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clip_tags.c
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#include <volume_io/internal_volume_io.h>
#include <special_geometry.h>
#define X_FACTOR 5.0
#define Y_FACTOR 5.0
#define GRID 40
private void find_plane(
Point points[],
Vector *normal );
private void create_plane_from_points(
Point points[],
Real dist,
polygons_struct *polygons );
private void get_plane_normal(
Vector *base_normal,
Real angle,
Vector *normal );
private Real get_voxel_plane_volume(
Volume volume,
Real x,
Real y,
Real z,
int n_planes,
Vector normals[],
Real constants[] );
private int get_voxel_plane_status(
Volume volume,
Real x,
Real y,
Real z,
int n_planes,
Vector normals[],
Real constants[] );
private void create_segment_plane(
Point *origin,
Vector *normal,
Real size,
polygons_struct *polygons );
int main(
int argc,
char *argv[] )
{
BOOLEAN create_plane, volume_desired, segment;
Real sum_x, sum_y, sum_z, sum_yy, sum_yz, sum_zz;
Real separations[MAX_DIMENSIONS], angle;
STRING three_tags_filename, input_tags_filename;
STRING output_tags_filename, plane_filename;
STRING volume_filename;
Real min_dist, max_dist, dist, voxel_volume;
Real angle_increment, angle_offset;
int i, n_objects, plane_status;
Point points[3], origin, point, centroid;
Vector normal, plane_normal;
Vector left_normal, right_normal;
Real left_constant, right_constant;
object_struct *object, **object_list;
Vector princ_normal, normals[4];
Real plane_constants[4];
int n_volumes, n_tag_points, *structure_ids, *patient_ids;
Real **tags1, **tags2, *weights, volume;
STRING *labels;
int n_new_tags, *new_structure_ids, *new_patient_ids;
Real **new_tags1, **new_tags2, *new_weights;
STRING *new_labels;
#ifdef PROGRESS
progress_struct progress;
#endif
Volume vol;
volume_input_struct volume_input;
initialize_argument_processing( argc, argv );
if( !get_string_argument( "", &three_tags_filename ) ||
!get_string_argument( "", &input_tags_filename ) ||
!get_string_argument( "", &output_tags_filename ) ||
!get_real_argument( 0.0, &min_dist ) ||
!get_real_argument( 0.0, &max_dist ) )
{
print( "Usage: %s 3_tags_file input.tag output.tag -distance +distance [mnc_file_if_you_want_volume] [angle_increment] [angle_offset] [plane_filename]\n", argv[0] );
return( 1 );
}
volume_desired = get_string_argument( "", &volume_filename );
segment = get_real_argument( 0.0, &angle_increment );
(void) get_real_argument( 0.0, &angle_offset );
create_plane = get_string_argument( "", &plane_filename );
if( min_dist > max_dist )
{
Real swap;
swap = min_dist;
min_dist = max_dist;
max_dist = swap;
}
if( input_tag_file( three_tags_filename, &n_volumes, &n_tag_points,
&tags1, &tags2, &weights, &structure_ids,
&patient_ids, &labels ) != OK )
return( 1 );
if( n_tag_points != 3 )
{
print( "Usage: %s 3_tags_file input.tag output.tag\n", argv[0] );
print( "First file must contain exactly 3 tags.\n" );
return( 1 );
}
for_less( i, 0, 3 )
fill_Point( points[i], tags1[i][X], tags1[i][Y], tags1[i][Z] );
free_tag_points( n_volumes, n_tag_points, tags1, tags2,
weights, structure_ids, patient_ids, labels );
find_plane( points, &normal );
