void scale_volume(VIO_Volume * vol, double o_min, double o_max, double min, double max)
{
double value, a, b;
int sizes[MAX_VAR_DIMS];
int i, j, k, v;
VIO_progress_struct progress;
get_volume_sizes(*vol, sizes);
/* rescale the volume */
a = (max - min) / (o_max - o_min);
b = min - (o_min * a);
initialize_progress_report(&progress, FALSE, sizes[Z_IDX], "Rescaling Volume");
for(k = sizes[Z_IDX]; k--;){
for(j = sizes[Y_IDX]; j--;){
for(i = sizes[X_IDX]; i--;){
for(v = sizes[V_IDX]; v--;){
value = (get_volume_real_value(*vol, k, j, i, v, 0) * a) + b;
set_volume_real_value(*vol, k, j, i, v, 0, value);
}
}
}
update_progress_report(&progress, k + 1);
}
terminate_progress_report(&progress);
if(verbose){
fprintf(stdout, " + rescaled data range: [%g:%g]\n", min, max);
}
set_volume_real_range(*vol, min, max);
}
void get_volume(float *data, VIO_Volume vol, int *sizes){
int i,j,k;
for (i=0;i<sizes[0];i++)
for (j=0;j<sizes[1];j++)
for (k=0;k<sizes[2];k++)
set_volume_real_value(vol,i,j,k,0,0,data[i*sizes[1]*sizes[2]+j*sizes[2]+k]);
}
/* perform an erosion on a volume */
Volume *erosion_kernel(Kernel * K, Volume * vol)
{
int x, y, z, c;
double value;
int sizes[MAX_VAR_DIMS];
progress_struct progress;
Volume tmp_vol;
if(verbose){
fprintf(stdout, "Erosion kernel\n");
}
get_volume_sizes(*vol, sizes);
initialize_progress_report(&progress, FALSE, sizes[2], "Erosion");
/* copy the volume */
tmp_vol = copy_volume(*vol);
for(z = -K->pre_pad[2]; z < sizes[0] - K->post_pad[2]; z++){
for(y = -K->pre_pad[1]; y < sizes[1] - K->post_pad[1]; y++){
for(x = -K->pre_pad[0]; x < sizes[2] - K->post_pad[0]; x++){
value = get_volume_real_value(tmp_vol, z, y, x, 0, 0);
for(c = 0; c < K->nelems; c++){
if(get_volume_real_value(*vol,
z + K->K[c][2],
y + K->K[c][1],
x + K->K[c][0],
0 + K->K[c][3], 0 + K->K[c][4]) > value){
set_volume_real_value(*vol,
z + K->K[c][2],
y + K->K[c][1],
x + K->K[c][0],
0 + K->K[c][3],
0 + K->K[c][4], value * K->K[c][5]);
}
}
value = get_volume_real_value(tmp_vol, z, y, x, 0, 0);
}
}
update_progress_report(&progress, z + 1);
}
delete_volume(tmp_vol);
terminate_progress_report(&progress);
return (vol);
}
/* pad a volume using the background value */
Volume *pad(Kernel * K, Volume * vol, double bg)
{
int x, y, z;
int sizes[MAX_VAR_DIMS];
get_volume_sizes(*vol, sizes);
/* z */
for(y = 0; y < sizes[1]; y++){
for(x = 0; x < sizes[2]; x++){
for(z = 0; z < -K->pre_pad[2]; z++){
set_volume_real_value(*vol, z, y, x, 0, 0, bg);
}
for(z = sizes[0] - K->post_pad[2]; z < sizes[0]; z++){
set_volume_real_value(*vol, z, y, x, 0, 0, bg);
}
}
}
/* y */
for(z = 0; z < sizes[0]; z++){
for(x = 0; x < sizes[2]; x++){
for(y = 0; y < -K->pre_pad[1]; y++){
set_volume_real_value(*vol, z, y, x, 0, 0, bg);
}
for(y = sizes[1] - K->post_pad[1]; y < sizes[1]; y++){
set_volume_real_value(*vol, z, y, x, 0, 0, bg);
}
}
}
/* x */
for(z = 0; z < sizes[0]; z++){
for(y = 0; y < sizes[1]; y++){
for(x = 0; x < -K->pre_pad[0]; x++){
set_volume_real_value(*vol, z, y, x, 0, 0, bg);
}
for(x = sizes[2] - K->post_pad[0]; x < sizes[2]; x++){
set_volume_real_value(*vol, z, y, x, 0, 0, bg);
}
}
}
return (vol);
}
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);
}
/* xcorr = sum((a*b)^2) / (sqrt(sum(a^2)) * sqrt(sum(b^2)) */
