def rescue1ch(filetrnk, xunits="ms", yunits="mV", dt=0.02):
sys.stdout.write("NICOMEDI: Rescuing file: Reading temp files...\n")
sys.stdout.flush()
fntmp = filetrnk + "_tmp.bin"
fntmp2 = filetrnk + "_tmp2.bin"
entmp = filetrnk + "_edge.bin"
fn = filetrnk + ".h5"
ftmp = open(fntmp, 'rb')
ftmp2 = open(fntmp2, 'rb')
databstr = ftmp.read()
databstr2 = ftmp2.read()
sys.stdout.write("NICOMEDI: Saving to file: Processing data...\n")
sys.stdout.flush()
datalist = np.fromstring(databstr, np.float32)
frames = np.fromstring(databstr2, np.int8)
# Write to hdf5:
sys.stdout.write("NICOMEDI: Saving to file: Converting to hdf5...\n")
sys.stdout.flush()
chlist = [
stfio.Channel([
stfio.Section(np.array(datalist, dtype=np.float)),
]),
]
chlist[0].yunits = yunits
rec = stfio.Recording(chlist)
rec.dt = dt # set sampling interval
rec.xunits = xunits # set time units
sys.stdout.write("NICOMEDI: Saving to file: Writing hdf5...")
sys.stdout.flush()
rec.write(fn)
sys.stdout.write("done\n")
sys.stdout.flush()
# Write frame transition times
if frames[0] != 0:
sys.stdout.write("NICOMEDI: Warning: first frame isn't 0\n")
edges = find_edges(frames)
etmp = open(entmp, 'wb')
etmp.write(edges.astype(np.int32).tostring())
etmp.close()
# Close and delete temp file:
ftmp.close()
ftmp2.close()
os.remove(fntmp)
os.remove(fntmp2)
sys.stdout.write("\nNICOMEDI: Stopping acquisition, read %d samples\n" \
% len(datalist))
sys.stdout.flush()
def convert_ws_to_stfio(infile):
wsfile = ws.wsfile(infile)
data = wsfile.data()
units = wsfile.unitslist
chlist = []
for channel, traces in data.iteritems():
seclist = [stfio.Section(trace) for trace in traces if np.any(trace)]
chlist.append(stfio.Channel(seclist))
chlist[-1].yunits = units[channel]
chlist[-1].name = channel
rec = stfio.Recording(chlist)
rec.date = wsfile.dstamp.strftime("%Y-%m-%d")
rec.time = wsfile.dstamp.strftime("%H-%M-%S")
rec.dt = 1000.0 / wsfile.SampleRate
rec.dt
rec.xunits = 'ms'
return rec
def neo2stfio(neo_obj):
"""Convert neo object to stfio recording.
Restrictions:
* Only converts the first block
* Assumes that the sampling rate is constant throughout segments
* Assumes that we have the same number of channels throughout segments
* Assumes that the channel units do not change
Usage:
>>> import neo
>>> neo_obj = neo.io.AxonIO("filename.abf")
>>> import stfio
>>> stfio_obj = stfio.neo.neo2stfio(neo_obj)
>>> assert(stfio_obj[0][0][0] == neo_obj.read()[0].segments[0].analogsignals[0][0])
"""
blocks = neo_obj.read()
if len(blocks) > 1:
sys.stderr.write("Warning: Only the first block" +
"of this neo object will be converted\n")
reference_signal = blocks[0].segments[0].analogsignals
nchannels = len(reference_signal)
rec = stfio.Recording([
stfio.Channel([
stfio.Section(np.array(seg.analogsignals[nc], dtype=np.float64))
for seg in blocks[0].segments
], reference_signal[nc].units.dimensionality.string)
for nc in range(nchannels)
])
rec.dt = float(reference_signal[0].sampling_period.rescale('ms'))
rec.xunits = "ms"
return rec
def stop(aichIC, aichEC, aichFR, dt, xunits, yunitsIC, yunitsEC, gainIC,
gainEC, fn, ftmpIC, fntmpIC, ftmpEC, fntmpEC, ftmpFR, fntmpFR, entmp,
s, connic, connec, connfr, plot_sample, databstr_old):
# Close device:
ret = c.comedi_cancel(aichIC.dev, aichIC.subdev)
# time stamp for last sample
s.send(np.array([
time.time(),
], dtype=np.float64).tostring())
if ret != 0:
comedi_errcheck()
# Empty buffer:
# ret = c.comedi_poll(aich.dev, aich.subdev)
# if ret < 0:
# comedi_errcheck()
read_buffer(aichIC, aichEC, aichFR, gainIC, gainEC, connic, connec, connfr,
plot_sample, ftmpIC, ftmpEC, ftmpFR, databstr_old)
ftmpIC.close()
ftmpEC.close()
ftmpFR.close()
# Scale temporary file:
sys.stdout.write("NICOMEDI: Saving to file: Reading temp file...\n")
sys.stdout.flush()
ftmpIC = open(fntmpIC, 'rb')
ftmpEC = open(fntmpEC, 'rb')
ftmpFR = open(fntmpFR, 'rb')
databstrIC = ftmpIC.read()
databstrEC = ftmpEC.read()
databstrFR = ftmpFR.read()
sys.stdout.write("NICOMEDI: Saving to file: Processing data...\n")
sys.stdout.flush()
datalistIC = np.fromstring(databstrIC, np.float32)
