gtPlaceSubVolume.m

function output=gtPlaceSubVolume(output, input, shift)
% GTPLACESUBVOLUME  Analogous to gtPlaceSubImage
%     output = gtPlaceSubVolume(output, input, shift)
%     -----------------------------------------------
%     places the input volume in the output vol, with the origin of the input
%     volume at point defined by shift=[y x z] in the output volume.  Any part of the
%     input volume falling outside of the output volume is cropped.  Origin
%     can contain negative coordinates, again anything outside the output
%     volume is cropped.
%     so...  shift=[0 0 0] means that the voxel (a,b,c) in input will be at
%     point (a,b,c) in the output.
%     shift=[2 -2 0] means that voxel (a,b,c) will be at (a+2, b-2, c) in
%     output.
%
%     Note - this used to add on volume to another, rather than place one image
%     in the other.  I have modified so it no longer adds.  Hope this doesn't
%     break anything.

[sizeYi, sizeXi, sizeZi]=size(input);
[sizeYo, sizeXo, sizeZo]=size(output);

%output(y1o:y2o, x1o:x2o, z1o:z2o)=output(y1o:y2o, x1o:x2o, z1o:z2o)+input(y1i:y2i, x1i:x2i, z1i:z2i);
y=shift(1);x=shift(2);z=shift(3);

%output volume limits
y1o=max(1, y+1);
y2o=min(sizeYo, y+sizeYi);
x1o=max(1, x+1);
x2o=min(sizeXo, x+sizeXi);
z1o=max(1, z+1);
z2o=min(sizeZo, z+sizeZi);

%input volume limits
y1i=max(1, -y+1);
y2i=min(sizeYi, sizeYo-y);
x1i=max(1, -x+1);
x2i=min(sizeXi, sizeXo-x);
z1i=max(1, -z+1);
z2i=min(sizeZi, sizeZo-z);

%output(y1o:y2o, x1o:x2o, z1o:z2o)=output(y1o:y2o, x1o:x2o,z1o:z2o)+input(y1i:y2i, x1i:x2i, z1i:z2i);
output(y1o:y2o, x1o:x2o, z1o:z2o)=input(y1i:y2i, x1i:x2i, z1i:z2i);

end