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#include "fileio.h"
#ifdef ISMRMRDSUPPORT
#include <ismrmrd/dataset.h>
#include <ismrmrd/ismrmrd.h>
#define HDF_DATASET_STR "dataset"
#define HDF_IMAGE_STR "image"
/////////////////////////////////////////////////////////////
struct IsmrmrdFormat : public FileFormat{
STD_string description() const {return "ISMRMRD Image";}
svector suffix() const {
svector result; result.resize(1);
result[0]="h5";
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("IsmrmrdFormat","read");
ISMRMRD::Dataset dataset(filename.c_str(), HDF_DATASET_STR, false);
int nimages=dataset.getNumberOfImages(HDF_IMAGE_STR);
ODINLOG(odinlog,normalDebug) << "nimages=" << nimages << STD_endl;
int nread=-1;
int nphase=-1;
int nslice=-1;
Geometry& geometry=prot.geometry;
ISMRMRD::Image<float> image;
for(int i=0; i<nimages; i++) {
dataset.readImage(HDF_IMAGE_STR, i, image);
if(i==0) {
nread =image.getMatrixSizeX();
nphase=image.getMatrixSizeY();
nslice=image.getMatrixSizeZ();
ODINLOG(odinlog,normalDebug) << "nslice/nphase/nread=" << nslice << "/" << nphase << "/" << nread << STD_endl;
data.resize(nimages, nslice, nphase, nread);
geometry.set_FOV(readDirection,image.getFieldOfViewX());
geometry.set_FOV(phaseDirection,image.getFieldOfViewY());
geometry.set_FOV(sliceDirection,image.getFieldOfViewZ());
float slicethick=secureDivision(image.getFieldOfViewZ(), nslice);
geometry.set_sliceThickness(slicethick);
geometry.set_sliceDistance(slicethick);
dvector readvec(3);
readvec[0]=image.getReadDirectionX();
readvec[1]=image.getReadDirectionY();
readvec[2]=image.getReadDirectionZ();
dvector phasevec(3);
phasevec[0]=image.getPhaseDirectionX();
phasevec[1]=image.getPhaseDirectionY();
phasevec[2]=image.getPhaseDirectionZ();
dvector slicevec(3);
slicevec[0]=image.getSliceDirectionX();
slicevec[1]=image.getSliceDirectionY();
slicevec[2]=image.getSliceDirectionZ();
dvector centervec(3);
centervec[0]=image.getPositionX();
centervec[1]=image.getPositionY();
centervec[2]=image.getPositionZ();
geometry.set_orientation_and_offset(readvec, phasevec, slicevec, centervec);
} else {
if(nread!=image.getMatrixSizeX() || nphase!=image.getMatrixSizeY() || nslice!=image.getMatrixSizeZ()) {
ODINLOG(odinlog,errorLog) << "size mismatch nslice/nphase/nread=" << nslice << "/" << nphase << "/" << nread << STD_endl;
return -1;
}
}
for(int iz=0; iz<nslice; iz++) {
for(int iy=0; iy<nphase; iy++) {
for(int ix=0; ix<nread; ix++) {
data(i,iz,iy,ix)=image(ix,iy,iz);
}
}
}
}
return nimages*nslice;
}
int write(const Data<float,4>& data, const STD_string& filename, const FileWriteOpts& opts, const Protocol& prot) {
Log<FileIO> odinlog("IsmrmrdFormat","write");
rmfile(filename.c_str()); // remove old file
ISMRMRD::Dataset dataset(filename.c_str(), HDF_DATASET_STR, true);
const TinyVector<int, 4> shape(data.shape());
ISMRMRD::Image<float> image(shape(readDim), shape(phaseDim), shape(sliceDim), 1); // only one channel
image.setImageType(ISMRMRD::ISMRMRD_IMTYPE_MAGNITUDE);
const Geometry& geometry=prot.geometry;
image.setFieldOfView(geometry.get_FOV(readDirection), geometry.get_FOV(phaseDirection), geometry.get_FOV(sliceDirection));
dvector center(geometry.get_center());
image.setPosition(center[0], center[1], center[2]);
dvector readvec(geometry.get_readVector());
image.setReadDirection(readvec[0], readvec[1], readvec[2]);
dvector phasevec(geometry.get_phaseVector());
image.setPhaseDirection(phasevec[0], phasevec[1], phasevec[2]);
dvector slicevec(geometry.get_sliceVector());
image.setSliceDirection(slicevec[0], slicevec[1], slicevec[2]);
for(int itime=0; itime<shape(timeDim); itime++) {
for(int iz=0; iz<shape(sliceDim); iz++) {
for(int iy=0; iy<shape(phaseDim); iy++) {
for(int ix=0; ix<shape(readDim); ix++) {
image(ix,iy,iz) = data(itime,iz,iy,ix);
}
}
}
image.setRepetition(itime);
dataset.appendImage(HDF_IMAGE_STR, image);
}
return 1;
}
};
#endif // ISMRMRDSUPPORT
//////////////////////////////////////////////////////////////
void register_ismrmrd_format() {
#ifdef ISMRMRDSUPPORT
static IsmrmrdFormat irf;
irf.register_format();
#endif
}
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