diff --git a/volume.cc b/volume.cc
index 8929716df79d622ae14cb488723c1eb9ec9a2fdd..7bb1c0319d7fb24549afd5714833c8b867baadbb 100644
--- a/volume.cc
+++ b/volume.cc
@@ -8,7 +8,7 @@
#include <iostream>
#include <cstdlib>
-#include "avwio/avwio.h"
+#include "fslio/fslio.h"
#include "newmatap.h"
#include "newmatio.h"
@@ -129,12 +129,12 @@ namespace MISCMATHS {
float fmin, fmax;
const ColumnVector& outputvol = *this;
- AVW* OP = AvwOpen(fname.c_str(), "wc");
+ FSLIO* OP = FslOpen(fname.c_str(), "wc");
- AvwSetDim(OP,volinfo.x, volinfo.y, volinfo.z, 1);
- AvwSetVoxDim(OP,volinfo.vx, volinfo.vy, volinfo.vz, 0);
- AvwSetDataType(OP, DT_FLOAT);
- AvwSetOriginator(OP, volinfo.originator);
+ FslSetDim(OP,volinfo.x, volinfo.y, volinfo.z, 1);
+ FslSetVoxDim(OP,volinfo.vx, volinfo.vy, volinfo.vz, 0);
+ FslSetDataType(OP, DT_FLOAT);
+ FslSetOriginator(OP, volinfo.originator);
int sizeVol = outputvol.Nrows();
@@ -152,15 +152,15 @@ namespace MISCMATHS {
qv[i-1] = outputvol(i);
}
- AvwSetMinMax(OP, (short)fmin, (short)fmax);
+ FslSetMinMax(OP, (short)fmin, (short)fmax);
// fwrite(qv,sizeVol*sizeof(float),1,OP->imgfp);
//fwrite(&OP->header,sizeof(OP->header),1,OP->hdrfp);
- AvwWriteVolumes(OP, qv, 1);
+ FslWriteVolumes(OP, qv, 1);
delete [] qv;
- AvwClose(OP);
+ FslClose(OP);
}
void Volume::writeAsInt(const string& fname)
@@ -169,12 +169,12 @@ namespace MISCMATHS {
int fmin, fmax;
const ColumnVector& outputvol = *this;
- AVW* OP = AvwOpen(fname.c_str(), "wc");
+ FSLIO* OP = FslOpen(fname.c_str(), "wc");
- AvwSetDim(OP, volinfo.x, volinfo.y, volinfo.z, 1);
- AvwSetVoxDim(OP, volinfo.vx, volinfo.vy, volinfo.vz, 0);
- AvwSetDataType(OP, DT_SIGNED_SHORT);
- AvwSetOriginator(OP, volinfo.originator);
+ FslSetDim(OP, volinfo.x, volinfo.y, volinfo.z, 1);
+ FslSetVoxDim(OP, volinfo.vx, volinfo.vy, volinfo.vz, 0);
+ FslSetDataType(OP, DT_SIGNED_SHORT);
+ FslSetOriginator(OP, volinfo.originator);
int sizeVol = outputvol.Nrows();
@@ -192,34 +192,34 @@ namespace MISCMATHS {
qv[i-1] = (short)outputvol(i);
}
- AvwSetMinMax(OP, (short)fmin, (short)(fmax+0.9999));
+ FslSetMinMax(OP, (short)fmin, (short)(fmax+0.9999));
- AvwWriteVolumes(OP, qv, 1);
+ FslWriteVolumes(OP, qv, 1);
delete [] qv;
- AvwClose(OP);
+ FslClose(OP);
}
void Volume::read(const string& fname)
{
Time_Tracer ts(string("Volume::read" + fname).c_str());
- AVW* IP = AvwOpen(fname.c_str(), "r");
+ FSLIO* IP = FslOpen(fname.c_str(), "r");
ColumnVector& output = *this;
short x,y,z,v,type;
float vx,vy,vz,tr;
- AvwGetDim(IP,&x,&y,&z,&v);
- AvwGetVoxDim(IP,&vx,&vy,&vz,&tr);
- AvwGetOriginator(IP,volinfo.originator);
+ FslGetDim(IP,&x,&y,&z,&v);
+ FslGetVoxDim(IP,&vx,&vy,&vz,&tr);
+ FslGetOriginator(IP,volinfo.originator);
volinfo.x = x; volinfo.y = y; volinfo.z = z; volinfo.v = v;
volinfo.vx = vx; volinfo.vy = vy; volinfo.vz = vz; volinfo.tr = tr;
size_t imagesize=x*y*z;
- AvwGetDataType(IP,&type);
+ FslGetDataType(IP,&type);
output.ReSize(x*y*z);
@@ -228,7 +228,7 @@ namespace MISCMATHS {
case DT_SIGNED_SHORT:
{
short* sbuffer=new short[imagesize];
- AvwReadVolumes(IP,sbuffer,v);
+ FslReadVolumes(IP,sbuffer,v);
for(size_t j = 1; j<=(size_t)x*y*z; j++)
{
@@ -241,7 +241,7 @@ namespace MISCMATHS {
case DT_FLOAT:
{
float* fbuffer=new float[imagesize];
- AvwReadVolumes(IP,fbuffer,v);
+ FslReadVolumes(IP,fbuffer,v);
for(size_t j = 1; j<=(size_t)x*y*z; j++)
