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Commit 6f7aea28 authored by marwan's avatar marwan
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fix clustering coeff. bug

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crp.m
+ 6
− 3
View file @ 6f7aea28
......@@ -84,6 +84,9 @@ function xout=crp(varargin)
% $Revision$
%
% $Log$
% Revision 5.21 2016/09/23 12:54:02 marwan
% link axis of RP and data for simultaneous effects when zooming etc.
%
% Revision 5.20 2016/06/14 11:52:12 marwan
% fix for option 'rr' in order to exclude the LOI
%
......@@ -301,7 +304,7 @@ if isnumeric(varargin{1}) % read commandline input
Nx=length(x); Ny=length(y);
NX=Nx-t*(m-1);NY=Ny-t*(m-1);
if (NX<1 | NY<1) & nogui==0;
errordlg('The embedding vectors cannot be created. Dimension M and/ or delay T are to big. Please use smaller values.','Dimension/ delay to big')
errordlg('The embedding vectors cannot be created. Dimension M and/ or delay T are too big. Please use smaller values.','Dimension/ delay too big')
waitforbuttonpress
end
% normalise the data
......@@ -392,7 +395,7 @@ else % read input from the GUI
Nx=length(x); Ny=length(y);
NX=Nx-t*(m-1);NY=Ny-t*(m-1);
if (NX<1 | NY<1) & strcmpi(action,'apply');
errordlg('The embedding vectors cannot be created. Dimension M and/ or delay T are to big. Please use smaller values.','Dimension/ delay to big')
errordlg('The embedding vectors cannot be created. Dimension M and/ or delay T are too big. Please use smaller values.','Dimension/ delay too big')
waitforbuttonpress
action='';
end
......@@ -440,7 +443,7 @@ if nogui>0
action='compute';
if (NX<1 | NY<1)
disp('Warning: The embedding vectors cannot be created.')
disp('Dimension M and/ or delay T are to big. Please use smaller values.')
disp('Dimension M and/ or delay T are too big. Please use smaller values.')
action='';
end
end
......
crp2.m
+ 5
− 2
View file @ 6f7aea28
......@@ -86,6 +86,9 @@ function xout=crp2(varargin)
% $Revision$
%
% $Log$
% Revision 5.23 2016/09/23 12:54:02 marwan
% link axis of RP and data for simultaneous effects when zooming etc.
%
% Revision 5.22 2016/03/03 14:57:40 marwan
% updated input/output check (because Mathworks is removing downwards compatibility)
% bug in crqad_big fixed (calculation of xcf).
......@@ -404,7 +407,7 @@ else % read input from the GUI
NX=Nx-t*(m-1);NY=Ny-t*(m-1);
xscale=1:Nx; yscale=1:Ny;
if (NX<1 | NY<1) & strcmpi(action,'apply');
errordlg('The embedding vectors cannot be created. Dimension M and/ or delay T are to big. Please use smaller values.','Dimension/ delay to big')
errordlg('The embedding vectors cannot be created. Dimension M and/ or delay T are too big. Please use smaller values.','Dimension/ delay too big')
waitforbuttonpress
action='';
end
......@@ -484,7 +487,7 @@ if nogui>0
action='compute';
if (NX<1 | NY<1)
disp('Warning: The embedding vectors cannot be created.')
disp('Dimension M and/ or delay T are to big. Please use smaller values.')
disp('Dimension M and/ or delay T are too big. Please use smaller values.')
action='';
end
end
......
crp_big.m
+ 6
− 3
View file @ 6f7aea28
......@@ -82,6 +82,9 @@ function xout=crp_big(varargin)
% $Revision$
%
% $Log$
% Revision 5.18 2016/09/23 12:54:02 marwan
% link axis of RP and data for simultaneous effects when zooming etc.
%
% Revision 5.17 2016/03/03 14:57:40 marwan
% updated input/output check (because Mathworks is removing downwards compatibility)
% bug in crqad_big fixed (calculation of xcf).
......@@ -288,7 +291,7 @@ if isnumeric(varargin{1})==1 % read commandline input
Nx=length(x); Ny=length(y);
NX=Nx-t*(m-1);NY=Ny-t*(m-1);
if (NX<1 | NY<1) & nogui==0;
errordlg('The embedding vectors cannot be created. Dimension M and/ or delay T are to big. Please use smaller values.','Dimension/ delay to big')
errordlg('The embedding vectors cannot be created. Dimension M and/ or delay T are too big. Please use smaller values.','Dimension/ delay too big')
waitforbuttonpress
end
% normalise the data
......@@ -378,7 +381,7 @@ else % read input from the GUI
Nx=length(x); Ny=length(y);
NX=Nx-t*(m-1);NY=Ny-t*(m-1);
if (NX<1 | NY<1) & strcmpi(action,'apply');
errordlg('The embedding vectors cannot be created. Dimension M and/ or delay T are to big. Please use smaller values.','Dimension/ delay to big')
errordlg('The embedding vectors cannot be created. Dimension M and/ or delay T are too big. Please use smaller values.','Dimension/ delay too big')
waitforbuttonpress
action='';
end
......@@ -424,7 +427,7 @@ if nogui>0
action='compute';
if (NX<1 | NY<1)
disp('Warning: The embedding vectors cannot be created.')
