def buildChildren(self, child_, nodeName_):
if child_.nodeType == Node.ELEMENT_NODE and nodeName_ == "mxv1InputCharacterisation":
obj_ = XSDataInputCharacterisation()
obj_.build(child_)
self.setMxv1InputCharacterisation(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and nodeName_ == "mxv1ResultCharacterisation_Reference":
obj_ = XSDataResultCharacterisation()
obj_.build(child_)
self.setMxv1ResultCharacterisation_Reference(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and nodeName_ == "mxv2DataCollection":
obj_ = XSDataCollection()
obj_.build(child_)
self.setMxv2DataCollection(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and nodeName_ == "mxv2DataCollection_Reference":
obj_ = XSDataCollection()
obj_.build(child_)
self.setMxv2DataCollection_Reference(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and nodeName_ == "possibleOrientations":
obj_ = kappa_alignment_response()
obj_.build(child_)
self.setPossibleOrientations(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and nodeName_ == "omega":
obj_ = XSDataAngle()
obj_.build(child_)
self.setOmega(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and nodeName_ == "kappa":
obj_ = XSDataAngle()
obj_.build(child_)
self.setKappa(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and nodeName_ == "phi":
obj_ = XSDataAngle()
obj_.build(child_)
self.setPhi(obj_)
XSDataInputInterface.buildChildren(self, child_, nodeName_)
def exportChildren(self, outfile, level, name_='XSDataInputInterfacev2_2'):
XSDataInputInterface.exportChildren(self, outfile, level, name_)
if self.__mxv1InputCharacterisation is not None:
self.mxv1InputCharacterisation.export(
outfile, level, name_='mxv1InputCharacterisation')
else:
warnEmptyAttribute("mxv1InputCharacterisation",
"XSDataInputCharacterisation")
if self.__mxv1ResultCharacterisation_Reference is not None:
self.mxv1ResultCharacterisation_Reference.export(
outfile, level, name_='mxv1ResultCharacterisation_Reference')
if self.__mxv2DataCollection is not None:
self.mxv2DataCollection.export(outfile,
level,
name_='mxv2DataCollection')
if self.__mxv2DataCollection_Reference is not None:
self.mxv2DataCollection_Reference.export(
outfile, level, name_='mxv2DataCollection_Reference')
if self.__possibleOrientations is not None:
self.possibleOrientations.export(outfile,
level,
name_='possibleOrientations')
if self.__omega is not None:
self.omega.export(outfile, level, name_='omega')
if self.__kappa is not None:
self.kappa.export(outfile, level, name_='kappa')
if self.__phi is not None:
self.phi.export(outfile, level, name_='phi')
def functionXMLout(_strXMLin, _strXMLout):
"""
This is an example of XMLout function ... it prints only the name of the file created
@param _srXMLin: The XML string used to launch the job
@type _strXMLin: python string with the input XML
@param _strXMLout: The XML string retrieved job
@type _strXMLout: python string with the output XML
@return: None
"""
xsDataInputInterface = XSDataInputInterface.parseString(_strXMLin)
strImagePath = xsDataInputInterface.getImagePath()[0].getPath().getValue()
EDVerbose.screen("Successful processing of image %s" % strImagePath)
strResultText = os.path.dirname(strImagePath) + " " + os.path.basename(strImagePath) + " "
xsDataResultInterface = XSDataResultInterface.parseString(_strXMLout)
xsDataResultCharacterisation = xsDataResultInterface.getResultCharacterisation()
#
xsDataIndexingResult = xsDataResultCharacterisation.getIndexingResult()
#strResultText = _strDirectoryVisit + " " + strFileName + " "
if (xsDataIndexingResult is None):
strResultText += "Indexing failed"
else:
xsDataSelectedSolution = xsDataIndexingResult.getSelectedSolution()
fMosaicityEstimation = xsDataSelectedSolution.getCrystal().getMosaicity().getValue()
strResultText += "Mosaicity: %.2f " % fMosaicityEstimation
xsDataStrategyResult = xsDataResultCharacterisation.getStrategyResult()
if (xsDataStrategyResult is None):
strResultText += "No strategy result"
else:
xsDataCollectionPlan = xsDataStrategyResult.getCollectionPlan()[0]
xsDataStrategySummary = xsDataCollectionPlan.getStrategySummary()
fRankingResolution = xsDataStrategySummary.getRankingResolution().getValue()
strResultText += "Resolution: %.2f" % fRankingResolution
writeToResultFile(strResultText)
def __init__(self, inputCharacterisation=None, comments=None, shortComments=None, dataCollectionId=None, transmission=None, wavelength=None, beamPosY=None, beamPosX=None, resultsFilePath=None, generatedTemplateFile=None, templateMode=None, beamSizeY=None, beamSizeX=None, beamSize=None, minExposureTimePerImage=None, flux=None, imagePath=None, sample=None, diffractionPlan=None, experimentalCondition=None, phi=None, kappa=None, omega=None, possibleOrientations=None, mxv2DataCollection_Reference=None, mxv2DataCollection=None, mxv1ResultCharacterisation_Reference=None, mxv1InputCharacterisation=None):
