ssoSegFunPerReg

 ssoSegFunPerReg : starts segmentation of phase image and sets error flags
 It creates the first set of good, bad and permanent segments and if
 CONST.seg.OPTI_FLAG is set to true it optimizes the region sizes.
 It uses perRegionOpti to optimize the regions.
 
 INPUT :
       phase_ : phase image
       CONST : segmentation constants
       header : string displayed with infromation
       dataname : 
       crop_box : information about alignement of the image
 
  OUTPUT :
       data : contains information about the segments and mask, for more
       information look at superSeggerOpti.
       err_flag : set to true if there are more segments than max
       

 Copyright (C) 2016 Wiggins Lab 
 Written by Stella Styliandou & 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 [data, err_flag] = ssoSegFunPerReg( phase, CONST, header, dataname, crop_box)
0002 % ssoSegFunPerReg : starts segmentation of phase image and sets error flags
0003 % It creates the first set of good, bad and permanent segments and if
0004 % CONST.seg.OPTI_FLAG is set to true it optimizes the region sizes.
0005 % It uses perRegionOpti to optimize the regions.
0006 %
0007 % INPUT :
0008 %       phase_ : phase image
0009 %       CONST : segmentation constants
0010 %       header : string displayed with infromation
0011 %       dataname :
0012 %       crop_box : information about alignement of the image
0013 %
0014 %  OUTPUT :
0015 %       data : contains information about the segments and mask, for more
0016 %       information look at superSeggerOpti.
0017 %       err_flag : set to true if there are more segments than max
0018 %
0019 %
0020 % Copyright (C) 2016 Wiggins Lab
0021 % Written by Stella Styliandou & Paul Wiggins.
0022 % University of Washington, 2016
0023 % This file is part of SuperSegger.
0024 %
0025 % SuperSegger is free software: you can redistribute it and/or modify
0026 % it under the terms of the GNU General Public License as published by
0027 % the Free Software Foundation, either version 3 of the License, or
0028 % (at your option) any later version.
0029 %
0030 % SuperSegger is distributed in the hope that it will be useful,
0031 % but WITHOUT ANY WARRANTY; without even the implied warranty of
0032 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
0033 % GNU General Public License for more details.
0034 %
0035 % You should have received a copy of the GNU General Public License
0036 % along with SuperSegger.  If not, see <http://www.gnu.org/licenses/>.
0037 
0038 if ~exist('header','var')
0039     header = '';
0040 end
0041 
0042 if ~exist('dataname','var')
0043     dataname = '';
0044 end
0045 
0046 if ~exist('crop_box','var')
0047     crop_box = '';
0048 end
0049 
0050 
0051 % create the masks and segments
0052 disp_seg = ~CONST.seg.OPTI_FLAG;
0053 data = superSeggerOpti( phase ,[], disp_seg ,CONST, 1, header, crop_box);
0054 
0055 if numel(data.segs.score) > CONST.superSeggerOpti.MAX_SEG_NUM;
0056     err_flag = true;
0057     save([dataname,'_too_many_segs'],'-STRUCT','data');
0058     disp( [header,'BSSO ',dataname,'_too_many_segs'] );
0059     return
0060 else
0061     err_flag = false;    
0062 end
0063 
0064 % optimize the regions with bad scores
0065 if CONST.seg.OPTI_FLAG
0066     data = perRegionOpti( data, 1, CONST,header);
0067     drawnow
0068 else
0069     data = intMakeRegs( data, CONST );
0070 end
0071 
0072 end
0073