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 generateXSDataMOSFLMInputIndexing(_xsDataIndexingInput):
"""
Translation from XSDataIndexingInput to XSDataMOSFLMInputIndexing.
"""
EDFactoryPluginStatic.loadModule("XSDataMOSFLMv10")
from XSDataMOSFLMv10 import XSDataMOSFLMInputIndexing
from XSDataMOSFLMv10 import XSDataMOSFLMBeamPosition
from XSDataMOSFLMv10 import XSDataMOSFLMImage
EDVerbose.DEBUG(
"EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputIndexing")
xsDataCollection = _xsDataIndexingInput.getDataCollection()
xsDataExperimentalCondition = _xsDataIndexingInput.getExperimentalCondition(
)
xsDataCrystal = _xsDataIndexingInput.getCrystal()
xsDataSubWedgeList = xsDataCollection.getSubWedge()
xsDataMOSFLMInputIndexing = XSDataMOSFLMInputIndexing()
if (xsDataExperimentalCondition is None):
xsDataExperimentalCondition = xsDataSubWedgeList[
0].getExperimentalCondition()
xsDataBeam = xsDataExperimentalCondition.getBeam()
xsDataDetector = xsDataExperimentalCondition.getDetector()
xsDataGoniostat = xsDataExperimentalCondition.getGoniostat()
dWavelength = xsDataBeam.getWavelength().getValue()
dDistance = xsDataDetector.getDistance().getValue()
dBeamPositionX = xsDataDetector.getBeamPositionX().getValue()
dBeamPositionY = xsDataDetector.getBeamPositionY().getValue()
xsDataMOSFLMBeamPosition = XSDataMOSFLMBeamPosition()
xsDataMOSFLMBeamPosition.setX(XSDataLength(dBeamPositionX))
xsDataMOSFLMBeamPosition.setY(XSDataLength(dBeamPositionY))
xsDataMOSFLMInputIndexing.setBeam(xsDataMOSFLMBeamPosition)
xsDataMOSFLMDetector = EDHandlerXSDataMOSFLMv10.getXSDataMOSFLMDetector(
xsDataDetector)
xsDataMOSFLMInputIndexing.setDetector(xsDataMOSFLMDetector)
xsDataMOSFLMInputIndexing.setWavelength(XSDataWavelength(dWavelength))
xsDataMOSFLMInputIndexing.setDistance(XSDataLength(dDistance))
xsDataSubWedgeFirst = xsDataSubWedgeList[0]
xsDataImageFirst = xsDataSubWedgeFirst.getImage()[0]
strPath = xsDataImageFirst.getPath().getValue()
strFileName = os.path.basename(strPath)
strDirectory = os.path.dirname(strPath)
if xsDataDetector.type.value == "eiger2_16m":
strMOSFLMTemplate = EDUtilsImage.getH5MasterTemplate(
strFileName, 1)
else:
strMOSFLMTemplate = EDUtilsImage.getTemplate(strFileName, "#")
xsDataMOSFLMInputIndexing.setTemplate(XSDataString(strMOSFLMTemplate))
xsDataMOSFLMInputIndexing.setDirectory(XSDataString(strDirectory))
if (xsDataCrystal is not None):
xsDataSpaceGroup = xsDataCrystal.getSpaceGroup()
if (xsDataSpaceGroup is not None):
xsDataStringName = xsDataSpaceGroup.getName()
if (xsDataStringName is not None):
xsDataMOSFLMInputIndexing.setSymmetry(
XSDataString(xsDataStringName.getValue()))
# Loop through the list of sub wedges
for xsDataSubWedge in xsDataSubWedgeList:
xsDataImageList = xsDataSubWedge.getImage()
xsDataGoniostat = xsDataSubWedge.getExperimentalCondition(
).getGoniostat()
fGonioStatOscillationStart = xsDataGoniostat.getRotationAxisStart(
).getValue()
fGonioStatOscillationRange = xsDataGoniostat.getOscillationWidth(
).getValue()
# First find the lowest image number
iLowestImageNumber = None
for xsDataImage in xsDataImageList:
iImageNumber = xsDataImage.getNumber().getValue()
if (iLowestImageNumber is None):
iLowestImageNumber = iImageNumber
elif (iImageNumber < iLowestImageNumber):
iLowestImageNumber = iImageNumber
# Loop through the list of images
for xsDataImage in xsDataImageList:
# Create the MOSFLM image object
xsDataMOSFLMImage = XSDataMOSFLMImage()
iImageNumber = xsDataImage.getNumber().getValue()
xsDataMOSFLMImage.setNumber(XSDataInteger(iImageNumber))
fImageOscillationStart = fGonioStatOscillationStart + (
iImageNumber -
iLowestImageNumber) * fGonioStatOscillationRange
xsDataMOSFLMImage.setRotationAxisStart(
XSDataAngle(fImageOscillationStart))
xsDataMOSFLMImage.setRotationAxisEnd(
XSDataAngle(fImageOscillationStart +
fGonioStatOscillationRange))
xsDataMOSFLMInputIndexing.addImage(xsDataMOSFLMImage)
return xsDataMOSFLMInputIndexing
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 generateXSDataMOSFLMInputIndexing(_xsDataIndexingInput):
"""
Translation from XSDataIndexingInput to XSDataMOSFLMInputIndexing.
