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 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;
}
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 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;
}
void QmitkDwiSoftwarePhantomView::GeneratePhantom()
{
typedef itk::DwiPhantomGenerationFilter< short > FilterType;
FilterType::GradientListType gradientList;
m_SignalRegions.clear();
for (int i=0; i<m_SignalRegionNodes.size(); i++)
{
mitk::Image::Pointer mitkBinaryImg = dynamic_cast<mitk::Image*>(m_SignalRegionNodes.at(i)->GetData());
ItkUcharImgType::Pointer signalRegion = ItkUcharImgType::New();
mitk::CastToItkImage<ItkUcharImgType>(mitkBinaryImg, signalRegion);
m_SignalRegions.push_back(signalRegion);
}
switch(m_Controls->m_TensorsToDWINumDirsSelect->currentIndex())
{
case 0:
gradientList = MakeGradientList<12>();
break;
case 1:
gradientList = MakeGradientList<42>();
break;
case 2:
gradientList = MakeGradientList<92>();
break;
case 3:
gradientList = MakeGradientList<162>();
break;
case 4:
gradientList = MakeGradientList<252>();
break;
case 5:
gradientList = MakeGradientList<362>();
break;
case 6:
gradientList = MakeGradientList<492>();
break;
case 7:
gradientList = MakeGradientList<642>();
break;
case 8:
gradientList = MakeGradientList<812>();
break;
case 9:
gradientList = MakeGradientList<1002>();
break;
default:
gradientList = MakeGradientList<92>();
}
double bVal = m_Controls->m_TensorsToDWIBValueEdit->value();
itk::ImageRegion<3> imageRegion;
imageRegion.SetSize(0, m_Controls->m_SizeX->value());
imageRegion.SetSize(1, m_Controls->m_SizeY->value());
imageRegion.SetSize(2, m_Controls->m_SizeZ->value());
mitk::Vector3D spacing;
spacing[0] = m_Controls->m_SpacingX->value();
spacing[1] = m_Controls->m_SpacingY->value();
spacing[2] = m_Controls->m_SpacingZ->value();
FilterType::Pointer filter = FilterType::New();
filter->SetGradientList(gradientList);
filter->SetBValue(bVal);
filter->SetSNR(m_Controls->m_NoiseLevel->value());
filter->SetSignalScale(m_Controls->m_SignalScale->value());
filter->SetImageRegion(imageRegion);
filter->SetSpacing(spacing);
filter->SetSignalRegions(m_SignalRegions);
filter->SetGreyMatterAdc(m_Controls->m_GmAdc->value());
std::vector< float > tensorFA;
std::vector< float > tensorADC;
std::vector< float > tensorWeight;
std::vector< vnl_vector_fixed<double, 3> > tensorDirection;
for (int i=0; i<m_SpinFa.size(); i++)
{
tensorFA.push_back(m_SpinFa.at(i)->value());
tensorADC.push_back(m_SpinAdc.at(i)->value());
vnl_vector_fixed<double, 3> dir;
dir[0] = m_SpinX.at(i)->value();
dir[1] = m_SpinY.at(i)->value();
dir[2] = m_SpinZ.at(i)->value();
dir.normalize();
tensorDirection.push_back(dir);
tensorWeight.push_back(m_SpinWeight.at(i)->value());
}
filter->SetTensorFA(tensorFA);
filter->SetTensorADC(tensorADC);
filter->SetTensorWeight(tensorWeight);
filter->SetTensorDirection(tensorDirection);
filter->Update();
mitk::DiffusionImage<short>::Pointer image = mitk::DiffusionImage<short>::New();
image->SetVectorImage( filter->GetOutput() );
image->SetB_Value(bVal);
image->SetDirections(gradientList);
image->InitializeFromVectorImage();
