def test1():
bl1 = generate_block_for_sorting(
nb_unit=2,
duration=3. * pq.s,
nb_segment=2,
)
oebl1 = OEBase.from_neo(bl1, dbinfo.mapped_classes, cascade=True)
oebl1.save()
bl2 = generate_block_for_sorting(
nb_unit=3,
duration=2.5 * pq.s,
nb_segment=1,
)
oebl2 = OEBase.from_neo(bl2, dbinfo.mapped_classes, cascade=True)
oebl2.save()
oebl3 = merge_blocks([oebl1, oebl2], )
print 'name', oebl3.name
#~ print oebl3.recordingchannelgroups
for rcg in oebl3.recordingchannelgroups:
print '#' * 3
print rcg
for rc in rcg.recordingchannels:
print rc
def test1():
bl1 = generate_block_for_sorting(nb_unit = 2,
duration = 3.*pq.s,
nb_segment = 2,
)
oebl1 = OEBase.from_neo(bl1, dbinfo.mapped_classes, cascade =True)
oebl1.save()
bl2 = generate_block_for_sorting(nb_unit = 3,
duration = 2.5*pq.s,
nb_segment = 1,
)
oebl2 = OEBase.from_neo(bl2, dbinfo.mapped_classes, cascade =True)
oebl2.save()
oebl3 = merge_blocks([oebl1, oebl2], )
print 'name', oebl3.name
#~ print oebl3.recordingchannelgroups
for rcg in oebl3.recordingchannelgroups:
print '#'*3
print rcg
for rc in rcg.recordingchannels:
print rc
url = 'sqlite:///test_spikesorting.sqlite'
dbinfo = open_db(url = url, use_global_session = True, myglobals = globals(),)
session = dbinfo.Session()
oebl = session.query(Block).first()
if oebl is None:
print 'do not exists: so create'
bl = generate_block_for_sorting(nb_unit = 6,
duration = 30.*pq.s,
noise_ratio = 0.2,
nb_segment = 2,
)
#~ for s, seg in enumerate(bl.segments):
#~ for k, sptr in enumerate(seg.spiketrains):
#~ print 's', s, 'k', k, sptr.size
print bl.recordingchannelgroups
oebl = OEBase.from_neo(bl, dbinfo.mapped_classes, cascade =True)
print oebl.recordingchannelgroups
oebl.save()
else:
print 'exist : transform to neo'
bl = oebl.to_neo(cascade = True)
rcg = bl.recordingchannelgroups[0]
sps = spikesorter = SpikeSorter(rcg)
if True:
#~ spikesorter.ButterworthFilter( f_low = 200.)
#~ spikesorter.MedianThresholdDetection(sign= '-', median_thresh = 6.,)
#~ spikesorter.AlignWaveformOnPeak(left_sweep = 1*pq.ms , right_sweep = 2*pq.ms, sign = '-')
#~ spikesorter.PcaFeature(n_components = 4)
)
session = dbinfo.Session()
oebl = session.query(Block).first()
if oebl is None:
print 'do not exists: so create'
bl = generate_block_for_sorting(
nb_unit=6,
duration=30. * pq.s,
noise_ratio=0.2,
nb_segment=2,
)
#~ for s, seg in enumerate(bl.segments):
#~ for k, sptr in enumerate(seg.spiketrains):
#~ print 's', s, 'k', k, sptr.size
print bl.recordingchannelgroups
oebl = OEBase.from_neo(bl, dbinfo.mapped_classes, cascade=True)
print oebl.recordingchannelgroups
oebl.save()
else:
print 'exist : transform to neo'
bl = oebl.to_neo(cascade=True)
rcg = bl.recordingchannelgroups[0]
sps = spikesorter = SpikeSorter(rcg)
if True:
#~ spikesorter.ButterworthFilter( f_low = 200.)
#~ spikesorter.MedianThresholdDetection(sign= '-', median_thresh = 6.,)
#~ spikesorter.AlignWaveformOnPeak(left_sweep = 1*pq.ms , right_sweep = 2*pq.ms, sign = '-')
#~ spikesorter.PcaFeature(n_components = 4)
spikesorter.CombineFeature(use_peak=True,
