int
Resample::UseCorner(const string &refname)
{
Cube refcube;
stringstream tmps;
if (refcube.ReadFile(refname)) {
Tes reftes;
if (!(reftes.ReadFile(refname))) {
refcube=reftes[0];
}
else {
printf("*** resample: invalid reference file: %s\n",refname.c_str());
return 501; // panic and exit
}
}
// first get the corner coordinates of both images
tokenlist ourline,refline;
ourline.ParseLine(mycube->GetHeader("AbsoluteCornerPosition:"));
refline.ParseLine(refcube.GetHeader("AbsoluteCornerPosition:"));
if (ourline.size()!=3) {
tmps.str("");
tmps << "resample: input image file doesn't have an absolute corner position tag";
printErrorMsg(VB_ERROR,tmps.str());
return 101;
}
if (refline.size()!=3) {
tmps.str("");
tmps << "resample: reference image file doesn't have an absolute corner position tag";
printErrorMsg(VB_ERROR,tmps.str());
return 101;
}
double ourpos[3],refpos[3];
ourpos[0]=strtod(ourline[0]);
ourpos[1]=strtod(ourline[1]);
ourpos[2]=strtod(ourline[2]);
refpos[0]=strtod(refline[0]);
refpos[1]=strtod(refline[1]);
refpos[2]=strtod(refline[2]);
// find the start point
x1=(refpos[0]-ourpos[0])/mycube->voxsize[0];
y1=(refpos[1]-ourpos[1])/mycube->voxsize[1];
z1=(refpos[2]-ourpos[2])/mycube->voxsize[2];
// the sampling interval should provide for 4x resolution in-plane
xstep=(refcube.voxsize[0]/4.0)/mycube->voxsize[0];
ystep=(refcube.voxsize[1]/4.0)/mycube->voxsize[1];
zstep=refcube.voxsize[2]/mycube->voxsize[2];
// the number of voxels should be the width of the target image
nx=refcube.dimx*4;
ny=refcube.dimy*4;
nz=refcube.dimz;
return 0;
}
void
Extractor::init(tokenlist &args)
{
// defaults
xvflag=0;
newdim[0]=41;
newdim[1]=51;
newdim[2]=27;
newcube.voxsize[0]=3.75;
newcube.voxsize[1]=3.75;
newcube.voxsize[2]=5.00;
newcube.origin[0]=21;
newcube.origin[1]=31;
newcube.origin[2]=10;
original.ReadFile(args[0]);
if (args.size()==1)
newcube.SetFileName((string)"m"+original.GetFileName());
if (args.size()==2 || args.size()==3) {
newcube.SetFileName(args[1]);
if (args.size()==3) {
xval=strtol(args[2]);
xvflag=1;
}
}
if (args.size()==11 || args.size()==12) {
newcube.SetFileName(args[1]);
newdim[0]=strtol(args[2]);
newdim[1]=strtol(args[3]);
newdim[2]=strtol(args[4]);
newcube.voxsize[0]=strtod(args[5]);
newcube.voxsize[1]=strtod(args[6]);
newcube.voxsize[2]=strtod(args[7]);
newcube.origin[0]=strtol(args[8]);
newcube.origin[1]=strtol(args[9]);
newcube.origin[2]=strtol(args[10]);
if (args.size()==12) {
xval=strtol(args[11]);
xvflag=1;
}
}
newcube.SetVolume(newdim[0],newdim[1],newdim[2],original.datatype);
}
int
process_singlemask(vector<VBRegion> &rlist,string fname)
{
Cube mask;
if (mask.ReadFile(fname)) {
return 101;
}
VBRegion reg;
reg=findregion_mask(mask,vb_gt,0.0);
reg.name=xfilename(fname);
if (!(reg.voxels.size()))
return 102;
rlist.push_back(reg);
return 0;
}
void
do_sumrfx(const string &fname,const string &mname,double thresh,vector<VBRegion> &rlist)
{
int i,j,k;
Tes rfx;
Cube mask;
rfx.ReadFile(fname);
if (!rfx.data_valid) {
