std::vector<float> get_scaled_layer_mask(
std::vector<uint16_t> labels_,
std::set<uint16_t> segment_labels,
std::vector<int> & big_to_small,
int small_size){
std::vector<float> mask(small_size, 0.0f);
std::vector<int> mask_count(small_size, 0);
for(uint big_idx = 0; big_idx < big_to_small.size(); big_idx++){
int small_idx = big_to_small[big_idx];
mask_count[small_idx]++;
uint16_t label = labels_[big_idx];
if(segment_labels.find(label) != segment_labels.end())
mask[small_idx]++;
}
for(int i = 0; i < small_size; i++){
mask[i] = mask_count[i] == 0 ? 0.0f : mask[i]/mask_count[i];
}
return mask;
}
void CowichanSerial::winnow(IntMatrix matrix, BoolMatrix mask,
PointVector points) {
index_t r, c;
index_t len; // number of points
index_t stride; // selection stride
index_t i, j;
// count set cell
len = mask_count (mask, nr, nc);
if (len < n) {
not_enough_points();
}
WeightedPointVector weightedPoints = NULL;
try {
weightedPoints = NEW_VECTOR_SZ(WeightedPoint, len);
}
catch (...) {out_of_memory();}
// fill temporary vector
i = 0;
for (r = 0; r < nr; r++) {
for (c = 0; c < nc; c++) {
if (MATRIX_RECT(mask, r, c)) {
weightedPoints[i++] = WeightedPoint((real)c, (real)r,
MATRIX_RECT(matrix, r, c));
}
}
}
#ifdef SORT_TIME
INT64 start, end;
start = get_ticks ();
#endif
// sort
std::sort(weightedPoints, &weightedPoints[len]);
#ifdef SORT_TIME
end = get_ticks ();
#endif
// copy over points
stride = len / n;
for (i = n - 1, j = len - 1; i >= 0; i--, j -= stride) {
#ifdef WINNOW_OUTPUT
std::cout << weightedPoints[j].weight << "\n";
#endif
points[i] = weightedPoints[j].point;
}
#ifdef SORT_TIME
std::cout << "winnow sort: ";
print_elapsed_time(start, end);
std::cout << std::endl;
#endif
delete [] weightedPoints;
}
int main( int argc , char * argv[] )
{
int iarg , nvox=0 , iv,ii,cnum , verb=1 ;
int automask=1 ; /* allow masks as input 14 Jul 2010 [rickr] */
THD_3dim_dataset *aset , *bset ;
byte *amm , *bmm ; int naa , nbb , nabu,nabi , naout , nbout ;
float paout , pbout , xrat,yrat,zrat ;
float_triple axyz , bxyz ;
/*-- read command line arguments --*/
if( argc < 2 || strncmp(argv[1],"-help",5) == 0 ){
printf(
"Usage: 3dABoverlap [options] A B\n"
"Output (to screen) is a count of various things about how\n"
"the automasks of datasets A and B overlap or don't overlap.\n"
"\n"
"* Dataset B will be resampled to match dataset A, if necessary,\n"
" which will be slow if A is high resolution. In such a case,\n"
" you should only use one sub-brick from dataset B.\n"
" ++ The resampling of B is done before the automask is generated.\n"
"* The values output are labeled thusly:\n"
" #A = number of voxels in the A mask\n"
" #B = number of voxels in the B mask\n"
" #(A uni B) = number of voxels in the either or both masks (set union)\n"
" #(A int B) = number of voxels present in BOTH masks (set intesection)\n"
" #(A \\ B) = number of voxels in A mask that aren't in B mask\n"
" #(B \\ A) = number of voxels in B mask that arent' in A mask\n"
" %%(A \\ B) = percentage of voxels from A mask that aren't in B mask\n"
" %%(B \\ A) = percentage of voxels from B mask that aren't in A mask\n"
" Rx(B/A) = radius of gyration of B mask / A mask, in x direction\n"
" Ry(B/A) = radius of gyration of B mask / A mask, in y direction\n"
" Rz(B/A) = radius of gyration of B mask / A mask, in z direction\n"
"* If B is an EPI dataset sub-brick, and A is a skull stripped anatomical\n"
" dataset, then %%(B \\ A) might be useful for assessing if the EPI\n"
" brick B is grossly misaligned with respect to the anatomical brick A.\n"
