towerMergeImages

 towerMergeImages : merges the towers of several cells.

 INPUT :
       imCell : cell array of individual cell images
       maskCell : image of tower mask
       ssCell : width and length of cells
       xdim : x dimensions for the towers
       skip : skip frame
       mag : used to set up the image dimensions
       CONST : Constants file that was used.

 OUTPUT :
         imColor : rescaled color (jet) consensus image
         imBW : rescaled bw consesus image
         towerIm : raw consensus image 
         maskCons : mask for consensus image
         nx : number of cells in x
         ny : number of cells in y
         max_x : max long axis length
         max_y : max short axis length

 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 [imColor, imBW, towerIm, maskCons, nx, ny, max_x, max_y ] = ...
0002     towerMergeImages( imCell, maskCell, ssCell, xdim, skip, mag, CONST )
0003 % towerMergeImages : merges the towers of several cells.
0004 %
0005 % INPUT :
0006 %       imCell : cell array of individual cell images
0007 %       maskCell : image of tower mask
0008 %       ssCell : width and length of cells
0009 %       xdim : x dimensions for the towers
0010 %       skip : skip frame
0011 %       mag : used to set up the image dimensions
0012 %       CONST : Constants file that was used.
0013 %
0014 % OUTPUT :
0015 %         imColor : rescaled color (jet) consensus image
0016 %         imBW : rescaled bw consesus image
0017 %         towerIm : raw consensus image
0018 %         maskCons : mask for consensus image
0019 %         nx : number of cells in x
0020 %         ny : number of cells in y
0021 %         max_x : max long axis length
0022 %         max_y : max short axis length
0023 %
0024 % Copyright (C) 2016 Wiggins Lab
0025 % Written by Stella Stylianidou, Paul Wiggins.
0026 % University of Washington, 2016
0027 % This file is part of SuperSegger.
0028 %
0029 % SuperSegger is free software: you can redistribute it and/or modify
0030 % it under the terms of the GNU General Public License as published by
0031 % the Free Software Foundation, either version 3 of the License, or
0032 % (at your option) any later version.
0033 %
0034 % SuperSegger is distributed in the hope that it will be useful,
0035 % but WITHOUT ANY WARRANTY; without even the implied warranty of
0036 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
0037 % GNU General Public License for more details.
0038 %
0039 % You should have received a copy of the GNU General Public License
0040 % along with SuperSegger.  If not, see <http://www.gnu.org/licenses/>.
0041 
0042 
0043 
0044 
0045 if ~exist('skip','var') || isempty (skip)
0046     skip = 1;
0047 end
0048 
0049 colormap_ = jet(256);
0050 max_x = 0;
0051 max_y = 0;
0052 
0053 
0054 % get number of time slices.
0055 T0 = numel(ssCell);
0056 
0057 for ii = 1:T0
0058     max_x = max([max_x, ssCell{ii}(2)]);
0059     max_y = max([max_y, ssCell{ii}(1)]);
0060 end
0061 
0062 
0063 if exist( 'xdim', 'var') && ~isempty(xdim)
0064     nx = xdim;
0065     ny = ceil(T0/nx/skip);
0066 else
0067     nx = ceil(sqrt(T0*max_y/max_x/skip));
0068     ny = ceil(T0/nx/skip);
0069 end
0070 
0071 max_x = max_x+mag;
0072 max_y = max_y+mag;
0073 
0074 imdim = [ max_y*ny + mag, max_x*nx + mag ];
0075 
0076 maskCons  = zeros(imdim(1), imdim(2));
0077 towerIm   = zeros(imdim(1), imdim(2));
0078 
0079 % make the composite image
0080 for ii = 1:T0
0081     
0082     yy = floor((ii-1)/nx/skip);
0083     xx = floor((ii-1)/skip)-yy*nx;
0084     
0085     ss = ssCell{ii};
0086     
0087     dx = floor((max_x-ss(2))/2);
0088     dy = floor((max_y-ss(1))/2);
0089     
0090     mask = maskCell{ii};
0091     
0092     try
0093         maskCons(1+yy*max_y+(1:ss(1))+dy, 1+xx*max_x+(1:ss(2))+dx) = mask;
0094         towerIm(1+yy*max_y+(1:ss(1))+dy, 1+xx*max_x+(1:ss(2))+dx) = imCell{ii};
0095     catch ME
0096         printError(ME);
0097         disp( 'Error in towerMergeImages' );
0098     end
0099 end
0100 
0101 % rescale the dynamic range of the image.
0102 f1mm = [min(towerIm( maskCons(:)>.5 )), max( towerIm( maskCons(:)>.5 ))];
0103 imBW = ag(towerIm.*maskCons,0,f1mm(2));
0104 
0105 
0106 if CONST.view.falseColorFlag
0107     % make the false color image
0108     imColor = ag(doColorMap( imBW, colormap_ ));
0109     mask3   = cat( 3, maskCons, maskCons, maskCons );
0110     imColor = uint8(uint8( double(imColor).*mask3));
0111 else
0112     % make normal image
0113     del = 0.15;     
0114     imColor = cat( 3, ...
0115         0*maskCons, ...
0116         uint8(double(imBW).*maskCons), ...
0117         del*ag(maskCons) );
0118 end
0119 
0120 end
0121 
0122