image_metadata * read_minc(char *filename, float **image, int *sizes){
VIO_Volume volume;
VIO_Real dummy[3];
image_metadata *meta;
if( input_volume(filename, 3, NULL, NC_UNSPECIFIED, FALSE, 0.0, 0.0, TRUE, &volume, (minc_input_options *) NULL ) != VIO_OK )
return( NULL );
meta = (image_metadata *)calloc( 1 , sizeof(image_metadata) ) ;
meta->start = calloc(3,sizeof(float));
meta->step = calloc(3,sizeof(float));
meta->length = calloc(3,sizeof(int));
get_volume_sizes(volume,sizes);
*image=malloc(sizes[0]*sizes[1]*sizes[2]*sizeof(**image));
set_volume(*image, volume, sizes);
meta->length[0]=sizes[0];
meta->length[1]=sizes[1];
meta->length[2]=sizes[2];
get_volume_starts(volume,dummy);
meta->start[0]=dummy[0];
meta->start[1]=dummy[1];
meta->start[2]=dummy[2];
get_volume_separations(volume,dummy);
meta->step[0]=dummy[0];
meta->step[1]=dummy[1];
meta->step[2]=dummy[2];
delete_volume(volume);
return meta;
}
VIOAPI void cancel_volume_input(
VIO_Volume volume,
volume_input_struct *input_info )
{
delete_volume( volume );
delete_volume_input( input_info );
}
int write_minc(char *filename, float *image, image_metadata *meta,VIO_BOOL binary_mask){
VIO_Volume volume;
int i,j,k,index;
float min=FLT_MAX,max=FLT_MIN;
VIO_Real dummy[3];
if(binary_mask)
{
volume = create_volume(3,NULL,NC_BYTE,FALSE,0.0,1.0);
printf("Writing a binary volume...\n");
}
else
volume = create_volume(3,NULL,NC_FLOAT,FALSE,FLT_MIN,FLT_MAX);
if(!volume)
return STATUS_ERR;
if(!binary_mask)
{
for (i=0;i<meta->length[0];i++){
for (j=0;j<meta->length[1];j++){
for (k=0;k<meta->length[2];k++){
index=i*meta->length[2]*meta->length[1] + j*meta->length[2] + k;
min=MIN(min,image[index]);
max=MAX(max,image[index]);
}
}
}
set_volume_real_range(volume,min,max);
} else {
set_volume_real_range(volume,0.0,1.0);
}
set_volume_sizes(volume,meta->length);
dummy[0]=meta->start[0];
dummy[1]=meta->start[1];
dummy[2]=meta->start[2];
set_volume_starts(volume,dummy);
dummy[0]=meta->step[0];
dummy[1]=meta->step[1];
dummy[2]=meta->step[2];
set_volume_separations(volume,dummy);
alloc_volume_data(volume);
get_volume(image, volume, meta->length);
if(!binary_mask)
output_volume( filename, NC_FLOAT,FALSE,min, max,volume,meta->history,(minc_output_options *)NULL);
else
output_volume( filename, NC_BYTE,FALSE,0, 1.0,volume,meta->history,(minc_output_options *)NULL);
delete_volume(volume);
return STATUS_OK;
}
VIOAPI VIO_Status input_volume(
VIO_STR filename,
int n_dimensions,
VIO_STR dim_names[],
nc_type volume_nc_data_type,
VIO_BOOL volume_signed_flag,
VIO_Real volume_voxel_min,
VIO_Real volume_voxel_max,
VIO_BOOL create_volume_flag,
VIO_Volume *volume,
minc_input_options *options )
{
VIO_Status status;
VIO_Real amount_done;
volume_input_struct input_info;
VIO_progress_struct progress;
static const int FACTOR = 1000;
VIO_Real volume_min=0.0,volume_max=0.0;
status = start_volume_input( filename, n_dimensions, dim_names,
volume_nc_data_type, volume_signed_flag,
volume_voxel_min, volume_voxel_max,
create_volume_flag, volume, options,
&input_info );
if( status == VIO_OK )
{
initialize_progress_report( &progress, FALSE, FACTOR, "Reading Volume");
while( input_more_of_volume( *volume, &input_info, &amount_done ) )
{
update_progress_report( &progress,
VIO_ROUND( (VIO_Real) FACTOR * amount_done));
}
if (amount_done < 1.0)
{
status = VIO_ERROR;
}
terminate_progress_report( &progress );
