void QmitkOdfMaximaExtractionView::TemplatedConvertShCoeffsFromFsl(mitk::Image* mitkImg)
{
typedef itk::FslShCoefficientImageConverter< float, shOrder > FilterType;
typedef mitk::ImageToItk< itk::Image< float, 4 > > CasterType;
CasterType::Pointer caster = CasterType::New();
caster->SetInput(mitkImg);
caster->Update();
typename FilterType::Pointer filter = FilterType::New();
filter->SetInputImage(caster->GetOutput());
filter->GenerateData();
typename FilterType::QballImageType::Pointer itkQbi = filter->GetQballImage();
typename FilterType::CoefficientImageType::Pointer itkCi = filter->GetCoefficientImage();
{
mitk::Image::Pointer img = mitk::Image::New();
img->InitializeByItk( itkCi.GetPointer() );
img->SetVolume( itkCi->GetBufferPointer() );
DataNode::Pointer node = DataNode::New();
node->SetData(img);
node->SetName("FSL_ShCoefficientImage");
GetDataStorage()->Add(node);
}
{
mitk::QBallImage::Pointer img = mitk::QBallImage::New();
img->InitializeByItk( itkQbi.GetPointer() );
img->SetVolume( itkQbi->GetBufferPointer() );
DataNode::Pointer node = DataNode::New();
node->SetData(img);
node->SetName("FSL_QballImage");
GetDataStorage()->Add(node);
}
}
void QmitkOdfMaximaExtractionView::ConvertPeaksFromMrtrix()
{
if (m_ImageNodes.empty())
return;
typedef itk::Image< float, 4 > ItkImageType;
typedef itk::MrtrixPeakImageConverter< float > FilterType;
FilterType::Pointer filter = FilterType::New();
// cast to itk
mitk::Image::Pointer mitkImg = dynamic_cast<mitk::Image*>(m_ImageNodes.at(0)->GetData());
mitk::Geometry3D::Pointer geom = mitkImg->GetGeometry();
typedef mitk::ImageToItk< FilterType::InputImageType > CasterType;
CasterType::Pointer caster = CasterType::New();
caster->SetInput(mitkImg);
caster->Update();
FilterType::InputImageType::Pointer itkImg = caster->GetOutput();
filter->SetInputImage(itkImg);
filter->GenerateData();
mitk::Vector3D outImageSpacing = geom->GetSpacing();
float maxSpacing = 1;
if(outImageSpacing[0]>outImageSpacing[1] && outImageSpacing[0]>outImageSpacing[2])
maxSpacing = outImageSpacing[0];
else if (outImageSpacing[1] > outImageSpacing[2])
maxSpacing = outImageSpacing[1];
else
maxSpacing = outImageSpacing[2];
mitk::FiberBundleX::Pointer directions = filter->GetOutputFiberBundle();
directions->SetGeometry(geom);
DataNode::Pointer node = DataNode::New();
node->SetData(directions);
QString name(m_ImageNodes.at(0)->GetName().c_str());
name += "_VectorField";
node->SetName(name.toStdString().c_str());
node->SetProperty("Fiber2DSliceThickness", mitk::FloatProperty::New(maxSpacing));
node->SetProperty("Fiber2DfadeEFX", mitk::BoolProperty::New(false));
GetDataStorage()->Add(node);
typedef FilterType::DirectionImageContainerType DirectionImageContainerType;
DirectionImageContainerType::Pointer container = filter->GetDirectionImageContainer();
for (int i=0; i<container->Size(); i++)
{
ItkDirectionImage3DType::Pointer itkImg = container->GetElement(i);
mitk::Image::Pointer img = mitk::Image::New();
img->InitializeByItk( itkImg.GetPointer() );
img->SetVolume( itkImg->GetBufferPointer() );
DataNode::Pointer node = DataNode::New();
node->SetData(img);
QString name(m_ImageNodes.at(0)->GetName().c_str());
name += "_Direction";
name += QString::number(i+1);
node->SetName(name.toStdString().c_str());
GetDataStorage()->Add(node);
}
}
void QmitkVirtualSurgery::MyCastPixelType(itk::Image<TPixel, VImageDimension> *itkImage, mitk::Image::Pointer *pointer)
{
std::cout<< "Function MyCastPixelType :Begin."<<std::endl;
/***************duplicate a image to clip 8 segment******************/
typedef itk::Image<TPixel, VImageDimension> TImageType;
typedef itk::ImageDuplicator< typename TImageType > DuplicatorType;
DuplicatorType::Pointer duplicator = DuplicatorType::New();
duplicator->SetInputImage( itkImage );
duplicator->Update();
typename TImageType::Pointer clonedImage = duplicator->GetOutput();
mitk::Image::Pointer resultImage = mitk::ImportItkImage( clonedImage );
mitk::DataTreeNode::Pointer newNode = mitk::DataTreeNode::New();
newNode->SetData(resultImage);
newNode->SetProperty("name", mitk::StringProperty::New("Liver Image"));
newNode->SetProperty("opacity", mitk::FloatProperty::New(0.0));
mitk::DataStorage::GetInstance()->Add( newNode );
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
/*********************************************************************/
//originalPixelType = (dynamic_cast<mitk::Image *>(selectedImage->Get()->GetData()))->GetPixelType();
if (originalPixelType == typeid(float))
{
std::cout<< "Function MyCastPixelType : Origin image pixel type is float."<<std::endl;
*pointer = mitk::ImportItkImage(itkImage);
}
else
{
typedef itk::Image<TPixel, VImageDimension> InputImageType;
typedef float OutputImagePixelType;
typedef itk::Image<OutputImagePixelType, VImageDimension> OutputImageType;
typedef itk::CastImageFilter<InputImageType, OutputImageType> CasterType;
CasterType::Pointer caster = CasterType::New();
caster->SetInput(itkImage);
try
{
caster->Update();
}
catch( itk::ExceptionObject & excp )
{
std::cerr << "CastPixelType exception thrown."
<< std::endl;
std::cerr << excp << std::endl;
return ;
}
OutputImageType::Pointer output = caster->GetOutput();
*pointer = mitk::ImportItkImage(output);
}
std::cout<< "Function MyCastPixelType End."<<std::endl;
}
typename itk::ShCoefficientImageImporter< float, shOrder >::QballImageType::Pointer TemplatedConvertShCoeffs(mitk::Image* mitkImg, int toolkit, bool noFlip = false)
{
typedef itk::ShCoefficientImageImporter< float, shOrder > FilterType;
typedef mitk::ImageToItk< itk::Image< float, 4 > > CasterType;
CasterType::Pointer caster = CasterType::New();
caster->SetInput(mitkImg);
caster->Update();
itk::Image< float, 4 >::Pointer itkImage = caster->GetOutput();
typename FilterType::Pointer filter = FilterType::New();
if (noFlip)
{
filter->SetInputImage(itkImage);
}
else
{
MITK_INFO << "Flipping image";
itk::FixedArray<bool, 4> flipAxes;
flipAxes[0] = true;
flipAxes[1] = true;
flipAxes[2] = false;
flipAxes[3] = false;
itk::FlipImageFilter< itk::Image< float, 4 > >::Pointer flipper = itk::FlipImageFilter< itk::Image< float, 4 > >::New();
flipper->SetInput(itkImage);
flipper->SetFlipAxes(flipAxes);
flipper->Update();
itk::Image< float, 4 >::Pointer flipped = flipper->GetOutput();
itk::Matrix< double,4,4 > m = itkImage->GetDirection(); m[0][0] *= -1; m[1][1] *= -1;
flipped->SetDirection(m);
itk::Point< float, 4 > o = itkImage->GetOrigin();
o[0] -= (flipped->GetLargestPossibleRegion().GetSize(0)-1);
o[1] -= (flipped->GetLargestPossibleRegion().GetSize(1)-1);
flipped->SetOrigin(o);
filter->SetInputImage(flipped);
}
switch (toolkit)
{
case 0:
filter->SetToolkit(FilterType::FSL);
break;
case 1:
filter->SetToolkit(FilterType::MRTRIX);
break;
default:
filter->SetToolkit(FilterType::FSL);
}
filter->GenerateData();
return filter->GetQballImage();
}
void CompareImages(mitk::PeakImage::ItkPeakImageType::Pointer testImage, std::string name)
{
typedef mitk::ImageToItk< mitk::PeakImage::ItkPeakImageType > CasterType;
