From e5011d65a9784813a39539bab8a9e1b9ad46c24f Mon Sep 17 00:00:00 2001
From: Stamatios Sotiropoulos <stam@fmrib.ox.ac.uk>
Date: Fri, 21 Jan 2011 11:28:03 +0000
Subject: [PATCH] Added pseudo-constrained non-linear optimization
---
pvmfit.cc | 30 ++++++++++++++++++++++--------
pvmfitOptions.h | 6 ++++++
2 files changed, 28 insertions(+), 8 deletions(-)
diff --git a/pvmfit.cc b/pvmfit.cc
index a8e6157..93d707d 100644
--- a/pvmfit.cc
+++ b/pvmfit.cc
@@ -116,15 +116,29 @@ int main(int argc, char** argv)
S(t+1)=data(i,j,k,t);
if(opts.modelnum.value()==1){
- PVM_single pvm(S,bvecs,bvals,opts.nfibres.value());
- pvm.fit();
+ if (opts.cnonlinear.value()){
+ PVM_single_c pvm(S,bvecs,bvals,opts.nfibres.value());
+ pvm.fit();
- S0(i-minx,j-miny,k-minz) = pvm.get_s0();
- dvol(i-minx,j-miny,k-minz) = pvm.get_d();
- for(int f=0;f<opts.nfibres.value();f++){
- fvol[f](i-minx,j-miny,k-minz) = pvm.get_f(f+1);
- thvol[f](i-minx,j-miny,k-minz) = pvm.get_th(f+1);
- phvol[f](i-minx,j-miny,k-minz) = pvm.get_ph(f+1);
+ S0(i-minx,j-miny,k-minz) = pvm.get_s0();
+ dvol(i-minx,j-miny,k-minz) = pvm.get_d();
+ for(int f=0;f<opts.nfibres.value();f++){
+ fvol[f](i-minx,j-miny,k-minz) = pvm.get_f(f+1);
+ thvol[f](i-minx,j-miny,k-minz) = pvm.get_th(f+1);
+ phvol[f](i-minx,j-miny,k-minz) = pvm.get_ph(f+1);
+ }
+ }
+ else{
+ PVM_single pvm(S,bvecs,bvals,opts.nfibres.value());
+ pvm.fit();
+
+ S0(i-minx,j-miny,k-minz) = pvm.get_s0();
+ dvol(i-minx,j-miny,k-minz) = pvm.get_d();
+ for(int f=0;f<opts.nfibres.value();f++){
+ fvol[f](i-minx,j-miny,k-minz) = pvm.get_f(f+1);
+ thvol[f](i-minx,j-miny,k-minz) = pvm.get_th(f+1);
+ phvol[f](i-minx,j-miny,k-minz) = pvm.get_ph(f+1);
+ }
}
}
else{
diff --git a/pvmfitOptions.h b/pvmfitOptions.h
index bf7c7b2..24deea9 100644
--- a/pvmfitOptions.h
+++ b/pvmfitOptions.h
@@ -36,6 +36,8 @@ class pvmfitOptions {
Option<string> bvalsfile;
Option<int> nfibres;
Option<int> modelnum;
+ Option<bool> cnonlinear;
+
bool parse_command_line(int argc, char** argv);
private:
@@ -84,6 +86,9 @@ class pvmfitOptions {
modelnum(string("--model"), 1,
string("1:monoexponential;2:non mono-exponential"),
false, requires_argument),
+ cnonlinear(string("--cnonlinear"),false,
+ string("Apply constrained nonlinear optimization on the diffusivity, volume fractions and their sum"),
+ false,no_argument),
options("pvmfit", "pvmfit -k <datafile> -m <maskfile> -r <bvecsfile> -b <bvalsfile> [-n 2]\n")
{
@@ -98,6 +103,7 @@ class pvmfitOptions {
options.add(bvalsfile);
options.add(nfibres);
options.add(modelnum);
+ options.add(cnonlinear);
}
catch(X_OptionError& e) {
options.usage();
--
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