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#include "fileio.h"
#include "filter.h"
#ifdef NIFTISUPPORT
#include <nifti1_io.h>
/////////////////////////////////////////////////////////////
struct NiftiFormat : public FileFormat{
STD_string description() const {return "NIFTI/ANALYZE";}
svector suffix() const{
svector result; result.resize(3);
result[0]="nii";
result[1]="hdr";
result[2]="analyze"; // for disambiguation
return result;
}
svector dialects() const{
svector result; result.resize(1);
result[0]="fsl";
return result;
}
bool read_orientation(const nifti_image &ni,Geometry &geometry, const FileReadOpts& opts) {
Log<FileIO> odinlog("NiftiFormat","read_orientation");
float spatscale=1.0;
if(ni.xyz_units==NIFTI_UNITS_METER) spatscale=1.0e3;
if(ni.xyz_units==NIFTI_UNITS_MICRON) spatscale=1.0e-3;
//@todo check me
geometry.set_FOV(readDirection,ni.dx*spatscale*ni.dim[1]);
geometry.set_FOV(phaseDirection,ni.dy*spatscale*ni.dim[2]);
geometry.set_sliceThickness(ni.dz*spatscale);
geometry.set_sliceDistance(ni.dz*spatscale); //no interslice distance in nifti - so use thickness
geometry.set_nSlices(ni.dim[3]);
if(ni.nifti_type>0) { // only for non-ANALYZE
dvector readvec(3),phasevec(3),slicevec(3),centervec(3);
// RotMatrix scaleMat;//method 2
if(ni.qform_code>0) {// just tranform to the nominal space of the scanner
ODINLOG(odinlog,normalDebug) << "Reading orientation from qform" << STD_endl;
for(unsigned short i=0;i<3;i++) {
readvec[i] =ni.qto_xyz.m[i][0]/ni.dx;
phasevec[i] =ni.qto_xyz.m[i][1]/ni.dy;
slicevec[i] =ni.qto_xyz.m[i][2]/ni.dz;
centervec[i]=ni.qto_xyz.m[i][3]*spatscale;
}
} else if(ni.sform_code>0) { // method 3
ODINLOG(odinlog,normalDebug) << "Reading orientation from sform" << STD_endl;
for(unsigned short i=0;i<3;i++) {
readvec[i] =ni.sto_xyz.m[i][0]/ni.dx;
phasevec[i] =ni.sto_xyz.m[i][1]/ni.dy;
slicevec[i] =ni.sto_xyz.m[i][2]/ni.dz;
centervec[i]=ni.sto_xyz.m[i][3]*spatscale;
}
} else {
ODINLOG(odinlog,infoLog) << "can't read Orientation"<< STD_endl;
}
const dvector ivector =//diagonale trougth the image in "normal" space
(geometry.get_FOV(readDirection)-ni.dx)*readvec+
(geometry.get_FOV(phaseDirection)-ni.dy)*phasevec+
(geometry.get_FOV(sliceDirection)-ni.dz)*slicevec;
centervec+=ivector/2;
ODINLOG(odinlog,normalDebug) << "FOV read/phase/slice:"<< geometry.get_FOV(readDirection) << "/" << geometry.get_FOV(phaseDirection) << "/" << geometry.get_FOV(sliceDirection) << STD_endl;
ODINLOG(odinlog,normalDebug) << "readvec:" << readvec.printbody() << STD_endl;
ODINLOG(odinlog,normalDebug) << "phasevec:"<< phasevec.printbody() << STD_endl;
ODINLOG(odinlog,normalDebug) << "slicevec:"<< slicevec.printbody() << STD_endl;
ODINLOG(odinlog,normalDebug) << "image diagonale "<< ivector.printbody() <<"/" << sqrt(ivector[0]*ivector[0]+ivector[1]*ivector[1]+ivector[2]*ivector[2])<< STD_endl;