XSDataInputInterface.__init__(self, inputCharacterisation, comments, shortComments, dataCollectionId, transmission, wavelength, beamPosY, beamPosX, resultsFilePath, generatedTemplateFile, templateMode, beamSizeY, beamSizeX, beamSize, minExposureTimePerImage, flux, imagePath, sample, diffractionPlan, experimentalCondition)
checkType("XSDataInputInterfacev2_2", "Constructor of XSDataInputInterfacev2_2", mxv1InputCharacterisation, "XSDataInputCharacterisation")
self.__mxv1InputCharacterisation = mxv1InputCharacterisation
checkType("XSDataInputInterfacev2_2", "Constructor of XSDataInputInterfacev2_2", mxv1ResultCharacterisation_Reference, "XSDataResultCharacterisation")
self.__mxv1ResultCharacterisation_Reference = mxv1ResultCharacterisation_Reference
checkType("XSDataInputInterfacev2_2", "Constructor of XSDataInputInterfacev2_2", mxv2DataCollection, "XSDataCollection")
self.__mxv2DataCollection = mxv2DataCollection
checkType("XSDataInputInterfacev2_2", "Constructor of XSDataInputInterfacev2_2", mxv2DataCollection_Reference, "XSDataCollection")
self.__mxv2DataCollection_Reference = mxv2DataCollection_Reference
checkType("XSDataInputInterfacev2_2", "Constructor of XSDataInputInterfacev2_2", possibleOrientations, "kappa_alignment_response")
self.__possibleOrientations = possibleOrientations
checkType("XSDataInputInterfacev2_2", "Constructor of XSDataInputInterfacev2_2", omega, "XSDataAngle")
self.__omega = omega
checkType("XSDataInputInterfacev2_2", "Constructor of XSDataInputInterfacev2_2", kappa, "XSDataAngle")
self.__kappa = kappa
checkType("XSDataInputInterfacev2_2", "Constructor of XSDataInputInterfacev2_2", phi, "XSDataAngle")
self.__phi = phi
def buildChildren(self, child_, nodeName_):
if child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'mxv1InputCharacterisation':
obj_ = XSDataInputCharacterisation()
obj_.build(child_)
self.setMxv1InputCharacterisation(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'mxv1ResultCharacterisation_Reference':
obj_ = XSDataResultCharacterisation()
obj_.build(child_)
self.setMxv1ResultCharacterisation_Reference(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'mxv2DataCollection':
obj_ = XSDataCollection()
obj_.build(child_)
self.setMxv2DataCollection(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'mxv2DataCollection_Reference':
obj_ = XSDataCollection()
obj_.build(child_)
self.setMxv2DataCollection_Reference(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'possibleOrientations':
obj_ = kappa_alignment_response()
obj_.build(child_)
self.setPossibleOrientations(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'omega':
obj_ = XSDataAngle()
obj_.build(child_)
self.setOmega(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'kappa':
obj_ = XSDataAngle()
obj_.build(child_)
self.setKappa(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'phi':
obj_ = XSDataAngle()
obj_.build(child_)
self.setPhi(obj_)
XSDataInputInterface.buildChildren(self, child_, nodeName_)
def exportChildren(self, outfile, level, name_='XSDataInputInterfacev2_2'):
XSDataInputInterface.exportChildren(self, outfile, level, name_)
if self.__mxv1InputCharacterisation is not None:
self.mxv1InputCharacterisation.export(outfile, level, name_='mxv1InputCharacterisation')
else:
warnEmptyAttribute("mxv1InputCharacterisation", "XSDataInputCharacterisation")
if self.__mxv1ResultCharacterisation_Reference is not None:
self.mxv1ResultCharacterisation_Reference.export(outfile, level, name_='mxv1ResultCharacterisation_Reference')
if self.__mxv2DataCollection is not None:
self.mxv2DataCollection.export(outfile, level, name_='mxv2DataCollection')
if self.__mxv2DataCollection_Reference is not None:
self.mxv2DataCollection_Reference.export(outfile, level, name_='mxv2DataCollection_Reference')
if self.__possibleOrientations is not None:
self.possibleOrientations.export(outfile, level, name_='possibleOrientations')
if self.__omega is not None:
self.omega.export(outfile, level, name_='omega')
if self.__kappa is not None:
self.kappa.export(outfile, level, name_='kappa')
if self.__phi is not None:
self.phi.export(outfile, level, name_='phi')
def functionXMLerror(_strXMLin):
"""
@param _strXMLin: The XML string used to launch the job
@type _strXMLin: python string with the input XML
@return: None
"""
xsDataInputInterface = XSDataInputInterface.parseString(_strXMLin)
strImagePath = xsDataInputInterface.getImagePath()[0].getPath().getValue()
strResultText = os.path.dirname(strImagePath) + " " + os.path.basename(strImagePath) + " "
strResultText = strResultText + "Processing failed."
