bool imageSort(const ImageType::Pointer &im1, const ImageType::Pointer &im2)
{
ImageType::PointType or1 = im1->GetOrigin();
ImageType::PointType or2 = im2->GetOrigin();
ImageType::DirectionType direction = im1->GetDirection();
itk::Vector<double, 3> dir, v1, v2, normed;
for(unsigned int i = 0; i < 3; i++)
{
dir[i] = direction(i,2);
v1[i] = or1[i];
v2[i] = or2[i];
}
std::cout << dir << std::endl;
double mul1 = v1[0] / dir[0];
double mul2 = v2[0] / dir[0];
return (mul1<mul2);
}
// ------------------------------------------------------------------------
void transformPointToPatient(const ImageType::Pointer &reference,
const SeriesTransform &series, const std::vector<int> &roiOffset,
const ImageType::PointType &input, ImageType::PointType &output)
{
// rotation is easy
MatrixType rotTemp = reference->GetDirection().GetVnlMatrix();
MatrixType rotation;
rotation.set_size(3,3);
for(unsigned int i = 0; i < 3; i++)
{
rotation(i,0) = rotTemp(i,1);
rotation(i,1) = rotTemp(i,0);
rotation(i,2) = rotTemp(i,2);
}
VectorType refOrig = reference->GetOrigin().GetVnlVector();
VectorType offset = vnl_inverse(rotation) * refOrig;
vnl_vector<double> vnl_output;
// translate the point
vnl_output = vnl_inverse(rotation) * input.GetVnlVector();
vnl_output = vnl_output - offset;
vnl_output /= reference->GetSpacing()[0];
for(unsigned int i = 0; i < 3; i++)
{
vnl_output[i] -= roiOffset[i];
vnl_output[i] -= series.translation[i];
}
output[0] = vnl_output[0];
output[1] = vnl_output[1];
output[2] = vnl_output[2];
}
void setup_snapshot_image(string basename, ImageType::Pointer model)
{
ImageType::SpacingType spacing = model->GetSpacing();
spacing[0] /= constants::SnapshotImageZoom;
spacing[1] /= constants::SnapshotImageZoom;
spacing[2] /= constants::SnapshotImageZoom;
g_snapshot_image = ImageType::New();
g_snapshot_image->SetSpacing( spacing );
g_snapshot_image->SetOrigin( model->GetOrigin() );
ImageType::RegionType const& region = model->GetLargestPossibleRegion();
ImageType::RegionType::SizeType size = region.GetSize();
// size is in pixels
ImageType::SizeType doubled_size(size);
doubled_size[0] *= constants::SnapshotImageZoom;
doubled_size[1] *= constants::SnapshotImageZoom;
doubled_size[2] *= constants::SnapshotImageZoom;
g_snapshot_image->SetRegions( doubled_size );
g_snapshot_image->Allocate();
s_snapshot_basename = basename;
}
// ------------------------------------------------------------------------
void buildOutput(const SeriesTransform::List &series, ImageType::Pointer &outputImage,
ImageType::Pointer &outputLabel, const unsigned int & timestep)
{
// get the output parameters
unsigned int slices = series.size();
unsigned int timeSteps = series.front().images.size();
ImageType::Pointer ref = series.front().images.front();
ImageType::SpacingType spacing = ref->GetSpacing();
spacing[2] = series.front().sliceThickness;
ImageType::DirectionType direction = ref->GetDirection();
ImageType::PointType origin = ref->GetOrigin();
ImageType::RegionType region = ref->GetLargestPossibleRegion();
region.SetSize(2,slices);
// create the outputs
outputImage->SetSpacing(spacing);
outputImage->SetDirection(direction);
outputImage->SetOrigin(origin);
outputImage->SetRegions(region);
outputImage->Allocate();
outputLabel->SetSpacing(spacing);
outputLabel->SetDirection(direction);
outputLabel->SetOrigin(origin);
outputLabel->SetRegions(region);
outputLabel->Allocate();
itk::ImageRegionIterator<ImageType> outLIt(outputLabel, outputLabel->GetLargestPossibleRegion());
itk::ImageRegionIterator<ImageType> outImIt(outputImage, outputImage->GetLargestPossibleRegion());
// loop through the slices
for(unsigned int i = 0; i < slices; i++)
{
ImageType::Pointer im = series[i].images[timestep];
ImageType::Pointer label = series[i].labelImages[timestep];
itk::ImageRegionConstIterator<ImageType> imIt(im, im->GetLargestPossibleRegion());
itk::ImageRegionConstIterator<ImageType> lIt(label, label->GetLargestPossibleRegion());
while(!imIt.IsAtEnd())
{
outLIt.Set(lIt.Get());
outImIt.Set(imIt.Get());
++imIt; ++lIt;
++outLIt; ++outImIt;
}
}
}
// ------------------------------------------------------------------------
void createOutput(const ImageType::Pointer &input, ImageType::Pointer &output)
{
output->SetDirection(input->GetDirection());
output->SetSpacing(input->GetSpacing());
output->SetRegions(input->GetLargestPossibleRegion());
output->SetOrigin(input->GetOrigin());
output->Allocate();
output->FillBuffer(0);
}
// ------------------------------------------------------------------------
void buildShortAxisVolume(const SeriesTransform::Map &transforms,
const unsigned int seriesNumber, ImageType::Pointer &saVolume)
{
// get the short axis transforms
SeriesTransform::Map::const_iterator mapIt = transforms.begin();
std::vector<SeriesTransform> saSlices;
while(mapIt != transforms.end())
{
if(mapIt->second.series == seriesNumber)
{
unsigned int sliceNum = mapIt->second.slice;
if(saSlices.size() < (sliceNum+1))
saSlices.resize(sliceNum+1);
saSlices[sliceNum] = mapIt->second;
}
++mapIt;
}
// get the dimensions of the output image
ImageType::Pointer reference = saSlices[0].images[0];
unsigned int x,y,z;
x = reference->GetLargestPossibleRegion().GetSize()[0];
y = reference->GetLargestPossibleRegion().GetSize()[1];
z = saSlices.size();
ImageType::RegionType region;
ImageType::SizeType size;
ImageType::IndexType index;
size[0] = x;
size[1] = y;
size[2] = z;
index.Fill(0);
region.SetSize(size);
region.SetIndex(index);
// get the other parts
ImageType::SpacingType spacing = reference->GetSpacing();
spacing[2] = saSlices[0].sliceThickness;
ImageType::DirectionType direction = reference->GetDirection();
ImageType::PointType origin = reference->GetOrigin();
saVolume->SetOrigin(origin);
saVolume->SetDirection(direction);
saVolume->SetSpacing(spacing);
saVolume->SetRegions(region);
saVolume->Allocate();
saVolume->FillBuffer(0);
}
// ------------------------------------------------------------------------
void DicomParser::writeSeries(const DicomSeries &series, const QString &outputFolder)
{
// create the series name
QString name = QString::fromStdString(series.description);
name.replace(" ","_");
name += "_" + QString::number(series.images.front().seriesNumber);
name += ".nrrd";
QDir path(outputFolder);
QString fullPath = path.absoluteFilePath(name);
std::vector<DicomImage> images = series.images;
std::sort(images.begin(), images.end());
// write and build the output images
typedef itk::Image<unsigned short, 3> ImageType;
typedef itk::Image<unsigned short, 4> OutputImageType;
typedef itk::ImageFileReader<ImageType> ReaderType;
typedef itk::JoinSeriesImageFilter<ImageType, OutputImageType> JoinerType;
JoinerType::Pointer joiner = JoinerType::New();
ImageType::Pointer orig;
for(unsigned int i = 0; i < images.size(); i++)
{
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(images[i].filename);
std::cout << images[i].filename << std::endl;
reader->SetImageIO(itk::GDCMImageIO::New());
reader->Update();
ImageType::Pointer im = reader->GetOutput();
if(i == 0) orig = im;
im->SetOrigin(orig->GetOrigin());
im->SetDirection(orig->GetDirection());
im->SetSpacing(orig->GetSpacing());
joiner->SetInput(i, reader->GetOutput());
}
std::cout << joiner->GetOutput()->GetDirection() << std::endl;
typedef itk::ImageFileWriter<OutputImageType> WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetInput(joiner->GetOutput());
writer->SetFileName(fullPath.toStdString());
writer->SetImageIO(itk::NrrdImageIO::New());
writer->Update();
}
// ------------------------------------------------------------------------
InitialTransformExtractor::TranslationType InitialTransformExtractor::ComputeTranslation(
const ImageType::Pointer &image,
const OptionsData &options)
{
// set the offsets
TranslationType translation;
translation.Fill(0);
translation[0] -= options.roiOffset[0];
translation[1] -= options.roiOffset[1];
translation[2] -= options.roiOffset[2];
ImageType::PointType origin = image->GetOrigin();
translation[0] -= origin[0];
translation[1] -= origin[1];
translation[2] -= origin[2];
return translation;
}
// ------------------------------------------------------------------------
void InitialTransformExtractor::Compute()
{
GetFilenames(m_Filenames);
BuildMapping(m_Mapping);
std::string referenceFilename = GetReferenceImageFilename();
// load the reference file
typedef itk::ImageFileReader<ImageType> ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(referenceFilename);
reader->SetImageIO(itk::GDCMImageIO::New());
reader->Update();
ImageType::Pointer refImage = reader->GetOutput();
// flip the x and y axis
typedef itk::PermuteAxesImageFilter<ImageType> FlipperType;
FlipperType::Pointer flipper = FlipperType::New();
itk::FixedArray<unsigned int, 3> order;
order[0] = 1;
order[1] = 0;
order[2] = 2;
flipper->SetOrder(order);
flipper->SetInput(refImage);
flipper->Update();
//refImage = flipper->GetOutput();
// transformation is the negative origin of the reference
ImageType::PointType origin = refImage->GetOrigin();
m_Translation[0] = -origin[0];
m_Translation[1] = -origin[1];
m_Translation[2] = -origin[2];
m_Rotation = refImage->GetDirection().GetInverse();
m_Reference = refImage;
}
void NrrdQBallImageReader
::GenerateData()
{
if ( m_FileName == "")
{
throw itk::ImageFileReaderException(__FILE__, __LINE__, "Sorry, the filename of the vessel tree to be read is empty!");
}
else
{
try
{
const std::string& locale = "C";
const std::string& currLocale = setlocale( LC_ALL, NULL );
if ( locale.compare(currLocale)!=0 )
{
try
{
setlocale(LC_ALL, locale.c_str());
}
catch(...)
{
MITK_INFO << "Could not set locale " << locale;
}
}
typedef itk::VectorImage<float,3> ImageType;
itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();
typedef itk::ImageFileReader<ImageType> FileReaderType;
FileReaderType::Pointer reader = FileReaderType::New();
reader->SetImageIO(io);
reader->SetFileName(this->m_FileName);
reader->Update();
ImageType::Pointer img = reader->GetOutput();
typedef itk::Image<itk::Vector<float,QBALL_ODFSIZE>,3> VecImgType;
VecImgType::Pointer vecImg = VecImgType::New();
vecImg->SetSpacing( img->GetSpacing() ); // Set the image spacing
vecImg->SetOrigin( img->GetOrigin() ); // Set the image origin
vecImg->SetDirection( img->GetDirection() ); // Set the image direction
vecImg->SetLargestPossibleRegion( img->GetLargestPossibleRegion());
vecImg->SetBufferedRegion( img->GetLargestPossibleRegion() );
vecImg->Allocate();
itk::ImageRegionIterator<VecImgType> ot (vecImg, vecImg->GetLargestPossibleRegion() );
ot = ot.Begin();
itk::ImageRegionIterator<ImageType> it (img, img->GetLargestPossibleRegion() );
typedef ImageType::PixelType VarPixType;
typedef VecImgType::PixelType FixPixType;
for (it = it.Begin(); !it.IsAtEnd(); ++it)
{
VarPixType vec = it.Get();
FixPixType fixVec(vec.GetDataPointer());
ot.Set(fixVec);
++ot;
}
this->GetOutput()->InitializeByItk(vecImg.GetPointer());
this->GetOutput()->SetVolume(vecImg->GetBufferPointer());
try
{
setlocale(LC_ALL, currLocale.c_str());
}
catch(...)
