From 9800916fceab1317c6e02f06a4678c3fec8de8f2 Mon Sep 17 00:00:00 2001
From: marwan <>
Date: Wed, 16 Mar 2005 16:22:29 +0000
Subject: [PATCH] support for joint recurrence plots added
---
jrp.m | 895 ++++++++++++++++++++++++++++++++++++++++++++++
jrqa.m | 1078 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 files changed, 1973 insertions(+)
create mode 100644 jrp.m
create mode 100644 jrqa.m
diff --git a/jrp.m b/jrp.m
new file mode 100644
index 0000000..178b6e8
--- /dev/null
+++ b/jrp.m
@@ -0,0 +1,895 @@
+function xout=jrp(varargin)
+%JRP Creates a joint recurrence plot.
+% JRP(X [,Y] [,param1,param2,...]) creates a simple
+% joint recurrence plot/ recurrence plot of maximal
+% two data series. Embedding parameters will be the
+% same for both systems. Results can be stored into
+% the workspace.
+%
+% R=JRP(X,M,T,E) uses the dimension M, delay T
+% and the size of neighbourhood E and creates a recurrence
+% plot of X.
+%
+% R=JRP(X,Y,'order') creates an order matrix plot
+% with normalization of the data.
+%
+% R=JRP(X,Y,'distance','nonormalize') creates a
+% distance coded matrix plot without normalization
+% of the data.
+%
+% Allows to change the parameters interactively by
+% using a GUI.
+%
+% The source-data X and test-data Y can be one- or
+% a two-coloumn vectors (then, in the first column
+% have to be the time); if the test-data Y is not
+% specified, a simple recurrence plot is created.
+%
+% Parameters: dimension M, delay T and the size of
+% neighbourhood E are the first three numbers after
+% the data series; further parameters can be used
+% to switch between various methods of finding the
+% neighbours of the phasespace trajectory, to suppress
+% the normalization of the data and to suppress the
+% GUI (useful in order to use this programme by other
+% programmes).
+%
+% Methods of finding the neighbours/ of plot.
+% maxnorm - Maximum norm.
+% euclidean - Euclidean norm.
+% minnorm - Minimum norm.
+% nrmnorm - Euclidean norm between normalized vectors
+% (all vectors have the length one).
+% fan - Fixed amount of nearest neighbours.
+% inter - Interdependent neighbours.
+% omatrix - Order matrix.
+% opattern - Order patterns recurrence plot.
+% distance - Distance coded matrix (global JRP, Euclidean norm).
+%
+% Normalization of the data series.
+% normalize - Normalization of the data.
+% nonormalize - No normalization of the data.
+%
+% Suppressing the GUI.
+% gui - Creates the GUI and the output plot.
+% nogui - Suppresses the GUI and the output plot.
+% silent - Suppresses all output.
+%
+% Parameters not needed to be specified.
+%
+% Current limitation: for higher speed in
+% output the whole matrix of the recurrence
+% plot is in the work space - this limits
+% the application of long data series.
+%
+% Examples: a = sin((1:1000) * 2 * pi/67);
+% b = sin(.01 * ([1:1000] * 2 * pi/67) .^ 2);
+% jrp(a,b,3,12,'fan')
+%
+% See also CRP, JRQA.
+%
+% References:
+% Romano, M., Thiel, M., Kurths, J., von Bloh, W.:
+% Multivariate Recurrence Plots, Phys. Lett. A , 330, 2004.
+
+% Copyright (c) 2004-2005 by AMRON
+% Norbert Marwan, Potsdam University, Germany
+% http://www.agnld.uni-potsdam.de
+%
+% $Date$
+% $Revision$
+%
+% $Log$
+%
+%
+% This program is part of the new generation XXII series.
+%
+% 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 the Free Software Foundation; either version 2
+% of the License, or any later version.
+
+
+
+warning off
+global errcode props
+
+errcode=0;
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% programme properties
+
+init_properties
+hCRP=[];hCtrl=[];nogui=[];obj=[];mflag=[];
+set(0,'ShowHidden','On')
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% check and read the input
+
+error(nargchk(1,8,nargin));
+if nargout>1, error('Too many output arguments'), end
+
+check_meth={'ma','eu','mi','nr','fa','in','om','op','di'}; % maxnorm, euclidean, nrmnorm, fan, distance
+check_norm={'non','nor'}; % nonormalize, normalize
+check_gui={'gui','nog','sil'}; % gui, nogui, silent
+
+if isnumeric(varargin{1})==1 % read commandline input
+ varargin{9}=[];
+ i_double=find(cellfun('isclass',varargin,'double'));
+ i_char=find(cellfun('isclass',varargin,'char'));
+
+ % check the text input parameters for method, gui and normalization
+ temp_meth=0;
+ temp_norm=0;
+ temp_gui=0;
+ if ~isempty(i_char)
+ for i=1:length(i_char),
+ varargin{i_char(i)}(4)='0';
+ temp_meth=temp_meth+strcmpi(varargin{i_char(i)}(1:2),check_meth');
+ temp_norm=temp_norm+strcmpi(varargin{i_char(i)}(1:3),check_norm');
+ temp_gui=temp_gui+strcmpi(varargin{i_char(i)}(1:3),check_gui');
+ end
+ method=min(find(temp_meth));
+ nonorm=min(find(temp_norm))-1;
+ nogui=min(find(temp_gui))-1;
+ if isempty(method), method=1; end
+ if isempty(nonorm), nonorm=1; end
+ if isempty(nogui), nogui=0; end
+ if method>length(check_meth), method=length(check_meth); end
+ if nonorm>1, nonorm=1; end
+ if nogui>2, nogui=2; end
+ else
+ method=1; nonorm=1; nogui=0;
+ end
+ if nogui==0 & nargout>0, nogui=1; end
+
+ % get the parameters for creating RP
+ if max(size(varargin{1}))<=3
+ error('To less values in data X.')
+ end
+ x=double(varargin{1});
+% if isempty(varargin{2}) | ~isnumeric(varargin{2}), y=x; end
+% if ~isempty(varargin{2}) & isnumeric(varargin{2}), y=double(varargin{2}); end
+ if isempty(varargin{2}) | ~isnumeric(varargin{2}), y=x;
+ else, y=double(varargin{2}); end
+
+ if (isnumeric(varargin{2}) & max(size(varargin{2}))==1) | ~isnumeric(varargin{2})
+ y=x;
+ if ~isempty(varargin{i_double(2)}), m=varargin{i_double(2)}(1); else m=1; end
+ if ~isempty(varargin{i_double(3)}), t=varargin{i_double(3)}(1); else t=1; end
+ if ~isempty(varargin{i_double(4)}), e=varargin{i_double(4)}(1); else e=.1; end
+ else
+ if ~isempty(varargin{i_double(3)}), m=varargin{i_double(3)}(1); else m=1; end
+ if ~isempty(varargin{i_double(4)}), t=varargin{i_double(4)}(1); else t=1; end
+ if ~isempty(varargin{i_double(5)}), e=varargin{i_double(5)}(1); else e=.1; end
+ end
+ if e<0, e=1; disp('Warning: The threshold size E cannot be negative and is now set to 1.'), end
+ if t<1, t=1; disp('Warning: The delay T cannot be smaller than one and is now set to 1.'), end
+ t=round(t); m=round(m); mflag=method;
+ action='init';
+
+ if max(size(x))~=max(size(y)),
+ if ~nogui, errordlg('Data must have the same length.','Check Data'), waitforbuttonpress, return, else error('Data must have the same length.'), end
+ end
+
+ 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')
+ waitforbuttonpress
+ end
+ if size(x,1)<size(x,2), x=x'; end
+ if size(y,1)<size(y,2), y=y'; end
+
+ if ~isempty(find(isnan(x)))
+ disp('Warning: NaN detected (in first variable) - will be cleared.')
+ for k=1:size(x,2), x(find(isnan(x(:,k))),:)=[]; end
+ end
+ if ~isempty(find(isnan(y)))
+ disp('Warning: NaN detected (in second variable) - will be cleared.')
+ for k=1:size(y,2), y(find(isnan(y(:,k))),:)=[]; end
+ end
+
+ if size(x,2)>=2
+ xscale=x(:,1);
+ if ~isempty(find(diff(xscale)<0)), error('First column of the first vector must be monotonically non-decreasing.'),end
+ if nonorm==1, x=(x(:,2)-mean(x(:,2)))/std(x(:,2)); else x=x(:,2); end
+ else
+ if nonorm==1, x=(x-mean(x))/std(x); end
+ xscale=(1:length(x))';
+ end
+ if size(y,2)>=2
+ yscale=y(:,1);
+ if ~isempty(find(diff(yscale)<0)), error('First column of the second vector must be monotonically non-decreasing.'),end
+ if nonorm==1, y=(y(:,2)-mean(y(:,2)))/std(y(:,2)); else y=y(:,2); end
+ else
+ if nonorm==1, y=(y-mean(y))/std(y); end
+ yscale=(1:length(y))';
+ end
+ if method==7 & m > 1,
+ m=1;
+ disp('Warning: For order matrix a dimension of one is used.')
+ end
+ ds=eye(m);
+
+
+else % read input from the GUI
+ action=varargin{1};
+ nogui=0;
+ h=get(gcf,'Name');h=h(findstr(h,'(')+1:findstr(h,')')-1);
+ hCRP=findobj('Name',['Joint Recurrence Plot (' h ')']);
+ hCtrl=findobj('Name',['Control (' h ')']);
+ h=str2num(h);
+ xshuttle=get(findobj('Parent',hCRP,'Tag','DataPlot2'),'UserData');
+ if ~isempty(xshuttle)
+ xscale=xshuttle(:,1);
+ x=xshuttle(:,2);
+ yshuttle=get(findobj('Parent',hCRP,'Tag','DataPlot1'),'UserData');
+ yscale=yshuttle(:,1);
+ y=yshuttle(:,2);
+
+ if ~isempty(hCtrl)
+ if get(findobj('Tag','Unthresh','Parent',hCtrl),'Value')
+ mflag=length(check_meth);
+ else
+ mflag=get(findobj('Tag','Method','Parent',hCtrl),'Value');
+ end
+ m=get(findobj('Tag','Dim','Parent',hCtrl),'Value');
+ t=str2num(get(findobj('Tag','Delay','Parent',hCtrl),'String'));
+ e=str2num(get(findobj('Tag','Size','Parent',hCtrl),'String'));
+ if e<0, e=1;
+ errordlg('The threshold size E cannot be negative.','Threshold size to small')
+ waitforbuttonpress
+ set(findobj('Tag','Size','Parent',hCtrl),'String','1')
+ action='';
+ end
+ if t<1, t=1;
+ errordlg('The delay T cannot be smaller than one.','Delay to small')
+ waitforbuttonpress
+ set(findobj('Tag','Delay','Parent',hCtrl),'String','1')
+ action='';
+ end
+ ds = get(findobj('Tag','Dim','Parent',hCtrl),'UserData');
+ if mflag==7 | mflag==8 | mflag==length(check_meth)
+ set(findobj('Tag','Size','Parent',hCtrl),'enable','off');
+ set(findobj('Tag','Sizetext','Parent',hCtrl),'enable','off');
+ else
+ set(findobj('Tag','Size','Parent',hCtrl),'enable','on');
+ set(findobj('Tag','Sizetext','Parent',hCtrl),'enable','on');
+ end
+
+ if mflag==7 & m > 1,
+ m=1; ds = 1;
+ disp('Warning: For order matrix a dimension of one is used.')
