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Copy pathcreate_landmark_full_volume.c
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create_landmark_full_volume.c
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#include <volume_io/internal_volume_io.h>
#include <bicpl.h>
#define SCALE_FACTOR 1.0
private void increment_voxel_count(
Volume volume,
int x,
int y,
int z,
Real *max_value )
{
Real value;
GET_VOXEL_3D_TYPED( value, (Real), volume, x, y, z );
value += SCALE_FACTOR;
if( value > *max_value )
*max_value = value;
SET_VOXEL_3D( volume, x, y, z, value );
}
private BOOLEAN is_left_id(
int id )
{
if( id >= 1000 )
id -= 1000;
return( id >= 10 && id <= 19 || id == 30 );
}
private BOOLEAN is_right_id(
int id )
{
if( id >= 1000 )
id -= 1000;
return( id >= 20 && id <= 29 || id == 40 );
}
private BOOLEAN is_left_filename(
char filename[] )
{
return( strstr( filename, "cing_l" ) != (char *) NULL );
}
extern int get_filename_arguments( STRING *[] );
int main(
int argc,
char *argv[] )
{
Status status;
char *input_filename, *output_filename;
Real separations[MAX_DIMENSIONS];
Real voxel[MAX_DIMENSIONS];
Real max_value;
Real radius, radius_squared;
Real delta, dx2, dy2, dz2;
STRING history;
STRING *filenames;
bitlist_3d_struct bitlist;
Volume volume, new_volume;
volume_input_struct volume_input;
int n_objects, n_files, n_patients, structure_id;
object_struct **object_list;
int i, p, x, y, z, n;
int sizes[N_DIMENSIONS];
int c, min_voxel[N_DIMENSIONS], max_voxel[N_DIMENSIONS];
Real min_limit, max_limit;
marker_struct *marker;
initialize_argument_processing( argc, argv );
if( !get_string_argument( "", &input_filename ) ||
!get_string_argument( "", &output_filename ) ||
!get_int_argument( 0, &structure_id ) ||
!get_real_argument( 0.0, &radius ) ||
!get_int_argument( 0, &n ) )
{
print( "%s example_volume output_volume structure_id|-1 n|0 radius of tags tag_file1 tag_file2 [tag_file3] ...\n", argv[0] );
return( 1 );
}
n_files = get_filename_arguments( &filenames );
radius_squared = radius * radius;
status = start_volume_input( input_filename, 3, XYZ_dimension_names,
NC_UNSPECIFIED, FALSE, 0.0, 0.0,
TRUE, &volume, (minc_input_options *) NULL,
&volume_input );
get_volume_sizes( volume, sizes );
get_volume_separations( volume, separations );
/* --- create the output volume */
new_volume = copy_volume_definition( volume, NC_SHORT, FALSE, 0.0, 0.0 );
create_bitlist_3d( sizes[X], sizes[Y], sizes[Z], &bitlist );
for_less( x, 0, sizes[X] )
for_less( y, 0, sizes[Y] )
for_less( z, 0, sizes[Z] )
SET_VOXEL_3D( new_volume, x, y, z, 0.0 );
max_value = 0.0;
n_patients = 0;
for_less( p, 0, n_files )
{
if( is_left_id(structure_id) && !is_left_filename(filenames[p]) )
continue;
if( is_right_id(structure_id) && is_left_filename(filenames[p]) )
continue;
++n_patients;
print( "[%d/%d] Reading %s\n", p+1, n_files, filenames[p] );
(void) flush_file( stdout );
status = input_objects_any_format( volume, filenames[p],
GREEN, 1.0, BOX_MARKER,
&n_objects, &object_list );
if( status != OK )
return( 1 );
for_less( i, 0, n_objects )
{
if( object_list[i]->object_type == MARKER )
{
marker = get_marker_ptr( object_list[i] );
if( structure_id >= 0 &&
structure_id != marker->structure_id &&
structure_id != marker->structure_id + 1000 )
continue;
convert_world_to_voxel( volume,
(Real) Point_x(marker->position),
(Real) Point_y(marker->position),
(Real) Point_z(marker->position),
voxel );
if( voxel_is_within_volume( new_volume, voxel ) )
{
if( radius == 0.0 )
{
x = ROUND( voxel[X] );
y = ROUND( voxel[Y] );
z = ROUND( voxel[Z] );
if( !get_bitlist_bit_3d( &bitlist, x, y, z))
{
increment_voxel_count( new_volume, x, y, z,
&max_value );
set_bitlist_bit_3d( &bitlist, x, y, z, TRUE );
}
}
else
{
for_less( c, 0, N_DIMENSIONS )
{
min_limit = voxel[c] - radius / separations[c];
max_limit = voxel[c] + radius / separations[c];
min_voxel[c] = CEILING( min_limit );
if( min_voxel[c] < 0 )
min_voxel[c] = 0;
max_voxel[c] = (int) max_limit;
if( max_voxel[c] >= sizes[c] )
max_voxel[c] = sizes[c]-1;
}
for_inclusive( x, min_voxel[X], max_voxel[X] )
{
delta = ((Real) x - voxel[X]) * separations[X];
dx2 = delta * delta;
for_inclusive( y, min_voxel[Y], max_voxel[Y] )
{
delta = ((Real) y - voxel[Y]) * separations[Y];
dy2 = delta * delta;
for_inclusive( z, min_voxel[Z], max_voxel[Z] )
{
delta = ((Real) z - voxel[Z]) *
separations[Z];
dz2 = delta * delta;
if( dx2 + dy2 + dz2 <= radius_squared &&
!get_bitlist_bit_3d( &bitlist, x, y, z))
{
increment_voxel_count( new_volume,
x, y, z,
&max_value );
set_bitlist_bit_3d( &bitlist, x, y, z,
TRUE );
}
}
}
}
}
}
}
}
zero_bitlist_3d( &bitlist );
delete_object_list( n_objects, object_list );
}
delete_bitlist_3d( &bitlist );
if( structure_id != -1 && structure_id != 1 &&
!is_left_id(structure_id) && !is_right_id(structure_id) )
n_patients /= 2;
if( n > 0 )
n_patients = n;
print( "Number subjects: %d\n", n_patients );
set_volume_voxel_value( new_volume, 0, 0, 0, 0, 0,
(Real) n_patients * SCALE_FACTOR );
set_volume_voxel_range( new_volume, 0.0, (Real) n_patients * SCALE_FACTOR );
set_volume_real_range( new_volume, 0.0, 100.0 );
cancel_volume_input( volume, &volume_input );
print( "Writing %s\n", output_filename );
history = create_string( "Created by: " );
for_less( i, 0, argc )
{
concat_to_string( &history, " " );
concat_to_string( &history, argv[i] );
}
status = output_volume( output_filename, NC_BYTE, FALSE,
0.0, 255.0, new_volume, history,
(minc_output_options *) NULL );
return( status != OK );
}