small changes

SharpWaveRipples/DetectSWR.m

@@ -1,4 +1,4 @@
-function [ripples] = DetectSWR(Channels, varargin)
+function ripples = DetectSWR(Channels, varargin)
 
 %DetectSWR - Detect Sharp Wave Ripple in epochs of continuous data.
 %
@@ -1483,6 +1483,7 @@
 
 end
 
+% ------------------------------- Helper functions -------------------------------
 
 function logAnalysisFile(AnalysisFileName, writePath)
 % The purpose of this utility is to provide a record of analyses run by

lfp/FilterLFP.m

@@ -31,7 +31,7 @@
 %        gamma      [30 80]
 %        ripples    [100 250]
 
-% Copyright (C) 2004-2021 by Michaël Zugaro
+% Copyright (C) 2004-2021 by Michaël Zugaro (C) 2021 by Ralitsa Todorova
 %
 % This program is free software; you can redistribute it and/or modify
 % it under the terms of the GNU General Public License as published by

lfp/FindThetaCycles.m

@@ -118,4 +118,16 @@
 troughs = troughs(ok);
 peaktopeak = peaktopeak(ok,:);
 amplitude = amplitude(ok,2);
-end
+
+
+% ------------------------------- Helper functions -------------------------------
+function peaks = FindLocalMaxima(signal)
+%FindLocalMaxima - find local peaks
+if isdmatrix(signal,'@2'),
+    iPeaks = FindLocalMaxima(signal(:,2));
+    peaks = signal(iPeaks,1);
+    return
+end
+
+d = [nan;diff(signal(:))>0];
+peaks = strfind(d',[1 0])';

lfp/WaveletSpectrogram.m

@@ -16,7 +16,7 @@
 %    -------------------------------------------------------------------------
 %     'range'       frequency range (in Hz) (default = all)
 %     'resolution'  desired frequency resolution (sub-octaves per octave, default = 0.05)
-%     'step'        desired step between successive windows (default = window/2): 
+%     'step'        desired step between successive windows (default = window/2):
 %                   output will be downsampled to this value
 %     'interpolate' interpolate to create equidistant frequency bins instead
 %                   of bins in power of 2 (default = false)
@@ -167,7 +167,7 @@
 
 % loop through all scales and compute transform
 for a1 = 1:J1+1
-	[daughter,fourier_factor,coi,dofmin]=wave_bases(mother,k,scale(a1),param);	
+	[daughter,fourier_factor,coi,dofmin]=wave_bases(mother,k,scale(a1),param);
 	wave(a1,:) = ifft(f.*daughter);  % wavelet transform[Eqn(4)]
 end
 

plotting/PlotIntervals.m

@@ -25,7 +25,8 @@
 %    =========================================================================
 %
 
-% Copyright (C) 2008-2013 by Gabrielle Girardeau & Michaël Zugaro
+% Copyright (C) 2008-2013 by Gabrielle Girardeau & Michaël Zugaro, 
+% (C) 2023 by Ralitsa Todorova (graphics optimization for large numbers of intervals)
 %
 % This program is free software; you can redistribute it and/or modify
 % it under the terms of the GNU General Public License as published by
@@ -39,67 +40,67 @@
 direction = 'v';
 yLim = ylim;
 
-if nargin < 1,
+if nargin < 1
   error('Incorrect number of parameters (type ''help <a href="matlab:help PlotIntervals">PlotIntervals</a>'' for details).');
 end
-if size(intervals,2) ~= 2,
+if size(intervals,2) ~= 2
   error('Incorrect list of intervals (type ''help <a href="matlab:help PlotIntervals">PlotIntervals</a>'' for details).');
 end
 
 % Backward compatibility: previous versions used the syntax PlotIntervals(intervals,style,direction)
 parsed = false;
-if (nargin == 2 || nargin == 3) && isstring_FMAT(lower(varargin{1}),'rectangles','bars'),
+if (nargin == 2 || nargin == 3) && isastring(lower(varargin{1}),'rectangles','bars')
 	style = lower(varargin{1});
 	parsed = true;
 end
-if nargin == 3 && isstring_FMAT(lower(varargin{2}),'h','v'),
+if nargin == 3 && isastring(lower(varargin{2}),'h','v')
 	direction = lower(varargin{2});
 	parsed = true;
 end
 