delete_volume_input( &input_info );
if( !volume_is_alloced( *volume ) ) {
delete_volume( *volume );
*volume = NULL;
status = VIO_ERROR;
}
}
if (status == VIO_OK)
{
get_volume_voxel_range( *volume, &volume_min, &volume_max );
}
return( status );
}
/* 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);
}
VIOAPI VIO_Status start_volume_input(
VIO_STR filename,
int n_dimensions,
VIO_STR dim_names[],
nc_type volume_nc_data_type,
VIO_BOOL volume_signed_flag,
VIO_Real volume_voxel_min,
VIO_Real volume_voxel_max,
VIO_BOOL create_volume_flag,
VIO_Volume *volume,
minc_input_options *options,
volume_input_struct *input_info )
{
VIO_Status status;
int d;
VIO_STR expanded_filename;
minc_input_options default_options;
status = VIO_OK;
if( options == (minc_input_options *) NULL )
{
set_default_minc_input_options( &default_options );
options = &default_options;
}
if( create_volume_flag || *volume == (VIO_Volume) NULL )
{
if( n_dimensions < 1 || n_dimensions > VIO_MAX_DIMENSIONS )
{
n_dimensions = VIO_MAX_DIMENSIONS;
}
if( dim_names == (VIO_STR *) NULL )
dim_names = get_default_dim_names( n_dimensions );
*volume = create_volume( n_dimensions, dim_names, volume_nc_data_type,
volume_signed_flag,
volume_voxel_min, volume_voxel_max );
}
else if( n_dimensions != get_volume_n_dimensions( *volume ) &&
volume_is_alloced( *volume ) )
{
free_volume_data( *volume );
}
expanded_filename = expand_filename( filename );
if (filename_extension_matches( expanded_filename, FREE_ENDING ) ) {
input_info->file_format = FREE_FORMAT;
}
#ifdef LIBMINC_NIFTI_SUPPORT
else if (filename_extension_matches( expanded_filename, "mgh" ) ||
filename_extension_matches( expanded_filename, "mgz" )
) {
input_info->file_format = MGH_FORMAT; /* FreeSurfer */
}
else if (filename_extension_matches( expanded_filename, "nii" ) ||
filename_extension_matches( expanded_filename, "hdr" )) {
input_info->file_format = NII_FORMAT; /* NIfTI-1 */
}
else if (filename_extension_matches( expanded_filename, "nhdr" ) ||
filename_extension_matches( expanded_filename, "nrrd" )) {
input_info->file_format = NRRD_FORMAT; /* NRRD */
}
#endif /*LIBMINC_NIFTI_SUPPORT*/
else {
#if defined(HAVE_MINC1) && defined(HAVE_MINC2)
if(options->prefer_minc2_api) {
#endif
#if defined(HAVE_MINC2)
input_info->file_format = MNC2_FORMAT;
#endif
#if defined(HAVE_MINC1) && defined(HAVE_MINC2)
} else {
#endif
#ifdef HAVE_MINC1
input_info->file_format = MNC_FORMAT;
#endif
#if defined(HAVE_MINC1) && defined(HAVE_MINC2)
}
#endif
}
switch( input_info->file_format )
{
#ifdef HAVE_MINC1
case MNC_FORMAT:
if( !file_exists( expanded_filename ) )
{
file_exists_as_compressed( expanded_filename,
&expanded_filename );
}
input_info->minc_file = initialize_minc_input( expanded_filename,
*volume, options );
if( input_info->minc_file == (Minc_file) NULL )
status = VIO_ERROR;
else
{
for_less( d, 0, VIO_MAX_DIMENSIONS )
input_info->axis_index_from_file[d] = d;
}
break;
#endif /*HAVE_MINC1*/
#ifdef HAVE_MINC2
case MNC2_FORMAT:
input_info->minc_file = initialize_minc2_input( expanded_filename,
*volume, options );
if( input_info->minc_file == (Minc_file) NULL )
status = VIO_ERROR;
else
{
for_less( d, 0, VIO_MAX_DIMENSIONS )
input_info->axis_index_from_file[d] = d;
}
break;
#endif /*HAVE_MINC2*/
case FREE_FORMAT:
status = initialize_free_format_input( expanded_filename,
