class EDPluginControlInterfacev2_0(EDPluginControl):
"""
This plugin is an enhancement of EDPluginControlInterfacev1_2
"""
def __init__ (self):
"""
"""
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataDiffractionPlan, "diffractionPlan")
self.setXSDataInputClass(XSDataString, "imagePaths")
self.setXSDataInputClass(XSDataFloat, "flux")
self.setXSDataInputClass(XSDataFloat, "minExposureTimePerImage")
self.setXSDataInputClass(XSDataFloat, "beamSize")
self.setXSDataInputClass(XSDataBoolean, "templateMode")
self.setXSDataInputClass(XSDataString, "generatedTemplateFile")
self.setXSDataInputClass(XSDataString, "generatedTemplateFileMXv2")
self.setXSDataInputClass(XSDataString, "resultsFilePath")
self.setXSDataInputClass(XSDataFloat, "beamPosX")
self.setXSDataInputClass(XSDataFloat, "beamPosY")
self.setXSDataInputClass(XSDataDouble, "transmission")
self.setXSDataInputClass(XSDataInteger, "dataCollectionId")
self.setXSDataInputClass(XSDataString, "shortComments")
self.setXSDataInputClass(XSDataString, "comments")
self.setXSDataInputClass(XSDataInputCharacterisation, "inputCharacterisation")
self.setXSDataInputClass(XSDataMXv2.XSDataCollection, "mxv2DataCollection")
self.strEDPluginControlSubWedgeAssembleName = "EDPluginControlSubWedgeAssemblev1_1"
self.strEDPluginControlCharacterisationName = "EDPluginControlCharForReorientationv2_0"
self.strEDPluginControlISPyBName = "EDPluginControlISPyBv1_1"
self.edPluginControlSubWedgeAssemble = None
self.edPluginControlCharacterisation = None
self.edPluginControlISPyB = None
self.pyListImagePaths = None
self.xsDataInputCharacterisation = None
self.xsDataCollectionMXv2 = None
self.strComplexity = "none"
self.listImagePaths = []
self.fFlux = None
self.fMaxExposureTimePerDataCollection = 10000 # s, default prototype value
self.fMinExposureTimePerImage = None
self.fBeamSize = None
self.bTemplateMode = False
self.strGeneratedTemplateFile = None
self.strGeneratedTemplateFileMXv2 = None
self.strResultsFilePath = None
self.strForcedSpaceGroup = None
self.bAnomalousData = False
self.fBeamPosX = None
self.fBeamPosY = None
self.fTransmission = None
self.strStrategyOption = None
self.iDataCollectionId = None
self.strShortComments = None
self.strComments = None
def configure(self):
"""
Gets the configuration parameters (if any).
"""
EDPluginControl.configure(self)
self.DEBUG("EDPluginControlInterfacev2_0.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", False)
if not bUseISPyBPlugin:
self.strEDPluginControlISPyBName = None
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 process(self, _edPlugin=None):
"""
"""
EDPluginControl.process(self, _edPlugin)
self.DEBUG("EDPluginControlInterfacev2_0.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 postProcess(self, _edPlugin=None):
"""
"""
EDPluginControl.postProcess(self, _edPlugin)
self.DEBUG("EDPluginControlInterfacev2_0.postProcess...")
if (not self.edPluginControlCharacterisation is None):
if (self.edPluginControlCharacterisation.hasDataOutput()):
self.setDataOutput(self.edPluginControlCharacterisation.getDataOutput(), "resultCharacterisationv2_0")
if (not self.edPluginControlISPyB is None):
if (self.edPluginControlISPyB.hasDataOutput()):
self.setDataOutput(self.edPluginControlISPyB.getDataOutput(), "ISPyB")
def createInputCharacterisationFromImageHeaders(self, _edPlugin):
"""
"""
self.DEBUG("EDPluginControlInterfacev2_0.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("EDPluginControlInterfacev2_0.runCharacterisationPlugin")
self.edPluginControlCharacterisation.setDataInput(self.xsDataInputCharacterisation, "mxv1InputCharacterisation")
if self.xsDataCollectionMXv2 != None:
self.edPluginControlCharacterisation.setDataInput(self.xsDataCollectionMXv2, "mxv2DataCollection")
self.edPluginControlCharacterisation.executeSynchronous()
def storeResultsInISPyB(self, _edPlugin=None):
self.DEBUG("EDPluginControlInterfacev2_0.storeResultsInISPyB")
if (self.edPluginControlISPyB is not None):
# Execute the ISPyB control plugin
xsDataInputControlISPyB = XSDataInputControlISPyB()
xsDataInputControlISPyB.setCharacterisationResult(self.edPluginControlCharacterisation.getDataOutput().getMxv1ResultCharacterisation())
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")
self.edPluginControlISPyB.setDataInput(xsDataInputControlISPyB)
self.edPluginControlISPyB.executeSynchronous()
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 generateTemplateFile(self, _edPlugin):
self.DEBUG("EDPluginControlInterfacev2_0.generateTemplateFile")
self.createInputCharacterisationFromSubWedges()
if self.strGeneratedTemplateFile is not None:
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 MXv1 xml template input file: " + self.strGeneratedTemplateFile + "...")
