mitk::TbssImage::Pointer mitk::TbssImporter::ImportMeta()
{
mitk::TbssImage::Pointer tbssImg = mitk::TbssImage::New();
m_Data = DataImageType::New();
std::vector< std::pair<mitk::TbssImage::MetaDataFunction, int> > metaInfo;
// Gradient images are vector images, so they will add more dimensions to the vector
int vecLength = m_MetaFiles.size();
//Check if there is a gradient image
for(int i=0; i < m_MetaFiles.size(); i++)
{
std::pair<std::string, std::string> p = m_MetaFiles.at(i);
if(RetrieveTbssFunction(p.first) == mitk::TbssImage::GRADIENT_X)
{
vecLength += 2;
}
}
int currIndex = 0;
for(int i=0; i < m_MetaFiles.size(); i++)
{
std::pair<std::string, std::string> p = m_MetaFiles.at(i);
std::string function = p.first;
std::string file = p.second;
// Add to metainfo to give the tbss image a function-index pair
std::pair<mitk::TbssImage::MetaDataFunction, int> pair;
pair.first = RetrieveTbssFunction(function);
pair.second = i;
if(pair.first == mitk::TbssImage::GRADIENT_X)
{
metaInfo.push_back(std::pair<mitk::TbssImage::MetaDataFunction, int>(mitk::TbssImage::GRADIENT_X, i));
metaInfo.push_back(std::pair<mitk::TbssImage::MetaDataFunction, int>(mitk::TbssImage::GRADIENT_Y, i+1));
metaInfo.push_back(std::pair<mitk::TbssImage::MetaDataFunction, int>(mitk::TbssImage::GRADIENT_Z, i+2));
VectorReaderType::Pointer fileReader = VectorReaderType::New();
fileReader->SetFileName(file);
itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();
fileReader->SetImageIO(io);
fileReader->Update();
VectorImageType::Pointer img = fileReader->GetOutput();
VectorImageType::SizeType size = img->GetLargestPossibleRegion().GetSize();
if(i==0)
{
// First image in serie. Properties should be used to initialize m_Data
m_Data->SetRegions(img->GetLargestPossibleRegion().GetSize());
m_Data->SetSpacing(img->GetSpacing());
m_Data->SetOrigin(img->GetOrigin());
m_Data->SetDirection(img->GetDirection());
m_Data->SetVectorLength(vecLength);
m_Data->Allocate();
}
/* Dealing with a gradient image, so the size of the vector need to be increased by 2
since this image contains 3 volumes. Old data should not be deleted*/
for(int x=0; x<size[0]; x++)
{
for(int y=0; y<size[1]; y++)
{
for(int z=0; z<size[2]; z++)
{
itk::Index<3> ix;
ix[0] = x;
ix[1] = y;
ix[2] = z;
itk::VariableLengthVector<int> vec = img->GetPixel(ix);
itk::VariableLengthVector<float> pixel = m_Data->GetPixel(ix);
for(int j=0; j<vec.Size(); j++)
{
int pos = currIndex+j;
float f = vec.GetElement(j);
pixel.SetElement(pos, f);
}
m_Data->SetPixel(ix, pixel);
}
}
}
currIndex += img->GetVectorLength();
tbssImg->SetContainsGradient(true);
// Read vector image and add to m_Data
}
else {
metaInfo.push_back(pair);
FileReaderType3D::Pointer fileReader = FileReaderType3D::New();
fileReader->SetFileName(file);
fileReader->Update();
FloatImage3DType::Pointer img = fileReader->GetOutput();
FloatImage3DType::SizeType size = img->GetLargestPossibleRegion().GetSize();
if(i==0)
{
// First image in serie. Properties should be used to initialize m_Data
m_Data->SetRegions(img->GetLargestPossibleRegion().GetSize());
m_Data->SetSpacing(img->GetSpacing());
m_Data->SetOrigin(img->GetOrigin());
m_Data->SetDirection(img->GetDirection());
m_Data->SetVectorLength(vecLength);
m_Data->Allocate();
}
for(int x=0; x<size[0]; x++)
{
for(int y=0; y<size[1]; y++)
{
