def doSuccessExecMetadata(self, _edPlugin=None):
self.DEBUG("EDPluginBioSaxsNormalizev1_0.doSuccessExecMetadata")
self.retrieveSuccessMessages(_edPlugin, "EDPluginBioSaxsNormalizev1_0.doSuccessExecMetadata")
if os.path.isfile(self.strNormalizedImage):
xsNormFile = XSDataImage()
xsNormFile.setPath(XSDataString(self.strNormalizedImage))
self.xsdResult.setNormalizedImage(xsNormFile)
def buildChildren(self, child_, nodeName_): if child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'image': obj_ = XSDataImage() obj_.build(child_) self.image.append(obj_) XSDataInput.buildChildren(self, child_, nodeName_)
def doSuccessExecMetadata(self, _edPlugin=None):
self.DEBUG("EDPluginBioSaxsNormalizev1_0.doSuccessExecMetadata")
self.retrieveSuccessMessages(_edPlugin, "EDPluginBioSaxsNormalizev1_0.doSuccessExecMetadata")
if os.path.isfile(self.strNormalizedImage):
xsNormFile = XSDataImage()
xsNormFile.setPath(XSDataString(self.strNormalizedImage))
self.xsdResult.setNormalizedImage(xsNormFile)
def testCheckParameters(self):
xsDataInput = XSDataInputBioSaxsHPLCv1_0()
xsDataInput.rawImage = XSDataImage()
xsDataInput.sample = XSDataBioSaxsSample()
xsDataInput.experimentSetup = XSDataBioSaxsExperimentSetup()
xsDataInput.logFile = XSDataFile()
xsDataInput.normalizedImage = XSDataImage()
xsDataInput.rawImageSize = XSDataInteger()
edPluginExecBioSaxsNormalize = self.createPlugin()
edPluginExecBioSaxsNormalize.setDataInput(xsDataInput)
edPluginExecBioSaxsNormalize.checkParameters()
def postProcess(self, _edObject=None):
EDPluginControl.postProcess(self)
self.DEBUG("EDPluginBioSaxsNormalizev1_1.postProcess")
if os.path.isfile(self.strNormalizedImage):
xsNormFile = XSDataImage()
xsNormFile.setPath(XSDataString(self.strNormalizedImage))
self.xsdResult.setNormalizedImage(xsNormFile)
self.xsdResult.status = XSDataStatus(executiveSummary=XSDataString(os.linesep.join(self.lstProcessLog)))
# Create some output data
self.setDataOutput(self.xsdResult)
def createDataMOSFLMOutputGeneratePrediction(self):
EDVerbose.DEBUG("EDPluginMOSFLMGeneratePredictionv10.createDataMOSFLMOutputIntegration")
xsDataMOSFLMInputGeneratePrediction = self.getDataInput()
xsDataMOSFLMImage = xsDataMOSFLMInputGeneratePrediction.getImage()
iImageNumber = xsDataMOSFLMImage.getNumber().getValue()
xsDataMOSFLMOutputGeneratePrediction = XSDataMOSFLMOutputGeneratePrediction()
xsDataImage = XSDataImage()
xsDataImage.setNumber(XSDataInteger(iImageNumber))
xsDataImage.setPath(XSDataString(os.path.join(self.getWorkingDirectory(), self.getPredictionImageFileName())))
xsDataMOSFLMOutputGeneratePrediction.setPredictionImage(xsDataImage)
return xsDataMOSFLMOutputGeneratePrediction
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
EDVerbose.DEBUG("EDPluginExecSaxsMacv1_0.postProcess")
# Create some output data
xsDataResult = XSDataResultSaxsMacv1_0()
if self.outputImage is None:
self.outputImage = "output.edf"
if os.path.isfile(self.outputImage):
xsdFile = XSDataImage()
xsdFile.setPath(XSDataString(os.path.abspath(self.outputImage)))
xsDataResult.setOutputImage(xsdFile)
self.setDataOutput(xsDataResult)
def makeXML(self, filename):
"""Here we create the XML string to be passed to the EDNA plugin from the input filename
This can / should be modified by the final user
@param filename: full path of the input file
@type filename: python string representing the path
@rtype: XML string
@return: python string
"""
bProcessFile = False
basename = os.path.basename(filename)
for oneExt in self.listExtensions:
if basename.endswith(oneExt):
bProcessFile = True
break
if bProcessFile:
for onePref in self.listExcludedPrefix:
if basename.startswith(onePref):
bProcessFile = False
if not bProcessFile:
EDVerbose.screen("Not processing file: %s" % filename)
return
xsdimage = XSDataImage()
xsdimage.setPath(XSDataString(filename))
xsd = XSDataInputDiffractionCT()
xsd.setImage(xsdimage)
xsd.setDestinationDirectory(self.destinationDirectory)
xsd.setSinogramFileNamePrefix(self.sinogramFileNamePrefix)
xsd.setPowderDiffractionSubdirectory(self.powderDiffractionSubdirectory)
xsd.setPowderDiffractionFormat(self.powderDiffractionFormat)
if self.indexOffset is not None and self.fastMotorSteps is not None:
idx = 0
basename = list(os.path.splitext(os.path.basename(filename))[0])
basename.reverse()
number = ""
for i in basename:
if i.isdigit():
number = i + number
else: break
idx = int(number) - self.indexOffset
if idx < 0:return
self.forceInstrument.set_tomo_spec_displ_x(XSDataLength(idx % (self.fastMotorSteps + 1)))