VIO_Volume *lcorr_kernel(Kernel * K, VIO_Volume * vol, VIO_Volume *cmp)
{
int x, y, z, c;
double value, v1, v2;
double ssum_v1, ssum_v2, sum_prd, denom;
int sizes[MAX_VAR_DIMS];
progress_struct progress;
Volume tmp_vol;
if(verbose){
fprintf(stdout, "Local Correlation kernel\n");
}
get_volume_sizes(*vol, sizes);
initialize_progress_report(&progress, FALSE, sizes[2], "Local Correlation");
/* copy the volume */
tmp_vol = copy_volume(*vol);
/* zero the output volume */
for(z = sizes[0]; z--;){
for(y = sizes[1]; y--;){
for(x = sizes[2]; x--;){
set_volume_voxel_value(*vol, z, y, x, 0, 0, 0);
}
}
}
/* set output range */
set_volume_real_range(*vol, 0.0, 1.0);
for(z = -K->pre_pad[2]; z < sizes[0] - K->post_pad[2]; z++){
for(y = -K->pre_pad[1]; y < sizes[1] - K->post_pad[1]; y++){
for(x = -K->pre_pad[0]; x < sizes[2] - K->post_pad[0]; x++){
/* init counters */
ssum_v1 = ssum_v2 = sum_prd = 0;
for(c = 0; c < K->nelems; c++){
v1 = get_volume_real_value(tmp_vol,
z + K->K[c][2],
y + K->K[c][1],
x + K->K[c][0], 0 + K->K[c][3],
0 + K->K[c][4]) * K->K[c][5];
v2 = get_volume_real_value(*cmp,
z + K->K[c][2],
y + K->K[c][1],
x + K->K[c][0], 0 + K->K[c][3],
0 + K->K[c][4]) * K->K[c][5];
/* increment counters */
ssum_v1 += v1*v1;
ssum_v2 += v2*v2;
sum_prd += v1*v2;
}
denom = sqrt(ssum_v1 * ssum_v2);
value = (denom == 0.0) ? 0.0 : sum_prd / denom;
set_volume_real_value(*vol, z, y, x, 0, 0, value);
}
}
update_progress_report(&progress, z + 1);
}
terminate_progress_report(&progress);
/* tidy up */
delete_volume(tmp_vol);
return (vol);
}
/* from the original 2 pass Borgefors alg */
Volume *distance_kernel(Kernel * K, Volume * vol, double bg)
{
int x, y, z, c;
double value, min;
int sizes[MAX_VAR_DIMS];
progress_struct progress;
Kernel *k1, *k2;
/* split the Kernel */
k1 = new_kernel(K->nelems);
k2 = new_kernel(K->nelems);
split_kernel(K, k1, k2);
setup_pad_values(k1);
setup_pad_values(k2);
if(verbose){
fprintf(stdout, "Distance kernel - background %g\n", bg);
fprintf(stdout, "forward direction kernel:\n");
print_kernel(k1);
fprintf(stdout, "\nreverse direction kernel:\n");
print_kernel(k2);
}
get_volume_sizes(*vol, sizes);
initialize_progress_report(&progress, FALSE, sizes[2] * 2, "Distance");
/* forward raster direction */
for(z = -K->pre_pad[2]; z < sizes[0] - K->post_pad[2]; z++){
for(y = -K->pre_pad[1]; y < sizes[1] - K->post_pad[1]; y++){
for(x = -K->pre_pad[0]; x < sizes[2] - K->post_pad[0]; x++){
if(get_volume_real_value(*vol, z, y, x, 0, 0) != bg){
/* find the minimum */
min = DBL_MAX;
for(c = 0; c < k1->nelems; c++){
value = get_volume_real_value(*vol,
z + k1->K[c][2],
y + k1->K[c][1],
x + k1->K[c][0],
0 + k1->K[c][3], 0 + k1->K[c][4]) + 1;
if(value < min){
min = value;
}
}
set_volume_real_value(*vol, z, y, x, 0, 0, min);
}
}
}
update_progress_report(&progress, z + 1);
}
/* reverse raster direction */
for(z = sizes[0] - k2->post_pad[2] - 1; z >= -k2->pre_pad[2]; z--){
for(y = sizes[1] - k2->post_pad[1] - 1; y >= -k2->pre_pad[1]; y--){
for(x = sizes[2] - k2->post_pad[0] - 1; x >= -k2->pre_pad[0]; x--){
min = get_volume_real_value(*vol, z, y, x, 0, 0);
if(min != bg){
/* find the minimum distance to bg in the neighbouring vectors */
for(c = 0; c < k2->nelems; c++){
value = get_volume_real_value(*vol,
