def testGenerateMOSFLMCommands(self):
"""
"""
pluginGeneratePrediction = self.createPlugin()
pluginGeneratePrediction.setScriptExecutable("cat")
pluginGeneratePrediction.configure()
xsDataMOSFLMInputGeneratePrediction = self.generateDataMOSFLMInputGeneratePrediction(
)
pluginGeneratePrediction.setDataInput(
xsDataMOSFLMInputGeneratePrediction)
pluginGeneratePrediction.generateMOSFLMCommands()
listCommandsReference = [
'WAVELENGTH 0.934', 'DISTANCE 198.4', 'BEAM 102.5 104.7',
'DETECTOR ADSC', 'DIRECTORY ' + self.strDataImagePath,
'TEMPLATE ref-testscale_1_###.img', 'XGUI ON',
'IMAGE 1 PHI 0.000000 TO 1.000000', 'GO', 'PREDICT_SPOTS',
'CREATE_IMAGE PREDICTION ON BINARY TRUE FILENAME ' +
pluginGeneratePrediction.getPredictionImageFileName(), 'RETURN',
'EXIT'
]
listCommands = pluginGeneratePrediction.getListCommandExecution()
#print listCommandsReference
#print listCommands
EDAssert.equal(listCommandsReference, listCommands)
self.cleanUp(pluginGeneratePrediction)
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 testParseMosflmScriptsOutput(self):
"""
This method tests the parsing of the MOSFLM script generated by Labelit.
"""
edPluginLabelitv10 = self.createPlugin()
# First file from version 1000rc11
strPathToMOSFLMScript = os.path.join(self.getPluginTestsDataHome(), "integration05_csh_v1000rc11.txt")
strMOSFLMScript = self.readAndParseFile(strPathToMOSFLMScript)
xsDataLabelitMosflmScriptsOutput = edPluginLabelitv10.parseMosflmScriptsOutput(strMOSFLMScript)
xsDataLabelitMosflmScriptsOutput.exportToFile("XSDataLabelitMosflmScriptsOutput_reference.xml")
strLabelitMosflmScriptsOutputFile = os.path.join(self.getPluginTestsDataHome(), "XSDataLabelitMosflmScriptsOutput_reference.xml")
strLabelitMosflmScriptsOutputXML = self.readAndParseFile(strLabelitMosflmScriptsOutputFile)
from XSDataLabelitv10 import XSDataLabelitMosflmScriptsOutput
xsDataLabelitMosflmScriptsOutputReference = XSDataLabelitMosflmScriptsOutput.parseString(strLabelitMosflmScriptsOutputXML)
EDAssert.equal(xsDataLabelitMosflmScriptsOutputReference.marshal(), xsDataLabelitMosflmScriptsOutput.marshal())
# Second file from version 1000b1
strPathToMOSFLMScript = os.path.join(self.getPluginTestsDataHome(), "integration05_csh_v1000b1.txt")
strMOSFLMScript = self.readAndParseFile(strPathToMOSFLMScript)
xsDataLabelitMosflmScriptsOutput = edPluginLabelitv10.parseMosflmScriptsOutput(strMOSFLMScript)
xsDataLabelitMosflmScriptsOutput.exportToFile("XSDataLabelitMosflmScriptsOutput_v1000b1_reference.xml")
strLabelitMosflmScriptsOutputFile = os.path.join(self.getPluginTestsDataHome(), "XSDataLabelitMosflmScriptsOutput_v1000b1_reference.xml")
strLabelitMosflmScriptsOutputXML = self.readAndParseFile(strLabelitMosflmScriptsOutputFile)
from XSDataLabelitv10 import XSDataLabelitMosflmScriptsOutput
xsDataLabelitMosflmScriptsOutputReference = XSDataLabelitMosflmScriptsOutput.parseString(strLabelitMosflmScriptsOutputXML)
EDAssert.equal(xsDataLabelitMosflmScriptsOutputReference.marshal(), xsDataLabelitMosflmScriptsOutput.marshal())
def testCopyHTMLFilesAndDir(self):
if not os.path.exists(EDUtilsPath.getEdnaUserTempFolder()):
os.mkdir(EDUtilsPath.getEdnaUserTempFolder())
strTestFromDir = os.path.join(EDUtilsPath.getEdnaUserTempFolder(), "TestFromDir")
shutil.rmtree(strTestFromDir, ignore_errors=True)
os.mkdir(strTestFromDir)
strTestHtmlFilePath = os.path.join(strTestFromDir, "index.html")
strTestHtmlDirPath = os.path.join(strTestFromDir, "index")
EDUtilsFile.writeFile(strTestHtmlFilePath, "Test content")
if not os.path.exists(strTestHtmlDirPath):
os.mkdir(strTestHtmlDirPath)
strTestHtmlDirFilePath = os.path.join(strTestHtmlDirPath, "test.txt")
EDUtilsFile.writeFile(strTestHtmlDirFilePath, "Test content")
#
strTestToDir = os.path.join(EDUtilsPath.getEdnaUserTempFolder(), "TestToDir")
shutil.rmtree(strTestToDir, ignore_errors=True)
os.mkdir(strTestToDir)
EDHandlerESRFPyarchv1_0.copyHTMLDir(strTestFromDir, strTestToDir)
#
# Check that files exist in strTestToDir:
EDAssert.isFile(os.path.join(strTestToDir, "index", "index.html"))
EDAssert.isFile(os.path.join(strTestToDir, "index", "index", "test.txt"))
#
shutil.rmtree(strTestFromDir, ignore_errors=True)
shutil.rmtree(strTestToDir, ignore_errors=True)
def testGenerateExecutableScript(self):
listCommands = ['COMMAND1', 'COMMAND2 BANANA']
edPluginExecProcessScript = EDPluginExecProcessScript()
edPluginExecProcessScript.setScriptShell("/bin/bash")
edPluginExecProcessScript.setScriptBaseName("TestCaseGenerateScript")
edPluginExecProcessScript.setListCommandExecution(listCommands)
edPluginExecProcessScript.setRequireCCP4(True)
edPluginExecProcessScript.setSetupCCP4("/usr/local/xtal/ccp4-6.0.2/include/ccp4.setup-bash")
edPluginExecProcessScript.setScriptExecutable("cat")
edPluginExecProcessScript.configure()
strScript = edPluginExecProcessScript.prepareScript()
edPluginExecProcessScript.writeExecutableScript(strScript)
strScriptFileName = edPluginExecProcessScript.getScriptFileName()
strScriptFromFile = edPluginExecProcessScript.readProcessFile(strScriptFileName)
lstScriptReference = ["#!/bin/bash",
"cd %s" % edPluginExecProcessScript.getWorkingDirectory(),
". /usr/local/xtal/ccp4-6.0.2/include/ccp4.setup-bash",
"cat > TestCaseGenerateScript.log 2> TestCaseGenerateScript.err << EOF-EDPluginExecProcessScript &",
"COMMAND1",
"COMMAND2 BANANA",
"EOF-EDPluginExecProcessScript",
"ednaJobPid=$!",
"ednaJobHostName=$(hostname)",
'echo "$ednaJobHostName $ednaJobPid" > %s' % edPluginExecProcessScript.getPathToHostNamePidFile(),
"wait $ednaJobPid",
""]
strScriptReference = EDUtilsPlatform.linesep.join(lstScriptReference)
EDAssert.equal(strScriptFromFile, strScriptReference)
def testExecute(self):
self.run()
# Checks that there are no error messages
plugin = self.getPlugin()
# Checks the expected result
strExpectedOutput = self.readAndParseFile(self.strReferenceDataOutputFile)
# Check that all the paths in the prediction results actaully exists
from XSDataMXv1 import XSDataIndexingResult
xsDataIndexingResultObtained = plugin.getDataOutput()
xsDataIndexingResultExpected = XSDataIndexingResult.parseString(strExpectedOutput)
xsDataGeneratePredictionResult = xsDataIndexingResultObtained.getPredictionResult()
for predictionImage in xsDataGeneratePredictionResult.getPredictionImage():
strImagePath = predictionImage.getPath().getValue()
bImageExists = os.path.exists(strImagePath)
EDAssert.equal(True, bImageExists)
# Check that we found the right space group
xsDataIndexingSolutionSelectedObtained = xsDataIndexingResultObtained.getSelectedSolution()
xsDataIndexingSolutionSelectedExpected = xsDataIndexingResultExpected.getSelectedSolution()
xsDataCrystalObtained = xsDataIndexingSolutionSelectedObtained.getCrystal()
xsDataCrystalExpected = xsDataIndexingSolutionSelectedExpected.getCrystal()
xsDataSpaceGroupObtained = xsDataCrystalObtained.getSpaceGroup()
xsDataSpaceGroupExpected = xsDataCrystalExpected.getSpaceGroup()
strSpacegroupNameObtained = xsDataSpaceGroupObtained.getName().getValue()
strSpacegroupNameExpected = xsDataSpaceGroupExpected.getName().getValue()
EDAssert.equal(strSpacegroupNameExpected, strSpacegroupNameObtained)
def testExecute(self):
"""
"""
self.run()
# plugin = self.getPlugin()
strExpectedOutput = self.readAndParseFile(
self.getReferenceDataOutputFile())
strObtainedOutput = self.readAndParseFile(
self.m_edObtainedOutputDataFile)
EDVerbose.DEBUG("Checking obtained result...")
