def testCreateDataMOSFLMOutputGeneratePrediction(self):
"""
"""
pluginGeneratePrediction = self.createPlugin()
pluginGeneratePrediction.setScriptExecutable("cat")
pluginGeneratePrediction.configure()
pluginGeneratePrediction.setPredictionImageFileName("prediction.jpg")
stringBaseName = pluginGeneratePrediction.getBaseName()
stringNewmatFile = os.path.join(
self.strUnitTestDataHome, "EDPluginMOSFLMv10_autoindexMat_ok.txt")
pluginGeneratePrediction.setNewmatFileName(stringNewmatFile)
from XSDataMOSFLMv10 import XSDataMOSFLMInputGeneratePrediction
xsDataMOSFLMInputGeneratePrediction = XSDataMOSFLMInputGeneratePrediction.parseFile(
os.path.join(self.strUnitTestDataHome,
"XSDataMOSFLMInputGeneratePrediction_reference.xml"))
pluginGeneratePrediction.setDataInput(
xsDataMOSFLMInputGeneratePrediction)
xsDataMOSFLMOutputGeneratePrediction = pluginGeneratePrediction.createDataMOSFLMOutputGeneratePrediction(
)
stringImagePath = xsDataMOSFLMOutputGeneratePrediction.getPredictionImage(
).getPath().getValue()
stringReferenceXML = self.readAndParseFile(
self.strReferenceDataOutputFile)
from XSDataMOSFLMv10 import XSDataMOSFLMOutputGeneratePrediction
xsDataMOSFLMOutputGeneratePredictionReference = XSDataMOSFLMOutputGeneratePrediction.parseString(
stringReferenceXML)
xsDataImage = xsDataMOSFLMOutputGeneratePredictionReference.getPredictionImage(
)
xsDataImage.setPath(XSDataString(stringImagePath))
xsDataMOSFLMOutputGeneratePredictionReference.setPredictionImage(
xsDataImage)
# Replace path to log file since it cannot be determined by the unit test
xsDataMOSFLMOutputGeneratePrediction.setPathToLogFile(
XSDataFile(XSDataString("MOSFLMGeneratePredictionv10.log")))
EDAssert.equal(xsDataMOSFLMOutputGeneratePredictionReference.marshal(),
xsDataMOSFLMOutputGeneratePrediction.marshal())
self.cleanUp(pluginGeneratePrediction)
def testCreateDataMOSFLMOutputGeneratePrediction(self):
"""
"""
pluginGeneratePrediction = self.createPlugin()
pluginGeneratePrediction.setScriptExecutable("cat")
pluginGeneratePrediction.configure()
pluginGeneratePrediction.setPredictionImageFileName("prediction.jpg")
stringBaseName = pluginGeneratePrediction.getBaseName()
stringNewmatFile = os.path.join(self.strUnitTestDataHome, "EDPluginMOSFLMv10_autoindexMat_ok.txt")
pluginGeneratePrediction.setNewmatFileName(stringNewmatFile)
from XSDataMOSFLMv10 import XSDataMOSFLMInputGeneratePrediction
xsDataMOSFLMInputGeneratePrediction = XSDataMOSFLMInputGeneratePrediction.parseFile(
os.path.join(self.strUnitTestDataHome, "XSDataMOSFLMInputGeneratePrediction_reference.xml")
)
pluginGeneratePrediction.setDataInput(xsDataMOSFLMInputGeneratePrediction)
xsDataMOSFLMOutputGeneratePrediction = pluginGeneratePrediction.createDataMOSFLMOutputGeneratePrediction()
stringImagePath = xsDataMOSFLMOutputGeneratePrediction.getPredictionImage().getPath().getValue()
stringReferenceXML = self.readAndParseFile(self.strReferenceDataOutputFile)
from XSDataMOSFLMv10 import XSDataMOSFLMOutputGeneratePrediction
xsDataMOSFLMOutputGeneratePredictionReference = XSDataMOSFLMOutputGeneratePrediction.parseString(
stringReferenceXML
)
xsDataImage = xsDataMOSFLMOutputGeneratePredictionReference.getPredictionImage()
xsDataImage.setPath(XSDataString(stringImagePath))
xsDataMOSFLMOutputGeneratePredictionReference.setPredictionImage(xsDataImage)
# Replace path to log file since it cannot be determined by the unit test
xsDataMOSFLMOutputGeneratePrediction.setPathToLogFile(
XSDataFile(XSDataString("MOSFLMGeneratePredictionv10.log"))
)
EDAssert.equal(
xsDataMOSFLMOutputGeneratePredictionReference.marshal(), xsDataMOSFLMOutputGeneratePrediction.marshal()
)
self.cleanUp(pluginGeneratePrediction)
def generateXSDataMOSFLMInputGeneratePrediction(
xsDataGeneratePredictionInput):
"""
Translation from XSDataGeneratePredictionInput to XSDataMOSFLMInputGeneratePrediction.
