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Commit 3fb4e2f4 authored by Mark Jenkinson's avatar Mark Jenkinson
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Added label option and checked basic functionality is giving zero diffs

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with 96 additions and 75 deletions
fslmeants.cc
+ 96
− 75
View file @ 3fb4e2f4
......@@ -51,6 +51,9 @@ Option<string> inname(string("-i"), string(""),
Option<string> maskname(string("-m"), string(""),
string("~<filename>\tinput 3D mask"),
false, requires_argument);
Option<string> labelname(string("--label"), string(""),
string("input 3D label image (generate separate mean for each integer label value - cannot be used with showall)"),
false, requires_argument);
Option<string> outmat(string("-o"), string(""),
string("~<filename>\toutput text matrix"),
false, requires_argument);
......@@ -89,6 +92,7 @@ int main(int argc,char *argv[])
options.add(eig);
options.add(order);
options.add(bin_mask);
options.add(labelname);
options.add(transpose);
options.add(verbose);
options.add(help);
......@@ -109,7 +113,7 @@ int main(int argc,char *argv[])
volume4D<float> vin;
read_volume4D(vin,inname.value());
volume<float> mask;
volume<float> mask, label;
volume4D<float> mask_nonbin;
if (maskname.set()) {
read_volume(mask,maskname.value());
......@@ -118,8 +122,19 @@ int main(int argc,char *argv[])
mask = 1.0;
}
int nlabs=1;
if (labelname.set() && showall.unset()) {
read_volume(label,labelname.value());
if (verbose.value()) { print_volume_info(label,"label"); }
float labmax=label.max();
if (labmax>=0.99) {
mask *= label;
}
nlabs=MISCMATHS::round(labmax);
if (nlabs<1) nlabs=1;
}
// override the mask if a coordinate is specified
// override the mask (and label) if a coordinate is specified
if (coordval.set()) {
mask = vin[0];
mask = 0.0;
......@@ -139,97 +154,103 @@ int main(int argc,char *argv[])
x = v(1); y = v(2); z = v(3);
mask(MISCMATHS::round(x),MISCMATHS::round(y),MISCMATHS::round(z)) = 1.0;
}
if (!samesize(vin[0],mask)) {
cerr << "ERROR: Mask and Input volumes have different (x,y,z) size."
<< endl;
return -1;
}
mask_nonbin.addvolume(mask);
mask.binarise(1e-8); // arbitrary "0" threshold
if(eig.value()){
Matrix dat, evecs, scales;
scales = mask_nonbin.matrix(mask);
dat = vin.matrix(mask);
if(!bin_mask.value())
dat = SP (dat, ones(dat.Nrows(),1) * scales);
dat = remmean(dat,1);
if (labelname.unset()) { mask.binarise(1e-8); } // arbitrary "0" threshold
Matrix meants;
int nt = vin.tsize();
int nvox = nlabs;
if (showall.value()) {
nvox = no_mask_voxels(mask);
nt += 3;
}
meants.ReSize(nt,nvox);
meants = 0;
for (int iter=1; iter<=nlabs; iter++) {
if (eig.value()) {
Matrix dat, evecs, scales;
scales = mask_nonbin.matrix(mask);
dat = vin.matrix(mask);
if(!bin_mask.value())
dat = SP (dat, ones(dat.Nrows(),1) * scales);
dat = remmean(dat,1);
if (verbose.value()) {
cout << "Number of voxels used = " << dat.Ncols() << endl;
}
if (verbose.value()) {
cout << "Number of voxels used = " << dat.Ncols() << endl;
}
SymmetricMatrix Corr;
Corr << dat * dat.t() / dat.Ncols();