xsDataResultReference = XSDataResultNormalize.parseString(
strExpectedOutput)
xsDataResultObtained = XSDataResultNormalize.parseString(
strObtainedOutput)
#EDAssert.strAlmostEqual(xsDataResultReference.marshal(), xsDataResultObtained.marshal(), "Result XML are the same")
npaReference = EDUtilsArray.getArray(xsDataResultReference.output)
npaObtained = EDUtilsArray.getArray(xsDataResultObtained.output)
EDAssert.arraySimilar(npaReference,
npaObtained,
"Arrays are the same",
_fAbsMaxDelta=1e-6)
EDAssert.equal(npaReference.dtype, npaObtained.dtype,
"Datatypes are the same")
def testDefaultChemicalComposition(self):
edPluginStrategy = self.createPlugin()
from XSDataCommon import XSDataAngle
from XSDataCommon import XSDataLength
from XSDataMXv1 import XSDataSampleCrystalMM
from XSDataMXv1 import XSDataCrystal
from XSDataMXv1 import XSDataCell
xsDataSampleCrystalMM = XSDataSampleCrystalMM()
xsDataCrystal = XSDataCrystal()
xsDataCell = XSDataCell(XSDataAngle(90.0),
XSDataAngle(90.0),
XSDataAngle(90.0),
XSDataLength(78.9),
XSDataLength(95.162),
XSDataLength(104.087))
xsDataCrystal.setCell(xsDataCell)
xsDataSampleCrystalMM.setCrystal(xsDataCrystal)
inumOperators = 4
xsDataSample2 = edPluginStrategy.getDefaultChemicalComposition(xsDataSampleCrystalMM, inumOperators)
strChainType = xsDataSample2.getStructure().getChain()[0].getType()
EDAssert.equal("protein", strChainType.getValue())
def testParseLabelitDistlOutput(self):
"""
This method test the parsing of the distl.signal_strength results in the log file.
"""
edPluginDistlSignalStrengthv1_1 = self.createPlugin()
strPathToLabelitLogText = os.path.join(self.getPluginTestsDataHome(),
"dstl.signal_strength.log")
strLabelitLogText = self.readAndParseFile(strPathToLabelitLogText)
xsDataImageQualityIndicators = edPluginDistlSignalStrengthv1_1.parseLabelitDistlOutput(
strLabelitLogText)
xmlInput1 = self.readAndParseFile(self.__strReferenceInputFile1)
xsDataInputDistlSignalStrength = XSDataInputDistlSignalStrength.parseString(
xmlInput1)
xsDataImageQualityIndicators.setImage(
xsDataInputDistlSignalStrength.getReferenceImage())
strResultDistlSignalStrengthFile = os.path.join(
self.getPluginTestsDataHome(),
"XSDataResultDistlSignalStrength_reference.xml")
strResultDistlSignalStrength = self.readAndParseFile(
strResultDistlSignalStrengthFile)
xsDataResultDistlSignalStrength = XSDataResultDistlSignalStrength.parseString(
strResultDistlSignalStrength)
xsDataImageQualityIndicatorsReference = xsDataResultDistlSignalStrength.getImageQualityIndicators(
)
EDAssert.equal(xsDataImageQualityIndicatorsReference.marshal(),
xsDataImageQualityIndicators.marshal())
def preProcess(self, _edObject=None):
EDPluginHDF5.preProcess(self)
self.DEBUG("EDPluginHDF5StackImagesv10test.preProcess")
for onefile in self.dataInput.inputImageFile:
if onefile.path is not None:
self.listImageFilenames.append(onefile.path.value)
if onefile.date is not None:
self.listImageDates.append(onefile.date.value)
if onefile.number is not None:
self.listForcedPositions.append(onefile.number.value)
self.listArray.append(EDUtilsArray.getArray(onefile))
for oneArray in self.dataInput.getInputArray():
self.listArray.append(EDUtilsArray.xsDataToArray(oneArray))
if self.dataInput.index != []:
self.listForcedPositions = [i.value for i in self.dataInput.index]
if self.dataInput.getDeleteInputImage() is not None:
self.bDeleteImage = bool(self.dataInput.deleteInputImage.value)
if self.listForcedPositions != []:
EDAssert.equal(len(self.listForcedPositions), max(len(self.listImageFilenames), len(self.listArray)), "Forced position list has a good length")
if self.listImageDates != []:
EDAssert.equal(len(self.listImageDates) , len(self.listImageFilenames), "listImageDates has the same size as listImageFilenames")
def testExecute(self):
"""
"""
self.run()
# Checks that there are no error messages
plugin = self.getPlugin()
# Checks the expected result
strExpectedOutput = self.readAndParseFile (self.getReferenceDataOutputFile())
# strObtainedOutput = plugin.getDataOutput().marshal() # EDUtilsTest.readAndParseFile ( self.m_edObtainedOutputDataFile )
EDVerbose.DEBUG("Checking obtained result...")