NORMALIZE_VECTOR( normal, normal );
origin = points[0];
print( "Normal is: %g %g %g\n",
Vector_x(normal), Vector_y(normal), Vector_z(normal) );
print( "Origin is: %g %g %g\n",
Point_x(origin), Point_y(origin), Point_z(origin) );
if( input_tag_file( input_tags_filename, &n_volumes, &n_tag_points,
&tags1, &tags2, &weights, &structure_ids,
&patient_ids, &labels ) != OK )
return( 1 );
n_new_tags = 0;
if( volume_desired )
{
if( start_volume_input( volume_filename, 3, XYZ_dimension_names,
NC_UNSPECIFIED, FALSE, 0.0, 0.0,
TRUE, &vol, (minc_input_options *) NULL,
&volume_input ) != OK )
return( 1 );
get_volume_separations( vol, separations );
voxel_volume = separations[0] * separations[1] * separations[2];
volume = 0.0;
right_normal = normal;
right_constant = -distance_from_plane( &origin, &right_normal, 0.0 )
- max_dist;
left_normal = normal;
left_constant = -distance_from_plane( &origin, &right_normal, 0.0 )
-min_dist;
SCALE_VECTOR( right_normal, right_normal, -1.0 );
right_constant = - right_constant;
}
normals[0] = left_normal;
plane_constants[0] = left_constant;
normals[1] = right_normal;
plane_constants[1] = right_constant;
#ifdef PROGRESS
initialize_progress_report( &progress, FALSE, n_tag_points,
"Clipping" );
#endif
new_tags1 = NULL;
new_tags2 = NULL;
new_weights = NULL;
new_structure_ids = NULL;
new_patient_ids = NULL;
new_labels = NULL;
for_less( i, 0, n_tag_points )
{
fill_Point( point, tags1[i][X], tags1[i][Y], tags1[i][Z] );
dist = distance_from_plane( &point, &normal,
-DOT_POINT_VECTOR(origin,normal) );
if( dist >= min_dist && dist <= max_dist )
{
/*--- increase the memory allocation of the tag points */
SET_ARRAY_SIZE( new_tags1, n_new_tags, n_new_tags+1, 10 );
ALLOC( new_tags1[n_new_tags], 3 );
SET_ARRAY_SIZE( new_weights, n_new_tags, n_new_tags+1, 10 );
SET_ARRAY_SIZE( new_structure_ids, n_new_tags, n_new_tags+1, 10 );
SET_ARRAY_SIZE( new_patient_ids, n_new_tags, n_new_tags+1, 10 );
SET_ARRAY_SIZE( new_labels, n_new_tags, n_new_tags+1, 10 );
/*--- copy from the input tags to the new tags */
new_tags1[n_new_tags][0] = tags1[i][0];
new_tags1[n_new_tags][1] = tags1[i][1];
new_tags1[n_new_tags][2] = tags1[i][2];
if( n_volumes == 2 )
{
SET_ARRAY_SIZE( new_tags2, n_new_tags, n_new_tags+1, 10 );
ALLOC( new_tags2[n_new_tags], 3 );
new_tags2[n_new_tags][0] = tags2[i][0];
new_tags2[n_new_tags][1] = tags2[i][1];
new_tags2[n_new_tags][2] = tags2[i][2];
}
new_weights[n_new_tags] = weights[i];
new_structure_ids[n_new_tags] = structure_ids[i];
new_patient_ids[n_new_tags] = patient_ids[i];
new_labels[n_new_tags] = create_string( labels[i] );
/*--- increment the number of new tags */
++n_new_tags;
}
if( volume_desired )
{
plane_status = get_voxel_plane_status( vol,
tags1[i][X], tags1[i][Y], tags1[i][Z],
2, normals, plane_constants );
if( plane_status == 1 )
{
volume += voxel_volume;
}
else if( plane_status == 0 )
{
volume += get_voxel_plane_volume( vol,
tags1[i][X], tags1[i][Y], tags1[i][Z],
2, normals, plane_constants );
}
}
#ifdef PROGRESS
update_progress_report( &progress, i+1 );
#endif
}
#ifdef PROGRESS
terminate_progress_report( &progress );
#endif
if( volume_desired )
