def preProcess(self, _edPlugin=None):
"""
Prepares the execution plugin
"""
EDPluginControl.preProcess(self, _edPlugin)
EDVerbose.DEBUG("EDPluginControlImageQualityIndicatorsv1_1.preProcess...")
# List containing instances of all the exeuction plugins
self.listPluginExecImageQualityIndicator = []
# Loop through all the incoming reference images
self.edPluginWaitMultiFile = self.loadPlugin(self.strPluginExecWaitMultiFileName)
listXSDataImage = self.getDataInput().getImage()
xsDataInputWaitMultiFile = XSDataInputWaitMultiFile()
for xsDataImage in listXSDataImage:
xsDataInputWaitMultiFile.addExpectedFile(XSDataFile(xsDataImage.getPath()))
xsDataInputWaitMultiFile.setExpectedSize(XSDataInteger(100000))
xsDataInputWaitMultiFile.setTimeOut(XSDataTime(self.fWaitFileTimeOut))
self.DEBUG("Wait file timeOut set to %f" % self.fWaitFileTimeOut)
self.edPluginWaitMultiFile.setDataInput(xsDataInputWaitMultiFile)
self.xsDataResultControlImageQualityIndicators = XSDataResultControlImageQualityIndicators()
def preProcess(self, _edPlugin=None):
"""
Prepares the execution plugin
"""
EDPluginControl.preProcess(self, _edPlugin)
EDVerbose.DEBUG("EDPluginControlImageQualityIndicatorsv1_1.preProcess...")
# List containing instances of all the exeuction plugins
self.listPluginExecImageQualityIndicator = []
# Loop through all the incoming reference images
self.edPluginWaitMultiFile = self.loadPlugin(self.strPluginExecWaitMultiFileName)
listXSDataImage = self.getDataInput().getImage()
xsDataInputWaitMultiFile = XSDataInputWaitMultiFile()
for xsDataImage in listXSDataImage:
xsDataInputWaitMultiFile.addExpectedFile(XSDataFile(xsDataImage.getPath()))
xsDataInputWaitMultiFile.setExpectedSize(XSDataInteger(100000))
xsDataInputWaitMultiFile.setTimeOut(XSDataTime(self.fWaitFileTimeOut))
self.DEBUG("Wait file timeOut set to %f" % self.fWaitFileTimeOut)
self.edPluginWaitMultiFile.setDataInput(xsDataInputWaitMultiFile)
self.xsDataResultControlImageQualityIndicators = XSDataResultControlImageQualityIndicators()
class EDPluginControlImageQualityIndicatorsv1_1(EDPluginControl):
"""
This plugin that control the plugin that generates the image quality indicators.
"""
def __init__(self):
EDPluginControl.__init__(self)
self.strPluginExecWaitMultiFileName = "EDPluginWaitMultiFile"
self.strPluginExecImageQualityIndicatorName = "EDPluginDistlSignalStrengthv1_1"
self.setXSDataInputClass(XSDataInputControlImageQualityIndicators)
self.listPluginExecImageQualityIndicator = None
self.xsDataResultControlImageQualityIndicators = None
self.edPluginWaitMultiFile = None
# Default time out for wait file
self.fWaitFileTimeOut = 30 #s
def checkParameters(self):
"""
Checks the mandatory parameters
"""
EDVerbose.DEBUG(
"EDPluginControlImageQualityIndicatorsv1_1.checkParameters")
self.checkMandatoryParameters(self.getDataInput().getImage(), "Image")
def configure(self, _edPlugin=None):
EDPluginControl.configure(self)
self.DEBUG("EDPluginControlReadImageHeaderv10.configure")
if self.getConfiguration():
xsDataStringParameter = EDConfiguration.getParamItem(
self.getConfiguration(), "waitFileTimeOut")
if xsDataStringParameter:
self.fWaitFileTimeOut = float(xsDataStringParameter.getValue())
def preProcess(self, _edPlugin=None):
"""
Prepares the execution plugin
"""
EDPluginControl.preProcess(self, _edPlugin)
EDVerbose.DEBUG(
"EDPluginControlImageQualityIndicatorsv1_1.preProcess...")
# List containing instances of all the exeuction plugins
self.listPluginExecImageQualityIndicator = []
# Loop through all the incoming reference images
self.edPluginWaitMultiFile = self.loadPlugin(
self.strPluginExecWaitMultiFileName)
listXSDataImage = self.getDataInput().getImage()
xsDataInputWaitMultiFile = XSDataInputWaitMultiFile()
for xsDataImage in listXSDataImage:
xsDataInputWaitMultiFile.addExpectedFile(
XSDataFile(xsDataImage.getPath()))
xsDataInputWaitMultiFile.setExpectedSize(XSDataInteger(100000))
xsDataInputWaitMultiFile.setTimeOut(XSDataTime(self.fWaitFileTimeOut))
self.DEBUG("Wait file timeOut set to %f" % self.fWaitFileTimeOut)
self.edPluginWaitMultiFile.setDataInput(xsDataInputWaitMultiFile)
self.xsDataResultControlImageQualityIndicators = XSDataResultControlImageQualityIndicators(
)
def process(self, _edPlugin=None):
"""
Executes the execution plugins
"""
EDPluginControl.process(self, _edPlugin)
EDVerbose.DEBUG("EDPluginControlImageQualityIndicatorsv1_1.process")
self.edPluginWaitMultiFile.connectSUCCESS(self.doSuccessWaitMultiFile)
self.edPluginWaitMultiFile.connectFAILURE(self.doFailureWaitMultiFile)
self.executePluginSynchronous(self.edPluginWaitMultiFile)
def finallyProcess(self, _edPlugin=None):
EDPluginControl.finallyProcess(self, _edPlugin)
EDVerbose.DEBUG(
"EDPluginControlImageQualityIndicatorsv1_1.finallyProcess")
self.setDataOutput(self.xsDataResultControlImageQualityIndicators)
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 doFailureWaitMultiFile(self, _edPlugin):
"""
The file has not appeared on the disk
"""
self.DEBUG(
"EDPluginControlImageQualityIndicatorsv1_0.doFailureWaitMultiFile")
self.retrieveFailureMessages(
_edPlugin,
"EDPluginControlReadImageHeaderv10.doFailureWaitMultiFile")
self.ERROR("Timeout when waiting for images")
self.setFailure()
def doSuccessExecPlugin(self, _edPlugin=None):
EDVerbose.DEBUG(
"EDPluginControlImageQualityIndicatorsv1_1.doSuccessExecPlugin")
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlImageQualityIndicatorsv1_1.doSuccessExecPlugin")
xsDataImageQualityIndicators = _edPlugin.getDataOutput(
).getImageQualityIndicators()
self.synchronizeOn()
self.xsDataResultControlImageQualityIndicators.addImageQualityIndicators(
XSDataImageQualityIndicators.parseString(
xsDataImageQualityIndicators.marshal()))
self.synchronizeOff()
def doFailureExecPlugin(self, _edPlugin=None):
EDVerbose.DEBUG(
"EDPluginControlImageQualityIndicatorsv1_1.doFailureGeneratePrediction"
)
#self.retrieveFailureMessages(_edPlugin, "EDPluginControlImageQualityIndicatorsv1_1.doFailureExecPlugin")
def generateExecutiveSummary(self, _edPlugin=None):
EDVerbose.DEBUG(
"EDPluginControlImageQualityIndicatorsv1_1.generateExecutiveSummary"
)
self.addErrorWarningMessagesToExecutiveSummary(
"Image quality indicator plugin execution failure! Error messages: "
)
self.addExecutiveSummaryLine(
"Summary of image quality indicators with %s :" %
self.strPluginExecImageQualityIndicatorName)
for edPluginPluginExecImageQualityIndicator in self.listPluginExecImageQualityIndicator:
self.addExecutiveSummaryLine("")
if edPluginPluginExecImageQualityIndicator is not None:
self.appendExecutiveSummary(
edPluginPluginExecImageQualityIndicator,
"Distl.signal_strength : ",
_bAddSeparator=False)
class EDPluginControlImageQualityIndicatorsv1_3(EDPluginControl):
"""
This plugin that control the plugin that generates the image quality indicators.
"""
def __init__(self):
EDPluginControl.__init__(self)
self.strPluginMXWaitFileName = "EDPluginMXWaitFilev1_1"
self.strPluginName = "EDPluginDistlSignalStrengthv1_1"
self.strPluginNameThinClient = "EDPluginDistlSignalStrengthThinClientv1_1"
self.strPluginNameControlBackground3D = "EDPluginControlBackground3Dv1_0"
self.strISPyBPluginName = "EDPluginISPyBStoreListOfImageQualityIndicatorsv1_4"
self.strIndexingMOSFLMPluginName = "EDPluginMOSFLMIndexingv10"
self.edPluginMOSFLMIndexing = None
self.strPluginReadImageHeaderName = "EDPluginControlReadImageHeaderv10"
self.edPluginReadImageHeader = None
self.edPluginControlBackground3D = None
self.setXSDataInputClass(XSDataInputControlImageQualityIndicators)
self.listPluginExecImageQualityIndicator = []
self.listPluginControlBackground3D = []
self.xsDataResultControlImageQualityIndicators = None
self.edPluginMXWaitFile = None
# Default time out for wait file
self.fMXWaitFileTimeOut = 30 # s
# Flag for using the thin client - disabled as of 2016/07/20
self.bUseThinClient = False
self.edPluginISPyB = None
self.listPluginMOSFLM = []
self.defaultMinImageSize = 1000000
self.minImageSize = None
def checkParameters(self):
"""
Checks the mandatory parameters
"""
self.DEBUG("EDPluginControlImageQualityIndicatorsv1_3.checkParameters")
self.checkMandatoryParameters(self.getDataInput().getImage(), "Image")
def configure(self, _edPlugin=None):
EDPluginControl.configure(self)
self.DEBUG("EDPluginControlReadImageHeaderv10.configure")
self.fMXWaitFileTimeOut = float(
self.config.get("MXWaitFileTimeOut", self.fMXWaitFileTimeOut))
self.minImageSize = self.config.get("minImageSize")
if self.minImageSize is None:
self.minImageSize = self.defaultMinImageSize
def process(self, _edPlugin=None):
"""
Executes the execution plugins
"""
EDPluginControl.process(self, _edPlugin)
self.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
xsDataInputMXWaitFile = XSDataInputMXWaitFile()
self.xsDataResultControlImageQualityIndicators = XSDataResultControlImageQualityIndicators(
)
listPlugin = []
for xsDataImage in listXSDataImage:
self.edPluginMXWaitFile = self.loadPlugin(
self.strPluginMXWaitFileName)
xsDataInputMXWaitFile.file = XSDataFile(xsDataImage.path)
xsDataInputMXWaitFile.setSize(XSDataInteger(self.minImageSize))
xsDataInputMXWaitFile.setTimeOut(
XSDataTime(self.fMXWaitFileTimeOut))
self.DEBUG("Wait file timeOut set to %f" % self.fMXWaitFileTimeOut)
self.edPluginMXWaitFile.setDataInput(xsDataInputMXWaitFile)
self.edPluginMXWaitFile.executeSynchronous()
if not os.path.exists(xsDataImage.path.value):
self.edPluginMXWaitFile = self.loadPlugin(
self.strPluginMXWaitFileName)
xsDataInputMXWaitFile.file = XSDataFile(xsDataImage.path)
xsDataInputMXWaitFile.setSize(XSDataInteger(5000000))
xsDataInputMXWaitFile.setTimeOut(
XSDataTime(self.fMXWaitFileTimeOut))
self.DEBUG("Wait file timeOut set to %f" %
self.fMXWaitFileTimeOut)
self.edPluginMXWaitFile.setDataInput(xsDataInputMXWaitFile)
self.edPluginMXWaitFile.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
# print xsDataIndexingResult.marshal()
# xsDataResultISPyB = edPluginISPyB.dataOutput
# if xsDataResultISPyB is not None:
# print xsDataResultISPyB.marshal()
def finallyProcess(self, _edPlugin=None):
EDPluginControl.finallyProcess(self, _edPlugin)
if self.edPluginISPyB is not None:
# Synchronize ISPyB plugin
self.DEBUG(
"EDPluginControlImageQualityIndicatorsv1_3.finallyProcess")
self.edPluginISPyB.synchronize()
listId = []
for xsDataInteger in self.edPluginISPyB.dataOutput.imageQualityIndicatorsId:
listId.append(xsDataInteger.value)
self.DEBUG("ISPyB imageQualityIndicatorIds = %r" % listId)
self.setDataOutput(self.xsDataResultControlImageQualityIndicators)
def generateExecutiveSummary(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlImageQualityIndicatorsv1_3.generateExecutiveSummary"
)
self.addErrorWarningMessagesToExecutiveSummary(
"Image quality indicator plugin execution failure! Error messages: "
)
self.addExecutiveSummaryLine(
"Summary of image quality indicators with %s :" %
self.strPluginName)
for edPluginPluginExecImageQualityIndicator in self.listPluginExecImageQualityIndicator:
self.addExecutiveSummaryLine("")
if edPluginPluginExecImageQualityIndicator is not None:
self.appendExecutiveSummary(
edPluginPluginExecImageQualityIndicator,
"Distl.signal_strength : ",
_bAddSeparator=False)
def process(self, _edPlugin=None):
"""
Executes the execution plugins
"""
EDPluginControl.process(self, _edPlugin)
self.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
xsDataInputMXWaitFile = XSDataInputMXWaitFile()
self.xsDataResultControlImageQualityIndicators = XSDataResultControlImageQualityIndicators(
)
listPlugin = []
for xsDataImage in listXSDataImage:
self.edPluginMXWaitFile = self.loadPlugin(
self.strPluginMXWaitFileName)
xsDataInputMXWaitFile.file = XSDataFile(xsDataImage.path)
xsDataInputMXWaitFile.setSize(XSDataInteger(self.minImageSize))
xsDataInputMXWaitFile.setTimeOut(
XSDataTime(self.fMXWaitFileTimeOut))
self.DEBUG("Wait file timeOut set to %f" % self.fMXWaitFileTimeOut)
self.edPluginMXWaitFile.setDataInput(xsDataInputMXWaitFile)
self.edPluginMXWaitFile.executeSynchronous()
if not os.path.exists(xsDataImage.path.value):
self.edPluginMXWaitFile = self.loadPlugin(
self.strPluginMXWaitFileName)
xsDataInputMXWaitFile.file = XSDataFile(xsDataImage.path)
xsDataInputMXWaitFile.setSize(XSDataInteger(5000000))
xsDataInputMXWaitFile.setTimeOut(
XSDataTime(self.fMXWaitFileTimeOut))
self.DEBUG("Wait file timeOut set to %f" %
self.fMXWaitFileTimeOut)
self.edPluginMXWaitFile.setDataInput(xsDataInputMXWaitFile)
self.edPluginMXWaitFile.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
class EDPluginControlImageQualityIndicatorsv1_2(EDPluginControl):
"""
This plugin that control the plugin that generates the image quality indicators.
