From fb8fc81b51da63630c1671e6bee2922580dd0bd4 Mon Sep 17 00:00:00 2001
From: Tim Behrens <behrens@fmrib.ox.ac.uk>
Date: Fri, 10 Jun 2005 15:26:50 +0000
Subject: [PATCH] *** empty log message ***
---
xfibres.cc | 44 +++++++++++++-------------------------------
xfibresoptions.h | 4 ++--
2 files changed, 15 insertions(+), 33 deletions(-)
diff --git a/xfibres.cc b/xfibres.cc
index b7784e4..57c1fa5 100644
--- a/xfibres.cc
+++ b/xfibres.cc
@@ -202,7 +202,7 @@ class xfibresVoxelManager{
Multifibre m_multifibre;
public:
xfibresVoxelManager(const ColumnVector& data,const ColumnVector& alpha,
- const ColumnVector& beta, const Matrix& b, const Matrix& Amat,
+ const ColumnVector& beta, const Matrix& b,
Samples& samples,int voxelnumber):
opts(xfibresOptions::getInstance()),
m_samples(samples),m_voxelnumber(voxelnumber),m_data(data),
@@ -327,7 +327,7 @@ int main(int argc, char *argv[])
Matrix datam, bvals,bvecs;
- volume<char> mask;
+ volume<float> mask;
bvals=read_ascii_matrix(opts.bvalsfile.value());
bvecs=read_ascii_matrix(opts.bvecsfile.value());
@@ -338,40 +338,22 @@ int main(int argc, char *argv[])
datam=data.matrix(mask);
}
- Samples samples(datam.Ncols());
-
-
- //if(opts.debuglevel.value()==1)
- //Tracer_Plus::setrunningstackon();
-
- //if(opts.timingon.value())
- //Tracer_Plus::settimingon();
+ Matrix Amat;
+ ColumnVector alpha, beta;
+ Amat=form_Amat(bvecs,bvals);
+ cart2sph(bvecs,alpha,beta);
+ Samples samples(datam.Ncols());
- // read data
-
- //VolumeSeries data;
- //data.read(opts.datafile.value());
- // data.writeAsFloat(LogSingleton::getInstance().appendDir("data"));
-// cout<<"done"<<endl;
-// return 0;
- //int ntpts = data.tsize();
- //Matrix bvecs = read_ascii_matrix(opts.bvecsfile.value());
- //Matrix bvals = read_ascii_matrix(opts.bvalsfile.value());
- // mask:
- //Volume mask;
- ///mask.read(opts.maskfile.value());
- //mask.threshold(1e-16);
- // threshold using mask:
- //data.setPreThresholdPositions(mask.getPreThresholdPositions());
- //data.thresholdSeries();
- ColumnVector A,B,C;
+ for(int vox=1;vox<=datam.Ncols();vox++){
+ xfibresVoxelManager vm(datam.Column(vox),alpha,beta,bvals,samples,vox);
+ vm.initialise(Amat);
+ vm.runmcmc();
+ }
- Matrix b,Amat;
- int n;
+ samples.save();
- Multifibre(A,B,C,b,n);
}
catch(Exception& e)
{
diff --git a/xfibresoptions.h b/xfibresoptions.h
index 57ec3e7..a8a4aa6 100644
--- a/xfibresoptions.h
+++ b/xfibresoptions.h
@@ -41,7 +41,7 @@ class xfibresOptions {
Option<int> nburn;
Option<int> sampleevery;
Option<int> updateproposalevery;
- Option<float> seed;
+ Option<int> seed;
void parse_command_line(int argc, char** argv, Log& logger);
private:
@@ -103,7 +103,7 @@ class xfibresOptions {
updateproposalevery(string("--upe,--updateproposalevery"),40,
string("Num of jumps for each update to the proposal density std (MCMC) (default is 40)"),
false,requires_argument),
- seed(string("--seed"),0.76986654,string("seed for pseudo random number generator"),
+ seed(string("--seed"),8665904,string("seed for pseudo random number generator"),
false,requires_argument),
options("xfibres", "xfibres -k <filename>\n xfibres --verbose\n")
{
--
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