ODINLOG(odinlog,normalDebug) << "center " << centervec.printbody() << STD_endl;
// @todo should be set here
// for(unsigned short i=0;i<3;i++)
// scaleMat[i][i]=1/ni.pixdim[i+1];
geometry.set_orientation_and_offset(readvec,phasevec,slicevec,centervec);
ODINLOG(odinlog,normalDebug) << "set up gradrot matrix " << geometry.get_gradrotmatrix().print() << STD_endl;
ODINLOG(odinlog,normalDebug) << "set up center (offset) " << geometry.get_center().printbody() << STD_endl;
}
return true;
}
template<class T> void copy_from(const T* src,Data<float,4> &dst, const FileReadOpts& opts) {
convert_from_ptr(dst, src, dst.shape());
}
int read(Data<float,4>& data, const STD_string& filename, const FileReadOpts& opts, Protocol& prot) {
Log<FileIO> odinlog("NiftiFormat","read");
nifti_image* ni=nifti_image_read(filename.c_str(), true);
if(!read_orientation(*ni,prot.geometry,opts)) return -1;
data.resize(
ni->ndim>=4 ? ni->dim[4]:1,
ni->ndim>=3 ? ni->dim[3]:1,
ni->ndim>=2 ? ni->dim[2]:1,
ni->dim[1]
);
const TinyVector<int, 4> shape(data.shape());
ODINLOG(odinlog,normalDebug) << "shape/ndim=" << shape << "/" << ni->ndim << STD_endl;
if(int(ni->nvox)!=product(shape)) {
ODINLOG(odinlog,errorLog) << "ni->nvox=" << ni->nvox << " != product(shape)=" << product(shape) << STD_endl;
}
STD_string type;
//copy ni->data to data
switch(ni->datatype) {
case DT_UINT8:
type=TypeTraits::type2label((u8bit)0);
copy_from((u8bit*)ni->data, data,opts);
break;
case DT_INT8:
type=TypeTraits::type2label((s8bit)0);
copy_from((s8bit*)ni->data, data,opts);
break;
case DT_UINT16:
type=TypeTraits::type2label((u16bit)0);
copy_from((u16bit*)ni->data, data,opts);
break;
case DT_INT16:
type=TypeTraits::type2label((s16bit)0);
copy_from((s16bit*)ni->data, data,opts);
break;
case DT_UINT32:
type=TypeTraits::type2label((u32bit)0);
copy_from((u32bit*)ni->data, data,opts);
break;
case DT_INT32:
type=TypeTraits::type2label((s32bit)0);
copy_from((s32bit*)ni->data, data,opts);
break;
case DT_FLOAT32:
type=TypeTraits::type2label((float)0);
copy_from((float*)ni->data, data,opts);
break;
case DT_FLOAT64:
type=TypeTraits::type2label((double)0);
copy_from((double*)ni->data, data,opts);
break;
default:
ODINLOG(odinlog,errorLog) << "Unsupported datatype " << ni->datatype << STD_endl;
return -1;
break;
}
ODINLOG(odinlog,normalDebug) << "type=" << type << STD_endl;
if(type=="")return -1;
if(ni->nifti_type>0) { // only for non-ANALYZE
if(ni->scl_slope!=1.0 || ni->scl_inter!=0.0) {
ODINLOG(odinlog,normalDebug) << "ni->scl_slope/ni->scl_inter=" << ni->scl_slope << "/" <<ni->scl_inter << STD_endl;
if(ni->scl_slope) { // apply only if slope is non-zero
data=data*ni->scl_slope+ni->scl_inter;
}
}
}
//set some metadata
prot.system.set_data_type(type);
prot.seqpars.set_NumOfRepetitions(ni->dim[4]);
float timescale=1.0;
if(ni->time_units==NIFTI_UNITS_SEC) timescale=1.0e3;
if(ni->time_units==NIFTI_UNITS_USEC) timescale=1.0e-3;
