diff --git a/find_the_biggest.cc b/find_the_biggest.cc
deleted file mode 100644
index efc0f85fd80439aa8e5cfe9d2be6365ea76f64ec..0000000000000000000000000000000000000000
--- a/find_the_biggest.cc
+++ /dev/null
@@ -1,217 +0,0 @@
-/* Copyright (C) 2004 University of Oxford */
-
-/* CCOPYRIGHT */
-
-#include <iostream>
-#include <fstream>
-#include "newimage/newimageall.h"
-#include <vector>
-using namespace std;
-using namespace NEWIMAGE;
-
-void biggest_from_volumes(vector<string> innames,string oname){
- vector<volume<float> > tmpvec;
- tmpvec.reserve(innames.size());
- volume<float> tmp;
- cout<<"number of inputs "<<innames.size()<<endl;
- cout<<"Indices"<<endl;
- for(unsigned int i=0;i<innames.size();i++){
- cout<<i+1<<" "<<innames[i]<<endl;
- read_volume(tmp,innames[i]);
- tmpvec.push_back(tmp);
- }
- volume<int> output(tmp.xsize(),tmp.ysize(),tmp.zsize());
- copybasicproperties(tmp,output);output=0;
-
- for(int z=tmp.minz();z<=tmp.maxz();z++){
- for(int y=tmp.miny();y<=tmp.maxy();y++){
- for(int x=tmp.minx();x<=tmp.maxx();x++){
- RowVector bum(innames.size());
- Matrix bugger;
- ColumnVector index;
- for(unsigned int i=0;i<innames.size();i++ ){
- bum(i+1)=tmpvec[i](x,y,z);
- }
- bugger=max(bum,index);
- bool flag=true;
- if(index.AsScalar()==1){
- // Check to see whether they're all zero.
- flag=false;
- for(unsigned int i=1;i<=innames.size();i++ ){
- if(bum(i)!=0){
- flag=true;break;
- }
-
- }
- }
- if(flag)
- output(x,y,z)=(int)index.AsScalar();
- else
- output(x,y,z)=0;
- }
- }
- }
-
- output.setDisplayMaximumMinimum(innames.size(),0);
- save_volume(output,oname);
-
-}
-
-ReturnMatrix read_label(const string& labelfile,string& firstline){
- Matrix L;
- ifstream fs(labelfile.c_str());
- if (!fs) {
- cerr << "Could not open label file " << labelfile << endl;
- L.Release();
- return L;
- }
-
- // read first line
- char str[200];
- FILE *fp;
- fp = fopen(labelfile.c_str(), "r");
- fscanf(fp, "%[^\n]", str);
- firstline = str;
-
- string cline;
- // skip header
- cline = skip_alpha(fs);
- // read number of vertices
- string ss="";
- fs >> ss;
- float nrows = atof(ss.c_str());
- L.ReSize(int(nrows),5);
- for(int r=1;r<=nrows;r++)
- for(int c=1;c<=5;c++){
- if(!fs.eof()){
- fs >> ss;
- while ( !isNumber(ss) && !fs.eof() ) {
- fs >> ss;
- }
- L(r,c) = atof(ss.c_str());
- }
- }
-
- L.Release();
- return L;
-}
-void write_label(const Matrix& L,const string& filename,const string& firstline){
- ofstream fs(filename.c_str());
- if (!fs) {
- cerr << "Could not open file " << filename << " for writing" << endl;
- exit(1);
- }
- fs << firstline << endl;
- fs << L.Nrows() << endl;
-
-#ifdef PPC64
- int n=0;
-#endif
- for (int i=1; i<=L.Nrows(); i++) {
- for (int j=1; j<=L.Ncols(); j++) {
- fs << L(i,j) << " ";
-#ifdef PPC64
- if ((n++ % 50) == 0) fs.flush();
-#endif
- }
- fs << endl;
- }
-
-
- fs.close();
-}
-
-void biggest_from_matrix(vector<string> innames,string oname){
- if(innames.size()!=2){
- cerr<<"usage: find_the_biggest <Matrix> <Label> <Output>"<<endl;
- exit(1);
- }
-
- cout << innames[0] << endl;
- Matrix M = read_ascii_matrix(innames[0]);
- ColumnVector maxMrow(M.Nrows()),coordMax(M.Nrows());
- maxMrow = sum(abs(M),2);
-
- cout << "number of vertices: " << M.Nrows() << endl;
- cout << "number of targets: " << M.Ncols() << endl;
-
- cout << endl << "read label file" << endl;
- string firstline;
- Matrix L = read_label(innames[1],firstline);
-
- cout << "number of vertices: " << L.Nrows() << endl;
- cout << "number of columns: " << L.Ncols() << endl;
-
- if(M.Nrows() != L.Nrows()){
- cerr<<"Error: matrix and label file do not have the same number of entries"<<endl;
- exit(1);
- }
-
- // test this (i think M and L do not come in the same order...)