*volume, input_info );
break;
#ifdef LIBMINC_NIFTI_SUPPORT
case MGH_FORMAT:
status = initialize_mgh_format_input( expanded_filename,
*volume, input_info );
break;
case NII_FORMAT:
status = initialize_nifti_format_input( expanded_filename,
*volume, input_info );
break;
case NRRD_FORMAT:
status = initialize_nrrd_format_input( expanded_filename,
*volume, input_info );
break;
#endif /*LIBMINC_NIFTI_SUPPORT*/
default:
/*Unsupported file format*/
status = VIO_ERROR;
break;
}
if( status != VIO_OK && create_volume_flag )
delete_volume( *volume );
delete_string( expanded_filename );
return( status );
}
void normalize_data_to_match_target(VIO_Volume d1, VIO_Volume m1, VIO_Real thresh1,
VIO_Volume d2, VIO_Volume m2, VIO_Real thresh2,
Arg_Data *globals)
{
VectorR
vector_step;
PointR
starting_position,
slice,
row,
col,
pos2,
voxel;
double
tx,ty,tz;
int
i,j,k,
r,c,s;
VIO_Real
min_range, max_range,
data_vox, data_val,
value1, value2;
VIO_Real
t1,t2, /* temporary threshold values */
s1,s2,s3; /* to store the sums for f1,f2,f3 */
float
*ratios,
result; /* the result */
int
sizes[VIO_MAX_DIMENSIONS],ratios_size,count1,count2;
VIO_Volume
vol;
VIO_progress_struct
progress;
VIO_Data_types
data_type;
set_feature_value_threshold(d1,d2,
&thresh1, &thresh2,
&t1, &t2);
if (globals->flags.debug) {
print ("In normalize_data_to_match_target, thresh = %10.3f %10.3f\n",t1,t2) ;
}
ratios_size = globals->count[ROW_IND] * globals->count[COL_IND] * globals->count[SLICE_IND];
ALLOC(ratios, ratios_size);
fill_Point( starting_position, globals->start[VIO_X], globals->start[VIO_Y], globals->start[VIO_Z]);
s1 = s2 = s3 = 0.0;
count1 = count2 = 0;
for(s=0; s<=globals->count[SLICE_IND]; s++) {
SCALE_VECTOR( vector_step, globals->directions[SLICE_IND], s);
ADD_POINT_VECTOR( slice, starting_position, vector_step );
for(r=0; r<=globals->count[ROW_IND]; r++) {
SCALE_VECTOR( vector_step, globals->directions[ROW_IND], r);
ADD_POINT_VECTOR( row, slice, vector_step );
SCALE_POINT( col, row, 1.0); /* init first col position */
for(c=0; c<=globals->count[COL_IND]; c++) {
convert_3D_world_to_voxel(d1, Point_x(col), Point_y(col), Point_z(col), &tx, &ty, &tz);
fill_Point( voxel, tx, ty, tz ); /* build the voxel POINT */
if (point_not_masked(m1, Point_x(col), Point_y(col), Point_z(col))) {
value1 = get_value_of_point_in_volume( Point_x(col), Point_y(col), Point_z(col), d1);
if ( value1 > t1 ) {
count1++;
DO_TRANSFORM(pos2, globals->trans_info.transformation, col);
convert_3D_world_to_voxel(d2, Point_x(pos2), Point_y(pos2), Point_z(pos2), &tx, &ty, &tz);
fill_Point( voxel, tx, ty, tz ); /* build the voxel POINT */
if (point_not_masked(m2, Point_x(pos2), Point_y(pos2), Point_z(pos2))) {
value2 = get_value_of_point_in_volume( Point_x(pos2), Point_y(pos2), Point_z(pos2), d2);
if ( (value2 > t2) &&
((value2 < -1e-15) || (value2 > 1e-15)) ) {
ratios[count2++] = value1 / value2 ;
s1 += value1*value2;
s2 += value1*value1;
s3 += value2*value2;
} /* if voxel in d2 */
} /* if point in mask volume two */
} /* if voxel in d1 */
} /* if point in mask volume one */
ADD_POINT_VECTOR( col, col, globals->directions[COL_IND] );
} /* for c */
} /* for r */
} /* for s */
if (count2 > 0) {
if (globals->flags.debug) (void)print ("Starting qsort of ratios...");
qs_list (ratios,0,count2);
if (globals->flags.debug) (void)print ("Done.\n");
