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)
def setParams(self,optargs=sys.argv[1:]):
self.parser = OptionParser()
self.setupParserOptions()
self.params = apParam.convertParserToParams(self.parser)
self.checkForDuplicateCommandLineInputs(optargs)