added distance weighting option

ccops.cc

@@ -270,6 +270,31 @@ void rem_cols(Matrix& myOMmat,Matrix& tractcoordmat,const bool tractcoordbool,co
   
 }
 
+void add_connexity(SymmetricMatrix& CtCt,const Matrix& coord){
+  // compute CtCt range
+  float r=CtCt.Minimum();
+  float R=CtCt.Maximum();
+
+  // compute distance matrix
+  SymmetricMatrix D(coord.Nrows());
+  for(int i=1;i<=coord.Nrows();i++)
+    for(int j=1;j<=i;j++){
+      D(i,j)=std::sqrt((coord.Row(i)-coord.Row(j)).SumSquare());
+    }
+  D=D.MaximumAbsoluteValue()-D;
+
+  // change distance range
+  float m=D.Minimum(),M=D.Maximum();
+  D=(D-m)*(R-r)/(M-m)+r;
+
+  // add distance to CtCt matrix
+  for(int i=1;i<=coord.Nrows();i++)
+    for(int j=1;j<=i;j++){
+      CtCt(i,j)=std::sqrt(CtCt(i,j)*CtCt(i,j)+D(i,j)*D(i,j));
+    }
+ 
+}
+
 
 
 int main ( int argc, char **argv ){
@@ -405,9 +430,20 @@ int main ( int argc, char **argv ){
   SymmetricMatrix CtCt;
   CtCt << corrcoef(newOMmat.t());
   CtCt << CtCt+1;
+
+  // adding connexity constraint
+  if(opts.connexity.value()){
+    if(!coordbool){
+      cerr<<"WARNING !! No coordinates provided. I cannot apply any connexity constraint."<<endl;
+    }
+    else{
+      add_connexity(CtCt,mycoordmat);
+    }
+  }
   if(opts.power.value()!=1){
     CtCt << pow(CtCt,opts.power.value());
   }
+
  
   if(!opts.reord1.value()){
      

ccopsOptions.h

@@ -31,6 +31,7 @@ class ccopsOptions {
   Option<string> excl_mask;
   Option<bool> reord1;
   Option<bool> reord2;
+  Option<bool> connexity;
   Option<int> bin;
   Option<float> power;
   bool parse_command_line(int argc, char** argv);
@@ -72,6 +73,9 @@ class ccopsOptions {
    reord2(string("--r2"), bool(false),
 	     string("do tractspace reordering (default no)"),
 	     false, no_argument), 
+   connexity(string("--con"), bool(false),
+	     string("add connexity constraint (default no)"),
+	     false, no_argument), 
    bin(string("--bin"), 0, 
 	 string("binarise at (default 0 - no binarisation)"), 
 	 false, requires_argument),
@@ -89,6 +93,7 @@ class ccopsOptions {
        options.add(excl_mask);
        options.add(reord1);
        options.add(reord2);
+       options.add(connexity);
        options.add(bin);
        options.add(power);