diff --git a/Makefile b/Makefile
index 8f445a1f6997ad89e1b72a180436d5b10dfaa447..42d7cb86e7c34802b41b44ba71326518a28a4025 100644
--- a/Makefile
+++ b/Makefile
@@ -6,15 +6,15 @@ PROJNAME = avwutils
USRINCFLAGS = -I${INC_NEWMAT} -I${INC_PROB} -I${INC_ZLIB}
USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_ZLIB}
-LIBS = -lnewimage -lmiscmaths -lprob -lfslio -lnewmat -lutils -lniftiio -lznz -lm -lz
+LIBS = -lnewimage -lmiscmaths -lprob -lfslio -lNewNifti -lnewmat -lutils -lniftiio -lznz -lm -lz
IOLIBS = -lfslio -lniftiio -lznz -lm -lz
XFILES = fslorient fslstats fslmerge \
fslpspec fslroi fslnvols fsl2ascii fslascii2img \
fslsplit fslcc fslinterleave \
- fslhd fslcpgeom fslcreatehd fslcorrecthd fslmaths \
- fslcomplex fslfft fslmeants fslslice fslswapdim_exe fslchfiletype_exe
+ fslhd fslcpgeom fslcreatehd fslcorrecthd \
+ fslmeants fslslice fslswapdim_exe fslchfiletype_exe fslmaths fslcomplex fslfft
SCRIPTS = fslval fslchpixdim fslanimate fslsize sliceanimate fslinfo fsledithd avw2fsl fslswapdim fslchfiletype fslreorient2std
diff --git a/fsl2ascii.cc b/fsl2ascii.cc
index c790df21876b77a6f4e4e6c889da6337aa41e755..92ded9cefcf986045d49b546ea62dc65023c9745 100755
--- a/fsl2ascii.cc
+++ b/fsl2ascii.cc
@@ -25,14 +25,14 @@ int fmrib_main(int argc, char *argv[])
string output_name=string(argv[2]);
ofstream output_file;
int i,j,k,t;
- for(t=0;t<=input_volume.maxt();t++)
+ for(t=0;t<input_volume.tsize();t++)
{
output_file.open((output_name+num2str(t,5)).c_str(),ofstream::out);
- for(k=0;k<=input_volume.maxz();k++)
+ for(k=0;k<input_volume.zsize();k++)
{
- for(j=0;j<=input_volume.maxy();j++)
+ for(j=0;j<input_volume.ysize();j++)
{
- for(i=0;i<=input_volume.maxx();i++)
+ for(i=0;i<input_volume.xsize();i++)
{
output_file << input_volume(i,j,k,t) << " ";
}
diff --git a/fslcc.cc b/fslcc.cc
index 08407325fc033ee5eef3b9a49eaa48d22e85f4bd..13626f1e31fefb2e8eed890821b3eba28e8f4c47 100755
--- a/fslcc.cc
+++ b/fslcc.cc
@@ -44,16 +44,16 @@ int fmrib_main(int argc, char *argv[])
input_volume1-=input_volume1.mean();
input_volume2-=input_volume2.mean();
}
- for(int t1=0;t1<=input_volume1.maxt();t1++)
+ for(int t1=0;t1<input_volume1.tsize();t1++)
{
- double ss1=sqrt(input_volume1[t1].sumsquares());
- for(int t2=0;t2<=input_volume2.maxt();t2++)
+ double ss1=sqrt(input_volume1.constantSubVolume(t1).sumsquares());
+ for(int t2=0;t2<input_volume2.tsize();t2++)
{
- double ss2=sqrt(input_volume2[t2].sumsquares());
+ double ss2=sqrt(input_volume2.constantSubVolume(t2).sumsquares());
double score=0;
- for(int k=0;k<=input_volume1.maxz();k++)
- for(int j=0;j<=input_volume1.maxy();j++)
- for(int i=0;i<=input_volume1.maxx();i++)
+ for(int k=0;k<input_volume1.zsize();k++)
+ for(int j=0;j<input_volume1.ysize();j++)
+ for(int i=0;i<=input_volume1.xsize();i++)
score+=(double)input_volume1(i,j,k,t1)*(double)input_volume2(i,j,k,t2);
if (!noabs.value())
score=fabs(score);
diff --git a/fslcreatehd.cc b/fslcreatehd.cc
index 4823ae3880ddb8668cc4cb47638da40bf31aaec4..1faf1eb8763eae5e8dbb404097ffbfb4c129c60d 100755
--- a/fslcreatehd.cc
+++ b/fslcreatehd.cc