{
MITK_INFO << "Could not reset locale " << currLocale;
}
}
catch(std::exception& e)
{
throw itk::ImageFileReaderException(__FILE__, __LINE__, e.what());
}
catch(...)
{
throw itk::ImageFileReaderException(__FILE__, __LINE__, "Sorry, an error occurred while reading the requested vessel tree file!");
}
}
}
std::vector<itk::SmartPointer<BaseData> > NrrdTensorImageReader::Read()
{
std::vector<itk::SmartPointer<mitk::BaseData> > result;
std::string location = GetInputLocation();
if ( location == "")
{
throw itk::ImageFileReaderException(__FILE__, __LINE__, "Sorry, the filename is empty!");
}
else
{
try
{
mitk::LocaleSwitch localeSwitch("C");
try
{
std::string fname3 = mitk::IOUtil::GetTempPath()+"/temp_dti.nii.gz";
int c = 0;
while( itksys::SystemTools::FileExists(fname3) )
{
fname3 = mitk::IOUtil::GetTempPath()+"/temp_dti_" + boost::lexical_cast<std::string>(c) + ".nii.gz";
++c;
}
itksys::SystemTools::CopyAFile(location.c_str(), fname3.c_str());
typedef itk::VectorImage<float,3> ImageType;
itk::NiftiImageIO::Pointer io = itk::NiftiImageIO::New();
typedef itk::ImageFileReader<ImageType> FileReaderType;
FileReaderType::Pointer reader = FileReaderType::New();
reader->SetImageIO(io);
reader->SetFileName(fname3);
reader->Update();
ImageType::Pointer img = reader->GetOutput();
TensorImage::ItkTensorImageType::Pointer vecImg = TensorImage::ItkTensorImageType::New();
vecImg->SetSpacing( img->GetSpacing() ); // Set the image spacing
vecImg->SetOrigin( img->GetOrigin() ); // Set the image origin
vecImg->SetDirection( img->GetDirection() ); // Set the image direction
vecImg->SetRegions( img->GetLargestPossibleRegion());
vecImg->Allocate();
itk::ImageRegionIterator<TensorImage::ItkTensorImageType> ot (vecImg, vecImg->GetLargestPossibleRegion() );
ot.GoToBegin();
itk::ImageRegionIterator<ImageType> it (img, img->GetLargestPossibleRegion() );
it.GoToBegin();
typedef ImageType::PixelType VarPixType;
typedef TensorImage::PixelType FixPixType;
int numComponents = img->GetNumberOfComponentsPerPixel();
if (numComponents==6)
{
MITK_INFO << "Trying to load dti as 6-comp nifti ...";
while (!it.IsAtEnd())
{
VarPixType vec = it.Get();
FixPixType fixVec(vec.GetDataPointer());
TensorImage::PixelType tensor;
tensor.SetElement(0, vec.GetElement(0));
tensor.SetElement(1, vec.GetElement(1));
tensor.SetElement(2, vec.GetElement(2));
tensor.SetElement(3, vec.GetElement(3));
tensor.SetElement(4, vec.GetElement(4));
tensor.SetElement(5, vec.GetElement(5));
fixVec = tensor;
ot.Set(fixVec);
++ot;
++it;
}
}
else if(numComponents==9)
{
MITK_INFO << "Trying to load dti as 9-comp nifti ...";
while (!it.IsAtEnd())
{
VarPixType vec = it.Get();
TensorImage::PixelType tensor;
tensor.SetElement(0, vec.GetElement(0));
tensor.SetElement(1, vec.GetElement(1));
tensor.SetElement(2, vec.GetElement(2));
tensor.SetElement(3, vec.GetElement(4));
tensor.SetElement(4, vec.GetElement(5));
tensor.SetElement(5, vec.GetElement(8));
FixPixType fixVec(tensor);
ot.Set(fixVec);
++ot;
++it;
}
}
else if (numComponents==1)
{
MITK_INFO << "Trying to load dti as 4D nifti ...";
typedef itk::Image<float,4> ImageType;
typedef itk::ImageFileReader<ImageType> FileReaderType;
FileReaderType::Pointer reader = FileReaderType::New();
reader->SetImageIO(io);
reader->SetFileName(fname3);
reader->Update();
ImageType::Pointer img = reader->GetOutput();
itk::Size<4> size = img->GetLargestPossibleRegion().GetSize();
while (!ot.IsAtEnd())
{
TensorImage::PixelType tensor;
ImageType::IndexType idx;
idx[0] = ot.GetIndex()[0]; idx[1] = ot.GetIndex()[1]; idx[2] = ot.GetIndex()[2];
if (size[3]==6)
{
for (unsigned int te=0; te<size[3]; te++)
{
idx[3] = te;
tensor.SetElement(te, img->GetPixel(idx));
}
}
else if (size[3]==9)
{
idx[3] = 0;
tensor.SetElement(0, img->GetPixel(idx));
idx[3] = 1;
tensor.SetElement(1, img->GetPixel(idx));
idx[3] = 2;
tensor.SetElement(2, img->GetPixel(idx));
idx[3] = 4;
tensor.SetElement(3, img->GetPixel(idx));
idx[3] = 5;
tensor.SetElement(4, img->GetPixel(idx));
idx[3] = 8;
tensor.SetElement(5, img->GetPixel(idx));
}
else
throw itk::ImageFileReaderException(__FILE__, __LINE__, "Unknown number of components for DTI file. Should be 6 or 9!");
FixPixType fixVec(tensor);
ot.Set(fixVec);
++ot;
}
}
OutputType::Pointer resultImage = OutputType::New();
resultImage->InitializeByItk( vecImg.GetPointer() );
resultImage->SetVolume( vecImg->GetBufferPointer() );
result.push_back( resultImage.GetPointer() );
}
catch(...)
{
MITK_INFO << "Trying to load dti as nrrd ...";
typedef itk::VectorImage<float,3> ImageType;
itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();
typedef itk::ImageFileReader<ImageType> FileReaderType;
FileReaderType::Pointer reader = FileReaderType::New();
reader->SetImageIO(io);
reader->SetFileName(location);
reader->Update();
ImageType::Pointer img = reader->GetOutput();
TensorImage::ItkTensorImageType::Pointer vecImg = TensorImage::ItkTensorImageType::New();
vecImg->SetSpacing( img->GetSpacing() ); // Set the image spacing
vecImg->SetOrigin( img->GetOrigin() ); // Set the image origin
vecImg->SetDirection( img->GetDirection() ); // Set the image direction
vecImg->SetRegions( img->GetLargestPossibleRegion());
vecImg->Allocate();
itk::ImageRegionIterator<TensorImage::ItkTensorImageType> ot (vecImg, vecImg->GetLargestPossibleRegion() );
ot.GoToBegin();
itk::ImageRegionIterator<ImageType> it (img, img->GetLargestPossibleRegion() );
it.GoToBegin();
typedef ImageType::PixelType VarPixType;
typedef TensorImage::PixelType FixPixType;
int numComponents = img->GetNumberOfComponentsPerPixel();
itk::MetaDataDictionary imgMetaDictionary = img->GetMetaDataDictionary();
std::vector<std::string> imgMetaKeys = imgMetaDictionary.GetKeys();
std::vector<std::string>::const_iterator itKey = imgMetaKeys.begin();
std::string metaString;
bool readFrame = false;
double xx, xy, xz, yx, yy, yz, zx, zy, zz;
MeasurementFrameType measFrame;
measFrame.SetIdentity();
MeasurementFrameType measFrameTransp;
measFrameTransp.SetIdentity();
for (; itKey != imgMetaKeys.end(); itKey ++)
{
itk::ExposeMetaData<std::string> (imgMetaDictionary, *itKey, metaString);
if (itKey->find("measurement frame") != std::string::npos)
{
sscanf(metaString.c_str(), " ( %lf , %lf , %lf ) ( %lf , %lf , %lf ) ( %lf , %lf , %lf ) \n", &xx, &xy, &xz, &yx, &yy, &yz, &zx, &zy, &zz);
if (xx>10e-10 || xy>10e-10 || xz>10e-10 ||
yx>10e-10 || yy>10e-10 || yz>10e-10 ||
zx>10e-10 || zy>10e-10 || zz>10e-10 )
{
readFrame = true;
measFrame(0,0) = xx;
measFrame(0,1) = xy;
measFrame(0,2) = xz;
measFrame(1,0) = yx;
measFrame(1,1) = yy;
measFrame(1,2) = yz;
measFrame(2,0) = zx;
measFrame(2,1) = zy;
measFrame(2,2) = zz;
measFrameTransp = measFrame.GetTranspose();
}
}
}
if (numComponents==6)
{
while (!it.IsAtEnd())
{
// T'=RTR'
VarPixType vec = it.Get();
FixPixType fixVec(vec.GetDataPointer());
if(readFrame)
{
TensorImage::PixelType tensor;
tensor.SetElement(0, vec.GetElement(0));
tensor.SetElement(1, vec.GetElement(1));
tensor.SetElement(2, vec.GetElement(2));
tensor.SetElement(3, vec.GetElement(3));
tensor.SetElement(4, vec.GetElement(4));
tensor.SetElement(5, vec.GetElement(5));
tensor = ConvertMatrixTypeToFixedArrayType(tensor.PreMultiply(measFrame));
tensor = ConvertMatrixTypeToFixedArrayType(tensor.PostMultiply(measFrameTransp));
fixVec = tensor;
}
ot.Set(fixVec);
++ot;
++it;
}
}
else if(numComponents==9)
{
while (!it.IsAtEnd())
{
VarPixType vec = it.Get();
TensorImage::PixelType tensor;
tensor.SetElement(0, vec.GetElement(0));
tensor.SetElement(1, vec.GetElement(1));
tensor.SetElement(2, vec.GetElement(2));
tensor.SetElement(3, vec.GetElement(4));
tensor.SetElement(4, vec.GetElement(5));
tensor.SetElement(5, vec.GetElement(8));
if(readFrame)
{
tensor = ConvertMatrixTypeToFixedArrayType(tensor.PreMultiply(measFrame));
tensor = ConvertMatrixTypeToFixedArrayType(tensor.PostMultiply(measFrameTransp));
}
FixPixType fixVec(tensor);
ot.Set(fixVec);
++ot;
++it;
}
}
else if (numComponents==1)
{
typedef itk::Image<float,4> ImageType;
itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();
typedef itk::ImageFileReader<ImageType> FileReaderType;
FileReaderType::Pointer reader = FileReaderType::New();
reader->SetImageIO(io);
reader->SetFileName(location);
reader->Update();
ImageType::Pointer img = reader->GetOutput();
itk::Size<4> size = img->GetLargestPossibleRegion().GetSize();
while (!ot.IsAtEnd())
{
TensorImage::PixelType tensor;
ImageType::IndexType idx;
idx[0] = ot.GetIndex()[0]; idx[1] = ot.GetIndex()[1]; idx[2] = ot.GetIndex()[2];
if (size[3]==6)
{
for (unsigned int te=0; te<size[3]; te++)
{
idx[3] = te;
tensor.SetElement(te, img->GetPixel(idx));
}
}
else if (size[3]==9)
{
idx[3] = 0;
tensor.SetElement(0, img->GetPixel(idx));
idx[3] = 1;
tensor.SetElement(1, img->GetPixel(idx));
idx[3] = 2;
tensor.SetElement(2, img->GetPixel(idx));
idx[3] = 4;
tensor.SetElement(3, img->GetPixel(idx));
idx[3] = 5;
tensor.SetElement(4, img->GetPixel(idx));
idx[3] = 8;
tensor.SetElement(5, img->GetPixel(idx));
}
else
throw itk::ImageFileReaderException(__FILE__, __LINE__, "Unknown number of komponents for DTI file. Should be 6 or 9!");
if(readFrame)
{
tensor = ConvertMatrixTypeToFixedArrayType(tensor.PreMultiply(measFrame));
tensor = ConvertMatrixTypeToFixedArrayType(tensor.PostMultiply(measFrameTransp));
}
FixPixType fixVec(tensor);
ot.Set(fixVec);
++ot;
}
}
else
{
throw itk::ImageFileReaderException(__FILE__, __LINE__, "Image has wrong number of pixel components!");
}
OutputType::Pointer resultImage = OutputType::New();
resultImage->InitializeByItk( vecImg.GetPointer() );
resultImage->SetVolume( vecImg->GetBufferPointer() );
result.push_back( resultImage.GetPointer() );
}
}
catch(std::exception& e)
{
throw itk::ImageFileReaderException(__FILE__, __LINE__, e.what());
}
catch(...)
