From 3d21fa580c34e599ab13d49eae54caf9522fb2c0 Mon Sep 17 00:00:00 2001
From: Matthew Webster <mwebster@fmrib.ox.ac.uk>
Date: Fri, 9 Jan 2015 15:54:22 +0000
Subject: [PATCH] Current Version Jan 15
---
fslchfiletype.cc | 14 +++++++-----
fslcomplex.cc | 58 ++++++++++++++++++++++++------------------------
fslselectvols.cc | 12 +++++-----
3 files changed, 43 insertions(+), 41 deletions(-)
diff --git a/fslchfiletype.cc b/fslchfiletype.cc
index ec99898..f70b836 100644
--- a/fslchfiletype.cc
+++ b/fslchfiletype.cc
@@ -5,6 +5,7 @@
#include "newimage/newimageall.h"
#include "newimage/fmribmain.h"
+#include <cstdlib>
using namespace NEWIMAGE;
@@ -20,9 +21,9 @@ int printUsage(const string& progname)
template <class T>
int fmrib_main(int argc, char *argv[])
{
- volume4D<T> input;
- read_volume4D(input,string(argv[0]));
- save_volume4D_dtype(input,string(argv[1]),dtype(string(argv[0])));
+ volume<T> input;
+ read_volume(input,string(argv[0]));
+ save_volume_dtype(input,string(argv[1]),dtype(string(argv[0])));
return 0;
}
@@ -44,13 +45,14 @@ int main(int argc,char *argv[])
else if (string(argv[1])=="NIFTI_PAIR_GZ") outputType=FSL_TYPE_NIFTI_PAIR_GZ;
else return printUsage(string(argv[0]));
- FslSetOverrideOutputType(outputType);
+ //argv[1] has a valid outtype at this point
+ setenv("FSLOUTPUTTYPE",argv[1], true);
if (dtype(inputFile)==DT_COMPLEX)
{
volume4D<float> real, imaginary;
- read_complexvolume4D(real, imaginary, inputFile);
- save_complexvolume4D(real, imaginary, outputFile);
+ read_complexvolume(real, imaginary, inputFile);
+ save_complexvolume(real, imaginary, outputFile);
}
else
{
diff --git a/fslcomplex.cc b/fslcomplex.cc
index b832e3b..1731849 100644
--- a/fslcomplex.cc
+++ b/fslcomplex.cc
@@ -45,21 +45,21 @@ void fix_start_and_end(int& start, int& end, int mint, int maxt)
void realpolar(const string& fin, const string& fabs, const string& fphase,
int start, int end)
{
- volume4D<float> vreal, vimag;
- read_complexvolume4D(vreal, vimag, fin);
+ volume<float> vreal, vimag;
+ read_complexvolume(vreal, vimag, fin);
fix_start_and_end(start,end,vreal.mint(),vreal.maxt());
if (fabs.size()>0) {
- volume4D<float> vabs;
+ volume<float> vabs;
for (int n=start; n<=end; n++) {
vabs.addvolume(abs(vreal[n],vimag[n]));
}
vabs.copyproperties(vreal);
- save_volume4D(vabs,fabs);
+ save_volume(vabs,fabs);
}
if (fphase.size()>0) {
- volume4D<float> vphase;
+ volume<float> vphase;
for (int n=start; n<=end; n++) {
vphase.addvolume(phase(vreal[n],vimag[n]));
}
@@ -71,26 +71,26 @@ void realpolar(const string& fin, const string& fabs, const string& fphase,
void realcartesian(const string& fin, const string& freal, const string& fimag,
int start, int end)
{
- volume4D<float> vreal, vimag;
- read_complexvolume4D(vreal, vimag, fin);
+ volume<float> vreal, vimag;
+ read_complexvolume(vreal, vimag, fin);
fix_start_and_end(start,end,vreal.mint(),vreal.maxt());
if (freal.size()>0) {
- volume4D<float> vre;
+ volume<float> vre;
for (int n=start; n<=end; n++) {
vre.addvolume(vreal[n]);
}
vre.copyproperties(vreal);
- save_volume4D(vre,freal);
+ save_volume(vre,freal);
}
if (fimag.size()>0) {
- volume4D<float> vim;
+ volume<float> vim;
for (int n=start; n<=end; n++) {
vim.addvolume(vimag[n]);
}
vim.copyproperties(vimag);
- save_volume4D(vim,fimag);
+ save_volume(vim,fimag);
}
}
@@ -98,21 +98,21 @@ void realcartesian(const string& fin, const string& freal, const string& fimag,
void complexsave(const string& freal, const string& fimag,
const string& fcomplex, int start, int end)
{
- volume4D<float> vreal, vimag;
- read_volume4D(vreal, freal);
- read_volume4D(vimag, fimag);