self.forceInstrument.set_tomo_spec_displ_rotation(XSDataLength(idx // (self.fastMotorSteps + 1)))
xsd.setOverrideScanParam(self.forceInstrument)
xsd.setOverrideImageParam(self.forceImage)
return xsd.marshal()
def doSucessGetMetadata(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginBioSaxsAveragev1_0.doSuccessGetMetadata")
# self.strProcessLog += "Averaging EDF images to '%s'\n" % (self.averagedImage)
self.xsdMetadata = _edPlugin.getDataOutput()
xsdSaxsMac = XSDataInputSaxsMacv1_0()
prefix = os.path.commonprefix(self.integratedImages)
listFilesReversed = []
for oneFile in self.integratedImages:
revLst = list(oneFile)
revLst.reverse()
listFilesReversed.append("".join(revLst))
revLst = list(os.path.commonprefix(listFilesReversed))
revLst.reverse()
suffix = "".join(revLst)
lenSuffix = len(suffix)
lenPrefix = len(prefix)
maxdif = 0
maxInt = 0
miniInt = sys.maxint
for oneFile in self.integratedImages:
lenOneFile = len(oneFile)
if lenOneFile - lenSuffix - lenPrefix > maxdif:
maxdif = lenOneFile - lenSuffix - lenPrefix
try:
val = int(oneFile[lenPrefix:-lenSuffix])
except Exception:
val = None
pass
if val is not None:
if val < miniInt:
miniInt = val
if val > maxInt:
maxInt = val
strImages = prefix + """%""" * maxdif + suffix + ",%i,%i" % (miniInt, maxInt)
self.strProcessLog += "Averaging images '%s' to %s\n" % (strImages, self.averagedImage)
EDVerbose.DEBUG("Averaging '%s'\n" % (strImages))
xsdImage = XSDataImage()
xsdImage.setPath(XSDataString(strImages))
xsdiSaxsMac = XSDataInputSaxsMacv1_0()
xsdiSaxsMac.setInputImage(xsdImage)
xsdiSaxsMac.setOutputImage(self.dataInput.getAveragedImage())
xsdiSaxsMac.setOptions(XSDataString("+pass -omod n +var -add %d" % len(self.integratedImages)))
xsdiSaxsMac.setMultConst(XSDataDouble(1.0 / len(self.integratedImages)))
self.__edPluginSaxsMac.setDataInput(xsdiSaxsMac)
self.__edPluginSaxsMac.connectSUCCESS(self.doSuccessSaxsMac)
self.__edPluginSaxsMac.connectFAILURE(self.doFailureSaxsMac)
self.__edPluginSaxsMac.executeSynchronous()
def doSuccessReadImageHeader(self, _edPlugin=None):
self.DEBUG("EDPluginControlGridScreeningv1_0.doSuccessReadImageHeader")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlGridScreeningv1_0.doSuccessReadImageHeader")
xsDataResultReadImageHeader = self.edPluginControlReadImageHeader.getDataOutput()
if xsDataResultReadImageHeader is not None:
xsDataSubWedge = xsDataResultReadImageHeader.getSubWedge()
self.xsDataCollection = XSDataCollection()
self.xsDataCollection.addSubWedge(xsDataSubWedge)
self.xsDataCollection.setDiffractionPlan(self.xsDataDiffractionPlan)
if not self.bDoOnlyIntegrationWithXMLOutput:
xsDataInputControlImageQualityIndicators = XSDataInputControlImageQualityIndicators()
if self.bStoreImageQualityIndicatorsInISPyB:
xsDataInputControlImageQualityIndicators.doUploadToIspyb = XSDataBoolean(True)
else:
xsDataInputControlImageQualityIndicators.doUploadToIspyb = XSDataBoolean(False)
xsDataInputControlImageQualityIndicators.addImage(XSDataImage(path=XSDataString(self.strImageFile)))
self.edPluginControlIndicators.setDataInput(xsDataInputControlImageQualityIndicators)
self.edPluginControlIndicators.connectSUCCESS(self.doSuccessIndicators)
self.edPluginControlIndicators.connectFAILURE(self.doFailureIndicators)
self.executePluginSynchronous(self.edPluginControlIndicators)
else:
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.setDataCollection(self.xsDataCollection)
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
xsDataMOSFLMIndexingInput = EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputIndexing(xsDataIndexingInput)
self.edPluginMOSFLMIndexing.connectSUCCESS(self.doSuccessIndexingMOSFLM)
self.edPluginMOSFLMIndexing.connectFAILURE(self.doFailureIndexingMOSFLM)
self.edPluginMOSFLMIndexing.setDataInput(xsDataMOSFLMIndexingInput)
self.edPluginMOSFLMIndexing.executeSynchronous()
def doSuccessGeneratePrediction(self, _edPlugin=None):
self.DEBUG("EDPluginControlGeneratePredictionv10.doSuccessGeneratePrediction")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlGeneratePredictionv10.doSuccessGeneratePrediction")
if (self.__xsDataGeneratePredictionResult is None):
self.__xsDataGeneratePredictionResult = XSDataGeneratePredictionResult()
xsDataMOSFLMOutputGeneratePrediction = _edPlugin.getDataOutput()
xsDataImage = xsDataMOSFLMOutputGeneratePrediction.getPredictionImage()
self.__xsDataGeneratePredictionResult.addPredictionImage(XSDataImage.parseString(xsDataImage.marshal()))
def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
self.DEBUG("EDPluginControlGeneratePredictionv10.preProcess...")
