edPluginControlISPyB is not None):
self.edPluginControlISPyB.connectSUCCESS(self.doSuccessActionISPyB)
self.edPluginControlISPyB.connectFAILURE(self.doFailureActionISPyB)
if (self.xsDataInputCharacterisation is None):
self.createInputCharacterisationFromImageHeaders(
self.edPluginControlSubWedgeAssemble)
else:
self.runCharacterisationPlugin(
self.edPluginControlCharacterisation)
def finallyProcess(self, _edPlugin=None):
EDPluginControl.finallyProcess(self, _edPlugin)
EDVerbose.DEBUG("EDPluginControlInterfacev1_2.finallyProcess...")
if (not self.edPluginControlCharacterisation is None):
if (self.edPluginControlCharacterisation.hasDataOutput()):
self.setDataOutput(
self.edPluginControlCharacterisation.getDataOutput(),
"characterisation")
if (not self.edPluginControlISPyB is None):
if (self.edPluginControlISPyB.hasDataOutput()):
self.setDataOutput(self.edPluginControlISPyB.getDataOutput(),
"ISPyB")
if self.hasDataInput():
xsDataResultInterface = XSDataResultInterface()
if self.edPluginControlCharacterisation:
xsDataResultInterface.setResultCharacterisation(
self.edPluginControlCharacterisation.getDataOutput())
if self.edPluginControlISPyB:
xsDataResultInterface.setResultControlISPyB(
self.edPluginControlISPyB.getDataOutput())
self.setDataOutput(xsDataResultInterface)
def createInputCharacterisationFromImageHeaders(self, _edPlugin):
EDVerbose.DEBUG(
"EDPluginControlInterfacev1_2.createInputCharacterisationFromImageHeaders"
)
xsDataInputSubWedgeAssemble = XSDataInputSubWedgeAssemble()
for xsDataStringImagePath in self.listImagePaths:
xsDataFile = XSDataFile()
xsDataFile.setPath(xsDataStringImagePath)
xsDataInputSubWedgeAssemble.addFile(xsDataFile)
_edPlugin.setDataInput(xsDataInputSubWedgeAssemble)
_edPlugin.executeSynchronous()
def runCharacterisationPlugin(self, _edPlugin=None):
EDVerbose.DEBUG(
"EDPluginControlInterfacev1_2.runCharacterisationPlugin")
self.edPluginControlCharacterisation.setDataInput(
self.xsDataInputCharacterisation)
self.edPluginControlCharacterisation.executeSynchronous()
def storeResultsInISPyB(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlInterfacev1_2.storeResultsInISPyB")
if (self.edPluginControlISPyB is not None):
# Execute the ISPyB control plugin
xsDataInputControlISPyB = XSDataInputControlISPyB()
xsDataInputControlISPyB.setCharacterisationResult(
self.edPluginControlCharacterisation.getDataOutput())
if (not self.iDataCollectionId is None):
xsDataInputControlISPyB.setDataCollectionId(
XSDataInteger(self.iDataCollectionId))
if (not self.strShortComments is None):
self.edPluginControlISPyB.setDataInput(
XSDataString(self.strShortComments), "shortComments")
if (not self.strComments is None):
self.edPluginControlISPyB.setDataInput(
XSDataString(self.strComments), "comments")
if (not self.strStatusMessage is None):
self.edPluginControlISPyB.setDataInput(
XSDataString(self.strStatusMessage), "statusMessage")
self.edPluginControlISPyB.setDataInput(xsDataInputControlISPyB)
self.edPluginControlISPyB.executeSynchronous()
def createInputCharacterisationFromSubWedges(self):
EDVerbose.DEBUG(
"EDPluginControlInterfacev1_2.createInputCharacterisationFromSubWedges"
)
xsDataResultSubWedgeAssemble = self.edPluginControlSubWedgeAssemble.getDataOutput(
)
self.xsDataInputCharacterisation = XSDataInputCharacterisation()
xsDataCollection = XSDataCollection()
# Default exposure time (for the moment, this value should be
# possible to read from the command line)
if self.xsDataDiffractionPlan is None:
self.xsDataDiffractionPlan = XSDataDiffractionPlan()
if (not xsDataResultSubWedgeAssemble is None):
pyListSubWedge = xsDataResultSubWedgeAssemble.getSubWedge()
xsDataCollection.setSubWedge(pyListSubWedge)
for xsDataSubWedge in pyListSubWedge:
if (self.strComplexity is not None):
self.xsDataDiffractionPlan.setComplexity(
XSDataString(self.strComplexity))
if (self.fFlux is not None):
xsDataSubWedge.getExperimentalCondition().getBeam(
).setFlux(XSDataFlux(self.fFlux))
if (self.fBeamSizeX is not None) and (self.fBeamSizeY
is not None):
xsDataSize = XSDataSize()
xsDataSize.setX(XSDataLength(self.fBeamSizeX))
xsDataSize.setY(XSDataLength(self.fBeamSizeY))
xsDataSubWedge.getExperimentalCondition().getBeam(
).setSize(xsDataSize)
if (self.fBeamPosX is not None):
xsDataSubWedge.getExperimentalCondition().getDetector(
).setBeamPositionX(XSDataLength(self.fBeamPosX))
if (self.fBeamPosY is not None):
xsDataSubWedge.getExperimentalCondition().getDetector(
).setBeamPositionY(XSDataLength(self.fBeamPosY))
if (self.fMinExposureTimePerImage is not None):
xsDataSubWedge.getExperimentalCondition().getBeam(
).setMinExposureTimePerImage(
XSDataTime(self.fMinExposureTimePerImage))
if (self.fTransmission is not None):
xsDataSubWedge.getExperimentalCondition().getBeam(
).setTransmission(XSDataDouble(self.fTransmission))
if (self.fWavelength is not None):
xsDataSubWedge.getExperimentalCondition().getBeam(
).setWavelength(XSDataWavelength(self.fWavelength))
if self.fMinOscillationWidth != None:
xsDataSubWedge.getExperimentalCondition().getGoniostat(
).setMinOscillationWidth(
XSDataAngle(self.fMinOscillationWidth))
if self.fMaxOscillationSpeed != None:
xsDataSubWedge.getExperimentalCondition().getGoniostat(
).setMaxOscillationSpeed(
XSDataAngularSpeed(self.fMaxOscillationSpeed))
if (self.strForcedSpaceGroup is not None):
self.xsDataDiffractionPlan.setForcedSpaceGroup(
XSDataString(self.strForcedSpaceGroup))
self.xsDataDiffractionPlan.setAnomalousData(
XSDataBoolean(self.bAnomalousData))
self.xsDataDiffractionPlan.setMaxExposureTimePerDataCollection(
XSDataTime(self.fMaxExposureTimePerDataCollection))
if (self.strStrategyOption is not None):
self.xsDataDiffractionPlan.setStrategyOption(
XSDataString(self.strStrategyOption))
xsDataCollection.setDiffractionPlan(self.xsDataDiffractionPlan)
if self.xsDataSample is not None:
xsDataCollection.setSample(
XSDataSampleCrystalMM.parseString(self.xsDataSample.marshal()))
self.xsDataInputCharacterisation.setDataCollection(xsDataCollection)
def generateTemplateFile(self, _edPlugin):
EDVerbose.DEBUG("EDPluginControlInterfacev1_2.generateTemplateFile")
self.createInputCharacterisationFromSubWedges()
if (self.strGeneratedTemplateFile is None):
EDVerbose.screen(
"No argument for command line --generateTemplate key word found!"
)
elif (self.xsDataInputCharacterisation is None):
EDVerbose.screen(
"ERROR! Cannot generate template file %s, please check the log files."
% self.strGeneratedTemplateFile)
else:
EDVerbose.screen("Generating xml template input file for edna: " +
self.strGeneratedTemplateFile + "...")
self.xsDataInputCharacterisation.exportToFile(
self.strGeneratedTemplateFile)
def doSubWedgeAssembleSUCCESS(self, _edPlugin):
EDVerbose.DEBUG(
"EDPluginControlInterfacev1_2.doSubWedgeAssembleSUCCESS")
self.createInputCharacterisationFromSubWedges()
self.runCharacterisationPlugin(_edPlugin)
def doSubWedgeAssembleFAILURE(self, _edPlugin):
EDVerbose.DEBUG(
"EDPluginControlInterfacev1_2.doSubWedgeAssembleFAILURE")
EDVerbose.screen("Execution of " +
self.strEDPluginControlSubWedgeAssembleName +
" failed.")
EDVerbose.screen(
"Please inspect the log file for further information.")
self.setFailure()
def doFailureActionCharacterisation(self, _edPlugin=None):
"""
retrieve the potential warning messages
retrieve the potential error messages
"""
EDVerbose.DEBUG(
"EDPluginControlInterfacev1_2.doFailureActionCharacterisation")
self.retrieveFailureMessages(
self.edPluginControlCharacterisation,
"EDPluginControlInterfacev1_2.doSuccessActionISPyB")
if _edPlugin.hasDataOutput("statusMessage"):
self.strStatusMessage = _edPlugin.getDataOutput(
"statusMessage")[0].getValue()
self.generateExecutiveSummary(self)
self.storeResultsInISPyB(_edPlugin)
self.setFailure()
def doSuccessActionCharacterisation(self, _edPlugin=None):
"""
retrieve the potential warning messages
"""
EDVerbose.DEBUG(
"EDPluginControlInterfacev1_2.doSuccessActionCharacterisation")
# Store the results if requested
if (self.strResultsFilePath is not None):
xsDataCharacterisationResult = _edPlugin.getDataOutput()
if (xsDataCharacterisationResult is not None):
xsDataCharacterisationResult.exportToFile(
self.strResultsFilePath)
if _edPlugin.hasDataOutput("statusMessage"):
self.strStatusMessage = _edPlugin.getDataOutput(
"statusMessage")[0].getValue()
self.storeResultsInISPyB(_edPlugin)
def doSuccessActionISPyB(self, _edPlugin):
EDVerbose.DEBUG("EDPluginControlInterfacev1_2.doSuccessActionISPyB...")
self.retrieveSuccessMessages(
self.edPluginControlISPyB,
"EDPluginControlInterfacev1_2.doSuccessActionISPyB")
def doFailureActionISPyB(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlInterfacev1_2.doFailureActionISpyB...")
