def doSuccessWaitMultiFile(self, _edPlugin):
"""
The file has appeared on the disk
"""
self.DEBUG(
"EDPluginControlImageQualityIndicatorsv1_0.doSuccessWaitMultiFile")
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlReadImageHeaderv10.doSuccessWaitMultiFile")
#
listXSDataImage = self.getDataInput().getImage()
for (iIndex, xsDataImage) in enumerate(listXSDataImage):
edPluginPluginExecImageQualityIndicator = self.loadPlugin(self.strPluginExecImageQualityIndicatorName, \
"%s-%d" % (self.strPluginExecImageQualityIndicatorName, iIndex + 1))
xsDataInputDistlSignalStrength = XSDataInputDistlSignalStrength()
xsDataInputDistlSignalStrength.setReferenceImage(xsDataImage)
edPluginPluginExecImageQualityIndicator.setDataInput(
xsDataInputDistlSignalStrength)
self.listPluginExecImageQualityIndicator.append(
edPluginPluginExecImageQualityIndicator)
# Prepare the action cluster
for edPluginPluginExecImageQualityIndicator in self.listPluginExecImageQualityIndicator:
edPluginPluginExecImageQualityIndicator.connectSUCCESS(
self.doSuccessExecPlugin)
edPluginPluginExecImageQualityIndicator.connectFAILURE(
self.doFailureExecPlugin)
self.addPluginToActionCluster(
edPluginPluginExecImageQualityIndicator)
# Launch the cluster
self.executeActionCluster()
self.synchronizeActionCluster()
def testParseLabelitDistlOutput(self):
"""
This method test the parsing of the distl.signal_strength results in the log file.
"""
edPluginDistlSignalStrengthThinClientv1_1 = self.createPlugin()
strPathToLabelitLogText = os.path.join(
self.getPluginTestsDataHome(),
"phenix.distl_thin_client_v17_650.txt")
strLabelitLogText = self.readAndParseFile(strPathToLabelitLogText)
xsDataImageQualityIndicators = edPluginDistlSignalStrengthThinClientv1_1.parseLabelitDistlOutput(
strLabelitLogText)
xmlInput1 = self.readAndParseFile(self.__strReferenceInputFile1)
xsDataInputDistlSignalStrength = XSDataInputDistlSignalStrength.parseString(
xmlInput1)
xsDataImageQualityIndicators.setImage(
xsDataInputDistlSignalStrength.getReferenceImage())
strResultDistlSignalStrengthFile = os.path.join(
self.getPluginTestsDataHome(),
"XSDataResultDistlSignalStrengthThinClient_reference.xml")
strResultDistlSignalStrength = self.readAndParseFile(
strResultDistlSignalStrengthFile)
xsDataResultDistlSignalStrength = XSDataResultDistlSignalStrength.parseString(
strResultDistlSignalStrength)
xsDataImageQualityIndicatorsReference = xsDataResultDistlSignalStrength.getImageQualityIndicators(
)
EDAssert.equal(xsDataImageQualityIndicatorsReference.marshal(),
xsDataImageQualityIndicators.marshal())
def doSuccessWaitMultiFile(self, _edPlugin):
"""
The file has appeared on the disk
"""
self.DEBUG("EDPluginControlImageQualityIndicatorsv1_0.doSuccessWaitMultiFile")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlReadImageHeaderv10.doSuccessWaitMultiFile")
#
listXSDataImage = self.getDataInput().getImage()
for (iIndex, xsDataImage) in enumerate(listXSDataImage):
edPluginPluginExecImageQualityIndicator = self.loadPlugin(self.strPluginExecImageQualityIndicatorName, \
"%s-%d" % (self.strPluginExecImageQualityIndicatorName, iIndex + 1))
xsDataInputDistlSignalStrength = XSDataInputDistlSignalStrength()
xsDataInputDistlSignalStrength.setReferenceImage(xsDataImage)
edPluginPluginExecImageQualityIndicator.setDataInput(xsDataInputDistlSignalStrength)
self.listPluginExecImageQualityIndicator.append(edPluginPluginExecImageQualityIndicator)
# Prepare the action cluster
for edPluginPluginExecImageQualityIndicator in self.listPluginExecImageQualityIndicator:
edPluginPluginExecImageQualityIndicator.connectSUCCESS(self.doSuccessExecPlugin)
edPluginPluginExecImageQualityIndicator.connectFAILURE(self.doFailureExecPlugin)
self.addPluginToActionCluster(edPluginPluginExecImageQualityIndicator)
# Launch the cluster
self.executeActionCluster()
self.synchronizeActionCluster()
def testParseLabelitDistlOutput(self):
"""
This method test the parsing of the distl.signal_strength results in the log file.
