def generateXSDataISPyBScreeningInput(_xsDataInputControlISPyB):
"""
"""
EDFactoryPluginStatic.loadModule("XSDataISPyBv1_2")
from XSDataISPyBv1_2 import XSDataISPyBScreeningInput
from XSDataISPyBv1_2 import XSDataDouble
xsDataResultCharacterisation = _xsDataInputControlISPyB.getCharacterisationResult()
xsDataISPyBScreeningInput = XSDataISPyBScreeningInput()
xsDataCollection = EDHandlerXSDataISPyBv2_0.getDataCollectionFromSuggestedStrategy(xsDataResultCharacterisation)
# Data collection information
if (xsDataCollection is not None):
xsDataSubWedgeList = xsDataCollection.getSubWedge()
if (xsDataSubWedgeList is not None):
xsDataSubWedgeFirst = xsDataSubWedgeList[0]
xsDataExperimentalCondition = xsDataSubWedgeFirst.getExperimentalCondition()
if (xsDataExperimentalCondition is not None):
xsDataDetector = xsDataExperimentalCondition.getDetector()
if (xsDataDetector is not None):
fBeamPositionX = xsDataDetector.getBeamPositionX().getValue()
fBeamPositionY = xsDataDetector.getBeamPositionY().getValue()
xsDataISPyBScreeningInput.setBeamX(XSDataDouble(fBeamPositionX))
xsDataISPyBScreeningInput.setBeamY(XSDataDouble(fBeamPositionY))
return xsDataISPyBScreeningInput
def writeKappaSettings(self):
'''
# future version for getting motor positions related to images under processing
# checking in order:
# - value got as input
# - mosflm.descr file in process subdir (if BCM (like mxcube) registered it)
# - {imageTemplate}_kappa_settings.xml file (if BCM (like DNA) registered it)
# - read it now (and try to register as {imageTemplate}_kappa_settings.xml)
# - just use the datum (0,0,0)
'''
#code for using a predefined datum (0;0;0)
#EDUtilsFile.writeFile( EDDiskExplorer.mergePath( self.getWorkingDirectory(), "DNA_STAC_Kappa_Settings" ), "<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?><kappa_collect_settings><motorSettings><motorName>Omega</motorName><motorValue>0</motorValue></motorSettings><motorSettings><motorName>Kappa</motorName><motorValue>0.000000</motorValue></motorSettings><motorSettings><motorName>Phi</motorName><motorValue>0</motorValue></motorSettings><motorSettings><motorName>X</motorName><motorValue>0.261444</motorValue></motorSettings><motorSettings><motorName>Y</motorName><motorValue>-0.085559</motorValue></motorSettings><motorSettings><motorName>Z</motorName><motorValue>0.659333</motorValue></motorSettings><comment>BCM query performed by STAC</comment></kappa_collect_settings>")
# gonio settings from DC descriptor object
EDFactoryPluginStatic.loadModule("XSDataMXv2")
#import XSDataMXv2
#dc = XSDataMXv2.XSDataCollection()
from XSDataMXv2 import XSDataCollection
dc = XSDataCollection()
dc = self.getDataInput("dataCollection")[0]
omega = dc.getXSSubWedge()[0].getXSRotationalGoniostatSetting().getBaseaxissetting()
[kappa, phi] = dc.getXSSubWedge()[0].getXSRotationalGoniostatSetting().getAxissetting()
EDUtilsFile.writeFile(os.path.join(self.getWorkingDirectory(), "DNA_STAC_Kappa_Settings"), "<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?><kappa_collect_settings><motorSettings><motorName>Omega</motorName><motorValue>%e</motorValue></motorSettings><motorSettings><motorName>Kappa</motorName><motorValue>%e</motorValue></motorSettings><motorSettings><motorName>Phi</motorName><motorValue>%e</motorValue></motorSettings><motorSettings><motorName>X</motorName><motorValue>0.261444</motorValue></motorSettings><motorSettings><motorName>Y</motorName><motorValue>-0.085559</motorValue></motorSettings><motorSettings><motorName>Z</motorName><motorValue>0.659333</motorValue></motorSettings><comment>BCM query performed by STAC</comment></kappa_collect_settings>" % (omega.getValue(), kappa.getValue(), phi.getValue()))
'''
def generateXSDataISPyBScreeningInput(_xsDataInputControlISPyB):
"""
"""
EDFactoryPluginStatic.loadModule("XSDataISPyBv1_2")
from XSDataISPyBv1_2 import XSDataISPyBScreeningInput
from XSDataISPyBv1_2 import XSDataDouble
xsDataResultCharacterisation = _xsDataInputControlISPyB.getCharacterisationResult(
)
xsDataISPyBScreeningInput = XSDataISPyBScreeningInput()
# Data collection information
xsDataCollection = xsDataResultCharacterisation.getDataCollection()
if (xsDataCollection is not None):
xsDataSubWedgeList = xsDataCollection.getSubWedge()
if (xsDataSubWedgeList is not None):
xsDataSubWedgeFirst = xsDataSubWedgeList[0]
xsDataExperimentalCondition = xsDataSubWedgeFirst.getExperimentalCondition(
)
if (xsDataExperimentalCondition is not None):
xsDataDetector = xsDataExperimentalCondition.getDetector()
if (xsDataDetector is not None):
fBeamPositionX = xsDataDetector.getBeamPositionX(
).getValue()
fBeamPositionY = xsDataDetector.getBeamPositionY(
).getValue()
xsDataISPyBScreeningInput.setBeamX(
XSDataDouble(fBeamPositionX))
xsDataISPyBScreeningInput.setBeamY(
XSDataDouble(fBeamPositionY))
return xsDataISPyBScreeningInput
def generateXSDataISPyBImage(_xsDataInputControlISPyB):
"""
"""
EDFactoryPluginStatic.loadModule("XSDataISPyBv1_2")
from XSDataISPyBv1_2 import XSDataString
from XSDataISPyBv1_2 import XSDataISPyBImage
xsDataResultCharacterisationv2_0 = _xsDataInputControlISPyB.getCharacterisationResult()
xsDataResultCharacterisation = xsDataResultCharacterisationv2_0.getMxv1ResultCharacterisation()
xsDataISPyBImage = None
# Find path to first image from data collection information
strPathToFirstImage = None
xsDataCollection = xsDataResultCharacterisation.getDataCollection()
if (xsDataCollection is not None):
lXSDataSubWedge = xsDataCollection.getSubWedge()
if (lXSDataSubWedge is not None):
xsDataSubWedgeFirst = lXSDataSubWedge[0]
lXSDataImage = xsDataSubWedgeFirst.getImage()
if (lXSDataImage is not None):
xsDataImageFirst = lXSDataImage[ 0 ]
strPathToFirstImage = xsDataImageFirst.getPath().getValue()
# Add an image path if the dataCollectionId is not present...
if (strPathToFirstImage is not None):
xsDataISPyBImage = XSDataISPyBImage()
strImageBaseName = EDUtilsFile.getBaseName(strPathToFirstImage)
strDirectoryName = EDUtilsPath.getFolderName(strPathToFirstImage)
xsDataISPyBImage.setFileName(XSDataString(strImageBaseName))
xsDataISPyBImage.setFileLocation(XSDataString(strDirectoryName))
return xsDataISPyBImage
def __init__ (self):
"""
"""
EDPluginControl.__init__(self)
#self.setXSDataInputClass( XSDataInputCharacterisation )
#self.setXSDataInputClass(EDList)
#self.strPluginIndexingName = "EDPluginControlIndexingv2_0"
self.strPluginIndexingName = "EDPluginControlIndexingv10"
self.edPluginIndexing = None
self.strPluginIntegrationName = "EDPluginControlIntegrationv10"
self.edPluginIntegration = None
self.strPluginStrategyName = "EDPluginControlKappaStrategyv2_0"
self.edPluginStrategy = None
self.xsDataResultCharacterisationv2_0 = None
self.xsDataResultCharacterisation = None
self.xsDataInputStrategy = None
self.setXSDataInputClass(XSDataInputCharacterisationv2_0)
EDFactoryPluginStatic.loadModule("XSDataMXv1")
import XSDataMXv1
self.setXSDataInputClass(XSDataMXv1.XSDataInputCharacterisation, "mxv1InputCharacterisation")
EDFactoryPluginStatic.loadModule("XSDataMXv2")
import XSDataMXv2
self.setXSDataInputClass(XSDataMXv2.XSDataCollection, "mxv2DataCollection")
def preProcess(self, _edPlugin=None):
"""
This method prepares the input for the CCP4i plugin and loads it.
