/matlab_tools/Converted/kDeconvAxial.m
Objective C | 196 lines | 193 code | 3 blank | 0 comment | 58 complexity | 7f8411302b9ad8a6b1a48c1995dcf98e MD5 | raw file
Possible License(s): BSD-3-Clause
- %kDeconvAxial 'Deconvolution using ML/EM algorithm '
- % This MatLab function was automatically generated by a converter (KhorosToMatLab) from the Khoros DeconvAxial.pane file
- %
- % Parameters:
- % Integer: n 'Iterations', default: 60: 'Number of iterations until algorythm stops'
- % Integer: rW 'Border (Pixels)', default: 4: 'a gaussian Window will be applied'
- % Toggle: norichardson 'No Richardson', default: 0: 'do not use the richardson iteration, but the stadard ML-correction method instead'
- % Toggle: noPSFnorm 'Do not normalize PSFs', default: 0: 'The integral intensity of the PSFs will then not be normalized'
- % Double: mf 'Maximal Rel. Frequency X/Y', default: 0.8: 'Higher frequencies are suppressed in X/Y direction'
- % Double: mzf 'Z', default: 0.4: 'Higher frequencies are suppressed in Z-direction'
- % InputFile: i 'Measured Image', required: 'Measured confocal image'
- % InputFile: p 'PSF', required: 'PSF needed for ML algorithm (same size as measured data)'
- % InputFile: s 'Start File', optional: 'file to start iteration with'
- % InputFile: Over 'Overrelaxation Table', optional: 'Table for Overrelaxation Factors'
- % InputFile: patterns 'Pattern File', optional: 'File containing the different patterns (along elements)'
- % Toggle: patsep 'Separable Patterns', default: 0: 'If selected, it is assumed, that the pattern can be described as a sum of separable components. In this case, the pattern-file has to consist of N planes (stacked along depth) for each element. The PSF elements are then assumed to contain the Z-modified PSFs.'
- % Toggle: HolmesLiu 'Holmes & Liu', default: 0: 'If selected, the overrelaxation is choosen according to the Holmes&Liu paper. This specific implementation is however rather slow.'
- % OutputFile: o 'Recon. Image', required: 'Resulting output data object'
- % OutputFile: c 'Correction Image', required: 'Correction Image'
- % OutputFile: f 'Fwd Projected File', optional: 'forward proj. guess'
- % OutputFile: hf 'HF Content Output', optional: 'energy of highest 10% frequences'
- % Toggle: background 'Estimate Background', default: 0: 'For patterned excitation data, a background (out-of-focus, not deconvolved) can be estimated.'
- % OutputFile: bgFile 'Background', optional: 'Only for patterned excitation data, Estimate Background active'
- %
- % Example: [o, c, f, hf, bgFile] = kDeconvAxial({i, p, s, Over, patterns}, {'n',60;'rW',4;'norichardson',0;'noPSFnorm',0;'mf',0.8;'mzf',0.4;'i','';'p','';'s','';'Over','';'patterns','';'patsep',0;'HolmesLiu',0;'o','';'c','';'f','';'hf','';'background',0;'bgFile',''})
- %
- % Khoros helpfile follows below:
- %
- % PROGRAM
- % DeconvAxial - Deconvolutes using many Psfs
- %
- % DESCRIPTION
- %
- %
- %
- % EXAMPLES
- %
- % "SEE ALSO"
- %
- % RESTRICTIONS
- %
- % REFERENCES
- %
- % COPYRIGHT
- % Copyright (C) 1996-2003, Rainer Heintzmann, All rights reserved.
- %
- function varargout = kDeconvAxial(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,..] = kDeconvAxial(Inputs,arglist).');
- end
- if size(arglist,2)~=2
- error('arglist must be of form {''ParameterTag1'',value1;''ParameterTag2'',value2}')
- end
- narglist={'n', 60;'rW', 4;'norichardson', 0;'noPSFnorm', 0;'mf', 0.8;'mzf', 0.4;'i', '__input';'p', '__input';'s', '__input';'Over', '__input';'patterns', '__input';'patsep', 0;'HolmesLiu', 0;'o', '__output';'c', '__output';'f', '__output';'hf', '__output';'background', 0;'bgFile', '__output'};
- maxval={1000,2,0,0,2,2,0,0,1,1,1,0,0,0,0,1,1,0,1};
- minval={1,2,0,0,0,0,0,0,1,1,1,0,0,0,0,1,1,0,1};
- istoggle=[0,1,1,1,1,1,0,0,1,1,1,1,1,0,0,1,1,1,1];
- was_set=istoggle * 0;
- paramtype={'Integer','Integer','Toggle','Toggle','Double','Double','InputFile','InputFile','InputFile','InputFile','InputFile','Toggle','Toggle','OutputFile','OutputFile','OutputFile','OutputFile','Toggle','OutputFile'};
- % identify the input arrays and assign them to the arguments as stated by the user
- if ~iscell(Inputs)
- Inputs = {Inputs};
- end
- NumReqOutputs=2; 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 'axialrec" -k'],Inputs,narglist);