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)