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)
#EDVerbose.DEBUG(str([ "bioSaxsIntegrated%02i.edf" % i for i in range(1, 11) ] + ["bioSaxsAveraged.dat", "bioSaxsAveraged.edf"]))
self.loadTestImage([ "bioSaxsIntegrated%02i.edf" % i for i in range(1, 11) ] + ["bioSaxsAveraged.dat", "bioSaxsAveraged.edf"])
strExpectedOutput = self.readAndParseFile (self.getReferenceDataOutputFile())
EDVerbose.DEBUG("strExpectedOutput:" + strExpectedOutput)
xsDataResultReference = XSDataResultBioSaxsAveragev1_0.parseString(strExpectedOutput)
self.averagedCurve = xsDataResultReference.getAveragedCurve().getPath().value
EDVerbose.DEBUG("Output file is %s" % self.averagedCurve)
if not os.path.isdir(os.path.dirname(self.averagedCurve)):
os.makedirs(os.path.dirname(self.averagedCurve))
if os.path.isfile(self.averagedCurve):
EDVerbose.DEBUG(" Output Averaged Curve file exists %s, I will remove it" % self.averagedCurve)
os.remove(self.averagedCurve)
self.AveragedImage = xsDataResultReference.getAveragedImage().getPath().value
EDVerbose.DEBUG("Output Integrated Image file is %s" % self.AveragedImage)
if not os.path.isdir(os.path.dirname(self.AveragedImage)):
os.makedirs(os.path.dirname(self.AveragedImage))
if os.path.isfile(self.AveragedImage):
EDVerbose.DEBUG(" Output Integrated Image file exists %s, I will remove it" % self.AveragedImage)
os.remove(self.AveragedImage)
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)
#EDVerbose.DEBUG(str([ "bioSaxsIntegrated%02i.edf" % i for i in range(1, 11) ] + ["bioSaxsAveraged.dat", "bioSaxsAveraged.edf"]))
self.loadTestImage([ "bioSaxsIntegrated%02i.edf" % i for i in range(1, 11) ] + ["bioSaxsAveraged.dat", "bioSaxsAveraged.edf"])
strExpectedOutput = self.readAndParseFile (self.getReferenceDataOutputFile())
EDVerbose.DEBUG("strExpectedOutput:" + strExpectedOutput)
xsDataResultReference = XSDataResultBioSaxsAveragev1_0.parseString(strExpectedOutput)
self.averagedCurve = xsDataResultReference.getAveragedCurve().getPath().value
EDVerbose.DEBUG("Output file is %s" % self.averagedCurve)
if not os.path.isdir(os.path.dirname(self.averagedCurve)):
os.makedirs(os.path.dirname(self.averagedCurve))
if os.path.isfile(self.averagedCurve):
EDVerbose.DEBUG(" Output Averaged Curve file exists %s, I will remove it" % self.averagedCurve)
os.remove(self.averagedCurve)
self.AveragedImage = xsDataResultReference.getAveragedImage().getPath().value
EDVerbose.DEBUG("Output Integrated Image file is %s" % self.AveragedImage)
if not os.path.isdir(os.path.dirname(self.AveragedImage)):
os.makedirs(os.path.dirname(self.AveragedImage))
if os.path.isfile(self.AveragedImage):
EDVerbose.DEBUG(" Output Integrated Image file exists %s, I will remove it" % self.AveragedImage)
os.remove(self.AveragedImage)
def __init__(self):
"""
"""
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputBioSaxsAveragev1_0)
self.__strControlledPluginWaitMultiFile = "EDPluginWaitMultiFile"
self.__strControlledPluginSaxsMac = "EDPluginExecSaxsMacv1_0"
self.__strControlledPluginAsciiExport = "EDPluginBioSaxsAsciiExportv1_0"
self.__strControlledPluginSaxsGetMetadata = "EDPluginBioSaxsMetadatav1_1"
self.__strControlledPluginSaxsSetMetadata = "EDPluginBioSaxsMetadatav1_1"
self.__edPluginWaitMultiFile = None
self.__edPluginSaxsMac = None
self.__edPluginAsciiExport = None
self.__edPluginSaxsGetMetadata = None
self.__edPluginSaxsSetMetadata = None
self.xsdMetadata = None
self.averagedImage = None
self.integratedImages = []
self.averagedCurve = None
self.normalizationFactor = None
self.correctedImage = None
self.concentration = None
self.comments = None
self.code = None
self.strLogFile = None
self.strProcessLog = ""
self.xsdResult = XSDataResultBioSaxsAveragev1_0()
def testExecute(self):
"""
"""
self.run()
plugin = self.getPlugin()
################################################################################
# Compare XSDataResults
################################################################################
strExpectedOutput = self.readAndParseFile (self.getReferenceDataOutputFile())
# strObtainedOutput = self.readAndParseFile (self.m_edObtainedOutputDataFile)
EDVerbose.DEBUG("Checking obtained result...")