CasterType::Pointer caster = CasterType::New();
caster->SetInput(mitk::IOUtil::Load<mitk::Image>(GetTestDataFilePath("DiffusionImaging/FiberFit/out/" + name)));
caster->Update();
mitk::PeakImage::ItkPeakImageType::Pointer refImage = caster->GetOutput();
itk::ImageRegionConstIterator< mitk::PeakImage::ItkPeakImageType > it1(testImage, testImage->GetLargestPossibleRegion());
itk::ImageRegionConstIterator< mitk::PeakImage::ItkPeakImageType > it2(refImage, refImage->GetLargestPossibleRegion());
while(!it1.IsAtEnd())
{
if (it2.Get()>0.0001)
{
if (fabs( it1.Get()/it2.Get()-1 )>0.01)
{
itk::ImageFileWriter< mitk::PeakImage::ItkPeakImageType >::Pointer writer = itk::ImageFileWriter< mitk::PeakImage::ItkPeakImageType >::New();
writer->SetInput(testImage);
writer->SetFileName(mitk::IOUtil::GetTempPath()+name);
writer->Update();
MITK_INFO << it1.Get() << " - " << it2.Get();
CPPUNIT_ASSERT_MESSAGE("Peak images should be equal 1", false);
}
}
else if (it1.Get()>0.0001)
{
itk::ImageFileWriter< mitk::PeakImage::ItkPeakImageType >::Pointer writer = itk::ImageFileWriter< mitk::PeakImage::ItkPeakImageType >::New();
writer->SetInput(testImage);
writer->SetFileName(mitk::IOUtil::GetTempPath()+name);
writer->Update();
CPPUNIT_ASSERT_MESSAGE("Peak images should be equal 2", false);
}
++it1;
++it2;
}
}
void setUp() override
{
std::vector<mitk::FiberBundle::Pointer> tracts;
tracts.push_back(LoadFib("Cluster_0.fib"));
tracts.push_back(LoadFib("Cluster_1.fib"));
tracts.push_back(LoadFib("Cluster_2.fib"));
tracts.push_back(LoadFib("Cluster_3.fib"));
tracts.push_back(LoadFib("Cluster_4.fib"));
mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor({"Peak Image"}, {});
mitk::PeakImage::Pointer peaks = mitk::IOUtil::Load<mitk::PeakImage>(GetTestDataFilePath("DiffusionImaging/FiberFit/csd_peak_image.nii.gz"), &functor);
typedef mitk::ImageToItk< mitk::PeakImage::ItkPeakImageType > CasterType;
CasterType::Pointer caster = CasterType::New();
caster->SetInput(peaks);
caster->Update();
mitk::PeakImage::ItkPeakImageType::Pointer peak_image = caster->GetOutput();
fitter = FitterType::New();
fitter->SetPeakImage(peak_image);
fitter->SetTractograms(tracts);
}
typename itk::ShCoefficientImageImporter< float, shOrder >::QballImageType::Pointer TemplatedConvertShCoeffs(mitk::Image* mitkImg, int toolkit)
{
typedef itk::ShCoefficientImageImporter< float, shOrder > FilterType;
typedef mitk::ImageToItk< itk::Image< float, 4 > > CasterType;
CasterType::Pointer caster = CasterType::New();
caster->SetInput(mitkImg);
caster->Update();
typename FilterType::Pointer filter = FilterType::New();
switch (toolkit)
{
case 0:
filter->SetToolkit(FilterType::FSL);
break;
case 1:
filter->SetToolkit(FilterType::MRTRIX);
break;
default:
filter->SetToolkit(FilterType::FSL);
}
filter->SetInputImage(caster->GetOutput());
filter->GenerateData();
return filter->GetQballImage();
}
// ------------------------------------------------------------------------
void OpenCVValve::ConvertImage(const ImageType::Pointer &input, MatPtr &mat)
{
// cast the image to uchar
typedef itk::Image<unsigned char, 2> OutputImageType;
typedef itk::RescaleIntensityImageFilter<ImageType, OutputImageType> CasterType;
CasterType::Pointer caster = CasterType::New();
caster->SetOutputMaximum(255);
caster->SetOutputMinimum(0);
caster->SetInput(input);
caster->Update();
OutputImageType::Pointer output = caster->GetOutput();
typedef itk::ImageFileWriter<OutputImageType> WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetImageIO(itk::PNGImageIO::New());
writer->SetInput(output);
writer->SetFileName("test.png");
writer->Update();
ImageType::SizeType size = input->GetLargestPossibleRegion().GetSize();
unsigned int rows = size[1];
unsigned int cols = size[0];
mat = new MatType(rows,cols, CV_8UC1);
itk::ImageRegionConstIterator<OutputImageType> it(output, output->GetLargestPossibleRegion());
it.GoToBegin();
while(!it.IsAtEnd())
{
OutputImageType::IndexType index = it.GetIndex();
unsigned char val = it.Get();
mat->at<unsigned char>(cv::Point(index[0], index[1])) = val;
++it;
}
}
int mitkLocalFiberPlausibilityTest(int argc, char* argv[])
{
MITK_TEST_BEGIN("mitkLocalFiberPlausibilityTest");
MITK_TEST_CONDITION_REQUIRED(argc==8,"check for input data")
string fibFile = argv[1];
vector< string > referenceImages;
referenceImages.push_back(argv[2]);
referenceImages.push_back(argv[3]);
string LDFP_ERROR_IMAGE = argv[4];
string LDFP_NUM_DIRECTIONS = argv[5];
string LDFP_VECTOR_FIELD = argv[6];
string LDFP_ERROR_IMAGE_IGNORE = argv[7];
float angularThreshold = 25;
try
{
typedef itk::Image<unsigned char, 3> ItkUcharImgType;
typedef itk::Image< itk::Vector< float, 3>, 3 > ItkDirectionImage3DType;
typedef itk::VectorContainer< unsigned int, ItkDirectionImage3DType::Pointer > ItkDirectionImageContainerType;
typedef itk::EvaluateDirectionImagesFilter< float > EvaluationFilterType;
// load fiber bundle
mitk::FiberBundleX::Pointer inputTractogram = dynamic_cast<mitk::FiberBundleX*>(mitk::IOUtil::LoadDataNode(fibFile)->GetData());
// load reference directions
ItkDirectionImageContainerType::Pointer referenceImageContainer = ItkDirectionImageContainerType::New();
for (unsigned int i=0; i<referenceImages.size(); i++)
{
try
{
mitk::Image::Pointer img = dynamic_cast<mitk::Image*>(mitk::IOUtil::LoadDataNode(referenceImages.at(i))->GetData());
typedef mitk::ImageToItk< ItkDirectionImage3DType > CasterType;
CasterType::Pointer caster = CasterType::New();
caster->SetInput(img);
caster->Update();
ItkDirectionImage3DType::Pointer itkImg = caster->GetOutput();
referenceImageContainer->InsertElement(referenceImageContainer->Size(),itkImg);
}
catch(...) {
MITK_INFO << "could not load: " << referenceImages.at(i);
}
}
ItkUcharImgType::Pointer itkMaskImage = ItkUcharImgType::New();
ItkDirectionImage3DType::Pointer dirImg = referenceImageContainer->GetElement(0);
itkMaskImage->SetSpacing( dirImg->GetSpacing() );
itkMaskImage->SetOrigin( dirImg->GetOrigin() );
itkMaskImage->SetDirection( dirImg->GetDirection() );
itkMaskImage->SetLargestPossibleRegion( dirImg->GetLargestPossibleRegion() );
itkMaskImage->SetBufferedRegion( dirImg->GetLargestPossibleRegion() );
itkMaskImage->SetRequestedRegion( dirImg->GetLargestPossibleRegion() );
itkMaskImage->Allocate();
itkMaskImage->FillBuffer(1);
// extract directions from fiber bundle
itk::TractsToVectorImageFilter<float>::Pointer fOdfFilter = itk::TractsToVectorImageFilter<float>::New();
fOdfFilter->SetFiberBundle(inputTractogram);
fOdfFilter->SetMaskImage(itkMaskImage);
fOdfFilter->SetAngularThreshold(cos(angularThreshold*M_PI/180));
fOdfFilter->SetNormalizeVectors(true);
fOdfFilter->SetUseWorkingCopy(false);
fOdfFilter->SetNumberOfThreads(1);
fOdfFilter->Update();
ItkDirectionImageContainerType::Pointer directionImageContainer = fOdfFilter->GetDirectionImageContainer();
// Get directions and num directions image
ItkUcharImgType::Pointer numDirImage = fOdfFilter->GetNumDirectionsImage();
mitk::Image::Pointer mitkNumDirImage = mitk::Image::New();