self.generateExecutiveSummary(self)
self.setFailure()
def generateExecutiveSummary(self, _edPlugin=None):
"""
Prints the executive summary from the plugin
"""
EDVerbose.DEBUG(
"EDPluginControlInterfacev1_2.generateExecutiveSummary")
if (self.edPluginControlSubWedgeAssemble is not None):
if self.edPluginControlSubWedgeAssemble.getListExecutiveSummaryLines(
) != []:
self.addExecutiveSummaryLine(
"Summary of plugin %s:" %
self.strEDPluginControlSubWedgeAssembleName)
self.appendExecutiveSummary(
self.edPluginControlSubWedgeAssemble)
if (self.edPluginControlCharacterisation is not None):
self.addExecutiveSummaryLine(
"Summary of plugin %s:" %
self.strEDPluginControlCharacterisationName)
self.appendExecutiveSummary(self.edPluginControlCharacterisation)
if (self.edPluginControlISPyB is not None):
self.addExecutiveSummaryLine("Summary of plugin %s:" %
self.strEDPluginControlISPyBName)
self.appendExecutiveSummary(self.edPluginControlISPyB)
self.verboseScreenExecutiveSummary()
def testSetDataModelInput(self):
from XSDataCCP4iv1_1 import XSDataInputCCP4i
xsDataInputCCP4i = XSDataInputCCP4i()
# Beam
from XSDataCommon import XSDataFlux
from XSDataCommon import XSDataSize
from XSDataCommon import XSDataLength
from XSDataCommon import XSDataFloat
from XSDataMXv1 import XSDataBeam
from XSDataMXv1 import XSDataExperimentalCondition
xsExperimentalCondition = XSDataExperimentalCondition()
xsBeam = XSDataBeam()
xsBeam.setFlux(XSDataFlux(1e+12))
xsBeam.setSize(XSDataSize(XSDataLength(0.1), XSDataLength(0.1)))
xsBeam.setMinExposureTimePerImage(XSDataFloat(0.1))
xsExperimentalCondition.setBeam(xsBeam)
# Goniostat
from XSDataCommon import XSDataSpeed
from XSDataCommon import XSDataAngle
from XSDataMXv1 import XSDataGoniostat
xsDataGoniostat = XSDataGoniostat()
xsDataGoniostat.setMaxOscillationSpeed(XSDataSpeed(0.2))
xsDataGoniostat.setMinOscillationWidth(XSDataAngle(0.1))
xsExperimentalCondition.setGoniostat(xsDataGoniostat)
xsDataInputCCP4i.setExperimentalCondition(xsExperimentalCondition)
# Sample
from XSDataCommon import XSDataString
from XSDataCommon import XSDataFloat
from XSDataCommon import XSDataString
from XSDataMXv1 import XSDataStructure
from XSDataMXv1 import XSDataChain
from XSDataMXv1 import XSDataAtom
from XSDataMXv1 import XSDataLigand
from XSDataMXv1 import XSDataSampleCrystalMM
from XSDataMXv1 import XSDataChemicalCompositionMM
from XSDataMXv1 import XSDataAtomicComposition
from XSDataMXv1 import XSDataSolvent
xsDataSampleCrystalMM = XSDataSampleCrystalMM()
xsDataStructure = XSDataStructure()
xsDataComposition = XSDataChemicalCompositionMM()
xsDataChain = XSDataChain()
xsDataChain.setType(XSDataString("protein"))
xsDataChain.setNumberOfCopies(XSDataFloat(2))
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtom1 = XSDataAtom()
xsDataAtom1.setSymbol(XSDataString("Se"))
xsDataAtom1.setNumberOf(XSDataFloat(4))
xsDataAtomicComposition.addAtom(xsDataAtom1)
xsDataChain.setHeavyAtoms(xsDataAtomicComposition)
xsDataChain.setNumberOfMonomers(XSDataFloat(100))
xsDataStructure.addChain(xsDataChain)
xsDataChain2 = XSDataChain()
xsDataChain2.setType(XSDataString("rna"))
xsDataChain2.setNumberOfCopies(XSDataFloat(1))
xsDataChain2.setNumberOfMonomers(XSDataFloat(60))
xsDataStructure.addChain(xsDataChain2)
xsDataLigand = XSDataLigand()
xsDataLigand.setNumberOfCopies(XSDataFloat(2))
xsDataLigand.setNumberOfLightAtoms(XSDataFloat(42))
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtom2 = XSDataAtom()
xsDataAtom2.setSymbol(XSDataString("Fe"))
xsDataAtom2.setNumberOf(XSDataFloat(1))
xsDataAtomicComposition.addAtom(xsDataAtom2)
xsDataLigand.setHeavyAtoms(xsDataAtomicComposition)
xsDataStructure.addLigand(xsDataLigand)
xsDataStructure.setNumberOfCopiesInAsymmetricUnit(XSDataFloat(0.25))
xsDataSolvent = XSDataSolvent()
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtom3 = XSDataAtom()
xsDataAtom3.setSymbol(XSDataString("Na"))
xsDataAtom3.setConcentration(XSDataFloat(1000))
xsDataAtom4 = XSDataAtom()
xsDataAtom4.setSymbol(XSDataString("Cl"))
xsDataAtom4.setConcentration(XSDataFloat(1000))
xsDataAtomicComposition.addAtom(xsDataAtom3)
xsDataAtomicComposition.addAtom(xsDataAtom4)
xsDataSolvent.setAtoms(xsDataAtomicComposition)
xsDataComposition.setStructure(xsDataStructure)
xsDataComposition.setSolvent(xsDataSolvent)
xsDataSampleCrystalMM.setChemicalComposition(xsDataComposition)
xsDataSampleCrystalMM.setSize(XSDataSize(XSDataLength(0.2), XSDataLength(0.2), XSDataLength(0.2)))
xsDataSampleCrystalMM.setSusceptibility(XSDataFloat(1.5))
xsDataSampleCrystalMM.setShape(XSDataFloat(2))
xsDataInputCCP4i.setSample(xsDataSampleCrystalMM)
from XSDataMXv1 import XSDataDiffractionPlan
xsDataDiffractionPlan = XSDataDiffractionPlan()
xsDataDiffractionPlan.setAimedCompleteness(XSDataFloat(95.5))
xsDataDiffractionPlan.setAimedIOverSigmaAtHighestResolution(XSDataFloat(2.5))
xsDataDiffractionPlan.setAimedMultiplicity(XSDataFloat(95.5))
xsDataDiffractionPlan.setAimedResolution(XSDataFloat(3))
xsDataDiffractionPlan.setComplexity(XSDataString("full"))
xsDataDiffractionPlan.setForcedSpaceGroup(XSDataString("P222"))
xsDataDiffractionPlan.setMaxExposureTimePerDataCollection(XSDataFloat(10000))
xsDataInputCCP4i.setDiffractionPlan(xsDataDiffractionPlan)
from XSDataCommon import XSDataFile
listInputDataFile = []
xsDataFile = XSDataFile(XSDataString(self.strXSDataGenerateTemplateFile))
listInputDataFile.append(xsDataFile)
xsDataInputCCP4i.setDataFile(listInputDataFile)
class EDPluginControlGridScreeningv1_0(EDPluginControl):
"""
This plugin is a "light-weight" characterisation to be used for processing
images from grid scans.
"""
def __init__(self):
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputGridScreening)
self.strControlReadImageHeaderPluginName = "EDPluginControlReadImageHeaderv10"
self.edPluginControlReadImageHeader = None
self.strControlledIndicatorsPluginName = "EDPluginControlImageQualityIndicatorsv1_1"
self.edPluginControlIndicators = None
self.strISPyBStoreImageQualityIndicatorsPluginName = "EDPluginISPyBStoreImageQualityIndicatorsv1_3"
self.edPluginISPyBStoreImageQualityIndicators = None
self.strIndexingMOSFLMPluginName = "EDPluginMOSFLMIndexingv10"
self.edPluginMOSFLMIndexing = None
self.strPluginControlIntegration = "EDPluginControlIntegrationv10"
self.edPluginControlIntegration = None
self.strPluginControlStrategy = "EDPluginControlStrategyv1_2"
self.edPluginControlStrategy = None
self.strPluginExecMtz2Various = "EDPluginExecMtz2Variousv1_0"
self.edPluginExecMtz2Various = None
self.strImageFile = None
self.xsDataIndexingResultMOSFLM = None
self.xsDataCrystal = None
self.strCharacterisationShortSummary = ""
self.strStatusMessage = ""
self.xsDataDiffractionPlan = None
self.xsDataCollection = None
self.xsDataIndexingResult = None
self.xsDataStrategyResult = None
self.xsDataImageQualityIndicators = None
self.bStoreImageQualityIndicatorsInISPyB = False
self.bDoOnlyImageQualityIndicators = False
self.bDoOnlyIntegrationWithXMLOutput = False
self.iImageQualityIndicatorsId = None
self.xsDataGridScreeningResultIntegration = None
def checkParameters(self):
"""
Checks the mandatory parameters.
"""
self.DEBUG("EDPluginControlGridScreeningv1_0.checkParameters")
self.checkMandatoryParameters(self.getDataInput(),
"Data Input is None")
self.checkMandatoryParameters(self.getDataInput().getImageFile(),
"imageFile")
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginControlGridScreeningv1_0.preProcess")
# Load the plugins
self.edPluginControlReadImageHeader = self.loadPlugin(self.strControlReadImageHeaderPluginName, \
"ReadImageHeader")
self.edPluginControlIndicators = self.loadPlugin(self.strControlledIndicatorsPluginName, \
"ControlIndicators")
self.edPluginMOSFLMIndexing = self.loadPlugin(self.strIndexingMOSFLMPluginName, \
"IndexingMOSFLM")
self.edPluginControlIntegration = self.loadPlugin(self.strPluginControlIntegration, \
"Integration")
self.edPluginControlStrategy = self.loadPlugin(self.strPluginControlStrategy, \
"Strategy")
self.edPluginExecMtz2Various = self.loadPlugin(self.strPluginExecMtz2Various, \
"Mtz2Various")
# Input data
self.strImageFile = self.getDataInput().getImageFile().getPath(
).getValue()
self.xsDataGridScreeningFileNameParameters = self.getFileNameParameters(
self.strImageFile)
self.xsDataDiffractionPlan = self.getDataInput().getDiffractionPlan()
if self.xsDataDiffractionPlan is None:
self.xsDataDiffractionPlan = XSDataDiffractionPlan()
if self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection(
) is None:
# Default max esposure time: 10000s
self.xsDataDiffractionPlan.setMaxExposureTimePerDataCollection(
XSDataTime(10000))
self.xsDataDiffractionPlan.setEstimateRadiationDamage(
XSDataBoolean(False))
# Image quality indicators
if self.getDataInput().getStoreImageQualityIndicatorsInISPyB():
self.bStoreImageQualityIndicatorsInISPyB = self.getDataInput(
).getStoreImageQualityIndicatorsInISPyB().getValue()
if self.getDataInput().getDoOnlyImageQualityIndicators():
self.bDoOnlyImageQualityIndicators = self.getDataInput(
).getDoOnlyImageQualityIndicators().getValue()
if self.getDataInput().getDoOnlyIntegrationWithXMLOutput():
self.bDoOnlyIntegrationWithXMLOutput = self.getDataInput(
).getDoOnlyIntegrationWithXMLOutput().getValue()
if self.bStoreImageQualityIndicatorsInISPyB:
self.edPluginISPyBStoreImageQualityIndicators = self.loadPlugin(self.strISPyBStoreImageQualityIndicatorsPluginName, \
"ISPyBStoreImageQualityIndicators")
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlGridScreeningv1_0.process")
xsDataInputReadImageHeader = XSDataInputReadImageHeader()
xsDataInputReadImageHeader.setImage(image=XSDataFile(
path=XSDataString(self.strImageFile)))
self.edPluginControlReadImageHeader.setDataInput(
xsDataInputReadImageHeader)
self.edPluginControlReadImageHeader.connectSUCCESS(
self.doSuccessReadImageHeader)
self.edPluginControlReadImageHeader.connectFAILURE(
self.doFailureReadImageHeader)
self.executePluginSynchronous(self.edPluginControlReadImageHeader)
def finallyProcess(self, _edObject=None):
EDPluginControl.finallyProcess(self)
self.DEBUG("EDPluginControlGridScreeningv1_0.finallyProcess")
# Synchronise if necessary
if self.edPluginISPyBStoreImageQualityIndicators is not None:
self.edPluginISPyBStoreImageQualityIndicators.synchronize()
# Build up the output object
strComment = ""
xsDataResultGridScreening = XSDataResultGridScreening()
if self.xsDataGridScreeningFileNameParameters is not None:
xsDataResultGridScreening.setFileNameParameters(
self.xsDataGridScreeningFileNameParameters)
if self.xsDataImageQualityIndicators is None:
strComment = "No image quality indicators"
else:
xsDataResultGridScreening.setImageQualityIndicators(
self.xsDataImageQualityIndicators)
if self.xsDataImageQualityIndicators.getIceRings().getValue() > 1:
strComment = "Ice rings detected"
if self.xsDataIndexingResult is None:
if strComment == "":
strComment = "No indexing result"
else:
strComment += ", no indexing result"
else:
xsDataSelectedSolution = self.xsDataIndexingResult.getSelectedSolution(
)
xsDataResultGridScreening.setMosaicity(
xsDataSelectedSolution.getCrystal().getMosaicity())
if self.xsDataStrategyResult is None:
if strComment == "":
strComment = "No strategy result"
else:
strComment += ", no strategy result"
else:
xsDataCollectionPlan = self.xsDataStrategyResult.getCollectionPlan(
)[0]
xsDataStrategySummary = xsDataCollectionPlan.getStrategySummary(
)
xsDataResultGridScreening.setRankingResolution(
xsDataStrategySummary.getRankingResolution())
xsDataResultGridScreening.setResultIntegration(
self.xsDataGridScreeningResultIntegration)
xsDataResultGridScreening.setComment(XSDataString(strComment))
if self.iImageQualityIndicatorsId is not None:
xsDataResultGridScreening.setImageQualityIndicatorsId(
XSDataInteger(self.iImageQualityIndicatorsId))
#print xsDataResultGridScreening.marshal()
self.setDataOutput(xsDataResultGridScreening)
def doSuccessReadImageHeader(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doSuccessReadImageHeader")
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlGridScreeningv1_0.doSuccessReadImageHeader")
xsDataResultReadImageHeader = self.edPluginControlReadImageHeader.getDataOutput(
)
if xsDataResultReadImageHeader is not None:
xsDataSubWedge = xsDataResultReadImageHeader.getSubWedge()
self.xsDataCollection = XSDataCollection()
self.xsDataCollection.addSubWedge(xsDataSubWedge)
self.xsDataCollection.setDiffractionPlan(
self.xsDataDiffractionPlan)
if not self.bDoOnlyIntegrationWithXMLOutput:
xsDataInputControlImageQualityIndicators = XSDataInputControlImageQualityIndicators(
)
xsDataInputControlImageQualityIndicators.addImage(
XSDataImage(path=XSDataString(self.strImageFile)))
self.edPluginControlIndicators.setDataInput(
xsDataInputControlImageQualityIndicators)
self.edPluginControlIndicators.connectSUCCESS(
self.doSuccessIndicators)
self.edPluginControlIndicators.connectFAILURE(
self.doFailureIndicators)
self.executePluginSynchronous(self.edPluginControlIndicators)
else:
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.setDataCollection(self.xsDataCollection)
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
xsDataMOSFLMIndexingInput = EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputIndexing(
xsDataIndexingInput)
self.edPluginMOSFLMIndexing.connectSUCCESS(
self.doSuccessIndexingMOSFLM)
self.edPluginMOSFLMIndexing.connectFAILURE(
self.doFailureIndexingMOSFLM)
self.edPluginMOSFLMIndexing.setDataInput(
xsDataMOSFLMIndexingInput)
self.edPluginMOSFLMIndexing.executeSynchronous()
def doFailureReadImageHeader(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doFailureReadImageHeader")
self.retrieveFailureMessages(
_edPlugin,
"EDPluginControlGridScreeningv1_0.doSuccessReadImageHeader")
def doSuccessIndicators(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doSuccessIndicators")
#self.retrieveSuccessMessages(_edPlugin, "EDPluginControlGridScreeningv1_0.doSuccessIndexingIndicators")
if self.edPluginControlIndicators.hasDataOutput():
self.xsDataImageQualityIndicators = self.edPluginControlIndicators.getDataOutput(
).getImageQualityIndicators()[0]
# Store results in ISPyB if requested
if self.bStoreImageQualityIndicatorsInISPyB:
xsDataInputStoreImageQualityIndicators = XSDataInputStoreImageQualityIndicators(
)
xsDataISPyBImageQualityIndicators = XSDataISPyBImageQualityIndicators.parseString(
self.xsDataImageQualityIndicators.marshal())
xsDataInputStoreImageQualityIndicators.setImageQualityIndicators(
xsDataISPyBImageQualityIndicators)
self.edPluginISPyBStoreImageQualityIndicators.setDataInput(
xsDataInputStoreImageQualityIndicators)
self.edPluginISPyBStoreImageQualityIndicators.connectSUCCESS(
self.doSuccessISPyBStoreImageQualityIndicators)
self.edPluginISPyBStoreImageQualityIndicators.connectFAILURE(
self.doFailureISPyBStoreImageQualityIndicators)
self.edPluginISPyBStoreImageQualityIndicators.execute()
# Continue only if requested
if not self.bDoOnlyImageQualityIndicators:
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.setDataCollection(self.xsDataCollection)
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
xsDataMOSFLMIndexingInput = EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputIndexing(
xsDataIndexingInput)
self.edPluginMOSFLMIndexing.connectSUCCESS(
self.doSuccessIndexingMOSFLM)
self.edPluginMOSFLMIndexing.connectFAILURE(
self.doFailureIndexingMOSFLM)
self.edPluginMOSFLMIndexing.setDataInput(
xsDataMOSFLMIndexingInput)
self.edPluginMOSFLMIndexing.executeSynchronous()
def doFailureIndicators(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doFailureIndicators")
strErrorMessage = "Execution of Indexing and Indicators plugin failed. Execution of characterisation aborted."