for(int z=0; z<size[2]; z++)
{
itk::Index<3> ix;
ix[0] = x;
ix[1] = y;
ix[2] = z;
float f = img->GetPixel(ix);
itk::VariableLengthVector<float> pixel = m_Data->GetPixel(ix);
pixel.SetElement(currIndex, f);
m_Data->SetPixel(ix, pixel);
}
}
}
}
if(pair.first == mitk::TbssImage::MEAN_FA_SKELETON)
{
tbssImg->SetContainsMeanSkeleton(true);
}
else if(pair.first == mitk::TbssImage::MEAN_FA_SKELETON_MASK)
{
tbssImg->SetContainsSkeletonMask(true);
}
else if(pair.first == mitk::TbssImage::DISTANCE_MAP)
{
tbssImg->SetContainsDistanceMap(true);
}
currIndex++;
}
tbssImg->SetIsMeta(true);
tbssImg->SetImage(m_Data);
tbssImg->SetMetaInfo(metaInfo);
tbssImg->InitializeFromVectorImage();
return tbssImg;
}
void otb::Wrapper::ObjectsRadiometricStatistics::DoExecute()
{
VectorImageType::Pointer referenceImage = GetParameterImage("im");
otb::ogr::DataSource::Pointer ogrDS;
ogrDS = otb::ogr::DataSource::New(GetParameterString("in"), otb::ogr::DataSource::Modes::Update_LayerUpdate);
m_OGRDataSourceRendering = OGRDataSourceToMapFilterType::New();
m_OGRDataSourceRendering->AddOGRDataSource(ogrDS);
m_OGRDataSourceRendering->SetOutputSize(referenceImage->GetLargestPossibleRegion().GetSize());
m_OGRDataSourceRendering->SetOutputOrigin(referenceImage->GetOrigin());
m_OGRDataSourceRendering->SetOutputSpacing(referenceImage->GetSpacing());
m_OGRDataSourceRendering->SetOutputProjectionRef(referenceImage->GetProjectionRef());
// m_OGRDataSourceRendering->SetOutputParametersFromImage(referenceImage); // A tester
m_OGRDataSourceRendering->SetBackgroundValue(GetParameterInt("background"));
m_OGRDataSourceRendering->SetBurnAttributeMode(true);
m_OGRDataSourceRendering->SetBurnAttribute(GetParameterString("field"));
// Write label image from OGR
/*
WriterType::Pointer writer = WriterType::New();
writer->SetInput(m_OGRDataSourceRendering->GetOutput());
writer->SetFileName("label_image.tif");
writer->Update();
*/
// Label image from OGR to statistics label map
ConverterStatisticsType::Pointer converterStats = ConverterStatisticsType::New();
converterStats->SetInput(m_OGRDataSourceRendering->GetOutput());
converterStats->SetBackgroundValue(GetParameterInt("background"));
converterStats->Update();
// Prepare channel extraction
ExtractROIFilterType::Pointer m_ExtractROIFilter = ExtractROIFilterType::New();
m_ExtractROIFilter->SetInput(referenceImage);
// Update dataset with new fields
otb::ogr::Layer layer = ogrDS->GetLayerChecked(0);
OGRFieldDefn fieldNbPixels("NbPixels", OFTInteger);
layer.CreateField(fieldNbPixels, true);
OGRFieldDefn fieldFlatness("Flat", OFTReal);
layer.CreateField(fieldFlatness, true);
OGRFieldDefn fieldRoundness("Round", OFTReal);
layer.CreateField(fieldRoundness, true);
OGRFieldDefn fieldElongation("Elong", OFTReal);
layer.CreateField(fieldElongation, true);
OGRFieldDefn fieldPerimeter("Perim", OFTReal);
layer.CreateField(fieldPerimeter, true);
for(unsigned int i = 0; i < referenceImage->GetNumberOfComponentsPerPixel(); i++)
{
std::ostringstream fieldoss;
fieldoss<<"meanB"<<i+1;
OGRFieldDefn field(fieldoss.str().c_str(), OFTReal);
layer.CreateField(field, true);
}
for(unsigned int i = 0; i < referenceImage->GetNumberOfComponentsPerPixel(); i++)
{
std::ostringstream fieldoss;
fieldoss<<"stdB"<<i+1;
OGRFieldDefn field(fieldoss.str().c_str(), OFTReal);
layer.CreateField(field, true);