"""
EDVerbose.DEBUG(
"EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputGeneratePrediction"
)
EDFactoryPluginStatic.loadModule("XSDataMOSFLMv10")
from XSDataMOSFLMv10 import XSDataMOSFLMBeamPosition
from XSDataMOSFLMv10 import XSDataMOSFLMImage
from XSDataMOSFLMv10 import XSDataMOSFLMNewmat
from XSDataMOSFLMv10 import XSDataMOSFLMMissettingsAngles
from XSDataMOSFLMv10 import XSDataMOSFLMInputGeneratePrediction
xsDataIndexingSolutionSelected = xsDataGeneratePredictionInput.getSelectedIndexingSolution(
)
xsDataCollection = xsDataGeneratePredictionInput.getDataCollection()
xsDataSubWedge = xsDataCollection.getSubWedge()[0]
xsDataImageList = xsDataSubWedge.getImage()
xsDataImageFirst = xsDataImageList[0]
xsDataCrystal = xsDataIndexingSolutionSelected.getCrystal()
xsDataOrientation = xsDataIndexingSolutionSelected.getOrientation()
xsDataExperimentalCondition = xsDataIndexingSolutionSelected.getExperimentalConditionRefined(
)
xsDataDetector = xsDataExperimentalCondition.getDetector()
xsDataBeam = xsDataExperimentalCondition.getBeam()
xsDataMatrixA = xsDataOrientation.getMatrixA()
xsDataMatrixU = xsDataOrientation.getMatrixU()
xsDataCell = xsDataCrystal.getCell()
xsDataMOSFLMInputGeneratePrediction = XSDataMOSFLMInputGeneratePrediction(
)
xsDataMOSFLMNewmat = XSDataMOSFLMNewmat()
xsDataMOSFLMNewmat.setRefinedCell(xsDataCell)
xsDataMOSFLMNewmat.setAMatrix(xsDataMatrixA)
xsDataMOSFLMNewmat.setUMatrix(xsDataMatrixU)
xsDataMOSFLMInputGeneratePrediction.setMatrix(xsDataMOSFLMNewmat)
xsDataMOSFLMMissettingsAngles = XSDataMOSFLMMissettingsAngles()
xsDataMOSFLMMissettingsAngles.setPhix(XSDataAngle(0.0))
xsDataMOSFLMMissettingsAngles.setPhiy(XSDataAngle(0.0))
xsDataMOSFLMMissettingsAngles.setPhiz(XSDataAngle(0.0))
xsDataMOSFLMNewmat.setMissettingAngles(xsDataMOSFLMMissettingsAngles)
xsDataMOSFLMBeamPosition = XSDataMOSFLMBeamPosition()
xsDataMOSFLMBeamPosition.setX(xsDataDetector.getBeamPositionX())
xsDataMOSFLMBeamPosition.setY(xsDataDetector.getBeamPositionY())
xsDataMOSFLMInputGeneratePrediction.setBeam(xsDataMOSFLMBeamPosition)
xsDataMOSFLMInputGeneratePrediction.setMosaicity(
xsDataCrystal.getMosaicity())
xsDataMOSFLMInputGeneratePrediction.setSymmetry(
xsDataCrystal.getSpaceGroup().getName())