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
def doSuccessISPyBStoreImageQualityIndicators(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlGridScreeningv1_0.doSuccessISPyBStoreImageQualityIndicators"
)
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlGridScreeningv1_0.doSuccessISPyBStoreImageQualityIndicators"
)
self.iImageQualityIndicatorsId = self.edPluginISPyBStoreImageQualityIndicators.getDataOutput(
).getImageQualityIndicatorsId().getValue()
if self.iImageQualityIndicatorsId is None:
self.WARNING(
"Image quality indicators result not stored in ISPyB!")
def doFailureISPyBStoreImageQualityIndicators(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlGridScreeningv1_0.doFailureISPyBStoreImageQualityIndicators"
)
strErrorMessage = "Execution of store ISPyB image quality indicators plugin failed."
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
def doSuccessIndexingMOSFLM(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doSuccessIndexingMOSFLM")
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlGridScreeningv1_0.doIntegrationToStrategyTransition"
)
xsDataMOSFLMIndexingOutput = self.edPluginMOSFLMIndexing.getDataOutput(
)
xsDataExperimentalConditionRefined = None
if self.hasDataInput("refinedExperimentalCondition"):
xsDataExperimentalConditionRefined = self.getDataInput(
"refinedExperimentalCondition")[0]
else:
# Use the experimental condition from the xsDataCollection
xsDataExperimentalConditionRefined = self.xsDataCollection.getSubWedge(
)[0].getExperimentalCondition()
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
self.xsDataIndexingResult = EDHandlerXSDataMOSFLMv10.generateXSDataIndexingResult(
xsDataMOSFLMIndexingOutput, xsDataExperimentalConditionRefined)
xsDataIntegrationInput = XSDataIntegrationInput()
xsDataIntegrationInput.setDataCollection(self.xsDataCollection)
xsDataIntegrationInput.setExperimentalConditionRefined(
self.xsDataIndexingResult.getSelectedSolution(
).getExperimentalConditionRefined())
xsDataIntegrationInput.setSelectedIndexingSolution(
self.xsDataIndexingResult.getSelectedSolution())
self.edPluginControlIntegration.connectSUCCESS(
self.doSuccessIntegration)
self.edPluginControlIntegration.connectFAILURE(
self.doFailureIntegration)
self.edPluginControlIntegration.setDataInput(xsDataIntegrationInput)
self.executePluginSynchronous(self.edPluginControlIntegration)
def doFailureIndexingMOSFLM(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doFailureActionIndexing")
self.retrieveFailureMessages(
_edPlugin,
"EDPluginControlCharacterisationv1_1.doFailureActionIndexing")
def doSuccessIntegration(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doSuccessIntegration")
self.retrieveSuccessMessages(
_edPlugin, "EDPluginControlGridScreeningv1_0.doSuccessIntegration")
self.addStatusMessage("Integration successful.")
self.xsDataIntegrationOutput = self.edPluginControlIntegration.getDataOutput(
)
# Integration short summary
if self.edPluginControlIntegration.hasDataOutput(
"integrationShortSummary"):
self.strCharacterisationShortSummary += self.edPluginControlIntegration.getDataOutput(
"integrationShortSummary")[0].getValue()
#self.DEBUG( self.xsDataExperimentCharacterisation.marshal() )
if self.bDoOnlyIntegrationWithXMLOutput:
# Run mtz2various
xsDataInputMtz2Various = XSDataInputMtz2Various()
xsDataInputMtz2Various.setMtzfile(
self.edPluginControlIntegration.getDataOutput(
).getIntegrationSubWedgeResult()[0].getGeneratedMTZFile())
xsDataInputMtz2Various.addLabin(XSDataString("I=I"))
xsDataInputMtz2Various.addLabin(XSDataString("SIGI=SIGI"))
xsDataInputMtz2Various.setOutput(
XSDataString("USER '(3I4,2F10.1)'"))
self.edPluginExecMtz2Various.setDataInput(xsDataInputMtz2Various)
self.edPluginExecMtz2Various.executeSynchronous()
strHklFilePath = self.edPluginExecMtz2Various.getDataOutput(
).getHklfile().getPath().getValue()
strIntegration = EDUtilsFile.readFile(strHklFilePath)
# Output the result in XML format
self.xsDataGridScreeningResultIntegration = XSDataGridScreeningResultIntegration(
)
self.xsDataGridScreeningResultIntegration.setFileName(
os.path.basename(self.strImageFile))
self.xsDataGridScreeningResultIntegration.setFileDirectory(
os.path.dirname(self.strImageFile))
self.xsDataGridScreeningResultIntegration.setIntegratedData(
strIntegration)
else:
# We continue with the strategy calculation
xsDataInputStrategy = XSDataInputStrategy()
xsDataSolutionSelected = self.xsDataIndexingResult.getSelectedSolution(
)
xsDataInputStrategy.setCrystalRefined(
xsDataSolutionSelected.getCrystal())
xsDataInputStrategy.setSample(self.xsDataCollection.getSample())
xsDataIntegrationSubWedgeResultList = self.xsDataIntegrationOutput.getIntegrationSubWedgeResult(
)
xsDataInputStrategy.setBestFileContentDat(
xsDataIntegrationSubWedgeResultList[0].getBestfileDat())
xsDataInputStrategy.setBestFileContentPar(
xsDataIntegrationSubWedgeResultList[0].getBestfilePar())
xsDataInputStrategy.setExperimentalCondition(
xsDataIntegrationSubWedgeResultList[0].
getExperimentalConditionRefined())
for xsDataIntegrationSubWedgeResult in xsDataIntegrationSubWedgeResultList:
xsDataInputStrategy.addBestFileContentHKL(
xsDataIntegrationSubWedgeResult.getBestfileHKL())
xsDataInputStrategy.setDiffractionPlan(self.xsDataDiffractionPlan)
self.edPluginControlStrategy.connectSUCCESS(self.doSuccessStrategy)
self.edPluginControlStrategy.connectFAILURE(self.doFailureStrategy)
self.edPluginControlStrategy.setDataInput(xsDataInputStrategy)
self.executePluginSynchronous(self.edPluginControlStrategy)
def doFailureIntegration(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doFailureIntegration")
strErrorMessage = "Execution of integration plugin failed."
self.addStatusMessage("Integration FAILURE.")
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
def doSuccessStrategy(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doSuccessStrategy")
self.retrieveSuccessMessages(
self.edPluginControlStrategy,
"EDPluginControlGridScreeningv1_0.doSuccessStrategy")
self.xsDataStrategyResult = self.edPluginControlStrategy.getDataOutput(
)
def doFailureStrategy(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doFailureStrategy")
self.retrieveFailureMessages(
self.edPluginControlStrategy,
"EDPluginControlGridScreeningv1_0.doFailureStrategy")
strErrorMessage = "Execution of strategy plugin failed."
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
# def generateExecutiveSummary(self, _edPlugin):
# """
# Generates a summary of the execution of the plugin.
# """
# self.DEBUG("EDPluginControlGridScreeningv1_0.generateExecutiveSummary")
# self.addExecutiveSummaryLine("Summary of characterisation:")
# xsDataInputStrategy = self.getDataInput()
# xsDataCollection = xsDataInputStrategy.getDataCollection()
# xsDataDiffractionPlan = xsDataCollection.getDiffractionPlan()
# self.addExecutiveSummaryLine("Diffraction plan:")
# if (xsDataDiffractionPlan.getComplexity() is not None):
# self.addExecutiveSummaryLine("BEST complexity : %s" % xsDataDiffractionPlan.getComplexity().getValue())
# if (xsDataDiffractionPlan.getAimedCompleteness() is not None):
# self.addExecutiveSummaryLine("Aimed completeness : %6.1f [%%]" % (100.0 * xsDataDiffractionPlan.getAimedCompleteness().getValue()))
# if (xsDataDiffractionPlan.getRequiredCompleteness() is not None):
# self.addExecutiveSummaryLine("Required completeness : %6.1f [%%]" % (100.0 * xsDataDiffractionPlan.getRequiredCompleteness().getValue()))
# if (xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution() is not None):
# self.addExecutiveSummaryLine("Aimed I/sigma at highest resolution : %6.1f" % xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution().getValue())
# if (xsDataDiffractionPlan.getAimedResolution() is not None):
# self.addExecutiveSummaryLine("Aimed resolution : %6.1f [A]" % xsDataDiffractionPlan.getAimedResolution().getValue())
# if (xsDataDiffractionPlan.getRequiredResolution() is not None):
# self.addExecutiveSummaryLine("Required resolution : %6.1f [A]" % xsDataDiffractionPlan.getRequiredResolution().getValue())
# if (xsDataDiffractionPlan.getAimedMultiplicity() is not None):
# self.addExecutiveSummaryLine("Aimed multiplicity : %6.1f" % xsDataDiffractionPlan.getAimedMultiplicity().getValue())
# if (xsDataDiffractionPlan.getRequiredMultiplicity() is not None):
# self.addExecutiveSummaryLine("Required multiplicity : %6.1f" % xsDataDiffractionPlan.getRequiredMultiplicity().getValue())
# if (xsDataDiffractionPlan.getForcedSpaceGroup() is not None):
# self.addExecutiveSummaryLine("Forced space group : %6s" % xsDataDiffractionPlan.getForcedSpaceGroup().getValue())
# if (xsDataDiffractionPlan.getMaxExposureTimePerDataCollection() is not None):
# self.addExecutiveSummaryLine("Max exposure time per data collection : %6.1f [s]" % xsDataDiffractionPlan.getMaxExposureTimePerDataCollection().getValue())
# self.addExecutiveSummarySeparator()
# if self.edPluginControlIndexingIndicators is not None:
# self.appendExecutiveSummary(self.edPluginControlIndexingIndicators, "")
# if self.edPluginControlIndexingLabelit is not None:
# self.appendExecutiveSummary(self.edPluginControlIndexingLabelit, "")
# if self.edPluginControlIntegration is not None:
# self.appendExecutiveSummary(self.edPluginControlIntegration, "")
# if self.edPluginControlStrategy is not None:
# self.appendExecutiveSummary(self.edPluginControlStrategy, "")
# self.addExecutiveSummarySeparator()
# if self.strCharacterisationShortSummary is not None:
# self.addExecutiveSummaryLine("Characterisation short summary:")
# self.addExecutiveSummaryLine("")
# if self.strStatusMessage != None:
# for strLine in self.strStatusMessage.split(". "):
# if strLine.endswith("."):
# self.addExecutiveSummaryLine(strLine)
# else:
# self.addExecutiveSummaryLine(strLine + ".")
# self.addExecutiveSummaryLine("")
# for strLine in self.strCharacterisationShortSummary.split("\n"):
# if strLine != "\n":
# self.addExecutiveSummaryLine(strLine)
# self.addErrorWarningMessagesToExecutiveSummary("Characterisation error and warning messages: ")
# self.addExecutiveSummarySeparator()
def addStatusMessage(self, _strStatusMessage):
if self.strStatusMessage != "":
self.strStatusMessage += " "
self.strStatusMessage += _strStatusMessage
def getFileNameParameters(self, _strFileName):
"""Method for extracting the rotation start angle, the two motor positions and the grid scan image no from the file name"""
# Typical file name: mesh_0_21.676_-0.051_22_001.mccd
listParts = os.path.basename(_strFileName).split("_")
xsDataGridScreeningFileNameParameters = XSDataGridScreeningFileNameParameters(
)
try:
strScanId1 = listParts[1]
xsDataGridScreeningFileNameParameters.setScanId1(
XSDataString(strScanId1))
strMotorPosition1 = listParts[2]
xsDataGridScreeningFileNameParameters.setMotorPosition1(
XSDataString(strMotorPosition1))
strMotorPosition2 = listParts[3]
xsDataGridScreeningFileNameParameters.setMotorPosition2(
XSDataString(strMotorPosition2))
strScanId2 = listParts[4]
xsDataGridScreeningFileNameParameters.setScanId2(
XSDataString(strScanId2))
except:
xsDataGridScreeningFileNameParameters = None
return xsDataGridScreeningFileNameParameters
def preProcess(self, _edPlugin=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edPlugin)
self.DEBUG("EDPluginControlInterfacev1_3.preProcess...")