{
throw itk::ImageFileReaderException(__FILE__, __LINE__, "Sorry, an error occurred while reading the requested DTI file!");
}
}
return result;
}
virtual ReadResult readImage(const std::string& file, const osgDB::ReaderWriter::Options* options) const
{
std::string ext = osgDB::getLowerCaseFileExtension(file);
if (!acceptsExtension(ext)) return ReadResult::FILE_NOT_HANDLED;
std::string fileName = osgDB::findDataFile( file, options );
if (fileName.empty()) return ReadResult::FILE_NOT_FOUND;
notice()<<"Reading DICOM file "<<fileName<<std::endl;
typedef unsigned short PixelType;
const unsigned int Dimension = 3;
typedef itk::Image< PixelType, Dimension > ImageType;
typedef itk::ImageFileReader< ImageType > ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName( fileName.c_str() );
typedef itk::GDCMImageIO ImageIOType;
ImageIOType::Pointer gdcmImageIO = ImageIOType::New();
reader->SetImageIO( gdcmImageIO );
try
{
reader->Update();
}
catch (itk::ExceptionObject & e)
{
std::cerr << "exception in file reader " << std::endl;
std::cerr << e.GetDescription() << std::endl;
std::cerr << e.GetLocation() << std::endl;
return ReadResult::ERROR_IN_READING_FILE;
}
ImageType::Pointer inputImage = reader->GetOutput();
ImageType::RegionType region = inputImage->GetBufferedRegion();
ImageType::SizeType size = region.GetSize();
ImageType::IndexType start = region.GetIndex();
//inputImage->GetSpacing();
//inputImage->GetOrigin();
unsigned int width = size[0];
unsigned int height = size[1];
unsigned int depth = size[2];
osg::RefMatrix* matrix = new osg::RefMatrix;
notice()<<"width = "<<width<<" height = "<<height<<" depth = "<<depth<<std::endl;
for(unsigned int i=0; i<Dimension; ++i)
{
(*matrix)(i,i) = inputImage->GetSpacing()[i];
(*matrix)(3,i) = inputImage->GetOrigin()[i];
}
osg::Image* image = new osg::Image;
image->allocateImage(width, height, depth, GL_LUMINANCE, GL_UNSIGNED_BYTE, 1);
unsigned char* data = image->data();
typedef itk::ImageRegionConstIterator< ImageType > IteratorType;
IteratorType it(inputImage, region);
it.GoToBegin();
while (!it.IsAtEnd())
{
*data = it.Get();
++data;
++it;
}
image->setUserData(matrix);
matrix->preMult(osg::Matrix::scale(double(image->s()), double(image->t()), double(image->r())));
return image;
}
// ------------------------------------------------------------------------
void NormaliseImage(const ImageType::Pointer &input,
const ImageType::Pointer &reference,
ImageType::Pointer &output,
SeriesTransform &trans)
{
// flip the x and y axis
typedef itk::PermuteAxesImageFilter<ImageType> FlipperType;
FlipperType::Pointer flipper = FlipperType::New();
itk::FixedArray<unsigned int, 3> order;
order[0] = 1;
order[1] = 0;
order[2] = 2;
flipper->SetOrder(order);
flipper->SetInput(input);
flipper->Update();
output = flipper->GetOutput();
// get the reference offset
vnl_vector<double> refOrigin(3);
refOrigin[0] = reference->GetOrigin()[0];// + trans.translation[0];
refOrigin[1] = reference->GetOrigin()[1];// + trans.translation[1];
refOrigin[2] = reference->GetOrigin()[2];// + trans.translation[2];
vnl_matrix<double> refRot = reference->GetDirection().GetVnlMatrix();
vnl_matrix<double> refRotInv = vnl_inverse(refRot);
vnl_vector<double> refOffset = refRotInv * refOrigin;
// get the image origin
vnl_vector<double> origin(3);
origin[0] = output->GetOrigin()[0];
origin[1] = output->GetOrigin()[1];
origin[2] = output->GetOrigin()[2];
// apply the rotation to the origin
origin = refRotInv * origin;
// apply the offset to the origin
origin = origin - refOffset;
// apply the scaling
origin /= reference->GetSpacing()[0];
// put the values into the output image
ImageType::PointType itkOrigin;
itkOrigin[0] = origin[0];
itkOrigin[1] = origin[1];
itkOrigin[2] = origin[2];
ImageType::SpacingType spacing;
spacing.Fill(output->GetSpacing()[0] / reference->GetSpacing()[0]);
// get the new direction
ImageType::DirectionType dirOut = output->GetDirection();
dirOut = reference->GetDirection().GetInverse() * dirOut.GetVnlMatrix();
output->SetSpacing(spacing);
output->SetDirection(dirOut);
output->SetOrigin(itkOrigin);
}
void QmitkBasicImageProcessing::StartButtonClicked()
{
if(!m_SelectedImageNode->GetNode()) return;
this->BusyCursorOn();
mitk::Image::Pointer newImage;
try
{
newImage = dynamic_cast<mitk::Image*>(m_SelectedImageNode->GetNode()->GetData());
}
catch ( std::exception &e )
{
QString exceptionString = "An error occured during image loading:\n";
exceptionString.append( e.what() );
QMessageBox::warning( NULL, "Basic Image Processing", exceptionString , QMessageBox::Ok, QMessageBox::NoButton );
this->BusyCursorOff();
return;
}
// check if input image is valid, casting does not throw exception when casting from 'NULL-Object'
if ( (! newImage) || (newImage->IsInitialized() == false) )
{
this->BusyCursorOff();
QMessageBox::warning( NULL, "Basic Image Processing", "Input image is broken or not initialized. Returning.", QMessageBox::Ok, QMessageBox::NoButton );
return;
}
// check if operation is done on 4D a image time step
if(newImage->GetDimension() > 3)
{
mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New();
timeSelector->SetInput(newImage);
timeSelector->SetTimeNr( ((QmitkSliderNavigatorWidget*)m_Controls->sliceNavigatorTime)->GetPos() );
timeSelector->Update();
newImage = timeSelector->GetOutput();
}
// check if image or vector image
ImageType::Pointer itkImage = ImageType::New();
VectorImageType::Pointer itkVecImage = VectorImageType::New();
int isVectorImage = newImage->GetPixelType().GetNumberOfComponents();
if(isVectorImage > 1)
{
CastToItkImage( newImage, itkVecImage );
}
else
{
CastToItkImage( newImage, itkImage );
}
std::stringstream nameAddition("");
int param1 = m_Controls->sbParam1->value();
int param2 = m_Controls->sbParam2->value();
double dparam1 = m_Controls->dsbParam1->value();
double dparam2 = m_Controls->dsbParam2->value();
double dparam3 = m_Controls->dsbParam3->value();
try{
switch (m_SelectedAction)
{
case GAUSSIAN:
{
GaussianFilterType::Pointer gaussianFilter = GaussianFilterType::New();
gaussianFilter->SetInput( itkImage );
gaussianFilter->SetVariance( param1 );
gaussianFilter->UpdateLargestPossibleRegion();
newImage = mitk::ImportItkImage(gaussianFilter->GetOutput())->Clone();
nameAddition << "_Gaussian_var_" << param1;
std::cout << "Gaussian filtering successful." << std::endl;
break;
}
case MEDIAN:
{
MedianFilterType::Pointer medianFilter = MedianFilterType::New();
MedianFilterType::InputSizeType size;
size.Fill(param1);
medianFilter->SetRadius( size );
medianFilter->SetInput(itkImage);
medianFilter->UpdateLargestPossibleRegion();
newImage = mitk::ImportItkImage(medianFilter->GetOutput())->Clone();
nameAddition << "_Median_radius_" << param1;
std::cout << "Median Filtering successful." << std::endl;
break;
}
case TOTALVARIATION:
{
if(isVectorImage > 1)
{
VectorTotalVariationFilterType::Pointer TVFilter
= VectorTotalVariationFilterType::New();
TVFilter->SetInput( itkVecImage.GetPointer() );
TVFilter->SetNumberIterations(param1);
TVFilter->SetLambda(double(param2)/1000.);
TVFilter->UpdateLargestPossibleRegion();
newImage = mitk::ImportItkImage(TVFilter->GetOutput())->Clone();
}
else
{
ImagePTypeToFloatPTypeCasterType::Pointer floatCaster = ImagePTypeToFloatPTypeCasterType::New();
floatCaster->SetInput( itkImage );
floatCaster->Update();
FloatImageType::Pointer fImage = floatCaster->GetOutput();
TotalVariationFilterType::Pointer TVFilter
= TotalVariationFilterType::New();
TVFilter->SetInput( fImage.GetPointer() );
TVFilter->SetNumberIterations(param1);
TVFilter->SetLambda(double(param2)/1000.);
TVFilter->UpdateLargestPossibleRegion();
newImage = mitk::ImportItkImage(TVFilter->GetOutput())->Clone();
}
nameAddition << "_TV_Iter_" << param1 << "_L_" << param2;
std::cout << "Total Variation Filtering successful." << std::endl;
break;
}
case DILATION:
{
BallType binaryBall;
binaryBall.SetRadius( param1 );
binaryBall.CreateStructuringElement();
DilationFilterType::Pointer dilationFilter = DilationFilterType::New();
dilationFilter->SetInput( itkImage );
dilationFilter->SetKernel( binaryBall );
dilationFilter->UpdateLargestPossibleRegion();
newImage = mitk::ImportItkImage(dilationFilter->GetOutput())->Clone();
nameAddition << "_Dilated_by_" << param1;
std::cout << "Dilation successful." << std::endl;
break;
}
case EROSION:
{
BallType binaryBall;
binaryBall.SetRadius( param1 );
binaryBall.CreateStructuringElement();
ErosionFilterType::Pointer erosionFilter = ErosionFilterType::New();
erosionFilter->SetInput( itkImage );
erosionFilter->SetKernel( binaryBall );
erosionFilter->UpdateLargestPossibleRegion();
newImage = mitk::ImportItkImage(erosionFilter->GetOutput())->Clone();
nameAddition << "_Eroded_by_" << param1;
std::cout << "Erosion successful." << std::endl;
break;
}
case OPENING:
{
BallType binaryBall;
binaryBall.SetRadius( param1 );
binaryBall.CreateStructuringElement();
OpeningFilterType::Pointer openFilter = OpeningFilterType::New();
openFilter->SetInput( itkImage );
openFilter->SetKernel( binaryBall );