+ end
+ 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')
+ waitforbuttonpress
+ action='';
+ end
+ end
+ end
+ clear xshuttle yshuttle
+ cm_old=get(hCRP,'Colormap');
+ cm=[{hsv(256)}; {hot(256)}; {gray(256)};...
+ {french(256)}; {bone(256)}; {copper(256)}; {pink(256)};...
+ {flag(256)}; {lines(256)}; {colorcube(256)};...
+ {jet(256)}; {prism(256)}; {cool(256)};...
+ {autumn(256)}; {spring(256)}; {winter(256)};...
+ {summer(256)}; {flipud(gray(2))}; {flipud(cm_old)}];
+
+ if isempty(findobj('Tag','CRPFig')) & nogui==0
+ action='init';
+ end
+
+end
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% splash the GPL
+
+splash_gpl('jrp')
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% nogui
+
+if nogui>0
+ hCRP=9999;
+ if nogui~=2
+ tx(1)={'maximum norm'};
+ tx(2)={'Euclidean norm'};
+ tx(3)={'minimum norm'};
+ tx(4)={'Euclidean norm of normalized distance'};
+ tx(5)={'fixed amount of nearest neighbours'};
+ tx(6)={'interdependent neighbours'};
+ tx(7)={'order matrix'};
+ tx(8)={'order pattern'};
+ tx(9)={'distance plot'};
+ disp(['use method: ', char(tx(method))]);
+ if nonorm==1, disp('normalize data'); else disp('do not normalize data'); end
+ end
+ 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.')
+ action='';
+ end
+end
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% switch routines
+
+try
+switch(action)
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% initialization
+
+ case 'init'
+
+ errcode=1;
+ xshuttle(:,1)=xscale;
+ yshuttle(:,1)=yscale;
+ xshuttle(:,2)=x;
+ yshuttle(:,2)=y;
+ ds=eye(m);
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% create GUI
+
+ errcode=2;
+ root_ud=get(0,'UserData');
+ if isstruct(root_ud)
+ if isfield(root_ud,'crp')
+ if ~isempty(root_ud.crp)
+ root_ud.crp=[root_ud.crp max(root_ud.crp)+1];
+ else
+ root_ud.crp=1;
+ end
+ h=num2str(root_ud.crp(end));
+ else
+ root_ud.crp=1;
+ h=num2str(1);
+ end
+ else
+ root_ud.old=root_ud;
+ root_ud.crp=1;
+ h=num2str(1);
+ end
+ set(0,'UserData',root_ud)
+
+ %%%%%%%%%%%%%%%%% JRP Figure
+
+ h_axes=create_JRPfig(h,xshuttle,yshuttle);
+ if nargout>0, xout=haxes; end
+
+ %%%%%%%%%%%%%%%%% Control Figure
+
+ errcode=3;
+ create_Ctrlfig('jrp',h,ds,m,t,e,method)
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% vectorswitch
+
+ case 'vectorswitch'
+
+ errcode=4;
+ vectorswitch
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% fit dimension display
+
+ case 'fitdim'
+
+ errcode=5;
+ ds2=eye(m);
+ if m>length(ds)
+ ds2(1:length(ds),1:length(ds))=ds;
+ else
+ ds2=ds(1:m,1:m);
+ end
+ ds=ds2; clear ds2
+ set(findobj('Tag','Dim','Parent',gcf),'UserData', ds);
+ for i=1:20
+ if i>m, set(findobj('Tag',['DimShift' num2str(i)],'Parent',gcf), 'Enable', 'off');
+ else, set(findobj('Tag',['DimShift' num2str(i)],'Parent',gcf), 'Enable', 'on'); end
+ end
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% unthresh
+
+ case 'unthresh'
+
+ errcode=6;
+ switch_unthresholded(hCRP)
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stretch
+
+ case 'stretch'
+
+ errcode=7;
+ stretch(hCRP,xscale,yscale,Nx,Ny)
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% change colormap
+
+ case 'log'
+
+ errcode=82;
+ change_colormapscale(hCRP,cm)
+
+
+ case 'colormap'
+
+ errcode=81;
+ change_colormap(hCtrl,hCRP,cm)
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% store
+
+ case 'store'
+
+ errcode=9;
+ X=get(findobj('Tag','CRPData','Parent',findobj('Parent',hCRP,'Tag','CRPPlot')),'UserData');
+ if isempty(X)
+ warndlg('The JRP matrix is still empty. Please start the computation before storing.','Empty JRP')
+ waitforbuttonpress
+ else
+ assignin('base','X', double(X))
+ end
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% handlevisON
+
+ case 'handlevisON'
+
+ set(hCRP, 'HandleVis','on')
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% close
+
+ case 'close'
+ errcode=101;
+ close_all
+
+
+ case 'smartclose'
+ errcode=102;
+ if ishandle(hCRP) & ishandle(hCtrl)
+ smart_close(hCRP,hCtrl)
+ end
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% computation
+
+ case 'compute'
+
+ errcode=11;
+ txt_cross='Joint ';
+ if size(x)==size(y)
+ if x==y, txt_cross=''; end
+ end
+ if nogui==0
+ setptr([hCRP,hCtrl],'watch')
+ h=findobj('Tag','Apply','Parent',hCtrl);
+ obj.children=get(hCtrl,'Children');
+ obj.enable=get(obj.children,'Enable');
+ set(obj.children,'Enable','off')
+ set(h(1),'String','Stop',...
+ 'ToolTip','Stops the computation.',...
+ 'Enable','on',...
+ 'Callback','set(gcbo,''String'',''Stopped'')')
+ end
+ set(findobj('Tag','Status','Parent',findobj('Parent',hCRP,'Tag','CRPPlot')),'Visible','on')
+ set(findobj('Tag','CRPData','Parent',findobj('Parent',hCRP,'Tag','CRPPlot')),'Visible','off')
+ set(findobj('Tag','Status','Parent',findobj('Parent',hCRP,'Tag','CRPPlot')),'String','Building Embedding Vectors'),drawnow
+ X=uint8(zeros(NY,NX));
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+
+ i=(1:NX)';j=0:t:0+(m-1)*t;
+ i=reshape(i(:,ones(1,m))+j(ones(NX,1),:),m*NX,1);
+ x1=x(i);
+ x2=reshape(x1,NX,m);
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+
+ i=(1:NY)';j=0:t:0+(m-1)*t;
+ i=reshape(i(:,ones(1,m))+j(ones(NY,1),:),m*NY,1);
+ y1=y(i);
+ y2=reshape(y1,NY,m);
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+
+ y2=y2*ds; % switch vectors
+
+ [NX, mx] = size(x2);
+ [NY, my] = size(y2);
+
+ clear jx jy x1 y1
+
+ switch(mflag)
+
+ %%%%%%%%%%%%%%%%% local JRP, fixed distance
+
+ case {1,2,3}
+
+ errcode=111;
+
+ set(findobj('Tag','Status','Parent',findobj('Parent',hCRP,'Tag','CRPPlot')),'String','Reshape Embedding Vectors (1)'),drawnow
+ px = permute(x2, [ 1 3 2 ]);
+ py = permute(x2, [ 3 1 2 ]);
+ set(findobj('Tag','Status','Parent',findobj('Parent',hCRP,'Tag','CRPPlot')),'String','Compute Distance Matrix (1)'),drawnow
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+ s1 = px(:,ones(1,NX),:) - py(ones(1,NX),:,:);
+
+ set(findobj('Tag','Status','Parent',findobj('Parent',hCRP,'Tag','CRPPlot')),'String','Reshape Embedding Vectors (2)'),drawnow
+ px = permute(y2, [ 1 3 2 ]);
+ py = permute(y2, [ 3 1 2 ]);
+ set(findobj('Tag','Status','Parent',findobj('Parent',hCRP,'Tag','CRPPlot')),'String','Compute Distance Matrix (2)'),drawnow
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+ s2 = px(:,ones(1,NY),:) - py(ones(1,NY),:,:);
+
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+ switch mflag
+ case 1
+ %%%%%%%%%%%%%%%%% maximum norm
+ sx = max(abs(s1),[],3);
+ sy = max(abs(s2),[],3);
+ matext=[num2str(round(100*e)/100) '\sigma (fixed distance maximum norm)'];
+ case 2
+ %%%%%%%%%%%%%%%%% euclidean norm
+ errcode=112;
+ sx = sqrt(sum(s1.^2, 3));
+ sy = sqrt(sum(s2.^2, 3));
+ matext=[num2str(round(100*e)/100) '\sigma (fixed distance euclidean norm)'];
+ case 3
+ %%%%%%%%%%%%%%%%% minimum norm
+ errcode=113;
+ sx = sum(abs(s1), 3);
+ sy = sum(abs(s2), 3);
+ matext=[num2str(round(100*e)/100) '\sigma (fixed distance minimum norm)'];
+ end
+
+ set(findobj('Tag','Status','Parent',findobj('Parent',hCRP,'Tag','CRPPlot')'),'String','Building JRP Matrix'),drawnow
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+ X1=sx<e;
+ X2=sy<e;
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+ X = uint8(X1)' .* uint8(X2)'; clear s s1 s2 sx sy x1 y1 px py X1 X2
+
+
+ %%%%%%%%%%%%%%%%% local JRP, normalized distance euclidean norm
+
+ case 4
+
+ errcode=114;
+ set(findobj('Tag','Status','Parent',findobj('Parent',hCRP,'Tag','CRPPlot')),'String','Normalize Embedding Vectors'),drawnow
+ Dx=sqrt(sum(((x2(:,:)).^2)'))';
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+ Dy=sqrt(sum(((y2(:,:)).^2)'))';
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+ x1=x2./repmat(Dx,1,m);x2=x1;
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+ y1=y2./repmat(Dy,1,m);y2=y1; clear Dx Dy y1 x1
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+
+ set(findobj('Tag','Status','Parent',findobj('Parent',hCRP,'Tag','CRPPlot')),'String','Reshape Embedding Vectors (1)'),drawnow
+ px = permute(x2, [ 1 3 2 ]);
+ py = permute(x2, [ 3 1 2 ]);
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+ set(findobj('Tag','Status','Parent',findobj('Parent',hCRP,'Tag','CRPPlot')),'String','Compute Distance Matrix (1)'),drawnow
+ s1 = px(:,ones(1,NX),:) - py(ones(1,NX),:,:);
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+ sx = sqrt(sum(s1.^2, 3));
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+
+ set(findobj('Tag','Status','Parent',findobj('Parent',hCRP,'Tag','CRPPlot')),'String','Reshape Embedding Vectors (2)'),drawnow
+ px = permute(y2, [ 1 3 2 ]);
+ py = permute(y2, [ 3 1 2 ]);
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+ set(findobj('Tag','Status','Parent',findobj('Parent',hCRP,'Tag','CRPPlot')),'String','Compute Distance Matrix (2)'),drawnow
+ s1 = px(:,ones(1,NY),:) - py(ones(1,NY),:,:);
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+ sy = sqrt(sum(s1.^2, 3));
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+
+ set(findobj('Tag','Status','Parent',findobj('Parent',hCRP,'Tag','CRPPlot')'),'String','Building JRP Matrix'),drawnow
+ X=(uint8(255*sx/max(sx(:)))<(255*e/max(sx(:))))' .* (uint8(255*sy/max(sy(:)))<(255*e/max(sy(:))))'; clear sx sy s1 x1 y1 px py
+ matext=[num2str(round(100*e)/100) '\sigma (normalized distance euclidean norm)'];
+
+
+ %%%%%%%%%%%%%%%%% local JRP, fixed neigbours amount
+
+ case 5
+
+ errcode=115;
+ if e>=1
+ e=round(e)/100;
+ txt=['The value for fixed neigbours amount has to be smaller '...