}
for(unsigned int i = 0; i < referenceImage->GetNumberOfComponentsPerPixel(); i++)
{
std::ostringstream fieldoss;
fieldoss<<"MedB"<<i+1;
OGRFieldDefn field(fieldoss.str().c_str(), OFTReal);
layer.CreateField(field, true);
}
for(unsigned int i = 0; i < referenceImage->GetNumberOfComponentsPerPixel(); i++)
{
std::ostringstream fieldoss;
fieldoss<<"VarB"<<i+1;
OGRFieldDefn field(fieldoss.str().c_str(), OFTReal);
layer.CreateField(field, true);
}
for(unsigned int i = 0; i < referenceImage->GetNumberOfComponentsPerPixel(); i++)
{
std::ostringstream fieldoss;
fieldoss<<"KurtB"<<i+1;
OGRFieldDefn field(fieldoss.str().c_str(), OFTReal);
layer.CreateField(field, true);
}
for(unsigned int i = 0; i < referenceImage->GetNumberOfComponentsPerPixel(); i++)
{
std::ostringstream fieldoss;
fieldoss<<"SkewB"<<i+1;
OGRFieldDefn field(fieldoss.str().c_str(), OFTReal);
layer.CreateField(field, true);
}
for(unsigned int i = 0; i < referenceImage->GetNumberOfComponentsPerPixel(); i++)
{
// Channel selection
m_ExtractROIFilter->SetChannel(i + 1);
// Statistics computation
StatisticsFilterType::Pointer statistics = StatisticsFilterType::New();
statistics->SetInput(converterStats->GetOutput());
statistics->SetFeatureImage(m_ExtractROIFilter->GetOutput());
statistics->SetComputePerimeter(true);
statistics->Update();
// Write shape attributes only one time
if(i==0)
{
for(otb::ogr::Layer::iterator featIt = layer.begin(); featIt!=layer.end(); ++featIt)
{
otb::ogr::Feature m_Feature = *featIt;
unsigned int label = m_Feature.ogr().GetFieldAsInteger(layer.GetLayerDefn().GetFieldIndex(GetParameterString("field").c_str()));
if(statistics->GetOutput()->HasLabel(label))
{
const StatisticsLabelObjectType *labelObjectStats = statistics->GetOutput()->GetLabelObject(label);
m_Feature.ogr().SetField("NbPixels", (int)labelObjectStats->GetNumberOfPixels());
m_Feature.ogr().SetField("Flat", labelObjectStats->GetFlatness());
m_Feature.ogr().SetField("Round", labelObjectStats->GetRoundness());
m_Feature.ogr().SetField("Elong", labelObjectStats->GetElongation());
m_Feature.ogr().SetField("Perim", labelObjectStats->GetPerimeter());
layer.SetFeature(m_Feature);
}
}
}
// Features iteration
for(otb::ogr::Layer::iterator featIt = layer.begin(); featIt!=layer.end(); ++featIt)
{
otb::ogr::Feature m_Feature = *featIt;
unsigned int label = m_Feature.ogr().GetFieldAsInteger(layer.GetLayerDefn().GetFieldIndex(GetParameterString("field").c_str()));
if(statistics->GetOutput()->HasLabel(label))
{
const StatisticsLabelObjectType *labelObjectStats = statistics->GetOutput()->GetLabelObject(label);
std::ostringstream fieldoss;
fieldoss<<"meanB"<<i+1;
m_Feature.ogr().SetField(fieldoss.str().c_str(),labelObjectStats->GetMean());
fieldoss.str("");
fieldoss<<"stdB"<<i+1;
m_Feature.ogr().SetField(fieldoss.str().c_str(),labelObjectStats->GetStandardDeviation());
fieldoss.str("");
fieldoss<<"medB"<<i+1;
m_Feature.ogr().SetField(fieldoss.str().c_str(),labelObjectStats->GetMedian());
fieldoss.str("");
fieldoss<<"varB"<<i+1;
m_Feature.ogr().SetField(fieldoss.str().c_str(),labelObjectStats->GetVariance());
fieldoss.str("");
fieldoss<<"kurtB"<<i+1;
m_Feature.ogr().SetField(fieldoss.str().c_str(),labelObjectStats->GetKurtosis());
fieldoss.str("");
fieldoss<<"skewB"<<i+1;
m_Feature.ogr().SetField(fieldoss.str().c_str(),labelObjectStats->GetSkewness());
