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segment.c
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#include <mni.h>
typedef enum { SAME, INCREASING, NUM_CLASSES } Classes;
#define USER_SET_BIT 128
#define FACE_NEIGHBOURS
#undef EDGE_NEIGHBOURS
#define EDGE_NEIGHBOURS
#undef CORNER_NEIGHBOURS
#define CORNER_NEIGHBOURS
private int neighbour_deltas[][N_DIMENSIONS] = {
#ifdef FACE_NEIGHBOURS
{ 1, 0, 0 },
{ -1, 0, 0 },
{ 0, 1, 0 },
{ 0, -1, 0 },
{ 0, 0, 1 },
{ 0, 0, -1 }
#endif
#ifdef EDGE_NEIGHBOURS
, { 1, 1, 0 },
{ 1, -1, 0 },
{ -1, 1, 0 },
{ -1, -1, 0 },
{ 1, 0, 1 },
{ 1, 0, -1 },
{ -1, 0, 1 },
{ -1, 0, -1 },
{ 0, 1, 1 },
{ 0, 1, -1 },
{ 0, -1, 1 },
{ 0, -1, -1 }
#endif
#ifdef CORNER_NEIGHBOURS
, { 1, 1, 1 },
{ 1, 1, -1 },
{ 1, -1, 1 },
{ 1, -1, -1 },
{ -1, 1, 1 },
{ -1, 1, -1 },
{ -1, -1, 1 },
{ -1, -1, -1 }
#endif
};
#define FOR_LOOP_NEIGHBOURS( i, x, y, z, nx, ny, nz ) \
for_less( i, 0, SIZEOF_STATIC_ARRAY( neighbour_deltas ) ) \
{ \
(nx) = (x) + neighbour_deltas[i][X]; \
(ny) = (y) + neighbour_deltas[i][Y]; \
(nz) = (z) + neighbour_deltas[i][Z];
private void create_to_do_list(
int min_range[],
int max_range[],
bitlist_3d_struct *to_do )
{
create_bitlist_3d( max_range[X] - min_range[X] + 1,
max_range[Y] - min_range[Y] + 1,
max_range[Z] - min_range[Z] + 1, to_do );
}
private void clear_to_do_list(
bitlist_3d_struct *to_do )
{
zero_bitlist_3d( to_do );
}
private void set_to_do_list(
int min_range[],
bitlist_3d_struct *to_do,
int x,
int y,
int z )
{
set_bitlist_bit_3d( to_do,
x - min_range[X],
y - min_range[Y],
z - min_range[Z], TRUE );
}
private void set_to_do_list_neighbours_no_check(
int min_range[],
bitlist_3d_struct *to_do,
int x,
int y,
int z )
{
int i, nx, ny, nz;
FOR_LOOP_NEIGHBOURS( i, x, y, z, nx, ny, nz )
set_to_do_list( min_range, to_do, nx, ny, nz );
}
}
private void set_to_do_list_neighbours(
int min_range[],
int max_range[],
bitlist_3d_struct *to_do,
int x,
int y,
int z )
{
int i, nx, ny, nz;
FOR_LOOP_NEIGHBOURS( i, x, y, z, nx, ny, nz )
if( min_range[X] <= nx && nx <= max_range[X] &&
min_range[Y] <= ny && ny <= max_range[Y] &&
min_range[Z] <= nz && nz <= max_range[Z] )
{
set_to_do_list( min_range, to_do, nx, ny, nz );
}
}
}
private BOOLEAN must_do_voxel(
int min_range[],
bitlist_3d_struct *to_do,
int x,
int y,
int z )
{
return( get_bitlist_bit_3d( to_do,
x - min_range[X],
y - min_range[Y],
z - min_range[Z] ) );
}
private void delete_to_do_list(
bitlist_3d_struct *to_do )
{
delete_bitlist_3d( to_do );
}
#define INVALID_DIST 255
private Smallest_int ***make_distance_transform(
Volume volume,
int n_dimensions,
int axis,
int min_range[],
int max_range[],
Real min_threshold,
Real max_threshold )
{
int i, x, y, z, nx, ny, nz, *neigh[MAX_DIMENSIONS];
int iteration;
Real value;
int this_dist, dist, new_value;
BOOLEAN changed, found;
BOOLEAN x_okay, y_okay, away_from_boundary;
Smallest_int ***distance[2];
