def bcpnn_offline_noColumns(params, conn_list, sim_cnt=0, save_all=False, comm=None):
"""
This function computes the weight and bias values based on spiketimes during the simulation.
Arguments:
params: parameter dictionary
conn_list: two-dim numpy array storing cell-to-cell connections (only non-zero elements will be processed)
in the format (src, tgt, weight, delay)
or
file name in which the date is stored in this way
sim_cnt: int for recording to file
save_all: if True all traces will be saved
comm = MPI communicator
"""
if (type(conn_list) == type('')):
d = np.load(conn_list)
if (comm != None):
pc_id, n_proc = comm.rank, comm.size
else:
pc_id, n_proc = 0, 1
# extract the local list of elements 'my_conns' from the global conn_list
n_total = len(conn_list)
(min_id, max_id) = utils.distribute_n(n_total, n_proc, pc_id)
my_conns = [(conn_list[i, 0], conn_list[i, 1], conn_list[i, 2], conn_list[i, 3]) for i in xrange(min_id, max_id)]
fn = params['exc_spiketimes_fn_merged'] + str(sim_cnt) + '.ras'
spklist = nts.load_spikelist(fn)#, range(params['n_exc_per_mc']), t_start=0, t_stop=params['t_sim'])
spiketrains = spklist.spiketrains
new_conn_list = np.zeros((len(my_conns), 4)) # (src, tgt, weight, delay)
bias_dict = {}
for i in xrange(params['n_exc']):
bias_dict[i] = None
for i in xrange(len(my_conns)):
# for i in xrange(2):
pre_id = my_conns[i][0]
post_id = my_conns[i][1]
# create traces from spiketimes
# pre
spiketimes_pre = spiketrains[pre_id+1.].spike_times
pre_trace = utils.convert_spiketrain_to_trace(spiketimes_pre, params['t_sim'] + 1) # + 1 is to handle spikes in the last time step
# post
spiketimes_post = spiketrains[post_id+1.].spike_times
post_trace = utils.convert_spiketrain_to_trace(spiketimes_post, params['t_sim'] + 1) # + 1 is to handle spikes in the last time step
# compute
# print "%d Computing traces for %d -> %d; %.2f percent " % (pc_id, pre_id, post_id, i / float(len(my_conns)) * 100.)
get_traces = save_all
if (get_traces):
wij, bias, pi, pj, pij, ei, ej, eij, zi, zj = get_spiking_weight_and_bias(pre_trace, post_trace, get_traces)
dw = (wij.max() - wij.min()) * params['dw_scale']
# bias update
new_bias = bias.max()
else:
dw, new_bias = get_spiking_weight_and_bias(pre_trace, post_trace, get_traces)
dw *= params['dw_scale']
# bias update
if bias_dict[post_id] == None:
bias_dict[post_id] = new_bias
# weight update
new_conn_list[i, 0] = pre_id
new_conn_list[i, 1] = post_id
new_conn_list[i, 2] = dw + my_conns[i][2]
new_conn_list[i, 3] = my_conns[i][3]
# print "DEBUG Pc %d \t%d\t%d\t%.1e\t%.1e\tbias:%.4e\tconn:" % (pc_id, new_conn_list[i, 0], new_conn_list[i, 1], new_conn_list[i, 2], new_conn_list[i, 3], new_bias[i, 1]), my_conns[i]
if (save_all):
# save
output_fn = params['weights_fn_base'] + "%d_%d.npy" % (pre_id, post_id)
np.save(output_fn, wij)
output_fn = params['bias_fn_base'] + "%d.npy" % (post_id)
np.save(output_fn, bias)
output_fn = params['ztrace_fn_base'] + "%d.npy" % pre_id
np.save(output_fn, zi)
output_fn = params['ztrace_fn_base'] + "%d.npy" % post_id
np.save(output_fn, zj)
output_fn = params['etrace_fn_base'] + "%d.npy" % pre_id
np.save(output_fn, ei)
output_fn = params['etrace_fn_base'] + "%d.npy" % post_id
np.save(output_fn, ej)
output_fn = params['etrace_fn_base'] + "%d_%d.npy" % (pre_id, post_id)
np.save(output_fn, eij)
output_fn = params['ptrace_fn_base'] + "%d.npy" % pre_id
np.save(output_fn, pi)
output_fn = params['ptrace_fn_base'] + "%d.npy" % post_id
np.save(output_fn, pj)
output_fn = params['ptrace_fn_base'] + "%d_%d.npy" % (pre_id, post_id)
np.save(output_fn, pij)
if (n_proc > 1):
output_fn_conn_list = params['conn_list_ee_fn_base'] + str(sim_cnt+1) + '.dat'
utils.gather_conn_list(comm, new_conn_list, n_total, output_fn_conn_list)
