#maglist.magnet_lists['VV'][vvswap][0]=buildlist[line,5] maglist.swap('VV',maglist.magnet_lists['VV'].index([buildlist[line,5],1,0]) , vvswap) maglist.magnet_lists['VV'][vvswap][1]=int(buildlist[line,4]) vvswap+=1 outfile = (os.path.split(filename)[1]+'.h5') #fg.output_fields(outfile, options.id_filename, options.id_template, options.magnets_filename, maglist) fp = open(os.path.split(filename)[1]+'.genome','w') pickle.dump(maglist, fp) fp.close() if options.readable: for filename in args[0::]: print("Making file %s human readable." % (filename)) human_output(options.id_filename, filename) if options.analysis: for filename in args[0::]: print("Processing file %s" % (filename)) # load the genome maglists = pickle.load( open( filename, "rb" ) ) outfile = (os.path.split(filename)[1]+'.h5') fg.output_fields(outfile, options.id_filename, options.id_template, options.magnets_filename, maglists)
mag_num=int(maglists.magnet_lists['VV'][vv][0]) mag_flip=maglists.magnet_lists['VV'][vv][1] vv+=1 if mag_type==2: mag_num=int(maglists.magnet_lists['HH'][hh][0]) mag_flip=maglists.magnet_lists['HH'][hh][1] hh+=1 if mag_type==3: mag_num=int(maglists.magnet_lists['VE'][ve][0]) mag_flip=maglists.magnet_lists['VE'][ve][1] ve+=1 if mag_type==4: mag_num=int(maglists.magnet_lists['HE'][he][0]) mag_flip=maglists.magnet_lists['HE'][he][1] he+=1 line= ("%5i %4i %4i %4i %4i %4i\n"%(b+1,a+1,mag_type,info['beams'][b]['mags'][a]['direction'][0],mag_flip, mag_num)) f3.write(line) a+=1 f3.write("\n") f3.close() fg.output_fields('/home/gdy32713/DAWN_stable/optid/Opt-ID/IDSort/src/v2/4.62409644e-07_000_00bc026cfae7.h5', '/home/gdy32713/DAWN_stable/optid/Opt-ID/IDSort/src/v2/2015test.json', '/home/gdy32713/DAWN_stable/optid/Opt-ID/IDSort/src/v2/2015test.h5', '/home/gdy32713/DAWN_stable/optid/Opt-ID/IDSort/src/v2/magnets.mag', maglists)
(options, args) = parser.parse_args() print("Loading magnets") mags = magnets.Magnets() mags.load(options.magnets_filename) if options.build: for filename in args[1::]: print("Processing file %s" % (filename)) # load the genome genome = ID_BCell() genome.load(filename) outfile = os.path.join(args[0], os.path.split(filename)[1] + '.h5') fg.output_fields(outfile, options.id_filename, options.lookup_filename, options.magnets_filename, genome.genome) sys.exit(0) if options.setup > 0: print("Running setup") for i in range(options.setup): # create a fresh maglist maglist = magnets.MagLists(mags) maglist.shuffle_all() genome = ID_BCell(options.id_filename, options.lookup_filename, options.magnets_filename) genome.create(maglist) genome.save(args[0]) for filename in args[1::]:
hh += 1 if mag_type == 3: mag_num = int(maglists.magnet_lists['VE'][ve][0]) mag_flip = maglists.magnet_lists['VE'][ve][1] ve += 1 if mag_type == 4: mag_num = int(maglists.magnet_lists['HE'][he][0]) mag_flip = maglists.magnet_lists['HE'][he][1] he += 1 line = ("%5i %4i %4i %4i %4i %4i\n" % (b + 1, a + 1, mag_type, info['beams'][b]['mags'][a]['direction'][0], mag_flip, mag_num)) f3.write(line) a += 1 f3.write("\n") f3.close() fg.output_fields( '/home/gdy32713/DAWN_stable/optid/Opt-ID/IDSort/src/v2/4.62409644e-07_000_00bc026cfae7.h5', '/home/gdy32713/DAWN_stable/optid/Opt-ID/IDSort/src/v2/2015test.json', '/home/gdy32713/DAWN_stable/optid/Opt-ID/IDSort/src/v2/2015test.h5', '/home/gdy32713/DAWN_stable/optid/Opt-ID/IDSort/src/v2/magnets.mag', maglists)