ODINLOG(odinlog,normalDebug) << "ni->time_units/timescale/ni->dt=" << ni->time_units << "/" << timescale << "/" << ni->dt << STD_endl;
prot.seqpars.set_RepetitionTime(timescale*ni->dt);
nifti_image_free(ni);
return shape(0)*shape(1);
}
void store_orientation(nifti_image &ni,const Data<float,4>& data,const Geometry &geometry, const FileWriteOpts& opts) {
Log<FileIO> odinlog("NiftiFormat","store_orientation");
ni.sform_code=ni.qform_code=NIFTI_XFORM_SCANNER_ANAT; //set scanner aligned space
const RotMatrix rot(geometry.get_gradrotmatrix());//orientation of the image in "normal" space
const TinyVector<int, 4> shape(data.shape());//size of the image in voxels
const dvector center(geometry.get_center());//position of the image in "normal" space
ni.dx=ni.pixdim[1]=voxel_extent(geometry,readDirection, shape(3));
ni.dy=ni.pixdim[2]=voxel_extent(geometry,phaseDirection, shape(2));
ni.dz=ni.pixdim[3]=voxel_extent(geometry,sliceDirection, shape(1));
const dvector ivector =//diagonale trougth the image (from first voxel, to the last) in "normal" space
(geometry.get_FOV(readDirection)-ni.dx)*geometry.get_readVector()+
(geometry.get_FOV(phaseDirection)-ni.dy)*geometry.get_phaseVector()+
(geometry.get_FOV(sliceDirection)-ni.dz)*geometry.get_sliceVector();
// double heightAng,azimutAng,inplaneAng;
// geometry.get_orientation(heightAng,azimutAng,inplaneAng);
ODINLOG(odinlog,normalDebug) << "get_gradrotmatrix "<< rot.print() << STD_endl;
ODINLOG(odinlog,normalDebug) << "get_readVector "<< geometry.get_readVector().printbody() << STD_endl;
ODINLOG(odinlog,normalDebug) << "get_phaseVector "<< geometry.get_phaseVector().printbody() << STD_endl;
ODINLOG(odinlog,normalDebug) << "get_sliceVector "<< geometry.get_sliceVector().printbody() << STD_endl;
ODINLOG(odinlog,normalDebug) << "get_center "<< center.printbody() << STD_endl;
ODINLOG(odinlog,normalDebug) << "FOV read/phase/slice "<< geometry.get_FOV(readDirection) << "/" << geometry.get_FOV(phaseDirection) << "/" << geometry.get_FOV(sliceDirection) << STD_endl;
ODINLOG(odinlog,normalDebug) << "image diagonale "<< ivector.printbody() <<"/" << sqrt(ivector[0]*ivector[0]+ivector[1]*ivector[1]+ivector[2]*ivector[2])<< STD_endl;
// ODINLOG(odinlog,normalDebug) << "heightAng,azimutAng,inplaneAng " << heightAng << "," << azimutAng << "," << inplaneAng << STD_endl;
//create space tranformation matrices - transforms the space when reading _NOT_ the data
//@todo maybe we can get the quaternions directly from the given rotation angles
for(int y =0;y<3;y++) {
ni.qto_xyz.m[0][y]=rot[0][y];
ni.qto_xyz.m[1][y]=rot[1][y];
ni.qto_xyz.m[2][y]=rot[2][y];
ni.qto_xyz.m[y][3]=center[y]-ivector[y]/2;
}
memcpy(ni.sto_xyz.m,ni.qto_xyz.m,sizeof(ni.sto_xyz.m));
//add scaling to the sform
for(int y =0;y<3;y++){
ni.sto_xyz.m[0][y]*=ni.pixdim[1+y];
ni.sto_xyz.m[1][y]*=ni.pixdim[1+y];
ni.sto_xyz.m[2][y]*=ni.pixdim[1+y];
}