+ 'than one. Continue the computation with a value of ' ...
+ num2str(e)];
+ if nogui==0
+ warndlg(txt,'Threshold value mismatch');
+ drawnow
+ waitforbuttonpress
+ set(findobj('Tag','Size','Parent',gcf),'String',num2str(e))
+ end
+ end
+
+ set(findobj('Tag','Status','Parent',findobj('Parent',hCRP,'Tag','CRPPlot')),'String','Reshape Embedding Vectors (1)'),drawnow
+ px = permute(x2, [ 1 3 2 ]);
+ py = permute(x2, [ 3 1 2 ]);
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+ set(findobj('Tag','Status','Parent',findobj('Parent',hCRP,'Tag','CRPPlot')),'String','Compute Distance Matrix (1)'),drawnow
+ s1 = px(:,ones(1,NX),:) - py(ones(1,NX),:,:);
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+% s = sqrt(sum(s1.^2, 3));
+ s = (sum(s1.^2, 3));
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+
+ set(findobj('Tag','Status','Parent',findobj('Parent',hCRP,'Tag','CRPPlot')),'String','Sort Distance Matrix (1)'),drawnow
+ mine=round(NY*e);
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+ [SS, JJ]=sort(s');
+ JJ=JJ';
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+
+ X1(NX*NX)=uint8(0); X1(JJ(:,1:mine)+repmat([0:NX:NX*NX-1]',1,mine))=uint8(1);
+
+
+ set(findobj('Tag','Status','Parent',findobj('Parent',hCRP,'Tag','CRPPlot')),'String','Reshape Embedding Vectors (2)'),drawnow
+ px = permute(y2, [ 1 3 2 ]);
+ py = permute(y2, [ 3 1 2 ]);
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+ set(findobj('Tag','Status','Parent',findobj('Parent',hCRP,'Tag','CRPPlot')),'String','Compute Distance Matrix (2)'),drawnow
+ s1 = px(:,ones(1,NY),:) - py(ones(1,NY),:,:);
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+% s = sqrt(sum(s1.^2, 3));
+ s = (sum(s1.^2, 3));
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+
+ set(findobj('Tag','Status','Parent',findobj('Parent',hCRP,'Tag','CRPPlot')),'String','Sort Distance Matrix (2)'),drawnow
+ mine=round(NY*e);
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+ [SS, JJ]=sort(s');
+ JJ=JJ';
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+
+ X2(NY*NY)=uint8(0); X2(JJ(:,1:mine)+repmat([0:NY:NY*NY-1]',1,mine))=uint8(1);
+
+
+ set(findobj('Tag','Status','Parent',findobj('Parent',hCRP,'Tag','CRPPlot')),'String','Building JRP Matrix'),drawnow
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+ X=reshape(X1,NX,NX) .* reshape(X2,NY,NY); clear X1 X2 SS JJ s px py
+
+ matext=[num2str(round(1000*mine/NY)/10) '% (fixed neighbours amount)'];
+
+
+ %%%%%%%%%%%%%%%%% local JRP, interdependent neigbours
+
+ case 6
+
+ errcode=116;
+ if e>=1
+ e=round(e)/100;
+ txt=['The value for fixed neigbours amount has to be smaller '...
+ 'than one. Continue the computation with a value of ' ...
+ num2str(e)];
+ if nogui==0
+ warndlg(txt,'Threshold value mismatch');
+ drawnow
+ waitforbuttonpress
+ set(findobj('Tag','Size','Parent',gcf),'String',num2str(e))
+ end
+ end
+
+ set(findobj('Tag','Status','Parent',findobj('Parent',hCRP,'Tag','CRPPlot')),'String','Reshape Embedding Vectors (1)'),drawnow
+ px = permute(x2, [ 1 3 2 ]);
+ py = permute(x2, [ 1 3 2 ]);
+ px2 = permute(x2, [ 3 1 2 ]);
+ py2 = permute(x2, [ 3 1 2 ]);
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+
+ set(findobj('Tag','Status','Parent',findobj('Parent',hCRP,'Tag','CRPPlot')),'String','Compute Distance Matrix (1)'),drawnow
+ s1 = px(:,ones(1,NX),:) - px2(ones(1,NX),:,:);
+ sx = sqrt(sum(s1.^2, 3));
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+ s1 = py(:,ones(1,NX),:) - py2(ones(1,NX),:,:);
+ sy = sqrt(sum(s1.^2, 3));
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+
+ set(findobj('Tag','Status','Parent',findobj('Parent',hCRP,'Tag','CRPPlot')),'String','Sort Distance Matrix (1)'),drawnow
+ mine=round(min(NX,NX)*e);
+ [SSx, JJx]=sort(sx);%SSx(1,:)=[]; JJx(1,:)=[];
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+ [SSy, JJy]=sort(sy);%SSy(1,:)=[]; JJy(1,:)=[];
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+ e=mean(SSy(mine:mine+1,:));
+ set(findobj('Tag','Status','Parent',findobj('Parent',hCRP,'Tag','CRPPlot')),'String','Building RP Matrix (1)'),drawnow
+ for i=1:min(NX,NX),
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+ JJx((JJx(1:mine,i)>min(NX,NX)),i)=1;
+ X1(i,JJx(1:mine,i))=sy(i,JJx(1:mine,i))<=e(i);
+ end
+
+
+ set(findobj('Tag','Status','Parent',findobj('Parent',hCRP,'Tag','CRPPlot')),'String','Reshape Embedding Vectors (2)'),drawnow
+ px = permute(y2, [ 1 3 2 ]);
+ py = permute(y2, [ 1 3 2 ]);
+ px2 = permute(y2, [ 3 1 2 ]);
+ py2 = permute(y2, [ 3 1 2 ]);
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+
+ set(findobj('Tag','Status','Parent',findobj('Parent',hCRP,'Tag','CRPPlot')),'String','Compute Distance Matrix (2)'),drawnow
+ s1 = px(:,ones(1,NY),:) - px2(ones(1,NY),:,:);
+ sx = sqrt(sum(s1.^2, 3));
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+ s1 = py(:,ones(1,NY),:) - py2(ones(1,NY),:,:);
+ sy = sqrt(sum(s1.^2, 3));
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+
+ set(findobj('Tag','Status','Parent',findobj('Parent',hCRP,'Tag','CRPPlot')),'String','Sort Distance Matrix (2)'),drawnow
+ mine=round(min(NY,NY)*e);
+ [SSx, JJx]=sort(sx);%SSx(1,:)=[]; JJx(1,:)=[];
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+ [SSy, JJy]=sort(sy);%SSy(1,:)=[]; JJy(1,:)=[];
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+ e=mean(SSy(mine:mine+1,:));
+ set(findobj('Tag','Status','Parent',findobj('Parent',hCRP,'Tag','CRPPlot')),'String','Building RP Matrix (2)'),drawnow
+ for i=1:min(NY,NY),
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+ JJx((JJx(1:mine,i)>min(NY,NY)),i)=1;
+ X2(i,JJx(1:mine,i))=sy(i,JJx(1:mine,i))<=e(i);
+ end
+
+ set(findobj('Tag','Status','Parent',findobj('Parent',hCRP,'Tag','CRPPlot')),'String','Building JRP Matrix'),drawnow
+ X = X1.* X2;
+
+ clear X1 X2 SS* JJ* s sx sy s1 px py px2 py2
+ matext=[num2str(round(1000*mine/NY)/10) '% (interdependent neighbours)'];
+
+
+ %%%%%%%%%%%%%%%%% order matrix
+
+ case 7
+
+ errcode=117;
+
+ set(findobj('Tag','Status','Parent',findobj('Parent',hCRP,'Tag','CRPPlot')),'String','Compute Order Matrix (1)'),drawnow
+ px = permute(x2, [ 1 3 2 ]);
+ py = permute(x2, [ 3 1 2 ]);
+ X1 = px(:,ones(1,NX),:) >= py(ones(1,NX),:,:) - e;
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+
+ set(findobj('Tag','Status','Parent',findobj('Parent',hCRP,'Tag','CRPPlot')),'String','Compute Order Matrix (2)'),drawnow
+ px = permute(y2, [ 1 3 2 ]);
+ py = permute(y2, [ 3 1 2 ]);
+ X2 = px(:,ones(1,NY),:) >= py(ones(1,NY),:,:) - e;
+ X = X1' .* X2';
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+
+ clear X1 X2 s sx sy s1 px py
+ matext='';
+
+ %%%%%%%%%%%%%%%%% order pattern recurrence plot
+
+ case 8
+
+ errcode=118;
+
+ set(findobj('Tag','Status','Parent',findobj('Parent',hCRP,'Tag','CRPPlot')),'String','Compute Order Patterns'),drawnow
+
+ % create a order pattern test
+ cmdStr = '';
+ for i=2:m;
+ cmdStr = [cmdStr, ' permX(:,', num2str(i-1) ,') < permX(:,', num2str(i), ') + eps'];
+ if i < m, cmdStr = [cmdStr, ' &']; end
+ end
+ if m==1
+ cmdStr = '1';
+ disp('Warning: No order patterns for dimension one; please use higher dimension!')