writeToResultFile(strResultText)
return None
def exportChildren(self, outfile, level, name_="XSDataInputInterfacev2_2"):
XSDataInputInterface.exportChildren(self, outfile, level, name_)
if self._mxv1InputCharacterisation is not None:
self.mxv1InputCharacterisation.export(outfile, level, name_="mxv1InputCharacterisation")
else:
warnEmptyAttribute("mxv1InputCharacterisation", "XSDataInputCharacterisation")
if self._mxv1ResultCharacterisation_Reference is not None:
self.mxv1ResultCharacterisation_Reference.export(
outfile, level, name_="mxv1ResultCharacterisation_Reference"
)
if self._mxv2DataCollection is not None:
self.mxv2DataCollection.export(outfile, level, name_="mxv2DataCollection")
if self._mxv2DataCollection_Reference is not None:
self.mxv2DataCollection_Reference.export(outfile, level, name_="mxv2DataCollection_Reference")
if self._possibleOrientations is not None:
self.possibleOrientations.export(outfile, level, name_="possibleOrientations")
if self._omega is not None:
self.omega.export(outfile, level, name_="omega")
if self._kappa is not None:
self.kappa.export(outfile, level, name_="kappa")
if self._phi is not None:
self.phi.export(outfile, level, name_="phi")
def testExecute(self):
"""
Runs the plugin and marshals the obtained XML file into an XSDataInputInterface object
"""
self.run()
edPlugin = self.getPlugin()
xsDataOutputObtained = edPlugin.getDataOutput()
strXMLFile = xsDataOutputObtained.getPath().getValue()
strObtainedOutput = self.readAndParseFile(strXMLFile)
xsDataInputInterfaceObtained = XSDataInputInterface.parseString(strObtainedOutput)
EDVerbose.DEBUG("Checking obtained result...")
EDVerbose.DEBUG("Found class of type: %s" % xsDataInputInterfaceObtained.__class__.__name__)
# Just quickly check that we have an actual XSDataInputInterface object
EDAssert.equal(xsDataInputInterfaceObtained.__class__.__name__ == "XSDataInputInterface", True)
def testExecute(self):
"""
Runs the plugin and marshals the obtained XML file into an XSDataInputInterface object
"""
self.run()
edPlugin = self.getPlugin()
xsDataOutputObtained = edPlugin.getDataOutput()
strXMLFile = xsDataOutputObtained.getPath().getValue()
strObtainedOutput = self.readAndParseFile(strXMLFile)
xsDataInputInterfaceObtained = XSDataInputInterface.parseString(
strObtainedOutput)
self.DEBUG("Checking obtained result...")
self.DEBUG("Found class of type: %s" %
xsDataInputInterfaceObtained.__class__.__name__)
# Just quickly check that we have an actual XSDataInputInterface object
EDAssert.equal(
xsDataInputInterfaceObtained.__class__.__name__ ==
"XSDataInputInterface", True)
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 __init__(self,
inputCharacterisation=None,
comments=None,
shortComments=None,
dataCollectionId=None,
transmission=None,
wavelength=None,
beamPosY=None,
beamPosX=None,
resultsFilePath=None,
generatedTemplateFile=None,
templateMode=None,
beamSizeY=None,
beamSizeX=None,
beamSize=None,
minExposureTimePerImage=None,
flux=None,
imagePath=None,
sample=None,
diffractionPlan=None,
experimentalCondition=None,
phi=None,
kappa=None,
omega=None,
possibleOrientations=None,
mxv2DataCollection_Reference=None,
mxv2DataCollection=None,
mxv1ResultCharacterisation_Reference=None,
mxv1InputCharacterisation=None):
XSDataInputInterface.__init__(
self, inputCharacterisation, comments, shortComments,
dataCollectionId, transmission, wavelength, beamPosY, beamPosX,
resultsFilePath, generatedTemplateFile, templateMode, beamSizeY,
beamSizeX, beamSize, minExposureTimePerImage, flux, imagePath,
sample, diffractionPlan, experimentalCondition)
checkType("XSDataInputInterfacev2_2",
"Constructor of XSDataInputInterfacev2_2",
mxv1InputCharacterisation, "XSDataInputCharacterisation")
self.__mxv1InputCharacterisation = mxv1InputCharacterisation