"""
edPluginDistlSignalStrengthThinClientv1_1 = self.createPlugin()
strPathToLabelitLogText = os.path.join(self.getPluginTestsDataHome(), "phenix.distl_thin_client_v17_650.txt")
strLabelitLogText = self.readAndParseFile(strPathToLabelitLogText)
xsDataImageQualityIndicators = edPluginDistlSignalStrengthThinClientv1_1.parseLabelitDistlOutput(strLabelitLogText)
xmlInput1 = self.readAndParseFile(self.__strReferenceInputFile1)
xsDataInputDistlSignalStrength = XSDataInputDistlSignalStrength.parseString(xmlInput1)
xsDataImageQualityIndicators.setImage(xsDataInputDistlSignalStrength.getReferenceImage())
strResultDistlSignalStrengthFile = os.path.join(self.getPluginTestsDataHome(), "XSDataResultDistlSignalStrengthThinClient_reference.xml")
strResultDistlSignalStrength = self.readAndParseFile(strResultDistlSignalStrengthFile)
xsDataResultDistlSignalStrength = XSDataResultDistlSignalStrength.parseString(strResultDistlSignalStrength)
xsDataImageQualityIndicatorsReference = xsDataResultDistlSignalStrength.getImageQualityIndicators()
EDAssert.equal(xsDataImageQualityIndicatorsReference.marshal(), xsDataImageQualityIndicators.marshal())
def process(self, _edPlugin=None):
"""
Executes the execution plugins
"""
EDPluginControl.process(self, _edPlugin)
EDVerbose.DEBUG("EDPluginControlImageQualityIndicatorsv1_2.process")
EDUtilsParallel.initializeNbThread()
# Check if we should do indexing:
bDoIndexing = False
if self.dataInput.doIndexing is not None:
if self.dataInput.doIndexing.value:
bDoIndexing = True
# Loop through all the incoming reference images
listXSDataImage = self.dataInput.image
xsDataInputWaitFile = XSDataInputWaitFile()
self.xsDataResultControlImageQualityIndicators = XSDataResultControlImageQualityIndicators(
)
listPlugin = []
for xsDataImage in listXSDataImage:
if not os.path.exists(xsDataImage.path.value):
self.screen("Waiting for image %s" % xsDataImage.path.value)
self.edPluginWaitFile = self.loadPlugin(
self.strPluginWaitFileName)
xsDataInputWaitFile.expectedFile = XSDataFile(xsDataImage.path)
xsDataInputWaitFile.setExpectedSize(XSDataInteger(100000))
xsDataInputWaitFile.setTimeOut(
XSDataTime(self.fWaitFileTimeOut))
self.DEBUG("Wait file timeOut set to %f" %
self.fWaitFileTimeOut)
self.edPluginWaitFile.setDataInput(xsDataInputWaitFile)
self.edPluginWaitFile.executeSynchronous()
if not os.path.exists(xsDataImage.path.value):
strError = "Time-out while waiting for image %s" % xsDataImage.path.value
self.error(strError)
self.addErrorMessage(strError)
self.setFailure()
else:
if self.bUseThinClient:
strPluginName = self.strPluginNameThinClient
else:
strPluginName = self.strPluginName
edPluginPluginExecImageQualityIndicator = self.loadPlugin(
strPluginName)
listPlugin.append(edPluginPluginExecImageQualityIndicator)
self.listPluginExecImageQualityIndicator.append(
edPluginPluginExecImageQualityIndicator)
xsDataInputDistlSignalStrength = XSDataInputDistlSignalStrength(
)
xsDataInputDistlSignalStrength.setReferenceImage(xsDataImage)
edPluginPluginExecImageQualityIndicator.setDataInput(
xsDataInputDistlSignalStrength)
edPluginPluginExecImageQualityIndicator.execute()