fieldoss.str("");
}
else
{
otbAppLogINFO( << "Object number " << label << " is skipped. This could happen during the rasterisation process when an object is smaller than 1 pixel.");
}
}
}
}
bool itkDataTensorImageReaderBase::read (const QString &path)
{
if (this->io.IsNull())
return false;
this->readInformation ( path );
qDebug() << "Read with: " << this->identifier();
if (medAbstractData *medData = dynamic_cast<medAbstractData*>(this->data()) ) {
if (medData->identifier()=="itkDataTensorImageDouble3") {
if (this->io->GetNumberOfComponents()==6) {
typedef itk::Tensor<double, 3> TensorType;
typedef itk::Image<TensorType, 3> TensorImageType;
typedef itk::Vector<double, 6> VectorType;
typedef itk::Image<VectorType, 3> VectorImageType;
typedef itk::ImageFileReader<VectorImageType> ReaderType;
VectorImageType::Pointer image = 0;
{
ReaderType::Pointer reader = ReaderType::New();
reader->SetImageIO (this->io);
reader->SetFileName ( path.toAscii().constData() );
try {
reader->Update();
}
catch (itk::ExceptionObject &e) {
qDebug() << e.GetDescription();
return false;
}
image = reader->GetOutput();
}
TensorImageType::Pointer tensors = TensorImageType::New();
TensorImageType::RegionType region = image->GetLargestPossibleRegion();
tensors->SetRegions (region);
tensors->SetSpacing (image->GetSpacing());
tensors->SetOrigin (image->GetOrigin());
tensors->SetDirection (image->GetDirection());
try {
tensors->Allocate();
}
catch (itk::ExceptionObject &e) {
qDebug() << e.GetDescription();
return false;
}
itk::ImageRegionConstIteratorWithIndex<VectorImageType> itIn (image,
image->GetLargestPossibleRegion());
itk::ImageRegionIteratorWithIndex<TensorImageType> itOut(tensors,
tensors->GetLargestPossibleRegion());
while(!itOut.IsAtEnd()) {
VectorType vec = itIn.Get();
TensorType tensor;
for( unsigned int j=0; j<6; j++) {
tensor[j] = vec[j];
}
itOut.Set (tensor);
++itOut;
++itIn;
}
medData->setData (tensors);
}
else if (this->io->GetNumberOfComponents()==9) {
typedef itk::Tensor<double, 3> TensorType;
typedef itk::Image<TensorType, 3> TensorImageType;
typedef itk::Vector<double, 9> VectorType;
typedef itk::Image<VectorType, 3> VectorImageType;
typedef itk::ImageFileReader<VectorImageType> ReaderType;
VectorImageType::Pointer image = 0;
{
ReaderType::Pointer reader = ReaderType::New();
reader->SetImageIO (this->io);
reader->SetFileName ( path.toAscii().constData() );
try {
reader->Update();
}
catch (itk::ExceptionObject &e) {
qDebug() << e.GetDescription();
return false;
}
image = reader->GetOutput();
}
TensorImageType::Pointer tensors = TensorImageType::New();
TensorImageType::RegionType region = image->GetLargestPossibleRegion();
tensors->SetRegions (region);
tensors->SetSpacing (image->GetSpacing());
tensors->SetOrigin (image->GetOrigin());
tensors->SetDirection (image->GetDirection());
try {
tensors->Allocate();
}
catch (itk::ExceptionObject &e) {
qDebug() << e.GetDescription();
return false;
}
itk::ImageRegionConstIteratorWithIndex<VectorImageType> itIn (image,
image->GetLargestPossibleRegion());
itk::ImageRegionIteratorWithIndex<TensorImageType> itOut(tensors,
tensors->GetLargestPossibleRegion());
while(!itOut.IsAtEnd()) {
VectorType vec = itIn.Get();
TensorType tensor;
for (unsigned int i=0; i<3; i++)
for (unsigned int j=0; j<3; j++)
tensor.SetComponent (i, j, vec[i*3+j]);