checkType("XSDataInputInterfacev2_2",
"Constructor of XSDataInputInterfacev2_2",
mxv1ResultCharacterisation_Reference,
"XSDataResultCharacterisation")
self.__mxv1ResultCharacterisation_Reference = mxv1ResultCharacterisation_Reference
checkType("XSDataInputInterfacev2_2",
"Constructor of XSDataInputInterfacev2_2",
mxv2DataCollection, "XSDataCollection")
self.__mxv2DataCollection = mxv2DataCollection
checkType("XSDataInputInterfacev2_2",
"Constructor of XSDataInputInterfacev2_2",
mxv2DataCollection_Reference, "XSDataCollection")
self.__mxv2DataCollection_Reference = mxv2DataCollection_Reference
checkType("XSDataInputInterfacev2_2",
"Constructor of XSDataInputInterfacev2_2",
possibleOrientations, "kappa_alignment_response")
self.__possibleOrientations = possibleOrientations
checkType("XSDataInputInterfacev2_2",
"Constructor of XSDataInputInterfacev2_2", omega,
"XSDataAngle")
self.__omega = omega
checkType("XSDataInputInterfacev2_2",
"Constructor of XSDataInputInterfacev2_2", kappa,
"XSDataAngle")
self.__kappa = kappa
checkType("XSDataInputInterfacev2_2",
"Constructor of XSDataInputInterfacev2_2", phi,
"XSDataAngle")
self.__phi = phi
def preProcess(self, _edPlugin=None):
"""
This method prepares the input for the CCP4i plugin and loads it.
"""
EDPluginControl.preProcess(self, _edPlugin)
self.DEBUG("EDPluginControlInterfaceToMXCuBEv1_3.preProcess...")
self.tStart = time.time()
xsDataInputMXCuBE = self.getDataInput()
xsDataInputInterface = XSDataInputInterface()
self.edPluginControlInterface = self.loadPlugin(self.strPluginControlInterface)
for xsDataSetMXCuBE in xsDataInputMXCuBE.getDataSet():
for xsDataFile in xsDataSetMXCuBE.getImageFile():
xsDataInputInterface.addImagePath(xsDataFile)
xsDataInputInterface.setExperimentalCondition(xsDataInputMXCuBE.getExperimentalCondition())
xsDataInputInterface.setDiffractionPlan(xsDataInputMXCuBE.getDiffractionPlan())
xsDataInputInterface.setSample(xsDataInputMXCuBE.getSample())
xsDataInputInterface.setDataCollectionId(xsDataInputMXCuBE.getDataCollectionId())
self.edPluginControlInterface.setDataInput(xsDataInputInterface)
#self.edPluginExecOutputHTML = self.loadPlugin(self.strPluginExecOutputHTMLName, "OutputHTML")
self.edPluginExecSimpleHTML = self.loadPlugin(self.strPluginExecSimpleHTMLName, "SimpleHTML")
self.xsDataResultMXCuBE = XSDataResultMXCuBE()
def process(self, _edPlugin=None):
EDPluginControl.process(self, _edPlugin)
self.DEBUG("EDPluginControlInterfaceToMXCuBEv1_3.process...")
xsDataInputMXCuBE = self.getDataInput()
xsDataInputInterface = XSDataInputInterface()
self.edPluginControlInterface = self.loadPlugin(
self.strPluginControlInterface)
xsDataFirstImage = None
for xsDataSetMXCuBE in xsDataInputMXCuBE.getDataSet():
for xsDataFile in xsDataSetMXCuBE.getImageFile():
xsDataInputInterface.addImagePath(xsDataFile)
if xsDataFirstImage is None:
xsDataFirstImage = xsDataFile
xsDataExperimentalCondition = self.getFluxAndBeamSizeFromISPyB(xsDataFirstImage, \
xsDataInputMXCuBE.getExperimentalCondition())
xsDataInputInterface.setExperimentalCondition(
xsDataExperimentalCondition)
xsDataInputInterface.setDiffractionPlan(
xsDataInputMXCuBE.getDiffractionPlan())
xsDataInputInterface.setSample(xsDataInputMXCuBE.getSample())
xsDataInputInterface.setDataCollectionId(
xsDataInputMXCuBE.getDataCollectionId())
self.edPluginControlInterface.setDataInput(xsDataInputInterface)
if self.edPluginControlInterface is not None:
self.connectProcess(
self.edPluginControlInterface.executeSynchronous)
self.edPluginControlInterface.connectSUCCESS(
self.doSuccessActionInterface)
self.edPluginControlInterface.connectFAILURE(
self.doFailureActionInterface)
def process(self, _edPlugin=None):
EDPluginControl.process(self, _edPlugin)
self.DEBUG("EDPluginControlInterfaceToMXCuBEv1_3.process...")
