def testGenerateXSDataInputXDSIndexing(self):
filename = "XSDataIndexingInput_reference.xml"
path = os.path.join(self.dataPath, filename)
xmlIndexingInput = EDUtilsTest.readAndParseFile(path)
from XSDataMXv1 import XSDataIndexingInput
xsDataIndexingInput = XSDataIndexingInput.parseString(xmlIndexingInput)
from EDHandlerXSDataXDSv1_0 import EDHandlerXSDataXDSv1_0
xsDataInputXDSIndexing = EDHandlerXSDataXDSv1_0.generateXSDataInputXDSIndexing(xsDataIndexingInput)
referenceFilename = "XSDataInputXDSIndexing_reference.xml"
referencePath = os.path.join(self.dataPath, referenceFilename)
xmlInputXDSIndexingReference = EDUtilsTest.readAndParseFile(referencePath)
EDAssert.equal(xmlInputXDSIndexingReference, xsDataInputXDSIndexing.marshal())
def testGenerateXSDataIndexingResult(self):
strFilename = "XSDataMOSFLMOutputIndexing_reference.xml"
strPath = os.path.join(self.m_strDataPath, strFilename)
strXMLMOSFLMOutputIndexing = EDUtilsTest.readAndParseFile(strPath)
from XSDataMOSFLMv10 import XSDataMOSFLMOutputIndexing
xsDataMOSFLMOutputIndexing = XSDataMOSFLMOutputIndexing.parseString(strXMLMOSFLMOutputIndexing)
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
xsDataIndexingResult = EDHandlerXSDataMOSFLMv10.generateXSDataIndexingResult(xsDataMOSFLMOutputIndexing)
strReferenceFilename = "XSDataIndexingResult_reference.xml"
strReferencePath = os.path.join(self.m_strDataPath, strReferenceFilename)
strXMLIndexingOutputReference = EDUtilsTest.readAndParseFile(strReferencePath)
from XSDataMXv1 import XSDataIndexingResult
xsdataIndexingResultReference = XSDataIndexingResult.parseString(strXMLIndexingOutputReference)
EDAssert.equal(xsdataIndexingResultReference.marshal(), xsDataIndexingResult.marshal())
def testGenerateXSDataMOSFLMInputIntegration(self):
strFilename = "XSDataIntegrationInput_reference.xml"
strPath = os.path.join(self.m_strDataPath, strFilename)
strXMLIntegrationInput = EDUtilsTest.readAndParseFile(strPath)
from XSDataMXv1 import XSDataIntegrationInput
xsDataIntegrationInput = XSDataIntegrationInput.parseString(strXMLIntegrationInput)
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
xsDataMOSFLMInputIntegration = EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputIntegration(xsDataIntegrationInput)
strReferenceFilename = "XSDataMOSFLMInputIntegration_reference.xml"
strReferencePath = os.path.join(self.m_strDataPath, strReferenceFilename)
strXMLIntegrationInputReference = EDUtilsTest.readAndParseFile(strReferencePath)
EDFactoryPluginStatic.loadModule("XSDataMOSFLMv10")
from XSDataMOSFLMv10 import XSDataMOSFLMInputIntegration
xsDataMOSFLMInputIntegrationReference = XSDataMOSFLMInputIntegration.parseString(strXMLIntegrationInputReference)
EDAssert.equal(xsDataMOSFLMInputIntegrationReference.marshal(), xsDataMOSFLMInputIntegration.marshal())
def testGenerateXSDataResultPowderIntegration(self):
strReferenceInputFile = os.path.join(self.m_strDataPath, "XSDataResultFIT2DCake_reference.xml")
strXMLInput = EDUtilsTest.readAndParseFile(strReferenceInputFile)
EDApplication.loadModule("XSDataFIT2Dv1_0")
from XSDataFIT2Dv1_0 import XSDataResultFIT2DCake
xsDataResultFIT2DCake = XSDataResultFIT2DCake.parseString(strXMLInput)
from EDHandlerXSDataFIT2Dv1_0 import EDHandlerXSDataFIT2Dv1_0
edHandlerXSDataFIT2Dv1_0 = EDHandlerXSDataFIT2Dv1_0()
xsDataResultPowderDiffraction = edHandlerXSDataFIT2Dv1_0.getXSDataResultPowderIntegration(xsDataResultFIT2DCake)
strReferencePath = os.path.join(self.m_strDataPath, "XSDataResultPowderIntegration_reference.xml")
strXMLResultReference = EDUtilsTest.readAndParseFile(strReferencePath)
EDApplication.loadModule("XSDataDiffractionCTv1")
from XSDataDiffractionCTv1 import XSDataResultPowderIntegration
xsDataResultPowderIntegrationReference = XSDataResultPowderIntegration.parseString(strXMLResultReference)
EDAssert.equal(xsDataResultPowderIntegrationReference.marshal(), xsDataResultPowderDiffraction.marshal())
def testGenerateXSDataInputBestv1_2(
self, _strFileNameXSDataInputStrategy_reference,
_strFileNameXSDataInputBest_reference):
"""
This method is testing the generation of the XSDataInputBest object given a XSDataIndexingStrategy object.
