def mergeTwoSubWedgesAdjascentInRotationAxis(self, _subWedge1, _subWedge2):
"""
This method takes as input two sub wedges and merges them to an unique subwedge, if possible,
and returns the resulting merged sub wedge. If the merge is not possible a None is returned.
"""
EDVerbose.DEBUG(
"EDPluginSubWedgeMergev1_1.mergeTwoSubWedgesAdjascentInRotationAxis"
)
xsDataSubWedgeMerged = None
# First check that the two sub wedges have identical experimental conditions
if (self.isSameExperimentalConditionInSubWedge(_subWedge1,
_subWedge2)):
# Check if sub wedges are adjascent:
dRoationAxisEnd1 = _subWedge1.getExperimentalCondition(
).getGoniostat().getRotationAxisEnd().getValue()
dRoationAxisStart2 = _subWedge2.getExperimentalCondition(
).getGoniostat().getRotationAxisStart().getValue()
#print dRoationAxisEnd1, dRoationAxisStart2
if (self.compareTwoValues(dRoationAxisEnd1, dRoationAxisStart2,
0.001)):
# Same sub wedge! Let's merge them
xsDataSubWedgeMerged = XSDataSubWedge.parseString(
_subWedge1.marshal())
xsDataSubWedge2 = XSDataSubWedge.parseString(
_subWedge2.marshal())
dRoationAxisEnd2 = xsDataSubWedge2.getExperimentalCondition(
).getGoniostat().getRotationAxisEnd().getValue()
xsDataSubWedgeMerged.getExperimentalCondition().getGoniostat(
).setRotationAxisEnd(XSDataAngle(dRoationAxisEnd2))
for xsDataImage in xsDataSubWedge2.getImage():
xsDataSubWedgeMerged.addImage(xsDataImage)
return xsDataSubWedgeMerged
def mergeListOfSubWedgesWithAdjascentRotationAxis(self, _listOfSubWedgesWithIdenticalExperimentalConditions):
"""
This method merges sub wedges in a list if they are adjascent in phi.
"""
self.DEBUG("EDPluginSubWedgeMergev1_1.mergeSubWedgesWithAdjascentRotationAxis")
# Copy the incoming list to a new list
listOfSubWedgesWithIdenticalExperimentalConditions = []
for xsDataSubWedge in _listOfSubWedgesWithIdenticalExperimentalConditions:
listOfSubWedgesWithIdenticalExperimentalConditions.append(XSDataSubWedge.parseString(xsDataSubWedge.marshal()))
listOfMergedSubWedges = []
if (len(listOfSubWedgesWithIdenticalExperimentalConditions) == 0):
pass
elif (len(listOfSubWedgesWithIdenticalExperimentalConditions) == 1):
listOfMergedSubWedges = listOfSubWedgesWithIdenticalExperimentalConditions
else:
# First sort the list as function of rotation axis start
listOfSubWedgesWithIdenticalExperimentalConditions.sort(lambda x, y: cmp(x.getExperimentalCondition().getGoniostat().getRotationAxisStart().getValue(), \
y.getExperimentalCondition().getGoniostat().getRotationAxisStart().getValue()))
# Then loop through the subwedges and merge them if possible
listRemainingSubWedges = listOfSubWedgesWithIdenticalExperimentalConditions
oCurrentSubWedge = listRemainingSubWedges[0]
listRemainingSubWedges = listRemainingSubWedges[1:]
while (len(listRemainingSubWedges) > 0):
oNextSubWedge = listRemainingSubWedges[0]
listRemainingSubWedges = listRemainingSubWedges[1:]
xsDataSubWedgeMerged = self.mergeTwoSubWedgesAdjascentInRotationAxis(oCurrentSubWedge, oNextSubWedge)
if (xsDataSubWedgeMerged is None):
listOfMergedSubWedges.append(oCurrentSubWedge)
oCurrentSubWedge = oNextSubWedge
else:
oCurrentSubWedge = xsDataSubWedgeMerged
listOfMergedSubWedges.append(oCurrentSubWedge)
return listOfMergedSubWedges
def mergeListOfSubWedgesWithAdjascentRotationAxis(self, _listOfSubWedgesWithIdenticalExperimentalConditions):
"""
This method merges sub wedges in a list if they are adjascent in phi.
