def __init__(self, _strTestName=None):
EDTestCasePluginExecute.__init__(self, "EDPluginControlEDNAprocv1_0")
self.strTestDir = os.path.join(self.getPluginTestsDataHome(), "id29_20140505")
self.setDataInputFile(os.path.join(self.strTestDir,
"edna-autoproc-input.xml"))
self.setNoExpectedWarningMessages(1)
self.setNoExpectedErrorMessages(1) # insufficient percentage of indexed reflections
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)
self.loadTestImage([ "bioSaxsMask.edf", "bioSaxsNormalized.edf", "bioSaxsIntegratedv1_3.dat", "bioSaxsCorrected.edf"])
strExpectedOutput = self.readAndParseFile (self.getReferenceDataOutputFile())
EDVerbose.DEBUG("strExpectedOutput:" + strExpectedOutput)
xsDataResultReference = XSDataResultBioSaxsAzimutIntv1_0.parseString(strExpectedOutput)
self.integratedCurve = xsDataResultReference.getIntegratedCurve().getPath().value
EDVerbose.DEBUG("Output file is %s" % self.integratedCurve)
if not os.path.isdir(os.path.dirname(self.integratedCurve)):
os.makedirs(os.path.dirname(self.integratedCurve))
if os.path.isfile(self.integratedCurve):
EDVerbose.DEBUG(" Output Integrated Curve file exists %s, I will remove it" % self.integratedCurve)
os.remove(self.integratedCurve)
EDUtilsParallel.initializeNbThread()
# self.correctedImage = xsDataResultReference.getCorrectedImage().getPath().value
# EDVerbose.DEBUG("Output Corrected Image file is %s" % self.correctedImage)
# if not os.path.isdir(os.path.dirname(self.correctedImage)):
# os.makedirs(os.path.dirname(self.correctedImage))
# if os.path.isfile(self.correctedImage):
# EDVerbose.DEBUG(" Output Corrected Image file exists %s, I will remove it" % self.correctedImage)
# os.remove(self.correctedImage)
if not pyFAI.version.startswith("0.7"):
EDVerbose.ERROR('pyFAI is not the right version, tested only with 0.7.2, here running version %s' % pyFAI.version)
def __init__(self, _strTestName=None):
EDTestCasePluginExecute.__init__(self, "EDPluginBioSaxsFlushHPLCv1_2")
self.setDataInputFile(os.path.join(self.getPluginTestsDataHome(), "XSDataInputHPLCFlush_reference.xml"))
self.setReferenceDataOutputFile(
os.path.join(self.getPluginTestsDataHome(), "BioSaxsFlushHPLCv1_2_dataOutput.xml")
)
def __init__(self, _strTestName=None):
"""
"""
EDTestCasePluginExecute.__init__(self, "EDPluginExecGnomv0_2")
self.setConfigurationFile(self.getRefConfigFile())
self.setDataInputFile(os.path.join(self.getPluginTestsDataHome(), "XSDataInputGnom_reference.xml"))
self.setReferenceDataOutputFile(os.path.join(self.getPluginTestsDataHome(), "XSDataResultGnom_reference.xml"))
def __init__(self, _strTestName=None):
EDTestCasePluginExecute.__init__(self, _strTestName)
self.setConfigurationFile(self.getRefConfigFile())
edPluginMOSFLM = self.createPlugin()
xsPluginItem = edPluginMOSFLM.getConfiguration()
if xsPluginItem is None:
xsPluginItem = EDApplication.getApplicationPluginConfiguration(self.getPluginName())
if xsPluginItem is None:
# No application wide configuration file found! Try to find a project specific config file:
xsPluginItem = EDApplication.getProjectPluginConfiguration(self.getPluginName())
if xsPluginItem is None:
EDVerbose.DEBUG("EDPlugin.configure: No plugin configuration found for " + self.getPluginName())
xsPluginItem = XSPluginItem()
else:
edPluginMOSFLM.setConfiguration(xsPluginItem)
# edPluginMOSFLM.configure()
strMOSFLMVersion = edPluginMOSFLM.getStringConfigurationParameterValue("execProcessScriptVersionString")
if strMOSFLMVersion.find("7.0.1") != -1:
strResultDir = "executionTestResult_v701_20070820"
elif strMOSFLMVersion.find("7.0.5") != -1:
strResultDir = "executionTestResult_v706_20090812"
elif strMOSFLMVersion.find("7.0.6") != -1:
strResultDir = "executionTestResult_v706_20100126"
else:
strResultDir = "executionTestResult_v707_20101220"