int which;
bitlist_3d_struct to_do[2];
neigh[X] = &nx;
neigh[Y] = &ny;
neigh[Z] = &nz;
ALLOC3D( distance[0], max_range[X]+1, max_range[Y]+1, max_range[Z]+1 );
ALLOC3D( distance[1], max_range[X]+1, max_range[Y]+1, max_range[Z]+1 );
create_to_do_list( min_range, max_range, &to_do[0] );
create_to_do_list( min_range, max_range, &to_do[1] );
which = 0;
for_inclusive( x, min_range[X], max_range[X] )
{
for_inclusive( y, min_range[Y], max_range[Y] )
{
for_inclusive( z, min_range[Z], max_range[Z] )
{
value = get_volume_real_value( volume, x, y, z, 0, 0 );
if( min_threshold <= value && value <= max_threshold )
{
set_to_do_list( min_range, &to_do[which], x, y, z );
distance[which][x][y][z] = INVALID_DIST;
}
else
distance[which][x][y][z] = 0;
}
}
}
iteration = 0;
do
{
clear_to_do_list( &to_do[1-which] );
++iteration;
print( "Distance Transform Iteration: %d\n", iteration );
changed = FALSE;
for_inclusive( x, min_range[X], max_range[X] )
{
x_okay = x > min_range[X] && x < max_range[X];
for_inclusive( y, min_range[Y], max_range[Y] )
{
y_okay = x_okay && y > min_range[Y] && y < max_range[Y];
for_inclusive( z, min_range[Z], max_range[Z] )
{
this_dist = distance[which][x][y][z];
if( this_dist != INVALID_DIST ||
!must_do_voxel( min_range, &to_do[which], x, y, z ) )
{
distance[1-which][x][y][z] = this_dist;
continue;
}
away_from_boundary = y_okay &&
z > min_range[Z] && z < max_range[Z];
found = FALSE;
FOR_LOOP_NEIGHBOURS( i, x, y, z, nx, ny, nz )
if( n_dimensions == 2 &&
(*(neigh[axis]) < min_range[axis] ||
*(neigh[axis]) > max_range[axis]) )
continue;
if( !away_from_boundary &&
(nx < min_range[X] || nx > max_range[X] ||
ny < min_range[Y] || ny > max_range[Y] ||
nz < min_range[Z] || nz > max_range[Z]) )
{
dist = INVALID_DIST;
}
else
dist =distance[which][nx][ny][nz];
if( dist == iteration-1 )
{
found = TRUE;
break;
}
}
if( found )
{
new_value = iteration;
changed = TRUE;
if( away_from_boundary )
set_to_do_list_neighbours_no_check( min_range,
&to_do[1-which], x, y, z );
else
set_to_do_list_neighbours( min_range, max_range,
&to_do[1-which], x, y, z );
}
else
new_value = this_dist;
distance[1-which][x][y][z] = new_value;
}
}
}
which = 1 - which;
}
while( changed );
delete_to_do_list( &to_do[0] );
delete_to_do_list( &to_do[1] );
FREE3D( distance[1-which] );
return( distance[which] );
}
private int get_cut_class(
int cut,
Classes *class )
{
*class = (Classes) (cut % NUM_CLASSES);
return( cut / NUM_CLASSES );
}
private int create_cut_class(
int cut,
Classes class )
{
return( NUM_CLASSES * cut + (int) class );
}
private void get_voxel_range(
Volume volume,
int n_dimensions,
int voxel_pos,
int axis,
int min_range[],
int max_range[] )
{
int c, sizes[MAX_DIMENSIONS];
get_volume_sizes( volume, sizes );
for_less( c, 0, get_volume_n_dimensions(volume) )
{
min_range[c] = 0;
max_range[c] = sizes[c]-1;
}
if( n_dimensions == 2 )
{