printf("sumrfx: invalid 4D file %s.\n",fname.c_str());
return;
}
// specified mask, intersect with tes mask
if (mname.size()) {
mask.ReadFile(mname);
for (i=0; i<mask.dimx; i++)
for (j=0; j<mask.dimy; j++)
for (k=0; k<mask.dimz; k++)
if (rfx.GetMaskValue(i,j,k)<0.5)
mask.SetValue(i,j,k,0);
}
// default mask
else {
mask.SetVolume(rfx.dimx,rfx.dimy,rfx.dimz,vb_byte);
for (i=0; i<mask.dimx; i++)
for (j=0; j<mask.dimy; j++)
for (k=0; k<mask.dimz; k++)
mask.SetValue(i,j,k,rfx.GetMaskValue(i,j,k));
}
if (!mask.data_valid) {
printf("sumrfx: invalid mask file %s.\n",mname.c_str());
return;
}
if (mask.dimx != rfx.dimx || mask.dimy != rfx.dimy || mask.dimz != rfx.dimz) {
printf("sumrfx: mask and rfx volume dimensions don't match\n");
return;
}
printf("sumrfx: thresh %.2f mask file: %s\n",thresh,mname.c_str());
for (i=0; i<rfx.dimt; i++) {
Cube mycube;
rfx.getCube(i,mycube);
if (!mycube.data_valid) continue;
do_sumcube(rfx.GetFileName(),i,mycube,mask,thresh,rlist);
}
}
int
process_multimask(vector<VBRegion> &rlist,string fname)
{
Cube mask;
tokenlist args;
if (mask.ReadFile(fname)) {
return 101;
}
for (int i=0; i<(int)mask.header.size(); i++) {
args.ParseLine(mask.header[i]);
if (args[0]!="vb_maskspec:") continue;
int value=strtol(args[1]);
VBRegion reg;
reg=findregion_mask(mask,vb_eq,(double)value);
if (reg.voxels.size())
rlist.push_back(reg);
}
return 0;
}
int
Resample::SetAlign(const string mode,const string ref)
{
Cube refcube;
if (refcube.ReadFile(refname))
return 100;
if (mode=="-aa" || mode=="-ax") {
if (ref=="origin")
x1=(float)mycube->origin[0]-(((float)refcube.origin[0]*refcube.voxsize[0])/mycube->voxsize[0]);
}
if (mode=="-aa" || mode=="-ay") {
if (ref=="origin")
y1=(float)mycube->origin[1]-(((float)refcube.origin[1]*refcube.voxsize[1])/mycube->voxsize[1]);
}
if (mode=="-aa" || mode=="-az") {
if (ref=="origin")
z1=(float)mycube->origin[2]-(((float)refcube.origin[2]*refcube.voxsize[2])/mycube->voxsize[2]);
}
return 0;
}
int
VBri::openconfig(string configfile)
{
ifstream infile;
infile.open(configfile.c_str());
if (!infile) {
QMessageBox::critical(this,"Error","Couldn't open config file.");
return 2;
}
chdir(xdirname(configfile).c_str());
char buf[STRINGLEN];
tokenlist args;
while (infile.getline(buf,STRINGLEN,'\n')) {
args.ParseLine(buf);
if (args.size()==0) continue;
if (args[0][0]=='#' || args[0][0] == ';')
continue;
if (args[0]=="image" && args.size()==3) {
Cube cb;
if (cb.ReadFile(args[2])) {
QMessageBox::critical(this,"Error",(format("Couldn't open image %s")%args[2]).str().c_str());
infile.close();
return 3;
}
find_origin(cb);
cubelist.push_back(cb);
cubemap[args[1]]=--cubelist.end();
}
else if (args[0]=="left") {
leftimg=args[1];
}
else if (args[0]=="right") {
rightimg=args[1];
}
else if (args[0]=="mask") {
VBmask vbm;
vbm.imgname=args[1];
if (args.size()>2) {
vbm.rating=strtol(args[2]);
vbm.xslice=strtol(args[3]);
vbm.yslice=strtol(args[3]);
vbm.zslice=strtol(args[3]);
vbm.notes=args.Tail(4);
}
else if (cubemap.count(vbm.imgname)) {
// FIXME get it from the header...