strPluginTestDataHome = self.getPluginTestsDataHome()
self.strExecutionTestDataInputHome = os.path.join(strPluginTestDataHome, "executionTestInput")
self.strExecutionTestDataResultHome = os.path.join(strPluginTestDataHome, strResultDir)
def __init__(self, _strTestName=None):
"""
"""
EDTestCasePluginExecute.__init__(self, "EDPluginExecMtz2Variousv1_0")
# self.setConfigurationFile(os.path.join(self.getPluginTestsDataHome(),
# "XSConfiguration_Mtz2Variousv1_0.xml"))
self.setDataInputFile(os.path.join(self.getPluginTestsDataHome(), "XSDataInputMtz2Various_reference.xml"))
def preProcess(self):
EDTestCasePluginExecute.preProcess(self)
listTestImage = []
for iImageNumber in range(1, 10):
strImageName = "testscale_1_%03d.img" % iImageNumber
listTestImage.append(strImageName)
self.loadTestImage(listTestImage)
def __init__(self, _strTestName="EDPluginSubWedgeMergev10"):
EDTestCasePluginExecute.__init__(self, _strTestName)
self.setConfigurationFile(self.getRefConfigFile())
self.setDataInputFile(os.path.join(self.getPluginTestsDataHome(), "XSDataInputSubWedgeMerge_reference.xml"))
self.setReferenceDataOutputFile(
os.path.join(self.getPluginTestsDataHome(), "XSDataResultSubWedgeMerge_reference.xml")
)
def __init__(self,):
"""
"""
self.EPSILON_REL = 0.01 #1 percent error
self.EPSILON_ABS = 0.0001 #1 percent error
EDTestCasePluginExecute.__init__(self, "EDPluginFIT2DCakev1_1", "EDPluginControlFIT2D-v1.0")
self.setConfigurationFile(self.getRefConfigFile())
self.setDataInputFile(os.path.join(self.getPluginTestsDataHome(), \
"XSDataInputFIT2DCake_reference.xml"))
self.setReferenceDataOutputFile(os.path.join(self.getPluginTestsDataHome(), \
"XSDataResultFIT2DCake_reference.xml"))
self.m_edObtainedOutputDataFile = self.getPluginName() + "_output.xml"
strSplineFileName = "frelon_spline_file_to_correct_SPD.spline"
strPathToSplineFile = os.path.join(self.getTestsDataImagesHome(), strSplineFileName)
if (not os.path.exists(strPathToSplineFile)):
EDUtilsFile.copyFile(os.path.join(self.getPluginTestsDataHome(), strSplineFileName), \
strPathToSplineFile)
self.m_iNoErrorMessages = 0
self.m_iNoWarningMessages = 0
def __init__(self, _edStringTestName=None):
EDTestCasePluginExecute.__init__(self, "EDPluginControlImageQualityIndicatorsv1_1")
self.setRequiredPluginConfiguration("EDPluginDistlSignalStrengthv1_1")
self.setConfigurationFile(os.path.join(self.getPluginTestsDataHome(), "XSConfiguration.xml"))
self.setDataInputFile(os.path.join(self.getPluginTestsDataHome(), "XSDataInputControlImageQualityIndicators_timeOut.xml"))
self.setNoExpectedErrorMessages(1)
self.setAcceptPluginFailure(True)
def __init__(self, _edStringTestName=None):
EDTestCasePluginExecute.__init__(self, "EDPluginControlStrategyv10", "EDPluginControlStrategy-v1.0", _edStringTestName)
self.setRequiredPluginConfiguration("EDPluginBestv1_1")
self.setRequiredPluginConfiguration("EDPluginRaddosev10")
self.setConfigurationFile(self.getRefConfigFile())
self.setDataInputFile(os.path.join(self.getPluginTestsDataHome(), "XSDataStrategyv10Input_reference_03.xml"))
self.setReferenceDataOutputFile(os.path.join(self.getPluginTestsDataHome(), "XSDataStrategyv10Output_reference_03.xml"))
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([ "autosubtracted.dat"])
def __init__(self, _strTestName=None):
EDTestCasePluginExecute.__init__(self, "EDPluginControlIndexingIndicatorsv1_1")
self.setRequiredPluginConfiguration("EDPluginMOSFLMIndexingv10")
self.setRequiredPluginConfiguration("EDPluginLabelitDistlv1_1")
self.setConfigurationFile(self.getRefConfigFile())
self.setDataInputFile(os.path.join(self.getPluginTestsDataHome(), \
"XSDataCollection_reference.xml"), "dataCollection")
def preProcess(self):
EDTestCasePluginExecute.preProcess(self)
