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segment_callosum.c
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#include <volume_io/internal_volume_io.h>
#include <special_geometry.h>
#define X_FACTOR 5.0
#define Y_FACTOR 40.0
private void get_plane_normal(
Vector *base_normal,
Real angle,
Vector *normal );
private void create_plane(
Point *origin,
Vector *normal,
Real size,
polygons_struct *polygons );
private Real get_voxel_plane_volume(
Volume volume,
Real x,
Real y,
Real z,
Vector *left_normal,
Real left_constant,
Vector *right_normal,
Real right_constant );
private int get_voxel_plane_status(
Volume volume,
Real x,
Real y,
Real z,
Vector *left_normal,
Real left_constant,
Vector *right_normal,
Real right_constant );
#define DEFAULT_ANGLE 30.0
#define GRID 80
int main(
int argc,
char *argv[] )
{
BOOLEAN create_planes;
Real separations[MAX_DIMENSIONS], current_angle;
Real angle_increment;
char *three_tags_filename, *input_tags_filename;
char *output_tags_filename, *plane_filename;
char *volume_filename;
Real min_dist, max_dist, dist, voxel_volume;
Real sum_x, sum_y, sum_z, sum_yy, sum_yz, sum_zz;
int i, n_objects, plane_status, p;
Point origin, point, centroid;
Vector normal, plane_normal;
Vector left_normal, right_normal;
Real left_constant, right_constant;
object_struct *object, **object_list;
int n_volumes, n_tag_points, *structure_ids, *patient_ids;
Real **tags1, **tags2, *weights, volume, true_volume;
char **labels;
progress_struct progress;
polygons_struct voxel, tmp, clipped;
Volume vol;
volume_input_struct volume_input;
initialize_argument_processing( argc, argv );
if( !get_string_argument( "", &volume_filename ) ||
!get_string_argument( "", &input_tags_filename ) )
{
print( "Usage: %s volume.mnc input.tag [angle]\n" );
return( 1 );
}
(void) get_real_argument( DEFAULT_ANGLE, &angle_increment;
create_planes = get_string_argument( "plane", &plane_filename );
if( input_tag_file( input_tags_filename, &n_volumes, &n_tag_points,
&tags1, &tags2, &weights, &structure_ids,
&patient_ids, &labels ) != OK )
return( 1 );
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 );
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( normal, 0.0, -sum_yz / sum_yy, 1.0 );
}
else if( sum_zz > 0.0 )
{
fill_Vector( normal, 0.0, 1.0, -sum_yz / sum_zz );
}
else
handle_internal_error( "Oh oh\n" );
if( Vector_y( normal ) < 0.0 )
SCALE_VECTOR( normal, normal, -1.0 );
NORMALIZE_VECTOR( normal, normal );
get_volume_separations( vol, separations );
voxel_volume = separations[0] * separations[1] * separations[2];
plane_constant = -distance_from_plane( ¢roid, &normal, 0.0 );
initialize_progress_report( &progress, FALSE, 360.0 / angle_increment,
"Clipping" );
current_angle = 0.0;
while( current_angle < 360.0 )
{
get_plane_normal( &normal, current_angle, &left_normal );
left_constant = plane_constant;
get_plane_normal( &normal, current_angle + angle_increment,
&right_normal );
SCALE_VECTOR( right_normal, right_normal, -1.0 );
right_constant = -plane_constant;
volume = 0.0;
for_less( i, 0, n_tag_points )
{
plane_status = get_voxel_plane_status( vol,
tags1[i][X], tags1[i][Y], tags1[i][Z],
&left_normal, left_constant,
&right_normal, right_constant );
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],
&left_normal, left_constant,
&right_normal, right_constant );
}
}
print( "Angle: %.0g to %.0g, Volume: %g\n",
current_angle,
current_angle + angle_increment, volume );
current_angle += angle_increment;
update_progress_report( &progress,
ROUND( current_angle / angle_increment ) );
}
terminate_progress_report( &progress );
if( create_planes )
{
n_objects = 0;
current_angle = 0.0;
while( current_angle < 180.0 )
{
get_plane_normal( &normal, current_angle, &plane_normal );
object = create_object( POLYGONS );
create_plane( ¢roid, &plane_normal, 100.0,
get_polygons_ptr(object) );
add_object_to_list( &n_objects, &object_list, object );
current_angle += angle;
}
(void) output_graphics_file( plane_filename, ASCII_FORMAT,
n_objects, object_list );
}
return( 0 );
}
private void create_plane(
Point *origin,
Vector *normal,
Real size,
polygons_struct *polygons )
{
int i;
Vector v1, v2, offset;
Real x_min, x_max, y_min, y_max, x, y, dx, dy;
Point point;
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 Real get_voxel_plane_volume(
Volume volume,
Real x,
Real y,
Real z,
Vector *left_normal,
Real left_constant,
Vector *right_normal,
Real right_constant )
{
int i, j, axis, a1, a2;
Real v[MAX_DIMENSIONS], voxel[MAX_DIMENSIONS];
Real separations[MAX_DIMENSIONS], max_axis_len;
Real l1, l2, r1, r2;
Real xw, yw, zw, vol, alpha_l, alpha_r, 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] = ROUND( voxel[0] );
voxel[1] = ROUND( voxel[1] );
voxel[2] = ROUND( voxel[2] );
max_axis_len = MAX3( ABS( Vector_x(*left_normal) ),
ABS( Vector_y(*left_normal) ),
ABS( Vector_z(*left_normal) ) );
if( ABS( Vector_x(*left_normal) ) == max_axis_len )
axis = X;
else if( ABS( Vector_y(*left_normal) ) == max_axis_len )
axis = Y;
else
axis = Z;
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;
v[axis] = voxel[axis] - 0.5;
convert_voxel_to_world( volume, v, &xw, &yw, &zw );
fill_Point( point, xw, yw, zw );
l1 = distance_from_plane( &point, left_normal, left_constant );
r1 = distance_from_plane( &point, right_normal, right_constant );
v[axis] = voxel[axis] + 0.5;
convert_voxel_to_world( volume, v, &xw, &yw, &zw );
fill_Point( point, xw, yw, zw );
l2 = distance_from_plane( &point, left_normal, left_constant );
r2 = distance_from_plane( &point, right_normal, right_constant );
if( l1 == l2 || r1 == r2 )
{
if( l1 >= 0.0 && r1 >= 0.0 )
vol += 1.0;
}
else
{
alpha_l = l1 / (l1 - l2);
alpha_r = r1 / (r1 - r2);
t_min = 0.0;
t_max = 1.0;
if( l1 < l2 )
t_min = MAX( t_min, alpha_l );
else
t_max = MIN( t_max, alpha_l );
if( r1 < r2 )
t_min = MAX( t_min, alpha_r );
else
t_max = MIN( t_max, alpha_r );
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,
Vector *left_normal,
Real left_constant,
Vector *right_normal,
Real right_constant )
{
Real separations[MAX_DIMENSIONS];
Real l, r, 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 );
l = distance_from_plane( &point, left_normal, left_constant );
r = distance_from_plane( &point, right_normal, right_constant );
if( l < 0.0 && l * l >= max_dist )
return( -1 );
if( r < 0.0 && r * r >= max_dist )
return( -1 );
if( l > 0.0 && l * l >= max_dist &&
r > 0.0 && r * r >= max_dist )
{
return( 1 );
}
else
return( 0 );
}
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,
Vector_x(*base_normal),
Vector_y(*base_normal),
Vector_z(*base_normal),
&x, &y, &z );
fill_Vector( *normal, x, y, z );
}