VIO_BOOL vol_to_cov(VIO_Volume d1, VIO_Volume m1, float centroid[4], float covar[4][4], double *step)
{
VectorR
vector_step,
slice_step,
row_step,
col_step;
PointR
starting_offset,
starting_origin,
starting_position,
slice,
row,
col,
voxel;
VIO_Real
tx,ty,tz;
int
i,r,c,s,
limits[VOL_NDIMS];
float
t,
sxx,syy,szz,
sxy,syz,sxz,
sx,sy,sz,si;
VIO_Real
thickness[3];
int
sizes[3];
VIO_Real
true_value;
get_volume_separations(d1, thickness);
get_volume_sizes(d1, sizes);
/* build sampling lattice info */
for(i=0; i<3; i++) {
step[i] *= thickness[i] / fabs( thickness[i]);
}
fill_Vector( col_step, step[COL_IND], 0.0, 0.0 );
fill_Vector( row_step, 0.0, step[ROW_IND], 0.0 );
fill_Vector( slice_step, 0.0, 0.0, step[SLICE_IND] );
convert_3D_voxel_to_world(d1, 0.0, 0.0, 0.0, &tx, &ty, &tz);
fill_Point( starting_origin, tx, ty, tz);
for(i=0; i<3; i++) { /* for each dim, get # of steps in that direction,
and set starting offset */
t = sizes[i] * thickness[i] / step[i];
limits[i] = abs( t );
Point_coord( starting_offset, (i) ) =
( (sizes[i]-1)*thickness[i] - (limits[i] * step[i] ) ) / 2.0;
}
ADD_POINTS( starting_position, starting_origin, starting_offset ); /* */
/* calculate centroids first */
sx = 0.0;
sy = 0.0;
sz = 0.0;
si = 0.0;
for(s=0; s<=limits[SLICE_IND]; s++) {
SCALE_VECTOR( vector_step, slice_step, s);
ADD_POINT_VECTOR( slice, starting_position, vector_step );
for(r=0; r<=limits[ROW_IND]; r++) {
SCALE_VECTOR( vector_step, row_step, r);
ADD_POINT_VECTOR( row, slice, vector_step );
SCALE_POINT( col, row, 1.0); /* init first col position */
for(c=0; c<=limits[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))) {
if (INTERPOLATE_TRUE_VALUE( d1, &voxel, &true_value )) {
sx += Point_x(col) * true_value;
sy += Point_y(col) * true_value;
sz += Point_z(col) * true_value;
si += true_value;
}
/* else requested voxel is just outside volume., so ignore it */
}
ADD_POINT_VECTOR( col, col, col_step );
}
}
}
if (si!=0.0) {
centroid[1] = sx/ si;
centroid[2] = sy/ si;
centroid[3] = sz/ si;
sxx = syy = szz = 0.0;
sxy = syz = sxz = 0.0;
/* now calculate variances and co-variances */
for(s=0; s<=limits[VIO_Z]; s++) {
SCALE_VECTOR( vector_step, slice_step, s);
ADD_POINT_VECTOR( slice, starting_position, vector_step );
for(r=0; r<=limits[VIO_Y]; r++) {
SCALE_VECTOR( vector_step, row_step, r);
ADD_POINT_VECTOR( row, slice, vector_step );
SCALE_POINT( col, row, 1.0); /* init first col position */
for(c=0; c<=limits[VIO_X]; 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))) {
if (INTERPOLATE_TRUE_VALUE( d1, &voxel, &true_value )) {
sxx += (Point_x( col )-centroid[1]) * (Point_x( col )-centroid[1]) * true_value;
syy += (Point_y( col )-centroid[2]) * (Point_y( col )-centroid[2]) * true_value;
szz += (Point_z( col )-centroid[3]) * (Point_z( col )-centroid[3]) * true_value;
sxy += (Point_x( col )-centroid[1]) * (Point_y( col )-centroid[2]) * true_value;
syz += (Point_y( col )-centroid[2]) * (Point_z( col )-centroid[3]) * true_value;
sxz += (Point_x( col )-centroid[1]) * (Point_z( col )-centroid[3]) * true_value;
}
/* else requested voxel is just outside volume., so ignore it */
}
ADD_POINT_VECTOR( col, col, col_step );
}
}
}
covar[1][1] = sxx/si; covar[1][2] = sxy/si; covar[1][3] = sxz/si;
covar[2][1] = sxy/si; covar[2][2] = syy/si; covar[2][3] = syz/si;
covar[3][1] = sxz/si; covar[3][2] = syz/si; covar[3][3] = szz/si;
return(TRUE);
}
else {
return(FALSE);
}
}
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);
}
void add_speckle_to_volume(VIO_Volume d1,
float speckle,
double *start, int *count, VectorR directions[])
{
VectorR
vector_step;
PointR
starting_position,
slice,
row,
col;
VIO_Real valid_min_voxel, valid_max_voxel;
double
tx,ty,tz,
voxel_value;
int
xi,yi,zi,
flip_flag,r,c,s;
flip_flag = FALSE;
get_volume_voxel_range(d1, &valid_min_voxel, &valid_max_voxel);
fill_Point( starting_position, start[0], start[1], start[2]);
for(s=0; s<count[SLICE_IND]; s++) {
SCALE_VECTOR( vector_step, directions[SLICE_IND], s);
ADD_POINT_VECTOR( slice, starting_position, vector_step );
for(r=0; r<count[ROW_IND]; r++) {
SCALE_VECTOR( vector_step, 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<count[COL_IND]; c++) {
convert_3D_world_to_voxel(d1, Point_x(col), Point_y(col), Point_z(col), &tx, &ty, &tz);
xi = (int)floor(tx + 0.5);
yi = (int)floor( ty + 0.5);
zi = (int)floor( tz + 0.5 );
GET_VOXEL_3D( voxel_value, d1 , xi, yi, zi );
if (voxel_value >= valid_min_voxel && voxel_value <= valid_max_voxel) {
if (flip_flag)
voxel_value = voxel_value * (1 + 0.01*speckle);
else
voxel_value = voxel_value * (1 - 0.01*speckle);
SET_VOXEL_3D( d1 , xi, yi, zi, voxel_value );
}
flip_flag = !flip_flag;
ADD_POINT_VECTOR( col, col, directions[COL_IND] );
}
}
}
}
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);
}
}