self.loadTestImage([ "ref-testscale_1_001_pred.jpg", "ref-testscale_1_002_pred.jpg",
"B.jpg", "phi_overlap.jpg", "compl.jpg", "I2D.jpg",
"ref-testscale_1_001.jpg", "ref-testscale_1_002.jpg",
"ref-testscale_1_001.thumbnail.jpg", "ref-testscale_1_002.thumbnail.jpg",
])
def preProcess(self):
"""
PreProcess of the execution test: download an EDF file from http://www.edna-site.org
and remove any existing output file, i.e. /tmp/diff6105.edf
"""
EDTestCasePluginExecute.preProcess(self)
self.loadTestImage([self.im1 , self.im2 ])
def __init__(self, _strTestName=None):
# EDTestCasePluginExecute.__init__(self, "EDPluginControlCharAtNewOrientationv2_0", "EDPluginControlCharacterisation-v1.0", _strTestName)
EDTestCasePluginExecute.__init__(
self, "EDPluginControlCharAtNewOrientationv2_0", "EDPluginControlCharAtNewOrientation-v2.0", _strTestName
)
self.setRequiredPluginConfiguration("EDPluginMOSFLMIndexingv10")
self.setRequiredPluginConfiguration("EDPluginMOSFLMIntegrationv10")
self.setRequiredPluginConfiguration("EDPluginMOSFLMGeneratePredictionv10")
self.setRequiredPluginConfiguration("EDPluginBestv1_1")
self.setRequiredPluginConfiguration("EDPluginRaddosev10")
self.setConfigurationFile(self.getRefConfigFile())
self.setDataInputFile(
os.path.join(self.getPluginTestsDataHome(), "XSDataInputCharacterisation_reference_KAPPA_Anomalous.xml"),
"mxv1InputCharacterisation",
)
self.setDataInputFile(
os.path.join(self.getPluginTestsDataHome(), "mxv2_XSDataCollection_reference.xml"), "mxv2DataCollection"
)
self.setDataInputFile(
os.path.join(
self.getPluginTestsDataHome(), "ControlCharForReorientationv2_0_dataOutput_betterResolution.xml"
),
"mxv1ResultCharacterisation_Reference",
)
self.setDataInputFile(
os.path.join(self.getPluginTestsDataHome(), "mxv2_XSDataCollection_Orig_reference.xml"),
"mxv2DataCollection_Reference",
)
self.setDataInputFile(
os.path.join(self.getPluginTestsDataHome(), "STAC_DNA_kappa_alignment_response"), "possibleOrientations"
)
def __init__(self, _strTestName=None):
EDTestCasePluginExecute.__init__(self, "EDPluginControlSubWedgeAssemblyv2_0")
self.setConfigurationFile(self.getRefConfigFile())
self.setDataInputFile(os.path.join(self.getPluginTestsDataHome(), "XSDataInputSubWedgeAssemble_reference.xml"))
self.setReferenceDataOutputFile(os.path.join(self.getPluginTestsDataHome(), "XSDataResultSubWedgeAssemble_reference.xml"), "mxv1Assemble")
self.setReferenceDataOutputFile(os.path.join(self.getPluginTestsDataHome(), "mxv2_XSDataCollection_reference.xml"), "mxv2DataCollection")
def preProcess(self):
"""
PreProcess of the execution test: download an EDF file from http://www.edna-site.org
and remove any existing output file, i.e. /tmp/diff6105.edf
"""
EDTestCasePluginExecute.preProcess(self)
self.loadTestImage([ "FullFieldXAS_00.jpg.key.gz", "FullFieldXAS_01.jpg.key.gz" ])
def __init__(self, _pyStrTestName=None):
EDTestCasePluginExecute.__init__(self, "EDPluginControlStrategyv1_2")
self.setRequiredPluginConfiguration("EDPluginBestv1_2")
self.setRequiredPluginConfiguration("EDPluginRaddosev10")
self.setConfigurationFile(self.getRefConfigFile())
self.setDataInputFile(os.path.join(self.getPluginTestsDataHome(), "XSDataInputStrategy_reference.xml"))
self.setReferenceDataOutputFile(os.path.join(self.getPluginTestsDataHome(), "XSDataResultStrategy_reference.xml"))
def __init__(self, _edStringTestName=None):
EDTestCasePluginExecute.__init__(self, "EDPluginControlCopyUnitCellMTZtoPDBv10")
self.setDataInputFile(
os.path.join(self.getPluginTestsDataHome(), "XSDataInputCopyUnitCellMTZtoPDB_reference.xml")
)
self.setReferenceDataOutputFile(
os.path.join(self.getPluginTestsDataHome(), "XSDataResultCopyUnitCellMTZtoPDB_reference.xml")
)
def __init__(self, _strTestName = None):
