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;
}
int write_volume(char *name, VIO_Volume vol, float *data){
int i,j,k,index,sizes[5];
float min=FLT_MAX,max=FLT_MIN;
fprintf(stderr,"Writing %s\n",name);
get_volume_sizes(vol,sizes);
for (i=0;i<sizes[0];i++){
for (j=0;j<sizes[1];j++){
for (k=0;k<sizes[2];k++){
index=i*sizes[2]*sizes[1] + j*sizes[2] + k;
min=MIN(min,data[index]);
max=MAX(max,data[index]);
}
}
}
set_volume_real_range(vol,min,max);
get_volume(data, vol, sizes);
output_volume( name, NC_FLOAT,FALSE,min,max,vol,NULL, (minc_output_options *)NULL);
return STATUS_OK;
}
void save_volume(VIO_Volume d, char *filename)
{
VIO_Status status;
status = output_volume(filename,NC_UNSPECIFIED, FALSE, 0.0, 0.0, d, (char *)NULL,
(minc_output_options *)NULL);
if (status != OK)
print_error_and_line_num("problems writing volume `%s'.",__FILE__, __LINE__, filename);
}
int main(int argc, char *argv[]) {
int v1, v2, v3, v4;
int sizes[VIO_MAX_DIMENSIONS], grid_sizes[4];
int n_concat_transforms, i;
VIO_STR arg_string;
char *input_volume_name;
char *input_xfm;
VIO_STR outfile;
VIO_Real w1, w2, w3;
VIO_Real nw1, nw2, nw3;
VIO_Real original[3], transformed[3];
VIO_Real value;
VIO_Real cosine[3];
VIO_Real original_separation[3], grid_separation[4];
VIO_Real original_starts[3], grid_starts[4];
VIO_Volume eval_volume, new_grid;
VIO_General_transform xfm, *voxel_to_world;
VIO_STR *dimnames, dimnames_grid[4];
VIO_progress_struct progress;
arg_string = time_stamp(argc, argv);
/* Check arguments */
if(ParseArgv(&argc, argv, argTable, 0) || (argc != 4)){
fprintf(stderr, "\nUsage: %s [options] input.mnc input.xfm output_grid.mnc\n", argv[0]);
fprintf(stderr, " %s -help\n\n", argv[0]);
exit(EXIT_FAILURE);
}
input_volume_name = argv[1];
input_xfm = argv[2];
outfile = argv[3];
/* check for the infile and outfile */
if(access(input_volume_name, F_OK) != 0){
fprintf(stderr, "%s: Couldn't find %s\n\n", argv[0], input_volume_name);
exit(EXIT_FAILURE);
}
if(access(input_xfm, F_OK) != 0) {
fprintf(stderr, "%s: Couldn't find %s\n\n", argv[0], input_xfm);
exit(EXIT_FAILURE);
}
if(access(outfile, F_OK) == 0 && !clobber){
fprintf(stderr, "%s: %s exists! (use -clobber to overwrite)\n\n", argv[0], outfile);
exit(EXIT_FAILURE);
}
/*--- input the volume */
/*
if( input_volume( input_volume_name, 3, NULL, MI_ORIGINAL_TYPE,
FALSE, 0.0, 0.0, TRUE, &eval_volume,(minc_input_options *) NULL ) != OK )
return( 1 );
*/
if (input_volume_header_only( input_volume_name, 3, NULL, &eval_volume,(minc_input_options *) NULL ) != VIO_OK ) {
return( 1 );
}
/* get information about the volume */
get_volume_sizes( eval_volume, sizes );
voxel_to_world = get_voxel_to_world_transform(eval_volume);
dimnames = get_volume_dimension_names(eval_volume);
get_volume_separations(eval_volume, original_separation);
get_volume_starts(eval_volume, original_starts);
/* create new 4D volume, last three dims same as other volume,
first dimension being the vector dimension. */
for(i=1; i < 4; i++) {
dimnames_grid[i] = dimnames[i-1];
grid_separation[i] = original_separation[i-1];
grid_sizes[i] = sizes[i-1];
grid_starts[i] = original_starts[i-1];
}
dimnames_grid[0] = "vector_dimension";
grid_sizes[0] = 3;
grid_separation[0] = 1;
grid_starts[0] = 0;
new_grid = create_volume(4, dimnames_grid, NC_SHORT, FALSE, 0.0, 0.0);
//set_voxel_to_world_transform(new_grid, voxel_to_world);
// initialize the new grid volume, otherwise the output will be
// garbage...
set_volume_real_range(new_grid, -100, 100);
set_volume_sizes(new_grid, grid_sizes);
set_volume_separations(new_grid, grid_separation);
set_volume_starts(new_grid, grid_starts);
/*
for (i=0; i < 3; i++) {
get_volume_direction_cosine(eval_volume, i, cosine);
set_volume_direction_cosine(new_grid, i+1, cosine);
}
*/
alloc_volume_data(new_grid);
/* get the transforms */
if( input_transform_file( input_xfm, &xfm ) != VIO_OK )
return( 1 );
/* see how many transforms will be applied */
n_concat_transforms = get_n_concated_transforms( &xfm );
printf("Number of transforms to be applied: %d\n", n_concat_transforms);
initialize_progress_report(&progress, FALSE, sizes[0], "Processing");
/* evaluate the transform at every voxel, keep the displacement
in the three cardinal directions */
for( v1 = 0; v1 < sizes[0]; ++v1 ) {
update_progress_report(&progress, v1 + 1);
for( v2 = 0; v2 < sizes[1]; ++v2 ) {
for( v3 = 0; v3 < sizes[2]; ++v3 ) {
convert_3D_voxel_to_world(eval_volume,
v1, v2, v3,
&original[0], &original[1], &original[2]);
general_transform_point(&xfm,
original[0], original[1], original[2],
&transformed[0], &transformed[1], &transformed[2]);
for(i=0; i < 3; i++) {
value = transformed[i] - original[i];
set_volume_real_value(new_grid, i, v1, v2, v3, 0, value);
}
}
}
}
terminate_progress_report(&progress);
printf("Outputting volume.\n");
output_volume(outfile, MI_ORIGINAL_TYPE, TRUE, 0.0, 0.0, new_grid, arg_string, NULL);
return(0);
}
int main(int argc, char *argv[])
{
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);
}
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 );
}