- vector< pair<int,int> > labels(L.Nrows());
- for(unsigned int i=0;i<labels.size();i++){
- labels[i].first=(int)L(i+1,1);
- labels[i].second=i+1;
- }
- sort(labels.begin(),labels.end());
- Matrix sL=L;
- for(int i=1;i<=L.Nrows();i++)
- sL.Row(i)=L.Row(labels[i-1].second);
-
-
- vector< vector<int> > Clusters(M.Ncols());
- float val;
- int cmax;
- for(int i=1;i<=M.Nrows();i++){
- val=(M.Row(i)).MaximumAbsoluteValue1(cmax);
- if(val!=0)
- Clusters[cmax-1].push_back(int(i));
- }
- // now store these into files
- for(unsigned int i=0;i<Clusters.size();i++){
- if(Clusters[i].size()>0){
- Matrix C(Clusters[i].size(),5);
- for(unsigned int j=0;j<Clusters[i].size();j++){
- C.Row(labels[j].second) = L.Row(Clusters[i][j]);
- C(labels[j].second,5) = i+1;
- }
- write_label(C,oname+"_"+num2str(i+1)+".label",firstline);
- }
- }
-
-}
-
-int main ( int argc, char **argv ){
- if(argc<3){
- cerr<<" "<<endl;
- cerr<<"usage: find_the_biggest <lots of volumes> output"<<endl;
- cerr<<"output is index in order of inputs"<<endl;
- cerr<<"Or: find_the_biggest <singleMatrixFile> <labelfile> output"<<endl;
- cerr<<" "<<endl;
- exit(1);
- }
-
- vector<string> innames;
- innames.clear();
- for(int i=1;i<=argc-2;i++){
- innames.push_back(argv[i]);
- }
- if(!fsl_imageexists(innames[0])){
- biggest_from_matrix(innames,argv[argc-1]);
- }
- else{
- biggest_from_volumes(innames,argv[argc-1]);
- }
-
- return(0);
-
-}
-
-
-
-
-
-
-
-
-
diff --git a/proj_thresh.cc b/proj_thresh.cc
deleted file mode 100644
index fb59ee7b3af75bea406fe4e62c82088107604c41..0000000000000000000000000000000000000000
--- a/proj_thresh.cc
+++ /dev/null
@@ -1,59 +0,0 @@
-/* Copyright (C) 2004 University of Oxford */
-
-/* CCOPYRIGHT */
-
-#include <iostream>
-#include <fstream>
-#include "newimage/newimageall.h"
-#include <vector>
-using namespace std;
-using namespace NEWIMAGE;
-
-int main ( int argc, char **argv ){
- if(argc<3){
- cerr<<"usage:proj_thresh <lots of volumes> threshold"<<endl;
- exit(1);
- }
- vector<volume<float> > tmpvec;
- // vector<volume<float> > outvec;
- float thresh=atof(argv[argc-1]);
- tmpvec.reserve(argc-2);
- // outvec.reserve(argc-2);
- volume<float> tmp;
- cout<<"number of inputs "<<argc-2<<endl;
- for(int i=1;i<=argc-2;i++){
- cout<<i<<" "<<argv[i]<<endl;
- read_volume(tmp,argv[i]);
- tmpvec.push_back(tmp);
- }
- cerr<<"threshold "<<thresh<<endl;
-
- volume<float> total;
- volume<float> total_thresh;
- total=tmp*0;
-
- for(unsigned int i=0;i<tmpvec.size();i++){
- total+=tmpvec[i];
- }
-
- total_thresh=binarise(total,thresh);
- save_volume(total,"total");
- for(unsigned int i=0;i<tmpvec.size();i++){
- tmp=divide(tmpvec[i],total,total_thresh);
- string outname =argv[i+1];
- make_basename(outname);
- string thrname="_thr_"+num2str(thresh);
- save_volume(tmp,outname+"_proj_seg"+thrname);
- }
-
-}
-
-
-
-
-
-
-
-
-
-