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cross_correlation_3d.c
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#include <volume_io/internal_volume_io.h>
#include <bicpl.h>
private Real compute_cross_correlation(
Volume volume1,
Volume volume2,
Transform *transform,
int nx,
int ny,
int nz );
private void usage(
STRING executable )
{
STRING usage_str = "\n\
Usage: %s input1.mnc input2.mnc output.obj xs ys zs ns xr yr zr xt yt zt\n\
\n\
Evaluates the cross correlation of the two volumes, with the set of\n\
offsets.\n\n";
print_error( usage_str, executable );
}
int main(
int argc,
char *argv[] )
{
STRING input_filename1, input_filename2, output_filename;
Volume volume1, volume2;
Real x_sampling, y_sampling, z_sampling, x_rot, y_rot, z_rot;
Real x_trans, y_trans, z_trans, xr, yr, zr, xt, yt, zt, alpha;
Real value, separations[3], min_value, max_value;
Transform transform, x_rot_trans, y_rot_trans, z_rot_trans;
Transform translation;
int n_samples, sample, sizes[3], nx, ny, nz;
object_struct *objects[2];
lines_struct *lines;
progress_struct progress;
initialize_argument_processing( argc, argv );
if( !get_string_argument( NULL, &input_filename1 ) ||
!get_string_argument( NULL, &input_filename2 ) ||
!get_string_argument( NULL, &output_filename ) ||
!get_real_argument( 0.0, &x_sampling ) ||
!get_real_argument( 0.0, &y_sampling ) ||
!get_real_argument( 0.0, &z_sampling ) ||
!get_int_argument( 0, &n_samples ) ||
!get_real_argument( 0.0, &x_rot ) ||
!get_real_argument( 0.0, &y_rot ) ||
!get_real_argument( 0.0, &z_rot ) ||
!get_real_argument( 0.0, &x_trans ) ||
!get_real_argument( 0.0, &y_trans ) ||
!get_real_argument( 0.0, &z_trans ) )
{
usage( argv[0] );
return( 1 );
}
if( input_volume( input_filename1, 3, File_order_dimension_names,
NC_UNSPECIFIED, FALSE, 0.0, 0.0,
TRUE, &volume1, NULL ) != OK )
return( 1 );
get_volume_sizes( volume1, sizes );
get_volume_separations( volume1, separations );
nx = ROUND( (Real) sizes[X] * FABS(separations[X]) / x_sampling );
ny = ROUND( (Real) sizes[Y] * FABS(separations[Y]) / y_sampling );
nz = ROUND( (Real) sizes[Z] * FABS(separations[Z]) / z_sampling );
if( equal_strings( input_filename1, input_filename2 ) )
{
volume2 = volume1;
}
else
{
if( input_volume( input_filename2, 3, File_order_dimension_names,
NC_UNSPECIFIED, FALSE, 0.0, 0.0,
TRUE, &volume2, NULL ) != OK )
return( 1 );
}
objects[0] = create_object( LINES );
lines = get_lines_ptr( objects[0] );
initialize_lines_with_size( lines, GREEN, n_samples, FALSE );
initialize_progress_report( &progress, FALSE, n_samples,
"Computing cross correlation" );
min_value = 0.0;
max_value = 0.0;
for_less( sample, 0, n_samples )
{
alpha = 2.0 * (Real) sample / (Real) (n_samples-1) - 1.0;
xr = alpha * x_rot;
yr = alpha * y_rot;
zr = alpha * z_rot;
xt = alpha * x_trans;
yt = alpha * y_trans;
zt = alpha * z_trans;
make_rotation_transform( DEG_TO_RAD * xr, X, &x_rot_trans );
make_rotation_transform( DEG_TO_RAD * yr, Y, &y_rot_trans );
make_rotation_transform( DEG_TO_RAD * zr, Z, &z_rot_trans );