strPathFirst = xsDataImageFirst.getPath().getValue()
strDirectoryFirst = os.path.dirname(strPathFirst)
strFilenameFirst = os.path.basename(strPathFirst)
xsDataMOSFLMInputGeneratePrediction.setWavelength(
xsDataBeam.getWavelength())
xsDataMOSFLMInputGeneratePrediction.setDistance(
xsDataDetector.getDistance())
xsDataMOSFLMInputGeneratePrediction.setDirectory(
XSDataString(strDirectoryFirst))
xsDataMOSFLMDetector = EDHandlerXSDataMOSFLMv10.getXSDataMOSFLMDetector(
xsDataDetector)
xsDataMOSFLMInputGeneratePrediction.setDetector(xsDataMOSFLMDetector)
# The MOSFLM plugin can only handle one image
xsDataImage = xsDataSubWedge.getImage()[0]
xsDataGoniostat = xsDataSubWedge.getExperimentalCondition(
).getGoniostat()
iImageNumber = xsDataImage.getNumber().getValue()
if xsDataDetector.type.value == "eiger2_16m":
strMOSFLMTemplate = EDUtilsImage.getH5MasterTemplate(
strFilenameFirst, iImageNumber)
else:
strMOSFLMTemplate = EDUtilsImage.getTemplate(strFilenameFirst, "#")
xsDataMOSFLMInputGeneratePrediction.setTemplate(
XSDataString(strMOSFLMTemplate))
xsDataMOSFLMImage = XSDataMOSFLMImage()
xsDataMOSFLMImage.setNumber(XSDataInteger(iImageNumber))
fOscillationStart = xsDataGoniostat.getRotationAxisStart().getValue()
fOscillationRange = xsDataGoniostat.getOscillationWidth().getValue()
xsDataMOSFLMImage.setRotationAxisStart(XSDataAngle(fOscillationStart))
xsDataMOSFLMImage.setRotationAxisEnd(
XSDataAngle(fOscillationStart + fOscillationRange))
xsDataMOSFLMInputGeneratePrediction.setImage(xsDataMOSFLMImage)
return xsDataMOSFLMInputGeneratePrediction
def generateDataMOSFLMInputGeneratePrediction(self):
"""
"""
from XSDataMOSFLMv10 import XSDataMOSFLMBeamPosition
xsDataMOSFLMBeamPosition = XSDataMOSFLMBeamPosition()
xsDataMOSFLMBeamPosition.setX(XSDataLength(102.5))
xsDataMOSFLMBeamPosition.setY(XSDataLength(104.7))
from XSDataMOSFLMv10 import XSDataMOSFLMDetector
xsDataMOSFLMDetector = XSDataMOSFLMDetector()
xsDataMOSFLMDetector.setType(XSDataString("ADSC"))
from XSDataMOSFLMv10 import XSDataMOSFLMImage
xsDataMOSFLMImage1 = XSDataMOSFLMImage()
xsDataMOSFLMImage1.setNumber(XSDataInteger(1))
xsDataMOSFLMImage1.setRotationAxisStart(XSDataAngle(0.0))
xsDataMOSFLMImage1.setRotationAxisEnd(XSDataAngle(1.0))