xsDataGeneratePredictionInput = self.getDataInput()
xsDataSelectedIndexingSolution = xsDataGeneratePredictionInput.getSelectedIndexingSolution()
xsDataExperimentalConditionRefined = xsDataSelectedIndexingSolution.getExperimentalConditionRefined()
xsDataCollection = xsDataGeneratePredictionInput.getDataCollection()
xsDataSubWedgeList = xsDataCollection.getSubWedge()
# List containing instances of all the generate prediction plugins
self.__listPluginGeneratePrediction = []
# Loop through all subwedges
iIndex = 0
for xsDataSubWedge in xsDataSubWedgeList:
xsDataImageList = xsDataSubWedge.getImage()
# First find the lowest image number
iLowestImageNumber = None
for xsDataImage in xsDataImageList:
iImageNumber = xsDataImage.getNumber().getValue()
if (iLowestImageNumber is None):
iLowestImageNumber = iImageNumber
elif (iImageNumber < iLowestImageNumber):
iLowestImageNumber = iImageNumber
# Then loop through all images in a sub wedge
for xsDataImage in xsDataImageList:
iIndex += 1
edPluginGeneratePrediction = self.loadPlugin(self.__strPluginGeneratePredictionName,
"%s-%02d" % (self.__strPluginGeneratePredictionName, iIndex))
xsDataGeneratePredictionInput = XSDataGeneratePredictionInput()
xsDataGeneratePredictionInput.setSelectedIndexingSolution(XSDataIndexingSolutionSelected.parseString(xsDataSelectedIndexingSolution.marshal()))
xsDataCollectionNew = XSDataCollection()
xsDataSubWedgeNew = XSDataSubWedge()
xsDataSubWedgeNew.addImage(XSDataImage.parseString(xsDataImage.marshal()))
xsDataSubWedgeNew.setExperimentalCondition(XSDataExperimentalCondition.parseString(xsDataSubWedge.getExperimentalCondition().marshal()))
# We must modify the rotationOscillationStart for the new subwedge
xsDataGoniostatNew = xsDataSubWedgeNew.getExperimentalCondition().getGoniostat()
fGoniostatRotationAxisStart = xsDataGoniostatNew.getRotationAxisStart().getValue()
fGonioStatOscillationRange = xsDataGoniostatNew.getOscillationWidth().getValue()
iImageNumber = xsDataImage.getNumber().getValue()
fGoniostatRotationAxisStartNew = fGoniostatRotationAxisStart + (iImageNumber - iLowestImageNumber) * fGonioStatOscillationRange
xsDataGoniostatNew.setRotationAxisStart(XSDataAngle(fGoniostatRotationAxisStartNew))
#
xsDataCollectionNew.addSubWedge(xsDataSubWedgeNew)
xsDataGeneratePredictionInput.setDataCollection(xsDataCollectionNew)
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
xsDataMOSFLMInputGeneratePrediction = EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputGeneratePrediction(xsDataGeneratePredictionInput)
edPluginGeneratePrediction.setDataInput(xsDataMOSFLMInputGeneratePrediction)
self.__listPluginGeneratePrediction.append(edPluginGeneratePrediction)
def generateListXSDataImageReference(_xsDataIndexingInput):
listXSDataImageReference = []
xsDataCollection = _xsDataIndexingInput.getDataCollection()
xsDataSubWedgeList = xsDataCollection.getSubWedge()
xsDataImageFirst = xsDataSubWedgeList[0].getImage()[0]
listXSDataImageReference.append(XSDataImage.parseString(xsDataImageFirst.marshal()))
fPhiStartFirst = xsDataSubWedgeList[0].getExperimentalCondition().getGoniostat().getRotationAxisStart().getValue()
if (len(xsDataSubWedgeList) > 1):
xsDataImageSecond = xsDataSubWedgeList[-1].getImage()[0]
fPhiStartSecond = xsDataSubWedgeList[-1].getExperimentalCondition().getGoniostat().getRotationAxisStart().getValue()
# Add modulus!
if (abs(fPhiStartSecond - fPhiStartFirst) > 4):
listXSDataImageReference.append(XSDataImage.parseString(xsDataImageSecond.marshal()))
return listXSDataImageReference
def fileName2xml(filename):
"""Here we create the XML string to be passed to the EDNA plugin from the input filename
This can / should be modified by the final user
@param filename: full path of the input file
@type filename: python string representing the path
@rtype: XML string
@return: python string
"""
if not filename.endswith(".edf"):
return
basename = os.path.basename(filename)
upperDir = os.path.dirname(os.path.dirname(filename))
if not os.path.isdir(os.path.join(upperDir, "MedianFiltered")):
os.makedirs(os.path.join(upperDir, "MedianFiltered"), int("775", 8))
destinationPath = os.path.join(upperDir, "MedianFiltered", basename)
xsd = XSDataInputMedianFilterImage()
xsd.setFilterWidth(XSDataInteger(FilterWidth))
xsd.setInputImage(XSDataImage(XSDataString(filename)))
xsd.setMedianFilteredImage(XSDataImage(XSDataString(destinationPath)))
return xsd.marshal()
def testCheckParameters(self):
xsDataInput = XSDataInputBioSaxsProcessOneFilev1_0()
xsDataInput.rawImage = XSDataImage()
xsDataInput.sample = XSDataBioSaxsSample()
xsDataInput.experimentSetup = XSDataBioSaxsExperimentSetup()
xsDataInput.logFile = XSDataFile()
xsDataInput.normalizedImage = XSDataImage()
xsDataInput.rawImageSize = XSDataInteger()
# xsDataInput.beamStopDiode = XSDataDouble()
# xsDataInput.normalizationFactor = XSDataDouble()
# xsDataInput.machineCurrent = XSDataDouble()
# xsDataInput.maskFile = XSDataImage()
# xsDataInput.detectorDistance = XSDataLength()
# xsDataInput.wavelength = XSDataWavelength()
# xsDataInput.pixelSize_1 = XSDataLength()
# xsDataInput.pixelSize_2 = XSDataLength()
# xsDataInput.beamCenter_1 = XSDataDouble()
# xsDataInput.beamCenter_2 = XSDataDouble()
edPluginExecBioSaxsNormalize = self.createPlugin()
edPluginExecBioSaxsNormalize.setDataInput(xsDataInput)
edPluginExecBioSaxsNormalize.checkParameters()
def generateImageList(self, _xsDataCollection):
"""
Make a list of all images in the subwedges
"""
self.verboseDebug("EDPluginControlIndexingIndicatorsv1_1.generateImageList")
listImage = None
if (_xsDataCollection is not None):
listImage = []
xsDataSubWedgeList = _xsDataCollection.getSubWedge()
for xsDataSubWedge in xsDataSubWedgeList:
xsDataImageList = xsDataSubWedge.getImage()
for xsDataImage in xsDataImageList:
listImage.append(XSDataImage.parseString(xsDataImage.marshal()))
return listImage
def testParseLabelitDistlOutput(self):
"""
This method test the parsing of the Labelit results in the log file.
