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[])
{
int
count,
i,j,k, p,r,s, flag,
sizes1[3],sizes2[3], sizes3[3];
VIO_Real
thresh;
VIO_Real
mean1, std1, mean2, std2,
corr, v1, v2, v3, s1, s2, s12,
u,v,w, x,y,z;
VIO_Status status;
VIO_Volume
data1, data2, mask;
char *f1, *f2, *mf;
if (argc<4) {
print ("usage: xcorr_vol.c vol1.mnc vol2.mnc threshold [mask.mnc]\n");
exit(EXIT_FAILURE);
}
prog_name = argv[0];
f1 = argv[1];
f2 = argv[2];
thresh = atof(argv[3]);
if (argc==5)
mf = argv[4];
status = input_volume(f1, 3, default_dim_names, NC_UNSPECIFIED, FALSE, 0.0,0.0,
TRUE, &data1, (minc_input_options *)NULL);
if (status!=VIO_OK) {
print ("Error reading %s.\n",f1);
exit(EXIT_FAILURE);
}
status = input_volume(f2, 3, default_dim_names, NC_UNSPECIFIED, FALSE, 0.0,0.0,
TRUE, &data2, (minc_input_options *)NULL);
if (status!=VIO_OK) {
print ("Error reading %s.\n",f2);
exit(EXIT_FAILURE);
}
if (argc==5) {
status = input_volume(mf, 3, default_dim_names, NC_UNSPECIFIED, FALSE, 0.0,0.0,
TRUE, &mask, (minc_input_options *)NULL);
if (status!=VIO_OK) {
print ("Error reading %s.\n",mf);
exit(EXIT_FAILURE);
}
get_volume_sizes(mask,sizes3);
}
else
mask = (VIO_Volume)NULL;
get_volume_sizes(data1,sizes1);
get_volume_sizes(data2,sizes2);
if (sizes1[0] != sizes2[0] || sizes1[1] != sizes2[1] || sizes1[2] != sizes2[2]) {
print ("Size mismatch between %s and %s.\n",f1,f2);
print ("%d,%d,%d != %d,%d,%d\n",
sizes1[0],sizes1[1],sizes1[2],
sizes2[0],sizes2[1],sizes2[2]);
exit(EXIT_FAILURE);
}
get_zscore_values(data1, mask, thresh, &mean1, &std1);
get_zscore_values(data2, mask, thresh, &mean2, &std2);
if (std1==0.0 || std2==0.0) {
print ("No standard deviation in one of %s and %s.\n",f1,f2);
exit(EXIT_FAILURE);
}
count = 0;
s1 = s2 = s12 = 0.0;
for(i=0; i<sizes1[0]; i++) {
for(j=0; j<sizes1[1]; j++) {
for(k=0; k<sizes1[2]; k++) {
flag = TRUE;
if (mask != NULL) {
convert_3D_voxel_to_world(data1, i,j,k, &x, &y, &z);
convert_3D_world_to_voxel(mask, x,y,z, &u, &v, &w);
p = VIO_ROUND(u);
r = VIO_ROUND(v);
s = VIO_ROUND(w);
if (p>=0 && p<sizes3[0] &&
r>=0 && r<sizes3[1] &&
s>=0 && s<sizes3[2]) {
GET_VALUE_3D( v3 , mask, p, r, s);
if (v3 < 0.5)
flag = FALSE;
}
else
flag = FALSE;
}
if (flag ) {
GET_VALUE_3D( v1 , data1, i, j, k);
GET_VALUE_3D( v2 , data2, i, j, k);
v1 = (v1 - mean1) / std1;
v2 = (v2 - mean2) / std2;
v1 = v1 - v2;
s12 += fabs(v1);
count++;
}
}
}
}
if (count==0) {
exit(EXIT_FAILURE);
print ("No masked voxels\n");
}
else {
corr = s12 / count;
print ("%15.12f\n",corr);
exit(EXIT_SUCCESS);
}
}