@@ -58,11 +58,6 @@ int fslcreatehd_main(int argc, char *argv[])
filetype = FslGetFileType(fslio);
}
- if (FslBaseFileType(FslGetFileType(fslio))==FSL_TYPE_MINC) {
- cerr << "Minc file type is not supported yet" << endl;
- exit(EXIT_FAILURE);
- }
-
if (argc>3) {
/* set uninteresting defaults */
if (existingimage) {
diff --git a/fslhd.cc b/fslhd.cc
index 767b3e84c4ba99a3d73c7636e543e9498965e743..17088f8cab09317f4567ffbe839f78b7c97be74c 100755
--- a/fslhd.cc
+++ b/fslhd.cc
@@ -1,6 +1,6 @@
// fslhd.cc - show image header
// Steve Smith, Mark Jenkinson and Matthew Webster, FMRIB Image Analysis Group
-// Copyright (C) 2000-2005 University of Oxford
+// Copyright (C) 2000-2012 University of Oxford
// CCOPYRIGHT
#include "newimage/newimageall.h"
@@ -25,10 +25,6 @@ void ShowNifti(FSLIO* fslio)
cout << nifti_image_to_ascii(fslio->niftiptr) << endl;
return;
}
- if (fslio->mincptr!=NULL) {
- cerr << "ERROR: Minc is not currently supported" << endl;
- return;
- }
return;
}
@@ -46,11 +42,6 @@ void ShowHdr(char *fileName, FSLIO* fslio)
}
ft = FslGetFileType(fslio);
- if (FslBaseFileType(ft)==FSL_TYPE_MINC)
- {
- cerr << "ERROR: Minc is not currently supported" << endl;
- return;
- }
if (fslio->niftiptr == NULL)
{
diff --git a/fslmaths.cc b/fslmaths.cc
index 8d5f6bb6869dff093daf24ef854fdd8a1eaa6b39..d1649738b1151ca353154ee7b5c9c4c2520d3b9c 100755
--- a/fslmaths.cc
+++ b/fslmaths.cc
@@ -144,7 +144,7 @@ void loadNewImage(volume4D<T> &oldI, volume4D<T> &newI, string filename)
volume4D<T> tmpvol=oldI;
oldI.reinitialize(oldI.xsize(),oldI.ysize(),oldI.zsize(),newI.tsize());
oldI.copyproperties(tmpvol);
- for (int t=0;t<newI.tsize();t++) oldI[t]=tmpvol[0];
+ for (int t=0;t<newI.tsize();t++) oldI[t]=tmpvol.constantSubVolume(0);
}
// sanity check on valid orientation info (it should be consistent)
diff --git a/fslmeants.cc b/fslmeants.cc
index bd775216efa437c72d97dca76f78782509567d3e..df8fdde13b70e14ee26af3243e0e44ad83a0ad30 100644
--- a/fslmeants.cc
+++ b/fslmeants.cc
@@ -123,7 +123,7 @@ int main(int argc,char *argv[])
if (maskname.set()) {
read_volume(mask,maskname.value());
} else {
- mask = vin[0];
+ mask = vin.constantSubVolume(0);
mask = 1.0;
}
@@ -167,7 +167,7 @@ int main(int argc,char *argv[])
// override the mask (and label) if a coordinate is specified
if (coordval.set()) {
- mask = vin[0];
+ mask = vin.constantSubVolume(0);
mask = 0.0;
float x, y, z;
x = coordval.value(0);
@@ -177,16 +177,16 @@ int main(int argc,char *argv[])
v << x << y << z << 1.0;
if (usemm.value()) {
// convert from mm to newimage voxels
- v = (vin[0].newimagevox2mm_mat()).i() * v;
+ v = (vin.constantSubVolume(0).newimagevox2mm_mat()).i() * v;
} else {
// convert from nifti voxels (input) to newimage voxels (internal)
- v = vin[0].niftivox2newimagevox_mat() * v;
+ v = vin.constantSubVolume(0).niftivox2newimagevox_mat() * v;
}
x = v(1); y = v(2); z = v(3);
mask(MISCMATHS::round(x),MISCMATHS::round(y),MISCMATHS::round(z)) = 1.0;
}
- if (!samesize(vin[0],mask)) {
+ if (!samesize(vin.constantSubVolume(0),mask)) {
cerr << "ERROR: Mask and Input volumes have different (x,y,z) size."