result = ratios[ (int)(count2/2) ]; /* the median value */
if (globals->flags.debug) (void)print ("Normalization: %7d %7d -> %10.8f\n",count1,count2,result);
if ( fabs(result) < 1e-15) {
print_error_and_line_num("Error computing normalization ratio `%f'.",__FILE__, __LINE__, result);
}
else {
data_type = get_volume_data_type(d1);
switch( data_type ) {
case SIGNED_BYTE:
case UNSIGNED_BYTE:
case SIGNED_SHORT:
case UNSIGNED_SHORT:
/* build temporary working volume */
vol = copy_volume_definition_no_alloc(d1, NC_UNSPECIFIED, FALSE, 0.0, 0.0);
get_volume_minimum_maximum_real_value(d1, &min_range, &max_range);
min_range /= result;
max_range /= result;
set_volume_real_range(vol, min_range, max_range);
get_volume_sizes(d1, sizes);
initialize_progress_report(&progress, FALSE, sizes[0]*sizes[1]*sizes[2] + 1,
"Normalizing source data" );
count1 = 0;
/* reset values in the data volume */
for(i=0; i<sizes[0]; i++)
for(j=0; j<sizes[1]; j++) {
count1++;
update_progress_report( &progress, count1);
for(k=0; k<sizes[2]; k++) {
GET_VOXEL_3D( data_vox, d1, i, j, k );
data_val = CONVERT_VOXEL_TO_VALUE(d1, data_vox);
data_val /= result;
data_vox = CONVERT_VALUE_TO_VOXEL( vol, data_val);
SET_VOXEL_3D( d1 , i, j, k, data_vox );
}
}
terminate_progress_report( &progress );
set_volume_real_range(d1, min_range, max_range);
if (globals->flags.debug) (void)print ("After normalization min,max, thresh = %f %f %f\n",
min_range, max_range, t1/result);
delete_volume(vol);
break;
default: /* then volume should be either float or double */
get_volume_sizes(d1, sizes);
initialize_progress_report(&progress, FALSE, sizes[0]*sizes[1]*sizes[2] + 1,
"Normalizing source data" );
count1 = 0;
/* nomalize the values in the data volume */
for(i=0; i<sizes[0]; i++)
for(j=0; j<sizes[1]; j++) {
count1++;
update_progress_report( &progress, count1);
for(k=0; k<sizes[2]; k++) { /* it should be possible to directly stream through the voxels, without indexing... */
GET_VOXEL_3D( data_vox, d1, i, j, k );
data_val = CONVERT_VOXEL_TO_VALUE(d1, data_vox);
data_val /= result;
data_vox = CONVERT_VALUE_TO_VOXEL( d1, data_val);
SET_VOXEL_3D( d1 , i, j, k, data_vox );
}
}
terminate_progress_report( &progress );
}
}
}
FREE(ratios);
}
void make_zscore_volume(VIO_Volume d1, VIO_Volume m1,
VIO_Real *threshold)
{
unsigned long
count;
int
stat_count,
sizes[VIO_MAX_DIMENSIONS],
s,r,c;
VIO_Real
wx,wy,wz,
valid_min_dvoxel, valid_max_dvoxel,
min,max,
sum, sum2, mean, var, std,
data_vox,data_val,
thick[VIO_MAX_DIMENSIONS];
PointR
voxel;
VIO_Volume
vol;
VIO_progress_struct
progress;
/* get default information from data and mask */
/* build temporary working volume */
vol = copy_volume_definition(d1, NC_UNSPECIFIED, FALSE, 0.0, 0.0);
set_volume_real_range(vol, MIN_ZRANGE, MAX_ZRANGE);
get_volume_sizes(d1, sizes);
get_volume_separations(d1, thick);
get_volume_voxel_range(d1, &valid_min_dvoxel, &valid_max_dvoxel);
/* initialize counters and sums */
count = 0;
sum = 0.0;
sum2 = 0.0;
min = 1e38;
max = -1e38;
stat_count = 0;
initialize_progress_report(&progress, FALSE, sizes[0]*sizes[1]*sizes[2] + 1,
"Tally stats" );
/* do first pass, to get mean and std */
for(s=0; s<sizes[0]; s++) {
for(r=0; r<sizes[1]; r++) {
for(c=0; c<sizes[2]; c++) {
stat_count++;
update_progress_report( &progress, stat_count);
convert_3D_voxel_to_world(d1, (VIO_Real)s, (VIO_Real)r, (VIO_Real)c, &wx, &wy, &wz);