itOut.Set (tensor);
++itOut;
++itIn;
}
medData->setData (tensors);
}
else {
qDebug() << "Unsupported number of components";
return false;
}
}
else if (medData->identifier()=="itkDataTensorImageFloat3") {
if (this->io->GetNumberOfComponents()==6) {
typedef itk::Tensor<float, 3> TensorType;
typedef itk::Image<TensorType, 3> TensorImageType;
typedef itk::Vector<float, 6> VectorType;
typedef itk::Image<VectorType, 3> VectorImageType;
typedef itk::ImageFileReader<VectorImageType> ReaderType;
VectorImageType::Pointer image = 0;
{
ReaderType::Pointer reader = ReaderType::New();
reader->SetImageIO (this->io);
reader->SetFileName ( path.toAscii().constData() );
try {
reader->Update();
}
catch (itk::ExceptionObject &e) {
qDebug() << e.GetDescription();
return false;
}
image = reader->GetOutput();
}
TensorImageType::Pointer tensors = TensorImageType::New();
TensorImageType::RegionType region = image->GetLargestPossibleRegion();
tensors->SetRegions (region);
tensors->SetSpacing (image->GetSpacing());
tensors->SetOrigin (image->GetOrigin());
tensors->SetDirection (image->GetDirection());
try {
tensors->Allocate();
}
catch (itk::ExceptionObject &e) {
qDebug() << e.GetDescription();
return false;
}
itk::ImageRegionConstIteratorWithIndex<VectorImageType> itIn (image,
image->GetLargestPossibleRegion());
itk::ImageRegionIteratorWithIndex<TensorImageType> itOut(tensors,
tensors->GetLargestPossibleRegion());
while(!itOut.IsAtEnd()) {
VectorType vec = itIn.Get();
TensorType tensor;
for( unsigned int j=0; j<6; j++) {
tensor[j] = vec[j];
}
itOut.Set (tensor);
++itOut;
++itIn;
}
medData->setData (tensors);
}
else if (this->io->GetNumberOfComponents()==9) {
typedef itk::Tensor<float, 3> TensorType;
typedef itk::Image<TensorType, 3> TensorImageType;
typedef itk::Vector<float, 9> VectorType;
typedef itk::Image<VectorType, 3> VectorImageType;
typedef itk::ImageFileReader<VectorImageType> ReaderType;
VectorImageType::Pointer image = 0;
{
ReaderType::Pointer reader = ReaderType::New();
reader->SetImageIO (this->io);
reader->SetFileName ( path.toAscii().constData() );
try {
reader->Update();
}
catch (itk::ExceptionObject &e) {
qDebug() << e.GetDescription();
return false;
}
image = reader->GetOutput();
}
TensorImageType::Pointer tensors = TensorImageType::New();
TensorImageType::RegionType region = image->GetLargestPossibleRegion();
tensors->SetRegions (region);
tensors->SetSpacing (image->GetSpacing());
tensors->SetOrigin (image->GetOrigin());
tensors->SetDirection (image->GetDirection());
try {
tensors->Allocate();
}
catch (itk::ExceptionObject &e) {
qDebug() << e.GetDescription();
return false;
}
itk::ImageRegionConstIteratorWithIndex<VectorImageType> itIn (image,
image->GetLargestPossibleRegion());
itk::ImageRegionIteratorWithIndex<TensorImageType> itOut(tensors,
tensors->GetLargestPossibleRegion());
while(!itOut.IsAtEnd()) {
VectorType vec = itIn.Get();
TensorType tensor;
for (unsigned int i=0; i<3; i++)
for (unsigned int j=0; j<3; j++)
tensor.SetComponent (i, j, vec[i*3+j]);
itOut.Set (tensor);
++itOut;
++itIn;
}
medData->setData (tensors);
}
else {
qDebug() << "Unsupported number of components";
return false;
}
}
else {
qDebug() << "Unsupported data type";
return false;
}
}
else {
qDebug() << "No data set or could not create one";
return false;
}
return true;
}