xsDataResultReference = XSDataResultDiffractionCT.parseString(strExpectedOutput)
xsDataResultObtained = plugin.getDataOutput()# XSDataResultDiffractionCT.parseString(strObtainedOutput)
EDAssert.equal(xsDataResultReference.marshal(), xsDataResultObtained.marshal())
ref = self.readAndParseFile(os.path.join(self.getTestsDataImagesHome(), "DCT2011March.chi"))
obt = self.readAndParseFile(xsDataResultObtained.getIntegratedIntensities().getPath().getValue())
EDAssert.strAlmostEqual(ref, obt, "Chi files are the same", 0.001)
# clean up SPD when finished
EDFactoryPluginStatic.loadPlugin("EDPluginSPDCorrectv10").killAllWorkers()
def testExecute(self):
"""
"""
self.run()
plugin = self.getPlugin()
strExpectedOutput = self.readAndParseFile(
self.getReferenceDataOutputFile())
xsDataResultReference = XSDataResultSPDCake.parseString(
strExpectedOutput)
xsDataResultObtained = plugin.getDataOutput()
# EDVerbose.DEBUG("Reference XML:%s" + xsDataResultReference.marshal())
# EDVerbose.DEBUG("Obtained XML:%s" + xsDataResultObtained.marshal())
EDAssert.strAlmostEqual(xsDataResultReference.marshal(),
xsDataResultObtained.marshal(),
"XSDataResult output are the same")
# Checking obtained results
xsDataResultsSPDCake = plugin.getDataOutput()
strPathToChiOutput = xsDataResultsSPDCake.getCakedFile().getPath(
).getValue()
strDataObtained = EDUtilsFile.readFile(strPathToChiOutput)
strDataReference = EDUtilsFile.readFile(
os.path.join(self.getTestsDataImagesHome(),
"EDPluginSPDCakev1_1.cif"))
EDAssert.strAlmostEqual(strDataReference,
strDataObtained,
"Comparing PowderCIF output",
_fAbsError=2e-3)
def preProcess(self, _edObject=None):
EDPluginHDF5.preProcess(self)
self.DEBUG("EDPluginHDF5StackImagesv10.preProcess")
for onefile in self.dataInput.inputImageFile:
if onefile is None:
self.ERROR("Please investigate why EDPluginHDF5StackImagesv10.dataInput.inputImageFile is a list containing None !!!!")
self.setFailure()
continue
if onefile.path is not None:
self.listImageFilenames.append(onefile.path.value)
if onefile.date is not None:
self.listImageDates.append(onefile.date.value)
if onefile.number is not None:
self.listForcedPositions.append(onefile.number.value)
self.listArray.append(EDUtilsArray.getArray(onefile))
for oneArray in self.dataInput.inputArray:
self.listArray.append(EDUtilsArray.xsDataToArray(oneArray))
if self.dataInput.index != []:
self.listForcedPositions = [i.value for i in self.dataInput.index]
if self.dataInput.getDeleteInputImage() is not None:
self.bDeleteImage = bool(self.dataInput.deleteInputImage.value)
if self.listForcedPositions != []:
EDAssert.equal(len(self.listForcedPositions), max(len(self.listImageFilenames), len(self.listArray)), "Forced position list has a good length")
if self.listImageDates != []:
EDAssert.equal(len(self.listImageDates) , len(self.listImageFilenames), "listImageDates has the same size as listImageFilenames")
self.hdf5group = EDPluginHDF5.createStructure(self.strHDF5Filename, self.strHDF5Path, self.dictExtraAttributes)
def testDropFileCreation( self ):
"""
This test will check to make sure the dropfile is created correctly and saved properly
"""
try :
os.remove("../data/out/test2.drop")
except :
print "nothing to delete"
try :
os.rename("../data/create-ds.xml.icat","../data/create-ds.xml")
except :
print "nothing to delete"
# Create the plugin instance
edPluginExecSRBRegister = self.createPlugin()
# Read in the data from the XML, for the big xml
edStringInputExecSRBRegisterv10XML = EDUtilsTest.readAndParseFile( self.m_edStringReferenceDataInputFile )
# gives the data to the plugin
edPluginExecSRBRegister.setDataInput( edStringInputExecSRBRegisterv10XML )
# call the method
edPluginExecSRBRegister.createDropFile();
# finalise the process
edPluginExecSRBRegister.moveGeneratedFiles()
# check that the file has been created
EDAssert.equal(True, os.path.isfile("../data/out/test2.drop"))
EDAssert.equal(True, os.path.isfile("../data/create-ds.xml.icat"))
def testSetDataOutput(self):
"""
Test the setDataOutput method with different arguments
"""
# Test 1: default output
edPlugin = EDPlugin()
xsDataStringTest = XSDataString("Test")
edPlugin.setDataOutput(xsDataStringTest)
EDAssert.equal(xsDataStringTest.marshal(), edPlugin.getDataOutput().marshal(), "Test 1: default output")
# Test 2: named output
edPlugin = EDPlugin()
xsDataStringTest = XSDataString("Test")
edPlugin.setDataOutput(xsDataStringTest, "testData")
EDAssert.equal(xsDataStringTest.marshal(), edPlugin.getDataOutput("testData")[0].marshal(), "Test 2: named output")
# Test 3: several inputs with the same name
edPlugin = EDPlugin()
xsDataStringTest1 = XSDataString("Test1")
xsDataStringTest2 = XSDataString("Test2")
edPlugin.setDataOutput(xsDataStringTest1, "testData")
edPlugin.setDataOutput(xsDataStringTest2, "testData")
pyListDataOutput = edPlugin.getDataOutput("testData")
EDAssert.equal(xsDataStringTest1.marshal(), pyListDataOutput[0].marshal(), "Test 3: several inputs with the same name, 1")
EDAssert.equal(xsDataStringTest2.marshal(), pyListDataOutput[1].marshal(), "Test 3: several inputs with the same name, 2")
# Test 6: test of delDataOutput
edPlugin = EDPlugin()
xsDataStringTest = XSDataString("Test")
edPlugin.setDataOutput(xsDataStringTest.marshal())
edPlugin.delDataOutput()
EDAssert.equal(None, edPlugin.getDataOutput(), "Test 6: test of delDataOutput")
def testFileNameExtraction( self ):
"""
This method should test to make sure that the plugin is extracting the correct file
list from the xml ingest file
"""
try :
os.rename("../data/create-ds.xml.icat","../data/create-ds.xml")
except :
print "nothing to delete"
# Create the plugin instance
edPluginExecSRBRegister = self.createPlugin()
# Read in the data from the XML
edStringInputExecSRBRegisterv10XML = EDUtilsTest.readAndParseFile( self.m_edStringReferenceDataInputFile )
# gives the data to the plugin
edPluginExecSRBRegister.setDataInput( edStringInputExecSRBRegisterv10XML )
edPluginExecSRBRegister.openXMLTree()
edFilelist = edPluginExecSRBRegister.processFileList()
# assert that the filelist is correct
edTestlist = ["EDPluginExecSRBRegisterv10_output.xml\n"]
EDAssert.equal(edFilelist,edTestlist)
def testCreateBaseName(self):
# Test 1 : naming of working directory
edPlugin = EDPlugin()
edPlugin.setBaseName("EDPlugin_testCreateBaseName")
edPlugin.configure()
strWorkingDir = edPlugin.getWorkingDirectory()
EDAssert.equal(True, os.path.exists(strWorkingDir), "Test 1 : naming of working directory")
def testExecute(self):
"""
"""
self.run()