"""
def __init__(self):
EDPluginControl.__init__(self)
self.strPluginMXWaitFileName = "EDPluginMXWaitFilev1_1"
self.strPluginName = "EDPluginDistlSignalStrengthv1_1"
self.strPluginNameThinClient = "EDPluginDistlSignalStrengthv1_1"
self.strISPyBPluginName = "EDPluginISPyBStoreListOfImageQualityIndicatorsv1_4"
self.strIndexingMOSFLMPluginName = "EDPluginMOSFLMIndexingv10"
self.edPluginMOSFLMIndexing = None
self.strPluginReadImageHeaderName = "EDPluginControlReadImageHeaderv10"
self.edPluginReadImageHeader = None
self.setXSDataInputClass(XSDataInputControlImageQualityIndicators)
self.listPluginExecImageQualityIndicator = []
self.xsDataResultControlImageQualityIndicators = None
self.edPluginMXWaitFile = None
# Default time out for wait file
self.fMXWaitFileTimeOut = 30 #s
# Flag for using the thin client
self.bUseThinClient = True
self.edPluginISPyB = None
self.listPluginMOSFLM = []
self.bDoISPyBUpload = True
self.defaultMinImageSize = 1000000
self.minImageSize = None
def checkParameters(self):
"""
Checks the mandatory parameters
"""
self.DEBUG("EDPluginControlImageQualityIndicatorsv1_2.checkParameters")
self.checkMandatoryParameters(self.getDataInput().getImage(), "Image")
def configure(self, _edPlugin=None):
EDPluginControl.configure(self)
self.DEBUG("EDPluginControlReadImageHeaderv10.configure")
self.fMXWaitFileTimeOut = float(
self.config.get("MXWaitFileTimeOut", self.fMXWaitFileTimeOut))
self.bDoISPyBUpload = self.config.get("do_ispyb_upload")
if self.bDoISPyBUpload is None or self.bDoISPyBUpload == "false":
self.bDoISPyBUpload = False
self.minImageSize = self.config.get("minImageSize")
if self.minImageSize is None:
self.minImageSize = self.defaultMinImageSize
def process(self, _edPlugin=None):
"""
Executes the execution plugins
"""
EDPluginControl.process(self, _edPlugin)
self.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
xsDataInputMXWaitFile = XSDataInputMXWaitFile()
self.xsDataResultControlImageQualityIndicators = XSDataResultControlImageQualityIndicators(
)
listPlugin = []
for xsDataImage in listXSDataImage:
self.edPluginMXWaitFile = self.loadPlugin(
self.strPluginMXWaitFileName)
xsDataInputMXWaitFile.file = XSDataFile(xsDataImage.path)
xsDataInputMXWaitFile.setSize(XSDataInteger(self.minImageSize))
xsDataInputMXWaitFile.setTimeOut(
XSDataTime(self.fMXWaitFileTimeOut))
self.DEBUG("Wait file timeOut set to %f" % self.fMXWaitFileTimeOut)
self.edPluginMXWaitFile.setDataInput(xsDataInputMXWaitFile)
self.edPluginMXWaitFile.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()
if self.bDoISPyBUpload:
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
# print xsDataIndexingResult.marshal()
# xsDataResultISPyB = edPluginISPyB.dataOutput
# if xsDataResultISPyB is not None:
#print xsDataResultISPyB.marshal()
def finallyProcess(self, _edPlugin=None):
EDPluginControl.finallyProcess(self, _edPlugin)
# Synchronize ISPyB plugin
self.DEBUG("EDPluginControlImageQualityIndicatorsv1_2.finallyProcess")
if self.bDoISPyBUpload:
self.edPluginISPyB.synchronize()
listId = []
for xsDataInteger in self.edPluginISPyB.dataOutput.imageQualityIndicatorsId:
listId.append(xsDataInteger.value)
self.DEBUG("ISPyB imageQualityIndicatorIds = %r" % listId)
self.setDataOutput(self.xsDataResultControlImageQualityIndicators)
def generateExecutiveSummary(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlImageQualityIndicatorsv1_2.generateExecutiveSummary"
)
self.addErrorWarningMessagesToExecutiveSummary(
"Image quality indicator plugin execution failure! Error messages: "
)
self.addExecutiveSummaryLine(
"Summary of image quality indicators with %s :" %
self.strPluginName)
for edPluginPluginExecImageQualityIndicator in self.listPluginExecImageQualityIndicator:
self.addExecutiveSummaryLine("")
if edPluginPluginExecImageQualityIndicator is not None:
self.appendExecutiveSummary(
edPluginPluginExecImageQualityIndicator,
"Distl.signal_strength : ",
_bAddSeparator=False)
def process(self, _edPlugin=None):
"""
Executes the execution plugins
"""
EDPluginControl.process(self, _edPlugin)
self.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
xsDataInputMXWaitFile = XSDataInputMXWaitFile()
self.xsDataResultControlImageQualityIndicators = XSDataResultControlImageQualityIndicators(
)
listPlugin = []
for xsDataImage in listXSDataImage:
self.edPluginMXWaitFile = self.loadPlugin(
self.strPluginMXWaitFileName)
xsDataInputMXWaitFile.file = XSDataFile(xsDataImage.path)
xsDataInputMXWaitFile.setSize(XSDataInteger(self.minImageSize))
xsDataInputMXWaitFile.setTimeOut(
XSDataTime(self.fMXWaitFileTimeOut))
self.DEBUG("Wait file timeOut set to %f" % self.fMXWaitFileTimeOut)
self.edPluginMXWaitFile.setDataInput(xsDataInputMXWaitFile)
self.edPluginMXWaitFile.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()
if self.bDoISPyBUpload:
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
class EDPluginControlImageQualityIndicatorsv1_5(EDPluginControl):
"""
This plugin that control the plugin that generates the image quality indicators.
"""
def __init__ (self):
EDPluginControl.__init__(self)
self.strPluginMXWaitFileName = "EDPluginMXWaitFilev1_1"
self.strPluginName = "EDPluginDistlSignalStrengthv1_1"
self.strPluginNameThinClient = "EDPluginDistlSignalStrengthThinClientv1_1"
self.strPluginNameControlDozor = "EDPluginControlDozorv1_0"
self.strISPyBPluginName = "EDPluginISPyBStoreListOfImageQualityIndicatorsv1_5"
self.strIndexingLabelitPluginName = "EDPluginLabelitIndexingv1_1"
self.edPluginLabelitIndexing = None
self.strPluginReadImageHeaderName = "EDPluginControlReadImageHeaderv10"
self.edPluginReadImageHeader = None
self.edPluginControlDozor = None
self.setXSDataInputClass(XSDataInputControlImageQualityIndicators)
self.listPluginExecImageQualityIndicator = []
self.listPluginControlDozor = []
self.xsDataResultControlImageQualityIndicators = None
self.edPluginMXWaitFile = None
# Default time out for wait file
self.fMXWaitFileTimeOut = 30 # s
# Flag for using the thin client
if EDUtilsPath.isEMBL():
self.bUseThinClient = False
else:
self.bUseThinClient = True
self.edPluginISPyB = None
self.listPluginLabelit = []
self.defaultMinImageSize = 1000000
self.minImageSize = None
def checkParameters(self):
"""
Checks the mandatory parameters
"""
self.DEBUG("EDPluginControlImageQualityIndicatorsv1_5.checkParameters")
self.checkMandatoryParameters(self.getDataInput().getImage(), "Image")
def configure(self, _edPlugin=None):
EDPluginControl.configure(self)
self.DEBUG("EDPluginControlReadImageHeaderv10.configure")
self.fMXWaitFileTimeOut = float(self.config.get("MXWaitFileTimeOut", self.fMXWaitFileTimeOut))
self.minImageSize = self.config.get("minImageSize")
if self.minImageSize is None:
self.minImageSize = self.defaultMinImageSize
def process(self, _edPlugin=None):
"""
Executes the execution plugins
"""
EDPluginControl.process(self, _edPlugin)
self.DEBUG("EDPluginControlImageQualityIndicatorsv1_5.process")
EDUtilsParallel.initializeNbThread()
# Check batch size
if self.dataInput.batchSize is None:
batchSize = 1
else:
batchSize = self.dataInput.batchSize.value
# Check if we should do distlSignalStrength:
bDoDistlSignalStrength = True
if self.dataInput.doDistlSignalStrength is not None:
if not self.dataInput.doDistlSignalStrength.value:
bDoDistlSignalStrength = False
# 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
xsDataInputMXWaitFile = XSDataInputMXWaitFile()
self.xsDataResultControlImageQualityIndicators = XSDataResultControlImageQualityIndicators()
listPluginDistl = []
listPluginDozor = []
listBatch = []
indexBatch = 0
for xsDataImage in listXSDataImage:
self.edPluginMXWaitFile = self.loadPlugin(self.strPluginMXWaitFileName)
xsDataInputMXWaitFile.file = XSDataFile(xsDataImage.path)
xsDataInputMXWaitFile.setSize(XSDataInteger(self.minImageSize))
xsDataInputMXWaitFile.setTimeOut(XSDataTime(self.fMXWaitFileTimeOut))
self.DEBUG("Wait file timeOut set to %f" % self.fMXWaitFileTimeOut)
self.edPluginMXWaitFile.setDataInput(xsDataInputMXWaitFile)
self.edPluginMXWaitFile.executeSynchronous()
if not os.path.exists(xsDataImage.path.value):
self.edPluginMXWaitFile = self.loadPlugin(self.strPluginMXWaitFileName)
xsDataInputMXWaitFile.file = XSDataFile(xsDataImage.path)
xsDataInputMXWaitFile.setSize(XSDataInteger(5000000))
xsDataInputMXWaitFile.setTimeOut(XSDataTime(self.fMXWaitFileTimeOut))
self.DEBUG("Wait file timeOut set to %f" % self.fMXWaitFileTimeOut)
self.edPluginMXWaitFile.setDataInput(xsDataInputMXWaitFile)
self.edPluginMXWaitFile.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:
# Check if we should run distl.signalStrength
edPluginPluginExecImageQualityIndicator = None
if bDoDistlSignalStrength:
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()
listPluginDistl.append((xsDataImage.copy(), edPluginPluginExecImageQualityIndicator))
listBatch.append(xsDataImage.copy())
if len(listBatch) == batchSize:
edPluginControlDozor = self.loadPlugin(self.strPluginNameControlDozor)
xsDataInputControlDozor = XSDataInputControlDozor()
for image in listBatch:
xsDataInputControlDozor.addImage(XSDataFile(image.path))
xsDataInputControlDozor.batchSize = XSDataInteger(batchSize)
edPluginControlDozor.dataInput = xsDataInputControlDozor
edPluginControlDozor.execute()
listPluginDozor.append((edPluginControlDozor, listBatch))
listBatch = []
if len(listBatch) > 0:
# Process the remaining images...
edPluginControlDozor = self.loadPlugin(self.strPluginNameControlDozor)
xsDataInputControlDozor = XSDataInputControlDozor()
for image in listBatch:
xsDataInputControlDozor.addImage(XSDataFile(image.path))
xsDataInputControlDozor.batchSize = XSDataInteger(batchSize)
edPluginControlDozor.dataInput = xsDataInputControlDozor
edPluginControlDozor.execute()
listPluginDozor.append([edPluginControlDozor, listBatch])
listIndexing = []
# Synchronize all image quality indicator plugins and upload to ISPyB
xsDataInputStoreListOfImageQualityIndicators = XSDataInputStoreListOfImageQualityIndicators()
for (xsDataImage, edPluginPluginExecImageQualityIndicator) in listPluginDistl:
xsDataImageQualityIndicators = XSDataImageQualityIndicators()
xsDataImageQualityIndicators.image = xsDataImage.copy()
if edPluginPluginExecImageQualityIndicator is not None:
edPluginPluginExecImageQualityIndicator.synchronize()
if edPluginPluginExecImageQualityIndicator.dataOutput.imageQualityIndicators is not None:
xsDataImageQualityIndicators = XSDataImageQualityIndicators.parseString(\
edPluginPluginExecImageQualityIndicator.dataOutput.imageQualityIndicators.marshal())
self.xsDataResultControlImageQualityIndicators.addImageQualityIndicators(xsDataImageQualityIndicators)
for (edPluginControlDozor, listBatch) in listPluginDozor:
edPluginControlDozor.synchronize()
for imageDozor in edPluginControlDozor.dataOutput.imageDozor:
for xsDataImageQualityIndicators in self.xsDataResultControlImageQualityIndicators.imageQualityIndicators:
if xsDataImageQualityIndicators.image.path.value == imageDozor.image.path.value:
xsDataImageQualityIndicators.dozor_score = imageDozor.mainScore
xsDataImageQualityIndicators.dozorSpotFile = imageDozor.spotFile
xsDataImageQualityIndicators.dozorSpotsIntAver = imageDozor.spotsIntAver
xsDataImageQualityIndicators.dozorSpotsResolution = imageDozor.spotsResolution
if self.xsDataResultControlImageQualityIndicators.inputDozor is None:
if edPluginControlDozor.dataOutput.inputDozor is not None:
self.xsDataResultControlImageQualityIndicators.inputDozor = XSDataDozorInput().parseString(
edPluginControlDozor.dataOutput.inputDozor.marshal())
if self.dataInput.doUploadToIspyb is not None and self.dataInput.doUploadToIspyb.value:
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 dozor_score from all images:
has_dozor_score = True
for imageQualityIndicators in self.xsDataResultControlImageQualityIndicators.imageQualityIndicators:
if imageQualityIndicators.dozor_score is None:
has_dozor_score = False
if has_dozor_score:
listSorted = sorted(self.xsDataResultControlImageQualityIndicators.imageQualityIndicators,
key=lambda imageQualityIndicators: imageQualityIndicators.dozor_score.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:
edPluginLabelitIndexing = self.loadPlugin(self.strIndexingLabelitPluginName)
xsDataInputLabelitIndexing = XSDataInputLabelitIndexing()
xsDataInputLabelitIndexing.image.append(XSDataImage(xsDataResultControlImageQualityIndicator.image.path))
edPluginLabelitIndexing.setDataInput(xsDataInputLabelitIndexing)
self.listPluginLabelit.append([edPluginLabelitIndexing, xsDataResultControlImageQualityIndicator])
edPluginLabelitIndexing.execute()
for tupleLabelit in self.listPluginLabelit:
edPluginLabelitIndexing = tupleLabelit[0]
xsDataResultControlImageQualityIndicator = tupleLabelit[1]
edPluginLabelitIndexing.synchronize()
if not edPluginLabelitIndexing.isFailure() and edPluginLabelitIndexing.dataOutput is not None:
xsDataResultLabelitIndexing = edPluginLabelitIndexing.getDataOutput()
xsDataIndexingResult = EDHandlerXSDataPhenixv1_1.generateXSDataIndexingResult(xsDataResultLabelitIndexing)
selectedSolution = xsDataIndexingResult.selectedSolution
if selectedSolution is not None:
xsDataResultControlImageQualityIndicator.selectedIndexingSolution = selectedSolution
def finallyProcess(self, _edPlugin=None):
EDPluginControl.finallyProcess(self, _edPlugin)
if self.edPluginISPyB is not None:
# Synchronize ISPyB plugin
self.DEBUG("EDPluginControlImageQualityIndicatorsv1_5.finallyProcess")
self.edPluginISPyB.synchronize()
listId = []
for xsDataInteger in self.edPluginISPyB.dataOutput.imageQualityIndicatorsId:
listId.append(xsDataInteger.value)
self.DEBUG("ISPyB imageQualityIndicatorIds = %r" % listId)
self.setDataOutput(self.xsDataResultControlImageQualityIndicators)
def generateExecutiveSummary(self, _edPlugin=None):
self.DEBUG("EDPluginControlImageQualityIndicatorsv1_5.generateExecutiveSummary")
self.addErrorWarningMessagesToExecutiveSummary("Image quality indicator plugin execution failure! Error messages: ")
self.addExecutiveSummaryLine("Summary of image quality indicators with %s :" % self.strPluginName)
for edPluginPluginExecImageQualityIndicator in self.listPluginExecImageQualityIndicator:
self.addExecutiveSummaryLine("")
if edPluginPluginExecImageQualityIndicator is not None:
self.appendExecutiveSummary(edPluginPluginExecImageQualityIndicator, "Distl.signal_strength : ", _bAddSeparator=False)
def process(self, _edPlugin=None):
"""
Executes the execution plugins
"""
EDPluginControl.process(self, _edPlugin)
self.DEBUG("EDPluginControlImageQualityIndicatorsv1_5.process")
EDUtilsParallel.initializeNbThread()
# Check batch size
if self.dataInput.batchSize is None:
batchSize = 1
else:
batchSize = self.dataInput.batchSize.value
# Check if we should do distlSignalStrength:
bDoDistlSignalStrength = True
if self.dataInput.doDistlSignalStrength is not None:
if not self.dataInput.doDistlSignalStrength.value:
bDoDistlSignalStrength = False
# 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
xsDataInputMXWaitFile = XSDataInputMXWaitFile()
self.xsDataResultControlImageQualityIndicators = XSDataResultControlImageQualityIndicators()
listPluginDistl = []
listPluginDozor = []
listBatch = []
indexBatch = 0
for xsDataImage in listXSDataImage:
self.edPluginMXWaitFile = self.loadPlugin(self.strPluginMXWaitFileName)
xsDataInputMXWaitFile.file = XSDataFile(xsDataImage.path)
xsDataInputMXWaitFile.setSize(XSDataInteger(self.minImageSize))
xsDataInputMXWaitFile.setTimeOut(XSDataTime(self.fMXWaitFileTimeOut))
self.DEBUG("Wait file timeOut set to %f" % self.fMXWaitFileTimeOut)
self.edPluginMXWaitFile.setDataInput(xsDataInputMXWaitFile)
self.edPluginMXWaitFile.executeSynchronous()
if not os.path.exists(xsDataImage.path.value):
self.edPluginMXWaitFile = self.loadPlugin(self.strPluginMXWaitFileName)
xsDataInputMXWaitFile.file = XSDataFile(xsDataImage.path)
xsDataInputMXWaitFile.setSize(XSDataInteger(5000000))
xsDataInputMXWaitFile.setTimeOut(XSDataTime(self.fMXWaitFileTimeOut))
self.DEBUG("Wait file timeOut set to %f" % self.fMXWaitFileTimeOut)
self.edPluginMXWaitFile.setDataInput(xsDataInputMXWaitFile)
self.edPluginMXWaitFile.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:
# Check if we should run distl.signalStrength
edPluginPluginExecImageQualityIndicator = None
if bDoDistlSignalStrength:
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()
listPluginDistl.append((xsDataImage.copy(), edPluginPluginExecImageQualityIndicator))
listBatch.append(xsDataImage.copy())
if len(listBatch) == batchSize:
edPluginControlDozor = self.loadPlugin(self.strPluginNameControlDozor)
xsDataInputControlDozor = XSDataInputControlDozor()
for image in listBatch:
xsDataInputControlDozor.addImage(XSDataFile(image.path))
xsDataInputControlDozor.batchSize = XSDataInteger(batchSize)
edPluginControlDozor.dataInput = xsDataInputControlDozor
edPluginControlDozor.execute()
listPluginDozor.append((edPluginControlDozor, listBatch))
listBatch = []
if len(listBatch) > 0:
# Process the remaining images...
edPluginControlDozor = self.loadPlugin(self.strPluginNameControlDozor)
xsDataInputControlDozor = XSDataInputControlDozor()
for image in listBatch:
xsDataInputControlDozor.addImage(XSDataFile(image.path))
xsDataInputControlDozor.batchSize = XSDataInteger(batchSize)
edPluginControlDozor.dataInput = xsDataInputControlDozor
edPluginControlDozor.execute()
listPluginDozor.append([edPluginControlDozor, listBatch])
listIndexing = []
# Synchronize all image quality indicator plugins and upload to ISPyB
xsDataInputStoreListOfImageQualityIndicators = XSDataInputStoreListOfImageQualityIndicators()
for (xsDataImage, edPluginPluginExecImageQualityIndicator) in listPluginDistl:
xsDataImageQualityIndicators = XSDataImageQualityIndicators()
xsDataImageQualityIndicators.image = xsDataImage.copy()
if edPluginPluginExecImageQualityIndicator is not None:
edPluginPluginExecImageQualityIndicator.synchronize()
if edPluginPluginExecImageQualityIndicator.dataOutput.imageQualityIndicators is not None:
xsDataImageQualityIndicators = XSDataImageQualityIndicators.parseString(\
edPluginPluginExecImageQualityIndicator.dataOutput.imageQualityIndicators.marshal())
self.xsDataResultControlImageQualityIndicators.addImageQualityIndicators(xsDataImageQualityIndicators)
for (edPluginControlDozor, listBatch) in listPluginDozor:
edPluginControlDozor.synchronize()
for imageDozor in edPluginControlDozor.dataOutput.imageDozor:
for xsDataImageQualityIndicators in self.xsDataResultControlImageQualityIndicators.imageQualityIndicators:
if xsDataImageQualityIndicators.image.path.value == imageDozor.image.path.value:
xsDataImageQualityIndicators.dozor_score = imageDozor.mainScore
xsDataImageQualityIndicators.dozorSpotFile = imageDozor.spotFile
xsDataImageQualityIndicators.dozorSpotsIntAver = imageDozor.spotsIntAver
xsDataImageQualityIndicators.dozorSpotsResolution = imageDozor.spotsResolution
if self.xsDataResultControlImageQualityIndicators.inputDozor is None:
if edPluginControlDozor.dataOutput.inputDozor is not None:
self.xsDataResultControlImageQualityIndicators.inputDozor = XSDataDozorInput().parseString(
edPluginControlDozor.dataOutput.inputDozor.marshal())
if self.dataInput.doUploadToIspyb is not None and self.dataInput.doUploadToIspyb.value:
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 dozor_score from all images:
has_dozor_score = True
for imageQualityIndicators in self.xsDataResultControlImageQualityIndicators.imageQualityIndicators:
if imageQualityIndicators.dozor_score is None:
has_dozor_score = False
if has_dozor_score:
listSorted = sorted(self.xsDataResultControlImageQualityIndicators.imageQualityIndicators,
key=lambda imageQualityIndicators: imageQualityIndicators.dozor_score.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:
edPluginLabelitIndexing = self.loadPlugin(self.strIndexingLabelitPluginName)
xsDataInputLabelitIndexing = XSDataInputLabelitIndexing()
xsDataInputLabelitIndexing.image.append(XSDataImage(xsDataResultControlImageQualityIndicator.image.path))
edPluginLabelitIndexing.setDataInput(xsDataInputLabelitIndexing)
self.listPluginLabelit.append([edPluginLabelitIndexing, xsDataResultControlImageQualityIndicator])
edPluginLabelitIndexing.execute()
for tupleLabelit in self.listPluginLabelit:
edPluginLabelitIndexing = tupleLabelit[0]
xsDataResultControlImageQualityIndicator = tupleLabelit[1]
edPluginLabelitIndexing.synchronize()
if not edPluginLabelitIndexing.isFailure() and edPluginLabelitIndexing.dataOutput is not None:
xsDataResultLabelitIndexing = edPluginLabelitIndexing.getDataOutput()
xsDataIndexingResult = EDHandlerXSDataPhenixv1_1.generateXSDataIndexingResult(xsDataResultLabelitIndexing)
selectedSolution = xsDataIndexingResult.selectedSolution
if selectedSolution is not None:
xsDataResultControlImageQualityIndicator.selectedIndexingSolution = selectedSolution
class EDPluginControlImageQualityIndicatorsv1_4(EDPluginControl):
"""
This plugin that control the plugin that generates the image quality indicators.
"""
def __init__ (self):
EDPluginControl.__init__(self)
self.strPluginMXWaitFileName = "EDPluginMXWaitFilev1_1"
self.strPluginName = "EDPluginDistlSignalStrengthv1_1"
self.strPluginNameThinClient = "EDPluginDistlSignalStrengthThinClientv1_1"
self.strPluginNameControlDozor = "EDPluginControlDozorv1_0"
self.strISPyBPluginName = "EDPluginISPyBStoreListOfImageQualityIndicatorsv1_4"
self.strIndexingMOSFLMPluginName = "EDPluginMOSFLMIndexingv10"
self.edPluginMOSFLMIndexing = None
self.strPluginReadImageHeaderName = "EDPluginControlReadImageHeaderv10"
self.edPluginReadImageHeader = None
self.edPluginControlDozor = None
self.strPluginControlH5ToCBF = "EDPluginControlH5ToCBFv1_1"
self.setXSDataInputClass(XSDataInputControlImageQualityIndicators)
self.listPluginExecImageQualityIndicator = []
self.listPluginControlDozor = []
self.xsDataResultControlImageQualityIndicators = None
self.edPluginMXWaitFile = None
# Default time out for wait file
self.fMXWaitFileTimeOut = 30 # s
# Flag for using the thin client
self.bUseThinClient = True
self.edPluginISPyB = None
self.listPluginMOSFLM = []
self.defaultMinImageSize = 1000000
self.minImageSize = None
def checkParameters(self):
"""
Checks the mandatory parameters
"""
self.DEBUG("EDPluginControlImageQualityIndicatorsv1_4.checkParameters")
self.checkMandatoryParameters(self.getDataInput().getImage(), "Image")
def configure(self, _edPlugin=None):
EDPluginControl.configure(self)
self.DEBUG("EDPluginControlImageQualityIndicatorsv1_4.configure")
self.fMXWaitFileTimeOut = float(self.config.get("MXWaitFileTimeOut", self.fMXWaitFileTimeOut))
self.minImageSize = self.config.get("minImageSize")
if self.minImageSize is None:
self.minImageSize = self.defaultMinImageSize
def process(self, _edPlugin=None):
"""
Executes the execution plugins
"""
EDPluginControl.process(self, _edPlugin)
self.DEBUG("EDPluginControlImageQualityIndicatorsv1_4.process")
EDUtilsParallel.initializeNbThread()
# Check batch size
if self.dataInput.batchSize is None:
batchSize = 1
else:
batchSize = self.dataInput.batchSize.value
self.screen("Batch size: {0}".format(batchSize))
# Check if we should do distlSignalStrength:
bDoDistlSignalStrength = True
if self.dataInput.doDistlSignalStrength is not None:
if not self.dataInput.doDistlSignalStrength.value:
bDoDistlSignalStrength = False
# 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
xsDataInputMXWaitFile = XSDataInputMXWaitFile()
self.xsDataResultControlImageQualityIndicators = XSDataResultControlImageQualityIndicators()
listPluginDistl = []
listPluginDozor = []
listBatch = []
indexBatch = 0
listH5FilePath = []
ispybDataCollection = None
for xsDataImage in listXSDataImage:
strPathToImage = xsDataImage.path.value
# If Eiger, just wait for the h5 file
if "id30a3" in strPathToImage:
h5MasterFilePath, h5DataFilePath, hdf5ImageNumber = self.getH5FilePath(strPathToImage, batchSize)
# print(h5FilePath)
# print(hdf5ImageNumber)
if not h5DataFilePath in listH5FilePath:
self.screen("ID30a3 Eiger data, waiting for master and data files...")
listH5FilePath.append(h5DataFilePath)
self.edPluginMXWaitFile = self.loadPlugin(self.strPluginMXWaitFileName)
xsDataInputMXWaitFile.file = XSDataFile(XSDataString(h5DataFilePath))
xsDataInputMXWaitFile.setSize(XSDataInteger(self.minImageSize))
xsDataInputMXWaitFile.setTimeOut(XSDataTime(self.fMXWaitFileTimeOut))
self.screen("Waiting for file {0}".format(h5DataFilePath))
self.DEBUG("Wait file timeOut set to %f" % self.fMXWaitFileTimeOut)
self.edPluginMXWaitFile.setDataInput(xsDataInputMXWaitFile)
self.edPluginMXWaitFile.executeSynchronous()
# hdf5FilePath = strPathToImage.replace(".cbf", ".h5")
ispybDataCollection = None
time.sleep(1)
indexLoop = 1
continueLoop = True
while continueLoop:
xsDataInputControlH5ToCBF = XSDataInputControlH5ToCBF()
xsDataInputControlH5ToCBF.hdf5File = XSDataFile(XSDataString(strPathToImage))
imageNumber = EDUtilsImage.getImageNumber(strPathToImage)
xsDataInputControlH5ToCBF.imageNumber = XSDataInteger(imageNumber)
xsDataInputControlH5ToCBF.hdf5ImageNumber = XSDataInteger(hdf5ImageNumber)
xsDataInputControlH5ToCBF.ispybDataCollection = ispybDataCollection
edPluginControlH5ToCBF = self.loadPlugin(self.strPluginControlH5ToCBF, "ControlH5ToCBF_%04d_%02d" % (imageNumber, indexLoop))
edPluginControlH5ToCBF.dataInput = xsDataInputControlH5ToCBF
edPluginControlH5ToCBF.executeSynchronous()
cbfFile = edPluginControlH5ToCBF.dataOutput.outputCBFFile
# print(cbfFile)
# print(indexLoop)
if cbfFile is not None:
strPathToImage = cbfFile.path.value
# print(cbfFile.path.value)
if os.path.exists(strPathToImage):
self.screen("Image has been converted to CBF file: {0}".format(strPathToImage))
continueLoop = False
# print(continueLoop)
if continueLoop:
self.screen("Still waiting for converting to CBF file: {0}".format(strPathToImage))
indexLoop += 1
time.sleep(5)
if indexLoop > 10:
continueLoop = False
ispybDataCollection = edPluginControlH5ToCBF.dataOutput.ispybDataCollection
elif not os.path.exists(strPathToImage):
self.screen("Waiting for file {0}".format(strPathToImage))
self.edPluginMXWaitFile = self.loadPlugin(self.strPluginMXWaitFileName)
xsDataInputMXWaitFile.file = XSDataFile(XSDataString(strPathToImage))
xsDataInputMXWaitFile.setSize(XSDataInteger(self.minImageSize))
xsDataInputMXWaitFile.setTimeOut(XSDataTime(self.fMXWaitFileTimeOut))
self.DEBUG("Wait file timeOut set to %f" % self.fMXWaitFileTimeOut)
self.edPluginMXWaitFile.setDataInput(xsDataInputMXWaitFile)
self.edPluginMXWaitFile.executeSynchronous()
if not os.path.exists(strPathToImage):
strError = "Time-out while waiting for image %s" % strPathToImage
self.error(strError)
self.addErrorMessage(strError)
self.setFailure()
else:
# Check if we should run distl.signalStrength
xsDataImageNew = XSDataImage(XSDataString(strPathToImage))
edPluginPluginExecImageQualityIndicator = None
if bDoDistlSignalStrength:
if self.bUseThinClient:
strPluginName = self.strPluginNameThinClient
else:
strPluginName = self.strPluginName
edPluginPluginExecImageQualityIndicator = self.loadPlugin(strPluginName)
self.listPluginExecImageQualityIndicator.append(edPluginPluginExecImageQualityIndicator)
xsDataInputDistlSignalStrength = XSDataInputDistlSignalStrength()
xsDataInputDistlSignalStrength.setReferenceImage(xsDataImageNew)
edPluginPluginExecImageQualityIndicator.setDataInput(xsDataInputDistlSignalStrength)
edPluginPluginExecImageQualityIndicator.execute()
listPluginDistl.append((xsDataImageNew.copy(), edPluginPluginExecImageQualityIndicator))
listBatch.append(xsDataImageNew.copy())
if len(listBatch) == batchSize:
edPluginControlDozor = self.loadPlugin(self.strPluginNameControlDozor)
xsDataInputControlDozor = XSDataInputControlDozor()
for image in listBatch:
xsDataInputControlDozor.addImage(XSDataFile(image.path))
xsDataInputControlDozor.batchSize = XSDataInteger(batchSize)
edPluginControlDozor.dataInput = xsDataInputControlDozor
edPluginControlDozor.execute()
listPluginDozor.append((edPluginControlDozor, listBatch))
listBatch = []
if len(listBatch) > 0:
# Process the remaining images...
edPluginControlDozor = self.loadPlugin(self.strPluginNameControlDozor)
xsDataInputControlDozor = XSDataInputControlDozor()
for image in listBatch:
xsDataInputControlDozor.addImage(XSDataFile(image.path))
xsDataInputControlDozor.batchSize = XSDataInteger(batchSize)
edPluginControlDozor.dataInput = xsDataInputControlDozor
edPluginControlDozor.execute()
listPluginDozor.append([edPluginControlDozor, listBatch])
listIndexing = []
# Synchronize all image quality indicator plugins and upload to ISPyB
xsDataInputStoreListOfImageQualityIndicators = XSDataInputStoreListOfImageQualityIndicators()
for (xsDataImage, edPluginPluginExecImageQualityIndicator) in listPluginDistl:
xsDataImageQualityIndicators = XSDataImageQualityIndicators()
xsDataImageQualityIndicators.image = xsDataImage.copy()
if edPluginPluginExecImageQualityIndicator is not None:
edPluginPluginExecImageQualityIndicator.synchronize()
if edPluginPluginExecImageQualityIndicator.dataOutput.imageQualityIndicators is not None:
xsDataImageQualityIndicators = XSDataImageQualityIndicators.parseString(\
edPluginPluginExecImageQualityIndicator.dataOutput.imageQualityIndicators.marshal())
self.xsDataResultControlImageQualityIndicators.addImageQualityIndicators(xsDataImageQualityIndicators)
for (edPluginControlDozor, listBatch) in listPluginDozor:
edPluginControlDozor.synchronize()
for imageDozor in edPluginControlDozor.dataOutput.imageDozor:
for xsDataImageQualityIndicators in self.xsDataResultControlImageQualityIndicators.imageQualityIndicators:
if xsDataImageQualityIndicators.image.path.value == imageDozor.image.path.value:
xsDataImageQualityIndicators.dozor_score = imageDozor.mainScore
xsDataImageQualityIndicators.dozorSpotFile = imageDozor.spotFile
if imageDozor.spotFile is not None:
if os.path.exists(imageDozor.spotFile.path.value):
numpyArray = numpy.loadtxt(imageDozor.spotFile.path.value, skiprows=3)
xsDataImageQualityIndicators.dozorSpotList = XSDataString(base64.b64encode(numpyArray.tostring()))
xsDataImageQualityIndicators.addDozorSpotListShape(XSDataInteger(numpyArray.shape[0]))
if len(numpyArray.shape) > 1:
xsDataImageQualityIndicators.addDozorSpotListShape(XSDataInteger(numpyArray.shape[1]))
xsDataImageQualityIndicators.dozorSpotsIntAver = imageDozor.spotsIntAver
xsDataImageQualityIndicators.dozorSpotsResolution = imageDozor.spotsResolution
if self.xsDataResultControlImageQualityIndicators.inputDozor is None:
if edPluginControlDozor.dataOutput.inputDozor is not None:
self.xsDataResultControlImageQualityIndicators.inputDozor = XSDataDozorInput().parseString(
edPluginControlDozor.dataOutput.inputDozor.marshal())
if self.dataInput.doUploadToIspyb is not None and self.dataInput.doUploadToIspyb.value:
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 dozor_score from all images:
has_dozor_score = True
for imageQualityIndicators in self.xsDataResultControlImageQualityIndicators.imageQualityIndicators:
if imageQualityIndicators.dozor_score is None:
has_dozor_score = False
if has_dozor_score:
listSorted = sorted(self.xsDataResultControlImageQualityIndicators.imageQualityIndicators,
key=lambda imageQualityIndicators: imageQualityIndicators.dozor_score.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
# print xsDataIndexingResult.marshal()
# xsDataResultISPyB = edPluginISPyB.dataOutput
# if xsDataResultISPyB is not None:
# print xsDataResultISPyB.marshal()
def finallyProcess(self, _edPlugin=None):
EDPluginControl.finallyProcess(self, _edPlugin)
if self.edPluginISPyB is not None:
# Synchronize ISPyB plugin
self.DEBUG("EDPluginControlImageQualityIndicatorsv1_4.finallyProcess")
self.edPluginISPyB.synchronize()
listId = []
for xsDataInteger in self.edPluginISPyB.dataOutput.imageQualityIndicatorsId:
listId.append(xsDataInteger.value)
self.DEBUG("ISPyB imageQualityIndicatorIds = %r" % listId)
self.setDataOutput(self.xsDataResultControlImageQualityIndicators)
def generateExecutiveSummary(self, _edPlugin=None):
self.DEBUG("EDPluginControlImageQualityIndicatorsv1_4.generateExecutiveSummary")
self.addErrorWarningMessagesToExecutiveSummary("Image quality indicator plugin execution failure! Error messages: ")
self.addExecutiveSummaryLine("Summary of image quality indicators with %s :" % self.strPluginName)
for edPluginPluginExecImageQualityIndicator in self.listPluginExecImageQualityIndicator:
self.addExecutiveSummaryLine("")
if edPluginPluginExecImageQualityIndicator is not None:
self.appendExecutiveSummary(edPluginPluginExecImageQualityIndicator, "Distl.signal_strength : ", _bAddSeparator=False)
def getH5FilePath(self, filePath, batchSize=1):
imageNumber = EDUtilsImage.getImageNumber(filePath)
prefix = EDUtilsImage.getPrefix(filePath)
h5FileNumber = int((imageNumber - 1) / batchSize) * batchSize + 1
h5MasterFileName = "{prefix}_{h5FileNumber}_master.h5".format(prefix=prefix,
h5FileNumber=h5FileNumber)
h5MasterFilePath = os.path.join(os.path.dirname(filePath), h5MasterFileName)
h5DataFileName = "{prefix}_{h5FileNumber}_data_000001.h5".format(prefix=prefix,
h5FileNumber=h5FileNumber)
h5DataFilePath = os.path.join(os.path.dirname(filePath), h5DataFileName)
return h5MasterFilePath, h5DataFilePath, h5FileNumber
def process(self, _edPlugin=None):
"""
Executes the execution plugins
"""
EDPluginControl.process(self, _edPlugin)
self.DEBUG("EDPluginControlImageQualityIndicatorsv1_4.process")
EDUtilsParallel.initializeNbThread()
# Check batch size
if self.dataInput.batchSize is None:
batchSize = 1
else:
batchSize = self.dataInput.batchSize.value
self.screen("Batch size: {0}".format(batchSize))
# Check if we should do distlSignalStrength:
bDoDistlSignalStrength = True
if self.dataInput.doDistlSignalStrength is not None:
if not self.dataInput.doDistlSignalStrength.value:
bDoDistlSignalStrength = False
# 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
xsDataInputMXWaitFile = XSDataInputMXWaitFile()
self.xsDataResultControlImageQualityIndicators = XSDataResultControlImageQualityIndicators()
listPluginDistl = []
listPluginDozor = []
listBatch = []
indexBatch = 0
listH5FilePath = []
ispybDataCollection = None
for xsDataImage in listXSDataImage:
strPathToImage = xsDataImage.path.value
# If Eiger, just wait for the h5 file
if "id30a3" in strPathToImage:
h5MasterFilePath, h5DataFilePath, hdf5ImageNumber = self.getH5FilePath(strPathToImage, batchSize)
# print(h5FilePath)
# print(hdf5ImageNumber)
if not h5DataFilePath in listH5FilePath:
self.screen("ID30a3 Eiger data, waiting for master and data files...")
