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']