+ end
+
+
+ % order patterns by permutation of the set of values
+ clear patt*
+ for i=1:length(x2)
+ permX=perms(x2(i,:));
+ orderPattern = find(eval(cmdStr));
+ if isempty(orderPattern) orderPattern = 0; end
+ pattX(i) = orderPattern(1);
+ end
+ for i=1:length(y2)
+ permX=perms(y2(i,:));
+ orderPattern = find(eval(cmdStr));
+ if isempty(orderPattern) orderPattern = 0; end
+ pattY(i) = orderPattern(1);
+ end
+
+ set(findobj('Tag','Status','Parent',findobj('Parent',hCRP,'Tag','CRPPlot')),'String','Create Order Patterns Matrix (1)'),drawnow
+
+ px = permute(pattX', [ 1 3 2 ]);
+ py = permute(pattX', [ 3 1 2 ]);
+ X1 = px(:,ones(1,length(x2)),:) == py(ones(1,length(x2)),:,:);
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+
+ set(findobj('Tag','Status','Parent',findobj('Parent',hCRP,'Tag','CRPPlot')),'String','Create Order Patterns Matrix (2)'),drawnow
+
+ px = permute(pattY', [ 1 3 2 ]);
+ py = permute(pattY', [ 3 1 2 ]);
+ X2 = px(:,ones(1,length(y2)),:) == py(ones(1,length(y2)),:,:);
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+
+ set(findobj('Tag','Status','Parent',findobj('Parent',hCRP,'Tag','CRPPlot')),'String','Building JRP Matrix'),drawnow
+ X = X1' .* X2';
+
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+
+ clear X1 X2 sx sy s1 px py pattY pattX orderPattern permX permY
+
+ matext='';
+
+
+ %%%%%%%%%%%%%%%%% global JRP
+
+ case length(check_meth)
+
+ errcode=110+length(check_meth);
+
+ set(findobj('Tag','Status','Parent',findobj('Parent',hCRP,'Tag','CRPPlot')),'String','Compute Distance Matrix (1)'),drawnow
+ px = permute(x2, [ 1 3 2 ]);
+ py = permute(x2, [ 3 1 2 ]);
+ s1 = px(:,ones(1,NX),:) - py(ones(1,NX),:,:);
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+ sx = sqrt(sum(s1.^2, 3))';
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+
+ set(findobj('Tag','Status','Parent',findobj('Parent',hCRP,'Tag','CRPPlot')),'String','Compute Distance Matrix (2)'),drawnow
+ px = permute(y2, [ 1 3 2 ]);
+ py = permute(y2, [ 3 1 2 ]);
+ s1 = px(:,ones(1,NY),:) - py(ones(1,NY),:,:);
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+ sy = sqrt(sum(s1.^2, 3))';
+ if check_stop(hCRP,hCtrl,nogui,obj), return, end
+
+ set(findobj('Tag','Status','Parent',findobj('Parent',hCRP,'Tag','CRPPlot')),'String','Building JRP Matrix'),drawnow
+% s=exp(-(s^2)/(4*.1^2));
+ X=double(sx) .* double(sy);
+ matext='';
+
+ clear sx sy s1 px py
+
+ end
+ if nogui==0
+ for i=1:length(obj.enable), set(obj.children(i),'Enable',obj.enable{i}); end
+ set(h(1),'String','Apply',...
+ 'ToolTip','Starts the computation - be patient.',...
+ 'Callback','jrp compute')
+ setptr([hCRP,hCtrl],'arrow')
+ end
+
+ %%%%%%%%%%%%%%%%% show JRP
+
+ if nogui==0
+ Shuttle.hCRP=hCRP;
+ Shuttle.hCtrl=hCtrl;
+ Shuttle.matext=matext;
+ Shuttle.xscale=xscale;
+ Shuttle.yscale=yscale;
+ Shuttle.mflag=mflag;
+ Shuttle.m=m;
+ Shuttle.t=t;
+ Shuttle.cm=cm;
+ Shuttle.txt_cross=txt_cross;
+ show_crp(X,Shuttle)
+ else
+ if nargout==1, xout=X;end
+ end
+
+end
+warning on
+try, set(0,props.root), end
+set(0,'ShowHidden','Off')
+
+%%%%%%% error handling
+
+%if 0
+catch
+ try, if nogui==0
+ for i=1:length(obj.enable), set(obj.children(i),'Enable',obj.enable{i}); end
+ set(h(1),'String','Apply',...
+ 'ToolTip','Starts the computation - be patient.',...
+ 'Callback','jrp compute')
+ setptr([hCRP,hCtrl],'arrow')
+ end, end
+ z=whos;x=lasterr;y=lastwarn;in=varargin{1};
+ print_error('jrp',z,x,y,in,mflag,action)
+ try, set(0,props.root), end
+end
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
diff --git a/jrqa.m b/jrqa.m
new file mode 100644
index 0000000..c2f6ba4
--- /dev/null
+++ b/jrqa.m
@@ -0,0 +1,1078 @@
+function xout=jrqa(varargin)
+%JRQA Computes and plots the JRQA measures.
+% Y=JRQA(X [,Y] [,param1,param2,...])
+% Recurrence quantification analysis of the joint recurrence
+% plot of the vectors X and Y.
+%
+% The input vectors can be multi-column vectors, where
+% each column will be used as a component of the
+% phase-space vector. However, if the first column is
+% monotonically increasing, it will be used as an
+% time scale for plotting.
+%
+% Y=JRQA(X,M,T,E,W,WS,LMIN,VMIN,TW) computes the
+% recurrence quantification analysis of the recurrence
+% plot of X by using the dimension M, delay T, the
+% size of neighbourhood E, the window size W and
+% a window shifting value of WS. LMIN and VMIN
+% specify the minimal length of diagonal and vertical
+% line structures (default is 2) and TW specifies the
+% Theiler window (default is 1).
+%
+% JRQA(...) without any output arguments opens a
+% GUI for interactively control the JRQA. If an
+% output is specified with using the option 'gui',
+% then the output will contain the figure handle.
+%
+% Parameters:
+% Dimension M, delay T, the size of
+% neighbourhood E, the window size W and the shift
+% value WS are the first five numbers after the data
+% series; if W is empty, the whole plot will be calculated.
+% The next two optional numeric parameters LMIN and VMIN
+% specify the minimal length of line structures.
+%
+% As the last numeric parameter, the size of the Theiler
+% window TW can be specified (default is 1). This window
+% excludes the recurrence points parallel to the main
+% diagonal from the analysis. The application of the
+% Theiler window is useful only for recurrence plots. In
+% joint recurrence plots, the size of the Theiler window will
+% be set automatically to zero.
+%
+% Further parameters can be used to switch between various
+% methods of finding the neighbours of the phasespace
+% trajectory, to suppress the normalization of the data
+% and to suppress the GUI (useful in order to use this
+% programme by other programmes). The minimal length of
+% diagonal and vertical structures can be setted only in
+% the GUI.
+%
+% Methods of finding the neighbours.
+% maxnorm - Maximum norm.
+% euclidean - Euclidean norm.
+% minnorm - Minimum norm.
+% nrmnorm - Euclidean norm between normalized vectors
+% (all vectors have the length one).
+% fan - Fixed amount of nearest neighbours.
+% inter - Interdependent neighbours.
+% omatrix - Order matrix.
+% opattern - Order patterns recurrence plot.
+%
+% Normalization of the data series.
+% normalize - Normalization of the data.
+% nonormalize - No normalization of the data.
+%
+% Suppressing the GUI.
+% gui - Creates the GUI.
+% nogui - Suppresses the GUI.
+% silent - Suppresses all output.
+%
+% Parameters not needed to be specified.
+%
+% Output:
+% Y(:, 1) = RR (recurrence rate)
+% Y(:, 2) = DET (determinism)
+% Y(:, 3) = <L> (mean diagonal line length)
+% Y(:, 4) = Lmax (maximal diagonal line length)
+% Y(:, 5) = ENTR (entropy of the diagonal line lengths)
+% Y(:, 6) = LAM (laminarity)
+% Y(:, 7) = TT (trapping time)
+% Y(:, 8) = Vmax (maximal vertical line length)
+% Y(:, 9) = T1 (recurrence time of 1st type)
+% Y(:,10) = T2 (recurrence time of 2nd type)
+%
+% Examples: N = 500; w = 40; ws = 10;
+% b = .4; a = .6; mu = .8:-0.7/N:.1;
+% % two mutually coupled logistic maps
+% for i = 2:N,
+% a(i) = 3.6 * a(i-1) * (1 - a(i-1));
+% b(i) = 4 * b(i-1) * (1 - b(i-1)) - mu(i)*a(i);
+% end
+% plot(b)
+% % coupling is obtained by higher RR and DET values
+% jrqa(a,b,1,1,.2,w,ws);
+%
+%
+% See also CRQA, JRP and CRP.
+%
+% References:
+% Trulla, L. L., Giuliani, A., Zbilut, J. P., Webber Jr., C. L.:
+% Recurrence quantification analysis of the logistic equation with
+% transients, Phys. Lett. A, 223, 1996.
