/matlab_tools/Converted/kMAPPR.m

%kMAPPR 'maximum a posteriory likelihood, poisson, Good\'s roughness '
% This MatLab function was automatically generated by a converter (KhorosToMatLab) from the Khoros MAPPR.pane file
%
% Parameters: 
% InputFile: i 'Measured data', required: 'First Input data object'
% InputFile: p 'PSF', required: 'Psf with identical sampling (total sizes may differ)'
% InputFile: patterns 'Patterns', optional: 'File containing the exact patterns (in real space) used for illumination'
% InputFile: s 'Start File', optional: 'If supplied, the iterations start with this image.'
% Integer: n 'Iterations', default: 25: 'number of iteratons to perform'
% Toggle: noPSFnorm 'Do not normalize PSF', default: 0: 'If activated the PSFs will not be normalized'
% Double: Backgr 'Background Estimate', default: 0: 'level of pure offset background in data'
% Double: Backgr1 'Bg 1', default: 0: 'estimat for element 1'
% Double: Backgr2 'Bg 2', default: 0: 'estimat for element 2'
% Double: w1 'Weight1', default: 1: 'Weight to attach to first element (0)'
% Double: w2 'Wght 2', default: 1: 'Weight to attach to second element'
% Double: w3 'Wght3', default: 1: 'Weight to attach to thrid element'
% Double: Gamma 'Gamma', default: 0.02: 'Regularization Parameter'
% Toggle: Steepest 'Steepest Descent', default: 0: 'use steepest descent instead of conjugate gradient'
% Double: alpha0 'Starting Alpha', default: 1: 'Overrelaxation factor alpha to start the search with'
% Toggle: PR 'Polak-Ribiere method', default: 0: 'If selected, the Polak-Ribiere method is used, otherwise Fletcher-Reves'
% Toggle: FGM 'First guess is Measured image', default: 0: 'If selected, the measured image (element 0) will be used as a first guess.'
% OutputFile: o 'Output', required: 'Resulting output data object'
%
% Example: o = kMAPPR({i, p, patterns, s}, {'i','';'p','';'patterns','';'s','';'n',25;'noPSFnorm',0;'Backgr',0;'Backgr1',0;'Backgr2',0;'w1',1;'w2',1;'w3',1;'Gamma',0.02;'Steepest',0;'alpha0',1;'PR',0;'FGM',0;'o',''})
%
% Khoros helpfile follows below:
%
%  PROGRAM
% MAPPR - maximum a posteriory likelihood, poisson, Good's roughness
%
%  DESCRIPTION
%
%  
%
%  EXAMPLES
%
%  "SEE ALSO"
%
%  RESTRICTIONS 
%
%  REFERENCES 
%
%  COPYRIGHT
% Copyright (C) 1996-2003, Rainer Heintzmann,  All rights reserved.
% 


function varargout = kMAPPR(varargin)
if nargin ==0
  Inputs={};arglist={'',''};
elseif nargin ==1
  Inputs=varargin{1};arglist={'',''};
elseif nargin ==2
  Inputs=varargin{1}; arglist=varargin{2};
else error('Usage: [out1,..] = kMAPPR(Inputs,arglist).');
end
if size(arglist,2)~=2
  error('arglist must be of form {''ParameterTag1'',value1;''ParameterTag2'',value2}')
 end
narglist={'i', '__input';'p', '__input';'patterns', '__input';'s', '__input';'n', 25;'noPSFnorm', 0;'Backgr', 0;'Backgr1', 0;'Backgr2', 0;'w1', 1;'w2', 1;'w3', 1;'Gamma', 0.02;'Steepest', 0;'alpha0', 1;'PR', 0;'FGM', 0;'o', '__output'};
maxval={0,0,1,1,2,0,1,1,1,1,1,1,1,0,1,0,0,0};
minval={0,0,1,1,2,0,1,1,1,1,1,1,1,0,1,0,0,0};
istoggle=[0,0,1,1,0,1,0,0,0,0,0,0,0,1,0,1,1,0];
was_set=istoggle * 0;
paramtype={'InputFile','InputFile','InputFile','InputFile','Integer','Toggle','Double','Double','Double','Double','Double','Double','Double','Toggle','Double','Toggle','Toggle','OutputFile'};
% identify the input arrays and assign them to the arguments as stated by the user
if ~iscell(Inputs)
Inputs = {Inputs};
end
NumReqOutputs=1; nextinput=1; nextoutput=1;
  for ii=1:size(arglist,1)
  wasmatched=0;
  for jj=1:size(narglist,1)
   if strcmp(arglist{ii,1},narglist{jj,1})  % a given argument was matched to the possible arguments
     wasmatched = 1;
     was_set(jj) = 1;
     if strcmp(narglist{jj,2}, '__input')
      if (nextinput > length(Inputs)) 
        error(['Input ' narglist{jj,1} ' has no corresponding input!']); 
      end
      narglist{jj,2} = 'OK_in';
      nextinput = nextinput + 1;
     elseif strcmp(narglist{jj,2}, '__output')
      if (nextoutput > nargout) 
        error(['Output nr. ' narglist{jj,1} ' is not present in the assignment list of outputs !']); 
      end
      if (isempty(arglist{ii,2}))
        narglist{jj,2} = 'OK_out';
      else
        narglist{jj,2} = arglist{ii,2};
      end