"""
strReferenceInputFile = os.path.join(
self.strDataPath, _strFileNameXSDataInputStrategy_reference)
strPath = os.path.join(self.strDataPath, strReferenceInputFile)
from XSDataMXv1 import XSDataInputStrategy
xsDataInputStrategy = XSDataInputStrategy.parseFile(strPath)
from EDHandlerXSDataBestv1_2 import EDHandlerXSDataBestv1_2
edHandlerXSDataBestv1_2 = EDHandlerXSDataBestv1_2()
xsDataInputBestv1_2 = edHandlerXSDataBestv1_2.getXSDataInputBest(
xsDataInputStrategy)
strReferencePath = os.path.join(self.strDataPath,
_strFileNameXSDataInputBest_reference)
strXMLInputBestReference = EDUtilsTest.readAndParseFile(
strReferencePath)
EDFactoryPluginStatic.loadModule("XSDataBestv1_2")
from XSDataBestv1_2 import XSDataInputBest
xsDataInputBestReference = XSDataInputBest.parseString(
strXMLInputBestReference)
EDAssert.equal(xsDataInputBestReference.marshal(),
xsDataInputBestv1_2.marshal())
def testCheckParameters(self):
edPluginSPD = self.createPlugin()
edStringXMLInput = EDUtilsTest.readAndParseFile(
self.m_edStringReferenceInputFileName)
xsDataInputSPDCake = XSDataInputSPDCake.parseString(edStringXMLInput)
edPluginSPD.setDataInput(xsDataInputSPDCake)
edPluginSPD.checkParameters()
def testGenerateXSDataIndexingResult(self):
"""
This method tests the generation of an XSDataIndexingResult object given an XSDataResultLabelit object.
"""
strPath = os.path.join(self.strDataPath, self.strReferenceOutputFile)
strXMLResultLabelit = EDUtilsTest.readAndParseFile(strPath)
EDFactoryPluginStatic.loadModule("XSDataLabelitv10")
from XSDataLabelitv10 import XSDataResultLabelit
xsDataResultLabelit = XSDataResultLabelit.parseString(strXMLResultLabelit)
from EDHandlerXSDataLabelitv10 import EDHandlerXSDataLabelitv10
xsDataIndexingResult = EDHandlerXSDataLabelitv10.generateXSDataIndexingResult(xsDataResultLabelit)
strReferencePath = os.path.join(self.strDataPath, "XSDataIndexingResult_reference.xml")
strIndexingResultReferenceXML = EDUtilsTest.readAndParseFile(strReferencePath)
from XSDataMXv1 import XSDataIndexingResult
xsDataIndexingResultReference = XSDataIndexingResult.parseString(strIndexingResultReferenceXML)
EDAssert.equal(xsDataIndexingResultReference.marshal(), xsDataIndexingResult.marshal())
def testSetDataInput(self):
"""
This method test the setDataInput method of the Labelit plugin by providing an XML string
and then retriving an XSDataInputLabelit object.
"""
#Create the plugin instance
edPluginControlDLSArchiver = self.createPlugin()
# create an object which contains the test information
edStringInputPluginControlDLSArchiverv10XML = EDUtilsTest.readAndParseFile(
self.m_edStringReferenceDataInputFile)
# gives the data to the plugin
edPluginControlDLSArchiver.setDataInput(
edStringInputPluginControlDLSArchiverv10XML)
# get the data from the plugin
xsDataInputPluginControlDLSArchiver = edPluginControlDLSArchiver.getDataInput(
)
# get the string of the path
edStringPath = EDString(xsDataInputPluginControlDLSArchiver.
getDropZonePath().getPath().getValue())
# create the test path
edStringPathReference = EDString("../data/test/ingest/")
# Actually test the data.
EDAssert.equal(edStringPath, edStringPathReference)
#check out that the list is getting read in properly
#FIXME, add in some proper test code here
print xsDataInputPluginControlDLSArchiver.getDropZonePath().getPath(
).getValue()
print xsDataInputPluginControlDLSArchiver.getIgnoreList()[1].getValue()
def testSpatialDistortion(self):
strRefX = "spline-3-18x.edf"
strRefY = "spline-3-18y.edf"
self.loadTestImage([strRefX, strRefY])
edPluginSPD = self.createPlugin()
strXMLInput = EDUtilsTest.readAndParseFile(self.strReferenceInputFileName)
xsDataInputSPDCake = XSDataInputSPDCake.parseString(strXMLInput)
edPluginSPD.setDataInput(xsDataInputSPDCake)
edPluginSPD.configure()
edPluginSPD.getInputParameter()
########################################################################
# Enforce some values
########################################################################
edPluginSPD.dictGeometry["SpatialDistortionFile"] = os.path.join(self.getPluginTestsDataHome(), "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 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 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 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 testGenerateXSDataInputLabelit(self, _strFileNameXSDataIndexingInput_reference,
_strFileNameXSDataLabelitInput_reference):
"""
This method is testing the generation of the XSDataInputLabelit object given a XSDataIndexingInput object.
