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#include "fileio.h"
/////////////////////////////////////////////////////////////
struct MhdFormat : public FileFormat {
STD_string description() const {return "MetaImage";}
svector suffix() const {
svector result; result.resize(1);
result[0]="mhd";
return result;
}
svector dialects() const {return svector();}
int read(Data<float,4>& data, const STD_string& filename, const FileReadOpts& opts, Protocol& prot) {
Log<FileIO> odinlog("MhdFormat","read");
STD_string mhdfile;
if(::load(mhdfile,filename)<0) return -1;
mhdfile=replaceStr(mhdfile,"=", " = "); // make sure key, value and '=' are separated by whitespaces
svector toks=tokens(mhdfile);
int ndims=-1;
int i;
int ntoks=toks.size();
for(i=0; i<ntoks; i++) {
if(toks[i]=="NDims" && i<(ntoks-2) && toks[i+1]=="=") {
ndims=atoi(toks[i+2].c_str());
break;
}
}
ODINLOG(odinlog,normalDebug) << "ndims=" << ndims << STD_endl;
if(ndims<0 || ndims>4) {
ODINLOG(odinlog,errorLog) << "Invalid NDims=" << ndims << STD_endl;
return -1;
}
fvector spacing(3);
TinyVector<int,4> shape; shape=1;
STD_string format;
STD_string rawfname;
for(i=0; i<ntoks; i++) {
if(toks[i]=="DimSize" && i<(ntoks-1-ndims) && toks[i+1]=="=") {
for(int idim=0; idim<ndims; idim++) {
shape(3-idim)=atoi(toks[i+2+idim].c_str());
}
}
if(toks[i]=="ElementSpacing" && i<(ntoks-1-ndims) && toks[i+1]=="=") {
for(int idim=0; idim<ndims; idim++) {
spacing[2-idim]=atof(toks[i+2+idim].c_str());
}
}
if(toks[i]=="ElementType" && i<(ntoks-2) && toks[i+1]=="=") {
STD_string eltype=toks[i+2];
if(eltype=="MET_FLOAT") format="float";
if(eltype=="MET_DOUBLE") format="double";
if(eltype=="MET_SHORT") format="short";
if(eltype=="MET_LONG") format="long";
if(format=="") {
ODINLOG(odinlog,errorLog) << "Unrecognized ElementType=" << eltype << STD_endl;
return -1;
}
}
if(toks[i]=="ElementDataFile" && i<(ntoks-2) && toks[i+1]=="=") rawfname=toks[i+2];
}
ODINLOG(odinlog,normalDebug) << "spacing/format/rawfname=" << spacing.printbody() << "/" << format << "/" << rawfname << STD_endl;
LDRfileName fname(filename);
data.resize(shape);
if(data.read(format, fname.get_dirname()+rawfname)<0) {
ODINLOG(odinlog,errorLog) << "Unable to ElementDataFile =" << fname.get_dirname()+rawfname << STD_endl;
return -1;
}
prot.geometry.set_sliceThickness(spacing[0]).set_sliceDistance(spacing[0]);
prot.geometry.set_FOV(phaseDirection,float(shape(2))*spacing[1]);
prot.geometry.set_FOV(readDirection, float(shape(3))*spacing[2]);
return shape(0)*shape(1);
}
int write(const Data<float,4>& data, const STD_string& filename, const FileWriteOpts& opts, const Protocol& prot) {
Log<FileIO> odinlog("MhdFormat","write");
TinyVector<int,4> shape=data.shape();
farray fa(data);
ndim nn=fa.get_extent();
nn.autosize(); // get rid of 1-size dims
fvector res(nn.dim()); res=1.0;
ODINLOG(odinlog,normalDebug) << "fa.dim()=" << fa.dim() << STD_endl;
if(fa.dim()>2) {
dvector soffset=prot.geometry.get_sliceOffsetVector();
ODINLOG(odinlog,normalDebug) << "soffset=" << soffset.printbody() << STD_endl;
if(soffset.size()>1) res[nn.dim()-3]=fabs(soffset[1]-soffset[0]);
else res[nn.dim()-3]=prot.geometry.get_sliceThickness();
}
if(nn.dim()>1) res[nn.dim()-2]=secureDivision(prot.geometry.get_FOV(phaseDirection),prot.seqpars.get_MatrixSize(phaseDirection));
if(nn.dim()>0) res[nn.dim()-1]=secureDivision(prot.geometry.get_FOV(readDirection), prot.seqpars.get_MatrixSize(readDirection));
LDRfileName fname(filename);
STD_string rawfname=fname.get_basename_nosuffix()+".raw";
STD_string header;
header+="NDims = "+itos(nn.dim())+"\n";
header+="DimSize =";
for(unsigned int idim=0; idim<nn.dim(); idim++) header+=" "+itos(nn[nn.dim()-idim-1]);
header+="\n";
header+="ElementType = MET_FLOAT\n";
header+="ElementSpacing =";
for(unsigned int idim=0; idim<nn.dim(); idim++) header+=" "+ftos(res[nn.dim()-idim-1]);
header+="\n";
header+="ElementByteOrderMSB = False\n";
header+="ElementDataFile = "+rawfname+"\n";
if(::write(header,filename)<0) return -1;
return data.write<float>(fname.get_dirname()+rawfname);
}
};
//////////////////////////////////////////////////////////////
void register_mhd_format() {
static MhdFormat mf;
mf.register_format();
}
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