 % Parse parameter list
-if ~parsed,
-	for i = 1:2:length(varargin),
-		if ~ischar(varargin{i}),
+if ~parsed
+	for i = 1:2:length(varargin)
+		if ~ischar(varargin{i})
 			error(['Parameter ' num2str(i+1) ' is not a property (type ''help <a href="matlab:help PlotIntervals">PlotIntervals</a>'' for details).']);
 		end
-		switch(lower(varargin{i})),
-			case 'style',
+		switch(lower(varargin{i}))
+			case 'style'
 				style = lower(varargin{i+1});
-				if ~isstring_FMAT(style,'bars','rectangles'),
+				if ~isastring(style,'bars','rectangles')
 					error('Incorrect value for property ''style'' (type ''help <a href="matlab:help PlotIntervals">PlotIntervals</a>'' for details).');
 				end
-			case 'direction',
+			case 'direction'
 				direction = lower(varargin{i+1});
-				if ~isstring_FMAT(direction,'h','v'),
+				if ~isastring(direction,'h','v')
 					error('Incorrect value for property ''direction'' (type ''help <a href="matlab:help PlotIntervals">PlotIntervals</a>'' for details).');
 				end
-			case 'color',
+			case 'color'
 				color = lower(varargin{i+1});
-				if ~isstring_FMAT(color,'r','g','b','c','m','y','k','w') && ~isdvector(color,'#3','>=0','<=1'),
+				if ~isastring(color,'r','g','b','c','m','y','k','w') && ~isdvector(color,'#3','>=0','<=1')
 					error('Incorrect value for property ''direction'' (type ''help <a href="matlab:help PlotIntervals">PlotIntervals</a>'' for details).');
 				end
-			case 'alpha',
+			case 'alpha'
                 alphaValue = varargin{i+1};
-                if ~isdscalar(alphaValue,'>=0','<=1'),
+                if ~isdscalar(alphaValue,'>=0','<=1')
                     error('Incorrect value for property ''alpha'' (type ''help <a href="matlab:help PlotIntervals">PlotIntervals</a>'' for details).');
                 end
-            case 'ylim',
+            case 'ylim'
                 yLim = varargin{i+1};
-                if ~isdvector(yLim,'<'),
+                if ~isdvector(yLim,'<')
                     error('Incorrect value for property ''yLim'' (type ''help <a href="matlab:help PlotIntervals">PlotIntervals</a>'' for details).');
                 end
-			otherwise,
+            otherwise
 				error(['Unknown property ''' num2str(varargin{i}) ''' (type ''help <a href="matlab:help PlotIntervals">PlotIntervals</a>'' for details).']);
 		end
 	end
 end
 
 hold on;
 xLim = xlim;
-if strcmp(style,'bars'),
-	for i = 1:size(intervals,1),
-		if strcmp(direction,'v'),
+if strcmp(style,'bars')
+	for i = 1:size(intervals,1)
+		if strcmp(direction,'v')
 			plot([intervals(i,1) intervals(i,1)],yLim,'Color',[0 0.75 0]);
 			plot([intervals(i,2) intervals(i,2)],yLim,'Color',[0.9 0 0]);
 		else
@@ -108,8 +109,8 @@
 		end
 	end
 else
-	for i=1:size(intervals,1),
-		if strcmp(direction,'v'),
+	for i=1:size(intervals,1)
+		if strcmp(direction,'v')
 			dx = intervals(i,2)-intervals(i,1);
 			dy = yLim(2)-yLim(1);
 			rec(i) = patch(intervals(i,1)+[0 0 dx dx],yLim(1)+[0 dy dy 0],color,'LineStyle','none');
@@ -127,7 +128,7 @@
     end
 end
 
-if nargout>0, 
+if nargout>0
     varargout{1} = rec;
 end
 

plotting/RasterPlot.m

@@ -13,7 +13,7 @@
 % the Free Software Foundation; either version 3 of the License, or
 % (at your option) any later version.
 
-if nargin==1,
+if nargin==1
     height = 1;
 end
 

plotting/semplot.m

@@ -1,4 +1,4 @@
-function varargout = semplot(x,y,color,smooth)
+function varargout = semplot(x,y,color,smooth,solid)
 
 %semplot - plot mean (line) +/- s.e.m. (shaded area) of a matrix "y"
 % semplot(x,y,color,smooth)
@@ -12,32 +12,34 @@
 % the Free Software Foundation; either version 3 of the License, or
 % (at your option) any later version.
 