openFilter->UpdateLargestPossibleRegion();
newImage = mitk::ImportItkImage(openFilter->GetOutput())->Clone();
nameAddition << "_Opened_by_" << param1;
std::cout << "Opening successful." << std::endl;
break;
}
case CLOSING:
{
BallType binaryBall;
binaryBall.SetRadius( param1 );
binaryBall.CreateStructuringElement();
ClosingFilterType::Pointer closeFilter = ClosingFilterType::New();
closeFilter->SetInput( itkImage );
closeFilter->SetKernel( binaryBall );
closeFilter->UpdateLargestPossibleRegion();
newImage = mitk::ImportItkImage(closeFilter->GetOutput())->Clone();
nameAddition << "_Closed_by_" << param1;
std::cout << "Closing successful." << std::endl;
break;
}
case GRADIENT:
{
GradientFilterType::Pointer gradientFilter = GradientFilterType::New();
gradientFilter->SetInput( itkImage );
gradientFilter->SetSigma( param1 );
gradientFilter->UpdateLargestPossibleRegion();
newImage = mitk::ImportItkImage(gradientFilter->GetOutput())->Clone();
nameAddition << "_Gradient_sigma_" << param1;
std::cout << "Gradient calculation successful." << std::endl;
break;
}
case LAPLACIAN:
{
// the laplace filter requires a float type image as input, we need to cast the itkImage
// to correct type
ImagePTypeToFloatPTypeCasterType::Pointer caster = ImagePTypeToFloatPTypeCasterType::New();
caster->SetInput( itkImage );
caster->Update();
FloatImageType::Pointer fImage = caster->GetOutput();
LaplacianFilterType::Pointer laplacianFilter = LaplacianFilterType::New();
laplacianFilter->SetInput( fImage );
laplacianFilter->UpdateLargestPossibleRegion();
newImage = mitk::ImportItkImage(laplacianFilter->GetOutput())->Clone();
nameAddition << "_Second_Derivative";
std::cout << "Laplacian filtering successful." << std::endl;
break;
}
case SOBEL:
{
// the sobel filter requires a float type image as input, we need to cast the itkImage
// to correct type
ImagePTypeToFloatPTypeCasterType::Pointer caster = ImagePTypeToFloatPTypeCasterType::New();
caster->SetInput( itkImage );
caster->Update();
FloatImageType::Pointer fImage = caster->GetOutput();
SobelFilterType::Pointer sobelFilter = SobelFilterType::New();
sobelFilter->SetInput( fImage );
sobelFilter->UpdateLargestPossibleRegion();
newImage = mitk::ImportItkImage(sobelFilter->GetOutput())->Clone();
nameAddition << "_Sobel";
std::cout << "Edge Detection successful." << std::endl;
break;
}
case THRESHOLD:
{
ThresholdFilterType::Pointer thFilter = ThresholdFilterType::New();
thFilter->SetLowerThreshold(param1 < param2 ? param1 : param2);
thFilter->SetUpperThreshold(param2 > param1 ? param2 : param1);
thFilter->SetInsideValue(1);
thFilter->SetOutsideValue(0);
thFilter->SetInput(itkImage);
thFilter->UpdateLargestPossibleRegion();
newImage = mitk::ImportItkImage(thFilter->GetOutput())->Clone();
nameAddition << "_Threshold";
std::cout << "Thresholding successful." << std::endl;
break;
}
case INVERSION:
{
InversionFilterType::Pointer invFilter = InversionFilterType::New();
mitk::ScalarType min = newImage->GetScalarValueMin();
mitk::ScalarType max = newImage->GetScalarValueMax();
invFilter->SetMaximum( max + min );
invFilter->SetInput(itkImage);
invFilter->UpdateLargestPossibleRegion();
newImage = mitk::ImportItkImage(invFilter->GetOutput())->Clone();
nameAddition << "_Inverted";
std::cout << "Image inversion successful." << std::endl;
break;
}
case DOWNSAMPLING:
{
ResampleImageFilterType::Pointer downsampler = ResampleImageFilterType::New();
downsampler->SetInput( itkImage );
NearestInterpolatorType::Pointer interpolator = NearestInterpolatorType::New();
downsampler->SetInterpolator( interpolator );
downsampler->SetDefaultPixelValue( 0 );
ResampleImageFilterType::SpacingType spacing = itkImage->GetSpacing();
spacing *= (double) param1;
downsampler->SetOutputSpacing( spacing );
downsampler->SetOutputOrigin( itkImage->GetOrigin() );
downsampler->SetOutputDirection( itkImage->GetDirection() );
ResampleImageFilterType::SizeType size = itkImage->GetLargestPossibleRegion().GetSize();
for ( int i = 0; i < 3; ++i )
{
size[i] /= param1;
}
downsampler->SetSize( size );
downsampler->UpdateLargestPossibleRegion();
newImage = mitk::ImportItkImage(downsampler->GetOutput())->Clone();
nameAddition << "_Downsampled_by_" << param1;
std::cout << "Downsampling successful." << std::endl;
break;
}
case FLIPPING:
{
FlipImageFilterType::Pointer flipper = FlipImageFilterType::New();
flipper->SetInput( itkImage );
itk::FixedArray<bool, 3> flipAxes;
for(int i=0; i<3; ++i)
{
if(i == param1)
{
flipAxes[i] = true;
}
else
{
flipAxes[i] = false;
}
}
flipper->SetFlipAxes(flipAxes);
flipper->UpdateLargestPossibleRegion();
newImage = mitk::ImportItkImage(flipper->GetOutput())->Clone();
std::cout << "Image flipping successful." << std::endl;
break;
}
case RESAMPLING:
{
std::string selectedInterpolator;
ResampleImageFilterType::Pointer resampler = ResampleImageFilterType::New();
switch (m_SelectedInterpolation)
{
case LINEAR:
{
LinearInterpolatorType::Pointer interpolator = LinearInterpolatorType::New();
resampler->SetInterpolator(interpolator);
selectedInterpolator = "Linear";
break;
}
case NEAREST:
{
NearestInterpolatorType::Pointer interpolator = NearestInterpolatorType::New();
resampler->SetInterpolator(interpolator);
selectedInterpolator = "Nearest";
break;
}
default:
{
LinearInterpolatorType::Pointer interpolator = LinearInterpolatorType::New();
resampler->SetInterpolator(interpolator);
selectedInterpolator = "Linear";
break;
}
}
resampler->SetInput( itkImage );
resampler->SetOutputOrigin( itkImage->GetOrigin() );
ImageType::SizeType input_size = itkImage->GetLargestPossibleRegion().GetSize();
ImageType::SpacingType input_spacing = itkImage->GetSpacing();
ImageType::SizeType output_size;
ImageType::SpacingType output_spacing;
output_size[0] = input_size[0] * (input_spacing[0] / dparam1);
output_size[1] = input_size[1] * (input_spacing[1] / dparam2);
output_size[2] = input_size[2] * (input_spacing[2] / dparam3);
output_spacing [0] = dparam1;
output_spacing [1] = dparam2;
output_spacing [2] = dparam3;
resampler->SetSize( output_size );
resampler->SetOutputSpacing( output_spacing );
resampler->SetOutputDirection( itkImage->GetDirection() );
resampler->UpdateLargestPossibleRegion();
ImageType::Pointer resampledImage = resampler->GetOutput();
newImage = mitk::ImportItkImage( resampledImage );
nameAddition << "_Resampled_" << selectedInterpolator;
std::cout << "Resampling successful." << std::endl;
break;
}
case RESCALE:
{
FloatImageType::Pointer floatImage = FloatImageType::New();
CastToItkImage( newImage, floatImage );
itk::RescaleIntensityImageFilter<FloatImageType,FloatImageType>::Pointer filter = itk::RescaleIntensityImageFilter<FloatImageType,FloatImageType>::New();
filter->SetInput(0, floatImage);
filter->SetOutputMinimum(dparam1);
filter->SetOutputMaximum(dparam2);
filter->Update();
floatImage = filter->GetOutput();
newImage = mitk::Image::New();
newImage->InitializeByItk(floatImage.GetPointer());
newImage->SetVolume(floatImage->GetBufferPointer());
nameAddition << "_Rescaled";
std::cout << "Rescaling successful." << std::endl;
break;
}
default:
this->BusyCursorOff();
return;
}
}
catch (...)
{
this->BusyCursorOff();
QMessageBox::warning(NULL, "Warning", "Problem when applying filter operation. Check your input...");
return;
}
newImage->DisconnectPipeline();
// adjust level/window to new image
mitk::LevelWindow levelwindow;
levelwindow.SetAuto( newImage );
mitk::LevelWindowProperty::Pointer levWinProp = mitk::LevelWindowProperty::New();
levWinProp->SetLevelWindow( levelwindow );
// compose new image name
std::string name = m_SelectedImageNode->GetNode()->GetName();
if (name.find(".pic.gz") == name.size() -7 )
{
name = name.substr(0,name.size() -7);
}
name.append( nameAddition.str() );
// create final result MITK data storage node
mitk::DataNode::Pointer result = mitk::DataNode::New();
result->SetProperty( "levelwindow", levWinProp );
result->SetProperty( "name", mitk::StringProperty::New( name.c_str() ) );
result->SetData( newImage );
// for vector images, a different mapper is needed
if(isVectorImage > 1)
{
mitk::VectorImageMapper2D::Pointer mapper =
mitk::VectorImageMapper2D::New();
result->SetMapper(1,mapper);
}
// reset GUI to ease further processing
// this->ResetOneImageOpPanel();
// add new image to data storage and set as active to ease further processing
GetDefaultDataStorage()->Add( result, m_SelectedImageNode->GetNode() );
if ( m_Controls->cbHideOrig->isChecked() == true )
m_SelectedImageNode->GetNode()->SetProperty( "visible", mitk::BoolProperty::New(false) );
// TODO!! m_Controls->m_ImageSelector1->SetSelectedNode(result);
// show the results
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
this->BusyCursorOff();
}
void NrrdTensorImageReader
::GenerateData()
{
if ( m_FileName == "")
{
throw itk::ImageFileReaderException(__FILE__, __LINE__, "Sorry, the filename is empty!");
}
else
{
try
{
const std::string& locale = "C";
const std::string& currLocale = setlocale( LC_ALL, NULL );
if ( locale.compare(currLocale)!=0 )
{
try
{
setlocale(LC_ALL, locale.c_str());
}
catch(...)