z + k2->K[c][2],
y + k2->K[c][1],
x + k2->K[c][0],
0 + k2->K[c][3], 0 + k2->K[c][4]) + 1;
if(value < min){
min = value;
}
}
set_volume_real_value(*vol, z, y, x, 0, 0, min);
}
}
}
update_progress_report(&progress, sizes[2] + z + 1);
}
free(k1);
free(k2);
terminate_progress_report(&progress);
return (vol);
}
int main(
int argc,
char *argv[] )
{
STRING volume_filename;
STRING output_filename;
Real x, y, z, xc, yc, zc, xp, yp, zp, len, pos;
Real value, scaling, min_value, max_value;
int v[MAX_DIMENSIONS], sizes[MAX_DIMENSIONS];
Real voxel[MAX_DIMENSIONS], scale;
Volume volume;
initialize_argument_processing( argc, argv );
if( !get_string_argument( "", &volume_filename ) ||
!get_string_argument( "", &output_filename ) ||
!get_real_argument( 0.0, &x ) ||
!get_real_argument( 0.0, &y ) ||
!get_real_argument( 0.0, &z ) ||
!get_real_argument( 0.0, &scaling ) )
{
return( 1 );
}
len = sqrt( x * x + y * y + z * z );
x /= len;
y /= len;
z /= len;
if( input_volume( volume_filename, 3, File_order_dimension_names,
NC_UNSPECIFIED, FALSE, 0.0, 0.0,
TRUE, &volume, NULL ) != OK )
return( 1 );
get_volume_sizes( volume, sizes );
get_volume_real_range( volume, &min_value, &max_value );
voxel[0] = (Real) (sizes[0]-1) / 2.0;
voxel[1] = (Real) (sizes[1]-1) / 2.0;
voxel[2] = (Real) (sizes[2]-1) / 2.0;
convert_voxel_to_world( volume, voxel, &xc, &yc, &zc );
BEGIN_ALL_VOXELS( volume, v[0], v[1], v[2], v[3], v[4] )
voxel[0] = (Real) v[0];
voxel[1] = (Real) v[1];
voxel[2] = (Real) v[2];
convert_voxel_to_world( volume, voxel, &xp, &yp, &zp );
pos = (xp - xc) * x + (yp - yc) * y + (zp - zc) * z;
scale = 1.0 + pos * scaling;
value = get_volume_real_value( volume, v[0], v[1], v[2], v[3], v[4] );
value *= scale;
if( value < min_value )
value = min_value;
else if( value > max_value )
value = max_value;
set_volume_real_value( volume, v[0], v[1], v[2], v[3], v[4], value );
END_ALL_VOXELS
(void) output_modified_volume( output_filename, NC_UNSPECIFIED, FALSE,
0.0, 0.0, volume, volume_filename,
"Scaled\n", 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);
}
/* regrid a point in a file using the input co-ordinate and data */
void regrid_point(VIO_Volume * totals, VIO_Volume * weights,
double x, double y, double z, int v_size, double *data_buf)
{
int sizes[MAX_VAR_DIMS];
VIO_Real steps[MAX_VAR_DIMS];
VIO_Real starts[MAX_VAR_DIMS];
int start_idx[3];
int stop_idx[3];
double value, weight;
double euc_dist;
double euc[3];
double c_pos[3];
int i, j, k, v;
double coord[3]; /* target point in mm coordinates, in X, Y, Z order */
VIO_Transform dircos, invdircos;
VIO_Vector vector;
VIO_Real dir[3];
/* the coord used below has to be in mm coordinates in the dircos space of the
target volume. Hence the manipulations with the vols direction_cosines */
make_identity_transform(&dircos);
get_volume_direction_cosine(*totals, perm[0], dir);
fill_Vector(vector, dir[0], dir[1], dir[2]);
set_transform_x_axis(&dircos, &vector);
get_volume_direction_cosine(*totals, perm[1], dir);
fill_Vector(vector, dir[0], dir[1], dir[2]);
set_transform_y_axis(&dircos, &vector);
get_volume_direction_cosine(*totals, perm[2], dir);
fill_Vector(vector, dir[0], dir[1], dir[2]);
set_transform_z_axis(&dircos, &vector);
for(i = 0; i < 4; i++){
for(j = 0; j < 4; j++){
