def getSymmetry(self, reconrunid, msg=True):
"""
get the symmetry from the last iteration of a refinement
"""
symmdata = apSymmetry.getSymmetryFromReconRunId(reconrunid, msg)
symmname = symmdata['eman_name']
return symmname
def getSymmetry(self, reconrunid, msg=True): """ get the symmetry from the last iteration of a refinement """ symmdata = apSymmetry.getSymmetryFromReconRunId(reconrunid, msg) symmname = symmdata['eman_name'] return symmname
def checkConflicts(self):
"""
make sure the necessary parameters are set correctly
"""
if self.cursor is None:
# connect
self.dbconf = sinedon.getConfig('appiondata')
self.db = MySQLdb.connect(**self.dbconf)
self.db.autocommit(True)
# create a cursor
self.cursor = self.db.cursor()
if not self.params['reconid']:
apDisplay.printError("Enter a Reconstruction Run ID, e.g. --reconid=243")
if not self.params['tiltrunid']:
self.params['tiltrunid'] = self.getTiltRunIDFromReconID(self.params['reconid'])
self.params['symmetry'] = apSymmetry.getSymmetryFromReconRunId(self.params['reconid'])
self.params['symmname'] = self.params['symmetry']['eman_name']
if not self.params['stackid']:
self.params['stackid'] = apStack.getStackIdFromRecon(self.params['reconid'])
def checkConflicts(self):
"""
make sure the necessary parameters are set correctly
"""
if self.cursor is None:
# connect
self.dbconf = sinedon.getConfig('appiondata')
self.db = MySQLdb.connect(**self.dbconf)
self.db.autocommit(True)
# create a cursor
self.cursor = self.db.cursor()
if not self.params['reconid']:
apDisplay.printError("Enter a Reconstruction Run ID, e.g. --reconid=243")
if not self.params['tiltrunid']:
self.params['tiltrunid'] = self.getTiltRunIDFromReconID(self.params['reconid'])
self.params['symmetry'] = apSymmetry.getSymmetryFromReconRunId(self.params['reconid'])
self.params['symmname'] = self.params['symmetry']['eman_name']
if not self.params['stackid']:
self.params['stackid'] = apStack.getStackIdFromRecon(self.params['reconid'])
def checkConflicts(self):
if self.params['reconid'] is None:
apDisplay.printError("enter a reconstruction ID from the database")
if self.params['mask'] is None:
apDisplay.printError("enter a mask radius")
if self.params['iter'] is None:
apDisplay.printError("enter an iteration for the final Eulers")
if self.params['keeplist'] is None:
apDisplay.printError("enter an keep list file")
self.params['keeplist'] = os.path.abspath(self.params['keeplist'])
if not os.path.isfile(self.params['keeplist']):
apDisplay.printError("could not find list file")
self.params['stackid'] = apStack.getStackIdFromRecon(self.params['reconid'])
if self.params['stackname'][-4:] != ".hed":
s = os.path.splitext(self.params['stackname'])[0]
s += ".hed"
self.params['stackname'] = s
apDisplay.printMsg("Stack name: "+self.params['stackname'])
self.params['symmetry'] = apSymmetry.getSymmetryFromReconRunId(self.params['reconid'])
self.params['symmname'] = self.params['symmetry']['eman_name']
