//internal static List<int> GetShell6List(ImageRaster3D<bool> image)
//{
// ITopologyElement topology = new TopologyElementRaster3D6Connectivity(image.Raster);
// int[] element_neigbour_array = new int[topology.MaximumConnectivity];
// List<int> shell_list = new List<int>();
// for (int element_index = 0; element_index < image.Raster.ElementCount; element_index++)
// {
// if (image.GetElementValue(element_index))
// {
// bool is_shell = false;
// topology.ElementNeighboursRBA(element_index, element_neigbour_array);
// foreach (int other_element_index in element_neigbour_array)
// {
// if (other_element_index != -1)
// {
// if (!image.GetElementValue(other_element_index))
// {
// is_shell = true;
// }
// }
// }
// if (is_shell)
// {
// shell_list.Add(element_index);
// }
// }
// }
// return shell_list;
//}
public static ImageRaster3D <bool> GetShell3D26C(ImageRaster3D <bool> source, bool border_is_shell = false)
{
ITopologyElement topology = new TopologyElementRaster3D26Connectivity(source.Raster);
ImageRaster3D <bool> target = new ImageRaster3D <bool>(source.Raster);
GetShellRBA(source, topology, target, border_is_shell);
return(target);
}
public IImageRaster3D <bool> FindMedialAxes(IImageRaster3D <bool> image)
{
ImageRaster3D <bool> skeleton_image = ToolsImageRaster.Pad(image, false, 1, 1, 1);
ITopologyElement topology = new TopologyElementRaster3D26Connectivity(skeleton_image.Raster);
int[] euler_table = BuildEulerLookupTable();
bool changes = true;
while (changes)
{
changes = false;
List <int> candidates = ToolsImageRaster.GetShell3D6C(skeleton_image).GetElementIndexesWithValue(true);
if (candidates.Count != 0)
{
// get 26 - neighbourhoods of candidates in volume
List <int[]> neigbourhoods = new List <int[]>();
List <int> end_point_indexes = new List <int>();
for (int candidate_index = 0; candidate_index < candidates.Count; candidate_index++)
{
int[] element_neigbour_array = new int[26];
bool[] element_neigbour_true_array = new bool[26];
topology.ElementNeighboursRBA(candidates[candidate_index], element_neigbour_array);
//int count = 0;
for (int neigbour_index = 0; neigbour_index < topology.MaximumConnectivity; neigbour_index++)
{
//TODO something here
}
}
// remove all endpoints (exactly one nb) from list
neigbourhoods.RemoveAt(end_point_indexes);
candidates.RemoveAt(end_point_indexes);
// remove all non-Euler - invariant points from list
List <int> euler_variate_indexes = new List <int>();
for (int candidate_index = 0; candidate_index < candidates.Count; candidate_index++)
{
if (compute_euler_characteristic(neigbourhoods[candidate_index], euler_table))
{
euler_variate_indexes.Add(candidate_index);
}
}
neigbourhoods.RemoveAt(euler_variate_indexes);
candidates.RemoveAt(euler_variate_indexes);
List <int> is_simple_indexes = new List <int>();
for (int candidate_index = 0; candidate_index < candidates.Count; candidate_index++)
{
if (is_simple(neigbourhoods[candidate_index]))
{
is_simple_indexes.Add(candidate_index);
}
}
// remove all non-simple points from list
candidates.RemoveAt(is_simple_indexes);
//get subscript indices of remaining candidates
//TODO [x, y, z] = ind2sub(padded_image_size, candidates);
// if any candidates left: divide into 8 independent subvolumes TODO this is silly
if (candidates.Count != 0)
{
// do re-checking for all points in each subvolume
List <int> removal_indexes = new List <int>(); //sub2ind(padded_image_size, x(idx), y(idx), z(idx));
skeleton_image.SetElementValues(removal_indexes, false); // remove points
List <int[]> nh = GetNeigbourhoods(skeleton_image, removal_indexes);
List <int> di_rc = new List <int>();
for (int index = 0; index < nh.Count; index++)
{
if (!is_simple(nh[index]))
{
di_rc.Add(index);
}
}
if (di_rc.Count != 0)
{
changes = true; //% at least one voxel removed
skeleton_image.SetElementValues(di_rc, true); // TODO this seems weird
}
}
}
}
return(skeleton_image);
}