<< endl;
return -1;
@@ -251,7 +251,7 @@ int main(int argc,char *argv[])
if (showall.value()) {
ColumnVector v(4);
v << x << y << z << 1.0;
- v = (vin[0].niftivox2newimagevox_mat()).i() * v;
+ v = (vin.constantSubVolume(0).niftivox2newimagevox_mat()).i() * v;
meants(1,num) = v(1);
meants(2,num) = v(2);
meants(3,num) = v(3);
diff --git a/fslmerge.cc b/fslmerge.cc
index ccf1d20cd646a9360b38440d5bb2d38f5a2e984c..50f95a6d9f78201b4134a6242b403c0b90fd535c 100755
--- a/fslmerge.cc
+++ b/fslmerge.cc
@@ -23,10 +23,11 @@ template <class T>
int fmrib_main(int argc, char *argv[])
{
volume4D<T> input_volume;
- float newTR(-1);
int direction,dimerror=0,xoffset=0,yoffset=0,zoffset=0,toffset=0;
- read_volume4D_hdr_only(input_volume,string(argv[3]));
- newTR = input_volume.TR();
+
+ NiftiIO reader;
+ NiftiHeader header(reader.loadHeader(string(argv[3])));
+ float newTR(header.pixdim[3]);
if (!strcmp(argv[1], "-t")) direction=0;
else if (!strcmp(argv[1], "-x")) direction=1;
@@ -43,27 +44,21 @@ int fmrib_main(int argc, char *argv[])
return(1);
}
- int xdimtot(input_volume.xsize());
- int ydimtot(input_volume.ysize());
- int zdimtot(input_volume.zsize());
- int tdimtot(input_volume.tsize());
+ int xdimtot(header.dim[0]), ydimtot(header.dim[1]), zdimtot(header.dim[2]), tdimtot(header.dim[3]);
if(direction==4)
{
- if( (zdimtot<2) && (tdimtot<2) ) direction=3;
+ if( zdimtot<2 && tdimtot<2 ) direction=3;
else direction=0;
}
- input_volume.destroy(); //Remove when new newimage comes out
for(int vol = 4; vol < argc; vol++)
- {
- read_volume4D_hdr_only(input_volume,string(argv[vol]));
- if (direction==0) tdimtot+=input_volume.tsize();
- // cerr << tdimtot << endl; //This will give errors in tdimtot if input_volume.destroy not present
- if (direction==1) xdimtot+=input_volume.xsize();
- if (direction==2) ydimtot+=input_volume.ysize();
- if (direction==3) zdimtot+=input_volume.zsize();
- input_volume.destroy(); //Remove when new newimage comes out
+ {
+ header=reader.loadHeader(string(argv[vol]));
+ if (direction==0) tdimtot+=header.dim[3];
+ if (direction==1) xdimtot+=header.dim[0];
+ if (direction==2) ydimtot+=header.dim[1];
+ if (direction==3) zdimtot+=header.dim[2];
}
volume4D<T> output_volume(xdimtot,ydimtot,zdimtot,tdimtot);
read_volume4D(input_volume,string(argv[3]));
@@ -104,7 +99,6 @@ int fmrib_main(int argc, char *argv[])