{
MITK_INFO << "Could not set locale " << locale;
}
}
try
{
MITK_INFO << "Trying to load dti as nifti ...";
std::string fname3 = "temp_dti.nii";
itksys::SystemTools::CopyAFile(m_FileName.c_str(), fname3.c_str());
typedef itk::Image<float,4> ImageType;
itk::NiftiImageIO::Pointer io = itk::NiftiImageIO::New();
typedef itk::ImageFileReader<ImageType> FileReaderType;
FileReaderType::Pointer reader = FileReaderType::New();
reader->SetImageIO(io);
reader->SetFileName(fname3);
reader->Update();
itksys::SystemTools::RemoveFile(fname3.c_str());
ImageType::Pointer img = reader->GetOutput();
itk::Size<4> size = img->GetLargestPossibleRegion().GetSize();
itk::ImageRegion< 3 > region;
region.SetSize(0,size[0]);
region.SetSize(1,size[1]);
region.SetSize(2,size[2]);
itk::Vector<double,3> spacing;
spacing[0] = img->GetSpacing()[0];
spacing[1] = img->GetSpacing()[1];
spacing[2] = img->GetSpacing()[2];
itk::Point<double,3> origin;
origin[0] = img->GetOrigin()[0];
origin[1] = img->GetOrigin()[1];
origin[2] = img->GetOrigin()[2];
itk::Matrix<double,3,3> direction;
direction[0][0] = img->GetDirection()[0][0];
direction[1][0] = img->GetDirection()[1][0];
direction[2][0] = img->GetDirection()[2][0];
direction[0][1] = img->GetDirection()[0][1];
direction[1][1] = img->GetDirection()[1][1];
direction[2][1] = img->GetDirection()[2][1];
direction[0][2] = img->GetDirection()[0][2];
direction[1][2] = img->GetDirection()[1][2];
direction[2][2] = img->GetDirection()[2][2];
typedef itk::Image<itk::DiffusionTensor3D<float>,3> VecImgType;
typedef VecImgType::PixelType FixPixType;
VecImgType::Pointer vecImg = VecImgType::New();
vecImg->SetSpacing( spacing );
vecImg->SetOrigin( origin );
vecImg->SetDirection( direction );
vecImg->SetRegions( region );
vecImg->Allocate();
itk::ImageRegionIterator<VecImgType> ot (vecImg, vecImg->GetLargestPossibleRegion() );
ot = ot.Begin();
while (!ot.IsAtEnd())
{
itk::DiffusionTensor3D<float> tensor;
ImageType::IndexType idx;
idx[0] = ot.GetIndex()[0]; idx[1] = ot.GetIndex()[1]; idx[2] = ot.GetIndex()[2];
if (size[3]==6)
{
for (int te=0; te<size[3]; te++)
{
idx[3] = te;
tensor.SetElement(te, img->GetPixel(idx));
}
}
else if (size[3]==9)
{
idx[3] = 0;
tensor.SetElement(0, img->GetPixel(idx));
idx[3] = 1;
tensor.SetElement(1, img->GetPixel(idx));
idx[3] = 2;
tensor.SetElement(2, img->GetPixel(idx));
idx[3] = 4;
tensor.SetElement(3, img->GetPixel(idx));
idx[3] = 5;
tensor.SetElement(4, img->GetPixel(idx));
idx[3] = 8;
tensor.SetElement(5, img->GetPixel(idx));
}
else
throw itk::ImageFileReaderException(__FILE__, __LINE__, "Unknown number of komponents for DTI file. Should be 6 or 9!");
FixPixType fixVec(tensor);
ot.Set(fixVec);
++ot;
}
this->GetOutput()->InitializeByItk(vecImg.GetPointer());
this->GetOutput()->SetVolume(vecImg->GetBufferPointer());
}
catch(...)
{
MITK_INFO << "Trying to load dti as nrrd ...";
typedef itk::VectorImage<float,3> ImageType;
itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();
typedef itk::ImageFileReader<ImageType> FileReaderType;
FileReaderType::Pointer reader = FileReaderType::New();
reader->SetImageIO(io);
reader->SetFileName(this->m_FileName);
reader->Update();
ImageType::Pointer img = reader->GetOutput();
typedef itk::Image<itk::DiffusionTensor3D<float>,3> VecImgType;
VecImgType::Pointer vecImg = VecImgType::New();
vecImg->SetSpacing( img->GetSpacing() ); // Set the image spacing
vecImg->SetOrigin( img->GetOrigin() ); // Set the image origin
vecImg->SetDirection( img->GetDirection() ); // Set the image direction
vecImg->SetRegions( img->GetLargestPossibleRegion());
vecImg->Allocate();
itk::ImageRegionIterator<VecImgType> ot (vecImg, vecImg->GetLargestPossibleRegion() );
ot = ot.Begin();
itk::ImageRegionIterator<ImageType> it (img, img->GetLargestPossibleRegion() );
it = it.Begin();
typedef ImageType::PixelType VarPixType;
typedef VecImgType::PixelType FixPixType;
int numComponents = img->GetNumberOfComponentsPerPixel();
itk::MetaDataDictionary imgMetaDictionary = img->GetMetaDataDictionary();
std::vector<std::string> imgMetaKeys = imgMetaDictionary.GetKeys();
std::vector<std::string>::const_iterator itKey = imgMetaKeys.begin();
std::string metaString;
bool readFrame = false;
double xx, xy, xz, yx, yy, yz, zx, zy, zz;
MeasurementFrameType measFrame;
measFrame.SetIdentity();
MeasurementFrameType measFrameTransp;
measFrameTransp.SetIdentity();
for (; itKey != imgMetaKeys.end(); itKey ++)
{
itk::ExposeMetaData<std::string> (imgMetaDictionary, *itKey, metaString);
if (itKey->find("measurement frame") != std::string::npos)
{
sscanf(metaString.c_str(), " ( %lf , %lf , %lf ) ( %lf , %lf , %lf ) ( %lf , %lf , %lf ) \n", &xx, &xy, &xz, &yx, &yy, &yz, &zx, &zy, &zz);
if (xx>10e-10 || xy>10e-10 || xz>10e-10 ||
yx>10e-10 || yy>10e-10 || yz>10e-10 ||
zx>10e-10 || zy>10e-10 || zz>10e-10 )
{
readFrame = true;
measFrame(0,0) = xx;
measFrame(0,1) = xy;
measFrame(0,2) = xz;
measFrame(1,0) = yx;
measFrame(1,1) = yy;
measFrame(1,2) = yz;
measFrame(2,0) = zx;
measFrame(2,1) = zy;
measFrame(2,2) = zz;
measFrameTransp = measFrame.GetTranspose();
}
}
}
if (numComponents==6)
{
while (!it.IsAtEnd())
{
// T'=RTR'
VarPixType vec = it.Get();
FixPixType fixVec(vec.GetDataPointer());
if(readFrame)
{
itk::DiffusionTensor3D<float> tensor;
tensor.SetElement(0, vec.GetElement(0));
tensor.SetElement(1, vec.GetElement(1));
tensor.SetElement(2, vec.GetElement(2));
tensor.SetElement(3, vec.GetElement(3));
tensor.SetElement(4, vec.GetElement(4));
tensor.SetElement(5, vec.GetElement(5));
tensor = ConvertMatrixTypeToFixedArrayType(tensor.PreMultiply(measFrame));
tensor = ConvertMatrixTypeToFixedArrayType(tensor.PostMultiply(measFrameTransp));
fixVec = tensor;
}
ot.Set(fixVec);
++ot;
++it;
}
}
else if(numComponents==9)
{
while (!it.IsAtEnd())
{
VarPixType vec = it.Get();
itk::DiffusionTensor3D<float> tensor;
tensor.SetElement(0, vec.GetElement(0));
tensor.SetElement(1, vec.GetElement(1));
tensor.SetElement(2, vec.GetElement(2));
tensor.SetElement(3, vec.GetElement(4));
tensor.SetElement(4, vec.GetElement(5));
tensor.SetElement(5, vec.GetElement(8));
if(readFrame)
{
tensor = ConvertMatrixTypeToFixedArrayType(tensor.PreMultiply(measFrame));
tensor = ConvertMatrixTypeToFixedArrayType(tensor.PostMultiply(measFrameTransp));
}
FixPixType fixVec(tensor);
ot.Set(fixVec);
++ot;
++it;
}
}
else if (numComponents==1)
{
typedef itk::Image<float,4> ImageType;
itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();
typedef itk::ImageFileReader<ImageType> FileReaderType;
FileReaderType::Pointer reader = FileReaderType::New();
reader->SetImageIO(io);
reader->SetFileName(this->m_FileName);
reader->Update();
ImageType::Pointer img = reader->GetOutput();
itk::Size<4> size = img->GetLargestPossibleRegion().GetSize();
MITK_INFO << size;
while (!ot.IsAtEnd())
{
itk::DiffusionTensor3D<float> tensor;
ImageType::IndexType idx;
idx[0] = ot.GetIndex()[0]; idx[1] = ot.GetIndex()[1]; idx[2] = ot.GetIndex()[2];
if (size[3]==6)
{
for (int te=0; te<size[3]; te++)
{
idx[3] = te;
tensor.SetElement(te, img->GetPixel(idx));
}
// idx[3] = 0;
// tensor.SetElement(0, img->GetPixel(idx));
// idx[3] = 1;
// tensor.SetElement(1, img->GetPixel(idx));
// idx[3] = 3;
// tensor.SetElement(2, img->GetPixel(idx));
// idx[3] = 2;
// tensor.SetElement(3, img->GetPixel(idx));
// idx[3] = 4;
// tensor.SetElement(4, img->GetPixel(idx));
// idx[3] = 5;
// tensor.SetElement(5, img->GetPixel(idx));
}
else if (size[3]==9)
{
idx[3] = 0;
tensor.SetElement(0, img->GetPixel(idx));
idx[3] = 1;
tensor.SetElement(1, img->GetPixel(idx));
idx[3] = 2;
tensor.SetElement(2, img->GetPixel(idx));
idx[3] = 4;
tensor.SetElement(3, img->GetPixel(idx));
idx[3] = 5;
tensor.SetElement(4, img->GetPixel(idx));
idx[3] = 8;
tensor.SetElement(5, img->GetPixel(idx));
}
else
throw itk::ImageFileReaderException(__FILE__, __LINE__, "Unknown number of komponents for DTI file. Should be 6 or 9!");
if(readFrame)
{
tensor = ConvertMatrixTypeToFixedArrayType(tensor.PreMultiply(measFrame));
tensor = ConvertMatrixTypeToFixedArrayType(tensor.PostMultiply(measFrameTransp));
}
FixPixType fixVec(tensor);
ot.Set(fixVec);
++ot;
}
}
else
{
throw itk::ImageFileReaderException(__FILE__, __LINE__, "Image has wrong number of pixel components!");
}
this->GetOutput()->InitializeByItk(vecImg.GetPointer());
this->GetOutput()->SetVolume(vecImg->GetBufferPointer());
}
try
{
setlocale(LC_ALL, currLocale.c_str());
}
catch(...)
{
MITK_INFO << "Could not reset locale " << currLocale;
}
}
catch(std::exception& e)
{
throw itk::ImageFileReaderException(__FILE__, __LINE__, e.what());
}
catch(...)