"""
edPluginLabelitDistlv1_1 = self.createPlugin()
strPathToLabelitLogText = os.path.join(self.getPluginTestsDataHome(), "labelit.distl_v116.log")
strLabelitLogText = self.readAndParseFile(strPathToLabelitLogText)
xsDataImageQualityIndicators = edPluginLabelitDistlv1_1.parseLabelitDistlOutput(strLabelitLogText)
xmlInput1 = self.readAndParseFile(self.__strReferenceInputFile1)
xsDataImage1 = XSDataImage.parseString(xmlInput1)
xsDataImageQualityIndicators.setImage(xsDataImage1)
strLabelitDistlOutputFile = os.path.join(self.getPluginTestsDataHome(), "XSDataImageQualityIndicators_reference.xml")
strLabelitDistlOutputXML = self.readAndParseFile(strLabelitDistlOutputFile)
from XSDataLabelitv1_1 import XSDataImageQualityIndicators
xsDataImageQualityIndicatorsReference = XSDataImageQualityIndicators.parseString(strLabelitDistlOutputXML)
EDAssert.equal(xsDataImageQualityIndicatorsReference.marshal(), xsDataImageQualityIndicators.marshal())
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlH5ToCBFv1_0.process")
imageNumber = self.dataInput.imageNumber.value
if self.dataInput.hdf5ImageNumber is None:
hdf5ImageNumber = imageNumber
else:
hdf5ImageNumber = self.dataInput.hdf5ImageNumber.value
if self.dataInput.ispybDataCollection is None:
xsDataInputRetrieveDataCollection = XSDataInputRetrieveDataCollection(
)
xsDataImage = XSDataImage(self.dataInput.hdf5File.path)
xsDataInputRetrieveDataCollection.image = xsDataImage
self.edPluginISPyBRetrieveDataCollection.dataInput = xsDataInputRetrieveDataCollection
self.edPluginISPyBRetrieveDataCollection.executeSynchronous()
xsDataResultRetrieveDataCollection = self.edPluginISPyBRetrieveDataCollection.dataOutput
dataCollection = xsDataResultRetrieveDataCollection.dataCollection
else:
dataCollection = self.dataInput.ispybDataCollection
if dataCollection is not None:
if dataCollection.overlap is None:
overlap = 0.0
else:
overlap = dataCollection.overlap
axisStart = dataCollection.axisStart
oscillationRange = dataCollection.axisRange
axisStartNew = axisStart - (overlap +
oscillationRange) * (imageNumber - 1)
dataCollection.axisStart = axisStartNew
xsDataISPyBDataCollection = XSDataISPyBDataCollection.parseString(
dataCollection.marshal())
else:
xsDataISPyBDataCollection = None
xsDataInputH5ToCBF = XSDataInputH5ToCBF()
xsDataInputH5ToCBF.hdf5File = self.dataInput.hdf5File
xsDataInputH5ToCBF.imageNumber = self.dataInput.imageNumber
xsDataInputH5ToCBF.hdf5ImageNumber = XSDataInteger(hdf5ImageNumber)
xsDataInputH5ToCBF.dataCollection = xsDataISPyBDataCollection
xsDataInputH5ToCBF.forcedOutputDirectory = self.dataInput.forcedOutputDirectory
self.edPluginEDPluginH5ToCBF.dataInput = xsDataInputH5ToCBF
self.edPluginEDPluginH5ToCBF.executeSynchronous()
if self.edPluginEDPluginH5ToCBF.dataOutput is not None:
self.dataOutput.outputCBFFile = self.edPluginEDPluginH5ToCBF.dataOutput.outputCBFFile
if dataCollection is not None:
self.dataOutput.ispybDataCollection = XSDataISPyBDataCollection.parseString(
dataCollection.marshal())
def postProcess(self, _edObject=None):
EDPluginControl.postProcess(self)
EDVerbose.DEBUG("EDPluginBioSaxsMetadatav1_0.postProcess")
# Create some output data
xsDataResult = XSDataResultBioSaxsMetadatav1_0()
if self.strOutputImage is not None:
xsdImage = XSDataImage()
xsdImage.setPath(XSDataString(self.strOutputImage))
xsDataResult.setOutputImage(xsdImage)
if self.detector is not None:
# EDVerbose.DEBUG("Detector=%s" % self.detector)
xsDataResult.setDetector(XSDataString(self.detector))
if self.detectorDistance is not None:
# EDVerbose.DEBUG("DetectorDistance %s(%s)" % (self.detectorDistance, self.detectorDistance.__class__))
xsDataResult.setDetectorDistance(XSDataLength(self.detectorDistance))
if self.pixelSize_1 is not None:
# EDVerbose.DEBUG("pixelSize_1 %s(%s)" % (self.pixelSize_1, self.pixelSize_1.__class__))
xsDataResult.setPixelSize_1(XSDataLength(self.pixelSize_1))
if self.pixelSize_2 is not None:
# EDVerbose.DEBUG("pixelSize_2 %s(%s)" % (self.pixelSize_2, self.pixelSize_2.__class__))
xsDataResult.setPixelSize_2(XSDataLength(self.pixelSize_2))
if self.beamCenter_1 is not None:
# EDVerbose.DEBUG("beamCenter_1 %s(%s)" % (self.beamCenter_1, self.beamCenter_1.__class__))
xsDataResult.setBeamCenter_1(XSDataDouble(self.beamCenter_1))
if self.beamCenter_2 is not None:
# EDVerbose.DEBUG("beamCenter_2 %s(%s)" % (self.beamCenter_2, self.beamCenter_2.__class__))
xsDataResult.setBeamCenter_2(XSDataDouble(self.beamCenter_2))
if self.beamStopDiode is not None:
# EDVerbose.DEBUG("beamStopDiode %s(%s)" % (self.beamStopDiode, self.beamStopDiode.__class__))
xsDataResult.setBeamStopDiode(XSDataDouble(self.beamStopDiode))
if self.wavelength is not None:
xsDataResult.setWavelength(XSDataWavelength(self.wavelength))
if self.maskFile is not None:
xsdFile = XSDataImage()
xsdFile.setPath(XSDataString(self.maskFile))
xsDataResult.setMaskFile(xsdFile)
if self.normalizationFactor is not None:
xsDataResult.setNormalizationFactor(XSDataDouble(self.normalizationFactor))
if self.machineCurrent is not None:
xsDataResult.setMachineCurrent(XSDataDouble(self.machineCurrent))
if self.code is not None:
xsDataResult.setCode(XSDataString(self.code))
if self.comments is not None:
xsDataResult.setComments(XSDataString(self.comments))
if self.concentration is not None:
xsDataResult.setConcentration(XSDataDouble(self.concentration))
EDVerbose.DEBUG("xsDataResult=%s" % xsDataResult.marshal())
self.setDataOutput(xsDataResult)
def testParseLabelitDistlOutput(self):
"""
This method test the parsing of the Labelit results in the log file.