"""
EDPluginControl.preProcess(self, _edPlugin)
EDVerbose.DEBUG("EDPluginControlInterfaceToMXCuBEv1_2.preProcess...")
EDFactoryPluginStatic.loadModule("XSDataCCP4iv1_1")
from XSDataCCP4iv1_1 import XSDataInputCCP4i
xsDataInputCCP4i = XSDataInputCCP4i()
xsDataInputMXCuBE = self.getDataInput()
xsDataInputCCP4i.setDataSet(xsDataInputMXCuBE.getDataSet())
#xsDataInputCCP4i.setDataFile( xsDataInputMXCuBE.getDataFile() )
xsDataInputCCP4i.setExperimentalCondition(xsDataInputMXCuBE.getExperimentalCondition())
xsDataInputCCP4i.setDiffractionPlan(xsDataInputMXCuBE.getDiffractionPlan())
xsDataInputCCP4i.setSample(xsDataInputMXCuBE.getSample())
self.__edPluginControlCCP4i = self.loadPlugin(self.__strPluginControlCCP4i, "CCP4i")
self.__edPluginControlCCP4i.setDataInput(xsDataInputCCP4i)
self.__xsDataIntegerDataCollectionId = xsDataInputMXCuBE.getDataCollectionId()
if (self.__xsDataIntegerDataCollectionId is not None):
self.__edPluginControlISPyB = self.loadPlugin(self.__strPluginControlISPyB, "ISPyB")
self.__edPluginExecOutputHTML = self.loadPlugin(self.__strPluginExecOutputHTMLName, "OutputHTML")
def mergeAtomicComposition(self, _xsDataAtomicComposition1, _xsDataAtomicComposition2):
EDFactoryPluginStatic.loadModule("XSDataRaddosev10")
mergedAtomicComposition = XSDataAtomicComposition()
dictionary = {}
for atom in _xsDataAtomicComposition2.getAtom():
dictionary[atom.getSymbol().getValue()] = atom.getNumberOf().getValue()
for atom1 in _xsDataAtomicComposition1.getAtom():
symbol = atom1.getSymbol().getValue()
if (self.exists(symbol, _xsDataAtomicComposition2) == True):
mergedAtom = XSDataAtom()
mergedAtom.setNumberOf(XSDataDouble(atom1.getNumberOf().getValue() + dictionary[symbol]))
mergedAtom.setSymbol(XSDataString(symbol))
mergedAtomicComposition.addAtom(mergedAtom)
else:
mergedAtomicComposition.addAtom(atom1)
for atom2 in _xsDataAtomicComposition2.getAtom():
symbol = atom2.getSymbol().getValue()
if (self.exists(symbol, _xsDataAtomicComposition1) == False):
mergedAtomicComposition.addAtom(atom2)
return mergedAtomicComposition
def generateXSDataISPyBImage(_xsDataInputControlISPyB):
"""
"""
EDFactoryPluginStatic.loadModule("XSDataISPyBv1_2")
from XSDataISPyBv1_2 import XSDataString
from XSDataISPyBv1_2 import XSDataISPyBImage
xsDataResultCharacterisation = _xsDataInputControlISPyB.getCharacterisationResult(
)
xsDataISPyBImage = None
# Find path to first image from data collection information
strPathToFirstImage = None
xsDataCollection = xsDataResultCharacterisation.getDataCollection()
if (xsDataCollection is not None):
lXSDataSubWedge = xsDataCollection.getSubWedge()
if (lXSDataSubWedge is not None):
xsDataSubWedgeFirst = lXSDataSubWedge[0]
lXSDataImage = xsDataSubWedgeFirst.getImage()
if (lXSDataImage is not None):
xsDataImageFirst = lXSDataImage[0]
strPathToFirstImage = xsDataImageFirst.getPath().getValue()
# Add an image path if the dataCollectionId is not present...
if (strPathToFirstImage is not None):
xsDataISPyBImage = XSDataISPyBImage()
strImageBaseName = EDUtilsFile.getBaseName(strPathToFirstImage)
strDirectoryName = EDUtilsPath.getFolderName(
strPathToFirstImage)
xsDataISPyBImage.setFileName(XSDataString(strImageBaseName))
xsDataISPyBImage.setFileLocation(
XSDataString(strDirectoryName))
return xsDataISPyBImage
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 generateXSDataISPyBScreening(_xsDataInputControlISPyB,
_strShortComments=None,
_strComments=None):
"""
"""
EDFactoryPluginStatic.loadModule("XSDataISPyBv1_2")
from XSDataISPyBv1_2 import XSDataString
from XSDataISPyBv1_2 import XSDataISPyBScreening
xsDataIntegerDataCollectionId = _xsDataInputControlISPyB.getDataCollectionId(
)
# General information
xsDataISPyBScreening = XSDataISPyBScreening()
xsDataISPyBScreening.setProgramVersion(XSDataString("EDNA MXv1"))
pyStrTimeStamp = time.strftime("%Y-%m-%d %H:%M:%S")
xsDataISPyBScreening.setTimeStamp(XSDataString(pyStrTimeStamp))
if (not _strShortComments is None):
xsDataISPyBScreening.setShortComments(
XSDataString(_strShortComments))
if (not _strComments is None):
xsDataISPyBScreening.setComments(XSDataString(_strComments))
# Use dataCollectionId if provided in the input
if (xsDataIntegerDataCollectionId is not None):
xsDataISPyBScreening.setDataCollectionId(
xsDataIntegerDataCollectionId)
return xsDataISPyBScreening
def __init__(self):
"""
"""
EDPluginControl.__init__(self)
#self.setXSDataInputClass( XSDataInputCharacterisation )
#self.setXSDataInputClass(EDList)
#self.strPluginIndexingName = "EDPluginControlIndexingv2_0"
self.strPluginIndexingName = "EDPluginControlIndexingv10"
self.edPluginIndexing = None
self.strPluginIntegrationName = "EDPluginControlIntegrationv10"
self.edPluginIntegration = None
self.xsDataResultCharacterisationv2_0 = None
self.xsDataResultCharacterisation = None
self.xsDataInputStrategy = None
self.setXSDataInputClass(XSDataInputCharacterisationv2_0)
EDFactoryPluginStatic.loadModule("XSDataMXv1")
import XSDataMXv1
self.setXSDataInputClass(XSDataMXv1.XSDataInputCharacterisation,
"mxv1InputCharacterisation")
EDFactoryPluginStatic.loadModule("XSDataMXv2")
import XSDataMXv2
self.setXSDataInputClass(XSDataMXv2.XSDataCollection,
"mxv2DataCollection")
def testCreateOutputFileDictionary(self):
strPathToCCP4iResult = os.path.join(self.getPluginTestsDataHome(),
"XSDataResultCCP4i_reference.xml")
strXML = self.readAndParseFile(strPathToCCP4iResult)
EDFactoryPluginStatic.loadModule("XSDataCCP4iv1_1")
from XSDataCCP4iv1_1 import XSDataResultCCP4i
xsDataResultCCP4i = XSDataResultCCP4i.parseString(strXML)
xsDataStringListOfOutputFiles = xsDataResultCCP4i.getListOfOutputFiles(
)
pluginMXCuBE = self.createPlugin()
pluginMXCuBE.configure()
strResultCharacterisationFileName = "XSDataResultCharacterisation_reference.xml"
strPathToReferenceFile = os.path.join(
self.getPluginTestsDataHome(), strResultCharacterisationFileName)
strXML = self.readAndParseFile(strPathToReferenceFile)
xsDataResultCharacterisation = XSDataResultCharacterisation.parseString(
strXML)
strDNAFileDirectoryPath = pluginMXCuBE.createDNAFileDirectoryPath(
xsDataResultCharacterisation)
pluginMXCuBE.createDNAFileDirectory(strDNAFileDirectoryPath)
xsDataDictionary = pluginMXCuBE.createOutputFileDictionary(
xsDataStringListOfOutputFiles, xsDataResultCharacterisation,
strDNAFileDirectoryPath)
EDAssert.equal(False, xsDataDictionary is None)
shutil.rmtree(strDNAFileDirectoryPath)
def preProcess(self, _edPlugin=None):
"""
This method prepares the input for the CCP4i plugin and loads it.
