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",
"bioSaxsProcessIntegrated.dat"
])
strExpectedOutput = self.readAndParseFile(
self.getReferenceDataOutputFile())
EDVerbose.DEBUG("strExpectedOutput:" + strExpectedOutput)
xsDataResultReference = XSDataResultBioSaxsProcessOneFilev1_0.parseString(
strExpectedOutput)
self.refNormImg = xsDataResultReference.normalizedImage.path.value
self.refIntImg = xsDataResultReference.integratedImage.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.refIntImg):
os.remove(self.refIntImg)
if os.path.isfile(self.refIntCrv):
os.remove(self.refIntCrv)
def testExecute(self):
"""
"""
self.run()
plugin = self.getPlugin()
################################################################################
# Compare XSDataResults
################################################################################
strExpectedOutput = self.readAndParseFile (self.getReferenceDataOutputFile())
EDVerbose.DEBUG("Checking obtained result...")
xsDataResultReference = XSDataResultBioSaxsProcessOneFilev1_0.parseString(strExpectedOutput)
xsDataResultObtained = plugin.getDataOutput()
EDAssert.strAlmostEqual(xsDataResultReference.marshal(), xsDataResultObtained.marshal(), "XSDataResult output are the same", _strExcluded="bioSaxs")
################################################################################
# Compare Ascii HEADER files
################################################################################
asciiObt = os.linesep.join([i.strip() for i in open(xsDataResultObtained.integratedCurve.path.value) if i.startswith("#") and "Raster" not in i])
asciiRef = os.linesep.join([i.strip() for i in open(os.path.join(self.getTestsDataImagesHome(), "bioSaxsProcessIntegrated1_2.dat")) if i.startswith("#") and "Raster" not in i])
EDAssert.strAlmostEqual(asciiObt, asciiRef, _strComment="ascii header files are the same", _fRelError=0.1, _strExcluded=os.environ["USER"])
dataObt = numpy.loadtxt(xsDataResultObtained.integratedCurve.path.value)
dataRef = numpy.loadtxt(os.path.join(self.getTestsDataImagesHome(), "bioSaxsProcessIntegrated1_2.dat"))
EDAssert.curveSimilar((dataObt[:, 0], dataObt[:, 1]), (dataRef[:, 0], dataRef[:, 1]), "data are the same", 0.6)
EDAssert.curveSimilar((dataObt[:, 0], dataObt[:, 2]), (dataRef[:, 0], dataRef[:, 2]), "errors are the same", 0.6)
EDVerbose.screen("Execution time for %s: %.3fs" % (plugin.getClassName(), plugin.getRunTime()))
def testExecute(self):
"""
"""
self.run()
plugin = self.getPlugin()
################################################################################
# Compare XSDataResults
################################################################################
strExpectedOutput = self.readAndParseFile (self.getReferenceDataOutputFile())
EDVerbose.DEBUG("Checking obtained result...")
xsDataResultReference = XSDataResultBioSaxsProcessOneFilev1_0.parseString(strExpectedOutput)
xsDataResultObtained = plugin.getDataOutput()
EDAssert.strAlmostEqual(xsDataResultReference.marshal(), xsDataResultObtained.marshal(), "XSDataResult output are the same", _strExcluded="bioSaxs")
################################################################################
# Compare dictionary
################################################################################
obtFile = xsDataResultObtained.integratedImage.path.value
refFile = os.path.join(self.getTestsDataImagesHome(), "bioSaxsProcessIntegrated.edf")
EDVerbose.DEBUG("fileRef=%s fileObt=%s" % (refFile, obtFile))
edfRef = openimage(refFile)
edfObt = openimage(obtFile)
headerRef = edfRef.header
headerObt = edfObt.header
keysRef = headerRef.keys()
keysObt = headerObt.keys()
keysRef.sort()
keysObt.sort()
# EDAssert.equal(keysRef, keysObt, _strComment="Same keys in the header dict")
for key in keysRef:
if not (key.startswith("History") or key in [ "Compression", "DDummy", "Dummy", "EDF_HeaderSize", "HeaderID", "Image", "filename", "RasterOrientation"]):
EDAssert.strAlmostEqual(headerRef[key], headerObt[key], _strComment="header value %s are the same" % key, _strExcluded="bioSaxs")
################################################################################
# Compare images
################################################################################
outputData = edfRef.data
referenceData = edfObt.data
EDAssert.arraySimilar(numpy.maximum(outputData, 0), numpy.maximum(referenceData, 0) , _fScaledMaxDelta=0.05, _strComment="Images-data are the same")
outputData = edfRef.next().data
referenceData = edfObt.next().data
EDAssert.arraySimilar(numpy.maximum(outputData, 0), numpy.maximum(referenceData, 0) , _fScaledMaxDelta=0.05, _strComment="Images-ESD are the same")
################################################################################
# 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_1.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 testExecute(self):
"""
"""
self.run()
plugin = self.getPlugin()
################################################################################
# Compare XSDataResults
################################################################################
strExpectedOutput = self.readAndParseFile (self.getReferenceDataOutputFile())
EDVerbose.DEBUG("Checking obtained result...")