DiagonalMatrix tmpD;
EigenValues(Corr,tmpD,evecs);
evecs = fliplr(evecs.Columns(evecs.Ncols()-order.value()+1 , evecs.Ncols())) * std::sqrt(dat.Nrows());
SymmetricMatrix Corr;
Corr << dat * dat.t() / dat.Ncols();
DiagonalMatrix tmpD;
EigenValues(Corr,tmpD,evecs);
evecs = fliplr(evecs.Columns(evecs.Ncols()-order.value()+1 , evecs.Ncols())) * std::sqrt(dat.Nrows());
Matrix res2 = mean(dat,2);
res2 = res2.Column(1).t() * evecs.Column(1);
Matrix res2 = mean(dat,2);
res2 = res2.Column(1).t() * evecs.Column(1);
if((float)res2.AsScalar()<0)
evecs = -1.0 * evecs;
if((float)res2.AsScalar()<0)
evecs = -1.0 * evecs;
if (transpose.value()) { evecs=evecs.t(); }
if (outmat.set()) {
write_ascii_matrix(evecs,outmat.value());
} else {
cout << evecs << endl;
}
if (transpose.value()) { evecs=evecs.t(); }
}
else{
int nt = vin.tsize();
int nvox = 1;
if (showall.value()) {
nvox = MISCMATHS::round(mask.sum());
nt += 3;
}
Matrix meants(nt,nvox);
meants = 0;
long int num=0;
if (transpose.value()) { evecs=evecs.t(); }
if (outmat.set()) {
write_ascii_matrix(evecs,outmat.value());
} else {
cout << evecs << endl;
}
if (transpose.value()) { evecs=evecs.t(); }
} else {
// NOT EIG
long int num=0;
for (int z=mask.minz(); z<=mask.maxz(); z++) {
for (int y=mask.miny(); y<=mask.maxy(); y++) {
for (int x=mask.minx(); x<=mask.maxx(); x++) {
if (mask(x,y,z)>0.5) {
num++;
if (showall.value()) {
ColumnVector v(4);
v << x << y << z << 1.0;
v = (vin[0].niftivox2newimagevox_mat()).i() * v;
meants(1,num) = v(1);
meants(2,num) = v(2);
meants(3,num) = v(3);
meants.SubMatrix(4,nt,num,num) = vin.voxelts(x,y,z);
} else {
meants += vin.voxelts(x,y,z);
for (int z=mask.minz(); z<=mask.maxz(); z++) {
for (int y=mask.miny(); y<=mask.maxy(); y++) {
for (int x=mask.minx(); x<=mask.maxx(); x++) {
if (MISCMATHS::round(mask(x,y,z))==iter) {
num++;
if (showall.value()) {
ColumnVector v(4);
v << x << y << z << 1.0;
v = (vin[0].niftivox2newimagevox_mat()).i() * v;
meants(1,num) = v(1);
meants(2,num) = v(2);
meants(3,num) = v(3);
meants.SubMatrix(4,nt,num,num) = vin.voxelts(x,y,z);
} else {
meants.SubMatrix(1,nt,iter,iter) = meants.SubMatrix(1,nt,iter,iter) + vin.voxelts(x,y,z);
}
}
}
}
}
}
}
if (verbose.value()) {
cout << "Number of voxels used = " << num << endl;
}
// normalise for number of valid entries if averaging
if (!showall.value()) {
if (num>0) meants /= (float) num;
}
if (verbose.value()) {
cout << "Number of voxels used = " << num << endl;
}
// save the result
if (transpose.value()) { meants=meants.t(); }
if (outmat.set()) {
write_ascii_matrix(meants,outmat.value());
} else {
cout << meants << endl;
// normalise for number of valid entries if averaging
if (!showall.value()) {
if (num>0) meants.SubMatrix(1,nt,iter,iter) = meants.SubMatrix(1,nt,iter,iter) / ((float) num);
}
// save the result
if (transpose.value()) { meants=meants.t(); }
if (outmat.set()) {
write_ascii_matrix(meants,outmat.value());
} else {
cout << meants << endl;
}
if (transpose.value()) { meants=meants.t(); }
}
if (transpose.value()) { meants=meants.t(); }
}
return 0;
}
......
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