vbm.xslice=cubemap[vbm.imgname]->origin[0];
vbm.yslice=cubemap[vbm.imgname]->origin[1];
vbm.zslice=cubemap[vbm.imgname]->origin[2];
}
masklist.push_back(vbm);
}
else if (args[0]=="outfile") {
if (args.size()>1)
outfile=args[1];
}
else if (args[0]=="randomize") {
randomizemasks();
}
else {
QMessageBox::critical(this,"Error",((string)"Bad config line: "+buf).c_str());
infile.close();
return 4;
}
}
infile.close();
return 0;
}
int
main(int argc,char *argv[])
{
tokenlist args;
string maskfile;
vector<string> filelist;
args.Transfer(argc-1,argv+1);
for (size_t i=0; i<args.size(); i++) {
if (args[i]=="-m" && i<args.size()-1)
maskfile=args[++i];
else if (args[i]=="-h") {
vbcmp_help();
exit(0);
}
else if (args[i]=="-v") {
vbcmp_version();
exit(0);
}
else
filelist.push_back(args[i]);
}
if (filelist.size() < 2) {
vbcmp_help();
exit(0);
}
Cube mask;
if (maskfile.size()) {
if (mask.ReadFile(maskfile)) {
cout << format("[E] vbcmp: error reading mask file %s\n")%maskfile;
exit(2);
}
}
string spacer;
if (filelist.size()>2) spacer=" ";
for (size_t i=0; i<filelist.size(); i++) {
for (size_t j=0; j<filelist.size(); j++) {
if (i>=j) continue;
if (filelist.size()>2)
cout << format("[I] vbcmp: comparing %s and %s\n")%filelist[i]%filelist[j];
int err1,err2;
Cube cb1,cb2;
err1=cb1.ReadFile(filelist[i]);
err2=cb2.ReadFile(filelist[j]);
if (!err1 && !err2) {
cmp3d(cb1,cb2,mask,spacer);
continue;
}
Tes ts1,ts2;
err1=ts1.ReadFile(filelist[i]);
err2=ts2.ReadFile(filelist[j]);
if (!err1 && !err2) {
cmp4d(ts1,ts2,mask,spacer);
continue;
}
// try vectors before matrices, because all vectors are matrices
VB_Vector v1,v2;
err1=v1.ReadFile(filelist[i]);
err2=v2.ReadFile(filelist[j]);
if (!err1 && !err2) {
cmp1d(v1,v2,spacer);
continue;
}
VBMatrix m1,m2;
err1=m1.ReadFile(filelist[i]);
err2=m2.ReadFile(filelist[j]);
if (!err1 && !err2) {
cmp2d(m1,m2,spacer);
continue;
}
cout << format("[E] vbcmp: couldn't read %s and %s as same type\n")%filelist[i]%filelist[j];
}
}
exit(100);
}
int
main(int argc,char *argv[])
{
if (argc<2) {
vbcmap_help();
exit(0);
}
tokenlist args;
vector<string>filelist;
string dvname,ivname,outfile,maskfile,pfile,pmapname;
args.Transfer(argc-1,argv+1);
int part=1,nparts=1;
string perm_mat;
int perm_index=-1;
int minlesions=2;
bool f_yates=0;
bool f_fisher=0;
bool f_zscore=0;
bool f_flip=0;
bool f_fdr=0;
bool f_twotailed=0;
bool f_nodup=0;
float q=0;
for (size_t i=0; i<args.size(); i++) {
if (args[i]=="-v")
vbcmap_version();
else if (args[i]=="-h")
vbcmap_help();
else if (args[i]=="-2")
f_twotailed=1;
else if (args[i]=="-z")
f_zscore=1;
else if (args[i]=="-f")
