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#include "fileio.h"
#include "image.h"
/////////////////////////////////////////////////////////////
void resize4dim(farray& fdata) {
if(fdata.dim()==4) return; // leave untouched if it is already 4dim
fdata.autosize();
ndim nn=fdata.get_extent();
bool add_first_dim=true;
if(nn.dim()==1) add_first_dim=false;
while(nn.dim()<4) nn.add_dim(1,add_first_dim);
while(nn.dim()>4) --nn;
fdata.redim(nn);
}
/////////////////////////////////////////////////////////////
struct JdxFormat : public FileFormat {
STD_string description() const {return "JCAMP-DX data sets";}
svector suffix() const {
svector result; result.resize(2);
result[0]="smp";
result[1]="coi";
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("JdxFormat","read");
STD_string arrlabel=opts.ldr;
if(arrlabel=="") {
if(LDRfileName(filename).get_suffix()=="smp") arrlabel="spinDensity";
else {
ODINLOG(odinlog,errorLog) << "No array label provided, use the option '-" << opts.ldr.get_cmdline_option() <<"' to specify one" << STD_endl;
return -1;
}
}
LDRblock block;
farray fdata;
bool valid_type=false;
if(!valid_type) {
LDRdoubleArr dpar;
dpar.set_label(arrlabel);
block.clear(); block.append(dpar);
if(block.load(filename,serializer)>0) {
ODINLOG(odinlog,normalDebug) << "LDRdoubleArr detected" << STD_endl;
fdata.redim(dpar.get_extent());
for(unsigned int i=0; i<dpar.length(); i++) fdata[i]=dpar[i];
valid_type=true;
}
}
if(!valid_type) {
LDRfloatArr fpar;
fpar.set_label(arrlabel);
block.clear(); block.append(fpar);
if(block.load(filename,serializer)>0) {
ODINLOG(odinlog,normalDebug) << "LDRfloatArr detected" << STD_endl;
fdata.redim(fpar.get_extent());
for(unsigned int i=0; i<fpar.length(); i++) fdata[i]=fpar[i];
valid_type=true;
}
}
if(!valid_type) {
LDRcomplexArr cpar;
cpar.set_label(arrlabel);
block.clear(); block.append(cpar);
if(block.load(filename,serializer)>0) {
ODINLOG(odinlog,normalDebug) << "LDRcomplexArr detected" << STD_endl;
ndim nn=cpar.get_extent();
nn[0]*=2;
fvector amp=amplitude(cpar);
fvector pha=phase(cpar);
ODINLOG(odinlog,normalDebug) << "nn=" << STD_string(nn) << STD_endl;
fdata.redim(nn);
unsigned int n=cpar.length();
for(unsigned int i=0; i<n; i++) {
fdata[i]=amp[i];
fdata[n+i]=pha[i];
}
valid_type=true;
}
}
if(!valid_type) {
ODINLOG(odinlog,errorLog) << "Array parameter " << arrlabel << " not found" << STD_endl;
return -1;
}
resize4dim(fdata);
data=fdata;
return data.extent(0)*data.extent(1);
}
int write(const Data<float,4>& data, const STD_string& filename, const FileWriteOpts&, const Protocol& prot) {
Log<FileIO> odinlog("JdxFormat","write");
ODINLOG(odinlog,errorLog) << "Not implemented" << STD_endl;
return -1;
}
private:
LDRserJDX serializer;
};
/////////////////////////////////////////////////////////////
template<class Serializer>
struct ImageFormat : public FileFormat {
STD_string description() const {return "ODIN Image based on "+serializer.get_description();}
svector suffix() const {
svector result; result.resize(1);
result[0]=serializer.get_default_file_prefix();
return result;
}
svector dialects() const {return svector();}
int read(FileIO::ProtocolDataMap& pdmap, const STD_string& filename, const FileReadOpts& opts, const Protocol& protocol_template) {
Log<FileIO> odinlog("ImageFormat","read");
int result=0;
ImageSet imgset;
if(imgset.load(filename,serializer)<0) return -1;
int nsets=imgset.get_numof_images();
if(nsets<=0) return -1;
ODINLOG(odinlog,normalDebug) << "nsets=" << nsets << STD_endl;
Protocol prot(protocol_template);
for(int i=0; i<nsets; i++) {
prot.geometry=imgset.get_image(i).get_geometry();
prot.study.set_Series(imgset.get_image(i).get_label(), i); // Make protocols distinguishable
Data<float,4>& data=pdmap[prot];
farray fdata=imgset.get_image(i).get_magnitude();
resize4dim(fdata);
data=fdata;
result+=data.extent(0)*data.extent(1);
}
return result;
}
int write(const FileIO::ProtocolDataMap& pdmap, const STD_string& filename, const FileWriteOpts& opts) {
Log<FileIO> odinlog("ImageFormat","write");
int result=0;
ImageSet imgset(LDRfileName(filename).get_basename());
for(FileIO::ProtocolDataMap::const_iterator pdit=pdmap.begin(); pdit!=pdmap.end(); ++pdit) {
STD_string series;
int number;
pdit->first.study.get_Series(series, number);
Image img(series); // use series description as image label
img.set_geometry(pdit->first.geometry);
img.set_magnitude(pdit->second);
imgset.append_image(img);
result+=pdit->second.extent(0)*pdit->second.extent(1);
}
if(imgset.write(filename,serializer)<0) return -1;
return result;
}
private:
Serializer serializer;
};
/////////////////////////////////////////////////////////////
template<class Serializer>
struct ProtFormat : public FileFormat {
STD_string description() const {return "ODIN protocols based on "+serializer.get_description();}
svector suffix() const {
svector result; result.resize(1);
if(serializer.get_default_file_prefix()=="xml") result[0]="x";
result[0]+="pro";
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("ProtFormat","read");
if(prot.load(filename,serializer)<0) return false;
int nslices=prot.geometry.get_nSlices();
if(prot.geometry.get_Mode()==voxel_3d) nslices=prot.seqpars.get_MatrixSize(sliceDirection);
data.resize(1, nslices, prot.seqpars.get_MatrixSize(phaseDirection), prot.seqpars.get_MatrixSize(readDirection)); // only one repetition
data=0.0;
return data.extent(0)*data.extent(1);
}
int write(const Data<float,4>& data, const STD_string& filename, const FileWriteOpts&, const Protocol& prot) {
Log<FileIO> odinlog("ProtFormat","write");
return prot.write(filename,serializer);
}
private:
Serializer serializer;
};
//////////////////////////////////////////////////////////////
void register_ser_format() {
static JdxFormat jf;
static ImageFormat<LDRserJDX> jdximf;
static ImageFormat<LDRserXML> xmlimf;
static ProtFormat<LDRserJDX> jdxpf;
static ProtFormat<LDRserXML> xmlpf;
jf.register_format();
jdximf.register_format();
xmlimf.register_format();
jdxpf.register_format();
xmlpf.register_format();
}
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