Final Source Code Example

This is an example which attempts to illustrate a typical processing task incorporating use of volumes, tag points, and transformations. This is a full program which, when linked to the BIC Volume IO Library, reads two volumes in MINC format, a set of tag points from file, and a transformation from file. The tag points are assumed to be in the world space of the first volume, and the transformation is assumed to transform points in the world space of the first volume to the world space of the second volume. The program transforms each tag point by the transformation input (presumably transforming from the world space of the first volume to that of the second volume), then transforms the result to the voxel space of the second volume. If the voxel coordinate is within the second volume, then the value of the corresponding voxel is printed.

#include  <volume_io.h>

int  main(
    int   argc,
    char  *argv[] )
{
    int                 v1, v2, v3, sizes[MAX_DIMENSIONS];
    Real                x_world2, y_world2, z_world2;
    Real                voxel2[MAX_DIMENSIONS];
    Real                voxel_value;
    Volume              volume1, volume2;
    int                 i, n_volumes, n_tag_points;
    int                 *structure_ids, *patient_ids;
    Real                **tags1, **tags2, *weights;
    char                **labels;
    General_transform   transform;

    /*--- input the two volumes */

    if( input_volume( "volume1.mnc", 3, NULL, NC_UNSPECIFIED, FALSE,
            0.0, 0.0, TRUE, &volume1,
            (minc_input_options *) NULL ) != OK )
        return( 1 );

    if( input_volume( "volume2.mnc", 3, NULL, NC_UNSPECIFIED, FALSE,
            0.0, 0.0, TRUE, &volume2,
            (minc_input_options *) NULL ) != OK )
        return( 1 );

    /*--- input the tag points */

    if( input_tag_file( "tags_volume1.tag", &n_volumes, &n_tag_points,
                        &tags1, &tags2, &weights, &structure_ids,
                        &patient_ids, &labels ) != OK )
        return( 1 );

    /*--- input the general transform */

    if( input_transform_file( "vol1_to_vol2.xfm", &transform ) != OK )
        return( 1 );

    /*--- convert each tag point */

    get_volume_sizes( volume2, sizes );

    for_less( i, 0, n_tag_points )
    {
        /*--- transform the tag points from volume 1 to volume 2
              world space */

        general_transform_point( &transform,
                                 tags1[i][X], tags1[i][Y], tags1[i][Z],
                                 &x_world2, &y_world2, &z_world2 );

        /*--- transform from volume 2 world space to
              volume 2 voxel space */

        convert_world_to_voxel( volume2, x_world2, y_world2, z_world2,
                                voxel2 );

        /*--- convert voxel coordinates to voxel indices */

        v1 = ROUND( voxel2[0] );
        v2 = ROUND( voxel2[1] );
        v3 = ROUND( voxel2[2] );

        /*--- check if voxel indices inside volume */
     
        if( v1 >= 0 && v1 < sizes[0] &&
            v2 >= 0 && v2 < sizes[1] &&
            v3 >= 0 && v3 < sizes[2] )
        {
            GET_VALUE_3D( voxel_value, volume2, v1, v2, v3 );

            print( "The value for tag point %d (%s) is: %g\n",
                   i, labels[i], voxel_value );
        }
        else
            print( "The tag point %d (%s) is outside.\n" );
    }

    /*--- free up memory */

    delete_volume( volume1 );
    delete_volume( volume2 );
    free_tag_points( n_volumes, n_tag_points, tags1, tags2,
                 weights, structure_ids, patient_ids, labels );
    delete_general_transform( &transform );

    return( 0 );
}