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 );
}
int main(int argc, char *argv[])
{
Volume volume;
volume_input_struct input_info;
char *filename;
double v0, v1, v2, wx, wy, wz;
static char *dim_names[] =
{ANY_SPATIAL_DIMENSION, ANY_SPATIAL_DIMENSION, ANY_SPATIAL_DIMENSION};
milog_init(argv[0]);
/* Check arguments */
if (ParseArgv(&argc, argv, argTable, 0) || argc != 5) {
(void) fprintf(stderr,
"Usage: %s <image file> <voxel index 1 (slowest)> <index 2> <index 3>\n",
argv[0]);
exit(EXIT_FAILURE);
}
filename = argv[1];
v0 = atof(argv[2]);
v1 = atof(argv[3]);
v2 = atof(argv[4]);
/* Open the image file */
set_print_function(print_to_stderr);
if (start_volume_input(filename, 3, dim_names, MI_ORIGINAL_TYPE, TRUE,
0.0, 0.0, TRUE, &volume, NULL, &input_info) != OK) {
(void) fprintf(stderr, "Error opening file %s for input.\n",
filename);
exit(EXIT_FAILURE);
}
/* Convert the voxel to world coordinates */
convert_3D_voxel_to_world(volume, v0, v1, v2, &wx, &wy, &wz);
/* Write out the result */
(void) printf("%.20g %.20g %.20g\n", wx, wy, wz);
exit(EXIT_SUCCESS);
}
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);
}
/* ----------------------------- 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;
}