from XSDataMOSFLMv10 import XSDataMOSFLMInputGeneratePrediction
xsDataMOSFLMInputGeneratePrediction = XSDataMOSFLMInputGeneratePrediction(
)
xsDataMOSFLMInputGeneratePrediction.setDistance(XSDataLength(198.4))
xsDataMOSFLMInputGeneratePrediction.setWavelength(
XSDataWavelength(0.9340))
xsDataMOSFLMInputGeneratePrediction.setBeam(xsDataMOSFLMBeamPosition)
xsDataMOSFLMInputGeneratePrediction.setDetector(xsDataMOSFLMDetector)
xsDataMOSFLMInputGeneratePrediction.setDirectory(
XSDataString(self.strDataImagePath))
xsDataMOSFLMInputGeneratePrediction.setTemplate(
XSDataString("ref-testscale_1_###.img"))
xsDataMOSFLMInputGeneratePrediction.setImage(xsDataMOSFLMImage1)
return xsDataMOSFLMInputGeneratePrediction
def generateDataMOSFLMInputGeneratePrediction(self):
"""
"""
from XSDataMOSFLMv10 import XSDataMOSFLMBeamPosition
xsDataMOSFLMBeamPosition = XSDataMOSFLMBeamPosition()
xsDataMOSFLMBeamPosition.setX(XSDataLength(102.5))
xsDataMOSFLMBeamPosition.setY(XSDataLength(104.7))
from XSDataMOSFLMv10 import XSDataMOSFLMDetector
xsDataMOSFLMDetector = XSDataMOSFLMDetector()
xsDataMOSFLMDetector.setType(XSDataString("ADSC"))
from XSDataMOSFLMv10 import XSDataMOSFLMImage
xsDataMOSFLMImage1 = XSDataMOSFLMImage()
xsDataMOSFLMImage1.setNumber(XSDataInteger(1))
xsDataMOSFLMImage1.setRotationAxisStart(XSDataAngle(0.0))
xsDataMOSFLMImage1.setRotationAxisEnd(XSDataAngle(1.0))
from XSDataMOSFLMv10 import XSDataMOSFLMInputGeneratePrediction
xsDataMOSFLMInputGeneratePrediction = XSDataMOSFLMInputGeneratePrediction()
xsDataMOSFLMInputGeneratePrediction.setDistance(XSDataLength(198.4))
xsDataMOSFLMInputGeneratePrediction.setWavelength(XSDataWavelength(0.9340))
xsDataMOSFLMInputGeneratePrediction.setBeam(xsDataMOSFLMBeamPosition)
xsDataMOSFLMInputGeneratePrediction.setDetector(xsDataMOSFLMDetector)
xsDataMOSFLMInputGeneratePrediction.setDirectory(XSDataString(self.strDataImagePath))
xsDataMOSFLMInputGeneratePrediction.setTemplate(XSDataString("ref-testscale_1_###.img"))
xsDataMOSFLMInputGeneratePrediction.setImage(xsDataMOSFLMImage1)
return xsDataMOSFLMInputGeneratePrediction
def generateXSDataMOSFLMInputGeneratePrediction(xsDataGeneratePredictionInput):
"""
Translation from XSDataGeneratePredictionInput to XSDataMOSFLMInputGeneratePrediction.
