void process_concatenated_transform( VIO_General_transform* t )
{
int n = get_n_concated_transforms( t );
int i;
print("[CONCATENATED TRANSFORM]\n");
for( i = 0; i < n; ++i ) {
print("Transform %d: ", i+1);
process_general_transform( get_nth_general_transform(t,i) );
print("\n\n");
}
}
void build_default_deformation_field(Arg_Data *globals)
{
if (get_n_concated_transforms(globals->trans_info.transformation)==1) {
append_new_default_deformation_field(globals);
}
else { /* we are starting with concatenated transforms,
so go get a point to the linear part.... */
resample_the_deformation_field(globals);
}
}
int main(int argc, char *argv[]) {
int v1, v2, v3, v4;
int sizes[VIO_MAX_DIMENSIONS], grid_sizes[4];
int n_concat_transforms, i;
VIO_STR arg_string;
char *input_volume_name;
char *input_xfm;
VIO_STR outfile;
VIO_Real w1, w2, w3;
VIO_Real nw1, nw2, nw3;
VIO_Real original[3], transformed[3];
VIO_Real value;
VIO_Real cosine[3];
VIO_Real original_separation[3], grid_separation[4];
VIO_Real original_starts[3], grid_starts[4];
VIO_Volume eval_volume, new_grid;
VIO_General_transform xfm, *voxel_to_world;
VIO_STR *dimnames, dimnames_grid[4];
VIO_progress_struct progress;
arg_string = time_stamp(argc, argv);
/* Check arguments */
if(ParseArgv(&argc, argv, argTable, 0) || (argc != 4)){
fprintf(stderr, "\nUsage: %s [options] input.mnc input.xfm output_grid.mnc\n", argv[0]);
fprintf(stderr, " %s -help\n\n", argv[0]);
exit(EXIT_FAILURE);
}
input_volume_name = argv[1];
input_xfm = argv[2];
outfile = argv[3];
/* check for the infile and outfile */
if(access(input_volume_name, F_OK) != 0){
fprintf(stderr, "%s: Couldn't find %s\n\n", argv[0], input_volume_name);
exit(EXIT_FAILURE);
}
if(access(input_xfm, F_OK) != 0) {
fprintf(stderr, "%s: Couldn't find %s\n\n", argv[0], input_xfm);
exit(EXIT_FAILURE);
}
if(access(outfile, F_OK) == 0 && !clobber){
fprintf(stderr, "%s: %s exists! (use -clobber to overwrite)\n\n", argv[0], outfile);
exit(EXIT_FAILURE);
}
/*--- input the volume */
/*
if( input_volume( input_volume_name, 3, NULL, MI_ORIGINAL_TYPE,
FALSE, 0.0, 0.0, TRUE, &eval_volume,(minc_input_options *) NULL ) != OK )
return( 1 );
*/
if (input_volume_header_only( input_volume_name, 3, NULL, &eval_volume,(minc_input_options *) NULL ) != VIO_OK ) {
return( 1 );
}
/* get information about the volume */
get_volume_sizes( eval_volume, sizes );
voxel_to_world = get_voxel_to_world_transform(eval_volume);
dimnames = get_volume_dimension_names(eval_volume);
get_volume_separations(eval_volume, original_separation);
get_volume_starts(eval_volume, original_starts);
/* create new 4D volume, last three dims same as other volume,
first dimension being the vector dimension. */
for(i=1; i < 4; i++) {
dimnames_grid[i] = dimnames[i-1];
grid_separation[i] = original_separation[i-1];
grid_sizes[i] = sizes[i-1];
grid_starts[i] = original_starts[i-1];
}
dimnames_grid[0] = "vector_dimension";
grid_sizes[0] = 3;
grid_separation[0] = 1;
grid_starts[0] = 0;
new_grid = create_volume(4, dimnames_grid, NC_SHORT, FALSE, 0.0, 0.0);
//set_voxel_to_world_transform(new_grid, voxel_to_world);
// initialize the new grid volume, otherwise the output will be
// garbage...