xsDataInputMXCuBE = self.getDataInput()
xsDataInputInterface = XSDataInputInterface()
self.edPluginControlInterface = self.loadPlugin(self.strPluginControlInterface)
xsDataFirstImage = None
for xsDataSetMXCuBE in xsDataInputMXCuBE.getDataSet():
for xsDataFile in xsDataSetMXCuBE.getImageFile():
xsDataInputInterface.addImagePath(xsDataFile)
if xsDataFirstImage is None:
xsDataFirstImage = xsDataFile
xsDataExperimentalCondition = self.getFluxAndBeamSizeFromISPyB(xsDataFirstImage, \
xsDataInputMXCuBE.getExperimentalCondition())
xsDataInputInterface.setExperimentalCondition(xsDataExperimentalCondition)
xsDataInputInterface.setDiffractionPlan(xsDataInputMXCuBE.getDiffractionPlan())
xsDataInputInterface.setSample(xsDataInputMXCuBE.getSample())
xsDataInputInterface.setDataCollectionId(xsDataInputMXCuBE.getDataCollectionId())
self.edPluginControlInterface.setDataInput(xsDataInputInterface)
if self.edPluginControlInterface is not None:
self.connectProcess(self.edPluginControlInterface.executeSynchronous)
self.edPluginControlInterface.connectSUCCESS(self.doSuccessActionInterface)
self.edPluginControlInterface.connectFAILURE(self.doFailureActionInterface)
def process(self, _edPlugin=None):
EDPluginControl.process(self, _edPlugin)
self.DEBUG("EDPluginControlInterfaceToMXCuBEv1_4.process...")
xsDataInputMXCuBE = self.getDataInput()
xsDataInputInterface = XSDataInputInterface()
self.edPluginControlInterface = self.loadPlugin(self.strPluginControlInterface)
self.xsDataFirstImage = None
for xsDataSetMXCuBE in xsDataInputMXCuBE.getDataSet():
for xsDataFile in xsDataSetMXCuBE.getImageFile():
if xsDataFile.path.value.endswith(".h5"):
self.bIsEigerDetector = True
self.xsDataFirstImage = xsDataFile
xsDataInputControlH5ToCBF = XSDataInputControlH5ToCBF()
xsDataInputControlH5ToCBF.hdf5File = XSDataFile(xsDataFile.path)
xsDataInputControlH5ToCBF.imageNumber = XSDataInteger(EDUtilsImage.getImageNumber(xsDataFile.path.value))
edPluginControlH5ToCBF = self.loadPlugin(self.strPluginControlH5ToCBF, "ControlH5ToCBF")
edPluginControlH5ToCBF.dataInput = xsDataInputControlH5ToCBF
edPluginControlH5ToCBF.executeSynchronous()
cbfFile = edPluginControlH5ToCBF.dataOutput.outputCBFFile
xsDataInputInterface.addImagePath(cbfFile)
else:
xsDataInputInterface.addImagePath(xsDataFile)
if self.xsDataFirstImage is None:
self.xsDataFirstImage = xsDataFile
# Check that images are on disk, otherwise wait
for xsDataImagePath in xsDataInputInterface.imagePath:
imagePath = xsDataImagePath.path.value
if os.path.exists(imagePath):
message = "Input file ok: {0}".format(imagePath)
self.screen(message)
self.sendMessageToMXCuBE(message)
else:
self.sendMessageToMXCuBE("Waiting for file: {0}, timeout {1} s".format(imagePath, self.fMXWaitFileTimeOut))
edPluginMXWaitFile = self.loadPlugin(self.strPluginMXWaitFileName)
xsDataInputMXWaitFile = XSDataInputMXWaitFile()
xsDataInputMXWaitFile.file = XSDataFile(XSDataString(imagePath))
xsDataInputMXWaitFile.setSize(XSDataInteger(self.minImageSize))
xsDataInputMXWaitFile.setTimeOut(XSDataTime(self.fMXWaitFileTimeOut))
self.DEBUG("Wait file timeOut set to %f" % self.fMXWaitFileTimeOut)
edPluginMXWaitFile.setDataInput(xsDataInputMXWaitFile)
edPluginMXWaitFile.executeSynchronous()
if edPluginMXWaitFile.dataOutput.timedOut.value:
errorMessage = "ERROR! File {0} does not exist on disk.".format(imagePath)
self.ERROR(errorMessage)
self.sendMessageToMXCuBE(errorMessage, "error")
self.setFailure()
break
xsDataExperimentalCondition = self.getFluxAndBeamSizeFromISPyB(self.xsDataFirstImage, \
xsDataInputMXCuBE.getExperimentalCondition())
xsDataInputInterface.setExperimentalCondition(xsDataExperimentalCondition)
xsDataInputInterface.setDiffractionPlan(xsDataInputMXCuBE.getDiffractionPlan())
xsDataInputInterface.setSample(xsDataInputMXCuBE.getSample())
xsDataInputInterface.setDataCollectionId(xsDataInputMXCuBE.getDataCollectionId())
self.edPluginControlInterface.setDataInput(xsDataInputInterface)
if not self.isFailure() and self.edPluginControlInterface is not None:
self.connectProcess(self.edPluginControlInterface.executeSynchronous)
self.edPluginControlInterface.connectSUCCESS(self.doSuccessActionInterface)
self.edPluginControlInterface.connectFAILURE(self.doFailureActionInterface)
def process(self, _edPlugin=None):
EDPluginControl.process(self, _edPlugin)
self.DEBUG("EDPluginControlInterfaceToMXCuBEv1_4.process...")