mitkNumDirImage->InitializeByItk( numDirImage.GetPointer() );
mitkNumDirImage->SetVolume( numDirImage->GetBufferPointer() );
mitk::FiberBundleX::Pointer testDirections = fOdfFilter->GetOutputFiberBundle();
// evaluate directions with missing directions
EvaluationFilterType::Pointer evaluationFilter = EvaluationFilterType::New();
evaluationFilter->SetImageSet(directionImageContainer);
evaluationFilter->SetReferenceImageSet(referenceImageContainer);
evaluationFilter->SetMaskImage(itkMaskImage);
evaluationFilter->SetIgnoreMissingDirections(false);
evaluationFilter->Update();
EvaluationFilterType::OutputImageType::Pointer angularErrorImage = evaluationFilter->GetOutput(0);
mitk::Image::Pointer mitkAngularErrorImage = mitk::Image::New();
mitkAngularErrorImage->InitializeByItk( angularErrorImage.GetPointer() );
mitkAngularErrorImage->SetVolume( angularErrorImage->GetBufferPointer() );
// evaluate directions without missing directions
evaluationFilter->SetIgnoreMissingDirections(true);
evaluationFilter->Update();
EvaluationFilterType::OutputImageType::Pointer angularErrorImageIgnore = evaluationFilter->GetOutput(0);
mitk::Image::Pointer mitkAngularErrorImageIgnore = mitk::Image::New();
mitkAngularErrorImageIgnore->InitializeByItk( angularErrorImageIgnore.GetPointer() );
mitkAngularErrorImageIgnore->SetVolume( angularErrorImageIgnore->GetBufferPointer() );
mitk::Image::Pointer gtAngularErrorImageIgnore = dynamic_cast<mitk::Image*>(mitk::IOUtil::LoadDataNode(LDFP_ERROR_IMAGE_IGNORE)->GetData());
mitk::Image::Pointer gtAngularErrorImage = dynamic_cast<mitk::Image*>(mitk::IOUtil::LoadDataNode(LDFP_ERROR_IMAGE)->GetData());
mitk::Image::Pointer gtNumTestDirImage = dynamic_cast<mitk::Image*>(mitk::IOUtil::LoadDataNode(LDFP_NUM_DIRECTIONS)->GetData());
mitk::FiberBundleX::Pointer gtTestDirections = dynamic_cast<mitk::FiberBundleX*>(mitk::IOUtil::LoadDataNode(LDFP_VECTOR_FIELD)->GetData());
MITK_TEST_CONDITION_REQUIRED(mitk::Equal(gtAngularErrorImageIgnore, mitkAngularErrorImageIgnore, 0.0001, true), "Check if error images are equal (ignored missing directions).");
MITK_TEST_CONDITION_REQUIRED(mitk::Equal(gtAngularErrorImage, mitkAngularErrorImage, 0.0001, true), "Check if error images are equal.");
MITK_TEST_CONDITION_REQUIRED(testDirections->Equals(gtTestDirections), "Check if vector fields are equal.");
MITK_TEST_CONDITION_REQUIRED(mitk::Equal(gtNumTestDirImage, mitkNumDirImage, 0.0001, true), "Check if num direction images are equal.");
}
catch (itk::ExceptionObject e)
{
MITK_INFO << e;
return EXIT_FAILURE;
}
catch (std::exception e)
{
MITK_INFO << e.what();
return EXIT_FAILURE;
}
catch (...)
{
MITK_INFO << "ERROR!?!";
return EXIT_FAILURE;
}
MITK_TEST_END();
}
int LocalDirectionalFiberPlausibility(int argc, char* argv[])
{
ctkCommandLineParser parser;
parser.setArgumentPrefix("--", "-");
parser.addArgument("input", "i", ctkCommandLineParser::String, "input tractogram (.fib, vtk ascii file format)", us::Any(), false);
parser.addArgument("reference", "r", ctkCommandLineParser::StringList, "reference direction images", us::Any(), false);
parser.addArgument("out", "o", ctkCommandLineParser::String, "output root", us::Any(), false);
parser.addArgument("mask", "m", ctkCommandLineParser::StringList, "mask images");
parser.addArgument("athresh", "a", ctkCommandLineParser::Float, "angular threshold in degrees. closer fiber directions are regarded as one direction and clustered together.", 25, true);
parser.addArgument("verbose", "v", ctkCommandLineParser::Bool, "output optional and intermediate calculation results");
parser.addArgument("ignore", "n", ctkCommandLineParser::Bool, "don't increase error for missing or too many directions");
map<string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
if (parsedArgs.size()==0)
return EXIT_FAILURE;
ctkCommandLineParser::StringContainerType referenceImages = us::any_cast<ctkCommandLineParser::StringContainerType>(parsedArgs["reference"]);
ctkCommandLineParser::StringContainerType maskImages;
if (parsedArgs.count("mask"))
maskImages = us::any_cast<ctkCommandLineParser::StringContainerType>(parsedArgs["mask"]);
string fibFile = us::any_cast<string>(parsedArgs["input"]);
float angularThreshold = 25;
if (parsedArgs.count("athresh"))
angularThreshold = us::any_cast<float>(parsedArgs["athresh"]);
string outRoot = us::any_cast<string>(parsedArgs["out"]);
bool verbose = false;
if (parsedArgs.count("verbose"))
verbose = us::any_cast<bool>(parsedArgs["verbose"]);
bool ignore = false;
if (parsedArgs.count("ignore"))
ignore = us::any_cast<bool>(parsedArgs["ignore"]);
try
{
RegisterDiffusionCoreObjectFactory();
RegisterFiberTrackingObjectFactory();
typedef itk::Image<unsigned char, 3> ItkUcharImgType;
typedef itk::Image< itk::Vector< float, 3>, 3 > ItkDirectionImage3DType;
typedef itk::VectorContainer< int, ItkDirectionImage3DType::Pointer > ItkDirectionImageContainerType;
typedef itk::EvaluateDirectionImagesFilter< float > EvaluationFilterType;
// load fiber bundle
mitk::FiberBundleX::Pointer inputTractogram = dynamic_cast<mitk::FiberBundleX*>(mitk::IOUtil::LoadDataNode(fibFile)->GetData());
// load reference directions
ItkDirectionImageContainerType::Pointer referenceImageContainer = ItkDirectionImageContainerType::New();
for (int i=0; i<referenceImages.size(); i++)
{
try
{
mitk::Image::Pointer img = dynamic_cast<mitk::Image*>(mitk::IOUtil::LoadDataNode(referenceImages.at(i))->GetData());
typedef mitk::ImageToItk< ItkDirectionImage3DType > CasterType;
CasterType::Pointer caster = CasterType::New();
caster->SetInput(img);
caster->Update();
ItkDirectionImage3DType::Pointer itkImg = caster->GetOutput();
referenceImageContainer->InsertElement(referenceImageContainer->Size(),itkImg);
}
catch(...){ MITK_INFO << "could not load: " << referenceImages.at(i); }
}
ItkUcharImgType::Pointer itkMaskImage = ItkUcharImgType::New();
ItkDirectionImage3DType::Pointer dirImg = referenceImageContainer->GetElement(0);
itkMaskImage->SetSpacing( dirImg->GetSpacing() );
itkMaskImage->SetOrigin( dirImg->GetOrigin() );
itkMaskImage->SetDirection( dirImg->GetDirection() );
itkMaskImage->SetLargestPossibleRegion( dirImg->GetLargestPossibleRegion() );
itkMaskImage->SetBufferedRegion( dirImg->GetLargestPossibleRegion() );
itkMaskImage->SetRequestedRegion( dirImg->GetLargestPossibleRegion() );
itkMaskImage->Allocate();
itkMaskImage->FillBuffer(1);
// extract directions from fiber bundle
itk::TractsToVectorImageFilter<float>::Pointer fOdfFilter = itk::TractsToVectorImageFilter<float>::New();
fOdfFilter->SetFiberBundle(inputTractogram);
fOdfFilter->SetMaskImage(itkMaskImage);
fOdfFilter->SetAngularThreshold(cos(angularThreshold*M_PI/180));
fOdfFilter->SetNormalizeVectors(true);
fOdfFilter->SetUseWorkingCopy(false);
fOdfFilter->Update();
ItkDirectionImageContainerType::Pointer directionImageContainer = fOdfFilter->GetDirectionImageContainer();
if (verbose)
{
// write vector field
mitk::FiberBundleX::Pointer directions = fOdfFilter->GetOutputFiberBundle();