Transform_elem(invdircos, i, j) = Transform_elem(dircos, j, i);
}
}
transform_point(&invdircos, x, y, z, &coord[0], &coord[1], &coord[2]);
get_volume_sizes(*totals, sizes); /* in volume voxel order, ie z,y,x with x fastest */
get_volume_separations(*totals, steps);
get_volume_starts(*totals, starts);
/* figure out the neighbouring voxels start and stop (in voxel co-ordinates) */
for(i = 0; i < 3; i++){ /* go through x, y and z */
start_idx[i] =
(int)rint((coord[i] - starts[perm[i]] - regrid_radius[i]) / steps[perm[i]]);
stop_idx[i] = start_idx[i] + rint((regrid_radius[i] * 2) / steps[perm[i]]);
/* flip if required */
if(start_idx[i] > stop_idx[i]){
value = start_idx[i];
start_idx[i] = stop_idx[i];
stop_idx[i] = value;
}
/* check that we aren't off the edge */
if(start_idx[i] < 0){
start_idx[i] = 0;
}
if(stop_idx[i] >= sizes[perm[i]]){
stop_idx[i] = sizes[perm[i]] - 1;
}
}
/* loop over the neighbours, getting euclidian distance */
c_pos[0] = starts[perm[0]] + (start_idx[0] * steps[perm[0]]);
for(i = start_idx[0]; i <= stop_idx[0]; i++){
euc[0] = fabs(c_pos[0] - coord[0]);
c_pos[1] = starts[perm[1]] + (start_idx[1] * steps[perm[1]]);
for(j = start_idx[1]; j <= stop_idx[1]; j++){
euc[1] = fabs(c_pos[1] - coord[1]);
c_pos[2] = starts[perm[2]] + (start_idx[2] * steps[perm[2]]);
for(k = start_idx[2]; k <= stop_idx[2]; k++){
euc[2] = fabs(c_pos[2] - coord[2]);
euc_dist = sqrt(SQR2(euc[0]) + SQR2(euc[1]) + SQR2(euc[2]));
if((regrid_radius[0] == 0 || euc[0] <= regrid_radius[0]) &&
(regrid_radius[1] == 0 || euc[1] <= regrid_radius[1]) &&
(regrid_radius[2] == 0 || euc[2] <= regrid_radius[2])){
/* calculate the weighting factor */
switch (regrid_type){
default:
fprintf(stderr, "Erk! unknown regrid_type. File: %s Line: %d\n",
__FILE__, __LINE__);
exit(EXIT_FAILURE);
break;
case NEAREST_FUNC:
case LINEAR_FUNC:
weight = euc_dist;
break;
case KAISERBESSEL_FUNC:
weight =
gsl_sf_bessel_I0(regrid_sigma[0] *
sqrt(1 - SQR2(euc[0] / regrid_radius[0]))) *
gsl_sf_bessel_I0(regrid_sigma[1] *
sqrt(1 - SQR2(euc[1] / regrid_radius[1]))) *
gsl_sf_bessel_I0(regrid_sigma[2] *
sqrt(1 - SQR2(euc[2] / regrid_radius[2]))) /
SQR3((regrid_radius[0] + regrid_radius[1] + regrid_radius[2]) / 3);
break;
case GAUSSIAN_FUNC:
weight = exp(-SQR2(euc[0]) / SQR2(regrid_sigma[0])) *
exp(-SQR2(euc[1]) / SQR2(regrid_sigma[1])) *
exp(-SQR2(euc[2]) / SQR2(regrid_sigma[2]));
break;
}
/* set data values */
if(regrid_type == NEAREST_FUNC){
value = get_volume_real_value(*weights, k, j, i, 0, 0);
if(weight < value){
set_volume_real_value(*weights, k, j, i, 0, 0, weight);
for(v = 0; v < v_size; v++){
set_volume_real_value(*totals, k, j, i, v, 0,
data_buf[0 + v] * weight);
}
}
}
else{
for(v = 0; v < v_size; v++){
value = get_volume_real_value(*totals, k, j, i, v, 0);
set_volume_real_value(*totals, k, j, i, v, 0,
value + (data_buf[0 + v] * weight));
}
/* increment count value */
value = get_volume_real_value(*weights, k, j, i, 0, 0);
set_volume_real_value(*weights, k, j, i, 0, 0, value + weight);
}
}
c_pos[2] += steps[perm[2]];
}
c_pos[1] += steps[perm[1]];
}
c_pos[0] += steps[perm[0]];
}
}
int main(int argc, char *argv[])
{
char **infiles;
int n_infiles;
char *out_fn;
char *history;
VIO_progress_struct progress;
VIO_Volume totals, weights;