"""
EDVerbose.DEBUG("EDPluginSubWedgeMergev10.mergeSubWedgesWithAdjascentRotationAxis")
# Copy the incoming list to a new list
listOfSubWedgesWithIdenticalExperimentalConditions = []
for xsDataSubWedge in _listOfSubWedgesWithIdenticalExperimentalConditions:
listOfSubWedgesWithIdenticalExperimentalConditions.append(XSDataSubWedge.parseString(xsDataSubWedge.marshal()))
listOfMergedSubWedges = []
if (len(listOfSubWedgesWithIdenticalExperimentalConditions) == 0):
pass
elif (len(listOfSubWedgesWithIdenticalExperimentalConditions) == 1):
listOfMergedSubWedges = listOfSubWedgesWithIdenticalExperimentalConditions
else:
# First sort the list as function of rotation axis start
listOfSubWedgesWithIdenticalExperimentalConditions.sort(lambda x, y: cmp(x.getExperimentalCondition().getGoniostat().getRotationAxisStart().getValue(), \
y.getExperimentalCondition().getGoniostat().getRotationAxisStart().getValue()))
# Then loop through the subwedges and merge them if possible
listRemainingSubWedges = listOfSubWedgesWithIdenticalExperimentalConditions
oCurrentSubWedge = listRemainingSubWedges[0]
listRemainingSubWedges = listRemainingSubWedges[1:]
while (len(listRemainingSubWedges) > 0):
oNextSubWedge = listRemainingSubWedges[0]
listRemainingSubWedges = listRemainingSubWedges[1:]
xsDataSubWedgeMerged = self.mergeTwoSubWedgesAdjascentInRotationAxis(oCurrentSubWedge, oNextSubWedge)
if (xsDataSubWedgeMerged is None):
listOfMergedSubWedges.append(oCurrentSubWedge)
oCurrentSubWedge = oNextSubWedge
else:
oCurrentSubWedge = xsDataSubWedgeMerged
listOfMergedSubWedges.append(oCurrentSubWedge)
return listOfMergedSubWedges
def testMergeTwoSubWedgesAdjascentInRotationAxis(self):
# First check two sub wedges which shouldn't be merged
edPluginSubWedgeMergev10 = self.createPlugin()
edPluginSubWedgeMergev10.configure()
xsDataInputSubWedgeMerge = XSDataInputSubWedgeMerge.parseFile(
self.__strPathToReferenceInput)
xsDataSubWedge1 = xsDataInputSubWedgeMerge.getSubWedge()[0]
xsDataSubWedge2 = xsDataInputSubWedgeMerge.getSubWedge()[1]
xsDataSubWedgeMerged = edPluginSubWedgeMergev10.mergeTwoSubWedgesAdjascentInRotationAxis(
xsDataSubWedge1, xsDataSubWedge2)
EDAssert.equal(xsDataSubWedgeMerged, None)
# Then check two adjascent images
strPathToInputTwoAdjascentImages = os.path.join(
self.getPluginTestsDataHome(),
"XSDataInputSubWedgeMerge_twoAdjascentImages.xml")
xsDataInputSubWedgeMerge2 = XSDataInputSubWedgeMerge.parseFile(
strPathToInputTwoAdjascentImages)
xsDataSubWedge1 = xsDataInputSubWedgeMerge2.getSubWedge()[0]
xsDataSubWedge2 = xsDataInputSubWedgeMerge2.getSubWedge()[1]
xsDataSubWedgeMerged = edPluginSubWedgeMergev10.mergeTwoSubWedgesAdjascentInRotationAxis(
xsDataSubWedge1, xsDataSubWedge2)
xsDataSubWedgeMergedReference = XSDataSubWedge.parseFile(
os.path.join(self.getPluginTestsDataHome(),
"XSDataSubWedgeMerged_twoImages.xml"))
EDAssert.equal(xsDataSubWedgeMerged.marshal(),
xsDataSubWedgeMergedReference.marshal())
def testMergeListOfSubWedgesWithAdjascentRotationAxis(self):
edPluginSubWedgeMergev10 = self.createPlugin()
edPluginSubWedgeMergev10.configure()