self.xsDataInputCharacterisation.outputFile(self.strGeneratedTemplateFile)
if self.strGeneratedTemplateFileMXv2 is not None:
if(self.strGeneratedTemplateFileMXv2 is None):
self.screen("No argument for command line --generateTemplateMXv2 key word found!")
elif (self.xsDataInputCharacterisation is None):
self.screen("ERROR! Cannot generate template file %s, please check the log files." % self.strGeneratedTemplateFileMXv2)
else:
# TEMP: generates the file to be read in
##PARAMS
calibDate = '2009-12-10'
omegaR = (0, 0, 1)
kappaR = (0, 0.707106781187, 0.707106781187)
phiR = (0, 0, 1)
beamD = (1, 0, 0)
polarisationP = (0, 1, 0)
exposuretime = 1.0
imagewidth = 1.0
numberimages = 1
wavelength = 1.0
OmegaV = 0.0
KappaV = 90.0
PhiV = 40.0
imgFnames = []
xsDataResultSubWedgeAssemble = self.edPluginControlSubWedgeAssemble.getDataOutput()
for xsDataImage in xsDataResultSubWedgeAssemble.getSubWedge()[0].getImage():
imgFnames.append(xsDataImage.getPath().getValue())
xsDC_v2 = self.generateDataCollectionDescriptorForSubWedge(calibDate, omegaR, kappaR, phiR, beamD, polarisationP, exposuretime, imagewidth, numberimages, wavelength, OmegaV, KappaV, PhiV, imgFnames)
self.screen("Generating MXv2 xml template input file: " + self.strGeneratedTemplateFileMXv2 + "...")
xsDC_v2.outputFile(self.strGeneratedTemplateFileMXv2)
def doSubWedgeAssembleSUCCESS(self, _edPlugin):
self.DEBUG("EDPluginControlInterfacev2_0.doSubWedgeAssembleSUCCESS")
self.createInputCharacterisationFromSubWedges()
self.runCharacterisationPlugin(_edPlugin)
def doSubWedgeAssembleFAILURE(self, _edPlugin):
self.DEBUG("EDPluginControlInterfacev2_0.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("EDPluginControlInterfacev2_0.doFailureActionCharacterisation")
self.retrieveFailureMessages(self.edPluginControlCharacterisation, "EDPluginControlInterfacev2_0.doSuccessActionISPyB")
self.generateExecutiveSummary(self)
self.setFailure()
def doSuccessActionCharacterisation(self, _edPlugin=None):
"""
retrieve the potential warning messages
"""
self.DEBUG("EDPluginControlInterfacev2_0.doSuccessActionCharacterisation")
# Store the results if requested
if (self.strResultsFilePath is not None):
xsDataCharacterisationResult = _edPlugin.getDataOutput()
if (xsDataCharacterisationResult is not None):
xsDataCharacterisationResult.outputFile(self.strResultsFilePath)
self.storeResultsInISPyB(_edPlugin)
def doSuccessActionISPyB(self, _edPlugin):
self.DEBUG("EDPluginControlInterfacev2_0.doSuccessActionISPyB...")
self.retrieveSuccessMessages(self.edPluginControlISPyB, "EDPluginControlInterfacev2_0.doSuccessActionISPyB")
def doFailureActionISPyB(self, _edPlugin=None):
self.DEBUG("EDPluginControlInterfacev2_0.doFailureActionISpyB...")
