void
cmp3d(Cube &c1,Cube &c2,Cube &mask,string spacer)
{
if (!(c1.dimsequal(c2))) {
printf("[I] vbcmp: %sdimensions don't match, can't compare.\n",spacer.c_str());
return;
}
if (mask.data && !(c1.dimsequal(mask))) {
printf("[I] vbcmp: %smask dimensions don't agree with images\n",spacer.c_str());
return;
}
double totaldiff,maxdiff=0.0,v1,v2,diff;
uint32 diffcount,voxelcount;
int i,j,k;
diffcount=0;
totaldiff=0.0;
int maxx=0,maxy=0,maxz=0;
voxelcount=c1.dimx * c1.dimy * c1.dimz;
// pre-count mask
if (mask.data) {
int newvoxelcount=0;
for (size_t i=0; i<voxelcount; i++)
if (mask.testValue(i))
newvoxelcount++;
voxelcount=newvoxelcount;
}
VB_Vector vec1(voxelcount),vec2(voxelcount);
uint64 ind=0;
for (i=0; i<c1.dimx; i++) {
for (j=0; j<c1.dimy; j++) {
for (k=0; k<c1.dimz; k++) {
if (mask.data)
if (!(mask.testValue(i,j,k))) continue;
v1=c1.GetValue(i,j,k);
v2=c2.GetValue(i,j,k);
// to support correlation, smush into vectors:
vec1[ind]=v1; vec2[ind]=v2; ind++;
if (v1 != v2) {
if (isnan(v1) && isnan(v2)) continue;
if (isinf(v1) && isinf(v2)) continue;
diffcount++;
diff=fabs(v1-v2);
totaldiff += diff;
if (diff>maxdiff) {
maxdiff=diff;
maxx=i;
maxy=j;
maxz=k;
}
}
}
}
}
if (!diffcount) {
printf("[I] vbcmp: %sthe data are identical\n",spacer.c_str());
}
else {
cout << format("[I] vbcmp: %sdifferent voxels: %ld of %ld (%.0f%%)\n")
% spacer % diffcount % voxelcount % ((diffcount*100.0)/voxelcount);
cout << format("[I] vbcmp: %smean difference: %.8f\n") % spacer % (totaldiff/diffcount);
cout << format("[I] vbcmp: %smax difference: %.8f (%d,%d,%d)\n")
% spacer % maxdiff % maxx % maxy % maxz;
cout << format("[I] vbcmp: %scorrelation between images: %g\n")%spacer%correlation(vec1,vec2);
}
}
void
do_sumcube(string fname,int index,Cube &mycube,Cube &mask,double thresh,vector<VBRegion> &rlist)
{
Cube tmpmask=mask;
int i,j,k;
printf("%s-%02d\n",fname.c_str(),index);
// eliminate from mask any sub-threshold voxels
for (i=0; i<mycube.dimx; i++) {
for (j=0; j<mycube.dimy; j++) {
for (k=0; k<mycube.dimz; k++) {
if (mycube.GetValue(i,j,k) < thresh)
tmpmask.SetValue(i,j,k,0);
}
}
}
// now find regions
vector<VBRegion> regionlist;
regionlist=findregions(tmpmask,vb_gt,0.0);
// now that we have a list of regions we can go through them and produce some stats
double grandsum=0.0;
double val;
int grandcnt=0;
for (i=0; i<(int)regionlist.size(); i++) {
double sum=0.0,x=0.0,y=0.0,z=0.0;
int cnt=0;
for (VI myvox=regionlist[i].begin(); myvox!=regionlist[i].end(); myvox++) {
if (val==0.0 && nozeroflag)
continue;
sum+=val;
grandsum+=val;
x+=myvox->second.x; y+=myvox->second.y; z+=myvox->second.z;
cnt++;
grandcnt++;
}
if (detailflag)
printf(" region %d: %d voxels, mean %.2f (%d,%d,%d)\n",i,cnt,sum/(double)cnt,
(int)x/cnt,(int)y/cnt,(int)z/cnt);
}
printf(" sum: %.3f count: %d average(sum/cnt): %.6f\n",grandsum,grandcnt,grandsum/(double)grandcnt);
// now do the region comparisons
if (rlist.size()) {
// build a vb_vector for each regionlist
vector<VB_Vector> myvecs;
