def __init__(self): """ """ EDPluginControl.__init__(self) self.__edPluginExecDatcmp = None self.__edPluginExecDataver = None self.__edPluginExecWaitFile = None self.__edPluginExecAutoSub = None self.__edPluginSaxsAnalysis = None self.__edPluginSaxsISPyB = None self.setXSDataInputClass(XSDataInputBioSaxsSmartMergev1_0) self.__edPluginExecDatCmp = None self.lstInput = [] self.curves = [] self.lstMerged = [] self.lstXsdInput = [] self.absoluteFidelity = None self.relativeFidelity = None self.dictSimilarities = {} # key: 2-tuple of images, similarities self.lstSummary = [] self.lstStrInput = [] self.autoRg = None self.gnom = None self.volume = None self.strRadiationDamage = None self.strMergedFile = None self.lstSub = [] self.strSubFile = None self.fConcentration = None self.xsDataResult = XSDataResultBioSaxsSmartMergev1_0() self.xsBestBuffer = None
def testExecute(self): """ """ plugin = self.getPlugin() plugin.__class__.lastBuffer = XSDataFile( XSDataString( os.path.join(EDUtilsPath.EDNA_TESTIMAGES, "buffer_before.dat"))) plugin.__class__.lastSample = XSDataFile( XSDataString( os.path.join(EDUtilsPath.EDNA_TESTIMAGES, "bioSaxsAveraged.dat"))) self.run() plugin = self.getPlugin() xsdRef = XSDataResultBioSaxsSmartMergev1_0.parseString( self.readAndParseFile(self.getReferenceDataOutputFile())) xsdRef.autoRg = None xsdObt = plugin.getDataOutput() xsdObt.status = None #Executive summary is too complicated to test EDAssert.strAlmostEqual(xsdRef.marshal(), xsdObt.marshal(), "XML output structures are the same", _fAbsError=0.1) # ref = " ".join([" ".join(i.split()) for i in open(self.destFile)]) # obt = " ".join([" ".join(i.split()) for i in open(xsdObt.mergedCurve.path.value)]) # EDAssert.strAlmostEqual(ref, obt, "Files are the same", _fAbsError=0.1) print plugin.__class__.lastBuffer.path.value print plugin.__class__.lastSample.path.value
def postProcess(self, _edObject=None): EDPluginControl.postProcess(self) self.DEBUG("EDPluginBioSaxsSmartMergev1_0.postProcess") # Create some output data xsDataResult = XSDataResultBioSaxsSmartMergev1_0() xsDataResult.mergedCurve = self.dataInput.mergedCurve executiveSummary = os.linesep.join(self.lstSummary) xsDataResult.status = XSDataStatus( executiveSummary=XSDataString(executiveSummary)) self.setDataOutput(xsDataResult) self.DEBUG(executiveSummary)
def testExecute(self): """ """ self.run() plugin = self.getPlugin() xsdRef = XSDataResultBioSaxsSmartMergev1_0.parseString(self.readAndParseFile(self.getReferenceDataOutputFile())) xsdObt = plugin.getDataOutput() xsdObt.status = None #Executive summary is too complicated to test EDAssert.strAlmostEqual(xsdRef.marshal(), xsdObt.marshal(), "XML output structures are the same", _fAbsError=0.1) ref = " ".join([" ".join(i.split()) for i in open(self.destFile)]) obt = " ".join([" ".join(i.split()) for i in open(xsdObt.mergedCurve.path.value)]) EDAssert.strAlmostEqual(ref, obt, "Files are the same", _fAbsError=0.1)
def testExecute(self): """ """ self.run() plugin = self.getPlugin() xsdRef = XSDataResultBioSaxsSmartMergev1_0.parseString(self.readAndParseFile(self.getReferenceDataOutputFile())) xsdObt = plugin.getDataOutput() xsdObt.status = None #Executive summary is too complicated to test EDAssert.strAlmostEqual(xsdRef.marshal(), xsdObt.marshal(), "XML output structures are the same", _fAbsError=0.1) ref = " ".join([" ".join(i.split()) for i in open(self.destFile)]) obt = " ".join([" ".join(i.split()) for i in open(xsdObt.mergedCurve.path.value)]) EDAssert.strAlmostEqual(ref, obt, "Files are the same", _fAbsError=0.1)
def postProcess(self, _edObject=None): EDPluginControl.postProcess(self) self.DEBUG("EDPluginBioSaxsSmartMergev1_3.postProcess") # Create some output data xsDataResult = XSDataResultBioSaxsSmartMergev1_0() xsDataResult.mergedCurve = self.dataInput.mergedCurve executiveSummary = os.linesep.join(self.lstSummary) xsDataResult.status = XSDataStatus(executiveSummary=XSDataString(executiveSummary)) if self.autoRg is not None: xsDataResult.autoRg = self.autoRg if self.strSubFile is not None and os.path.isfile(self.strSubFile): xsDataResult.subtractedCurve = XSDataFile(XSDataString(self.strSubFile)) self.setDataOutput(xsDataResult)
def testExecute(self): """ """ plugin = self.getPlugin() plugin.__class__.lastBuffer = XSDataFile(XSDataString(os.path.join(EDUtilsPath.EDNA_TESTIMAGES, "buffer_before.dat"))) plugin.__class__.lastSample = XSDataFile(XSDataString(os.path.join(EDUtilsPath.EDNA_TESTIMAGES, "bioSaxsAveraged.dat"))) self.run() plugin = self.getPlugin() xsdRef = XSDataResultBioSaxsSmartMergev1_0.parseString(self.readAndParseFile(self.getReferenceDataOutputFile())) xsdRef.autoRg = None xsdObt = plugin.getDataOutput() xsdObt.status = None #Executive summary is too complicated to test EDAssert.strAlmostEqual(xsdRef.marshal(), xsdObt.marshal(), "XML output structures are the same", _fAbsError=0.1) # ref = " ".join([" ".join(i.split()) for i in open(self.destFile)]) # obt = " ".join([" ".join(i.split()) for i in open(xsdObt.mergedCurve.path.value)]) # EDAssert.strAlmostEqual(ref, obt, "Files are the same", _fAbsError=0.1) print plugin.__class__.lastBuffer.path.value print plugin.__class__.lastSample.path.value
def __init__(self): """ """ EDPluginControl.__init__(self) #self.__edPluginExecDatcmp = None self.__edPluginExecDataver = None self.__edPluginExecWaitFile = None self.__edPluginExecAutoSub = None self.__edPluginSaxsAnalysis = None self.__edPluginSaxsISPyB = None self.setXSDataInputClass(XSDataInputBioSaxsSmartMergev1_0) #self.__edPluginExecDatCmp = None self.lstInput = [] self.curves = [] self.forgetLastSample = False self.lstMerged = [] self.lstDiscarded = [] self.lstXsdInput = [] self.absoluteFidelity = 0.01 #None self.relativeFidelity = 0.01 #None self.dictSimilarities = {} # key: 2-tuple of images, similarities self.lstStrInput = [] self.autoRg = None self.gnom = None self.volume = None self.rti = None self.strRadiationDamage = None self.strMergedFile = None self.lstSub = [] self.strSubFile = None self.fConcentration = None self.xsDataResult = XSDataResultBioSaxsSmartMergev1_0() self.xsBestBuffer = None self.bestBufferType = "" self.bufferFrames = [] self.xsScatterPlot = None self.xsGuinierPlot = None self.xsKratkyPlot = None self.xsDensityPlot = None self.xsdSubtractedCurve = None self.outdir = None #directory on rnice for analysis results to go to