From 63c93a94ecbd6bade95e8d87f82f07d5646c4f0a Mon Sep 17 00:00:00 2001
From: Saad Jbabdi <saad@fmrib.ox.ac.uk>
Date: Thu, 30 Nov 2006 14:28:20 +0000
Subject: [PATCH] *** empty log message ***
---
probtrackxOptions.h | 11 ++++--
streamlines.cc | 94 +++++++++++++++++++++++++++++++++++----------
2 files changed, 81 insertions(+), 24 deletions(-)
diff --git a/probtrackxOptions.h b/probtrackxOptions.h
index 36431e5..07724aa 100644
--- a/probtrackxOptions.h
+++ b/probtrackxOptions.h
@@ -35,13 +35,14 @@ class probtrackxOptions {
Option<string> mode;
Option<string> targetfile;
Option<bool> simpleout;
- Option<int> pathdist;
+ Option<bool> pathdist;
Option<bool> s2tout;
FmribOption<bool> matrix1out;
FmribOption<bool> matrix2out;
FmribOption<bool> maskmatrixout;
Option<string> outfile;
Option<string> rubbishfile;
+ Option<string> stopfile;
Option<string> seeds_to_dti;
FmribOption<string> skipmask;
Option<string> seedref;
@@ -110,9 +111,9 @@ class probtrackxOptions {
simpleout(string("--opd"), false,
string("output path distribution"),
false, no_argument),
- pathdist(string("--pd"), 1,
+ pathdist(string("--pd"), false,
string("path distribution, 1:probability,2:distance corrected value"),
- false, requires_argument),
+ false, no_argument),
s2tout(string("--os2t"), false,
string("output seeds to targets"),
false, no_argument),
@@ -131,6 +132,9 @@ class probtrackxOptions {
rubbishfile(string("--rubbish"), string(""),
string("Rubbish file"),
false, requires_argument),
+ stopfile(string("--stop"), string(""),
+ string("Stop tracking at locations given by this mask file"),
+ false, requires_argument),
seeds_to_dti(string("--xfm"), string(""),
string("Transform Matrix taking seed space to DTI space default is to use the identity"),false, requires_argument),
skipmask(string("--no_integrity"), string(""),
@@ -215,6 +219,7 @@ class probtrackxOptions {
options.add(maskmatrixout);
options.add(outfile);
options.add(rubbishfile);
+ options.add(stopfile);
options.add(seeds_to_dti);
options.add(nparticles);
options.add(nsteps);
diff --git a/streamlines.cc b/streamlines.cc
index 330b214..fb42395 100644
--- a/streamlines.cc
+++ b/streamlines.cc
@@ -37,6 +37,9 @@ namespace TRACT{
if(opts.rubbishfile.value()!=""){
read_volume(m_rubbish,opts.rubbishfile.value());
}
+ if(opts.stopfile.value()!=""){
+ read_volume(m_stop,opts.stopfile.value());
+ }
vector<string> masknames;
if(opts.waypoints.value()!=""){
@@ -90,7 +93,8 @@ namespace TRACT{
x=xst;y=yst;z=zst;
m_part.change_xyz(x,y,z);
int partlength=0;
- //NB - this only goes in one direction!!
+ bool rubbish_passed=false;
+ //NB - this only goes in one direction!!
for(unsigned int pf=0;pf<m_passed_flags.size();pf++) {
m_passed_flags[pf]=false; /// only keep it if this streamline went through all the masks
}
@@ -139,9 +143,17 @@ namespace TRACT{
if(opts.rubbishfile.value()!=""){
- if(m_rubbish(x_s,y_s,z_s)>0) break;
+ if(m_rubbish(x_s,y_s,z_s)!=0){
+ rubbish_passed=true;
+ break;
+ }
}
-
+ if(opts.stopfile.value()!=""){
+ if(m_stop(x_s,y_s,z_s)!=0){
+ m_path.pop_back();
+ break;
+ }
+ }
if(opts.skipmask.value() == ""){
@@ -189,6 +201,8 @@ namespace TRACT{
if(!m_passed_flags[i])
accept_path=false;
}
+ if(rubbish_passed)
+ accept_path=false;
return accept_path;
}
@@ -363,7 +377,7 @@ namespace TRACT{
void Counter::update_pathdist(){
const vector<ColumnVector>& path=m_stline.get_path_ref();
- if(opts.pathdist.value()==1){
+ if(!opts.pathdist.value()){