output_fn_bias = params['bias_values_fn_base'] + str(sim_cnt+1) + '.dat'
utils.gather_bias(comm, bias_dict, n_total, output_fn_bias)
else:
print "Debug saving to", params['conn_list_ee_fn_base'] + str(sim_cnt+1) + '.dat'
np.savetxt(params['conn_list_ee_fn_base'] + str(sim_cnt+1) + '.dat', my_conns)#conn_list)
print "Debug saving to", params['bias_values_fn_base'] + str(sim_cnt+1) + '.dat'
np.savetxt(params['bias_values_fn_base'] + str(sim_cnt+1) + '.dat', bias)
def bcpnn_offline(params, connection_matrix, sim_cnt=0, pc_id=0, n_proc=1, save_all=False):
"""
Arguments:
params: parameter dictionary
connection_matrix: two-dim numpy array storing cell-to-cell connections (only non-zero elements will be processed)
or
file name
sim_cnt: int for recording to file
This function does basically the same thing as the script bcpnn_offline.py
"""
if (type(connection_matrix) == type('')):
connection_matrix = np.load(connection_matrix)
non_zeros = connection_matrix.nonzero()
conns = zip(non_zeros[0], non_zeros[1])
my_conns = utils.distribute_list(conns, n_proc, pc_id)
n, m = connection_matrix.shape
for i in xrange(len(my_conns)):
# for i in xrange(2):
pre_id = my_conns[i][0]
post_id = my_conns[i][1]
# extract the spike times from the file where all cells belonging to one minicolumn are stored
# pre
mc_index_pre = pre_id / params['n_exc_per_mc']
fn_pre = params['exc_spiketimes_fn_base'] + str(pre_id) + '.ras'
spklist_pre = nts.load_spikelist(fn_pre, range(params['n_exc_per_mc']), t_start=0, t_stop=params['t_sim'])
spiketimes_pre = spklist_pre[pre_id % params['n_exc_per_mc']].spike_times # TODO: check: + 1 for NeuroTools
pre_trace = utils.convert_spiketrain_to_trace(spiketimes_pre, params['t_sim'] + 1) # + 1 is to handle spikes in the last time step
# post
mc_index_post = post_id / params['n_exc_per_mc']
fn_post = params['exc_spiketimes_fn_base'] + str(post_id) + '.ras'
spklist_post = nts.load_spikelist(fn_post, range(params['n_exc_per_mc']), t_start=0, t_stop=params['t_sim'])
spiketimes_post = spklist_post[post_id % params['n_exc_per_mc']].spike_times# TODO: check: + 1 for NeuroTools
post_trace = utils.convert_spiketrain_to_trace(spiketimes_post, params['t_sim'] + 1)
# compute
wij, bias, pi, pj, pij, ei, ej, eij, zi, zj = get_spiking_weight_and_bias(pre_trace, post_trace)
# update
dw = (wij.max() - wij.min()) * params['dw_scale']
print "DEBUG, updating weight[%d, %d] by %.1e to %.1e" % (pre_id, post_id, dw, connection_matrix[pre_id, post_id] + dw)
connection_matrix[pre_id, post_id] += dw
bias[post_id] = bias.max()
ids_to_save = []
if (save_all):
ids_to_save = []
if (save_all):
# save
output_fn = params['weights_fn_base'] + "%d_%d.npy" % (pre_id, post_id)
np.save(output_fn, wij)
output_fn = params['bias_fn_base'] + "%d.npy" % (post_id)
np.save(output_fn, bias)
output_fn = params['ztrace_fn_base'] + "%d.npy" % pre_id
np.save(output_fn, zi)
output_fn = params['ztrace_fn_base'] + "%d.npy" % post_id
np.save(output_fn, zj)
output_fn = params['etrace_fn_base'] + "%d.npy" % pre_id
np.save(output_fn, ei)
output_fn = params['etrace_fn_base'] + "%d.npy" % post_id
np.save(output_fn, ej)
output_fn = params['etrace_fn_base'] + "%d_%d.npy" % (pre_id, post_id)
np.save(output_fn, eij)
output_fn = params['ptrace_fn_base'] + "%d.npy" % pre_id
np.save(output_fn, pi)
output_fn = params['ptrace_fn_base'] + "%d.npy" % post_id
np.save(output_fn, pj)
output_fn = params['ptrace_fn_base'] + "%d_%d.npy" % (pre_id, post_id)
np.save(output_fn, pij)
print "debug", params['conn_mat_ee_fn_base'] + str(sim_cnt+1) + '.npy'
np.savetxt(params['conn_mat_ee_fn_base'] + str(sim_cnt+1) + '.npy', connection_matrix)
print "debug", params['bias_values_fn_base'] + str(sim_cnt+1) + '.npy'
np.savetxt(params['bias_values_fn_base'] + str(sim_cnt+1) + '.npy', bias)
return connection_matrix, bias