From 03486a0ea42fc3ec016d4510b72ef54835285af9 Mon Sep 17 00:00:00 2001
From: Saad Jbabdi <saad@fmrib.ox.ac.uk>
Date: Thu, 5 Mar 2009 18:40:57 +0000
Subject: [PATCH] added possibility of saving seed-to-target counter as a text
file
---
probtrackxOptions.h | 6 +++++-
streamlines.cc | 43 +++++++++++++++++++++++++++++++++++++++++++
streamlines.h | 3 +++
3 files changed, 51 insertions(+), 1 deletion(-)
diff --git a/probtrackxOptions.h b/probtrackxOptions.h
index 83ed8ab..fa2f5f7 100644
--- a/probtrackxOptions.h
+++ b/probtrackxOptions.h
@@ -66,7 +66,7 @@ class probtrackxOptions {
Option<int> fibst;
Option<bool> modeuler;
Option<int> rseed;
-
+ Option<bool> seedcountastext;
void parse_command_line(int argc, char** argv,Log& logger);
void modecheck();
@@ -206,6 +206,9 @@ class probtrackxOptions {
rseed(string("--rseed"), 12345,
string("Random seed"),
false, requires_argument),
+ seedcountastext(string("--seedcountastext"), false,
+ string("Output seed-to-target counts as a text file"),
+ false, no_argument),
options("probtrackx","probtrackx -s <basename> -m <maskname> -x <seedfile> -o <output> --targetmasks=<textfile>\n probtrackx --help\n")
{
@@ -249,6 +252,7 @@ class probtrackxOptions {
options.add(fibst);
options.add(modeuler);
options.add(rseed);
+ options.add(seedcountastext);
}
catch(X_OptionError& e) {
options.usage();
diff --git a/streamlines.cc b/streamlines.cc
index ed69306..a0f71fb 100644
--- a/streamlines.cc
+++ b/streamlines.cc
@@ -299,6 +299,33 @@ namespace TRACT{
m_seedcounts.push_back(tmpint);
//m_particle_numbers.push_back(tmpvec);
}
+
+ // where we save the seed counts in text files
+ if(opts.seedcountastext.value()){
+
+ int numseeds=0;
+ if(opts.meshfile.value()==""){
+ for(int Wz=m_seeds.minz();Wz<=m_seeds.maxz();Wz++)
+ for(int Wy=m_seeds.miny();Wy<=m_seeds.maxy();Wy++)
+ for(int Wx=m_seeds.minx();Wx<=m_seeds.maxx();Wx++)
+ if(m_seeds.value(Wx,Wy,Wz)!=0)
+ numseeds++;
+ }
+ else{
+ ifstream fs(opts.seedfile.value().c_str());
+ if(fs){
+ char buffer[1024];
+ fs.getline(buffer,1024);
+ fs >>numseeds;
+ cout<<numseeds<<endl;
+ }
+ }
+
+ m_SeedCountMat.ReSize(numseeds,m_targetmasknames.size());
+ m_SeedCountMat=0;
+ m_SeedRow=1;
+ }
+
}
@@ -426,6 +453,9 @@ namespace TRACT{
if(opts.matrix2out.value()){
next_matrix2_row();
}
+ if(opts.seedcountastext.value()){
+ m_SeedRow++;
+ }
}
@@ -499,6 +529,10 @@ namespace TRACT{
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.seedcountastext.value())
+ m_SeedCountMat(m_SeedRow,m+1) += 1;
+
}
}
}
@@ -515,6 +549,10 @@ namespace TRACT{
m_seedcounts[m](xseedvox,yseedvox,zseedvox)+=(int)d;
m_targflags[m]=1;
//m_particle_numbers[m].push_back(particle_number);
+
+ if(opts.seedcountastext.value())
+ m_SeedCountMat(m_SeedRow,m+1) += d;
+
}
}
@@ -678,6 +716,11 @@ namespace TRACT{
save_volume(m_seedcounts[m],logger.appendDir("seeds_to_"+tmpname));
}
+
+ if(opts.seedcountastext.value()){
+ write_ascii_matrix(m_SeedCountMat,logger.appendDir("matrix_seeds_to_all_targets"));
+ }
+
}
// the following is a helper function for save_matrix*
diff --git a/streamlines.h b/streamlines.h
index 2f9d912..39748fc 100644
--- a/streamlines.h
+++ b/streamlines.h
@@ -98,6 +98,9 @@ namespace TRACT{
vector<ColumnVector> m_path;
vector<volume<int> > m_seedcounts;
+ Matrix m_SeedCountMat;
+ int m_SeedRow;
+
vector<volume<float> > m_targetmasks;
vector<string> m_targetmasknames;
vector<int> m_targflags;
--
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