def createDataInputCharacterisationFromDataFiles(self, _pyListXSDataFile):
"""
This method takes as input a list of paths to XML data files. It parses
these files and create a single XSDataInputCharacterisation object.
"""
EDVerbose.DEBUG("EDPluginControlCCP4iv1_1.createDataInputCharacterisationFromDataFiles")
xsDataInputCharacterisation = None
for xsDataInputFile in _pyListXSDataFile:
try:
pyStrInputFileContent = EDUtilsFile.readFile(xsDataInputFile.getPath().getValue())
xsDataInputCharacterisationCurrent = XSDataInputCharacterisation.parseString(pyStrInputFileContent)
except Exception, detail:
errorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginControlCCP4iv1_1.preProcess', 'EDPluginControlCCP4iv1_1', detail)
EDVerbose.error(errorMessage)
self.addErrorMessage(errorMessage)
raise RuntimeError, errorMessage
if (xsDataInputCharacterisationCurrent is None):
errorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginControlCCP4iv1_1.preProcess', 'EDPluginControlCCP4iv1_1', "None data collection")
EDVerbose.error(errorMessage)
self.addErrorMessage(errorMessage)
raise RuntimeError, errorMessage
else:
# Instantiate the xsDataInputCharacterisation object if it's not already done.
if (xsDataInputCharacterisation is None):
xsDataInputCharacterisation = XSDataInputCharacterisation()
xsDataInputCharacterisation.setDataCollection(xsDataInputCharacterisationCurrent.getDataCollection())
def createDataInputCharacterisationFromDataSets(self,
_pyListXSDataCCP4iDataSet):
"""
This method takes as input a list of ccp4i data sets. Each data set can contain several
paths to image files. It runs the EDPluginControlSubWedgeAssemble plugin to read the
experimental information from the image headers and then creates a single XSDataInputCharacterisation object.
"""
EDVerbose.DEBUG(
"EDPluginControlCCP4iv1_1.createDataInputCharacterisationFromDataSets"
)
xsDataInputCharacterisation = None
# We might have to run the plugin several times
edActionCluster = EDActionCluster()
pyListPluginControlSubWedgeAssemble = []
# Prepare the action cluster
iIndex = 1
for xsDataCCP4iDataSet in _pyListXSDataCCP4iDataSet:
edPluginControlSubWedgeAssemble = self.loadPlugin(
self.__strPluginControlSubWedgeAssembleName,
"SubWedgeAssemble-%02d" % iIndex)
edPluginControlSubWedgeAssemble.connectSUCCESS(
self.doSuccessActionSubWedgeAssemble)
edPluginControlSubWedgeAssemble.connectFAILURE(
self.doFailureActionSubWedgeAssemble)
# Prepare the input for the sub wedge assemble plugin
xsDataInputSubWedgeAssemble = XSDataInputSubWedgeAssemble()
for xsDataImageFile in xsDataCCP4iDataSet.getImageFile():
xsDataInputSubWedgeAssemble.addFile(xsDataImageFile)
edPluginControlSubWedgeAssemble.setDataInput(
xsDataInputSubWedgeAssemble)
pyListPluginControlSubWedgeAssemble.append(
edPluginControlSubWedgeAssemble)
self.addPluginToActionCluster(edPluginControlSubWedgeAssemble)
iIndex += 1
# Run the action cluster synchronously
self.executeActionCluster()
self.synchronizeActionCluster()
# Recuperate the output
for edPluginControlSubWedgeAssemble in pyListPluginControlSubWedgeAssemble:
if (edPluginControlSubWedgeAssemble.isFailure()):
self.setFailure()
else:
xsDataResultSubWedgeAssemble = edPluginControlSubWedgeAssemble.getDataOutput(
)
for xsDataSubWedge in xsDataResultSubWedgeAssemble.getSubWedge(
):
# Instantiate the xsDataInputCharacterisation object if it's not already done.
xsDataCollection = None
if (xsDataInputCharacterisation is None):
xsDataInputCharacterisation = XSDataInputCharacterisation(
)
else:
xsDataCollection = xsDataInputCharacterisation.getDataCollection(
)
if (xsDataCollection is None):
xsDataCollection = XSDataCollection()
xsDataCollection.addSubWedge(xsDataSubWedge)
xsDataInputCharacterisation.setDataCollection(
xsDataCollection)
return xsDataInputCharacterisation
def createDataInputCharacterisationFromDataFiles(self, _pyListXSDataFile):
"""
This method takes as input a list of paths to XML data files. It parses
these files and create a single XSDataInputCharacterisation object.