# Check a list of nine adjascent images
strPathToInputNineAdjascentImages = os.path.join(self.getPluginTestsDataHome(), "XSDataInputSubWedgeMerge_nineAdjascentImages.xml")
xsDataInputSubWedgeMergeNine = XSDataInputSubWedgeMerge.parseFile(strPathToInputNineAdjascentImages)
xsDataSubWedgeMerged = edPluginSubWedgeMergev10.mergeListOfSubWedgesWithAdjascentRotationAxis(xsDataInputSubWedgeMergeNine.getSubWedge())
xsDataSubWedgeMergedReference = XSDataSubWedge.parseFile(os.path.join(self.getPluginTestsDataHome(), "XSDataSubWedgeMerged_nineImages.xml"))
EDAssert.equal(xsDataSubWedgeMerged[0].marshal(), xsDataSubWedgeMergedReference.marshal())
def getXSDataResultStrategy(self, _xsDataResultBest, _xsDataExperimentalCondition, _xsDataSample):
xsDataResultStrategy = XSDataResultStrategy()
#xsDataCollectionRunsBest = _xsDataResultBest.getCollectionRun()
xsDataCollectionPlansBest = _xsDataResultBest.getCollectionPlan()
for xsDataCollectionPlanBest in xsDataCollectionPlansBest:
xsDataCollectionPlan = XSDataCollectionPlan()
xsDataCollectionStrategy = XSDataCollection()
xsDataDoubleTransmission = xsDataCollectionPlanBest.getStrategySummary().getAttenuation()
for xsDataCollectionRunBest in xsDataCollectionPlanBest.getCollectionRun():
xsDataSubWedge = XSDataSubWedge()
strXmlStringDataExperimentalCondition = _xsDataExperimentalCondition.marshal()
xsDataExperimentalCondition = XSDataExperimentalCondition.parseString(strXmlStringDataExperimentalCondition)
xsDataExperimentalCondition.getBeam().setExposureTime(xsDataCollectionRunBest.getExposureTime())
xsDataExperimentalCondition.getBeam().setTransmission(xsDataDoubleTransmission)
xsDataExperimentalCondition.getDetector().setDistance(xsDataCollectionRunBest.getDistance())
xsDataExperimentalCondition.getGoniostat().setRotationAxisStart(xsDataCollectionRunBest.getPhiStart())
xsDataExperimentalCondition.getGoniostat().setOscillationWidth(xsDataCollectionRunBest.getPhiWidth())
fRotationAxisEnd = xsDataCollectionRunBest.getPhiStart().getValue() + xsDataCollectionRunBest.getNumberOfImages().getValue() * xsDataCollectionRunBest.getPhiWidth().getValue()
xsDataExperimentalCondition.getGoniostat().setRotationAxisEnd(XSDataAngle(fRotationAxisEnd))
xsDataSubWedge.setExperimentalCondition(xsDataExperimentalCondition)
xsDataSubWedge.setSubWedgeNumber(xsDataCollectionRunBest.getCollectionRunNumber())
xsDataCollectionStrategy.addSubWedge(xsDataSubWedge)
xsDataCollectionStrategy.setSample(_xsDataSample)
xsDataCollectionPlan.setCollectionStrategy(xsDataCollectionStrategy)
xsDataStrategySummary = xsDataCollectionPlanBest.getStrategySummary()
xsDataCollectionPlan.setStrategySummary(xsDataStrategySummary)
xsDataStatistics = xsDataCollectionPlanBest.getStatisticalPrediction()
xsDataCollectionPlan.setStatistics(xsDataStatistics)
xsDataCollectionPlan.setCollectionPlanNumber(xsDataCollectionPlanBest.getCollectionPlanNumber())
xsDataResultStrategy.addCollectionPlan(xsDataCollectionPlan)
return xsDataResultStrategy
def mergeTwoSubWedgesAdjascentInRotationAxis(self, _subWedge1, _subWedge2):
"""
This method takes as input two sub wedges and merges them to an unique subwedge, if possible,
and returns the resulting merged sub wedge. If the merge is not possible a None is returned.