{
throw itk::ImageFileReaderException(__FILE__, __LINE__, "Sorry, an error occurred while reading the requested DTI file!");
}
}
}
int main(int, char ** argv)
{
OptionsData options;
readXMLValues(argv[2], options);
exit(1);
// parse the dicom directory
gdcm::Directory dir;
dir.Load(argv[1], true);
gdcm::Directory::FilenamesType filenames = dir.GetFilenames();
gdcm::Tag seriesDescription = gdcm::Tag(0x0008,0x103e);
gdcm::Tag seriesNumber = gdcm::Tag(0x0020,0x0011);
gdcm::Tag instanceNumber = gdcm::Tag(0x0020,0x0013);
gdcm::Tag sliceThickness = gdcm::Tag(0x0018,0x0050);
gdcm::Tag triggerTime = gdcm::Tag(0x0018,0x1060);
gdcm::Tag numberOfImages = gdcm::Tag(0x0018,0x1090);
gdcm::Tag slicePosition = gdcm::Tag(0x0019,0x1015);
gdcm::Tag imagePosition = gdcm::Tag(0x0020,0x0032);
gdcm::Tag imageOrientation = gdcm::Tag(0x0020,0x0037);
gdcm::Tag sliceLocation = gdcm::Tag(0x0020,0x1041);
gdcm::Tag rows = gdcm::Tag(0x0028,0x0010);
gdcm::Tag cols = gdcm::Tag(0x0028,0x0011);
gdcm::Tag pixelSpacing = gdcm::Tag(0x0028,0x0030);
gdcm::Scanner scanner;
scanner.AddTag(seriesDescription);
scanner.AddTag(seriesNumber);
scanner.AddTag(instanceNumber);
scanner.AddTag(sliceThickness);
scanner.AddTag(triggerTime);
scanner.AddTag(numberOfImages);
scanner.AddTag(slicePosition);
scanner.AddTag(imagePosition);
scanner.AddTag(imageOrientation);
scanner.AddTag(sliceLocation);
scanner.AddTag(rows);
scanner.AddTag(cols);
scanner.AddTag(pixelSpacing);
scanner.Scan(filenames);
gdcm::Scanner::MappingType mapping = scanner.GetMappings();
// extract all the images that are Short axis and are the first instance
gdcm::Directory::FilenamesType targetFilenames;
for(unsigned int i = 0; i < filenames.size(); i++)
{
const char * fname = filenames[i].c_str();
if(mapping.count(fname) == 0) continue;
// extract the image information
std::string descriptionStr = mapping[fname][seriesDescription];
std::string instanceNumberStr = mapping[fname][instanceNumber];
QString description = QString::fromStdString(descriptionStr);
unsigned int instanceNumber = QString::fromStdString(instanceNumberStr).toInt();
// check that the description is a short axis one and is instance 1
if(instanceNumber == 1 && description.contains("sa", Qt::CaseInsensitive))
{
targetFilenames.push_back(filenames[i]);
}
}
// sort the images based on their slice position
/*
gdcm::Sorter sorter;
sorter.SetSortFunction(position_sort);
sorter.StableSort(targetFilenames);
gdcm::Directory::FilenamesType sorted = sorter.GetFilenames();
for(unsigned int i = 0; i < sorted.size(); i++)
{
const char * fname = sorted[i].c_str();
std::string position = mapping[fname][imagePosition];
std::cout << position << std::endl;
std::cout << mapping[fname][sliceLocation] << std::endl;
}
*/
std::cout << targetFilenames.size() << std::endl;
// find the slice with the smallest slice position
double smallest = 1000000.0;
int smallestIndex;
for(unsigned int i = 0; i < targetFilenames.size(); i++)
{
const char * fname = targetFilenames[i].c_str();
std::string slicePosition = mapping[fname][sliceLocation];
double pos = QString::fromStdString(slicePosition).toDouble();
std::cout << pos << std::endl;
if(pos < smallest)
{
smallest = pos;
smallestIndex = i;
}
}
// load the image
typedef itk::Image<unsigned short, 3> ImageType;
typedef itk::ImageFileReader<ImageType> ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(targetFilenames[smallestIndex]);
reader->SetImageIO(itk::GDCMImageIO::New());
reader->Update();
// flip the x and y axis
typedef itk::PermuteAxesImageFilter<ImageType> FlipperType;
FlipperType::Pointer flipper = FlipperType::New();
itk::FixedArray<unsigned int, 3> order;
order[0] = 1;
order[1] = 0;
order[2] = 2;
flipper->SetOrder(order);
flipper->SetInput(reader->GetOutput());
flipper->Update();
ImageType::Pointer referenceImage = flipper->GetOutput();
ImageType::DirectionType direction = referenceImage->GetDirection();
direction.SetIdentity();
referenceImage->SetDirection(direction);
ImageType::PointType origin = referenceImage->GetOrigin();
origin.Fill(20.0);
referenceImage->SetOrigin(origin);
ImageType::SpacingType spacing;
spacing.Fill(1.0);
referenceImage->SetSpacing(spacing);
flipper->GetOutput()->Print(std::cout);
typedef itk::ImageFileWriter<ImageType> WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetInput(referenceImage);
writer->SetImageIO(itk::NrrdImageIO::New());
writer->SetFileName("test.nrrd");
writer->Update();
std::cout << targetFilenames[smallestIndex] << std::endl;
return 0;
}
void NrrdTensorImageReader
::GenerateData()
{
if ( m_FileName == "")
{
throw itk::ImageFileReaderException(__FILE__, __LINE__, "Sorry, the filename is empty!");
}
else
{
try
{
const std::string& locale = "C";
const std::string& currLocale = setlocale( LC_ALL, NULL );
if ( locale.compare(currLocale)!=0 )
{
try
{
setlocale(LC_ALL, locale.c_str());
}
catch(...)
{
MITK_INFO << "Could not set locale " << locale;
}
}
typedef itk::VectorImage<float,3> ImageType;
itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();
typedef itk::ImageFileReader<ImageType> FileReaderType;
FileReaderType::Pointer reader = FileReaderType::New();
reader->SetImageIO(io);
reader->SetFileName(this->m_FileName);
reader->Update();
ImageType::Pointer img = reader->GetOutput();
typedef itk::Image<itk::DiffusionTensor3D<float>,3> VecImgType;
VecImgType::Pointer vecImg = VecImgType::New();
vecImg->SetSpacing( img->GetSpacing() ); // Set the image spacing
vecImg->SetOrigin( img->GetOrigin() ); // Set the image origin
vecImg->SetDirection( img->GetDirection() ); // Set the image direction
vecImg->SetRegions( img->GetLargestPossibleRegion());
vecImg->Allocate();
itk::ImageRegionIterator<VecImgType> ot (vecImg, vecImg->GetLargestPossibleRegion() );
ot = ot.Begin();
itk::ImageRegionIterator<ImageType> it (img, img->GetLargestPossibleRegion() );
it = it.Begin();
typedef ImageType::PixelType VarPixType;
typedef VecImgType::PixelType FixPixType;
int numComponents = img->GetNumberOfComponentsPerPixel();
itk::MetaDataDictionary imgMetaDictionary = img->GetMetaDataDictionary();
std::vector<std::string> imgMetaKeys = imgMetaDictionary.GetKeys();
std::vector<std::string>::const_iterator itKey = imgMetaKeys.begin();
std::string metaString;
bool readFrame = false;
double xx, xy, xz, yx, yy, yz, zx, zy, zz;
MeasurementFrameType measFrame;
measFrame.SetIdentity();
MeasurementFrameType measFrameTransp;
measFrameTransp.SetIdentity();
for (; itKey != imgMetaKeys.end(); itKey ++)
{
itk::ExposeMetaData<std::string> (imgMetaDictionary, *itKey, metaString);
if (itKey->find("measurement frame") != std::string::npos)
{
sscanf(metaString.c_str(), " ( %lf , %lf , %lf ) ( %lf , %lf , %lf ) ( %lf , %lf , %lf ) \n", &xx, &xy, &xz, &yx, &yy, &yz, &zx, &zy, &zz);
if (xx>10e-10 || xy>10e-10 || xz>10e-10 ||
yx>10e-10 || yy>10e-10 || yz>10e-10 ||
zx>10e-10 || zy>10e-10 || zz>10e-10 )
{
readFrame = true;
measFrame(0,0) = xx;
measFrame(0,1) = xy;
measFrame(0,2) = xz;
measFrame(1,0) = yx;
measFrame(1,1) = yy;
measFrame(1,2) = yz;
measFrame(2,0) = zx;
measFrame(2,1) = zy;
measFrame(2,2) = zz;
measFrameTransp = measFrame.GetTranspose();
}
}
}
if (numComponents==6)
{
while (!it.IsAtEnd())
{
// T'=RTR'
VarPixType vec = it.Get();
FixPixType fixVec(vec.GetDataPointer());
if(readFrame)
{
itk::DiffusionTensor3D<float> tensor;
tensor.SetElement(0, vec.GetElement(0));
tensor.SetElement(1, vec.GetElement(1));
tensor.SetElement(2, vec.GetElement(2));
tensor.SetElement(3, vec.GetElement(3));
tensor.SetElement(4, vec.GetElement(4));
tensor.SetElement(5, vec.GetElement(5));
tensor = tensor.PreMultiply(measFrame);
tensor = tensor.PostMultiply(measFrameTransp);
fixVec = tensor;
}
ot.Set(fixVec);
++ot;
++it;
}
}
else if(numComponents==9)
{
while (!it.IsAtEnd())
{
VarPixType vec = it.Get();
itk::DiffusionTensor3D<float> tensor;
tensor.SetElement(0, vec.GetElement(0));
tensor.SetElement(1, vec.GetElement(1));
tensor.SetElement(2, vec.GetElement(2));
tensor.SetElement(3, vec.GetElement(4));
tensor.SetElement(4, vec.GetElement(5));
tensor.SetElement(5, vec.GetElement(8));
if(readFrame)
{
tensor = tensor.PreMultiply(measFrame);
tensor = tensor.PostMultiply(measFrameTransp);
}
FixPixType fixVec(tensor);
ot.Set(fixVec);
++ot;
++it;
}
}
else
{
throw itk::ImageFileReaderException(__FILE__, __LINE__, "Image has wrong number of pixel components!");
}
this->GetOutput()->InitializeByItk(vecImg.GetPointer());
this->GetOutput()->SetVolume(vecImg->GetBufferPointer());
try
{
setlocale(LC_ALL, currLocale.c_str());
}
catch(...)
{
MITK_INFO << "Could not reset locale " << currLocale;
}
}
catch(std::exception& e)
{
throw itk::ImageFileReaderException(__FILE__, __LINE__, e.what());
}
catch(...)