f_flip=1;
else if (args[i]=="-x")
f_fisher=1;
else if (args[i]=="-y")
f_yates=1;
else if (args[i]=="-nodup")
f_nodup=1;
else if (args[i]=="-pfile" && i<args.size()-1) {
pfile=args[++i];
}
else if (args[i]=="-pmap" && i<args.size()-1) {
pmapname=args[++i];
}
else if (args[i]=="-m" && i<args.size()-1) {
maskfile=args[++i];
}
else if (args[i]=="-q" && i<args.size()-1) {
f_fdr=1;
q=strtod(args[++i]);
}
else if (args[i]=="-n" && i<args.size()-1) {
minlesions=strtol(args[++i]);
if (minlesions<2) minlesions=2;
}
else if (args[i]=="-op" && i<args.size()-2) {
perm_mat=args[++i];
perm_index=strtol(args[++i]);
}
else if (args[i]=="-p" && i<args.size()-2) {
part=strtol(args[++i]);
nparts=strtol(args[++i]);
}
else
filelist.push_back(args[i]);
}
if (filelist.size()!=3) {
vbcmap_help();
exit(112);
}
ivname=filelist[0];
dvname=filelist[1];
outfile=filelist[2];
Cube tmap,mask;
Tes ts;
VB_Vector depvar;
if (ts.ReadFile(ivname)) {
printf("[E] vbcmap: couldn't get grouping info from %s\n",ivname.c_str());
exit(101);
}
if (depvar.ReadFile(dvname)) {
printf("[E] vbcmap: couldn't get dependent variable info from %s\n",dvname.c_str());
exit(102);
}
// build our mask
ts.ExtractMask(mask);
if (maskfile.size()) {
Cube tmask;
if (tmask.ReadFile(maskfile)) {
printf("[E] vbcmap: couldn't read mask file %s\n",maskfile.c_str());
exit(103);
}
if (!(tmask.dimsequal(mask))) {
printf("[E] vbcmap: lesion maps and mask files have inconsistent dimensions\n");
exit(104);
}
mask.intersect(tmask);
}
// permute order of dv if requested
VB_Vector perm_order;
if (perm_index>-1) {
VBMatrix vm(perm_mat,0,0,perm_index,perm_index);
perm_order=vm.GetColumn(0);
VB_Vector tmp(depvar.size());
for (uint32 i=0; i<depvar.size(); i++)
tmp[i]=depvar[(int)perm_order[i]];
depvar=tmp;
}
// convert dv to bitmask
bitmask dvbm;
dvbm.resize(depvar.size());
dvbm.clear();
for (size_t i=0; i<depvar.size(); i++) {
if (!f_flip && fabs(depvar[i])>FLT_MIN)
dvbm.set(i);
if (f_flip && !(fabs(depvar[i])>FLT_MIN))
dvbm.set(i);
}
string partstring;
if (nparts>1)
partstring="_part_"+strnum(part);
bitmask bm;
bm.resize(ts.dimt);
map<bitmask,x2val> statlookup;
map<bitmask,x2val>::iterator iter;
Cube statmap(ts.dimx,ts.dimy,ts.dimz,vb_float);
Cube pmap;
Tes cimap;
x2val res;
Cube fdrmask;
if (f_fdr || pmapname.size()) {
pmap.SetVolume(ts.dimx,ts.dimy,ts.dimz,vb_float);
fdrmask=mask;
fdrmask.zero();
}
vector<double> pvals; // all p vals used in fdr calculation
bool f_non1=0;
int16 val;
for (int i=0; i<ts.dimx; i++) {
for (int j=0; j<ts.dimy; j++) {
for (int k=0; k<ts.dimz; k++) {
if (!mask.testValue(i,j,k))