"""
EDVerbose.DEBUG("EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputGeneratePrediction")
EDFactoryPluginStatic.loadModule("XSDataMOSFLMv10")
from XSDataMOSFLMv10 import XSDataMOSFLMBeamPosition
from XSDataMOSFLMv10 import XSDataMOSFLMImage
from XSDataMOSFLMv10 import XSDataMOSFLMNewmat
from XSDataMOSFLMv10 import XSDataMOSFLMMissettingsAngles
from XSDataMOSFLMv10 import XSDataMOSFLMInputGeneratePrediction
xsDataIndexingSolutionSelected = xsDataGeneratePredictionInput.getSelectedIndexingSolution()
xsDataCollection = xsDataGeneratePredictionInput.getDataCollection()
xsDataSubWedge = xsDataCollection.getSubWedge()[0]
xsDataImageList = xsDataSubWedge.getImage()
xsDataImageFirst = xsDataImageList[0]
xsDataCrystal = xsDataIndexingSolutionSelected.getCrystal()
xsDataOrientation = xsDataIndexingSolutionSelected.getOrientation()
xsDataExperimentalCondition = xsDataIndexingSolutionSelected.getExperimentalConditionRefined()
xsDataDetector = xsDataExperimentalCondition.getDetector()
xsDataBeam = xsDataExperimentalCondition.getBeam()
xsDataMatrixA = xsDataOrientation.getMatrixA()
xsDataMatrixU = xsDataOrientation.getMatrixU()
xsDataCell = xsDataCrystal.getCell()
xsDataMOSFLMInputGeneratePrediction = XSDataMOSFLMInputGeneratePrediction()
xsDataMOSFLMNewmat = XSDataMOSFLMNewmat()
xsDataMOSFLMNewmat.setRefinedCell(xsDataCell)
xsDataMOSFLMNewmat.setAMatrix(xsDataMatrixA)
xsDataMOSFLMNewmat.setUMatrix(xsDataMatrixU)
xsDataMOSFLMInputGeneratePrediction.setMatrix(xsDataMOSFLMNewmat)
xsDataMOSFLMMissettingsAngles = XSDataMOSFLMMissettingsAngles()
xsDataMOSFLMMissettingsAngles.setPhix(XSDataAngle(0.0))
xsDataMOSFLMMissettingsAngles.setPhiy(XSDataAngle(0.0))
xsDataMOSFLMMissettingsAngles.setPhiz(XSDataAngle(0.0))
xsDataMOSFLMNewmat.setMissettingAngles(xsDataMOSFLMMissettingsAngles)
xsDataMOSFLMBeamPosition = XSDataMOSFLMBeamPosition()
xsDataMOSFLMBeamPosition.setX(xsDataDetector.getBeamPositionX())
xsDataMOSFLMBeamPosition.setY(xsDataDetector.getBeamPositionY())
xsDataMOSFLMInputGeneratePrediction.setBeam(xsDataMOSFLMBeamPosition)
xsDataMOSFLMInputGeneratePrediction.setMosaicity(xsDataCrystal.getMosaicity())
xsDataMOSFLMInputGeneratePrediction.setSymmetry(xsDataCrystal.getSpaceGroup().getName())
strPathFirst = xsDataImageFirst.getPath().getValue()
strDirectoryFirst = os.path.dirname(strPathFirst)
strFilenameFirst = os.path.basename(strPathFirst)
xsDataMOSFLMInputGeneratePrediction.setWavelength(xsDataBeam.getWavelength())
xsDataMOSFLMInputGeneratePrediction.setDistance(xsDataDetector.getDistance())
xsDataMOSFLMInputGeneratePrediction.setDirectory(XSDataString(strDirectoryFirst))
xsDataMOSFLMDetector = EDHandlerXSDataMOSFLMv10.getXSDataMOSFLMDetector(xsDataDetector)
xsDataMOSFLMInputGeneratePrediction.setDetector(xsDataMOSFLMDetector)
strMOSFLMTemplate = EDUtilsImage.getTemplate(strFilenameFirst, "#")
xsDataMOSFLMInputGeneratePrediction.setTemplate(XSDataString(strMOSFLMTemplate))
# The MOSFLM plugin can only handle one image
xsDataImage = xsDataSubWedge.getImage()[0]
xsDataGoniostat = xsDataSubWedge.getExperimentalCondition().getGoniostat()
xsDataMOSFLMImage = XSDataMOSFLMImage()
iImageNumber = xsDataImage.getNumber().getValue()
xsDataMOSFLMImage.setNumber(XSDataInteger(iImageNumber))
fOscillationStart = xsDataGoniostat.getRotationAxisStart().getValue()
fOscillationRange = xsDataGoniostat.getOscillationWidth().getValue()
xsDataMOSFLMImage.setRotationAxisStart(XSDataAngle(fOscillationStart))
xsDataMOSFLMImage.setRotationAxisEnd(XSDataAngle(fOscillationStart + fOscillationRange))
xsDataMOSFLMInputGeneratePrediction.setImage(xsDataMOSFLMImage)
return xsDataMOSFLMInputGeneratePrediction