function aligned_photo=align2(photo, template, rows, columns)
% align2(photo, template, rows, columns)
% returns a shifted version of the photo
% to make it best align with the template.
% If template is the same size as the photo,
% then align2 merely "rotates" some of the rows of the photo
% from the top to the bottom (or vice versa) (and columns)
% to make it best align with the template.
%
% usage:
% » aligned_photo = align2(photo, template, 100:200, 1:40)
% » aligned_photo = align2(photo, template, 1:size(photo,1), 1:size(photo,2) )
% 1998-08-31:DAV: fixed correlation/convolution bug.
% 1998-08-31:DAV: subtracted mean intensity,
% so it wouldn't always give shifts of 0,0.
% 1998-08-29:DAV: fixed so it works with both odd and even size photos.
% 1998-08-29:DAV: written by David Cary <d.cary at ieee.org>
% Is this made practically obsolete with XCORR2 ?
% See also XCORR2, CONV2, FILTER2, 
% FIXME:
% My code uses a photo and template of the the *same* size.
% It probably does the Right Thing if 
% template is much smaller than photo; but this hasn't been tested.

% speedup: Reduce the amount of data, to make it go a bit faster
% FIXME: this assumes there's a nice hot spot somewhere in
% this region. This is true for all the boards I've seen so far...
% I picked the column of small chips on the left edge.
small_photo = photo( rows, columns);
small_photo = small_photo - mean(small_photo(:));
small_template = template( rows, columns);
% rotate so we do correlation, not convolution.
small_template = rot90(small_template,2) - mean(small_template(:));
% end of speedup.

Height=size(small_photo,1)+size(small_template,1)-1;
Width=size(small_photo,2)+size(small_template,2)-1;
%'doing correlation'
padded_correlation = abs( ifft2(...
    fft2(small_photo, Height, Width) .* ...
    fft2(small_template, Height, Width)...
    ));
%'finding shift'
%correlation=padded_correlation(...
%    (0:(size(small_photo,1)-1)) + floor(size(small_template,1)/2)+1, ... 
%    (0:(size(small_photo,2)-1)) + floor(size(small_template,2)/2)+1 ...
%    );
% to reduce false hits, only allow +-6 pixel shifts in y direction.
%trimmed_correlation = correlation;
%half_size = floor(size(small_photo,1)/2 );
%top = 1:(half_size-6);
%trimmed_correlation( top, :) = 0;
%bottom = (half_size+6):size(small_photo,1);
%trimmed_correlation( bottom, :) = 0;

% max_match = max( trimmed_correlation(:) );
max_match = max( padded_correlation(:) );
[y,x] = find( max_match == padded_correlation );
% arbitrarily pick the 1st match --
% since a few pathological cases have multiple matches.
yshift = y(1)- size(small_photo,1)
xshift = x(1)- size(small_photo,2)

% positive shift values mean that
% photo is shifted to the right/down relative to template,
% and now needs to be shifted to the left/up to make it line up.
%'shifting image'
% shuffle columns
reordered_columns = 1 + mod( (0:size(photo,2)-1) + xshift, size(photo,2) );
columns_aligned = photo( :, reordered_columns );

% shuffle rows
reordered_rows = 1 + mod( (0:size(photo,1)-1) + yshift, size(photo,1) );
aligned_photo = columns_aligned( reordered_rows, : );

% end align2.m