print( "Total volume inside planes: %g\n", volume );
/*--- output the new tags, the subset of the input tags */
if( output_tag_file( output_tags_filename, "Removed negative X's",
n_volumes, n_new_tags, new_tags1, new_tags2,
new_weights, new_structure_ids,
new_patient_ids, new_labels ) != OK )
return( 1 );
free_tag_points( n_volumes, n_new_tags, new_tags1, new_tags2,
new_weights, new_structure_ids, new_patient_ids,
new_labels );
if( segment )
{
sum_x = 0.0;
sum_y = 0.0;
sum_z = 0.0;
sum_yy = 0.0;
sum_yz = 0.0;
sum_zz = 0.0;
for_less( i, 0, n_tag_points )
{
sum_x += tags1[i][X];
sum_y += tags1[i][Y];
sum_z += tags1[i][Z];
sum_yy += tags1[i][Y] * tags1[i][Y];
sum_yz += tags1[i][Y] * tags1[i][Z];
sum_zz += tags1[i][Z] * tags1[i][Z];
}
fill_Point( centroid, sum_x / (Real) n_tag_points,
sum_y / (Real) n_tag_points,
sum_z / (Real) n_tag_points );
if( sum_yy > 0.0 )
{
fill_Vector( princ_normal, 0.0, -sum_yz / sum_yy, 1.0 );
}
else if( sum_zz > 0.0 )
{
fill_Vector( princ_normal, 0.0, 1.0, -sum_yz / sum_zz );
}
else
handle_internal_error( "Oh oh\n" );
if( Vector_y( princ_normal ) < 0.0f )
SCALE_VECTOR( princ_normal, princ_normal, -1.0 );
NORMALIZE_VECTOR( princ_normal, princ_normal );
angle = 0.0;
while( angle < 360.0 )
{
get_plane_normal( &princ_normal, angle + angle_offset,
&normals[2] );
get_plane_normal( &princ_normal,
angle + angle_offset + angle_increment,
&normals[3] );
SCALE_VECTOR( normals[3], normals[3], -1.0 );
plane_constants[2] = -distance_from_plane( ¢roid, &normals[2],
0.0 );
plane_constants[3] = -distance_from_plane( ¢roid, &normals[3],
0.0 );
volume = 0.0;
#ifdef PROGRESS
initialize_progress_report( &progress, FALSE,
angle / angle_increment, "Segmenting" );
#endif
for_less( i, 0, n_tag_points )
{
fill_Point( point, tags1[i][X], tags1[i][Y], tags1[i][Z] );
plane_status = get_voxel_plane_status( vol,
tags1[i][X], tags1[i][Y], tags1[i][Z],
4, normals, plane_constants );
if( plane_status == 1 )
{
volume += voxel_volume;
}
else if( plane_status == 0 )
{
volume += get_voxel_plane_volume( vol,
tags1[i][X], tags1[i][Y], tags1[i][Z],
4, normals, plane_constants );
}
}
print( "Angle: %4.0f to %4.0f, Volume: %g\n",
angle, angle + angle_increment, volume );
angle += angle_increment;
}
#ifdef PROGRESS
update_progress_report( &progress, i+1 );
#endif
}
#ifdef PROGRESS
terminate_progress_report( &progress );
#endif
if( create_plane )
{
n_objects = 0;
object = create_object( POLYGONS );
create_plane_from_points( points, min_dist, get_polygons_ptr(object) );
add_object_to_list( &n_objects, &object_list, object );
object = create_object( POLYGONS );
create_plane_from_points( points, max_dist, get_polygons_ptr(object) );
add_object_to_list( &n_objects, &object_list, object );
if( segment )
{
angle = 0.0;
while( angle < 180.0 )
{
get_plane_normal( &princ_normal, angle+angle_offset,
&plane_normal );
object = create_object( POLYGONS );
create_segment_plane( ¢roid, &plane_normal, 100.0,
get_polygons_ptr(object) );
if( angle == 0.0 )
get_polygons_ptr(object)->colours[0] = GREEN;
else if( angle == angle_increment )
get_polygons_ptr(object)->colours[0] = RED;
add_object_to_list( &n_objects, &object_list, object );