set_volume_real_range(new_grid, -100, 100);
set_volume_sizes(new_grid, grid_sizes);
set_volume_separations(new_grid, grid_separation);
set_volume_starts(new_grid, grid_starts);
/*
for (i=0; i < 3; i++) {
get_volume_direction_cosine(eval_volume, i, cosine);
set_volume_direction_cosine(new_grid, i+1, cosine);
}
*/
alloc_volume_data(new_grid);
/* get the transforms */
if( input_transform_file( input_xfm, &xfm ) != VIO_OK )
return( 1 );
/* see how many transforms will be applied */
n_concat_transforms = get_n_concated_transforms( &xfm );
printf("Number of transforms to be applied: %d\n", n_concat_transforms);
initialize_progress_report(&progress, FALSE, sizes[0], "Processing");
/* evaluate the transform at every voxel, keep the displacement
in the three cardinal directions */
for( v1 = 0; v1 < sizes[0]; ++v1 ) {
update_progress_report(&progress, v1 + 1);
for( v2 = 0; v2 < sizes[1]; ++v2 ) {
for( v3 = 0; v3 < sizes[2]; ++v3 ) {
convert_3D_voxel_to_world(eval_volume,
v1, v2, v3,
&original[0], &original[1], &original[2]);
general_transform_point(&xfm,
original[0], original[1], original[2],
&transformed[0], &transformed[1], &transformed[2]);
for(i=0; i < 3; i++) {
value = transformed[i] - original[i];
set_volume_real_value(new_grid, i, v1, v2, v3, 0, value);
}
}
}
}
terminate_progress_report(&progress);
printf("Outputting volume.\n");
output_volume(outfile, MI_ORIGINAL_TYPE, TRUE, 0.0, 0.0, new_grid, arg_string, NULL);
return(0);
}
int main(int argc, char *argv[])
{
VIO_General_transform
transform,
*grid_transform_ptr,
forward_transform;
VIO_Volume
target_vol,
volume;
volume_input_struct
input_info;
VIO_Real
voxel[VIO_MAX_DIMENSIONS],
steps[VIO_MAX_DIMENSIONS],
start[VIO_N_DIMENSIONS],
target_steps[VIO_MAX_DIMENSIONS],
wx,wy,wz, inv_x, inv_y, inv_z,
def_values[VIO_MAX_DIMENSIONS];
static int
clobber_flag = FALSE,
verbose = TRUE,
debug = FALSE;
static char
*target_file;
int
parse_flag,
prog_count,
sizes[VIO_MAX_DIMENSIONS],
target_sizes[VIO_MAX_DIMENSIONS],
xyzv[VIO_MAX_DIMENSIONS],
target_xyzv[VIO_MAX_DIMENSIONS],
index[VIO_MAX_DIMENSIONS],
i,
trans_count;
VIO_progress_struct
progress;
static ArgvInfo argTable[] = {
{"-like", ARGV_STRING, (char *) 0, (char *) &target_file,
"Specify target volume sampling information."},
{"-no_clobber", ARGV_CONSTANT, (char *) FALSE, (char *) &clobber_flag,
"Do not overwrite output file (default)."},
{"-clobber", ARGV_CONSTANT, (char *) TRUE, (char *) &clobber_flag,
"Overwrite output file."},
{"-verbose", ARGV_CONSTANT, (char *) TRUE, (char *) &verbose,
"Write messages indicating progress (default)"},
{"-quiet", ARGV_CONSTANT, (char *) FALSE, (char *) &verbose,
"Do not write log messages"},
{"-debug", ARGV_CONSTANT, (char *) TRUE, (char *) &debug,
"Print out debug info."},
{NULL, ARGV_END, NULL, NULL, NULL}
};
prog_name = argv[0];
target_file = malloc(1024);
strcpy(target_file,"");
/* Call ParseArgv to interpret all command line args (returns TRUE if error) */
parse_flag = ParseArgv(&argc, argv, argTable, 0);
/* Check remaining arguments */
if (parse_flag || argc != 3) print_usage_and_exit(prog_name);
