From c92c823a3f7bb02825df23481e5e9088884e675b Mon Sep 17 00:00:00 2001
From: Saad Jbabdi <saad@fmrib.ox.ac.uk>
Date: Wed, 8 Apr 2009 08:53:54 +0000
Subject: [PATCH] streamline stops when entering a termination mask
---
streamlines.cc | 67 +++++++++++++++++++++++++++++++++++++++++---------
1 file changed, 56 insertions(+), 11 deletions(-)
diff --git a/streamlines.cc b/streamlines.cc
index a0f71fb..b218252 100644
--- a/streamlines.cc
+++ b/streamlines.cc
@@ -203,8 +203,8 @@ namespace TRACT{
if(m_stop(x_s,y_s,z_s)!=0){
stop_flag=true;
}
- else
- if(stop_flag)break;
+ //else
+ if(stop_flag)break;
}
if(opts.skipmask.value() == ""){
@@ -378,7 +378,7 @@ namespace TRACT{
char buffer[1024];
fs.getline(buffer,1024);
fs >>numseeds;
- cout<<numseeds<<endl;
+ cout<<"numseeds="<<numseeds<<endl;
}
}
@@ -397,7 +397,10 @@ namespace TRACT{
cerr<<" Although, it must stay in line with the seeds"<<endl;
exit(-1);
}
+
m_ConMat2.reinitialize(numseeds,numnz,1);
+ OUT(m_ConMat2.xsize());
+
m_CoordMat2.reinitialize(numseeds,3,1);
m_CoordMat_tract2.reinitialize(numnz,3,1);
@@ -745,14 +748,56 @@ namespace TRACT{
}
void Counter::save_matrix2(){
- save_volume(m_ConMat2,logger.appendDir("fdt_matrix2"));
- applycoordchange(m_CoordMat2, m_seeds.niftivox2newimagevox_mat().i());
- save_volume(m_CoordMat2,logger.appendDir("coords_for_fdt_matrix2"));
- applycoordchange(m_CoordMat2, m_seeds.niftivox2newimagevox_mat());
- applycoordchange(m_CoordMat_tract2, m_lrmask.niftivox2newimagevox_mat().i());
- save_volume(m_CoordMat_tract2,logger.appendDir("tract_space_coords_for_fdt_matrix2"));
- applycoordchange(m_CoordMat_tract2, m_lrmask.niftivox2newimagevox_mat());
- save_volume4D(m_lookup2,logger.appendDir("lookup_tractspace_fdt_matrix2"));
+ if(!opts.splitmatrix2.value()){
+ save_volume(m_ConMat2,logger.appendDir("fdt_matrix2"));
+ applycoordchange(m_CoordMat2, m_seeds.niftivox2newimagevox_mat().i());
+ save_volume(m_CoordMat2,logger.appendDir("coords_for_fdt_matrix2"));
+ applycoordchange(m_CoordMat2, m_seeds.niftivox2newimagevox_mat());
+ applycoordchange(m_CoordMat_tract2, m_lrmask.niftivox2newimagevox_mat().i());
+ save_volume(m_CoordMat_tract2,logger.appendDir("tract_space_coords_for_fdt_matrix2"));
+ applycoordchange(m_CoordMat_tract2, m_lrmask.niftivox2newimagevox_mat());
+ save_volume4D(m_lookup2,logger.appendDir("lookup_tractspace_fdt_matrix2"));
+ }
+ else{
+ cout << "saving matrix2 into splitted files" << endl;
+
+ int nsplits = 10;
+ while( float(m_ConMat2.xsize()/nsplits) >= 32767 ){
+ nsplits++;
+ }
+
+ int nrows = std::floor(float(m_ConMat2.xsize()/nsplits))+1;
+ volume<int> tmpmat;
+
+ applycoordchange(m_CoordMat2, m_seeds.niftivox2newimagevox_mat().i());
+
+ for(int i=1;i<=nsplits;i++){
+ int first_row = (i-1)*nrows+1;
+ int last_row = i*nrows > m_ConMat2.xsize() ? m_ConMat2.xsize() : i*nrows;
+ if(first_row > m_ConMat2.xsize()) break;
+
+ // set limits
+ m_ConMat2.setROIlimits(first_row-1,m_ConMat2.miny(),m_ConMat2.minz(),last_row-1,m_ConMat2.maxy(),m_ConMat2.maxz());
+ m_ConMat2.activateROI();
+ tmpmat = m_ConMat2.ROI();
+ save_volume(tmpmat,logger.appendDir("fdt_matrix2_"+num2str(i)));
+
+ m_CoordMat2.setROIlimits(first_row-1,m_CoordMat2.miny(),m_CoordMat2.minz(),last_row-1,m_CoordMat2.maxy(),m_CoordMat2.maxz());
+ m_CoordMat2.activateROI();
+ tmpmat = m_CoordMat2.ROI();
+ save_volume(tmpmat,logger.appendDir("coords_for_fdt_matrix2_"+num2str(i)));
+
+
+ }
+
+ applycoordchange(m_CoordMat_tract2, m_lrmask.niftivox2newimagevox_mat());
+ save_volume4D(m_lookup2,logger.appendDir("lookup_tractspace_fdt_matrix2"));
+
+ applycoordchange(m_CoordMat2, m_seeds.niftivox2newimagevox_mat());
+ applycoordchange(m_CoordMat_tract2, m_lrmask.niftivox2newimagevox_mat().i());
+ save_volume(m_CoordMat_tract2,logger.appendDir("tract_space_coords_for_fdt_matrix2"));
+
+ }
}
int Seedmanager::run(const float& x,const float& y,const float& z,bool onewayonly, int fibst){
--
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