if (direction==1) xoffset+=input_volume.xsize();
if (direction==2) yoffset+=input_volume.ysize();
if (direction==3) zoffset+=input_volume.zsize();
- input_volume.destroy(); //Remove when new newimage comes out
}
output_volume.setTR(newTR);
save_volume4D(output_volume,string(argv[2]));
diff --git a/fslnvols.cc b/fslnvols.cc
index 41bc57d31354e4c786ecca29598cec4554e81b82..78b3ad5d1c103971cab5050962d6f3c875264813 100755
--- a/fslnvols.cc
+++ b/fslnvols.cc
@@ -18,13 +18,10 @@ void print_usage(const string& progname)
template <class T>
int fmrib_main(int argc, char *argv[])
{
- FSLIO *IP1;
- IP1 = NewFslOpen(string(argv[1]), "r");
- if (IP1==0) throw Exception(("Failed to read volume "+string(argv[1])).c_str());
- short sx=0,sy=0,sz=0,st=0;
- FslGetDim(IP1,&sx,&sy,&sz,&st);
- FslClose(IP1);
- cout << st << endl;
+
+ NiftiIO reader;
+ NiftiHeader header(reader.loadHeader(string(argv[1])));
+ cout << header.dim[4] << endl;
return 0;
}
diff --git a/fslorient.cc b/fslorient.cc
index c2a2b2a177c2faea902005234608058e09956257..591855158965f02245c94b1fd9e24be8f6facdac 100644
--- a/fslorient.cc
+++ b/fslorient.cc
@@ -2,7 +2,7 @@
Mark Jenkinson and Matthew Webster, FMRIB Image Analysis Group
- Copyright (C) 2003-20047 University of Oxford */
+ Copyright (C) 2003-2012 University of Oxford */
/* CCOPYRIGHT */
@@ -69,16 +69,6 @@ int getorient(const volume4D<T>& invol)
return 0;
}
-
-template <class T>
-int getorient(const string& filename)
-{
- volume4D<T> invol;
- read_orig_volume4D(invol,filename);
- return getorient(invol);
-}
-
-
int showmat(const Matrix& mat) {
for (int a=1; a<=4; a++) {
for (int b=1; b<=4; b++) {
@@ -102,16 +92,13 @@ int testminargs(int argnum, int argc) {
template <class T>
int fmrib_main(int argc,char *argv[])
{
- bool modified=false;
- int retval=0;
- string option=argv[1], filename;
-
+ bool modified(false);
+ string option(argv[1]), filename(argv[argc-1]);
volume4D<T> invol;
- filename=argv[argc-1];
read_orig_volume4D(invol,filename);
- if (option=="-getorient") {
+ if ( argc==2 || option=="-getorient") {
getorient(invol);
} else if (option=="-getsformcode") {
cout << invol.sform_code() << endl;
@@ -171,20 +158,16 @@ int fmrib_main(int argc,char *argv[])
if (invol.left_right_order()==FSL_RADIOLOGICAL) {
swaporient(invol);
}
- } else{
- // does the first arg exist as an image file?