listH5FilePath.append(h5DataFilePath)
self.edPluginMXWaitFile = self.loadPlugin(self.strPluginMXWaitFileName)
xsDataInputMXWaitFile.file = XSDataFile(XSDataString(h5DataFilePath))
xsDataInputMXWaitFile.setSize(XSDataInteger(self.minImageSize))
xsDataInputMXWaitFile.setTimeOut(XSDataTime(self.fMXWaitFileTimeOut))
self.screen("Waiting for file {0}".format(h5DataFilePath))
self.DEBUG("Wait file timeOut set to %f" % self.fMXWaitFileTimeOut)
self.edPluginMXWaitFile.setDataInput(xsDataInputMXWaitFile)
self.edPluginMXWaitFile.executeSynchronous()
# hdf5FilePath = strPathToImage.replace(".cbf", ".h5")
ispybDataCollection = None
time.sleep(1)
indexLoop = 1
continueLoop = True
while continueLoop:
xsDataInputControlH5ToCBF = XSDataInputControlH5ToCBF()
xsDataInputControlH5ToCBF.hdf5File = XSDataFile(XSDataString(strPathToImage))
imageNumber = EDUtilsImage.getImageNumber(strPathToImage)
xsDataInputControlH5ToCBF.imageNumber = XSDataInteger(imageNumber)
xsDataInputControlH5ToCBF.hdf5ImageNumber = XSDataInteger(hdf5ImageNumber)
xsDataInputControlH5ToCBF.ispybDataCollection = ispybDataCollection
edPluginControlH5ToCBF = self.loadPlugin(self.strPluginControlH5ToCBF, "ControlH5ToCBF_%04d_%02d" % (imageNumber, indexLoop))
edPluginControlH5ToCBF.dataInput = xsDataInputControlH5ToCBF
edPluginControlH5ToCBF.executeSynchronous()
cbfFile = edPluginControlH5ToCBF.dataOutput.outputCBFFile
# print(cbfFile)
# print(indexLoop)
if cbfFile is not None:
strPathToImage = cbfFile.path.value
# print(cbfFile.path.value)
if os.path.exists(strPathToImage):
self.screen("Image has been converted to CBF file: {0}".format(strPathToImage))
continueLoop = False
# print(continueLoop)
if continueLoop:
self.screen("Still waiting for converting to CBF file: {0}".format(strPathToImage))
indexLoop += 1
time.sleep(5)
if indexLoop > 10:
continueLoop = False
ispybDataCollection = edPluginControlH5ToCBF.dataOutput.ispybDataCollection
elif not os.path.exists(strPathToImage):
self.screen("Waiting for file {0}".format(strPathToImage))
self.edPluginMXWaitFile = self.loadPlugin(self.strPluginMXWaitFileName)
xsDataInputMXWaitFile.file = XSDataFile(XSDataString(strPathToImage))
xsDataInputMXWaitFile.setSize(XSDataInteger(self.minImageSize))
xsDataInputMXWaitFile.setTimeOut(XSDataTime(self.fMXWaitFileTimeOut))
self.DEBUG("Wait file timeOut set to %f" % self.fMXWaitFileTimeOut)
self.edPluginMXWaitFile.setDataInput(xsDataInputMXWaitFile)
self.edPluginMXWaitFile.executeSynchronous()
if not os.path.exists(strPathToImage):
strError = "Time-out while waiting for image %s" % strPathToImage
self.error(strError)
self.addErrorMessage(strError)
self.setFailure()
else:
# Check if we should run distl.signalStrength
xsDataImageNew = XSDataImage(XSDataString(strPathToImage))
edPluginPluginExecImageQualityIndicator = None
if bDoDistlSignalStrength:
if self.bUseThinClient:
strPluginName = self.strPluginNameThinClient
else:
strPluginName = self.strPluginName
edPluginPluginExecImageQualityIndicator = self.loadPlugin(strPluginName)
self.listPluginExecImageQualityIndicator.append(edPluginPluginExecImageQualityIndicator)
xsDataInputDistlSignalStrength = XSDataInputDistlSignalStrength()
xsDataInputDistlSignalStrength.setReferenceImage(xsDataImageNew)
edPluginPluginExecImageQualityIndicator.setDataInput(xsDataInputDistlSignalStrength)
edPluginPluginExecImageQualityIndicator.execute()
listPluginDistl.append((xsDataImageNew.copy(), edPluginPluginExecImageQualityIndicator))
listBatch.append(xsDataImageNew.copy())
if len(listBatch) == batchSize:
edPluginControlDozor = self.loadPlugin(self.strPluginNameControlDozor)
xsDataInputControlDozor = XSDataInputControlDozor()
for image in listBatch:
xsDataInputControlDozor.addImage(XSDataFile(image.path))
xsDataInputControlDozor.batchSize = XSDataInteger(batchSize)
edPluginControlDozor.dataInput = xsDataInputControlDozor
edPluginControlDozor.execute()
listPluginDozor.append((edPluginControlDozor, listBatch))
listBatch = []
if len(listBatch) > 0:
# Process the remaining images...
edPluginControlDozor = self.loadPlugin(self.strPluginNameControlDozor)
xsDataInputControlDozor = XSDataInputControlDozor()
for image in listBatch:
xsDataInputControlDozor.addImage(XSDataFile(image.path))
xsDataInputControlDozor.batchSize = XSDataInteger(batchSize)
edPluginControlDozor.dataInput = xsDataInputControlDozor
edPluginControlDozor.execute()
listPluginDozor.append([edPluginControlDozor, listBatch])
listIndexing = []
# Synchronize all image quality indicator plugins and upload to ISPyB
xsDataInputStoreListOfImageQualityIndicators = XSDataInputStoreListOfImageQualityIndicators()
for (xsDataImage, edPluginPluginExecImageQualityIndicator) in listPluginDistl:
xsDataImageQualityIndicators = XSDataImageQualityIndicators()
xsDataImageQualityIndicators.image = xsDataImage.copy()
if edPluginPluginExecImageQualityIndicator is not None:
edPluginPluginExecImageQualityIndicator.synchronize()
if edPluginPluginExecImageQualityIndicator.dataOutput.imageQualityIndicators is not None:
xsDataImageQualityIndicators = XSDataImageQualityIndicators.parseString(\
edPluginPluginExecImageQualityIndicator.dataOutput.imageQualityIndicators.marshal())
self.xsDataResultControlImageQualityIndicators.addImageQualityIndicators(xsDataImageQualityIndicators)
for (edPluginControlDozor, listBatch) in listPluginDozor:
edPluginControlDozor.synchronize()
for imageDozor in edPluginControlDozor.dataOutput.imageDozor:
for xsDataImageQualityIndicators in self.xsDataResultControlImageQualityIndicators.imageQualityIndicators:
if xsDataImageQualityIndicators.image.path.value == imageDozor.image.path.value:
xsDataImageQualityIndicators.dozor_score = imageDozor.mainScore
xsDataImageQualityIndicators.dozorSpotFile = imageDozor.spotFile
if imageDozor.spotFile is not None:
if os.path.exists(imageDozor.spotFile.path.value):
numpyArray = numpy.loadtxt(imageDozor.spotFile.path.value, skiprows=3)
xsDataImageQualityIndicators.dozorSpotList = XSDataString(base64.b64encode(numpyArray.tostring()))
xsDataImageQualityIndicators.addDozorSpotListShape(XSDataInteger(numpyArray.shape[0]))
if len(numpyArray.shape) > 1:
xsDataImageQualityIndicators.addDozorSpotListShape(XSDataInteger(numpyArray.shape[1]))
xsDataImageQualityIndicators.dozorSpotsIntAver = imageDozor.spotsIntAver
xsDataImageQualityIndicators.dozorSpotsResolution = imageDozor.spotsResolution
if self.xsDataResultControlImageQualityIndicators.inputDozor is None:
if edPluginControlDozor.dataOutput.inputDozor is not None:
self.xsDataResultControlImageQualityIndicators.inputDozor = XSDataDozorInput().parseString(
edPluginControlDozor.dataOutput.inputDozor.marshal())
if self.dataInput.doUploadToIspyb is not None and self.dataInput.doUploadToIspyb.value:
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 dozor_score from all images:
has_dozor_score = True
for imageQualityIndicators in self.xsDataResultControlImageQualityIndicators.imageQualityIndicators:
if imageQualityIndicators.dozor_score is None:
has_dozor_score = False
if has_dozor_score:
listSorted = sorted(self.xsDataResultControlImageQualityIndicators.imageQualityIndicators,
key=lambda imageQualityIndicators: imageQualityIndicators.dozor_score.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
class EDPluginControlImageQualityIndicatorsv1_5(EDPluginControl):
"""
This plugin that control the plugin that generates the image quality indicators.
"""
def __init__(self):
EDPluginControl.__init__(self)
self.strPluginMXWaitFileName = "EDPluginMXWaitFilev1_1"
self.strPluginName = "EDPluginDistlSignalStrengthv1_1"
self.strPluginNameThinClient = "EDPluginDistlSignalStrengthThinClientv1_1"
self.strPluginNameControlDozor = "EDPluginControlDozorv1_0"
self.strISPyBPluginName = "EDPluginISPyBStoreListOfImageQualityIndicatorsv1_5"
self.strIndexingLabelitPluginName = "EDPluginLabelitIndexingv1_1"
self.edPluginLabelitIndexing = None
self.strPluginReadImageHeaderName = "EDPluginControlReadImageHeaderv10"
self.edPluginReadImageHeader = None
self.edPluginControlDozor = None
self.strPluginControlH5ToCBF = "EDPluginControlH5ToCBFv1_1"
self.setXSDataInputClass(XSDataInputControlImageQualityIndicators)
self.listPluginExecImageQualityIndicator = []
self.listPluginControlDozor = []
self.xsDataResultControlImageQualityIndicators = None
self.edPluginMXWaitFile = None
# Default time out for wait file
self.fMXWaitFileTimeOut = 120 # s
# Flag for using the thin client - disabled as of 2016/07/20
self.bUseThinClient = False
self.edPluginISPyB = None
self.listPluginLabelit = []
self.defaultMinImageSize = 1000000
self.minImageSize = None
self.strEDPluginControlReadImageHeaderName = "EDPluginControlReadImageHeaderv10"
self.hasOverlap = False
def checkParameters(self):
"""
Checks the mandatory parameters
"""
self.DEBUG("EDPluginControlImageQualityIndicatorsv1_5.checkParameters")
# self.checkMandatoryParameters(self.getDataInput().getImage(), "Image")
def configure(self, _edPlugin=None):
EDPluginControl.configure(self)
self.DEBUG("EDPluginControlReadImageHeaderv10.configure")
self.fMXWaitFileTimeOut = float(
self.config.get("MXWaitFileTimeOut", self.fMXWaitFileTimeOut))
self.minImageSize = self.config.get("minImageSize")
if self.minImageSize is None:
self.minImageSize = self.defaultMinImageSize
def process(self, _edPlugin=None):
"""
Executes the execution plugins
"""
EDPluginControl.process(self, _edPlugin)
self.DEBUG("EDPluginControlImageQualityIndicatorsv1_5.process")
EDUtilsParallel.initializeNbThread()
# Check batch size
if self.dataInput.batchSize is None:
batchSize = 1
else:
batchSize = self.dataInput.batchSize.value
self.screen(
"Image quality indicators batch size: {0}".format(batchSize))
# Check if we should do distlSignalStrength:
bDoDistlSignalStrength = True
if self.dataInput.doDistlSignalStrength is not None:
if not self.dataInput.doDistlSignalStrength.value:
bDoDistlSignalStrength = False
# Check if we should do indexing:
bDoIndexing = False
if self.dataInput.doIndexing is not None:
if self.dataInput.doIndexing.value:
bDoIndexing = True
# Check if fast mesh (for HDF5)
isFastMesh = False
if self.dataInput.fastMesh:
isFastMesh = self.dataInput.fastMesh.value
# Loop through all the incoming reference images
if len(self.dataInput.image) == 0:
directory = self.dataInput.directory.path.value
template = self.dataInput.template.value
startNo = self.dataInput.startNo.value
endNo = self.dataInput.endNo.value
listXSDataImage = []
for index in range(startNo, endNo + 1):
imageName = template.replace("####", "{0:04d}".format(index))
imagePath = os.path.join(directory, imageName)
xsDataImage = XSDataImage(path=XSDataString(imagePath),
number=XSDataInteger(index))
listXSDataImage.append(xsDataImage)
else:
listXSDataImage = self.dataInput.image
xsDataInputMXWaitFile = XSDataInputMXWaitFile()
self.xsDataResultControlImageQualityIndicators = XSDataResultControlImageQualityIndicators(
)
listPluginDistl = []
listPluginDozor = []
listOfImagesInBatch = []
listOfAllBatches = []
indexBatch = 0
listH5FilePath = []
# Process data in batches
for xsDataImage in listXSDataImage:
listOfImagesInBatch.append(xsDataImage.copy())
if len(listOfImagesInBatch) == batchSize:
listOfAllBatches.append(listOfImagesInBatch)
listOfImagesInBatch = []
if len(listOfImagesInBatch) > 0:
listOfAllBatches.append(listOfImagesInBatch)
listOfImagesInBatch = []
# Loop over batches
for listOfImagesInBatch in listOfAllBatches:
# First wait for images
for image in listOfImagesInBatch:
strPathToImage = image.path.value
# If Eiger, just wait for the h5 file
if strPathToImage.endswith(".h5"):
h5MasterFilePath, h5DataFilePath, hdf5ImageNumber = self.getH5FilePath(
strPathToImage,
batchSize=batchSize,
isFastMesh=isFastMesh)
# print(h5FilePath)
# print(hdf5ImageNumber)
if not h5DataFilePath in listH5FilePath:
self.screen(
"ID30a3 Eiger data, waiting for master and data files..."