+%
+% Marwan, N., Wessel, N., Meyerfeldt, U., Schirdewan, A., Kurths, J.:
+% Recurrence Plot Based Measures of Complexity and its Application to
+% Heart Rate Variability Data, Phys. Rev. E, 66(2), 2002.
+%
+% Romano, M., Thiel, M., Kurths, J., von Bloh, W.:
+% Multivariate Recurrence Plots, Phys. Lett. A , 330, 2004.
+
+% Copyright (c) 1998-2004 by AMRON
+% Norbert Marwan, Potsdam University, Germany
+% http://www.agnld.uni-potsdam.de
+%
+% $Date$
+% $Revision$
+%
+% $Log$
+%
+%
+% This program is part of the new generation XXII series.
+%
+% 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 the Free Software Foundation; either version 2
+% of the License, or any later version.
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% programme properties
+
+global errcode props
+
+
+init_properties
+
+lmin=2;
+vmin=2;
+nonorm=1;
+theiler_window=1;
+hw=-1;
+xscale = [];
+yscale = [];
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% check the input
+
+error(nargchk(1,13,nargin));
+if nargout>1, error('Too many output arguments'), end
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% splash the GPL
+
+splash_gpl('crp');
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% check and read the input
+
+try
+errcode=1;
+
+ set(0,'ShowHidden','on')
+ varargin{14}=[];
+ i_double=find(cellfun('isclass',varargin,'double'));
+ i_char=find(cellfun('isclass',varargin,'char'));
+ t=1;
+ w=[];wstep=0; method='max'; method_n=1;
+ time_scale_flag=1; time_scale_flag_x=1;
+ nogui=0;
+ check_meth={'ma','eu','mi','nr','fa','in','om','op','di'}; % maxnorm, euclidean, nrmnorm, fan, distance
+ check_gui={'gui','nog','sil'}; % gui, nogui, silent
+ check_norm={'non','nor'}; % nonormalize, normalize
+
+ if nargin & ischar(varargin{1})
+ set(0,'ShowHidden','on');h=findobj('Tag','Msgbox_Check Input');delete(h)
+ action=varargin{1};
+ h=findobj('Tag','crqa_Fig');
+ temp=get(h(1),'UserData');
+ x=temp{1}; y=temp{2};
+ h=findobj('Tag','crqa_axes_Data','Parent',h(1)); % get handle of plot-axes object
+ h_crqa_axes_Data = h(1);
+ h=findobj('Type','line','Parent',h(1)); % get handle of line-object
+ xscale=get(h(1),'xdata');
+ h=findobj('Tag','crqa_m');
+ m=str2num(get(h(1),'String'));
+ h=findobj('Tag','crqa_maxLag');
+ t=str2num(get(h(1),'String'));
+ h=findobj('Tag','crqa_eps');
+ e=str2num(get(h(1),'String'));
+ h=findobj('Tag','crqa_method');
+ method={'Maximum Norm','Euclidean Norm','Minimum Norm','Normalized Norm','FAN','Interdependent','Order Matrix','Order Pattern','Distance Plot'};
+ method=method{get(h(1),'Value')};
+ nonorm=get(h(1),'UserData');
+ h=findobj('Tag','crqa_lmin');
+ lmin=str2num(get(h(1),'String'));
+ h=findobj('Tag','crqa_vmin');
+ vmin=str2num(get(h(1),'String'));
+ h=findobj('Tag','crqa_theiler');
+ theiler_window=str2num(get(h(1),'String'));
+ h=findobj('Tag','crqa_w');
+ w=str2num(get(h(1),'String'));
+ h=findobj('Tag','crqa_ws');
+ wstep=str2num(get(h(1),'String'));
+
+ elseif nargin & isnumeric(varargin{1})
+
+ % check the text input parameters for method, gui
+ temp_meth=0;
+ temp_norm=0;
+ temp_gui=0;
+ if ~isempty(i_char)
+ for i=1:length(i_char),
+ varargin{i_char(i)}(4)='0';
+ temp_gui=temp_gui+strcmpi(varargin{i_char(i)}(1:3),check_gui');
+ temp_norm=temp_norm+strcmpi(varargin{i_char(i)}(1:3),check_norm');
+ temp_meth=temp_meth+strcmpi(varargin{i_char(i)}(1:2),check_meth');
+ end
+ method_n=min(find(temp_meth));
+ nogui=min(find(temp_gui))-1;
+ nonorm=min(find(temp_norm))-1;
+ for i=1:length(i_char); temp2(i,:)=varargin{i_char(i)}(1:3); end
+ i_char(strmatch(check_gui(find(temp_gui)),temp2))=[];
+ if isempty(nonorm), nonorm=1; end
+ if nonorm>1, nonorm=1; end
+ if isempty(nogui), nogui=0; end
+ if isempty(method_n), method_n=1; end
+ if nogui>2, nogui=1; end
+ if method_n>length(check_meth), method0=length(check_meth); end
+ method=check_meth{method_n};
+ else
+ nogui=0;
+ if nargout
+ nogui=1;
+ action='compute';
+ end
+ end
+ if nogui==0
+ action='init';
+ else
+ action='compute';
+ end
+
+ % get the parameters for creating RP
+ if max(size(varargin{1}))<=3
+ disp('Error using ==> jrqa')
+ disp('To less values in data X.')
+ return
+ end
+ x=double(varargin{1});
+ if isempty(varargin{2}) | ~isnumeric(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})
+ y=x;
+ if ~isempty(varargin{i_double(2)}), m=varargin{i_double(2)}(1); else m=1; end
+ if ~isempty(varargin{i_double(3)}), t=varargin{i_double(3)}(1); else t=1; end
+ if ~isempty(varargin{i_double(4)}), e=varargin{i_double(4)}(1); else e=.1; end
+ if ~isempty(varargin{i_double(5)}), w=varargin{i_double(5)}(1); else w=varargin{i_double(5)}; end
+ if ~isempty(varargin{i_double(6)}), wstep=varargin{i_double(6)}(1); else wstep=1; end
+ if ~isempty(varargin{i_double(7)}), lmin=varargin{i_double(7)}(1); end
+ if ~isempty(varargin{i_double(8)}), vmin=varargin{i_double(8)}(1); end
+ if ~isempty(varargin{i_double(9)}), theiler_window=varargin{i_double(9)}(1); end
+ else
+ if ~isempty(varargin{i_double(3)}), m=varargin{i_double(3)}(1); else m=1; end
+ if ~isempty(varargin{i_double(4)}), t=varargin{i_double(4)}(1); else t=1; end
+ if ~isempty(varargin{i_double(5)}), e=varargin{i_double(5)}(1); else e=.1; end
+ if ~isempty(varargin{i_double(6)}), w=varargin{i_double(6)}(1); else w=varargin{i_double(6)}; end
+ if ~isempty(varargin{i_double(7)}), wstep=varargin{i_double(7)}(1); else wstep=1; end
+ if ~isempty(varargin{i_double(8)}), lmin=varargin{i_double(8)}(1); end
+ if ~isempty(varargin{i_double(9)}), vmin=varargin{i_double(9)}(1); end
+ if ~isempty(varargin{i_double(10)}), theiler_window=varargin{i_double(10)}(1); end
+ end
+ else
+ disp('Error using ==> jrqa')
+ disp('No valid arguments.')
+ return
+ end
+
+
+ if max(size(x))~=max(size(y)),
+ if ~nogui, errordlg('Data must have the same length.','Check Data'), waitforbuttonpress, return, else error('Data must have the same length.'), end
+ end
+
+ Nx=length(x); Ny=length(y);
+ if size(x,1)<size(x,2), x=x'; end
+ if size(y,1)<size(y,2), y=y'; end
+
+ if size(x,2)>=2
+ xscale=x(:,1);
+ if ~isempty(find(diff(xscale)<0)) % multi-column data vector, each column used as vector component
+ time_scale_flag=0;
+ time_scale_flag_x=0;
+ xscale=(1:length(x))';
+ end
+ else
+ xscale=(1:length(x))';
+ time_scale_flag=0;
+ time_scale_flag_x=0;
+ end
+
+ if size(y,2)>=2
+ yscale=y(:,1);
+ time_scale_flag=1;
+ if ~isempty(find(diff(yscale)<0))
+ time_scale_flag=0;
+ yscale=(1:length(y))';
+ end
+ if time_scale_flag && ~time_scale_flag_x % if time-scale given in y, but not in x -> error
+ if ~nogui
+ errordlg(['A time-scale for the second data is series given, but not for the first!',10,'(The time-scale has to be inlcuded as the first colummn of the first data vector.)'],'Check Data')
+ waitforbuttonpress
+ return
+ else
+ error(['A time-scale for the second data series is given, but not for the first!',10,'(The time-scale has to be inlcuded as the first colummn of the first data vector.)'])
+ end
+ end
+ else
+ yscale=(1:length(y))';
+ time_scale_flag=0;
+ end
+ if time_scale_flag_x && ~time_scale_flag % if time-scale given in x, but not in y
+ if length(x) ~= length(y)
+ if ~nogui
+ errordlg(['If you are using the time-scale given by the first vector also for',10,'the second vector, both vectors should have the same size!'],'Check Data')
+ waitforbuttonpress
+ return
+ else
+ error(['If you are using the time-scale given by the first vector also for',10,'the second vector, both vectors should have the same size!'])
+ end
+ end
+ y = [xscale, y];
+ yscale = xscale;
+ time_scale_flag=1;
+ end
+ if e<0,
+ e=1;
+ if ~nogui
+ warndlg('The threshold size E can not be negative and is now set to 1.','Check Data')
+ waitforbuttonpress
+ h=findobj('Tag','crqa_eps');
+ if ~isempty(h), set(h(1),'String',num2str(e)), end
+ else
+ disp('The threshold size E can not be negative and is now set to 1.'),
+ end
+ end
+ if t<1,
+ t=1;
+ if ~nogui
+ warndlg('The delay T can not be smaller than one and is now set to 1.','Check Data')
+ waitforbuttonpress
+ h=findobj('Tag','crqa_maxLag');
+ if ~isempty(h), set(h(1),'String',num2str(t)), end
+ else
+ disp('The delay T can not be smaller than one and is now set to 1.')
