doColorMap

 doColorMap : Applies colormap to an image.

 INPUT :
       im_ : image
       colormap_ : coloramp to be used for image (default jet)
       caxis_ : 

 OUTPUT :
       im_new : image with the colormap applied

 holdcoldinv : inverts hot to cold in colormap.

 
 Copyright (C) 2016 Wiggins Lab 
 Written by 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 im_new = doColorMap( imOriginal, colormap_ , caxis_ )
0002 % doColorMap : Applies colormap to an image.
0003 %
0004 % INPUT :
0005 %       im_ : image
0006 %       colormap_ : coloramp to be used for image (default jet)
0007 %       caxis_ :
0008 %
0009 % OUTPUT :
0010 %       im_new : image with the colormap applied
0011 %
0012 % holdcoldinv : inverts hot to cold in colormap.
0013 %
0014 %
0015 % Copyright (C) 2016 Wiggins Lab
0016 % Written by Paul Wiggins.
0017 % University of Washington, 2016
0018 % This file is part of SuperSegger.
0019 %
0020 % SuperSegger is free software: you can redistribute it and/or modify
0021 % it under the terms of the GNU General Public License as published by
0022 % the Free Software Foundation, either version 3 of the License, or
0023 % (at your option) any later version.
0024 %
0025 % SuperSegger is distributed in the hope that it will be useful,
0026 % but WITHOUT ANY WARRANTY; without even the implied warranty of
0027 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
0028 % GNU General Public License for more details.
0029 %
0030 % You should have received a copy of the GNU General Public License
0031 % along with SuperSegger.  If not, see <http://www.gnu.org/licenses/>.
0032 
0033 
0034 
0035 if ~exist( 'caxis_', 'var' ) || isempty( caxis_ )
0036     caxis_ = [min(imOriginal(:)),max(imOriginal(:))];
0037 end
0038 
0039 im = double((imOriginal-caxis_(1)))/double((caxis_(2)-caxis_(1)));
0040 im(im<0)=0;
0041 im(isnan(im)) = 0;
0042 ss_c = size(colormap_);
0043 
0044 im = floor( ss_c(1)*im)+1;
0045 im(im>ss_c(1))=ss_c(1);
0046 
0047 ss  = size( im );
0048 im_new = im(:);
0049 im_new = colormap_(im_new,:);
0050 im_new = reshape( im_new, [ss,3]);
0051 
0052 end