angle += angle_increment;
}
}
(void) output_graphics_file( plane_filename, ASCII_FORMAT,
n_objects, object_list );
}
return( 0 );
}
private void find_plane(
Point points[],
Vector *normal )
{
Vector v1, v2;
SUB_POINTS( v1, points[1], points[0] );
SUB_POINTS( v2, points[2], points[0] );
CROSS_VECTORS( *normal, v1, v2 );
}
private void get_xy_pos(
Vector x_axis,
Vector y_axis,
Real x,
Real y,
Point *point )
{
Vector x_offset, y_offset, v;
SCALE_VECTOR( x_offset, x_axis, x );
SCALE_VECTOR( y_offset, y_axis, y );
ADD_VECTORS( v, x_offset, y_offset );
CONVERT_VECTOR_TO_POINT( *point, v );
}
private void create_plane_from_points(
Point points[],
Real dist,
polygons_struct *polygons )
{
int i;
Vector v1, v2, v3, offset, v;
Real x_min, x_max, y_min, y_max, x, y, dx, dy;
Point point;
SUB_POINTS( v1, points[1], points[0] );
SUB_POINTS( v2, points[2], points[0] );
CROSS_VECTORS( v3, v1, v2 );
CROSS_VECTORS( v2, v3, v1 );
NORMALIZE_VECTOR( v1, v1 );
NORMALIZE_VECTOR( v2, v2 );
NORMALIZE_VECTOR( v3, v3 );
SCALE_VECTOR( offset, v3, dist );
CONVERT_POINT_TO_VECTOR( v, points[0] );
ADD_VECTORS( offset, offset, v );
x_min = 0.0;
x_max = 0.0;
y_min = 0.0;
y_max = 0.0;
for_less( i, 0, 3 )
{
x = DOT_VECTORS( v1, points[i] );
y = DOT_VECTORS( v2, points[i] );
if( i == 0 || x < x_min )
x_min = x;
if( i == 0 || x > x_max )
x_max = x;
if( i == 0 || y < y_min )
y_min = y;
if( i == 0 || y > y_max )
y_max = y;
}
initialize_polygons( polygons, WHITE, NULL );
polygons->n_points = 4;
ALLOC( polygons->points, polygons->n_points );
ALLOC( polygons->normals, polygons->n_points );
polygons->n_items = 1;
ALLOC( polygons->end_indices, polygons->n_items );
polygons->end_indices[0] = 4;
ALLOC( polygons->indices, 4 );
polygons->indices[0] = 0;
polygons->indices[1] = 1;
polygons->indices[2] = 2;
polygons->indices[3] = 3;
dx = x_max - x_min;
dy = y_max - y_min;
get_xy_pos( v1, v2, x_min - X_FACTOR * dx, y_min - Y_FACTOR * dy, &point );
polygons->points[0] = point;
polygons->normals[0] = v3;
get_xy_pos( v1, v2, x_max + X_FACTOR * dx, y_min - Y_FACTOR * dy, &point );
polygons->points[1] = point;
polygons->normals[1] = v3;
get_xy_pos( v1, v2, x_max + X_FACTOR * dx, y_max + Y_FACTOR * dy, &point );
polygons->points[2] = point;
polygons->normals[2] = v3;
get_xy_pos( v1, v2, x_min - X_FACTOR * dx, y_max + Y_FACTOR * dy, &point );
polygons->points[3] = point;
polygons->normals[3] = v3;
for_less( i, 0, 4 )
{
ADD_POINT_VECTOR( polygons->points[i], polygons->points[i], offset );
}
}
private Real get_voxel_plane_volume(
Volume volume,
Real x,
Real y,
Real z,
int n_planes,
Vector normals[],
Real constants[] )
{
int i, j, axis, a1, a2, p;
Real v[MAX_DIMENSIONS], voxel[MAX_DIMENSIONS];
Real separations[MAX_DIMENSIONS];
Real d1, d2;
Real xw, yw, zw, vol, alpha, t_min, t_max;
Point point;
get_volume_separations( volume, separations );
convert_3D_world_to_voxel( volume, x, y, z,
&voxel[0], &voxel[1], &voxel[2] );
voxel[0] = (Real) ROUND( voxel[0] );
voxel[1] = (Real) ROUND( voxel[1] );
voxel[2] = (Real) ROUND( voxel[2] );
axis = X;
a1 = (axis + 1) % N_DIMENSIONS;
a2 = (axis + 2) % N_DIMENSIONS;
vol = 0.0;
for_less( i, 0, GRID )
{
