def setParams(self, optargs, useglobalparams=True): self.parser = OptionParser() if useglobalparams is True: self.setupGlobalParserOptions() self.setupParserOptions() self.params = apParam.convertParserToParams(self.parser) self.checkForDuplicateCommandLineInputs(optargs)
def setParams(self,optargs,useglobalparams=True): self.parser = OptionParser() if useglobalparams is True: self.setupGlobalParserOptions() self.setupParserOptions() self.params = apParam.convertParserToParams(self.parser) self.checkForDuplicateCommandLineInputs(optargs)
def parseOptions(): parser=OptionParser() parser.add_option('--tiltid', dest='tiltid', help= 'Primary key for a tilt series from appion database') parser.add_option('--outtiltfile', dest='tiltfile', help='PROTOMO tilt file to output') parser.add_option('--seriesname', dest='seriesname', help='Prefix to use as the name of the tilt series for processing') parser.add_option('--tar', action="store_true", dest='tar', default=False, help="Create a tarball containing files and directories") params=apParam.convertParserToParams(parser) return params
def parseOptions(): parser = OptionParser() parser.add_option( '--tiltid', dest='tiltid', help='Primary key for a tilt series from appion database') parser.add_option('--outtiltfile', dest='tiltfile', help='PROTOMO tilt file to output') parser.add_option( '--seriesname', dest='seriesname', help='Prefix to use as the name of the tilt series for processing') parser.add_option('--tar', action="store_true", dest='tar', default=False, help="Create a tarball containing files and directories") params = apParam.convertParserToParams(parser) return params
def setParams(self,optargs=sys.argv[1:]): self.parser = OptionParser() self.setupParserOptions() self.params = apParam.convertParserToParams(self.parser) self.checkForDuplicateCommandLineInputs(optargs)
help="Second input image", metavar="FILE") parser.add_option("--p1", "--pickfile1", dest="pickfile1", help="First particle pick file", metavar="FILE") parser.add_option("--p2", "--pickfile2", dest="pickfile2", help="Second particle pick file", metavar="FILE") parser.add_option("-t", "--tiltangle", dest="tiltangle", type="float", help="Absolute tilt angle," +" negative, image 1 is more compressed (tilted), " +" positive, image 2 is more compressed (tilted)", metavar="#") parser.add_option("-o", "--outfile", dest="outfile", help="Particle picks and tilt parameters output file", metavar="FILE") parser.add_option("-d", "--diam", "--pixdiam", dest="pixdiam", type="float", help="Approximate diameter of particle in pixels", metavar="#") parser.add_option("-x", "--tiltaxis", dest="tiltaxis", type="float", help="Approximate tilt axis angle", metavar="#") params = apParam.convertParserToParams(parser) checkConflicts(params) ### set important parameters imgfile1 = params['imgfile1'] imgfile2 = params['imgfile2'] picks1 = readPickFile(params['pickfile1']) picks2 = readPickFile(params['pickfile2']) theta = params['tiltangle'] outfile = params['outfile'] pixdiam = params['pixdiam'] tiltaxis = params['tiltaxis'] ### run tilt automation autotilter = autotilt.autoTilt()
### floats parser.add_option("-c", "--cc-cut", dest="cccut", type="float", default=0.5, help="Cross-correlation cutoff", metavar="#") ### strings parser.add_option("-s", "--sym", dest="sym", help="EMAN symmetry", metavar=".") ### true/false parser.add_option("-e", "--eotest", dest="eotest", default=False, action="store_true", help="Determine resolution by even/odd FSC") ### choices prefvalues = ( "median", "minimum", "minlessrange" ) parser.add_option("--preftype", "--preference-type", dest="preftype", help="Set preference value type", metavar="TYPE", type="choice", choices=prefvalues, default="minlessrange" ) params = apParam.convertParserToParams(parser) if params['iter'] is None: apDisplay.printError("Please provide a EMAN iteration number") if params['hard'] is None: apDisplay.printError("Please provide a EMAN hard value") if params['sym'] is None: apDisplay.printError("Please provide a EMAN sym value") if params['mask'] is None: apDisplay.printError("Please provide a EMAN mask value") params['emandir'] = os.path.abspath(os.getcwd()) params['rundir'] = os.path.join(params['emandir'], ("affprop%d"%(params['iter']))) if not os.path.isdir(params['rundir']): os.mkdir(params['rundir']) start(params)