"""
edPluginLabelitDistlv1_1 = self.createPlugin()
strPathToLabelitLogText = os.path.join(self.getPluginTestsDataHome(),
"labelit.distl_v116.log")
strLabelitLogText = self.readAndParseFile(strPathToLabelitLogText)
xsDataImageQualityIndicators = edPluginLabelitDistlv1_1.parseLabelitDistlOutput(
strLabelitLogText)
xmlInput1 = self.readAndParseFile(self.__strReferenceInputFile1)
xsDataImage1 = XSDataImage.parseString(xmlInput1)
xsDataImageQualityIndicators.setImage(xsDataImage1)
strLabelitDistlOutputFile = os.path.join(
self.getPluginTestsDataHome(),
"XSDataImageQualityIndicators_reference.xml")
strLabelitDistlOutputXML = self.readAndParseFile(
strLabelitDistlOutputFile)
from XSDataLabelitv1_1 import XSDataImageQualityIndicators
xsDataImageQualityIndicatorsReference = XSDataImageQualityIndicators.parseString(
strLabelitDistlOutputXML)
EDAssert.equal(xsDataImageQualityIndicatorsReference.marshal(),
xsDataImageQualityIndicators.marshal())
def process(self, _edObject=None):
EDPluginExec.process(self)
EDVerbose.DEBUG("*** EDPluginExecReadImageHeaderADSCv10.process")
xsDataInputReadImageHeader = self.getDataInput()
xsDataFile = xsDataInputReadImageHeader.getImage()
strPath = xsDataFile.getPath().getValue()
strAbsolutePath = os.path.abspath(strPath)
dictHeader = self.readHeaderADSC(strPath)
if (dictHeader is None):
strErrorMessage = "EDPluginExecReadImageHeaderADSCv10.process : error when reading header from %s" % strAbsolutePath
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
else:
xsDataExperimentalCondition = XSDataExperimentalCondition()
xsDataDetector = XSDataDetector()
xsDataDetector.setBeamPositionX(XSDataLength(float(dictHeader[ "BEAM_CENTER_X" ])))
xsDataDetector.setBeamPositionY(XSDataLength(float(dictHeader[ "BEAM_CENTER_Y" ])))
xsDataDetector.setDistance(XSDataLength(float(dictHeader[ "DISTANCE" ])))
fPixelSize = float(dictHeader[ "PIXEL_SIZE" ])
xsDataDetector.setPixelSizeX(XSDataLength(fPixelSize))
xsDataDetector.setPixelSizeY(XSDataLength(fPixelSize))
if "TWOTHETA" in dictHeader.keys():
xsDataDetector.setTwoTheta(XSDataAngle(float(dictHeader[ "TWOTHETA" ])))
xsDataDetector.setNumberBytesInHeader(XSDataInteger(float(dictHeader[ "HEADER_BYTES" ])))
xsDataDetector.setSerialNumber(XSDataString(dictHeader[ "DETECTOR_SN" ]))
xsDataDetector.setNumberPixelX(XSDataInteger(int(dictHeader[ "SIZE1" ])))
xsDataDetector.setNumberPixelY(XSDataInteger(int(dictHeader[ "SIZE2" ])))
xsDataDetector.setBin(XSDataString(dictHeader[ "BIN" ]))
xsDataDetector.setDataType(XSDataString(dictHeader[ "TYPE" ]))
xsDataDetector.setByteOrder(XSDataString(dictHeader[ "BYTE_ORDER" ]))
if "CCD_IMAGE_SATURATION" in dictHeader.keys():
xsDataDetector.setImageSaturation(XSDataInteger(int(dictHeader[ "CCD_IMAGE_SATURATION" ])))
# Determine type of detector...
iNoPixelsX = xsDataDetector.getNumberPixelX().getValue()
iNoPixelsY = xsDataDetector.getNumberPixelY().getValue()
if (iNoPixelsX == 2304 and iNoPixelsY == 2304):
xsDataDetector.setName(XSDataString("ADSC Q4"))
xsDataDetector.setType(XSDataString("q4"))
elif (iNoPixelsX == 1152 and iNoPixelsY == 1152):
xsDataDetector.setName(XSDataString("ADSC Q4 bin 2x2"))
xsDataDetector.setType(XSDataString("q4-2x"))
elif (iNoPixelsX == 4096 and iNoPixelsY == 4096):
xsDataDetector.setName(XSDataString("ADSC Q210"))
xsDataDetector.setType(XSDataString("q210"))
elif (iNoPixelsX == 2048 and iNoPixelsY == 2048):
xsDataDetector.setName(XSDataString("ADSC Q210 bin 2x2"))
xsDataDetector.setType(XSDataString("q210-2x"))
elif (iNoPixelsX == 6144 and iNoPixelsY == 6144):
xsDataDetector.setName(XSDataString("ADSC Q315"))
xsDataDetector.setType(XSDataString("q315"))
elif (iNoPixelsX == 3072 and iNoPixelsY == 3072):
xsDataDetector.setName(XSDataString("ADSC Q315 bin 2x2"))
xsDataDetector.setType(XSDataString("q315-2x"))
else:
strErrorMessage = EDMessage.ERROR_DATA_HANDLER_02 % ("EDPluginExecReadImageHeaderADSCv10.process", "Unknown detector type")
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
xsDataExperimentalCondition.setDetector(xsDataDetector)
# Beam object
xsDataBeam = XSDataBeam()
xsDataBeam.setWavelength(XSDataWavelength(float(dictHeader[ "WAVELENGTH" ])))
xsDataBeam.setExposureTime(XSDataTime(float(dictHeader[ "TIME" ])))
xsDataExperimentalCondition.setBeam(xsDataBeam)
# Goniostat object
xsDataGoniostat = XSDataGoniostat()
fRotationAxisStart = float(dictHeader[ "OSC_START" ])
fOscillationWidth = float(dictHeader[ "OSC_RANGE" ])
xsDataGoniostat.setRotationAxisStart(XSDataAngle(fRotationAxisStart))
xsDataGoniostat.setRotationAxisEnd(XSDataAngle(fRotationAxisStart + fOscillationWidth))
xsDataGoniostat.setOscillationWidth(XSDataAngle(fOscillationWidth))
strRotationAxis = None
if ("AXIS" in dictHeader.keys()):
strRotationAxis = dictHeader[ "AXIS" ]
elif ("OSC_AXIS" in dictHeader.keys()):
strRotationAxis = dictHeader[ "OSC_AXIS" ]
else:
strErrorMessage = "EDPluginExecReadImageHeaderADSCv10.process : Neither AXIS nor OSC_AXIS header item found."
