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/// NewSpmOutputter.cpp
/**
*/
#include <string>
#include <vector>
#include "SeriesHandler.h"
#include "NewSpmVolume.h"
#include "NewSpmOutputter.h"
using namespace jcs;
///
/**
*/
NewSpmOutputter::NewSpmOutputter() :
Basic3DOutputter(CreateOptions())
{
}
///
/**
*/
Options
NewSpmOutputter::CreateOptions()
{
Options options = Get3DOptions();
options.pathname = "SpmAnalyze";
return options;
}
///
/**
*/
BasicVolumeFormat*
NewSpmOutputter::GetOutputVolume(const char* file)
{
return new NewSpmVolume(file, headerExtension.mb_str(wxConvLocal), rawExtension.mb_str(wxConvLocal));
}
///
/**
*/
int
NewSpmOutputter::ConvertSeries(SeriesHandler* handler)
{
int bits_allocated, pixel_rep = 0;
handler->Find("BitsAllocated", bits_allocated);
handler->Find("PixelRepresentation", pixel_rep);
switch (bits_allocated + pixel_rep) {
case 8 : {
SpmConversion<wxUint8> conversion(this, handler);
conversion.Convert();
break;
}
case 9 : {
SpmConversion<wxInt8> conversion(this, handler);
conversion.Convert();
break;
}
case 16 : {
SpmConversion<wxUint16> conversion(this, handler);
conversion.Convert();
break;
}
case 17 : {
SpmConversion<wxInt16> conversion(this, handler);
conversion.Convert();
break;
}
case 32 : {
SpmConversion<wxUint32> conversion(this, handler);
conversion.Convert();
break;
}
case 33 : {
SpmConversion<wxInt32> conversion(this, handler);
conversion.Convert();
break;
}
default : {
wxLogMessage(_("BitsAllocated and PixelRepresentation values (%d, %d) not supported."), bits_allocated, pixel_rep);
}
}
return 1;
}
///
/**
*/
template <class T>
SpmConversion<T>::SpmConversion(Basic3DOutputter* outputter, SeriesHandler* handler)
: Basic3DConversion<T>(outputter, handler)
{
mHeader = new NewSpmHeader();
}
///
/**
*/
template <class T>
SpmConversion<T>::~SpmConversion()
{
delete mHeader;
}
///
/**
*/
template <class T> void
SpmConversion<T>::ProcessSlice(std::vector<T>& slice)
{
std::reverse(slice.begin(), slice.end());
}
///
/**
*/
template <class T> void
SpmConversion<T>::GetHeaderForSeries()
{
mHeader->InitHeader();
std::string s;
this->mHandler->Find("SeriesDate", s);
s.copy(mHeader->hist.exp_date, sizeof(mHeader->hist.exp_date));
this->mHandler->Find("SeriesTime", s);
s.copy(mHeader->hist.exp_time, sizeof(mHeader->hist.exp_time));
this->mHandler->Find("SeriesDescription", s);
s.copy(mHeader->hist.descrip, sizeof(mHeader->hist.descrip));
this->mHandler->Find("PatientName", s);
s.copy(mHeader->hist.patient_id, sizeof(mHeader->hist.patient_id));
float fvar;
this->mHandler->Find("RepetitionTime", fvar);
mHeader->dime.pixdim[4] = fvar;
mHeader->dime.dim[1] = this->mHandler->GetColumns();
mHeader->dime.dim[2] = this->mHandler->GetRows();
mHeader->dime.dim[3] = this->mHandler->GetNumberOfSlices();
// dim[3] recalculated in mConvert
std::vector<double>voxel_size = this->mHandler->GetVoxelSize();
mHeader->dime.pixdim[1] = voxel_size[0];
mHeader->dime.pixdim[2] = voxel_size[1];
mHeader->dime.pixdim[3] = voxel_size[2];
// pixdim[3] recalculated in mConvert
this->mHandler->Find("PhotometricInterpretation", s);
if (s == "RGB") {
mHeader->dime.datatype = 128; // DT_RGB
}
else {
this->mHandler->Find("BitsAllocated", mHeader->dime.bitpix);
// Standard Analyze data types don't include
// either unsigned 16 bit or signed 8 bit
switch (mHeader->dime.bitpix) {
case 16 :
mHeader->dime.datatype = 4; // DT_SIGNED_SHORT
break;
case 8 :
mHeader->dime.datatype = 8; // DT_UNSIGNED_CHAR
break;
default :
mHeader->dime.datatype = 0; // DT_UNKNOWN
}
}
// Write/calculate remaining fields
mHeader->hk.sizeof_hdr = 348;
mHeader->dime.dim[0] = 4;
mHeader->dime.dim[4] = 1; // one volume per file by default
int dimensionality = this->mOutputter->GetDimensionality(this->mHandler->GetSeriesUid());
if (dimensionality == 4) {
mHeader->dime.dim[4] = this->GetNumberOfVolumes();
}
mHeader->hk.regular = 'r'; // all volumes same size
mHeader->dime.vox_offset = 0;
mHeader->hist.origin[0] = mHeader->dime.dim[1]/2;
mHeader->hist.origin[1] = mHeader->dime.dim[2]/2;
mHeader->hist.origin[2] = mHeader->dime.dim[3]/2;
}
///
/**
\param volPair A volume identifier and a volume.
*/
template <class T> void
SpmConversion<T>::CompleteHeaderForVolume(std::pair<VolId, Volume<T> > volPair)
{
// Calculate number of slices for this volume
int n_slices = volPair.second.size();
mHeader->SetNumberOfSlices(n_slices);
// Calculate voxel size in Z from slice spacing for multi-slice files
if (n_slices > 1) {
mHeader->SetSliceSpacing(volPair.second.GetSpacing());
}
double slope, intercept;
if (this->mOutputter->rescale == false &&
this->mHandler->GetRescaleSlopeAndIntercept(volPair.first, slope, intercept)) {
mHeader->dime.scale = slope;
mHeader->dime.intercept = intercept;
}
else {
mHeader->dime.scale = 1;
mHeader->dime.intercept = 0;
}
}
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