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Jan Grewe
2014-10-16 17:15:55 +02:00
parent d4b147103f
commit d799c2b4cf
3 changed files with 153 additions and 47 deletions
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61
programming/exercises/psths.m
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@@ -4,48 +4,57 @@ max_time = 0;
for i = 1:size(times,2)
max_time = max([max_time, max(times{i})]);
end
fig = figure();
set(gcf,'Color', 'white')
%% create PSTH on the basis of the interspike intervals
subplot(3,1,1)
hold on
% 1. get the interspike intervals for each trial
for i = 1:size(times,2)
t = times{i};
isi = diff(t);
plot(t(2:end), 1./isi)
t = times{1};
firing_rate = [0 1./diff(t)];
start = 1;
resp = zeros(1, round(max_time * sample_rate));
for i = 1:length(t)
resp(1,start:round(t(i) * sample_rate)) = firing_rate(i);
start = round(t(i) * sample_rate);
end
fig = figure();
set(gcf, 'PaperUnits', 'centimeters');
set(gcf, 'PaperSize', [11.7 9.0]);
set(gcf, 'PaperPosition',[0.0 0.0 11.7 9.0]);
set(gcf,'Color', 'white')
plot((1/sample_rate:1/sample_rate:max_time), resp)
xlabel('time [s]')
ylabel('firing rate [Hz]')
box('off')
ylim([0 300])
xlim([0 1])
title('instanataneous firing rate')
%% create PSTH using the binning method
subplot(3,1,2)
box('off')
bin_width = 0.02; % s
bin_width = 0.0125; % s
edges = 0:bin_width:max_time;
firing_rate = [];
for i = 1:size(times,2)
t = times{i};
[n, t] = hist(t, edges);
[n, time] = hist(t, edges);
if isempty(firing_rate)
firing_rate = n / bin_width;
firing_rate = n / bin_width / size(times,2);
else
firing_rate = firing_rate + (n / bin_width / size(times,2));
end
end
plot(t,firing_rate)
fig = figure();
set(gcf, 'PaperUnits', 'centimeters');
set(gcf, 'PaperSize', [11.7 9.0]);
set(gcf, 'PaperPosition',[0.0 0.0 11.7 9.0]);
set(gcf,'Color', 'white')
plot(time, firing_rate)
ylim([0 300])
xlim([0 1])
xlabel('time [s]')
ylabel('firing rate [Hz]')
title('binning method')
%% create PSTH using the kernel-convolution method
subplot(3,1,3)
kernel_width = 0.0125; %s
binary_spikes = zeros(size(times,2), round(max_time*sample_rate));
resps = zeros(size(binary_spikes));
window = hann(bin_width/4*sample_rate,'symmetric');
window = hann(kernel_width*sample_rate,'symmetric');
window = window/sum(window);
for i = 1:size(times,2)
@@ -55,6 +64,16 @@ for i = 1:size(times,2)
temp(1) = 1;
end
binary_spikes(i, temp) = 1;
resps(i,:) = conv(binary_spikes(i,:), window, 'same');
resps(i,:) = conv(binary_spikes(i,:), window, 'same')*sample_rate;
end
plot((0:1/sample_rate:max_time), mean(resps,2))
fig = figure();
set(gcf, 'PaperUnits', 'centimeters');
set(gcf, 'PaperSize', [11.7 9.0]);
set(gcf, 'PaperPosition',[0.0 0.0 11.7 9.0]);
set(gcf,'Color', 'white')
plot((1/sample_rate:1/sample_rate:max_time), mean(resps,1))
ylim([0 300])
xlim([0 1])
xlabel('time [s]')
ylabel('firing rate [Hz]')
title('convolution method')