min_range[axis] = voxel_pos;
max_range[axis] = voxel_pos;
}
}
public void initialize_segmenting_3d(
Volume volume,
Volume label_volume,
int n_dimensions,
int voxel_pos,
int axis,
Real min_threshold,
Real max_threshold,
Smallest_int ****distance_transform,
Smallest_int ****cuts,
bitlist_3d_struct *to_do )
{
int label, dist, cut, x, y, z;
int min_range[MAX_DIMENSIONS], max_range[MAX_DIMENSIONS];
get_voxel_range( volume, n_dimensions, voxel_pos, axis,
min_range, max_range );
*distance_transform = make_distance_transform( volume, n_dimensions,
axis, min_range, max_range,
min_threshold,
max_threshold );
ALLOC3D( *cuts, max_range[X]+1, max_range[Y]+1, max_range[Z]+1 );
create_to_do_list( min_range, max_range, to_do );
for_inclusive( x, min_range[X], max_range[X] )
{
for_inclusive( y, min_range[Y], max_range[Y] )
{
for_inclusive( z, min_range[Z], max_range[Z] )
{
label = (int) get_volume_voxel_value( volume, x, y, z, 0, 0 );
if( label & USER_SET_BIT )
{
label = 0;
set_volume_voxel_value( label_volume, x, y, z, 0, 0, 0.0 );
}
dist = (*distance_transform)[x][y][z];
if( dist == 0 )
cut = 0;
else
{
if( label != 0 )
{
cut = create_cut_class( dist, INCREASING );
set_to_do_list_neighbours( min_range, max_range,
to_do, x, y, z );
}
else
cut = create_cut_class( 0, INCREASING );
}
(*cuts)[x][y][z] = cut;
}
}
}
}
private void propagate_neighbour_cut(
int bound_dist,
int neigh_cut,
Classes neigh_class,
int neigh_bound_dist,
int *new_cut,
Classes *new_class )
{
switch( neigh_class )
{
case INCREASING:
if( bound_dist > neigh_bound_dist )
{
*new_cut = bound_dist;
*new_class = INCREASING;
}
else if( bound_dist == neigh_bound_dist )
{
*new_cut = MIN( neigh_cut, bound_dist );
*new_class = SAME;
}
else
{
*new_cut = neigh_cut;
*new_class = SAME;
}
break;
case SAME:
if( bound_dist >= neigh_bound_dist )
{
*new_cut = MIN( neigh_cut, neigh_bound_dist );
*new_class = SAME;
}
else
{
*new_cut = neigh_cut;
*new_class = SAME;
}
break;
default:
HANDLE_INTERNAL_ERROR( "propagate_cuts" );
}
}
public BOOLEAN expand_labels_3d(
Volume label_volume,
Smallest_int ***distance_transform,
Smallest_int ***cuts,
bitlist_3d_struct *to_do,
int n_dimensions,
int voxel_pos,
int axis )
{
int i, x, y, z, nx, ny, nz, x_size, y_size;
int label, dist, cut;
int neigh_dist, neigh_cut;
int best_label, neigh_label, best_cut;
int new_cut;
BOOLEAN x_okay, y_okay, away_from_boundary;
BOOLEAN changed, better, user_set_it;
Classes class, new_class, neigh_class, best_class;
Smallest_int ***new_cuts, ***new_labels;
int min_range[MAX_DIMENSIONS], max_range[MAX_DIMENSIONS];
progress_struct progress;
bitlist_3d_struct next_to_do;
get_voxel_range( label_volume, n_dimensions, voxel_pos, axis,
min_range, max_range );
ALLOC3D( new_cuts, max_range[X]+1, max_range[Y]+1, max_range[Z]+1 );
ALLOC3D( new_labels, max_range[X]+1, max_range[Y]+1, max_range[Z]+1 );
create_to_do_list( min_range, max_range, &next_to_do );
