--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/m-toolbox/classes/@ao/cohere.m	Wed Nov 23 19:22:13 2011 +0100
@@ -0,0 +1,114 @@
+% COHERE estimates the coherence between time-series objects
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% DESCRIPTION: COHERE estimates the coherence between the
+%              time-series objects in the input analysis objects. 
+%              The estimate is done by taking 
+%              the ratio of the CPSD between the two inputs, Sxy, divided by 
+%              the product of the PSDs of the inputs, Sxx and Syy,              
+%              and is either magnitude-squared: (abs(Sxy))^2 / (Sxx * Syy) 
+%              or complex value: Sxy / sqrt(Sxx * Syy)
+%              Here x is the first input, y is the second input
+%
+% CALL:        b = cohere(a1,a2,pl)
+%
+% INPUTS:      a1   - input analysis object
+%              a2   - input analysis object
+%              pl   - input parameter list
+%
+% OUTPUTS:     b    - output analysis object
+%
+% <a href="matlab:utils.helper.displayMethodInfo('ao', 'cohere')">Parameters Description</a>
+%
+% VERSION:    $Id: cohere.m,v 1.43 2011/04/08 08:56:16 hewitson Exp $
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+function varargout = cohere(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);
+
+  if nargout == 0
+    error('### cohere cannot be used as a modifier. Please give an output variable.');
+  end
+
+  % Collect input variable names
+  in_names = cell(size(varargin));
+  for ii = 1:nargin,in_names{ii} = inputname(ii);end
+
+  % Collect all AOs
+  [as, ao_invars] = utils.helper.collect_objects(varargin(:), 'ao', in_names);
+
+  % Apply defaults to plist
+  pl = applyDefaults(getDefaultPlist, varargin{:});
+
+  % Throw an error if input is not two AOs
+  if numel(as) ~= 2
+    error('### cohere only accepts two inputs AOs.');
+  end
+  
+  % Compute coherence with xspec
+  scale_type = find(pl, 'Type');
+  switch lower(scale_type)
+    case 'c'
+      bs = xspec(as, pl, 'cohere', getInfo, ao_invars);
+    case 'ms'
+      bs = xspec(as, pl, 'mscohere', getInfo, ao_invars);
+    otherwise
+      error(['### Unknown coherence type: [' scale_type ']']);
+  end
+
+  % Set output
+  varargout{1} = bs;
+
+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: cohere.m,v 1.43 2011/04/08 08:56:16 hewitson Exp $', sets, pl);
+  ii.setModifier(false);
+  ii.setArgsmin(2);
+end
+
+%--------------------------------------------------------------------------
+% Get Default Plist
+%--------------------------------------------------------------------------
+
+function plout = getDefaultPlist()
+  persistent pl;  
+  if ~exist('pl', 'var') || isempty(pl)
+    pl = buildplist();
+  end
+  plout = pl;  
+end
+
+function pl = buildplist()
+  
+  % General plist for Welch-based, linearly spaced spectral estimators
+  pl = plist.WELCH_PLIST;
+  
+  % Type
+  p = param({'Type',['type of output scaling. Choose from:<ul>', ...
+    '<li>MS - Magnitude-Squared Coherence:<br><tt>(abs(Sxy))^2 / (Sxx * Syy)</tt></li>', ...
+    '<li>C  - Complex Coherence:<br><tt>Sxy / sqrt(Sxx * Syy)</tt></li></ul>']}, {1, {'C', 'MS'}, paramValue.SINGLE});
+  pl.append(p);
+  
+end
+