EDTestCasePluginExecute.__init__(self, "EDPluginControlISPyB")
# self.setConfigurationFile(os.path.join(self.getPluginTestsDataHome(),
# "XSConfiguration_ISPyB.xml"))
self.setDataInputFile(os.path.join(self.getPluginTestsDataHome(), \
"XSDataInputISPyB_reference.xml"))
self.setReferenceDataOutputFile(os.path.join(self.getPluginTestsDataHome(), \
"XSDataResultISPyB_reference.xml"))
def __init__(self, _strTestName=None):
EDTestCasePluginExecute.__init__(self, "EDPluginControlSaxsModelingv1_1")
self.setConfigurationFile(os.path.join(self.getPluginTestsDataHome(),
"XSConfiguration_SaxsModelingv1_0.xml"))
self.setDataInputFile(os.path.join(self.getPluginTestsDataHome(), \
"XSDataInputSaxsModelingv1_0_reference.xml"))
self.setReferenceDataOutputFile(os.path.join(self.getPluginTestsDataHome(), \
"XSDataResultSaxsModelingv1_0_reference.xml"))
def preProcess(self):
"""
Download reference 1D curves
"""
EDTestCasePluginExecute.preProcess(self)
self.loadTestImage([ "noise1.dat", "noise2.dat" ])
self.setReferenceDataOutputFile(os.path.join(self.getPluginTestsDataHome(), \
"XSDataResultDatcmp_reference.xml-" + self.plugin.config.get("atsasVersion", "2.5.2")))
def __init__(self, _strTestName=None):
EDTestCasePluginExecute.__init__(self, "EDPluginBioSaxsAzimutIntv1_2")
# self.setConfigurationFile(os.path.join(self.getPluginTestsDataHome(),
# "XSConfiguration_<basePluginName>.xml"))
self.setDataInputFile(os.path.join(self.getPluginTestsDataHome(), \
"XSDataInputBioSaxsAzimutIntv1_1_reference.xml"))
self.setReferenceDataOutputFile(os.path.join(self.getPluginTestsDataHome(), \
"XSDataResultBioSaxsAzimutIntv1_2_reference.xml"))
def __init__(self, _strTestName=None):
EDTestCasePluginExecute.__init__(self, "EDPluginBioSaxsProcessOneFilev1_2")
# self.setConfigurationFile(os.path.join(self.getPluginTestsDataHome(),
# "XSConfiguration_BioSaxsProcessOneFile.xml"))
self.setDataInputFile(os.path.join(self.getPluginTestsDataHome(), \
"XSDataInputBioSaxsProcessOneFile_reference.xml"))
self.setReferenceDataOutputFile(os.path.join(self.getPluginTestsDataHome(), \
"XSDataResultBioSaxsProcessOneFile_reference_v1_2.xml"))
def preProcess(self):
"""
PreProcess of the execution test: download an EDF file from http://www.edna-site.org
and remove any existing output file, i.e. /tmp/diff6105.edf
"""
EDTestCasePluginExecute.preProcess(self)
self.loadTestImage([ "normaliseImageDark10.edf", "normaliseImageDark15.edf", "normaliseImageDark2.edf", "normaliseImageDark3.edf", "normaliseImageData10.edf", "normaliseImageData15.edf", "normaliseImageFlat2.edf", "normaliseImageFlat3.edf"])
strExpectedOutput = self.readAndParseFile (self.getReferenceDataOutputFile())
def __init__(self, _strTestName=None):
EDTestCasePluginExecute.__init__(self, "EDPluginControlMedianFilterImagev1_0")
# self.setConfigurationFile(os.path.join(self.getPluginTestsDataHome(),
# "XSConfiguration_MedianFilterImage.xml"))
self.setDataInputFile(os.path.join(self.getPluginTestsDataHome(), \
"XSDataInputMedianFilterImage_reference.xml"))
self.setReferenceDataOutputFile(os.path.join(self.getPluginTestsDataHome(), \
"XSDataResultMedianFilterImage_empty.xml"))
def __init__(self, _edStringTestName=None):
"""
"""
EDTestCasePluginExecute.__init__(self, "EDPluginControlIntegrationv10", "EDPluginControlIntegration-v0.1", _edStringTestName)
self.setRequiredPluginConfiguration("EDPluginMOSFLMIntegrationv10")
self.setConfigurationFile(self.getRefConfigFile())
self.setDataInputFile(os.path.join(self.getPluginTestsDataHome(), "XSDataIntegrationInput_reference.xml"))
self.setReferenceDataOutputFile(os.path.join(self.getPluginTestsDataHome(), "XSDataIntegrationResult_reference.xml"))
def __init__(self, _edStringTestName=None):
"""
Sets config file + input and output reference files.