"""
self.DEBUG("EDPluginSubWedgeMergev1_1.mergeTwoSubWedgesAdjascentInRotationAxis")
xsDataSubWedgeMerged = None
# First check that the two sub wedges have identical experimental conditions
if (self.isSameExperimentalConditionInSubWedge(_subWedge1, _subWedge2)):
# Check if sub wedges are adjascent:
dRoationAxisEnd1 = _subWedge1.getExperimentalCondition().getGoniostat().getRotationAxisEnd().getValue()
dRoationAxisStart2 = _subWedge2.getExperimentalCondition().getGoniostat().getRotationAxisStart().getValue()
#print dRoationAxisEnd1, dRoationAxisStart2
if (self.compareTwoValues(dRoationAxisEnd1, dRoationAxisStart2, 0.001)):
# Same sub wedge! Let's merge them
xsDataSubWedgeMerged = XSDataSubWedge.parseString(_subWedge1.marshal())
xsDataSubWedge2 = XSDataSubWedge.parseString(_subWedge2.marshal())
dRoationAxisEnd2 = xsDataSubWedge2.getExperimentalCondition().getGoniostat().getRotationAxisEnd().getValue()
xsDataSubWedgeMerged.getExperimentalCondition().getGoniostat().setRotationAxisEnd(XSDataAngle(dRoationAxisEnd2))
for xsDataImage in xsDataSubWedge2.getImage():
xsDataSubWedgeMerged.addImage(xsDataImage)
return xsDataSubWedgeMerged
def getXSDataStrategyResult(self, _xsDataBestOutput, _xsDataExperimentalCondition, _xsDataSample):
xsDataStrategyResult = XSDataStrategyResult()
#xsDataCollectionRunsBest = _xsDataBestOutput.getCollectionRun()
xsDataCollectionPlansBest = _xsDataBestOutput.getCollectionPlan()
for xsDataCollectionPlanBest in xsDataCollectionPlansBest:
xsDataCollectionPlan = XSDataCollectionPlan()
xsDataCollectionStrategy = XSDataCollection()
for xsDataCollectionRunBest in xsDataCollectionPlanBest.getCollectionRun():
xsDataSubWedge = XSDataSubWedge()
strXmlStringDataExperimentalCondition = _xsDataExperimentalCondition.marshal()
xsDataExperimentalCondition = XSDataExperimentalCondition.parseString(strXmlStringDataExperimentalCondition)
xsDataExperimentalCondition.getBeam().setExposureTime(xsDataCollectionRunBest.getExposureTime())
xsDataExperimentalCondition.getDetector().setDistance(xsDataCollectionRunBest.getDistance())
xsDataExperimentalCondition.getGoniostat().setRotationAxisStart(xsDataCollectionRunBest.getPhiStart())
xsDataExperimentalCondition.getGoniostat().setOscillationWidth(xsDataCollectionRunBest.getPhiWidth())
fRotationAxisEnd = xsDataCollectionRunBest.getPhiStart().getValue() + xsDataCollectionRunBest.getNumberOfImages().getValue() * xsDataCollectionRunBest.getPhiWidth().getValue()
xsDataExperimentalCondition.getGoniostat().setRotationAxisEnd(XSDataAngle(fRotationAxisEnd))
xsDataSubWedge.setExperimentalCondition(xsDataExperimentalCondition)
xsDataCollectionStrategy.addSubWedge(xsDataSubWedge)
xsDataCollectionStrategy.setSample(_xsDataSample)
xsDataCollectionPlan.setCollectionStrategy(xsDataCollectionStrategy)
xsDataStrategySummary = xsDataCollectionPlanBest.getStrategySummary()
xsDataCollectionPlan.setStrategySummary(xsDataStrategySummary)
xsDataStatistics = xsDataCollectionPlanBest.getStatisticalPrediction()
xsDataCollectionPlan.setStatistics(xsDataStatistics)
xsDataStrategyResult.addCollectionPlan(xsDataCollectionPlan)