      nextoutput = nextoutput + 1;
      if (minval{jj} == 0)  
         NumReqOutputs = NumReqOutputs - 1;
      end
     elseif isstr(arglist{ii,2})
      narglist{jj,2} = arglist{ii,2};
     else
        if strcmp(paramtype{jj}, 'Integer') & (round(arglist{ii,2}) ~= arglist{ii,2})
            error(['Argument ' arglist{ii,1} ' is of integer type but non-integer number ' arglist{ii,2} ' was supplied']);
        end
        if (minval{jj} ~= 0 | maxval{jj} ~= 0)
          if (minval{jj} == 1 & maxval{jj} == 1 & arglist{ii,2} < 0)
            error(['Argument ' arglist{ii,1} ' must be bigger or equal to zero!']);
          elseif (minval{jj} == -1 & maxval{jj} == -1 & arglist{ii,2} > 0)
            error(['Argument ' arglist{ii,1} ' must be smaller or equal to zero!']);
          elseif (minval{jj} == 2 & maxval{jj} == 2 & arglist{ii,2} <= 0)
            error(['Argument ' arglist{ii,1} ' must be bigger than zero!']);
          elseif (minval{jj} == -2 & maxval{jj} == -2 & arglist{ii,2} >= 0)
            error(['Argument ' arglist{ii,1} ' must be smaller than zero!']);
          elseif (minval{jj} ~= maxval{jj} & arglist{ii,2} < minval{jj})
            error(['Argument ' arglist{ii,1} ' must be bigger than ' num2str(minval{jj})]);
          elseif (minval{jj} ~= maxval{jj} & arglist{ii,2} > maxval{jj})
            error(['Argument ' arglist{ii,1} ' must be smaller than ' num2str(maxval{jj})]);
          end
        end
     end
     if ~strcmp(narglist{jj,2},'OK_out') &  ~strcmp(narglist{jj,2},'OK_in') 
       narglist{jj,2} = arglist{ii,2};
     end
   end
   end
   if (wasmatched == 0 & ~strcmp(arglist{ii,1},''))
        error(['Argument ' arglist{ii,1} ' is not a valid argument for this function']);
   end
end
% match the remaining inputs/outputs to the unused arguments and test for missing required inputs
 for jj=1:size(narglist,1)
     if  strcmp(paramtype{jj}, 'Toggle')
        if (narglist{jj,2} ==0)
          narglist{jj,1} = ''; 
        end;
        narglist{jj,2} = ''; 
     end;
     if  ~strcmp(narglist{jj,2},'__input') && ~strcmp(narglist{jj,2},'__output') && istoggle(jj) && ~ was_set(jj)
          narglist{jj,1} = ''; 
          narglist{jj,2} = ''; 
     end;
     if strcmp(narglist{jj,2}, '__input')
      if (minval{jj} == 0)  % meaning this input is required
        if (nextinput > size(Inputs)) 
           error(['Required input ' narglist{jj,1} ' has no corresponding input in the list!']); 
        else
          narglist{jj,2} = 'OK_in';
          nextinput = nextinput + 1;
        end
      else  % this is an optional input
        if (nextinput <= length(Inputs)) 
          narglist{jj,2} = 'OK_in';
          nextinput = nextinput + 1;
        else 
          narglist{jj,1} = '';
          narglist{jj,2} = '';
        end;
      end;
     else 
     if strcmp(narglist{jj,2}, '__output')
      if (minval{jj} == 0) % this is a required output
        if (nextoutput > nargout & nargout > 1) 
           error(['Required output ' narglist{jj,1} ' is not stated in the assignment list!']); 
        else
          narglist{jj,2} = 'OK_out';
          nextoutput = nextoutput + 1;
          NumReqOutputs = NumReqOutputs-1;
        end
      else % this is an optional output
        if (nargout - nextoutput >= NumReqOutputs) 
          narglist{jj,2} = 'OK_out';
          nextoutput = nextoutput + 1;
        else 
          narglist{jj,1} = '';
          narglist{jj,2} = '';
        end;
      end
     end
  end
end
if nargout
   varargout = cell(1,nargout);
else
  varargout = cell(1,1);
end
global KhorosRoot
if exist('KhorosRoot') && ~isempty(KhorosRoot)
w=['"' KhorosRoot];
else
if ispc
  w='"C:\Program Files\dip\khorosBin\';
else
[s,w] = system('which cantata');
w=['"' w(1:end-8)];
end
end
[varargout{:}]=callKhoros([w 'mappr"  -k'],Inputs,narglist);