OPT: adapt get_non_zero_coordinates to 2D data --> put zero value to z
OPT: adapt get_non_zero_coordinates to 2D data --> put zero value to z

Former-commit-id: 7a9101aaeb561f0d3381589c8a264c87905499a2
neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox