To interpolate without the gaps you need to remove them from the data before interpolating, request values on the full grid (including gap sites), then add the gaps back in.
- If you leave the gaps in the original data, then those 0's will affect the interpolation results at neighboring sites, so they need to be discarded for the purposes of interpolation.
- If you don't request values on the full grid from griddata, adding the gaps back in afterward is harder.
For example:
idx = (z ~= 0); %logical mask to keep nonzeros in z
x_adj = x(idx);
y_adj = y(idx);
z_adj = z(idx);
% interpolate on the full grid (x,y) using only the adjusted data
z_gridded = griddata(x_adj,y_adj,z_adj,x,y);
% use the mask again to restore the gaps.
% z_gridded then includes interpolated data + gaps over the full grid (x,y)
z_gridded(~idx) = 0;