self.generateExecutiveSummary(self)
self.setFailure()
def generateExecutiveSummary(self, _edPlugin=None):
"""
Prints the executive summary from the plugin
"""
self.DEBUG("EDPluginControlInterfacev2_0.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 generateDataCollectionDescriptorForSubWedge(self, calibDate, omegaR, kappaR, phiR, beamD, polarisationP, exposuretime, imagewidth, numberimages, wavelength, OmegaV, KappaV, PhiV, imgFnames):
##CONTAINER
xsDC_v2 = XSDataCollection_v2()
##GonioCalib
calib = XSDataMXv2.XSCalibration()
cdate = XSDataMXv2.XSDataDate()
cdate.setValue(calibDate)
calib.setDate(cdate)
#OmegaCalib
omegacal = XSDataMXv2.XSCalibratedDisplacementAxis()
zdir = XSDataMXv2.XSDataUnitVector()
zdir.setV1(omegaR[0])
zdir.setV2(omegaR[1])
zdir.setV3(omegaR[2])
omegacal.setZerodirection(zdir)
omegacal.setXSCalibration(calib)
#KappaCalib
kappacal = XSDataMXv2.XSCalibratedDisplacementAxis()
zdir = XSDataMXv2.XSDataUnitVector()
zdir.setV1(kappaR[0])
zdir.setV2(kappaR[1])
zdir.setV3(kappaR[2])
kappacal.setZerodirection(zdir)
kappacal.setXSCalibration(calib)
#PhiCalib
phical = XSDataMXv2.XSCalibratedDisplacementAxis()
zdir = XSDataMXv2.XSDataUnitVector()
zdir.setV1(phiR[0])
zdir.setV2(phiR[1])
zdir.setV3(phiR[2])
phical.setZerodirection(zdir)
phical.setXSCalibration(calib)
##goni
actgonio = XSDataMXv2.XSRotationalGoniostat()
#omega
omega = XSDataMXv2.XSGoniostatBaseAxis()
omega.setName(XSDataMXv2.XSDataString('Omega'))
omega.setIsscannable(XSDataMXv2.XSDataBoolean(1))
omega.addXSCalibratedDisplacementAxis(omegacal)
actgonio.setXSGoniostatBaseAxis(omega)
#kappa
kappa = XSDataMXv2.XSGoniostatRotatableAxis()
kappa.setName(XSDataMXv2.XSDataString('Kappa'))
kappa.setIsscannable(XSDataMXv2.XSDataBoolean(0))
kappa.addXSCalibratedDisplacementAxis(kappacal)
actgonio.addXSGoniostatRotatableAxis(kappa)
#phi
phi = XSDataMXv2.XSGoniostatRotatableAxis()
phi.setName(XSDataMXv2.XSDataString('Phi'))
phi.setIsscannable(XSDataMXv2.XSDataBoolean(0))
phi.addXSCalibratedDisplacementAxis(phical)
actgonio.addXSGoniostatRotatableAxis(phi)
##beam
beam = XSDataMXv2.XSBeam()
zdir = XSDataMXv2.XSDataUnitVector()
zdir.setV1(polarisationP[0])
zdir.setV2(polarisationP[1])
zdir.setV3(polarisationP[2])
beam.setPolarisatation(zdir)
zdir = XSDataMXv2.XSDataUnitVector()
zdir.setV1(beamD[0])
zdir.setV2(beamD[1])
zdir.setV3(beamD[2])
beam.setDirection(zdir)
##detector
detector = XSDataMXv2.XSDetector()
detector.setName(XSDataMXv2.XSDataString('detector'))
###detector.set
##SUBWEDGE
sw = XSSubWedge_v2()
# template
sw.setImagefilenametemplate(XSDataMXv2.XSDataString(EDUtilsImage.getTemplate(imgFnames[0], "#")))
# images
for imgFname in imgFnames:
img = XSDiffractionImages_v2()
img.setFilename(XSDataMXv2.XSDataString(imgFname))
sw.addXSDiffractionImages(img)
#RotationExposure
rotexp = XSRotationExposure_v2()
rotexp.setExposuretime(XSDataMXv2.XSDataTime(exposuretime))
rotexp.setImagewidth(XSDataMXv2.XSDataAngle(imagewidth))
rotexp.setNumberimages(XSDataMXv2.XSDataInteger(numberimages))
rotexp.setXSGoniostatAxis(omega)
sw.setXSRotationExposure(rotexp)
#Beamsetting
beams = XSBeamSetting_v2()
w = XSDataMXv2.XSDataWavelength()
w.setValue(wavelength)
beams.setWavelength(w)
beams.setXSBeam(beam)
sw.setXSBeamSetting(beams)
#RotationalGonioSetting
rotgset = XSDataMXv2.XSRotationalGoniostatSetting()
rotgset.setXSRotationalGoniostat(actgonio)
oang = XSDataMXv2.XSDataAngle()
oang.setValue(OmegaV)
rotgset.setBaseaxissetting(oang)
kang = XSDataMXv2.XSDataAngle()
kang.setValue(KappaV)
rotgset.addAxissetting(kang)
pang = XSDataMXv2.XSDataAngle()
pang.setValue(PhiV)
rotgset.addAxissetting(pang)
sw.setXSRotationalGoniostatSetting(rotgset)
#DetectorSetting TODOTODO
detset = XSDataMXv2.XSDetectorSetting()
#axissetting=(XSDataMXv2.XSDataAngle().setValue(KappaV),XSDataMXv2.XSDataAngle().setValue(PhiV))
#detset.setAxissetting(axissetting)
xsDC_v2.addXSSubWedge(sw)
return xsDC_v2
