seed masks no longer need to be binarised

ptx_meshmask.cc

@@ -25,7 +25,7 @@ void meshmask()
   mseeds.load_fs_label(opts.seedfile.value());
 
   // internally create seed mask in voxel space
-  volume<int> seeds;
+  volume<float> seeds;
   if(opts.seedref.value()!="")
     read_volume(seeds,opts.seedref.value());
   else

ptx_nmasks.cc

@@ -20,8 +20,8 @@ void nmasks()
 
   ////////////////////////////////
   //  Log& logger = LogSingleton::getInstance();
-  vector< volume<int> > seeds;
-  volume<int> tmpvol;
+  vector< volume<float> > seeds;
+  volume<float> tmpvol;
   vector<string> masknames;
 
   if(fsl_imageexists(opts.seedfile.value())){

ptx_seedmask.cc

@@ -20,7 +20,7 @@ void seedmask()
 
   ////////////////////////////////
   //  Log& logger = LogSingleton::getInstance();
-  volume<int> seeds;
+  volume<float> seeds;
   read_volume(seeds,opts.seedfile.value());
   Streamliner stline;
   Counter counter(seeds,stline);

ptx_simple.cc

@@ -22,7 +22,7 @@ void track(){
     logger.makeDir("particles","particle0",true,false);
   }
   
-  volume<int> seedref;
+  volume<float> seedref;
   if(opts.seedref.value()!=""){
     read_volume(seedref,opts.seedref.value());
   }

ptx_twomasks.cc

@@ -20,7 +20,7 @@ void twomasks()
 
   ////////////////////////////////
   //  Log& logger = LogSingleton::getInstance();
-  volume<int> seeds,seeds2;
+  volume<float> seeds,seeds2;
   read_volume(seeds,opts.seedfile.value());
   read_volume(seeds2,opts.mask2.value());
 

streamlines.cc

@@ -51,7 +51,7 @@ namespace TRACT{
       }
 
       for( unsigned int m = 0; m < masknames.size(); m++ ){
-	volume<int>* tmpptr =new volume<int>;
+	volume<float>* tmpptr =new volume<float>;
 	if(opts.verbose.value()>0)
 	  cout<<masknames[m]<<endl;
 	read_volume(*tmpptr,masknames[m]);
@@ -648,17 +648,23 @@ namespace TRACT{
   int Seedmanager::run(const float& x,const float& y,const float& z,bool onewayonly, int fibst,const ColumnVector& dir){
     //onewayonly for mesh things..
     cout <<x<<" "<<y<<" "<<z<<endl;
-    if(fibst == -1){
-      fibst=0;//m_seeds(int(round(x)),int(round(y)),int(round(z)))-1;//fibre to start with is taken from seed volume..
-    }
-    if(opts.randfib.value()){
-      float tmp=rand()/RAND_MAX * float(m_stline.nfibres()-1);
-      fibst = (int)round(tmp);
-      //if(tmp>0.5)
-      //fibst=0;
-      //else
-      //fibst=1;// fix this for > 2 fibres
-    } 
+    if(opts.fibst.set()){
+      fibst=opts.fibst.value()-1;
+      OUT(fibst);
+   }
+    else{
+      if(fibst == -1){
+	fibst=0;//m_seeds(int(round(x)),int(round(y)),int(round(z)))-1;//fibre to start with is taken from seed volume..
+    }
+      if(opts.randfib.value()){
+	float tmp=rand()/RAND_MAX * float(m_stline.nfibres()-1);
+	fibst = (int)round(tmp);
+	//if(tmp>0.5)
+	//fibst=0;
+	//else
+	//fibst=1;// fix this for > 2 fibres
+      } 
+    }
     
     int nlines=0;
     for(int p=0;p<opts.nparticles.value();p++){

streamlines.h

@@ -30,7 +30,7 @@ namespace TRACT{
     volume<int> m_rubbish;
     volume<int> m_stop;
     volume4D<float> m_loopcheck;
-    vector<volume<int>* > m_waymasks;
+    vector<volume<float>* > m_waymasks;
     vector<bool> m_passed_flags;
     vector<bool> m_own_waymasks;
     Matrix m_Seeds_to_DTI;
@@ -46,7 +46,7 @@ namespace TRACT{
       for(unsigned int i=0;i<m_waymasks.size();i++)
 	if(m_own_waymasks[i]) delete m_waymasks[i];
     }
-    void add_waymask(volume<int>& myway,const bool& ownership=false){
+    void add_waymask(volume<float>& myway,const bool& ownership=false){
       //make sure that the waymask to add will not be deleted before
       //this streamliner goes out of scope!!
       m_waymasks.push_back(&myway);
@@ -54,7 +54,7 @@ namespace TRACT{
       m_passed_flags.push_back(false);
     }
     void pop_waymasks(){
-      volume<int>* tmpptr=m_waymasks[m_waymasks.size()-1];
+      volume<float>* tmpptr=m_waymasks[m_waymasks.size()-1];
       m_waymasks.pop_back();
       m_passed_flags.pop_back();
       if(m_own_waymasks[m_own_waymasks.size()-1]){
@@ -115,13 +115,13 @@ namespace TRACT{
     int m_Conrow2;
     ColumnVector m_lrdim;
     
-    const volume<int>& m_seeds;
+    const volume<float>& m_seeds;
     ColumnVector m_seedsdim;
     const Streamliner& m_stline;
     Streamliner& m_nonconst_stline;
     
   public:
-    Counter(const volume<int>& seeds,Streamliner& stline):opts(probtrackxOptions::getInstance()),
+    Counter(const volume<float>& seeds,Streamliner& stline):opts(probtrackxOptions::getInstance()),
 							  logger(LogSingleton::getInstance()),
 							  m_seeds(seeds),m_stline(stline),
 							  m_nonconst_stline(stline){
@@ -136,7 +136,8 @@ namespace TRACT{
     void initialise();
     
     void initialise_path_dist(){
-      m_prob=m_seeds;
+      m_prob.reinitialize(m_seeds.xsize(),m_seeds.ysize(),m_seeds.zsize());
+      copybasicproperties(m_seeds,m_prob);
       m_prob=0;
     }
     void initialise_seedcounts();
@@ -184,7 +185,7 @@ namespace TRACT{
 
     inline const Streamliner& get_streamline() const {return m_stline;}
     inline Streamliner& get_nonconst_streamline() const {return m_nonconst_stline;}
-    inline const volume<int>& get_seeds() const {return m_seeds;}
+    inline const volume<float>& get_seeds() const {return m_seeds;}
 
     
   };
@@ -194,7 +195,7 @@ namespace TRACT{
     Log& logger;
     Counter& m_counter;    
     Streamliner& m_stline;
-    const volume<int>& m_seeds;
+    const volume<float>& m_seeds;
     ColumnVector m_seeddims;
   public:
     Seedmanager(Counter& counter):opts(probtrackxOptions::getInstance()),