"""
EDVerbose.DEBUG(
"EDPluginControlCCP4iv1_1.createDataInputCharacterisationFromDataFiles"
)
xsDataInputCharacterisation = None
for xsDataInputFile in _pyListXSDataFile:
try:
pyStrInputFileContent = EDUtilsFile.readFile(
xsDataInputFile.getPath().getValue())
xsDataInputCharacterisationCurrent = XSDataInputCharacterisation.parseString(
pyStrInputFileContent)
except Exception, detail:
errorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginControlCCP4iv1_1.preProcess',
'EDPluginControlCCP4iv1_1', detail)
EDVerbose.error(errorMessage)
self.addErrorMessage(errorMessage)
raise RuntimeError, errorMessage
if (xsDataInputCharacterisationCurrent is None):
errorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginControlCCP4iv1_1.preProcess',
'EDPluginControlCCP4iv1_1', "None data collection")
EDVerbose.error(errorMessage)
self.addErrorMessage(errorMessage)
raise RuntimeError, errorMessage
else:
# Instantiate the xsDataInputCharacterisation object if it's not already done.
if (xsDataInputCharacterisation is None):
xsDataInputCharacterisation = XSDataInputCharacterisation()
xsDataInputCharacterisation.setDataCollection(
xsDataInputCharacterisationCurrent.getDataCollection())
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 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 createDataInputCharacterisationFromDataSets(self, _pyListXSDataCCP4iDataSet):
"""
This method takes as input a list of ccp4i data sets. Each data set can contain several
paths to image files. It runs the EDPluginControlSubWedgeAssemble plugin to read the
experimental information from the image headers and then creates a single XSDataInputCharacterisation object.
"""
EDVerbose.DEBUG("EDPluginControlCCP4iv1_1.createDataInputCharacterisationFromDataSets")
xsDataInputCharacterisation = None
# We might have to run the plugin several times
edActionCluster = EDActionCluster()
pyListPluginControlSubWedgeAssemble = []
# Prepare the action cluster
iIndex = 1
for xsDataCCP4iDataSet in _pyListXSDataCCP4iDataSet:
edPluginControlSubWedgeAssemble = self.loadPlugin(self.__strPluginControlSubWedgeAssembleName, "SubWedgeAssemble-%02d" % iIndex)
edPluginControlSubWedgeAssemble.connectSUCCESS(self.doSuccessActionSubWedgeAssemble)
edPluginControlSubWedgeAssemble.connectFAILURE(self.doFailureActionSubWedgeAssemble)
# Prepare the input for the sub wedge assemble plugin
xsDataInputSubWedgeAssemble = XSDataInputSubWedgeAssemble()
for xsDataImageFile in xsDataCCP4iDataSet.getImageFile():
xsDataInputSubWedgeAssemble.addFile(xsDataImageFile)
edPluginControlSubWedgeAssemble.setDataInput(xsDataInputSubWedgeAssemble)
pyListPluginControlSubWedgeAssemble.append(edPluginControlSubWedgeAssemble)
self.addPluginToActionCluster(edPluginControlSubWedgeAssemble)
iIndex += 1
# Run the action cluster synchronously
self.executeActionCluster()
self.synchronizeActionCluster()
# Recuperate the output
for edPluginControlSubWedgeAssemble in pyListPluginControlSubWedgeAssemble:
if (edPluginControlSubWedgeAssemble.isFailure()):
self.setFailure()
else:
xsDataResultSubWedgeAssemble = edPluginControlSubWedgeAssemble.getDataOutput()
for xsDataSubWedge in xsDataResultSubWedgeAssemble.getSubWedge():