changed = FALSE;
x_size = max_range[X] - min_range[X] + 1;
y_size = max_range[Y] - min_range[Y] + 1;
initialize_progress_report( &progress, FALSE, x_size * y_size,
"Expanding Labels" );
for_inclusive( x, min_range[X], max_range[X] )
{
x_okay = x > min_range[X] && x < max_range[X];
for_inclusive( y, min_range[Y], max_range[Y] )
{
y_okay = x_okay && y > min_range[Y] && y < max_range[Y];
for_inclusive( z, min_range[Z], max_range[Z] )
{
away_from_boundary = y_okay &&
z > min_range[Z] && z < max_range[Z];
label = (int) get_volume_voxel_value( label_volume, x, y, z,
0, 0 );
user_set_it = FALSE;
if( (label & USER_SET_BIT) != 0 )
label -= USER_SET_BIT;
else if( label != 0 )
user_set_it = TRUE;
dist = distance_transform[x][y][z];
cut = get_cut_class( cuts[x][y][z], &class );
best_label = label;
best_cut = cut;
best_class = class;
if( dist != 0 && !user_set_it &&
must_do_voxel( min_range, to_do, x, y, z ) )
{
FOR_LOOP_NEIGHBOURS( i, x, y, z, nx, ny, nz )
if( away_from_boundary ||
nx >= min_range[X] && nx <= max_range[X] &&
ny >= min_range[Y] && ny <= max_range[Y] &&
nz >= min_range[Z] && nz <= max_range[Z] )
{
neigh_dist = distance_transform[nx][ny][nz];
if( neigh_dist == 0 )
continue;
neigh_label = (int) get_volume_voxel_value(
label_volume, nx, ny, nz, 0, 0 );
if( neigh_label == 0 )
continue;
if( (neigh_label & USER_SET_BIT) != 0 )
neigh_label -= USER_SET_BIT;
neigh_cut = get_cut_class( cuts[nx][ny][nz],
&neigh_class );
propagate_neighbour_cut( dist,
neigh_cut,
neigh_class,
neigh_dist,
&new_cut,
&new_class );
if( new_class < best_class )
better = TRUE;
else if( new_class == best_class &&
(new_cut > best_cut ||
new_cut == best_cut &&
neigh_label < best_label) )
better = TRUE;
else
better = FALSE;
if( better )
{
best_label = neigh_label;
best_cut = new_cut;
best_class = new_class;
}
}
}
}
if( best_label != label ||
best_cut != cut ||
best_class != class )
{
new_labels[x][y][z] = best_label | USER_SET_BIT;
changed = TRUE;
if( away_from_boundary )
set_to_do_list_neighbours_no_check(
min_range,
&next_to_do, x, y, z );
else
set_to_do_list_neighbours( min_range, max_range,
&next_to_do, x, y, z );
}
else
{
if( !user_set_it && best_label != 0 )
best_label |= USER_SET_BIT;
new_labels[x][y][z] = best_label;
}
cut = create_cut_class( best_cut, best_class );
new_cuts[x][y][z] = cut;
}
update_progress_report( &progress, (x - min_range[X]) * y_size +
y - min_range[Y] + 1 );
}
}
terminate_progress_report( &progress );
if( changed )
{
for_inclusive( x, min_range[X], max_range[X] )
{
for_inclusive( y, min_range[Y], max_range[Y] )
{
for_inclusive( z, min_range[Z], max_range[Z] )
{
label = new_labels[x][y][z];
set_volume_voxel_value( label_volume, x, y, z, 0, 0,
(Real) label );
cuts[x][y][z] = new_cuts[x][y][z];
}
}
}
}
FREE3D( new_cuts );
FREE3D( new_labels );
delete_to_do_list( to_do );
*to_do = next_to_do;
return( changed );
}