# Checks that there are no error messages
plugin = self.getPlugin()
edPlugin = self.getPlugin()
strBestVersion = self.getPlugin().getStringVersion()
if strBestVersion.find("3.1.0") != -1 :
self.setReferenceDataOutputFile(os.path.join(self.getPluginTestsDataHome(), "XSDataResultBest_reference.xml"))
elif strBestVersion.find("3.2.0") != -1 :
self.setReferenceDataOutputFile(os.path.join(self.getPluginTestsDataHome(), "XSDataResultBest_reference_BESTv320.xml"))
# Checks the expected result
strExpectedOutput = self.readAndParseFile(self.getReferenceDataOutputFile())
from XSDataBestv1_1 import XSDataResultBest
xsDataOutputExpected = XSDataResultBest.parseString(strExpectedOutput)
xsDataOutputObtained = edPlugin.getDataOutput()
EDAssert.equal(xsDataOutputExpected.marshal(), xsDataOutputObtained.marshal())
def testRasterConfiguration(self):
strPathToTestConfigFile = os.path.join(self.strUnitTestDataHome, "XSConfiguration_raster.xml")
edConfiguration = EDConfiguration(strPathToTestConfigFile)
edConfiguration.load()
xsPluginItem = edConfiguration.getPluginItem("EDPluginMOSFLMv10")
xsDataMOSFLMInput = XSDataMOSFLMInput()
xsDataMOSFLMBeam = XSDataMOSFLMBeamPosition()
xsDataMOSFLMBeam.setX(XSDataLength(1.0))
xsDataMOSFLMBeam.setY(XSDataLength(2.0))
xsDataMOSFLMInput.setBeam(xsDataMOSFLMBeam)
xsDataMOSFLMDetector = XSDataMOSFLMDetector()
xsDataMOSFLMDetector.setType(XSDataString("ADSC"))
xsDataMOSFLMInput.setDetector(xsDataMOSFLMDetector)
xsDataMOSFLMInput.setDirectory(XSDataString("/tmp"))
xsDataMOSFLMInput.setTemplate(XSDataString("testdata_1_###.img"))
xsDataMOSFLMInput.setWavelength(XSDataWavelength(1.1111))
xsDataMOSFLMInput.setDistance(XSDataLength(222.22))
edPluginMOSFLMv10 = self.createPlugin()
edPluginMOSFLMv10.setScriptExecutable("cat")
edPluginMOSFLMv10.setConfiguration(xsPluginItem)
edPluginMOSFLMv10.configure()
edPluginMOSFLMv10.setXSDataInputClass(XSDataMOSFLMInput)
edPluginMOSFLMv10.setDataInput(xsDataMOSFLMInput)
edPluginMOSFLMv10.generateMOSFLMCommands()
edListCommands = edPluginMOSFLMv10.getListCommandExecution()
edListCommandsReference = ['WAVELENGTH 1.1111', 'DISTANCE 222.22', 'BEAM 1.0 2.0', 'DETECTOR ADSC', 'DIRECTORY /tmp', 'TEMPLATE testdata_1_###.img', 'RASTER 15 15 3 3 3']
EDAssert.equal(edListCommandsReference, edListCommands, "MOSFLM commands with ratser configured")
def testExecute(self):
"""
"""
self.run()
plugin = self.getPlugin()
################################################################################
# Compare XSDataResults
################################################################################
strExpectedOutput = self.readAndParseFile(
self.getReferenceDataOutputFile())
EDVerbose.DEBUG("Checking obtained result...")
xsDataResultObtained = plugin.getDataOutput()
EDAssert.strAlmostEqual(self.xsDataResultReference.marshal(),
xsDataResultObtained.marshal(),
"XSDataResult output are the same")
################################################################################
# Compare image Files
################################################################################
outputData = Image.open(self.outputFile)
referenceData = Image.open(
os.path.join(self.getTestsDataImagesHome(),
os.path.basename(self.outputFile)))
delta = ImageChops.difference(outputData, referenceData)
deltaColor = delta.getextrema()
i = 0
for color in deltaColor:
EDAssert.lowerThan(
color[1], 12, "Maximum tone variation is %s for channel %s" %
(color[1], "RGBA"[i]))
i += 1
def testExecute(self):
self.run()
plugin = self.getPlugin()
output = plugin.dataOutput
EDAssert.equal(output.succeeded.value, True,
"HDF5 processing succeeded.")
def testSpatialDistortion(self):
strRefX = "spline-3-18x.edf"
strRefY = "spline-3-18y.edf"
self.loadTestImage([strRefX, strRefY])
edPluginSPD = self.createPlugin()
strXMLInput = EDUtilsFile.readFileAndParseVariables(self.strReferenceInputFileName)
xsDataInputSPDCake = XSDataInputSPDCake.parseString(strXMLInput)
edPluginSPD.setDataInput(xsDataInputSPDCake)
edPluginSPD.configure()
edPluginSPD.getInputParameter()
########################################################################
# Enforce some values
########################################################################
edPluginSPD.dictGeometry["SpatialDistortionFile"] = os.path.join(self.getTestsDataImagesHome(), "frelon_spline_file_to_correct_SPD.spline")
edPluginSPD.dictGeometry["TiltRotation"] = 18
edPluginSPD.dictGeometry["AngleOfTilt"] = 3
spline = Spline()
spline.read(edPluginSPD.dictGeometry["SpatialDistortionFile"])
edPluginSPD.dictGeometry["PixelSizeX"], edPluginSPD.dictGeometry["PixelSizeY"] = spline.getPixelSize()
edPluginSPD.createDisplacementMatrix(spline)
edPluginSPD.cleanDispMat(edPluginSPD.getWorkingDirectory())
refX = fabio.openimage.openimage(os.path.join(self.getTestsDataImagesHome(), strRefX)).data
obtX = fabio.openimage.openimage(os.path.join(edPluginSPD.getWorkingDirectory(), "frelon_spline_file_to_correct_SPD-tilted-x.edf")).data
refY = fabio.openimage.openimage(os.path.join(self.getTestsDataImagesHome(), strRefY)).data
obtY = fabio.openimage.openimage(os.path.join(edPluginSPD.getWorkingDirectory(), "frelon_spline_file_to_correct_SPD-tilted-y.edf")).data
# print edPluginSPD.dictGeometry
EDAssert.arraySimilar(obtX, refX , _fAbsMaxDelta=0.1, _strComment="X displacement Matrix is the same")
EDAssert.arraySimilar(obtY, refY , _fAbsMaxDelta=0.1, _strComment="Y displacement Matrix is the same")
def test_createHtmlPage(self):
strDimpleOutput = os.path.join(self.strDataPath, "dimple",
"Dimplev1_0_dataOutput.xml")
strResultDimple = self.readAndParseFile(strDimpleOutput)
xsDataResultDimple = XSDataResultDimple.parseString(strResultDimple)
strPdfPath = os.path.join(
xsDataResultDimple.resultsDirectory.path.value, "DIMPLE.pdf")
edPlugin = self.getPlugin()
strPyarchRootDir = tempfile.mkdtemp(prefix="html_",
dir=os.path.join(
self.strDataPath, "dimple"))
strPrefix = "xtal5w1_1"
strProposal = "mx415"
strSessionDate = "2015-02-23"
strBeamline = "id29"
strResultsDirectory = strPyarchRootDir
listPath = edPlugin.copyResults(strPrefix, strPyarchRootDir,
xsDataResultDimple, strPdfPath)
listPathHtml = edPlugin.createHtmlPage(strPrefix, xsDataResultDimple,
strResultsDirectory,
strPyarchRootDir, strProposal,
strSessionDate, strBeamline)
for pathHtml in listPathHtml:
EDAssert.equal(True, os.path.exists(pathHtml),
"HTML page generated")
shutil.rmtree(strPyarchRootDir)
def testExecute(self):
"""
"""
self.run()
# Checks that there are no error messages
plugin = self.getPlugin()
plugin.killAllWorkers()