datalistEC = np.fromstring(databstrEC, np.float32)
frames = np.fromstring(databstrFR, np.int8)
# Write to hdf5:
sys.stdout.write("NICOMEDI: Saving to file: Converting to hdf5...\n")
sys.stdout.flush()
chlist = [
stfio.Channel([
stfio.Section(np.array(datalistIC, dtype=np.float)),
]),
stfio.Channel([
stfio.Section(np.array(datalistEC, dtype=np.float)),
])
]
chlist[0].yunits = yunitsIC
chlist[1].yunits = yunitsEC
rec = stfio.Recording(chlist)
rec.dt = dt # set sampling interval
rec.xunits = xunits # set time units
sys.stdout.write("NICOMEDI: Saving to file: Writing hdf5 to %s..." % fn)
sys.stdout.flush()
if sys.version_info >= (3, ):
rec.write(fn)
else:
rec.write(fn.encode('latin-1'))
sys.stdout.write("done\n")
sys.stdout.flush()
# Write frame transition times
if frames[0] != 0:
sys.stdout.write("NICOMEDI: Warning: first frame isn't 0\n")
edges = find_edges(frames)
etmp = open(entmp, 'wb')
etmp.write(edges.astype(np.int32).tostring())
etmp.close()
# Close and delete temp file:
ftmpIC.close()
ftmpEC.close()
ftmpFR.close()
# Do not remove temp files, CSH 2013-10-11
# os.remove(fntmpIC)
# os.remove(fntmpEC)
# os.remove(fntmpFR)
sys.stdout.write("\nNICOMEDI: Stopping acquisition, read %d samples\n" \
% len(datalistIC))
sys.stdout.flush()
sys.stdout.write("NICOMEDI: Synchronizing in background\n")
locald = os.path.dirname(fn)
netd = os.path.dirname(
locald.replace(settings.local_data_dir,
settings.net_data_dir_mnt)) + '/'
if not os.path.exists(netd):
args = ["/usr/local/bin/sync_rackstation.sh"]
else:
netd = os.path.dirname(
locald.replace(settings.local_data_dir,
settings.net_data_dir)) + """/'"""
args = ["/usr/bin/rsync", "-a", locald, netd]
subprocess.Popen(args)
def run(dt_nrn, tstop, mean_f):
module_dir = os.path.dirname(__file__)
if os.path.exists("%s/dat/events.h5" % module_dir):
rec = stfio.read("%s/dat/events.h5" % module_dir)
spiketimes = np.load("%s/dat/spiketimes.npy" % module_dir)
return rec, spiketimes
if os.path.exists("%s/dat/events_nonoise.npy" % module_dir):
mrec = np.load("%s/dat/events_nonoise.npy" % module_dir)
spiketimes = np.load("%s/dat/spiketimes.npy" % module_dir)
else:
from neuron import h
h.load_file('stdrun.hoc')
soma, dend = ball_and_stick(h)
h.tstop = tstop
trange = np.arange(0, tstop + dt_nrn, dt_nrn)
spiketimes = generate_events(trange, mean_f)
np.save("%s/dat/spiketimes.npy" % module_dir, spiketimes)
syn_AMPA, spiketimes_nrn, vecstim, netcon = [], [], [], []
for spike in spiketimes:
loc = 0.8 * np.random.normal(1.0, 0.03)
if loc < 0:
loc = 0
if loc > 1:
loc = 1
syn_AMPA.append(h.Exp2Syn(dend(loc), sec=dend))
spiketimes_nrn.append(h.Vector([spike]))
vecstim.append(h.VecStim())
netcon.append(h.NetCon(vecstim[-1], syn_AMPA[-1]))
syn_AMPA[-1].tau1 = 0.2 * np.random.normal(1.0, 0.3)
if syn_AMPA[-1].tau1 < 0.05:
syn_AMPA[-1].tau1 = 0.05
syn_AMPA[-1].tau2 = 2.5 * np.random.normal(1.0, 0.3)
if syn_AMPA[-1].tau2 < syn_AMPA[-1].tau1 * 1.5:
syn_AMPA[-1].tau2 = syn_AMPA[-1].tau1 * 1.5
syn_AMPA[-1].e = 0
vecstim[-1].play(spiketimes_nrn[-1])
netcon[-1].weight[0] = np.random.normal(1.0e-3, 1.0e-4)
if netcon[-1].weight[0] < 0:
netcon[-1].weight[0] = 0
netcon[-1].threshold = 0.0
vclamp = h.SEClamp(soma(0.5), sec=soma)
vclamp.dur1 = tstop
vclamp.amp1 = -80.0
vclamp.rs = 5.0
mrec = h.Vector()
mrec.record(vclamp._ref_i)
h.dt = dt_nrn # ms
h.steps_per_ms = 1.0 / h.dt
h.v_init = -80.0
h.run()
mrec = np.array(mrec)
np.save("%s/dat/events_nonoise.npy" % module_dir, mrec)
plt.plot(np.arange(len(mrec), dtype=np.float) * dt_nrn, mrec)
peak_window_i = 20.0 / dt_nrn
amps_i = np.array([
int(np.argmin(mrec[onset_i:onset_i + peak_window_i]) + onset_i)
for onset_i in spiketimes / dt_nrn
],
dtype=np.int)
plt.plot(amps_i * dt_nrn, mrec[amps_i], 'o')
mean_amp = np.abs(mrec[amps_i].mean())
print(mean_amp)
mrec = add_noise(mrec, dt_nrn, mean_amp)
plt.plot(np.arange(len(mrec), dtype=np.float) * dt_nrn, mrec)
seclist = [
stfio.Section(mrec),
]
chlist = [
stfio.Channel(seclist),
]
chlist[0].yunits = "pA"
rec = stfio.Recording(chlist)
rec.dt = dt_nrn
rec.xunits = "ms"
rec.write("%s/dat/events.h5" % module_dir)
return rec, spiketimes