mitk::CoreObjectFactory::FileWriterList fileWriters = mitk::CoreObjectFactory::GetInstance()->GetFileWriters();
for (mitk::CoreObjectFactory::FileWriterList::iterator it = fileWriters.begin() ; it != fileWriters.end() ; ++it)
{
if ( (*it)->CanWriteBaseDataType(directions.GetPointer()) ) {
string outfilename = outRoot;
outfilename.append("_VECTOR_FIELD.fib");
(*it)->SetFileName( outfilename.c_str() );
(*it)->DoWrite( directions.GetPointer() );
}
}
// write direction images
for (int i=0; i<directionImageContainer->Size(); i++)
{
itk::TractsToVectorImageFilter<float>::ItkDirectionImageType::Pointer itkImg = directionImageContainer->GetElement(i);
typedef itk::ImageFileWriter< itk::TractsToVectorImageFilter<float>::ItkDirectionImageType > WriterType;
WriterType::Pointer writer = WriterType::New();
string outfilename = outRoot;
outfilename.append("_DIRECTION_");
outfilename.append(boost::lexical_cast<string>(i));
outfilename.append(".nrrd");
MITK_INFO << "writing " << outfilename;
writer->SetFileName(outfilename.c_str());
writer->SetInput(itkImg);
writer->Update();
}
// write num direction image
{
ItkUcharImgType::Pointer numDirImage = fOdfFilter->GetNumDirectionsImage();
typedef itk::ImageFileWriter< ItkUcharImgType > WriterType;
WriterType::Pointer writer = WriterType::New();
string outfilename = outRoot;
outfilename.append("_NUM_DIRECTIONS.nrrd");
MITK_INFO << "writing " << outfilename;
writer->SetFileName(outfilename.c_str());
writer->SetInput(numDirImage);
writer->Update();
}
}
string logFile = outRoot;
logFile.append("_ANGULAR_ERROR.csv");
ofstream file;
file.open (logFile.c_str());
if (maskImages.size()>0)
{
for (int i=0; i<maskImages.size(); i++)
{
mitk::Image::Pointer mitkMaskImage = dynamic_cast<mitk::Image*>(mitk::IOUtil::LoadDataNode(maskImages.at(i))->GetData());
mitk::CastToItkImage<ItkUcharImgType>(mitkMaskImage, itkMaskImage);
// evaluate directions
EvaluationFilterType::Pointer evaluationFilter = EvaluationFilterType::New();
evaluationFilter->SetImageSet(directionImageContainer);
evaluationFilter->SetReferenceImageSet(referenceImageContainer);
evaluationFilter->SetMaskImage(itkMaskImage);
evaluationFilter->SetIgnoreMissingDirections(ignore);
evaluationFilter->Update();
if (verbose)
{
EvaluationFilterType::OutputImageType::Pointer angularErrorImage = evaluationFilter->GetOutput(0);
typedef itk::ImageFileWriter< EvaluationFilterType::OutputImageType > WriterType;
WriterType::Pointer writer = WriterType::New();
string outfilename = outRoot;
outfilename.append("_ERROR_IMAGE.nrrd");
MITK_INFO << "writing " << outfilename;
writer->SetFileName(outfilename.c_str());
writer->SetInput(angularErrorImage);
writer->Update();
}
string sens = itksys::SystemTools::GetFilenameWithoutExtension(itksys::SystemTools::GetFilenameName(fibFile));
sens.append(",");
sens.append(itksys::SystemTools::GetFilenameWithoutExtension(itksys::SystemTools::GetFilenameName(maskImages.at(i))));
sens.append(",");
sens.append(boost::lexical_cast<string>(evaluationFilter->GetMeanAngularError()));
sens.append(",");
sens.append(boost::lexical_cast<string>(evaluationFilter->GetMedianAngularError()));
sens.append(",");
sens.append(boost::lexical_cast<string>(evaluationFilter->GetMaxAngularError()));
sens.append(",");
sens.append(boost::lexical_cast<string>(evaluationFilter->GetMinAngularError()));
sens.append(",");
sens.append(boost::lexical_cast<string>(std::sqrt(evaluationFilter->GetVarAngularError())));
sens.append(";\n");
file << sens;
}
}
else
{
// evaluate directions
EvaluationFilterType::Pointer evaluationFilter = EvaluationFilterType::New();
evaluationFilter->SetImageSet(directionImageContainer);
evaluationFilter->SetReferenceImageSet(referenceImageContainer);
evaluationFilter->SetMaskImage(itkMaskImage);
evaluationFilter->SetIgnoreMissingDirections(ignore);
evaluationFilter->Update();
if (verbose)
{
EvaluationFilterType::OutputImageType::Pointer angularErrorImage = evaluationFilter->GetOutput(0);
typedef itk::ImageFileWriter< EvaluationFilterType::OutputImageType > WriterType;
WriterType::Pointer writer = WriterType::New();
string outfilename = outRoot;
outfilename.append("_ERROR_IMAGE.nrrd");
MITK_INFO << "writing " << outfilename;
writer->SetFileName(outfilename.c_str());
writer->SetInput(angularErrorImage);
writer->Update();
}
string sens = itksys::SystemTools::GetFilenameWithoutExtension(itksys::SystemTools::GetFilenameName(fibFile));
sens.append(",");
sens.append("FULL");
sens.append(",");
sens.append(boost::lexical_cast<string>(evaluationFilter->GetMeanAngularError()));
sens.append(",");
sens.append(boost::lexical_cast<string>(evaluationFilter->GetMedianAngularError()));
sens.append(",");
sens.append(boost::lexical_cast<string>(evaluationFilter->GetMaxAngularError()));
sens.append(",");
sens.append(boost::lexical_cast<string>(evaluationFilter->GetMinAngularError()));
sens.append(",");
sens.append(boost::lexical_cast<string>(std::sqrt(evaluationFilter->GetVarAngularError())));
sens.append(";\n");
file << sens;
}
file.close();
MITK_INFO << "DONE";
}
catch (itk::ExceptionObject e)
{
MITK_INFO << e;
return EXIT_FAILURE;
}
catch (std::exception e)
{
MITK_INFO << e.what();
return EXIT_FAILURE;
}
catch (...)
{
MITK_INFO << "ERROR!?!";
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
int StartPeakExtraction(int argc, char* argv[])
{
mitkCommandLineParser parser;
parser.setArgumentPrefix("--", "-");
parser.addArgument("image", "i", mitkCommandLineParser::InputFile, "Input image", "sh coefficient image", us::Any(), false);
parser.addArgument("outroot", "o", mitkCommandLineParser::OutputDirectory, "Output directory", "output root", us::Any(), false);
parser.addArgument("mask", "m", mitkCommandLineParser::InputFile, "Mask", "mask image");
parser.addArgument("normalization", "n", mitkCommandLineParser::Int, "Normalization", "0=no norm, 1=max norm, 2=single vec norm", 1, true);
parser.addArgument("numpeaks", "p", mitkCommandLineParser::Int, "Max. number of peaks", "maximum number of extracted peaks", 2, true);
parser.addArgument("peakthres", "r", mitkCommandLineParser::Float, "Peak threshold", "peak threshold relative to largest peak", 0.4, true);
parser.addArgument("abspeakthres", "a", mitkCommandLineParser::Float, "Absolute peak threshold", "absolute peak threshold weighted with local GFA value", 0.06, true);
parser.addArgument("shConvention", "s", mitkCommandLineParser::String, "Use specified SH-basis", "use specified SH-basis (MITK, FSL, MRtrix)", string("MITK"), true);
parser.addArgument("noFlip", "f", mitkCommandLineParser::Bool, "No flip", "do not flip input image to match MITK coordinate convention");
parser.addArgument("clusterThres", "c", mitkCommandLineParser::Float, "Clustering threshold", "directions closer together than the specified angular threshold will be clustered (in rad)", 0.9);
parser.addArgument("flipX", "fx", mitkCommandLineParser::Bool, "Flip X", "Flip peaks in x direction");
parser.addArgument("flipY", "fy", mitkCommandLineParser::Bool, "Flip Y", "Flip peaks in y direction");
