From 97b20b576a4268aff38161dc5fde326eff5796e7 Mon Sep 17 00:00:00 2001
From: Matthew Webster <matthew.webster@ndcn.ox.ac.uk>
Date: Mon, 20 Jan 2020 16:35:09 +0000
Subject: [PATCH] Changes as requested by MC
---
fslselectvols.cc | 70 +++++++++++++++++++++++-------------------------
1 file changed, 33 insertions(+), 37 deletions(-)
diff --git a/fslselectvols.cc b/fslselectvols.cc
index caa1742..9577272 100644
--- a/fslselectvols.cc
+++ b/fslselectvols.cc
@@ -16,7 +16,7 @@ using namespace Utilities;
int parse_filterstring(vector<int>& comps,const string& vols){
- int ctr=0;
+ int ctr=0;
char *p;
char t[1024];
const char *discard = ", [];{(})abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ~!@#$%^&*_-=+|\':><./?";
@@ -31,7 +31,7 @@ int parse_filterstring(vector<int>& comps,const string& vols){
p=strtok(NULL,discard);
if(p){
ctr = atoi(p);
- if(ctr>0){
+ if(ctr>=0){
comps.push_back(ctr);
}
}
@@ -46,7 +46,7 @@ bool file_exists (const std::string& name) {
} else {
f.close();
return false;
- }
+ }
}
int get_vols(Matrix& id_vols,const string& vols){
@@ -105,60 +105,56 @@ int main(int argc,char *argv[]){
if ( (help.value()) || (!options.check_compulsory_arguments(true)) ){
options.usage();
exit(EXIT_FAILURE);
- }
- else{
-
- volume4D<float> data;
- volume4D<float> subdata;
+ } else {
+ volume4D<float> data, subdata;
read_volume4D(data,ifilename.value());
Matrix list;
get_vols(list,vols.value());
- bool meancalc=calc_mean.value(), varcalc=calc_var.value();
+ bool meancalc( calc_mean.value() ), varcalc( calc_var.value() );
if(!meancalc && !varcalc)
- subdata.reinitialize(data.xsize(),data.ysize(),data.zsize(),list.Ncols());
+ subdata.reinitialize(data.xsize(),data.ysize(),data.zsize(),list.Ncols());
else
- subdata.reinitialize(data.xsize(),data.ysize(),data.zsize(),1);
+ subdata.reinitialize(data.xsize(),data.ysize(),data.zsize(),1);
subdata=0;
copybasicproperties(data,subdata);
-
- float v,v2;
- for(int z=0;z<data.zsize();z++){
- for(int y=0;y<data.ysize();y++){
- for(int x=0;x<data.xsize();x++){
- v=0;v2=0;
- for(int i=1;i<=list.Ncols();i++){
- v += data[list(1,i)](x,y,z);
- v2 += data[list(1,i)](x,y,z)*data[list(1,i)](x,y,z);
- if(!meancalc && !varcalc)
- subdata[i-1](x,y,z)= data[list(1,i)](x,y,z);
- }
- if(meancalc)
- subdata(x,y,z,0)= v/float(list.Ncols());
- if(varcalc)
- subdata(x,y,z,0)= v2/float(list.Ncols()) -v*v/float(list.Ncols()*list.Ncols());
- }
- }
- }
-
+ float nImages(list.Ncols()); //float to avoid risk of integer math
+ for(int z=0;z<data.zsize();z++)
+ for(int y=0;y<data.ysize();y++)
+ for(int x=0;x<data.xsize();x++) {
+ double v(0),v2(0);
+ for(int i=1;i<=list.Ncols();i++) {
+ int index( list(1,i) );
+ double value( data(x,y,z,index) );
+ if( varcalc || meancalc ) {
+ v += value;
+ v2 += value * value;
+ } else
+ subdata(x,y,z,i-1) = value;
+ }
+ if(meancalc)
+ subdata(x,y,z,0)= v/nImages;
+ if(varcalc)
+ subdata(x,y,z,0)=(nImages/(nImages-1)) * (v2/nImages - v*v/(nImages*nImages));
+ }
save_volume4D(subdata,ofilename.value());
return 0;
-
}
- }catch(X_OptionError& e) {
+ } catch(X_OptionError& e) {
options.usage();
cerr << endl << e.what() << endl;
exit(EXIT_FAILURE);
- }catch(std::exception &e) {
+ }
+ catch(std::exception &e) {
cerr << e.what() << endl;
- }
+ }
// either mean or variance but not both
if(calc_mean.value() && calc_var.value()){
cerr<<" Cannot output mean *and* variance. Please choose one or the other but not both"<<endl;
exit(1);
}
-
-
+
+
}
--
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