xsDataResultReference = XSDataResultBioSaxsAveragev1_0.parseString(strExpectedOutput)
xsDataResultObtained = plugin.getDataOutput()
EDAssert.strAlmostEqual(xsDataResultReference.marshal(), xsDataResultObtained.marshal(), "XSDataResult output are the same", _strExcluded="bioSaxs")
################################################################################
# Compare spectrum ascii Files
################################################################################
outputData = open(xsDataResultObtained.getAveragedCurve().getPath().value, "rb").read()
referenceData = open(os.path.join(self.getTestsDataImagesHome(), "bioSaxsAveraged.dat"), "rb").read()
EDAssert.strAlmostEqual(referenceData, outputData, _strComment="3-column ascii spectra files spectra are the same", _fRelError=0.1, _fAbsError=0.1, _strExcluded="bioSaxs")
################################################################################
# Compare images
################################################################################
edfObt = EdfFile.EdfFile(xsDataResultObtained.getAveragedImage().getPath().value)
edfRef = EdfFile.EdfFile(os.path.join(self.getTestsDataImagesHome(), "bioSaxsAveraged.edf"))
outputData = edfObt.GetData(0)
referenceData = edfRef.GetData(0)
EDAssert.arraySimilar(outputData, referenceData , _fAbsMaxDelta=0.1, _fScaledMaxDelta=0.05, _strComment="Averaged images are the same")
headerRef = edfRef.GetHeader(0)
headerObt = edfObt.GetHeader(0)
keysRef = headerRef.keys()
keysObt = headerObt.keys()
keysRef.sort()
keysObt.sort()
for key in ["HeaderID", "Image", 'EDF_BinarySize', "EDF_DataBlockID", "EDF_HeaderSize", "filename", "RasterOrientation", "History-1", "History-1~1" ]:
if key in keysObt: keysObt.remove(key)
if key in keysRef: keysRef.remove(key)
EDAssert.equal(keysRef, keysObt, _strComment="Same keys in the header dictionary for Corrected Images")
for key in keysRef:
EDAssert.strAlmostEqual(headerRef[key], headerObt[key], _strComment="header value in Averaged %s are the same" % key, _strExcluded="bioSaxs")
def testExecute(self):
"""
"""
self.run()
plugin = self.getPlugin()
################################################################################
# Compare XSDataResults
################################################################################
strExpectedOutput = self.readAndParseFile (self.getReferenceDataOutputFile())
# strObtainedOutput = self.readAndParseFile (self.m_edObtainedOutputDataFile)
EDVerbose.DEBUG("Checking obtained result...")
xsDataResultReference = XSDataResultBioSaxsAveragev1_0.parseString(strExpectedOutput)
xsDataResultObtained = plugin.getDataOutput()
EDAssert.strAlmostEqual(xsDataResultReference.marshal(), xsDataResultObtained.marshal(), "XSDataResult output are the same", _strExcluded="bioSaxs")
################################################################################
# Compare spectrum ascii Files
################################################################################
outputData = open(xsDataResultObtained.getAveragedCurve().getPath().value, "rb").read()
referenceData = open(os.path.join(self.getTestsDataImagesHome(), "bioSaxsAveraged.dat"), "rb").read()
EDAssert.strAlmostEqual(referenceData, outputData, _strComment="3-column ascii spectra files spectra are the same", _fRelError=0.1, _fAbsError=0.1, _strExcluded="bioSaxs")
################################################################################
# Compare images
################################################################################
edfObt = EdfFile.EdfFile(xsDataResultObtained.getAveragedImage().getPath().value)
edfRef = EdfFile.EdfFile(os.path.join(self.getTestsDataImagesHome(), "bioSaxsAveraged.edf"))
outputData = edfObt.GetData(0)
referenceData = edfRef.GetData(0)
EDAssert.arraySimilar(outputData, referenceData , _fAbsMaxDelta=0.1, _fScaledMaxDelta=0.05, _strComment="Averaged images are the same")
headerRef = edfRef.GetHeader(0)
headerObt = edfObt.GetHeader(0)
keysRef = headerRef.keys()
keysObt = headerObt.keys()
keysRef.sort()
keysObt.sort()
for key in ["HeaderID", "Image", 'EDF_BinarySize', "EDF_DataBlockID", "EDF_HeaderSize", "filename", "RasterOrientation", "History-1", "History-1~1" ]:
if key in keysObt: keysObt.remove(key)
if key in keysRef: keysRef.remove(key)
EDAssert.equal(keysRef, keysObt, _strComment="Same keys in the header dictionary for Corrected Images")
for key in keysRef:
EDAssert.strAlmostEqual(headerRef[key], headerObt[key], _strComment="header value in Averaged %s are the same" % key, _strExcluded="bioSaxs")