listIndexing = []
# Synchronize all image quality indicator plugins and upload to ISPyB
xsDataInputStoreListOfImageQualityIndicators = XSDataInputStoreListOfImageQualityIndicators(
)
for edPluginPluginExecImageQualityIndicator in listPlugin:
edPluginPluginExecImageQualityIndicator.synchronize()
xsDataImageQualityIndicators = XSDataImageQualityIndicators.parseString( \
edPluginPluginExecImageQualityIndicator.dataOutput.imageQualityIndicators.marshal())
self.xsDataResultControlImageQualityIndicators.addImageQualityIndicators(
xsDataImageQualityIndicators)
xsDataISPyBImageQualityIndicators = \
XSDataISPyBImageQualityIndicators.parseString(xsDataImageQualityIndicators.marshal())
xsDataInputStoreListOfImageQualityIndicators.addImageQualityIndicators(
xsDataISPyBImageQualityIndicators)
# print xsDataInputStoreListOfImageQualityIndicators.marshal()
self.edPluginISPyB = self.loadPlugin(self.strISPyBPluginName)
self.edPluginISPyB.dataInput = xsDataInputStoreListOfImageQualityIndicators
self.edPluginISPyB.execute()
#
if bDoIndexing:
# Find the 5 most intensive images (TIS):
listImage = []
listSorted = sorted(
self.xsDataResultControlImageQualityIndicators.
imageQualityIndicators,
key=lambda imageQualityIndicators: imageQualityIndicators.
totalIntegratedSignal.value)
for xsDataResultControlImageQualityIndicator in listSorted[-5:]:
if xsDataResultControlImageQualityIndicator.goodBraggCandidates.value > 30:
xsDataInputReadImageHeader = XSDataInputReadImageHeader()
xsDataInputReadImageHeader.image = XSDataFile(
xsDataResultControlImageQualityIndicator.image.path)
self.edPluginReadImageHeader = self.loadPlugin(
self.strPluginReadImageHeaderName)
self.edPluginReadImageHeader.dataInput = xsDataInputReadImageHeader
self.edPluginReadImageHeader.executeSynchronous()
xsDataResultReadImageHeader = self.edPluginReadImageHeader.dataOutput
if xsDataResultReadImageHeader is not None:
xsDataSubWedge = xsDataResultReadImageHeader.subWedge
self.xsDataCollection = XSDataCollection()
self.xsDataCollection.addSubWedge(xsDataSubWedge)
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.setDataCollection(
self.xsDataCollection)
xsDataMOSFLMIndexingInput = EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputIndexing(
xsDataIndexingInput)
edPluginMOSFLMIndexing = self.loadPlugin(
self.strIndexingMOSFLMPluginName)
self.listPluginMOSFLM.append([
edPluginMOSFLMIndexing,
xsDataResultControlImageQualityIndicator
])
edPluginMOSFLMIndexing.setDataInput(
xsDataMOSFLMIndexingInput)
edPluginMOSFLMIndexing.execute()
for tupleMOSFLM in self.listPluginMOSFLM:
edPluginMOSFLMIndexing = tupleMOSFLM[0]
xsDataResultControlImageQualityIndicator = tupleMOSFLM[1]
edPluginMOSFLMIndexing.synchronize()
if not edPluginMOSFLMIndexing.isFailure():
xsDataMOSFLMOutput = edPluginMOSFLMIndexing.dataOutput
xsDataIndexingResult = EDHandlerXSDataMOSFLMv10.generateXSDataIndexingResult(
xsDataMOSFLMOutput)
selectedSolution = xsDataIndexingResult.selectedSolution
if selectedSolution is not None:
xsDataResultControlImageQualityIndicator.selectedIndexingSolution = selectedSolution
def process(self, _edPlugin=None):
"""