parser.addArgument("flipZ", "fz", mitkCommandLineParser::Bool, "Flip Z", "Flip peaks in z direction");
parser.setCategory("Preprocessing Tools");
parser.setTitle("Peak Extraction");
parser.setDescription("");
parser.setContributor("MIC");
map<string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
if (parsedArgs.size()==0)
return EXIT_FAILURE;
// mandatory arguments
string imageName = us::any_cast<string>(parsedArgs["image"]);
string outRoot = us::any_cast<string>(parsedArgs["outroot"]);
// optional arguments
string maskImageName("");
if (parsedArgs.count("mask"))
maskImageName = us::any_cast<string>(parsedArgs["mask"]);
int normalization = 1;
if (parsedArgs.count("normalization"))
normalization = us::any_cast<int>(parsedArgs["normalization"]);
int numPeaks = 2;
if (parsedArgs.count("numpeaks"))
numPeaks = us::any_cast<int>(parsedArgs["numpeaks"]);
float peakThres = 0.4;
if (parsedArgs.count("peakthres"))
peakThres = us::any_cast<float>(parsedArgs["peakthres"]);
float absPeakThres = 0.06;
if (parsedArgs.count("abspeakthres"))
absPeakThres = us::any_cast<float>(parsedArgs["abspeakthres"]);
float clusterThres = 0.9;
if (parsedArgs.count("clusterThres"))
clusterThres = us::any_cast<float>(parsedArgs["clusterThres"]);
bool noFlip = false;
if (parsedArgs.count("noFlip"))
noFlip = us::any_cast<bool>(parsedArgs["noFlip"]);
bool flipX = false;
if (parsedArgs.count("flipX"))
flipX = us::any_cast<bool>(parsedArgs["flipX"]);
bool flipY = false;
if (parsedArgs.count("flipY"))
flipY = us::any_cast<bool>(parsedArgs["flipY"]);
bool flipZ = false;
if (parsedArgs.count("flipZ"))
flipZ = us::any_cast<bool>(parsedArgs["flipZ"]);
std::cout << "image: " << imageName;
std::cout << "outroot: " << outRoot;
if (!maskImageName.empty())
std::cout << "mask: " << maskImageName;
else
std::cout << "no mask image selected";
std::cout << "numpeaks: " << numPeaks;
std::cout << "peakthres: " << peakThres;
std::cout << "abspeakthres: " << absPeakThres;
std::cout << "shOrder: " << shOrder;
try
{
mitk::Image::Pointer image = dynamic_cast<mitk::Image*>(mitk::IOUtil::Load(imageName)[0].GetPointer());
mitk::Image::Pointer mask = dynamic_cast<mitk::Image*>(mitk::IOUtil::Load(maskImageName)[0].GetPointer());
typedef itk::Image<unsigned char, 3> ItkUcharImgType;
typedef itk::FiniteDiffOdfMaximaExtractionFilter< float, shOrder, 20242 > MaximaExtractionFilterType;
typename MaximaExtractionFilterType::Pointer filter = MaximaExtractionFilterType::New();
int toolkitConvention = 0;
if (parsedArgs.count("shConvention"))
{
string convention = us::any_cast<string>(parsedArgs["shConvention"]).c_str();
if ( boost::algorithm::equals(convention, "FSL") )
{
toolkitConvention = 1;
std::cout << "Using FSL SH-basis";
}
else if ( boost::algorithm::equals(convention, "MRtrix") )
{
toolkitConvention = 2;
std::cout << "Using MRtrix SH-basis";
}
else
std::cout << "Using MITK SH-basis";
}
else
std::cout << "Using MITK SH-basis";
ItkUcharImgType::Pointer itkMaskImage = nullptr;
if (mask.IsNotNull())
{
try{
itkMaskImage = ItkUcharImgType::New();
mitk::CastToItkImage(mask, itkMaskImage);
filter->SetMaskImage(itkMaskImage);
}
catch(...)
{
}
}
if (toolkitConvention>0)
{
std::cout << "Converting coefficient image to MITK format";
typedef itk::ShCoefficientImageImporter< float, shOrder > ConverterType;
typedef mitk::ImageToItk< itk::Image< float, 4 > > CasterType;
CasterType::Pointer caster = CasterType::New();
caster->SetInput(image);
caster->Update();
itk::Image< float, 4 >::Pointer itkImage = caster->GetOutput();
typename ConverterType::Pointer converter = ConverterType::New();
if (noFlip)
{
converter->SetInputImage(itkImage);
}
else
{
std::cout << "Flipping image";
itk::FixedArray<bool, 4> flipAxes;
flipAxes[0] = true;
flipAxes[1] = true;
flipAxes[2] = false;
flipAxes[3] = false;
itk::FlipImageFilter< itk::Image< float, 4 > >::Pointer flipper = itk::FlipImageFilter< itk::Image< float, 4 > >::New();
flipper->SetInput(itkImage);
flipper->SetFlipAxes(flipAxes);
flipper->Update();
itk::Image< float, 4 >::Pointer flipped = flipper->GetOutput();
itk::Matrix< double,4,4 > m = itkImage->GetDirection(); m[0][0] *= -1; m[1][1] *= -1;
flipped->SetDirection(m);
itk::Point< float, 4 > o = itkImage->GetOrigin();
o[0] -= (flipped->GetLargestPossibleRegion().GetSize(0)-1);
o[1] -= (flipped->GetLargestPossibleRegion().GetSize(1)-1);
flipped->SetOrigin(o);
converter->SetInputImage(flipped);
}
std::cout << "Starting conversion";
switch (toolkitConvention)
{
case 1:
converter->SetToolkit(ConverterType::FSL);
filter->SetToolkit(MaximaExtractionFilterType::FSL);
break;
case 2:
converter->SetToolkit(ConverterType::MRTRIX);
filter->SetToolkit(MaximaExtractionFilterType::MRTRIX);
break;
default:
converter->SetToolkit(ConverterType::FSL);
filter->SetToolkit(MaximaExtractionFilterType::FSL);
break;
}
converter->GenerateData();
filter->SetInput(converter->GetCoefficientImage());
}
else
{
try{
typedef mitk::ImageToItk< typename MaximaExtractionFilterType::CoefficientImageType > CasterType;
typename CasterType::Pointer caster = CasterType::New();
caster->SetInput(image);
caster->Update();
filter->SetInput(caster->GetOutput());
}
catch(...)
{
std::cout << "wrong image type";
return EXIT_FAILURE;
}
}
filter->SetMaxNumPeaks(numPeaks);
filter->SetPeakThreshold(peakThres);
filter->SetAbsolutePeakThreshold(absPeakThres);
filter->SetAngularThreshold(1);
filter->SetClusteringThreshold(clusterThres);
filter->SetFlipX(flipX);
filter->SetFlipY(flipY);
filter->SetFlipZ(flipZ);
switch (normalization)
{
case 0:
filter->SetNormalizationMethod(MaximaExtractionFilterType::NO_NORM);
break;
case 1:
filter->SetNormalizationMethod(MaximaExtractionFilterType::MAX_VEC_NORM);
break;
case 2:
filter->SetNormalizationMethod(MaximaExtractionFilterType::SINGLE_VEC_NORM);
break;
}
std::cout << "Starting extraction";
filter->Update();
// write direction image
{
typename MaximaExtractionFilterType::PeakImageType::Pointer itkImg = filter->GetPeakImage();
string outfilename = outRoot;
outfilename.append("_PEAKS.nrrd");
typedef itk::ImageFileWriter< typename MaximaExtractionFilterType::PeakImageType > WriterType;
typename WriterType::Pointer writer = WriterType::New();
writer->SetFileName(outfilename);
writer->SetInput(itkImg);
writer->Update();
}
// write num directions image
{
ItkUcharImgType::Pointer numDirImage = filter->GetNumDirectionsImage();
if (itkMaskImage.IsNotNull())
{
numDirImage->SetDirection(itkMaskImage->GetDirection());
numDirImage->SetOrigin(itkMaskImage->GetOrigin());
}
string outfilename = outRoot.c_str();
outfilename.append("_NUM_PEAKS.nrrd");
typedef itk::ImageFileWriter< ItkUcharImgType > WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetFileName(outfilename);
writer->SetInput(numDirImage);
writer->Update();
}
}
catch (itk::ExceptionObject e)
{
std::cout << e;
return EXIT_FAILURE;
}
catch (std::exception e)
{
std::cout << e.what();
return EXIT_FAILURE;
}
catch (...)
{
std::cout << "ERROR!?!";
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
/*!