{
throw itk::ImageFileReaderException(__FILE__, __LINE__, "Sorry, an error occurred while reading the requested DTI file!");
}
}
}
int main(int argc, char ** argv)
{
// load the input matrix
utils::MatrixReader::Pointer reader = utils::MatrixReader::New();
reader->SetFilename("/home/om0000/ValveTracking/TrainingData/conf6/conf6-MV-2C-0.hdf5");
reader->Read();
Params pparams("/home/om0000/ValveTracking/TrainingData/conf6/extract_features.json");
MatrixType pos = reader->GetOutput()->doubleData["p1-pos"];
MatrixType neg = reader->GetOutput()->doubleData["p1-neg"];
for(unsigned int tNum = 0; tNum < pos.rows(); tNum++)
{
MatrixType test = pos.row(tNum);
MatrixType others(pos.rows()-1, pos.cols());
unsigned int count = 0;
for(unsigned int i = 0; i < pos.rows(); i++)
{
if(i != tNum)
{
others.row(count) = pos.row(i);
count++;
}
}
unsigned int T = others.rows();
unsigned int Knn = 5;
unsigned int newCount = 0;
unsigned int NN = 50;
srand (time(NULL));
MatrixType smotePos(NN*T, pos.cols());
for(unsigned int i = 0; i < T; i++)
{
MatrixType s1 = others.row(i);
MatrixType dists(T,1);
std::vector<IndexDistPair> sortList;
for(unsigned int j = 0; j < T; j++)
{
if(i == j) continue;
std::pair<int, double> p(j, (others.row(j)-s1).norm());
sortList.push_back(p);
}
std::sort(sortList.begin(), sortList.end(), index_sort);
unsigned int N = NN;
while(N != 0)
{
int nn = sortList[rand() % Knn].first;
MatrixType newF(1, others.cols());
for(unsigned int j = 0; j < others.cols(); j++)
{
double diff = others(nn,j) - s1(0,j);
double gap = (double) rand() / RAND_MAX;
smotePos(newCount, j) = round(s1(0,j) + (gap*diff));
}
newCount++;
N--;
}
}
// combine the pos and neg
MatrixType newAll, all;
IntMatrixType newLabels, labels;
combine(others, neg, all, labels);
combine(smotePos, neg, newAll, newLabels);
/*
cv::Mat vType = cv::Mat(pos.cols()+1, 1, CV_8U);
vType.setTo(cv::Scalar(CV_VAR_NUMERICAL));
vType.at<uchar>(pos.cols(), 0) = CV_VAR_CATEGORICAL;
cv::Mat X = convert(newAll);
cv::Mat y = convert(newLabels);
cv::Mat cvtest = convert(test);
cv::BoostParams params;
params.boost_type = CvBoost::GENTLE;
cv::Boost cls;
std::cout << "Training" << std::endl;
//cls.train(X, CV_ROW_SAMPLE, y,
//cv::Mat(), cv::Mat(), vType, cv::Mat(), params);
cls.load("cls.cls", "hello");
std::cout << "Testing" << std::endl;
std::cout << cls.predict(cvtest, cv::Mat(), cv::Range::all(), false, true) << std::endl;
/*
cv::RandomTreeParams params;
params.max_depth = 25;
params.regression_accuracy = 0.00001;
cv::NormalBayesClassifier cls;
cls.train(X, y);
cv::Mat out;
cls.predict(cvtest, &out);
std::cout << out << std::endl;
*/
//cv::RandomTrees trees;
//trees.train(X, CV_ROW_SAMPLE, y,
//cv::Mat(), cv::Mat(), vType, cv::Mat(), params);
//std::cout << trees.predict(cvtest) << std::endl;
/*
MatrixType probs1, probs2;
IntMatrixType cls1, cls2;
*/
vt::SVMClassifier::Pointer svm1 = vt::SVMClassifier::New();
svm1->Train(all, labels);
vt::SVMClassifier::Pointer svm2 = vt::SVMClassifier::New();
svm2->Train(newAll, newLabels);
// load the image
ValveSequenceReader<3>::Pointer reader = ValveSequenceReader<3>::New();
reader->SetFileName(argv[1]);
ValveSequence<3>::Pointer sequence = reader->GetOutput();
typedef ValveLine<3> ValveType;
typedef ValveType::ImageType ImageType;
ValveType::Pointer valve = sequence->GetValveLine(0);
ImageType::Pointer image = valve->GetImage();
typedef itk::Image<double, 3> RealImageType;
RealImageType::Pointer output = RealImageType::New();
output->SetOrigin(image->GetOrigin());
output->SetSpacing(image->GetSpacing());
output->SetRegions(image->GetLargestPossibleRegion());
output->SetDirection(image->GetDirection());
output->Allocate();
RealImageType::Pointer output2 = RealImageType::New();
output2->SetOrigin(image->GetOrigin());
output2->SetSpacing(image->GetSpacing());
output2->SetRegions(image->GetLargestPossibleRegion());
output2->SetDirection(image->GetDirection());
output2->Allocate();
itk::ImageRegionIterator<RealImageType> it(output, output->GetLargestPossibleRegion());
itk::ImageRegionIterator<RealImageType> it2(output2, output2->GetLargestPossibleRegion());
while(!it.IsAtEnd())
{
ImageType::IndexType index = it.GetIndex();
ImageType::PointType pt;
output->TransformIndexToPhysicalPoint(index, pt);
MatrixType feature;
extractLBPFeature(pparams, valve, pt, feature);
MatrixType p1,p2;
IntMatrixType c1, c2;
svm1->PredictProbability(feature, c1, p1);
svm2->PredictProbability(feature, c2, p2);
it.Set(p1(0,0));
it2.Set(p2(0,0));
++it2;
++it;
}
utils::RealVolumeIO::Write("votes.nrrd", output);
utils::RealVolumeIO::Write("votes2.nrrd", output);
utils::ImageVolumeIO::Write("image.nrrd", image);
return 0;
}
return 0;
}
void mitk::DiffusionPropertyHelper::AverageRedundantGradients(double precision)
{
mitk::GradientDirectionsProperty* DirectionsProperty = static_cast<mitk::GradientDirectionsProperty*>( m_Image->GetProperty(mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() );
GradientDirectionsContainerType::Pointer oldDirs = DirectionsProperty->GetGradientDirectionsContainer();
GradientDirectionsContainerType::Pointer newDirs =
CalcAveragedDirectionSet(precision, oldDirs);
// if sizes equal, we do not need to do anything in this function
if(oldDirs->size() == newDirs->size())
return;
// new image
ImageType::Pointer oldImage = ImageType::New();
mitk::CastToItkImage( m_Image, oldImage);
ImageType::Pointer newITKImage = ImageType::New();
newITKImage->SetSpacing( oldImage->GetSpacing() ); // Set the image spacing
newITKImage->SetOrigin( oldImage->GetOrigin() ); // Set the image origin
newITKImage->SetDirection( oldImage->GetDirection() ); // Set the image direction
newITKImage->SetLargestPossibleRegion( oldImage->GetLargestPossibleRegion() );
newITKImage->SetVectorLength( newDirs->size() );
newITKImage->SetBufferedRegion( oldImage->GetLargestPossibleRegion() );
newITKImage->Allocate();
// average image data that corresponds to identical directions
itk::ImageRegionIterator< ImageType > newIt(newITKImage, newITKImage->GetLargestPossibleRegion());
newIt.GoToBegin();
itk::ImageRegionIterator< ImageType > oldIt(oldImage, oldImage->GetLargestPossibleRegion());
oldIt.GoToBegin();
// initial new value of voxel
ImageType::PixelType newVec;
newVec.SetSize(newDirs->size());
newVec.AllocateElements(newDirs->size());
// find which gradients should be averaged
GradientDirectionsContainerType::Pointer oldDirections = oldDirs;
std::vector<std::vector<int> > dirIndices;
for(GradientDirectionsContainerType::ConstIterator gdcitNew = newDirs->Begin();
gdcitNew != newDirs->End(); ++gdcitNew)
{
dirIndices.push_back(std::vector<int>(0));
for(GradientDirectionsContainerType::ConstIterator gdcitOld = oldDirs->Begin();
gdcitOld != oldDirections->End(); ++gdcitOld)
{
if(AreAlike(gdcitNew.Value(), gdcitOld.Value(), precision))
{
//MITK_INFO << gdcitNew.Value() << " " << gdcitOld.Value();
dirIndices[gdcitNew.Index()].push_back(gdcitOld.Index());
}
}
}
//int ind1 = -1;
while(!newIt.IsAtEnd())
{
// progress
//typename ImageType::IndexType ind = newIt.GetIndex();
//ind1 = ind.m_Index[2];
// init new vector with zeros
newVec.Fill(0.0);
// the old voxel value with duplicates
ImageType::PixelType oldVec = oldIt.Get();
for(unsigned int i=0; i<dirIndices.size(); i++)
{
// do the averaging
const unsigned int numavg = dirIndices[i].size();
unsigned int sum = 0;
for(unsigned int j=0; j<numavg; j++)
{
//MITK_INFO << newVec[i] << " << " << oldVec[dirIndices[i].at(j)];
sum += oldVec[dirIndices[i].at(j)];
}
if(numavg == 0)
{
MITK_ERROR << "VectorImage: Error on averaging. Possibly due to corrupted data";
return;
}
newVec[i] = sum / numavg;
}
newIt.Set(newVec);
++newIt;
++oldIt;
}
mitk::GrabItkImageMemory( newITKImage, m_Image );
m_Image->SetProperty( mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str(), mitk::GradientDirectionsProperty::New( newDirs ) );
m_Image->SetProperty( mitk::DiffusionPropertyHelper::ORIGINALGRADIENTCONTAINERPROPERTYNAME.c_str(), mitk::GradientDirectionsProperty::New( newDirs ) );
ApplyMeasurementFrame();
UpdateBValueMap();
std::cout << std::endl;
}
int main( int argc, char* argv[] )
{
if( argc != 3 )
{
std::cerr << "Usage: "<< std::endl;
std::cerr << argv[0];
std::cerr << " <InputFileName> n";
std::cerr << std::endl;
return EXIT_FAILURE;
}
int operations = atoi(argv[2]);
//sscanf(&operations,"%d",argv[2]);
//printf("%d\n", operations);
itk::TimeProbe itkClock;
double t0 = 0.0;
double tf = 0.0;
itk::MultiThreader::SetGlobalDefaultNumberOfThreads(1);
// Loading file
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName( argv[1] );
reader->Update();
ImageType::Pointer image = reader->GetOutput();
#ifdef GPU
GPUReaderType::Pointer gpureader = GPUReaderType::New();
gpureader->SetFileName( argv[1] );
gpureader->Update();
GPUImageType::Pointer gpuImage = gpureader->GetOutput();
#endif
saveFile((char*) "/tmp/itk_input.dcm", image);
// Allocate output image
ImageType::Pointer output = ImageType::New();
ImageType::RegionType region = image->GetBufferedRegion();
output->SetRegions( region );
output->SetOrigin( image->GetOrigin() );
output->SetSpacing( image->GetSpacing() );
output->Allocate();
// Negative
typedef itk::UnaryFunctorImageFilter<ImageType,ImageType,
Negate<ImageType::PixelType,ImageType::PixelType> > NegateImageFilterType;
NegateImageFilterType::Pointer negateFilter = NegateImageFilterType::New();
negateFilter = NegateImageFilterType::New();
negateFilter->SetInput(image);
#ifndef GPU_only
itkClock.Start();
TimerStart();
for(int n = 0; n < operations; n++)
{
negateFilter->Modified();
negateFilter->Update();
}
itkClock.Stop();
printf("Tempo gasto para fazer %d negative: %s\n",operations, getTimeElapsedInSeconds());
tf = itkClock.GetTotal();
std::cout << "My: " << (tf - t0) << std::endl;
t0 = tf;
#endif
// Saving Not result