# Instantiate the xsDataInputCharacterisation object if it's not already done.
xsDataCollection = None
if (xsDataInputCharacterisation is None):
xsDataInputCharacterisation = XSDataInputCharacterisation()
else:
xsDataCollection = xsDataInputCharacterisation.getDataCollection()
if (xsDataCollection is None):
xsDataCollection = XSDataCollection()
xsDataCollection.addSubWedge(xsDataSubWedge)
xsDataInputCharacterisation.setDataCollection(xsDataCollection)
return xsDataInputCharacterisation
def runMXv1Pipeline():
strLogFileName = os.path.join(returnWorkingDirectory(), "wsgi-server.log")
EDVerbose.setLogFileName(strLogFileName)
strInput = str(request['wsgi.input'].read(int(request['CONTENT_LENGTH'])))
if strInput:
# Take the parameters string, split off the title and run the bash script to generate the input char. XML
listParams = shlex.split(strInput)
strComments = listParams[0] # the 1st item
strShortComments = listParams[1] # the 2nd item
strWorkingDir = listParams[2] # the 3rd item
strHTMLResultDir = listParams[3] # the 4th item
os.chdir(strWorkingDir)
strParamString = " ".join(listParams[4:]) # all but the first four items
edPluginMxv1ParamsToXML = EDFactoryPluginStatic.loadPlugin('EDPluginMxv1ParamsToXMLv1_0')
edPluginMxv1ParamsToXML.setDataInput(XSDataString(strParamString), "paramString")
edPluginMxv1ParamsToXML.executeSynchronous()
xsDataFile = edPluginMxv1ParamsToXML.getDataOutput()
# Read the XML and parse it into an object hierarchy
strXMLFile = xsDataFile.getPath().getValue()
f = open(strXMLFile, 'r')
xml = f.read()
f.close()
xsDataInputCharacterisation = XSDataInputCharacterisation.parseString(xml)
# Run the MXv1 application pipeline
edApplicationMXv1Characterisation = EDApplicationMXv1Characterisation(_strPluginName="EDPluginControlInterfacev1_2", \
_strConfigurationFileName=strConfigurationFilePath, \
_xsDataInputCharacterisation=xsDataInputCharacterisation, \
_strComments=strComments, \
_strShortComments=strShortComments)
edApplicationMXv1Characterisation.execute()
# Run the EDNA2HTML generator on the output from the MXv1 application
edPluginExecOutputHTML = EDFactoryPluginStatic.loadPlugin('EDPluginExecOutputHTMLv1_0')
edPluginExecOutputHTML.setDataInput(XSDataString(strComments), "title")
strWorkingDir = os.path.join(strWorkingDir, edApplicationMXv1Characterisation.getWorkingDir())
edPluginExecOutputHTML.setDataInput(XSDataString(strWorkingDir), "workingDir")
#strBaseDir = os.path.join(strHTMLResultDir, "edna")
#edPluginExecOutputHTML.setDataInput(XSDataString(strBaseDir), "basename")
edPluginExecOutputHTML.setDataInput(XSDataString(strHTMLResultDir), "basename")
edPluginExecOutputHTML.executeSynchronous()
strPathToHTMLFile = ""
if (edPluginExecOutputHTML.hasDataOutput("htmlFile")):
strPathToHTMLFile = edPluginExecOutputHTML.getDataOutput("htmlFile")[0].getPath().getValue()
else:
EDVerbose.ERROR("edna-mxv1-wsgi-server: edPluginExecOutputHTML has no dataOutput htmlFile!")
if strPathToHTMLFile =="":
EDVerbose.ERROR("edna-mxv1-wsgi-server: Returning empty string")
return strPathToHTMLFile
else:
return strInput
def testSetDataInput(self):
edPluginControlCharacterisationv1_1 = self.createPlugin()
xsPluginItemGood01 = self.getPluginConfiguration(os.path.join(self.getPluginTestsDataHome(), "XSConfiguration.xml"))
edPluginControlCharacterisationv1_1.setConfiguration(xsPluginItemGood01)
edPluginControlCharacterisationv1_1.configure()
edStringXMLInput = self.readAndParseFile(self.strReferenceInputFile)
edPluginControlCharacterisationv1_1.setDataInput(edStringXMLInput)
from XSDataMXv1 import XSDataInputCharacterisation
xsDataInputCharacterisationReference = XSDataInputCharacterisation.parseString(edStringXMLInput)
xsDataInputCharacterisationv11 = edPluginControlCharacterisationv1_1.getDataInput()
EDAssert.equal(xsDataInputCharacterisationReference.marshal(), xsDataInputCharacterisationv11.marshal())
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 testSetDataInput(self):
edPluginControlCharacterisationv1_1 = self.createPlugin()
xsPluginItemGood01 = self.getPluginConfiguration(
os.path.join(self.getPluginTestsDataHome(), "XSConfiguration.xml"))
edPluginControlCharacterisationv1_1.setConfiguration(
xsPluginItemGood01)
edPluginControlCharacterisationv1_1.configure()
edStringXMLInput = self.readAndParseFile(self.strReferenceInputFile)
edPluginControlCharacterisationv1_1.setDataInput(edStringXMLInput)
from XSDataMXv1 import XSDataInputCharacterisation
xsDataInputCharacterisationReference = XSDataInputCharacterisation.parseString(
edStringXMLInput)
xsDataInputCharacterisationv11 = edPluginControlCharacterisationv1_1.getDataInput(