- if (fsl_imageexists(string(argv[1]))) {
- getorient<T>(string(argv[1]));
- } else {
- cerr << "Unrecognised option: " << option << endl;
- print_usage();
- retval = -1;
- }
+ } else {
+ cerr << "Unrecognised option: " << option << endl;
+ print_usage();
+ return(-1);
}
+
if (modified) {
- if (FslBaseFileType(fslFileType(filename))!=FSL_TYPE_ANALYZE) {
+ if ( FslBaseFileType(fslFileType(filename)) != FSL_TYPE_ANALYZE ) {
FslSetOverrideOutputType(fslFileType(filename));
save_orig_volume4D(invol,filename);
FslSetOverrideOutputType(-1); // restore to default
@@ -192,10 +175,10 @@ int fmrib_main(int argc,char *argv[])
cerr << "Cannot modify orientation for Analyze files" << endl;
cerr << " All Analyze files are treated as radiological" << endl;
cerr << " To change the data storage use fslswapdim" << endl;
- retval=-1;
+ return(-1);
}
}
- return retval;
+ return 0;
}
@@ -205,10 +188,6 @@ int main(int argc,char *argv[])
print_usage();
return -1;
}
-
- string inname;
- inname = argv[argc-1];
- // call the templated main
- return call_fmrib_main(dtype(inname),argc,argv);
+ return call_fmrib_main(dtype(string(argv[argc-1])),argc,argv);
}
diff --git a/fslroi.cc b/fslroi.cc
index 040fafd7978f0ba73f9ad4783a99213b1878f2f5..90dc85358ac588922c5340a6008f18b132e84f75 100755
--- a/fslroi.cc
+++ b/fslroi.cc
@@ -21,11 +21,11 @@ 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,input_name);
+ string input_name(string(argv[1]));
+ string output_name(string(argv[2]));
+ 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;
+ 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
if (argc==5) //4D Timeseries only
{
@@ -99,10 +99,7 @@ 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; }
- input_vol.setROIlimits(minx,miny,minz,mint,maxx,maxy,maxz,maxt);
- input_vol.activateROI(); //is this needed? //yes!
- output_vol=input_vol.ROI();
- save_volume4D(output_vol,output_name);
+ save_volume4D(input_vol.ROI(minx,miny,minz,mint,maxx,maxy,maxz,maxt),"foo2");
return 0;
}
diff --git a/fslslice.cc b/fslslice.cc
index 5c9257a384d9136915a188757ca5f69e36045105..8aaa47c664b36c3f5fb26b0f27f4b8548c591334 100644
--- a/fslslice.cc
+++ b/fslslice.cc
@@ -40,14 +40,10 @@ int fmrib_main(int argc, char *argv[])
make_basename(base);
for(int z=0;z<grot.zsize();z++){
- grot.setROIlimits(grot.minx(),grot.miny(),z,grot.mint(),grot.maxx(),grot.maxy(),z,grot.maxt());
- grot.activateROI();
- tmp=grot.ROI();
+ tmp=grot.ROI(0,0,z,0,grot.maxx(),grot.maxy(),z,grot.maxt());
string oname=base+"_slice_"+zeropad_numeric_string(num2str(z),4);
- //cout<<"writing slice "<<z<<'\r';
save_volume4D(tmp,oname);
}
- //cout<<'\n';
return 0;
}
@@ -63,7 +59,6 @@ int main(int argc,char *argv[])
cout<<endl;
return -1;
}
- string iname=string(argv[1]);
- return call_fmrib_main(dtype(iname),argc,argv);
+ return call_fmrib_main(dtype(string(argv[1])),argc,argv);
}
diff --git a/fslsplit.cc b/fslsplit.cc
index 9d17207cdbe1f905905e80132de695e8f52e6123..68f1b7bfb8bab4003c4717d985152819dc94b067 100755
--- a/fslsplit.cc
+++ b/fslsplit.cc
@@ -41,10 +41,8 @@ int fmrib_main(int argc, char *argv[])
nsize=xoff*yoff*zoff*toff;
for(int j=0;j<nsize;j++)
{
