def __init__(self, ednaOutputFile):
"""
Parse
ControlInterfaceToMXCuBEv1_3_dataOutput.xml
"""
self.ednaOutputFile = ednaOutputFile
self.log = localLogger.LocalLogger("edna")
self.log.logger.debug("Parsing edna Output File file: " +
self.ednaOutputFile)
# Workaround to process old EDNA characterisation XML format
# ControlInterfaceToMXCuBEv1_2/CCP4i/Characterisation/ControlCharacterisationv1_2_dataOutput.xml
if self.ednaOutputFile.find('ControlCharacterisationv1_2') > 0:
self._outputXMLContent = XSDataMXv1.XSDataCharacterisation.parseString(
open(self.ednaOutputFile, "rb").read())
# Workaround to read file sent by Sandor
elif self.ednaOutputFile.find('mxv1StrategyResult') > 0:
self._outputXMLContent = XSDataMXv1.XSDataResultStrategy.parseString(
open(self.ednaOutputFile, "rb").read())
else:
self._outputXMLContent = XSDataMXCuBEv1_3.XSDataResultMXCuBE.parseString(
open(self.ednaOutputFile, "rb").read())
# variables
self.subWedgesList = [] # list of dictionaries for parsed subwedges
def getParTestFile ( self, section, option, default = None ):
"""
ini.getPar("BEST", "besthome")
Same but tests if file exists and give complete path
"""
if self.cfg.has_section ( section ):
#print 'Has Section'
if self.cfg.has_option ( section, option ):
#print 'Has Option'
value = self.cfg.get ( section, option ).strip()
else:
value = default
else:
value = default
completeFilePath = self.testIfFileExists(value)
if completeFilePath is None :
localLogger.LocalLogger("ini").logger.error("Trying tro fetch a file that does not exist: " + value)
return None
else :
return completeFilePath
def __init__(self, xdsRunFolder):
self.xdsRunFolder = xdsRunFolder
self.log = localLogger.LocalLogger("xds")
self.cell = None
self.spaceGroupNumber = None
self.firstImage = None
self.lastImage = None
self.referenceDataSet = None
def __init__(self, processPath, ednaPath, keysFileName):
self._ednaRaddoseExecutable = os.path.join(
ednaPath,
ini.Ini().getPar("EDNA", "edna_raddose_executable"))
self.log = localLogger.LocalLogger("raddose")
self._keywords = None
self.results = None
self.realAbsorbedDoseRate = None
self.keysFileName = keysFileName
self.log.logger.debug("Using raddose keywords file: " +
self.keysFileName)
def __init__(self, wedge):
'''
Constructor:
@param wedge: wedgeHandler - the folder name contents parsed...
'''
self.wedge = wedge
self.log = localLogger.LocalLogger("burntWedge")
self.log.logger.debug("BurntWedgesHandler...")
self.wedgeList = []
def __init__(self, x, y):
'''
Constructor
'''
self.log = localLogger.LocalLogger("fitting")
self.discrete_x = x
self.discrete_y = y
self.continuous_x = None
self.continuous_y = None
self.function = None
self.coefficients = None
self.error = None
def __init__(self, wedgeFolderPath):
'''
Constructor
Two types of wedgeFolderPath
# old : /data/id23eh1/inhouse/opid231/20100930/HUM/Ricardo/Lyso1/process/xds_t4w1_run1_1
# new : /data/id23eh1/inhouse/opid231/20101103/PROCESSED_DATA/LYS_T/xds_t3w7_run1_1
'''
self.log = localLogger.LocalLogger("wedge")
# normalize path (just for safety...)
if os.path.isabs(wedgeFolderPath) and os.path.exists(wedgeFolderPath):
self.wedgeFolderPath = os.path.normpath(wedgeFolderPath)
# if is relative path, build complete path
elif not os.path.isabs(wedgeFolderPath) and os.path.exists(
os.path.abspath(wedgeFolderPath)):
self.wedgeFolderPath = os.path.abspath(wedgeFolderPath)
else:
self.log.logger.error("Wedge folder does not exist: " +
wedgeFolderPath)
sys.exit(-1)
self.log.logger.debug("Parsing: " + self.wedgeFolderPath)
#
self.baseFolderPath = None
self.processFolderPath = None
self._getBaseFolderPath()
#
self.wedgeFolderName = None
self.wedgeSoftware = None
self.wedgeName = None
self.subWedgeNumber = None
self.wedgeRunNumber = None
self.wedgeDatasetNumber = None
self._parseCurrentWedgeNumber()
def __init__(self,condorRunFolder) :
self.condorRunFolder = condorRunFolder
self.log = localLogger.LocalLogger("condor")
def __init__(self, oarRunFolder):
self.oarRunFolder = oarRunFolder
self.log = localLogger.LocalLogger("oar")
def __init__(self, runFolder):
self.runFolder = runFolder
self.log = localLogger.LocalLogger("best")
return 2
except Usage, err:
print >> sys.stderr, sys.argv[0].split("/")[-1] + ": " + str(err.msg)
print >> sys.stderr, ""
print >> sys.stderr, "For help use the -h or the --help option."
print >> sys.stderr, ""
return 2
#===============================================================================
# Fun starts here!!
#===============================================================================
# Mandatory initialisations!
ini.Ini(configIniFileName)
myLog = localLogger.LocalLogger()
#
if ednaFolderName is None and (wedgeFolderPath is None
or wedgeFolderTemplate is None):
myLog.logger.info("InducedRadDam v0.3")
myLog.logger.info(
"Both ednaFolderName and wedgeFolderPath are mandatory!")
sys.exit(0)
# get wedge details from the wedgeFolderPath
wedge = wedgeHandler.WedgeHandler(wedgeFolderPath)
wedge.buildEdnaFolderPath(ednaFolderName)
if currentQueueItem is None:
def __init__(self):
'''
Constructor
'''
self.log = localLogger.LocalLogger("data")
self.listOfDicts = []
def __init__(self):
'''
Constructor
'''
self.log = localLogger.LocalLogger("plot")