"""
strPath = os.path.join(self.strDataPath, _strFileNameXSDataIndexingInput_reference)
strXMLIndexingInput = EDUtilsTest.readAndParseFile(strPath)
from XSDataMXv1 import XSDataIndexingInput
xsDataIndexingInput = XSDataIndexingInput.parseString(strXMLIndexingInput)
from EDHandlerXSDataLabelitv10 import EDHandlerXSDataLabelitv10
xsDataInputLabelit = EDHandlerXSDataLabelitv10.generateXSDataInputLabelit(xsDataIndexingInput)
strReferencePath = os.path.join(self.strDataPath, _strFileNameXSDataLabelitInput_reference)
strXMLInputLabelitReference = EDUtilsTest.readAndParseFile(strReferencePath)
EDFactoryPluginStatic.loadModule("XSDataLabelitv10")
from XSDataLabelitv10 import XSDataInputLabelit
xsDataInputLabelitReference = XSDataInputLabelit.parseString(strXMLInputLabelitReference)
EDAssert.equal(xsDataInputLabelitReference.marshal(), xsDataInputLabelit.marshal())
def testGenerateXSDataInputXDSIndexing(self):
filename = "XSDataIndexingInput_reference.xml"
path = os.path.join(self.dataPath, filename)
xmlIndexingInput = EDUtilsTest.readAndParseFile(path)
from XSDataMXv1 import XSDataIndexingInput
xsDataIndexingInput = XSDataIndexingInput.parseString(xmlIndexingInput)
from EDHandlerXSDataXDSv1_0 import EDHandlerXSDataXDSv1_0
xsDataInputXDSIndexing = EDHandlerXSDataXDSv1_0.generateXSDataInputXDSIndexing(
xsDataIndexingInput)
referenceFilename = "XSDataInputXDSIndexing_reference.xml"
referencePath = os.path.join(self.dataPath, referenceFilename)
xmlInputXDSIndexingReference = EDUtilsTest.readAndParseFile(
referencePath)
EDAssert.equal(xmlInputXDSIndexingReference,
xsDataInputXDSIndexing.marshal())
def testCleanDispMat(self):
edPluginSPD = self.createPlugin()
strXMLInput = EDUtilsTest.readAndParseFile(self.strReferenceInputFileName)
xsDataInputSPDCake = XSDataInputSPDCake.parseString(strXMLInput)
edPluginSPD.setDataInput(xsDataInputSPDCake)
if EDVerbose.isVerboseDebug():
edPluginSPD.cleanDispMat(edPluginSPD.getWorkingDirectory())
else:
edPluginSPD.cleanDispMat()
def testGenerateXSDataResultPowderIntegration(self):
strReferenceInputFile = os.path.join(
self.m_strDataPath, "XSDataResultFIT2DCake_reference.xml")
strXMLInput = EDUtilsTest.readAndParseFile(strReferenceInputFile)
EDApplication.loadModule("XSDataFIT2Dv1_0")
from XSDataFIT2Dv1_0 import XSDataResultFIT2DCake
xsDataResultFIT2DCake = XSDataResultFIT2DCake.parseString(strXMLInput)
from EDHandlerXSDataFIT2Dv1_0 import EDHandlerXSDataFIT2Dv1_0
edHandlerXSDataFIT2Dv1_0 = EDHandlerXSDataFIT2Dv1_0()
xsDataResultPowderDiffraction = edHandlerXSDataFIT2Dv1_0.getXSDataResultPowderIntegration(
xsDataResultFIT2DCake)
strReferencePath = os.path.join(
self.m_strDataPath, "XSDataResultPowderIntegration_reference.xml")
strXMLResultReference = EDUtilsTest.readAndParseFile(strReferencePath)
EDApplication.loadModule("XSDataDiffractionCTv1")
from XSDataDiffractionCTv1 import XSDataResultPowderIntegration
xsDataResultPowderIntegrationReference = XSDataResultPowderIntegration.parseString(
strXMLResultReference)
EDAssert.equal(xsDataResultPowderIntegrationReference.marshal(),
xsDataResultPowderDiffraction.marshal())
def testGenerateXSDataIndexingResult(self):
strFilename = "XSDataMOSFLMOutputIndexing_reference.xml"
strPath = os.path.join(self.m_strDataPath, strFilename)
strXMLMOSFLMOutputIndexing = EDUtilsTest.readAndParseFile(strPath)
from XSDataMOSFLMv10 import XSDataMOSFLMOutputIndexing
xsDataMOSFLMOutputIndexing = XSDataMOSFLMOutputIndexing.parseString(
strXMLMOSFLMOutputIndexing)
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
xsDataIndexingResult = EDHandlerXSDataMOSFLMv10.generateXSDataIndexingResult(
xsDataMOSFLMOutputIndexing)