mitk::DataNode::Pointer node = mitk::DataNode::New();
node->SetData( image );
node->SetName(m_Controls->m_ImageName->text().toStdString());
GetDataStorage()->Add(node);
if (m_Controls->m_OutputNumDirectionsBox->isChecked())
{
ItkUcharImgType::Pointer numDirImage = filter->GetNumDirectionsImage();
mitk::Image::Pointer image2 = mitk::Image::New();
image2->InitializeByItk( numDirImage.GetPointer() );
image2->SetVolume( numDirImage->GetBufferPointer() );
mitk::DataNode::Pointer node2 = mitk::DataNode::New();
node2->SetData(image2);
QString name(m_Controls->m_ImageName->text());
name += "_NumDirections";
node2->SetName(name.toStdString().c_str());
GetDataStorage()->Add(node2);
}
if (m_SignalRegionNodes.size()==0)
return;
if (m_Controls->m_OutputDirectionImagesBox->isChecked())
{
typedef FilterType::ItkDirectionImageContainer ItkDirectionImageContainer;
ItkDirectionImageContainer::Pointer container = filter->GetDirectionImageContainer();
for (int i=0; i<container->Size(); i++)
{
FilterType::ItkDirectionImage::Pointer itkImg = container->GetElement(i);
mitk::Image::Pointer img = mitk::Image::New();
img->InitializeByItk( itkImg.GetPointer() );
img->SetVolume( itkImg->GetBufferPointer() );
mitk::DataNode::Pointer node = mitk::DataNode::New();
node->SetData(img);
QString name(m_Controls->m_ImageName->text());
name += "_Direction";
name += QString::number(i+1);
node->SetName(name.toStdString().c_str());
GetDataStorage()->Add(node);
}
}
if (m_Controls->m_OutputVectorFieldBox->isChecked())
{
mitk::Geometry3D::Pointer geometry = image->GetGeometry();
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);
mitk::DataNode::Pointer node = mitk::DataNode::New();
node->SetData(directions);
QString name(m_Controls->m_ImageName->text());
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);
}
}
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);
}
}
void QmitkOdfMaximaExtractionView::StartTensor()
{
if (m_TensorImageNodes.empty())
return;
typedef itk::DiffusionTensorPrincipalDirectionImageFilter< float, float > MaximaExtractionFilterType;
MaximaExtractionFilterType::Pointer filter = MaximaExtractionFilterType::New();
mitk::Geometry3D::Pointer geometry;
try{
TensorImage::Pointer img = dynamic_cast<TensorImage*>(m_TensorImageNodes.at(0)->GetData());
ItkTensorImage::Pointer itkImage = ItkTensorImage::New();
CastToItkImage<ItkTensorImage>(img, itkImage);
filter->SetInput(itkImage);
geometry = img->GetGeometry();
}
catch(itk::ExceptionObject &e)
{
MITK_INFO << "wrong image type: " << e.what();
throw e;
}
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);
}
if (m_Controls->m_NormalizationBox->currentIndex()==0)
filter->SetNormalizeVectors(false);
filter->Update();
if (m_Controls->m_OutputDirectionImagesBox->isChecked())
{
MaximaExtractionFilterType::OutputImageType::Pointer itkImg = filter->GetOutput();
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_TensorImageNodes.at(0)->GetName().c_str());
name += "_PrincipalDirection";
node->SetName(name.toStdString().c_str());
GetDataStorage()->Add(node);
}
if (m_Controls->m_OutputNumDirectionsBox->isChecked())
{
