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live_edbn.m
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live_edbn.m
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function [spike_list, edbn, opts] = live_edbn(edbn, x, opts)
% Set defaults
if ~isfield(edbn,'fw_conns'), edbn.fw_conns=num2cell([2:numel(edbn.sizes) 0]); end;
if ~isfield(edbn,'fb_conns'), edbn.fb_conns=num2cell([0 1:numel(edbn.sizes)-1]); end;
if ~isfield(edbn,'fw_erbm'), edbn.fw_erbm=[1:numel(edbn.erbm) 0]; end
if ~isfield(opts,'recreate'), opts.recreate = 1; end;
if ~isfield(opts,'timespan'), opts.timespan = 4; end;
if ~isfield(opts,'numspikes'), opts.numspikes = 2000; end;
if ~isfield(opts,'delay'), opts.delay = 0.001; end;
if ~isfield(opts,'show_dt'), opts.show_dt = 0.010; end;
if ~isfield(opts,'vis_tau'), opts.vis_tau = 0.05; end;
if ~isfield(opts,'makespikes'), opts.makespikes = 1; end;
if ~isfield(opts,'makevisdim'), opts.makevisdim = 1; end;
if ~isfield(opts,'vis_handle'), opts.vis_handle = figure; end;
if ~isfield(opts,'vis_layers'), opts.vis_layers = 1:numel(edbn.sizes); end;
if ~isfield(opts,'ff'), opts.ff = [ones(1, numel(edbn.sizes)-1) 0]; end;
if ~isfield(opts,'fb'), opts.fb = zeros(1, numel(edbn.sizes)); end;
% Create reconstruction layer as necessary
if(opts.recreate)
edbn.sizes = [edbn.sizes edbn.sizes(1)];
edbn.erbm = [edbn.erbm edbn.erbm(1)];
edbn.fb_conns{2} = numel(edbn.sizes);
edbn.fw_conns = [edbn.fw_conns edbn.fw_conns{1}];
edbn.fb_conns = [edbn.fb_conns 0];
opts.ff = [opts.ff 0];
opts.fb(2) = 1;
opts.fb = [opts.fb 0];
edbn.fw_erbm = [edbn.fw_erbm numel(edbn.erbm)];
opts.vis_layers = [opts.vis_layers numel(edbn.sizes)];
end
% Create spikes proportional to intensity and assign a random time
if(opts.makespikes)
inp.addr = randsample(numel(x), opts.numspikes, true, x(:))';
inp.times = sort(rand(1,opts.numspikes)) .* opts.timespan;
x = inp;
end
% Initialize neurons
layers = numel(edbn.sizes);
mem = cell(1, layers);
mem_time = cell(1, layers);
refrac_end = cell(1, layers);
for i = 1:layers
mem{i} = zeros(1, edbn.sizes(i));
mem_time{i} = 0;
refrac_end{i} = zeros(1, edbn.sizes(i));
end
% Initialize spike queues
queue.times = x.times;
queue.layers = 1 * ones(1, numel(x.addr));
queue.addrs = num2cell(x.addr);
% Build show dimensions
if(opts.makevisdim)
for i = 1:layers
factors = factor(edbn.sizes(i));
opts.show_dims{i} = [prod(factors(2:2:end)) prod(factors(1:2:end))];
end
end
% Build plotspace
figure(opts.vis_handle); clf;
last_spiked = cell(1, layers);
image_handle = cell(1, layers);
for i=1:numel(edbn.sizes)
% Create storage for visualization
last_spiked{i} = zeros(1, edbn.sizes(i));
if(any(i==opts.vis_layers))
% Plot and store a handle
subplot(1, numel(opts.vis_layers), find(i==opts.vis_layers));
image(reshape(last_spiked{i}, opts.show_dims{i})', 'CDataMapping','scaled');
colormap bone; axis image; axis off;
image_handle{i} = get(gca,'Children');
end
end
% Run the event-based network
tic;
idx = 1;
last_show = 0;
while(idx < size(queue.times, 2))
% Pull out spikes to process
curr_time = queue.times(idx);
from_addr = queue.addrs{idx};
from_layer = queue.layers(idx);
% Update display
last_spiked{from_layer}(from_addr) = last_spiked{from_layer}(from_addr) + 1;
% Process forward and backward connections
for direction=1:2
if(direction == 1), conns = opts.ff(from_layer) .* edbn.fw_conns{from_layer}; end
if(direction == 2), conns = opts.fb(from_layer) .* edbn.fb_conns{from_layer}; end
% Skip if nothing to do
if(~any(conns)), continue; end
for l_idx = 1:numel(conns)
layer = conns(l_idx);
% Decay
time_gap = curr_time - mem_time{layer};
decayfac = exp(-time_gap / opts.tau_m);
mem{layer} = mem{layer} .* decayfac;
% Add Impulse
not_refrac = curr_time > refrac_end{layer};
if(direction == 1)
impulse = edbn.erbm{edbn.fw_erbm(from_layer)}.W(:, from_addr)';
else
impulse = edbn.erbm{edbn.fw_erbm(layer)}.W(from_addr, :);
end
mem{layer} = mem{layer} + sum(bsxfun(@times, not_refrac, impulse), 1);
% Store new 'old' time
mem_time{layer} = curr_time;
% Check for firing; reset potential and store refrac
firings = find(mem{layer} > opts.v_thr);
mem{layer}(firings) = 0;
refrac_end{layer}(firings) = curr_time + opts.t_ref;
% Update queues
if(numel(firings > 0))
insert_idx = find(curr_time + opts.delay < queue.times, 1, 'first');
if(isempty(insert_idx))
insert_idx = size(queue, 2);
end
queue.times = horzcat(queue.times(1:insert_idx-1), ...
curr_time + opts.delay, ...
queue.times(insert_idx:end));
queue.layers = horzcat(queue.layers(1:insert_idx-1), ...
layer, ...
queue.layers(insert_idx:end));
queue.addrs = horzcat(queue.addrs(1:insert_idx-1), ...
{firings}, ...
queue.addrs(insert_idx:end));
end
end
end
% Display if desired
if(curr_time - last_show > opts.show_dt)
for i = 1:numel(edbn.sizes)
last_spiked{i} = last_spiked{i} .* exp(-opts.show_dt / opts.vis_tau);
if(any(i==opts.vis_layers))
set(image_handle{i}, 'CData', reshape(last_spiked{i}, opts.show_dims{i})');
end
end
pause(0.01);
last_show = curr_time;
end
% Pick next time
idx = idx + 1;
end
% Report finish and the timing
fprintf('Completed %i input spikes occurring over %2.2f seconds, in %2.3f seconds of real time.\n', ...
opts.numspikes, opts.timespan, toc);
% De-parallelize output
spike_list.addrs = cell2mat(queue.addrs);
numrepeats = cellfun(@(x)size(x,2),queue.addrs);
spike_list.times = cell2mat(arrayfun(@(time, repeats) ones(1,repeats)*time, queue.times, numrepeats, 'UniformOutput', 0));
spike_list.layers = cell2mat(arrayfun(@(layer, repeats) ones(1,repeats)*layer, queue.layers, numrepeats, 'UniformOutput', 0));