strReferenceFilename = "XSDataIndexingResult_reference.xml"
strReferencePath = os.path.join(self.m_strDataPath,
strReferenceFilename)
strXMLIndexingOutputReference = EDUtilsTest.readAndParseFile(
strReferencePath)
from XSDataMXv1 import XSDataIndexingResult
xsdataIndexingResultReference = XSDataIndexingResult.parseString(
strXMLIndexingOutputReference)
EDAssert.equal(xsdataIndexingResultReference.marshal(),
xsDataIndexingResult.marshal())
def testGenerateXSDataMOSFLMInputIntegration(self):
strFilename = "XSDataIntegrationInput_reference.xml"
strPath = os.path.join(self.m_strDataPath, strFilename)
strXMLIntegrationInput = EDUtilsTest.readAndParseFile(strPath)
from XSDataMXv1 import XSDataIntegrationInput
xsDataIntegrationInput = XSDataIntegrationInput.parseString(
strXMLIntegrationInput)
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
xsDataMOSFLMInputIntegration = EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputIntegration(
xsDataIntegrationInput)
strReferenceFilename = "XSDataMOSFLMInputIntegration_reference.xml"
strReferencePath = os.path.join(self.m_strDataPath,
strReferenceFilename)
strXMLIntegrationInputReference = EDUtilsTest.readAndParseFile(
strReferencePath)
EDFactoryPluginStatic.loadModule("XSDataMOSFLMv10")
from XSDataMOSFLMv10 import XSDataMOSFLMInputIntegration
xsDataMOSFLMInputIntegrationReference = XSDataMOSFLMInputIntegration.parseString(
strXMLIntegrationInputReference)
EDAssert.equal(xsDataMOSFLMInputIntegrationReference.marshal(),
xsDataMOSFLMInputIntegration.marshal())
def testIgnoreFile(self):
# Create the plugin instance
edPluginExecSRBRegister = self.createPlugin()
# Read in the data from the XML, for the big xml
edStringInputExecSRBRegisterv10XML = EDUtilsTest.readAndParseFile( self.m_edStringReferenceDataInputFile3)
# gives the data to the plugin
edPluginExecSRBRegister.setDataInput( edStringInputExecSRBRegisterv10XML )
# first load the tree
edPluginExecSRBRegister.openXMLTree()
edPluginExecSRBRegister.checkAgainstIgnoreList()
EDAssert.equal(False,edPluginExecSRBRegister.forArchiving)
def testGenerateSPDCommand(self):
edPluginSPD = self.createPlugin()
strXMLInput = EDUtilsTest.readAndParseFile(self.strReferenceInputFileName)
xsDataInputSPDCake = XSDataInputSPDCake.parseString(strXMLInput)
edPluginSPD.setDataInput(xsDataInputSPDCake)
edPluginSPD.configure()
edPluginSPD.getInputParameter()
#edPluginSPD.preProcess()
edPluginSPD.generateSPDCommand()
EDVerbose.screen("SPD configuration:\n%s" % edPluginSPD.getSPDConfig())
if EDVerbose.isVerboseDebug():
expected = """off_1=0 off_2=0 verbose=2 src_ext=.edf cor_ext=.cor wvl=1.000000e-10 cen_1=1.050000e+03 cen_2=1.000000e+03 dis=1.000000e-01 pix_1=4.722440e-05 pix_2=4.683150e-05 do_distortion=0 do_dark=0"""
#"do_distortion=2 off_1=0 off_2=0 verbose=2 src_ext=.edf cor_ext=.cor wvl=1.000000e-10 cen_1=1.050000e+03 cen_2=1.000000e+03 dis=1.000000e-01 pix_1=4.722440e-05 pix_2=4.683150e-05 do_dark=0"
else:
expected = """off_1=0 off_2=0 verbose=0 src_ext=.edf cor_ext=.cor wvl=1.000000e-10 cen_1=1.050000e+03 cen_2=1.000000e+03 dis=1.000000e-01 pix_1=4.722440e-05 pix_2=4.683150e-05 do_distortion=0 do_dark=0"""
#do_distortion=2 off_1=0 off_2=0 verbose=0 src_ext=.edf cor_ext=.cor wvl=1.000000e-10 cen_1=1.050000e+03 cen_2=1.000000e+03 dis=1.000000e-01 pix_1=4.722440e-05 pix_2=4.683150e-05 do_dark=0"
EDAssert.equal(edPluginSPD.getSPDConfig(), expected)
def testGenerateXSDataInputBestv1_2(self, _strFileNameXSDataInputStrategy_reference, _strFileNameXSDataInputBest_reference):
"""
This method is testing the generation of the XSDataInputBest object given a XSDataIndexingStrategy object.
