From 00ed20cc083430c2ec8c1cd8afd58741871b36ed Mon Sep 17 00:00:00 2001
From: Saad Jbabdi <saad@fmrib.ox.ac.uk>
Date: Fri, 15 Aug 2014 12:01:19 +0000
Subject: [PATCH] Added fslselectvols
---
Makefile | 8 ++-
fslselectvols.cc | 179 +++++++++++++++++++++++++++++++++++++++++++++++
2 files changed, 184 insertions(+), 3 deletions(-)
create mode 100644 fslselectvols.cc
diff --git a/Makefile b/Makefile
index abf96c5..181d6c2 100644
--- a/Makefile
+++ b/Makefile
@@ -6,15 +6,15 @@ PROJNAME = avwutils
USRINCFLAGS = -I${INC_NEWMAT} -I${INC_PROB} -I${INC_ZLIB}
USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_ZLIB}
-LIBS = -lnewimage -lmiscmaths -lprob -lfslio -lNewNifti -lnewmat -lutils -lniftiio -lznz -lm -lz
+LIBS = -lnewimage -lmiscmaths -lprob -lfslio -lnewmat -lutils -lniftiio -lznz -lm -lz
IOLIBS = -lfslio -lniftiio -lznz -lm -lz
XFILES = fslorient fslstats fslmerge \
fslpspec fslroi fslnvols fsl2ascii fslascii2img \
fslsplit fslcc fslinterleave \
- fslhd fslcpgeom fslcreatehd fslcorrecthd \
- fslmeants fslslice fslswapdim_exe fslchfiletype_exe fslmaths fslcomplex fslfft fslsmoothfill
+ fslhd fslcpgeom fslcreatehd fslcorrecthd fslmaths \
+ fslcomplex fslfft fslmeants fslslice fslswapdim_exe fslchfiletype_exe calc_grad_perc_dev fslsmoothfill fslselectvols
SCRIPTS = fslval fslchpixdim fslanimate fslsize sliceanimate fslinfo fsledithd avw2fsl fslswapdim fslchfiletype fslreorient2std fslmodhd fsladd
@@ -102,3 +102,5 @@ calc_grad_perc_dev: calc_grad_perc_dev.o
fslsmoothfill: fslsmoothfill.o
${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ fslsmoothfill.o ${LIBS}
+fslselectvols: fslselectvols.o
+ ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ fslselectvols.o ${LIBS}
diff --git a/fslselectvols.cc b/fslselectvols.cc
new file mode 100644
index 0000000..d77c5b2
--- /dev/null
+++ b/fslselectvols.cc
@@ -0,0 +1,179 @@
+/* fslselectvols.cc
+
+ Saad Jbabdi, FMRIB Image Analysis Group
+
+ Copyright (C) 2012 University of Oxford */
+
+/* CCOPYRIGHT */
+
+#include "miscmaths/miscmaths.h"
+#include "newimage/newimageall.h"
+#include "utils/options.h"
+
+using namespace MISCMATHS;
+using namespace NEWIMAGE;
+using namespace Utilities;
+
+
+int parse_filterstring(vector<int>& comps,const string& vols){
+ int ctr=0;
+ char *p;
+ char t[1024];
+ const char *discard = ", [];{(})abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ~!@#$%^&*_-=+|\':><./?";
+ comps.clear();
+
+ strcpy(t, vols.c_str());
+ p=strtok(t,discard);
+ ctr = atoi(p);
+ if(ctr>=0)
+ comps.push_back(ctr);
+ do{
+ p=strtok(NULL,discard);
+ if(p){
+ ctr = atoi(p);
+ if(ctr>0){
+ comps.push_back(ctr);
+ }
+ }
+ }while(p);
+ return 0;
+}
+bool file_exists (const std::string& name) {
+ ifstream f(name.c_str());
+ if (f.good()) {
+ f.close();
+ return true;
+ } else {
+ f.close();
+ return false;
+ }
+}
+
+int get_vols(Matrix& id_vols,const string& vols){
+ vector<int> comps;
+ if(file_exists(vols)){
+ id_vols = read_ascii_matrix(vols);
+ if(id_vols.Ncols()==1){id_vols=id_vols.t();}