return xsDataStrategyResult
def testMergeListOfSubWedgesWithAdjascentRotationAxis(self):
edPluginSubWedgeMergev10 = self.createPlugin()
edPluginSubWedgeMergev10.configure()
# Check a list of nine adjascent images
strPathToInputNineAdjascentImages = os.path.join(
self.getPluginTestsDataHome(),
"XSDataInputSubWedgeMerge_nineAdjascentImages.xml")
xsDataInputSubWedgeMergeNine = XSDataInputSubWedgeMerge.parseFile(
strPathToInputNineAdjascentImages)
xsDataSubWedgeMerged = edPluginSubWedgeMergev10.mergeListOfSubWedgesWithAdjascentRotationAxis(
xsDataInputSubWedgeMergeNine.getSubWedge())
xsDataSubWedgeMergedReference = XSDataSubWedge.parseFile(
os.path.join(self.getPluginTestsDataHome(),
"XSDataSubWedgeMerged_nineImages.xml"))
EDAssert.equal(xsDataSubWedgeMerged[0].marshal(),
xsDataSubWedgeMergedReference.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 testMergeTwoSubWedgesAdjascentInRotationAxis(self):
# First check two sub wedges which shouldn't be merged
edPluginSubWedgeMergev10 = self.createPlugin()
edPluginSubWedgeMergev10.configure()
xsDataInputSubWedgeMerge = XSDataInputSubWedgeMerge.parseFile(self.__strPathToReferenceInput)
xsDataSubWedge1 = xsDataInputSubWedgeMerge.getSubWedge()[0]
xsDataSubWedge2 = xsDataInputSubWedgeMerge.getSubWedge()[1]
xsDataSubWedgeMerged = edPluginSubWedgeMergev10.mergeTwoSubWedgesAdjascentInRotationAxis(xsDataSubWedge1, xsDataSubWedge2)
EDAssert.equal(xsDataSubWedgeMerged, None)
# Then check two adjascent images
strPathToInputTwoAdjascentImages = os.path.join(self.getPluginTestsDataHome(), "XSDataInputSubWedgeMerge_twoAdjascentImages.xml")
xsDataInputSubWedgeMerge2 = XSDataInputSubWedgeMerge.parseFile(strPathToInputTwoAdjascentImages)
xsDataSubWedge1 = xsDataInputSubWedgeMerge2.getSubWedge()[0]
xsDataSubWedge2 = xsDataInputSubWedgeMerge2.getSubWedge()[1]
xsDataSubWedgeMerged = edPluginSubWedgeMergev10.mergeTwoSubWedgesAdjascentInRotationAxis(xsDataSubWedge1, xsDataSubWedge2)
xsDataSubWedgeMergedReference = XSDataSubWedge.parseFile(os.path.join(self.getPluginTestsDataHome(), "XSDataSubWedgeMerged_twoImages.xml"))
EDAssert.equal(xsDataSubWedgeMerged.marshal(), xsDataSubWedgeMergedReference.marshal())
def process(self, _edObject=None):
EDPluginExec.process(self)
self.DEBUG("EDPluginExecReadImageHeaderEiger4Mv10.process")
xsDataInputReadImageHeader = self.getDataInput()
xsDataFile = xsDataInputReadImageHeader.getImage()
strPath = xsDataFile.getPath().getValue()
dictEiger4MHeader = self.readHeaderEiger4M(strPath)
if (dictEiger4MHeader is None):
strErrorMessage = "EDPluginExecReadImageHeaderEiger4Mv10.process : Cannot read header : %s" % strPath
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
else:
xsDataExperimentalCondition = XSDataExperimentalCondition()
xsDataDetector = XSDataDetector()
iNoPixelsX = 2070
iNoPixelsY = 2167
xsDataDetector.setNumberPixelX(XSDataInteger(iNoPixelsX))
xsDataDetector.setNumberPixelY(XSDataInteger(iNoPixelsY))
# Pixel size
listPixelSizeXY = dictEiger4MHeader[ "Pixel_size" ].split(" ")
fPixelSizeX = float(listPixelSizeXY[0]) * 1000
xsDataDetector.setPixelSizeX(XSDataLength(fPixelSizeX))