v[a1] = voxel[a1] + ((Real) i + 0.5) / (Real) GRID - 0.5;
for_less( j, 0, GRID )
{
v[a2] = voxel[a2] + ((Real) j + 0.5) / (Real) GRID - 0.5;
t_min = 0.0;
t_max = 1.0;
for_less( p, 0, n_planes )
{
v[axis] = voxel[axis] - 0.5;
convert_voxel_to_world( volume, v, &xw, &yw, &zw );
fill_Point( point, xw, yw, zw );
d1 = distance_from_plane( &point, &normals[p], constants[p] );
v[axis] = voxel[axis] + 0.5;
convert_voxel_to_world( volume, v, &xw, &yw, &zw );
fill_Point( point, xw, yw, zw );
d2 = distance_from_plane( &point, &normals[p], constants[p] );
if( d1 == d2 )
{
if( d1 < 0.0 )
{
t_min = 0.0;
t_max = 0.0;
break;
}
}
else
{
alpha = d1 / (d1 - d2);
if( d1 < d2 )
t_min = MAX( t_min, alpha );
else
t_max = MIN( t_max, alpha );
}
}
if( t_min < t_max )
vol += t_max - t_min;
}
}
vol = (Real) vol / (Real) (GRID * GRID) *
separations[0] * separations[1] * separations[2];
return( vol );
}
private int get_voxel_plane_status(
Volume volume,
Real x,
Real y,
Real z,
int n_planes,
Vector normals[],
Real constants[] )
{
int i;
Real separations[MAX_DIMENSIONS];
Real d, max_dist;
Point point;
get_volume_separations( volume, separations );
max_dist = separations[0] * separations[0] +
separations[1] * separations[1] +
separations[2] * separations[2];
fill_Point( point, x, y, z );
for_less( i, 0, n_planes )
{
d = distance_from_plane( &point, &normals[i], constants[i] );
if( d < 0.0 && d * d >= max_dist )
return( -1 );
else if( d * d < max_dist )
return( 0 );
}
return( 1 );
}
private void create_segment_plane(
Point *origin,
Vector *normal,
Real size,
polygons_struct *polygons )
{
Vector v1, v2;
create_two_orthogonal_vectors( normal, &v1, &v2 );
NORMALIZE_VECTOR( v1, v1 );
NORMALIZE_VECTOR( v2, v2 );
SCALE_VECTOR( v1, v1, size );
SCALE_VECTOR( v2, v2, size );
initialize_polygons( polygons, WHITE, NULL );
polygons->n_points = 4;
ALLOC( polygons->points, polygons->n_points );
ALLOC( polygons->normals, polygons->n_points );
polygons->n_items = 1;
ALLOC( polygons->end_indices, polygons->n_items );
polygons->end_indices[0] = 4;
ALLOC( polygons->indices, 4 );
polygons->indices[0] = 0;
polygons->indices[1] = 1;
polygons->indices[2] = 2;
polygons->indices[3] = 3;
polygons->normals[0] = *normal;
polygons->normals[1] = *normal;
polygons->normals[2] = *normal;
polygons->normals[3] = *normal;
ADD_POINT_VECTOR( polygons->points[0], *origin, v1 );
SUB_POINT_VECTOR( polygons->points[0], polygons->points[0], v2 );
ADD_POINT_VECTOR( polygons->points[1], *origin, v1 );
ADD_POINT_VECTOR( polygons->points[1], polygons->points[1], v2 );
SUB_POINT_VECTOR( polygons->points[2], *origin, v1 );
ADD_POINT_VECTOR( polygons->points[2], polygons->points[2], v2 );
SUB_POINT_VECTOR( polygons->points[3], *origin, v1 );
SUB_POINT_VECTOR( polygons->points[3], polygons->points[3], v2 );
}
private void get_plane_normal(
Vector *base_normal,
Real angle,
Vector *normal )
{
Real x, y, z;
Transform transform;
make_rotation_transform( angle * DEG_TO_RAD, X, &transform );
transform_vector( &transform,
(Real) Vector_x(*base_normal),
(Real) Vector_y(*base_normal),
(Real) Vector_z(*base_normal),
&x, &y, &z );
fill_Vector( *normal, x, y, z );
NORMALIZE_VECTOR( *normal, *normal );
}