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#include "filter_slicetime.h"
void FilterSliceTime::init(){
sliceorderstr.set_description("space-separated list of slice indices in order of acquisition");
append_arg(sliceorderstr,"sliceorderstr");
}
bool FilterSliceTime::process(Data<float,4>& data, Protocol& prot) const {
Log<Filter> odinlog(c_label(),"process");
Range all=Range::all();
TinyVector<int,4> shape=data.shape();
int nrep=shape(0);
int nslices=shape(1);
if(nrep<=1) return true;
ivector sliceorder;
if(sliceorderstr=="") {
// try protocol
LDRbase* soptr=prot.get_parameter("SliceOrder");
if(soptr) {
iarray* sovec=0;
sovec=soptr->cast(sovec);
if(sovec) {
sliceorder=(*sovec);
}
}
} else {
svector toks=tokens(sliceorderstr);
sliceorder.resize(toks.size());
for(unsigned int i=0; i<toks.size(); i++) sliceorder[i]=atoi(toks[i].c_str());
}
ODINLOG(odinlog,normalDebug) << "sliceorderstr=" << sliceorderstr << STD_endl;
ODINLOG(odinlog,normalDebug) << "sliceorder=" << sliceorder.printbody() << STD_endl;
if(int(sliceorder.size())!=nslices) {
ODINLOG(odinlog,errorLog) << "size mismatch: nslices/sliceorder.size()=" << nslices << "/" << sliceorder.printbody() << STD_endl;
return false;
}
dvector sliceshift(nslices); sliceshift=0.0;
for(int islice=0; islice<nslices; islice++) {
sliceshift[sliceorder[islice]]=secureDivision(islice,nslices);
}
ODINLOG(odinlog,normalDebug) << "sliceshift=" << sliceshift.printbody() << STD_endl;
Data<float,1> tcourse(nrep);
TinyVector<float,1> subpixel_shift;
for(int islice=0; islice<nslices; islice++) {
for(int iphase=0; iphase<shape(2); iphase++) {
for(int iread=0; iread<shape(3); iread++) {
tcourse(all)=data(all,islice,iphase,iread);
subpixel_shift(0)=sliceshift[islice];
tcourse.congrid(tcourse.shape(), &subpixel_shift);
data(all,islice,iphase,iread)=tcourse(all);
}
}
}
return true;
}
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