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
Example #3
0
 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)
Example #5
0
 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
Example #8
0
    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