void get_volume_XYZV_indices(VIO_Volume data, int xyzv[]){
int
axis, i, vol_dims;
char
**data_dim_names;
vol_dims = get_volume_n_dimensions(data);
data_dim_names = get_volume_dimension_names(data);
for(i=0; i<VIO_N_DIMENSIONS+1; i++) xyzv[i] = -1;
for(i=0; i<vol_dims; i++) {
if (convert_dim_name_to_spatial_axis(data_dim_names[i], &axis )) {
xyzv[axis] = i;
}
else { /* not a spatial axis */
xyzv[VIO_Z+1] = i;
}
}
delete_dimension_names(data, data_dim_names);
}
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 );
}
/* ----------------------------- 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;
}