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
xsDataGoniostat.setRotationAxis(XSDataString(strRotationAxis))
xsDataExperimentalCondition.setGoniostat(xsDataGoniostat)
# Create the image object
xsDataImage = XSDataImage()
xsDataImage.setPath(XSDataString(strAbsolutePath))
xsDataImage.setDate(XSDataString(dictHeader[ "DATE" ]))
strFileName = os.path.basename(strPath)
iImageNumber = EDUtilsImage.getImageNumber(strFileName)
xsDataImage.setNumber(XSDataInteger(iImageNumber))
xsDataSubWedge = XSDataSubWedge()
xsDataSubWedge.setExperimentalCondition(xsDataExperimentalCondition)
xsDataSubWedge.addImage(xsDataImage)
self.__xsDataResultReadImageHeader = XSDataResultReadImageHeader()
self.__xsDataResultReadImageHeader.setSubWedge(xsDataSubWedge)
def postProcess(self, _edObject=None):
"""
complex type XSDataBioSaxsExperimentSetup extends XSData{
detector : XSDataString optional
detectorDistance : XSDataLength optional
pixelSize_1 : XSDataLength optional
pixelSize_2 : XSDataLength optional
beamCenter_1 : XSDataDouble optional
beamCenter_2 : XSDataDouble optional
beamStopDiode : XSDataDouble optional
wavelength : XSDataWavelength optional
machineCurrent : XSDataDouble optional
maskFile : XSDataImage optional
normalizationFactor : XSDataDouble optional
storageTemperature: XSDataDouble optional
exposureTemperature: XSDataDouble optional
exposureTime: XSDataTime optional
frameNumber: XSDataInteger optional
frameMax: XSDataInteger optional
}
complex type XSDataBioSaxsSample extends XSData {
concentration : XSDataDouble optional
comments : XSDataString optional
code : XSDataString optional
temperature: XSDataDouble optional
"""
EDPluginExec.postProcess(self)
EDVerbose.DEBUG("EDPluginBioSaxsMetadatav1_1.postProcess")
# Create some output data
xsDataResult = XSDataResultBioSaxsMetadatav1_0()
xsdSample = XSDataBioSaxsSample()
xsdExperiment = XSDataBioSaxsExperimentSetup()
if self.strOutputImage is not None:
xsdImage = XSDataImage()
xsdImage.setPath(XSDataString(self.strOutputImage))
xsDataResult.setOutputImage(xsdImage)
if self.detector is not None:
xsdExperiment.detector = xsDataResult.detector = XSDataString(self.detector)
if self.detectorDistance is not None:
xsdExperiment.detectorDistance = xsDataResult.detectorDistance = XSDataLength(self.detectorDistance)
if self.pixelSize_1 is not None:
xsDataResult.pixelSize_1 = XSDataLength(self.pixelSize_1)
xsdExperiment.pixelSize_1 = xsDataResult.pixelSize_1
if self.pixelSize_2 is not None:
xsDataResult.pixelSize_2 = XSDataLength(self.pixelSize_2)
xsdExperiment.pixelSize_2 = xsDataResult.pixelSize_2
if self.beamCenter_1 is not None:
xsDataResult.beamCenter_1 = XSDataDouble(self.beamCenter_1)
xsdExperiment.beamCenter_1 = xsDataResult.beamCenter_1
if self.beamCenter_2 is not None:
xsDataResult.beamCenter_2 = XSDataDouble(self.beamCenter_2)
xsdExperiment.beamCenter_2 = xsDataResult.beamCenter_2
if self.beamStopDiode is not None:
xsdExperiment.beamStopDiode = xsDataResult.beamStopDiode = XSDataDouble(self.beamStopDiode)
if self.wavelength is not None:
xsdExperiment.wavelength = xsDataResult.wavelength = XSDataWavelength(self.wavelength)
if self.maskFile is not None:
xsdFile = XSDataImage()
xsdFile.setPath(XSDataString(self.maskFile))
xsdExperiment.maskFile = xsDataResult.maskFile = xsdFile
if self.normalizationFactor is not None:
xsdExperiment.normalizationFactor = xsDataResult.normalizationFactor = XSDataDouble(self.normalizationFactor)
if self.machineCurrent is not None:
xsdExperiment.machineCurrent = xsDataResult.machineCurrent = XSDataDouble(self.machineCurrent)
if self.storageTemperature is not None:
xsdExperiment.storageTemperature = xsDataResult.storageTemperature = XSDataDouble(self.storageTemperature)
if self.exposureTemperature is not None:
xsdExperiment.exposureTemperature = xsDataResult.exposureTemperature = XSDataDouble(self.exposureTemperature)
