def main():
if len(sys.argv) < 3:
print 'plot_PSTH.py <out prefix> <in1.psf.pk> [in2.psf.pk] ...'
print
print 'Options:'
print ' --n_bins=# Number of 1-ms bins'
return
# -- parse options and arguments
args, opts = parse_opts2(sys.argv[1:])
of = args[0]
files = args[1:]
print 'OF =', of
print 'FILES =', files
n_bins = DEF_NBINS
if 'n_bins' in opts:
n_bins = int(opts['n_bins'])
print ' * n_bins =', n_bins
db = {}
load_db(files, db, n_bins=n_bins)
# -- plot
init()
fpic = of + '.pdf'
flog = of + '.bstim.log'
flog2 = of + '.snr.log'
pp = PdfPages(fpic)
plot_all(db, pp, log=flog, log2=flog2)
pp.close()
print 'Done.'
def main():
if len(sys.argv) < 3:
print USAGE
return
args, opts = parse_opts2(sys.argv[1:])
mode = args[0]
# -- parsing extra arguments (mainly for backward compatibility)
if mode == 'feature':
get_features(args[1], args[2], opts)
elif mode == 'cluster':
cluster(args[1], args[2], opts)
elif mode == 'collate':
collate(args[1], args[2], opts)
else:
raise ValueError('Invalid mode')
print 'Done. '
def main():
if len(sys.argv) < 3:
print 'cmp_impedance.py [opts] <impedance log 1a.txt> <impedance log' \
'1b.txt> [<log 2a.txt> <log 2b.txt>] ...'
print 'cmp_impedance.py: compare pairs of impedance log files.'
print 'Options:'
print ' --plot=<filename.pdf>'
return
# -- parse options and arguments
args, opts = parse_opts2(sys.argv[1:])
plot = None
if 'plot' in opts:
plot = opts['plot']
print '* Plotting into', plot
# -- do the work
files = args
cmp_impedance_all(files, plot=plot)
def main():
if len(sys.argv) < 3:
print USAGE
return
args, opts = parse_opts2(sys.argv[1:])
of = args[0]
files = args[1:]
print 'Output prefix:', of
# -- process options
if 'flist' in opts:
flistpx = ''
if 'flistpx' in opts:
flistpx = opts['flistpx']
for f in open(opts['flist']).readlines():
fp = f.strip()
if flistpx != '':
fp = os.path.join(flistpx, fp)
files.append(fp)
print 'Using the followings:'
for f in files:
print ' ', f
multi = False
fkey = FKEY
if 'multi' in opts:
multi = True
if 'key' in opts:
fkey = opts['key'].split(',')
print 'Enable multiple array data processing'
print 'Multiple array data key:', fkey
noerr = True
for f in files:
found = False
for i_k, k in enumerate(fkey):
if k in f:
found = True
break
if not found:
noerr = False
print '** Not matching file name:', f
if not noerr:
print '** Error occured!'
return
exclude_img = None
if 'exclude_img' in opts:
exclude_img = opts['exclude_img'].split(',')
print 'Exclude unwanted images:', exclude_img
n_maxtrial = N_MAXTRIAL
if 'n_maxtrial' in opts:
n_maxtrial = int(opts['n_maxtrial'])
print 'Setting n_maxtrial:', n_maxtrial
n_bins = N_BINS
if 'n_bins' in opts:
n_bins = int(opts['n_bins'])
print 'Setting n_bins:', n_bins
assert all([os.path.exists(f) for f in files])
# -- main loop
try:
signal.signal(signal.SIGINT, signal_handler)
signal.signal(signal.SIGTERM, signal_handler)
convert(files, of, multi=multi, fkey=fkey, \
exclude_img=exclude_img, n_maxtrial=n_maxtrial, n_bins=n_bins)
finally:
print 'Cleaning up...'
cleanup()
print 'Done.'
def main(rseed=RSEED):
if len(sys.argv) < 2:
print 'Prep Mode:'
print 'summarizedp_cv.py prep <d\'-CV output.pk> <combined frate.pk>'
print 'Note: input pickle files are made by combine_firrate_data.py'
print
print 'Result Formatting Mode:'
print 'summarizedp_cv.py res [options] <d\'-CV output A.pk> <d\'-CV output M.pk> <d\'-CV output P.pk>'
print 'Options:'
print ' --prndp Print d\' values'
print ' --doplot Plot PSTHs of blanks for each channel'
print ' --px=prefix Prefix of output files'
print ' --bad=ch1,ch2,.. Comma separated list of 1-based bad channels'
print ' --ng=ch1,ch2,... Comma separated list of 1-based not-so-good channels'
print ' --topn=# Pick top # channels'
return
# parse options and arguments
args, opts = parse_opts2(sys.argv[1:])
mode = args[0]
np.random.seed(rseed)
# prepare d'-cv computation
if mode == 'prep':
fo = args[1]
fi = args[2]
print '* Output d\'-CV result:', fo
db = pk.load(open(fi))
res = dp_cv(db)
pk.dump(res, open(fo, 'wb'))
# or give the results...
elif mode == 'res':
doplot, prndp, topn, px = False, False, TOPN, PREF
bad = []
ng = []
if 'doplot' in opts:
from matplotlib import rc, use
use('pdf')
import pylab as pl
init()
doplot = True
print '* DOPLOT'
if 'prndp' in opts:
prndp = True
print '* PRNDP'
if 'topn' in opts:
topn = int(opts['topn'])
print '* TOPN =', topn
if 'bad' in opts:
bad = [int(b) for b in opts['bad'].split(',')]
print '* BAD =', bad
if 'ng' in opts:
ng = [int(b) for b in opts['ng'].split(',')]
print '* NG =', ng
if 'px' in opts:
px = opts['px']
print '* PX =', px
files = args[1:]
db = load_all(files, skipchk=True)
pick_top(db, topn, bad=bad, ng=ng, prndp=prndp, px=px)
if doplot:
ipage = plot_all(db, px=px)
pl.savefig(px +'_p%d.pdf' % (ipage))
print 'Done.'
#pl.show()
else:
print 'Unrecognized mode. Aborting.'
