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 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
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))
print cmd os.system(cmd) os.system("mpcIngest.pl *.MPC") os.system("cp *.MPC /home/cadc/kavelaar/results/05AQ06B") return (0) 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") parser.add_option("--triple", "-t", 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",
if os.access(astrom, os.R_OK): return (1) else: return (0) 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") parser.add_option("--triple", "-t", action="store", type="int", dest="triple", help="Triple to search") parser.add_option( "--epoch", "-e", action="store", default="discovery", help="Epoch to search. Choose from [discovery|checkup|recovery]") parser.add_option("--block",
def _quit(): """ Quit application """ print __appname__ + " terminated" # Stop SWAP manager manager.stop() # Exit application raise SystemExit if __name__ == "__main__": """ Command-line SWAP Device Management Tool """ print __appname__ parser = OptionParser() # Print version parser.add_option("--version", action="store_true", default="False", dest="version", help="Print version number") # Monitor network activity parser.add_option("--monitor", action="store_true", default="False", dest="monitor", help="Monitor SWAP network activity") # Sniff SWAP network parser.add_option("--sniff", action="store_true", default="False", dest="sniff", help="Sniff SWAP network") # Configure device parser.add_option("-c", "--config", action="store_true", default="False", dest="config", help="Configure SWAP device") parser.add_option("-d", "--device", type="string", dest="device", help="Product name") # Address of the target device parser.add_option("-a", "--address", type="int", dest="devAddr", help="Address of the target device (1-255). Ommit for sync mode")
#* #* Modification History: #* #**** C A N A D I A N A S T R O N O M Y D A T A C E N T R E ***** # Run J-M.'s and Matt's object finding systems... then intersect the # results. 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") parser.add_option("--triple", "-t", action="store", type="int", 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",
This script is designed to work with MEGAPRIME images from CFHT""" author="JJ Kavelaars" version=1.0 import sys import optik from optik import OptionParser 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"""
#* #* Modification History: #* #**** C A N A D I A N A S T R O N O M Y D A T A C E N T R E ***** # Run J-M.'s and Matt's object finding systems... then intersect the # results. 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") parser.add_option("--triple","-t", action="store", type="int", 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",
print "Result: %d matches" % len(resultset) lst = list(resultset.items()) lst.sort(lambda x,y : -cmp(x[1],y[1])) for docid,score in lst: print "%-2d %s %d" % (docid, docs[docid].getId(), score) except: traceback.print_exc() if __name__== '__main__': usage = "Usage: %prog [options] " parser = OptionParser(usage=usage) parser.add_option('-d','--directory', action='store',type='string', dest='directory',help='directory to be search for input files') parser.add_option('-l','--left', action='store_true', dest='extra_truncate_left', help='enable left truncation',default=0) parser.add_option('-n','--neardistance', action='store',type='int', dest='extra_near_distance', help='max. distance between words for near search',default=5) parser.add_option('-C','--converter', action='store',type='int', dest='extra_use_converters', help='use document converters',default=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',
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>")
This script is designed to work with MEGAPRIME images from CFHT""" author = "JJ Kavelaars" version = 1.0 import sys import optik from optik import OptionParser 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)
__Version__ = "$Revision: 1.1 $" __Id__ = "$Id: ctio_mkpsf.py,v 1.1 2005/01/16 04:56:55 observe Exp $" if __name__ == '__main__': ### Import some standard python. import os, sys, string, tempfile, shutil import optik from optik import OptionParser ### parse the commandline arguements parser = OptionParser() parser.add_option("-f", "--file", action="store", type="string", dest="filename", help="create PSF for FILE", metavar="FILE") parser.add_option("-e", "--expnum", action="store", type="string", dest="expnum", help="exposure to get from AD", metavar="EXPNUM") parser.add_option( "-u", "--update", action="store_true", dest="update",
#* #**** C A N A D I A N A S T R O N O M Y D A T A C E N T R E ***** #************************************************************************ #-*/ """Update the WCS of a megaprime image by taking an input star list """ __Version__ = "$Revision 0.1$" import optik, sys from optik import OptionParser if __name__=='__main__': parser=OptionParser() parser.add_option("--image", action="store", help="Image to modified WCS of", dest="image") parser.add_option("--usno", action="store", help="USNO catalog stars", dest="usno") parser.add_option("--stars", action="store", help="x,y location of stars in input image") (opt, args) = parser.parse_args() cmd = "imwcs -p is -h 200 -d "+opt.stars+" -c "+opt.usno+" -w "+opt.image
#* #**** C A N A D I A N A S T R O N O M Y D A T A C E N T R E ***** # Run J-M.'s and Matt's object finding systems... then intersect the # results. """Given a list of directories that have the format triple.ccd look for *.real.astrom and *.NONE.astrom file and update the 'status' line in the process table of the cfeps database""" 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('.')