continue;
for (int m=0; m<ts.dimt; m++) {
val=ts.getValue<int16>(i,j,k,m);
if (val) {
bm.set(m);
if (val!=1) f_non1=1;
}
else
bm.unset(m);
}
if (bm.count()<minlesions)
continue;
if (ts.dimt-bm.count()<2)
continue;
iter=statlookup.find(bm);
if (iter==statlookup.end()) {
// this is a new pattern
if (f_fdr)
fdrmask.SetValue(i,j,k,1);
if (f_fisher)
res=calc_fisher(bm,dvbm);
else
res=calc_chisquared(bm,dvbm,f_yates);
if (f_twotailed)
res.p*=2.0;
// FIXME??? if we need the p value or z score, get it
// if doing fdr, stash the p value
if (f_fdr || pmapname.size()) {
pmap.SetValue(i,j,k,res.p);
pvals.push_back(res.p);
}
// if doing confidence intervals, stash that
if (f_zscore)
statmap.SetValue(i,j,k,res.z);
else
statmap.SetValue(i,j,k,res.x2);
statlookup[bm]=res;
}
else {
// this is a previously encountered pattern
if (f_fdr && !f_nodup) {
fdrmask.SetValue(i,j,k,1);
pvals.push_back(iter->second.p);
}
statmap.SetValue(i,j,k,iter->second.x2);
if (f_fdr || pmapname.size())
pmap.SetValue(i,j,k,iter->second.p);
}
}
}
}
if (f_non1) {
cout << "[W] vbcmap: non-0/1 values found in lesion map" << endl;
}
if (f_fdr) {
vector<fdrstat> ffs=calc_multi_fdr_thresh(statmap,pmap,fdrmask,q);
if (ffs.size()) {
cout << (format("[I] vbcmap: FDR calculation included %d voxels with p values from %.4f to %.4f\n")
%ffs[0].nvoxels%ffs[0].low%ffs[0].high).str();
statmap.AddHeader("# the following thresholds must be exceeded for FDR control");
vbforeach(fdrstat ff,ffs) {
if (ff.maxind>=0)
cout << (format("[I] vbcmap: FDR threhsold for q=%.2f is %.4f\n")%ff.q%ff.statval).str();
else
cout << (format("[I] vbcmap: no FDR threhsold could be identified for q=%.2f\n")%ff.q).str();
string tmps=(format("fdrthresh: %g %g")%ff.q%ff.statval).str().c_str();
statmap.AddHeader(tmps);
}
}
}
int
VBSim::Go(int argc,char *argv[])
{
tokenlist args;
rng=NULL;
dimx=0;
dimy=0;
dimz=0;
dimt=0;
n_mean=10.0;
n_variance=5.0;
n_fwhm=0.0;
float vx=1.0;
float vy=1.0;
float vz=1.0;
float vt=2000;
uint32 rngseed=VBRandom();
args.Transfer(argc,argv);
if (args.size() == 0) {
vbsim_help();
exit(0);
}
for (size_t i=0; i<args.size(); i++) {
// -d x y z for dims
if (args[i]=="-d" && i<args.size()-4) {
dimx=strtol(args[i+1]);
dimy=strtol(args[i+2]);
dimz=strtol(args[i+3]);
dimt=strtol(args[i+4]);
i+=4;
}
// -c for loading anatomy
else if (args[i]=="-c" && i<args.size()-1) {
anatname=args[i+1];
i++;
}
// -z for voxel sizes
else if (args[i]=="-z" && i<args.size()-3) {
vx=strtod(args[++i]);
vy=strtod(args[++i]);
vz=strtod(args[++i]);
vt=strtod(args[++i]);
}
// -n for per-volume noise
else if (args[i]=="-n" && i<args.size()-3) {