/* Read in file that has a def field to invert */
if (input_transform_file(argv[1], &transform) != OK) {
(void) fprintf(stderr, "%s: Error reading transform file %s\n",
argv[0], argv[1]);
exit(EXIT_FAILURE);
}
for(trans_count=0; trans_count<get_n_concated_transforms(&transform); trans_count++ ) {
grid_transform_ptr = get_nth_general_transform(&transform, trans_count );
if (grid_transform_ptr->type == GRID_TRANSFORM) {
copy_general_transform(grid_transform_ptr,
&forward_transform);
/*
this is the call that should be made
with the latest version of internal_libvolume_io
invert_general_transform(&forward_transform); */
forward_transform.inverse_flag = !(forward_transform.inverse_flag);
volume = grid_transform_ptr->displacement_volume;
if (strlen(target_file)!=0) {
if (debug) print ("Def field will be resampled like %s\n",target_file);
if (!file_exists( target_file ) ) {
(void) fprintf(stderr, "%s: Target file '%s' does not exist\n",
prog_name,target_file);
exit(EXIT_FAILURE);
}
start_volume_input(target_file, 3, (char **)NULL,
NC_UNSPECIFIED, FALSE, 0.0, 0.0,
TRUE, &target_vol,
(minc_input_options *)NULL,
&input_info);
get_volume_XYZV_indices(volume, xyzv);
get_volume_separations (volume, steps);
get_volume_sizes (volume, sizes);
get_volume_XYZV_indices(target_vol, target_xyzv);
get_volume_separations (target_vol, target_steps);
get_volume_sizes (target_vol, target_sizes);
for(i=0; i<VIO_MAX_DIMENSIONS; i++) {
index[i] = 0;
voxel[i] = 0.0;
}
convert_voxel_to_world(target_vol, voxel, &start[VIO_X], &start[VIO_Y], &start[VIO_Z]);
if( volume != (void *) NULL ){
free_volume_data( volume );
}
for(i=VIO_X; i<=VIO_Z; i++) {
steps[ xyzv[i] ] = target_steps[ target_xyzv[i] ] ;
sizes[ xyzv[i] ] = target_sizes[ target_xyzv[i] ] ;
}
set_volume_separations(volume, steps);
set_volume_sizes( volume, sizes);
set_volume_starts(volume, start);
alloc_volume_data( volume );
}
get_volume_sizes(volume, sizes);
get_volume_XYZV_indices(volume,xyzv);
for(i=0; i<VIO_MAX_DIMENSIONS; i++){
index[i] = 0;
}
if (verbose){
initialize_progress_report(&progress, FALSE,
sizes[xyzv[VIO_X]]*sizes[xyzv[VIO_Y]]*sizes[xyzv[VIO_Z]]+1,
"Inverting def field");
}
prog_count = 0;
for(index[xyzv[VIO_X]]=0; index[xyzv[VIO_X]]<sizes[xyzv[VIO_X]]; index[xyzv[VIO_X]]++)
for(index[xyzv[VIO_Y]]=0; index[xyzv[VIO_Y]]<sizes[xyzv[VIO_Y]]; index[xyzv[VIO_Y]]++)
for(index[xyzv[VIO_Z]]=0; index[xyzv[VIO_Z]]<sizes[xyzv[VIO_Z]]; index[xyzv[VIO_Z]]++) {
index[ xyzv[VIO_Z+1] ] = 0;
for(i=0; i<VIO_MAX_DIMENSIONS; i++) voxel[i] = (VIO_Real)index[i];
convert_voxel_to_world(volume, voxel, &wx, &wy, &wz);
if (sizes[ xyzv[VIO_Z] ] ==1)
general_inverse_transform_point_in_trans_plane(&forward_transform,
wx, wy, wz,
&inv_x, &inv_y, &inv_z);
else
grid_inverse_transform_point(&forward_transform,
wx, wy, wz,
&inv_x, &inv_y, &inv_z);
def_values[VIO_X] = inv_x - wx;
def_values[VIO_Y] = inv_y - wy;
def_values[VIO_Z] = inv_z - wz;
for(index[xyzv[VIO_Z+1]]=0; index[xyzv[VIO_Z+1]]<3; index[xyzv[VIO_Z+1]]++)
set_volume_real_value(volume,
