removing filtred when counting fluorescence channels. Needed when run…

…ning for the second time foci finding steps onwards.

cell/trackOptiMakeCell.m

@@ -139,7 +139,9 @@ function trackOptiMakeCell(dirname,CONST,header)
         tmp_fn = fieldnames( data_c );
         nf = numel( tmp_fn );
         for j = 1:nf;
-            if numel(strfind(tmp_fn{j},'fluor')==1)&& ~numel((strfind(tmp_fn{j},'fluor0')))
+            if numel(strfind(tmp_fn{j},'fluor')==1) && ...
+                    ~numel((strfind(tmp_fn{j},'fluor0'))) && ...
+                    ~numel((strfind(tmp_fn{j},'filtered')))
                 nc = nc+1;
             end
         end

fluorescence/trackOptiFluor.m

@@ -1,12 +1,12 @@
 function trackOptiFluor(dirname,CONST,header)
 % trackOptiFluor calculates the mean background fluorescence for each frame.
-% This is the fluroscence outside the background mask. It does not do any focus
-% fitting at this stage. It saves the information in the err/seg
-% files under data_c.fl1bg for channel 1 and data_c.fl2bg for channel 2.
+% This is the mean fluorescence of the non cell regions. No focus fitting is
+% done at this stage. It saves the information in the err/seg
+% files under data_c.fl1bg for channel 1, data_c.fl2bg for channel 2, etc.
 %
 % INPUT :
 %   dirname: seg folder eg. maindirectory/xy1/seg
-%   CONST: are the segmentation constants.
+%   CONST: segmentation constants.
 %   header : string displayed with information
 %
 % Copyright (C) 2016 Wiggins Lab
@@ -32,10 +32,8 @@ function trackOptiFluor(dirname,CONST,header)
     header = [];
 end
 
-
 SE = strel( 'disk', 5 );
 
-
 if(nargin<1 || isempty(dirname))
     dirname = '.';
 end
@@ -53,26 +51,26 @@ function trackOptiFluor(dirname,CONST,header)
 end
 
 nc = 0;
-
 if numel(contents) > 0
     data_c = loaderInternal([dirname,contents(1).name]);
     datacFields = fieldnames(data_c);
     nf = numel(datacFields);
     % goes through the fields in data_c and calculates the number of fluorescence channels
     for j = 1:nf;
-        if numel(strfind(datacFields{j},'fluor')==1) && ~numel((strfind(datacFields{j},'fluor0')))
+        if numel(strfind(datacFields{j},'fluor')==1) && ...
+                ~numel(strfind(datacFields{j},'filtered')) && ...
+                ~numel((strfind(datacFields{j},'fluor0')))
             nc = nc+1;
         end
     end
 end
 
-
 % loop through all the cells.
 if nc > 0
     for i = 1:num_im
         data_c = loaderInternal([dirname,contents(i).name]);
 
-        % Compute the background fluorescence level in both channel
+        % Compute the background fluorescence level in every channel
         ss = size( data_c.mask_cell );
 
         for j = 1 : nc