fPixelSizeY = float(listPixelSizeXY[3]) * 1000
xsDataDetector.setPixelSizeY(XSDataLength(fPixelSizeY))
# Beam position
listBeamPosition = dictEiger4MHeader["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(dictEiger4MHeader[ "Detector_distance" ].split(" ")[0]) * 1000
xsDataDetector.setDistance(XSDataLength(fDistance))
# xsDataDetector.setNumberBytesInHeader(XSDataInteger(float(dictEiger4MHeader[ "header_size" ])))
xsDataDetector.setSerialNumber(XSDataString(dictEiger4MHeader[ "Detector:" ]))
# #xsDataDetector.setBin( XSDataString( dictEiger4MHeader[ "BIN" ] ) ) )
# #xsDataDetector.setDataType( XSDataString( dictEiger4MHeader[ "TYPE" ] ) ) )
# #xsDataDetector.setByteOrder( XSDataString( dictEiger4MHeader[ "BYTE_ORDER" ] ) ) )
# xsDataDetector.setImageSaturation(XSDataInteger(int(dictEiger4MHeader[ "saturation_level" ])))
xsDataDetector.setName(XSDataString("EIGER 4M"))
xsDataDetector.setType(XSDataString("eiger4m"))
xsDataExperimentalCondition.setDetector(xsDataDetector)
# Beam object
xsDataBeam = XSDataBeam()
xsDataBeam.setWavelength(XSDataWavelength(float(dictEiger4MHeader[ "Wavelength" ].split(" ")[0])))
xsDataBeam.setExposureTime(XSDataTime(float(dictEiger4MHeader[ "Exposure_time" ].split(" ")[0])))
xsDataExperimentalCondition.setBeam(xsDataBeam)
# Goniostat object
xsDataGoniostat = XSDataGoniostat()
fRotationAxisStart = float(dictEiger4MHeader[ "Start_angle" ].split(" ")[0])
fOscillationWidth = float(dictEiger4MHeader[ "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 dictEiger4MHeader:
strTimeStamp = dictEiger4MHeader[ "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 preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
EDVerbose.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 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 getXSDataResultStrategy(self, _xsDataResultBest,
_xsDataExperimentalCondition, _xsDataSample):
xsDataResultStrategy = XSDataResultStrategy()
listXSDataBestCollectionPlan = _xsDataResultBest.getCollectionPlan()
for xsDataBestCollectionPlan in listXSDataBestCollectionPlan:
xsDataCollectionPlan = XSDataCollectionPlan()
xsDataCollectionStrategy = XSDataCollection()
xsDataBestStrategySummary = xsDataBestCollectionPlan.getStrategySummary(
)
xsDataDoubleTransmission = xsDataBestStrategySummary.getTransmission(
)
for xsDataBestCollectionRun in xsDataBestCollectionPlan.getCollectionRun(
):
xsDataSubWedge = XSDataSubWedge()
strXmlStringDataExperimentalCondition = _xsDataExperimentalCondition.marshal(
)
xsDataExperimentalCondition = XSDataExperimentalCondition.parseString(
strXmlStringDataExperimentalCondition)
xsDataExperimentalCondition.getBeam().setExposureTime(
xsDataBestCollectionRun.getExposureTime())
if (xsDataBestCollectionRun.getTransmission() is None):
xsDataExperimentalCondition.getBeam().setTransmission(
xsDataDoubleTransmission)
else:
xsDataExperimentalCondition.getBeam().setTransmission(
xsDataBestCollectionRun.getTransmission())
xsDataExperimentalCondition.getDetector().setDistance(
xsDataBestStrategySummary.getDistance())
xsDataExperimentalCondition.getGoniostat(
