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 = XSDataResultBioSaxsMetadatav1_0.parseString(
strExpectedOutput)
xsDataResultObtained = plugin.getDataOutput()
EDAssert.strAlmostEqual(xsDataResultReference.marshal(),
xsDataResultObtained.marshal(),
"XSDataResult output are the same",
_strExcluded="bioSaxs")
################################################################################
# Compare dictionary:
################################################################################
edfRef = EdfFile.EdfFile(
xsDataResultObtained.getOutputImage().getPath().value)
edfObt = EdfFile.EdfFile(
os.path.join(self.getTestsDataImagesHome(), "bioSaxsMetadata.edf"))
########################################################################
# DEPRECATED PLUGIN => DEPREFCATED TESTS
########################################################################
# 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", "Center_1", "Center_2", "Code", "Comments", "Concentration",
# "VersionNumber",'time_of_day', ]:
# 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 key in keysRef:
# EDAssert.strAlmostEqual(headerRef[key], headerObt[key], _strComment="header value %s are the same" % key, _strExcluded="bioSaxs")
################################################################################
# Compare images
################################################################################
outputData = edfObt.GetData(0)
referenceData = edfRef.GetData(0)
EDAssert.arraySimilar(outputData,
referenceData,
_fAbsMaxDelta=0.1,
_fScaledMaxDelta=0.05,
_strComment="Images-data are the same")
def postProcess(self, _edObject=None):
EDPluginControl.postProcess(self)
EDVerbose.DEBUG("EDPluginBioSaxsMetadatav1_0.postProcess")
# Create some output data
xsDataResult = XSDataResultBioSaxsMetadatav1_0()
if self.strOutputImage is not None:
xsdImage = XSDataImage()
xsdImage.setPath(XSDataString(self.strOutputImage))
xsDataResult.setOutputImage(xsdImage)
if self.detector is not None:
# EDVerbose.DEBUG("Detector=%s" % self.detector)
xsDataResult.setDetector(XSDataString(self.detector))
if self.detectorDistance is not None:
# EDVerbose.DEBUG("DetectorDistance %s(%s)" % (self.detectorDistance, self.detectorDistance.__class__))
xsDataResult.setDetectorDistance(
XSDataLength(self.detectorDistance))
if self.pixelSize_1 is not None:
# EDVerbose.DEBUG("pixelSize_1 %s(%s)" % (self.pixelSize_1, self.pixelSize_1.__class__))
xsDataResult.setPixelSize_1(XSDataLength(self.pixelSize_1))
if self.pixelSize_2 is not None:
# EDVerbose.DEBUG("pixelSize_2 %s(%s)" % (self.pixelSize_2, self.pixelSize_2.__class__))
xsDataResult.setPixelSize_2(XSDataLength(self.pixelSize_2))
if self.beamCenter_1 is not None:
# EDVerbose.DEBUG("beamCenter_1 %s(%s)" % (self.beamCenter_1, self.beamCenter_1.__class__))
xsDataResult.setBeamCenter_1(XSDataDouble(self.beamCenter_1))
if self.beamCenter_2 is not None:
# EDVerbose.DEBUG("beamCenter_2 %s(%s)" % (self.beamCenter_2, self.beamCenter_2.__class__))
xsDataResult.setBeamCenter_2(XSDataDouble(self.beamCenter_2))
if self.beamStopDiode is not None:
# EDVerbose.DEBUG("beamStopDiode %s(%s)" % (self.beamStopDiode, self.beamStopDiode.__class__))
xsDataResult.setBeamStopDiode(XSDataDouble(self.beamStopDiode))
if self.wavelength is not None:
xsDataResult.setWavelength(XSDataWavelength(self.wavelength))
if self.maskFile is not None:
xsdFile = XSDataImage()
xsdFile.setPath(XSDataString(self.maskFile))
xsDataResult.setMaskFile(xsdFile)
if self.normalizationFactor is not None:
xsDataResult.setNormalizationFactor(
XSDataDouble(self.normalizationFactor))
if self.machineCurrent is not None:
xsDataResult.setMachineCurrent(XSDataDouble(self.machineCurrent))
if self.code is not None:
xsDataResult.setCode(XSDataString(self.code))
if self.comments is not None:
xsDataResult.setComments(XSDataString(self.comments))
if self.concentration is not None:
xsDataResult.setConcentration(XSDataDouble(self.concentration))