disp('Dimension M and/ or delay T are to big. Please use smaller values.')
disp('Dimension M and/ or delay T are too big. Please use smaller values.')
action='';
end
end
......
crqa.m
+ 43
− 23
View file @ 6f7aea28
......@@ -149,6 +149,9 @@ function xout=crqa(varargin)
% $Revision$
%
% $Log$
% Revision 5.60 2017/03/30 14:33:27 marwan
% fixing a bug in tt.m if applied to CRP
%
% Revision 5.59 2016/09/30 15:11:02 marwan
% bug with wrong axes handle for the results plots fixed
%
......@@ -361,7 +364,7 @@ splash_gpl('crp');
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% check and read the input
try
%try
errcode=1;
set(0,'ShowHidden','on')
......@@ -477,8 +480,11 @@ errcode=1;
return
end
x=double(varargin{1});
if isempty(varargin{2}) | ~isnumeric(varargin{2}), y=x; else
y=double(varargin{2}); end
if isempty(varargin{2}) | ~isnumeric(varargin{2}) | all(size(varargin{2}))
y=x;
else
y=double(varargin{2});
end
% if sum(double(diff(x(:,1))<=0)), time_scale_flag=0; end
if (isnumeric(varargin{2}) & max(size(varargin{2}))==1) | ~isnumeric(varargin{2})
......@@ -684,9 +690,14 @@ errcode=1;
% normalize data if necessary
if nonorm
x = (x - repmat(mean(x),length(x),1)) ./ repmat(std(x),length(x),1);
y = (y - repmat(mean(y),length(y),1)) ./ repmat(std(y),length(y),1);
xMean = mean(x(~isnan(x)));
yMean = mean(y(~isnan(y)));
xStd = std(x(~isnan(x)));
yStd = std(y(~isnan(y)));
x = (x - repmat(xMean,length(x),1)) ./ repmat(xStd,length(x),1);
y = (y - repmat(yMean,length(y),1)) ./ repmat(yStd,length(y),1);
end
......@@ -749,6 +760,7 @@ case 'init'
axes_height = 5.8;
axes_base = 3;
axes_hoffset = 2.5;
h = 0;
h(1)=axes(props.axes,...
'Tag','crqa_axes_Data',...
'Box','On',...
......@@ -756,10 +768,10 @@ case 'init'
if time_scale_flag
plot(xscale,x(:,2:end),'color',props.line.Color)
if ~all(x(:)==y(:)) hold on; plot(yscale,y(:,2:end),'r'), end
if ~isequal(x(~isnan(x)),y(~isnan(y))) hold on; plot(yscale,y(:,2:end),'r'), end
else
plot(xscale,x(:,1:end),'color',props.line.Color)
if ~all(x(:)==y(:)) hold on; plot(yscale,y(:,1),'r'), end
if ~isequal(x(~isnan(x)),y(~isnan(y))) hold on; plot(yscale,y(:,1),'r'), end
end
set(h(1),'Tag','crqa_axes_Data','color',props.axes.Color)
ylabel('Data')
......@@ -780,7 +792,7 @@ case 'init'
cla
text(0.5,0.5,sprintf('%6.4f',x_var(1,2)),'FontWeight','bold','HorizontalAlign','Center')
end
if ~all(x(:)==y(:))
if ~isequal(x(~isnan(x)),y(~isnan(y)))
hold on;
if time_scale_flag
y_var = winplot(y(:,2),w,wstep,2);
......@@ -794,12 +806,13 @@ case 'init'
text(0.5,0.5,sprintf('%6.5f, %6.5f',x_var(2,2),y_var(1,2)),'FontWeight','bold','HorizontalAlign','Center')
end
h3=axes('Units','Char',...
'Pos',get(h,'Pos'),...
'XLim',get(h,'XLim'),...
'YLim',get(h,'YLim'),...
'Position',get(h(2),'Position'),...
'XLim',get(h(2),'XLim'),...
'YLim',get(h(2),'YLim'),...
'YAxisLocation','right',...
'Color','none',...
'Tag','crqa_axes_CoVar',...
'XTick',[],...