"""
strReferenceInputFile = os.path.join(self.strDataPath, _strFileNameXSDataInputStrategy_reference)
strPath = os.path.join(self.strDataPath, strReferenceInputFile)
from XSDataMXv1 import XSDataInputStrategy
xsDataInputStrategy = XSDataInputStrategy.parseFile(strPath)
from EDHandlerXSDataBestv1_2 import EDHandlerXSDataBestv1_2
edHandlerXSDataBestv1_2 = EDHandlerXSDataBestv1_2()
xsDataInputBestv1_2 = edHandlerXSDataBestv1_2.getXSDataInputBest(xsDataInputStrategy)
strReferencePath = os.path.join(self.strDataPath, _strFileNameXSDataInputBest_reference)
strXMLInputBestReference = EDUtilsTest.readAndParseFile(strReferencePath)
EDFactoryPluginStatic.loadModule("XSDataBestv1_2")
from XSDataBestv1_2 import XSDataInputBest
xsDataInputBestReference = XSDataInputBest.parseString(strXMLInputBestReference)
EDAssert.equal(xsDataInputBestReference.marshal(), xsDataInputBestv1_2.marshal())
def testGenerateSPDCommand(self):
edPluginSPD = self.createPlugin()
edStringXMLInput = EDUtilsTest.readAndParseFile(self.m_edStringReferenceInputFileName)
xsDataInputSPDCake = XSDataInputSPDCake.parseString(edStringXMLInput)
edPluginSPD.setDataInput(xsDataInputSPDCake)
edPluginSPD.configure()
edPluginSPD.getInputParameter()
#edPluginSPD.preProcess()
edPluginSPD.generateSPDCommand()
EDVerbose.screen("SPD configuration:\n %s" % edPluginSPD.getSPDConfig())
if EDVerbose.isVerboseDebug():
expected = """off_1=0 off_2=0 verbose=2 src_ext=.edf wvl=1.000000e-10 cen_1=1.050000e+03 cen_2=1.000000e+03 dis=1.000000e-01 pix_1=4.722440e-05 pix_2=4.683150e-05 do_distortion=0 do_dark=0 cor_ext=.cor azim_int=1 azim_pass=0 azim_ext=.cor azim_r_num=1489"""
# """do_distortion=2 off_1=0 off_2=0 verbose=2 src_ext=.edf wvl=1.000000e-10 cen_1=1.050000e+03 cen_2=1.000000e+03 dis=1.000000e-01 pix_1=4.722440e-05 pix_2=4.683150e-05 do_dark=0 cor_ext=.cor azim_int=1 azim_pass=0 azim_ext=.cor azim_r_num=1489"""
else:
expected = """off_1=0 off_2=0 verbose=0 src_ext=.edf wvl=1.000000e-10 cen_1=1.050000e+03 cen_2=1.000000e+03 dis=1.000000e-01 pix_1=4.722440e-05 pix_2=4.683150e-05 do_distortion=0 do_dark=0 cor_ext=.cor azim_int=1 azim_pass=0 azim_ext=.cor azim_r_num=1489"""
# """do_distortion=2 off_1=0 off_2=0 verbose=0 src_ext=.edf wvl=1.000000e-10 cen_1=1.050000e+03 cen_2=1.000000e+03 dis=1.000000e-01 pix_1=4.722440e-05 pix_2=4.683150e-05 do_dark=0 cor_ext=.cor azim_int=1 azim_pass=0 azim_ext=.cor azim_r_num=1489"""
EDAssert.equal(edPluginSPD.getSPDConfig(), expected)
def testSetDataInput( self ):
"""
This method test the setDataInput method of the Labelit plugin by providing an XML string
and then retriving an XSDataInputLabelit object.
"""
#Create the plugin instance
edPluginExecICATIngester = self.createPlugin()
# create an object which contains the test information
edStringInputExecICATIngesterv10XML = EDUtilsTest.readAndParseFile( self.m_edStringReferenceDataInputFile )
# gives the data to the plugin
edPluginExecICATIngester.setDataInput( edStringInputExecICATIngesterv10XML )
# get the data from the plugin
xsDataInputPluginExecICATIngester = edPluginExecICATIngester.getDataInput()
# get the string of the path
edStringPath = EDString( xsDataInputPluginExecICATIngester.getXmlIngestFileName().getPath().getValue() )
# create the test path
edStringPathReference = EDString( "/tmp/xmlingest/" )
# Actualy test the data.
EDAssert.equal( edStringPathReference, edStringPath )
def testSetDataInput(self):
"""
This method test the setDataInput method of the Labelit plugin by providing an XML string
and then retriving an XSDataInputLabelit object.
"""
#Create the plugin instance
edPluginExecICATIngester = self.createPlugin()
# create an object which contains the test information
edStringInputExecICATIngesterv10XML = EDUtilsTest.readAndParseFile(
self.m_edStringReferenceDataInputFile)
# gives the data to the plugin
edPluginExecICATIngester.setDataInput(
edStringInputExecICATIngesterv10XML)
# get the data from the plugin
xsDataInputPluginExecICATIngester = edPluginExecICATIngester.getDataInput(
)
# get the string of the path
edStringPath = EDString(xsDataInputPluginExecICATIngester.
getXmlIngestFileName().getPath().getValue())
# create the test path
edStringPathReference = EDString("/tmp/xmlingest/")
# Actualy test the data.
EDAssert.equal(edStringPathReference, edStringPath)
def testSetDataInput( self ):
"""
This method test the setDataInput method of the Labelit plugin by providing an XML string
and then retriving an XSDataInputLabelit object.