)
EDAssert.equal(xsDataInputCharacterisationReference.marshal(),
xsDataInputCharacterisationv11.marshal())
def preProcess(self):
"""
Processes the command line, creates the plugins
"""
EDApplication.preProcess(self)
EDVerbose.DEBUG("EDApplicationMXv1Characterisation.preProcess")
if self.__xsDataInputCharacterisation == None:
# Read command line parameters and check if they are ok
self.__bProcess = self.readAndProcessCommandLine()
if (self.__bProcess) and not (self.__strDatasetFileName is None):
# Check if XML data is given as input :
if (self.__strDatasetFileName is not None):
try:
self.__xsDataInputCharacterisation = XSDataInputCharacterisation.parseFile(self.__strDatasetFileName)
except:
errorMessage = EDMessage.ERROR_CANNOT_READ_FILE_02 % ("EDApplicationMXv1Characterisation.process", self.__strDatasetFileName)
EDVerbose.error(errorMessage)
raise RuntimeError, errorMessage
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 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 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_)
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 testCheckParameters(self):
strXMLInput = self.readAndParseFile(self.strPathToReferenceInput)
xsDataInput = XSDataInputCharacterisation.parseString(strXMLInput)
edPluginExecCharacterisation = self.createPlugin()
edPluginExecCharacterisation.setDataInput(xsDataInput)
edPluginExecCharacterisation.checkParameters()
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
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_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 testCheckParameters(self):
strXMLInput = self.readAndParseFile(self.strPathToReferenceInput)
xsDataInput = XSDataInputCharacterisation.parseString(strXMLInput)
edPluginExecCharacterisation = self.createPlugin()
edPluginExecCharacterisation.setDataInput(xsDataInput)
edPluginExecCharacterisation.checkParameters()
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 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 runMXv1Pipeline():
strLogFileName = os.path.join(returnWorkingDirectory(), "wsgi-server.log")
EDVerbose.setLogFileName(strLogFileName)
strInput = str(request['wsgi.input'].read(int(request['CONTENT_LENGTH'])))
if strInput:
# Take the parameters string, split off the title and run the bash script to generate the input char. XML
listParams = shlex.split(strInput)
strComments = listParams[0] # the 1st item
strShortComments = listParams[1] # the 2nd item
strWorkingDir = listParams[2] # the 3rd item
strHTMLResultDir = listParams[3] # the 4th item
os.chdir(strWorkingDir)
strParamString = " ".join(
listParams[4:]) # all but the first four items
edPluginMxv1ParamsToXML = EDFactoryPluginStatic.loadPlugin(
'EDPluginMxv1ParamsToXMLv1_0')
edPluginMxv1ParamsToXML.setDataInput(XSDataString(strParamString),
"paramString")
edPluginMxv1ParamsToXML.executeSynchronous()
xsDataFile = edPluginMxv1ParamsToXML.getDataOutput()
# Read the XML and parse it into an object hierarchy
strXMLFile = xsDataFile.getPath().getValue()
f = open(strXMLFile, 'r')
xml = f.read()
f.close()
xsDataInputCharacterisation = XSDataInputCharacterisation.parseString(
xml)
# Run the MXv1 application pipeline
edApplicationMXv1Characterisation = EDApplicationMXv1Characterisation(_strPluginName="EDPluginControlInterfacev1_2", \
_strConfigurationFileName=strConfigurationFilePath, \
_xsDataInputCharacterisation=xsDataInputCharacterisation, \
_strComments=strComments, \
_strShortComments=strShortComments)
edApplicationMXv1Characterisation.execute()
# Run the EDNA2HTML generator on the output from the MXv1 application
edPluginExecOutputHTML = EDFactoryPluginStatic.loadPlugin(
'EDPluginExecOutputHTMLv1_0')
edPluginExecOutputHTML.setDataInput(XSDataString(strComments), "title")
strWorkingDir = os.path.join(
strWorkingDir, edApplicationMXv1Characterisation.getWorkingDir())
edPluginExecOutputHTML.setDataInput(XSDataString(strWorkingDir),
"workingDir")
#strBaseDir = os.path.join(strHTMLResultDir, "edna")
#edPluginExecOutputHTML.setDataInput(XSDataString(strBaseDir), "basename")
edPluginExecOutputHTML.setDataInput(XSDataString(strHTMLResultDir),
"basename")
edPluginExecOutputHTML.executeSynchronous()
strPathToHTMLFile = ""
if (edPluginExecOutputHTML.hasDataOutput("htmlFile")):
strPathToHTMLFile = edPluginExecOutputHTML.getDataOutput(
"htmlFile")[0].getPath().getValue()
else:
EDVerbose.ERROR(
"edna-mxv1-wsgi-server: edPluginExecOutputHTML has no dataOutput htmlFile!"
)
if strPathToHTMLFile == "":
EDVerbose.ERROR("edna-mxv1-wsgi-server: Returning empty string")
return strPathToHTMLFile
else:
return strInput