Executes the execution plugins
"""
EDPluginControl.process(self, _edPlugin)
EDVerbose.DEBUG("EDPluginControlImageQualityIndicatorsv1_3.process")
EDUtilsParallel.initializeNbThread()
# Check if we should do indexing:
bDoIndexing = False
if self.dataInput.doIndexing is not None:
if self.dataInput.doIndexing.value:
bDoIndexing = True
# Loop through all the incoming reference images
listXSDataImage = self.dataInput.image
xsDataInputWaitFile = XSDataInputWaitFile()
self.xsDataResultControlImageQualityIndicators = XSDataResultControlImageQualityIndicators()
listPlugin = []
for xsDataImage in listXSDataImage:
if not os.path.exists(xsDataImage.path.value):
self.screen("Waiting for image %s" % xsDataImage.path.value)
self.edPluginWaitFile = self.loadPlugin(self.strPluginWaitFileName)
xsDataInputWaitFile.expectedFile = XSDataFile(xsDataImage.path)
xsDataInputWaitFile.setExpectedSize(XSDataInteger(100000))
xsDataInputWaitFile.setTimeOut(XSDataTime(self.fWaitFileTimeOut))
self.DEBUG("Wait file timeOut set to %f" % self.fWaitFileTimeOut)
self.edPluginWaitFile.setDataInput(xsDataInputWaitFile)
self.edPluginWaitFile.executeSynchronous()
if not os.path.exists(xsDataImage.path.value):
strError = "Time-out while waiting for image %s" % xsDataImage.path.value
self.error(strError)
self.addErrorMessage(strError)
self.setFailure()
else:
if self.bUseThinClient:
strPluginName = self.strPluginNameThinClient
else:
strPluginName = self.strPluginName
edPluginPluginExecImageQualityIndicator = self.loadPlugin(strPluginName)
self.listPluginExecImageQualityIndicator.append(edPluginPluginExecImageQualityIndicator)
xsDataInputDistlSignalStrength = XSDataInputDistlSignalStrength()
xsDataInputDistlSignalStrength.setReferenceImage(xsDataImage)
edPluginPluginExecImageQualityIndicator.setDataInput(xsDataInputDistlSignalStrength)
edPluginPluginExecImageQualityIndicator.execute()
edPluginControlBackground3D = self.loadPlugin(self.strPluginNameControlBackground3D)
listPlugin.append([edPluginPluginExecImageQualityIndicator, edPluginControlBackground3D])
xsDataInputControlBackground3D = XSDataInputControlBackground3D()
xsDataInputControlBackground3D.addImage(XSDataFile(xsDataImage.path))
edPluginControlBackground3D.dataInput = xsDataInputControlBackground3D
edPluginControlBackground3D.execute()
listIndexing = []
# Synchronize all image quality indicator plugins and upload to ISPyB
xsDataInputStoreListOfImageQualityIndicators = XSDataInputStoreListOfImageQualityIndicators()
for pluginPair in listPlugin:
edPluginPluginExecImageQualityIndicator = pluginPair[0]
edPluginControlBackground3D = pluginPair[1]
edPluginPluginExecImageQualityIndicator.synchronize()
edPluginControlBackground3D.synchronize()
xsDataImageQualityIndicators = XSDataImageQualityIndicators.parseString(\
edPluginPluginExecImageQualityIndicator.dataOutput.imageQualityIndicators.marshal())
if edPluginControlBackground3D.dataOutput.imageBackground != []:
xsDataImageQualityIndicators.background3D_estimate = edPluginControlBackground3D.dataOutput.imageBackground[0].estimate
self.xsDataResultControlImageQualityIndicators.addImageQualityIndicators(xsDataImageQualityIndicators)