)
listH5FilePath.append(h5DataFilePath)
self.edPluginMXWaitFile = self.loadPlugin(
self.strPluginMXWaitFileName)
xsDataInputMXWaitFile.file = XSDataFile(
XSDataString(h5DataFilePath))
xsDataInputMXWaitFile.setSize(
XSDataInteger(self.minImageSize))
xsDataInputMXWaitFile.setTimeOut(
XSDataTime(self.fMXWaitFileTimeOut))
self.screen(
"Waiting for file {0}".format(h5DataFilePath))
self.DEBUG("Wait file timeOut set to %f" %
self.fMXWaitFileTimeOut)
self.edPluginMXWaitFile.setDataInput(
xsDataInputMXWaitFile)
self.edPluginMXWaitFile.executeSynchronous()
# hdf5FilePath = strPathToImage.replace(".cbf", ".h5")
time.sleep(1)
if not os.path.exists(h5DataFilePath):
strError = "Time-out while waiting for image %s" % h5DataFilePath
self.error(strError)
self.addErrorMessage(strError)
self.setFailure()
else:
if not os.path.exists(strPathToImage):
# self.screen("Waiting for file {0}".format(strPathToImage))
self.edPluginMXWaitFile = self.loadPlugin(
self.strPluginMXWaitFileName)
xsDataInputMXWaitFile.file = XSDataFile(
XSDataString(strPathToImage))
xsDataInputMXWaitFile.setSize(
XSDataInteger(self.minImageSize))
xsDataInputMXWaitFile.setTimeOut(
XSDataTime(self.fMXWaitFileTimeOut))
self.screen("Wait file timeOut set to %.0f s" %
self.fMXWaitFileTimeOut)
self.edPluginMXWaitFile.setDataInput(
xsDataInputMXWaitFile)
self.edPluginMXWaitFile.executeSynchronous()
if not os.path.exists(strPathToImage):
strError = "Time-out while waiting for image %s" % strPathToImage
self.error(strError)
self.addErrorMessage(strError)
self.setFailure()
if not self.isFailure():
strPathToFirstImage = listOfImagesInBatch[0].path.value
if strPathToImage.endswith(".h5"):
indexLoop = 1
continueLoop = True
while continueLoop:
directory = os.path.dirname(strPathToFirstImage)
firstImage = EDUtilsImage.getImageNumber(
listOfImagesInBatch[0].path.value)
lastImage = EDUtilsImage.getImageNumber(
listOfImagesInBatch[-1].path.value)
xsDataInputH5ToCBF = XSDataInputH5ToCBF()
xsDataInputH5ToCBF.hdf5File = XSDataFile(
listOfImagesInBatch[0].path)
xsDataInputH5ToCBF.hdf5ImageNumber = XSDataInteger(1)
xsDataInputH5ToCBF.startImageNumber = XSDataInteger(
firstImage)
xsDataInputH5ToCBF.endImageNumber = XSDataInteger(
lastImage)
xsDataInputH5ToCBF.forcedOutputDirectory = XSDataFile(
XSDataString(directory))
edPluginH5ToCBF = self.loadPlugin(
"EDPluginH5ToCBFv1_1")
edPluginH5ToCBF.dataInput = xsDataInputH5ToCBF
edPluginH5ToCBF.execute()
edPluginH5ToCBF.synchronize()
outputCBFFileTemplate = edPluginH5ToCBF.dataOutput.outputCBFFileTemplate
if outputCBFFileTemplate is not None:
lastCbfFile = outputCBFFileTemplate.path.value.replace(
"######", "{0:06d}".format(
EDUtilsImage.getImageNumber(
listOfImagesInBatch[-1].path.value)))
strPathToImage = os.path.join(
directory, lastCbfFile)
# print(cbfFile.path.value)
if os.path.exists(strPathToImage):
# Rename all images
for image in listOfImagesInBatch:
image.path.value = image.path.value.replace(
".h5", ".cbf")
imageNumber = EDUtilsImage.getImageNumber(
image.path.value)
oldPath = os.path.join(
directory,
outputCBFFileTemplate.path.value.
replace("######",
"{0:06d}".format(imageNumber)))
newPath = os.path.join(
directory,
outputCBFFileTemplate.path.value.
replace("######",
"{0:04d}".format(imageNumber)))
os.rename(oldPath, newPath)
lastCbfFile = outputCBFFileTemplate.path.value.replace(
"######", "{0:04d}".format(
EDUtilsImage.getImageNumber(
listOfImagesInBatch[-1].path.value)
))
strPathToImage = os.path.join(
directory, lastCbfFile)
self.screen(
"Image has been converted to CBF file: {0}"
.format(strPathToImage))
continueLoop = False
# print(continueLoop)
if continueLoop:
self.screen(
"Still waiting for converting to CBF file: {0}"
.format(strPathToImage))
indexLoop += 1
time.sleep(5)
if indexLoop > 10:
continueLoop = False
for image in listOfImagesInBatch:
strPathToImage = image.path.value
# Check if we should run distl.signalStrength
xsDataImageNew = XSDataImage(XSDataString(strPathToImage))
xsDataImageNew.number = XSDataInteger(
EDUtilsImage.getImageNumber(image.path.value))
edPluginPluginExecImageQualityIndicator = None
if bDoDistlSignalStrength:
if self.bUseThinClient:
strPluginName = self.strPluginNameThinClient
else:
strPluginName = self.strPluginName
edPluginPluginExecImageQualityIndicator = self.loadPlugin(
strPluginName)
self.listPluginExecImageQualityIndicator.append(
edPluginPluginExecImageQualityIndicator)
xsDataInputDistlSignalStrength = XSDataInputDistlSignalStrength(
)
xsDataInputDistlSignalStrength.setReferenceImage(
xsDataImageNew)
edPluginPluginExecImageQualityIndicator.setDataInput(
xsDataInputDistlSignalStrength)
edPluginPluginExecImageQualityIndicator.execute()
listPluginDistl.append(
(xsDataImageNew.copy(),
edPluginPluginExecImageQualityIndicator))
edPluginControlDozor = self.loadPlugin(
self.strPluginNameControlDozor, "ControlDozor_{0}".format(
os.path.splitext(
os.path.basename(strPathToFirstImage))[0]))
xsDataInputControlDozor = XSDataInputControlDozor()
for image in listOfImagesInBatch:
xsDataInputControlDozor.addImage(XSDataFile(image.path))
xsDataInputControlDozor.batchSize = XSDataInteger(
len(listOfImagesInBatch))
edPluginControlDozor.dataInput = xsDataInputControlDozor
edPluginControlDozor.execute()
listPluginDozor.append(
(edPluginControlDozor, list(listOfImagesInBatch)))
if not self.isFailure():
listIndexing = []
# Synchronize all image quality indicator plugins and upload to ISPyB
xsDataInputStoreListOfImageQualityIndicators = XSDataInputStoreListOfImageQualityIndicators(
)
for (xsDataImage,
edPluginPluginExecImageQualityIndicator) in listPluginDistl:
xsDataImageQualityIndicators = XSDataImageQualityIndicators()
xsDataImageQualityIndicators.image = xsDataImage.copy()
if edPluginPluginExecImageQualityIndicator is not None:
edPluginPluginExecImageQualityIndicator.synchronize()
if edPluginPluginExecImageQualityIndicator.dataOutput is not None:
if edPluginPluginExecImageQualityIndicator.dataOutput.imageQualityIndicators is not None:
xsDataImageQualityIndicators = XSDataImageQualityIndicators.parseString(\
edPluginPluginExecImageQualityIndicator.dataOutput.imageQualityIndicators.marshal())
self.xsDataResultControlImageQualityIndicators.addImageQualityIndicators(
xsDataImageQualityIndicators)
for (edPluginControlDozor, listBatch) in listPluginDozor:
edPluginControlDozor.synchronize()
# Check that we got at least one result
if len(edPluginControlDozor.dataOutput.imageDozor) == 0:
# Run the dozor plugin again, this time synchronously
firstImage = os.path.basename(listBatch[0].path.value)
lastImage = os.path.basename(listBatch[-1].path.value)
self.screen(
"No dozor results! Re-executing Dozor for images {0} to {1}"
.format(firstImage, lastImage))
time.sleep(5)
edPluginControlDozor = self.loadPlugin(
self.strPluginNameControlDozor,
"ControlDozor_reexecution_{0}".format(
os.path.splitext(firstImage)[0]))
xsDataInputControlDozor = XSDataInputControlDozor()
for image in listBatch:
xsDataInputControlDozor.addImage(XSDataFile(
image.path))
xsDataInputControlDozor.batchSize = XSDataInteger(
batchSize)
edPluginControlDozor.dataInput = xsDataInputControlDozor
edPluginControlDozor.executeSynchronous()
for imageDozor in edPluginControlDozor.dataOutput.imageDozor:
for xsDataImageQualityIndicators in self.xsDataResultControlImageQualityIndicators.imageQualityIndicators:
if xsDataImageQualityIndicators.image.path.value == imageDozor.image.path.value:
xsDataImageQualityIndicators.dozor_score = imageDozor.mainScore
xsDataImageQualityIndicators.dozorSpotFile = imageDozor.spotFile
if imageDozor.spotFile is not None:
if os.path.exists(
imageDozor.spotFile.path.value):
numpyArray = numpy.loadtxt(
imageDozor.spotFile.path.value,
skiprows=3)
xsDataImageQualityIndicators.dozorSpotList = XSDataString(
base64.b64encode(
numpyArray.tostring()))
xsDataImageQualityIndicators.addDozorSpotListShape(
XSDataInteger(numpyArray.shape[0]))
if len(numpyArray.shape) > 1:
xsDataImageQualityIndicators.addDozorSpotListShape(
XSDataInteger(numpyArray.shape[1]))
xsDataImageQualityIndicators.dozorSpotsIntAver = imageDozor.spotsIntAver
xsDataImageQualityIndicators.dozorSpotsResolution = imageDozor.spotsResolution
xsDataImageQualityIndicators.dozorVisibleResolution = imageDozor.visibleResolution
if self.xsDataResultControlImageQualityIndicators.inputDozor is None:
if edPluginControlDozor.dataOutput.inputDozor is not None:
self.xsDataResultControlImageQualityIndicators.inputDozor = XSDataDozorInput(
).parseString(
edPluginControlDozor.dataOutput.
inputDozor.marshal())
if self.dataInput.doUploadToIspyb is not None and self.dataInput.doUploadToIspyb.value:
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 dozor_score from all images:
has_dozor_score = True
for imageQualityIndicators in self.xsDataResultControlImageQualityIndicators.imageQualityIndicators:
if imageQualityIndicators.dozor_score is None:
has_dozor_score = False
if has_dozor_score:
listSorted = sorted(
self.xsDataResultControlImageQualityIndicators.
imageQualityIndicators,
key=lambda imageQualityIndicators:
imageQualityIndicators.dozor_score.value)
else:
listSorted = sorted(
self.xsDataResultControlImageQualityIndicators.
imageQualityIndicators,
key=lambda imageQualityIndicators:
imageQualityIndicators.totalIntegratedSignal.value)
for xsDataResultControlImageQualityIndicator in listSorted[
-5:]:
if xsDataResultControlImageQualityIndicator.dozor_score.value > 1:
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:
edPluginLabelitIndexing = self.loadPlugin(
self.strIndexingLabelitPluginName)
xsDataInputLabelitIndexing = XSDataInputLabelitIndexing(
)
xsDataInputLabelitIndexing.image.append(
XSDataImage(
xsDataResultControlImageQualityIndicator.
image.path))
edPluginLabelitIndexing.setDataInput(
xsDataInputLabelitIndexing)
self.listPluginLabelit.append([
edPluginLabelitIndexing,
xsDataResultControlImageQualityIndicator
])
edPluginLabelitIndexing.execute()
for tupleLabelit in self.listPluginLabelit:
edPluginLabelitIndexing = tupleLabelit[0]
xsDataResultControlImageQualityIndicator = tupleLabelit[1]
edPluginLabelitIndexing.synchronize()
if not edPluginLabelitIndexing.isFailure(
) and edPluginLabelitIndexing.dataOutput is not None:
xsDataResultLabelitIndexing = edPluginLabelitIndexing.getDataOutput(
)
xsDataIndexingResult = EDHandlerXSDataPhenixv1_1.generateXSDataIndexingResult(
xsDataResultLabelitIndexing)
selectedSolution = xsDataIndexingResult.selectedSolution
if selectedSolution is not None:
xsDataResultControlImageQualityIndicator.selectedIndexingSolution = selectedSolution
def finallyProcess(self, _edPlugin=None):
EDPluginControl.finallyProcess(self, _edPlugin)
if self.edPluginISPyB is not None:
# Synchronize ISPyB plugin
self.DEBUG(
"EDPluginControlImageQualityIndicatorsv1_5.finallyProcess")
self.edPluginISPyB.synchronize()
listId = []
for xsDataInteger in self.edPluginISPyB.dataOutput.imageQualityIndicatorsId:
listId.append(xsDataInteger.value)
self.DEBUG("ISPyB imageQualityIndicatorIds = %r" % listId)
self.setDataOutput(self.xsDataResultControlImageQualityIndicators)
def generateExecutiveSummary(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlImageQualityIndicatorsv1_5.generateExecutiveSummary"
)
self.addErrorWarningMessagesToExecutiveSummary(
"Image quality indicator plugin execution failure! Error messages: "
)
self.addExecutiveSummaryLine(
"Summary of image quality indicators with %s :" %
self.strPluginName)
for edPluginPluginExecImageQualityIndicator in self.listPluginExecImageQualityIndicator:
self.addExecutiveSummaryLine("")
if edPluginPluginExecImageQualityIndicator is not None:
self.appendExecutiveSummary(
edPluginPluginExecImageQualityIndicator,
"Distl.signal_strength : ",
_bAddSeparator=False)
def getH5FilePath(self, filePath, batchSize=1, isFastMesh=False):
imageNumber = EDUtilsImage.getImageNumber(filePath)
prefix = EDUtilsImage.getPrefix(filePath)
if isFastMesh:
h5ImageNumber = int((imageNumber - 1) / 100) + 1
h5FileNumber = 1
else:
h5ImageNumber = 1
h5FileNumber = int((imageNumber - 1) / batchSize) * batchSize + 1
h5MasterFileName = "{prefix}_{h5FileNumber}_master.h5".format(
prefix=prefix, h5FileNumber=h5FileNumber)
h5MasterFilePath = os.path.join(os.path.dirname(filePath),
h5MasterFileName)
h5DataFileName = "{prefix}_{h5FileNumber}_data_{h5ImageNumber:06d}.h5".format(
prefix=prefix,
h5FileNumber=h5FileNumber,
h5ImageNumber=h5ImageNumber)
h5DataFilePath = os.path.join(os.path.dirname(filePath),
h5DataFileName)
return h5MasterFilePath, h5DataFilePath, h5FileNumber
class EDPluginControlImageQualityIndicatorsv1_1(EDPluginControl):
"""
This plugin that control the plugin that generates the image quality indicators.
"""
def __init__ (self):
EDPluginControl.__init__(self)
self.strPluginExecWaitMultiFileName = "EDPluginWaitMultiFile"
self.strPluginExecImageQualityIndicatorName = "EDPluginDistlSignalStrengthv1_1"
self.setXSDataInputClass(XSDataInputControlImageQualityIndicators)
self.listPluginExecImageQualityIndicator = None
self.xsDataResultControlImageQualityIndicators = None
self.edPluginWaitMultiFile = None
# Default time out for wait file
self.fWaitFileTimeOut = 30 #s
def checkParameters(self):
"""
Checks the mandatory parameters
"""
EDVerbose.DEBUG("EDPluginControlImageQualityIndicatorsv1_1.checkParameters")
self.checkMandatoryParameters(self.getDataInput().getImage(), "Image")
def configure(self, _edPlugin = None):
EDPluginControl.configure(self)
self.DEBUG("EDPluginControlReadImageHeaderv10.configure")
if self.getConfiguration():
xsDataStringParameter = EDConfiguration.getParamItem(self.getConfiguration(), "waitFileTimeOut")
if xsDataStringParameter:
self.fWaitFileTimeOut = float(xsDataStringParameter.getValue())
def preProcess(self, _edPlugin=None):
"""
Prepares the execution plugin
"""
EDPluginControl.preProcess(self, _edPlugin)
EDVerbose.DEBUG("EDPluginControlImageQualityIndicatorsv1_1.preProcess...")