"* The radius of gyration ratios might be useful for determining if one\n"
" dataset is grossly larger or smaller than the other.\n"
"\n"
"OPTIONS\n"
"-------\n"
" -no_automask = consider input datasets as masks\n"
" (automask does not work on mask datasets)\n"
" -quiet = be as quiet as possible (without being entirely mute)\n"
" -verb = print out some progress reports (to stderr)\n"
"\n"
"NOTES\n"
"-----\n"
" * If an input dataset is comprised of bytes and contains only one\n"
" sub-brick, then this program assumes it is already an automask-\n"
" generated dataset and the automask operation will be skipped.\n"
) ;
PRINT_COMPILE_DATE ; exit(0) ;
}
iarg = 1 ;
/*-- 20 Apr 2001: addto the arglist, if user wants to [RWCox] --*/
/* check options */
while( iarg < argc && argv[iarg][0] == '-' ){
if( strcmp(argv[iarg],"-verb") == 0 ){
verb++ ; iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-quiet") == 0 ){
verb = 0 ; iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-no_automask") == 0 ){
automask = 0 ; iarg++ ; continue ;
}
ERROR_exit("Illegal option: %s",argv[iarg]) ;
}
mainENTRY("3dOverlap main") ; machdep() ;
if( verb ) PRINT_VERSION("3dOverlap") ;
AFNI_logger("3dOverlap",argc,argv) ;
/* input datasets */
if( iarg+1 >= argc ) ERROR_exit("Need 2 input datasets on command line") ;
aset = THD_open_dataset(argv[iarg]) ; CHECK_OPEN_ERROR(aset,argv[iarg]) ; iarg++ ;
bset = THD_open_dataset(argv[iarg]) ; CHECK_OPEN_ERROR(bset,argv[iarg]) ; iarg++ ;
nvox = DSET_NVOX(aset) ;
if( !EQUIV_GRIDS(aset,bset) ){ /** must resample **/
THD_3dim_dataset *cset ;
if( verb ) INFO_message("resampling dataset B to match dataset A") ;
cset = r_new_resam_dset( bset, aset, 0.0,0.0,0.0,NULL,
MRI_BILINEAR, NULL, 1, 0 ) ;
DSET_delete(bset) ; bset = cset ;
}
if( iarg < argc ) WARNING_message("Extra arguments?") ;
DSET_load(aset); CHECK_LOAD_ERROR(aset);
DSET_load(bset); CHECK_LOAD_ERROR(bset);
/* 10 Aug 2009: keep input datasets without automask, if appropriate */
if( DSET_NVALS(aset) > 1 || DSET_BRICK_TYPE(aset,0) != MRI_byte ){
/* allow masks as input (via -no_automask) 14 Jul 2010 [rickr] */
if( automask ) amm = THD_automask(aset);
else amm = THD_makemask(aset, 0, 1, 0); /* use any non-zero */
DSET_unload(aset);
} else {
amm = DSET_BRICK_ARRAY(aset,0) ;
}
if( DSET_NVALS(bset) > 1 || DSET_BRICK_TYPE(bset,0) != MRI_byte ){
/* allow masks as input (via -no_automask) 14 Jul 2010 [rickr] */
if( automask ) bmm = THD_automask(bset);
else bmm = THD_makemask(bset, 0, 1, 0); /* use any non-zero */
DSET_unload(bset);
} else {
bmm = DSET_BRICK_ARRAY(bset,0) ;
}
naa = mask_count ( nvox , amm ) ;
nbb = mask_count ( nvox , bmm ) ;
nabi = mask_intersect_count( nvox , amm , bmm ) ;
nabu = mask_union_count ( nvox , amm , bmm ) ;
naout = naa - nabi ;
nbout = nbb - nabi ;
paout = (naa > 0) ? naout/(float)naa : 0.0f ;
pbout = (nbb > 0) ? nbout/(float)nbb : 0.0f ;
axyz = mask_rgyrate( DSET_NX(aset),DSET_NY(aset),DSET_NZ(aset) , amm ) ;
bxyz = mask_rgyrate( DSET_NX(bset),DSET_NY(bset),DSET_NZ(bset) , bmm ) ;
xrat = (axyz.a > 0.0f && bxyz.a > 0.0f) ? bxyz.a / axyz.a : 0.0f ;
yrat = (axyz.b > 0.0f && bxyz.b > 0.0f) ? bxyz.b / axyz.b : 0.0f ;
zrat = (axyz.c > 0.0f && bxyz.c > 0.0f) ? bxyz.c / axyz.c : 0.0f ;
if( verb )
printf("#A=%s B=%s\n",DSET_BRIKNAME(aset),DSET_BRIKNAME(bset)) ;
if( verb )
printf("#A #B #(A uni B) #(A int B) "
"#(A \\ B) #(B \\ A) %%(A \\ B) %%(B \\ A) "
"Rx(B/A) Ry(B/A) Rz(B/A)\n") ;
printf("%-12d %-12d %-12d %-12d %-12d %-12d %7.4f %7.4f %7.4f %7.4f %7.4f\n",
naa , nbb , nabu, nabi, naout,nbout,100.0f*paout,100.0f*pbout,
xrat,yrat,zrat ) ;
exit(0) ;
}