#!/usr/bin/python import FASTA import random import sys from optik import OptionParser usage = "usage: %prog [options] < faInput > faOutput" parser = OptionParser(usage) parser.add_option("-r", "--rate", type="float", dest="rate", help="probability that a given base mutates", default=0.1) parser.add_option("-s", "--seed", type="int", dest="seed", help="seed for initializing RNG", default=None) (options, args) = parser.parse_args() if len(args) != 0: parser.error("incorrect number of arguments") mutations = {'A': ('C', 'G', 'T'), 'C': ('A', 'G', 'T'), 'G': ('A', 'C', 'T'), 'T': ('A', 'C', 'G')} def mutateCharacter(char, rate): if random.random() < rate: return random.choice(mutations[char]) else: return char def mutateSequence(seq, rate):
### set the version flag for this program __Version__ = "$Revision: 1.1 $" __Id__ = "$Id: ctio_mkpsf.py,v 1.1 2005/01/16 04:56:55 observe Exp $" if __name__ == "__main__": ### Import some standard python. import os, sys, string, tempfile, shutil import optik from optik import OptionParser ### parse the commandline arguements parser = OptionParser() parser.add_option( "-f", "--file", action="store", type="string", dest="filename", help="create PSF for FILE", metavar="FILE" ) parser.add_option( "-e", "--expnum", action="store", type="string", dest="expnum", help="exposure to get from AD", metavar="EXPNUM" ) parser.add_option( "-u", "--update", action="store_true", dest="update", default=0, help="Update AD with new file? (before possible removal)", ) parser.add_option( "-r", "--remove", action="store_true", dest="remove", default=0, help="Remove file when done updating?" )
print os.access(astrom,os.R_OK) if os.access(astrom,os.R_OK): print cmd os.system(cmd) os.system("mpcIngest.pl *.MPC") os.system("cp *.MPC /home/cadc/kavelaar/results/05AQ06B") return(0) 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") parser.add_option("--triple","-t", 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",
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)
print __appname__ + " terminated" # Stop SWAP manager manager.stop() # Exit application raise SystemExit if __name__ == "__main__": """ Command-line SWAP Device Management Tool """ print __appname__ parser = OptionParser() # Print version parser.add_option("--version", action="store_true", default="False", dest="version", help="Print version number") # Monitor network activity parser.add_option("--monitor", action="store_true", default="False", dest="monitor", help="Monitor SWAP network activity") # Sniff SWAP network parser.add_option("--sniff", action="store_true", default="False", dest="sniff", help="Sniff SWAP network") # Configure device
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))
#!/usr/bin/python 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)
astrom=filenames[0]+".measure3.cands.astrom" if os.access(astrom,os.R_OK): return(1) else: return(0) 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") parser.add_option("--triple","-t", action="store", type="int", dest="triple", help="Triple to search") parser.add_option("--epoch","-e", action="store", default="discovery", help="Epoch to search. Choose from [discovery|checkup|recovery]" ) parser.add_option("--block","-b", action="store", dest="block", help="CFEPS block to search")