crqa.m

function xout=crqa(varargin)
%CRQA   Computes and plots the CRQA measures.
%    Y=CRQA(X [,Y] [,param1,param2,...]) 
%    Recurrence quantification analysis of the cross 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=CRQA(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).
%
%    CRQA(...) without any output arguments opens a
%    GUI for interactively control the CRQA. 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
%    cross 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.
%      distance    - Distance coded matrix (global CRP, 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.
%      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)
%
%    Warning:
%    The RQA measures may differ from those of the RQA programmes by
%    Charles Webber Jr. For compatibility use a Theiler window of
%    size one and ensure that the data are normalized before by the
%    same distance which is used in the RQA programmes; e.g. normalize
%    with the maximal phase space diameter, which can be estimated 
%    with the programme PSS:
%
%      RQA=crqa(100*x/pss(x,dim,lag,'euclidean'),...
%               dim,lag,e,[],[],l_min,v_min,1,...
%               'euclidean','nonormalize','silent')
%
%    Examples: a=randn(300,1);
%              crqa(a,1,1,.2,40,2,'euc')
%
%              N=500; w=40; ws=2;
%              a=3.4:.6/(N-1):4;
%              b=.5; for i=2:N, b(i)=a(i)*b(i-1)*(1-b(i-1));end
%              y=crqa(b,3,2,.1,w,ws);
%              subplot(2,1,1), plot(a,b,'.','markersize',.1)
%              title('logistic map'), axis([3.4 4 0 1])
%              subplot(2,1,2), plot(a(1:ws:N-w),y(1:ws:N-w,1))
%              ylabel('recurrence rate'), axis([3.4 4 0 1])
%
%      
%    See also CRQAD, CRP, CRP2, CRP_BIG, DL, TT, PSS.
%
%    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.
%
%    Gao, J. B.: 
%    Recurrence Time Statistics for Chaotic Systems and Their 
%    Applications, Phys. Rev. Lett., 83(16), 1999.
%
%    Thiel, M., Romano, M. C., Kurths, J., Meucci, R., Allaria, E., 
%    Arecchi, F. T.:
%    Influence of observational noise on the recurrence quantification 
%    analysis, Physica D, 171(3), 2002.

% 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;


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 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;
   embed_flag=1;
   nogui=0;
      check_meth={'ma','eu','mi','nr','fa','in','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_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'};
     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>7, method0=7; 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 ==> crqa')
	 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)), embed_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 ==> crqa')
      disp('No valid arguments.')
      return
    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)), embed_flag=0; end
   else
      xscale=(1:length(x))'; 
   end
   if size(y,2)>=2
      yscale=y(:,1); 
      if ~isempty(find(diff(yscale)<0)), embed_flag=0; end
   else
       yscale=(1:length(y))';
   end
      
      if max(size(x))~=max(size(y)),
        if ~nogui, errordlg('Data must have the same length.','Check Data'), waitforbuttonpress, else error('Data must have the same length.'), end
      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},...
  	    'Name','Cross 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 Cross Recurrence Quantification Analysis','Callback','helpwin crqa');
  else
    h1=flipud(get(h(1),'Children'));
    set(h1(1),'Separator','on')
    h2=uimenu('Parent',h(1),'Label','&Help Cross Recurrence Quantification Analysis','Callback','helpwin crqa');
    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','1998-2004'});
  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]);    
  plot(xscale,x,'color',props.line.Color)
  if ~all(x==y) hold on; plot(yscale,y,'r'), 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]);    
  x_var = winplot(x,w,wstep,2);
  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; y_var = winplot(y,w,wstep,2); 
    if size(y_var,1) > 2
      stairs(yscale(round(y_var(:,1))),y_var(:,2),'r')
      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');
    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
  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',...
            '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]);    

%%%%%%%%%%% crqa parameters
  h=uicontrol(props.frame,...
            'Tag','frame',...
            'Position',[86+30 11+.5 29 12.2]);    
 
  h=uicontrol(props.text,...
            'Tag','text',...
            'Fontangle','italic',...
	    'String','CRQA 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 CRQA analysis into a variable in the workspace.',...
  	      'Callback','crqa store',...
  	      'Position',[100.5+30  7.4+.5 10.5  2.2143]);

  h=uicontrol(props.button,...
            'Tag','crqa_button_print',...
	    'CallBack','crqa print',...
  	      'ToolTip','Prints the CRQA window.',...
	    'String','Print',...
            'Position',[89+30  7.4+.5 10.5  2.2143]);    

  h=uicontrol(props.button,...
            'Tag','crqa_button_close',...
	    'CallBack','crqa close',...
  	      'ToolTip','Closes the CRQA 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','crqa 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(['CRQA 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 ~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

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
try
%  X=crp_big(x(i:i+w-1,:),y(i:i+w-1,:),m,t,e,'fan','silent');
  if embed_flag
    X=crp_big(x(i:i+w-1,:),y(i:i+w-1,:),m,t,e,method,'silent',check_norm{nonorm+1});
  else
%    X=crp2(x(i:i+w-1,:),y(i:i+w-1,:),m,t,e,method,varargin{i_char},'silent');
    X=crp2(x(i:i+w-1,:),y(i:i+w-1,:),m,t,e,method,check_norm{nonorm+1},'silent');
  end
%  X=crp(x(i:i+w-1,:),y(i:i+w-1,:),m,t,e,varargin{i_char},'silent');
  x_var=var(x(i:i+w-1,:)); y_var=var(y(i:i+w-1,:)); temp=cov(x(i:i+w-1,:),y(i:i+w-1,:)); 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','crqa 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(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(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(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(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')
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('crqa',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','crqa 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