static void append_new_default_deformation_field(Arg_Data *globals)
{
VIO_Volume
new_field;
VIO_Real
zero,
st[VIO_MAX_DIMENSIONS],
wst[VIO_MAX_DIMENSIONS],
step[VIO_MAX_DIMENSIONS],
XYZstart[ VIO_MAX_DIMENSIONS ],
XYZstep[ VIO_MAX_DIMENSIONS ],
voxel[VIO_MAX_DIMENSIONS],
point[VIO_N_DIMENSIONS],
dir[3][3];
int
index[VIO_MAX_DIMENSIONS],
xyzv[VIO_MAX_DIMENSIONS],
i,
count[VIO_MAX_DIMENSIONS],
XYZcount[VIO_MAX_DIMENSIONS],
count_extended[VIO_MAX_DIMENSIONS];
VIO_General_transform
*grid_trans;
VectorR
XYZdirections[ VIO_MAX_DIMENSIONS ];
/* build a vector volume to store the Grid VIO_Transform */
/* ALLOC(new_field,1); not needed since create volume allocs it
internally and returns a pointer*/
if (globals->flags.debug) { print ("In append_new_default_deformation_field...\n"); }
new_field = create_volume(4, dim_name_vector_vol, NC_DOUBLE, TRUE, 0.0, 0.0);
get_volume_XYZV_indices(new_field, xyzv);
/* get the global voxel count and voxel size */
for(i=0; i<VIO_N_DIMENSIONS; i++) {
count[xyzv[i]] = globals->count[i];
count_extended[xyzv[i]] = count[xyzv[i]];
step[xyzv[i]] = globals->step[i];
}
/* add info for the vector dimension */
count[xyzv[VIO_Z+1]] = 3;
count_extended[xyzv[VIO_Z+1]] = 3;
step[xyzv[VIO_Z+1]] = 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, now using floats */
for(i=0; i<VIO_N_DIMENSIONS; i++) {
dir[VIO_X][i]=globals->directions[VIO_X].coords[i];
dir[VIO_Y][i]=globals->directions[VIO_Y].coords[i];
dir[VIO_Z][i]=globals->directions[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]);
for(i=0; i<VIO_MAX_DIMENSIONS; i++) /* set the voxel origin, used in the vol def */
voxel[i] = 0.0;
set_volume_translation( new_field, voxel, globals->start);
if (globals->flags.debug) {
print("in append new def, the start is: %8.3f %8.3f %8.3f\n", globals->start[VIO_X], globals->start[VIO_Y], globals->start[VIO_Z]);
}
/* now pad the volume along the spatial axis
to ensure good coverage of the data space
with the deformation field */
for(i=0; i<VIO_N_DIMENSIONS; i++) {
if (globals->count[i]>1) {
voxel[xyzv[i]] = -2.5;
count_extended[xyzv[i]] = globals->count[i]+5;
}
else {
voxel[xyzv[i]] = 0.0;
count_extended[xyzv[i]] = 1;
}
}
if (globals->flags.debug) {
print("in append_new_default_deformation_field:\n\tcount_extended= %d %d %d %d\n",
count_extended[0],count_extended[1],count_extended[2],count_extended[3]);
}
set_volume_sizes(new_field, count_extended);
for(i=0; i<VIO_MAX_DIMENSIONS; i++) count[i] = count_extended[i];
/* reset the first voxel position with the new origin */
convert_voxel_to_world(new_field, voxel,
&(point[VIO_X]), &(point[VIO_Y]), &(point[VIO_Z]));
for(i=0; i<VIO_MAX_DIMENSIONS; i++) voxel[i] = 0;
set_volume_translation(new_field, voxel, point);
if (globals->flags.debug) {
print (" point: %8.3f %8.3f %8.3f \n", point[VIO_X], point[VIO_Y], point[VIO_Z]);
get_volume_starts(new_field, st);
print (" start: %8.3f %8.3f %8.3f \n", st[xyzv[VIO_X]], st[xyzv[VIO_Y]], st[xyzv[VIO_Z]]);
voxel[0] = 0;
voxel[1] = 0;
voxel[2] = 0;
get_volume_translation(new_field, voxel, wst);
print (" wstrt: %8.3f %8.3f %8.3f \n", wst[VIO_X], wst[VIO_Y], wst[VIO_Z]);
print (" voxel: %8.3f %8.3f %8.3f \n", voxel[xyzv[VIO_X]], voxel[xyzv[VIO_Y]], voxel[xyzv[VIO_Z]]);
for(i=0; i<3; i++) {
get_volume_direction_cosine(new_field,xyzv[i], wst);
print (" dirs: %8.3f %8.3f %8.3f \n", wst[VIO_X], wst[VIO_Y], wst[VIO_Z]);
}
}
/* allocate space for the deformation field data */
alloc_volume_data(new_field);
/* Initilize the field to zero deformation */
/* zero = CONVERT_VALUE_TO_VOXEL(new_field, 0.0); not needed, defs are now doubles */
for(index[0]=0; index[0]<count[0]; index[0]++)
for(index[1]=0; index[1]<count[1]; index[1]++)
for(index[2]=0; index[2]<count[2]; index[2]++)
for(index[3]=0; index[3]<count[3]; index[3]++)
{
SET_VOXEL(new_field, index[0],index[1],index[2],index[3],0, 0.0); /* was set to 'zero', but now as a double,can be set to 0.0 */
}
/* build the new GRID_TRANSFORM */
ALLOC(grid_trans, 1);
create_grid_transform(grid_trans, new_field, NULL);
/* append the deforamation to the current transformation */
concat_general_transforms(globals->trans_info.transformation, grid_trans,
globals->trans_info.transformation);
delete_volume(new_field);
delete_general_transform(grid_trans);
}
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);
}
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;
}