if (m1 != NULL) {
convert_3D_world_to_voxel(m1, wx, wy, wz, &Point_x(voxel), &Point_y(voxel), &Point_z(voxel));
}
else {
wx = 0.0; wy = 0.0; wz = 0.0;
}
if (point_not_masked(m1, wx,wy,wz)) {
GET_VOXEL_3D( data_vox, d1 , s, r, c );
if (data_vox >= valid_min_dvoxel && data_vox <= valid_max_dvoxel) {
data_val = CONVERT_VOXEL_TO_VALUE(d1, data_vox);
if (data_val > *threshold) {
sum += data_val;
sum2 += data_val*data_val;
count++;
if (data_val < min)
min = data_val;
else
if (data_val > max)
max = data_val;
}
}
}
}
}
}
terminate_progress_report( &progress );
stat_count = 0;
initialize_progress_report(&progress, FALSE, sizes[0]*sizes[1]*sizes[2] + 1,
"Zscore convert" );
/* calc mean and std */
mean = sum / (float)count;
var = ((float)count*sum2 - sum*sum) / ((float)count*((float)count-1));
std = sqrt(var);
min = 1e38;
max = -1e38;
/* replace the voxel values */
for(s=0; s<sizes[0]; s++) {
for(r=0; r<sizes[1]; r++) {
for(c=0; c<sizes[2]; c++) {
stat_count++;
update_progress_report( &progress, stat_count);
GET_VOXEL_3D( data_vox, d1, s, r, c );
if (data_vox >= valid_min_dvoxel && data_vox <= valid_max_dvoxel) {
data_val = CONVERT_VOXEL_TO_VALUE(d1, data_vox);
if (data_val > *threshold) {
/* instead of
data_val = CONVERT_VALUE_TO_VOXEL(d1, data_vox);
i will use
data_val = CONVERT_VALUE_TO_VOXEL(d1, vol);
since the values in vol are changed with respect to the
new z-score volume */
data_val = (data_val - mean) / std;
if (data_val< MIN_ZRANGE) data_val = MIN_ZRANGE;
if (data_val> MAX_ZRANGE) data_val = MAX_ZRANGE;
data_vox = CONVERT_VALUE_TO_VOXEL( vol, data_val);
if (data_val < min) {
min = data_val;
}
else {
if (data_val > max)
max = data_val;
}
}
else
data_vox = -DBL_MAX; /* should be fill_value! */
SET_VOXEL_3D( d1 , s, r, c, data_vox );
}
}
}
}
terminate_progress_report( &progress );
set_volume_real_range(d1, MIN_ZRANGE, MAX_ZRANGE); /* reset the data volume's range */
*threshold = (*threshold - mean) / std;
delete_volume(vol);
}
/* 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);
}
/* resulting groups are sorted WRT size */
Volume *group_kernel(Kernel * K, Volume * vol, double bg)
{
int x, y, z;
int sizes[MAX_VAR_DIMS];
progress_struct progress;
Volume tmp_vol;
Kernel *k1, *k2;
unsigned int *equiv;
unsigned int *counts;
unsigned int *trans;
unsigned int neighbours[K->nelems];
/* counters */
unsigned int c;
unsigned int value;
unsigned int group_idx; /* label for the next group */
unsigned int num_groups;
unsigned int min_label;
unsigned int curr_label;
unsigned int prev_label;
unsigned int num_matches;
/* structure for group data */
Group_info *group_data;
/* split the Kernel into forward and backwards kernels */
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, "Group 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], "Groups");
/* copy and then zero out the original volume */
tmp_vol = copy_volume(*vol);
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);
}
}
}
/* pass 1 - forward direction (we assume a symmetric kernel) */
/* our first group is given the label 1 */
group_idx = 1;
/* initialise the equiv and counts arrays */
SET_ARRAY_SIZE(equiv, 0, group_idx, 500);
equiv[0] = 0;
SET_ARRAY_SIZE(counts, 0, group_idx, 500);
counts[0] = 0;
for(z = -k1->pre_pad[2]; z < sizes[0] - k1->post_pad[2]; z++){
for(y = -k1->pre_pad[1]; y < sizes[1] - k1->post_pad[1]; y++){