\brief Copies transformation matrix of one image to another
*/
int main(int argc, char* argv[])
{
mitkCommandLineParser parser;
parser.setTitle("Flip Peaks");
parser.setCategory("Preprocessing Tools");
parser.setDescription("Flips the peaks of the input peak image along the given dimensions.");
parser.setContributor("MIC");
parser.setArgumentPrefix("--", "-");
parser.addArgument("", "i", mitkCommandLineParser::String, "Input", "input image", us::Any(), false, false, false, mitkCommandLineParser::Input);
parser.addArgument("", "o", mitkCommandLineParser::String, "Output", "output image", us::Any(), false, false, false, mitkCommandLineParser::Output);
parser.addArgument("", "x", mitkCommandLineParser::Bool, "Flip x", "flip along x-axis");
parser.addArgument("", "y", mitkCommandLineParser::Bool, "Flip y", "flip along y-axis");
parser.addArgument("", "z", mitkCommandLineParser::Bool, "Flip z", "flip along z-axis");
std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
if (parsedArgs.size()==0)
return EXIT_FAILURE;
std::string imageName = us::any_cast<std::string>(parsedArgs["i"]);
std::string outImage = us::any_cast<std::string>(parsedArgs["o"]);
bool x = false;
if (parsedArgs.count("x"))
x = us::any_cast<bool>(parsedArgs["x"]);
bool y = false;
if (parsedArgs.count("y"))
y = us::any_cast<bool>(parsedArgs["y"]);
bool z = false;
if (parsedArgs.count("z"))
z = us::any_cast<bool>(parsedArgs["z"]);
try
{
mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor({"Peak Image"}, {});
mitk::PeakImage::Pointer image = mitk::IOUtil::Load<mitk::PeakImage>(imageName, &functor);
typedef mitk::ImageToItk< mitk::PeakImage::ItkPeakImageType > CasterType;
CasterType::Pointer caster = CasterType::New();
caster->SetInput(image);
caster->Update();
mitk::PeakImage::ItkPeakImageType::Pointer itkImg = caster->GetOutput();
itk::FlipPeaksFilter< float >::Pointer flipper = itk::FlipPeaksFilter< float >::New();
flipper->SetInput(itkImg);
flipper->SetFlipX(x);
flipper->SetFlipY(y);
flipper->SetFlipZ(z);
flipper->Update();
mitk::Image::Pointer resultImage = dynamic_cast<mitk::Image*>(mitk::PeakImage::New().GetPointer());
mitk::CastToMitkImage(flipper->GetOutput(), resultImage);
resultImage->SetVolume(flipper->GetOutput()->GetBufferPointer());
mitk::IOUtil::Save(resultImage, outImage);
}
catch (itk::ExceptionObject e)
{
std::cout << e;
return EXIT_FAILURE;
}
catch (std::exception e)
{
std::cout << e.what();
return EXIT_FAILURE;
}
catch (...)
{
std::cout << "ERROR!?!";
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
int TractogramAngularError(int argc, char* argv[])
{
ctkCommandLineParser parser;
parser.setArgumentPrefix("--", "-");
parser.addArgument("input", "i", ctkCommandLineParser::String, "input tractogram (.fib, vtk ascii file format)", us::Any(), false);
parser.addArgument("reference", "r", ctkCommandLineParser::StringList, "reference direction images", us::Any(), false);
parser.addArgument("out", "o", ctkCommandLineParser::String, "output root", us::Any(), false);
parser.addArgument("mask", "m", ctkCommandLineParser::String, "mask image");
parser.addArgument("verbose", "v", ctkCommandLineParser::Bool, "output optional and intermediate calculation results");
parser.addArgument("ignore", "n", ctkCommandLineParser::Bool, "don't increase error for missing or too many directions");
parser.addArgument("trilinear", "t", ctkCommandLineParser::Bool, "use trilinear instead of nearest neighbor interpolation");
map<string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
if (parsedArgs.size()==0)
return EXIT_FAILURE;
ctkCommandLineParser::StringContainerType referenceImages = us::any_cast<ctkCommandLineParser::StringContainerType>(parsedArgs["reference"]);
string fibFile = us::any_cast<string>(parsedArgs["input"]);
string maskImage("");
if (parsedArgs.count("mask"))
maskImage = us::any_cast<string>(parsedArgs["mask"]);
string outRoot = us::any_cast<string>(parsedArgs["out"]);
bool verbose = false;
if (parsedArgs.count("verbose"))
verbose = us::any_cast<bool>(parsedArgs["verbose"]);
bool ignore = false;
if (parsedArgs.count("ignore"))
ignore = us::any_cast<bool>(parsedArgs["ignore"]);
bool interpolate = false;
if (parsedArgs.count("interpolate"))
interpolate = us::any_cast<bool>(parsedArgs["interpolate"]);
try
{
RegisterDiffusionCoreObjectFactory();
RegisterFiberTrackingObjectFactory();
typedef itk::Image<unsigned char, 3> ItkUcharImgType;
typedef itk::Image< itk::Vector< float, 3>, 3 > ItkDirectionImage3DType;
typedef itk::VectorContainer< int, ItkDirectionImage3DType::Pointer > ItkDirectionImageContainerType;
typedef itk::EvaluateTractogramDirectionsFilter< float > EvaluationFilterType;
// load fiber bundle
mitk::FiberBundleX::Pointer inputTractogram = dynamic_cast<mitk::FiberBundleX*>(mitk::IOUtil::LoadDataNode(fibFile)->GetData());
if (!inputTractogram)
return EXIT_FAILURE;
// load reference directions
ItkDirectionImageContainerType::Pointer referenceImageContainer = ItkDirectionImageContainerType::New();
for (int i=0; i<referenceImages.size(); i++)
{
try
{
mitk::Image::Pointer img = dynamic_cast<mitk::Image*>(mitk::IOUtil::LoadDataNode(referenceImages.at(i))->GetData());
typedef mitk::ImageToItk< ItkDirectionImage3DType > CasterType;
CasterType::Pointer caster = CasterType::New();
caster->SetInput(img);
caster->Update();
ItkDirectionImage3DType::Pointer itkImg = caster->GetOutput();
referenceImageContainer->InsertElement(referenceImageContainer->Size(),itkImg);
}
catch(...) {
MITK_INFO << "could not load: " << referenceImages.at(i);
}
}
// load/create mask image
ItkUcharImgType::Pointer itkMaskImage = ItkUcharImgType::New();
if (maskImage.compare("")==0)
{
ItkDirectionImage3DType::Pointer dirImg = referenceImageContainer->GetElement(0);
itkMaskImage->SetSpacing( dirImg->GetSpacing() );
itkMaskImage->SetOrigin( dirImg->GetOrigin() );
itkMaskImage->SetDirection( dirImg->GetDirection() );
itkMaskImage->SetLargestPossibleRegion( dirImg->GetLargestPossibleRegion() );
itkMaskImage->SetBufferedRegion( dirImg->GetLargestPossibleRegion() );
itkMaskImage->SetRequestedRegion( dirImg->GetLargestPossibleRegion() );
itkMaskImage->Allocate();
itkMaskImage->FillBuffer(1);
}
else
{
mitk::Image::Pointer mitkMaskImage = dynamic_cast<mitk::Image*>(mitk::IOUtil::LoadDataNode(maskImage)->GetData());
mitk::CastToItkImage<ItkUcharImgType>(mitkMaskImage, itkMaskImage);
}
// evaluate directions
EvaluationFilterType::Pointer evaluationFilter = EvaluationFilterType::New();
evaluationFilter->SetTractogram(inputTractogram);
evaluationFilter->SetReferenceImageSet(referenceImageContainer);
evaluationFilter->SetMaskImage(itkMaskImage);
evaluationFilter->SetIgnoreMissingDirections(ignore);
evaluationFilter->SetUseInterpolation(interpolate);
evaluationFilter->Update();
if (verbose)
{
EvaluationFilterType::OutputImageType::Pointer angularErrorImage = evaluationFilter->GetOutput(0);
typedef itk::ImageFileWriter< EvaluationFilterType::OutputImageType > WriterType;
WriterType::Pointer writer = WriterType::New();
string outfilename = outRoot;
outfilename.append("_ERROR_IMAGE.nrrd");
MITK_INFO << "writing " << outfilename;
writer->SetFileName(outfilename.c_str());
writer->SetInput(angularErrorImage);
writer->Update();
}
string logFile = outRoot;
logFile.append("_ANGULAR_ERROR.csv");
ofstream file;
file.open (logFile.c_str());
string sens = "Mean:";
sens.append(",");
sens.append(boost::lexical_cast<string>(evaluationFilter->GetMeanAngularError()));
sens.append(";\n");
sens.append("Median:");
sens.append(",");
sens.append(boost::lexical_cast<string>(evaluationFilter->GetMedianAngularError()));
sens.append(";\n");
sens.append("Maximum:");
sens.append(",");
sens.append(boost::lexical_cast<string>(evaluationFilter->GetMaxAngularError()));
sens.append(";\n");
sens.append("Minimum:");
sens.append(",");
sens.append(boost::lexical_cast<string>(evaluationFilter->GetMinAngularError()));
sens.append(";\n");
sens.append("STDEV:");
sens.append(",");
sens.append(boost::lexical_cast<string>(std::sqrt(evaluationFilter->GetVarAngularError())));
sens.append(";\n");
file << sens;
file.close();
MITK_INFO << "DONE";
}
catch (itk::ExceptionObject e)
{
MITK_INFO << e;
return EXIT_FAILURE;
}
catch (std::exception e)
{
MITK_INFO << e.what();
return EXIT_FAILURE;
}
catch (...)
{
MITK_INFO << "ERROR!?!";
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
/*!
\brief Fits the tractogram to the input peak image by assigning a weight to each fiber (similar to https://doi.org/10.1016/j.neuroimage.2015.06.092).
