intAlignIm

 intAlignIm : aligning image A to image B with given precision

 INPUT :
      imA : image A
      imB : image B
      precision :  Upsampling factor (integer). Images will be registered to 
           within 1/precision of a pixel. 

 OUTPUT :
       out :  [error,diffphase,net_row_shift,net_col_shift]
           error : Translation invariant normalized RMS error between f and g
           diffphase : Global phase difference between the two images (should be
           zero if images are non-negative).
           net_row_shift, net_col_shift : Pixel shifts between images
       errNum : error value of alignment
       focusNum : score of how focused the images are

 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  [out, errNum, focusNum] = intAlignIm( imA, imB, precision )
0002 % intAlignIm : aligning image A to image B with given precision
0003 %
0004 % INPUT :
0005 %      imA : image A
0006 %      imB : image B
0007 %      precision :  Upsampling factor (integer). Images will be registered to
0008 %           within 1/precision of a pixel.
0009 %
0010 % OUTPUT :
0011 %       out :  [error,diffphase,net_row_shift,net_col_shift]
0012 %           error : Translation invariant normalized RMS error between f and g
0013 %           diffphase : Global phase difference between the two images (should be
0014 %           zero if images are non-negative).
0015 %           net_row_shift, net_col_shift : Pixel shifts between images
0016 %       errNum : error value of alignment
0017 %       focusNum : score of how focused the images are
0018 %
0019 % Copyright (C) 2016 Wiggins Lab
0020 % Written by Paul Wiggins.
0021 % University of Washington, 2016
0022 % This file is part of SuperSegger.
0023 %
0024 % SuperSegger is free software: you can redistribute it and/or modify
0025 % it under the terms of the GNU General Public License as published by
0026 % the Free Software Foundation, either version 3 of the License, or
0027 % (at your option) any later version.
0028 %
0029 % SuperSegger is distributed in the hope that it will be useful,
0030 % but WITHOUT ANY WARRANTY; without even the implied warranty of
0031 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
0032 % GNU General Public License for more details.
0033 %
0034 % You should have received a copy of the GNU General Public License
0035 % along with SuperSegger.  If not, see <http://www.gnu.org/licenses/>.
0036 
0037 
0038 
0039 % fourier transform images
0040 fftA = fft2(imA);
0041 fftB = fft2(imB);
0042 
0043 % subpixel image registration by crosscorrelation
0044 try
0045     out = dftregistration(fftA,fftB,precision);
0046 catch ME
0047    printError( ME )
0048 end
0049 
0050 % calculate error
0051 lamMin = 5;
0052 lamMax = 100;
0053 errNum = compErrInt( fftA, fftB, lamMin, lamMax );
0054 
0055 % calculates how in focus image A is
0056 focusNum = isFocus( fftA );
0057 
0058 end