def testGenerateXSDataMOSFLMInputIndexing(self):
strFilename = "XSDataIndexingInput_reference.xml"
strPath = os.path.join(self.m_strDataPath, strFilename)
strXMLIndexingInput = EDUtilsTest.readAndParseFile(strPath)
from XSDataMXv1 import XSDataIndexingInput
xsDataIndexingInput = XSDataIndexingInput.parseString(strXMLIndexingInput)
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
xsDataMOSFLMInputIndexing = EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputIndexing(xsDataIndexingInput)
xsDataMOSFLMInputIndexing.outputFile("XSDataMOSFLMInputIndexing_reference.xml")
strReferenceFilename = "XSDataMOSFLMInputIndexing_reference.xml"
strReferencePath = os.path.join(self.m_strDataPath, strReferenceFilename)
strXMLMOSFLMInputIndexingReference = EDUtilsTest.readAndParseFile(strReferencePath)
EDFactoryPluginStatic.loadModule("XSDataMOSFLMv10")
from XSDataMOSFLMv10 import XSDataMOSFLMInputIndexing
xsDataMOSFLMInputIndexingReference = XSDataMOSFLMInputIndexing.parseString(strXMLMOSFLMInputIndexingReference)
EDAssert.equal(xsDataMOSFLMInputIndexingReference.marshal(), xsDataMOSFLMInputIndexing.marshal())
def testGenerateExecutiveSummary(self):
"""
"""
pluginIndexing = self.createPlugin()
pluginIndexing.setScriptExecutable("cat")
pluginIndexing.configure()
from XSDataMOSFLMv10 import XSDataMOSFLMInputIndexing
from XSDataMOSFLMv10 import XSDataMOSFLMOutputIndexing
strMOSFLMInputIndexingXML = self.readAndParseFile(self.strReferenceDataInputFile)
strMOSFLMOutputIndexingXML = self.readAndParseFile(self.strReferenceDataOutputFile)
xsDataMOSFLMInputIndexing = XSDataMOSFLMInputIndexing.parseString(strMOSFLMInputIndexingXML)
xsDataMOSFLMOutputIndexing = XSDataMOSFLMOutputIndexing.parseString(strMOSFLMOutputIndexingXML)
pluginIndexing.setDataInput(xsDataMOSFLMInputIndexing)
pluginIndexing.setDataOutput(xsDataMOSFLMOutputIndexing)
pluginIndexing.generateExecutiveSummary(pluginIndexing)
pluginIndexing.verboseScreenExecutiveSummary()
self.cleanUp(pluginIndexing)
def testGenerateExecutiveSummary(self):
"""
"""
pluginIndexing = self.createPlugin()
pluginIndexing.setScriptExecutable("cat")
pluginIndexing.configure()
from XSDataMOSFLMv10 import XSDataMOSFLMInputIndexing
from XSDataMOSFLMv10 import XSDataMOSFLMOutputIndexing
strMOSFLMInputIndexingXML = self.readAndParseFile(self.strReferenceDataInputFile)
strMOSFLMOutputIndexingXML = self.readAndParseFile(self.strReferenceDataOutputFile)
xsDataMOSFLMInputIndexing = XSDataMOSFLMInputIndexing.parseString(strMOSFLMInputIndexingXML)
xsDataMOSFLMOutputIndexing = XSDataMOSFLMOutputIndexing.parseString(strMOSFLMOutputIndexingXML)
pluginIndexing.setDataInput(xsDataMOSFLMInputIndexing)
pluginIndexing.setDataOutput(xsDataMOSFLMOutputIndexing)
pluginIndexing.generateExecutiveSummary(pluginIndexing)
pluginIndexing.verboseScreenExecutiveSummary()
self.cleanUp(pluginIndexing)
def testGenerateXSDataMOSFLMInputIndexing(self):
strFilename = "XSDataIndexingInput_reference.xml"
strPath = os.path.join(self.m_strDataPath, strFilename)
