/matlab_tools/Converted/kcROIfromcoords.m
Objective C | 199 lines | 196 code | 3 blank | 0 comment | 59 complexity | 4292846558541e5bf63ee01eb898bbfd MD5 | raw file
Possible License(s): BSD-3-Clause
- %kcROIfromcoords 'Extract rectangular ROIs from an image using coordinates'
- % This MatLab function was automatically generated by a converter (KhorosToMatLab) from the Khoros cROIfromcoords.pane file
- %
- % Parameters:
- % InputFile: i 'Input image file', required: 'Input file with the image to be used for ROI extraction'
- % InputFile: icoords 'Input Coord file', required: 'input Coord file with coordinates for ROI extraction'
- % MultiChoice: setwhat 'ROIs will be everything', default: 1: 'flag for setting if ROIs are inside or outside coords'
- % Choices are:
- % 1: 'Inside coords'
- % 2: 'Outside coords'
- % Toggle: autocrop 'Auto-crop image (extract minimum area)', default: 0: 'if set will reduce image dimensions to bounding box'
- % OutputFile: o 'Output', required: 'output image with the ROIs masked or set to values'
- % Toggle: masknonROIs 'Masked as 0 (non-valid)', default: 0: 'if set will mask all non-ROIs pixels in the image'
- % Toggle: assignnonROIs 'Assigned to value:', default: 0: 'if set will assign a value to the non-ROI pixels in the image'
- %
- % Example: o = kcROIfromcoords({i, icoords}, {'i','';'icoords','';'setwhat',1;'autocrop',0;'o','';'masknonROIs',0;'assignnonROIs',0})
- %
- % Khoros helpfile follows below:
- %
- % PROGRAM
- % cROIfromcoords - Extract rectangular ROIs from an image using coordinates
- %
- % DESCRIPTION
- % Read a file with 4 integers as coordinates specifying a rectangle and set the value or mask regions of the input object to be considered as \fBR"egions \fBO\fPf \fBI\fPnterest depending on the parameters.
- % The Coords file is an ASCII file that specifies the rectangles. Its format is very simple:
- % * lines starting with # or / are considered as comments
- % * lines with less than 7 characters on it are ignored
- % * each line should have 4 coordinates: start column, start row, width, height.
- % ROIs can be specified as being masked (with the [-masknonROIs] flag) or set to a value (with the [-assignnonROIs] flag and specifying real and complex values with [-valuei] and [-valuej]), and being the regions inside or outside the coordinates with the [-setwhat] toggle.
- % \fBImportant:" the optional argument [-autocrop] should be used only when the ROIs are \fBnot\fP going to be joined later by "kappend\fP or a similar routine because there is the possibility that the different objects created by this routine with [-autocrop] will have different sizes and then joining them with \fIkappend\fP will create padding areas with values 0, which surely is not a good idea for some classification methods which will consider all those padding points as valid samples.
- %
- %
- %
- % EXAMPLES
- % All examples for the Classify toolbox are listed on the Classify Toolbox Manual. For an example of usage of the cROIfromcoords kroutine for ROI extraction, see the example workspace Classify:workspaces:KNN.
- %
- % "SEE ALSO"
- % cROIfrommcoords, lcROIfromcoords, Coord file format in the Classify Toolbox Manual.
- %
- % RESTRICTIONS
- % The coordinates specified in the file must be inside the range of the image file, i.e. they must contain valid coordinates.
- % \fBImportant:" Workspaces that were created with the version 1.0 of this program must be checked - the regions outside the ROIs will be by default set to 0, which will create errors in the signatures.
- %
- % REFERENCES
- % All references for the Classify toolbox are listed on the Classify Toolbox Manual.
- %
- % COPYRIGHT
- % Copyright (C) 1997 Rafael Santos. Khoros (C) Khoral Research, Inc.
- %
- function varargout = kcROIfromcoords(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,..] = kcROIfromcoords(Inputs,arglist).');
- end
- if size(arglist,2)~=2
- error('arglist must be of form {''ParameterTag1'',value1;''ParameterTag2'',value2}')
- end
- narglist={'i', '__input';'icoords', '__input';'setwhat', 1;'autocrop', 0;'o', '__output';'masknonROIs', 0;'assignnonROIs', 0};
- maxval={0,0,0,0,0,0,0};
- minval={0,0,0,0,0,0,0};
- istoggle=[0,0,0,1,0,1,1];
- was_set=istoggle * 0;
- paramtype={'InputFile','InputFile','MultiChoice','Toggle','OutputFile','Toggle','Toggle'};
- % 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 'cROIfromcoords" '],Inputs,narglist);