def testGenerateExecutiveSummary(self):
strInputBest = self.readAndParseFile(self.strReferenceInputFile)
strResultBest = self.readAndParseFile(self.strReferenceResultFile)
from XSDataBestv1_1 import XSDataInputBest
from XSDataBestv1_1 import XSDataResultBest
xsDataInputBest = XSDataInputBest.parseString(strInputBest)
xsDataResultBest = XSDataResultBest.parseString(strResultBest)
edPluginBest = self.createPlugin()
edPluginBest.setDataInput(xsDataInputBest)
edPluginBest.setDataOutput(xsDataResultBest)
edPluginBest.generateExecutiveSummary(edPluginBest)
def testGenerateExecutiveSummary(self):
strInputBest = self.readAndParseFile(self.strReferenceInputFile)
strResultBest = self.readAndParseFile(self.strReferenceResultFile)
from XSDataBestv1_1 import XSDataInputBest
from XSDataBestv1_1 import XSDataResultBest
xsDataInputBest = XSDataInputBest.parseString(strInputBest)
xsDataResultBest = XSDataResultBest.parseString(strResultBest)
edPluginBest = self.createPlugin()
edPluginBest.setDataInput(xsDataInputBest)
edPluginBest.setDataOutput(xsDataResultBest)
edPluginBest.generateExecutiveSummary(edPluginBest)
def setDataInput( self, _dataInput ):
"""
Sets the Plugin Input Data
_dataInput could be either an String XML or an XSData
The XML String should be parsed as an Output Object by the final Plugin
"""
self.DEBUG( "EDPluginSTACv10Alignment.setDataInput" )
# Check the type
if( isinstance( _dataInput, EDString ) ):
self.DEBUG( "EDPluginSTACv10.setDataInput: Input Data is of EDString " )
self.m_xsDataInput = XSDataInputBest.parseString( _dataInput )
elif ( isinstance( _dataInput, XSDataInputBest ) ):
self.m_xsDataInput = _dataInput
else:
errorMessage = EDMessage.ERROR_WRONG_DATA_TYPE_02 % ('EDPluginSTACv10.setDataInput', "XMLString or XSDataBestv01Input expected" )
self.error( errorMessage )
self.addErrorMessage( errorMessage )
raise RuntimeError, errorMessage
def setDataInput(self, _dataInput):
"""
Sets the Plugin Input Data
_dataInput could be either an String XML or an XSData
The XML String should be parsed as an Output Object by the final Plugin
"""
self.DEBUG("EDPluginSTACv10Alignment.setDataInput")
# Check the type
if (isinstance(_dataInput, EDString)):
self.DEBUG(
"EDPluginSTACv10.setDataInput: Input Data is of EDString ")
self.m_xsDataInput = XSDataInputBest.parseString(_dataInput)
elif (isinstance(_dataInput, XSDataInputBest)):
self.m_xsDataInput = _dataInput
else:
errorMessage = EDMessage.ERROR_WRONG_DATA_TYPE_02 % (
'EDPluginSTACv10.setDataInput',
"XMLString or XSDataBestv01Input expected")
self.error(errorMessage)
self.addErrorMessage(errorMessage)
raise RuntimeError, errorMessage
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 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(0.22E+06))
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 getXSDataInputBest(self, _xsDataBeam, _xsDataSample, _xsDataDetector, _xsDataGoniostat, _xsDataDiffractionPlan,
_edStrBestFileContentDat, _edStrBestFileContentPar, _edListBestFileContentHKL):
"""
"""
xsDataInputBest = XSDataInputBest()
# Sample
xdDataAbsorbedDose = None
xsDataSusceptibility = None
# Could be None if sample has not been set
# It could be not None in case Raddose has calculated an absorbed dose with default sample values
if(_xsDataSample is not None):
xdDataAbsorbedDose = _xsDataSample.getAbsorbedDoseRate()
xsDataSusceptibility = _xsDataSample.getSusceptibility()
# Could be None if Raddose failed to calculate the absorbed dose
if(xdDataAbsorbedDose is not None):
xsDataInputBest.setCrystalAbsorbedDoseRate(_xsDataSample.getAbsorbedDoseRate())
xsDataInputBest.setCrystalSusceptibility(xsDataSusceptibility)
# crystalShape
# Default value is 1 (We assume that Xtal is smaller than beam)
xsDataFloatCrystalShape = _xsDataSample.getShape()