+ end
+ end
+ if isempty(w), w=Nx; wstep=1; end
+ if w < 5+(m-1)*t,
+ w=5+(m-1)*t;
+ if ~nogui, warndlg('The window size W exceeds the valid range.','Check Data')
+ waitforbuttonpress
+ h=findobj('Tag','crqa_w');
+ if ~isempty(h), set(h(1),'String',num2str(w)), end
+ else, disp('The window size W exceeds the valid range.'), end
+ end
+ if w>Nx,
+ w=Nx; wstep=1;;
+ if ~nogui, warndlg('The window size W exceeds the valid range.','Check Data')
+ waitforbuttonpress
+ h=findobj('Tag','crqa_w');
+ if ~isempty(h), set(h(1),'String',num2str(w)), end
+ else, disp('The window size W exceeds the valid range.'), end
+ end
+ if wstep<1 | wstep>Nx/3,
+ wstep=2;
+ if ~nogui, warndlg('The window shifting value WS exceeds the valid range.','Check Data')
+ waitforbuttonpress
+ h=findobj('Tag','crqa_ws');
+ if ~isempty(h), set(h(1),'String',num2str(wstep)), end
+ else, disp('The window shifting value WS exceeds the valid range.'), end
+ end
+ if vmin<1 | vmin>Nx,
+ vmin=2;
+ if ~nogui, warndlg('The minimal length for vertical lines is not valid.','Check Data')
+ waitforbuttonpress
+ h=findobj('Tag','crqa_vmin');
+ if ~isempty(h), set(h(1),'String',num2str(vmin)), end
+ else, disp('The minimal length for vertical lines is not valid.'), end
+ end
+ if lmin<1 | lmin>Nx,
+ lmin=2;
+ if ~nogui, warndlg('The minimal length for diagonal lines is not valid.','Check Input')
+ waitforbuttonpress
+ h=findobj('Tag','crqa_lmin');
+ if ~isempty(h), set(h(1),'String',num2str(lmin)), end
+ else, disp('The minimal length for diagonal lines is not valid.'), end
+ end
+ if theiler_window<0 | theiler_window>Nx,
+ theiler_window=1;
+ if ~nogui, warndlg('The value for the Theiler window is not valid.','Check Input')
+ waitforbuttonpress
+ h=findobj('Tag','crqa_theiler');
+ if ~isempty(h), set(h(1),'String',num2str(theiler_window)), end
+ else, disp('The value for the Theiler window is not valid.'), end
+ end
+ if x~=y, theiler_window=0; end
+ t=round(t); m=round(m); w=round(w); wstep=round(wstep); vmin=round(vmin); lmin=round(lmin); theiler_window=round(theiler_window);
+
+switch(action)
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% create gui
+
+case 'init'
+
+ errcode=3;
+
+ oldunit=get(0,'unit');
+ set(0,'Unit','char')
+ scr=get(0,'ScreenSize');
+ set(0,'Unit',oldunit)
+
+ h8=figure(props.window,... % Plot Figure
+ 'Tag','crqa_Fig',...
+ 'MenuBar','Figure',...
+ 'Position',[(scr(3)-150)/2 scr(4)-50 150.0000 44],...
+ 'PaperType','a4',...
+ 'PaperPosition',[0.25 0.25 7.7677 11.193],...
+ 'PaperOrientation','portrait',...
+ 'UserData',{x,y,time_scale_flag},...
+ 'Name','Joint Recurrence Quantification Analysis');
+
+ set(0,'showhidden','on')
+ h=findobj('Label','&Help','Type','uimenu');
+ if isempty(h)
+ h=uimenu('Label','&Help');
+ h2=uimenu('Parent',h(1),'Label','&Help Joint Recurrence Quantification Analysis','Callback','helpwin jrqa');
+ else
+ h1=flipud(get(h(1),'Children'));
+ set(h1(1),'Separator','on')
+ h2=uimenu('Parent',h(1),'Label','&Help Joint Recurrence Quantification Analysis','Callback','helpwin jrqa');
+ copyobj(h1,h(1))
+ delete(h1)
+ end
+ set(0,'showhidden','off')
+
+
+ h=axes(props.axes,...
+ 'Position',[89+30 24.8+14.5 6.8 3.5]);
+ logo=load('logo');
+ h2=imagesc([logo.logo fliplr(logo.logo)]);
+ set(h2,'Tag','uniLogo')
+ set(h,props.logo,'Tag','axes_logo')
+ h=uicontrol(props.text,...
+ 'Tag','text_logo',...
+ 'String','Uni Potsdam',...
+ 'Position',[97+30 24.2143+14.5 22 3.5714]);
+ h2=textwrap(h,{'© AGNLD','University of Potsdam','1998-2005'});
+ set(h,'String',h2)
+
+
+%%%%%%%%%%% plots
+
+ axes_height = 5.8;
+ axes_base = 3;
+ axes_hoffset = 2.5;
+ h=axes(props.axes,...
+ 'Tag','crqa_axes_Data',...
+ 'Box','On',...
+ 'Position',[11.2017 axes_base+4*(axes_height+axes_hoffset) 28.1785+15 axes_height]);
+
+ 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
+ else
+ plot(xscale,x(:,1),'color',props.line.Color)
+ if ~all(x(:)==y(:)) hold on; plot(yscale,y(:,1),'r'), end
+ end
+ set(h,'Tag','crqa_axes_Data','color',props.axes.Color)
+ ylabel('Data')
+
+ h=axes(props.axes,...
+ 'Tag','crqa_axes_Var',...
+ 'Box','On',...
+ 'Position',[49.8023+15 axes_base+4*(axes_height+axes_hoffset) 28.1785+15 axes_height]);
+ if time_scale_flag
+ x_var = winplot(x(:,2:end),w,wstep,2);
+ else
+ x_var = winplot(x(:,1),w,wstep,2);
+ end
+ if size(x_var,1) > 2
+ h2=stairs(xscale(round(x_var(:,1))),x_var(:,2));
+ set(h2,'color',props.line.Color)
+ else
+ cla
+ text(0.5,0.5,sprintf('%6.4f',x_var(1,2)),'FontWeight','bold','HorizontalAlign','Center')
+ end
+ if ~all(x(:)==y(:))
+ hold on;
+ if time_scale_flag
+ y_var = winplot(y(:,2:end),w,wstep,2);
+ else
+ y_var = winplot(y(:,1),w,wstep,2);
+ end
+ if size(y_var,1) > 2
+ stairs(yscale(round(y_var(:,1))),y_var(:,2),'r')
+ else
+ cla
+ 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'),...
+ 'YAxisLocation','right',...
+ 'Color','none',...
+ 'Tag','crqa_axes_CoVar',...
+ 'visible','off');
+ end
+ set(gcf,'CurrentAxes',h);
+ ylabel('Variance')
+ set(h,'Tag','crqa_axes_Var','color',props.axes.Color)
+
+
+ h=axes(props.axes,...
+ 'Tag','crqa_axes_RR',...
+ 'Box','On',...
+ 'Position',[11.2017 axes_base+3*(axes_height+axes_hoffset) 28.1785+15 axes_height]);
+ ylabel('RR')
+
+ h=axes(props.axes,...
+ 'Tag','crqa_axes_DET',...
+ 'Box','On',...
+ 'Position',[49.8023+15 axes_base+3*(axes_height+axes_hoffset) 28.1785+15 axes_height]);
+ ylabel('DET')
+
+ h=axes(props.axes,...
+ 'Tag','crqa_axes_L',...
+ 'Box','On',...
+ 'Position',[11.2017 axes_base+2*(axes_height+axes_hoffset) 28.1785+15 axes_height]);
+ ylabel('L')
+
+ h=axes(props.axes,...
+ 'Tag','crqa_axes_ENTR',...
+ 'Box','On',...
+ 'Position',[49.8023+15 axes_base+2*(axes_height+axes_hoffset) 28.1785+15 axes_height]);
+ ylabel('ENTR')
+
+ h=axes(props.axes,...
+ 'Tag','crqa_axes_LAM',...
+ 'Box','On',...
+ 'Position',[11.2017 axes_base+1*(axes_height+axes_hoffset) 28.1785+15 axes_height]);
+ ylabel('LAM')
+
+ h=axes(props.axes,...
+ 'Tag','crqa_axes_TT',...
+ 'Box','On',...
+ 'Position',[49.8023+15 axes_base+1*(axes_height+axes_hoffset) 28.1785+15 axes_height]);
+ ylabel('TT')
+
+ h=axes(props.axes,...
+ 'Tag','crqa_axes_T1',...
+ 'Box','On',...
+ 'Position',[11.2017 axes_base+0*(axes_height+axes_hoffset) 28.1785+15 axes_height]);
+ ylabel('T_1')
+
+ h=axes(props.axes,...
+ 'Tag','crqa_axes_T2',...
+ 'Box','On',...
+ 'Position',[49.8023+15 axes_base+0*(axes_height+axes_hoffset) 28.1785+15 axes_height]);
+ ylabel('T_2')
+
+%%%%%%%%%%% embedding
+ h=uicontrol(props.frame,...
+ 'Tag','frame',...
+ 'Position',[86+30 29.+2.8 29 5.7]);
+
+ h=uicontrol(props.text,...
+ 'Tag','text',...
+ 'Fontangle','italic',...
+ 'String','Embedding parameters',...
+ 'Position',[87+30 34.2+1.6 16.8333 1.5000]);
+
+ h=uicontrol(props.text,...
+ 'Tag','text',...
+ 'String','Dimension:',...
+ 'Position',[89+30 32+2.2 16.8333 1.5000]);
+
+ h=uicontrol(props.edit,...
+ 'Tag','crqa_m',...
+ 'String',num2str(m),...
+ 'ToolTip','Select the embedding dimension.',...
+ 'Position',[104+30 32+.2+2.2 7 1.5000]);
+
+ h=uicontrol(props.text,...
+ 'Tag','text',...
+ 'String','Delay:',...
+ 'Position',[89+30 30+2.32 16.8333 1.5000]);
+
+ h=uicontrol(props.edit,...
+ 'Tag','crqa_maxLag',...
+ 'String',num2str(t),...
+ 'ToolTip','Insert the embedding delay time.',...
+ 'Position',[104+30 30+.2+2.32 7 1.5000]);
+
+%%%%%%%%%%% neigbourhood
+ h=uicontrol(props.frame,...
+ 'Tag','frame',...
