From 4938cf7bbf7932b62a73f4c537f9e5c471a5c897 Mon Sep 17 00:00:00 2001
From: Mark Jenkinson <mark@fmrib.ox.ac.uk>
Date: Fri, 5 Aug 2005 11:16:17 +0000
Subject: [PATCH] Hopefully fixed bugs in avwstats++, except -r and -R when -l
and -u are used - but this is an old, existing bug
---
fslstats.cc | 66 ++++++++++++++++++++++++-----------------------------
1 file changed, 30 insertions(+), 36 deletions(-)
diff --git a/fslstats.cc b/fslstats.cc
index 7202436..25901f9 100644
--- a/fslstats.cc
+++ b/fslstats.cc
@@ -11,7 +11,6 @@
#include "miscmaths/miscmaths.h"
#include "newimage/newimageall.h"
-#include "newimage/fmribmain.h"
#include "newimage/costfns.h"
using namespace NEWIMAGE;
@@ -53,8 +52,7 @@ void print_usage(const string& progname) {
// Some specialised nonzero functions just for speedup
// (it avoids generating masks when not absolutely necessary)
-template <class T>
-long int nonzerocount(const volume4D<T>& vol)
+long int nonzerocount(const volume4D<float>& vol)
{
long int totn=0;
for (int t=vol.mint(); t<=vol.maxt(); t++) {
@@ -71,8 +69,7 @@ long int nonzerocount(const volume4D<T>& vol)
return totn;
}
-template <class T>
-double nonzeromean(const volume4D<T>& vol)
+double nonzeromean(const volume4D<float>& vol)
{
double totv=0.0;
long int totn=0;
@@ -95,8 +92,7 @@ double nonzeromean(const volume4D<T>& vol)
return meanval;
}
-template <class T>
-double nonzerostddev(const volume4D<T>& vol)
+double nonzerostddev(const volume4D<float>& vol)
{
double totv=0.0, totvv=0.0;
long int totn=0;
@@ -105,7 +101,7 @@ double nonzerostddev(const volume4D<T>& vol)
for (int y=vol.miny(); y<=vol.maxy(); y++) {
for (int x=vol.minx(); x<=vol.maxx(); x++) {
if (vol(x,y,z,t)!=0.0) {
- T v=vol(x,y,z,t);
+ float v=vol(x,y,z,t);
totvv+=(double) v*v;
totv+=(double) v;
totn++;
@@ -122,27 +118,24 @@ double nonzerostddev(const volume4D<T>& vol)
return std::sqrt(var);
}
-template <class T>
-int generate_masks(volume4D<T> &mask, volume4D<T> &masknz, const volume4D<T> &vin,
- T& lthr, T& uthr)
+int generate_masks(volume4D<float> &mask, volume4D<float> &masknz, const volume4D<float> &vin,
+ float& lthr, float& uthr)
{
if (!lthr_used) { lthr=vin.min()-1; }
if (!uthr_used) { uthr=vin.max()+1; }
mask = binarise(vin,lthr,uthr,exclusive);
- masknz = mask * ((T) 1 - binarise(vin,(T) 0.0, (T) 0.0));
+ masknz = mask * (1.0f - binarise(vin,0.0f, 0.0f));
return 0;
}
-template <class T>
-int generate_masks(const volume4D<T> &mask, volume4D<T> &masknz, const volume4D<T> &vin)
+int generate_masks(const volume4D<float> &mask, volume4D<float> &masknz, const volume4D<float> &vin)
{
- masknz = mask * ((T) 1 - binarise(vin,(T) 0.0, (T) 0.0));
+ masknz = mask * (1.0f - binarise(vin,0.0f, 0.0f));
return 0;
}
-template <class T>
-int fmrib_main(int argc, char* argv[])
+int fmrib_main_float(int argc, char* argv[])
{
cout.setf(ios::dec);
@@ -150,10 +143,10 @@ int fmrib_main(int argc, char* argv[])
cout.setf(ios::left, ios::adjustfield);
cout.precision(6);
- volume4D<T> vin, vol, mask, masknz;
+ volume4D<float> vin, vol, mask, masknz;
read_volume4D(vol,argv[1]);
- T lthr=0, uthr=0; // these initial values are not used
+ float lthr=0, uthr=0; // these initial values are not used
if (masks_used) {
vin = vol;
generate_masks(mask,masknz,vin,lthr,uthr);
@@ -205,8 +198,8 @@ int fmrib_main(int argc, char* argv[])
for(int z=masknz.minz();z<=masknz.maxz();z++) {
for(int y=masknz.miny();y<=masknz.maxy();y++) {
for(int x=masknz.minx();x<=masknz.maxx();x++) {
- if (masknz(x,y,z,t)>(T) 0.5) {
- // if (masknz(x,y,z)>(T) 0.5) {
+ if (masknz(x,y,z,t)>0.5) {
+ // if (masknz(x,y,z)>0.5) {
if (x<xmin) xmin=x;
if (x>xmax) xmax=x;
if (y<ymin) ymin=y;
@@ -278,18 +271,18 @@ int fmrib_main(int argc, char* argv[])
masks_used=true;
vin = vol;
}
- T th=(T) 0.5;
+ float th= 0.5;
if (th!=0) {
mask.binarise(th);
} else {
- mask.binarise((T) 1);
+ mask.binarise(1);
}
- generate_masks<T>(mask,masknz,vin);
+ generate_masks(mask,masknz,vin);
vol = vin * mask;
} else if (sarg=="-l") {
narg++;
if (narg<argc) {
- lthr = (T) atof(argv[narg]);
+ lthr = atof(argv[narg]);
} else {
cerr << "Must specify an argument to -l" << endl;
exit(2);
@@ -299,12 +292,12 @@ int fmrib_main(int argc, char* argv[])
masks_used=true;
vin = vol;
}
- generate_masks<T>(mask,masknz,vin,lthr,uthr);
+ generate_masks(mask,masknz,vin,lthr,uthr);
vol = vin * mask;
} else if (sarg=="-u") {
narg++;
if (narg<argc) {
- uthr = (T) atof(argv[narg]);
+ uthr = atof(argv[narg]);
} else {
cerr << "Must specify an argument to -u" << endl;
exit(2);
@@ -314,7 +307,7 @@ int fmrib_main(int argc, char* argv[])
masks_used=true;
vin = vol;
}
- generate_masks<T>(mask,masknz,vin,lthr,uthr);
+ generate_masks(mask,masknz,vin,lthr,uthr);
vol = vin * mask;
} else if (sarg=="-a") {
vol = abs(vin);
@@ -350,7 +343,14 @@ int fmrib_main(int argc, char* argv[])
}
} else if (sarg=="-r") {
if (masks_used) {
- cout << vol.robustmin(mask) << " " << vol.robustmax(mask) << " ";
+ float rmin=vol.robustmin(mask);
+ float rmax=vol.robustmax(mask);
+ if (rmin>rmax) {
+ float tmp = rmax;
+ rmax = rmin;
+ rmin = tmp;
+ }
+ cout << rmin << " " << rmax << " ";
} else {
cout << vol.robustmin() << " " << vol.robustmax() << " ";
}
@@ -433,13 +433,7 @@ int main(int argc,char *argv[])
return 1;
}
- int datatype = dtype(string(argv[1]));
+ return fmrib_main_float(argc,argv);
- if (datatype==DT_UNSIGNED_CHAR) {
- // avoid using char as all print outs become non-numeric!
- return fmrib_main<short>(argc,argv);
- } else {
- return call_fmrib_main(datatype,argc,argv);
- }
}
--
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