ni.dx=ni.pixdim[1];
ni.dy=ni.pixdim[2];
ni.dz=ni.pixdim[3];
//generate matching quaternions
nifti_mat44_to_quatern(
ni.qto_xyz,
&ni.quatern_b,&ni.quatern_c,&ni.quatern_d,
&ni.qoffset_x,&ni.qoffset_y,&ni.qoffset_z,
NULL,NULL,NULL,
&ni.qfac);
}
template<typename T> void* copy_to(Data<float,4> &src,Data<T,4> &dst,nifti_image &ni, Geometry& geo,const FileWriteOpts& opts) {
Log<FileIO> odinlog("NiftiFormat","copy_to");
src.convert_to(dst,!opts.noscale);
const TinyVector<int, 4> shape(src.shape());
ni.ndim=ni.dim[0]=shape(0)>1 ? 4:3;
ni.nx=ni.dim[1]=shape(3);
ni.ny=ni.dim[2]=shape(2);
ni.nz=ni.dim[3]=shape(1);
ni.nt=ni.dim[4]=shape(0);
//@todo - is already done in autoscaled conversion - waste of time
ni.cal_max = max(dst);
ni.cal_min = min(dst);
ni.nvox=product(shape);
//and return pointer to the converted data
return dst.c_array();
}
int write(const Data<float,4>& data, const STD_string& filename, const FileWriteOpts& opts, const Protocol& prot) {
Log<FileIO> odinlog("NiftiFormat","write");
STD_string type=select_write_datatype(prot,opts);
ODINLOG(odinlog,normalDebug) << "type=" << type << STD_endl;
LDRfileName fname(filename);
Protocol protcopy(prot);
Geometry& geo=protcopy.geometry;
Data<float,4> src(data);
nifti_image ni;
memset(&ni,0, sizeof(nifti_image)); //set everything to zero - default value for "not used"
ni.nu=ni.nv=ni.nw=1;
if(tolowerstr(opts.dialect)=="fsl") {
bool do_transform=false;
STD_string sppart="s,p";
if(geo.get_orientation()==sagittal || geo.get_orientation()==coronal) {
ODINLOG(odinlog,infoLog) << "Rotating around read axis for fsl dialect" << STD_endl;
sppart="p-,s";
do_transform=true;
}
STD_string rsign;
double heightAng, azimutAng, inplaneAng;
bool revSlice;
geo.get_orientation(heightAng, azimutAng, inplaneAng, revSlice);
if(!revSlice) { // FSL needs 'radiological' handness
ODINLOG(odinlog,infoLog) << "Reversing handness for fsl dialect" << STD_endl;
rsign="-";
do_transform=true;
}
if(do_transform) FilterChain("-swapdim "+sppart+",r"+rsign+"").apply(protcopy,src);
}
// Compatabilty with FSL
STD_string newtype;
if(IS_TYPE(s8bit,type)) newtype=TypeTraits::type2label((u8bit)0);
else if(IS_TYPE(u16bit,type)) newtype=TypeTraits::type2label((s16bit)0);
else if(IS_TYPE(u32bit,type)) newtype=TypeTraits::type2label((s32bit)0);
if(newtype!="") {
if(tolowerstr(opts.dialect)=="fsl" || fname.get_suffix()=="hdr") {
ODINLOG(odinlog,infoLog) << "data type " << type << " is not supported, falling back to " << newtype << STD_endl;
type=newtype;
} else {
ODINLOG(odinlog,warningLog) << "data type " << type << " is not supported in FSL, use '-wdialect fsl' to correct this" << STD_endl;
}
}
store_orientation(ni,src,geo,opts);
//dummies to keep the data ni.data points to
Data< u8bit,4> u8bit_data;
Data< s8bit,4> s8bit_data;
Data<u16bit,4> u16bit_data;
Data<s16bit,4> s16bit_data;
Data<u32bit,4> u32bit_data;
Data<s32bit,4> s32bit_data;
