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Commit 4429fda5 authored by Tim Behrens's avatar Tim Behrens
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dtifit.cc
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...@@ -170,17 +170,17 @@ int main(int argc, char** argv) ...@@ -170,17 +170,17 @@ int main(int argc, char** argv)
int success=opts.parse_command_line(argc,argv); int success=opts.parse_command_line(argc,argv);
if(!success) return 0; if(!success) return 0;
if(opts.verbose.value()){ if(opts.verbose.value()){
cerr<<"data file "<<opts.dtidatafile.value()<<endl; cout<<"data file "<<opts.dtidatafile.value()<<endl;
cerr<<"mask file "<<opts.maskfile.value()<<endl; cout<<"mask file "<<opts.maskfile.value()<<endl;
cerr<<"bvecs "<<opts.bvecsfile.value()<<endl; cout<<"bvecs "<<opts.bvecsfile.value()<<endl;
cerr<<"bvals "<<opts.bvalsfile.value()<<endl; cout<<"bvals "<<opts.bvalsfile.value()<<endl;
if(opts.littlebit.value()){ if(opts.littlebit.value()){
cerr<<"min z "<<opts.z_min.value()<<endl; cout<<"min z "<<opts.z_min.value()<<endl;
cerr<<"max z "<<opts.z_max.value()<<endl; cout<<"max z "<<opts.z_max.value()<<endl;
cerr<<"min y "<<opts.y_min.value()<<endl; cout<<"min y "<<opts.y_min.value()<<endl;
cerr<<"max y "<<opts.y_max.value()<<endl; cout<<"max y "<<opts.y_max.value()<<endl;
cerr<<"min x "<<opts.x_min.value()<<endl; cout<<"min x "<<opts.x_min.value()<<endl;
cerr<<"max x "<<opts.x_max.value()<<endl; cout<<"max x "<<opts.x_max.value()<<endl;
} }
} }
...@@ -190,19 +190,19 @@ int main(int argc, char** argv) ...@@ -190,19 +190,19 @@ int main(int argc, char** argv)
volume4D<float> data; volume4D<float> data;
volume<int> mask; volume<int> mask;
volumeinfo tempinfo; volumeinfo tempinfo;
if(opts.verbose.value()) cerr<<"reading data"<<endl; if(opts.verbose.value()) cout<<"reading data"<<endl;
read_volume4D(data,opts.dtidatafile.value(),tempinfo); read_volume4D(data,opts.dtidatafile.value(),tempinfo);
if(opts.verbose.value()) cerr<<"reading mask"<<endl; if(opts.verbose.value()) cout<<"reading mask"<<endl;
read_volume(mask,opts.maskfile.value()); read_volume(mask,opts.maskfile.value());
if(opts.verbose.value()) cerr<<"ok"<<endl; if(opts.verbose.value()) cout<<"ok"<<endl;
int minx=opts.littlebit.value() ? opts.x_min.value():0; int minx=opts.littlebit.value() ? opts.x_min.value():0;
int maxx=opts.littlebit.value() ? opts.x_max.value():mask.xsize(); int maxx=opts.littlebit.value() ? opts.x_max.value():mask.xsize();
int miny=opts.littlebit.value() ? opts.y_min.value():0; int miny=opts.littlebit.value() ? opts.y_min.value():0;
int maxy=opts.littlebit.value() ? opts.y_max.value():mask.ysize(); int maxy=opts.littlebit.value() ? opts.y_max.value():mask.ysize();
int minz=opts.littlebit.value() ? opts.z_min.value():0; int minz=opts.littlebit.value() ? opts.z_min.value():0;
int maxz=opts.littlebit.value() ? opts.z_max.value():mask.zsize(); int maxz=opts.littlebit.value() ? opts.z_max.value():mask.zsize();
cerr<<minx<<" "<<maxx<<" "<<miny<<" "<<maxy<<" "<<minz<<" "<<maxz<<endl; cout<<minx<<" "<<maxx<<" "<<miny<<" "<<maxy<<" "<<minz<<" "<<maxz<<endl;
if(opts.verbose.value()) cerr<<"setting up vols"<<endl; if(opts.verbose.value()) cout<<"setting up vols"<<endl;
volume<float> l1(maxx-minx,maxy-miny,maxz-minz); volume<float> l1(maxx-minx,maxy-miny,maxz-minz);
volume<float> l2(maxx-minx,maxy-miny,maxz-minz); volume<float> l2(maxx-minx,maxy-miny,maxz-minz);
volume<float> l3(maxx-minx,maxy-miny,maxz-minz); volume<float> l3(maxx-minx,maxy-miny,maxz-minz);
...@@ -211,7 +211,7 @@ int main(int argc, char** argv) ...@@ -211,7 +211,7 @@ int main(int argc, char** argv)
volume4D<float> V1(maxx-minx,maxy-miny,maxz-minz,3); volume4D<float> V1(maxx-minx,maxy-miny,maxz-minz,3);
volume4D<float> V2(maxx-minx,maxy-miny,maxz-minz,3); volume4D<float> V2(maxx-minx,maxy-miny,maxz-minz,3);
volume4D<float> V3(maxx-minx,maxy-miny,maxz-minz,3); volume4D<float> V3(maxx-minx,maxy-miny,maxz-minz,3);
if(opts.verbose.value()) cerr<<"copying input properties to output volumes"<<endl; if(opts.verbose.value()) cout<<"copying input properties to output volumes"<<endl;
copybasicproperties(data[0],l1); copybasicproperties(data[0],l1);
copybasicproperties(data[0],l2); copybasicproperties(data[0],l2);
copybasicproperties(data[0],l3); copybasicproperties(data[0],l3);
...@@ -220,18 +220,18 @@ int main(int argc, char** argv) ...@@ -220,18 +220,18 @@ int main(int argc, char** argv)
copybasicproperties(data[0],V1[0]); copybasicproperties(data[0],V1[0]);
copybasicproperties(data[0],V2[0]); copybasicproperties(data[0],V2[0]);
copybasicproperties(data[0],V3[0]); copybasicproperties(data[0],V3[0]);
if(opts.verbose.value()) cerr<<"zeroing output volumes"<<endl; if(opts.verbose.value()) cout<<"zeroing output volumes"<<endl;
l1=0;l2=0;l3=0;FA=0;S0=0;V1=0;V2=0;V3=0; l1=0;l2=0;l3=0;FA=0;S0=0;V1=0;V2=0;V3=0;
if(opts.verbose.value()) cerr<<"ok"<<endl; if(opts.verbose.value()) cout<<"ok"<<endl;
DiagonalMatrix evals(3); DiagonalMatrix evals(3);
ColumnVector evec1(3),evec2(3),evec3(3); ColumnVector evec1(3),evec2(3),evec3(3);
ColumnVector S(data.tsize()); ColumnVector S(data.tsize());
float fa,s0; float fa,s0;
if(opts.verbose.value()) cerr<<"Forming A matrix"<<endl; if(opts.verbose.value()) cout<<"Forming A matrix"<<endl;
Matrix Amat = form_Amat(r,b); Matrix Amat = form_Amat(r,b);
if(opts.verbose.value()) cerr<<"starting the fits"<<endl; if(opts.verbose.value()) cout<<"starting the fits"<<endl;
for(int k = minz; k < maxz; k++){ for(int k = minz; k < maxz; k++){
cerr<<k<<" slices processed"<<endl; cout<<k<<" slices processed"<<endl;
for(int j=miny; j < maxy; j++){ for(int j=miny; j < maxy; j++){
for(int i =minx; i< maxx; i++){ for(int i =minx; i< maxx; i++){
......
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