From 751a13db71f5bc35fcc88739598affb42ae3181f Mon Sep 17 00:00:00 2001
From: Matthew Webster <mwebster@fmrib.ox.ac.uk>
Date: Fri, 9 Jan 2015 13:50:00 +0000
Subject: [PATCH] Current Version Jan 15
---
fslnvols.cc | 25 +++++--------------------
fslorient.cc | 11 +++++------
fslroi.cc | 11 ++++-------
3 files changed, 14 insertions(+), 33 deletions(-)
diff --git a/fslnvols.cc b/fslnvols.cc
index 78b3ad5..2557dcb 100755
--- a/fslnvols.cc
+++ b/fslnvols.cc
@@ -4,7 +4,6 @@
// CCOPYRIGHT
#include "newimage/newimageall.h"
-#include "newimage/fmribmain.h"
using namespace NEWIMAGE;
@@ -14,19 +13,6 @@ void print_usage(const string& progname)
cout << "Usage: fslnvols <input>" << endl;
}
-
-template <class T>
-int fmrib_main(int argc, char *argv[])
-{
-
- NiftiIO reader;
- NiftiHeader header(reader.loadHeader(string(argv[1])));
- cout << header.dim[4] << endl;
- return 0;
-}
-
-
-
int main(int argc,char *argv[])
{
string progname=argv[0];
@@ -35,15 +21,14 @@ int main(int argc,char *argv[])
print_usage(progname);
return 1;
}
- if (!FslFileExists(argv[1]))
+ if (!FslFileExists(string(argv[1])))
{
cout << "0" << endl;
return 0; // the intended usage is to return "0" and not show an error
}
- else
- {
- string iname=string(argv[1]);
- return call_fmrib_main(dtype(iname),argc,argv);
- }
+ NiftiIO reader;
+ NiftiHeader header(reader.loadHeader(return_validimagefilename(string(argv[1]))));
+ cout << header.dim[4] << endl;
+ return 0;
}
diff --git a/fslorient.cc b/fslorient.cc
index 5918551..192c39a 100644
--- a/fslorient.cc
+++ b/fslorient.cc
@@ -94,9 +94,9 @@ int fmrib_main(int argc,char *argv[])
{
bool modified(false);
string option(argv[1]), filename(argv[argc-1]);
- volume4D<T> invol;
+ volume<T> invol;
- read_orig_volume4D(invol,filename);
+ read_orig_volume(invol,filename);
if ( argc==2 || option=="-getorient") {
getorient(invol);
@@ -167,10 +167,9 @@ int fmrib_main(int argc,char *argv[])
if (modified) {
- if ( FslBaseFileType(fslFileType(filename)) != FSL_TYPE_ANALYZE ) {
- FslSetOverrideOutputType(fslFileType(filename));
- save_orig_volume4D(invol,filename);
- FslSetOverrideOutputType(-1); // restore to default
+ int filetype( fslFileType(filename) );
+ if ( filetype != FSL_TYPE_ANALYZE ) {
+ save_orig_volume(invol,filename,filetype);
} else {
cerr << "Cannot modify orientation for Analyze files" << endl;
cerr << " All Analyze files are treated as radiological" << endl;
diff --git a/fslroi.cc b/fslroi.cc
index 90dc853..3becf22 100755
--- a/fslroi.cc
+++ b/fslroi.cc
@@ -7,6 +7,8 @@
#include "newimage/fmribmain.h"
using namespace NEWIMAGE;
+using namespace MISCMATHS;
+
void print_usage(const string& progname) {
cout << endl;
@@ -21,9 +23,7 @@ template <class T>
int fmrib_main(int argc, char *argv[])
{
volume4D<T> input_vol,output_vol;
- string input_name(string(argv[1]));
- string output_name(string(argv[2]));
- read_volume4D(input_vol, string(argv[1]) );
+ read_volume4D(input_vol,string(argv[1]));
int minx(-1),miny(-1),minz(-1),mint(-1),maxx(-1),maxy(-1),maxz(-1),maxt(-1),argindex(3);
//Note there is currently no explicit bounds testing e.g. if maxx>inputvol.maxx() etc
@@ -99,16 +99,13 @@ int fmrib_main(int argc, char *argv[])
if (minx>maxx) { int tmpx=maxx; maxx=minx; minx=tmpx; }
if (miny>maxy) { int tmpy=maxy; maxy=miny; miny=tmpy; }
if (minz>maxz) { int tmpz=maxz; maxz=minz; minz=tmpz; }
- save_volume4D(input_vol.ROI(minx,miny,minz,mint,maxx,maxy,maxz,maxt),"foo2");
+ save_volume4D(input_vol.ROI(minx,miny,minz,mint,maxx,maxy,maxz,maxt),string(argv[2]));
return 0;
}
int main(int argc,char *argv[])
{
-
- Tracer tr("main");
-
try {
string progname=argv[0];
if (argc !=5 && argc !=9 && argc !=11)
--
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