self.listImagePaths = []
# Check if XSDataInputInterface is given as input
if self.hasDataInput():
xsDataInputInterface = self.getDataInput()
if xsDataInputInterface.getExperimentalCondition():
self.xsDataExperimentalCodition = xsDataInputInterface.getExperimentalCondition(
)
if self.xsDataExperimentalCodition.getGoniostat():
if self.xsDataExperimentalCodition.getGoniostat(
).getMinOscillationWidth():
self.fMinOscillationWidth = self.xsDataExperimentalCodition.getGoniostat(
).getMinOscillationWidth().getValue()
if self.xsDataExperimentalCodition.getGoniostat(
).getMaxOscillationSpeed():
self.fMaxOscillationSpeed = self.xsDataExperimentalCodition.getGoniostat(
).getMaxOscillationSpeed().getValue()
self.xsDataSample = xsDataInputInterface.getSample()
self.xsDataDiffractionPlan = self.getDataInput(
).getDiffractionPlan()
if self.xsDataDiffractionPlan:
if self.xsDataDiffractionPlan.getForcedSpaceGroup():
self.strForcedSpaceGroup = self.xsDataDiffractionPlan.getForcedSpaceGroup(
).getValue()
if self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection(
):
self.fMaxExposureTimePerDataCollection = self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection(
).getValue()
if self.xsDataDiffractionPlan.getAnomalousData():
self.bAnomalousData = self.xsDataDiffractionPlan.getAnomalousData(
).getValue()
if self.xsDataDiffractionPlan.getStrategyOption():
self.strStrategyOption = self.xsDataDiffractionPlan.getStrategyOption(
).getValue()
if self.xsDataDiffractionPlan.getComplexity():
self.strComplexity = self.xsDataDiffractionPlan.getComplexity(
).getValue()
if self.fMinOscillationWidth == None:
if self.xsDataDiffractionPlan.getGoniostatMinOscillationWidth(
):
self.fMinOscillationWidth = self.xsDataDiffractionPlan.getGoniostatMinOscillationWidth(
).getValue()
if self.fMaxOscillationSpeed == None:
if self.xsDataDiffractionPlan.getGoniostatMaxOscillationSpeed(
):
self.fMaxOscillationSpeed = self.xsDataDiffractionPlan.getGoniostatMaxOscillationSpeed(
).getValue()
self.xsDataSample = xsDataInputInterface.getSample()
if xsDataInputInterface.getImagePath():
for xsDataFile in xsDataInputInterface.getImagePath():
self.listImagePaths.append(xsDataFile.getPath())
if xsDataInputInterface.getFlux():
self.fFlux = xsDataInputInterface.getFlux().getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getFlux(
) != None:
self.fFlux = self.xsDataExperimentalCodition.getBeam(
).getFlux().getValue()
if xsDataInputInterface.getMinExposureTimePerImage():
self.fMinExposureTimePerImage = xsDataInputInterface.getMinExposureTimePerImage(
).getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam(
).getMinExposureTimePerImage() != None:
self.fMinExposureTimePerImage = self.xsDataExperimentalCodition.getBeam(
).getMinExposureTimePerImage().getValue()
if self.fMinExposureTimePerImage == None and xsDataInputInterface.getDiffractionPlan(
):
if xsDataInputInterface.getDiffractionPlan(
).getMinExposureTimePerImage() != None:
self.fMinExposureTimePerImage = xsDataInputInterface.getDiffractionPlan(
).getMinExposureTimePerImage().getValue()
if self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getSize(
) != None:
self.fBeamSizeX = self.xsDataExperimentalCodition.getBeam(
).getSize().getX().getValue()
self.fBeamSizeY = self.xsDataExperimentalCodition.getBeam(
).getSize().getY().getValue()
if self.xsDataExperimentalCodition.getBeam(
).getApertureSize() != None:
self.fApertureSize = self.xsDataExperimentalCodition.getBeam(
).getApertureSize().getValue()
if xsDataInputInterface.getBeamSize():
self.fBeamSizeX = xsDataInputInterface.getBeamSize().getValue()
self.fBeamSizeY = xsDataInputInterface.getBeamSize().getValue()
if xsDataInputInterface.getApertureSize():
self.fApertureSize = xsDataInputInterface.getApertureSize(
).getValue()
if xsDataInputInterface.getBeamSizeX():
self.fBeamSizeX = xsDataInputInterface.getBeamSizeX().getValue(
)
if xsDataInputInterface.getBeamSizeY():
self.fBeamSizeY = xsDataInputInterface.getBeamSizeY().getValue(
)
if xsDataInputInterface.getApertureSize():
self.fApertureSize = xsDataInputInterface.getApertureSize(
).getValue()
if xsDataInputInterface.getTemplateMode():
self.bTemplateMode = xsDataInputInterface.getTemplateMode(
).getValue()
if xsDataInputInterface.getBeamPosX():
self.fBeamPosX = xsDataInputInterface.getBeamPosX().getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getDetector() != None:
if self.xsDataExperimentalCodition.getDetector(
).getBeamPositionX() != None:
self.fBeamPosX = self.xsDataExperimentalCodition.getDetector(
).getBeamPositionX().getValue()
if xsDataInputInterface.getBeamPosY():
self.fBeamPosY = xsDataInputInterface.getBeamPosY().getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getDetector() != None:
if self.xsDataExperimentalCodition.getDetector(
).getBeamPositionY() != None:
self.fBeamPosY = self.xsDataExperimentalCodition.getDetector(
).getBeamPositionY().getValue()
if xsDataInputInterface.getWavelength():
self.fWavelength = xsDataInputInterface.getWavelength(
).getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getWavelength(
) != None:
self.fWavelength = self.xsDataExperimentalCodition.getBeam(
).getWavelength().getValue()
if xsDataInputInterface.getTransmission():
self.fTransmission = xsDataInputInterface.getTransmission(
).getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam(
).getTransmission() != None:
self.fTransmission = self.xsDataExperimentalCodition.getBeam(
).getTransmission().getValue()
if xsDataInputInterface.getGeneratedTemplateFile():
self.strGeneratedTemplateFile = xsDataInputInterface.getGeneratedTemplateFile(
).getPath().getValue()
if xsDataInputInterface.getResultsFilePath():
self.strResultsFilePath = xsDataInputInterface.getResultsFilePath(
).getPath().getValue()
if xsDataInputInterface.getDataCollectionId():
self.iDataCollectionId = xsDataInputInterface.getDataCollectionId(
).getValue()
if xsDataInputInterface.getShortComments():
self.strShortComments = xsDataInputInterface.getShortComments(
).getValue()
if xsDataInputInterface.getComments():
self.strComments = xsDataInputInterface.getComments().getValue(
)
if xsDataInputInterface.getInputCharacterisation():
self.xsDataInputCharacterisation = xsDataInputInterface.getInputCharacterisation(
)
if xsDataInputInterface.getDataCollectionId():
self.iDataCollectionId = xsDataInputInterface.getDataCollectionId(
).getValue()
else:
if self.hasDataInput("experimentalCondition"):
self.xsDataExperimentalCodition = self.getDataInput(
"experimentalCondition")[0]
if self.xsDataExperimentalCodition.getGoniostat():
if self.xsDataExperimentalCodition.getGoniostat(
).getMinOscillationWidth():
self.fMinOscillationWidth = self.xsDataExperimentalCodition.getGoniostat(
).getMinOscillationWidth().getValue()
if self.xsDataExperimentalCodition.getGoniostat(
).getMaxOscillationSpeed():
self.fMaxOscillationSpeed = self.xsDataExperimentalCodition.getGoniostat(
).getMaxOscillationSpeed().getValue()
if self.hasDataInput("sample"):
self.xsDataSample = self.getDataInput("sample")[0]
if (self.hasDataInput("diffractionPlan")):
if self.xsDataDiffractionPlan is None:
self.xsDataDiffractionPlan = XSDataDiffractionPlan()
xsDataDiffractionPlans = self.getDataInput("diffractionPlan")
if (not xsDataDiffractionPlans[0] is None):
self.xsDataDiffractionPlan = xsDataDiffractionPlans[0]
if self.xsDataDiffractionPlan.getForcedSpaceGroup():
self.strForcedSpaceGroup = self.xsDataDiffractionPlan.getForcedSpaceGroup(
).getValue()
if self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection(
):
self.fMaxExposureTimePerDataCollection = self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection(
).getValue()
if self.xsDataDiffractionPlan.getAnomalousData():
self.bAnomalousData = self.xsDataDiffractionPlan.getAnomalousData(
).getValue()
if self.xsDataDiffractionPlan.getStrategyOption():
self.strStrategyOption = self.xsDataDiffractionPlan.getStrategyOption(
).getValue()
if self.xsDataDiffractionPlan.getComplexity():
self.strComplexity = self.xsDataDiffractionPlan.getComplexity(
).getValue()
if self.fMinOscillationWidth == None:
if self.xsDataDiffractionPlan.getGoniostatMinOscillationWidth(
):
self.fMinOscillationWidth = self.xsDataDiffractionPlan.getGoniostatMinOscillationWidth(
).getValue()
if self.fMaxOscillationSpeed == None:
if self.xsDataDiffractionPlan.getGoniostatMaxOscillationSpeed(
):
self.fMaxOscillationSpeed = self.xsDataDiffractionPlan.getGoniostatMaxOscillationSpeed(
).getValue()
if self.hasDataInput("sample"):
self.xsDataSample = self.getDataInput("sample")[0]
if self.hasDataInput("imagePaths"):
for strImagePath in self.getDataInput("imagePaths"):
self.listImagePaths.append(strImagePath)
if self.hasDataInput("flux"):
self.fFlux = self.getDataInput("flux")[0].getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getFlux(
) != None:
self.fFlux = self.xsDataExperimentalCodition.getBeam(
).getFlux().getValue()
if self.hasDataInput("minExposureTimePerImage"):
self.fMinExposureTimePerImage = self.getDataInput(
"minExposureTimePerImage")[0].getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam(
).getMinExposureTimePerImage() != None:
self.fMinExposureTimePerImage = self.xsDataExperimentalCodition.getBeam(
).getMinExposureTimePerImage().getValue()
if self.fMinExposureTimePerImage == None and self.hasDataInput(
"diffractionPlan"):
if self.getDataInput("diffractionPlan"
)[0].getMinExposureTimePerImage() != None:
self.fMinExposureTimePerImage = self.getDataInput(
"diffractionPlan")[0].getMinExposureTimePerImage(
).getValue()
if self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getSize(
) != None:
self.fBeamSizeX = self.xsDataExperimentalCodition.getBeam(
).getSize().getX().getValue()
self.fBeamSizeY = self.xsDataExperimentalCodition.getBeam(
).getSize().getY().getValue()
if self.xsDataExperimentalCodition.getBeam(
).getApertureSize() != None:
self.fApertureSize = self.xsDataExperimentalCodition.getBeam(
).getApertureSize().getValue()
if self.hasDataInput("beamSize"):
self.fBeamSizeX = self.getDataInput("beamSize")[0].getValue()
self.fBeamSizeY = self.getDataInput("beamSize")[0].getValue()
if self.hasDataInput("apertureSize"):
self.fApertureSize = self.getDataInput(
"apertureSize")[0].getValue()
if self.hasDataInput("beamSizeX"):
self.fBeamSizeX = self.getDataInput("beamSizeX")[0].getValue()
if self.hasDataInput("beamSizeY"):
self.fBeamSizeY = self.getDataInput("beamSizeY")[0].getValue()
if self.hasDataInput("templateMode"):
self.bTemplateMode = self.getDataInput(
"templateMode")[0].getValue()
if (self.hasDataInput("beamPosX")):
self.fBeamPosX = self.getDataInput("beamPosX")[0].getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getDetector() != None:
if self.xsDataExperimentalCodition.getDetector(
).getBeamPositionX() != None:
self.fBeamPosX = self.xsDataExperimentalCodition.getDetector(
).getBeamPositionX().getValue()
if (self.hasDataInput("beamPosY")):
self.fBeamPosY = self.getDataInput("beamPosY")[0].getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getDetector() != None:
if self.xsDataExperimentalCodition.getDetector(
).getBeamPositionY() != None:
self.fBeamPosY = self.xsDataExperimentalCodition.getDetector(
).getBeamPositionY().getValue()
if (self.hasDataInput("wavelength")):
self.fWavelength = self.getDataInput(
"wavelength")[0].getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getWavelength(
) != None:
self.fWavelength = self.xsDataExperimentalCodition.getBeam(
).getWavelength().getValue()
if (self.hasDataInput("transmission")):
self.fTransmission = self.getDataInput(
"transmission")[0].getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam(
).getTransmission() != None:
self.fTransmission = self.xsDataExperimentalCodition.getBeam(
).getTransmission().getValue()
if self.hasDataInput("generatedTemplateFile"):
self.strGeneratedTemplateFile = self.getDataInput(
"generatedTemplateFile")[0].getValue()
if self.hasDataInput("resultsFilePath"):
self.strResultsFilePath = self.getDataInput(
"resultsFilePath")[0].getValue()
if self.hasDataInput("dataCollectionId"):
self.iDataCollectionId = self.getDataInput(
"dataCollectionId")[0].getValue()
if self.hasDataInput("shortComments"):
self.strShortComments = self.getDataInput(
"shortComments")[0].getValue()
if self.hasDataInput("comments"):
self.strComments = self.getDataInput("comments")[0].getValue()
if self.hasDataInput("inputCharacterisation"):
self.xsDataInputCharacterisation = self.getDataInput(
"inputCharacterisation")[0]
# Check if XML data is given as input :
if (self.xsDataInputCharacterisation is None):
self.edPluginControlSubWedgeAssemble = self.loadPlugin(
self.strEDPluginControlSubWedgeAssembleName,
"SubWedgeAssemble")
self.edPluginControlCharacterisation = self.loadPlugin(
self.strEDPluginControlCharacterisationName, "Characterisation")
if (self.strEDPluginControlISPyBName is not None):
self.edPluginControlISPyB = self.loadPlugin(
self.strEDPluginControlISPyBName, "ISPyB")
def buildChildren(self, child_, nodeName_):
if child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'experimentalCondition':
obj_ = XSDataExperimentalCondition()
obj_.build(child_)
self.setExperimentalCondition(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'diffractionPlan':
obj_ = XSDataDiffractionPlan()
obj_.build(child_)
self.setDiffractionPlan(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'sample':
obj_ = XSDataSampleCrystalMM()
obj_.build(child_)
self.setSample(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'imagePath':
obj_ = XSDataFile()
obj_.build(child_)
self.imagePath.append(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'flux':
obj_ = XSDataFloat()
obj_.build(child_)
self.setFlux(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'minExposureTimePerImage':
obj_ = XSDataTime()
obj_.build(child_)
self.setMinExposureTimePerImage(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'beamSize':
obj_ = XSDataLength()
obj_.build(child_)
self.setBeamSize(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'beamSizeX':
obj_ = XSDataLength()
obj_.build(child_)
self.setBeamSizeX(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'beamSizeY':
obj_ = XSDataLength()
obj_.build(child_)
self.setBeamSizeY(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'apertureSize':
obj_ = XSDataLength()
obj_.build(child_)
self.setApertureSize(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'templateMode':
obj_ = XSDataBoolean()
obj_.build(child_)
self.setTemplateMode(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'generatedTemplateFile':
obj_ = XSDataFile()
obj_.build(child_)
self.setGeneratedTemplateFile(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'resultsFilePath':
obj_ = XSDataFile()
obj_.build(child_)
self.setResultsFilePath(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'beamPosX':
obj_ = XSDataFloat()
obj_.build(child_)
self.setBeamPosX(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'beamPosY':
obj_ = XSDataFloat()
obj_.build(child_)
self.setBeamPosY(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'wavelength':
obj_ = XSDataWavelength()
obj_.build(child_)
self.setWavelength(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'transmission':
obj_ = XSDataDouble()
obj_.build(child_)
self.setTransmission(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'dataCollectionId':
obj_ = XSDataInteger()
obj_.build(child_)
self.setDataCollectionId(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'shortComments':
obj_ = XSDataString()
obj_.build(child_)
self.setShortComments(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'comments':
obj_ = XSDataString()
obj_.build(child_)
self.setComments(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'inputCharacterisation':
obj_ = XSDataInputCharacterisation()
obj_.build(child_)
self.setInputCharacterisation(obj_)
def preProcess(self, _edPlugin=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edPlugin)
self.DEBUG("EDPluginControlInterfacev1_3.preProcess...")
