--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/m-toolbox/classes/@ao/bicohere.m	Wed Nov 23 19:22:13 2011 +0100
@@ -0,0 +1,161 @@
+% BICOHERE computes the bicoherence of two input time-series
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% DESCRIPTION: BICOHERE computes the bicoherence of two input time-series.
+%
+% CALL:        bs = bicohere(a1,a2,pl)
+%
+% INPUTS:      aN    - input analysis objects
+%              a1,a2 - input analysis objects array
+%              pl    - input parameter list
+%
+% OUTPUTS:     bs   - xyz data analysis object
+%
+% <a href="matlab:utils.helper.displayMethodInfo('bicohere', 'psd')">Parameters Description</a>
+%
+% VERSION:    $Id: psd.m,v 1.59 2010/12/17 17:45:08 ingo Exp $
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+function varargout = bicohere(varargin)
+  
+  % Check if this is a call for parameters
+  if utils.helper.isinfocall(varargin{:})
+    varargout{1} = getInfo(varargin{3});
+    return
+  end
+  
+  import utils.const.*
+  utils.helper.msg(msg.PROC3, 'running %s/%s', mfilename('class'), mfilename);
+  
+  % Collect input variable names
+  in_names = cell(size(varargin));
+  for ii = 1:nargin,in_names{ii} = inputname(ii);end
+  
+  % Collect all AOs and plists
+  [as, ao_invars] = utils.helper.collect_objects(varargin(:), 'ao', in_names);
+  pl              = utils.helper.collect_objects(varargin(:), 'plist', in_names);
+  
+  if numel(as) ~= 2
+    error('bicohere only works with 2 time-series at the moment.');
+  end
+  
+  % Get data
+  a  = as(1);
+  b  = as(2);
+  
+  % same fs?
+  if a.data.fs ~= b.data.fs
+    error('### Two time-series have different sample rates.');
+  end
+  
+  % Same length vectors?
+  if a.len ~= b.len
+    error('### Two time-series must have same length');
+  end
+  
+  % Combine plists
+  pl = combine(pl, getDefaultPlist); 
+  usepl = utils.helper.process_spectral_options(pl, 'lin', a.len, a.fs);
+  
+  win     = find(usepl, 'Win');
+  nfft    = find(usepl, 'Nfft');
+  olap    = find(usepl, 'Olap')/100;
+  Xolap   = round(olap*nfft);
+  order   = find(usepl, 'order');
+    
+  fs = a.data.fs;
+  x  = {a.data.y; b.data.y};
+    
+  [x,M,isreal_x,y,Ly,win,winName,winParam,noverlap,k,L,options] = ...
+    ao.welchparse(x,'',win.win, Xolap, nfft, fs);
+  
+  select = 1:(nfft+1)/2;
+
+  % loop over segments
+  LminusOverlap = L-noverlap;
+  xStart = 1:LminusOverlap:k*LminusOverlap;
+  xEnd   = xStart+L-1;
+  
+  m = zeros(length(select), length(select));
+
+  for i = 1:k
+    if order < 0
+      Xseg = x(xStart(i):xEnd(i));
+      Yseg = x(xStart(i):xEnd(i));
+    else
+      [Xseg,coeffs] = ltpda_polyreg(x(xStart(i):xEnd(i)), order);
+      [Yseg,coeffs] = ltpda_polyreg(y(xStart(i):xEnd(i)), order);
+    end
+     
+    % window
+    xw = Xseg.*win.';
+    yw = Yseg.*win.';
+
+    % FFT
+    xx2s = fft(xw);    
+    xx   = xx2s(select);
+    yy2s = fft(yw);
+    yy   = yy2s(select);
+    
+    scalex = abs(xx);
+    scaley = abs(yy);
+    sc = scalex * scaley';
+    m = m + (xx * yy')./sc;
+        
+  end
+    
+  m = m./k;
+  
+  f = psdfreqvec('npts',nfft,'Fs',fs);
+  f = f(select);
+  do = xyzdata(f, f, m);
+  do.setXunits('Hz');
+  do.setYunits('Hz');
+  do.setZunits(a.yunits*b.yunits);
+  
+  ma = ao(do);
+  ma.setName(sprintf('%s, %s', a.name, b.name));
+  ma.addHistory(getInfo('None'), usepl, ao_invars, [a.hist b.hist]);
+
+  
+  % Set output
+  varargout{1} = ma;
+end
+
+%--------------------------------------------------------------------------
+% Get Info Object
+%--------------------------------------------------------------------------
+function ii = getInfo(varargin)
+  if nargin == 1 && strcmpi(varargin{1}, 'None')
+    sets = {};
+    pl   = [];
+  else
+    sets = {'Default'};
+    pl   = getDefaultPlist;
+  end
+  % Build info object
+  ii = minfo(mfilename, 'ao', 'ltpda', utils.const.categories.sigproc, '$Id: psd.m,v 1.59 2010/12/17 17:45:08 ingo Exp $', sets, pl);
+end
+
+%--------------------------------------------------------------------------
+% Get Default Plist
+%--------------------------------------------------------------------------
+function plout = getDefaultPlist()
+  persistent pl;  
+  if exist('pl', 'var')==0 || isempty(pl)
+    pl = buildplist();
+  end
+  plout = pl;  
+end
+
+function pl = buildplist()
+  
+  % General plist for Welch-based, linearly spaced spectral estimators
+  pl = plist.WELCH_PLIST;
+  
+  
+end
+% END
+