# if EDVerbose.isVerboseDebug():
# plugin.cleanDispMat(plugin.getWorkingDirectory())
# else:
# plugin.cleanDispMat()
# Checking obtained results
xsDataResultSPD = plugin.getDataOutput()
outputData = EDF(xsDataResultSPD.getCakedFile().getPath().getValue()).GetData(0)
referenceData = EDF(os.path.join(self.getTestsDataImagesHome(), self.refOutput)).GetData(0)
# print outputData.shape
# print referenceData.shape
relError = 100 * (abs(outputData - referenceData).max() - referenceData.min()) / (referenceData.max() - referenceData.min())
absError = abs(outputData - referenceData).max()
if relError > 5:
EDAssert.lowerThan(relError, 5, "Maximum relative error = %.2f%%, Maximum Absolute Error %.2f" % (relError, absError))
else:
EDAssert.lowerThan(absError, 5, "Maximum relative error = %.2f%%, Maximum Absolute Error %.2f " % (relError, absError))
def test_extractFinalResultsFromRefmac5RestrLog(self):
strRefmacLogFilePath = os.path.join(self.strDataPath, "dimple",
"08-refmac5_restr.log")
edPlugin = self.getPlugin()
strResults = edPlugin.extractFinalResultsFromRefmac5RestrLog(
strRefmacLogFilePath)
EDAssert.equal(True, strResults != "", "Read Refmac5restr log")
def testGetParamItem(self):
"""
Testing the XSParamItem inside an XSPluginItem
"""
xsPluginItem = self.___edConfiguration.getPluginItem("indexingMosflm")
xsParamItem = self.___edConfiguration.getParamItem(xsPluginItem, "workingDir")
EDAssert.equal("workingDir", xsParamItem.getName())
def testGenerateMOSFLMCommands(self):
"""
"""
pluginGeneratePrediction = self.createPlugin()
pluginGeneratePrediction.setScriptExecutable("cat")
pluginGeneratePrediction.configure()
xsDataMOSFLMInputGeneratePrediction = self.generateDataMOSFLMInputGeneratePrediction()
pluginGeneratePrediction.setDataInput(xsDataMOSFLMInputGeneratePrediction)
pluginGeneratePrediction.generateMOSFLMCommands()
listCommandsReference = [
"WAVELENGTH 0.934",
"DISTANCE 198.4",
"BEAM 102.5 104.7",
"DETECTOR ADSC",
"DIRECTORY " + self.strDataImagePath,
"TEMPLATE ref-testscale_1_###.img",
"XGUI ON",
"IMAGE 1 PHI 0.000000 TO 1.000000",
"GO",
"PREDICT_SPOTS",
"CREATE_IMAGE PREDICTION ON BINARY TRUE FILENAME " + pluginGeneratePrediction.getPredictionImageFileName(),
"RETURN",
"EXIT",
]
listCommands = pluginGeneratePrediction.getListCommandExecution()
# print listCommandsReference
# print listCommands
EDAssert.equal(listCommandsReference, listCommands)
self.cleanUp(pluginGeneratePrediction)
def testExecute(self):
"""
"""
self.run()
plugin = self.getPlugin()
strExpectedOutput = self.readAndParseFile(
self.getReferenceDataOutputFile())
# strObtainedOutput = self.readAndParseFile (self.m_edObtainedOutputDataFile)
EDVerbose.DEBUG("Checking obtained result...")
xsDataResultReference = XSDataResultSaxsMacv1_0.parseString(
strExpectedOutput)
xsDataResultObtained = plugin.getDataOutput()
EDAssert.strAlmostEqual(xsDataResultReference.marshal(),
xsDataResultObtained.marshal(),
"XSDataResult output are the same")
outputData = openimage(
xsDataResultObtained.getOutputImage().getPath().getValue()).data
referenceData = openimage(
os.path.join(self.getTestsDataImagesHome(), "moke.edf")).data
EDAssert.arraySimilar(outputData,
referenceData,
_fAbsMaxDelta=0.8,
_fScaledMaxDelta=0.05,
_fRfactor=5,
_fRelMaxDelta=1.5,
_strComment="Images are the same")
def testExecute(self):
"""
"""
plugin = self.getPlugin()
plugin.emptyItems()
plugin.emptyQueries()
plugin.addItem("data1")
plugin.addItem("data2")
plugin.addItem("data3")
plugin.addItem("data4")
plugin.addItem("data5")
self.run()
# Checking obtained results
# print plugin.getDataInput().marshal()
# print plugin.getDataOutput().marshal()
xsDataResult = plugin.getDataOutput()
strXMLRef = XSDataResultAccumulator.parseString(
EDUtilsFile.readFile(self.getReferenceDataOutputFile())).marshal()
EDAssert.equal(xsDataResult.marshal(), strXMLRef,
"XML results are conform")
# print plugin.getItems()
EDAssert.equal(plugin.getItems(),
['data1', 'data2', 'data3', 'data4', 'data5'],
"Remaining items are the same")
plugin.emptyItems()
def testGenerateMOSFLMIntegrationCommands(self):
strPathToTestConfigFile = os.path.join(self.strUnitTestDataHome,
"XSConfiguration_unitTest.xml")
edConfiguration = EDConfiguration(strPathToTestConfigFile)
xsPluginItem = edConfiguration.getXSConfigurationItem(
"EDPluginMOSFLMIntegrationv10")
pluginIntegration = self.createPlugin()
pluginIntegration.setScriptExecutable("cat")
pluginIntegration.setConfiguration(xsPluginItem)
pluginIntegration.configure()
strXMLInputData = self.readAndParseFile(self.strReferenceDataInputFile)
pluginIntegration.setDataInput(strXMLInputData)
pluginIntegration.generateMOSFLMCommands()
listCommandExecution = pluginIntegration.getListCommandExecution()
listCommandReference = [
'WAVELENGTH 0.934', 'DISTANCE 198.440994',
'BEAM 102.478996 104.8862', 'DETECTOR ADSC',
'DIRECTORY ' + self.strDataImagePath,
'TEMPLATE ref-testscale_1_###.img', 'SYMMETRY P222',
'MATRIX ' + pluginIntegration.getScriptBaseName() + '_matrix.mat',
'MOSAIC 0.75', 'HKLOUT process_1_1.mtz',
'PROCESS 1 TO 1 START 0.000000 ANGLE 1.000000', 'BEST ON', 'GO',
'BEST OFF'
]
EDAssert.equal(listCommandReference, listCommandExecution)
def testStartServer(self):
"""
check the status after a job creation
"""
edServer = EDServerXMLRCP.getInstance()
if not edServer:
EDAssert.equal(not None, edServer, "Server instance None")
def testSetDataInput( self ):
"""
This method test the setDataInput method of the SRBRegister plugin by providing an XML string
and then retriving an XSDataInputLabelit object. It checks both inputs
"""
#Create the plugin instance
edPluginExecSRBRegister = self.createPlugin()
# create an object which contains the test information
edStringInputExecSRBRegisterv10XML = EDUtilsTest.readAndParseFile( self.m_edStringReferenceDataInputFile )
# gives the data to the plugin
edPluginExecSRBRegister.setDataInput( edStringInputExecSRBRegisterv10XML )
# get the data from the plugin
xsDataInputPluginExecSRBRegister = edPluginExecSRBRegister.getDataInput()
# get the string of the path
edStringPath = EDString( xsDataInputPluginExecSRBRegister.getSrbDropFileName().getPath().getValue() )
# create the test path
edStringPathReference = EDString( "../data/out/test2.drop" )
# Actually test the data.
EDAssert.equal( edStringPathReference, edStringPath )
# test the reading of the other data
edStringPath = EDString( xsDataInputPluginExecSRBRegister.getXmlIngestFileName().getPath().getValue() )
# create the test path
edStringPathReference = EDString( "../data/create-ds.xml" )