xsDataInputMXCuBE = self.getDataInput()
xsDataInputInterface = XSDataInputInterface()
self.edPluginControlInterface = self.loadPlugin(self.strPluginControlInterface)
self.xsDataFirstImage = None
for xsDataSetMXCuBE in xsDataInputMXCuBE.getDataSet():
for xsDataFile in xsDataSetMXCuBE.getImageFile():
if xsDataFile.path.value.endswith(".h5"):
self.bIsEigerDetector = True
self.xsDataFirstImage = xsDataFile
xsDataInputControlH5ToCBF = XSDataInputControlH5ToCBF()
xsDataInputControlH5ToCBF.hdf5File = XSDataFile(xsDataFile.path)
xsDataInputControlH5ToCBF.imageNumber = XSDataInteger(
EDUtilsImage.getImageNumber(xsDataFile.path.value)
)
edPluginControlH5ToCBF = self.loadPlugin(self.strPluginControlH5ToCBF, "ControlH5ToCBF")
edPluginControlH5ToCBF.dataInput = xsDataInputControlH5ToCBF
edPluginControlH5ToCBF.executeSynchronous()
cbfFile = edPluginControlH5ToCBF.dataOutput.outputCBFFile
xsDataInputInterface.addImagePath(cbfFile)
else:
xsDataInputInterface.addImagePath(xsDataFile)
if self.xsDataFirstImage is None:
self.xsDataFirstImage = xsDataFile
xsDataExperimentalCondition = self.getFluxAndBeamSizeFromISPyB(
self.xsDataFirstImage, xsDataInputMXCuBE.getExperimentalCondition()
)
xsDataInputInterface.setExperimentalCondition(xsDataExperimentalCondition)
xsDataInputInterface.setDiffractionPlan(xsDataInputMXCuBE.getDiffractionPlan())
xsDataInputInterface.setSample(xsDataInputMXCuBE.getSample())
xsDataInputInterface.setDataCollectionId(xsDataInputMXCuBE.getDataCollectionId())
self.edPluginControlInterface.setDataInput(xsDataInputInterface)
if self.edPluginControlInterface is not None:
self.connectProcess(self.edPluginControlInterface.executeSynchronous)
self.edPluginControlInterface.connectSUCCESS(self.doSuccessActionInterface)
self.edPluginControlInterface.connectFAILURE(self.doFailureActionInterface)
def __init__(self,
inputCharacterisation=None,
comments=None,
shortComments=None,
dataCollectionId=None,
transmission=None,
wavelength=None,
beamPosY=None,
beamPosX=None,
resultsFilePath=None,
generatedTemplateFile=None,
templateMode=None,
beamSizeY=None,
beamSizeX=None,
beamSize=None,
minExposureTimePerImage=None,
flux=None,
imagePath=None,
sample=None,
diffractionPlan=None,
experimentalCondition=None,
phi=None,
kappa=None,
omega=None,
possibleOrientations=None,
mxv2DataCollection_Reference=None,
mxv2DataCollection=None,
mxv1ResultCharacterisation_Reference=None,
mxv1InputCharacterisation=None):
XSDataInputInterface.__init__(
self, inputCharacterisation, comments, shortComments,
dataCollectionId, transmission, wavelength, beamPosY, beamPosX,
resultsFilePath, generatedTemplateFile, templateMode, beamSizeY,
beamSizeX, beamSize, minExposureTimePerImage, flux, imagePath,
sample, diffractionPlan, experimentalCondition)
if mxv1InputCharacterisation is None:
self._mxv1InputCharacterisation = None
elif mxv1InputCharacterisation.__class__.__name__ == "XSDataInputCharacterisation":
self._mxv1InputCharacterisation = mxv1InputCharacterisation
else:
strMessage = "ERROR! XSDataInputInterfacev2_2 constructor argument 'mxv1InputCharacterisation' is not XSDataInputCharacterisation but %s" % self._mxv1InputCharacterisation.__class__.__name__
raise BaseException(strMessage)
if mxv1ResultCharacterisation_Reference is None:
self._mxv1ResultCharacterisation_Reference = None
elif mxv1ResultCharacterisation_Reference.__class__.__name__ == "XSDataResultCharacterisation":
self._mxv1ResultCharacterisation_Reference = mxv1ResultCharacterisation_Reference
else:
strMessage = "ERROR! XSDataInputInterfacev2_2 constructor argument 'mxv1ResultCharacterisation_Reference' is not XSDataResultCharacterisation but %s" % self._mxv1ResultCharacterisation_Reference.__class__.__name__
raise BaseException(strMessage)
if mxv2DataCollection is None:
self._mxv2DataCollection = None
elif mxv2DataCollection.__class__.__name__ == "XSDataCollection":
self._mxv2DataCollection = mxv2DataCollection
else:
strMessage = "ERROR! XSDataInputInterfacev2_2 constructor argument 'mxv2DataCollection' is not XSDataCollection but %s" % self._mxv2DataCollection.__class__.__name__
raise BaseException(strMessage)
if mxv2DataCollection_Reference is None:
self._mxv2DataCollection_Reference = None
elif mxv2DataCollection_Reference.__class__.__name__ == "XSDataCollection":
self._mxv2DataCollection_Reference = mxv2DataCollection_Reference
else:
strMessage = "ERROR! XSDataInputInterfacev2_2 constructor argument 'mxv2DataCollection_Reference' is not XSDataCollection but %s" % self._mxv2DataCollection_Reference.__class__.__name__
raise BaseException(strMessage)
if possibleOrientations is None:
self._possibleOrientations = None
elif possibleOrientations.__class__.__name__ == "kappa_alignment_response":
self._possibleOrientations = possibleOrientations
else:
strMessage = "ERROR! XSDataInputInterfacev2_2 constructor argument 'possibleOrientations' is not kappa_alignment_response but %s" % self._possibleOrientations.__class__.__name__
raise BaseException(strMessage)
if omega is None:
self._omega = None
elif omega.__class__.__name__ == "XSDataAngle":
self._omega = omega
else:
strMessage = "ERROR! XSDataInputInterfacev2_2 constructor argument 'omega' is not XSDataAngle but %s" % self._omega.__class__.__name__
raise BaseException(strMessage)
if kappa is None:
self._kappa = None
elif kappa.__class__.__name__ == "XSDataAngle":
self._kappa = kappa
else:
strMessage = "ERROR! XSDataInputInterfacev2_2 constructor argument 'kappa' is not XSDataAngle but %s" % self._kappa.__class__.__name__
raise BaseException(strMessage)
if phi is None:
self._phi = None
elif phi.__class__.__name__ == "XSDataAngle":
self._phi = phi
else:
strMessage = "ERROR! XSDataInputInterfacev2_2 constructor argument 'phi' is not XSDataAngle but %s" % self._phi.__class__.__name__
raise BaseException(strMessage)
def preProcess(self, _edPlugin=None):
"""
This method prepares the input for the CCP4i plugin and loads it.
"""
EDPluginControl.preProcess(self, _edPlugin)
self.DEBUG("EDPluginControlInterfaceToMXCuBEv1_3.preProcess...")