EDVerbose.DEBUG("xsDataResult=%s" % xsDataResult.marshal())
self.setDataOutput(xsDataResult)
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 = XSDataResultBioSaxsMetadatav1_0.parseString(strExpectedOutput)
xsDataResultObtained = plugin.getDataOutput()
EDAssert.strAlmostEqual(xsDataResultReference.marshal(), xsDataResultObtained.marshal(), "XSDataResult output are the same", _strExcluded="bioSaxs")
################################################################################
# Compare dictionary:
################################################################################
edfRef = EdfFile.EdfFile(xsDataResultObtained.getOutputImage().getPath().value)
edfObt = EdfFile.EdfFile(os.path.join(self.getTestsDataImagesHome(), "bioSaxsMetadata.edf"))
########################################################################
# DEPRECATED PLUGIN => DEPREFCATED TESTS
########################################################################
# 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", "Center_1", "Center_2", "Code", "Comments", "Concentration",
# "VersionNumber",'time_of_day', ]:
# 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 key in keysRef:
# EDAssert.strAlmostEqual(headerRef[key], headerObt[key], _strComment="header value %s are the same" % key, _strExcluded="bioSaxs")
################################################################################
# Compare images
################################################################################
outputData = edfObt.GetData(0)
referenceData = edfRef.GetData(0)
EDAssert.arraySimilar(outputData, referenceData , _fAbsMaxDelta=0.1, _fScaledMaxDelta=0.05, _strComment="Images-data are the same")
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", "bioSaxsMetadata.edf"])
strExpectedOutput = self.readAndParseFile (self.getReferenceDataOutputFile())
EDVerbose.DEBUG("strExpectedOutput:" + strExpectedOutput)
xsDataResultReference = XSDataResultBioSaxsMetadatav1_0.parseString(strExpectedOutput)
self.outputImage = xsDataResultReference.getOutputImage().getPath().value
EDVerbose.DEBUG("Output file is %s" % self.outputImage)
if not os.path.isdir(os.path.dirname(self.outputImage)):
os.makedirs(os.path.dirname(self.outputImage))
if os.path.isfile(self.outputImage):
EDVerbose.DEBUG(" Output Image file exists %s, I will remove it" % self.outputImage)
os.remove(self.outputImage)
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 = XSDataResultBioSaxsMetadatav1_0.parseString(strExpectedOutput)
xsDataResultObtained = plugin.getDataOutput()
EDAssert.strAlmostEqual(xsDataResultReference.marshal(), xsDataResultObtained.marshal(), "XSDataResult output are the same", _strExcluded="bioSaxs")
################################################################################
# Compare dictionary
################################################################################
edfRef = fabio.open(xsDataResultObtained.getOutputImage().getPath().value)
edfObt = fabio.open(os.path.join(self.getTestsDataImagesHome(), "bioSaxsMetadata.edf"))
keysRef = edfRef.header_keys
keysObt = edfObt.header_keys
keysRef.sort()
keysObt.sort()
for key in ["HeaderID", "Image", 'EDF_BinarySize', "EDF_DataBlockID", "EDF_HeaderSize", "filename", "RasterOrientation" ]:
if key in keysObt: keysObt.remove(key)
if key in keysRef: keysRef.remove(key)
# print edfObt.header
EDAssert.equal(keysRef, keysObt, _strComment="Same keys in the header dictionary")
for key in keysRef:
EDAssert.strAlmostEqual(edfRef.header[key], edfObt.header[key], _strComment="header value %s are the same" % key, _strExcluded="bioSaxs")
################################################################################
# Compare images
################################################################################
outputData = edfObt.data
referenceData = edfRef.data
EDAssert.arraySimilar(outputData, referenceData , _fAbsMaxDelta=0.1, _fScaledMaxDelta=0.05, _strComment="Images-data are the same")
def postProcess(self, _edObject=None):
"""