# Actually test the data.
EDAssert.equal( edStringPathReference, edStringPath )
def testGenerateMOSFLMCommands(self):
xsDataMOSFLMInput = XSDataMOSFLMInput()
xsDataMOSFLMBeam = XSDataMOSFLMBeamPosition()
xsDataMOSFLMBeam.setX(XSDataLength(1.0))
xsDataMOSFLMBeam.setY(XSDataLength(2.0))
xsDataMOSFLMInput.setBeam(xsDataMOSFLMBeam)
xsDataMOSFLMDetector = XSDataMOSFLMDetector()
xsDataMOSFLMDetector.setType(XSDataString("ADSC"))
xsDataMOSFLMInput.setDetector(xsDataMOSFLMDetector)
xsDataMOSFLMInput.setDirectory(XSDataString("/tmp"))
xsDataMOSFLMInput.setTemplate(XSDataString("testdata_1_###.img"))
xsDataMOSFLMInput.setWavelength(XSDataWavelength(1.1111))
xsDataMOSFLMInput.setDistance(XSDataLength(222.22))
edPluginMOSFLMv10 = self.createPlugin()
edPluginMOSFLMv10.setScriptExecutable("cat")
edPluginMOSFLMv10.configure()
edPluginMOSFLMv10.setXSDataInputClass(XSDataMOSFLMInput)
edPluginMOSFLMv10.setDataInput(xsDataMOSFLMInput)
edPluginMOSFLMv10.generateMOSFLMCommands()
edListCommands = edPluginMOSFLMv10.getListCommandExecution()
edListCommandsReference = [
'WAVELENGTH 1.1111', 'DISTANCE 222.22', 'BEAM 1.0 2.0',
'DETECTOR ADSC', 'DIRECTORY /tmp', 'TEMPLATE testdata_1_###.img'
]
EDAssert.equal(edListCommandsReference, edListCommands,
"MOSFLM commands")
self.cleanUp(edPluginMOSFLMv10)
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 = XSDataResultBioSaxsAsciiExportv1_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.getIntegratedCurve().getPath().value, "rb").read()
referenceData = open(os.path.join(self.getTestsDataImagesHome(), "bioSaxsAsciiExportv1_1.dat"), "rb").read()
EDAssert.strAlmostEqual(referenceData, outputData, _strComment="3-column ascii spectra files are the same", _fRelError=0.1, _fAbsError=0.1, _strExcluded="bioSaxs")
def testRasterConfiguration(self):
strPathToTestConfigFile = os.path.join(self.strUnitTestDataHome,
"XSConfiguration_raster.xml")
edConfiguration = EDConfiguration(strPathToTestConfigFile)
xsPluginItem = edConfiguration.getXSConfigurationItem(
"EDPluginMOSFLMv10")
xsDataMOSFLMInput = XSDataMOSFLMInput()
xsDataMOSFLMBeam = XSDataMOSFLMBeamPosition()
xsDataMOSFLMBeam.setX(XSDataLength(1.0))
xsDataMOSFLMBeam.setY(XSDataLength(2.0))
xsDataMOSFLMInput.setBeam(xsDataMOSFLMBeam)
xsDataMOSFLMDetector = XSDataMOSFLMDetector()
xsDataMOSFLMDetector.setType(XSDataString("ADSC"))
xsDataMOSFLMInput.setDetector(xsDataMOSFLMDetector)
xsDataMOSFLMInput.setDirectory(XSDataString("/tmp"))
xsDataMOSFLMInput.setTemplate(XSDataString("testdata_1_###.img"))
xsDataMOSFLMInput.setWavelength(XSDataWavelength(1.1111))
xsDataMOSFLMInput.setDistance(XSDataLength(222.22))
edPluginMOSFLMv10 = self.createPlugin()
edPluginMOSFLMv10.setScriptExecutable("cat")
edPluginMOSFLMv10.setConfiguration(xsPluginItem)
edPluginMOSFLMv10.configure()
edPluginMOSFLMv10.setXSDataInputClass(XSDataMOSFLMInput)
edPluginMOSFLMv10.setDataInput(xsDataMOSFLMInput)
edPluginMOSFLMv10.generateMOSFLMCommands()
edListCommands = edPluginMOSFLMv10.getListCommandExecution()
edListCommandsReference = [
'WAVELENGTH 1.1111', 'DISTANCE 222.22', 'BEAM 1.0 2.0',
'DETECTOR ADSC', 'DIRECTORY /tmp', 'TEMPLATE testdata_1_###.img',
'RASTER 15 15 3 3 3'
]
EDAssert.equal(edListCommandsReference, edListCommands,
"MOSFLM commands with ratser configured")
def testExecute(self):
"""
"""
self.run()
# Checks that there are no error messages
plugin = self.getPlugin()
edPlugin = self.getPlugin()
strBestVersion = self.getPlugin().getStringVersion()
if strBestVersion.find("3.1.0") != -1:
self.setReferenceDataOutputFile(
os.path.join(self.getPluginTestsDataHome(),
"XSDataResultBest_reference.xml"))
elif strBestVersion.find("3.2.0") != -1:
self.setReferenceDataOutputFile(
os.path.join(self.getPluginTestsDataHome(),
"XSDataResultBest_reference_BESTv320.xml"))
# Checks the expected result
strExpectedOutput = self.readAndParseFile(
self.getReferenceDataOutputFile())
from XSDataBestv1_1 import XSDataResultBest
xsDataOutputExpected = XSDataResultBest.parseString(strExpectedOutput)
xsDataOutputObtained = edPlugin.getDataOutput()
EDAssert.equal(xsDataOutputExpected.marshal(),
xsDataOutputObtained.marshal())
def unitTestLineSep(self):
"""
Test os.linesep
"""
EDVerbose.DEBUG("EDTestCaseEDUtilsPlatform.unitTestLineSep")
EDAssert.equal(os.linesep, EDUtilsPlatform.linesep,
"os.linesep equivalent")
def testExecute(self):
"""
"""
self.run()
plugin = self.getPlugin()
EDVerbose.DEBUG("Checking obtained result...")