+ volume<float> vreal, vimag;
+ read_volume(vreal, freal);
+ read_volume(vimag, fimag);
fix_start_and_end(start,end,Max(vreal.mint(),vimag.mint()),
Min(vreal.maxt(),vimag.maxt()));
if (fcomplex.size()>0) {
- volume4D<float> vre, vim;
+ volume<float> vre, vim;
for (int n=start; n<=end; n++) {
vre.addvolume(vreal[n]);
vim.addvolume(vimag[n]);
}
vre.copyproperties(vreal);
vim.copyproperties(vimag);
- save_complexvolume4D(vre,vim,fcomplex);
+ save_complexvolume(vre,vim,fcomplex);
}
}
@@ -120,21 +120,21 @@ void complexsave(const string& freal, const string& fimag,
void complexpolar(const string& fabsvol, const string& fphasevol,
const string& fcomplex, int start, int end)
{
- volume4D<float> vabs, vphase;
- read_volume4D(vabs, fabsvol);
- read_volume4D(vphase, fphasevol);
+ volume<float> vabs, vphase;
+ read_volume(vabs, fabsvol);
+ read_volume(vphase, fphasevol);
fix_start_and_end(start,end,Max(vabs.mint(),vphase.mint()),
Min(vabs.maxt(),vphase.maxt()));
if (fcomplex.size()>0) {
- volume4D<float> vre, vim;
+ volume<float> vre, vim;
for (int n=start; n<=end; n++) {
vre.addvolume(real(vabs[n],vphase[n]));
vim.addvolume(imag(vabs[n],vphase[n]));
}
vre.copyproperties(vabs);
vim.copyproperties(vphase);
- save_complexvolume4D(vre,vim,fcomplex);
+ save_complexvolume(vre,vim,fcomplex);
}
}
@@ -142,7 +142,7 @@ void complexsplit(const string& fsource, const string& fdest,
int start, int end)
{
volume4D<float> vreal, vimag;
- read_complexvolume4D(vreal, vimag, fsource);
+ read_complexvolume(vreal, vimag, fsource);
fix_start_and_end(start,end,Max(vreal.mint(),vimag.mint()),
Min(vreal.maxt(),vimag.maxt()));
@@ -154,16 +154,16 @@ void complexsplit(const string& fsource, const string& fdest,
}
vre.copyproperties(vreal);
vim.copyproperties(vimag);
- save_complexvolume4D(vre,vim,fdest);
+ save_complexvolume(vre,vim,fdest);
}
}
void complexmerge(const string& fsource1, const string& fsource2,
const string& fdest)
{
- volume4D<float> vr1, vi1, vr2, vi2;
- read_complexvolume4D(vr1, vi1, fsource1);
- read_complexvolume4D(vr2, vi2, fsource2);
+ volume<float> vr1, vi1, vr2, vi2;
+ read_complexvolume(vr1, vi1, fsource1);
+ read_complexvolume(vr2, vi2, fsource2);
if (!samesize(vr1,vi1)) {
cerr << "Could not process image " << fsource1 << " correctly." << endl;
@@ -185,7 +185,7 @@ void complexmerge(const string& fsource1, const string& fsource2,
}
vdr.copyproperties(vr1);
vdi.copyproperties(vr2);
- save_complexvolume4D(vdr,vdi,fdest);
+ save_complexvolume(vdr,vdi,fdest);
}
}
@@ -193,8 +193,8 @@ void complexmerge(const string& fsource1, const string& fsource2,
void copyonly(const string& fsource, const string& fdest)
{
volume4D<float> vreal, vimag;
- read_complexvolume4D(vreal, vimag, fsource);
- save_complexvolume4D(vreal, vimag, fdest);
+ read_complexvolume(vreal, vimag, fsource);
+ save_complexvolume(vreal, vimag, fdest);
}
diff --git a/fslselectvols.cc b/fslselectvols.cc
index d77c5b2..6b1d723 100644
--- a/fslselectvols.cc
+++ b/fslselectvols.cc
@@ -133,16 +133,16 @@ int main(int argc,char *argv[]){
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());
+ subdata.reinitialize(data.xsize(),data.ysize(),data.zsize(),list.Ncols());
else
- subdata.reinitialize(data[0].xsize(),data[0].ysize(),data[0].zsize(),1);
+ subdata.reinitialize(data.xsize(),data.ysize(),data.zsize(),1);
subdata=0;
- copybasicproperties(data[0],subdata[0]);
+ copybasicproperties(data,subdata);
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++){
+ 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);
--
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