for (i=0; i<(int)rlist.size(); i++) {
vector<double> vals;
for (VI myvox=rlist[i].begin(); myvox!=rlist[i].end(); myvox++) {
val=mycube.GetValue(myvox->second.x,myvox->second.y,myvox->second.z);
if (val==0.0 && nozeroflag)
continue;
if (val<thresh)
continue;
vals.push_back(val);
}
VB_Vector tmpv(vals.size());
for (j=0; j<(int)vals.size(); j++)
tmpv[j]=vals[j];
myvecs.push_back(tmpv);
}
for (i=0; i<(int)rlist.size()-1; i++) {
for (j=i+1; j<(int)rlist.size(); j++) {
double tvalue=ttest(myvecs[i],myvecs[j]);
cout << " region comparison: " << rlist[i].name << " vs. " << rlist[j].name << endl;
cout << " means: " << myvecs[i].getVectorMean() << " vs. " << myvecs[j].getVectorMean() << endl;
cout << " voxels: " << myvecs[i].getLength() << " vs. " << myvecs[j].getLength() << endl;
cout << " t value= " << tvalue << endl;
}
}
}
}
double
Extractor::regioncode(int x,int y,int z)
{
vector<value> valuelist;
double x0,x1,y0,y1,z0,z1;
int xx0,xx1,yy0,yy1,zz0,zz1;
double val;
int added;
// xyz are the newcube coordinates of the voxel we'd like. subtract
// the origin of the new cube and divide by newvox to get that in mm
// relative to the origin.
x0=(double)(x-newcube.origin[0])*newcube.voxsize[0];
x1=(double)((x+1)-newcube.origin[0])*newcube.voxsize[0];
y0=(double)(y-newcube.origin[1])*newcube.voxsize[1];
y1=(double)((y+1)-newcube.origin[1])*newcube.voxsize[1];
z0=(double)(z-newcube.origin[2])*newcube.voxsize[2];
z1=(double)((z+1)-newcube.origin[2])*newcube.voxsize[2];
// cout << "x: " << x0 << ":" << x1 << endl;
// cout << "y: " << y0 << ":" << y1 << endl;
// cout << "z: " << z0 << ":" << z1 << endl;
// now then divide by oldvox and subtract from original origin to
// get original cube voxel.
xx0=original.origin[0]+(int)(x0/original.voxsize[0]);
xx1=original.origin[0]+(int)(x1/original.voxsize[0]);
yy0=original.origin[1]+(int)(y0/original.voxsize[1]);
yy1=original.origin[1]+(int)(y1/original.voxsize[1]);
zz0=original.origin[2]+(int)(z0/original.voxsize[2]);
zz1=original.origin[2]+(int)(z1/original.voxsize[2]);
// cout << "coords: " << xx0 << ":" << xx1;
// cout << ", " << yy0 << ":" << yy1;
// cout << ", " << zz0 << ":" << zz1 << endl;
for (int i=xx0; i<xx1; i++) {
if (i<0 || i>=original.dimx)
continue;
for (int j=yy0; j<yy1; j++) {
if (j<0 || j>=original.dimy)
continue;
for (int k=zz0; k<zz1; k++) {
if (k<0 || k>=original.dimz)
continue;
val=original.GetValue(i,j,k);
added=0;
for (int m=0; m<(int)valuelist.size(); m++) {
if (valuelist[m].val==val) {
valuelist[m].cnt++;
added=1;
break;
}
}
if (added==0) {
value tmp;
tmp.val=val;
tmp.cnt=1;
valuelist.push_back(tmp);
}
break;
}
}
}
// cout << "voxels: " << (xx1-xx0)*(yy1-yy0)*(zz1-zz0) << " ";
// cout << "vals: " << valuelist.size() << " ";
int commoncnt=0;
double commonval=0.0;
for (int i=0; i<(int)valuelist.size(); i++) {
if (valuelist[i].cnt > commoncnt) {
commonval=valuelist[i].val;
commoncnt=valuelist[i].cnt;
}
}
// cout << "common: " << commonval << "(" << commoncnt << ")" << endl;
return (commonval);
}