"""
EDPluginControl.preProcess(self, _edPlugin)
EDVerbose.DEBUG("EDPluginControlInterfaceToMXCuBEv1_2.preProcess...")
EDFactoryPluginStatic.loadModule("XSDataCCP4iv1_1")
from XSDataCCP4iv1_1 import XSDataInputCCP4i
xsDataInputCCP4i = XSDataInputCCP4i()
xsDataInputMXCuBE = self.getDataInput()
xsDataInputCCP4i.setDataSet(xsDataInputMXCuBE.getDataSet())
#xsDataInputCCP4i.setDataFile( xsDataInputMXCuBE.getDataFile() )
xsDataInputCCP4i.setExperimentalCondition(xsDataInputMXCuBE.getExperimentalCondition())
xsDataInputCCP4i.setDiffractionPlan(xsDataInputMXCuBE.getDiffractionPlan())
xsDataInputCCP4i.setSample(xsDataInputMXCuBE.getSample())
self.__edPluginControlCCP4i = self.loadPlugin(self.__strPluginControlCCP4i, "CCP4i")
self.__edPluginControlCCP4i.setDataInput(xsDataInputCCP4i)
self.__xsDataIntegerDataCollectionId = xsDataInputMXCuBE.getDataCollectionId()
if (self.__xsDataIntegerDataCollectionId is not None):
self.__edPluginControlISPyB = self.loadPlugin(self.__strPluginControlISPyB, "ISPyB")
self.__edPluginExecOutputHTML = self.loadPlugin(self.__strPluginExecOutputHTMLName, "OutputHTML")
def testGenerateXSDataInputISPyB(self):
"""
This method is testing the generation of the XSDataInputISPyB object given a XSDataIndexingInput object.
"""
strReferenceInputControlISPyBFile = EDUtilsPath.mergePath(
self.strDataPath, "XSDataInputControlISPyB_reference.xml")
strPath = os.path.join(self.strDataPath,
strReferenceInputControlISPyBFile)
strXMLIndexingInput = self.readAndParseFile(strPath)
from XSDataMXv1 import XSDataInputControlISPyB
xsDataInputControlISPyB = XSDataInputControlISPyB.parseString(
strXMLIndexingInput)
from EDHandlerXSDataISPyBv1_1 import EDHandlerXSDataISPyBv1_1
xsDataInputISPyB = EDHandlerXSDataISPyBv1_1.generateXSDataInputISPyB(
xsDataInputControlISPyB)
strReferenceInputISPyBFile = EDUtilsPath.mergePath(
self.strDataPath, "XSDataInputISPyB_reference.xml")
strReferencePath = os.path.join(self.strDataPath,
strReferenceInputISPyBFile)
strXMLInputISPyBReference = self.readAndParseFile(strReferencePath)
EDFactoryPluginStatic.loadModule("XSDataISPyBv1_1")
from XSDataISPyBv1_1 import XSDataInputISPyB
xsDataInputISPyBReference = XSDataInputISPyB.parseString(
strXMLInputISPyBReference)
# Remove the time strings since they otherwise make the test fail
xsDataInputISPyBReference.getScreening().setTimeStamp(None)
xsDataInputISPyB.getScreening().setTimeStamp(None)
EDAssert.equal(xsDataInputISPyBReference.marshal(),
xsDataInputISPyB.marshal())
def writeKappaSettings(self):
'''
# future version for getting motor positions related to images under processing
# checking in order:
# - value got as input
# - mosflm.descr file in process subdir (if BCM (like mxcube) registered it)
# - {imageTemplate}_kappa_settings.xml file (if BCM (like DNA) registered it)
# - read it now (and try to register as {imageTemplate}_kappa_settings.xml)
# - just use the datum (0,0,0)
'''
#code for using a predefined datum (0;0;0)
#EDUtilsFile.writeFile( EDDiskExplorer.mergePath( self.getWorkingDirectory(), "DNA_STAC_Kappa_Settings" ), "<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?><kappa_collect_settings><motorSettings><motorName>Omega</motorName><motorValue>0</motorValue></motorSettings><motorSettings><motorName>Kappa</motorName><motorValue>0.000000</motorValue></motorSettings><motorSettings><motorName>Phi</motorName><motorValue>0</motorValue></motorSettings><motorSettings><motorName>X</motorName><motorValue>0.261444</motorValue></motorSettings><motorSettings><motorName>Y</motorName><motorValue>-0.085559</motorValue></motorSettings><motorSettings><motorName>Z</motorName><motorValue>0.659333</motorValue></motorSettings><comment>BCM query performed by STAC</comment></kappa_collect_settings>")
# gonio settings from DC descriptor object
EDFactoryPluginStatic.loadModule("XSDataMXv2")
#import XSDataMXv2
#dc = XSDataMXv2.XSDataCollection()
from XSDataMXv2 import XSDataCollection
dc = XSDataCollection()
dc = self.getDataInput("dataCollection")[0]
omega = dc.getXSSubWedge()[0].getXSRotationalGoniostatSetting(
).getBaseaxissetting()
[kappa, phi] = dc.getXSSubWedge()[0].getXSRotationalGoniostatSetting(
).getAxissetting()
EDUtilsFile.writeFile(
os.path.join(self.getWorkingDirectory(),
"DNA_STAC_Kappa_Settings"),
"<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?><kappa_collect_settings><motorSettings><motorName>Omega</motorName><motorValue>%e</motorValue></motorSettings><motorSettings><motorName>Kappa</motorName><motorValue>%e</motorValue></motorSettings><motorSettings><motorName>Phi</motorName><motorValue>%e</motorValue></motorSettings><motorSettings><motorName>X</motorName><motorValue>0.261444</motorValue></motorSettings><motorSettings><motorName>Y</motorName><motorValue>-0.085559</motorValue></motorSettings><motorSettings><motorName>Z</motorName><motorValue>0.659333</motorValue></motorSettings><comment>BCM query performed by STAC</comment></kappa_collect_settings>"
% (omega.getValue(), kappa.getValue(), phi.getValue()))
'''
def mergeAtomicComposition(self, _xsDataAtomicComposition1,
_xsDataAtomicComposition2):
EDFactoryPluginStatic.loadModule("XSDataRaddosev10")
mergedAtomicComposition = XSDataAtomicComposition()
dictionary = {}
for atom in _xsDataAtomicComposition2.getAtom():
dictionary[
atom.getSymbol().getValue()] = atom.getNumberOf().getValue()
for atom1 in _xsDataAtomicComposition1.getAtom():
symbol = atom1.getSymbol().getValue()
if (self.exists(symbol, _xsDataAtomicComposition2) == True):
mergedAtom = XSDataAtom()
mergedAtom.setNumberOf(
XSDataDouble(atom1.getNumberOf().getValue() +
dictionary[symbol]))
mergedAtom.setSymbol(XSDataString(symbol))
mergedAtomicComposition.addAtom(mergedAtom)
else:
mergedAtomicComposition.addAtom(atom1)
for atom2 in _xsDataAtomicComposition2.getAtom():
symbol = atom2.getSymbol().getValue()
if (self.exists(symbol, _xsDataAtomicComposition1) == False):
mergedAtomicComposition.addAtom(atom2)
return mergedAtomicComposition
def __init__(self):
"""
"""
EDPluginExecProcessScript.__init__(self)
EDFactoryPluginStatic.loadModule("XSDataMXv1")
EDFactoryPluginStatic.loadModule("XSDataMXv2")
from XSDataMXv2 import XSDataCollection
self.setXSDataInputClass(XSDataCollection, "dataCollection")
self.__pyStrBCMDEF = None
def __init__(self):
"""
"""
EDPluginExecProcessScript.__init__(self)
EDFactoryPluginStatic.loadModule("XSDataMXv1")
EDFactoryPluginStatic.loadModule("XSDataMXv2")
from XSDataMXv2 import XSDataCollection
self.setXSDataInputClass(XSDataCollection, "dataCollection")
self.__pyStrBCMDEF = None
def __init__(self, _strNameOfPlugin):
EDPlugin.__init__(self)
self.__strNameOfPlugin = _strNameOfPlugin
EDFactoryPluginStatic.loadModule(_strNameOfPlugin)
self.__dictXMLDataInput = {}
self.__dictXMLDataOutput = {}
self.__strPythonWrapperScriptName = "pluginWrapperForJobScheduler.py"
self.__strPathToPythonWrapper = None
self.__edServerXMLRCP = EDServerXMLRCP.getInstance()
self.__edServerXMLRCP.registerPlugin(self)
self.__bFinished = False
def __init__(self):
"""
"""
EDPluginSTACv2_0.__init__(self)
EDFactoryPluginStatic.loadModule("XSDataMXv1")
EDFactoryPluginStatic.loadModule("XSDataBestv1_2")
from XSDataMXv1 import XSDataIndexingResult
from XSDataBestv1_2 import XSDataInputBest
self.setXSDataInputClass(XSDataInputBest, "inputBest")
self.setXSDataInputClass(XSDataIndexingResult, "indexingResult")
from XSDataMXv1 import XSDataString
self.setXSDataInputClass(XSDataString, "KappaStrategyOption")
def __init__(self):
"""
"""
EDPluginSTACv2_0.__init__(self)
EDFactoryPluginStatic.loadModule("XSDataMXv1")
EDFactoryPluginStatic.loadModule("XSDataBestv1_2")
from XSDataMXv1 import XSDataIndexingResult
from XSDataBestv1_2 import XSDataInputBest
self.setXSDataInputClass(XSDataInputBest, "inputBest")
self.setXSDataInputClass(XSDataIndexingResult, "indexingResult")
from XSDataMXv1 import XSDataString
self.setXSDataInputClass(XSDataString, "KappaStrategyOption")
def testGenerateXSDataInputISPyB(self):
"""
This method is testing the generation of the XSDataInputISPyB object given a XSDataIndexingInput object.