int i, j, k, v;
double min, max;
double w_min, w_max;
long num_missed;
double weight, value;
double initial_weight;
VIO_Real dummy[3];
int sizes[MAX_VAR_DIMS];
double starts[MAX_VAR_DIMS];
double steps[MAX_VAR_DIMS];
long t = 0;
/* start the time counter */
current_realtime_seconds();
/* get the history string */
history = time_stamp(argc, argv);
/* get args */
if(ParseArgv(&argc, argv, argTable, 0) || (argc < 3)){
fprintf(stderr,
"\nUsage: %s [options] <in1.mnc> [<in2.mnc> [...]] <out.mnc>\n", argv[0]);
fprintf(stderr,
" %s [options] -arb_path pth.conf <infile.raw> <out.mnc>\n", argv[0]);
fprintf(stderr, " %s -help\n\n", argv[0]);
exit(EXIT_FAILURE);
}
/* get file names */
n_infiles = argc - 2;
infiles = (char **)malloc(sizeof(char *) * n_infiles);
for(i = 0; i < n_infiles; i++){
infiles[i] = argv[i + 1];
}
out_fn = argv[argc - 1];
/* check for infiles and outfile */
for(i = 0; i < n_infiles; i++){
if(!file_exists(infiles[i])){
fprintf(stderr, "%s: Couldn't find input file %s.\n\n", argv[0], infiles[i]);
exit(EXIT_FAILURE);
}
}
if(!clobber && file_exists(out_fn)){
fprintf(stderr, "%s: %s exists, -clobber to overwrite.\n\n", argv[0], out_fn);
exit(EXIT_FAILURE);
}
/* check for weights_fn if required */
if(weights_fn != NULL){
if(!clobber && file_exists(weights_fn)){
fprintf(stderr, "%s: %s exists, -clobber to overwrite.\n\n", argv[0],
weights_fn);
exit(EXIT_FAILURE);
}
}
/* set up parameters for reconstruction */
if(out_dtype == NC_UNSPECIFIED){
out_dtype = in_dtype;
}
if(out_is_signed == DEF_BOOL){
out_is_signed = in_is_signed;
}
/* check vector dimension size */
if(vect_size < 1){
fprintf(stderr, "%s: -vector (%d) must be 1 or greater.\n\n", argv[0], vect_size);
exit(EXIT_FAILURE);
}
/* check sigma */
if(regrid_sigma[0] <= 0 || regrid_sigma[1] <= 0 || regrid_sigma[2] <= 0 ){
fprintf(stderr, "%s: -sigma must be greater than 0\n\n", argv[0]);
exit(EXIT_FAILURE);
}
/* read in the output file config from a file is specified */
if(out_config_fn != NULL){
int ext_args_c;
char *ext_args[32]; /* max possible is 32 arguments */
ext_args_c = read_config_file(out_config_fn, ext_args);
if(ParseArgv(&ext_args_c, ext_args, argTable,
ARGV_DONT_SKIP_FIRST_ARG | ARGV_NO_LEFTOVERS | ARGV_NO_DEFAULTS)){
fprintf(stderr, "\nError in parameters in %s\n", out_config_fn);
exit(EXIT_FAILURE);
}
}
if(verbose){
fprintf_vol_def(stdout, &out_inf);
}
/* transpose the geometry arrays */
/* out_inf.*[] are in world xyz order, perm[] is the permutation
array to map world xyz to the right voxel order in the volume */
for(i = 0; i < WORLD_NDIMS; i++){
sizes[i] = out_inf.nelem[perm[i]]; /* sizes, starts, steps are in voxel volume order. */
starts[i] = out_inf.start[perm[i]];
steps[i] = out_inf.step[perm[i]];
}
sizes[WORLD_NDIMS] = vect_size;
/* create the totals volume */
totals = create_volume((vect_size > 1) ? 4 : 3,
(vect_size > 1) ? std_dimorder_v : std_dimorder,
out_dtype, out_is_signed, 0.0, 0.0);
set_volume_sizes(totals, sizes);
set_volume_starts(totals, starts);
set_volume_separations(totals, steps);
for(i = 0; i < WORLD_NDIMS; i++){
/* out_inf.dircos is in world x,y,z order, we have to use the perm array to
map each direction to the right voxel axis. */
set_volume_direction_cosine(totals, i, out_inf.dircos[perm[i]]);
