def _get_db_options(args): """Parse through a command line of arguments to over-ride the values in the users .dbrc file. If no user name is given then the environment variable $USERNAME is used. If $USERNAME is not defined then prompt for input. """ import optik, getpass, sys from optik import OptionParser parser = OptionParser() parser.add_option("-d", "--database", action="store", type="string", dest="database", default="cfht", help="Name of the SYBASE database containing TABLE", metavar="FILE") parser.add_option("-u", "--user", action="store", type="string", dest="user", default=getpass.getuser(), help="User name to access db with", metavar="USER") (opt, unused_args) = parser.parse_args(args) return opt.database, opt.user, unused_args
def main(): options_table = [ Option("-d", "--db", action="store", help="DB string to connect to"), ] parser = OptionParser(option_list=options_table) (options, args) = parser.parse_args() if not options.db: print "--db not specified" return 1 rhnSQL.initDB(options.db) if not args: print "No module specified" return 0 if '.' not in sys.path: sys.path.append('.') g = globals() for module_name in args: print "Checking module %s" % module_name pmn = proper_module_name(module_name) try: m = __import__(pmn) g[module_name] = m except ImportError, e: print "Unable to import module %s: %s" % (module_name, e) continue comps = string.split(pmn, '.') for c in comps[1:]: m = getattr(m, c) for mod, name, statement in get_class_instances(m, rhnSQL.Statement): try: rhnSQL.prepare(statement) except rhnSQL.SQLStatementPrepareError, e: print "Error: %s.%s: %s" % (mod.__name__, name, e)
def run_with_optik(): """parse the options with optik""" parser = OptionParser() parser.add_option("-o", "--output", action="store", type="string", dest="outputfilename", help="write output into FILE") output = sys.stdout close_output = 0 (options, args) = parser.parse_args() try: if options.outputfilename and options.outputfilename != "-": output = file(options.outputfilename, "w") close_output = 1 except IOError: print "could not open '%s' for writing." % options.outputfilename if output: convertProfFiles(output, args) if close_output: output.close()
def _get_db_options(args): """Parse through a command line of arguments to over-ride the values in the users .dbrc file. If no user name is given then the environment variable $USERNAME is used. If $USERNAME is not defined then prompt for input. """ import optik, getpass,sys from optik import OptionParser parser=OptionParser() parser.add_option("-d","--database", action="store", type="string", dest="database", default="cfht", help="Name of the SYBASE database containing TABLE", metavar="FILE") parser.add_option("-u","--user", action="store", type="string", dest="user", default=getpass.getuser(), help="User name to access db with", metavar="USER") (opt, unused_args) = parser.parse_args(args) return opt.database,opt.user,unused_args
import string import locale import codecs import sys from optik import OptionParser parser = OptionParser() parser.add_option("-i", "--input-file", dest="filename", help="wordlist FILE to parse and evaluate, use - to read form stdin", metavar="FILE") parser.add_option("-v", "--verbose", action="store_true", dest="verbose", default=0, help="print python dictionaries and frequency percentages") parser.add_option("-l", "--locale", dest="inputlocale", default=locale.getdefaultlocale(), help="locale to use for selection of valid characters, default is the current locale", metavar="LOCALE") (options, args) = parser.parse_args() if options.filename is None: parser.print_help() sys.exit() if options.filename == "-": options.filename = '/dev/stdin' input = open(options.filename, 'r') freq = {} locale.setlocale(locale.LC_ALL, options.inputlocale) line = input.readline() total = 0 #while line != "": # count, word = string.split(line, maxsplit=1) # for c in word:
dest="triple", help="Triple to search") parser.add_option("--block", "-b", action="store", default=None, dest="block", help="CFEPS Block to retrieve, (eg: 03BQ02)") parser.add_option("--pointing", "-p", action="store", default=None, dest="pointing", help="CFEPS POINTING to retrieve, (eg: 03BQ02)") (opt, file_ids) = parser.parse_args() import os, shutil import MOPdbaccess, MOPfits mysql = MOPdbaccess.connect('cfeps', 'cfhls', dbSystem='MYSQL') if not opt.triple and not opt.block: parser.print_help() sys.exit("\n\n You must specify either a triple or block\n") cfeps = mysql.cursor() if not opt.triple: sql = """SELECT DISTINCT(t.id) FROM triples t JOIN checkup d ON t.id=d.triple