"""
strReferenceInputControlISPyBFile = EDUtilsPath.mergePath(self.strDataPath, "XSDataInputControlISPyB_reference.xml")
strPath = os.path.join(self.strDataPath, strReferenceInputControlISPyBFile)
strXMLIndexingInput = EDUtilsFile.readFileAndParseVariables(strPath, self.dictReplace)
xsDataInputControlISPyB = XSDataInputControlISPyB.parseString(strXMLIndexingInput)
xsDataInputISPyB = EDHandlerXSDataISPyBv1_4.generateXSDataInputISPyBStoreScreening(xsDataInputControlISPyB)
strReferenceInputISPyBFile = EDUtilsPath.mergePath(self.strDataPath, "XSDataInputISPyB_reference.xml")
strReferencePath = os.path.join(self.strDataPath, strReferenceInputISPyBFile)
strXMLInputISPyBReference = EDUtilsFile.readFileAndParseVariables(strReferencePath, self.dictReplace)
EDFactoryPluginStatic.loadModule("XSDataISPyBv1_4")
def testGetXSDataResultCharacterisation(self):
strPathToCCP4iResult = os.path.join(self.getPluginTestsDataHome(),
"XSDataResultCCP4i_reference.xml")
strXML = self.readAndParseFile(strPathToCCP4iResult)
EDFactoryPluginStatic.loadModule("XSDataCCP4iv1_1")
from XSDataCCP4iv1_1 import XSDataResultCCP4i
xsDataResultCCP4i = XSDataResultCCP4i.parseString(strXML)
strListOfOutputFiles = xsDataResultCCP4i.getListOfOutputFiles().getValue()
pluginMXCuBE = self.createPlugin()
xsDataResultCharacterisation = pluginMXCuBE.getXSDataResultCharacterisation(strListOfOutputFiles)
strPathToResultCharacterisationReference = os.path.join(self.getPluginTestsDataHome(),
"EDPluginControlCharacterisationv1_1_dataOutput.xml")
xsDataResultCharacterisationReference = XSDataResultCharacterisation.parseFile(strPathToResultCharacterisationReference)
EDAssert.equal(xsDataResultCharacterisationReference.marshal(), xsDataResultCharacterisation.marshal())
def testGenerateXSDataInputISPyB(self):
"""
This method is testing the generation of the XSDataInputISPyB object given a XSDataIndexingInput object.
"""
strReferenceInputControlISPyBFile = EDUtilsPath.mergePath(self.strDataPath, "XSDataInputControlISPyB_reference.xml")
strPath = os.path.join(self.strDataPath, strReferenceInputControlISPyBFile)
strXMLIndexingInput = EDUtilsFile.readFileAndParseVariables(strPath, self.dictReplace)
xsDataInputControlISPyB = XSDataInputControlISPyB.parseString(strXMLIndexingInput)
xsDataInputISPyB = EDHandlerXSDataISPyBv1_3.generateXSDataInputISPyBStoreScreening(xsDataInputControlISPyB)
print xsDataInputISPyB.marshal()
strReferenceInputISPyBFile = EDUtilsPath.mergePath(self.strDataPath, "XSDataInputISPyB_reference.xml")
strReferencePath = os.path.join(self.strDataPath, strReferenceInputISPyBFile)
strXMLInputISPyBReference = EDUtilsFile.readFileAndParseVariables(strReferencePath, self.dictReplace)
EDFactoryPluginStatic.loadModule("XSDataISPyBv1_3")
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 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 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 __init__(self):
EDPluginControl.__init__(self)
self.setRequiredToHaveConfiguration(True)
self.strPluginRaddoseName = "EDPluginRaddosev10"
self.edPluginRaddose = None
self.edHandlerXSDataRaddose = None
self.strPluginBestName = "EDPluginBestv1_2"
self.edPluginBest = None
from EDHandlerXSDataBestv1_2 import EDHandlerXSDataBestv1_2
self.edHandlerXSDataBest = EDHandlerXSDataBestv1_2()
self.strPluginAlignmentName = "EDPluginSTACAlignmentv2_0"
self.edPluginAlignment = None
self.edHandlerXSDataAlignment = None
self.strPluginKappaStrategyName = "EDPluginSTACStrategyv2_0"
self.edPluginKappaStrategy = None
self.edHandlerXSDataKappaStrategy = None
self.setXSDataInputClass(XSDataInputStrategy, "mxv1InputStrategy")
EDFactoryPluginStatic.loadModule("XSDataMXv2")
import XSDataMXv2
self.setXSDataInputClass(XSDataMXv2.XSDataCollection, "mxv2DataCollection")
import XSDataMXv1
self.setXSDataInputClass(XSDataMXv1.XSDataIndexingResult, "mxv1IndexingResult")
# disable kappa by default
self.KappaStrategy = 0
self.strCONF_SYMOP_HOME = "symopHome"
# Default value for the location of the symop table
self.strSymopHome = os.path.normpath("/opt/pxsoft/ccp4-6.0.2/lib/data")
self.xsDataSampleCopy = None
# For default chemical composition
self.fAverageAminoAcidVolume = 135.49
self.fAverageCrystalSolventContent = 0.47
self.fAverageSulfurContentPerAminoacid = 0.05
self.fAverageSulfurConcentration = 314
def __init__(self):
EDPluginControl.__init__(self)
#self.setXSDataInputClass(EDList)
self.setRequiredToHaveConfiguration(True)
self.strPluginRaddoseName = "EDPluginRaddosev10"
self.edPluginRaddose = None
self.edHandlerXSDataRaddose = None
self.strPluginBestName = "EDPluginBestv1_2"
self.edPluginBest = None
from EDHandlerXSDataBestv1_2 import EDHandlerXSDataBestv1_2
self.edHandlerXSDataBest = EDHandlerXSDataBestv1_2()
self.strPluginAlignmentName = "EDPluginSTACAlignmentv2_0"
self.edPluginAlignment = None
self.edHandlerXSDataAlignment = None
self.strPluginKappaStrategyName = "EDPluginSTACStrategyv2_0"
self.edPluginKappaStrategy = None
self.edHandlerXSDataKappaStrategy = None
self.setXSDataInputClass(XSDataInputStrategy, "mxv1InputStrategy")
EDFactoryPluginStatic.loadModule("XSDataMXv2")
import XSDataMXv2
self.setXSDataInputClass(XSDataMXv2.XSDataCollection,
"mxv2DataCollection")
import XSDataMXv1
self.setXSDataInputClass(XSDataMXv1.XSDataIndexingResult,
"mxv1IndexingResult")
#disable kappa by default
self.KappaStrategy = 0
self.strCONF_SYMOP_HOME = "symopHome"
# Default value for the location of the symop table
self.strSymopHome = os.path.normpath("/opt/pxsoft/ccp4-6.0.2/lib/data")
self.xsDataSampleCopy = None
# For default chemical composition
self.fAverageAminoAcidVolume = 135.49
self.fAverageCrystalSolventContent = 0.47
self.fAverageSulfurContentPerAminoacid = 0.05
self.fAverageSulfurConcentration = 314
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 mergeStrategyToNewOrientation(_xsDataResultStrategy, _xsDataCollection, _fOmega, _fKappa, _fPhi):