"""
#Create the plugin instance
edPluginControlDLSArchiver = self.createPlugin()
# create an object which contains the test information
edStringInputPluginControlDLSArchiverv10XML = EDUtilsTest.readAndParseFile( self.m_edStringReferenceDataInputFile )
# gives the data to the plugin
edPluginControlDLSArchiver.setDataInput( edStringInputPluginControlDLSArchiverv10XML )
# get the data from the plugin
xsDataInputPluginControlDLSArchiver = edPluginControlDLSArchiver.getDataInput()
# get the string of the path
edStringPath = EDString( xsDataInputPluginControlDLSArchiver.getDropZonePath().getPath().getValue() )
# create the test path
edStringPathReference = EDString( "../data/test/ingest/" )
# Actually test the data.
EDAssert.equal( edStringPath, edStringPathReference)
#check out that the list is getting read in properly
#FIXME, add in some proper test code here
print xsDataInputPluginControlDLSArchiver.getDropZonePath().getPath().getValue()
print xsDataInputPluginControlDLSArchiver.getIgnoreList()[1].getValue()
def testCleanDispMat(self):
edPluginSPD = self.createPlugin()
edStringXMLInput = EDUtilsTest.readAndParseFile(self.m_edStringReferenceInputFileName)
xsDataInputSPDCake = XSDataInputSPDCake.parseString(edStringXMLInput)
edPluginSPD.setDataInput(xsDataInputSPDCake)
edPluginSPD.cleanDispMat()
def testKillAllWorkers(self):
edPluginSPD = self.createPlugin()
edStringXMLInput = EDUtilsTest.readAndParseFile(self.m_edStringReferenceInputFileName)
xsDataInputSPDCake = XSDataInputSPDCake.parseString(edStringXMLInput)
edPluginSPD.setDataInput(xsDataInputSPDCake)
edPluginSPD.killAllWorkers()
def testCheckParameters(self):
edPluginFIT2D = self.createPlugin()
edStringXMLInput = EDUtilsTest.readAndParseFile(self.m_edStringReferenceInputFileName)
xsDataInputFIT2DCake = XSDataInputFIT2DCake.parseString(edStringXMLInput)
edPluginFIT2D.setDataInput(xsDataInputFIT2DCake)
edPluginFIT2D.checkParameters()
def testCheckParameters(self):
edPluginSPD = self.createPlugin()
strXMLInput = EDUtilsTest.readAndParseFile(self.strReferenceInputFileName)
xsDataInputSPDCake = XSDataInputSPDCake.parseString(strXMLInput)
edPluginSPD.setDataInput(xsDataInputSPDCake)
edPluginSPD.checkParameters()
def testGetXSDataRaddoseInput(self):
"""
"""
from XSDataCommon import XSDataLength
from XSDataCommon import XSDataWavelength
from XSDataCommon import XSDataFlux
from XSDataCommon import XSDataSize
from XSDataCommon import XSDataDouble
from XSDataCommon import XSDataString
from XSDataCommon import XSDataAngle
from XSDataCommon import XSDataTime
from XSDataCommon import XSDataInteger
from XSDataMXv1 import XSDataBeam
from XSDataMXv1 import XSDataStructure
from XSDataMXv1 import XSDataChain
from XSDataMXv1 import XSDataAtom
from XSDataMXv1 import XSDataLigand
from XSDataMXv1 import XSDataCrystal
from XSDataMXv1 import XSDataSpaceGroup
from XSDataMXv1 import XSDataSampleCrystalMM
from XSDataMXv1 import XSDataChemicalCompositionMM
from XSDataMXv1 import XSDataAtomicComposition
from XSDataMXv1 import XSDataSolvent
from XSDataMXv1 import XSDataCell
from EDHandlerXSDataRaddosev10 import EDHandlerXSDataRaddosev10
EDFactoryPluginStatic.loadModule("XSDataRaddosev10")
from XSDataRaddosev10 import XSDataRaddoseInput
xsDataBeam = XSDataBeam()
xsDataBeam.setSize(XSDataSize(x=XSDataLength(0.1), y=XSDataLength(0.1)))
xsDataBeam.setWavelength(XSDataWavelength(2.41))
xsDataBeam.setFlux(XSDataFlux(1e+12))
xsDataSample = XSDataSampleCrystalMM()
xsDataStructure = XSDataStructure()
xsDataComposition = XSDataChemicalCompositionMM()
xsDataChain = XSDataChain()
xsDataChain.setType(XSDataString("protein"))
xsDataChain.setNumberOfCopies(XSDataDouble(2))
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtom1 = XSDataAtom()
xsDataAtom1.setSymbol(XSDataString("Se"))
xsDataAtom1.setNumberOf(XSDataDouble(4))
xsDataAtomicComposition.addAtom(xsDataAtom1)