{
@@ -254,7 +254,7 @@ namespace MISCMATHS {
case DT_UNSIGNED_CHAR:
{
unsigned char* cbuffer=new unsigned char[imagesize];
- AvwReadVolumes(IP,cbuffer,v);
+ FslReadVolumes(IP,cbuffer,v);
for(size_t j = 1; j<=(size_t)x*y*z; j++)
{
@@ -265,10 +265,10 @@ namespace MISCMATHS {
}
break;
default:
- perror("AvwRead: DT not supported");
+ perror("FslRead: DT not supported");
}
- AvwClose(IP);
+ FslClose(IP);
return;
}
diff --git a/volumeseries.cc b/volumeseries.cc
index 4587407fd86bde3b23602be39b534ee968b78ff5..8e2a7552ecf2bde3b25c1b058b8076b5af8b4a06 100644
--- a/volumeseries.cc
+++ b/volumeseries.cc
@@ -8,7 +8,7 @@
#include <iostream>
#include <cstdlib>
-#include "avwio/avwio.h"
+#include "fslio/fslio.h"
#include "newmatap.h"
#include "newmatio.h"
@@ -97,7 +97,8 @@ namespace MISCMATHS {
cerr << "j = " << j+1 << endl;
}
*/
- if(m > thresh && s > 0.0)
+
+ if(m > thresh && s > 1e-10)
{
j++;
preThresholdPositions(j) = i;
@@ -133,21 +134,21 @@ namespace MISCMATHS {
{
Time_Tracer ts(string("VolumeSeries::read-" + fname).c_str());
- AVW* IP = AvwOpen(fname.c_str(), "r");
+ FSLIO* IP = FslOpen(fname.c_str(), "r");
Matrix& output = *this;
short x,y,z,v,type;
float vx,vy,vz,tr;
- AvwGetDim(IP,&x,&y,&z,&v);
- AvwGetVoxDim(IP,&vx,&vy,&vz,&tr);
- AvwGetOriginator(IP,volinfo.originator);
+ FslGetDim(IP,&x,&y,&z,&v);
+ FslGetVoxDim(IP,&vx,&vy,&vz,&tr);
+ FslGetOriginator(IP,volinfo.originator);
volinfo.x = x; volinfo.y = y; volinfo.z = z; volinfo.v = v;
volinfo.vx = vx; volinfo.vy = vy; volinfo.vz = vz; volinfo.tr = tr;
size_t imagesize=x*y*z*v;
- AvwGetDataType(IP,&type);
+ FslGetDataType(IP,&type);
output.ReSize(v,x*y*z);
@@ -157,7 +158,7 @@ namespace MISCMATHS {
{
short* sbuffer=new short[imagesize];
- AvwReadVolumes(IP, sbuffer,v);
+ FslReadVolumes(IP, sbuffer,v);
size_t volsize = volinfo.x*volinfo.y*volinfo.z;
size_t volstart = 1;
@@ -177,7 +178,7 @@ namespace MISCMATHS {
case DT_FLOAT:
{
float* fbuffer=new float[imagesize];
- AvwReadVolumes(IP,fbuffer,v);
+ FslReadVolumes(IP,fbuffer,v);
size_t volsize = volinfo.x*volinfo.y*volinfo.z;
size_t volstart = 1;
@@ -195,7 +196,7 @@ namespace MISCMATHS {
case DT_UNSIGNED_CHAR:
{
unsigned char* cbuffer=new unsigned char[imagesize];
- AvwReadVolumes(IP,cbuffer,v);
+ FslReadVolumes(IP,cbuffer,v);
size_t volsize = volinfo.x*volinfo.y*volinfo.z;
size_t volstart = 1;
@@ -211,10 +212,10 @@ namespace MISCMATHS {
}
break;
default:
- perror("AvwRead: DT not supported");
+ perror("FslRead: DT not supported");
}
- AvwClose(IP);
+ FslClose(IP);
return;
}
@@ -230,12 +231,12 @@ namespace MISCMATHS {
{
Time_Tracer ts(string("VolumeSeries::writeAsFloat" + fname).c_str());
- AVW* OP = AvwOpen(fname.c_str(), "wc");
+ FSLIO* OP = FslOpen(fname.c_str(), "wc");
- AvwSetDim(OP,volinfo.x, volinfo.y, volinfo.z, volinfo.v);
- AvwSetVoxDim(OP,volinfo.vx, volinfo.vy, volinfo.vz, volinfo.tr);
- AvwSetDataType(OP, DT_FLOAT);
- AvwSetOriginator(OP, volinfo.originator);
+ FslSetDim(OP,volinfo.x, volinfo.y, volinfo.z, volinfo.v);
+ FslSetVoxDim(OP,volinfo.vx, volinfo.vy, volinfo.vz, volinfo.tr);
+ FslSetDataType(OP, DT_FLOAT);
+ FslSetOriginator(OP, volinfo.originator);
int volStart = 1;
int volSize = getNumSeries();
@@ -252,11 +253,11 @@ namespace MISCMATHS {
}
}
- AvwWriteVolumes(OP, qv, volNum);
+ FslWriteVolumes(OP, qv, volNum);
delete [] qv;
- AvwClose(OP);
+ FslClose(OP);
}