self.tStart = time.time()
xsDataInputMXCuBE = self.getDataInput()
xsDataInputInterface = XSDataInputInterface()
self.edPluginControlInterface = self.loadPlugin(
self.strPluginControlInterface)
for xsDataSetMXCuBE in xsDataInputMXCuBE.getDataSet():
for xsDataFile in xsDataSetMXCuBE.getImageFile():
xsDataInputInterface.addImagePath(xsDataFile)
xsDataInputInterface.setExperimentalCondition(
xsDataInputMXCuBE.getExperimentalCondition())
xsDataInputInterface.setDiffractionPlan(
xsDataInputMXCuBE.getDiffractionPlan())
xsDataInputInterface.setSample(xsDataInputMXCuBE.getSample())
xsDataInputInterface.setDataCollectionId(
xsDataInputMXCuBE.getDataCollectionId())
self.edPluginControlInterface.setDataInput(xsDataInputInterface)
#self.edPluginExecOutputHTML = self.loadPlugin(self.strPluginExecOutputHTMLName, "OutputHTML")
self.edPluginExecSimpleHTML = self.loadPlugin(
self.strPluginExecSimpleHTMLName, "SimpleHTML")
self.xsDataResultMXCuBE = XSDataResultMXCuBE()
def __init__(
self,
inputCharacterisation=None,
comments=None,
shortComments=None,
dataCollectionId=None,
transmission=None,
wavelength=None,
beamPosY=None,
beamPosX=None,
resultsFilePath=None,
generatedTemplateFile=None,
templateMode=None,
beamSizeY=None,
beamSizeX=None,
beamSize=None,
minExposureTimePerImage=None,
flux=None,
imagePath=None,
sample=None,
diffractionPlan=None,
experimentalCondition=None,
phi=None,
kappa=None,
omega=None,
possibleOrientations=None,
mxv2DataCollection_Reference=None,
mxv2DataCollection=None,
mxv1ResultCharacterisation_Reference=None,
mxv1InputCharacterisation=None,
):
XSDataInputInterface.__init__(
self,
inputCharacterisation,
comments,
shortComments,
dataCollectionId,
transmission,
wavelength,
beamPosY,
beamPosX,
resultsFilePath,
generatedTemplateFile,
templateMode,
beamSizeY,
beamSizeX,
beamSize,
minExposureTimePerImage,
flux,
imagePath,
sample,
diffractionPlan,
experimentalCondition,
)
if mxv1InputCharacterisation is None:
self._mxv1InputCharacterisation = None
elif mxv1InputCharacterisation.__class__.__name__ == "XSDataInputCharacterisation":
self._mxv1InputCharacterisation = mxv1InputCharacterisation
else:
strMessage = (
"ERROR! XSDataInputInterfacev2_2 constructor argument 'mxv1InputCharacterisation' is not XSDataInputCharacterisation but %s"
% self._mxv1InputCharacterisation.__class__.__name__
)
raise BaseException(strMessage)
if mxv1ResultCharacterisation_Reference is None:
self._mxv1ResultCharacterisation_Reference = None
elif mxv1ResultCharacterisation_Reference.__class__.__name__ == "XSDataResultCharacterisation":
self._mxv1ResultCharacterisation_Reference = mxv1ResultCharacterisation_Reference
else:
strMessage = (
"ERROR! XSDataInputInterfacev2_2 constructor argument 'mxv1ResultCharacterisation_Reference' is not XSDataResultCharacterisation but %s"
% self._mxv1ResultCharacterisation_Reference.__class__.__name__
)
raise BaseException(strMessage)
if mxv2DataCollection is None:
self._mxv2DataCollection = None
elif mxv2DataCollection.__class__.__name__ == "XSDataCollection":
self._mxv2DataCollection = mxv2DataCollection
else:
strMessage = (
"ERROR! XSDataInputInterfacev2_2 constructor argument 'mxv2DataCollection' is not XSDataCollection but %s"
% self._mxv2DataCollection.__class__.__name__
)
raise BaseException(strMessage)
if mxv2DataCollection_Reference is None:
self._mxv2DataCollection_Reference = None
elif mxv2DataCollection_Reference.__class__.__name__ == "XSDataCollection":
self._mxv2DataCollection_Reference = mxv2DataCollection_Reference
else:
strMessage = (
"ERROR! XSDataInputInterfacev2_2 constructor argument 'mxv2DataCollection_Reference' is not XSDataCollection but %s"
% self._mxv2DataCollection_Reference.__class__.__name__
)
raise BaseException(strMessage)
if possibleOrientations is None:
self._possibleOrientations = None
elif possibleOrientations.__class__.__name__ == "kappa_alignment_response":
self._possibleOrientations = possibleOrientations
else:
strMessage = (
"ERROR! XSDataInputInterfacev2_2 constructor argument 'possibleOrientations' is not kappa_alignment_response but %s"
% self._possibleOrientations.__class__.__name__
)
raise BaseException(strMessage)
if omega is None:
self._omega = None
elif omega.__class__.__name__ == "XSDataAngle":
self._omega = omega
else:
strMessage = (
"ERROR! XSDataInputInterfacev2_2 constructor argument 'omega' is not XSDataAngle but %s"
% self._omega.__class__.__name__
)
raise BaseException(strMessage)
if kappa is None:
self._kappa = None
elif kappa.__class__.__name__ == "XSDataAngle":
self._kappa = kappa
else:
strMessage = (
"ERROR! XSDataInputInterfacev2_2 constructor argument 'kappa' is not XSDataAngle but %s"
% self._kappa.__class__.__name__
)
raise BaseException(strMessage)
if phi is None:
self._phi = None
elif phi.__class__.__name__ == "XSDataAngle":
self._phi = phi
else:
strMessage = (
"ERROR! XSDataInputInterfacev2_2 constructor argument 'phi' is not XSDataAngle but %s"
% self._phi.__class__.__name__
)
raise BaseException(strMessage)
