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#include "fileio.h"
/////////////////////////////////////////////////////////////
struct InterfileFormat : public FileFormat {
STD_string description() const {return "Interfile";}
svector suffix() const{
svector result; result.resize(2);
result[0]="hdr";
result[1]="interfile"; // for disambiguation
return result;
}
svector dialects() const {
svector result; result.resize(1);
result[0]="neurostat";
return result;
}
static STD_string parse_header_entry(const STD_string& header, const STD_string& key) {
Log<FileIO> odinlog("InterfileFormat","parse_header_entry");
STD_string result;
STD_string afterkey=extract(header, key, "\n");
ODINLOG(odinlog,normalDebug) << "afterkey="<< afterkey << STD_endl;
result=replaceStr(afterkey, ":=", "", firstOccurence);
ODINLOG(odinlog,normalDebug) << "result="<< result << STD_endl;
if(result=="") {
ODINLOG(odinlog,warningLog) << "Cannot find key >" << key << "<" << STD_endl;
}
return result;
}
static STD_string get_imgfilename(const STD_string& filename) {
Log<FileIO> odinlog("InterfileFormat","get_imgfilename");
LDRfileName fname(filename);
STD_string imgfilename=fname.get_dirname()+SEPARATOR_STR+fname.get_basename_nosuffix()+".img";
ODINLOG(odinlog,normalDebug) << "imgfilename="<< imgfilename << STD_endl;
return imgfilename;
}
int read(Data<float,4>& data, const STD_string& filename, const FileReadOpts& opts, Protocol& prot) {
Log<FileIO> odinlog("InterfileFormat","read");
STD_string header;
if(load(header, filename)) {
ODINLOG(odinlog,errorLog) << "Cannot read header file" << STD_endl;
return -1;
}
header=dos2unix(header);
int nx=atoi(parse_header_entry(header, "matrix size [1]").c_str());
int ny=atoi(parse_header_entry(header, "matrix size [2]").c_str());
int nz=atoi(parse_header_entry(header, "number of slices").c_str());
TinyVector<int, 4> shape(1,nz,ny,nx);
ODINLOG(odinlog,normalDebug) << "shape="<< shape << STD_endl;
LONGEST_INT nvals=product(shape);
if(nvals<=0) {
ODINLOG(odinlog,errorLog) << "Cannot get shape of data" << STD_endl;
return -1;
}
int wordsize=atoi(parse_header_entry(header, "number of bytes per pixel").c_str());
ODINLOG(odinlog,normalDebug) << "wordsize="<< wordsize << STD_endl;
LONGEST_INT offset=atoi(parse_header_entry(header, "data offset in bytes").c_str());
ODINLOG(odinlog,normalDebug) << "offset="<< offset << STD_endl;
STD_string endianness=shrink(parse_header_entry(header, "imagedata byte order"));
ODINLOG(odinlog,normalDebug) << "endianness="<< endianness << STD_endl;
STD_string format=parse_header_entry(header, "number format");
ODINLOG(odinlog,normalDebug) << "format="<< format << STD_endl;
LONGEST_INT nbytes=wordsize*nvals;
ODINLOG(odinlog,normalDebug) << "nbytes="<< nbytes << STD_endl;
int fd;
void* ptr=filemap(get_imgfilename(filename), nbytes, offset, true, fd);
if(!ptr) return -1;
char* ptr_byteorder=(char*)ptr; // default
bool swapped=false;
bool little_endian_file=(endianness=="LITTLEENDIAN");
if(little_endian_file != little_endian_byte_order()) {
ptr_byteorder=new char[nbytes];
ODINLOG(odinlog,normalDebug) << "swabbing data" << STD_endl;
// swab(ptr, ptr_byteorder, wordsize);
char* from=(char*)ptr;
for(int ival=0; ival<nvals; ival++) {
for(int iw=0; iw<wordsize; iw++) {
LONGEST_INT base=ival*wordsize;
ptr_byteorder[base+iw]=from[base+wordsize-1-iw];
}
}
swapped=true;
}
STD_string type;
if(format.find("integer")!=STD_string::npos) {
if(format.find("unsigned")!=STD_string::npos) {
if(wordsize==1) {convert_from_ptr(data,(u8bit*)ptr_byteorder,shape); type=TypeTraits::type2label((u8bit)0);}
if(wordsize==2) {convert_from_ptr(data,(u16bit*)ptr_byteorder,shape); type=TypeTraits::type2label((u16bit)0);}
if(wordsize==4) {convert_from_ptr(data,(u32bit*)ptr_byteorder,shape); type=TypeTraits::type2label((u32bit)0);}
} else {
if(wordsize==1) {convert_from_ptr(data,(s8bit*)ptr_byteorder,shape); type=TypeTraits::type2label((s8bit)0);}
if(wordsize==2) {convert_from_ptr(data,(s16bit*)ptr_byteorder,shape); type=TypeTraits::type2label((s16bit)0);}
if(wordsize==4) {convert_from_ptr(data,(s32bit*)ptr_byteorder,shape); type=TypeTraits::type2label((s32bit)0);}
