def main():
warnings.simplefilter('once')
if len(sys.argv) < 3:
print 'mergy.py [options] <mwk> <nev/plx>'
print 'Aligns and merges mwk and nev/plx files.'
print
print 'Options:'
print ' --nowav - do not include waveform data (recommended)'
print ' --filter_inf=<.inf prefix> - reject any spikes not in the inf files'
print ' --cluster=<.inf/.clu prefix> - apply clustering information'
print ' --cluster_all=<.clu prefix 1,.clu prefix 2,...>'
print ' - use other clustering info (in this superset)'
return
args, opts = parse_opts_adapter(sys.argv[1:], 2)
fn_mwk, fn_nev = args[:2]
# -- parse options
if 'nowav' in opts:
print 'merge: no waveform processing'
proc_wav = False
else:
print 'merge: including waveform data'
proc_wav = True
callback_reject = None
if 'filter_inf' in opts:
inf_prefix = opts['filter_inf']
print 'merge: spike rejection based on', inf_prefix
reject_inf.prefix = inf_prefix
callback_reject = reject_inf
callback_cluster = None
if 'cluster' in opts:
prefixes = opts['cluster'].split(CLU_SEP)
if len(prefixes) != 2:
prefix = prefixes[0]
print 'merge: clustering based on', prefix
cluster.prefix_inf = prefix
cluster.prefix_clu = prefix
else:
print 'merge: clustering based on', prefixes
cluster.prefix_inf = prefixes[0]
cluster.prefix_clu = prefixes[1]
if 'cluster_all' in opts:
clu_all = prep_files(opts['cluster_all'], sep=CLU_SEP, extchk=False)
print 'merge: using other info', clu_all
cluster.prefix_clu_all = clu_all
callback_cluster = cluster
code_sent = 'wordout_var'
if 'code_sent' in opts:
code_sent = opts['code_sent']
print 'merge: code_sent =', code_sent
code_recv = 'wordSent'
if 'code_recv' in opts:
code_recv = opts['code_recv']
print 'merge: code_recv =', code_recv
adj_reject = None
amp_reject = None
if 'adj_reject' in opts:
adj_reject = float(opts['adj_reject'])
amp_reject = set_new_threshold_rng
print 'merge: amplitude rejection multiplier =', adj_reject
_force_timetransf = None
if 'force_timetransf' in opts:
a, b, delay = [float(e) for e in opts['force_timetransf'].split(',')]
_force_timetransf = {}
_force_timetransf['C'] = [a, b]
_force_timetransf['delay'] = delay
print 'merge: time transformation =', _force_timetransf
# -- execute
m = Merge(fn_mwk, fn_nev)
if m.merge(proc_wav=proc_wav, code_sent=code_sent, code_recv=code_recv, \
adj_reject=adj_reject, amp_reject=amp_reject, \
callback_reject=callback_reject, callback_cluster=callback_cluster, \
_force_timetransf=_force_timetransf):
print 'merge: merged successfully.'
def main():
if len(sys.argv) < 3:
print 'collect_PS_firing.py [options] <mwk> <output> ' \
'[override delay in us] [number of electrodes]'
print 'Collects spike timing around visual stimuli'
print
print 'Options:'
print ' --wav=<.nev file name> - collects waveform for spike' \
' sorting with the .nev file.'
print ' --extinfo - collects extra stimuli info' \
'rmation in addition to the names'
print ' --c_success=<code name> - code name for "success" signal'
print ' --proc_cluster - process extra spike sorting info' \
'rmation'
print ' --max_cluster=# - maximum number of clusters per' \
' channel'
return
args, opts = parse_opts_adapter(sys.argv[1:], 4)
fn_mwk = args[0]
fn_out = args[1]
fn_nev = None
# -- parsing extra arguments (mainly for backward compatibility)
if len(args) >= 3:
override_delay_us = long(args[2])
if override_delay_us < 0:
override_delay_us = None
print '* Delay override:', override_delay_us
else:
override_delay_us = None
if len(args) >= 4:
override_elecs = range(1, int(args[3]) + 1)
print '* Active electrodes override: [%d..%d]' % \
(min(override_elecs), max(override_elecs))
else:
override_elecs = DEFAULT_ELECS
# -- handle "opts"
mode = 'firrate'
if 'wav' in opts:
mode = 'wav'
fn_nev = opts['wav']
print '* Collecting waveforms for later spike sorting with', fn_nev
extinfo = False
if 'extinfo' in opts:
extinfo = True
print '* Collecting extra information of the stimuli'
if 'c_success' in opts:
c_success = opts['c_success']
print '* c_success:', c_success
else:
c_success = C_SUCCESS
if 't_success' in opts:
t_success = int(opts['t_success'])
print '* t_success:', t_success
else:
t_success = T_SUCCESS
proc_cluster = PROC_CLUSTER
if 'proc_cluster' in opts or 'proc_spksorting' in opts:
print '* Collecting spike sorting information'
proc_cluster = True
max_clus = MAX_CLUS
if 'max_cluster' in opts:
max_clus = int(opts['max_cluster'])
print '* Maximum number of clusters per channel:', max_clus
t_start0 = T_START
if 't_start' in opts:
t_start0 = int(opts['t_start'])
print '* t_start =', t_start0
t_stop0 = T_STOP
if 't_stop' in opts:
t_stop0 = int(opts['t_stop'])
print '* t_stop =', t_stop0
reject_sloppy = REJECT_SLOPPY
if 'reject_sloppy' in opts:
reject_sloppy = True
print '* Rejecting sloppy stimuli'
exclude_img = None
if 'exclude_img' in opts:
exclude_img = opts['exclude_img'].split(',')
print '* Exclude unwanted images:', exclude_img
movie_begin_fname = None
if 'movie_begin_fname' in opts:
movie_begin_fname = opts['movie_begin_fname']
print '* movie_begin_fname:', movie_begin_fname
ign_unregistered = False
if 'ign_unregistered' in opts:
ign_unregistered = True
print '* Ignore unregistered keys'
ch_shift = None
if 'ch_shift' in opts:
ch_shift = opts['ch_shift']
print '* Shifting based on this rule:', ch_shift
# -- go go go
kwargs = {'override_delay_us': override_delay_us,
'override_elecs': override_elecs,
'extinfo': extinfo, 'c_success': c_success,
't_success_lim': t_success,
'proc_cluster': proc_cluster, 'max_clus': max_clus,
't_start0': t_start0, 't_stop0': t_stop0,
'reject_sloppy': reject_sloppy,
'exclude_img': exclude_img,
'movie_begin_fname': movie_begin_fname,
'ign_unregistered': ign_unregistered,
'ch_shift': CH_SHIFT[ch_shift]
}
if mode == 'firrate':
get_firrate(fn_mwk, fn_out, **kwargs)
elif mode == 'wav':
get_waveform(fn_mwk, fn_nev, fn_out, **kwargs)
else:
raise ValueError('Invalid mode')
print 'Done. '