}
alloc_volume_data(totals);
/* create the "weights" volume */
weights = create_volume(3, std_dimorder, out_dtype, out_is_signed, 0.0, 0.0);
set_volume_sizes(weights, sizes);
set_volume_starts(weights, starts);
set_volume_separations(weights, steps);
for(i = 0; i < WORLD_NDIMS; i++){
set_volume_direction_cosine(weights, i, out_inf.dircos[perm[i]]);
}
alloc_volume_data(weights);
/* down below in regrid_loop, Andrew makes a nasty direct reference to the
voxel_to_world transformation in the volume. This
transformation is not necessarily up to date, particularly when
non-default direction cosines are used. In volume_io, the
direction cosines are set and a FLAG is also set to indicate
that the voxel-to-world xform is not up to date. If the stanrd
volume_io general transform code is used, it checks internally
to see if the matrix is up to date, and if not it is recomputed.
So here, we'll (LC + MK) force an update by calling a general
transform. */
// convert_world_to_voxel(weights, (Real) 0, (Real) 0, (Real) 0, dummy);
// convert_world_to_voxel(totals, (Real) 0, (Real) 0, (Real) 0, dummy);
fprintf(stderr, "2Sizes: [%d:%d:%d] \n", sizes[perm[0]], sizes[perm[1]], sizes[perm[2]]);
/* initialize weights to be arbitray large value if using NEAREST */
/* volume interpolation else initialize all to zero */
if(regrid_type == NEAREST_FUNC && ap_coord_fn == NULL){
initial_weight = LARGE_INITIAL_WEIGHT;
}
else{
initial_weight = 0.0;
}
/* initialize weights and totals */
for(k = sizes[Z_IDX]; k--;){
for(j = sizes[Y_IDX]; j--;){
for(i = sizes[X_IDX]; i--;){
set_volume_real_value(weights, k, j, i, 0, 0, initial_weight);
for(v = vect_size; v--;){
set_volume_real_value(totals, k, j, i, v, 0, 0.0);
}
}
}
}
/* if regridding via an arbitrary path */
if(ap_coord_fn != NULL){
if(n_infiles > 1){
fprintf(stderr, "%s: arb_path only works for one input file (so far).\n\n",
argv[0]);
exit(EXIT_FAILURE);
}
/* print some pretty output */
if(verbose){
fprintf(stdout, " | Input data: %s\n", infiles[0]);
fprintf(stdout, " | Arb path: %s\n", ap_coord_fn);
fprintf(stdout, " | Output range: [%g:%g]\n", out_range[0], out_range[1]);
fprintf(stdout, " | Output file: %s\n", out_fn);
}
regrid_arb_path(ap_coord_fn, infiles[0], max_buffer_size_in_kb,
&totals, &weights, vect_size, regrid_range[0], regrid_range[1]);
}
/* else if regridding via a series of input minc file(s) */
else {
for(i = 0; i < n_infiles; i++){
if(verbose){
fprintf(stdout, " | Input file: %s\n", infiles[i]);
}
regrid_minc(infiles[i], max_buffer_size_in_kb,
&totals, &weights, vect_size, regrid_range[0], regrid_range[1]);
}
}
/* initialise min and max counters and divide totals/weights */
num_missed = 0;
min = get_volume_real_value(totals, 0, 0, 0, 0, 0);
max = get_volume_real_value(totals, 0, 0, 0, 0, 0);
w_min = get_volume_real_value(weights, 0, 0, 0, 0, 0);
w_max = get_volume_real_value(weights, 0, 0, 0, 0, 0);
initialize_progress_report(&progress, FALSE, out_inf.nelem[Z_IDX], "Dividing through");
for(i = sizes[perm[0]]; i--;){
for(j = sizes[perm[1]]; j--;){
for(k = sizes[perm[2]]; k--;){
weight = get_volume_real_value(weights, k, j, i, 0, 0);
if(weight < w_min){
w_min = weight;
}
else if(weight > w_max){
w_max = weight;
}
if(weight != 0){