index[0],index[1],index[2],index[3],index[4],
def_values[ index[ xyzv[VIO_Z+1] ]]);
prog_count++;
if (verbose)
update_progress_report(&progress, prog_count);
}
if (verbose)
terminate_progress_report(&progress);
delete_general_transform(&forward_transform);
grid_transform_ptr->inverse_flag = !(grid_transform_ptr->inverse_flag);
}
}
/* Write out the transform */
if (output_transform_file(argv[2], NULL, &transform) != OK) {
(void) fprintf(stderr, "%s: Error writing transform file %s\n",
argv[0], argv[2]);
exit(EXIT_FAILURE);
}
exit(EXIT_SUCCESS);
}
static void resample_the_deformation_field(Arg_Data *globals)
{
VIO_Volume
existing_field,
new_field;
VIO_Real
vector_val[3],
XYZstart[ VIO_MAX_DIMENSIONS ],
wstart[ VIO_MAX_DIMENSIONS ],
start[ VIO_MAX_DIMENSIONS ],
XYZstep[ VIO_MAX_DIMENSIONS ],
step[ VIO_MAX_DIMENSIONS ],
step2[ VIO_MAX_DIMENSIONS ],
s1[ VIO_MAX_DIMENSIONS ],
voxel[ VIO_MAX_DIMENSIONS ],
dir[3][3];
int
i,
siz[ VIO_MAX_DIMENSIONS ],
index[ VIO_MAX_DIMENSIONS ],
xyzv[ VIO_MAX_DIMENSIONS ],
XYZcount[ VIO_MAX_DIMENSIONS ],
count[ VIO_MAX_DIMENSIONS ];
VIO_General_transform
*non_lin_part;
VectorR
XYZdirections[ VIO_MAX_DIMENSIONS ];
VIO_Real
del_x, del_y, del_z, wx, wy,wz;
VIO_progress_struct
progress;
char
**data_dim_names;
/* get the nonlinear part
of the transformation */
existing_field = (VIO_Volume)NULL;
non_lin_part = get_nth_general_transform(globals->trans_info.transformation,
get_n_concated_transforms(
globals->trans_info.transformation)
-1);
if (get_transform_type( non_lin_part ) == GRID_TRANSFORM){
existing_field = (VIO_Volume)(non_lin_part->displacement_volume);
}
else {
for(i=0; i<get_n_concated_transforms(globals->trans_info.transformation); i++)
print ("Transform %d is of type %d\n",i,
get_transform_type(
get_nth_general_transform(globals->trans_info.transformation,
i) ));
print_error_and_line_num("Cannot find the deformation field transform to resample",
__FILE__, __LINE__);
}
/* build a vector volume to store the Grid VIO_Transform */
new_field = create_volume(4, dim_name_vector_vol, NC_DOUBLE, TRUE, 0.0, 0.0);
get_volume_XYZV_indices(new_field, xyzv);
for(i=0; i<VIO_N_DIMENSIONS; i++)
step2[i] = globals->step[i];
/* get new start, count, step and directions,
all returned in X, Y, Z order. */
set_up_lattice(existing_field, step2, XYZstart, wstart, XYZcount, XYZstep, XYZdirections);
/* reset count and step to be in volume order */
for(i=0; i<VIO_N_DIMENSIONS; i++) {
start[ i ] = wstart[ i ];
count[ xyzv[i] ] = XYZcount[ i ];
step[ xyzv[i] ] = XYZstep[ i ];
}
/* add info for the vector dimension */
count[xyzv[VIO_Z+1]] = 3;
step[xyzv[VIO_Z+1]] = 0.0;
/* use the sign of the step returned to set the true step size */
for(i=0; i<VIO_N_DIMENSIONS; i++) {
if (step[xyzv[i]]<0)
step[xyzv[i]] = -1.0 * fabs(globals->step[i]);
else
step[xyzv[i]] = fabs(globals->step[i]);
}
for(i=0; i<VIO_MAX_DIMENSIONS; i++) /* set the voxel origin, used in the vol def */
voxel[i] = 0.0;
set_volume_sizes( new_field, count);
set_volume_separations( new_field, step);
/* set_volume_voxel_range( new_field, -MY_MAX_VOX, MY_MAX_VOX);
