def write_data_to_hdf5(self, filename='data'):
"""This is a function to call after simulation that writes the
data of all probes to filename using the Neo HDF5 IO module.
:param string filename: the name of the file to write out to
"""
import neo
from neo import hdf5io
# get list of probes
probe_list = [
self.nodes[node] for node in self.nodes if node[:5] == 'Probe'
]
# if no probes then just return
if len(probe_list) == 0: return
# open up hdf5 file
if not filename.endswith('.hd5'): filename += '.hd5'
iom = hdf5io.NeoHdf5IO(filename=filename)
#TODO: set up to write multiple trials/segments to same block
# for trials run at different points
# create the all encompassing block structure
block = neo.Block()
# create the segment, representing a trial
segment = neo.Segment()
# put the segment in the block
block.segments.append(segment)
# create the appropriate Neo structures from the Probes data
#TODO: pair any analog signals and spike trains from the same
# population together into a RecordingChannel
for probe in probe_list:
# decoded signals become AnalogSignals
if probe.target_name.endswith('decoded'):
segment.analogsignals.append(
neo.AnalogSignal(
probe.get_data() * quantities.dimensionless,
sampling_period=probe.dt_sample * quantities.s,
target_name=probe.target_name))
# spikes become spike trains
elif probe.target_name.endswith('spikes'):
# have to change spike train of 0s and 1s to list of times
for neuron in probe.get_data().T:
segment.spiketrains.append(
neo.SpikeTrain([
t * probe.dt_sample
for t, val in enumerate(neuron[0]) if val > 0
] * quantities.s,
t_stop=len(probe.data),
target_name=probe.target_name))
else:
print 'Do not know how to write %s to NeoHDF5 file' % probe.target_name
assert False
# write block to file
iom.save(block)
# close up hdf5 file
iom.close()
Bp = net.make_probe('B', dt_sample=dt_step)
BpSpikes = net.make_probe('B', data_type='spikes', dt_sample=dt_step)
build_time_end = time.time()
print "starting simulation"
net.run(timesteps * dt_step)
sim_time_end = time.time()
print "\nBuild time: %0.10fs" % (build_time_end - build_time_start)
print "Sim time: %0.10fs" % (sim_time_end - build_time_end)
net.write_data_to_hdf5()
# open up hdf5 file
iom = hdf5io.NeoHdf5IO(filename='data.hd5')
print iom.get_info()
# wtf i know right?
block_as = iom.read_analogsignal()
segment_as = block_as.segments[0]
block_st = iom.read_spiketrain()
segment_st = block_st.segments[0]
import matplotlib.pyplot as plt
plt.clf()
plt.subplot(211)
plt.title('analog signal')
plt.hold(1)
legend = []