for(v = vect_size; v--;){
value = get_volume_real_value(totals, k, j, i, v, 0) / weight;
if(value < min){
min = value;
}
else if(value > max){
max = value;
}
set_volume_real_value(totals, k, j, i, v, 0, value);
}
}
else {
num_missed++;
}
}
}
update_progress_report(&progress, k + 1);
}
terminate_progress_report(&progress);
/* set the volumes range */
if(verbose){
fprintf(stdout, " + data range: [%g:%g]\n", min, max);
fprintf(stdout, " + weight range: [%g:%g]\n", w_min, w_max);
}
set_volume_real_range(totals, min, max);
set_volume_real_range(weights, w_min, w_max);
if(num_missed > 0 && verbose){
int nvox;
nvox = out_inf.nelem[X_IDX] * out_inf.nelem[Y_IDX] * out_inf.nelem[Z_IDX];
fprintf(stdout,
"\n-regrid_radius possibly too small, no data in %ld/%d[%2.2f%%] voxels\n\n",
num_missed, nvox, ((float)num_missed / nvox * 100));
}
/* rescale data if required */
if(out_range[0] != -DBL_MAX && out_range[1] != DBL_MAX){
double o_min, o_max;
/* get the existing range */
get_volume_real_range(totals, &o_min, &o_max);
/* rescale it */
scale_volume(&totals, o_min, o_max, out_range[0], out_range[1]);
}
/* output the result */
if(verbose){
fprintf(stdout, " | Outputting %s...\n", out_fn);
}
if(output_volume(out_fn, out_dtype, out_is_signed,
0.0, 0.0, totals, history, NULL) != VIO_OK){
fprintf(stderr, "Problems outputing: %s\n\n", out_fn);
}
/* output weights volume if required */
if(weights_fn != NULL){
if(verbose){
fprintf(stdout, " | Outputting %s...\n", weights_fn);
}
if(output_volume(weights_fn, out_dtype, out_is_signed,
0.0, 0.0, weights, history, NULL) != VIO_OK){
fprintf(stderr, "Problems outputting: %s\n\n", weights_fn);
}
}
delete_volume(totals);
delete_volume(weights);
t = current_realtime_seconds();
printf("Total reconstruction time: %ld hours %ld minutes %ld seconds\n", t/3600, (t/60)%60, t%60);
return (EXIT_SUCCESS);
}
int main(int argc, char *argv[])
{
VIO_Volume
volume;
VIO_Real
variability,
rand_val,
voxel[VIO_MAX_DIMENSIONS];
int
progress_count,
sizes[VIO_MAX_DIMENSIONS],
index[VIO_MAX_DIMENSIONS],
i,j,k;
VIO_progress_struct
progress;
union
{
long l;
char c[4];
} seedval;
time_t t;
char tmp;
prog_name = argv[0];
/* Check arguments */
if (argc != 4) {
(void) fprintf(stderr, "Usage: %s input.mnc output.mnc std_dev\n",
argv[0]);
exit(EXIT_FAILURE);
}
if( input_volume( argv[1], 3, NULL, NC_UNSPECIFIED, FALSE,
0.0, 0.0, TRUE, &volume, (minc_input_options *)NULL ) != OK ) {
(void)fprintf(stderr, "Error opening input volume file %s.\n",
argv[1]);
exit(EXIT_FAILURE);
}
variability = atof( argv[3] );
/* initialize drand function */
t = 2*time(NULL);
seedval.l = t;
tmp = seedval.c[0]; seedval.c[0] = seedval.c[3]; seedval.c[3] = tmp;
tmp = seedval.c[1]; seedval.c[1] = seedval.c[2]; seedval.c[2] = tmp;
srand48(seedval.l);
set_volume_real_range(volume, -5.0*variability, 5.0*variability);
get_volume_sizes(volume,sizes);
initialize_progress_report(&progress, FALSE,
sizes[VIO_X]*sizes[VIO_Y]*sizes[VIO_Z]+1,
"Randomizing volume");
progress_count = 0;
for(i=0; i<MAX_DIMENSIONS; i++) index[i] = 0;
/* loop over all voxels */
for(index[X]=0; index[X]<sizes[X]; index[X]++)
for(index[Y]=0; index[Y]<sizes[Y]; index[Y]++)
for(index[Z]=0; index[Z]<sizes[Z]; index[Z]++) {
/* get a random value from a gaussian distribution */