xsDataResultReference = XSDataResultBioSaxsProcessOneFilev1_0.parseString(strExpectedOutput)
xsDataResultObtained = plugin.getDataOutput()
EDAssert.strAlmostEqual(xsDataResultReference.marshal(), xsDataResultObtained.marshal(), "XSDataResult output are the same", _strExcluded="bioSaxs")
################################################################################
# Compare dictionary
################################################################################
obtFile = xsDataResultObtained.integratedImage.path.value
refFile = os.path.join(self.getTestsDataImagesHome(), "bioSaxsProcessIntegrated.edf")
EDVerbose.DEBUG("fileRef=%s fileObt=%s" % (refFile, obtFile))
edfRef = openimage(refFile)
edfObt = openimage(obtFile)
headerRef = edfRef.header
headerObt = edfObt.header
keysRef = headerRef.keys()
keysObt = headerObt.keys()
keysRef.sort()
keysObt.sort()
# EDAssert.equal(keysRef, keysObt, _strComment="Same keys in the header dict")
for key in keysRef:
if not (key.startswith("History") or key in [ "Compression", "DDummy", "Dummy", "EDF_HeaderSize", "HeaderID", "Image", "filename", "RasterOrientation"]):
EDAssert.strAlmostEqual(headerRef[key], headerObt[key], _strComment="header value %s are the same" % key, _strExcluded="bioSaxs")
################################################################################
# Compare images
################################################################################
outputData = edfRef.data
referenceData = edfObt.data
EDAssert.arraySimilar(numpy.maximum(outputData, 0), numpy.maximum(referenceData, 0) , _fScaledMaxDelta=0.05, _strComment="Images-data are the same")
outputData = edfRef.next().data
referenceData = edfObt.next().data
EDAssert.arraySimilar(numpy.maximum(outputData, 0), numpy.maximum(referenceData, 0) , _fScaledMaxDelta=0.05, _strComment="Images-ESD are the same")
################################################################################
# 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_1.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 postProcess(self, _edObject=None):
EDPluginControl.postProcess(self)
self.DEBUG("EDPluginBioSaxsProcessOneFilev1_1.postProcess")
# Create some output data
xsDataResult = XSDataResultBioSaxsProcessOneFilev1_0()
xsDataResult.normalizedImage = self.normalizedImage
xsDataResult.integratedImage = self.integratedImage
xsDataResult.integratedCurve = self.integratedCurve
xsDataResult.status = XSDataStatus(executiveSummary=XSDataString(os.linesep.join(self.lstExecutiveSummary)))
self.setDataOutput(xsDataResult)
def postProcess(self, _edObject=None):
EDPluginControl.postProcess(self)
self.DEBUG("EDPluginBioSaxsProcessOneFilev1_3.postProcess")
# Create some output data
xsDataResult = XSDataResultBioSaxsProcessOneFilev1_0()
if os.path.exists(self.integratedCurve):
xsDataResult.integratedCurve = XSDataFile(XSDataString(self.integratedCurve))
xsDataResult.sample = self.sample
xsDataResult.experimentSetup = self.experimentSetup
xsDataResult.status = XSDataStatus(executiveSummary=XSDataString(os.linesep.join(self.lstExecutiveSummary)))
self.setDataOutput(xsDataResult)
def __init__(self):
"""
"""
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputBioSaxsProcessOneFilev1_0)
self.__edPluginWaitFile = None
self.rawImage = None
self.rawImageSize = XSDataInteger(1024)
self.normalizedImage = None
self.integratedCurve = None
self.integratedImage = None
self.lstExecutiveSummary = []
self.sample = None
self.experimentSetup = None
self.integrator_config = {}
self.scale = None
self.detector = None
self.xsDataResult = XSDataResultBioSaxsProcessOneFilev1_0()
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 = XSDataResultBioSaxsProcessOneFilev1_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()