'''
_xsDataResultStrategy: reference strategy results as the template for the new strategy
_xsDataCollection: The data collection that will be merged in
result:
suggestedStrategy(XSDataResultStrategy): the strategy resulted from the merge
'''
# suggestedStrategy = None
# try:
# newpossibleOrientations=XSDataSTACv01.kappa_alignment_response.parseString(_possible_orientation.marshal())
# except:
# newpossibleOrientations=None
#so we will copy the strategy of collecting the reference images inputed to here but at the new orientation
#get the full strategy from the Reference
EDFactoryPluginStatic.loadModule("XSDataMXv1")
from XSDataMXv1 import XSDataResultStrategy
suggestedStrategy = XSDataResultStrategy.parseString(_xsDataResultStrategy.marshal())
#take only the first CollectionPlan
if len(suggestedStrategy.getCollectionPlan()) > 0:
suggestedStrategy.setCollectionPlan([suggestedStrategy.getCollectionPlan()[0]])
#modify the DC part taking it from the input
suggestedStrategy.getCollectionPlan()[0].setCollectionStrategy(_xsDataCollection)
#and modify the Orientation
# dc = XSDataMXv2.XSDataCollection()
# dc = self.getDataInput("mxv2DataCollection_Reference")[0]
# Orients = _possible_orientation.getPossible_orientation()
# omega = Orients[0].getOmega()
# kappa = Orients[0].getKappa()
# phi = Orients[0].getPhi()
suggestedStrategy = EDHandlerXSDataMXv1v1_0.copyStrategyToNewOrientation(suggestedStrategy, _fOmega, _fKappa, _fPhi, "MERGED")
# for dcplan in suggestedStrategy.getCollectionPlan():
# dcplan.setComment(EDHandlerXSDataMXv1v1_0().replaceElements(dcplan.getComment(), "OMEGA=", omega))
# dcplan.setComment(EDHandlerXSDataMXv1v1_0().replaceElements(dcplan.getComment(), "KAPPA=", kappa))
# dcplan.setComment(EDHandlerXSDataMXv1v1_0().replaceElements(dcplan.getComment(), "PHI=", phi))
#finally take the suggested new orientation out of the list of further possible ones
# if newpossibleOrientations is not None:
# newpossibleOrientations.setPossible_orientation([])
# for i in range(1, Orients.__len__()):
# if (math.fabs(float(Orients[i].getKappa())-float(kappa))<tol and math.fabs(float(Orients[i].getPhi())-float(phi))<tol):
# newpossibleOrientations.addPossible_orientation(Orients[i])
# return [suggestedStrategy,newpossibleOrientations]
return suggestedStrategy
def testGetXSDataResultCharacterisation(self):
strPathToCCP4iResult = os.path.join(self.getPluginTestsDataHome(),
"XSDataResultCCP4i_reference.xml")
strXML = self.readAndParseFile(strPathToCCP4iResult)
EDFactoryPluginStatic.loadModule("XSDataCCP4iv1_1")
from XSDataCCP4iv1_1 import XSDataResultCCP4i
xsDataResultCCP4i = XSDataResultCCP4i.parseString(strXML)
strListOfOutputFiles = xsDataResultCCP4i.getListOfOutputFiles(
).getValue()
pluginMXCuBE = self.createPlugin()
xsDataResultCharacterisation = pluginMXCuBE.getXSDataResultCharacterisation(
strListOfOutputFiles)
strPathToResultCharacterisationReference = os.path.join(
self.getPluginTestsDataHome(),
"EDPluginControlCharacterisationv1_1_dataOutput.xml")
xsDataResultCharacterisationReference = XSDataResultCharacterisation.parseFile(
strPathToResultCharacterisationReference)
EDAssert.equal(xsDataResultCharacterisationReference.marshal(),
xsDataResultCharacterisation.marshal())
def generateXSDataInputLabelitIndexing(_xsDataIndexingInput):
EDFactoryPluginStatic.loadModule("XSDataPhenixv1_1")
from XSDataPhenixv1_1 import XSDataInputLabelitIndexing
inputLabelitIndexing = XSDataInputLabelitIndexing()
listXSDataImageReference = []
dataCollection = _xsDataIndexingInput.dataCollection
for subWedge in dataCollection.subWedge:
for image in subWedge.image:
inputLabelitIndexing.image.append(image.copy())
xsDataCrystal = _xsDataIndexingInput.getCrystal()
if xsDataCrystal is not None:
xsDataSpaceGroup = xsDataCrystal.getSpaceGroup()
if xsDataSpaceGroup is not None:
xsDataStringName = xsDataSpaceGroup.getName()
if xsDataStringName is not None:
inputLabelitIndexing.forcedSpaceGroup = xsDataStringName
return inputLabelitIndexing
def generateXSDataInputLabelitIndexing(_xsDataIndexingInput):
EDFactoryPluginStatic.loadModule("XSDataPhenixv1_1")
from XSDataPhenixv1_1 import XSDataInputLabelitIndexing
inputLabelitIndexing = XSDataInputLabelitIndexing()
listXSDataImageReference = []
dataCollection = _xsDataIndexingInput.dataCollection
for subWedge in dataCollection.subWedge:
for image in subWedge.image:
inputLabelitIndexing.image.append(image.copy())
xsDataCrystal = _xsDataIndexingInput.getCrystal()
if xsDataCrystal is not None:
xsDataSpaceGroup = xsDataCrystal.getSpaceGroup()
if xsDataSpaceGroup is not None:
xsDataStringName = xsDataSpaceGroup.getName()
if xsDataStringName is not None:
inputLabelitIndexing.forcedSpaceGroup = xsDataStringName
return inputLabelitIndexing
def getXSDataMOSFLMDetector(_xsDataDetector):
"""
Translates an XSDataDetector object to XSDataMOSFLMv10.
"""
EDFactoryPluginStatic.loadModule("XSDataMOSFLMv10")
from XSDataMOSFLMv10 import XSDataMOSFLMDetector
xsDataMOSFLMDetector = XSDataMOSFLMDetector()
strDetectorType = _xsDataDetector.getType().getValue()
if (strDetectorType == "q4") or \
(strDetectorType == "q4-2x") or \
(strDetectorType == "q210") or \
(strDetectorType == "q210-2x") or \
(strDetectorType == "q315") or \
(strDetectorType == "q315-2x"):
xsDataMOSFLMDetector.setType(XSDataString("ADSC"))
elif (strDetectorType == "mar165") or \
(strDetectorType == "mar225"):
xsDataMOSFLMDetector.setType(XSDataString("MARCCD"))
elif (strDetectorType == "pilatus6m"
or strDetectorType == "pilatus2m"):
xsDataMOSFLMDetector.setType(XSDataString("PILATUS"))
elif strDetectorType.startswith("eiger2"):
xsDataMOSFLMDetector.setType(XSDataString("EIGER2"))
elif strDetectorType.startswith("eiger"):
xsDataMOSFLMDetector.setType(XSDataString("EIGER"))
elif (strDetectorType == "raxis4"):
xsDataMOSFLMDetector.setType(XSDataString("RAXISIV"))
else:
# This is a temporary solution for the exception problem pointed out in bug #43.
# Instead of raising an exception with a known type we send the error message as a string.
strErrorMessage = "EDHandlerXSDataMOSFLMv10.getXSDataMOSFLMDetector: Unknown detector type : " + strDetectorType
raise BaseException(strErrorMessage)
if (_xsDataDetector.getNumberPixelX() is not None):
xsDataMOSFLMDetector.setNumberPixelX(
_xsDataDetector.getNumberPixelX())
if (_xsDataDetector.getNumberPixelY() is not None):
xsDataMOSFLMDetector.setNumberPixelY(
_xsDataDetector.getNumberPixelY())
if (_xsDataDetector.getPixelSizeX() is not None):
xsDataMOSFLMDetector.setPixelSizeX(_xsDataDetector.getPixelSizeX())
if (_xsDataDetector.getPixelSizeY() is not None):
xsDataMOSFLMDetector.setPixelSizeY(_xsDataDetector.getPixelSizeY())
return xsDataMOSFLMDetector
def testCreateOutputFileDictionary(self):
strPathToCCP4iResult = os.path.join(self.getPluginTestsDataHome(),
"XSDataResultCCP4i_reference.xml")
strXML = self.readAndParseFile(strPathToCCP4iResult)
EDFactoryPluginStatic.loadModule("XSDataCCP4iv1_1")
from XSDataCCP4iv1_1 import XSDataResultCCP4i
xsDataResultCCP4i = XSDataResultCCP4i.parseString(strXML)
xsDataStringListOfOutputFiles = xsDataResultCCP4i.getListOfOutputFiles()
pluginMXCuBE = self.createPlugin()
pluginMXCuBE.configure()
strResultCharacterisationFileName = "XSDataResultCharacterisation_reference.xml"
strPathToReferenceFile = os.path.join(self.getPluginTestsDataHome(),
strResultCharacterisationFileName)
strXML = self.readAndParseFile(strPathToReferenceFile)
xsDataResultCharacterisation = XSDataResultCharacterisation.parseString(strXML)
strDNAFileDirectoryPath = pluginMXCuBE.createDNAFileDirectoryPath(xsDataResultCharacterisation)
pluginMXCuBE.createDNAFileDirectory(strDNAFileDirectoryPath)
xsDataDictionary = pluginMXCuBE.createOutputFileDictionary(xsDataResultCharacterisation, strDNAFileDirectoryPath)
EDAssert.equal(False, xsDataDictionary is None)
shutil.rmtree(strDNAFileDirectoryPath)
def __init__(self):
EDPluginControl.__init__(self)
self.setRequiredToHaveConfiguration(True)
self.strPluginRaddoseName = "EDPluginRaddosev10"
self.edPluginRaddose = None
self.edHandlerXSDataRaddose = None
self.strPluginBestName = "EDPluginBestv1_2"
self.edPluginBest = None
from EDHandlerXSDataBestv1_2 import EDHandlerXSDataBestv1_2
self.edHandlerXSDataBest = EDHandlerXSDataBestv1_2()
self.strPluginAlignmentName = "EDPluginSTACAlignmentv2_0"
self.edPluginAlignment = None
self.edHandlerXSDataAlignment = None
self.strPluginKappaStrategyName = "EDPluginSTACStrategyv2_0"
self.edPluginKappaStrategy = None
self.edHandlerXSDataKappaStrategy = None
self.setXSDataInputClass(XSDataInputStrategy, "mxv1InputStrategy")
EDFactoryPluginStatic.loadModule("XSDataMXv2")
import XSDataMXv2
self.setXSDataInputClass(XSDataMXv2.XSDataCollection,
"mxv2DataCollection")
import XSDataMXv1
self.setXSDataInputClass(XSDataMXv1.XSDataIndexingResult,
"mxv1IndexingResult")
# disable kappa by default
self.KappaStrategy = 0
self.xsDataSampleCopy = None
# For default chemical composition
self.fAverageAminoAcidVolume = 135.49
self.fAverageCrystalSolventContent = 0.47
self.fAverageSulfurContentPerAminoacid = 0.05
self.fAverageSulfurConcentration = 314
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 copyStrategyToNewOrientation(_xsDataResultStrategy, _fOmega, _fKappa, _fPhi, _strategy = "COPIED"):
'''
_xsDataResultStrategy: the strategy results in which the orientation should be changed
omega,kappa,phi: the new orientation
result:
suggestedStrategy(XSDataResultStrategy): the strategy in which the orientation is changed
'''
#we suggest the currently calculated strategy
EDFactoryPluginStatic.loadModule("XSDataMXv1")
from XSDataMXv1 import XSDataResultStrategy
suggestedStrategy = XSDataResultStrategy.parseString(_xsDataResultStrategy.marshal())
#and we have to add the actual orientation
EDFactoryPluginStatic.loadModule("EDHandlerXSDataCommon")
from EDHandlerXSDataCommon import EDHandlerXSDataCommon
for dcplan in suggestedStrategy.getCollectionPlan():
dcplan.setComment(EDHandlerXSDataCommon.replaceElements(dcplan.getComment(), "OMEGA=", str(_fOmega)))
dcplan.setComment(EDHandlerXSDataCommon.replaceElements(dcplan.getComment(), "KAPPA=", str(_fKappa)))
dcplan.setComment(EDHandlerXSDataCommon.replaceElements(dcplan.getComment(), "PHI=", str(_fPhi)))
dcplan.setComment(EDHandlerXSDataCommon.replaceElements(dcplan.getComment(), "STRATEGY=", str(_strategy)))
return suggestedStrategy
def testGenerateXSDataInputISPyB(self):
"""
This method is testing the generation of the XSDataInputISPyB object given a XSDataIndexingInput object.
"""
strReferenceInputControlISPyBFile = EDUtilsPath.mergePath(self.strDataPath, "XSDataInputControlISPyB_reference.xml")
strPath = os.path.join(self.strDataPath, strReferenceInputControlISPyBFile)
strXMLIndexingInput = self.readAndParseFile(strPath)
from XSDataMXv1 import XSDataInputControlISPyB
xsDataInputControlISPyB = XSDataInputControlISPyB.parseString(strXMLIndexingInput)
from EDHandlerXSDataISPyBv1_1 import EDHandlerXSDataISPyBv1_1
xsDataInputISPyB = EDHandlerXSDataISPyBv1_1.generateXSDataInputISPyB(xsDataInputControlISPyB)
strReferenceInputISPyBFile = EDUtilsPath.mergePath(self.strDataPath, "XSDataInputISPyB_reference.xml")
strReferencePath = os.path.join(self.strDataPath, strReferenceInputISPyBFile)
strXMLInputISPyBReference = self.readAndParseFile(strReferencePath)
EDFactoryPluginStatic.loadModule("XSDataISPyBv1_1")
from XSDataISPyBv1_1 import XSDataInputISPyB
xsDataInputISPyBReference = XSDataInputISPyB.parseString(strXMLInputISPyBReference)
# Remove the time strings since they otherwise make the test fail
xsDataInputISPyBReference.getScreening().setTimeStamp(None)
xsDataInputISPyB.getScreening().setTimeStamp(None)
EDAssert.equal(xsDataInputISPyBReference.marshal(), xsDataInputISPyB.marshal())
def getXSDataMOSFLMDetector(_xsDataDetector):
"""
Translates an XSDataDetector object to XSDataMOSFLMv10.
"""
EDFactoryPluginStatic.loadModule("XSDataMOSFLMv10")
from XSDataMOSFLMv10 import XSDataMOSFLMDetector
xsDataMOSFLMDetector = XSDataMOSFLMDetector()
strDetectorType = _xsDataDetector.getType().getValue()
if (strDetectorType == "q4") or \
(strDetectorType == "q4-2x") or \
(strDetectorType == "q210") or \
(strDetectorType == "q210-2x") or \
(strDetectorType == "q315") or \
(strDetectorType == "q315-2x"):
xsDataMOSFLMDetector.setType(XSDataString("ADSC"))
elif (strDetectorType == "mar165") or \
(strDetectorType == "mar225"):
xsDataMOSFLMDetector.setType(XSDataString("MARCCD"))
elif (strDetectorType == "pilatus6m" or strDetectorType == "pilatus2m"):
xsDataMOSFLMDetector.setType(XSDataString("PILATUS"))
elif strDetectorType.startswith("eiger"):
xsDataMOSFLMDetector.setType(XSDataString("EIGER"))
elif (strDetectorType == "raxis4"):
xsDataMOSFLMDetector.setType(XSDataString("RAXISIV"))
else:
# This is a temporary solution for the exception problem pointed out in bug #43.
# Instead of raising an exception with a known type we send the error message as a string.
strErrorMessage = "EDHandlerXSDataMOSFLMv10.getXSDataMOSFLMDetector: Unknown detector type : " + strDetectorType
raise BaseException(strErrorMessage)
if (_xsDataDetector.getNumberPixelX() is not None):
xsDataMOSFLMDetector.setNumberPixelX(_xsDataDetector.getNumberPixelX())
if (_xsDataDetector.getNumberPixelY() is not None):
xsDataMOSFLMDetector.setNumberPixelY(_xsDataDetector.getNumberPixelY())
if (_xsDataDetector.getPixelSizeX() is not None):
xsDataMOSFLMDetector.setPixelSizeX(_xsDataDetector.getPixelSizeX())
if (_xsDataDetector.getPixelSizeY() is not None):
xsDataMOSFLMDetector.setPixelSizeY(_xsDataDetector.getPixelSizeY())
return xsDataMOSFLMDetector
def __init__( self ):
"""
"""
EDPluginSTACv2_0.__init__( self )
EDFactoryPluginStatic.loadModule( "XSDataMXv1" )
EDFactoryPluginStatic.loadModule( "XSDataMXv2" )
EDFactoryPluginStatic.loadModule( "XSDataSTACv2_0" )
EDFactoryPluginStatic.loadModule( "XSDataBestv1_2" )
from XSDataMXv1 import XSDataIndexingResult
from XSDataMXv1 import XSDataInputStrategy
from XSDataBestv1_2 import XSDataInputBest
self.setXSDataInputClass( kappa_strategy_request, "kappa_strategy_request" )
import XSDataMXv2
self.setXSDataInputClass( XSDataMXv2.XSDataCollection, "mxv2DataCollection" )
# not used: self.setXSDataInputClass( XSDataIndexingResult, "indexingResult" )
self.setXSDataInputClass( XSDataInputStrategy, "inputBest" )
def generateXSDataInputLabelit(_xsDataIndexingInput):
EDFactoryPluginStatic.loadModule("XSDataLabelitv10")
from XSDataLabelitv10 import XSDataInputLabelit
xsDataInputLabelit = XSDataInputLabelit()
xsDataCollection = _xsDataIndexingInput.getDataCollection()
xsDataSubWedgeList = xsDataCollection.getSubWedge()
xsDataInputLabelit.addImage(xsDataSubWedgeList[0].getImage()[0])
fPhiStartFirst = xsDataSubWedgeList[0].getExperimentalCondition().getGoniostat().getRotationAxisStart().getValue()
if (len(xsDataSubWedgeList) > 1):
xsDataImageSecond = xsDataSubWedgeList[-1].getImage()[0]
fPhiStartSecond = xsDataSubWedgeList[-1].getExperimentalCondition().getGoniostat().getRotationAxisStart().getValue()
# Add modulus!
if (abs(fPhiStartSecond - fPhiStartFirst) > 4):
xsDataInputLabelit.addImage(xsDataImageSecond)
return xsDataInputLabelit
def generateXSDataISPyBScreening(_xsDataInputControlISPyB, _strShortComments=None, _strComments=None):
"""
"""
EDFactoryPluginStatic.loadModule("XSDataISPyBv1_2")
from XSDataISPyBv1_2 import XSDataString
from XSDataISPyBv1_2 import XSDataISPyBScreening
xsDataIntegerDataCollectionId = _xsDataInputControlISPyB.getDataCollectionId()
# General information
xsDataISPyBScreening = XSDataISPyBScreening()
xsDataISPyBScreening.setProgramVersion(XSDataString("EDNA MXv1"))
pyStrTimeStamp = time.strftime("%Y-%m-%d %H:%M:%S")
xsDataISPyBScreening.setTimeStamp(XSDataString(pyStrTimeStamp))
if (not _strShortComments is None):
xsDataISPyBScreening.setShortComments(XSDataString(_strShortComments))
if (not _strComments is None):
xsDataISPyBScreening.setComments(XSDataString(_strComments))
# Use dataCollectionId if provided in the input
if (xsDataIntegerDataCollectionId is not None):
xsDataISPyBScreening.setDataCollectionId(xsDataIntegerDataCollectionId)
return xsDataISPyBScreening
def __init__(self):
"""
"""
EDPluginSTACv2_0.__init__(self)
EDFactoryPluginStatic.loadModule("XSDataMXv1")
EDFactoryPluginStatic.loadModule("XSDataBestv1_2")
from XSDataMXv1 import XSDataIndexingResult
from XSDataBestv1_2 import XSDataInputBest
self.setXSDataInputClass(XSDataInputBest, "inputBest")
self.setXSDataInputClass(XSDataIndexingResult, "indexingResult")
EDFactoryPluginStatic.loadModule( "XSDataSTACv2_0" )
from XSDataSTACv2_0 import kappa_alignment_request
self.setXSDataInputClass(kappa_alignment_request, "kappa_alignment_request")
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
__author__ = "Jérôme Kieffer"
__license__ = "GPLv3+"
__copyright__ = "2011, ESRF Grenoble"
import os, tempfile
from EDVerbose import EDVerbose
from EDAssert import EDAssert
from EDTestCasePluginExecute import EDTestCasePluginExecute
from EDFactoryPluginStatic import EDFactoryPluginStatic
EDFactoryPluginStatic.loadModule("XSDataEdnaSaxs")
EDFactoryPluginStatic.loadModule("XSDataBioSaxsv1_0")
from XSDataBioSaxsv1_0 import XSDataResultBioSaxsSmartMergev1_0
class EDTestCasePluginExecuteBioSaxsSmartMergev1_0(EDTestCasePluginExecute):
def __init__(self, _strTestName=None):
EDTestCasePluginExecute.__init__(self, "EDPluginBioSaxsSmartMergev1_0")
# self.setConfigurationFile(os.path.join(self.getPluginTestsDataHome(),
# "XSConfiguration_BioSaxsSmartMerge.xml"))
self.setDataInputFile(os.path.join(self.getPluginTestsDataHome(), \
"XSDataInputBioSaxsSmartMerge_reference.xml"))
self.setReferenceDataOutputFile(os.path.join(self.getPluginTestsDataHome(), \
"XSDataResultBioSaxsSmartMerge_reference.xml"))
self.destFile = os.path.join(tempfile.gettempdir(),
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
import threading, time, os
from EDVerbose import EDVerbose
from EDFactoryPluginStatic import EDFactoryPluginStatic
from EDFactoryPlugin import EDFactoryPlugin
from EDObject import EDObject
from EDSlot import EDSlot
from EDPluginWrapperForJobScheduler import EDPluginWrapperForJobScheduler
#asizeof does not work with Jython
if os.name == "java":
asizeof = None
else:
asizeof = EDFactoryPluginStatic.loadModule("asizeof")
class EDJob(EDObject):
PLUGIN_STATE_UNITIALIZED = "uninitialized"
PLUGIN_STATE_RUNNING = "running"
PLUGIN_STATE_SUCCESS = "success"
PLUGIN_STATE_FAILURE = "failure"
__edFactoryPlugin = EDFactoryPlugin()
__dictJobs = {}
__semaphore = threading.Semaphore()
__dictPluginLastId = {}
__fStartTime = time.time()
def __init__(self, _strPluginName):
#
__author__ = "Jérôme Kieffer"
__license__ = "GPLv3+"
__copyright__ = "ESRF"
__date__ = "2011-02-25"
import os, sys
from EDVerbose import EDVerbose
from EDTestCasePluginUnit import EDTestCasePluginUnit
from XSDataBioSaxsv1_0 import XSDataInputBioSaxsNormalizev1_0, XSDataBioSaxsSample, XSDataBioSaxsExperimentSetup
from XSDataCommon import XSDataInteger, XSDataDouble, XSDataImage, XSDataFile, XSDataString, \