self.listImagePaths = []
# Check if XSDataInputInterface is given as input
if self.hasDataInput():
xsDataInputInterface = self.getDataInput()
if xsDataInputInterface.getExperimentalCondition():
self.xsDataExperimentalCodition = xsDataInputInterface.getExperimentalCondition()
if self.xsDataExperimentalCodition.getGoniostat():
if self.xsDataExperimentalCodition.getGoniostat().getMinOscillationWidth():
self.fMinOscillationWidth = self.xsDataExperimentalCodition.getGoniostat().getMinOscillationWidth().getValue()
if self.xsDataExperimentalCodition.getGoniostat().getMaxOscillationSpeed():
self.fMaxOscillationSpeed = self.xsDataExperimentalCodition.getGoniostat().getMaxOscillationSpeed().getValue()
self.xsDataSample = xsDataInputInterface.getSample()
self.xsDataDiffractionPlan = self.getDataInput().getDiffractionPlan()
if self.xsDataDiffractionPlan:
if self.xsDataDiffractionPlan.getForcedSpaceGroup():
self.strForcedSpaceGroup = self.xsDataDiffractionPlan.getForcedSpaceGroup().getValue()
if self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection():
self.fMaxExposureTimePerDataCollection = self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection().getValue()
if self.xsDataDiffractionPlan.getAnomalousData():
self.bAnomalousData = self.xsDataDiffractionPlan.getAnomalousData().getValue()
if self.xsDataDiffractionPlan.getStrategyOption():
self.strStrategyOption = self.xsDataDiffractionPlan.getStrategyOption().getValue()
if self.xsDataDiffractionPlan.getComplexity():
self.strComplexity = self.xsDataDiffractionPlan.getComplexity().getValue()
if self.fMinOscillationWidth == None:
if self.xsDataDiffractionPlan.getGoniostatMinOscillationWidth():
self.fMinOscillationWidth = self.xsDataDiffractionPlan.getGoniostatMinOscillationWidth().getValue()
if self.fMaxOscillationSpeed == None:
if self.xsDataDiffractionPlan.getGoniostatMaxOscillationSpeed():
self.fMaxOscillationSpeed = self.xsDataDiffractionPlan.getGoniostatMaxOscillationSpeed().getValue()
self.xsDataSample = xsDataInputInterface.getSample()
if xsDataInputInterface.getImagePath():
for xsDataFile in xsDataInputInterface.getImagePath():
self.listImagePaths.append(xsDataFile.getPath())
if xsDataInputInterface.getFlux():
self.fFlux = xsDataInputInterface.getFlux().getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getFlux() != None:
self.fFlux = self.xsDataExperimentalCodition.getBeam().getFlux().getValue()
if xsDataInputInterface.getMinExposureTimePerImage():
self.fMinExposureTimePerImage = xsDataInputInterface.getMinExposureTimePerImage().getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getMinExposureTimePerImage() != None:
self.fMinExposureTimePerImage = self.xsDataExperimentalCodition.getBeam().getMinExposureTimePerImage().getValue()
if self.fMinExposureTimePerImage == None and xsDataInputInterface.getDiffractionPlan():
if xsDataInputInterface.getDiffractionPlan().getMinExposureTimePerImage() != None:
self.fMinExposureTimePerImage = xsDataInputInterface.getDiffractionPlan().getMinExposureTimePerImage().getValue()
if self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getSize() != None:
self.fBeamSizeX = self.xsDataExperimentalCodition.getBeam().getSize().getX().getValue()
self.fBeamSizeY = self.xsDataExperimentalCodition.getBeam().getSize().getY().getValue()
if self.xsDataExperimentalCodition.getBeam().getApertureSize() != None:
self.fApertureSize = self.xsDataExperimentalCodition.getBeam().getApertureSize().getValue()
if xsDataInputInterface.getBeamSize():
self.fBeamSizeX = xsDataInputInterface.getBeamSize().getValue()
self.fBeamSizeY = xsDataInputInterface.getBeamSize().getValue()
if xsDataInputInterface.getApertureSize():
self.fApertureSize = xsDataInputInterface.getApertureSize().getValue()
if xsDataInputInterface.getBeamSizeX():
self.fBeamSizeX = xsDataInputInterface.getBeamSizeX().getValue()
if xsDataInputInterface.getBeamSizeY():
self.fBeamSizeY = xsDataInputInterface.getBeamSizeY().getValue()
if xsDataInputInterface.getApertureSize():
self.fApertureSize = xsDataInputInterface.getApertureSize().getValue()
if xsDataInputInterface.getTemplateMode():
self.bTemplateMode = xsDataInputInterface.getTemplateMode().getValue()
if xsDataInputInterface.getBeamPosX():
self.fBeamPosX = xsDataInputInterface.getBeamPosX().getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getDetector() != None:
if self.xsDataExperimentalCodition.getDetector().getBeamPositionX() != None:
self.fBeamPosX = self.xsDataExperimentalCodition.getDetector().getBeamPositionX().getValue()
if xsDataInputInterface.getBeamPosY():
self.fBeamPosY = xsDataInputInterface.getBeamPosY().getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getDetector() != None:
if self.xsDataExperimentalCodition.getDetector().getBeamPositionY() != None:
self.fBeamPosY = self.xsDataExperimentalCodition.getDetector().getBeamPositionY().getValue()
if xsDataInputInterface.getWavelength():
self.fWavelength = xsDataInputInterface.getWavelength().getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getWavelength() != None:
self.fWavelength = self.xsDataExperimentalCodition.getBeam().getWavelength().getValue()
if xsDataInputInterface.getTransmission():
self.fTransmission = xsDataInputInterface.getTransmission().getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getTransmission() != None:
self.fTransmission = self.xsDataExperimentalCodition.getBeam().getTransmission().getValue()
if xsDataInputInterface.getGeneratedTemplateFile():
self.strGeneratedTemplateFile = xsDataInputInterface.getGeneratedTemplateFile().getPath().getValue()
if xsDataInputInterface.getResultsFilePath():
self.strResultsFilePath = xsDataInputInterface.getResultsFilePath().getPath().getValue()
if xsDataInputInterface.getDataCollectionId():
self.iDataCollectionId = xsDataInputInterface.getDataCollectionId().getValue()
if xsDataInputInterface.getShortComments():
self.strShortComments = xsDataInputInterface.getShortComments().getValue()
if xsDataInputInterface.getComments():
self.strComments = xsDataInputInterface.getComments().getValue()
if xsDataInputInterface.getInputCharacterisation():
self.xsDataInputCharacterisation = xsDataInputInterface.getInputCharacterisation()
if xsDataInputInterface.getDataCollectionId():
self.iDataCollectionId = xsDataInputInterface.getDataCollectionId().getValue()
else:
if self.hasDataInput("experimentalCondition"):
self.xsDataExperimentalCodition = self.getDataInput("experimentalCondition")[0]
if self.xsDataExperimentalCodition.getGoniostat():
if self.xsDataExperimentalCodition.getGoniostat().getMinOscillationWidth():
self.fMinOscillationWidth = self.xsDataExperimentalCodition.getGoniostat().getMinOscillationWidth().getValue()
if self.xsDataExperimentalCodition.getGoniostat().getMaxOscillationSpeed():
self.fMaxOscillationSpeed = self.xsDataExperimentalCodition.getGoniostat().getMaxOscillationSpeed().getValue()
if self.hasDataInput("sample"):
self.xsDataSample = self.getDataInput("sample")[0]
if (self.hasDataInput("diffractionPlan")):
if self.xsDataDiffractionPlan is None:
self.xsDataDiffractionPlan = XSDataDiffractionPlan()
xsDataDiffractionPlans = self.getDataInput("diffractionPlan")
if (not xsDataDiffractionPlans[0] is None):
self.xsDataDiffractionPlan = xsDataDiffractionPlans[0]
if self.xsDataDiffractionPlan.getForcedSpaceGroup():
self.strForcedSpaceGroup = self.xsDataDiffractionPlan.getForcedSpaceGroup().getValue()
if self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection():
self.fMaxExposureTimePerDataCollection = self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection().getValue()
if self.xsDataDiffractionPlan.getAnomalousData():
self.bAnomalousData = self.xsDataDiffractionPlan.getAnomalousData().getValue()
if self.xsDataDiffractionPlan.getStrategyOption():
self.strStrategyOption = self.xsDataDiffractionPlan.getStrategyOption().getValue()
if self.xsDataDiffractionPlan.getComplexity():
self.strComplexity = self.xsDataDiffractionPlan.getComplexity().getValue()
if self.fMinOscillationWidth == None:
if self.xsDataDiffractionPlan.getGoniostatMinOscillationWidth():
self.fMinOscillationWidth = self.xsDataDiffractionPlan.getGoniostatMinOscillationWidth().getValue()
if self.fMaxOscillationSpeed == None:
if self.xsDataDiffractionPlan.getGoniostatMaxOscillationSpeed():
self.fMaxOscillationSpeed = self.xsDataDiffractionPlan.getGoniostatMaxOscillationSpeed().getValue()
if self.hasDataInput("sample"):
self.xsDataSample = self.getDataInput("sample")[0]
if self.hasDataInput("imagePaths"):
for strImagePath in self.getDataInput("imagePaths"):
self.listImagePaths.append(strImagePath)
if self.hasDataInput("flux"):
self.fFlux = self.getDataInput("flux")[0].getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getFlux() != None:
self.fFlux = self.xsDataExperimentalCodition.getBeam().getFlux().getValue()
if self.hasDataInput("minExposureTimePerImage"):
self.fMinExposureTimePerImage = self.getDataInput("minExposureTimePerImage")[0].getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getMinExposureTimePerImage() != None:
self.fMinExposureTimePerImage = self.xsDataExperimentalCodition.getBeam().getMinExposureTimePerImage().getValue()
if self.fMinExposureTimePerImage == None and self.hasDataInput("diffractionPlan"):
if self.getDataInput("diffractionPlan")[0].getMinExposureTimePerImage() != None:
self.fMinExposureTimePerImage = self.getDataInput("diffractionPlan")[0].getMinExposureTimePerImage().getValue()
if self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getSize() != None:
self.fBeamSizeX = self.xsDataExperimentalCodition.getBeam().getSize().getX().getValue()
self.fBeamSizeY = self.xsDataExperimentalCodition.getBeam().getSize().getY().getValue()
if self.xsDataExperimentalCodition.getBeam().getApertureSize() != None:
self.fApertureSize = self.xsDataExperimentalCodition.getBeam().getApertureSize().getValue()
if self.hasDataInput("beamSize"):
self.fBeamSizeX = self.getDataInput("beamSize")[0].getValue()
self.fBeamSizeY = self.getDataInput("beamSize")[0].getValue()
if self.hasDataInput("apertureSize"):
self.fApertureSize = self.getDataInput("apertureSize")[0].getValue()
if self.hasDataInput("beamSizeX"):
self.fBeamSizeX = self.getDataInput("beamSizeX")[0].getValue()
if self.hasDataInput("beamSizeY"):
self.fBeamSizeY = self.getDataInput("beamSizeY")[0].getValue()
if self.hasDataInput("templateMode"):
self.bTemplateMode = self.getDataInput("templateMode")[0].getValue()
if (self.hasDataInput("beamPosX")):
self.fBeamPosX = self.getDataInput("beamPosX")[0].getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getDetector() != None:
if self.xsDataExperimentalCodition.getDetector().getBeamPositionX() != None:
self.fBeamPosX = self.xsDataExperimentalCodition.getDetector().getBeamPositionX().getValue()
if (self.hasDataInput("beamPosY")):
self.fBeamPosY = self.getDataInput("beamPosY")[0].getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getDetector() != None:
if self.xsDataExperimentalCodition.getDetector().getBeamPositionY() != None:
self.fBeamPosY = self.xsDataExperimentalCodition.getDetector().getBeamPositionY().getValue()
if (self.hasDataInput("wavelength")):
self.fWavelength = self.getDataInput("wavelength")[0].getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getWavelength() != None:
self.fWavelength = self.xsDataExperimentalCodition.getBeam().getWavelength().getValue()
if (self.hasDataInput("transmission")):
self.fTransmission = self.getDataInput("transmission")[0].getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getTransmission() != None:
self.fTransmission = self.xsDataExperimentalCodition.getBeam().getTransmission().getValue()
if self.hasDataInput("generatedTemplateFile"):
self.strGeneratedTemplateFile = self.getDataInput("generatedTemplateFile")[0].getValue()
if self.hasDataInput("resultsFilePath"):
self.strResultsFilePath = self.getDataInput("resultsFilePath")[0].getValue()
if self.hasDataInput("dataCollectionId"):
self.iDataCollectionId = self.getDataInput("dataCollectionId")[0].getValue()
if self.hasDataInput("shortComments"):
self.strShortComments = self.getDataInput("shortComments")[0].getValue()
if self.hasDataInput("comments"):
self.strComments = self.getDataInput("comments")[0].getValue()
if self.hasDataInput("inputCharacterisation"):
self.xsDataInputCharacterisation = self.getDataInput("inputCharacterisation")[0]
# Check if XML data is given as input :
if (self.xsDataInputCharacterisation is None):
self.edPluginControlSubWedgeAssemble = self.loadPlugin(self.strEDPluginControlSubWedgeAssembleName, "SubWedgeAssemble")
self.edPluginControlCharacterisation = self.loadPlugin(self.strEDPluginControlCharacterisationName, "Characterisation")
if (self.strEDPluginControlISPyBName is not None):
self.edPluginControlISPyB = self.loadPlugin(self.strEDPluginControlISPyBName, "ISPyB")
def setPluginInput(self, _edPlugin):
xsDataDiffractionPlan = XSDataDiffractionPlan()
if (not self.__fMaxExposureTimePerDataCollection is None):
xsDataDiffractionPlan.setMaxExposureTimePerDataCollection(XSDataTime(self.__fMaxExposureTimePerDataCollection))
if (not self.__strForcedSpaceGroup is None):
xsDataDiffractionPlan.setForcedSpaceGroup(XSDataString(self.__strForcedSpaceGroup))
if (not self.__bAnomalousData is None):
xsDataDiffractionPlan.setAnomalousData(XSDataBoolean(self.__bAnomalousData))
if (not self.__strStrategyOption is None):
xsDataDiffractionPlan.setStrategyOption(XSDataString(self.__strStrategyOption))
if (not self.__strComplexity is None):
xsDataDiffractionPlan.setComplexity(XSDataString(self.__strComplexity))
_edPlugin.setDataInput(xsDataDiffractionPlan, "diffractionPlan")
if (not self.__listImagePaths is None):
for strImagePath in self.__listImagePaths:
_edPlugin.setDataInput(XSDataString(strImagePath), "imagePaths")
if (not self.__xsDataInputCharacterisation is None):
_edPlugin.setDataInput(self.__xsDataInputCharacterisation, "inputCharacterisation")
if (not self.__fFlux is None):
_edPlugin.setDataInput(XSDataFloat(self.__fFlux), "flux")
if (not self.__fMinExposureTimePerImage is None):
_edPlugin.setDataInput(XSDataFloat(self.__fMinExposureTimePerImage), "minExposureTimePerImage")
if (not self.__fBeamSize is None):
_edPlugin.setDataInput(XSDataFloat(self.__fBeamSize), "beamSize")
if (not self.__bTemplateMode is None):
_edPlugin.setDataInput(XSDataBoolean(self.__bTemplateMode), "templateMode")
if (not self.__strGeneratedTemplateFile is None):
_edPlugin.setDataInput(XSDataString(self.__strGeneratedTemplateFile), "generatedTemplateFile")
if (not self.__strResultsFilePath is None):
_edPlugin.setDataInput(XSDataString(self.__strResultsFilePath), "resultsFilePath")
if (not self.__fBeamPosX is None):
_edPlugin.setDataInput(XSDataFloat(self.__fBeamPosX), "beamPosX")
if (not self.__fBeamPosY is None):
_edPlugin.setDataInput(XSDataFloat(self.__fBeamPosY), "beamPosY")
if (not self.__iDataCollectionId is None):
_edPlugin.setDataInput(XSDataInteger(self.__iDataCollectionId), "dataCollectionId")
if (not self.__strShortComments is None):
_edPlugin.setDataInput(XSDataString(self.__strShortComments), "shortComments")
if (not self.__strComments is None):
_edPlugin.setDataInput(XSDataString(self.__strComments), "comments")
if (not self.__fTransmission is None):
_edPlugin.setDataInput(XSDataDouble(self.__fTransmission), "transmission")
class EDPluginControlInterfacev1_3(EDPluginControl):
"""
This is the common class to all plugins managing user interfaces
"""
def __init__ (self):
"""
"""
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputInterface)
self.setXSDataInputClass(XSDataExperimentalCondition, "experimentalCondition")
self.setXSDataInputClass(XSDataDiffractionPlan, "diffractionPlan")
self.setXSDataInputClass(XSDataSampleCrystalMM, "sample")
self.setXSDataInputClass(XSDataString, "imagePaths")
self.setXSDataInputClass(XSDataFloat, "flux")
self.setXSDataInputClass(XSDataFloat, "minExposureTimePerImage")
self.setXSDataInputClass(XSDataFloat, "beamSize")
self.setXSDataInputClass(XSDataFloat, "beamSizeX")
self.setXSDataInputClass(XSDataFloat, "beamSizeY")
self.setXSDataInputClass(XSDataBoolean, "templateMode")
self.setXSDataInputClass(XSDataString, "generatedTemplateFile")
self.setXSDataInputClass(XSDataString, "resultsFilePath")
self.setXSDataInputClass(XSDataFloat, "beamPosX")
self.setXSDataInputClass(XSDataFloat, "beamPosY")
self.setXSDataInputClass(XSDataDouble, "wavelength")
self.setXSDataInputClass(XSDataDouble, "transmission")
self.setXSDataInputClass(XSDataInteger, "dataCollectionId")
self.setXSDataInputClass(XSDataString, "shortComments")
self.setXSDataInputClass(XSDataString, "comments")
self.setXSDataInputClass(XSDataInputCharacterisation, "inputCharacterisation")
self.strEDPluginControlSubWedgeAssembleName = "EDPluginControlSubWedgeAssemblev1_1"
self.strEDPluginControlCharacterisationName = "EDPluginControlCharacterisationv1_5"
self.strEDPluginControlISPyBName = "EDPluginControlISPyBv1_1"
self.edPluginControlSubWedgeAssemble = None
self.edPluginControlCharacterisation = None
self.edPluginControlISPyB = None
self.pyListImagePaths = None
self.xsDataInputCharacterisation = None
self.strComplexity = "none"
self.listImagePaths = []
self.fFlux = None
self.fMaxExposureTimePerDataCollection = 10000 # s, default prototype value
self.fMinExposureTimePerImage = None
self.fBeamSizeX = None
self.fBeamSizeY = None
self.fApertureSize = None
self.bTemplateMode = False
self.strGeneratedTemplateFile = None
self.strResultsFilePath = None
self.strForcedSpaceGroup = None
self.bAnomalousData = False
self.fBeamPosX = None
self.fBeamPosY = None
self.fMinOscillationWidth = None
self.fMaxOscillationSpeed = None
self.fWavelength = None
self.fTransmission = None
self.strStrategyOption = None
self.iDataCollectionId = None
self.strShortComments = None
self.strComments = None
self.strStatusMessage = None
self.xsDataExperimentalCodition = None
self.xsDataSample = None
self.xsDataDiffractionPlan = None
def configure(self):
"""
Gets the configuration parameters (if any).
"""
EDPluginControl.configure(self)
self.DEBUG("EDPluginControlInterfacev1_3.configure")
if (self.getControlledPluginName("subWedgeAssemblePlugin") is not None):
self.strEDPluginControlSubWedgeAssembleName = self.getControlledPluginName("subWedgeAssemblePlugin")
if (self.getControlledPluginName("characterisationPlugin") is not None):
self.strEDPluginControlCharacterisationName = self.getControlledPluginName("characterisationPlugin")
if (self.getControlledPluginName("ispybPlugin") is not None):
self.strEDPluginControlISPyBName = self.getControlledPluginName("ispybPlugin")
bUseISPyBPlugin = self.config.get("useISPyBPlugin")
if not bUseISPyBPlugin:
self.DEBUG("EDPluginControlInterfacev1_3 configured to not use ISPyB")
self.strEDPluginControlISPyBName = None
def preProcess(self, _edPlugin=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edPlugin)
self.DEBUG("EDPluginControlInterfacev1_3.preProcess...")
self.listImagePaths = []
# Check if XSDataInputInterface is given as input
if self.hasDataInput():
xsDataInputInterface = self.getDataInput()
if xsDataInputInterface.getExperimentalCondition():
self.xsDataExperimentalCodition = xsDataInputInterface.getExperimentalCondition()
if self.xsDataExperimentalCodition.getGoniostat():
if self.xsDataExperimentalCodition.getGoniostat().getMinOscillationWidth():
self.fMinOscillationWidth = self.xsDataExperimentalCodition.getGoniostat().getMinOscillationWidth().getValue()
if self.xsDataExperimentalCodition.getGoniostat().getMaxOscillationSpeed():
self.fMaxOscillationSpeed = self.xsDataExperimentalCodition.getGoniostat().getMaxOscillationSpeed().getValue()
self.xsDataSample = xsDataInputInterface.getSample()
self.xsDataDiffractionPlan = self.getDataInput().getDiffractionPlan()
if self.xsDataDiffractionPlan:
if self.xsDataDiffractionPlan.getForcedSpaceGroup():
self.strForcedSpaceGroup = self.xsDataDiffractionPlan.getForcedSpaceGroup().getValue()
if self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection():
self.fMaxExposureTimePerDataCollection = self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection().getValue()
if self.xsDataDiffractionPlan.getAnomalousData():
self.bAnomalousData = self.xsDataDiffractionPlan.getAnomalousData().getValue()
if self.xsDataDiffractionPlan.getStrategyOption():
self.strStrategyOption = self.xsDataDiffractionPlan.getStrategyOption().getValue()
if self.xsDataDiffractionPlan.getComplexity():
self.strComplexity = self.xsDataDiffractionPlan.getComplexity().getValue()
if self.fMinOscillationWidth == None:
if self.xsDataDiffractionPlan.getGoniostatMinOscillationWidth():
self.fMinOscillationWidth = self.xsDataDiffractionPlan.getGoniostatMinOscillationWidth().getValue()
if self.fMaxOscillationSpeed == None:
if self.xsDataDiffractionPlan.getGoniostatMaxOscillationSpeed():
self.fMaxOscillationSpeed = self.xsDataDiffractionPlan.getGoniostatMaxOscillationSpeed().getValue()
self.xsDataSample = xsDataInputInterface.getSample()
if xsDataInputInterface.getImagePath():
for xsDataFile in xsDataInputInterface.getImagePath():
self.listImagePaths.append(xsDataFile.getPath())
if xsDataInputInterface.getFlux():
self.fFlux = xsDataInputInterface.getFlux().getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getFlux() != None:
self.fFlux = self.xsDataExperimentalCodition.getBeam().getFlux().getValue()
if xsDataInputInterface.getMinExposureTimePerImage():
self.fMinExposureTimePerImage = xsDataInputInterface.getMinExposureTimePerImage().getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getMinExposureTimePerImage() != None:
self.fMinExposureTimePerImage = self.xsDataExperimentalCodition.getBeam().getMinExposureTimePerImage().getValue()
if self.fMinExposureTimePerImage == None and xsDataInputInterface.getDiffractionPlan():
if xsDataInputInterface.getDiffractionPlan().getMinExposureTimePerImage() != None:
self.fMinExposureTimePerImage = xsDataInputInterface.getDiffractionPlan().getMinExposureTimePerImage().getValue()
if self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getSize() != None:
