trackOptiFindFoci

 trackOptiFindFoci : Finds foci in cells. Note that this only
 runs if the number of foci to be fit is set in CONST.trackLoci.numSpots.
 It runs on the err.mat files and saves the new err.mat files with the
 found foci. This is done using the curve filter to find the foci in the 
 image and then by fitting gaussians and and assigning the foci 
 in all cells simultaneously.

 INPUT :
   dirname: is the seg directory in the xy directory
   CONST: are the segmentation constants.
   header : string displayed with information

 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 trackOptiFindFoci(dirname,CONST,header)
0002 % trackOptiFindFoci : Finds foci in cells. Note that this only
0003 % runs if the number of foci to be fit is set in CONST.trackLoci.numSpots.
0004 % It runs on the err.mat files and saves the new err.mat files with the
0005 % found foci. This is done using the curve filter to find the foci in the
0006 % image and then by fitting gaussians and and assigning the foci
0007 % in all cells simultaneously.
0008 %
0009 % INPUT :
0010 %   dirname: is the seg directory in the xy directory
0011 %   CONST: are the segmentation constants.
0012 %   header : string displayed with information
0013 %
0014 % Copyright (C) 2016 Wiggins Lab
0015 % Written by Stella Stylianidou & Paul Wiggins.
0016 % University of Washington, 2016
0017 % This file is part of SuperSegger.
0018 %
0019 % SuperSegger is free software: you can redistribute it and/or modify
0020 % it under the terms of the GNU General Public License as published by
0021 % the Free Software Foundation, either version 3 of the License, or
0022 % (at your option) any later version.
0023 %
0024 % SuperSegger is distributed in the hope that it will be useful,
0025 % but WITHOUT ANY WARRANTY; without even the implied warranty of
0026 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
0027 % GNU General Public License for more details.
0028 %
0029 % You should have received a copy of the GNU General Public License
0030 % along with SuperSegger.  If not, see <http://www.gnu.org/licenses/>.
0031 
0032 if ~exist('header','var')
0033     header = [];
0034 end
0035 
0036 dirname = fixDir( dirname );
0037 
0038 % Get the error data file names with the region information
0039 contents=dir([dirname,'*_err.mat']);
0040 num_im = numel(contents);
0041 
0042 data_c = loaderInternal([dirname,contents(1).name]);
0043 nc = 0;
0044 tmp_fn = fieldnames(data_c);
0045 nf = numel(tmp_fn);
0046 
0047 % goes through the fields in data_c and calculates the number of fluorescence channels
0048 for j = 1:nf; 
0049     if numel(strfind(tmp_fn{j},'fluor')==1) && ~numel((strfind(tmp_fn{j},'fluor0')))
0050         nc = nc+1;
0051     end
0052 end
0053 
0054 if ~isfield( data_c, 'fluor1' ) || ~isfield( CONST.trackLoci, 'numSpots' ) ||...
0055         ~any(CONST.trackLoci.numSpots)
0056     disp ('No foci were fit. Set the constants if you want foci.');
0057     return;
0058 end
0059 
0060 
0061 if CONST.parallel.show_status
0062     h = waitbar( 0, 'Find Loci.');
0063     cleanup = onCleanup( @()( delete( h ) ) );
0064 else
0065     h = [];
0066 end
0067 
0068 for i = 1:num_im; % finding loci through every image
0069     intDoFoci( i, dirname, contents, nc, CONST);
0070     if CONST.parallel.show_status
0071         waitbar(i/num_im,h,['Find Loci--Frame: ',num2str(i),'/',num2str(num_im)]);
0072     else
0073         disp( [header, 'FindLoci: No status bar. Frame ',num2str(i), ...
0074             ' of ', num2str(num_im),'.']);
0075    end
0076 end
0077 
0078 if CONST.parallel.show_status
0079     close(h);
0080 end
0081 
0082 
0083 end
0084 
0085 function data = loaderInternal( filename )
0086 data = load(filename);
0087 end
0088 
0089 function intDoFoci( i, dirname, contents, nc, CONST)
0090 % intDoLoci : finds the foci in image i
0091 %
0092 % INPUT :
0093 %       i : time frame number
0094 %       dirname : seg directory path in xy folder
0095 %       contents : seg/err data files
0096 %       nc : number of channels
0097 %       CONST : segmentation parameters
0098 
0099 data_c = loaderInternal([dirname,contents(i).name]);
0100 
0101 % Loop through the different fluorescence channels
0102 for channel_number = 1:nc
0103     if isfield( CONST.trackLoci, 'numSpots' ) && numel(CONST.trackLoci.numSpots)>=channel_number
0104         if CONST.trackLoci.numSpots(channel_number) 
0105             % only runs if non zero number of foci are set in constants
0106             % Fits the foci
0107             data_c = intFindFociCurve( data_c, CONST, channel_number );
0108         end
0109     end
0110 end
0111 
0112 dataname = [dirname,contents(i).name];
0113 save(dataname,'-STRUCT','data_c');
0114 
0115 end
0116