rand_val = variability * gaussian_random_0_1();
if (rand_val > 5.0*variability) rand_val = 5.0*variability;
if (rand_val < -5.0*variability) rand_val = -5.0*variability;
set_volume_real_value(volume,
index[0],index[1],index[2],index[3],index[4],
rand_val);
progress_count++;
update_progress_report(&progress, progress_count);
}
terminate_progress_report(&progress);
/* Write out the random volume */
if (output_volume(argv[2], NC_UNSPECIFIED, FALSE, 0.0, 0.0, volume,
(char *)NULL, (minc_output_options *)NULL) != OK) {
(void) fprintf(stderr, "%s: Error writing volume file %s\n",
argv[0], argv[2]);
exit(EXIT_FAILURE);
}
exit(EXIT_SUCCESS);
}
/* ----------------------------- MNI Header -----------------------------------
@NAME : average_smoothness
@INPUT : tmp_lambda_file - tmp file with unaveraged smoothness values
@OUTPUT : lambda_file - file where final values are to be placed
@RETURNS : nothing
@DESCRIPTION: routine to create buffers for calculating smoothness of field
@CREATED : Nov. 3, 1997, J. Taylor
@MODIFIED :
---------------------------------------------------------------------------- */
int average_smoothness(char *tmp_lambda_file, char *lambda_file, double scalar)
{
Volume volume;
nc_type in_nc_type;
int in_signed_flag = FALSE;
volume_input_struct volume_input;
int v1, v2, v3;
int num_dim;
int sizes[MAX_DIMENSIONS];
double avg, values[8];
int i;
if(start_volume_input(tmp_lambda_file, 3, NULL, NC_UNSPECIFIED, FALSE,
0.0, 0.0, TRUE, &volume,
(minc_input_options *) NULL, &volume_input) != OK){
fprintf(stderr,"\nError opening %s.\n", tmp_lambda_file);
exit(EXIT_FAILURE);
}
in_nc_type = get_volume_nc_data_type(volume, &in_signed_flag);
get_volume_sizes(volume, sizes);
num_dim = get_volume_n_dimensions(volume);
cancel_volume_input(volume, &volume_input);
if( input_volume(tmp_lambda_file, 3, NULL, NC_FLOAT, FALSE, 0.0, 0.0,
TRUE, &volume, (minc_input_options *) NULL) != OK) {
(void) fprintf(stderr, "Error reading file \"%s\"\n", tmp_lambda_file);
return FALSE;
}
for(v1=0; v1<sizes[0]; v1++) {
for(v2=0; v2<sizes[1]; v2++) {
for(v3=0; v3<sizes[2]; v3++) {
avg = 0.0;
if((v1<sizes[0]-1) && (v2<sizes[1]-1) && (v3<sizes[2])-1) {
values[0] = get_volume_real_value(volume, v1+1, v2, v3, 0, 0);
values[1] = get_volume_real_value(volume, v1, v2+1, v3, 0, 0);
values[2] = get_volume_real_value(volume, v1, v2, v3+1, 0, 0);
values[3] = get_volume_real_value(volume,v1+1, v2+1, v3, 0, 0);
values[4] = get_volume_real_value(volume, v1+1,v2, v3+1, 0, 0);
values[5] = get_volume_real_value(volume, v1, v2+1,v3+1, 0, 0);
values[6] = get_volume_real_value(volume, v1, v2, v3, 0, 0);
values[7] = get_volume_real_value(volume, v1+1, v2+1,v3+1,0,0);
for(i=0; i<8; i++) {
if(values[i] != INVALID_DATA)
avg += values[i];
else {
avg = INVALID_DATA;
i = 8;
}
}
}
else
avg = INVALID_DATA;
if (avg == 0.0)
avg = INVALID_DATA;
if (avg != INVALID_DATA)
avg = scalar * 8.0 / pow(avg, (1.0 / num_dim));
set_volume_real_value(volume, v1, v2, v3, 0, 0, avg);
}
}
}
if( output_modified_volume(lambda_file, in_nc_type, in_signed_flag,
0.0, 0.0, volume, tmp_lambda_file, NULL,
(minc_output_options *) NULL) != OK) {
(void) fprintf(stderr, "Error writing file \"%s\"\n", lambda_file);
return FALSE;
}
return TRUE;
}