self.fBeamSizeX = self.xsDataExperimentalCodition.getBeam().getSize().getX().getValue()
self.fBeamSizeY = self.xsDataExperimentalCodition.getBeam().getSize().getY().getValue()
if self.xsDataExperimentalCodition.getBeam().getApertureSize() != None:
self.fApertureSize = self.xsDataExperimentalCodition.getBeam().getApertureSize().getValue()
if xsDataInputInterface.getBeamSize():
self.fBeamSizeX = xsDataInputInterface.getBeamSize().getValue()
self.fBeamSizeY = xsDataInputInterface.getBeamSize().getValue()
if xsDataInputInterface.getApertureSize():
self.fApertureSize = xsDataInputInterface.getApertureSize().getValue()
if xsDataInputInterface.getBeamSizeX():
self.fBeamSizeX = xsDataInputInterface.getBeamSizeX().getValue()
if xsDataInputInterface.getBeamSizeY():
self.fBeamSizeY = xsDataInputInterface.getBeamSizeY().getValue()
if xsDataInputInterface.getApertureSize():
self.fApertureSize = xsDataInputInterface.getApertureSize().getValue()
if xsDataInputInterface.getTemplateMode():
self.bTemplateMode = xsDataInputInterface.getTemplateMode().getValue()
if xsDataInputInterface.getBeamPosX():
self.fBeamPosX = xsDataInputInterface.getBeamPosX().getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getDetector() != None:
if self.xsDataExperimentalCodition.getDetector().getBeamPositionX() != None:
self.fBeamPosX = self.xsDataExperimentalCodition.getDetector().getBeamPositionX().getValue()
if xsDataInputInterface.getBeamPosY():
self.fBeamPosY = xsDataInputInterface.getBeamPosY().getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getDetector() != None:
if self.xsDataExperimentalCodition.getDetector().getBeamPositionY() != None:
self.fBeamPosY = self.xsDataExperimentalCodition.getDetector().getBeamPositionY().getValue()
if xsDataInputInterface.getWavelength():
self.fWavelength = xsDataInputInterface.getWavelength().getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getWavelength() != None:
self.fWavelength = self.xsDataExperimentalCodition.getBeam().getWavelength().getValue()
if xsDataInputInterface.getTransmission():
self.fTransmission = xsDataInputInterface.getTransmission().getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getTransmission() != None:
self.fTransmission = self.xsDataExperimentalCodition.getBeam().getTransmission().getValue()
if xsDataInputInterface.getGeneratedTemplateFile():
self.strGeneratedTemplateFile = xsDataInputInterface.getGeneratedTemplateFile().getPath().getValue()
if xsDataInputInterface.getResultsFilePath():
self.strResultsFilePath = xsDataInputInterface.getResultsFilePath().getPath().getValue()
if xsDataInputInterface.getDataCollectionId():
self.iDataCollectionId = xsDataInputInterface.getDataCollectionId().getValue()
if xsDataInputInterface.getShortComments():
self.strShortComments = xsDataInputInterface.getShortComments().getValue()
if xsDataInputInterface.getComments():
self.strComments = xsDataInputInterface.getComments().getValue()
if xsDataInputInterface.getInputCharacterisation():
self.xsDataInputCharacterisation = xsDataInputInterface.getInputCharacterisation()
if xsDataInputInterface.getDataCollectionId():
self.iDataCollectionId = xsDataInputInterface.getDataCollectionId().getValue()
else:
if self.hasDataInput("experimentalCondition"):
self.xsDataExperimentalCodition = self.getDataInput("experimentalCondition")[0]
if self.xsDataExperimentalCodition.getGoniostat():
if self.xsDataExperimentalCodition.getGoniostat().getMinOscillationWidth():
self.fMinOscillationWidth = self.xsDataExperimentalCodition.getGoniostat().getMinOscillationWidth().getValue()
if self.xsDataExperimentalCodition.getGoniostat().getMaxOscillationSpeed():
self.fMaxOscillationSpeed = self.xsDataExperimentalCodition.getGoniostat().getMaxOscillationSpeed().getValue()
if self.hasDataInput("sample"):
self.xsDataSample = self.getDataInput("sample")[0]
if (self.hasDataInput("diffractionPlan")):
if self.xsDataDiffractionPlan is None:
self.xsDataDiffractionPlan = XSDataDiffractionPlan()
xsDataDiffractionPlans = self.getDataInput("diffractionPlan")
if (not xsDataDiffractionPlans[0] is None):
self.xsDataDiffractionPlan = xsDataDiffractionPlans[0]
if self.xsDataDiffractionPlan.getForcedSpaceGroup():
self.strForcedSpaceGroup = self.xsDataDiffractionPlan.getForcedSpaceGroup().getValue()
if self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection():
self.fMaxExposureTimePerDataCollection = self.xsDataDiffractionPlan.getMaxExposureTimePerDataCollection().getValue()
if self.xsDataDiffractionPlan.getAnomalousData():
self.bAnomalousData = self.xsDataDiffractionPlan.getAnomalousData().getValue()
if self.xsDataDiffractionPlan.getStrategyOption():
self.strStrategyOption = self.xsDataDiffractionPlan.getStrategyOption().getValue()
if self.xsDataDiffractionPlan.getComplexity():
self.strComplexity = self.xsDataDiffractionPlan.getComplexity().getValue()
if self.fMinOscillationWidth == None:
if self.xsDataDiffractionPlan.getGoniostatMinOscillationWidth():
self.fMinOscillationWidth = self.xsDataDiffractionPlan.getGoniostatMinOscillationWidth().getValue()
if self.fMaxOscillationSpeed == None:
if self.xsDataDiffractionPlan.getGoniostatMaxOscillationSpeed():
self.fMaxOscillationSpeed = self.xsDataDiffractionPlan.getGoniostatMaxOscillationSpeed().getValue()
if self.hasDataInput("sample"):
self.xsDataSample = self.getDataInput("sample")[0]
if self.hasDataInput("imagePaths"):
for strImagePath in self.getDataInput("imagePaths"):
self.listImagePaths.append(strImagePath)
if self.hasDataInput("flux"):
self.fFlux = self.getDataInput("flux")[0].getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getFlux() != None:
self.fFlux = self.xsDataExperimentalCodition.getBeam().getFlux().getValue()
if self.hasDataInput("minExposureTimePerImage"):
self.fMinExposureTimePerImage = self.getDataInput("minExposureTimePerImage")[0].getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getMinExposureTimePerImage() != None:
self.fMinExposureTimePerImage = self.xsDataExperimentalCodition.getBeam().getMinExposureTimePerImage().getValue()
if self.fMinExposureTimePerImage == None and self.hasDataInput("diffractionPlan"):
if self.getDataInput("diffractionPlan")[0].getMinExposureTimePerImage() != None:
self.fMinExposureTimePerImage = self.getDataInput("diffractionPlan")[0].getMinExposureTimePerImage().getValue()
if self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getSize() != None:
self.fBeamSizeX = self.xsDataExperimentalCodition.getBeam().getSize().getX().getValue()
self.fBeamSizeY = self.xsDataExperimentalCodition.getBeam().getSize().getY().getValue()
if self.xsDataExperimentalCodition.getBeam().getApertureSize() != None:
self.fApertureSize = self.xsDataExperimentalCodition.getBeam().getApertureSize().getValue()
if self.hasDataInput("beamSize"):
self.fBeamSizeX = self.getDataInput("beamSize")[0].getValue()
self.fBeamSizeY = self.getDataInput("beamSize")[0].getValue()
if self.hasDataInput("apertureSize"):
self.fApertureSize = self.getDataInput("apertureSize")[0].getValue()
if self.hasDataInput("beamSizeX"):
self.fBeamSizeX = self.getDataInput("beamSizeX")[0].getValue()
if self.hasDataInput("beamSizeY"):
self.fBeamSizeY = self.getDataInput("beamSizeY")[0].getValue()
if self.hasDataInput("templateMode"):
self.bTemplateMode = self.getDataInput("templateMode")[0].getValue()
if (self.hasDataInput("beamPosX")):
self.fBeamPosX = self.getDataInput("beamPosX")[0].getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getDetector() != None:
if self.xsDataExperimentalCodition.getDetector().getBeamPositionX() != None:
self.fBeamPosX = self.xsDataExperimentalCodition.getDetector().getBeamPositionX().getValue()
if (self.hasDataInput("beamPosY")):
self.fBeamPosY = self.getDataInput("beamPosY")[0].getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getDetector() != None:
if self.xsDataExperimentalCodition.getDetector().getBeamPositionY() != None:
self.fBeamPosY = self.xsDataExperimentalCodition.getDetector().getBeamPositionY().getValue()
if (self.hasDataInput("wavelength")):
self.fWavelength = self.getDataInput("wavelength")[0].getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getWavelength() != None:
self.fWavelength = self.xsDataExperimentalCodition.getBeam().getWavelength().getValue()
if (self.hasDataInput("transmission")):
self.fTransmission = self.getDataInput("transmission")[0].getValue()
elif self.xsDataExperimentalCodition != None:
if self.xsDataExperimentalCodition.getBeam() != None:
if self.xsDataExperimentalCodition.getBeam().getTransmission() != None:
self.fTransmission = self.xsDataExperimentalCodition.getBeam().getTransmission().getValue()
if self.hasDataInput("generatedTemplateFile"):
self.strGeneratedTemplateFile = self.getDataInput("generatedTemplateFile")[0].getValue()
if self.hasDataInput("resultsFilePath"):
self.strResultsFilePath = self.getDataInput("resultsFilePath")[0].getValue()
if self.hasDataInput("dataCollectionId"):
self.iDataCollectionId = self.getDataInput("dataCollectionId")[0].getValue()
if self.hasDataInput("shortComments"):
self.strShortComments = self.getDataInput("shortComments")[0].getValue()
if self.hasDataInput("comments"):
self.strComments = self.getDataInput("comments")[0].getValue()
if self.hasDataInput("inputCharacterisation"):
self.xsDataInputCharacterisation = self.getDataInput("inputCharacterisation")[0]
# Check if XML data is given as input :
if (self.xsDataInputCharacterisation is None):
self.edPluginControlSubWedgeAssemble = self.loadPlugin(self.strEDPluginControlSubWedgeAssembleName, "SubWedgeAssemble")
self.edPluginControlCharacterisation = self.loadPlugin(self.strEDPluginControlCharacterisationName, "Characterisation")
if (self.strEDPluginControlISPyBName is not None):
self.edPluginControlISPyB = self.loadPlugin(self.strEDPluginControlISPyBName, "ISPyB")
def process(self, _edPlugin=None):
EDPluginControl.process(self, _edPlugin)
self.DEBUG("EDPluginControlInterfacev1_3.process...")
if (self.edPluginControlSubWedgeAssemble is not None):
if(self.bTemplateMode == True):
self.edPluginControlSubWedgeAssemble.connectSUCCESS(self.generateTemplateFile)
else:
self.edPluginControlSubWedgeAssemble.connectSUCCESS(self.doSubWedgeAssembleSUCCESS)
self.edPluginControlSubWedgeAssemble.connectFAILURE(self.doSubWedgeAssembleFAILURE)
if(self.edPluginControlCharacterisation is not None):
self.edPluginControlCharacterisation.connectSUCCESS(self.doSuccessActionCharacterisation)
self.edPluginControlCharacterisation.connectFAILURE(self.doFailureActionCharacterisation)
if (self.edPluginControlISPyB is not None):
self.edPluginControlISPyB.connectSUCCESS(self.doSuccessActionISPyB)
self.edPluginControlISPyB.connectFAILURE(self.doFailureActionISPyB)
if (self.xsDataInputCharacterisation is None):
self.createInputCharacterisationFromImageHeaders(self.edPluginControlSubWedgeAssemble)
else:
self.runCharacterisationPlugin(self.edPluginControlCharacterisation)
def finallyProcess(self, _edPlugin=None):
EDPluginControl.finallyProcess(self, _edPlugin)
self.DEBUG("EDPluginControlInterfacev1_3.finallyProcess...")