+ 'Position',[86+30 21.9+2.5 29 6.7]);
+
+ h=uicontrol(props.text,...
+ 'Tag','text',...
+ 'Fontangle','italic',...
+ 'String','Neighbourhood',...
+ 'Position',[87+30 26.8+2.5 23 1.5000]);
+
+ h=uicontrol(props.popup,...
+ 'Tag','text',...
+ 'Tag','crqa_method',...
+ 'UserData',nonorm,...
+ 'Value',method_n,...
+ 'String','Maximum Norm|Euclidean Norm|Minimum Norm|Normalized Norm|Fixed Amount|Interdependent|Order Matrix|Order Patterns|Distance Plot',...
+ 'Position',[89+30 24.6+.2+2.5 22 1.7]);
+
+ h=uicontrol(props.text,...
+ 'Tag','text',...
+ 'String','Threshold:',...
+ 'Position',[89+30 22.6+2.5 16.8333 1.5]);
+
+ h=uicontrol(props.edit,...
+ 'Tag','crqa_eps',...
+ 'String',num2str(e),...
+ 'ToolTip','Insert the size of neighbourhood.',...
+ 'Position',[104+30 22.6+.2+2.5 7 1.5000]);
+
+%%%%%%%%%%% jrqa parameters
+ h=uicontrol(props.frame,...
+ 'Tag','frame',...
+ 'Position',[86+30 11+.5 29 12.2]);
+
+ h=uicontrol(props.text,...
+ 'Tag','text',...
+ 'Fontangle','italic',...
+ 'String','JRQA parameters',...
+ 'Position',[87+30 19.4+2.5 23 1.5000]);
+
+ h=uicontrol(props.text,...
+ 'Tag','text',...
+ 'String','min. Diagonal:',...
+ 'Position',[89+30 17.6+2.5 16.8333 1.5]);
+
+ h=uicontrol(props.edit,...
+ 'Tag','crqa_lmin',...
+ 'String',num2str(lmin),...
+ 'ToolTip','Insert the minimal length of a diagonal line.',...
+ 'Position',[104+30 17.6+.2+2.5 7 1.5000]);
+
+ h=uicontrol(props.text,...
+ 'Tag','text',...
+ 'String','min. Vertical:',...
+ 'Position',[89+30 15.6+2.5 16.8333 1.5]);
+
+ h=uicontrol(props.edit,...
+ 'Tag','crqa_vmin',...
+ 'String',num2str(vmin),...
+ 'ToolTip','Insert the minimal length of a vertical line.',...
+ 'Position',[104+30 15.6+.2+2.5 7 1.5000]);
+
+ h=uicontrol(props.text,...
+ 'Tag','text',...
+ 'String','Theiler wind.:',...
+ 'Position',[89+30 15.6+.5 16.8333 1.5]);
+
+ h=uicontrol(props.edit,...
+ 'Tag','crqa_theiler',...
+ 'String',num2str(theiler_window),...
+ 'ToolTip','Insert the size for the Theiler window.',...
+ 'Position',[104+30 15.6+.2+.5 7 1.5000]);
+ if x~=y; set(h,'enable','off'); end
+
+ h=uicontrol(props.text,...
+ 'Tag','text',...
+ 'String','Window size:',...
+ 'Position',[89+30 13.6+.5 16.8333 1.5]);
+
+ h=uicontrol(props.edit,...
+ 'Tag','crqa_w',...
+ 'String',num2str(w),...
+ 'ToolTip','Insert the size of the sliding window.',...
+ 'Position',[104+30 13.6+.2+.5 7 1.5000]);
+
+ h=uicontrol(props.text,...
+ 'Tag','text',...
+ 'String','Window step:',...
+ 'Position',[89+30 11.6+.5 16.8333 1.5]);
+
+ h=uicontrol(props.edit,...
+ 'Tag','crqa_ws',...
+ 'String',num2str(wstep),...
+ 'ToolTip','Insert the step width for sliding the window.',...
+ 'Position',[104+30 11.6+.2+.5 7 1.5000]);
+
+
+%%%%%%%%%%% buttons
+
+ h=uicontrol(props.frame,...
+ 'Tag','frame',...
+ 'Position',[86+30 1.3+.5 29 9]);
+
+
+ h=uicontrol(props.button,...
+ 'String','Store',...
+ 'Tag','crqa_button_store',...
+ 'Enable','Off',...
+ 'ToolTip','Stores the JRQA analysis into a variable in the workspace.',...
+ 'Callback','jrqa store',...
+ 'Position',[100.5+30 7.4+.5 10.5 2.2143]);
+
+ h=uicontrol(props.button,...
+ 'Tag','crqa_button_print',...
+ 'CallBack','jrqa print',...
+ 'ToolTip','Prints the JRQA window.',...
+ 'String','Print',...
+ 'Position',[89+30 7.4+.5 10.5 2.2143]);
+
+ h=uicontrol(props.button,...
+ 'Tag','crqa_button_close',...
+ 'CallBack','jrqa close',...
+ 'ToolTip','Closes the JRQA window.',...
+ 'String','Close',...
+ 'Position',[89+30 2.1+.5 22 2.2143]);
+
+ h=uicontrol(props.button,...
+ 'String','Apply',...
+ 'Tag','crqa_button_apply',...
+ 'ToolTip','Starts the computation.',...
+ 'Callback','jrqa compute',...
+ 'Position',[89+30 4.75+.5 22 2.2143]);
+
+ set(0,'ShowHidden','on')
+ set(h8, 'HandleVis','CallBack')
+ tags={'crqa_Fig';'axes_logo';'text_logo';'crqa_theiler';'frame';'text';'crqa_axes_Data';'crqa_axes_Var';'crqa_axes_CoVar';'crqa_axes_RR';'crqa_axes_DET';'crqa_axes_L';'crqa_axes_ENTR';'crqa_axes_LAM';'crqa_axes_TT';'crqa_axes_T1';'crqa_axes_T2';'crqa_m';'crqa_maxLag';'crqa_method';'crqa_eps';'crqa_lmin';'crqa_vmin';'crqa_w';'crqa_ws';'crqa_button_store';'crqa_button_print';'crqa_button_close';'crqa_button_apply'};
+ h=[];
+ for i=1:length(tags); h=[h; findobj('Tag',tags{i})]; end
+ set(h,'Units','Norm')
+ if nargout; xout=h8; end
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% close windows
+
+case 'close'
+ errcode=101;
+ set(0,props.root)
+ h=findobj('Tag','crqa_Fig');
+ if ~isempty(h), close(h(1)), end
+ clear all
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% store
+
+case 'store'
+ errcode=0;
+ if ~isempty(findobj('Tag','crqa_button_store'))
+ h=findobj('Tag','crqa_button_store');
+ h1=findobj('Tag','crqa_button_close');
+ if ~isempty(h1), vname_old=get(h1(1),'UserData'); else vname_old=''; end
+ if isempty(vname_old), vname_old=''; end
+ vname=char(inputdlg('Choose a variable name.','Store output',1,{vname_old}));
+ if isempty(vname)
+ return
+ else
+ crqa_values=get(h(1),'UserData');
+ assignin('base',vname, [crqa_values])
+ warndlg(['JRQA measures have been assigned to the workspace variable ''',vname,'''.'],'Store output');
+ waitforbuttonpress
+ set(h1(1),'UserData',vname)
+ end
+ end
+ set(0,props.root)
+
+ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% print
+ case 'print'
+
+ errcode=91;
+ h=findobj('Tag','crqa_axes_Data','Parent',gcf); h_axes.h(1)=h(1);
+ h=findobj('Tag','crqa_axes_Var','Parent',gcf); h_axes.h(2)=h(1);
+ h=findobj('Tag','crqa_axes_CoVar','Parent',gcf); h_axes.h(11)=h(1);
+ h=findobj('Tag','crqa_axes_RR','Parent',gcf); h_axes.h(3)=h(1);
+ h=findobj('Tag','crqa_axes_DET','Parent',gcf); h_axes.h(4)=h(1);
+ h=findobj('Tag','crqa_axes_L','Parent',gcf); h_axes.h(5)=h(1);
+ h=findobj('Tag','crqa_axes_ENTR','Parent',gcf); h_axes.h(6)=h(1);
+ h=findobj('Tag','crqa_axes_LAM','Parent',gcf); h_axes.h(7)=h(1);
+ h=findobj('Tag','crqa_axes_TT','Parent',gcf); h_axes.h(8)=h(1);
+ h=findobj('Tag','crqa_axes_T1','Parent',gcf); h_axes.h(9)=h(1);
+ h=findobj('Tag','crqa_axes_T2','Parent',gcf); h_axes.h(10)=h(1);
+ h=findobj('Tag','uniLogo');
+ tags={'text_logo';'frame';'text';'crqa_m';'crqa_maxLag';'crqa_method';'crqa_eps';'crqa_lmin';'crqa_vmin';'crqa_theiler';'crqa_w';'crqa_ws';'crqa_button_store';'crqa_button_print';'crqa_button_close';'crqa_button_apply';};
+ for i=1:length(tags); h=[h; findobj('Tag',tags{i},'Parent',gcf)]; end
+ set(h,'Visible','Off')
+
+ set(h_axes.h,'Units','Character');
+ h_axes.old_pos=get(h_axes.h,'Position');
+
+ axes_height = .13;
+ axes_base = 0.065;
+ axes_hoffset = .06;
+
+ for i=2:2:10
+ set(h_axes.h(i-1), 'Units','normalize','Position',[0.1300 axes_base+(5-i/2)*(axes_height+axes_hoffset) 0.3270 axes_height])
+ set(h_axes.h(i),'Units','normalize','Position',[0.5780 axes_base+(5-i/2)*(axes_height+axes_hoffset) 0.3270 axes_height])
+ end
+ set(h_axes.h(11), 'Units','normalize','Position',[0.5780 axes_base+(5-2/2)*(axes_height+axes_hoffset) 0.3270 axes_height])
+ h_dlg=printdlg;
+ waitfor(h_dlg)
+
+ for i=1:10, set(h_axes.h(i),'Units','Character','Position',h_axes.old_pos{i}), set(h_axes.h(i),'Units','Norm'),end
+ set(h_axes.h(11),'Units','Character','Position',h_axes.old_pos{11}), set(h_axes.h(11),'Units','Norm')
+ set(h,'Visible','On')
+ set(0,props.root)
+
+
+
+
+
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% compute
+case 'compute'
+
+ errcode=11;
+ if length(method)>1 & strcmpi(method(1:2),'di')
+ disp('Warning: RQA from distance plot not possible!')
