[pointprocesses] improved chapter

pointprocesses/code/counthist.m

@@ -1,16 +1,11 @@
-function [counts, bins] = counthist(spikes, w)
-% Compute and plot histogram of spike counts.
+function counthist(spikes, w)
+% Plot histogram of spike counts.
 %
-% [counts, bins] = counthist(spikes, w)
+% counthist(spikes, w)
 %
 % Arguments:
 %   spikes: a cell array of vectors of spike times in seconds
-%   w: observation window duration in seconds for computing the counts
-%
-% Returns:
-%   counts: the histogram of counts normalized to probabilities
-%   bins: the bin centers for the histogram
-
+%   w: duration of window in seconds for computing the counts
     % collect spike counts:
     tmax = spikes{1}(end);
     n = [];
@@ -21,12 +16,12 @@ function [counts, bins] = counthist(spikes, w)
 %         for tk = 0:w:tmax-w
 %             nn = sum((times >= tk) & (times < tk+w));
 %             %nn = length(find((times >= tk) & (times < tk+w)));
-%             n = [n nn];
+%             n = [n, nn];
 %         end
 %     alternative 2: use the hist() function to do that!
         tbins = 0.5*w:w:tmax-0.5*w;
         nn = hist(times, tbins);
-        n = [n nn];
+        n = [n, nn];
     end
 
     % histogram of spike counts:
@@ -36,9 +31,7 @@ function [counts, bins] = counthist(spikes, w)
     counts = counts / sum(counts);
 
     % plot:
-    if nargout == 0
-        bar(bins, counts);
-        xlabel('counts k');
-        ylabel('P(k)');
-    end
+    bar(bins, counts);
+    xlabel('counts k');
+    ylabel('P(k)');
 end

pointprocesses/code/isihist.m

@@ -8,7 +8,7 @@ function [pdf, centers] = isihist(isis, binwidth)
 %   binwidth: optional width in seconds to be used for the isi bins
 %
 % Returns:
-%   pdf: vector with probability density of interspike intervals in Hz
+%   pdf: vector with pdf of interspike intervals in Hertz
 %   centers: vector with centers of interspikeintervalls in seconds
 
     if nargin < 2

pointprocesses/code/isis.m

@@ -5,11 +5,9 @@ function isivec = isis(spikes)
 %
 % Arguments:
 %   spikes: a cell array of vectors of spike times in seconds
-%   isivec: a column vector with all the interspike intervalls
 %
 % Returns:
 %   isivec: a column vector with all the interspike intervalls
-
     isivec = [];
     for k = 1:length(spikes)
         difftimes = diff(spikes{k});

pointprocesses/code/isiserialcorr.m

@@ -1,15 +1,15 @@
-function isicorr = isiserialcorr(isivec, maxlag)
+function [isicorr, lags] = isiserialcorr(isivec, maxlag)
 % serial correlation of interspike intervals
 %
 % isicorr = isiserialcorr(isivec, maxlag)
 %
 % Arguments:
 %   isivec: vector of interspike intervals in seconds
-%   maxlag: the maximum lag in seconds
+%   maxlag: the maximum lag
 %
 % Returns:
 %   isicorr: vector with the serial correlations for lag 0 to maxlag
-
+%   lags: vector with the lags corresponding to isicorr
     lags = 0:maxlag;
     isicorr = zeros(size(lags));
     for k = 1:length(lags)
@@ -21,14 +21,4 @@ function isicorr = isiserialcorr(isivec, maxlag)
             isicorr(k) = corr(isivec(1:end-lag), isivec(lag+1:end));
         end
     end
-    
-    if nargout == 0
-        % plot:
-        plot(lags, isicorr, '-b');
-        hold on;
-        scatter(lags, isicorr, 50.0, 'b', 'filled');
-        hold off;
-        xlabel('Lag k')
-        ylabel('\rho_k')
-    end
 end

pointprocesses/code/plotisiserialcorr.m

@@ -0,0 +1,16 @@
+function isicorr = plotisiserialcorr(isivec, maxlag)
+% plot serial correlation of interspike intervals
+%
+% plotisiserialcorr(isivec, maxlag)
+%
+% Arguments:
+%   isivec: vector of interspike intervals in seconds
+%   maxlag: the maximum lag
+    [isicorr, lags] = isiserialcorr(isivec, maxlag);
+    plot(lags, isicorr, '-b');
+    hold on;
+    scatter(lags, isicorr, 20.0, 'b', 'filled');
+    hold off;
+    xlabel('Lag k')
+    ylabel('\rho_k')
+end

pointprocesses/code/rasterplot.m

@@ -2,21 +2,35 @@ function rasterplot(spikes, tmax)
 % Display a spike raster of the spike times given in spikes.
 %
 % rasterplot(spikes, tmax)
+%
+% Arguments:
 %   spikes: a cell array of vectors of spike times in seconds
-%   tmax: plot spike raster upto tmax seconds
-
+%   tmax: plot spike raster up to tmax seconds
+    in_msecs = tmax < 1.5
+    spiketimes = [];
+    trials = [];
     ntrials = length(spikes);
     for k = 1:ntrials
         times = spikes{k};
         times = times(times<tmax);
-        if tmax < 1.5
-            times = 1000.0*times; % conversion to ms
-        end
-        for i = 1:length( times )
-            line([times(i) times(i)],[k-0.4 k+0.4], 'Color', 'k'); 
+        if in_msecs
+            times = 1000.0*times;               % conversion to ms
         end
+        % (x,y) pairs for start and stop of stroke
+        % plus nan separating strokes:
+        spiketimes = [spiketimes, ...
+                       [times(:)'; times(:)'; times(:)'*nan]];
+        trials = [trials, ...
+                   [ones(1, length(times)) * (k-0.4); ...
+                    ones(1, length(times)) * (k+0.4); ...
+                    ones(1, length(times)) * nan]];
     end
-    if tmax < 1.5
+    % convert matrices into simple vectors of (x,y) pairs:
+    spiketimes = spiketimes(:);
+    trials = trials(:);
+    % plotting this is lightning fast:
+    plot(spiketimes, trials, 'k')
+    if in_msecs
         xlabel('Time [ms]');
         xlim([0.0 1000.0*tmax]);
     else