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Commit 1656c6aa authored by David Flitney's avatar David Flitney
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volume.cc
+ 27
− 27
View file @ 1656c6aa
...@@ -8,7 +8,7 @@ ...@@ -8,7 +8,7 @@
#include <iostream> #include <iostream>
#include <cstdlib> #include <cstdlib>
#include "avwio/avwio.h" #include "fslio/fslio.h"
#include "newmatap.h" #include "newmatap.h"
#include "newmatio.h" #include "newmatio.h"
...@@ -129,12 +129,12 @@ namespace MISCMATHS { ...@@ -129,12 +129,12 @@ namespace MISCMATHS {
float fmin, fmax; float fmin, fmax;
const ColumnVector& outputvol = *this; 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); FslSetDim(OP,volinfo.x, volinfo.y, volinfo.z, 1);
AvwSetVoxDim(OP,volinfo.vx, volinfo.vy, volinfo.vz, 0); FslSetVoxDim(OP,volinfo.vx, volinfo.vy, volinfo.vz, 0);
AvwSetDataType(OP, DT_FLOAT); FslSetDataType(OP, DT_FLOAT);
AvwSetOriginator(OP, volinfo.originator); FslSetOriginator(OP, volinfo.originator);
int sizeVol = outputvol.Nrows(); int sizeVol = outputvol.Nrows();
...@@ -152,15 +152,15 @@ namespace MISCMATHS { ...@@ -152,15 +152,15 @@ namespace MISCMATHS {
qv[i-1] = outputvol(i); 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(qv,sizeVol*sizeof(float),1,OP->imgfp);
//fwrite(&OP->header,sizeof(OP->header),1,OP->hdrfp); //fwrite(&OP->header,sizeof(OP->header),1,OP->hdrfp);
AvwWriteVolumes(OP, qv, 1); FslWriteVolumes(OP, qv, 1);
delete [] qv; delete [] qv;
AvwClose(OP); FslClose(OP);
} }
void Volume::writeAsInt(const string& fname) void Volume::writeAsInt(const string& fname)
...@@ -169,12 +169,12 @@ namespace MISCMATHS { ...@@ -169,12 +169,12 @@ namespace MISCMATHS {
int fmin, fmax; int fmin, fmax;
const ColumnVector& outputvol = *this; 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); FslSetDim(OP, volinfo.x, volinfo.y, volinfo.z, 1);
AvwSetVoxDim(OP, volinfo.vx, volinfo.vy, volinfo.vz, 0); FslSetVoxDim(OP, volinfo.vx, volinfo.vy, volinfo.vz, 0);
AvwSetDataType(OP, DT_SIGNED_SHORT); FslSetDataType(OP, DT_SIGNED_SHORT);
AvwSetOriginator(OP, volinfo.originator); FslSetOriginator(OP, volinfo.originator);
int sizeVol = outputvol.Nrows(); int sizeVol = outputvol.Nrows();
...@@ -192,34 +192,34 @@ namespace MISCMATHS { ...@@ -192,34 +192,34 @@ namespace MISCMATHS {
qv[i-1] = (short)outputvol(i); 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; delete [] qv;
AvwClose(OP); FslClose(OP);
} }
void Volume::read(const string& fname) void Volume::read(const string& fname)
{ {
Time_Tracer ts(string("Volume::read" + fname).c_str()); 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; ColumnVector& output = *this;
short x,y,z,v,type; short x,y,z,v,type;
float vx,vy,vz,tr; float vx,vy,vz,tr;
AvwGetDim(IP,&x,&y,&z,&v); FslGetDim(IP,&x,&y,&z,&v);
AvwGetVoxDim(IP,&vx,&vy,&vz,&tr); FslGetVoxDim(IP,&vx,&vy,&vz,&tr);
AvwGetOriginator(IP,volinfo.originator); FslGetOriginator(IP,volinfo.originator);
volinfo.x = x; volinfo.y = y; volinfo.z = z; volinfo.v = v; volinfo.x = x; volinfo.y = y; volinfo.z = z; volinfo.v = v;
volinfo.vx = vx; volinfo.vy = vy; volinfo.vz = vz; volinfo.tr = tr; volinfo.vx = vx; volinfo.vy = vy; volinfo.vz = vz; volinfo.tr = tr;
size_t imagesize=x*y*z; size_t imagesize=x*y*z;
AvwGetDataType(IP,&type); FslGetDataType(IP,&type);
output.ReSize(x*y*z); output.ReSize(x*y*z);
...@@ -228,7 +228,7 @@ namespace MISCMATHS { ...@@ -228,7 +228,7 @@ namespace MISCMATHS {
case DT_SIGNED_SHORT: case DT_SIGNED_SHORT:
{ {
short* sbuffer=new short[imagesize]; 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++) for(size_t j = 1; j<=(size_t)x*y*z; j++)
{ {
...@@ -241,7 +241,7 @@ namespace MISCMATHS { ...@@ -241,7 +241,7 @@ namespace MISCMATHS {
case DT_FLOAT: case DT_FLOAT:
{ {
float* fbuffer=new float[imagesize]; 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++) for(size_t j = 1; j<=(size_t)x*y*z; j++)
{ {
...@@ -254,7 +254,7 @@ namespace MISCMATHS { ...@@ -254,7 +254,7 @@ namespace MISCMATHS {
case DT_UNSIGNED_CHAR: case DT_UNSIGNED_CHAR:
{ {
unsigned char* cbuffer=new unsigned char[imagesize]; 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++) for(size_t j = 1; j<=(size_t)x*y*z; j++)
{ {
...@@ -265,10 +265,10 @@ namespace MISCMATHS { ...@@ -265,10 +265,10 @@ namespace MISCMATHS {
} }
break; break;
default: default:
perror("AvwRead: DT not supported"); perror("FslRead: DT not supported");
} }
AvwClose(IP); FslClose(IP);
return; return;
} }
......