- input_vol.setROIlimits(0+j*(xoff!=1),0+j*(yoff!=1),0+j*(zoff!=1),0+j*(toff!=1),input_vol.xsize()-1-(nsize-j-1)*(xoff!=1),input_vol.ysize()-1-(nsize-j-1)*(yoff!=1),input_vol.zsize()-1-(nsize-j-1)*(zoff!=1),input_vol.tsize()-1-(nsize-j-1)*(toff!=1));
- input_vol.activateROI();
- output_vol=input_vol.ROI();
- save_volume4D(output_vol,(output_name+num2str(j,4)));
+ output_vol=input_vol.ROI(0+j*(xoff!=1),0+j*(yoff!=1),0+j*(zoff!=1),0+j*(toff!=1),input_vol.xsize()-1-(nsize-j-1)*(xoff!=1),input_vol.ysize()-1-(nsize-j-1)*(yoff!=1),input_vol.zsize()-1-(nsize-j-1)*(zoff!=1),input_vol.tsize()-1-(nsize-j-1)*(toff!=1));
+ save_volume4D(output_vol,(output_name+num2str(j,4)));
}
return 0;
}
diff --git a/fslstats.cc b/fslstats.cc
index 7f4395398c12592d376e323cbdc8e44fe7b9ed12..f19da4a15455600f2e1daa0a8132259112e2fdc6 100644
--- a/fslstats.cc
+++ b/fslstats.cc
@@ -10,6 +10,7 @@
#include "newimage/newimageall.h"
#include "newimage/costfns.h"
#include "utils/fsl_isfinite.h"
+#include <limits>
using namespace NEWIMAGE;
@@ -47,64 +48,39 @@ void print_usage(const string& progname) {
// Some specialised nonzero functions just for speedup
// (it avoids generating masks when not absolutely necessary)
-long int nonzerocount(const volume4D<float>& vol)
+long nonzerocount(const volume4D<float>& vol)
{
- long int totn=0;
- for (int t=vol.mint(); t<=vol.maxt(); t++) {
- for (int z=vol.minz(); z<=vol.maxz(); z++) {
- 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) {
- totn++;
- }
- }
- }
- }
- }
+ long totn=0;
+ for(volume4D<float>::fast_const_iterator it=vol.fbegin(), end=vol.fend(); it<end; it++ )
+ if ( (*it) != 0 )
+ totn++;
return totn;
}
double nonzeromean(const volume4D<float>& vol)
{
- double totv=0.0;
+ double total=0.0;
long int totn=0;
- for (int t=vol.mint(); t<=vol.maxt(); t++) {
- for (int z=vol.minz(); z<=vol.maxz(); z++) {
- 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) {
- totv+=(double) vol(x,y,z,t);
- totn++;
- }
- }
- }
+ for(volume4D<float>::fast_const_iterator it=vol.fbegin(), end=vol.fend(); it<end; it++ )
+ if ( (*it) != 0 ) {
+ total+=(double)(*it);
+ totn++;
}
- }
- double meanval=0.0;
- if (totn>0) {
- meanval=totv/totn;
- }
- return meanval;
+ if (totn>0)
+ total/=totn;
+ return total;
}
double nonzerostddev(const volume4D<float>& vol)
{
double totv=0.0, totvv=0.0;
long int totn=0;
- for (int t=vol.mint(); t<=vol.maxt(); t++) {
- for (int z=vol.minz(); z<=vol.maxz(); z++) {
- 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) {
- float v=vol(x,y,z,t);
- totvv+=(double) v*v;
- totv+=(double) v;
- totn++;
- }
- }
- }
+ for(volume4D<float>::fast_const_iterator it=vol.fbegin(), end=vol.fend(); it<end; it++ )
+ if ( (*it) != 0 ) {
+ totvv+=(double)((*it)*(*it));
+ totv+=(double)(*it);
+ totn++;
}
- }
double var=0.0;
if (totn>1) {
double meanval = totv/totn;
@@ -113,11 +89,10 @@ double nonzerostddev(const volume4D<float>& vol)
return std::sqrt(var);
}
-int generateNonZeroMask(const volume4D<float> &mask, volume4D<float> &masknz, const volume4D<float> &input)
+template<class M>
+int generateNonZeroMask(const M &mask, volume4D<float> &masknz, const volume4D<float> &input)
{