# List containing instances of all the exeuction plugins
self.listPluginExecImageQualityIndicator = []
# Loop through all the incoming reference images
self.edPluginWaitMultiFile = self.loadPlugin(self.strPluginExecWaitMultiFileName)
listXSDataImage = self.getDataInput().getImage()
xsDataInputWaitMultiFile = XSDataInputWaitMultiFile()
for xsDataImage in listXSDataImage:
xsDataInputWaitMultiFile.addExpectedFile(XSDataFile(xsDataImage.getPath()))
xsDataInputWaitMultiFile.setExpectedSize(XSDataInteger(100000))
xsDataInputWaitMultiFile.setTimeOut(XSDataTime(self.fWaitFileTimeOut))
self.DEBUG("Wait file timeOut set to %f" % self.fWaitFileTimeOut)
self.edPluginWaitMultiFile.setDataInput(xsDataInputWaitMultiFile)
self.xsDataResultControlImageQualityIndicators = XSDataResultControlImageQualityIndicators()
def process(self, _edPlugin=None):
"""
Executes the execution plugins
"""
EDPluginControl.process(self, _edPlugin)
EDVerbose.DEBUG("EDPluginControlImageQualityIndicatorsv1_1.process")
self.edPluginWaitMultiFile.connectSUCCESS(self.doSuccessWaitMultiFile)
self.edPluginWaitMultiFile.connectFAILURE(self.doFailureWaitMultiFile)
self.executePluginSynchronous(self.edPluginWaitMultiFile)
def finallyProcess(self, _edPlugin= None):
EDPluginControl.finallyProcess(self, _edPlugin)
EDVerbose.DEBUG("EDPluginControlImageQualityIndicatorsv1_1.finallyProcess")
self.setDataOutput(self.xsDataResultControlImageQualityIndicators)
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 doFailureWaitMultiFile(self, _edPlugin):
"""
The file has not appeared on the disk
"""
self.DEBUG("EDPluginControlImageQualityIndicatorsv1_0.doFailureWaitMultiFile")
self.retrieveFailureMessages(_edPlugin, "EDPluginControlReadImageHeaderv10.doFailureWaitMultiFile")
self.ERROR("Timeout when waiting for images")
self.setFailure()
def doSuccessExecPlugin(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlImageQualityIndicatorsv1_1.doSuccessExecPlugin")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlImageQualityIndicatorsv1_1.doSuccessExecPlugin")
xsDataImageQualityIndicators = _edPlugin.getDataOutput().getImageQualityIndicators()
self.synchronizeOn()
self.xsDataResultControlImageQualityIndicators.addImageQualityIndicators(XSDataImageQualityIndicators.parseString(xsDataImageQualityIndicators.marshal()))
self.synchronizeOff()
def doFailureExecPlugin(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlImageQualityIndicatorsv1_1.doFailureGeneratePrediction")
#self.retrieveFailureMessages(_edPlugin, "EDPluginControlImageQualityIndicatorsv1_1.doFailureExecPlugin")
def generateExecutiveSummary(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlImageQualityIndicatorsv1_1.generateExecutiveSummary")
self.addErrorWarningMessagesToExecutiveSummary("Image quality indicator plugin execution failure! Error messages: ")
self.addExecutiveSummaryLine("Summary of image quality indicators with %s :" % self.strPluginExecImageQualityIndicatorName)
for edPluginPluginExecImageQualityIndicator in self.listPluginExecImageQualityIndicator:
self.addExecutiveSummaryLine("")
if edPluginPluginExecImageQualityIndicator is not None:
self.appendExecutiveSummary(edPluginPluginExecImageQualityIndicator, "Distl.signal_strength : ", _bAddSeparator=False)
def process(self, _edPlugin=None):
"""
Executes the execution plugins
"""
EDPluginControl.process(self, _edPlugin)
self.DEBUG("EDPluginControlImageQualityIndicatorsv1_4.process")
EDUtilsParallel.initializeNbThread()
# Check batch size
if self.dataInput.batchSize is None:
batchSize = 1
else:
batchSize = self.dataInput.batchSize.value
self.screen(
"Image quality indicators batch size: {0}".format(batchSize))
# Check if we should do distlSignalStrength:
bDoDistlSignalStrength = True
if self.dataInput.doDistlSignalStrength is not None:
if not self.dataInput.doDistlSignalStrength.value:
bDoDistlSignalStrength = False
# Check if we should do indexing:
bDoIndexing = False
if self.dataInput.doIndexing is not None:
if self.dataInput.doIndexing.value:
bDoIndexing = True
# Check if fast mesh (for HDF5)
isFastMesh = False
if self.dataInput.fastMesh:
isFastMesh = self.dataInput.fastMesh.value
# Loop through all the incoming reference images
if len(self.dataInput.image) == 0:
directory = self.dataInput.directory.path.value
template = self.dataInput.template.value
startNo = self.dataInput.startNo.value
endNo = self.dataInput.endNo.value
listXSDataImage = []
for index in range(startNo, endNo + 1):
imageName = template.replace("####", "{0:04d}".format(index))
imagePath = os.path.join(directory, imageName)
xsDataImage = XSDataImage(path=XSDataString(imagePath),
number=XSDataInteger(index))
listXSDataImage.append(xsDataImage)
else:
listXSDataImage = self.dataInput.image
xsDataInputMXWaitFile = XSDataInputMXWaitFile()
self.xsDataResultControlImageQualityIndicators = XSDataResultControlImageQualityIndicators(
)
listPluginDistl = []
listPluginDozor = []
listOfImagesInBatch = []
listOfAllBatches = []
indexBatch = 0
listH5FilePath = []
# Process data in batches
for xsDataImage in listXSDataImage:
listOfImagesInBatch.append(xsDataImage.copy())
if len(listOfImagesInBatch) == batchSize:
listOfAllBatches.append(listOfImagesInBatch)
listOfImagesInBatch = []
if len(listOfImagesInBatch) > 0:
listOfAllBatches.append(listOfImagesInBatch)
listOfImagesInBatch = []
# Loop over batches
for listOfImagesInBatch in listOfAllBatches:
# First wait for images
for image in listOfImagesInBatch:
strPathToImage = image.path.value
# If Eiger, just wait for the h5 file
if strPathToImage.endswith(".h5"):
h5MasterFilePath, h5DataFilePath, hdf5ImageNumber = self.getH5FilePath(
strPathToImage,
batchSize=batchSize,
isFastMesh=isFastMesh)
# print(h5FilePath)
# print(hdf5ImageNumber)
if not h5DataFilePath in listH5FilePath:
self.screen(
"ID30a3 Eiger data, waiting for master and data files..."
)
listH5FilePath.append(h5DataFilePath)
self.edPluginMXWaitFile = self.loadPlugin(
self.strPluginMXWaitFileName)
xsDataInputMXWaitFile.file = XSDataFile(
XSDataString(h5DataFilePath))
xsDataInputMXWaitFile.setSize(
XSDataInteger(self.minImageSize))
xsDataInputMXWaitFile.setTimeOut(
XSDataTime(self.fMXWaitFileTimeOut))
self.screen(
"Waiting for file {0}".format(h5DataFilePath))
self.DEBUG("Wait file timeOut set to %f" %
self.fMXWaitFileTimeOut)
self.edPluginMXWaitFile.setDataInput(
xsDataInputMXWaitFile)
self.edPluginMXWaitFile.executeSynchronous()
# hdf5FilePath = strPathToImage.replace(".cbf", ".h5")
time.sleep(1)
if not os.path.exists(h5DataFilePath):
strError = "Time-out while waiting for image %s" % h5DataFilePath
self.error(strError)
self.addErrorMessage(strError)
self.setFailure()
else:
if not os.path.exists(strPathToImage):
# self.screen("Waiting for file {0}".format(strPathToImage))
self.edPluginMXWaitFile = self.loadPlugin(
self.strPluginMXWaitFileName)
xsDataInputMXWaitFile.file = XSDataFile(
XSDataString(strPathToImage))
xsDataInputMXWaitFile.setSize(
XSDataInteger(self.minImageSize))
xsDataInputMXWaitFile.setTimeOut(
XSDataTime(self.fMXWaitFileTimeOut))
self.screen("Wait file timeOut set to %.0f s" %
self.fMXWaitFileTimeOut)
self.edPluginMXWaitFile.setDataInput(
xsDataInputMXWaitFile)
self.edPluginMXWaitFile.executeSynchronous()
if not os.path.exists(strPathToImage):
strError = "Time-out while waiting for image %s" % strPathToImage
self.error(strError)
self.addErrorMessage(strError)
self.setFailure()
if not self.isFailure():
strPathToFirstImage = listOfImagesInBatch[0].path.value
if strPathToImage.endswith(".h5"):
indexLoop = 1
continueLoop = True
while continueLoop:
directory = os.path.dirname(strPathToFirstImage)
firstImage = EDUtilsImage.getImageNumber(
listOfImagesInBatch[0].path.value)
lastImage = EDUtilsImage.getImageNumber(
listOfImagesInBatch[-1].path.value)
xsDataInputH5ToCBF = XSDataInputH5ToCBF()
xsDataInputH5ToCBF.hdf5File = XSDataFile(
listOfImagesInBatch[0].path)
xsDataInputH5ToCBF.hdf5ImageNumber = XSDataInteger(1)
xsDataInputH5ToCBF.startImageNumber = XSDataInteger(
firstImage)
xsDataInputH5ToCBF.endImageNumber = XSDataInteger(
lastImage)
xsDataInputH5ToCBF.forcedOutputDirectory = XSDataFile(
XSDataString(directory))
edPluginH5ToCBF = self.loadPlugin(
"EDPluginH5ToCBFv1_1")
edPluginH5ToCBF.dataInput = xsDataInputH5ToCBF
edPluginH5ToCBF.execute()
edPluginH5ToCBF.synchronize()
outputCBFFileTemplate = edPluginH5ToCBF.dataOutput.outputCBFFileTemplate
if outputCBFFileTemplate is not None:
lastCbfFile = outputCBFFileTemplate.path.value.replace(
"######", "{0:06d}".format(
EDUtilsImage.getImageNumber(
listOfImagesInBatch[-1].path.value)))
strPathToImage = os.path.join(
directory, lastCbfFile)
# print(cbfFile.path.value)
if os.path.exists(strPathToImage):
# Rename all images
for image in listOfImagesInBatch:
image.path.value = image.path.value.replace(
".h5", ".cbf")
imageNumber = EDUtilsImage.getImageNumber(
image.path.value)
oldPath = os.path.join(
directory,
outputCBFFileTemplate.path.value.
replace("######",
"{0:06d}".format(imageNumber)))
newPath = os.path.join(
directory,
outputCBFFileTemplate.path.value.
replace("######",
"{0:04d}".format(imageNumber)))
os.rename(oldPath, newPath)
lastCbfFile = outputCBFFileTemplate.path.value.replace(
"######", "{0:04d}".format(
EDUtilsImage.getImageNumber(
listOfImagesInBatch[-1].path.value)
))
strPathToImage = os.path.join(
directory, lastCbfFile)
self.screen(
"Image has been converted to CBF file: {0}"
.format(strPathToImage))
continueLoop = False
# print(continueLoop)
if continueLoop:
self.screen(
"Still waiting for converting to CBF file: {0}"
.format(strPathToImage))
indexLoop += 1
time.sleep(5)
if indexLoop > 10:
continueLoop = False
for image in listOfImagesInBatch:
strPathToImage = image.path.value
# Check if we should run distl.signalStrength
xsDataImageNew = XSDataImage(XSDataString(strPathToImage))
xsDataImageNew.number = XSDataInteger(
EDUtilsImage.getImageNumber(image.path.value))
edPluginPluginExecImageQualityIndicator = None
if bDoDistlSignalStrength:
if self.bUseThinClient:
strPluginName = self.strPluginNameThinClient
else:
strPluginName = self.strPluginName
edPluginPluginExecImageQualityIndicator = self.loadPlugin(
strPluginName)
self.listPluginExecImageQualityIndicator.append(
edPluginPluginExecImageQualityIndicator)
xsDataInputDistlSignalStrength = XSDataInputDistlSignalStrength(
)
xsDataInputDistlSignalStrength.setReferenceImage(
xsDataImageNew)
edPluginPluginExecImageQualityIndicator.setDataInput(
xsDataInputDistlSignalStrength)
edPluginPluginExecImageQualityIndicator.execute()
listPluginDistl.append(
(xsDataImageNew.copy(),
edPluginPluginExecImageQualityIndicator))
edPluginControlDozor = self.loadPlugin(
self.strPluginNameControlDozor, "ControlDozor_{0}".format(
os.path.splitext(
os.path.basename(strPathToFirstImage))[0]))
xsDataInputControlDozor = XSDataInputControlDozor()
for image in listOfImagesInBatch:
xsDataInputControlDozor.addImage(XSDataFile(image.path))
xsDataInputControlDozor.batchSize = XSDataInteger(
len(listOfImagesInBatch))
edPluginControlDozor.dataInput = xsDataInputControlDozor
edPluginControlDozor.execute()
listPluginDozor.append(
(edPluginControlDozor, list(listOfImagesInBatch)))
if not self.isFailure():
listIndexing = []
# Synchronize all image quality indicator plugins and upload to ISPyB
xsDataInputStoreListOfImageQualityIndicators = XSDataInputStoreListOfImageQualityIndicators(
)
for (xsDataImage,
edPluginPluginExecImageQualityIndicator) in listPluginDistl:
xsDataImageQualityIndicators = XSDataImageQualityIndicators()
xsDataImageQualityIndicators.image = xsDataImage.copy()
if edPluginPluginExecImageQualityIndicator is not None:
edPluginPluginExecImageQualityIndicator.synchronize()
if edPluginPluginExecImageQualityIndicator.dataOutput is not None:
if edPluginPluginExecImageQualityIndicator.dataOutput.imageQualityIndicators is not None:
xsDataImageQualityIndicators = XSDataImageQualityIndicators.parseString(\
edPluginPluginExecImageQualityIndicator.dataOutput.imageQualityIndicators.marshal())
self.xsDataResultControlImageQualityIndicators.addImageQualityIndicators(
xsDataImageQualityIndicators)
for (edPluginControlDozor, listBatch) in listPluginDozor:
edPluginControlDozor.synchronize()
# Check that we got at least one result
if len(edPluginControlDozor.dataOutput.imageDozor) == 0:
# Run the dozor plugin again, this time synchronously
firstImage = os.path.basename(listBatch[0].path.value)
lastImage = os.path.basename(listBatch[-1].path.value)
self.screen(
"No dozor results! Re-executing Dozor for images {0} to {1}"
.format(firstImage, lastImage))
time.sleep(5)
edPluginControlDozor = self.loadPlugin(
self.strPluginNameControlDozor,
"ControlDozor_reexecution_{0}".format(
os.path.splitext(firstImage)[0]))
xsDataInputControlDozor = XSDataInputControlDozor()
for image in listBatch:
xsDataInputControlDozor.addImage(XSDataFile(
image.path))
xsDataInputControlDozor.batchSize = XSDataInteger(
batchSize)
edPluginControlDozor.dataInput = xsDataInputControlDozor
edPluginControlDozor.executeSynchronous()
for imageDozor in edPluginControlDozor.dataOutput.imageDozor:
for xsDataImageQualityIndicators in self.xsDataResultControlImageQualityIndicators.imageQualityIndicators:
if xsDataImageQualityIndicators.image.path.value == imageDozor.image.path.value:
xsDataImageQualityIndicators.dozor_score = imageDozor.mainScore
xsDataImageQualityIndicators.dozorSpotFile = imageDozor.spotFile
if imageDozor.spotFile is not None:
if os.path.exists(
imageDozor.spotFile.path.value):
numpyArray = numpy.loadtxt(
imageDozor.spotFile.path.value,
skiprows=3)
xsDataImageQualityIndicators.dozorSpotList = XSDataString(
base64.b64encode(
numpyArray.tostring()))
xsDataImageQualityIndicators.addDozorSpotListShape(
XSDataInteger(numpyArray.shape[0]))
if len(numpyArray.shape) > 1:
xsDataImageQualityIndicators.addDozorSpotListShape(
XSDataInteger(numpyArray.shape[1]))
xsDataImageQualityIndicators.dozorSpotsIntAver = imageDozor.spotsIntAver
xsDataImageQualityIndicators.dozorSpotsResolution = imageDozor.spotsResolution
xsDataImageQualityIndicators.dozorVisibleResolution = imageDozor.visibleResolution
if self.xsDataResultControlImageQualityIndicators.inputDozor is None:
if edPluginControlDozor.dataOutput.inputDozor is not None:
self.xsDataResultControlImageQualityIndicators.inputDozor = XSDataDozorInput(
).parseString(
edPluginControlDozor.dataOutput.
inputDozor.marshal())
if self.dataInput.doUploadToIspyb is not None and self.dataInput.doUploadToIspyb.value:
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 dozor_score from all images:
has_dozor_score = True
for imageQualityIndicators in self.xsDataResultControlImageQualityIndicators.imageQualityIndicators:
if imageQualityIndicators.dozor_score is None:
has_dozor_score = False
if has_dozor_score:
listSorted = sorted(
self.xsDataResultControlImageQualityIndicators.
imageQualityIndicators,
key=lambda imageQualityIndicators:
imageQualityIndicators.dozor_score.value)
else:
listSorted = sorted(
self.xsDataResultControlImageQualityIndicators.
imageQualityIndicators,
key=lambda imageQualityIndicators:
imageQualityIndicators.totalIntegratedSignal.value)
for xsDataResultControlImageQualityIndicator in listSorted[
-5:]:
if xsDataResultControlImageQualityIndicator.dozor_score.value > 1:
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
class EDPluginControlImageQualityIndicatorsv1_5(EDPluginControl):
"""
This plugin that control the plugin that generates the image quality indicators.