for(unsigned int i=0;i<path.size();i++){
int x_s=int(round(float(path[i](1)))),y_s=int(round(float(path[i](2)))),z_s=int(round(float(path[i](3))));
if(m_beenhere(x_s,y_s,z_s)==0){
@@ -407,13 +421,34 @@ namespace TRACT{
int xseedvox=int(round(m_stline.get_x_seed()));
int yseedvox=int(round(m_stline.get_y_seed()));
int zseedvox=int(round(m_stline.get_z_seed()));
- for(unsigned int i=0;i<path.size();i++){
- int x_s=int(round(float(path[i](1)))),y_s=int(round(float(path[i](2)))),z_s=int(round(float(path[i](3))));
- for(unsigned int m=0;m<m_targetmasknames.size();m++){
- if(m_targetmasks[m](x_s,y_s,z_s)>0 && m_targflags[m]==0){
- m_seedcounts[m](xseedvox,yseedvox,zseedvox)=m_seedcounts[m](xseedvox,yseedvox,zseedvox)+1;
- m_targflags[m]=1;
- //m_particle_numbers[m].push_back(particle_number);
+
+ if(!opts.pathdist.value()){
+ for(unsigned int i=0;i<path.size();i++){
+ int x_s=int(round(float(path[i](1)))),y_s=int(round(float(path[i](2)))),z_s=int(round(float(path[i](3))));
+ for(unsigned int m=0;m<m_targetmasknames.size();m++){
+ if(m_targetmasks[m](x_s,y_s,z_s)>0 && m_targflags[m]==0){
+ m_seedcounts[m](xseedvox,yseedvox,zseedvox)=m_seedcounts[m](xseedvox,yseedvox,zseedvox)+1;
+ m_targflags[m]=1;
+ //m_particle_numbers[m].push_back(particle_number);
+ }
+ }
+ }
+ }
+ else{
+ int d=0;
+ int x_s=0,y_s=0,z_s=0,px,py,pz;
+ for(unsigned int i=0;i<path.size();i++){
+ px=(int)floor(x_s),py=(int)floor(y_s),pz=(int)floor(z_s);
+ x_s=int(round(float(path[i](1))));y_s=int(round(float(path[i](2))));z_s=int(round(float(path[i](3))));
+ if(i==0 | (floor(x_s)!=px | floor(y_s)!=py | floor(z_s)!=pz)){
+ d++;
+ for(unsigned int m=0;m<m_targetmasknames.size();m++){
+ if(m_targetmasks[m](x_s,y_s,z_s)>0 && m_targflags[m]==0){
+ m_seedcounts[m](xseedvox,yseedvox,zseedvox)+=d;
+ m_targflags[m]=1;
+ //m_particle_numbers[m].push_back(particle_number);
+ }
+ }
}
}
}
@@ -446,18 +481,35 @@ namespace TRACT{
void Counter::update_matrix2_row(){
//run this one every streamline - not every voxel..
const vector<ColumnVector>& path=m_stline.get_path_ref();
- for(unsigned int i=0;i<path.size();i++){
- ColumnVector xyz_seeds=path[i];
- ColumnVector xyz_lr=vox_to_vox(xyz_seeds,m_seedsdim,m_lrdim,m_I);
- int x_lr=int(round(float(xyz_lr(1)))),y_lr=int(round(float(xyz_lr(2)))),z_lr=int(round(float(xyz_lr(3))));
- int Concol2=m_lookup2(x_lr,y_lr,z_lr,0);
- if(Concol2!=0){
- if(m_beenhere2(x_lr,y_lr,z_lr)==0){
- m_ConMat2(m_Conrow2,Concol2,0)+=1;
- m_beenhere2(x_lr,y_lr,z_lr)=1;
+
+ if(!opts.pathdist.value())
+ for(unsigned int i=0;i<path.size();i++){
+ ColumnVector xyz_seeds=path[i];
+ ColumnVector xyz_lr=vox_to_vox(xyz_seeds,m_seedsdim,m_lrdim,m_I);
+ int x_lr=int(round(float(xyz_lr(1)))),y_lr=int(round(float(xyz_lr(2)))),z_lr=int(round(float(xyz_lr(3))));
+ int Concol2=m_lookup2(x_lr,y_lr,z_lr,0);
+ if(Concol2!=0){
+ if(m_beenhere2(x_lr,y_lr,z_lr)==0){
+ m_ConMat2(m_Conrow2,Concol2,0)+=1;
+ m_beenhere2(x_lr,y_lr,z_lr)=1;
+ }
+ }
+
+ }
+ else{
+ int d=1;
+ for(unsigned int i=0;i<path.size();i++){
+ ColumnVector xyz_seeds=path[i];
+ ColumnVector xyz_lr=vox_to_vox(xyz_seeds,m_seedsdim,m_lrdim,m_I);
+ int x_lr=int(round(float(xyz_lr(1)))),y_lr=int(round(float(xyz_lr(2)))),z_lr=int(round(float(xyz_lr(3))));
+ int Concol2=m_lookup2(x_lr,y_lr,z_lr,0);
+ if(Concol2!=0){
+ if(m_beenhere2(x_lr,y_lr,z_lr)==0){
+ m_ConMat2(m_Conrow2,Concol2,0)+=d;d++;
+ m_beenhere2(x_lr,y_lr,z_lr)=1;
+ }
}
}
-
}
}
--
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