xsDataAtom2 = XSDataAtom()
xsDataAtom2.setSymbol(XSDataString("S"))
xsDataAtom2.setNumberOf(XSDataDouble(5))
xsDataAtomicComposition.addAtom(xsDataAtom2)
xsDataChain.setHeavyAtoms(xsDataAtomicComposition)
xsDataChain.setNumberOfMonomers(XSDataDouble(100))
xsDataStructure.addChain(xsDataChain)
xsDataChain2 = XSDataChain()
xsDataChain2.setType(XSDataString("rna"))
xsDataChain2.setNumberOfCopies(XSDataDouble(1))
xsDataChain2.setNumberOfMonomers(XSDataDouble(60))
xsDataStructure.addChain(xsDataChain2)
xsDataLigand = XSDataLigand()
xsDataLigand.setNumberOfCopies(XSDataDouble(2))
xsDataLigand.setNumberOfLightAtoms(XSDataDouble(42))
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtom3 = XSDataAtom()
xsDataAtom3.setSymbol(XSDataString("Fe"))
xsDataAtom3.setNumberOf(XSDataDouble(1))
xsDataAtomicComposition.addAtom(xsDataAtom3)
xsDataLigand.setHeavyAtoms(xsDataAtomicComposition)
xsDataStructure.addLigand(xsDataLigand)
xsDataStructure.setNumberOfCopiesInAsymmetricUnit(XSDataDouble(0.25))
xsDataSolvent = XSDataSolvent()
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtomNa = XSDataAtom()
xsDataAtomNa.setSymbol(XSDataString("Na"))
xsDataAtomNa.setConcentration(XSDataDouble(1000))
xsDataAtomicComposition.addAtom(xsDataAtomNa)
xsDataAtomCl = XSDataAtom()
xsDataAtomCl.setSymbol(XSDataString("Cl"))
xsDataAtomCl.setConcentration(XSDataDouble(1000))
xsDataAtomicComposition.addAtom(xsDataAtomCl)
xsDataSolvent.setAtoms(xsDataAtomicComposition)
xsDataComposition.setStructure(xsDataStructure)
xsDataComposition.setSolvent(xsDataSolvent)
xsDataSample.setChemicalComposition(xsDataComposition)
xsDataSample.setSize(XSDataSize(XSDataLength(0.1), XSDataLength(0.1), XSDataLength(0.1)))
xsDataCell = XSDataCell(angle_alpha=XSDataAngle(90.0),
angle_beta=XSDataAngle(90.0),
angle_gamma=XSDataAngle(90.0),
length_a=XSDataLength(78.9),
length_b=XSDataLength(95.162),
length_c=XSDataLength(104.087))
xsDataCrystal = XSDataCrystal()
xsDataSpaceGroup = XSDataSpaceGroup()
xsDataCrystal.setCell(xsDataCell)
xsDataSpaceGroup.setITNumber(XSDataInteger(16))
xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
xsDataSample.setCrystal(xsDataCrystal)
iNumSymOperators = 4
xsDataRaddosev01Input = EDHandlerXSDataRaddosev10().getXSDataRaddoseInput(xsDataBeam,
xsDataSample,
iNumSymOperators)
xsDataRaddosev01Input.exportToFile(self.strObtainedInputFile2)
strExpectedInput = EDUtilsTest.readAndParseFile (self.strReferenceInputFile2)
strObtainedInput = EDUtilsTest.readAndParseFile (self.strObtainedInputFile2)
xsDataInputExpected = XSDataRaddoseInput.parseString(strExpectedInput)
xsDataInputObtained = XSDataRaddoseInput.parseString(strObtainedInput)
EDAssert.equal(xsDataInputExpected.marshal(), xsDataInputObtained.marshal())
def testCheckParameters(self):
pyStrXMLInput = EDUtilsTest.readAndParseFile(self.m_pyStrReferenceInputFile)
edPluginControlCopyUnitCellMTZtoPDB = self.createPlugin()
edPluginControlCopyUnitCellMTZtoPDB.setDataInput(pyStrXMLInput)
edPluginControlCopyUnitCellMTZtoPDB.checkParameters()
def testCheckParameters(self):
pyStrXMLInput = EDUtilsTest.readAndParseFile(self.m_pyStrReferenceInputFile)
edPluginExecPDBSETUnitCell = self.createPlugin()
edPluginExecPDBSETUnitCell.setDataInput(pyStrXMLInput)
edPluginExecPDBSETUnitCell.checkParameters()
def testGetXSDataRaddoseInput(self):
"""
"""
from XSDataCommon import XSDataLength
from XSDataCommon import XSDataWavelength
from XSDataCommon import XSDataFlux
from XSDataCommon import XSDataSize
from XSDataCommon import XSDataDouble
from XSDataCommon import XSDataString
from XSDataCommon import XSDataAngle
from XSDataCommon import XSDataTime
from XSDataCommon import XSDataInteger
from XSDataMXv1 import XSDataBeam
from XSDataMXv1 import XSDataStructure
from XSDataMXv1 import XSDataChain
from XSDataMXv1 import XSDataAtom
from XSDataMXv1 import XSDataLigand
from XSDataMXv1 import XSDataCrystal