+ return
+ end
+
+ if ~nogui
+ h_fig=findobj('tag','crqa_Fig');
+ setptr(gcf,'watch'),
+ obj=({'text';'crqa_m';'crqa_maxLag';'crqa_method';'crqa_eps';'crqa_lmin';'crqa_vmin';'crqa_theiler';'crqa_w';'crqa_ws';'crqa_button_store';'crqa_button_print';'crqa_button_close'});
+ for j=1:length(obj);
+ h=findobj('Tag',obj{j},'Parent',h_fig(1));
+ if ~isempty(h)
+ set(h,'Enable','Off')
+ end
+ end
+ h=findobj('tag','crqa_button_apply');
+ set(h(1),'ToolTip','Stops the computation.','String','Stop','Callback','set(0,''ShowHidden'',''on'');h=findobj(''tag'',''crqa_button_apply'');set(h(1),''String'',''Stopped'');set(0,''ShowHidden'',''off'')')
+ end
+
+if Nx==w & wstep<2, wstep=1; Nx=w+1; end
+if Nx==w, Nx=w+1; end
+if nogui~=2, hw=waitbar(0,['0/',num2str(Nx-w)]);set(hw,'Name','Please Wait!');h1=get(hw,'chil');h1=get(h1,'title'); drawnow; end
+if strcmpi(method,'Order Pattern') method = 'op'; end
+if strcmpi(method,'Order Matrx') method = 'om'; end
+
+for i=1:wstep:Nx-w;
+ if ~nogui
+ set(0,'ShowHidden','on')
+ h=findobj('tag','crqa_button_apply','Parent',h_fig(1));
+ if strcmpi(get(h(1),'string'),'stopped')
+ Y(i:Nx-w,1:6)=NaN;
+ break
+ end
+ end
+
+do_norm = {'non';'nor'};
+
+try
+% X=crp_big(x(i:i+w-1,:),y(i:i+w-1,:),m,t,e,'fan','silent');
+ if time_scale_flag
+ if length(x(i:i+w-1,:)) > 2000
+ Xx=crp_big(x(i:i+w-1,:),m,t,e,method,do_norm{nonorm+1},'silent');
+ Xy=crp_big(y(i:i+w-1,:),m,t,e,method,do_norm{nonorm+1},'silent');
+ X = Xx .* Xy;
+ else
+ X=jrp(x(i:i+w-1,:),y(i:i+w-1,:),m,t,e,method,do_norm{nonorm+1},'silent');
+ end
+ else
+ Xx=crp2(x(i:i+w-1,:),m,t,e,method,do_norm{nonorm+1},'silent');
+ Xy=crp2(y(i:i+w-1,:),m,t,e,method,do_norm{nonorm+1},'silent');
+ X = Xx .* Xy;
+ end
+% X=crp(x(i:i+w-1,:),y(i:i+w-1,:),m,t,e,varargin{i_char},'silent');
+ if time_scale_flag
+ x_var=var(x(i:i+w-1,2:end)); y_var=var(y(i:i+w-1,2:end));
+ temp=cov(x(i:i+w-1,2:end),y(i:i+w-1,2:end));
+ else
+ x_var=var(x(i:i+w-1,1)); y_var=var(y(i:i+w-1,1));
+ temp=cov(x(i:i+w-1,1),y(i:i+w-1,1));
+ end
+ xy_var=temp(1,2);
+
+warning off
+if nogui~=2 & ishandle(h1), set(h1,'str',[num2str(i),'/',num2str(Nx-w)]); waitbar(i/(Nx-w)); drawnow, end
+
+%if 0
+catch
+ error(lasterr)
+ if nogui~=2 & ishandle(hw), close(hw), end
+end
+
+errcode=20;
+t1=[0];t2=[];
+for i2=1:size(X,2)
+ rps2=find(diff(double(X(:,i2)))==1);
+ rps=find(X(:,i2));
+ t1=[t1;diff(rps)];
+ t2=[t2;diff(rps2)];
+end
+t1=mean(t1);
+t2=mean(t2);
+
+N=size(X);
+X_theiler=double(triu(X,theiler_window))+double(tril(X,-theiler_window));
+
+[a b]=dl(X_theiler);
+warning off
+errcode=201;
+b(find(b<=lmin))=[];
+[c d]=tt(X);
+warning off
+errcode=202;
+d(find(d<=vmin))=[];
+
+errcode=203;
+RR=sum(X_theiler(:))/(N(1)*N(2));
+%b(find(b>=max(N)-lmin))=[]; if isempty(b), b=0; end
+b(find(b>=max(N)))=[]; if isempty(b), b=0; end
+errcode=204;
+if sum(sum(X_theiler)) > 0
+ DET=sum(b)/sum(sum(X_theiler));
+else
+ DET=NaN;
+end
+errcode=205;
+L=mean(b);
+histL=hist(b(:));
+ENTR=entropy(histL(:));
+errcode=206;
+if sum(d)>0
+ LAM=sum(d)/sum(sum(X));
+else
+ LAM=NaN;
+end
+errcode=207;
+TT=mean(d);
+b=[b;0]; Lmax=max(b);
+d=[d;0]; Vmax=max(d);
+warning on
+
+errcode=208;
+Y(i,1)=RR;
+Y(i,2)=DET;
+Y(i,3)=L;
+Y(i,4)=Lmax;
+Y(i,5)=ENTR;
+Y(i,6)=LAM;
+Y(i,7)=TT;
+Y(i,8)=Vmax;
+Y(i,9)=t1;
+Y(i,10)=t2;
+Y(i,11)=x_var;
+Y(i,12)=y_var;
+Y(i,13)=xy_var;
+end
+if nogui~=2 & ishandle(hw), waitbar(1); drawnow; close(hw), end
+
+ if ~nogui
+ h=findobj('tag','crqa_button_apply');
+ set(h(1),'ToolTip','Starts the computation.','String','Apply','Callback','jrqa compute')
+ for j=1:length(obj);
+ h=findobj('Tag',obj{j},'Parent',h_fig(1));
+ if ~isempty(h)
+ set(h,'Enable','On')
+ end
+ end
+ end
+
+ if ~nogui,
+ h=findobj('Tag','crqa_Fig');
+ if ~isempty(h), set(0,'CurrentFigure',h(1)); end
+ setptr(gcf,'arrow'),
+ end
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% plot
+if ~nogui
+ set(0,'showhidden','on')
+ errcode=30;
+ h=findobj('Tag','crqa_Fig'); if ~isempty(h), set(0,'CurrentFigure',h(1)); end
+ tx={'RR';'DET';'L';'ENTR';'LAM';'TT';'T_1';'T_2';'Variance';'Covariance'};
+ index=[1,2,3,5,6,7,9,10,11,12,13];
+ tags={'crqa_axes_RR','crqa_axes_DET','crqa_axes_L','crqa_axes_ENTR','crqa_axes_LAM','crqa_axes_TT','crqa_axes_T1','crqa_axes_T2','crqa_axes_Var','crqa_axes_CoVar'};
+ h=findobj('Tag','crqa_axes_RR','Parent',gcf); h_axes.h(1)=h(1);
+ h=findobj('Tag','crqa_axes_DET','Parent',gcf); h_axes.h(2)=h(1);
+ h=findobj('Tag','crqa_axes_L','Parent',gcf); h_axes.h(3)=h(1);
+ h=findobj('Tag','crqa_axes_ENTR','Parent',gcf); h_axes.h(4)=h(1);
+ h=findobj('Tag','crqa_axes_LAM','Parent',gcf); h_axes.h(5)=h(1);
+ h=findobj('Tag','crqa_axes_TT','Parent',gcf); h_axes.h(6)=h(1);
+ h=findobj('Tag','crqa_axes_T1','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
+ for i=1:9,
+ set(gcf,'CurrentAxes',h_axes.h(i))
+ if size(Y,1)==1
+ cla
+ text(0.5,0.5,sprintf('%6.4f',Y(index(i))),'FontWeight','bold','HorizontalAlign','Center')
+% if ~all(x(:)==y(:)) & i==9
+% cla
+% text(0.5,0.5,sprintf('%6.5f, %6.5f',Y(index(i)),Y(index(i+1))),'FontWeight','bold','HorizontalAlign','Center')
+% set(gcf,'CurrentAxes',h_axes.h(i+1));cla
+% set(h_axes.h(i+1),'visible','off');
+% end
+ else
+ if i==9
+ cla
+ h2=stairs(xscale(1:wstep:length(Y)),Y(1:wstep:end,index(i)));
+ set(h2,'color',props.line.Color)
+ if ~all(x(:)==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
+ set(h_axes.h(10),'visible','on');
+ 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])
+ end
+ else
+ plot(xscale(1:wstep:length(Y)),Y(1:wstep:end,index(i)),'color',props.line.Color)
+ end
+ end
+ set(gcf,'CurrentAxes',h_axes.h(i));
+ ylabel(tx(i));
+ set(gca,'Tag',tags{i},'color',props.axes.Color,'Units','Norm')
+ end
+ h=findobj('Tag','crqa_button_store');
+ 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
+else
+ if nargout, xout=Y(:,1:10); end
+end
+
+if nargout, xout=Y(:,1:10); end
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% the end
+
+end
+
+
+
+
+%if 0
+catch
+ if nogui~=2, if ishandle(hw), close(hw), end , end
+
+ z=whos;x=lasterr;y=lastwarn;in=varargin{1};
+ print_error('jrqa',z,x,y,in,method,action)
+ try, if ~nogui
+ h=findobj('tag','crqa_button_apply');
+ set(h(1),'ToolTip','Starts the computation.','String','Apply','Callback','jrqa compute')
+ for j=1:length(obj);
+ h=findobj('Tag',obj{j},'Parent',h_fig(1));
+ if ~isempty(h)
+ set(h,'Enable','On')
+ end
+ end, end
+ end
+ set(0,'showhidden','on')
+ h=findobj('Tag','crqa_Fig'); if ~isempty(h), setptr(h(1),'arrow'); end
+ set(0,'showhidden','off')
+end
+
+
+try, set(0,props.root), end
+
+
+
+try
+ set(0,'ShowHidden','off')
+end
--
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