n_mean=strtod(args[i+1]);
n_variance=strtod(args[i+2]);
n_fwhm=strtod(args[i+3]);
i+=3;
}
else if (args[i]=="-s" && i<args.size()-1)
rngseed=strtol(args[++i]);
else if (args[i]=="-o" && i<args.size()-1) {
outfile=args[i+1];
i++;
}
else {
printf("[E] vbsim: unrecognized argument %s\n",args(i));
return 140;
}
}
if (dimx<1 || dimy<0 || dimz<0 || dimt<0) {
printf("[E] vbsim: bad dimensions\n");
return 110;
}
// initialize RNG
rng=gsl_rng_alloc(gsl_rng_mt19937);
assert(rng);
gsl_rng_set(rng,rngseed);
// FIXME tell the user here what we're doing
// CREATE ANATOMY (constant image)
if (anatname.size()) {
if (anat.ReadFile(anatname)) {
printf("[E] vbsim: couldn't read %s\n",anatname.c_str());
return 101;
}
if (anat.dimx!=dimx || anat.dimy!=dimy || anat.dimz != dimz) {
printf("[E] vbsim: %s doesn't match your dimensions\n",anatname.c_str());
return 102;
}
}
else {
// create volume according to dimensions, add random noise if requested
anat.SetVolume(dimx,dimy,dimz,vb_float);
}
// SPECIAL CASE-- vecs if dimy=dimz=dimt==0
if (dimt==0 && dimy==0 && dimz==0) {
printf("[I] vbsim: creating a vector with %d elements with N(%g,%g)\n",dimx,
n_mean,sqrt(n_variance));
if (outfile=="")
outfile="data.ref";
VB_Vector vv(dimx);
if (!(isnan(n_mean))) {
for (int32 i=0; i<dimx; i++)
vv[i]=n_mean+gaussian_random(sqrt(abs(n_variance)));
}
if (vv.WriteFile(outfile)) {
printf("[E] vbsim: error writing 1D file %s\n",outfile.c_str());
exit(120);
}
printf("[I] vbsim: wrote 1D file %s\n",outfile.c_str());
exit(0);
}
// SPECIAL CASE-- cubes if dimt==0
if (dimt==0) {
printf("[I] vbsim: creating a %dx%dx%d 3D volume with N(%g,%g)\n",dimx,dimy,dimz,
n_mean,sqrt(n_variance));
if (outfile=="")
outfile="data.cub";
Cube vol(dimx,dimy,dimz,vb_float);
if (!(isnan(n_mean)))
AddGaussian(vol,n_mean,n_variance,n_fwhm,n_fwhm,n_fwhm);
vol+=anat;
vol.setVoxSizes(vx,vy,vz,vt);
if (vol.WriteFile(outfile)) {
printf("[E] vbsim: error writing 3D volume %s\n",outfile.c_str());
exit(120);
}
printf("[I] vbsim: wrote 3D volume %s\n",outfile.c_str());
exit(0);
}
printf("[I] vbsim: creating a %dx%dx%dx%d 4D volume with N(%g,%g)\n",dimx,dimy,dimz,dimt,
n_mean,sqrt(n_variance));
if (outfile=="")
outfile="data.tes";
// CREATE FUNCTIONALS (variable images, one per time point)
mytes.SetVolume(dimx,dimy,dimz,dimt,vb_float);
for (int i=0; i<dimt; i++) {
Cube vol(dimx,dimy,dimz,vb_float);
if (!(isnan(n_mean)))
AddGaussian(vol,n_mean,n_variance,n_fwhm,n_fwhm,n_fwhm);
vol+=anat;
mytes.SetCube(i,vol);
}
mytes.setVoxSizes(vx,vy,vz,vt);
if (mytes.WriteFile(outfile)) {