from XSDataMXv1 import XSDataSpaceGroup
from XSDataMXv1 import XSDataSampleCrystalMM
from XSDataMXv1 import XSDataChemicalCompositionMM
from XSDataMXv1 import XSDataAtomicComposition
from XSDataMXv1 import XSDataSolvent
from XSDataMXv1 import XSDataCell
from EDHandlerXSDataRaddosev10 import EDHandlerXSDataRaddosev10
EDFactoryPluginStatic.loadModule("XSDataRaddosev10")
from XSDataRaddosev10 import XSDataRaddoseInput
xsDataBeam = XSDataBeam()
xsDataBeam.setSize(XSDataSize(x=XSDataLength(0.1),
y=XSDataLength(0.1)))
xsDataBeam.setWavelength(XSDataWavelength(2.41))
xsDataBeam.setFlux(XSDataFlux(1e+12))
xsDataBeam.setExposureTime(XSDataTime(0.037))
xsDataSample = XSDataSampleCrystalMM()
xsDataStructure = XSDataStructure()
xsDataComposition = XSDataChemicalCompositionMM()
xsDataChain = XSDataChain()
xsDataChain.setType(XSDataString("protein"))
xsDataChain.setNumberOfCopies(XSDataDouble(2))
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtom1 = XSDataAtom()
xsDataAtom1.setSymbol(XSDataString("Se"))
xsDataAtom1.setNumberOf(XSDataDouble(4))
xsDataAtomicComposition.addAtom(xsDataAtom1)
xsDataAtom2 = XSDataAtom()
xsDataAtom2.setSymbol(XSDataString("S"))
xsDataAtom2.setNumberOf(XSDataDouble(5))
xsDataAtomicComposition.addAtom(xsDataAtom2)
xsDataChain.setHeavyAtoms(xsDataAtomicComposition)
xsDataChain.setNumberOfMonomers(XSDataDouble(100))
xsDataStructure.addChain(xsDataChain)
xsDataChain2 = XSDataChain()
xsDataChain2.setType(XSDataString("rna"))
xsDataChain2.setNumberOfCopies(XSDataDouble(1))
xsDataChain2.setNumberOfMonomers(XSDataDouble(60))
xsDataStructure.addChain(xsDataChain2)
xsDataLigand = XSDataLigand()
xsDataLigand.setNumberOfCopies(XSDataDouble(2))
xsDataLigand.setNumberOfLightAtoms(XSDataDouble(42))
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtom3 = XSDataAtom()
xsDataAtom3.setSymbol(XSDataString("Fe"))
xsDataAtom3.setNumberOf(XSDataDouble(1))
xsDataAtomicComposition.addAtom(xsDataAtom3)
xsDataLigand.setHeavyAtoms(xsDataAtomicComposition)
xsDataStructure.addLigand(xsDataLigand)
xsDataStructure.setNumberOfCopiesInAsymmetricUnit(XSDataDouble(0.25))
xsDataSolvent = XSDataSolvent()
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtomNa = XSDataAtom()
xsDataAtomNa.setSymbol(XSDataString("Na"))
xsDataAtomNa.setConcentration(XSDataDouble(1000))
xsDataAtomicComposition.addAtom(xsDataAtomNa)
xsDataAtomCl = XSDataAtom()
xsDataAtomCl.setSymbol(XSDataString("Cl"))
xsDataAtomCl.setConcentration(XSDataDouble(1000))
xsDataAtomicComposition.addAtom(xsDataAtomCl)
xsDataSolvent.setAtoms(xsDataAtomicComposition)
xsDataComposition.setStructure(xsDataStructure)
xsDataComposition.setSolvent(xsDataSolvent)
xsDataSample.setChemicalComposition(xsDataComposition)
xsDataSample.setSize(
XSDataSize(XSDataLength(0.1), XSDataLength(0.1),
XSDataLength(0.1)))
xsDataCell = XSDataCell(angle_alpha=XSDataAngle(90.0),
angle_beta=XSDataAngle(90.0),
angle_gamma=XSDataAngle(90.0),
length_a=XSDataLength(78.9),
length_b=XSDataLength(95.162),
length_c=XSDataLength(104.087))
xsDataCrystal = XSDataCrystal()
xsDataSpaceGroup = XSDataSpaceGroup()
xsDataCrystal.setCell(xsDataCell)
xsDataSpaceGroup.setITNumber(XSDataInteger(16))
xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
xsDataSample.setCrystal(xsDataCrystal)
iNumSymOperators = 4
iNumberOfImages = 2
xsDataRaddosev01Input = EDHandlerXSDataRaddosev10(
).getXSDataRaddoseInput(xsDataBeam, xsDataSample, iNumSymOperators,
iNumberOfImages)
xsDataRaddosev01Input.exportToFile(self.strObtainedInputFile2)
strExpectedInput = EDUtilsTest.readAndParseFile(
self.strReferenceInputFile2)
strObtainedInput = EDUtilsTest.readAndParseFile(
self.strObtainedInputFile2)
xsDataInputExpected = XSDataRaddoseInput.parseString(strExpectedInput)
xsDataInputObtained = XSDataRaddoseInput.parseString(strObtainedInput)
EDAssert.equal(xsDataInputExpected.marshal(),
xsDataInputObtained.marshal())