- masknz.reinitialize(mask.xsize(),mask.ysize(),mask.zsize(),input.tsize());
- for (int t=input.mint(); t<=input.maxt(); t++)
- masknz[t]=((binarise(input[t],0.0f, 0.0f)-1.0f)*-1.0f*mask[t % mask.tsize()]);
+ masknz = ( binarise(input,0.0f, 0.0f ) -1.0f ) * -1.0f * mask;
return 0;
}
@@ -145,19 +120,19 @@ int fmrib_main_float(int argc, char* argv[],const bool timeseriesMode)
for ( int timepoint=0; timepoint < nTimepoints ; timepoint++ )
{
if ( timeseriesMode )
- vol=inputMaster[timepoint];
+ vol=inputMaster.constantSubVolume(timepoint);
volume4D<float> mask, masknz;
- float lthr(vol.min()-1);
- float uthr=(vol.max()+1);
+ float lthr(numeric_limits<float>::min());
+ float uthr(numeric_limits<float>::max());
int narg(2);
-
+
while (narg<argc) {
string sarg(argv[narg]);
if (sarg=="-n") {
- for (int t=vol.mint(); t<=vol.maxt(); t++)
- for (int z=vol.minz(); z<=vol.maxz(); z++)
- for (int y=vol.miny(); y<=vol.maxy(); y++)
- for (int x=vol.minx(); x<=vol.maxx(); x++)
+ for (int t=0; t<vol.tsize(); t++)
+ for (int z=0; z<vol.zsize(); z++)
+ for (int y=0; y<vol.ysize(); y++)
+ for (int x=0; x<vol.xsize(); x++)
if (!isfinite((double)vol(x,y,z,t)))
vol(x,y,z,t)=0;
} else if (sarg=="-m") {
@@ -172,32 +147,18 @@ int fmrib_main_float(int argc, char* argv[],const bool timeseriesMode)
}
} else if (sarg=="-X") {
ColumnVector coord(4);
- coord(4)=1.0;
- if (mask.nvoxels()>0) {
- coord(1) = vol.mincoordx(mask);
- coord(2) = vol.mincoordy(mask);
- coord(3) = vol.mincoordz(mask);
- } else {
- coord(1) = vol.mincoordx();
- coord(2) = vol.mincoordy();
- coord(3) = vol.mincoordz();
- }
- coord = (vol[0].niftivox2newimagevox_mat()).i() * coord;
+ vector<long long> iCoords;
+ vol.min(mask,iCoords);
+ coord << (Real)iCoords[7] << (Real)iCoords[8] << (Real)iCoords[9] << 1.0;
+ coord = (vol.constantSubVolume(0).niftivox2newimagevox_mat()).i() * coord;
cout << MISCMATHS::round(coord(1)) << " " <<
MISCMATHS::round(coord(2)) << " " << MISCMATHS::round(coord(3)) << " ";
} else if (sarg=="-x") {
ColumnVector coord(4);
- coord(4)=1.0;
- if (mask.nvoxels()>0) {
- coord(1) = vol.maxcoordx(mask);
- coord(2) = vol.maxcoordy(mask);
- coord(3) = vol.maxcoordz(mask);
- } else {
- coord(1) = vol.maxcoordx();
- coord(2) = vol.maxcoordy();
- coord(3) = vol.maxcoordz();
- }
- coord = (vol[0].niftivox2newimagevox_mat()).i() * coord;
+ vector<long long> iCoords;
+ vol.min(mask,iCoords);
+ coord << (Real)iCoords[0] << (Real)iCoords[1] << (Real)iCoords[2] << 1.0;
+ coord = (vol.constantSubVolume(0).niftivox2newimagevox_mat()).i() * coord;
cout << MISCMATHS::round(coord(1)) << " " <<
MISCMATHS::round(coord(2)) << " " << MISCMATHS::round(coord(3)) << " ";
} else if (sarg=="-w") {
@@ -205,14 +166,13 @@ int fmrib_main_float(int argc, char* argv[],const bool timeseriesMode)
generate_masks(mask,masknz,vol,lthr,uthr);
vol*=mask;
}
- int xmin=masknz.maxx(),xmax=masknz.minx(),ymin=masknz.maxy(),ymax=masknz.miny(),zmin=masknz.maxz(),zmax=masknz.minz(),tmin=masknz.maxt(),tmax=masknz.mint();
+ int xmin=masknz.xsize()-1,xmax(0),ymin=masknz.ysize()-1,ymax(0),zmin=masknz.zsize()-1,zmax(0),tmin=masknz.tsize()-1,tmax(0);
- for(int t=masknz.mint();t<=masknz.maxt();t++) {