if self.exposureTime is not None:
xsdExperiment.exposureTime = xsDataResult.exposureTime = XSDataTime(self.exposureTime)
if self.frameNumber is not None:
xsdExperiment.frameNumber = xsDataResult.frameNumber = XSDataInteger(self.frameNumber)
if self.frameMax is not None:
xsdExperiment.frameMax = xsDataResult.frameMax = XSDataInteger(self.frameMax)
if self.timeOfFrame is not None:
xsdExperiment.timeOfFrame = xsDataResult.timeOfFrame = XSDataTime(self.timeOfFrame)
if self.code is not None:
xsdSample.code = xsDataResult.code = XSDataString(self.code)
if self.comments is not None:
xsdSample.comments = xsDataResult.comments = XSDataString(self.comments)
if self.concentration is not None:
xsdSample.concentration = xsDataResult.concentration = XSDataDouble(self.concentration)
xsDataResult.sample = xsdSample
xsDataResult.experimentSetup = xsdExperiment
self.setDataOutput(xsDataResult)
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 process(self, _edObject=None):
EDPluginExec.process(self)
EDVerbose.DEBUG("EDPluginExecReadImageHeaderMARCCDv10.process")
xsDataInputReadImageHeader = self.getDataInput()
xsDataFile = xsDataInputReadImageHeader.getImage()
strPath = xsDataFile.getPath().getValue()
dictMARCCDHeader = self.readHeaderMarccd(strPath)
if (dictMARCCDHeader is None):
strErrorMessage = "EDPluginExecReadImageHeaderMARCCDv10.process : Cannot read header : %s" % strPath
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
else:
xsDataExperimentalCondition = XSDataExperimentalCondition()
xsDataDetector = XSDataDetector()
iNoPixelsX = int(dictMARCCDHeader[ "nslow" ])
iNoPixelsY = int(dictMARCCDHeader[ "nfast" ])
xsDataDetector.setNumberPixelX(XSDataInteger(iNoPixelsX))
xsDataDetector.setNumberPixelY(XSDataInteger(iNoPixelsY))
fPixelSizeX = float(dictMARCCDHeader[ "pixelsize_x" ]) / 1000.0
xsDataDetector.setPixelSizeX(XSDataLength(fPixelSizeX))
fPixelSizeY = float(dictMARCCDHeader[ "pixelsize_y" ]) / 1000.0
xsDataDetector.setPixelSizeY(XSDataLength(fPixelSizeY))
fBeamPositionX = float(dictMARCCDHeader[ "beam_x" ]) / 1000.0
fBeamPositionY = float(dictMARCCDHeader[ "beam_y" ]) / 1000.0
# Fix for bug 397 - check if the beam position is close to the centre of the image
fTwoTheta = float(dictMARCCDHeader[ "end_twotheta" ]) / 1000.0
xsDataDetector.setTwoTheta(XSDataAngle(fTwoTheta))
if (abs(fTwoTheta) < 0.1):
if (abs(fBeamPositionX / (fPixelSizeX / 1000.0) - iNoPixelsX / 2.0) > (2 * iNoPixelsX)):
fBeamPositionX = fBeamPositionX * fPixelSizeX / 1000.0
fBeamPositionY = fBeamPositionY * fPixelSizeY / 1000.0
xsDataDetector.setBeamPositionX(XSDataLength(fBeamPositionX))
xsDataDetector.setBeamPositionY(XSDataLength(fBeamPositionY))
fDistance = float(dictMARCCDHeader[ "xtal_to_detector" ]) / 1000.0
if (abs(fDistance) < 0.1):
fDistanceStart = float(dictMARCCDHeader[ "start_xtal_to_detector" ]) / 1000.0
fDistanceEnd = float(dictMARCCDHeader[ "end_xtal_to_detector" ]) / 1000.0
if (abs(fDistanceStart - fDistanceEnd) < 0.1):
fDistance = fDistanceStart
else:
# Somethings very wrong with the distances...
strErrorMessage = "EDPluginExecReadImageHeaderMARCCDv10.process : Inconsistency in MAR CCD image header: start_xtal_to_detector = %d, end_xtal_to_detector = %d" % \
(fDistanceStart, fDistanceEnd)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
xsDataDetector.setDistance(XSDataLength(fDistance))
xsDataDetector.setNumberBytesInHeader(XSDataInteger(float(dictMARCCDHeader[ "header_size" ])))
# xsDataDetector.setSerialNumber( XSDataInteger( dictMARCCDHeader[ "DETECTOR_SN" ] ) ) )
# xsDataDetector.setBin( XSDataString( dictMARCCDHeader[ "BIN" ] ) ) )
# xsDataDetector.setDataType( XSDataString( dictMARCCDHeader[ "TYPE" ] ) ) )
# xsDataDetector.setByteOrder( XSDataString( dictMARCCDHeader[ "BYTE_ORDER" ] ) ) )
xsDataDetector.setImageSaturation(XSDataInteger(int(dictMARCCDHeader[ "saturation_level" ])))