action="store", type="int", default=0, dest="triple", help="Triple to search") parser.add_option("--block","-b", action="store", dest="block", help="CFEPS block to search") parser.add_option("--ccd","-c", action="store", default=-1, type="int", dest="ccd", help="Provide feedback on what I'm doing") (opt, file_ids)=parser.parse_args() import os, shutil if os.getenv('_CONDOR_SCRATCH_DIR') != None: os.chdir(os.getenv('_CONDOR_SCRATCH_DIR')) import MOPdbaccess mysql=MOPdbaccess.connect('cfeps','cfhls',dbSystem='MYSQL') cfeps=mysql.cursor() if not opt.triple: sql="""SELECT DISTINCT(t.id) FROM triples t JOIN discovery d ON t.id=d.triple JOIN bucket.association a ON t.pointing=a.pointing JOIN bucket.blocks b ON a.expnum=b.expnum WHERE b.qname LIKE '%s'""" % ( opt.block, )
if __name__ =='__main__': parser=OptionParser() parser.add_option('--image',action='store', help='image to compute centroids of stars') parser.add_option('--input',action='store', help='coo file [in format approriate for iraf.digiphot.daophot.phot coo] ') parser.add_option('--output',action='store', help='file with output star coordinates [X,Y,MAG,MERR,ID]') parser.add_option('--aperture',action='store', help='phot aperture to use', default=15) (opt, args)=parser.parse_args() if not (opt.image and opt.input and opt.output ): parser.print_help() sys.exit(0) def centroid(image,input,output): """Compute the centroids and magnitudes of a bunch sources detected on CFHT-MEGAPRIME images""" print "Centroiding stars" print "IMAGE: %s " % (opt.image,) print "COORDINATES: %s " % ( opt.input,) print "RESULTS: %s" % ( opt.output, ) from pyraf import iraf from pyraf.irafpar import IrafParList import pyfits
from myTaskError import TaskError if __name__=='__main__': ### Must be running as a script import optik, sys from optik import OptionParser parser=OptionParser() parser.add_option("--verbose","-v", action="store_true", dest="verbose", help="Provide feedback on what I'm doing") (opt, dirs)=parser.parse_args() import os, shutil, sys, string import MOPdbaccess mysql=MOPdbaccess.connect('cfeps','cfhls',dbSystem='MYSQL') cfeps=mysql.cursor() foreach dir in dirs: [triple.ccd] = dirs.split('.') sql="""SELECT distinct(t.id),m.ccd FROM triples t JOIN %s d ON t.id=d.triple JOIN block_pointing b ON b.pointing=t.pointing
hdu.data=hdu.data + hdu._bzero del hdu.header['BSCALE'] del hdu.header['BZERO'] hdu.header['BITPIX']=pyfits._ImageBaseHDU.ImgCode[hdu.data.type()] temp.append(hdu) return temp if __name__ == '__main__': ### Import some standard python. import optik,sys from optik import OptionParser ### parse the commandline arguements parser = OptionParser() parser.add_option("-o","--outfile", action="store", type="string", dest="outfile", help="Name of output MEF file", metavar="MEF") parser.add_option("-q","--quiet", action="store_false", dest="verbose", default=1, help="run makepsf/iraf quietly?") ### the left over arguments are assumed to be fits images. (opt,infiles)=parser.parse_args() sys.exit(stack(opt.outfile,infiles,opt.verbose))
temp.append(hdu) return temp if __name__ == '__main__': ### Import some standard python. import optik, sys from optik import OptionParser ### parse the commandline arguements parser = OptionParser() parser.add_option("-o", "--outfile", action="store", type="string", dest="outfile", help="Name of output MEF file", metavar="MEF") parser.add_option("-q", "--quiet", action="store_false", dest="verbose", default=1, help="run makepsf/iraf quietly?") ### the left over arguments are assumed to be fits images. (opt, infiles) = parser.parse_args() sys.exit(stack(opt.outfile, infiles, opt.verbose))
# Or address unitary registers # Register id parser.add_option("-r", "--regid", type="int", dest="regId", help="Register ID") # Register value parser.add_option("-v", "--value", type="string", dest="value", help="Register value)") (options, args) = parser.parse_args() # Dispatch commands if options.version == True: print __version__ raise SystemExit try: # Start SWAP manager tool manager = SwapManager(options.sniff, options.monitor) # Configuration commands if options.config == True: listCfgRegs = None setCustomReg = False # Device passed as argument?
