/matlab_tools/Converted/kClassify.m
Objective C | 186 lines | 183 code | 3 blank | 0 comment | 58 complexity | 6fbecf207e2c20505f0a6a7887c859b3 MD5 | raw file
Possible License(s): BSD-3-Clause
- %kClassify 'classifies a series of images according to a number of color vectors '
- % This MatLab function was automatically generated by a converter (KhorosToMatLab) from the Khoros Classify.pane file
- %
- % Parameters:
- % InputFile: i1 'Images (along elements)', required: 'Series of images (also 3D) stacked along elment direction'
- % InputFile: i2 'Colors', required: 'Color vectors (along X) stacked along element direcition'
- % Double: t 'DAPI threshold', default: 10: 'Element 0 is assumed to contain the DAPI channel. Pixels below threshold are ignored.'
- % Double: minq 'Min Quality', default: 0.97: 'Defines the minimal quality for single channel matching. If not reached, method reverts to two channels'
- % Integer: co 'Color Optimize Iterations', default: 1: 'If selected, some iterations for finding the optimal color vectors are performed'
- % Double: mincq 'Min Color Quality', default: 0.8: 'Defines the minimum quality for adjusting the colors.'
- % OutputFile: o1 'Classified', required: 'Resulting classification image'
- % OutputFile: o2 'Quality Img', required: 'A classification quality is given for every pixel'
- % OutputFile: o3 'Output Colors', optional: 'The (eventually optimized) colors'
- %
- % Example: [o1, o2, o3] = kClassify({i1, i2}, {'i1','';'i2','';'t',10;'minq',0.97;'co',1;'mincq',0.8;'o1','';'o2','';'o3',''})
- %
- % Khoros helpfile follows below:
- %
- % PROGRAM
- % Classify - classifies a series of images according to a number of color vectors
- %
- % DESCRIPTION
- %
- %
- %
- % EXAMPLES
- %
- % "SEE ALSO"
- %
- % RESTRICTIONS
- %
- % REFERENCES
- %
- % COPYRIGHT
- % Copyright (C) 1996-2003, Rainer Heintzmann, All rights reserved.
- %
- function varargout = kClassify(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,..] = kClassify(Inputs,arglist).');
- end
- if size(arglist,2)~=2
- error('arglist must be of form {''ParameterTag1'',value1;''ParameterTag2'',value2}')
- end
- narglist={'i1', '__input';'i2', '__input';'t', 10;'minq', 0.97;'co', 1;'mincq', 0.8;'o1', '__output';'o2', '__output';'o3', '__output'};
- maxval={0,0,0,0,2,0,0,0,1};
- minval={0,0,0,0,2,0,0,0,1};
- istoggle=[0,0,1,1,1,1,0,0,1];
- was_set=istoggle * 0;
- paramtype={'InputFile','InputFile','Double','Double','Integer','Double','OutputFile','OutputFile','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 'classify" -k'],Inputs,narglist);