"""
EDFactoryPluginStatic.loadModule("XSDataMOSFLMv10")
from XSDataMOSFLMv10 import XSDataMOSFLMInputIndexing
from XSDataMOSFLMv10 import XSDataMOSFLMBeamPosition
from XSDataMOSFLMv10 import XSDataMOSFLMImage
EDVerbose.DEBUG("EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputIndexing")
xsDataCollection = _xsDataIndexingInput.getDataCollection()
xsDataExperimentalCondition = _xsDataIndexingInput.getExperimentalCondition()
xsDataCrystal = _xsDataIndexingInput.getCrystal()
xsDataSubWedgeList = xsDataCollection.getSubWedge()
xsDataMOSFLMInputIndexing = XSDataMOSFLMInputIndexing()
if (xsDataExperimentalCondition is None):
xsDataExperimentalCondition = xsDataSubWedgeList[0].getExperimentalCondition()
xsDataBeam = xsDataExperimentalCondition.getBeam()
xsDataDetector = xsDataExperimentalCondition.getDetector()
xsDataGoniostat = xsDataExperimentalCondition.getGoniostat()
dWavelength = xsDataBeam.getWavelength().getValue()
dDistance = xsDataDetector.getDistance().getValue()
dBeamPositionX = xsDataDetector.getBeamPositionX().getValue()
dBeamPositionY = xsDataDetector.getBeamPositionY().getValue()
xsDataMOSFLMBeamPosition = XSDataMOSFLMBeamPosition()
xsDataMOSFLMBeamPosition.setX(XSDataLength(dBeamPositionX))
xsDataMOSFLMBeamPosition.setY(XSDataLength(dBeamPositionY))
xsDataMOSFLMInputIndexing.setBeam(xsDataMOSFLMBeamPosition)
xsDataMOSFLMDetector = EDHandlerXSDataMOSFLMv10.getXSDataMOSFLMDetector(xsDataDetector)
xsDataMOSFLMInputIndexing.setDetector(xsDataMOSFLMDetector)
xsDataMOSFLMInputIndexing.setWavelength(XSDataWavelength(dWavelength))
xsDataMOSFLMInputIndexing.setDistance(XSDataLength(dDistance))
xsDataSubWedgeFirst = xsDataSubWedgeList[0]
xsDataImageFirst = xsDataSubWedgeFirst.getImage()[0]
strPath = xsDataImageFirst.getPath().getValue()
strFileName = os.path.basename(strPath)
strDirectory = os.path.dirname(strPath)
strMOSFLMTemplate = EDUtilsImage.getTemplate(strFileName, "#")
xsDataMOSFLMInputIndexing.setTemplate(XSDataString(strMOSFLMTemplate))
xsDataMOSFLMInputIndexing.setDirectory(XSDataString(strDirectory))
if (xsDataCrystal is not None):
xsDataSpaceGroup = xsDataCrystal.getSpaceGroup()
if (xsDataSpaceGroup is not None):
xsDataStringName = xsDataSpaceGroup.getName()
if (xsDataStringName is not None):
xsDataMOSFLMInputIndexing.setSymmetry(XSDataString(xsDataStringName.getValue()))
# Loop through the list of sub wedges
for xsDataSubWedge in xsDataSubWedgeList:
xsDataImageList = xsDataSubWedge.getImage()
xsDataGoniostat = xsDataSubWedge.getExperimentalCondition().getGoniostat()
fGonioStatOscillationStart = xsDataGoniostat.getRotationAxisStart().getValue()
fGonioStatOscillationRange = xsDataGoniostat.getOscillationWidth().getValue()
# First find the lowest image number
iLowestImageNumber = None
for xsDataImage in xsDataImageList:
iImageNumber = xsDataImage.getNumber().getValue()
if (iLowestImageNumber is None):
iLowestImageNumber = iImageNumber
elif (iImageNumber < iLowestImageNumber):
iLowestImageNumber = iImageNumber
# Loop through the list of images
for xsDataImage in xsDataImageList:
# Create the MOSFLM image object
xsDataMOSFLMImage = XSDataMOSFLMImage()
iImageNumber = xsDataImage.getNumber().getValue()
xsDataMOSFLMImage.setNumber(XSDataInteger(iImageNumber))
fImageOscillationStart = fGonioStatOscillationStart + (iImageNumber - iLowestImageNumber) * fGonioStatOscillationRange
xsDataMOSFLMImage.setRotationAxisStart(XSDataAngle(fImageOscillationStart))
xsDataMOSFLMImage.setRotationAxisEnd(XSDataAngle(fImageOscillationStart + fGonioStatOscillationRange))
xsDataMOSFLMInputIndexing.addImage(xsDataMOSFLMImage)
return xsDataMOSFLMInputIndexing
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