saveFile((char*) "/tmp/itk_not.dcm", negateFilter->GetOutput());
#ifdef GPU
// GPU Negative
typedef itk::GPUUnaryFunctorImageFilter<ImageType,ImageType,
Negate<ImageType::PixelType,ImageType::PixelType> > GPUNegateImageFilterType;
GPUNegateImageFilterType::Pointer gpuNegateFilter = GPUNegateImageFilterType::New();
gpuNegateFilter->SetInput(gpureader->GetOutput());
gpuNegateFilter->Update();
// Saving Not result
//saveFile("/tmp/itk_gpu_not.dcm", gpuNegateFilter->GetOutput());
#endif
// Common Threshold
int lowerThreshold = 100;
int upperThreshold = 200;
// Threshold
typedef itk::BinaryThresholdImageFilter <ImageType, ImageType>
BinaryThresholdImageFilterType;
BinaryThresholdImageFilterType::Pointer thresholdFilter
= BinaryThresholdImageFilterType::New();
thresholdFilter = BinaryThresholdImageFilterType::New();
thresholdFilter->SetInput(reader->GetOutput());
thresholdFilter->SetLowerThreshold(lowerThreshold);
thresholdFilter->SetUpperThreshold(upperThreshold);
thresholdFilter->SetInsideValue(255);
thresholdFilter->SetOutsideValue(0);
#ifndef GPU_only
itkClock.Start();
TimerStart();
for(int n = 0; n < operations; n++)
{
thresholdFilter->Modified();
thresholdFilter->Update();
}
itkClock.Stop();
printf("Tempo gasto para fazer %d threshold: %s\n",operations, getTimeElapsedInSeconds());
tf = itkClock.GetTotal();
std::cout << "My: " << (tf - t0) << std::endl;
t0 = tf;
// Saving Threshold result
saveFile((char*) "/tmp/itk_thresh.dcm", thresholdFilter->GetOutput());
#endif
#ifdef GPU
// GPU Threshold
typedef itk::GPUBinaryThresholdImageFilter <GPUImageType, GPUImageType>
GPUBinaryThresholdImageFilterType;
GPUBinaryThresholdImageFilterType::Pointer gpuThresholdFilter
= GPUBinaryThresholdImageFilterType::New();
gpuThresholdFilter->SetInput(gpureader->GetOutput());
gpuThresholdFilter->SetLowerThreshold(lowerThreshold);
gpuThresholdFilter->SetUpperThreshold(upperThreshold);
gpuThresholdFilter->SetInsideValue(255);
gpuThresholdFilter->SetOutsideValue(0);
itkClock.Start();
TimerStart();
for(int n = 0; n < operations; n++)
{
gpuThresholdFilter->Modified();
gpuThresholdFilter->Update();
}
itkClock.Stop();
printf("Tempo gasto para fazer %d GPU threshold: %s\n",operations, getTimeElapsedInSeconds());
tf = itkClock.GetTotal();
std::cout << "My: " << (tf - t0) << std::endl;
t0 = tf;
// Saving GPU Threshold result
gpuThresholdFilter->GetOutput()->UpdateBuffers();
saveFile((char*) "/tmp/itk_gpu_thresh.dcm", gpuThresholdFilter->GetOutput());
#endif
// Mean
typedef itk::MeanImageFilter< ImageType, ImageType > MeanFilterType;
MeanFilterType::Pointer meanFilter = MeanFilterType::New();
meanFilter = MeanFilterType::New();
meanFilter->SetInput( image );
meanFilter->SetRadius( 1 );
#ifndef GPU_only
itkClock.Start();
TimerStart();
for(int n = 0; n < operations; n++)
{
meanFilter->Modified();
meanFilter->Update();
}
itkClock.Stop();
printf("Tempo gasto para fazer %d mean blur: %s\n",operations, getTimeElapsedInSeconds());
tf = itkClock.GetTotal();
std::cout << "My: " << (tf - t0) << std::endl;
t0 = tf;
// Saving Convolution result
saveFile((char*) "/tmp/itk_mean3x3.dcm", meanFilter->GetOutput());
#endif
// Binomial Blur (aproximation of gaussian blur)
typedef itk::BinomialBlurImageFilter<ImageType, ImageType> BinomialBlurImageFilterType;
int repetitions = 1;
BinomialBlurImageFilterType::Pointer blurFilter = BinomialBlurImageFilterType::New();
blurFilter = BinomialBlurImageFilterType::New();
blurFilter->SetInput( reader->GetOutput() );
blurFilter->SetRepetitions( repetitions );
#ifndef GPU_only
itkClock.Start();
TimerStart();
for(int n = 0; n < operations; n++)
{
blurFilter->Modified();
blurFilter->Update();
}
itkClock.Stop();
printf("Tempo gasto para fazer %d blur: %s\n",operations, getTimeElapsedInSeconds());
tf = itkClock.GetTotal();
std::cout << "My: " << (tf - t0) << std::endl;
t0 = tf;
// Saving Blur result
saveFile((char*) "/tmp/itk_blur.dcm", blurFilter->GetOutput());
#endif
#ifdef GPU
// GPU Blur
typedef itk::BoxImageFilter< GPUImageType, GPUImageType > BoxImageFilterType;
typedef itk::GPUBoxImageFilter< GPUImageType, GPUImageType, BoxImageFilterType > GPUBoxImageFilterType;
GPUBoxImageFilterType::Pointer GPUBlurFilter = GPUBoxImageFilterType::New();
//ImageType::SizeType indexRadius;
//indexRadius[0] = 2;
//indexRadius[1] = 2;
//indexRadius[2] = 2;
GPUBlurFilter->SetInput(gpureader->GetOutput());
//GPUBlurFilter->SetRadius(indexRadius);
itkClock.Start();
TimerStart();
for(int n = 0; n < operations; n++)
{
GPUBlurFilter->Update();
GPUBlurFilter->Modified();
}
itkClock.Stop();
printf("Tempo gasto para fazer %d gpu blur: %s\n",operations, getTimeElapsedInSeconds());
tf = itkClock.GetTotal();
std::cout << "My: " << (tf - t0) << std::endl;
t0 = tf;
GPUBlurFilter->GetOutput()->UpdateBuffers();
// Saving GPU Blur result
saveFile((char*) "/tmp/itk_gpu_blur.dcm", GPUBlurFilter->GetOutput());
#endif
//Erosion Common
typedef itk::BinaryBallStructuringElement<
ImageType::PixelType, 3> StructuringElementType;
typedef itk::GrayscaleErodeImageFilter <ImageType, ImageType, StructuringElementType>
GrayscaleErodeImageFilterType;
unsigned int radius;
// Erosion 3x3
StructuringElementType structuringElement3x3;
radius = 1;
structuringElement3x3.SetRadius(radius);
structuringElement3x3.CreateStructuringElement();
GrayscaleErodeImageFilterType::Pointer erodeFilter3x3;
erodeFilter3x3= GrayscaleErodeImageFilterType::New();
erodeFilter3x3->SetInput(reader->GetOutput());
erodeFilter3x3->SetKernel(structuringElement3x3);
#ifndef GPU_only
itkClock.Start();
TimerStart();
for(int n = 0; n < operations; n++)
{
erodeFilter3x3->Modified();
erodeFilter3x3->Update();
}
itkClock.Stop();
printf("Tempo gasto para fazer %d erosion 3x3: %s\n",operations, getTimeElapsedInSeconds());
tf = itkClock.GetTotal();
std::cout << "My: " << (tf - t0) << std::endl;
t0 = tf;
// Saving Erosion result
saveFile((char*) "/tmp/itk_erode3x3.dcm", erodeFilter3x3->GetOutput());
#endif
// Erosion 5x5
StructuringElementType structuringElement5x5;
radius = 2;
structuringElement5x5.SetRadius(radius);
structuringElement5x5.CreateStructuringElement();
GrayscaleErodeImageFilterType::Pointer erodeFilter5x5;
erodeFilter5x5 = GrayscaleErodeImageFilterType::New();
erodeFilter5x5->SetInput(reader->GetOutput());
erodeFilter5x5->SetKernel(structuringElement5x5);
#ifndef GPU_only
itkClock.Start();
TimerStart();
for(int n = 0; n < operations; n++)
{
erodeFilter5x5->Modified();
erodeFilter5x5->Update();
}
itkClock.Stop();
printf("Tempo gasto para fazer %d erosion 5x5: %s\n",operations, getTimeElapsedInSeconds());
tf = itkClock.GetTotal();
std::cout << "My: " << (tf - t0) << std::endl;
t0 = tf;
// Saving Erosion result
saveFile((char*) "/tmp/itk_erode5x5.dcm", erodeFilter5x5->GetOutput());
#endif
// Copy
typedef itk::ImageDuplicator< ImageType > DuplicatorType;
DuplicatorType::Pointer duplicator;
duplicator = DuplicatorType::New();
duplicator->SetInputImage(image);
#ifndef GPU_only
itkClock.Start();
TimerStart();
for(int n = 0; n < operations; n++)
{
duplicator->Modified();
duplicator->Update();
}
itkClock.Stop();
printf("Tempo gasto para fazer %d copias cpu: %s\n",operations, getTimeElapsedInSeconds());
tf = itkClock.GetTotal();
std::cout << "My: " << (tf - t0) << std::endl;
t0 = tf;
// Saving Copy result
saveFile((char*) "/tmp/itk_copy.dcm", duplicator->GetOutput());
#endif
// Convolution common
typedef itk::ConvolutionImageFilter<ImageType> ConvolutionImageFilterType;
ConvolutionImageFilterType::Pointer convolutionFilter;
convolutionFilter = ConvolutionImageFilterType::New();
convolutionFilter->SetInput(reader->GetOutput());
int convWidth;
// Convolution 3x3
ImageType::Pointer kernel3x3 = ImageType::New();
convWidth = 3;
CreateKernel(kernel3x3, convWidth);
convolutionFilter->SetKernelImage(kernel3x3);
#ifndef GPU_only
itkClock.Start();
TimerStart();
for(int n = 0; n < operations; n++)
{
convolutionFilter->Modified();
convolutionFilter->Update();
}
itkClock.Stop();
printf("Tempo gasto para fazer %d convolucoes 3x3 cpu: %s\n",operations, getTimeElapsedInSeconds());
tf = itkClock.GetTotal();
std::cout << "My: " << (tf - t0) << std::endl;
t0 = tf;
// Saving Convolution result
saveFile((char*) "/tmp/itk_convolution3x3.dcm", convolutionFilter->GetOutput());
#endif
// Convolution 5x5
ImageType::Pointer kernel5x5 = ImageType::New();
convWidth = 5;
CreateKernel(kernel5x5, convWidth);
convolutionFilter->SetKernelImage(kernel5x5);
#ifndef GPU_only
itkClock.Start();
TimerStart();
for(int n = 0; n < operations; n++)
{
convolutionFilter->Modified();
convolutionFilter->Update();
}
itkClock.Stop();
printf("Tempo gasto para fazer %d convolucoes 5x5 cpu: %s\n",operations, getTimeElapsedInSeconds());
tf = itkClock.GetTotal();
std::cout << "My: " << (tf - t0) << std::endl;
t0 = tf;
// Saving Convolution result
saveFile((char*) "/tmp/itk_convolution5x5.dcm", convolutionFilter->GetOutput());
#endif
#ifdef GPU
// GPU Mean
typedef itk::GPUMeanImageFilter<GPUImageType, GPUImageType> GPUMeanFilterType;
GPUMeanFilterType::Pointer GPUMean = GPUMeanFilterType::New();
GPUMean->SetInput(gpureader->GetOutput());
GPUMean->SetRadius( 1 );
TimerStart();
for(int n = 0; n < operations; n++)
{
GPUMean->Update();
GPUMean->Modified();
}
itkClock.Stop();
printf("Tempo gasto para fazer %d GPU mean blur: %s\n",operations, getTimeElapsedInSeconds());
tf = itkClock.GetTotal();
std::cout << "My: " << (tf - t0) << std::endl;
t0 = tf;
GPUMean->GetOutput()->UpdateBuffers();
saveFile((char*) "/tmp/itk_gpu_blurmean.dcm", GPUMean->GetOutput());
#endif
// Visualize
/*
QuickView viewer;
viewer.AddImage<ImageType>(
image,true,
itksys::SystemTools::GetFilenameName(argv[1]));
std::stringstream desc;
desc << "ITK QuickView: "
<< argv[1];
viewer.Visualize();
*/
// Saving input image as is
saveFile((char*) "/tmp/itk_input.dcm", image);
return EXIT_SUCCESS;
}