complex type XSDataBioSaxsExperimentSetup extends XSData{
detector : XSDataString optional
detectorDistance : XSDataLength optional
pixelSize_1 : XSDataLength optional
pixelSize_2 : XSDataLength optional
beamCenter_1 : XSDataDouble optional
beamCenter_2 : XSDataDouble optional
beamStopDiode : XSDataDouble optional
wavelength : XSDataWavelength optional
machineCurrent : XSDataDouble optional
maskFile : XSDataImage optional
normalizationFactor : XSDataDouble optional
storageTemperature: XSDataDouble optional
exposureTemperature: XSDataDouble optional
exposureTime: XSDataTime optional
frameNumber: XSDataInteger optional
frameMax: XSDataInteger optional
}
complex type XSDataBioSaxsSample extends XSData {
concentration : XSDataDouble optional
comments : XSDataString optional
code : XSDataString optional
temperature: XSDataDouble optional
"""
EDPluginExec.postProcess(self)
EDVerbose.DEBUG("EDPluginBioSaxsMetadatav1_1.postProcess")
# Create some output data
xsDataResult = XSDataResultBioSaxsMetadatav1_0()
xsdSample = XSDataBioSaxsSample()
xsdExperiment = XSDataBioSaxsExperimentSetup()
if self.strOutputImage is not None:
xsdImage = XSDataImage()
xsdImage.setPath(XSDataString(self.strOutputImage))
xsDataResult.setOutputImage(xsdImage)
if self.detector is not None:
xsdExperiment.detector = xsDataResult.detector = XSDataString(
self.detector)
if self.detectorDistance is not None:
xsdExperiment.detectorDistance = xsDataResult.detectorDistance = XSDataLength(
self.detectorDistance)
if self.pixelSize_1 is not None:
xsDataResult.pixelSize_1 = XSDataLength(self.pixelSize_1)
xsdExperiment.pixelSize_1 = xsDataResult.pixelSize_1
if self.pixelSize_2 is not None:
xsDataResult.pixelSize_2 = XSDataLength(self.pixelSize_2)
xsdExperiment.pixelSize_2 = xsDataResult.pixelSize_2
if self.beamCenter_1 is not None:
xsDataResult.beamCenter_1 = XSDataDouble(self.beamCenter_1)
xsdExperiment.beamCenter_1 = xsDataResult.beamCenter_1
if self.beamCenter_2 is not None:
xsDataResult.beamCenter_2 = XSDataDouble(self.beamCenter_2)
xsdExperiment.beamCenter_2 = xsDataResult.beamCenter_2
if self.beamStopDiode is not None:
xsdExperiment.beamStopDiode = xsDataResult.beamStopDiode = XSDataDouble(
self.beamStopDiode)
if self.wavelength is not None:
xsdExperiment.wavelength = xsDataResult.wavelength = XSDataWavelength(
self.wavelength)
if self.maskFile is not None:
xsdFile = XSDataImage()
xsdFile.setPath(XSDataString(self.maskFile))
xsdExperiment.maskFile = xsDataResult.maskFile = xsdFile
if self.normalizationFactor is not None:
xsdExperiment.normalizationFactor = xsDataResult.normalizationFactor = XSDataDouble(
self.normalizationFactor)
if self.machineCurrent is not None:
xsdExperiment.machineCurrent = xsDataResult.machineCurrent = XSDataDouble(
self.machineCurrent)
if self.storageTemperature is not None:
xsdExperiment.storageTemperature = xsDataResult.storageTemperature = XSDataDouble(
self.storageTemperature)
if self.exposureTemperature is not None:
xsdExperiment.exposureTemperature = xsDataResult.exposureTemperature = XSDataDouble(
self.exposureTemperature)
if self.exposureTime is not None:
xsdExperiment.exposureTime = xsDataResult.exposureTime = XSDataTime(
self.exposureTime)
if self.frameNumber is not None:
xsdExperiment.frameNumber = xsDataResult.frameNumber = XSDataInteger(
self.frameNumber)
if self.frameMax is not None:
xsdExperiment.frameMax = xsDataResult.frameMax = XSDataInteger(
self.frameMax)
if self.timeOfFrame is not None:
xsdExperiment.timeOfFrame = xsDataResult.timeOfFrame = XSDataTime(
self.timeOfFrame)
if self.code is not None:
xsdSample.code = xsDataResult.code = XSDataString(self.code)
if self.comments is not None:
xsdSample.comments = xsDataResult.comments = XSDataString(
self.comments)
if self.concentration is not None:
xsdSample.concentration = xsDataResult.concentration = XSDataDouble(
self.concentration)
xsDataResult.sample = xsdSample
xsDataResult.experimentSetup = xsdExperiment
self.setDataOutput(xsDataResult)