*/
int main(int argc, char* argv[])
{
mitkCommandLineParser parser;
parser.setTitle("Fit Fibers To Image");
parser.setCategory("Fiber Tracking and Processing Methods");
parser.setDescription("Assigns a weight to each fiber in order to optimally explain the input peak image");
parser.setContributor("MIC");
parser.setArgumentPrefix("--", "-");
parser.addArgument("", "i1", mitkCommandLineParser::StringList, "Input tractograms:", "input tractograms (.fib, vtk ascii file format)", us::Any(), false);
parser.addArgument("", "i2", mitkCommandLineParser::InputFile, "Input image:", "input image", us::Any(), false);
parser.addArgument("", "o", mitkCommandLineParser::OutputDirectory, "Output:", "output root", us::Any(), false);
parser.addArgument("max_iter", "", mitkCommandLineParser::Int, "Max. iterations:", "maximum number of optimizer iterations", 20);
parser.addArgument("bundle_based", "", mitkCommandLineParser::Bool, "Bundle based fit:", "fit one weight per input tractogram/bundle, not for each fiber", false);
parser.addArgument("min_g", "", mitkCommandLineParser::Float, "Min. g:", "lower termination threshold for gradient magnitude", 1e-5);
parser.addArgument("lambda", "", mitkCommandLineParser::Float, "Lambda:", "modifier for regularization", 0.1);
parser.addArgument("save_res", "", mitkCommandLineParser::Bool, "Save Residuals:", "save residual images", false);
parser.addArgument("save_weights", "", mitkCommandLineParser::Bool, "Save Weights:", "save fiber weights in a separate text file", false);
parser.addArgument("filter_outliers", "", mitkCommandLineParser::Bool, "Filter outliers:", "perform second optimization run with an upper weight bound based on the first weight estimation (99% quantile)", false);
parser.addArgument("join_tracts", "", mitkCommandLineParser::Bool, "Join output tracts:", "outout tracts are merged into a single tractogram", false);
parser.addArgument("regu", "", mitkCommandLineParser::String, "Regularization:", "MSM, Variance, VoxelVariance (default), Lasso, GroupLasso, GroupVariance, NONE");
std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
if (parsedArgs.size()==0)
return EXIT_FAILURE;
mitkCommandLineParser::StringContainerType fib_files = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["i1"]);
std::string input_image_name = us::any_cast<std::string>(parsedArgs["i2"]);
std::string outRoot = us::any_cast<std::string>(parsedArgs["o"]);
bool single_fib = true;
if (parsedArgs.count("bundle_based"))
single_fib = !us::any_cast<bool>(parsedArgs["bundle_based"]);
bool save_residuals = false;
if (parsedArgs.count("save_res"))
save_residuals = us::any_cast<bool>(parsedArgs["save_res"]);
bool save_weights = false;
if (parsedArgs.count("save_weights"))
save_weights = us::any_cast<bool>(parsedArgs["save_weights"]);
std::string regu = "VoxelVariance";
if (parsedArgs.count("regu"))
regu = us::any_cast<std::string>(parsedArgs["regu"]);
bool join_tracts = false;
if (parsedArgs.count("join_tracts"))
join_tracts = us::any_cast<bool>(parsedArgs["join_tracts"]);
int max_iter = 20;
if (parsedArgs.count("max_iter"))
max_iter = us::any_cast<int>(parsedArgs["max_iter"]);
float g_tol = 1e-5;
if (parsedArgs.count("min_g"))
g_tol = us::any_cast<float>(parsedArgs["min_g"]);
float lambda = 0.1;
if (parsedArgs.count("lambda"))
lambda = us::any_cast<float>(parsedArgs["lambda"]);
bool filter_outliers = false;
if (parsedArgs.count("filter_outliers"))
filter_outliers = us::any_cast<bool>(parsedArgs["filter_outliers"]);
try
{
MITK_INFO << "Loading data";
std::streambuf *old = cout.rdbuf(); // <-- save
std::stringstream ss;
std::cout.rdbuf (ss.rdbuf()); // <-- redirect
std::vector< mitk::FiberBundle::Pointer > input_tracts;
mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor({"Peak Image", "Fiberbundles"}, {});
std::vector< std::string > fib_names;
for (auto item : fib_files)
{
if ( ist::FileIsDirectory(item) )
{
for ( auto fibFile : get_file_list(item) )
{
mitk::FiberBundle::Pointer inputTractogram = mitk::IOUtil::Load<mitk::FiberBundle>(fibFile);
if (inputTractogram.IsNull())
continue;
input_tracts.push_back(inputTractogram);
fib_names.push_back(fibFile);
}
}
else
{
mitk::FiberBundle::Pointer inputTractogram = mitk::IOUtil::Load<mitk::FiberBundle>(item);
if (inputTractogram.IsNull())
continue;
input_tracts.push_back(inputTractogram);
fib_names.push_back(item);
}
}
std::cout.rdbuf (old); // <-- restore
itk::FitFibersToImageFilter::Pointer fitter = itk::FitFibersToImageFilter::New();
mitk::BaseData::Pointer inputData = mitk::IOUtil::Load(input_image_name, &functor)[0].GetPointer();
mitk::Image::Pointer mitk_image = dynamic_cast<mitk::Image*>(inputData.GetPointer());
mitk::PeakImage::Pointer mitk_peak_image = dynamic_cast<mitk::PeakImage*>(inputData.GetPointer());
if (mitk_peak_image.IsNotNull())
{
typedef mitk::ImageToItk< mitk::PeakImage::ItkPeakImageType > CasterType;
CasterType::Pointer caster = CasterType::New();
caster->SetInput(mitk_peak_image);
caster->Update();
mitk::PeakImage::ItkPeakImageType::Pointer peak_image = caster->GetOutput();
fitter->SetPeakImage(peak_image);
}
else if (mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(mitk_image))
{
fitter->SetDiffImage(mitk::DiffusionPropertyHelper::GetItkVectorImage(mitk_image));
mitk::TensorModel<>* model = new mitk::TensorModel<>();
model->SetBvalue(1000);
model->SetDiffusivity1(0.0010);
model->SetDiffusivity2(0.00015);
model->SetDiffusivity3(0.00015);
model->SetGradientList(mitk::DiffusionPropertyHelper::GetGradientContainer(mitk_image));
fitter->SetSignalModel(model);
}
else if (mitk_image->GetDimension()==3)
{
itk::FitFibersToImageFilter::DoubleImgType::Pointer scalar_image = itk::FitFibersToImageFilter::DoubleImgType::New();
mitk::CastToItkImage(mitk_image, scalar_image);
fitter->SetScalarImage(scalar_image);
}
else
{
MITK_INFO << "Input image invalid. Valid options are peak image, 3D scalar image or raw diffusion-weighted image.";
return EXIT_FAILURE;
}
fitter->SetTractograms(input_tracts);
fitter->SetFitIndividualFibers(single_fib);
fitter->SetMaxIterations(max_iter);
fitter->SetGradientTolerance(g_tol);
fitter->SetLambda(lambda);
fitter->SetFilterOutliers(filter_outliers);
if (regu=="MSM")
fitter->SetRegularization(VnlCostFunction::REGU::MSM);
else if (regu=="Variance")
fitter->SetRegularization(VnlCostFunction::REGU::VARIANCE);
else if (regu=="Lasso")
fitter->SetRegularization(VnlCostFunction::REGU::LASSO);
else if (regu=="VoxelVariance")
fitter->SetRegularization(VnlCostFunction::REGU::VOXEL_VARIANCE);
else if (regu=="GroupLasso")
fitter->SetRegularization(VnlCostFunction::REGU::GROUP_LASSO);
else if (regu=="GroupVariance")
fitter->SetRegularization(VnlCostFunction::REGU::GROUP_VARIANCE);
else if (regu=="NONE")
fitter->SetRegularization(VnlCostFunction::REGU::NONE);
fitter->Update();
if (save_residuals && mitk_peak_image.IsNotNull())
{
itk::ImageFileWriter< PeakImgType >::Pointer writer = itk::ImageFileWriter< PeakImgType >::New();
writer->SetInput(fitter->GetFittedImage());
writer->SetFileName(outRoot + "_fitted.nii.gz");
writer->Update();
writer->SetInput(fitter->GetResidualImage());
writer->SetFileName(outRoot + "_residual.nii.gz");
writer->Update();
writer->SetInput(fitter->GetOverexplainedImage());
writer->SetFileName(outRoot + "_overexplained.nii.gz");