Data< float,4> float_data;
Data<double,4> double_data;
ni.datatype=DT_UNKNOWN;
if( IS_TYPE( u8bit,type)) {ni.datatype=DT_UINT8; ni.data=copy_to(src, u8bit_data,ni,geo,opts);}
else if(IS_TYPE( s8bit,type)) {ni.datatype=DT_INT8; ni.data=copy_to(src, s8bit_data,ni,geo,opts);}
else if(IS_TYPE(u16bit,type)) {ni.datatype=DT_UINT16; ni.data=copy_to(src,u16bit_data,ni,geo,opts);}
else if(IS_TYPE(s16bit,type)) {ni.datatype=DT_INT16; ni.data=copy_to(src,s16bit_data,ni,geo,opts);}
else if(IS_TYPE(u32bit,type)) {ni.datatype=DT_UINT32; ni.data=copy_to(src,u32bit_data,ni,geo,opts);}
else if(IS_TYPE(s32bit,type)) {ni.datatype=DT_INT32; ni.data=copy_to(src,s32bit_data,ni,geo,opts);}
else if(IS_TYPE(float,type)) {ni.datatype=DT_FLOAT32;ni.data=copy_to(src, float_data,ni,geo,opts);}
else if(IS_TYPE(double,type)) {ni.datatype=DT_FLOAT64;ni.data=copy_to(src,double_data,ni,geo,opts);}
ni.nbyper=TypeTraits::typesize(type);
ODINLOG(odinlog,normalDebug) << "nbyper/datatype=" << ni.nbyper << "/" << ni.datatype << STD_endl;
ODINLOG(odinlog,normalDebug) << "ni.pixdim[1/2/3]=" << ni.pixdim[1] << "/" << ni.pixdim[2] << "/" << ni.pixdim[3] << STD_endl;
if(src.extent(0)) ni.dt=ni.pixdim[4] = prot.seqpars.get_RepetitionTime();
//@todo we could save scale and offset here - intead of autoscale
ni.scl_slope=1;
ni.scl_inter=0.0;// http://209.85.135.104/search?q=cache:AxBp5gn9GzoJ:nifti.nimh.nih.gov/board/read.php%3Ff%3D1%26i%3D57%26t%3D57+nifti-1+scl_slope&hl=en&ct=clnk&cd=1&client=iceweasel-a
ni.freq_dim=1;
ni.phase_dim=2;
ni.slice_dim=3;
ni.xyz_units=NIFTI_UNITS_MM;
ni.time_units=NIFTI_UNITS_MSEC;
ni.fname=(char*)filename.c_str();
STD_string imgfile; // Keep in scope for valid char* pointer
if(fname.get_suffix()=="hdr") {
ni.nifti_type=0; // ANALYZE
imgfile=fname.get_dirname()+SEPARATOR_STR+fname.get_basename_nosuffix()+".img";
ODINLOG(odinlog,normalDebug) << "imgfile=" << imgfile << STD_endl;
ni.iname=(char*)imgfile.c_str();
} else {
ni.nifti_type=1; // NIFTI
ni.iname=(char*)filename.c_str();
}
STD_string studydescr;
STD_string physician;
prot.study.get_Context(studydescr, physician);
snprintf(ni.descrip, 80, "%s", studydescr.c_str());
STD_string seriesdescr;
int seriesnr;
prot.study.get_Series(seriesdescr, seriesnr);
snprintf(ni.intent_name, 16, "%s", seriesdescr.c_str());
errno=0; //reset errno
nifti_image_write(&ni); //write the image - in case of a failure errno should be set
if(errno) {
//if so, tell the user, clean up and return -1
ODINLOG(odinlog,errorLog) << "Could not write to "<< filename << "(" <<strerror(errno) << ")" << STD_endl;
rmfile(filename.c_str());
return -1;
}
else return 1;
}
};
#endif // NIFTISUPPORT
//////////////////////////////////////////////////////////////
void register_nifti_format() {
#ifdef NIFTISUPPORT
static NiftiFormat nf;
nf.register_format();
#endif
}
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