if (not self.edPluginControlCharacterisation is None):
if (self.edPluginControlCharacterisation.hasDataOutput()):
self.setDataOutput(self.edPluginControlCharacterisation.getDataOutput(), "characterisation")
if (not self.edPluginControlISPyB is None):
if (self.edPluginControlISPyB.hasDataOutput()):
self.setDataOutput(self.edPluginControlISPyB.getDataOutput(), "ISPyB")
if self.hasDataInput():
xsDataResultInterface = XSDataResultInterface()
if self.edPluginControlCharacterisation:
xsDataResultInterface.setResultCharacterisation(self.edPluginControlCharacterisation.getDataOutput())
if self.edPluginControlISPyB:
xsDataResultInterface.setResultControlISPyB(self.edPluginControlISPyB.getDataOutput())
self.setDataOutput(xsDataResultInterface)
def createInputCharacterisationFromImageHeaders(self, _edPlugin):
self.DEBUG("EDPluginControlInterfacev1_3.createInputCharacterisationFromImageHeaders")
xsDataInputSubWedgeAssemble = XSDataInputSubWedgeAssemble()
for xsDataStringImagePath in self.listImagePaths:
xsDataFile = XSDataFile()
xsDataFile.setPath(xsDataStringImagePath)
xsDataInputSubWedgeAssemble.addFile(xsDataFile)
_edPlugin.setDataInput(xsDataInputSubWedgeAssemble)
_edPlugin.executeSynchronous()
def runCharacterisationPlugin(self, _edPlugin=None):
self.DEBUG("EDPluginControlInterfacev1_3.runCharacterisationPlugin")
self.edPluginControlCharacterisation.setDataInput(self.xsDataInputCharacterisation)
self.edPluginControlCharacterisation.executeSynchronous()
def storeResultsInISPyB(self, _edPlugin=None):
self.DEBUG("EDPluginControlInterfacev1_3.storeResultsInISPyB")
if (self.edPluginControlISPyB is not None):
# Execute the ISPyB control plugin
xsDataInputControlISPyB = XSDataInputControlISPyB()
xsDataInputControlISPyB.setCharacterisationResult(self.edPluginControlCharacterisation.getDataOutput())
if (not self.iDataCollectionId is None):
dataCollectionGroupId = self.getDataCollectionGroupId(self.iDataCollectionId)
xsDataInputControlISPyB.setDataCollectionGroupId(XSDataInteger(dataCollectionGroupId))
if (not self.strShortComments is None):
self.edPluginControlISPyB.setDataInput(XSDataString(self.strShortComments), "shortComments")
if (not self.strComments is None):
self.edPluginControlISPyB.setDataInput(XSDataString(self.strComments), "comments")
if (not self.strStatusMessage is None):
self.edPluginControlISPyB.setDataInput(XSDataString(self.strStatusMessage), "statusMessage")
self.edPluginControlISPyB.setDataInput(xsDataInputControlISPyB)
self.edPluginControlISPyB.executeSynchronous()
self.checkDozorScores(self.edPluginControlCharacterisation.getDataOutput())
def createInputCharacterisationFromSubWedges(self):
self.DEBUG("EDPluginControlInterfacev1_3.createInputCharacterisationFromSubWedges")
xsDataResultSubWedgeAssemble = self.edPluginControlSubWedgeAssemble.getDataOutput()
self.xsDataInputCharacterisation = XSDataInputCharacterisation()
xsDataCollection = XSDataCollection()
# Default exposure time (for the moment, this value should be
# possible to read from the command line)
if self.xsDataDiffractionPlan is None:
self.xsDataDiffractionPlan = XSDataDiffractionPlan()
if (not xsDataResultSubWedgeAssemble is None):
pyListSubWedge = xsDataResultSubWedgeAssemble.getSubWedge()
xsDataCollection.setSubWedge(pyListSubWedge)
for xsDataSubWedge in pyListSubWedge:
if (self.strComplexity is not None):
self.xsDataDiffractionPlan.setComplexity(XSDataString(self.strComplexity))
if (self.fFlux is not None):
xsDataSubWedge.getExperimentalCondition().getBeam().setFlux(XSDataFlux(self.fFlux))
if (self.fBeamSizeX is not None) and (self.fBeamSizeY is not None):
xsDataSize = XSDataSize()
xsDataSize.setX(XSDataLength(self.fBeamSizeX))
xsDataSize.setY(XSDataLength(self.fBeamSizeY))
xsDataSubWedge.getExperimentalCondition().getBeam().setSize(xsDataSize)
if (self.fApertureSize is not None):
xsDataSubWedge.getExperimentalCondition().getBeam().setApertureSize(XSDataLength(self.fApertureSize))
if (self.fBeamPosX is not None):
xsDataSubWedge.getExperimentalCondition().getDetector().setBeamPositionX(XSDataLength(self.fBeamPosX))
if (self.fBeamPosY is not None):
xsDataSubWedge.getExperimentalCondition().getDetector().setBeamPositionY(XSDataLength(self.fBeamPosY))
if (self.fMinExposureTimePerImage is not None):
xsDataSubWedge.getExperimentalCondition().getBeam().setMinExposureTimePerImage(XSDataTime(self.fMinExposureTimePerImage))
if (self.fTransmission is not None):
xsDataSubWedge.getExperimentalCondition().getBeam().setTransmission(XSDataDouble(self.fTransmission))
if (self.fWavelength is not None):
xsDataSubWedge.getExperimentalCondition().getBeam().setWavelength(XSDataWavelength(self.fWavelength))
if self.fMinOscillationWidth != None:
xsDataSubWedge.getExperimentalCondition().getGoniostat().setMinOscillationWidth(XSDataAngle(self.fMinOscillationWidth))
if self.fMaxOscillationSpeed != None:
xsDataSubWedge.getExperimentalCondition().getGoniostat().setMaxOscillationSpeed(XSDataAngularSpeed(self.fMaxOscillationSpeed))
if (self.strForcedSpaceGroup is not None):
self.xsDataDiffractionPlan.setForcedSpaceGroup(XSDataString(self.strForcedSpaceGroup))
self.xsDataDiffractionPlan.setAnomalousData(XSDataBoolean(self.bAnomalousData))
self.xsDataDiffractionPlan.setMaxExposureTimePerDataCollection(XSDataTime(self.fMaxExposureTimePerDataCollection))
if (self.strStrategyOption is not None):
self.xsDataDiffractionPlan.setStrategyOption(XSDataString(self.strStrategyOption))
xsDataCollection.setDiffractionPlan(self.xsDataDiffractionPlan)
if self.xsDataSample is not None:
xsDataCollection.setSample(XSDataSampleCrystalMM.parseString(self.xsDataSample.marshal()))
self.xsDataInputCharacterisation.setDataCollection(xsDataCollection)
def generateTemplateFile(self, _edPlugin):
self.DEBUG("EDPluginControlInterfacev1_3.generateTemplateFile")
self.createInputCharacterisationFromSubWedges()
if(self.strGeneratedTemplateFile is None):
self.screen("No argument for command line --generateTemplate key word found!")
elif (self.xsDataInputCharacterisation is None):
self.screen("ERROR! Cannot generate template file %s, please check the log files." % self.strGeneratedTemplateFile)
else:
self.screen("Generating xml template input file for edna: " + self.strGeneratedTemplateFile + "...")
self.xsDataInputCharacterisation.exportToFile(self.strGeneratedTemplateFile)
def doSubWedgeAssembleSUCCESS(self, _edPlugin):
self.DEBUG("EDPluginControlInterfacev1_3.doSubWedgeAssembleSUCCESS")
self.createInputCharacterisationFromSubWedges()
self.runCharacterisationPlugin(_edPlugin)
def doSubWedgeAssembleFAILURE(self, _edPlugin):
self.DEBUG("EDPluginControlInterfacev1_3.doSubWedgeAssembleFAILURE")
self.screen("Execution of " + self.strEDPluginControlSubWedgeAssembleName + " failed.")
self.screen("Please inspect the log file for further information.")
self.setFailure()
def doFailureActionCharacterisation(self, _edPlugin=None):
"""
retrieve the potential warning messages
retrieve the potential error messages
"""
self.DEBUG("EDPluginControlInterfacev1_3.doFailureActionCharacterisation")
self.retrieveFailureMessages(self.edPluginControlCharacterisation, "EDPluginControlInterfacev1_3.doSuccessActionISPyB")
if _edPlugin.hasDataOutput("statusMessage"):
self.strStatusMessage = _edPlugin.getDataOutput("statusMessage")[0].getValue()
self.generateExecutiveSummary(self)
self.storeResultsInISPyB(_edPlugin)
self.setFailure()
def doSuccessActionCharacterisation(self, _edPlugin=None):
"""
retrieve the potential warning messages
"""
self.DEBUG("EDPluginControlInterfacev1_3.doSuccessActionCharacterisation")
# Store the results if requested
if (self.strResultsFilePath is not None):
xsDataCharacterisationResult = _edPlugin.getDataOutput()
if (xsDataCharacterisationResult is not None):
xsDataCharacterisationResult.exportToFile(self.strResultsFilePath)
if _edPlugin.hasDataOutput("statusMessage"):
self.strStatusMessage = _edPlugin.getDataOutput("statusMessage")[0].getValue()
self.storeResultsInISPyB(_edPlugin)
def doSuccessActionISPyB(self, _edPlugin):
self.DEBUG("EDPluginControlInterfacev1_3.doSuccessActionISPyB...")
self.retrieveSuccessMessages(self.edPluginControlISPyB, "EDPluginControlInterfacev1_3.doSuccessActionISPyB")
def doFailureActionISPyB(self, _edPlugin=None):
self.DEBUG("EDPluginControlInterfacev1_3.doFailureActionISpyB...")
self.generateExecutiveSummary(self)
self.setFailure()
def generateExecutiveSummary(self, _edPlugin=None):
"""
Prints the executive summary from the plugin
"""
self.DEBUG("EDPluginControlInterfacev1_3.generateExecutiveSummary")
if (self.edPluginControlSubWedgeAssemble is not None):
if self.edPluginControlSubWedgeAssemble.getListExecutiveSummaryLines() != []:
self.addExecutiveSummaryLine("Summary of plugin %s:" % self.strEDPluginControlSubWedgeAssembleName)
self.appendExecutiveSummary(self.edPluginControlSubWedgeAssemble)
if (self.edPluginControlCharacterisation is not None):
self.addExecutiveSummaryLine("Summary of plugin %s:" % self.strEDPluginControlCharacterisationName)
self.appendExecutiveSummary(self.edPluginControlCharacterisation)
if (self.edPluginControlISPyB is not None):
self.addExecutiveSummaryLine("Summary of plugin %s:" % self.strEDPluginControlISPyBName)
self.appendExecutiveSummary(self.edPluginControlISPyB)
self.verboseScreenExecutiveSummary()
def checkDozorScores(self, _xsDataResultCharacterisation):
# Check Dozor scores
listImageQualityIndicators = _xsDataResultCharacterisation.imageQualityIndicators
noWeakDiffraction = 0
noTotal = 0
newComment = None
referenceImagePath = None
listImageNoWithNoDiffraction = []
for imageQualityIndicators in listImageQualityIndicators:
if referenceImagePath is None:
referenceImagePath = imageQualityIndicators.image.path.value
if imageQualityIndicators.dozor_score is not None:
noTotal += 1
dozorScore = imageQualityIndicators.dozor_score.value
if dozorScore <= 0.001:
listImageNoWithNoDiffraction.append(imageQualityIndicators.image.number.value)
elif dozorScore < 1.0:
noWeakDiffraction += 1
if noTotal > 0:
if len(listImageNoWithNoDiffraction) == noTotal:
newComment = "No diffraction."
elif noWeakDiffraction + len(listImageNoWithNoDiffraction) == noTotal:
newComment = "Very weak diffraction."
else:
subComment = None
if len(listImageNoWithNoDiffraction) == 1:
subComment = "image {0}".format(listImageNoWithNoDiffraction[0])
elif len(listImageNoWithNoDiffraction) == 2:
subComment = "images {0} and {1}".format(listImageNoWithNoDiffraction[0], listImageNoWithNoDiffraction[1])
elif len(listImageNoWithNoDiffraction) > 2:
subComment = "images {0}".format(listImageNoWithNoDiffraction[0])
for imageNo in listImageNoWithNoDiffraction[1:-1]:
subComment += ", {0}".format(imageNo)
subComment += " and {0}".format(listImageNoWithNoDiffraction[-1])
if subComment is not None:
newComment = "No diffraction detected in {0} - hint: sample might not be accurately centred.".format(subComment)
if newComment is not None and self.iDataCollectionId is not None:
xsDataInput = XSDataInputISPyBUpdateDataCollectionGroupComment()
xsDataInput.newComment = XSDataString(newComment)
xsDataInput.dataCollectionId = XSDataInteger(self.iDataCollectionId)
edPluginISPyBUpdateDataCollectionGroupComment = self.loadPlugin("EDPluginISPyBUpdateDataCollectionGroupCommentv1_4")
edPluginISPyBUpdateDataCollectionGroupComment.dataInput = xsDataInput
self.executePluginSynchronous(edPluginISPyBUpdateDataCollectionGroupComment)
def getDataCollectionGroupId(self, _dataCollectionId):
self.DEBUG("EDPluginControlInterfacev1_2.getDataCollectionGroupId")
self.DEBUG("dataCollectionId = {0}".format(_dataCollectionId))
dataCollectionGroupId = None
xsDataInputRetrieveDataCollection = XSDataInputRetrieveDataCollection()
xsDataInputRetrieveDataCollection.dataCollectionId = XSDataInteger(_dataCollectionId)
edPluginISPyBRetrieveDataCollection = self.loadPlugin("EDPluginISPyBRetrieveDataCollectionv1_4")
edPluginISPyBRetrieveDataCollection.dataInput = xsDataInputRetrieveDataCollection
edPluginISPyBRetrieveDataCollection.executeSynchronous()
xsDataResultRetrieveDataCollection = edPluginISPyBRetrieveDataCollection.dataOutput
if xsDataResultRetrieveDataCollection is not None:
dataCollection = xsDataResultRetrieveDataCollection.dataCollection
if dataCollection is not None:
dataCollectionGroupId = dataCollection.dataCollectionGroupId
self.DEBUG("dataCollectionGroupId = {0}".format(dataCollectionGroupId))
return dataCollectionGroupId
def diffractionPlan(self):
# Do we have a diffracionPlan?
xsDataDiffractionPlan = self.xsDataResultCharacterisation.getDataCollection().getDiffractionPlan()
if xsDataDiffractionPlan is None:
xsDataDiffractionPlan = XSDataDiffractionPlan()
self.page.h2( "Diffraction Plan" )
self.page.table( class_='diffractionPlan', border_="1", cellpadding_="0")
self.page.tr( align_="CENTER", bgcolor_=self.strTableColourTitle2)
self.page.th("Forced<br>space group")
self.page.th("Anomalous<br>data")
self.page.th("Aimed<br>multiplicity")
self.page.th("Aimed<br>completeness")
self.page.th("Aimed I/sigma<br>at highest res.")
self.page.th("Aimed<br>resolution (Å)")
self.page.tr.close()
self.page.tr( align_="CENTER", bgcolor_=self.strTableColourRows)
# Forced space group
if xsDataDiffractionPlan.getForcedSpaceGroup() is None:
strForcedSpaceGroup = "None"
else:
strForcedSpaceGroup = xsDataDiffractionPlan.getForcedSpaceGroup().getValue()
self.page.th(strForcedSpaceGroup)
# Anomalous data
if xsDataDiffractionPlan.getAnomalousData() is None or xsDataDiffractionPlan.getAnomalousData().getValue() == False:
strAnomalousData = "False"
else:
strAnomalousData = "True"
self.page.th(strAnomalousData)
# Aimed multiplicity
if xsDataDiffractionPlan.getAimedMultiplicity() is None:
strAimedMultiplicity = "Default<br>(optimized)"
else:
strAimedMultiplicity = "%.2f" % xsDataDiffractionPlan.getAimedMultiplicity().getValue()
self.page.th(strAimedMultiplicity)
# Aimed completeness
if xsDataDiffractionPlan.getAimedCompleteness() is None:
strAimedCompleteness = "Default<br>(>= 0.99)"
else:
strAimedCompleteness = "%.2f" % xsDataDiffractionPlan.getAimedCompleteness().getValue()
self.page.th(strAimedCompleteness)
# Aimed aimedIOverSigmaAtHighestResolution
if xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution() is None:
strAimedIOverSigmaAtHighestResolution = "BEST Default"
else:
strAimedIOverSigmaAtHighestResolution = "%.2f" % xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution().getValue()
self.page.th(strAimedIOverSigmaAtHighestResolution)
# Aimed resolution
if xsDataDiffractionPlan.getAimedResolution() is None:
strAimedResolution = "Default<br>(highest possible)"
else:
strAimedResolution = "%0.2f" % xsDataDiffractionPlan.getAimedResolution().getValue()
self.page.th(strAimedResolution)
# Close the table
self.page.tr.close()
self.page.table.close()