(options, args) = parser.parse_args() print("Loading magnets") mags = magnets.Magnets() mags.load(options.magnets_filename) if options.build: for filename in args[1::]: print("Processing file %s" % (filename)) # load the genome genome = ID_BCell() genome.load(filename) outfile = os.path.join(args[0], os.path.split(filename)[1]+'.h5') fg.output_fields(outfile, options.id_filename, options.lookup_filename, options.magnets_filename, genome.genome); sys.exit(0) if options.setup > 0: print("Running setup") for i in range(options.setup): # create a fresh maglist maglist = magnets.MagLists(mags) maglist.shuffle_all() genome = ID_BCell(options.id_filename, options.lookup_filename, options.magnets_filename) genome.create(maglist) genome.save(args[0]) for filename in args[1::]: print("Processing file %s" % (filename))
def process(options, args): if options.create_genome: for filename in args[0::]: print("Turning file %s from Human Readable to Genome" % (filename)) f2 = open(filename, 'r') buildlist = np.genfromtxt(filename, dtype=str) f2.close() mags = magnets.Magnets() mags.load(options.magnets_filename) maglist = magnets.MagLists(mags) heswap = 0 veswap = 0 hhswap = 0 vvswap = 0 for line in range(buildlist.shape[0]): if int(buildlist[line, 2]) == 4: #maglist.magnet_lists['HE'][heswap][0]=buildlist[line,5] maglist.swap( 'HE', maglist.magnet_lists['HE'].index( [buildlist[line, 5], 1, 0]), heswap) maglist.magnet_lists['HE'][heswap][1] = int(buildlist[line, 4]) heswap += 1 elif int(buildlist[line, 2]) == 3: #maglist.magnet_lists['VE'][veswap][0]=buildlist[line,5] maglist.swap( 'VE', maglist.magnet_lists['VE'].index( [buildlist[line, 5], 1, 0]), veswap) maglist.magnet_lists['VE'][veswap][1] = int(buildlist[line, 4]) veswap += 1 elif int(buildlist[line, 2]) == 2: #maglist.magnet_lists['HH'][hhswap][0]=buildlist[line,5] maglist.swap( 'HH', maglist.magnet_lists['HH'].index( [buildlist[line, 5], 1, 0]), hhswap) maglist.magnet_lists['HH'][hhswap][1] = int(buildlist[line, 4]) hhswap += 1 elif int(buildlist[line, 2]) == 1: #maglist.magnet_lists['VV'][vvswap][0]=buildlist[line,5] maglist.swap( 'VV', maglist.magnet_lists['VV'].index( [buildlist[line, 5], 1, 0]), vvswap) maglist.magnet_lists['VV'][vvswap][1] = int(buildlist[line, 4]) vvswap += 1 outfile = (os.path.split(filename)[1] + '.h5') #fg.output_fields(outfile, options.id_filename, options.id_template, options.magnets_filename, maglist) fp = open(os.path.split(filename)[1] + '.genome', 'w') pickle.dump(maglist, fp) fp.close() if options.readable: for filename in args[0::]: print("Making file %s human readable." % (filename)) human_output(options.id_filename, filename) if options.analysis: for filename in args[0::]: print("Processing file %s" % (filename)) # load the genome maglists = pickle.load(open(filename, "rb")) outfile = (os.path.split(filename)[1] + '.h5') fg.output_fields(outfile, options.id_filename, options.id_template, options.magnets_filename, maglists)