strXMLIndexingInput = EDUtilsTest.readAndParseFile(strPath)
from XSDataMXv1 import XSDataIndexingInput
xsDataIndexingInput = XSDataIndexingInput.parseString(
strXMLIndexingInput)
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
xsDataMOSFLMInputIndexing = EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputIndexing(
xsDataIndexingInput)
xsDataMOSFLMInputIndexing.exportToFile(
"XSDataMOSFLMInputIndexing_reference.xml")
strReferenceFilename = "XSDataMOSFLMInputIndexing_reference.xml"
strReferencePath = os.path.join(self.m_strDataPath,
strReferenceFilename)
strXMLMOSFLMInputIndexingReference = EDUtilsTest.readAndParseFile(
strReferencePath)
EDFactoryPluginStatic.loadModule("XSDataMOSFLMv10")
from XSDataMOSFLMv10 import XSDataMOSFLMInputIndexing
xsDataMOSFLMInputIndexingReference = XSDataMOSFLMInputIndexing.parseString(
strXMLMOSFLMInputIndexingReference)
EDAssert.equal(xsDataMOSFLMInputIndexingReference.marshal(),
xsDataMOSFLMInputIndexing.marshal())
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 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 generateDataMOSFLMInputIndexing(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 XSDataMOSFLMImage
xsDataMOSFLMImage2 = XSDataMOSFLMImage()
xsDataMOSFLMImage2.setNumber(XSDataInteger(2))
xsDataMOSFLMImage2.setRotationAxisStart(XSDataAngle(90.0))
xsDataMOSFLMImage2.setRotationAxisEnd(XSDataAngle(91.0))
from XSDataMOSFLMv10 import XSDataMOSFLMInputIndexing
xsDataMOSFLMInputIndexing = XSDataMOSFLMInputIndexing()
xsDataMOSFLMInputIndexing.setDistance(XSDataLength(198.4))
xsDataMOSFLMInputIndexing.setWavelength(XSDataWavelength(0.9340))
xsDataMOSFLMInputIndexing.setBeam(xsDataMOSFLMBeamPosition)
xsDataMOSFLMInputIndexing.setDetector(xsDataMOSFLMDetector)
xsDataMOSFLMInputIndexing.setDirectory(XSDataString(self.strDataImagePath))
xsDataMOSFLMInputIndexing.setTemplate(XSDataString("ref-testscale_1_###.img"))
xsDataMOSFLMInputIndexing.addImage(xsDataMOSFLMImage1)
xsDataMOSFLMInputIndexing.addImage(xsDataMOSFLMImage2)
return xsDataMOSFLMInputIndexing
def generateDataMOSFLMInputIndexing(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 XSDataMOSFLMImage
xsDataMOSFLMImage2 = XSDataMOSFLMImage()
xsDataMOSFLMImage2.setNumber(XSDataInteger(2))
xsDataMOSFLMImage2.setRotationAxisStart(XSDataAngle(90.0))
xsDataMOSFLMImage2.setRotationAxisEnd(XSDataAngle(91.0))
from XSDataMOSFLMv10 import XSDataMOSFLMInputIndexing
xsDataMOSFLMInputIndexing = XSDataMOSFLMInputIndexing()
xsDataMOSFLMInputIndexing.setDistance(XSDataLength(198.4))
xsDataMOSFLMInputIndexing.setWavelength(XSDataWavelength(0.9340))
xsDataMOSFLMInputIndexing.setBeam(xsDataMOSFLMBeamPosition)
xsDataMOSFLMInputIndexing.setDetector(xsDataMOSFLMDetector)
xsDataMOSFLMInputIndexing.setDirectory(XSDataString(self.strDataImagePath))
xsDataMOSFLMInputIndexing.setTemplate(XSDataString("ref-testscale_1_###.img"))
xsDataMOSFLMInputIndexing.addImage(xsDataMOSFLMImage1)
xsDataMOSFLMInputIndexing.addImage(xsDataMOSFLMImage2)
return xsDataMOSFLMInputIndexing