make_translation_transform( xt, yt, zt, &translation );
concat_transforms( &transform, &x_rot_trans, &y_rot_trans );
concat_transforms( &transform, &transform, &z_rot_trans );
concat_transforms( &transform, &transform, &translation );
value = compute_cross_correlation( volume1, volume2, &transform,
nx, ny, nz );
if( sample == 0 || value < min_value )
min_value = value;
if( sample == 0 || value > max_value )
max_value = value;
fill_Point( lines->points[sample], alpha, value, 0.0 );
update_progress_report( &progress, sample+1 );
}
for_less( sample, 0, n_samples )
{
fill_Point( lines->points[sample],
Point_x(lines->points[sample]),
(Point_y(lines->points[sample]) - min_value) /
(max_value - min_value),
0.0 );
}
terminate_progress_report( &progress );
objects[1] = create_object( LINES );
lines = get_lines_ptr( objects[1] );
initialize_lines_with_size( lines, RED, 2, FALSE );
fill_Point( lines->points[0], 0.0, 0.0, 0.0 );
fill_Point( lines->points[1], 0.0, 1.0, 0.0 );
(void) output_graphics_file( output_filename, ASCII_FORMAT, 2, objects );
delete_object( objects[0] );
delete_object( objects[1] );
if( volume1 != volume2 )
delete_volume( volume2 );
delete_volume( volume1 );
return( 0 );
}
private Real compute_cross_correlation(
Volume volume1,
Volume volume2,
Transform *transform,
int nx,
int ny,
int nz )
{
Real voxel[MAX_DIMENSIONS];
Real voxel2[MAX_DIMENSIONS];
Real delta[MAX_DIMENSIONS];
int sizes[MAX_DIMENSIONS], grid[MAX_DIMENSIONS];
int i, j, k, dim;
Real value1, value2, corr, xw, yw, zw, diff;
corr = 0.0;
get_volume_sizes( volume1, sizes );
voxel[0] = 0.0;
voxel[1] = 0.0;
voxel[2] = INTERPOLATE( ((Real) 0 + 0.5) / (Real) nz,
-0.5, (Real) sizes[Z] - 0.5 );
convert_voxel_to_world( volume1, voxel, &xw, &yw, &zw );
transform_point( transform, xw, yw, zw, &xw, &yw, &zw );
convert_world_to_voxel( volume2, xw, yw, zw, voxel2 );
voxel[2] = INTERPOLATE( ((Real) 1 + 0.5) / (Real) nz,
-0.5, (Real) sizes[Z] - 0.5 );
convert_voxel_to_world( volume1, voxel, &xw, &yw, &zw );
transform_point( transform, xw, yw, zw, &xw, &yw, &zw );
convert_world_to_voxel( volume2, xw, yw, zw, delta );
delta[0] -= voxel2[0];
delta[1] -= voxel2[1];
delta[2] -= voxel2[2];
for_less( i, 0, nx )
{
voxel[X] = INTERPOLATE( ((Real) i + 0.5) / (Real) nx,
-0.5, (Real) sizes[X] - 0.5 );
for_less( j, 0, ny )
{
voxel[Y] = INTERPOLATE( ((Real) j + 0.5) / (Real) ny,
-0.5, (Real) sizes[Y] - 0.5 );
for_less( k, 0, nz )
{
voxel[Z] = INTERPOLATE( ((Real) k + 0.5) / (Real) nz,
-0.5, (Real) sizes[Z] - 0.5 );
if( k == 0 )
{
convert_voxel_to_world( volume1, voxel, &xw, &yw, &zw );
transform_point( transform, xw, yw, zw, &xw, &yw, &zw );
convert_world_to_voxel( volume2, xw, yw, zw, voxel2 );
}
else
{
voxel2[0] += delta[0];
voxel2[1] += delta[1];
voxel2[2] += delta[2];
}
(void) evaluate_volume( volume1, voxel, NULL, 0, FALSE, 0.0,
&value1, NULL, NULL );
(void) evaluate_volume( volume2, voxel2, NULL, 0, FALSE, 0.0,
&value2, NULL, NULL );
diff = value1 - value2;
corr += diff * diff;
}
}
}
corr /= (Real) (nx * ny * nz);
return( corr );
}