#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)