getInfoScores

 getInfoScores : gathers properties and predicted values to be used for
 model training.

 INPUT:
       dirname : directory with seg files
       xChoice : 'segs' or 'regs' for segments or regions
       CONST : segmentation constants
 OUPUT :
       X : properties (info) for segments or regions
       Y : boolean array with two fields for bad or good segment/region

 Copyright (C) 2016 Wiggins Lab
 Written by Stella Stylianidou.
 University of Washington, 2016
 This file is part of SuperSegger.

 SuperSegger is free software: you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
 the Free Software Foundation, either version 3 of the License, or
 (at your option) any later version.

 SuperSegger is distributed in the hope that it will be useful,
 but WITHOUT ANY WARRANTY; without even the implied warranty of
 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 GNU General Public License for more details.

 You should have received a copy of the GNU General Public License
 along with SuperSegger.  If not, see <http://www.gnu.org/licenses/>.

0001 function [X,Y] =  getInfoScores (dirname, xChoice, recalcInfo, CONST)
0002 % getInfoScores : gathers properties and predicted values to be used for
0003 % model training.
0004 %
0005 % INPUT:
0006 %       dirname : directory with seg files
0007 %       xChoice : 'segs' or 'regs' for segments or regions
0008 %       CONST : segmentation constants
0009 % OUPUT :
0010 %       X : properties (info) for segments or regions
0011 %       Y : boolean array with two fields for bad or good segment/region
0012 %
0013 % Copyright (C) 2016 Wiggins Lab
0014 % Written by Stella Stylianidou.
0015 % University of Washington, 2016
0016 % This file is part of SuperSegger.
0017 %
0018 % SuperSegger is free software: you can redistribute it and/or modify
0019 % it under the terms of the GNU General Public License as published by
0020 % the Free Software Foundation, either version 3 of the License, or
0021 % (at your option) any later version.
0022 %
0023 % SuperSegger is distributed in the hope that it will be useful,
0024 % but WITHOUT ANY WARRANTY; without even the implied warranty of
0025 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
0026 % GNU General Public License for more details.
0027 %
0028 % You should have received a copy of the GNU General Public License
0029 % along with SuperSegger.  If not, see <http://www.gnu.org/licenses/>.
0030 
0031 
0032 dirname = fixDir(dirname);
0033 if ~strcmp (xChoice,'segs') && ~strcmp (xChoice,'regs')
0034     disp('no x chosen, optimizing segments');
0035     xChoice = 'segs';
0036 end
0037 if strcmp (xChoice,'segs')
0038     contents = dir([dirname,'*_seg.mat']);
0039 else
0040     contents = dir([dirname,'*_seg*.mat']);
0041 end
0042 
0043 
0044 Y = [];
0045 X = [];
0046 
0047 for i = 1 : numel(contents)
0048     data = load([dirname,contents(i).name]);
0049     disp(contents(i).name);
0050     if recalcInfo && exist('CONST','var') && ~isempty(CONST)
0051         disp ('recalculating');
0052         data = calculateInfo (data,CONST,xChoice);
0053         save ([dirname,contents(i).name],'-struct','data');
0054     end
0055     
0056     if strcmp (xChoice,'segs')
0057         X = [X;data.segs.info];
0058         Y = [Y;data.segs.score];
0059        
0060     else       
0061         X = [X;data.regs.info];
0062         Y = [Y;data.regs.score];               
0063     end
0064     
0065 
0066     
0067 end
0068 
0069 [indices] = find(~isnan(Y));
0070 X = X(indices,:);
0071 Y = Y(indices);
0072 
0073 [indices] = find(isfinite(sum(X,2)));
0074 X = X(indices,:);
0075 Y = Y(indices);
0076 
0077 
0078     function [data] = calculateInfo (data,CONST,xChoice)
0079         if strcmp (xChoice,'regs')
0080             oldInfo = data.regs.info;
0081             ss = size(data.mask_cell);
0082             data.regs.regs_label = bwlabel(data.mask_cell);
0083             data.regs.props = regionprops( data.regs.regs_label,'BoundingBox','Orientation','Centroid','Area');
0084             data.regs.num_regs = max(data.regs.regs_label(:));
0085             data.regs.info = [];
0086             
0087             for ii = 1:data.regs.num_regs
0088                 [xx,yy] = getBBpad( data.regs.props(ii).BoundingBox, ss, 1);
0089                 mask = data.regs.regs_label(yy,xx)==ii;
0090                 data.regs.info(ii,:) = CONST.regionScoreFun.props( mask, data.regs.props(ii) );
0091             end
0092             
0093             
0094             
0095             newInfo = data.regs.info;
0096             if isempty(newInfo) || all(size (oldInfo)~=size(newInfo))
0097                 error('size')
0098             elseif all (oldInfo~=newInfo)
0099                 error('hi')
0100             end
0101             
0102         elseif strcmp (xChoice,'segs')
0103 
0104             data = superSeggerOpti( data, [], 0, CONST );
0105            % disp('hack');
0106            %ss = size(data.segs.info,1);
0107            %data.segs.info (1:ss,20:25)  = 0;
0108             
0109 
0110             
0111         end
0112     end
0113 
0114 end
0115 
0116