volumeseries.cc
+ 20
− 19
View file @ 1656c6aa
...@@ -8,7 +8,7 @@ ...@@ -8,7 +8,7 @@
#include <iostream> #include <iostream>
#include <cstdlib> #include <cstdlib>
#include "avwio/avwio.h" #include "fslio/fslio.h"
#include "newmatap.h" #include "newmatap.h"
#include "newmatio.h" #include "newmatio.h"
...@@ -97,7 +97,8 @@ namespace MISCMATHS { ...@@ -97,7 +97,8 @@ namespace MISCMATHS {
cerr << "j = " << j+1 << endl; cerr << "j = " << j+1 << endl;
} }
*/ */
if(m > thresh && s > 0.0)
if(m > thresh && s > 1e-10)
{ {
j++; j++;
preThresholdPositions(j) = i; preThresholdPositions(j) = i;
...@@ -133,21 +134,21 @@ namespace MISCMATHS { ...@@ -133,21 +134,21 @@ namespace MISCMATHS {
{ {
Time_Tracer ts(string("VolumeSeries::read-" + fname).c_str()); 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; Matrix& output = *this;
short x,y,z,v,type; short x,y,z,v,type;
float vx,vy,vz,tr; float vx,vy,vz,tr;
AvwGetDim(IP,&x,&y,&z,&v); FslGetDim(IP,&x,&y,&z,&v);
AvwGetVoxDim(IP,&vx,&vy,&vz,&tr); FslGetVoxDim(IP,&vx,&vy,&vz,&tr);
AvwGetOriginator(IP,volinfo.originator); FslGetOriginator(IP,volinfo.originator);
volinfo.x = x; volinfo.y = y; volinfo.z = z; volinfo.v = v; volinfo.x = x; volinfo.y = y; volinfo.z = z; volinfo.v = v;
volinfo.vx = vx; volinfo.vy = vy; volinfo.vz = vz; volinfo.tr = tr; volinfo.vx = vx; volinfo.vy = vy; volinfo.vz = vz; volinfo.tr = tr;
size_t imagesize=x*y*z*v; size_t imagesize=x*y*z*v;
AvwGetDataType(IP,&type); FslGetDataType(IP,&type);
output.ReSize(v,x*y*z); output.ReSize(v,x*y*z);
...@@ -157,7 +158,7 @@ namespace MISCMATHS { ...@@ -157,7 +158,7 @@ namespace MISCMATHS {
{ {
short* sbuffer=new short[imagesize]; short* sbuffer=new short[imagesize];
AvwReadVolumes(IP, sbuffer,v); FslReadVolumes(IP, sbuffer,v);
size_t volsize = volinfo.x*volinfo.y*volinfo.z; size_t volsize = volinfo.x*volinfo.y*volinfo.z;
size_t volstart = 1; size_t volstart = 1;
...@@ -177,7 +178,7 @@ namespace MISCMATHS { ...@@ -177,7 +178,7 @@ namespace MISCMATHS {
case DT_FLOAT: case DT_FLOAT:
{ {
float* fbuffer=new float[imagesize]; float* fbuffer=new float[imagesize];
AvwReadVolumes(IP,fbuffer,v); FslReadVolumes(IP,fbuffer,v);
size_t volsize = volinfo.x*volinfo.y*volinfo.z; size_t volsize = volinfo.x*volinfo.y*volinfo.z;
size_t volstart = 1; size_t volstart = 1;
...@@ -195,7 +196,7 @@ namespace MISCMATHS { ...@@ -195,7 +196,7 @@ namespace MISCMATHS {
case DT_UNSIGNED_CHAR: case DT_UNSIGNED_CHAR:
{ {
unsigned char* cbuffer=new unsigned char[imagesize]; 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 volsize = volinfo.x*volinfo.y*volinfo.z;
size_t volstart = 1; size_t volstart = 1;
...@@ -211,10 +212,10 @@ namespace MISCMATHS { ...@@ -211,10 +212,10 @@ namespace MISCMATHS {
} }
break; break;
default: default:
perror("AvwRead: DT not supported"); perror("FslRead: DT not supported");
} }
AvwClose(IP); FslClose(IP);
return; return;
} }
...@@ -230,12 +231,12 @@ namespace MISCMATHS { ...@@ -230,12 +231,12 @@ namespace MISCMATHS {
{ {
Time_Tracer ts(string("VolumeSeries::writeAsFloat" + fname).c_str()); 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); FslSetDim(OP,volinfo.x, volinfo.y, volinfo.z, volinfo.v);
AvwSetVoxDim(OP,volinfo.vx, volinfo.vy, volinfo.vz, volinfo.tr); FslSetVoxDim(OP,volinfo.vx, volinfo.vy, volinfo.vz, volinfo.tr);
AvwSetDataType(OP, DT_FLOAT); FslSetDataType(OP, DT_FLOAT);
AvwSetOriginator(OP, volinfo.originator); FslSetOriginator(OP, volinfo.originator);
int volStart = 1; int volStart = 1;
int volSize = getNumSeries(); int volSize = getNumSeries();
...@@ -252,11 +253,11 @@ namespace MISCMATHS { ...@@ -252,11 +253,11 @@ namespace MISCMATHS {
} }
} }
AvwWriteVolumes(OP, qv, volNum); FslWriteVolumes(OP, qv, volNum);
delete [] qv; delete [] qv;
AvwClose(OP); FslClose(OP);
} }
......
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