writer->Update();
writer->SetInput(fitter->GetUnderexplainedImage());
writer->SetFileName(outRoot + "_underexplained.nii.gz");
writer->Update();
}
else if (save_residuals && mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(mitk_image))
{
{
mitk::Image::Pointer outImage = mitk::GrabItkImageMemory( fitter->GetFittedImageDiff().GetPointer() );
mitk::DiffusionPropertyHelper::CopyProperties(mitk_image, outImage, true);
mitk::DiffusionPropertyHelper propertyHelper( outImage );
propertyHelper.InitializeImage();
mitk::IOUtil::Save(outImage, "application/vnd.mitk.nii.gz", outRoot + "_fitted_image.nii.gz");
}
{
mitk::Image::Pointer outImage = mitk::GrabItkImageMemory( fitter->GetResidualImageDiff().GetPointer() );
mitk::DiffusionPropertyHelper::CopyProperties(mitk_image, outImage, true);
mitk::DiffusionPropertyHelper propertyHelper( outImage );
propertyHelper.InitializeImage();
mitk::IOUtil::Save(outImage, "application/vnd.mitk.nii.gz", outRoot + "_residual_image.nii.gz");
}
{
mitk::Image::Pointer outImage = mitk::GrabItkImageMemory( fitter->GetOverexplainedImageDiff().GetPointer() );
mitk::DiffusionPropertyHelper::CopyProperties(mitk_image, outImage, true);
mitk::DiffusionPropertyHelper propertyHelper( outImage );
propertyHelper.InitializeImage();
mitk::IOUtil::Save(outImage, "application/vnd.mitk.nii.gz", outRoot + "_overexplained_image.nii.gz");
}
{
mitk::Image::Pointer outImage = mitk::GrabItkImageMemory( fitter->GetUnderexplainedImageDiff().GetPointer() );
mitk::DiffusionPropertyHelper::CopyProperties(mitk_image, outImage, true);
mitk::DiffusionPropertyHelper propertyHelper( outImage );
propertyHelper.InitializeImage();
mitk::IOUtil::Save(outImage, "application/vnd.mitk.nii.gz", outRoot + "_underexplained_image.nii.gz");
}
}
else if (save_residuals)
{
itk::ImageFileWriter< itk::FitFibersToImageFilter::DoubleImgType >::Pointer writer = itk::ImageFileWriter< itk::FitFibersToImageFilter::DoubleImgType >::New();
writer->SetInput(fitter->GetFittedImageScalar());
writer->SetFileName(outRoot + "_fitted_image.nii.gz");
writer->Update();
writer->SetInput(fitter->GetResidualImageScalar());
writer->SetFileName(outRoot + "_residual_image.nii.gz");
writer->Update();
writer->SetInput(fitter->GetOverexplainedImageScalar());
writer->SetFileName(outRoot + "_overexplained_image.nii.gz");
writer->Update();
writer->SetInput(fitter->GetUnderexplainedImageScalar());
writer->SetFileName(outRoot + "_underexplained_image.nii.gz");
writer->Update();
}
std::vector< mitk::FiberBundle::Pointer > output_tracts = fitter->GetTractograms();
if (!join_tracts)
{
for (unsigned int bundle=0; bundle<output_tracts.size(); bundle++)
{
std::string name = fib_names.at(bundle);
name = ist::GetFilenameWithoutExtension(name);
mitk::IOUtil::Save(output_tracts.at(bundle), outRoot + name + "_fitted.fib");
if (save_weights)
{
ofstream logfile;
logfile.open (outRoot + name + "_weights.txt");
for (int f=0; f<output_tracts.at(bundle)->GetNumFibers(); ++f)
logfile << output_tracts.at(bundle)->GetFiberWeight(f) << "\n";
logfile.close();
}
}
}
else
{
mitk::FiberBundle::Pointer out = mitk::FiberBundle::New();
out = out->AddBundles(output_tracts);
out->ColorFibersByFiberWeights(false, true);
mitk::IOUtil::Save(out, outRoot + "_fitted.fib");
if (save_weights)
{
ofstream logfile;
logfile.open (outRoot + "_weights.txt");
for (int f=0; f<out->GetNumFibers(); ++f)
logfile << out->GetFiberWeight(f) << "\n";
logfile.close();
}
}
}
catch (itk::ExceptionObject e)
{
std::cout << e;
return EXIT_FAILURE;
}
catch (std::exception e)
{
std::cout << e.what();
return EXIT_FAILURE;
}
catch (...)
{
std::cout << "ERROR!?!";
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
void QmitkOdfMaximaExtractionView::GenerateDataFromDwi()
{
typedef itk::OdfMaximaExtractionFilter< float > MaximaExtractionFilterType;
MaximaExtractionFilterType::Pointer filter = MaximaExtractionFilterType::New();
mitk::Geometry3D::Pointer geometry;
if (!m_ImageNodes.empty())
{
try{
Image::Pointer img = dynamic_cast<Image*>(m_ImageNodes.at(0)->GetData());
typedef ImageToItk< MaximaExtractionFilterType::CoefficientImageType > CasterType;
CasterType::Pointer caster = CasterType::New();
caster->SetInput(img);
caster->Update();
filter->SetShCoeffImage(caster->GetOutput());
geometry = img->GetGeometry();
}
catch(itk::ExceptionObject &e)
{
MITK_INFO << "wrong image type: " << e.what();
return;
}
}
else
return;
filter->SetMaxNumPeaks(m_Controls->m_MaxNumPeaksBox->value());
filter->SetPeakThreshold(m_Controls->m_PeakThresholdBox->value());
if (!m_BinaryImageNodes.empty())
{
ItkUcharImgType::Pointer itkMaskImage = ItkUcharImgType::New();
Image::Pointer mitkMaskImg = dynamic_cast<Image*>(m_BinaryImageNodes.at(0)->GetData());
CastToItkImage<ItkUcharImgType>(mitkMaskImg, itkMaskImage);
filter->SetMaskImage(itkMaskImage);
}
switch (m_Controls->m_NormalizationBox->currentIndex())
{
case 0:
filter->SetNormalizationMethod(MaximaExtractionFilterType::NO_NORM);
break;
case 1:
filter->SetNormalizationMethod(MaximaExtractionFilterType::MAX_VEC_NORM);
break;
case 2:
filter->SetNormalizationMethod(MaximaExtractionFilterType::SINGLE_VEC_NORM);
break;
}
filter->GenerateData();
ItkUcharImgType::Pointer numDirImage = filter->GetNumDirectionsImage();
if (m_Controls->m_OutputDirectionImagesBox->isChecked())
{
typedef MaximaExtractionFilterType::ItkDirectionImageContainer ItkDirectionImageContainer;
ItkDirectionImageContainer::Pointer container = filter->GetDirectionImageContainer();
for (int i=0; i<container->Size(); i++)
{
MaximaExtractionFilterType::ItkDirectionImage::Pointer itkImg = container->GetElement(i);
mitk::Image::Pointer img = mitk::Image::New();
img->InitializeByItk( itkImg.GetPointer() );
img->SetVolume( itkImg->GetBufferPointer() );
DataNode::Pointer node = DataNode::New();
node->SetData(img);
QString name(m_ImageNodes.at(0)->GetName().c_str());
name += "_Direction";
name += QString::number(i+1);
node->SetName(name.toStdString().c_str());
GetDataStorage()->Add(node);
}
}
if (m_Controls->m_OutputNumDirectionsBox->isChecked())
{
mitk::Image::Pointer image2 = mitk::Image::New();
image2->InitializeByItk( numDirImage.GetPointer() );
image2->SetVolume( numDirImage->GetBufferPointer() );
DataNode::Pointer node = DataNode::New();
node->SetData(image2);
QString name(m_ImageNodes.at(0)->GetName().c_str());
name += "_NumDirections";
node->SetName(name.toStdString().c_str());
GetDataStorage()->Add(node);
}
if (m_Controls->m_OutputVectorFieldBox->isChecked())
{
mitk::Vector3D outImageSpacing = geometry->GetSpacing();
float minSpacing = 1;
if(outImageSpacing[0]<outImageSpacing[1] && outImageSpacing[0]<outImageSpacing[2])
minSpacing = outImageSpacing[0];
else if (outImageSpacing[1] < outImageSpacing[2])
minSpacing = outImageSpacing[1];
else
minSpacing = outImageSpacing[2];
mitk::FiberBundleX::Pointer directions = filter->GetOutputFiberBundle();
directions->SetGeometry(geometry);
DataNode::Pointer node = DataNode::New();
node->SetData(directions);
QString name(m_ImageNodes.at(0)->GetName().c_str());
name += "_VectorField";
node->SetName(name.toStdString().c_str());
node->SetProperty("Fiber2DSliceThickness", mitk::FloatProperty::New(minSpacing));
node->SetProperty("Fiber2DfadeEFX", mitk::BoolProperty::New(false));
GetDataStorage()->Add(node);
}
}