).setRotationAxisStart(xsDataBestCollectionRun.getPhiStart())
xsDataExperimentalCondition.getGoniostat().setOscillationWidth(
xsDataBestCollectionRun.getPhiWidth())
fRotationAxisEnd = xsDataBestCollectionRun.getPhiStart(
).getValue(
) + xsDataBestCollectionRun.getNumberOfImages().getValue(
) * xsDataBestCollectionRun.getPhiWidth().getValue()
xsDataExperimentalCondition.getGoniostat().setRotationAxisEnd(
XSDataAngle(fRotationAxisEnd))
xsDataSubWedge.setExperimentalCondition(
xsDataExperimentalCondition)
xsDataSubWedge.setSubWedgeNumber(
xsDataBestCollectionRun.getCollectionRunNumber())
if xsDataBestCollectionRun.getCrystalPosition():
xsDataSubWedge.setAction(
XSDataString("Crystal position: %d" %
xsDataBestCollectionRun.
getCrystalPosition().getValue()))
else:
xsDataSubWedge.setAction(
xsDataBestCollectionRun.getAction())
xsDataCollectionStrategy.addSubWedge(xsDataSubWedge)
xsDataCollectionStrategy.setSample(_xsDataSample)
xsDataCollectionPlan.setCollectionStrategy(
xsDataCollectionStrategy)
xsDataStrategySummary = XSDataStrategySummary()
xsDataStrategySummary.setCompleteness(
xsDataBestStrategySummary.getCompleteness())
xsDataStrategySummary.setISigma(
xsDataBestStrategySummary.getISigma())
xsDataStrategySummary.setRankingResolution(
xsDataBestStrategySummary.getRankingResolution())
xsDataStrategySummary.setRedundancy(
xsDataBestStrategySummary.getRedundancy())
xsDataStrategySummary.setResolution(
xsDataBestStrategySummary.getResolution())
xsDataStrategySummary.setResolutionReasoning(
xsDataBestStrategySummary.getResolutionReasoning())
xsDataStrategySummary.setTotalDataCollectionTime(
xsDataBestStrategySummary.getTotalDataCollectionTime())
xsDataStrategySummary.setTotalExposureTime(
xsDataBestStrategySummary.getTotalExposureTime())
xsDataCollectionPlan.setStrategySummary(xsDataStrategySummary)
if xsDataBestCollectionPlan.getStatisticalPrediction() is not None:
xsDataStatisticsStrategy = XSDataStatisticsStrategy.parseString(
xsDataBestCollectionPlan.getStatisticalPrediction(
).marshal())
xsDataCollectionPlan.setStatistics(xsDataStatisticsStrategy)
xsDataCollectionPlan.setCollectionPlanNumber(
xsDataBestCollectionPlan.getCollectionPlanNumber())
xsDataResultStrategy.addCollectionPlan(xsDataCollectionPlan)
if _xsDataResultBest.getPathToLogFile() != None:
xsDataResultStrategy.setBestLogFile(
_xsDataResultBest.getPathToLogFile())
return xsDataResultStrategy
def getXSDataResultStrategy(self, _xsDataResultBest, _xsDataExperimentalCondition, _xsDataSample):
xsDataResultStrategy = XSDataResultStrategy()
listXSDataBestCollectionPlan = _xsDataResultBest.getCollectionPlan()
for xsDataBestCollectionPlan in listXSDataBestCollectionPlan:
xsDataCollectionPlan = XSDataCollectionPlan()
xsDataCollectionStrategy = XSDataCollection()
xsDataBestStrategySummary = xsDataBestCollectionPlan.getStrategySummary()
xsDataDoubleTransmission = xsDataBestStrategySummary.getTransmission()
for xsDataBestCollectionRun in xsDataBestCollectionPlan.getCollectionRun():
xsDataSubWedge = XSDataSubWedge()
strXmlStringDataExperimentalCondition = _xsDataExperimentalCondition.marshal()