ItkUcharImgType::Pointer numDirImage = filter->GetNumDirectionsImage();
mitk::Image::Pointer image2 = mitk::Image::New();
image2->InitializeByItk( numDirImage.GetPointer() );
image2->SetVolume( numDirImage->GetBufferPointer() );
DataNode::Pointer node2 = DataNode::New();
node2->SetData(image2);
QString name(m_TensorImageNodes.at(0)->GetName().c_str());
name += "_NumDirections";
node2->SetName(name.toStdString().c_str());
GetDataStorage()->Add(node2);
}
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_TensorImageNodes.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);
}
}
void DwiPhantomGenerationFilter< TOutputScalarType >
::GenerateData()
{
if (m_NoiseVariance < 0)
m_NoiseVariance = 0.001;
if (!m_SimulateBaseline)
{
MITK_INFO << "Baseline image values are set to default. Noise variance value is treated as SNR!";
if (m_NoiseVariance <= 0)
m_NoiseVariance = 0.0001;
if (m_NoiseVariance>99)
m_NoiseVariance = 0;
else
{
m_NoiseVariance = m_DefaultBaseline/(m_NoiseVariance*m_SignalScale);
m_NoiseVariance *= m_NoiseVariance;
}
}
m_RandGen = Statistics::MersenneTwisterRandomVariateGenerator::New();
m_RandGen->SetSeed();
typename OutputImageType::Pointer outImage = OutputImageType::New();
outImage->SetSpacing( m_Spacing );
outImage->SetOrigin( m_Origin );
outImage->SetDirection( m_DirectionMatrix );
outImage->SetLargestPossibleRegion( m_ImageRegion );
outImage->SetBufferedRegion( m_ImageRegion );
outImage->SetRequestedRegion( m_ImageRegion );
outImage->SetVectorLength(m_GradientList.size());
outImage->Allocate();
typename OutputImageType::PixelType pix;
pix.SetSize(m_GradientList.size());
pix.Fill(0.0);
outImage->FillBuffer(pix);
this->SetNthOutput (0, outImage);
double minSpacing = m_Spacing[0];
if (m_Spacing[1]<minSpacing)
minSpacing = m_Spacing[1];
if (m_Spacing[2]<minSpacing)
minSpacing = m_Spacing[2];
m_DirectionImageContainer = ItkDirectionImageContainer::New();
for (int i=0; i<m_SignalRegions.size(); i++)
{
itk::Vector< float, 3 > nullVec; nullVec.Fill(0.0);
ItkDirectionImage::Pointer img = ItkDirectionImage::New();
img->SetSpacing( m_Spacing );
img->SetOrigin( m_Origin );
img->SetDirection( m_DirectionMatrix );
img->SetRegions( m_ImageRegion );
img->Allocate();
img->FillBuffer(nullVec);
m_DirectionImageContainer->InsertElement(m_DirectionImageContainer->Size(), img);
}
m_NumDirectionsImage = ItkUcharImgType::New();
m_NumDirectionsImage->SetSpacing( m_Spacing );
m_NumDirectionsImage->SetOrigin( m_Origin );
m_NumDirectionsImage->SetDirection( m_DirectionMatrix );
m_NumDirectionsImage->SetRegions( m_ImageRegion );
m_NumDirectionsImage->Allocate();
m_NumDirectionsImage->FillBuffer(0);
m_SNRImage = ItkFloatImgType::New();
m_SNRImage->SetSpacing( m_Spacing );
m_SNRImage->SetOrigin( m_Origin );
m_SNRImage->SetDirection( m_DirectionMatrix );
m_SNRImage->SetRegions( m_ImageRegion );
m_SNRImage->Allocate();
m_SNRImage->FillBuffer(0);
vtkSmartPointer<vtkCellArray> m_VtkCellArray = vtkSmartPointer<vtkCellArray>::New();
vtkSmartPointer<vtkPoints> m_VtkPoints = vtkSmartPointer<vtkPoints>::New();
m_BaselineImages = 0;
for( unsigned int i=0; i<m_GradientList.size(); i++)