# Determine type of detector...
if (iNoPixelsX == 2048 and iNoPixelsY == 2048):
xsDataDetector.setName(XSDataString("MAR CCD 165"))
xsDataDetector.setType(XSDataString("mar165"))
elif (iNoPixelsX == 3072 and iNoPixelsY == 3072):
xsDataDetector.setName(XSDataString("MAR CCD 225"))
xsDataDetector.setType(XSDataString("mar225"))
elif (iNoPixelsX == 4096 and iNoPixelsY == 4096):
xsDataDetector.setName(XSDataString("MAR CCD 325"))
xsDataDetector.setType(XSDataString("mar325"))
else:
strErrorMessage = EDMessage.ERROR_DATA_HANDLER_02 % ("EDPluginExecReadImageHeaderMARCCDv10.process", "Unknown detector type")
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
xsDataExperimentalCondition.setDetector(xsDataDetector)
# Beam object
xsDataBeam = XSDataBeam()
xsDataBeam.setWavelength(XSDataWavelength(float(dictMARCCDHeader[ "source_wavelength" ]) / 100000.0))
xsDataBeam.setExposureTime(XSDataTime(float(dictMARCCDHeader[ "exposure_time" ]) / 1000.0))
xsDataExperimentalCondition.setBeam(xsDataBeam)
# Goniostat object
xsDataGoniostat = XSDataGoniostat()
fRotationAxisStart = float(dictMARCCDHeader[ "start_phi" ]) / 1000.0
fOscillationWidth = float(dictMARCCDHeader[ "rotation_range" ]) / 1000.0
xsDataGoniostat.setRotationAxisStart(XSDataAngle(fRotationAxisStart))
xsDataGoniostat.setRotationAxisEnd(XSDataAngle(fRotationAxisStart + fOscillationWidth))
xsDataGoniostat.setOscillationWidth(XSDataAngle(fOscillationWidth))
xsDataExperimentalCondition.setGoniostat(xsDataGoniostat)
# Create the image object
xsDataImage = XSDataImage()
xsDataImage.setPath(XSDataString(strPath))
strTimeStamp = dictMARCCDHeader[ "acquire_timestamp" ]
xsDataImage.setDate(XSDataString(strTimeStamp))
iImageNumber = EDUtilsImage.getImageNumber(strPath)
xsDataImage.setNumber(XSDataInteger(iImageNumber))
xsDataSubWedge = XSDataSubWedge()
xsDataSubWedge.setExperimentalCondition(xsDataExperimentalCondition)
xsDataSubWedge.addImage(xsDataImage)
self.__xsDataResultReadImageHeader = XSDataResultReadImageHeader()
self.__xsDataResultReadImageHeader.setSubWedge(xsDataSubWedge)
def process(self, _edObject=None):
EDPluginExec.process(self)
EDVerbose.DEBUG("EDPluginExecReadImageHeaderPilatus2Mv10.process")
xsDataInputReadImageHeader = self.getDataInput()
xsDataFile = xsDataInputReadImageHeader.getImage()
strPath = xsDataFile.getPath().getValue()
dictPilatus2MHeader = self.readHeaderPilatus2M(strPath)
if (dictPilatus2MHeader is None):
strErrorMessage = "EDPluginExecReadImageHeaderPilatus2Mv10.process : Cannot read header : %s" % strPath
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
else:
xsDataExperimentalCondition = XSDataExperimentalCondition()
xsDataDetector = XSDataDetector()
iNoPixelsX = 1475
iNoPixelsY = 1679
xsDataDetector.setNumberPixelX(XSDataInteger(iNoPixelsX))
xsDataDetector.setNumberPixelY(XSDataInteger(iNoPixelsY))
# Pixel size
listPixelSizeXY = dictPilatus2MHeader[ "Pixel_size" ].split(" ")
fPixelSizeX = float(listPixelSizeXY[0]) * 1000
xsDataDetector.setPixelSizeX(XSDataLength(fPixelSizeX))
fPixelSizeY = float(listPixelSizeXY[3]) * 1000
xsDataDetector.setPixelSizeY(XSDataLength(fPixelSizeY))
# Beam position
listBeamPosition = dictPilatus2MHeader["Beam_xy"].replace("(", " ").replace(")", " ").replace(",", " ").split()
fBeamPositionX = float(listBeamPosition[1]) * fPixelSizeX
fBeamPositionY = float(listBeamPosition[0]) * fPixelSizeY
xsDataDetector.setBeamPositionX(XSDataLength(fBeamPositionX))
xsDataDetector.setBeamPositionY(XSDataLength(fBeamPositionY))
fDistance = float(dictPilatus2MHeader[ "Detector_distance" ].split(" ")[0]) * 1000
xsDataDetector.setDistance(XSDataLength(fDistance))
# xsDataDetector.setNumberBytesInHeader(XSDataInteger(float(dictPilatus2MHeader[ "header_size" ])))
xsDataDetector.setSerialNumber(XSDataString(dictPilatus2MHeader[ "Detector:" ]))
# #xsDataDetector.setBin( XSDataString( dictPilatus2MHeader[ "BIN" ] ) ) )
# #xsDataDetector.setDataType( XSDataString( dictPilatus2MHeader[ "TYPE" ] ) ) )
# #xsDataDetector.setByteOrder( XSDataString( dictPilatus2MHeader[ "BYTE_ORDER" ] ) ) )
# xsDataDetector.setImageSaturation(XSDataInteger(int(dictPilatus2MHeader[ "saturation_level" ])))
xsDataDetector.setName(XSDataString("PILATUS2 3M"))
xsDataDetector.setType(XSDataString("pilatus2m"))
xsDataExperimentalCondition.setDetector(xsDataDetector)
# Beam object
xsDataBeam = XSDataBeam()
xsDataBeam.setWavelength(XSDataWavelength(float(dictPilatus2MHeader[ "Wavelength" ].split(" ")[0])))
xsDataBeam.setExposureTime(XSDataTime(float(dictPilatus2MHeader[ "Exposure_time" ].split(" ")[0])))
xsDataExperimentalCondition.setBeam(xsDataBeam)
# Goniostat object
xsDataGoniostat = XSDataGoniostat()
fRotationAxisStart = float(dictPilatus2MHeader[ "Start_angle" ].split(" ")[0])
fOscillationWidth = float(dictPilatus2MHeader[ "Angle_increment" ].split(" ")[0])
xsDataGoniostat.setRotationAxisStart(XSDataAngle(fRotationAxisStart))
xsDataGoniostat.setRotationAxisEnd(XSDataAngle(fRotationAxisStart + fOscillationWidth))
xsDataGoniostat.setOscillationWidth(XSDataAngle(fOscillationWidth))
xsDataExperimentalCondition.setGoniostat(xsDataGoniostat)
#
# Create the image object
xsDataImage = XSDataImage()
xsDataImage.setPath(XSDataString(strPath))
if "DateTime" in dictPilatus2MHeader:
strTimeStamp = dictPilatus2MHeader[ "DateTime" ]
xsDataImage.setDate(XSDataString(strTimeStamp))
iImageNumber = EDUtilsImage.getImageNumber(strPath)
xsDataImage.setNumber(XSDataInteger(iImageNumber))
xsDataSubWedge = XSDataSubWedge()
xsDataSubWedge.setExperimentalCondition(xsDataExperimentalCondition)
xsDataSubWedge.addImage(xsDataImage)
self.__xsDataResultReadImageHeader = XSDataResultReadImageHeader()
self.__xsDataResultReadImageHeader.setSubWedge(xsDataSubWedge)
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