systematic

 systematic: Finds the minimum energy configuration by trying all segment 
 combinations.

 INPUT :
       segs_list : list of ids of segments to be turned on and off
       data : seg data file
       cell_mask : mask of regions of cells to be optimized
       xx : xx from bounding box of cell_mask
       yy : yy from bounding box of cell_mask
       CONST : segmentation constants

 OUTPUT :
       minVect : vector of segments to be on for minimum energy found.
       regEmin : energy of every region for the minimum state


 Copyright (C) 2016 Wiggins Lab 
 Written by Stella Stylianidou, Paul Wiggins.
 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 [minVect,regEmin] = systematic( segs_list, data, cell_mask, xx, yy, CONST)
0002 % systematic: Finds the minimum energy configuration by trying all segment
0003 % combinations.
0004 %
0005 % INPUT :
0006 %       segs_list : list of ids of segments to be turned on and off
0007 %       data : seg data file
0008 %       cell_mask : mask of regions of cells to be optimized
0009 %       xx : xx from bounding box of cell_mask
0010 %       yy : yy from bounding box of cell_mask
0011 %       CONST : segmentation constants
0012 %
0013 % OUTPUT :
0014 %       minVect : vector of segments to be on for minimum energy found.
0015 %       regEmin : energy of every region for the minimum state
0016 %
0017 %
0018 % Copyright (C) 2016 Wiggins Lab
0019 % Written by Stella Stylianidou, Paul Wiggins.
0020 % University of Washington, 2016
0021 % This file is part of SuperSegger.
0022 %
0023 % SuperSegger is free software: you can redistribute it and/or modify
0024 % it under the terms of the GNU General Public License as published by
0025 % the Free Software Foundation, either version 3 of the License, or
0026 % (at your option) any later version.
0027 %
0028 % SuperSegger is distributed in the hope that it will be useful,
0029 % but WITHOUT ANY WARRANTY; without even the implied warranty of
0030 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
0031 % GNU General Public License for more details.
0032 %
0033 % You should have received a copy of the GNU General Public License
0034 % along with SuperSegger.  If not, see <http://www.gnu.org/licenses/>.
0035 
0036 debug_flag = 0;
0037 
0038 num_segs = numel(segs_list);
0039 num_comb = 2^num_segs;
0040 state = cell( 1, num_comb );
0041 regionScore = zeros( 1, num_comb );
0042 
0043 for jj = 1:num_comb;
0044     
0045     % goes through all combinations and turns on segments
0046     vect = makeVector(jj-1,num_segs)';
0047     
0048     % calculates state energy
0049     [regionScore(jj),state{jj}] = calculateStateEnergy(cell_mask,vect,segs_list,data,xx,yy,CONST);
0050     
0051 end
0052 
0053 % get the minimum score
0054 [Emin, jj_min] = min(regionScore);
0055 minVect = makeVector(jj_min-1,num_segs)';
0056 minState = state{jj_min};
0057 regEmin = minState.reg_E;
0058 
0059 if debug_flag
0060     % shows the minimum score found from systematic
0061     cell_mask_mod = cell_mask;    
0062     for kk = 1:num_segs
0063         cell_mask_mod = cell_mask_mod - minVect(kk)*(segs_list(kk)==data.segs.segs_label(yy,xx));
0064     end
0065     figure(1);
0066     clf;
0067     imshow( cat(3,ag(cell_mask),...
0068         ag(cell_mask_mod),...
0069         0*ag(cell_mask)),'InitialMagnification','fit');
0070     disp(['Total Region Score : ',num2str(Emin)]);
0071 end
0072 
0073 end
0074 
0075 function vect = makeVector( nn, n )
0076 vect = zeros(1,n);
0077 for i=n-1:-1:0;
0078     vect(i+1) = floor(nn/2^i);
0079     nn = nn - vect(i+1)*2^i;
0080 end
0081 end