"""
def __init__ (self):
EDPluginControl.__init__(self)
self.strPluginMXWaitFileName = "EDPluginMXWaitFilev1_1"
self.strPluginName = "EDPluginDistlSignalStrengthv1_1"
self.strPluginNameThinClient = "EDPluginDistlSignalStrengthThinClientv1_1"
self.strPluginNameControlDozor = "EDPluginControlDozorv1_0"
self.strISPyBPluginName = "EDPluginISPyBStoreListOfImageQualityIndicatorsv1_5"
self.strIndexingLabelitPluginName = "EDPluginLabelitIndexingv1_1"
self.edPluginLabelitIndexing = None
self.strPluginReadImageHeaderName = "EDPluginControlReadImageHeaderv10"
self.edPluginReadImageHeader = None
self.edPluginControlDozor = None
self.strPluginControlH5ToCBF = "EDPluginControlH5ToCBFv1_1"
self.setXSDataInputClass(XSDataInputControlImageQualityIndicators)
self.listPluginExecImageQualityIndicator = []
self.listPluginControlDozor = []
self.xsDataResultControlImageQualityIndicators = None
self.edPluginMXWaitFile = None
# Default time out for wait file
self.fMXWaitFileTimeOut = 120 # s
# Flag for using the thin client - disabled as of 2016/07/20
self.bUseThinClient = False
self.edPluginISPyB = None
self.listPluginLabelit = []
self.defaultMinImageSize = 1000000
self.minImageSize = None
self.strEDPluginControlReadImageHeaderName = "EDPluginControlReadImageHeaderv10"
self.hasOverlap = False
def checkParameters(self):
"""
Checks the mandatory parameters
"""
self.DEBUG("EDPluginControlImageQualityIndicatorsv1_5.checkParameters")
# self.checkMandatoryParameters(self.getDataInput().getImage(), "Image")
def configure(self, _edPlugin=None):
EDPluginControl.configure(self)
self.DEBUG("EDPluginControlReadImageHeaderv10.configure")
self.fMXWaitFileTimeOut = float(self.config.get("MXWaitFileTimeOut", self.fMXWaitFileTimeOut))
self.minImageSize = self.config.get("minImageSize")
if self.minImageSize is None:
self.minImageSize = self.defaultMinImageSize
def process(self, _edPlugin=None):
"""
Executes the execution plugins
"""
EDPluginControl.process(self, _edPlugin)
self.DEBUG("EDPluginControlImageQualityIndicatorsv1_5.process")
EDUtilsParallel.initializeNbThread()
# Check batch size
if self.dataInput.batchSize is None:
batchSize = 1
else:
batchSize = self.dataInput.batchSize.value
self.screen("Image quality indicators batch size: {0}".format(batchSize))
# Check if we should do distlSignalStrength:
bDoDistlSignalStrength = True
if self.dataInput.doDistlSignalStrength is not None:
if not self.dataInput.doDistlSignalStrength.value:
bDoDistlSignalStrength = False
# Check if we should do indexing:
bDoIndexing = False
if self.dataInput.doIndexing is not None:
if self.dataInput.doIndexing.value:
bDoIndexing = True
# Check if fast mesh (for HDF5)
isFastMesh = False
if self.dataInput.fastMesh:
isFastMesh = self.dataInput.fastMesh.value
# Loop through all the incoming reference images
if len(self.dataInput.image) == 0:
directory = self.dataInput.directory.path.value
template = self.dataInput.template.value
startNo = self.dataInput.startNo.value
endNo = self.dataInput.endNo.value
listXSDataImage = []
for index in range(startNo, endNo + 1):
imageName = template.replace("####", "{0:04d}".format(index))
imagePath = os.path.join(directory, imageName)
xsDataImage = XSDataImage(path=XSDataString(imagePath), number=XSDataInteger(index))
listXSDataImage.append(xsDataImage)
else:
listXSDataImage = self.dataInput.image
xsDataInputMXWaitFile = XSDataInputMXWaitFile()
self.xsDataResultControlImageQualityIndicators = XSDataResultControlImageQualityIndicators()
listPluginDistl = []
listPluginDozor = []
listOfImagesInBatch = []
listOfAllBatches = []
indexBatch = 0
listH5FilePath = []
# Process data in batches
for xsDataImage in listXSDataImage:
listOfImagesInBatch.append(xsDataImage.copy())
if len(listOfImagesInBatch) == batchSize:
listOfAllBatches.append(listOfImagesInBatch)
listOfImagesInBatch = []
if len(listOfImagesInBatch) > 0:
listOfAllBatches.append(listOfImagesInBatch)
listOfImagesInBatch = []
# Loop over batches
for listOfImagesInBatch in listOfAllBatches:
# First wait for images
for image in listOfImagesInBatch:
strPathToImage = image.path.value
# If Eiger, just wait for the h5 file
if strPathToImage.endswith(".h5"):
h5MasterFilePath, h5DataFilePath, hdf5ImageNumber = self.getH5FilePath(strPathToImage,
batchSize=batchSize,
isFastMesh=isFastMesh)
# print(h5FilePath)
# print(hdf5ImageNumber)
if not h5DataFilePath in listH5FilePath:
self.screen("ID30a3 Eiger data, waiting for master and data files...")
listH5FilePath.append(h5DataFilePath)
self.edPluginMXWaitFile = self.loadPlugin(self.strPluginMXWaitFileName)
xsDataInputMXWaitFile.file = XSDataFile(XSDataString(h5DataFilePath))
xsDataInputMXWaitFile.setSize(XSDataInteger(self.minImageSize))
xsDataInputMXWaitFile.setTimeOut(XSDataTime(self.fMXWaitFileTimeOut))
self.screen("Waiting for file {0}".format(h5DataFilePath))
self.DEBUG("Wait file timeOut set to %f" % self.fMXWaitFileTimeOut)
self.edPluginMXWaitFile.setDataInput(xsDataInputMXWaitFile)
self.edPluginMXWaitFile.executeSynchronous()
# hdf5FilePath = strPathToImage.replace(".cbf", ".h5")
time.sleep(1)
if not os.path.exists(h5DataFilePath):
strError = "Time-out while waiting for image %s" % h5DataFilePath
self.error(strError)
self.addErrorMessage(strError)
self.setFailure()
else:
if not os.path.exists(strPathToImage):
# self.screen("Waiting for file {0}".format(strPathToImage))
self.edPluginMXWaitFile = self.loadPlugin(self.strPluginMXWaitFileName)
xsDataInputMXWaitFile.file = XSDataFile(XSDataString(strPathToImage))
xsDataInputMXWaitFile.setSize(XSDataInteger(self.minImageSize))
xsDataInputMXWaitFile.setTimeOut(XSDataTime(self.fMXWaitFileTimeOut))
self.screen("Wait file timeOut set to %.0f s" % self.fMXWaitFileTimeOut)
self.edPluginMXWaitFile.setDataInput(xsDataInputMXWaitFile)
self.edPluginMXWaitFile.executeSynchronous()
if not os.path.exists(strPathToImage):
strError = "Time-out while waiting for image %s" % strPathToImage
self.error(strError)
self.addErrorMessage(strError)
self.setFailure()
if not self.isFailure():
strPathToFirstImage = listOfImagesInBatch[0].path.value
if strPathToImage.endswith(".h5"):
indexLoop = 1
continueLoop = True
while continueLoop:
directory = os.path.dirname(strPathToFirstImage)
firstImage = EDUtilsImage.getImageNumber(listOfImagesInBatch[0].path.value)
lastImage = EDUtilsImage.getImageNumber(listOfImagesInBatch[-1].path.value)
xsDataInputH5ToCBF = XSDataInputH5ToCBF()
xsDataInputH5ToCBF.hdf5File = XSDataFile(listOfImagesInBatch[0].path)
xsDataInputH5ToCBF.hdf5ImageNumber = XSDataInteger(1)
xsDataInputH5ToCBF.startImageNumber = XSDataInteger(firstImage)
xsDataInputH5ToCBF.endImageNumber = XSDataInteger(lastImage)
xsDataInputH5ToCBF.forcedOutputDirectory = XSDataFile(XSDataString(directory))
edPluginH5ToCBF = self.loadPlugin("EDPluginH5ToCBFv1_1")
edPluginH5ToCBF.dataInput = xsDataInputH5ToCBF
edPluginH5ToCBF.execute()
edPluginH5ToCBF.synchronize()
outputCBFFileTemplate = edPluginH5ToCBF.dataOutput.outputCBFFileTemplate
if outputCBFFileTemplate is not None:
lastCbfFile = outputCBFFileTemplate.path.value.replace("######", "{0:06d}".format(EDUtilsImage.getImageNumber(listOfImagesInBatch[-1].path.value)))
strPathToImage = os.path.join(directory, lastCbfFile)
# print(cbfFile.path.value)
if os.path.exists(strPathToImage):
# Rename all images
for image in listOfImagesInBatch:
image.path.value = image.path.value.replace(".h5", ".cbf")
imageNumber = EDUtilsImage.getImageNumber(image.path.value)
oldPath = os.path.join(directory, outputCBFFileTemplate.path.value.replace("######", "{0:06d}".format(imageNumber)))
newPath = os.path.join(directory, outputCBFFileTemplate.path.value.replace("######", "{0:04d}".format(imageNumber)))
os.rename(oldPath, newPath)
lastCbfFile = outputCBFFileTemplate.path.value.replace("######", "{0:04d}".format(EDUtilsImage.getImageNumber(listOfImagesInBatch[-1].path.value)))
strPathToImage = os.path.join(directory, lastCbfFile)
self.screen("Image has been converted to CBF file: {0}".format(strPathToImage))
continueLoop = False
# print(continueLoop)
if continueLoop:
self.screen("Still waiting for converting to CBF file: {0}".format(strPathToImage))
indexLoop += 1
time.sleep(5)
if indexLoop > 10:
continueLoop = False
for image in listOfImagesInBatch:
strPathToImage = image.path.value
# Check if we should run distl.signalStrength
xsDataImageNew = XSDataImage(XSDataString(strPathToImage))
xsDataImageNew.number = XSDataInteger(EDUtilsImage.getImageNumber(image.path.value))
edPluginPluginExecImageQualityIndicator = None
if bDoDistlSignalStrength:
if self.bUseThinClient:
strPluginName = self.strPluginNameThinClient
else:
strPluginName = self.strPluginName
edPluginPluginExecImageQualityIndicator = self.loadPlugin(strPluginName)
self.listPluginExecImageQualityIndicator.append(edPluginPluginExecImageQualityIndicator)
xsDataInputDistlSignalStrength = XSDataInputDistlSignalStrength()
xsDataInputDistlSignalStrength.setReferenceImage(xsDataImageNew)
edPluginPluginExecImageQualityIndicator.setDataInput(xsDataInputDistlSignalStrength)
edPluginPluginExecImageQualityIndicator.execute()
listPluginDistl.append((xsDataImageNew.copy(), edPluginPluginExecImageQualityIndicator))
edPluginControlDozor = self.loadPlugin(self.strPluginNameControlDozor,
"ControlDozor_{0}".format(os.path.splitext(os.path.basename(strPathToFirstImage))[0]))
xsDataInputControlDozor = XSDataInputControlDozor()
for image in listOfImagesInBatch:
xsDataInputControlDozor.addImage(XSDataFile(image.path))
xsDataInputControlDozor.batchSize = XSDataInteger(len(listOfImagesInBatch))
edPluginControlDozor.dataInput = xsDataInputControlDozor
edPluginControlDozor.execute()
listPluginDozor.append((edPluginControlDozor, list(listOfImagesInBatch)))
if not self.isFailure():
listIndexing = []
# Synchronize all image quality indicator plugins and upload to ISPyB
xsDataInputStoreListOfImageQualityIndicators = XSDataInputStoreListOfImageQualityIndicators()
for (xsDataImage, edPluginPluginExecImageQualityIndicator) in listPluginDistl:
xsDataImageQualityIndicators = XSDataImageQualityIndicators()
xsDataImageQualityIndicators.image = xsDataImage.copy()
if edPluginPluginExecImageQualityIndicator is not None:
edPluginPluginExecImageQualityIndicator.synchronize()
if edPluginPluginExecImageQualityIndicator.dataOutput is not None:
if edPluginPluginExecImageQualityIndicator.dataOutput.imageQualityIndicators is not None:
xsDataImageQualityIndicators = XSDataImageQualityIndicators.parseString(\
edPluginPluginExecImageQualityIndicator.dataOutput.imageQualityIndicators.marshal())
self.xsDataResultControlImageQualityIndicators.addImageQualityIndicators(xsDataImageQualityIndicators)
for (edPluginControlDozor, listBatch) in listPluginDozor:
edPluginControlDozor.synchronize()
# Check that we got at least one result
if len(edPluginControlDozor.dataOutput.imageDozor) == 0:
# Run the dozor plugin again, this time synchronously
firstImage = os.path.basename(listBatch[0].path.value)
lastImage = os.path.basename(listBatch[-1].path.value)
self.screen("No dozor results! Re-executing Dozor for images {0} to {1}".format(firstImage, lastImage))
time.sleep(5)
edPluginControlDozor = self.loadPlugin(self.strPluginNameControlDozor, "ControlDozor_reexecution_{0}".format(os.path.splitext(firstImage)[0]))
xsDataInputControlDozor = XSDataInputControlDozor()
for image in listBatch:
xsDataInputControlDozor.addImage(XSDataFile(image.path))
xsDataInputControlDozor.batchSize = XSDataInteger(batchSize)
edPluginControlDozor.dataInput = xsDataInputControlDozor
edPluginControlDozor.executeSynchronous()
for imageDozor in edPluginControlDozor.dataOutput.imageDozor:
for xsDataImageQualityIndicators in self.xsDataResultControlImageQualityIndicators.imageQualityIndicators:
if xsDataImageQualityIndicators.image.path.value == imageDozor.image.path.value:
xsDataImageQualityIndicators.dozor_score = imageDozor.mainScore
xsDataImageQualityIndicators.dozorSpotFile = imageDozor.spotFile
if imageDozor.spotFile is not None:
if os.path.exists(imageDozor.spotFile.path.value):
numpyArray = numpy.loadtxt(imageDozor.spotFile.path.value, skiprows=3)
xsDataImageQualityIndicators.dozorSpotList = XSDataString(base64.b64encode(numpyArray.tostring()))
xsDataImageQualityIndicators.addDozorSpotListShape(XSDataInteger(numpyArray.shape[0]))
if len(numpyArray.shape) > 1:
xsDataImageQualityIndicators.addDozorSpotListShape(XSDataInteger(numpyArray.shape[1]))
xsDataImageQualityIndicators.dozorSpotsIntAver = imageDozor.spotsIntAver
xsDataImageQualityIndicators.dozorSpotsResolution = imageDozor.spotsResolution
xsDataImageQualityIndicators.dozorVisibleResolution = imageDozor.visibleResolution
if self.xsDataResultControlImageQualityIndicators.inputDozor is None:
if edPluginControlDozor.dataOutput.inputDozor is not None:
self.xsDataResultControlImageQualityIndicators.inputDozor = XSDataDozorInput().parseString(
edPluginControlDozor.dataOutput.inputDozor.marshal())
if self.dataInput.doUploadToIspyb is not None and self.dataInput.doUploadToIspyb.value:
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 dozor_score from all images:
has_dozor_score = True
for imageQualityIndicators in self.xsDataResultControlImageQualityIndicators.imageQualityIndicators:
if imageQualityIndicators.dozor_score is None:
has_dozor_score = False
if has_dozor_score:
listSorted = sorted(self.xsDataResultControlImageQualityIndicators.imageQualityIndicators,
key=lambda imageQualityIndicators: imageQualityIndicators.dozor_score.value)
else:
listSorted = sorted(self.xsDataResultControlImageQualityIndicators.imageQualityIndicators,
key=lambda imageQualityIndicators: imageQualityIndicators.totalIntegratedSignal.value)
for xsDataResultControlImageQualityIndicator in listSorted[-5:]:
if xsDataResultControlImageQualityIndicator.dozor_score.value > 1:
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:
edPluginLabelitIndexing = self.loadPlugin(self.strIndexingLabelitPluginName)
xsDataInputLabelitIndexing = XSDataInputLabelitIndexing()
xsDataInputLabelitIndexing.image.append(XSDataImage(xsDataResultControlImageQualityIndicator.image.path))
edPluginLabelitIndexing.setDataInput(xsDataInputLabelitIndexing)
self.listPluginLabelit.append([edPluginLabelitIndexing, xsDataResultControlImageQualityIndicator])
edPluginLabelitIndexing.execute()
for tupleLabelit in self.listPluginLabelit:
edPluginLabelitIndexing = tupleLabelit[0]
xsDataResultControlImageQualityIndicator = tupleLabelit[1]