strExpectedOutput = self.readAndParseFile (self.getReferenceDataOutputFile())
xsDataResultReference = XSDataResultSPDCake.parseString(strExpectedOutput)
xsDataResultObtained = plugin.getDataOutput()
# EDVerbose.DEBUG("Reference XML:%s" + xsDataResultReference.marshal())
# EDVerbose.DEBUG("Obtained XML:%s" + xsDataResultObtained.marshal())
EDAssert.strAlmostEqual(xsDataResultReference.marshal(), xsDataResultObtained.marshal(), "XSDataResult output are the same")
# Checking obtained results
xsDataResultsSPDCake = plugin.getDataOutput()
strPathToChiOutput = xsDataResultsSPDCake.getCakedFile().getPath().getValue()
strPathToChiReference = os.path.join(self.getTestsDataImagesHome(), "EDPluginSPDCakev1_0.chi")
Xref, Yref = readChiPlot(strPathToChiReference)
Xobt, Yobt = readChiPlot(strPathToChiOutput)
EDVerbose.DEBUG("Output File: %s, Reference file: %s" % (strPathToChiOutput, strPathToChiReference))
bigX = Xref + Xobt
bigX.sort()
bigYobt = numpy.interp(bigX, Xobt, Yobt)
bigYref = numpy.interp(bigX, Xref, Yref)
EDVerbose.DEBUG("ref.shape= %s, obt.shape=%s" % (bigYobt.shape, bigYref.shape))
EDVerbose.DEBUG("Type of object ref= %s, obt=%s" % (bigYobt.__class__, bigYref.__class__))
EDAssert.arraySimilar(bigYobt, bigYref, _fAbsMaxDelta=0.1, _fScaledMaxDelta=0.1, _strComment="Comparing ChiPlot files")
def testMergeTwoSubWedgesAdjascentInRotationAxis(self):
# First check two sub wedges which shouldn't be merged
edPluginSubWedgeMergev1_1 = self.createPlugin()
edPluginSubWedgeMergev1_1.configure()
xsDataInputSubWedgeMerge = XSDataInputSubWedgeMerge.parseFile(
self.strPathToReferenceInput)
xsDataSubWedge1 = xsDataInputSubWedgeMerge.getSubWedge()[0]
xsDataSubWedge2 = xsDataInputSubWedgeMerge.getSubWedge()[1]
xsDataSubWedgeMerged = edPluginSubWedgeMergev1_1.mergeTwoSubWedgesAdjascentInRotationAxis(
xsDataSubWedge1, xsDataSubWedge2)
EDAssert.equal(xsDataSubWedgeMerged, None)
# Then check two adjascent images
strPathToInputTwoAdjascentImages = os.path.join(
self.getPluginTestsDataHome(),
"XSDataInputSubWedgeMerge_twoAdjascentImages.xml")
xsDataInputSubWedgeMerge2 = XSDataInputSubWedgeMerge.parseFile(
strPathToInputTwoAdjascentImages)
xsDataSubWedge1 = xsDataInputSubWedgeMerge2.getSubWedge()[0]
xsDataSubWedge2 = xsDataInputSubWedgeMerge2.getSubWedge()[1]
xsDataSubWedgeMerged = edPluginSubWedgeMergev1_1.mergeTwoSubWedgesAdjascentInRotationAxis(
xsDataSubWedge1, xsDataSubWedge2)
xsDataSubWedgeMergedReference = XSDataSubWedge.parseFile(
os.path.join(self.getPluginTestsDataHome(),
"XSDataSubWedgeMerged_twoImages.xml"))
EDAssert.equal(xsDataSubWedgeMerged.marshal(),
xsDataSubWedgeMergedReference.marshal())
def test_generateCommandLine(self):
edPlugin = self.getPlugin()
strInputXML = EDUtilsFile.readFile(os.path.join(self.strDataPath, "XSDataInputXia2DIALS_reference.xml"))
xsDataInput = XSDataInputXia2DIALS.parseString(strInputXML)
strCommandLine = edPlugin.generateCommandLine(xsDataInput)
# print(strCommandLine)
EDAssert.equal("-dials -ispyb_xml_out ispyb.xml image=/scisoft/pxsoft/data/AUTO_PROCESSING/id29/20130301/RAW_DATA/GaelleB/xtal5/xtal5w1_1_0001.cbf", strCommandLine, "Reference data input")
def testCopyHTMLFilesAndDir(self):
if not os.path.exists(EDUtilsPath.getEdnaUserTempFolder()):
os.mkdir(EDUtilsPath.getEdnaUserTempFolder())
strTestFromDir = os.path.join(EDUtilsPath.getEdnaUserTempFolder(), "TestFromDir")
shutil.rmtree(strTestFromDir, ignore_errors=True)
os.mkdir(strTestFromDir)
strTestHtmlFilePath = os.path.join(strTestFromDir, "index.html")
strTestHtmlDirPath = os.path.join(strTestFromDir, "index")
EDUtilsFile.writeFile(strTestHtmlFilePath, "Test content")
if not os.path.exists(strTestHtmlDirPath):
os.mkdir(strTestHtmlDirPath)
strTestHtmlDirFilePath = os.path.join(strTestHtmlDirPath, "test.txt")
EDUtilsFile.writeFile(strTestHtmlDirFilePath, "Test content")
#
strTestToDir = os.path.join(EDUtilsPath.getEdnaUserTempFolder(), "TestToDir")
shutil.rmtree(strTestToDir, ignore_errors=True)
os.mkdir(strTestToDir)
EDHandlerESRFPyarchv1_0.copyHTMLDir(strTestFromDir, strTestToDir)
#
# Check that files exist in strTestToDir:
EDAssert.isFile(os.path.join(strTestToDir, "index", "index.html"))
EDAssert.isFile(os.path.join(strTestToDir, "index", "index", "test.txt"))
#
shutil.rmtree(strTestFromDir, ignore_errors=True)
shutil.rmtree(strTestToDir, ignore_errors=True)
def testSortIdenticalObjects(self):
edListObjects = []
edPluginSubWedgeMergev10 = self.createPlugin()
edListSorted = edPluginSubWedgeMergev10.sortIdenticalObjects(
edListObjects, edPluginSubWedgeMergev10.compareTwoValues)
EDAssert.equal(edListSorted, [])
edListObjects = [1]
edPluginSubWedgeMergev10 = self.createPlugin()
edListSorted = edPluginSubWedgeMergev10.sortIdenticalObjects(
edListObjects, edPluginSubWedgeMergev10.compareTwoValues)
EDAssert.equal(edListSorted, [[1]])
edListObjects = [1, 2]
edPluginSubWedgeMergev10 = self.createPlugin()
edListSorted = edPluginSubWedgeMergev10.sortIdenticalObjects(
edListObjects, edPluginSubWedgeMergev10.compareTwoValues)
EDAssert.equal(edListSorted, [[1], [2]])
edListObjects = [1, 1]
edPluginSubWedgeMergev10 = self.createPlugin()
edListSorted = edPluginSubWedgeMergev10.sortIdenticalObjects(
edListObjects, edPluginSubWedgeMergev10.compareTwoValues)
EDAssert.equal(edListSorted, [[1, 1]])
edListObjects = [1, 2, 1, 3, 4, 1, 5, 2, 2, 9, 3, 2]
edPluginSubWedgeMergev10 = self.createPlugin()
edListSorted = edPluginSubWedgeMergev10.sortIdenticalObjects(
edListObjects, edPluginSubWedgeMergev10.compareTwoValues)
EDAssert.equal(edListSorted,
[[1, 1, 1], [2, 2, 2, 2], [3, 3], [4], [5], [9]])
def unitTestGetValueSILength(self):
"""
Test sub method specific to length: GetValueLength
"""
EDVerbose.DEBUG("EDTestCaseEDUtilsUnit.unitTestGetValueSILength")
EDAssert.equal(1.54E-10, EDUtilsUnit.getValueLength(1.54, "A"),
"Length Conversion A -> m ")
def testCreateDict(self):
pathToReferenceInput = os.path.join(self.getPluginTestsDataHome(), \
"XSDataInputControlDozor_reference.xml")
xsDataInputControlDozor = XSDataInputControlDozor.parseFile(pathToReferenceInput)
edPluginControlDozor = self.createPlugin()
dictImage = edPluginControlDozor.createImageDict(xsDataInputControlDozor)
EDAssert.equal(True, type(dictImage) == dict)
def unitTestGetValueSIAngle(self):
"""
Test sub method specific to length: GetValueLength
"""
EDVerbose.DEBUG("EDTestCaseEDUtilsUnit.unitTestGetValueSIAngle")
EDAssert.equal(math.pi / 2.0, EDUtilsUnit.getValueAngle(90, "deg"),
"Angle Conversion deg -> rad ")
def testSetDataModelInput(self):
"""
"""
edPluginBest = self.createPlugin()
xsPluginItemGood01 = self.getPluginConfiguration(os.path.join(self.strDataPath, "XSConfiguration.xml"))
edPluginBest.setConfiguration(xsPluginItemGood01)
edPluginBest.setScriptExecutable("cat")