-solid = false; % one day I will make this into an option
+if ~exist('solid','var')
+    solid = false;
+end
 
-if nargin<2 || (nargin==2 && ischar(y)),
-    if nargin==2,
+if nargin<2 || (nargin==2 && ischar(y))
+    if nargin==2
         color = y;
     end
     y = x;
     x = 1:size(y,2);
 end
 
-if ~exist('color','var'),
+if ~exist('color','var')
     color = [0 0 0];
 end
 
-if ~exist('smooth','var'),
+if ~exist('smooth','var')
     smooth = 0;
 end
 
-if size(y,2)~=length(x),
+if size(y,2)~=length(x)
     y = y';
-    if size(y,2)~=length(x),
+    if size(y,2)~=length(x)
         error('Y should have one column for each element in X');
     end
 end
 
-if isvector(y),
+if isvector(y)
     handles = plot(x,Smooth(y,smooth),'color',color);
     if nargout>0, varargout{1} = handles; end
     hold on;
@@ -54,7 +56,7 @@
 y = Smooth(nanmean(y),smooth);
 handles = fill(xx,yy,color);
 
-if solid,
+if solid
     set(handles,'FaceColor',mean([color;1 1 1]),'edgeAlpha',0);
 else % transparent
     set(handles,'FaceAlpha',0.5,'edgeAlpha',0);

reactivation/ActivityTemplates.m

@@ -45,7 +45,7 @@
 %
 %    See also ReactivationStrength.
 
-% Copyright (C) 2016-2022 by Michaël Zugaro, Ralitsa Todorova
+% Copyright (C) 2016-2024 by Michaël Zugaro, Ralitsa Todorova
 %
 % This program is free software; you can redistribute it and/or modify
 % it under the terms of the GNU General Public License as published by

spikes/DeconvolvePETH.m

@@ -1,12 +1,12 @@
 function [deconvolved,t] = DeconvolvePETH(signal,events,varargin)
 
-% [DeconvolvePETH] - [Compute a deconvolved version of PETH which removes the
-% smoothing effects of the events' autocorrelogram]
+%DeconvolvePETH - Compute a deconvolved version of PETH which removes the
+% smoothing effects of the events' autocorrelogram
 %
 %  INPUTS
-%    [signal]      [signal to find events for]
-%    [events]      [events for PETH]
-%    <options>   optional list of property-value pairs (see table below)
+%    signal         signal to find events for
+%    events         events for PETH
+%    <options>      optional list of property-value pairs (see table below)
 %    =========================================================================
 %     Properties    Values
 %    -------------------------------------------------------------------------
@@ -30,15 +30,15 @@
 %    =========================================================================
 %
 %  OUTPUTS
-%    [deconvolved]     [deconvolved PETH]
-%    [t]               [times of PETH]
+%    deconvolved    deconvolved PETH
+%    t              times of PETH
 
 %
 % SEE ALSO
 %
-%   [PETH. This is using similar script as PETH with deconvultion]
+%   PETH
 %
-% [Ralitsa Todorova] [2021-2022]
+% Copyright (C) 2021-2024 by Ralitsa Todorova
 %
 % This program is free software; you can redistribute it and/or modify
 % it under the terms of the GNU General Public License as published by
@@ -47,7 +47,7 @@
 
 % default values:
 durations = [-1 1];
-nBins = [100];
+nBins = 100;
 
 argsToPassOn = {};
 for i = 1:2:length(varargin)
@@ -85,7 +85,7 @@
 [~,t] = PETH(signal,events,'durations',durations,'nBins',nBins,argsToPassOn{:});
 [autoResponse,~] =  PETH(events,events,'durations',durations*2,'nBins',nBins*2-1,argsToPassOn{:});
 % make sure the binsize stays the same while you double the duration
-[rawResponse,~] = PETH(signal,events,'durations',durations*2,'nBins',nBins*2-1,argsToPassOn{:}); 
+[rawResponse,~] = PETH(signal,events,'durations',durations*2,'nBins',nBins*2-1,argsToPassOn{:});
 
 autocorrelogram = sum(autoResponse);
 rawPeth = sum(rawResponse);
@@ -102,17 +102,3 @@
 % add the baseline to the final PETH
 deconvolved = T \ rawPeth(round(nBins/2 + 0):round(nBins/2*3 - 1))' + const/length(events);
 end
-
-%% Old code:
-% function deconvolved = DeconvolvePETH(rawPeth,autocorrelogram)
-%
-% Note: "rawPETH" should be of double the duration of the autocorrelogram for this to work/
-
-% Example:
-% [autoResponse,t]=  PETH(events,events,'durations',durations,'nBins',nBins);
-% [rawResponse,~]=  PETH(signal,events,,'durations',durations*2,'nBins',nBins*2-1); % make sure the binsize stays the same while you double the duration
-% deconvolved = DeconvolvePETH(sum(rawResponse),sum(autoResponse));
-% plot(t,deconvolved);
-%
-% T = toeplitz([autocorrelogram(:); zeros(numel(rawPeth)-numel(autocorrelogram), 1)], [autocorrelogram(1), zeros(1, length(autocorrelogram)-1)]);
-% deconvolved = T \ rawPeth(:);