printf("[E] vbsim: error writing 4D volume %s\n",outfile.c_str());
return 120;
}
printf("[I] vbsim: wrote 4D volume %s\n",outfile.c_str());
return 0;
}
int
main(int argc,char *argv[])
{
if (argc==1) {
vbconv_help();
exit(0);
}
tokenlist args;
string outfile;
int floatflag=0,nanflag=0,extractflag=0;
set<int> includeset,excludeset;
list<string> filelist;
VBFF nullff;
args.Transfer(argc-1,argv+1);
for (size_t i=0; i<args.size(); i++) {
if (args[i]=="-f")
floatflag=1;
else if (args[i]=="-n")
nanflag=1;
else if (args[i]=="-i" && i<args.size()-1) {
includeset=numberset(args[++i]);
if (includeset.empty()) {
cout << "[E] vbconv: invalid inclusion range specified with -i\n";
exit(111);
}
}
else if (args[i]=="-e" && i<args.size()-1) {
excludeset=numberset(args[++i]);
if (excludeset.empty()) {
cout << "[E] vbconv: invalid exclusion range specified with -e\n";
exit(111);
}
}
else if (args[i]=="-x" && i<args.size()-1)
extractflag=1;
else if (args[i]=="-v") {
vbconv_version();
exit(0);
}
else if (args[i]=="-h") {
vbconv_help();
exit(0);
}
else if (args[i]=="-o" && i<args.size()-1)
outfile=args[++i];
else {
filelist.push_back(args[i]);
}
}
if (filelist.size()<1) {
printf("[E] vbconv: requires at least one input file\n");
exit(10);
}
// if there's no -o flag and exactly two files specified, convert
// the first to the second
if (filelist.size()==2 && outfile.size()==0) {
outfile=filelist.back();
filelist.pop_back();
}
if (outfile.size()==0) {
printf("[E] vbconv: requires an output filename be provided\n");
exit(11);
}
// multiple files, must be 3D/4D combination
if (filelist.size()>1) {
Tes newtes;
ConvertMultiple(filelist,nanflag,floatflag,newtes);
if (WriteTes(newtes,outfile,extractflag,floatflag,nanflag,includeset,excludeset))
exit(223);
exit(0); // just in case
}
int err;
// just one file, see what kind
Cube cb;
if (cb.ReadFile(filelist.front())==0) {
cb.fileformat=nullff;
if (floatflag && cb.datatype!=vb_float)
cb.convert_type(vb_float);
if (nanflag)
cb.removenans();
if ((err=cb.WriteFile(outfile))) {
printf("[E] vbconv: error %d writing %s\n",err,outfile.c_str());
exit(4);
}
else {
printf("[I] vbconv: wrote cube %s\n",outfile.c_str());
exit(0);
}
}
Tes ts;
if (ts.ReadFile(filelist.front())==0) {
ts.fileformat=nullff;
if ((err=WriteTes(ts,outfile,extractflag,floatflag,nanflag,includeset,excludeset))) {
printf("[E] vbconv: error %d writing %s\n",err,outfile.c_str());
exit(4);
}
else {
printf("[I] vbconv: wrote 4D volume %s\n",outfile.c_str());
exit(0);
}
}
VB_Vector vv;
if (vv.ReadFile(*filelist.begin())==0) {
// vv.fileformat=nullff; // FIXME -- can we set 1d fileformat?