"""
EDTestCasePluginExecute.__init__(self, "EDPluginISPyBStoreAutoProcv1_3")
self.setConfigurationFile(os.path.join(self.getPluginTestsDataHome(), "XSConfiguration_ESRF_testDataBase.xml"))
self.setDataInputFile(os.path.join(self.getPluginTestsDataHome(), "XSDataInputStoreAutoProc_failedProcessing.xml"))
def preProcess(self):
EDTestCasePluginExecute.preProcess(self)
self.loadTestImage(["FAE_1_1_00001.cbf"])
def __init__(self, _strTestName=None):
EDTestCasePluginExecute.__init__(self, "EDPluginExecReadDataBM23v1_0")
self.setDataInputFile(os.path.join(self.getPluginTestsDataHome(), \
"XSDataInputReadDataBM23_up.xml"))
def preProcess(self):
"""
upload reference file
"""
EDTestCasePluginExecute.preProcess(self)
self.loadTestImage(["BM23.up"])
def preProcess(self):
EDTestCasePluginExecute.preProcess(self)
self.loadTestImage(
["ref-testscale_1_001.img", "ref-testscale_1_002.img"])
def __init__(self, _strTestName=None):
EDTestCasePluginExecute.__init__(
self, "EDPluginControlPyarchThumbnailGeneratorParallelv1_0")
self.setDataInputFile(os.path.join(self.getPluginTestsDataHome(), \
"XSDataInputPyarchThumbnailGeneratorParallel_png.xml"))
def preProcess(self):
EDTestCasePluginExecute.preProcess(self)
self.loadTestImage([
"B.jpg", "I2D.jpg", "phi_overlap.jpg", "compl.jpg",
"ref-testscale_1_001_pred.jpg", "ref-testscale_1_002_pred.jpg"
])
def __init__(self, _oalStringTestName=None):
EDTestCasePluginExecute.__init__(self, "EDPluginDozorv1_0")
self.setConfigurationFile(self.getRefConfigFile())
self.setDataInputFile(
os.path.join(self.getPluginTestsDataHome(),
"XSDataInputDozor_wedgeNumber.xml"))
def preProcess(self):
EDTestCasePluginExecute.preProcess(self)
def __init__(self, _edStringTestName=None):
EDTestCasePluginExecute.__init__(self, "EDPluginControlISPyBv1_4")
self.setDataInputFile(os.path.join(self.getPluginTestsDataHome(), \
"XSDataInputControlISPyB_reference.xml"))
def preProcess(self):
"""
Download reference 1D curves
"""
EDTestCasePluginExecute.preProcess(self)
self.loadTestImage(["datgnom.out"])
def preProcess(self):
"""
Download reference 1D curves
"""
EDTestCasePluginExecute.preProcess(self)
self.loadTestImage([ "noise1.dat", "noise2.dat" ])
def __init__(self, _oalStringTestName=None):
EDTestCasePluginExecute.__init__(self, "EDPluginHTML2PDFv1_0")
self.setConfigurationFile(self.getRefConfigFile())
self.setDataInputFile(os.path.join(self.getPluginTestsDataHome(), "XSDataInputHTML2PDF_reference.xml"))
def preProcess(self):
EDTestCasePluginExecute.preProcess(self)
self.loadTestImage(
["THAU_1_0001.cbf", "THAU_1_0002.cbf", "THAU_1_0003.cbf"])
def preProcess(self):
"""
"""
EDTestCasePluginExecute.preProcess(self)
self.loadTestImage(["diff6105.edf"])