def main(): usage = "usage: %prog [options] sysName [ctp_id | rtpFileName=Run.rtp] [buildMode] [buildOpts]" dataSource = {"db2": 0, "xml": 1, "ff": 2} parser = OptionParser(usage) rtpName = 'Run.rtp' # sys_class option: parser.add_option("-c", "--sys_class", type="string", action="store", dest="sys_class", default="testing", help="(scratch | [testing] | production)") # source options: parser.add_option("-d", "--from-database", action="store_const", dest="source", const=dataSource["db2"], default=dataSource["db2"], help="look for system in database") parser.add_option("-x", "--from-xml", action="store_const", dest="source", const=dataSource["xml"], help="look for system in xml file") parser.add_option("-p", "--from-package", action="store_const", dest="source", const=dataSource["ff"], help="look for system in force field files") # force field identifier option (only used if source=package) parser.add_option("-f", "--forcefield", action="store", dest="forceField", default="unknown", help="define force field of system") # system id option (only used if source=db2) parser.add_option("-i", "--system-id", action="store", dest="sysId", default="-1", help="identify system in db2") # verbose/quiet options parser.add_option("-v", "--verbose", action="store_true", dest="verbose", default="store_false", help="sets output to be verbose") parser.add_option("-q", "--quiet", action="store_false", dest="verbose", help="sets output to be quiet") (options, args) = parser.parse_args() buildMode = "Opt" buildOpts = '' if len(args) < 1: parser.error("incorrect number of args") sysName = args[0] if len(args) == 2: rtpName = args[1] if len(args) == 3: buildMode = args[2] if len(args) == 4: buildOpts = args[3] if options.verbose: print("sys_class:", options.sys_class) print("source:", options.source) print("rtp file:", rtpName) print("force field:", options.forceField) # set xml creation object based on force field setting creator = None if options.forceField == 'charmm': creator = BuildUtils.createXmlForCharmm() elif options.forceField == 'oplsaa': creator = BuildUtils.createXmlForOplsaa() else: create = BuildUtils.createXml() sysId = options.sysId ctpId = -1 if options.source == dataSource["ff"]: if options.verbose: print("calling creator.fromSource()") creator.fromSource(sysName, None, options.verbose) if options.source == dataSource["xml"] or \ options.source == dataSource["ff"]: if options.verbose: print("calling BuildUtils.xml2db2(), BuildUtils.rtp2db2()") sysId=BuildUtils.xml2db2(sysName + '.' + options.forceField, \ options.verbose) if options.verbose: print("sysId =", str(sysId)) if rtpName.isdigit(): ctpId = rtpName else: ctpId = BuildUtils.rtp2db2(rtpName, options.verbose) if options.source == dataSource["xml"] or \ options.source == dataSource["ff"] or \ options.source == dataSource["db2"]: if options.verbose: print("calling BuildUtils.db2cpp(), BuildUtils.cpp2exe()") BuildUtils.db2cpp( str(sysName) + '.' + str(options.forceField), sysId, ctpId, options.verbose) BuildUtils.cpp2exe( str(sysName) + '.' + str(options.forceField), buildMode, buildOpts, options.verbose) return (0)
parser.add_option('-c','--casefolding', action='store_true', dest='extra_splitter_casefolding', help='enable casefolding', default=1) parser.add_option('-a','--autoexpand', action='store_true', dest='extra_autoexpand', help='auto expand', default=0) parser.add_option('-w','--stopwords', action='store',type='string', dest='extra_use_stopwords', help='name of stopword file') parser.add_option('-P','--parser', action='store', type='string', dest='extra_use_parser',default='PyQueryParser', help='parser name') parser.add_option('-X','--prof', action='store_true', dest='prof',default=0, help='profiling on/off') options,args = parser.parse_args() class extra: def __init__(self): self._keys = list() def set(self, k, v): setattr(self, k, v) self._keys.append(k) def keys(self): return self._keys E = extra() for k in dir(options): if k.startswith('extra_'):
def main(): usage = "usage: %prog [options] epsilon sigma/Rmin" parser = OptionParser(usage) parser.add_option("-s", "--sigma", action="store_true", dest="sigma", default="store_false", help="sets input type of sigma/Rmin to sigma") parser.add_option("-r", "--rmin", action="store_false", dest="sigma", default="store_false", help="sets input type of sigma/Rmin to Rmin") parser.add_option("-n", "--number", action="store", dest="count", default=4, help="particle count") parser.add_option("-c", "--chemcomp", action="store", dest="chemcomp", default="AR", help="chemical component") parser.add_option("-e", "--element", action="store", dest="element", default="Ar", help="element symbol") parser.add_option("-t", "--atomtag", action="store", dest="atomtag", default="AR_", help="atom tag") parser.add_option("-m", "--mass", action="store", dest="mass", default="39.948", help="mass (amu)") parser.add_option("-d", "--moleculename", action="store", dest="moleculename", default="Argon", help="molecule name") parser.add_option("-k", "--kelvin", action="store_true", dest="kelvin", default="store_false", help="energy units in kelvin") (options, args) = parser.parse_args() if len(args) < 2: parser.error("incorrect number of args") if int(options.count) <= 0: parser.error("Illegal value for particle number") epsilon = args[0] if options.kelvin: epsilon = epsilon + "*SciConst::KBoltzmann_IU" rMinValue = args[1] if options.sigma: rMinValue = rMinValue + "*SciConst::SixthRootOfTwo" outputXmlHeaderWithDtd() print("<ffparams>") outputHeaderParameterList() outputMoleculeName(options.moleculename, "SALT") outputChemicalComponentInstanceList(int(options.count), options.chemcomp) outputMoleculeInstanceList(int(options.count)) outputSiteList(int(options.count), options.mass, options.atomtag, epsilon, rMinValue, options.element) print("</ffparams>")
help='image to compute centroids of stars') parser.add_option( '--input', action='store', help= 'coo file [in format approriate for iraf.digiphot.daophot.phot coo] ') parser.add_option( '--output', action='store', help='file with output star coordinates [X,Y,MAG,MERR,ID]') parser.add_option('--aperture', action='store', help='phot aperture to use', default=15) (opt, args) = parser.parse_args() if not (opt.image and opt.input and opt.output): parser.print_help() sys.exit(0) def centroid(image, input, output): """Compute the centroids and magnitudes of a bunch sources detected on CFHT-MEGAPRIME images""" print "Centroiding stars" print "IMAGE: %s " % (opt.image, ) print "COORDINATES: %s " % (opt.input, ) print "RESULTS: %s" % (opt.output, )