--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/m-toolbox/classes/@pest/computePdf.m	Wed Nov 23 19:22:13 2011 +0100
@@ -0,0 +1,141 @@
+% computes Probability Density Function from a pest object
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% DESCRIPTION:  computes Probability Density Function from a pest object. 
+%              
+% CALL:         p = computePdf(p,pl)  
+%               p.computePdf(pl)     
+%              
+% INPUTS:       p   -  pest object 
+%               pl  -  parameter list (BurnIn,nbins)
+%
+% OUTPUTs:      p   -  pest object with the computed normilized pdf
+%
+% <a href="matlab:utils.helper.displayMethodInfo('pest', 'computePdf')">Parameters Description</a>
+%
+% VERSION:   $Id: computePdf.m,v 1.2 2011/06/06 14:02:12 nikos Exp $
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+function varargout = computePdf(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
+  [pests, pest_invars] = utils.helper.collect_objects(varargin(:), 'pest', in_names);
+  pl              = utils.helper.collect_objects(varargin(:), 'plist', in_names);
+  
+  % Decide on a deep copy or a modify
+  p = copy(pests, nargout);
+  
+  % combine plists
+  pl = parse(pl, getDefaultPlist());
+  BurnIn = find(pl, 'BurnIn');
+  nbins = find(pl, 'nbins');
+    
+  if ~all(isa(pests, 'pest'))
+    error('### computePdf must be only applied to pest objects.');
+  end
+  
+ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+  
+ N = numel(p); 
+ 
+ for ii=1:N     
+     a=p(ii).chain;
+     D=size(a);
+     [n(1,:),xout(1,:)]=hist(a(BurnIn:D(1),1),nbins);
+     sumbins = sum(n(1,:));
+     PDF = [xout(1,:) ; n(1,:)/sumbins]';
+     
+     for jj=2:D(2)
+     % creating histograms
+     [n(jj,:),xout(jj,:)]=hist(a(BurnIn:D(1),jj),nbins);
+     sumbins = sum(n(jj,:));
+     PDF = [PDF xout(jj,:)' (n(jj,:)')/sumbins];
+     end
+    PDFn(:,:,ii)= PDF;
+ end
+ 
+ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+  
+  % Output pest/pdf
+  if nargout == 1
+      for ii=1:N
+        p(ii).setPdf(PDFn(:,:,ii));
+      end
+      out = p;
+    elseif nargout == 0
+      for ii=1:N
+        p(ii).setPdf(PDFn(:,:,ii));
+      end
+      out = p;
+      out.addHistory(getInfo('None'), pl, pest_invars(:), [pests(:).hist]);
+    else
+      error('### The number of output arguments must be a one or zero');   
+  end
+   
+  name = p(1).name;
+  if N>1
+    for ii=2:N
+      name = [name ',' p(ii).name];
+    end
+  end
+       
+  % Set outputs
+  if nargout > 0
+    varargout{1} = out;
+  end
+  
+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, 'pest', 'ltpda', utils.const.categories.helper, '$Id: computePdf.m,v 1.2 2011/06/06 14:02:12 nikos 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()
+pl = plist();
+
+p = param({'BurnIn','Number of samples (of the chains) to be discarded'}, paramValue.DOUBLE_VALUE(1));
+pl.append(p);
+
+p = param({'nbins','Number of bins of the pdf histogram computed for every parameter'}, paramValue.DOUBLE_VALUE(10));
+pl.append(p);
+
+end
+