xsDataISPyBImageQualityIndicators = \
XSDataISPyBImageQualityIndicators.parseString(xsDataImageQualityIndicators.marshal())
xsDataInputStoreListOfImageQualityIndicators.addImageQualityIndicators(xsDataISPyBImageQualityIndicators)
# print xsDataInputStoreListOfImageQualityIndicators.marshal()
if self.dataInput.doUploadToIspyb is not None and self.dataInput.doUploadToIspyb.value:
self.edPluginISPyB = self.loadPlugin(self.strISPyBPluginName)
self.edPluginISPyB.dataInput = xsDataInputStoreListOfImageQualityIndicators
self.edPluginISPyB.execute()
#
if bDoIndexing:
# Find the 5 most intensive images (TIS):
listImage = []
# Check that we have background3D_estimate from all images:
has_background3D_estimate = True
for imageQualityIndicators in self.xsDataResultControlImageQualityIndicators.imageQualityIndicators:
if imageQualityIndicators.background3D_estimate is None:
has_background3D_estimate = False
if has_background3D_estimate:
listSorted = sorted(self.xsDataResultControlImageQualityIndicators.imageQualityIndicators,
key=lambda imageQualityIndicators: imageQualityIndicators.background3D_estimate.value)
else:
listSorted = sorted(self.xsDataResultControlImageQualityIndicators.imageQualityIndicators,
key=lambda imageQualityIndicators: imageQualityIndicators.totalIntegratedSignal.value)
for xsDataResultControlImageQualityIndicator in listSorted[-5:]:
if xsDataResultControlImageQualityIndicator.goodBraggCandidates.value > 30:
xsDataInputReadImageHeader = XSDataInputReadImageHeader()
xsDataInputReadImageHeader.image = XSDataFile(xsDataResultControlImageQualityIndicator.image.path)
self.edPluginReadImageHeader = self.loadPlugin(self.strPluginReadImageHeaderName)
self.edPluginReadImageHeader.dataInput = xsDataInputReadImageHeader
self.edPluginReadImageHeader.executeSynchronous()
xsDataResultReadImageHeader = self.edPluginReadImageHeader.dataOutput
if xsDataResultReadImageHeader is not None:
xsDataSubWedge = xsDataResultReadImageHeader.subWedge
self.xsDataCollection = XSDataCollection()
self.xsDataCollection.addSubWedge(xsDataSubWedge)
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.setDataCollection(self.xsDataCollection)
xsDataMOSFLMIndexingInput = EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputIndexing(xsDataIndexingInput)
edPluginMOSFLMIndexing = self.loadPlugin(self.strIndexingMOSFLMPluginName)
self.listPluginMOSFLM.append([edPluginMOSFLMIndexing, xsDataResultControlImageQualityIndicator])
edPluginMOSFLMIndexing.setDataInput(xsDataMOSFLMIndexingInput)
edPluginMOSFLMIndexing.execute()
for tupleMOSFLM in self.listPluginMOSFLM:
edPluginMOSFLMIndexing = tupleMOSFLM[0]
xsDataResultControlImageQualityIndicator = tupleMOSFLM[1]
edPluginMOSFLMIndexing.synchronize()
if not edPluginMOSFLMIndexing.isFailure():
xsDataMOSFLMOutput = edPluginMOSFLMIndexing.dataOutput
xsDataIndexingResult = EDHandlerXSDataMOSFLMv10.generateXSDataIndexingResult(xsDataMOSFLMOutput)
selectedSolution = xsDataIndexingResult.selectedSolution
if selectedSolution is not None:
xsDataResultControlImageQualityIndicator.selectedIndexingSolution = selectedSolution