for(x = -k1->pre_pad[0]; x < sizes[2] - k1->post_pad[0]; x++){
if(get_volume_voxel_value(tmp_vol, z, y, x, 0, 0) != bg){
/* search this voxels neighbours */
num_matches = 0;
min_label = INT_MAX;
for(c = 0; c < k1->nelems; c++){
value = (unsigned int)get_volume_voxel_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]);
if(value != 0){
if(value < min_label){
min_label = value;
}
neighbours[num_matches] = value;
num_matches++;
}
}
switch (num_matches){
case 0:
/* no neighbours, make a new label and increment */
set_volume_voxel_value(*vol, z, y, x, 0, 0, (Real) group_idx);
SET_ARRAY_SIZE(equiv, group_idx, group_idx + 1, 500);
equiv[group_idx] = group_idx;
SET_ARRAY_SIZE(counts, group_idx, group_idx + 1, 500);
counts[group_idx] = 1;
group_idx++;
break;
case 1:
/* only one neighbour, no equivalences needed */
set_volume_voxel_value(*vol, z, y, x, 0, 0, (Real) min_label);
counts[min_label]++;
break;
default:
/* more than one neighbour */
/* first sort the neighbours array */
qsort(&neighbours[0], (size_t) num_matches, sizeof(unsigned int),
&compare_ints);
/* find the minimum possible label for this voxel, */
/* this is done by descending through each neighbours */
/* equivalences until an equivalence equal to itself */
/* is found */
prev_label = -1;
for(c = 0; c < num_matches; c++){
curr_label = neighbours[c];
/* recurse this label if we haven't yet */
if(curr_label != prev_label){
while(equiv[curr_label] != equiv[equiv[curr_label]]){
curr_label = equiv[curr_label];
}
/* check against the current minimum value */
if(equiv[curr_label] < min_label){
min_label = equiv[curr_label];
}
}
prev_label = neighbours[c];
}
/* repeat, setting equivalences to the min_label */
prev_label = -1;
for(c = 0; c < num_matches; c++){
curr_label = neighbours[c];
if(curr_label != prev_label){
while(equiv[curr_label] != equiv[equiv[curr_label]]){
curr_label = equiv[curr_label];
equiv[curr_label] = min_label;
}
/* set the label itself */
if(equiv[neighbours[c]] != min_label){
equiv[neighbours[c]] = min_label;
}
}
prev_label = neighbours[c];
}
/* finally set the voxel in question to the minimum value */
set_volume_voxel_value(*vol, z, y, x, 0, 0, (Real) min_label);
counts[min_label]++;
break;
} /* end case */
}
}
}
update_progress_report(&progress, z + 1);
}
terminate_progress_report(&progress);
/* reduce the equiv and counts array */
num_groups = 0;
for(c = 0; c < group_idx; c++){
/* if this equivalence is not resolved yet */
if(c != equiv[c]){
/* find the min label value */
min_label = equiv[c];
while(min_label != equiv[min_label]){
min_label = equiv[min_label];
}
/* update the label and its counters */
equiv[c] = min_label;
counts[min_label] += counts[c];
counts[c] = 0;
}
else {
num_groups++;
}
}
/* Allocate space for the array of groups */
group_data = (Group_info *) malloc(num_groups * sizeof(Group_info));
num_groups = 0;
for(c = 0; c < group_idx; c++){
if(counts[c] > 0){
/* allocate space for this element */
group_data[num_groups] = malloc(sizeof(group_info_struct));
group_data[num_groups]->orig_label = equiv[c];
group_data[num_groups]->count = counts[c];
num_groups++;
}
}
/* sort the groups by the count size */
if(verbose){
fprintf(stdout, "Found %d unique groups from %d, sorting...\n", num_groups,
group_idx);
}
qsort(group_data, num_groups, sizeof(Group_info), &compare_groups);
/* set up the transpose array */