edPluginBest.configure()
from XSDataBestv1_1 import XSDataInputBest
xsDataInputBest = XSDataInputBest()
from XSDataCommon import XSDataAbsorbedDoseRate
from XSDataCommon import XSDataDouble
from XSDataCommon import XSDataTime
from XSDataCommon import XSDataSpeed
from XSDataCommon import XSDataString
from XSDataCommon import XSDataAngle
from XSDataCommon import XSDataBoolean
xsDataInputBest.setCrystalAbsorbedDoseRate(XSDataAbsorbedDoseRate(0.22e06))
xsDataInputBest.setCrystalShape(XSDataDouble(1))
xsDataInputBest.setCrystalSusceptibility(XSDataDouble(1.5))
xsDataInputBest.setDetectorType(XSDataString("q210-2x"))
xsDataInputBest.setBeamExposureTime(XSDataTime(1))
xsDataInputBest.setBeamMaxExposureTime(XSDataTime(10000))
xsDataInputBest.setBeamMinExposureTime(XSDataTime(0.1))
xsDataInputBest.setGoniostatMinRotationWidth(XSDataAngle(0.1))
xsDataInputBest.setGoniostatMaxRotationSpeed(XSDataSpeed(10))
xsDataInputBest.setAimedResolution(XSDataDouble(2))
xsDataInputBest.setAimedRedundancy(XSDataDouble(6.5))
xsDataInputBest.setAimedCompleteness(XSDataDouble(0.9))
xsDataInputBest.setAimedIOverSigma(XSDataDouble(3))
xsDataInputBest.setComplexity(XSDataString("min"))
xsDataInputBest.setAnomalousData(XSDataBoolean(True))
bestFileContentDat = EDUtilsFile.readFile(os.path.join(self.strDataPath, "bestfile.dat"))
xsDataInputBest.setBestFileContentDat(XSDataString(bestFileContentDat))
bestFileContentPar = EDUtilsFile.readFile(os.path.join(self.strDataPath, "bestfile.par"))
xsDataInputBest.setBestFileContentPar(XSDataString(bestFileContentPar))
bestFileContentHKL = EDUtilsFile.readFile(os.path.join(self.strDataPath, "bestfile1.hkl"))
listBestFileContentHKL = []
listBestFileContentHKL.append(XSDataString(bestFileContentHKL))
xsDataInputBest.setBestFileContentHKL(listBestFileContentHKL)
xsDataInputBest.outputFile(self.strObtainedInputFile)
strExpectedInput = self.readAndParseFile(self.strReferenceInputFile)
strObtainedInput = self.readAndParseFile(self.strObtainedInputFile)
xsDataInputExpected = XSDataInputBest.parseString(strExpectedInput)
xsDataInputObtained = XSDataInputBest.parseString(strObtainedInput)
EDAssert.equal(xsDataInputExpected.marshal(), xsDataInputObtained.marshal())
os.remove(self.strObtainedInputFile)
self.cleanUp(edPluginBest)
def unitTestGetValueSITime(self):
"""
Test sub method specific to length: GetValueTime
"""
EDVerbose.DEBUG("EDTestCaseEDUtilsUnit.unitTestGetValueSITime")
EDAssert.equal(1800, EDUtilsUnit.getValueTime(30, "mn"),
"Length Conversion mn -> s ")
def testGenerateMosflmScriptName(self):
"""
This method tests the generateMosflmScriptName method of the Labelit plugin.
"""
edPluginLabelitv10 = self.createPlugin()
EDAssert.equal("integration01.csh", edPluginLabelitv10.generateMosflmScriptName(1))
EDAssert.equal("integration10.csh", edPluginLabelitv10.generateMosflmScriptName(10))
def testExecute(self):
"""
"""
self.run()
plugin = self.getPlugin()
# Checking obtained results
xsDataResult = plugin.getDataOutput()
xsDataRef = XSDataResult1DPowderEDF.parseString(
self.readAndParseFile(self.getReferenceDataOutputFile()))
# EDAssert.strAlmostEqual(XSDataResult1DPowderEDF.parseString(self.readAndParseFile(self.getReferenceDataOutputFile())).marshal(), xsDataResult.marshal(), _strComment="XML structures are the same")
tthref = EDUtilsArray.xsDataToArray(xsDataRef.getTwoTheta(),
_bCheckMd5sum=False)
tthobt = EDUtilsArray.xsDataToArray(xsDataResult.getTwoTheta(),
_bCheckMd5sum=False)
Iref = EDUtilsArray.xsDataToArray(xsDataRef.getIntensity(),
_bCheckMd5sum=False)
Iobt = EDUtilsArray.xsDataToArray(xsDataResult.getIntensity(),
_bCheckMd5sum=False)
EDAssert.arraySimilar(_npaValue=tthobt,
_npaRef=tthref,
_fAbsMaxDelta=0.1,
_strComment="2theta arrays are the same")
EDAssert.arraySimilar(_npaValue=Iobt,
_npaRef=Iref,
_fAbsMaxDelta=0.1,
_strComment="Intensity arrays are the same")
def test_generateCommandLine(self):
edPlugin = self.getPlugin()
strInputXML = EDUtilsFile.readFile(os.path.join(self.strDataPath, "XSDataInputAutoPROC_reference.xml"))
xsDataInput = XSDataInputAutoPROC.parseString(strInputXML)
strCommandLine = edPlugin.generateCommandLine(xsDataInput)
print(strCommandLine)
EDAssert.equal("-B -xml -I /scisoft/pxsoft/data/AUTO_PROCESSING/id29/20130301/RAW_DATA/GaelleB/xtal5 -Id 1088454,/scisoft/pxsoft/data/AUTO_PROCESSING/id29/20130301/RAW_DATA/GaelleB/xtal5,xtal5w1_1_####.cbf,1,100 -R 5.0 2.0 -ANO", strCommandLine, "Reference data input")
def testExecute(self):
self.run()
# Checks that there are no error messages
plugin = self.getPlugin()
# Checks the expected result
xsDataResultCharacterisationv2_0 = plugin.getDataOutput()
# EDAssert.equal(True, xsDataResultCharacterisationv2_0.getMxv1ResultCharacterisation_Reference() is not None)
EDAssert.equal(
True,
xsDataResultCharacterisationv2_0.getMxv1ResultCharacterisation()
is not None)
EDAssert.equal(
True,
xsDataResultCharacterisationv2_0.getSuggestedStrategy()
is not None)
# EDAssert.equal(True, xsDataResultCharacterisationv2_0.getPossibleOrientations() is not None)
xsDataResultCharacterisation = xsDataResultCharacterisationv2_0.getMxv1ResultCharacterisation(
)
# There should be indexing results, integration results and strategy results
EDAssert.equal(
True,
xsDataResultCharacterisation.getIndexingResult() is not None)
EDAssert.equal(
True,
xsDataResultCharacterisation.getIntegrationResult() is not None)
EDAssert.equal(
True,
xsDataResultCharacterisation.getStrategyResult() is not None)
def testGetOutputDataFromDNATableFile(self):
edPluginRdfit = self.createPlugin()
strPathToTableFile = os.path.join(self.strDataPath, "rdfit.xml")
xsDataResultRdfit = edPluginRdfit.getOutputDataFromDNATableFile(strPathToTableFile)
strPathToReference = os.path.join(self.strDataPath, "XSDataResultRdfit_reference.xml")
xsDataResultRdfitReference = XSDataResultRdfit.parseFile(strPathToReference)
EDAssert.equal(xsDataResultRdfitReference.marshal(), xsDataResultRdfit.marshal(), "Test parsing result 'DNA' xml file")
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 = XSDataResultBioSaxsAzimutIntv1_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.getIntegratedCurve().getPath().value, "rb").read().split(os.linesep)
referenceData = EDUtilsFile.readFileAndParseVariables(os.path.join(self.getTestsDataImagesHome(), "bioSaxsIntegratedv1_3.dat"), EDUtilsPath.getDictOfPaths()).split(os.linesep)
outputData = os.linesep.join([i for i in outputData if not i.startswith("# History")])
referenceData = os.linesep.join([i for i in referenceData if not i.startswith("# History")])
EDAssert.strAlmostEqual(referenceData, outputData, _strComment="3column ascii spectra files are the same", _fRelError=0.1, _fAbsError=0.1, _strExcluded="bioSaxs")