From eebba49123a759843a598647a5cd09e66f429c2c Mon Sep 17 00:00:00 2001
From: Tim Behrens <behrens@fmrib.ox.ac.uk>
Date: Thu, 22 Oct 2009 08:28:43 +0000
Subject: [PATCH] Fixed randfib, fibst bugs. Updated options text to make it
clearer what these things do..
---
probtrackxOptions.h | 4 ++--
streamlines.cc | 14 ++++++++++----
streamlines.h | 1 +
tractvolsx.h | 15 +++++----------
4 files changed, 18 insertions(+), 16 deletions(-)
diff --git a/probtrackxOptions.h b/probtrackxOptions.h
index d11a53c..24f39b3 100644
--- a/probtrackxOptions.h
+++ b/probtrackxOptions.h
@@ -213,10 +213,10 @@ class probtrackxOptions {
string("Use anisotropy to constrain tracking"),
false, no_argument),
randfib(string("--randfib"), 0,
- string("Set to 1 to randomly sample initial fibres. Set to 2 to sample in proportion to f"),
+ string("Default 0. Set to 1 to randomly sample initial fibres (with f > fibthresh). \n Set to 2 to sample in proportion fibres (with f>fibthresh) to f. \n Set to 3 to sample ALL populations at random (even if f<fibthresh)"),
false, no_argument),
fibst(string("--fibst"),1,
- string("Force a starting fibre for tracking - default=1, i.e. first fibre orientation"),
+ string("Force a starting fibre for tracking - default=1, i.e. first fibre orientation. Only works if randfib==0"),
false, requires_argument),
modeuler(string("--modeuler"), false,
string("Use modified euler streamlining"),
diff --git a/streamlines.cc b/streamlines.cc
index 6eb14f3..83e2a86 100644
--- a/streamlines.cc
+++ b/streamlines.cc
@@ -1098,14 +1098,20 @@ void Counter::save_matrix3(){
int nlines=0;
for(int p=0;p<opts.nparticles.value();p++){
- if(opts.randfib.value()){
+
+ if(opts.randfib.value()>2){
+ //This bit of code just does random sampling from all fibre populations - even those whose f value is less than f-thresh.
+ //3 other possibilities - randfib==0 -> use fibst (default first fibre but can be set)
+ // randfib==1 - random sampling of fibres bigger than fthresh
+ // randfib==2 random sampling of fibres bigger than fthresh in proporthion to their f-values.
float tmp=rand()/float(RAND_MAX) * float(m_stline.nfibres()-1);
fibst = (int)round(tmp);
- }
+ }
+
if(opts.verbose.value()>1)
logger.setLogFile("particle"+num2str(p));
-
- m_stline.reset();
+
+ m_stline.reset(); //This now includes a vols.reset() in order to get fibst right.
bool forwardflag=false,backwardflag=false;
bool counted=false;
if(!onewayonly || opts.matrix3out.value()){//always go both ways in matrix3 mode
diff --git a/streamlines.h b/streamlines.h
index 9e5cb18..354d281 100644
--- a/streamlines.h
+++ b/streamlines.h
@@ -106,6 +106,7 @@ namespace TRACT{
inline vector<ColumnVector> get_path() const{return m_path;}
inline void reset(){
m_part.reset();
+ vols.reset(opts.fibst.value());
}
inline void reverse(){
m_part.restart_reverse();
diff --git a/tractvolsx.h b/tractvolsx.h
index 29203e2..f1206e5 100644
--- a/tractvolsx.h
+++ b/tractvolsx.h
@@ -153,9 +153,8 @@ namespace TRACTVOLSX{
float dotmax=0,dottmp=0;
int fibind=0;
if(thsamples.size()>1){//more than 1 fibre
-
+
if(init_sample){//go for the specified fibre on the first jump or generate at random
-
if(opts.randfib.value()==1){//this generates startfib at random (except for fibres where f<fibthresh)
vector<int> fibvec;
for(unsigned int fib=0;fib<thsamples.size();fib++){
@@ -172,10 +171,7 @@ namespace TRACTVOLSX{
float rtmp=rand()/float(RAND_MAX) * float(fibvec.size()-1);
fibst = fibvec[ (int)round(rtmp) ];
}
-
}
-
-
else if(opts.randfib.value()==2){ //this generates startfib with probability proportional to f (except for fibres where f<fibthresh).
//this chooses at random but in proportion to fsamples.
float fsumtmp=0;
@@ -204,11 +200,10 @@ namespace TRACTVOLSX{
}
}
-
- theta=(*thsamples[fibst])(int(newx),int(newy),int(newz),int(samp));
- phi=(*phsamples[fibst])(int(newx),int(newy),int(newz),int(samp));
-
- }
+ }
+
+ theta=(*thsamples[fibst])(int(newx),int(newy),int(newz),int(samp));
+ phi=(*phsamples[fibst])(int(newx),int(newy),int(newz),int(samp));
init_sample=false;
}
else{
--
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