void ReadImage(medAbstractData* medData,itk::DCMTKImageIO::Pointer io,const QStringList& paths) {
typename itk::ImageFileReader<itk::Image<TYPE,DIM> >::Pointer Reader = itk::ImageFileReader<itk::Image<TYPE,DIM> >::New();
Reader->SetImageIO(io);
Reader->SetFileName(paths[0].toAscii().constData());
medData->setData(Reader->GetOutput());
Reader->Update();
}
//! a helper function for image loading
template <class T> typename T::Pointer load_image(const char *file)
{
typename itk::ImageFileReader<T>::Pointer reader = itk::ImageFileReader<T>::New();
reader->SetFileName(file);
reader->Update();
return reader->GetOutput();
}
// a helper function for minc reading
template <class T> typename T::Pointer load_minc(const char *file)
{
typedef itk::MincImageIO ImageIOType;
ImageIOType::Pointer minc2ImageIO = ImageIOType::New();
typename itk::ImageFileReader<T>::Pointer reader = itk::ImageFileReader<T>::New();
reader->SetFileName(file);
reader->SetImageIO( minc2ImageIO );
reader->Update();
return reader->GetOutput();
}
bool itkDataImageReaderBase::read_image(const QString& path,const char* type)
{
medAbstractData* medData = dynamic_cast<medAbstractData*>(this->data());
if (medData && medData->identifier()!=type)
return false;
typedef itk::Image<T,DIM> Image;
typename itk::ImageFileReader<Image>::Pointer TReader = itk::ImageFileReader<Image>::New();
TReader->SetImageIO(this->io);
TReader->SetFileName(path.toAscii().constData());
TReader->SetUseStreaming(true);
typename Image::Pointer im = TReader->GetOutput();
medData->setData(im);
// Recover the pixel meaning from the intent_name.
const itk::MetaDataDictionary dict = im->GetMetaDataDictionary();
std::string PixMeaning;
if (itk::ExposeMetaData(dict,"intent_name",PixMeaning))
medData->addMetaData(medAbstractImageData::PixelMeaningMetaData,QString(PixMeaning.c_str()));
TReader->Update();
return true;
}
void readwarpfile(int nlhs,
mxArray *plhs[],
int nrhs,
const mxArray *prhs[])
{
typedef int PixelType;
typedef itk::Image< PixelType, Dimension > ImageType;
// mexPrintf("the dimentsion is ", Dimension);
// typedef PixelType;
typedef itk::Vector<PixelType, Dimension> VectorPixelType;
typedef itk::Image<VectorPixelType, Dimension> DeformationFieldType;
typedef itk::WarpImageFilter
<ImageType, ImageType, DeformationFieldType> WarperType;
mexPrintf("input number is: %d", nrhs);
mexPrintf("output parameternumber is: %d", nlhs);
// mexPrintf("the dimentsion is :%d", Dimension);
//boost::timer timer;
typename DeformationFieldType::SizeType size;
typename DeformationFieldType::IndexType start;
unsigned int numPix(1u);
char * inputDfFilename;
mwSize matlabdims[Dimension];
// here, we should read image parameter
for (unsigned int d=0; d<Dimension; d++)
{
matlabdims[d]= mxGetDimensions(prhs[1])[d];
size[d] = matlabdims[d];
start[d] = 0;
numPix *= size[d];
// inptrs[d] = static_cast<const MatlabPixelType *>(mxGetData(prhs[d]));
}
inputDfFilename = mxArrayToString(prhs[0]);
mexPrintf("output file name is %s", inputDfFilename);
typename itk::ImageFileReader<DeformationFieldType>::Pointer df_reader = itk::ImageFileReader<DeformationFieldType>::New();
df_reader->SetFileName(inputDfFilename);
df_reader->Update();
// Allocate images and deformation field
typename ImageType::Pointer image
= ImageType::New();
typename DeformationFieldType::Pointer field = DeformationFieldType::New();
// typename DeformationFieldType::Pointer field = 0;
typename DeformationFieldType::SpacingType spacing;
spacing.Fill( 1.0 );
typename DeformationFieldType::PointType origin;
origin.Fill( 0.0 );
typename DeformationFieldType::RegionType region;
field = df_reader->GetOutput();
region = field->GetLargestPossibleRegion();
// initialize output point
const mxClassID classID = mxGetClassID(prhs[1]);
MatlabPixelType * fieldoutptrs[Dimension];
for (unsigned int d=0; d<Dimension; d++)
{
plhs[d] = mxCreateNumericArray(
Dimension, matlabdims, classID, mxREAL);
fieldoutptrs[d] = static_cast<MatlabPixelType *>(mxGetData(plhs[d]));
}
// read field
VectorPixelType * fieldptr = field->GetBufferPointer();
const VectorPixelType * const buff_end = fieldptr + numPix;
while ( fieldptr != buff_end )
{
for (unsigned int d=0; d<Dimension; d++)
{
*(fieldoutptrs[d])++ = (*fieldptr)[d];
}
++fieldptr;
}
}