set_volume_real_range( new_field, -1.0*globals->trans_info.max_def_magnitude, globals->trans_info.max_def_magnitude); - no longer needed, because now using doubles*/
set_volume_translation( new_field, voxel, start);
for(i=0; i<VIO_N_DIMENSIONS; i++) {
dir[VIO_X][i]=XYZdirections[VIO_X].coords[i];
dir[VIO_Y][i]=XYZdirections[VIO_Y].coords[i];
dir[VIO_Z][i]=XYZdirections[VIO_Z].coords[i];
}
set_volume_direction_cosine(new_field,xyzv[VIO_X],dir[VIO_X]);
set_volume_direction_cosine(new_field,xyzv[VIO_Y],dir[VIO_Y]);
set_volume_direction_cosine(new_field,xyzv[VIO_Z],dir[VIO_Z]);
/* make sure that the vector dimension
is named! */
data_dim_names = get_volume_dimension_names(new_field);
if( strcmp( data_dim_names[ xyzv[VIO_Z+1] ] , MIvector_dimension ) != 0 ) {
ALLOC((new_field)->dimension_names[xyzv[VIO_Z+1]], \
strlen(MIvector_dimension ) + 1 );
(void) strcpy( (new_field)->dimension_names[xyzv[VIO_Z+1]], MIvector_dimension );
}
delete_dimension_names(new_field, data_dim_names);
if (globals->flags.debug) {
print ("in resample_deformation_field:\n");
print ("xyzv[axes] = %d, %d, %d, %d\n",xyzv[VIO_X],xyzv[VIO_Y],xyzv[VIO_Z],xyzv[VIO_Z+1]);
get_volume_sizes(new_field, siz);
get_volume_separations(new_field, s1);
print ("seps: %7.3f %7.3f %7.3f %7.3f %7.3f \n",s1[0],s1[1],s1[2],s1[3],s1[4]);
print ("size: %7d %7d %7d %7d %7d \n",siz[0],siz[1],siz[2],siz[3],siz[4]);
}
alloc_volume_data(new_field);
if (globals->flags.verbose>0)
initialize_progress_report( &progress, FALSE, count[xyzv[VIO_X]],
"Interpolating new field" );
/* now resample the values from the input deformation */
for(i=0; i<VIO_MAX_DIMENSIONS; i++) {
voxel[i] = 0.0;
index[i] = 0;
}
for(index[xyzv[VIO_X]]=0; index[xyzv[VIO_X]]<count[xyzv[VIO_X]]; index[xyzv[VIO_X]]++) {
voxel[xyzv[VIO_X]] = (VIO_Real)index[xyzv[VIO_X]];
for(index[xyzv[VIO_Y]]=0; index[xyzv[VIO_Y]]<count[xyzv[VIO_Y]]; index[xyzv[VIO_Y]]++) {
voxel[xyzv[VIO_Y]] = (VIO_Real)index[xyzv[VIO_Y]];
for(index[xyzv[VIO_Z]]=0; index[xyzv[VIO_Z]]<count[xyzv[VIO_Z]]; index[xyzv[VIO_Z]]++) {
voxel[xyzv[VIO_Z]] = (VIO_Real)index[xyzv[VIO_Z]];
convert_voxel_to_world(new_field, voxel, &wx,&wy,&wz);
grid_transform_point(non_lin_part, wx, wy, wz,
&del_x, &del_y, &del_z);
/* get just the deformation part */
del_x = del_x - wx;
del_y = del_y - wy;
del_z = del_z - wz;
/* del_x = del_y = del_z = 0.0;
*/
vector_val[0] = CONVERT_VALUE_TO_VOXEL(new_field, del_x);
vector_val[1] = CONVERT_VALUE_TO_VOXEL(new_field, del_y);
vector_val[2] = CONVERT_VALUE_TO_VOXEL(new_field, del_z);
for(index[xyzv[VIO_Z+1]]=0; index[xyzv[VIO_Z+1]]<3; index[xyzv[VIO_Z+1]]++) {
SET_VOXEL(new_field, \
index[0], index[1], index[2], index[3], index[4], \
vector_val[ index[ xyzv[ VIO_Z+1] ] ]);
}
}
}
if (globals->flags.verbose>0)
update_progress_report( &progress,index[xyzv[VIO_X]]+1);
}
if (globals->flags.verbose>0)
terminate_progress_report( &progress );
/* delete and free up old data */
delete_volume(non_lin_part->displacement_volume);
/* set new volumes into transform */
non_lin_part->displacement_volume = new_field;
}
