def preProcess(self):
"""
PreProcess of the execution test: download a set of images from http://www.edna-site.org
and remove any existing output file
"""
EDTestCasePluginExecute.preProcess(self)
self.loadTestImage([
"bioSaxsRaw.edf", "bioSaxsMask.edf", "bioSaxsCorrected.edf",
"bioSaxsProcessNormalized.edf", "bioSaxsProcessIntegrated.edf",
"bioSaxsProcessIntegrated1_2.dat", "averbuffer.dat"
])
strExpectedOutput = self.readAndParseFile(
self.getReferenceDataOutputFile())
EDVerbose.DEBUG("strExpectedOutput:" + strExpectedOutput)
xsDataResultReference = XSDataResultBioSaxsHPLCv1_0.parseString(
strExpectedOutput)
self.refNormImg = xsDataResultReference.normalizedImage.path.value
self.refIntCrv = xsDataResultReference.integratedCurve.path.value
if not os.path.isdir(os.path.dirname(self.refNormImg)):
os.makedirs(os.path.dirname(self.refNormImg))
if os.path.isfile(self.refNormImg):
os.remove(self.refNormImg)
if os.path.isfile(self.refIntCrv):
os.remove(self.refIntCrv)
EDUtilsParallel.initializeNbThread()
def testExecute(self):
"""
"""
plugin = self.getPlugin()
plugin.__class__.dictHPLC = {}
self.run()
################################################################################
# Compare XSDataResults
################################################################################
strExpectedOutput = self.readAndParseFile (self.getReferenceDataOutputFile())
EDVerbose.DEBUG("Checking obtained result...")
xsDataResultReference = XSDataResultBioSaxsHPLCv1_0.parseString(strExpectedOutput)
xsDataResultObtained = plugin.getDataOutput()
EDAssert.strAlmostEqual(xsDataResultReference.marshal(), xsDataResultObtained.marshal(), "XSDataResult output are the same", _strExcluded="bioSaxs")
################################################################################
# Compare Ascii files
################################################################################
asciiObt = os.linesep.join([i.strip() for i in open(xsDataResultObtained.integratedCurve.path.value) if "Raster" not in i])
asciiRef = os.linesep.join([i.strip() for i in open(os.path.join(self.getTestsDataImagesHome(), "bioSaxsProcessIntegrated1_2.dat")) if "Raster" not in i])
EDAssert.strAlmostEqual(asciiRef, asciiObt, _strComment="3 column ascii files are the same", _fRelError=0.1, _strExcluded=os.environ["USER"])
EDVerbose.screen("Execution time for %s: %.3fs" % (plugin.getClassName(), plugin.getRunTime()))
def __init__(self):
"""
"""
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputBioSaxsHPLCv1_0)
self.xsDataResult = XSDataResultBioSaxsHPLCv1_0()
self.runId = None
self.FrameId = None
self.hplc_run = None
self.curve = None
self.subtracted = None
self.lstExecutiveSummary = []
def push_event(self, event):
if event.attr_value is not None:
if event.attr_value.name.endswith("jobSuccess"):
print('jobSuccess')
# Get curve
jobid = event.attr_value.value # from event
print('jobid', jobid)
x = self._device.getJobOutput(jobid)
xsd = XSDataResultBioSaxsHPLCv1_0.parseString(x)
if not self._init and xsd.dataQ is not None:
q = xsDataToArray(xsd.dataQ)
w.setXData(q)
self._init = True
if xsd.dataI is not None:
i = xsDataToArray(xsd.dataI)
i[i <= 1] = 1 # Hack
w.appendCurves(i)
def __init__(self):
"""
"""
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputBioSaxsHPLCv1_0)
self.__edPluginProcessOneFile = None
self.__edPluginSubtract = None
self.__edPluginSaxsAnalysis = None
self.__edPluginDatCmp = None
self.xsDataResult = XSDataResultBioSaxsHPLCv1_0()
self.runId = None
self.frameId = None
self.frame = None
self.hplc_run = None
self.curve = None
self.subtracted = None
self.lstExecutiveSummary = []
self.isBuffer = False
def preProcess(self):
"""
PreProcess of the execution test: download a set of images from http://www.edna-site.org
and remove any existing output file
"""
EDTestCasePluginExecute.preProcess(self)
self.loadTestImage(["bioSaxsRaw.edf", "bioSaxsMask.edf",
"bioSaxsCorrected.edf", "bioSaxsProcessNormalized.edf",
"bioSaxsProcessIntegrated.edf", "bioSaxsProcessIntegrated1_2.dat"])
strExpectedOutput = self.readAndParseFile (self.getReferenceDataOutputFile())
EDVerbose.DEBUG("strExpectedOutput:" + strExpectedOutput)
xsDataResultReference = XSDataResultBioSaxsHPLCv1_0.parseString(strExpectedOutput)
self.refNormImg = xsDataResultReference.normalizedImage.path.value
self.refIntCrv = xsDataResultReference.integratedCurve.path.value
if not os.path.isdir(os.path.dirname(self.refNormImg)):
os.makedirs(os.path.dirname(self.refNormImg))
if os.path.isfile(self.refNormImg):
os.remove(self.refNormImg)
if os.path.isfile(self.refIntCrv):
os.remove(self.refIntCrv)
EDUtilsParallel.initializeNbThread()
def __init__(self):
"""
"""
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputBioSaxsHPLCv1_0)
self.edPluginProcessOneFile = None
self.edPluginSubtract = None
self.edPluginAutoRg = None
#self.edPluginDatCmp = None
self.xsDataResult = XSDataResultBioSaxsHPLCv1_0()
self.runId = None
self.frameId = None
self.frame = None
self.hplc_run = None
self.curve = None
self.subtracted = None
self.lstExecutiveSummary = []
self.isBuffer = False
self.intensity = None
self.stdError = None
self.ATSASRg = False