trans = (unsigned int *)malloc(sizeof(unsigned int) * group_idx);
for(c = 0; c < num_groups; c++){
trans[group_data[c]->orig_label] = c + 1; /* +1 to bump past 0 */
}
/* pass 2 - resolve equivalences in the output data */
if(verbose){
fprintf(stdout, "Resolving equivalences...\n");
}
for(z = sizes[0]; z--;){
for(y = sizes[1]; y--;){
for(x = sizes[2]; x--;){
value = (unsigned int)get_volume_voxel_value(*vol, z, y, x, 0, 0);
if(value != 0){
value = trans[equiv[value]];
set_volume_voxel_value(*vol, z, y, x, 0, 0, (Real) value);
}
}
}
}
/* tidy up */
delete_volume(tmp_vol);
for(c = 0; c < num_groups; c++){
free(group_data[c]);
}
free(group_data);
free(trans);
free(k1);
free(k2);
return (vol);
}
/* perform a median kernel operation on a volume */
Volume *median_dilation_kernel(Kernel * K, Volume * vol)
{
int x, y, z, c, i;
int sizes[MAX_VAR_DIMS];
progress_struct progress;
Volume tmp_vol;
double value;
unsigned int kvalue;
unsigned int neighbours[K->nelems];
if(verbose){
fprintf(stdout, "Median Dilation kernel\n");
}
get_volume_sizes(*vol, sizes);
initialize_progress_report(&progress, FALSE, sizes[2], "Median Dilation");
/* 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++){
/* only modify background voxels */
value = get_volume_voxel_value(tmp_vol, z, y, x, 0, 0);
if(value == 0.0){
i = 0;
for(c = 0; c < K->nelems; c++){
kvalue = (unsigned int)get_volume_voxel_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]);
if(kvalue != 0){
neighbours[i] = kvalue;
i++;
}
}
/* only run this for adjacent voxels */
if(i > 0){
/* find the median of our little array */
qsort(&neighbours[0], (size_t) i, sizeof(unsigned int), &compare_ints);
/* store the median value */
set_volume_voxel_value(*vol, z, y, x, 0, 0,
(double)neighbours[(int)floor((i - 1) / 2)]);
}
}
/* else just copy the original value over */
else {
set_volume_voxel_value(*vol, z, y, x, 0, 0, value);
}
}
}
update_progress_report(&progress, z + 1);
}
delete_volume(tmp_vol);
terminate_progress_report(&progress);
return (vol);
}
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[] )
{
Volume volume;
STRING input_filename, output_filename;
int n_slices, n_components;
pixels_struct *pixels;
nc_type vol_type;
BOOLEAN two_d_allowed;
initialize_argument_processing( argc, argv );
if( !get_string_argument( NULL, &output_filename ) ||
!get_int_argument( 0, &n_components ) )
{
print( "Usage: %s output.mnc 3|4|23|24 input1.rgb input2.rgb ...\n", argv[0] );
return( 1 );
}
if( n_components > 100 )
{
vol_type = NC_FLOAT;
n_components -= 100;
}
else
vol_type = NC_BYTE;
if( n_components > 20 )
{
two_d_allowed = TRUE;
n_components -= 20;
}
else
{
two_d_allowed = FALSE;
}
n_slices = 0;
pixels = NULL;
while( get_string_argument( "", &input_filename ) )
{
SET_ARRAY_SIZE( pixels, n_slices, n_slices+1, DEFAULT_CHUNK_SIZE );
if( input_rgb_file( input_filename, &pixels[n_slices] ) != OK )
return( 1 );
++n_slices;
}
volume = convert_pixels_to_volume( n_components, n_slices,
(two_d_allowed && n_slices == 1) ? 2 : 3,
vol_type, pixels );
if( volume != NULL )
{
(void) output_volume( output_filename, NC_UNSPECIFIED, FALSE,
0.0, 0.0,
volume, "Converted from pixels",
(minc_output_options *) NULL );
delete_volume( volume );
}
return( 0 );
}
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);
}
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;
}