'visible','off');
end
set(gcf,'CurrentAxes',h(2));
......@@ -1155,7 +1168,7 @@ if strcmpi(method,'Maximum Norm, fixed RR') method = 'rr'; end
if nogui == 1 & plugin_exist & ( method_n < 4 | method_n == 8 ) & length(x) == length(y)
disp('(plugin used)')
end
plugin_exist = 0;
errcode=20;
% general histograms of line structures for significance test
......@@ -1183,10 +1196,12 @@ for i=1:wstep:Nx-w+1;
if time_scale_flag
x_var=var(x(i:i+w-1,2)); y_var=var(y(i:i+w-1,2));
xx = x(i:i+w-1,2); yy = y(i:i+w-1,2);
x_var=var(xx(~isnan(xx))); y_var=var(yy(~isnan(yy)));
temp=cov(x(i:i+w-1,2),y(i:i+w-1,2));
else
x_var=var(x(i:i+w-1,1)); y_var=var(y(i:i+w-1,1));
xx = x(i:i+w-1,1); yy = y(i:i+w-1,1);
x_var=var(xx(~isnan(xx))); y_var=var(yy(~isnan(yy)));
temp=cov(x(i:i+w-1,1),y(i:i+w-1,1));
end
xy_var=temp(1,2);
......@@ -1237,6 +1252,10 @@ for i=1:wstep:Nx-w+1;
errcode=22;
% import RQA
rqa_in = [];
RR = NaN; DET = NaN; LAM = NaN; Lmax = NaN;
L = NaN; ENTR = NaN; Vmax = NaN; TT = NaN; t1 = NaN; t2 = NaN;
RT = NaN; RTmax = NaN; RF = NaN; ENTW = NaN;
try
fid = fopen(tmp_rqadatafile,'r'); % open RQA data file
while 1
......@@ -1290,7 +1309,7 @@ for i=1:wstep:Nx-w+1;
if time_scale_flag
if length(x(i:i+w-1,:)) > 2000
X=crp_big(x(i:i+w-1,:),y(i:i+w-1,:),m,t,e,method,'nonorm','silent');
else
else
X=crp(x(i:i+w-1,:),y(i:i+w-1,:),m,t,e,method,'nonorm','silent');
end
else
......@@ -1442,7 +1461,7 @@ for i=1:wstep:Nx-w+1;
% global clustering coefficient
errcode=279;
kv = sum(X_theiler,1); % degree of nodes
Clust = mean(diag(double(X_theiler)*double(X_theiler)*double(X_theiler))' ./ (kv .* (kv-1)));
Clust = nanmean(diag(double(X_theiler)*double(X_theiler)*double(X_theiler))' ./ (kv .* (kv-1)));
% transitivity
denom = sum(sum(double(X_theiler) * double(X_theiler)));
Trans = trace(double(X_theiler)*double(X_theiler)*double(X_theiler))/denom;
......@@ -1541,7 +1560,8 @@ if ~nogui
h=findobj('Tag','crqa_axes_RTE','Parent',gcf); h_axes.h(7)=h(1);
h=findobj('Tag','crqa_axes_T2','Parent',gcf); h_axes.h(8)=h(1);
h=findobj('Tag','crqa_axes_Var','Parent',gcf); h_axes.h(9)=h(1);
if ~all(x(:)==y(:)), h=findobj('Tag','crqa_axes_CoVar','Parent',gcf); h_axes.h(10)=h(1); end
if ~isequal(x(~isnan(x)),y(~isnan(y))), h=findobj('Tag','crqa_axes_CoVar','Parent',gcf); h_axes.h(10)=h(1); end
for i=1:9,
set(gcf,'CurrentAxes',h_axes.h(i))
if size(Y,1)==1
......@@ -1554,11 +1574,11 @@ if ~nogui
% set(h_axes.h(i+1),'visible','off');
% end
else
if i==9
if i==9 % Variance and covariance plot
cla
h2=stairs(xscale(1:wstep:length(Y)),Y(1:wstep:end,index(i)));
set(h2,'color',props.line.Color)
if ~all(x(:)==y(:))
if ~isequal(x(~isnan(x)),y(~isnan(y)))
set(gca,'Color','none')
hold on; h2=stairs(xscale(1:wstep:length(Y)),Y(1:wstep:end,index(10)),'r');
set(gcf,'CurrentAxes',h_axes.h(i+1));cla
......@@ -1566,7 +1586,7 @@ if ~nogui
h3=stairs(xscale(1:wstep:length(Y)),Y(1:wstep:end,index(11))); set(h3,'color',[0 .4 0]);
ylabel(tx(i+1));
set(h_axes.h(i+1),'Tag',tags{i+1},'Units','Norm','Color','none','YAxisLocation','right','YColor',[0 .4 0])
set(h_axes.h(i+1),'Tag',tags{i+1},'Units','Norm','Color','none','YAxisLocation','right','YColor',[0 .4 0],'xtick',[])
end
else
plot(xscale(1:wstep:length(Y)),Y(1:wstep:end,index(i)),'color',props.line.Color)
......@@ -1582,7 +1602,7 @@ if ~nogui
set(h(1),'UserData',Y,'Enable','On')
xlim = get(h_axes.h(9),'xlim');
if length(Y(:,1)) > 1, set(h_crqa_axes_Data,'xlim',xlim), end
if ~all(x(:)==y(:)) & length(Y(:,1)) == 1, set(h_axes.h(10),'visible','off'); delete(get(h_axes.h(10),'children')), end
if ~isequal(x(~isnan(x)),y(~isnan(y))) & length(Y(:,1)) == 1, set(h_axes.h(10),'visible','off'); delete(get(h_axes.h(10),'children')), end
else
if nargout, xout=Y(:,argout_index); end
end
......@@ -1597,8 +1617,8 @@ end
%if 0
catch
if 0
%catch
if nogui~=2, if ishandle(hw), close(hw), end , end
if nargout, xout = NaN; end
......
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