if(xsDataFloatCrystalShape is None):
xsDataInputBest.setCrystalShape(XSDataFloat(1))
else:
xsDataInputBest.setCrystalShape(xsDataFloatCrystalShape)
# Detector
xsDataInputBest.setDetectorType(_xsDataDetector.getType())
# Beam
xsDataInputBest.setBeamExposureTime(_xsDataBeam.getExposureTime())
xsDataInputBest.setBeamMinExposureTime(_xsDataBeam.getMinExposureTimePerImage())
# Goniostat
xsDataInputBest.setGoniostatMaxRotationSpeed(_xsDataGoniostat.getMaxOscillationSpeed())
xsDataInputBest.setGoniostatMinRotationWidth(_xsDataGoniostat.getMinOscillationWidth())
# Diffraction plan
xsDataInputBest.setAimedResolution(_xsDataDiffractionPlan.getAimedResolution())
xsDataInputBest.setAimedRedundancy(_xsDataDiffractionPlan.getAimedMultiplicity())
xsDataInputBest.setAimedCompleteness(_xsDataDiffractionPlan.getAimedCompleteness())
xsDataInputBest.setAimedIOverSigma(_xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution())
xsDataInputBest.setBeamMaxExposureTime(_xsDataDiffractionPlan.getMaxExposureTimePerDataCollection())
xsDataInputBest.setComplexity(_xsDataDiffractionPlan.getComplexity())
xsDataInputBest.setAnomalousData(_xsDataDiffractionPlan.getAnomalousData())
# Best Files
xsDataInputBest.setBestFileContentDat(_edStrBestFileContentDat)
xsDataInputBest.setBestFileContentPar(_edStrBestFileContentPar)
xsDataInputBest.setBestFileContentHKL(_edListBestFileContentHKL)
return xsDataInputBest
def getXSDataInputBest(self, _xsDataBeam, _xsDataSample, _xsDataDetector,
_xsDataGoniostat, _xsDataDiffractionPlan,
_edStrBestFileContentDat, _edStrBestFileContentPar,
_edListBestFileContentHKL):
"""
"""
xsDataInputBest = XSDataInputBest()
# Sample
xdDataAbsorbedDose = None
xsDataSusceptibility = None
# Could be None if sample has not been set
# It could be not None in case Raddose has calculated an absorbed dose with default sample values
if (_xsDataSample is not None):
xdDataAbsorbedDose = _xsDataSample.getAbsorbedDoseRate()
xsDataSusceptibility = _xsDataSample.getSusceptibility()
# Could be None if Raddose failed to calculate the absorbed dose
if (xdDataAbsorbedDose is not None):
xsDataInputBest.setCrystalAbsorbedDoseRate(
_xsDataSample.getAbsorbedDoseRate())
xsDataInputBest.setCrystalSusceptibility(xsDataSusceptibility)
# crystalShape
# Default value is 1 (We assume that Xtal is smaller than beam)
xsDataFloatCrystalShape = _xsDataSample.getShape()
if (xsDataFloatCrystalShape is None):
xsDataInputBest.setCrystalShape(XSDataFloat(1))
else:
xsDataInputBest.setCrystalShape(xsDataFloatCrystalShape)
# Detector
xsDataInputBest.setDetectorType(_xsDataDetector.getType())
# Beam
xsDataInputBest.setBeamExposureTime(_xsDataBeam.getExposureTime())
xsDataInputBest.setBeamMinExposureTime(
_xsDataBeam.getMinExposureTimePerImage())
# Goniostat
xsDataInputBest.setGoniostatMaxRotationSpeed(
_xsDataGoniostat.getMaxOscillationSpeed())
xsDataInputBest.setGoniostatMinRotationWidth(
_xsDataGoniostat.getMinOscillationWidth())
# Diffraction plan
xsDataInputBest.setAimedResolution(
_xsDataDiffractionPlan.getAimedResolution())
xsDataInputBest.setAimedRedundancy(
_xsDataDiffractionPlan.getAimedMultiplicity())
xsDataInputBest.setAimedCompleteness(
_xsDataDiffractionPlan.getAimedCompleteness())
xsDataInputBest.setAimedIOverSigma(
_xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution())
xsDataInputBest.setBeamMaxExposureTime(
_xsDataDiffractionPlan.getMaxExposureTimePerDataCollection())
xsDataInputBest.setComplexity(_xsDataDiffractionPlan.getComplexity())
xsDataInputBest.setAnomalousData(
_xsDataDiffractionPlan.getAnomalousData())
# Best Files
xsDataInputBest.setBestFileContentDat(_edStrBestFileContentDat)
xsDataInputBest.setBestFileContentPar(_edStrBestFileContentPar)
xsDataInputBest.setBestFileContentHKL(_edListBestFileContentHKL)
return xsDataInputBest