}
}
if(format.find("float")!=STD_string::npos) {
if(format.find("long")!=STD_string::npos) {convert_from_ptr(data,(double*)ptr_byteorder,shape); type=TypeTraits::type2label((double)0);}
else {convert_from_ptr(data,(float*) ptr_byteorder,shape); type=TypeTraits::type2label((float)0);}
}
prot.system.set_data_type(type);
fileunmap(fd, ptr, nbytes, offset);
if(swapped) delete[] ptr_byteorder;
// ignore pixel scaling value
// float scale=atof(parse_header_entry(header, "pixel scaling value").c_str());
float dx=atof(parse_header_entry(header, "scaling factor (mm/pixel) [1]").c_str());
float dy=atof(parse_header_entry(header, "scaling factor (mm/pixel) [2]").c_str());
if(dx>0.0) prot.geometry.set_FOV(readDirection, nx*dx);
if(dy>0.0) prot.geometry.set_FOV(phaseDirection, ny*dy);
float slicethick=atof(parse_header_entry(header, "slice thickness (mm/pixel)").c_str());
if(slicethick>0.0) {
prot.geometry.set_sliceThickness(slicethick);
prot.geometry.set_sliceDistance(slicethick);
}
return nz;
}
int write(const Data<float,4>& data, const STD_string& filename, const FileWriteOpts& opts, const Protocol& prot) {
Log<FileIO> odinlog("InterfileFormat","write");
Range all=Range::all();
TinyVector<int, 4> shape(data.shape());
STD_string header;
header+="!data offset in bytes :=0\n";
STD_string endian="BIGENDIAN";
if(little_endian_byte_order()) endian="LITTLEENDIAN";
header+="!imagedata byte order :="+endian+"\n";
header+="!matrix size [1] :="+itos(shape(readDim))+"\n";
header+="!matrix size [2] :="+itos(shape(phaseDim))+"\n";
STD_string type=select_write_datatype(prot,opts);
ODINLOG(odinlog,normalDebug) << "type=" << type << STD_endl;
char schar=' ';
if(type.size()) schar=type[0];
STD_string format;
if(schar=='u') format+="unsigned ";
if(schar=='s') format+="signed ";
if(type.find("bit")!=STD_string::npos) format+="integer";
if(type=="float") format="short float";
if(type=="double") format="long float";
header+="!number format :="+format+"\n";
header+="!number of bytes per pixel :="+itos(TypeTraits::typesize(type))+"\n";
const Geometry& geo=prot.geometry;
header+="scaling factor (mm/pixel) [1] :="+ftos(voxel_extent(geo, readDirection, data.extent(readDim )))+"\n";
header+="scaling factor (mm/pixel) [2] :="+ftos(voxel_extent(geo, phaseDirection, data.extent(phaseDim)))+"\n";
header+="!pixel scaling value :=32.767\n"; // for NEUROSTAT
header+="!number of slices :="+itos(data.extent(sliceDim))+"\n";
header+="!slice thickness (mm/pixel) :="+ftos(prot.geometry.get_sliceDistance())+"\n";
STD_string rlstr="0";
if(prot.geometry.get_readVector()[readDirection]<0.0) rlstr="1";
header+="!the right brain on the left :="+rlstr+"\n";
STD_string apstr="0";
if(prot.geometry.get_phaseVector()[phaseDirection]<0.0) apstr="1";
header+="!the anterior to the posterior :="+apstr+"\n";
STD_string sistr="0";
if(prot.geometry.get_sliceVector()[sliceDirection]<0.0) sistr="1";
header+="!the superior to the inferior :="+sistr+"\n";
header+="!END OF HEADER:=\n";
LDRfileName fname(filename);
int nrep=shape(timeDim);
Data<float,4> onefiledata(1,shape(sliceDim), shape(phaseDim), shape(readDim));
for(int irep=0; irep<nrep; irep++) {
STD_string onefilename=fname.get_dirname()+SEPARATOR_STR+fname.get_basename_nosuffix();
if(nrep>1) onefilename+="_time"+itos(irep,nrep-1);
onefilename+="."+fname.get_suffix();
ODINLOG(odinlog,normalDebug) << "Writing " << onefilename << STD_endl;
if(::write(header, onefilename)) return -1;
onefiledata(0,all,all,all)=data(irep,all,all,all);
if(opts.dialect=="neurostat" && type=="s16bit") { // signed datatype, but only positive values
Data<s16bit,4> posdata;
onefiledata.convert_to(posdata);
posdata=posdata/2;
posdata=posdata-min(posdata);
if(posdata.write(get_imgfilename(onefilename))) return -1;
} else {
if(onefiledata.write(type, get_imgfilename(onefilename))) return -1;
}
}
return data.extent(sliceDim)*data.extent(timeDim);
}
};
//////////////////////////////////////////////////////////////
void register_interfile_format() {
static InterfileFormat iff;
iff.register_format();
}
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