+
+ comps.resize(id_vols.Ncols());
+ for(int i=0;i<(int)comps.size();i++){
+ comps[i]=id_vols(1,i+1);
+ }
+ }
+ else{
+ if(vols.length()>0 && parse_filterstring(comps,vols)){
+ return 1;
+ }
+ }
+
+ //sort and remove duplicates
+ sort (comps.begin(), comps.end());
+ vector<int>::iterator it = unique (comps.begin(), comps.end());
+ comps.resize( it - comps.begin() );
+
+ id_vols.ReSize(1,comps.size());
+ for(int i=0;i<(int)comps.size();i++){
+ id_vols(1,i+1)=comps[i];
+ }
+
+
+ return 0;
+}
+
+
+
+string title=string("fslselectvols\n")+
+ string(" Select volumes from a 4D time series and output a subset 4D volume\n");
+string examples=string("fslselectvols -i <input> -o <output> --vols=0,1,6,7\n")+
+ string("fslselectvols -i <input> -o <output> --vols=volumes_list.txt");
+
+Option<bool> help(string("-h,--help"), false,
+ string("display this help text"),
+ false,no_argument);
+Option<string> ifilename(string("-i,--in"), string(""),
+ string("\tinput file name (4D image)"),
+ true, requires_argument);
+Option<string> ofilename(string("-o,--out"), string(""),
+ string("output file name (4D image)"),
+ true, requires_argument);
+Option<string> vols(string("--vols"), string(""),
+ string("\tlist of volumes to extract (comma-separated list or ascii file)"),
+ true, requires_argument);
+Option<bool> calc_mean(string("-m"), false,
+ string("\toutput mean instead of concat"),
+ false, no_argument);
+Option<bool> calc_var(string("-v"), false,
+ string("\toutput variance instead of concat"),
+ false, no_argument);
+
+
+int main(int argc,char *argv[]){
+ OptionParser options(title, examples);
+ try{
+ options.add(help);
+ options.add(ifilename);
+ options.add(ofilename);
+ options.add(vols);
+ options.add(calc_mean);
+ options.add(calc_var);
+ options.parse_command_line(argc, argv);
+ if ( (help.value()) || (!options.check_compulsory_arguments(true)) ){
+ options.usage();
+ exit(EXIT_FAILURE);
+ }
+ else{
+
+ volume4D<float> data;
+ volume4D<float> subdata;
+ read_volume4D(data,ifilename.value());
+
+ Matrix list;
+ get_vols(list,vols.value());
+
+ bool meancalc=calc_mean.value(), varcalc=calc_var.value();
+
+ if(!meancalc && !varcalc)
+ subdata.reinitialize(data[0].xsize(),data[0].ysize(),data[0].zsize(),list.Ncols());
+ else
+ subdata.reinitialize(data[0].xsize(),data[0].ysize(),data[0].zsize(),1);
+ subdata=0;
+ copybasicproperties(data[0],subdata[0]);
+
+ float v,v2;
+ for(int z=0;z<data[0].zsize();z++){
+ for(int y=0;y<data[0].ysize();y++){
+ for(int x=0;x<data[0].xsize();x++){
+ v=0;v2=0;
+ for(int i=1;i<=list.Ncols();i++){
+ v += data[list(1,i)](x,y,z);
+ v2 += v*v;
+ 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());
+ }
+ }
+ }
+
+ save_volume4D(subdata,ofilename.value());
+ return 0;
+
+ }
+ }catch(X_OptionError& e) {
+ options.usage();
+ cerr << endl << e.what() << endl;
+ exit(EXIT_FAILURE);
+ }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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