XSDataLength, XSDataWavelength
from EDFactoryPluginStatic import EDFactoryPluginStatic
# Needed for loading the plugin...
EDFactoryPluginStatic.loadModule("EDInstallNumpyv1_3")
EDFactoryPluginStatic.loadModule("EDInstallPILv1_1_7")
EDFactoryPluginStatic.loadModule("EDInstallFabio_v0_0_7")
class EDTestCasePluginUnitBioSaxsNormalizev1_1(EDTestCasePluginUnit):
def __init__(self, _edStringTestName=None):
EDTestCasePluginUnit.__init__(self, "EDPluginBioSaxsNormalizev1_1")
def testCheckParameters(self):
xsDataInput = XSDataInputBioSaxsNormalizev1_0()
xsDataInput.setRawImage(XSDataImage())
# xsDataInput.setLogFile(XSDataFile())
xsDataInput.setNormalizedImage(XSDataImage())
xsDataInput.setRawImageSize(XSDataInteger())
xsDataInput.setExperimentSetup(XSDataBioSaxsExperimentSetup())
__authors__ = ["Olof Svensson", "Karl Levik"]
__contact__ = "*****@*****.**"
__license__ = "GPLv3+"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
import os, tempfile
from EDAssert import EDAssert
from EDTestCase import EDTestCase
from EDUtilsTest import EDUtilsTest
from EDUtilsPath import EDUtilsPath
from EDUtilsFile import EDUtilsFile
from EDFactoryPluginStatic import EDFactoryPluginStatic
EDFactoryPluginStatic.loadModule("EDHandlerXSDataISPyBv1_4")
from EDHandlerXSDataISPyBv1_4 import EDHandlerXSDataISPyBv1_4
from XSDataMXv1 import XSDataInputControlISPyB
class EDTestCaseEDHandlerISPyBv1_4(EDTestCase):
def __init__(self, _pyStrTestName=None):
EDTestCase.__init__(self, _pyStrTestName)
strMXv1DataHome = EDUtilsTest.getPluginTestDataDirectory(self.getClassName())
strDataDir = "EDHandlerISPyBv1_4"
self.strDataPath = os.path.join(strMXv1DataHome, strDataDir)
self.dictReplace = {
"${EDNA_TESTIMAGES}": EDUtilsPath.EDNA_TESTIMAGES,
"${EDNA_HOME}": EDUtilsPath.getEdnaHome(),
"${USER}": os.getenv("USER", "UndefindedUser"),
from EDFactoryPluginStatic import EDFactoryPluginStatic
EDFactoryPluginStatic.loadModule("XSDataMXv1")
from XSDataMXv1 import XSDataResultStrategy
xsDataResultStrategy = XSDataResultStrategy.parseString(mxv1StrategyResult)
xsDataCollectionPlan = xsDataResultStrategy.getCollectionPlan()[0]
xsDataCollectionStrategy = xsDataCollectionPlan.getCollectionStrategy()
xsDataSubWedge = xsDataCollectionStrategy.getSubWedge()[0]
xsDataExperimentalCondition = xsDataSubWedge.getExperimentalCondition()
exposureTime = xsDataExperimentalCondition.getBeam().getExposureTime(
).getValue()
detectorDistance = xsDataExperimentalCondition.getDetector().getDistance(
).getValue()
oscillationWidth = xsDataExperimentalCondition.getGoniostat(
).getOscillationWidth().getValue()
rotationAxisStart = xsDataExperimentalCondition.getGoniostat(
).getRotationAxisStart().getValue()
rotationAxisEnd = xsDataExperimentalCondition.getGoniostat(
).getRotationAxisEnd().getValue()
noImages = int((rotationAxisEnd - rotationAxisStart) / oscillationWidth)
runNumberDataCollection = run_number
print "Suggested strategy:"
print "Oscillation start: %.2f" % rotationAxisStart
print "Oscillation width: %.2f" % oscillationWidth
print "No images: %d" % noImages
print "Exposure time: %.2f" % exposureTime
print "Detector distance: %.2f" % detectorDistance
print "Run number: %d " % runNumberDataCollection
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
from EDVerbose import EDVerbose
from EDFactoryPluginStatic import EDFactoryPluginStatic
from EDPluginControl import EDPluginControl
import XSDataMXv2
EDFactoryPluginStatic.loadModule("XSDataSTACv2_0")
import XSDataSTACv2_0
EDFactoryPluginStatic.loadModule("EDHandlerXSDataMXv1v1_0")
from EDHandlerXSDataMXv1v1_0 import EDHandlerXSDataMXv1v1_0
EDFactoryPluginStatic.loadModule("EDHandlerXSDataSTACv2_0")
from EDHandlerXSDataSTACv2_0 import EDHandlerXSDataSTACv2_0
EDFactoryPluginStatic.loadModule("XSDataMXv1")
from XSDataMXv1 import XSDataInputCharacterisation
from XSDataMXv1 import XSDataResultCharacterisation
from XSDataMXv2 import XSDataInputCharacterisationv2_0
from XSDataMXv2 import XSDataResultCharacterisationv2_0
from XSDataMXv2 import XSDataCollection
from XSDataMXv2 import kappa_alignment_response
#
__author__ = "Olof Svensson"
__contact__ = "*****@*****.**"
__license__ = "LGPLv3+"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
__date__ = "20120712"
__status__ = "production"
import os, datetime
from EDPluginExec import EDPluginExec
from EDFactoryPluginStatic import EDFactoryPluginStatic
EDFactoryPluginStatic.loadModule("EDInstallSudsv0_4")
from suds.client import Client
from suds.transport.http import HttpAuthenticated
from suds.sax.date import DateTime
from XSDataCommon import XSDataInteger
from XSDataISPyBv1_4 import XSDataInputStoreListOfImageQualityIndicators
from XSDataISPyBv1_4 import XSDataResultStoreListOfImageQualityIndicators
class EDPluginISPyBStoreListOfImageQualityIndicatorsv1_4(EDPluginExec):
"""
Plugin to store results in an ISPyB database using web services
"""
__license__ = "GPLv3+"
__copyright__ = "ESRF"
__status__ = "deprecated"
import os, shutil
from EDVerbose import EDVerbose
from EDPluginControl import EDPluginControl
from EDFactoryPluginStatic import EDFactoryPluginStatic
from XSDataCommon import XSDataString, XSDataInteger, XSDataFile
from XSDataBioSaxsv1_0 import (
XSDataInputBioSaxsAsciiExportv1_0,
XSDataResultBioSaxsAsciiExportv1_0,
XSDataInputBioSaxsMetadatav1_0,
)
EDFactoryPluginStatic.loadModule("XSDataWaitFilev1_0")
EDFactoryPluginStatic.loadModule("XSDataSaxsv1_0")
from XSDataWaitFilev1_0 import XSDataInputWaitFile
from XSDataSaxsv1_0 import XSDataInputSaxsCurvesv1_0
class EDPluginBioSaxsAsciiExportv1_0(EDPluginControl):
"""
Control for Bio Saxs ascii export of integrated data :
* Wait for the file to arrive
* Retrieve metadata from the header
* export as 3-column ascii file (EDPluginSaxsCurvesv1_0)
* rewrite metadata
"""
def __init__(self):
from EDVerbose import EDVerbose
from EDPluginControl import EDPluginControl
from EDFactoryPluginStatic import EDFactoryPluginStatic
from EDConfiguration import EDConfiguration
from XSDataCommon import XSDataFile
from XSDataCommon import XSDataInteger
from XSDataCommon import XSDataTime
from XSDataMXv1 import XSDataImageQualityIndicators
from XSDataMXv1 import XSDataInputControlImageQualityIndicators
from XSDataMXv1 import XSDataResultControlImageQualityIndicators
EDFactoryPluginStatic.loadModule("XSDataWaitFilev1_0")
from XSDataWaitFilev1_0 import XSDataInputWaitMultiFile
EDFactoryPluginStatic.loadModule("XSDataLabelitv1_1")
from XSDataLabelitv1_1 import XSDataInputDistlSignalStrength
class EDPluginControlImageQualityIndicatorsv1_1(EDPluginControl):
"""
This plugin that control the plugin that generates the image quality indicators.
"""
def __init__(self):
EDPluginControl.__init__(self)
self.strPluginExecWaitMultiFileName = "EDPluginWaitMultiFile"
self.strPluginExecImageQualityIndicatorName = "EDPluginDistlSignalStrengthv1_1"
self.setXSDataInputClass(XSDataInputControlImageQualityIndicators)
# If not, see <http://www.gnu.org/licenses/>.
#
__author__ = "Olof Svensson"
__contact__ = "*****@*****.**"
__license__ = "LGPLv3+"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
__date__ = "20120712"
__status__ = "production"
import os, datetime
from EDPluginExec import EDPluginExec
from EDFactoryPluginStatic import EDFactoryPluginStatic
EDFactoryPluginStatic.loadModule("EDInstallSudsv0_4")
from suds.client import Client
from suds.transport.http import HttpAuthenticated
from suds.sax.date import DateTime
from XSDataCommon import XSDataInteger
from XSDataISPyBv1_4 import XSDataISPyBScreeningStrategy
from XSDataISPyBv1_4 import XSDataInputISPyBStoreScreening
from XSDataISPyBv1_4 import XSDataResultISPyBStoreScreening
class EDPluginISPyBStoreScreeningv1_4(EDPluginExec):
"""
Plugin to store results in an ISPyB database using web services
"""
