Squashed commit of the sb-vbs branch.

Includes the SD-VBS benchmarks modified to:
- Use libextra to loop as realtime jobs
- Preallocate memory before starting their main computation
- Accept input via stdin instead of via argc

Does not include the SD-VBS matlab code.

Fixes libextra execution in LITMUS^RT.

1 files changed, 82 insertions, 0 deletions

diff --git a/SD-VBS/common/toolbox/toolbox_basic/affine/find_AD.m b/SD-VBS/common/toolbox/toolbox_basic/affine/find_AD.m
new file mode 100755
index 0000000..3cccefb
--- /dev/null
+++ b/SD-VBS/common/toolbox/toolbox_basic/affine/find_AD.m
@@ -0,0 +1,82 @@
+function [A,D] = find_AD(I,J,mask,w)
+%
+%  [A,D] = find_AD(I,J,mask,w)
+%
+%    find the matrix affine transform A and displacement D,
+%    such that SSD difference of  I(Ax-d)-J(x) is minimized,
+%   
+
+%
+% Jianbo Shi
+%
+
+
+[gy1,gx1] = grad(I,w);
+[gy2,gx2] = grad(J,w);
+
+gx = 0.5*(gx1+gx2);
+gy = 0.5*(gy1+gy2);
+
+[size_y,size_x] = size(I);
+[center_y,center_x] = find_center(size_y,size_x);
+mask = mask(w+1:size_y-w,w+1:size_x-w);
+
+[x,y] = meshgrid(1:size_x,1:size_y);
+x = x- center_x;
+y = y-center_y;
+
+x = x(w+1:size_y-w,w+1:size_x-w);
+y = y(w+1:size_y-w,w+1:size_x-w);
+
+gx_sqr = gx.*mask.*gx;
+gx_gy = gx.*mask.*gy;
+gy_sqr = gy.*mask.*gy;
+
+x_sqr = x.*x;
+x_y = x.*y;
+y_sqr = y.*y;
+
+T= zeros(6,6);
+T(1,1) = 0.5*trapz(trapz(gx_sqr.*x_sqr));
+T(2,1) = trapz(trapz(gx_gy.*x_y));
+T(3,1) = trapz(trapz(gx_sqr.*x_y));
+T(4,1) = trapz(trapz(gx_gy.*x_sqr));
+T(5,1) = trapz(trapz(gx_sqr.*x));
+T(6,1) = trapz(trapz(gx_gy.*x));
+T(2,2) = 0.5*trapz(trapz(gy_sqr.*y_sqr));
+T(3,2) = trapz(trapz(gx_gy.*y_sqr));
+T(4,2) = trapz(trapz(gy_sqr.*x_y));
+T(5,2) = trapz(trapz(gx_gy.*y));
+T(6,2) = trapz(trapz(gy_sqr.*y));
+T(3,3) = 0.5*trapz(trapz(gx_sqr.*y_sqr));
+T(4,3) = trapz(trapz(gx_gy.*x_y));
+T(5,3) = trapz(trapz(gx_sqr.*y));
+T(6,3) = trapz(trapz(gx_gy.*y));
+T(4,4) = 0.5*trapz(trapz(gy_sqr.*x_sqr));
+T(5,4) = trapz(trapz(gx_gy.*x));
+T(6,4) = trapz(trapz(gy_sqr.*x));
+T(5,5) = 0.5*trapz(trapz(gx_sqr));
+T(6,5) = trapz(trapz(gx_gy));
+T(6,6) = 0.5*trapz(trapz(gy_sqr));
+
+T = T+T';
+
+J = J(w+1:size_y-w,w+1:size_x-w);
+I = I(w+1:size_y-w,w+1:size_x-w);
+
+
+diff = (J-I).*mask;
+b(1) = trapz(trapz(diff.*gx.*x));
+b(2) = trapz(trapz(diff.*gy.*y));
+b(3) = trapz(trapz(diff.*gx.*y));
+b(4) = trapz(trapz(diff.*gy.*x));
+b(5) = trapz(trapz(diff.*gx));
+b(6) = trapz(trapz(diff.*gy));
+
+a = inv(T)*b';
+
+A = [1+a(1), a(3);
+a(4),1+a(2)];
+
+D= [a(5),a(6)];
+