- 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++) {
+ for(int t=0;t<masknz.tsize();t++)
+ for(int z=0;z<masknz.zsize();z++)
+ for(int y=0;y<masknz.ysize();y++)
+ for(int x=0;x<masknz.xsize();x++)
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;
@@ -222,10 +182,6 @@ int fmrib_main_float(int argc, char* argv[],const bool timeseriesMode)
if (t<tmin) tmin=t;
if (t>tmax) tmax=t;
}
- }
- }
- }
- }
// change voxel coords from newimage to nifti convention for output
ColumnVector v(4);
v << xmin << ymin << zmin << 1.0;
@@ -284,25 +240,23 @@ int fmrib_main_float(int argc, char* argv[],const bool timeseriesMode)
exit(2);
}
read_volume4D(mask,argv[narg]);
- if (!samesize(mask[0],vol[0])) {
+ if ( !samesize(mask.constantSubVolume(0),vol.constantSubVolume(0)) || mask.tsize() > vol.tsize() ) {
cerr << "Mask and image must be the same size" << endl;
exit(3);
}
- if ( mask.tsize() > vol.tsize() ) {
- cerr << "Mask and image must be the same size" << endl;
- exit(3);
- }
- if ( mask.tsize() != vol.tsize() && mask.tsize() != 1) {
- // copy the last max volume until the correct size is reached
- while (mask.tsize() < vol.tsize() ) {
- mask.addvolume(mask[mask.maxt()]);
+ if ( mask.tsize() != vol.tsize() && mask.tsize() != 1)
+ while (mask.tsize() < vol.tsize() ) { // copy the last max volume until the correct size is reached
+ mask.addvolume(mask.constantSubVolume(mask.tsize()-1));
}
- }
-
mask.binarise(0.5);
- generateNonZeroMask(mask,masknz,vol);
- if (mask.tsize()!=1) vol*=mask;
- else vol*=mask[0];
+ if (mask.tsize()!=1) {
+ generateNonZeroMask(mask,masknz,vol);
+ vol*=mask;
+ }
+ else {
+ generateNonZeroMask(mask.constantSubVolume(0),masknz,vol);
+ vol*=mask.constantSubVolume(0);
+ }
} else if (sarg=="-l") {
narg++;
if (narg<argc) {
@@ -359,21 +313,21 @@ int fmrib_main_float(int argc, char* argv[],const bool timeseriesMode)
if (mask.nvoxels()>0) cout << vol.robustmin(mask) << " " << vol.robustmax(mask) << " ";
else cout << vol.robustmin() << " " << vol.robustmax() << " ";
} else if (sarg=="-R") {
- if (mask.nvoxels()>0) cout << vol.min(mask) << " " << vol.max(mask) << " ";
- else cout << vol.min() << " " << vol.max() << " ";
+ if (mask.nvoxels()>0) cout << vol.min(mask) << " " << vol.max(mask) << " ";
+ else cout << vol.min() << " " << vol.max() << " ";
} else if (sarg=="-c") {
ColumnVector cog(4);
// convert from fsl mm to voxel to nifti sform coord
- cog.SubMatrix(1,3,1,1) = vol[0].cog();
+ cog.SubMatrix(1,3,1,1) = vol.constantSubVolume(0).cog();
cog(4) = 1.0;
- cog = vol[0].newimagevox2mm_mat() * cog;
+ cog = vol.constantSubVolume(0).newimagevox2mm_mat() * cog;
cout << cog(1) << " " << cog(2) << " " << cog(3) << " " ;
} else if (sarg=="-C") {
ColumnVector cog(4);
// convert from fsl mm to fsl voxel coord to nifti voxel coord
- cog.SubMatrix(1,3,1,1) = vol[0].cog();
+ cog.SubMatrix(1,3,1,1) = vol.constantSubVolume(0).cog();
cog(4) = 1.0;
- cog = (vol[0].niftivox2newimagevox_mat()).i() * cog;
+ cog = (vol.constantSubVolume(0).niftivox2newimagevox_mat()).i() * cog;
cout << cog(1) << " " << cog(2) << " " << cog(3) << " " ;
} else if (sarg=="-p") {
float n;