xsDataExperimentalCondition = XSDataExperimentalCondition.parseString(
strXmlStringDataExperimentalCondition
)
xsDataExperimentalCondition.getBeam().setExposureTime(xsDataBestCollectionRun.getExposureTime())
if xsDataBestCollectionRun.getTransmission() is None:
xsDataExperimentalCondition.getBeam().setTransmission(xsDataDoubleTransmission)
else:
xsDataExperimentalCondition.getBeam().setTransmission(xsDataBestCollectionRun.getTransmission())
xsDataExperimentalCondition.getDetector().setDistance(xsDataBestStrategySummary.getDistance())
xsDataExperimentalCondition.getGoniostat().setRotationAxisStart(xsDataBestCollectionRun.getPhiStart())
xsDataExperimentalCondition.getGoniostat().setOscillationWidth(xsDataBestCollectionRun.getPhiWidth())
fRotationAxisEnd = (
xsDataBestCollectionRun.getPhiStart().getValue()
+ xsDataBestCollectionRun.getNumberOfImages().getValue()
* xsDataBestCollectionRun.getPhiWidth().getValue()
)
xsDataExperimentalCondition.getGoniostat().setRotationAxisEnd(XSDataAngle(fRotationAxisEnd))
xsDataSubWedge.setExperimentalCondition(xsDataExperimentalCondition)
xsDataSubWedge.setSubWedgeNumber(xsDataBestCollectionRun.getCollectionRunNumber())
if xsDataBestCollectionRun.getCrystalPosition():
xsDataSubWedge.setAction(
XSDataString("Crystal position: %d" % xsDataBestCollectionRun.getCrystalPosition().getValue())
)
else:
xsDataSubWedge.setAction(xsDataBestCollectionRun.getAction())
xsDataCollectionStrategy.addSubWedge(xsDataSubWedge)
xsDataCollectionStrategy.setSample(_xsDataSample)
xsDataCollectionPlan.setCollectionStrategy(xsDataCollectionStrategy)
xsDataStrategySummary = XSDataStrategySummary()
xsDataStrategySummary.setCompleteness(xsDataBestStrategySummary.getCompleteness())
xsDataStrategySummary.setISigma(xsDataBestStrategySummary.getISigma())
xsDataStrategySummary.setRankingResolution(xsDataBestStrategySummary.getRankingResolution())
xsDataStrategySummary.setRedundancy(xsDataBestStrategySummary.getRedundancy())
xsDataStrategySummary.setResolution(xsDataBestStrategySummary.getResolution())
xsDataStrategySummary.setResolutionReasoning(xsDataBestStrategySummary.getResolutionReasoning())
xsDataStrategySummary.setTotalDataCollectionTime(xsDataBestStrategySummary.getTotalDataCollectionTime())
xsDataStrategySummary.setTotalExposureTime(xsDataBestStrategySummary.getTotalExposureTime())
xsDataCollectionPlan.setStrategySummary(xsDataStrategySummary)
if xsDataBestCollectionPlan.getStatisticalPrediction() is not None:
xsDataStatisticsStrategy = XSDataStatisticsStrategy.parseString(
xsDataBestCollectionPlan.getStatisticalPrediction().marshal()
)
xsDataCollectionPlan.setStatistics(xsDataStatisticsStrategy)
xsDataCollectionPlan.setCollectionPlanNumber(xsDataBestCollectionPlan.getCollectionPlanNumber())
xsDataResultStrategy.addCollectionPlan(xsDataCollectionPlan)
if _xsDataResultBest.getPathToLogFile() != None:
xsDataResultStrategy.setBestLogFile(_xsDataResultBest.getPathToLogFile())
return xsDataResultStrategy
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, _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)