edPluginLabelitIndexing.synchronize()
if not edPluginLabelitIndexing.isFailure() and edPluginLabelitIndexing.dataOutput is not None:
xsDataResultLabelitIndexing = edPluginLabelitIndexing.getDataOutput()
xsDataIndexingResult = EDHandlerXSDataPhenixv1_1.generateXSDataIndexingResult(xsDataResultLabelitIndexing)
selectedSolution = xsDataIndexingResult.selectedSolution
if selectedSolution is not None:
xsDataResultControlImageQualityIndicator.selectedIndexingSolution = selectedSolution
def finallyProcess(self, _edPlugin=None):
EDPluginControl.finallyProcess(self, _edPlugin)
if self.edPluginISPyB is not None:
# Synchronize ISPyB plugin
self.DEBUG("EDPluginControlImageQualityIndicatorsv1_5.finallyProcess")
self.edPluginISPyB.synchronize()
listId = []
for xsDataInteger in self.edPluginISPyB.dataOutput.imageQualityIndicatorsId:
listId.append(xsDataInteger.value)
self.DEBUG("ISPyB imageQualityIndicatorIds = %r" % listId)
self.setDataOutput(self.xsDataResultControlImageQualityIndicators)
def generateExecutiveSummary(self, _edPlugin=None):
self.DEBUG("EDPluginControlImageQualityIndicatorsv1_5.generateExecutiveSummary")
self.addErrorWarningMessagesToExecutiveSummary("Image quality indicator plugin execution failure! Error messages: ")
self.addExecutiveSummaryLine("Summary of image quality indicators with %s :" % self.strPluginName)
for edPluginPluginExecImageQualityIndicator in self.listPluginExecImageQualityIndicator:
self.addExecutiveSummaryLine("")
if edPluginPluginExecImageQualityIndicator is not None:
self.appendExecutiveSummary(edPluginPluginExecImageQualityIndicator, "Distl.signal_strength : ", _bAddSeparator=False)
def getH5FilePath(self, filePath, batchSize=1, isFastMesh=False):
imageNumber = EDUtilsImage.getImageNumber(filePath)
prefix = EDUtilsImage.getPrefix(filePath)
if isFastMesh:
h5ImageNumber = int((imageNumber - 1) / 100) + 1
h5FileNumber = 1
else:
h5ImageNumber = 1
h5FileNumber = int((imageNumber - 1) / batchSize) * batchSize + 1
h5MasterFileName = "{prefix}_{h5FileNumber}_master.h5".format(prefix=prefix,
h5FileNumber=h5FileNumber)
h5MasterFilePath = os.path.join(os.path.dirname(filePath), h5MasterFileName)
h5DataFileName = "{prefix}_{h5FileNumber}_data_{h5ImageNumber:06d}.h5".format(prefix=prefix,
h5FileNumber=h5FileNumber,
h5ImageNumber=h5ImageNumber)
h5DataFilePath = os.path.join(os.path.dirname(filePath), h5DataFileName)
return h5MasterFilePath, h5DataFilePath, h5FileNumber
def process(self, _edPlugin=None):
"""
Executes the execution plugins
"""
EDPluginControl.process(self, _edPlugin)
self.DEBUG("EDPluginControlImageQualityIndicatorsv1_4.process")
EDUtilsParallel.initializeNbThread()
# Check batch size
if self.dataInput.batchSize is None:
batchSize = 1
else:
batchSize = self.dataInput.batchSize.value
self.screen("Image quality indicators batch size: {0}".format(batchSize))
# Check if we should do distlSignalStrength:
bDoDistlSignalStrength = True
if self.dataInput.doDistlSignalStrength is not None:
if not self.dataInput.doDistlSignalStrength.value:
bDoDistlSignalStrength = False
# Check if we should do indexing:
bDoIndexing = False
if self.dataInput.doIndexing is not None:
if self.dataInput.doIndexing.value:
bDoIndexing = True
# Check if fast mesh (for HDF5)
isFastMesh = False
if self.dataInput.fastMesh:
isFastMesh = self.dataInput.fastMesh.value
# Loop through all the incoming reference images
if len(self.dataInput.image) == 0:
directory = self.dataInput.directory.path.value
template = self.dataInput.template.value
startNo = self.dataInput.startNo.value
endNo = self.dataInput.endNo.value
listXSDataImage = []
for index in range(startNo, endNo + 1):
imageName = template.replace("####", "{0:04d}".format(index))
imagePath = os.path.join(directory, imageName)
xsDataImage = XSDataImage(path=XSDataString(imagePath), number=XSDataInteger(index))
listXSDataImage.append(xsDataImage)
else:
listXSDataImage = self.dataInput.image
xsDataInputMXWaitFile = XSDataInputMXWaitFile()
self.xsDataResultControlImageQualityIndicators = XSDataResultControlImageQualityIndicators()
listPluginDistl = []
listPluginDozor = []
listOfImagesInBatch = []
listOfAllBatches = []
indexBatch = 0
listH5FilePath = []
# Process data in batches
for xsDataImage in listXSDataImage:
listOfImagesInBatch.append(xsDataImage.copy())
if len(listOfImagesInBatch) == batchSize:
listOfAllBatches.append(listOfImagesInBatch)
listOfImagesInBatch = []
if len(listOfImagesInBatch) > 0:
listOfAllBatches.append(listOfImagesInBatch)
listOfImagesInBatch = []
# Loop over batches
for listOfImagesInBatch in listOfAllBatches:
# First wait for images
for image in listOfImagesInBatch:
strPathToImage = image.path.value
# If Eiger, just wait for the h5 file
if strPathToImage.endswith(".h5"):
h5MasterFilePath, h5DataFilePath, hdf5ImageNumber = self.getH5FilePath(strPathToImage,
batchSize=batchSize,
isFastMesh=isFastMesh)
# print(h5FilePath)
# print(hdf5ImageNumber)
if not h5DataFilePath in listH5FilePath:
self.screen("ID30a3 Eiger data, waiting for master and data files...")
listH5FilePath.append(h5DataFilePath)
self.edPluginMXWaitFile = self.loadPlugin(self.strPluginMXWaitFileName)
xsDataInputMXWaitFile.file = XSDataFile(XSDataString(h5DataFilePath))
xsDataInputMXWaitFile.setSize(XSDataInteger(self.minImageSize))
xsDataInputMXWaitFile.setTimeOut(XSDataTime(self.fMXWaitFileTimeOut))
self.screen("Waiting for file {0}".format(h5DataFilePath))
self.DEBUG("Wait file timeOut set to %f" % self.fMXWaitFileTimeOut)
self.edPluginMXWaitFile.setDataInput(xsDataInputMXWaitFile)
self.edPluginMXWaitFile.executeSynchronous()
# hdf5FilePath = strPathToImage.replace(".cbf", ".h5")
time.sleep(1)
if not os.path.exists(h5DataFilePath):
strError = "Time-out while waiting for image %s" % h5DataFilePath
self.error(strError)
self.addErrorMessage(strError)
self.setFailure()
else:
if not os.path.exists(strPathToImage):
# self.screen("Waiting for file {0}".format(strPathToImage))
self.edPluginMXWaitFile = self.loadPlugin(self.strPluginMXWaitFileName)
xsDataInputMXWaitFile.file = XSDataFile(XSDataString(strPathToImage))
xsDataInputMXWaitFile.setSize(XSDataInteger(self.minImageSize))
xsDataInputMXWaitFile.setTimeOut(XSDataTime(self.fMXWaitFileTimeOut))
self.screen("Wait file timeOut set to %.0f s" % self.fMXWaitFileTimeOut)
self.edPluginMXWaitFile.setDataInput(xsDataInputMXWaitFile)
self.edPluginMXWaitFile.executeSynchronous()
if not os.path.exists(strPathToImage):
strError = "Time-out while waiting for image %s" % strPathToImage
self.error(strError)
self.addErrorMessage(strError)
self.setFailure()
if not self.isFailure():
strPathToFirstImage = listOfImagesInBatch[0].path.value
if strPathToImage.endswith(".h5"):
indexLoop = 1
continueLoop = True
while continueLoop:
directory = os.path.dirname(strPathToFirstImage)
firstImage = EDUtilsImage.getImageNumber(listOfImagesInBatch[0].path.value)
lastImage = EDUtilsImage.getImageNumber(listOfImagesInBatch[-1].path.value)
xsDataInputH5ToCBF = XSDataInputH5ToCBF()
xsDataInputH5ToCBF.hdf5File = XSDataFile(listOfImagesInBatch[0].path)
xsDataInputH5ToCBF.hdf5ImageNumber = XSDataInteger(1)
xsDataInputH5ToCBF.startImageNumber = XSDataInteger(firstImage)
xsDataInputH5ToCBF.endImageNumber = XSDataInteger(lastImage)
xsDataInputH5ToCBF.forcedOutputDirectory = XSDataFile(XSDataString(directory))
edPluginH5ToCBF = self.loadPlugin("EDPluginH5ToCBFv1_1")
edPluginH5ToCBF.dataInput = xsDataInputH5ToCBF
edPluginH5ToCBF.execute()
edPluginH5ToCBF.synchronize()
outputCBFFileTemplate = edPluginH5ToCBF.dataOutput.outputCBFFileTemplate
if outputCBFFileTemplate is not None:
lastCbfFile = outputCBFFileTemplate.path.value.replace("######", "{0:06d}".format(EDUtilsImage.getImageNumber(listOfImagesInBatch[-1].path.value)))
strPathToImage = os.path.join(directory, lastCbfFile)
# print(cbfFile.path.value)
if os.path.exists(strPathToImage):
# Rename all images
for image in listOfImagesInBatch:
image.path.value = image.path.value.replace(".h5", ".cbf")
imageNumber = EDUtilsImage.getImageNumber(image.path.value)
oldPath = os.path.join(directory, outputCBFFileTemplate.path.value.replace("######", "{0:06d}".format(imageNumber)))
newPath = os.path.join(directory, outputCBFFileTemplate.path.value.replace("######", "{0:04d}".format(imageNumber)))
os.rename(oldPath, newPath)
lastCbfFile = outputCBFFileTemplate.path.value.replace("######", "{0:04d}".format(EDUtilsImage.getImageNumber(listOfImagesInBatch[-1].path.value)))
strPathToImage = os.path.join(directory, lastCbfFile)
self.screen("Image has been converted to CBF file: {0}".format(strPathToImage))
continueLoop = False
# print(continueLoop)
if continueLoop:
self.screen("Still waiting for converting to CBF file: {0}".format(strPathToImage))
indexLoop += 1
time.sleep(5)
if indexLoop > 10:
continueLoop = False
for image in listOfImagesInBatch:
strPathToImage = image.path.value
# Check if we should run distl.signalStrength
xsDataImageNew = XSDataImage(XSDataString(strPathToImage))
xsDataImageNew.number = XSDataInteger(EDUtilsImage.getImageNumber(image.path.value))
edPluginPluginExecImageQualityIndicator = None
if bDoDistlSignalStrength:
if self.bUseThinClient:
strPluginName = self.strPluginNameThinClient
else:
strPluginName = self.strPluginName
edPluginPluginExecImageQualityIndicator = self.loadPlugin(strPluginName)
self.listPluginExecImageQualityIndicator.append(edPluginPluginExecImageQualityIndicator)
xsDataInputDistlSignalStrength = XSDataInputDistlSignalStrength()
xsDataInputDistlSignalStrength.setReferenceImage(xsDataImageNew)
edPluginPluginExecImageQualityIndicator.setDataInput(xsDataInputDistlSignalStrength)
edPluginPluginExecImageQualityIndicator.execute()
listPluginDistl.append((xsDataImageNew.copy(), edPluginPluginExecImageQualityIndicator))
edPluginControlDozor = self.loadPlugin(self.strPluginNameControlDozor,
"ControlDozor_{0}".format(os.path.splitext(os.path.basename(strPathToFirstImage))[0]))
xsDataInputControlDozor = XSDataInputControlDozor()
for image in listOfImagesInBatch:
xsDataInputControlDozor.addImage(XSDataFile(image.path))
xsDataInputControlDozor.batchSize = XSDataInteger(len(listOfImagesInBatch))
edPluginControlDozor.dataInput = xsDataInputControlDozor
edPluginControlDozor.execute()
listPluginDozor.append((edPluginControlDozor, list(listOfImagesInBatch)))
if not self.isFailure():
listIndexing = []
# Synchronize all image quality indicator plugins and upload to ISPyB
xsDataInputStoreListOfImageQualityIndicators = XSDataInputStoreListOfImageQualityIndicators()
for (xsDataImage, edPluginPluginExecImageQualityIndicator) in listPluginDistl:
xsDataImageQualityIndicators = XSDataImageQualityIndicators()
xsDataImageQualityIndicators.image = xsDataImage.copy()
if edPluginPluginExecImageQualityIndicator is not None:
edPluginPluginExecImageQualityIndicator.synchronize()
if edPluginPluginExecImageQualityIndicator.dataOutput is not None:
if edPluginPluginExecImageQualityIndicator.dataOutput.imageQualityIndicators is not None:
xsDataImageQualityIndicators = XSDataImageQualityIndicators.parseString(\
edPluginPluginExecImageQualityIndicator.dataOutput.imageQualityIndicators.marshal())
self.xsDataResultControlImageQualityIndicators.addImageQualityIndicators(xsDataImageQualityIndicators)
for (edPluginControlDozor, listBatch) in listPluginDozor:
edPluginControlDozor.synchronize()
# Check that we got at least one result
if len(edPluginControlDozor.dataOutput.imageDozor) == 0:
# Run the dozor plugin again, this time synchronously
firstImage = os.path.basename(listBatch[0].path.value)
lastImage = os.path.basename(listBatch[-1].path.value)
self.screen("No dozor results! Re-executing Dozor for images {0} to {1}".format(firstImage, lastImage))
time.sleep(5)
edPluginControlDozor = self.loadPlugin(self.strPluginNameControlDozor, "ControlDozor_reexecution_{0}".format(os.path.splitext(firstImage)[0]))
xsDataInputControlDozor = XSDataInputControlDozor()
for image in listBatch:
xsDataInputControlDozor.addImage(XSDataFile(image.path))
xsDataInputControlDozor.batchSize = XSDataInteger(batchSize)
edPluginControlDozor.dataInput = xsDataInputControlDozor
edPluginControlDozor.executeSynchronous()
for imageDozor in edPluginControlDozor.dataOutput.imageDozor:
for xsDataImageQualityIndicators in self.xsDataResultControlImageQualityIndicators.imageQualityIndicators:
if xsDataImageQualityIndicators.image.path.value == imageDozor.image.path.value:
xsDataImageQualityIndicators.dozor_score = imageDozor.mainScore
xsDataImageQualityIndicators.dozorSpotFile = imageDozor.spotFile
if imageDozor.spotFile is not None:
if os.path.exists(imageDozor.spotFile.path.value):
numpyArray = numpy.loadtxt(imageDozor.spotFile.path.value, skiprows=3)
xsDataImageQualityIndicators.dozorSpotList = XSDataString(base64.b64encode(numpyArray.tostring()))
xsDataImageQualityIndicators.addDozorSpotListShape(XSDataInteger(numpyArray.shape[0]))
if len(numpyArray.shape) > 1:
xsDataImageQualityIndicators.addDozorSpotListShape(XSDataInteger(numpyArray.shape[1]))
xsDataImageQualityIndicators.dozorSpotsIntAver = imageDozor.spotsIntAver
xsDataImageQualityIndicators.dozorSpotsResolution = imageDozor.spotsResolution
xsDataImageQualityIndicators.dozorVisibleResolution = imageDozor.visibleResolution
if self.xsDataResultControlImageQualityIndicators.inputDozor is None:
if edPluginControlDozor.dataOutput.inputDozor is not None:
self.xsDataResultControlImageQualityIndicators.inputDozor = XSDataDozorInput().parseString(
edPluginControlDozor.dataOutput.inputDozor.marshal())
if self.dataInput.doUploadToIspyb is not None and self.dataInput.doUploadToIspyb.value:
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 dozor_score from all images:
has_dozor_score = True
for imageQualityIndicators in self.xsDataResultControlImageQualityIndicators.imageQualityIndicators:
if imageQualityIndicators.dozor_score is None:
has_dozor_score = False
if has_dozor_score:
listSorted = sorted(self.xsDataResultControlImageQualityIndicators.imageQualityIndicators,
key=lambda imageQualityIndicators: imageQualityIndicators.dozor_score.value)
else:
listSorted = sorted(self.xsDataResultControlImageQualityIndicators.imageQualityIndicators,
key=lambda imageQualityIndicators: imageQualityIndicators.totalIntegratedSignal.value)
for xsDataResultControlImageQualityIndicator in listSorted[-5:]:
if xsDataResultControlImageQualityIndicator.dozor_score.value > 1:
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