if (vv.WriteFile(outfile)) {
printf("[E] vbconv: error writing %s\n",outfile.c_str());
exit(4);
}
else {
printf("[I] vbconv: wrote vector %s\n",outfile.c_str());
exit(0);
}
}
printf("[E] vbconv: couldn't make sense of file %s\n",filelist.front().c_str());
exit(100);
}
int
ConvertMultiple(list<string> &filelist,int nanflag,int floatflag,Tes &newtes)
{
// printf("[I] vbconv: converting %d files\n",(int)filelist.size());
// pre-scan for dimensions
int dimx=0,dimy=0,dimz=0,dimt=0;
VB_datatype dtype=vb_short;
for (list<string>::iterator ff=filelist.begin(); ff!=filelist.end(); ff++) {
Cube cb;
Tes ts;
VBImage *im;
if (cb.ReadHeader(*ff)==0) {
im=&cb;
dimt++;
}
else if (ts.ReadHeader(*ff)==0) {
im=&ts;
dimt+=ts.dimt;
}
else {
printf("[E] vbconv: couldn't read %s\n",ff->c_str());
exit(51);
}
if (ff==filelist.begin()) {
dimx=im->dimx;
dimy=im->dimy;
dimz=im->dimz;
dimt=1;
dtype=im->datatype;
}
else if (im->dimx!=dimx||im->dimy!=dimy||im->dimz!=dimz) {
printf("[E] vbconv: incompatible dimensions in file %s\n",ff->c_str());
exit(51);
}
}
int index=0;
if (floatflag)
dtype=vb_float;
// now grab all the images
newtes.SetVolume(dimx,dimy,dimz,dimt,dtype);
int findex=1;
for (list<string>::iterator ff=filelist.begin(); ff!=filelist.end(); ff++) {
printf("[I] vbconv: converting file %d of %d\n",findex++,(int)filelist.size());
newtes.AddHeader("vbconv: included file "+*ff);
Cube cb;
Tes ts;
if (cb.ReadFile(*ff)==0) {
newtes.SetCube(index++,cb);
}
else if (ts.ReadFile(*ff)==0) {
for (int i=0; i<ts.dimt; i++) {
ts.getCube(i,cb);
newtes.SetCube(index++,cb);
}
}
else {
printf("[E] vbconv: couldn't read data from %s\n",ff->c_str());
exit(5);
}
}
if (nanflag)
newtes.removenans();
return 0;
}
int
RenderMe::Go(tokenlist &args)
{
if (!args.size()) {
help();
return 102;
}
for (int i=0; i<args.size(); i++) {
if (args[i]=="-m" && i+1 < args.size()) {
maskname=args[i+1];
i++;
}
else if (args[i]=="-d" && i+1 < args.size()) {
overlayname=args[i+1];
i++;
}
else if (args[i]=="-o" && i+1 < args.size()) {
outfilename=args[i+1];
i++;
}
else if (args[i]=="-a" && i+1 < args.size()) {
anatomyname=args[i+1];
i++;
}
else if (args[i]=="-1") {
vbr.twotailed=0;
}
else if (args[i]=="-t" && i+2 < args.size()) {
vbr.low=strtod(args[i+1]);
vbr.high=strtod(args[i+2]);
i+=2;
}
}
if (outfilename.size() && !anatomyname.size() && !overlayname.size()) {
help();
return 101;
}
char tmp[STRINGLEN];
if (anatomyname.size()) {
anatomy.ReadFile(anatomyname);
if (!anatomy.data_valid){
sprintf(tmp,"vbrender: anatomy file %s not valid",anatomyname.c_str());
printErrorMsg(VB_ERROR,tmp);
return 102;
}
vbr.anatomy=&anatomy;
}
if (overlayname.size()) {
overlay.ReadFile(overlayname);
if (!overlay.data_valid){
sprintf(tmp,"vbrender: statistical overlay file %s not valid",overlayname.c_str());
printErrorMsg(VB_ERROR,tmp);
return 102;
}
vbr.overlay=&overlay;
}
if (maskname.size()) {
mask.ReadFile(maskname);
if (!mask.data_valid){
sprintf(tmp,"vbrender: mask file %s not valid",maskname.c_str());
printErrorMsg(VB_ERROR,tmp);
return 102;
}
vbr.mask=&mask;
}
QImage im;
if (vbr.RenderSlices())
return 103;
if (vbr.SavePNG(outfilename))
return 103;
return 0;
}