if (m_GradientList[i].GetNorm()<=0.0001)
m_BaselineImages++;
typedef ImageRegionIterator<OutputImageType> IteratorOutputType;
IteratorOutputType it (outImage, m_ImageRegion);
// isotropic tensor
itk::DiffusionTensor3D<float> isoTensor;
isoTensor.Fill(0);
float e1 = m_GreyMatterAdc;
float e2 = m_GreyMatterAdc;
float e3 = m_GreyMatterAdc;
isoTensor.SetElement(0,e1);
isoTensor.SetElement(3,e2);
isoTensor.SetElement(5,e3);
m_MaxBaseline = GetTensorL2Norm(isoTensor);
GenerateTensors();
// simulate measurement
m_MeanBaseline = 0;
double noiseStdev = sqrt(m_NoiseVariance);
while(!it.IsAtEnd())
{
pix = it.Get();
typename OutputImageType::IndexType index = it.GetIndex();
int numDirs = 0;
for (int i=0; i<m_SignalRegions.size(); i++)
{
ItkUcharImgType::Pointer region = m_SignalRegions.at(i);
if (region->GetPixel(index)!=0)
{
numDirs++;
pix += SimulateMeasurement(m_TensorList[i], m_TensorWeight[i]);
// set direction image pixel
ItkDirectionImage::Pointer img = m_DirectionImageContainer->GetElement(i);
itk::Vector< float, 3 > pixel = img->GetPixel(index);
vnl_vector_fixed<double, 3> dir = m_TensorDirection.at(i);
dir.normalize();
dir *= m_TensorWeight.at(i);
pixel.SetElement(0, dir[0]);
pixel.SetElement(1, dir[1]);
pixel.SetElement(2, dir[2]);
img->SetPixel(index, pixel);
vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
itk::ContinuousIndex<double, 3> center;
center[0] = index[0];
center[1] = index[1];
center[2] = index[2];
itk::Point<double> worldCenter;
outImage->TransformContinuousIndexToPhysicalPoint( center, worldCenter );
itk::Point<double> worldStart;
worldStart[0] = worldCenter[0]-dir[0]/2 * minSpacing;
worldStart[1] = worldCenter[1]-dir[1]/2 * minSpacing;
worldStart[2] = worldCenter[2]-dir[2]/2 * minSpacing;
vtkIdType id = m_VtkPoints->InsertNextPoint(worldStart.GetDataPointer());
container->GetPointIds()->InsertNextId(id);
itk::Point<double> worldEnd;
worldEnd[0] = worldCenter[0]+dir[0]/2 * minSpacing;
worldEnd[1] = worldCenter[1]+dir[1]/2 * minSpacing;
worldEnd[2] = worldCenter[2]+dir[2]/2 * minSpacing;
id = m_VtkPoints->InsertNextPoint(worldEnd.GetDataPointer());
container->GetPointIds()->InsertNextId(id);
m_VtkCellArray->InsertNextCell(container);
}
}
if (numDirs>1)
{
for (int i=0; i<m_GradientList.size(); i++)
pix[i] /= numDirs;
}
else if (numDirs==0)
{
if (m_SimulateBaseline)
pix = SimulateMeasurement(isoTensor, 1.0);
else
pix.Fill(0.0);
}
m_MeanBaseline += pix[0];
it.Set(pix);
m_NumDirectionsImage->SetPixel(index, numDirs);
if (m_NoiseVariance>0)
m_SNRImage->SetPixel(index, pix[0]/(noiseStdev*m_SignalScale));
++it;
}
m_MeanBaseline /= m_ImageRegion.GetNumberOfPixels();
if (m_NoiseVariance>0)
MITK_INFO << "Mean SNR: " << m_MeanBaseline/(noiseStdev*m_SignalScale);
else
MITK_INFO << "No noise added";
// add rician noise
it.GoToBegin();
while(!it.IsAtEnd())
{
pix = it.Get();
AddNoise(pix);
it.Set(pix);
++it;
}
// generate fiber bundle
vtkSmartPointer<vtkPolyData> directionsPolyData = vtkSmartPointer<vtkPolyData>::New();
directionsPolyData->SetPoints(m_VtkPoints);
directionsPolyData->SetLines(m_VtkCellArray);
m_OutputFiberBundle = mitk::FiberBundleX::New(directionsPolyData);
}