void transform(string inputFilename, string outputFilename)
{
typedef itk::Image< TPixelType, N > ImageType;
typedef itk::ImageFileReader< ImageType > ReaderType;
typedef itk::ImageFileWriter< ImageType > WriterType;
typename ReaderType::Pointer reader = ReaderType::New();
itk::NiftiImageIO::Pointer io = itk::NiftiImageIO::New();
reader->SetImageIO(io);
reader->SetFileName(inputFilename);
try {
reader->Update();
} catch( itk::ExceptionObject & e ) {
std::cerr << "Exception caught while reading image " << std::endl;
std::cerr << e << std::endl;
}
typename WriterType::Pointer writer = WriterType::New();
writer->SetImageIO(io);
writer->SetFileName(outputFilename);
writer->SetInput(reader->GetOutput());
try {
writer->Update();
} catch( itk::ExceptionObject & e ) {
std::cerr << "Exception caught while writing image " << std::endl;
std::cerr << e << std::endl;
}
}
void StrokeMask::
Write(const std::string& filename,
const TPixel& strokeValue)
{
typedef itk::Image<TPixel, 2> ImageType;
typename ImageType::Pointer image = ImageType::New();
image->SetRegions(this->GetLargestPossibleRegion());
image->Allocate();
itk::ImageRegionConstIteratorWithIndex<StrokeMask>
maskIterator(this,
this->GetLargestPossibleRegion());
while(!maskIterator.IsAtEnd())
{
if(maskIterator.Get() == StrokeMaskPixelTypeEnum::STROKE)
{
image->SetPixel(maskIterator.GetIndex(),
strokeValue);
}
else
{
image->SetPixel(maskIterator.GetIndex(), itk::NumericTraits<TPixel>::Zero);
}
++maskIterator;
}
typedef itk::ImageFileWriter<ImageType> WriterType;
typename WriterType::Pointer writer = WriterType::New();
writer->SetFileName(filename);
writer->SetInput(image);
writer->Update();
}
void _mitkItkPictureWriteComposite(itk::Image< TPixel, VImageDimension >* itkImage, const std::string& fileName)
{
typedef itk::Image< TPixel, VImageDimension > TImageType;
typedef itk::Image< TPixel, 2 > TImageType2D;
typedef itk::ImageSeriesWriter< TImageType, TImageType2D > WriterType;
typename WriterType::Pointer writer = WriterType::New();
// get the dimension info
unsigned int numberOfImages = 1;
if( itkImage->GetImageDimension() > 2)
numberOfImages = itkImage->GetLargestPossibleRegion().GetSize()[2];
// create output name(s)
SetOutputNames<WriterType>( writer, fileName, numberOfImages );
writer->SetInput( itkImage );
try
{
writer->Update();
}
catch(const itk::ExceptionObject &e)
{
MITK_ERROR << "ITK Exception occured: " << e.what();
mitkThrow() << "Caught ITK exception while writing image with composite type \n" << e.what();
}
}
template <typename T> int writeImage(typename T::Pointer im, const char* filename){
printf("Writing %s ... \n",filename);
typedef typename itk::ImageFileWriter< T > WriterType;
typename WriterType::Pointer writer = WriterType::New();
writer->SetFileName(filename); writer->SetInput(im);
try {
writer->Update();
}
catch(itk::ExceptionObject &err) {
std::cerr << "ExceptionObject caught!" <<std::endl;
std::cerr << err << std::endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
template<class TImage> void ttt::JSONTissueTrackingProject::storeImage(const typename TImage::Pointer & image, const std::string & table,unsigned int frame) {
std::stringstream ssQuery, ssFileName, ssPath;
typedef itk::ImageFileWriter<TImage> WriterType;
typename WriterType::Pointer writer = WriterType::New();
ssFileName << table << "-" << frame << ".tif";
ssPath << this->m_ProjectPath << "/" << ssFileName.str();
writer->SetFileName(ssPath.str());
writer->SetInput(image);
writer->Update();
try {
ssQuery << "INSERT into " << table
<< " (idProject, t, fileName) values (?, ?, ?) on duplicate key UPDATE fileName=VALUES(fileName)";
std::auto_ptr<sql::PreparedStatement> prep_stmt(
m_DB->prepareStatement(ssQuery.str()));
prep_stmt->setInt(1, m_ProjectID); //IDproject==2
prep_stmt->setInt(2, frame); //t==0
prep_stmt->setString(3, ssFileName.str());
prep_stmt->execute();
} catch (sql::SQLException &e) {
/*
The MySQL Connector/C++ throws three different exceptions:
- sql::MethodNotImplementedException (derived from sql::SQLException)
- sql::InvalidArgumentException (derived from sql::SQLException)
- sql::SQLException (derived from std::runtime_error)
*/
cout << "# ERR: SQLException in " << __FILE__;
// cout << "(" << EXAMPLE_FUNCTION << ") on line " << __LINE__ << endl;
/* Use what() (derived from std::runtime_error) to fetch the error message */
cout << "# ERR: " << e.what();
cout << " (MySQL error code: " << e.getErrorCode();
cout << ", SQLState: " << e.getSQLState() << " )" << endl;
}
}
void _mitkItkPictureWriteComposite(itk::Image< TPixel, VImageDimension >* itkImage, const std::string& fileName)
{
typedef itk::Image< TPixel, VImageDimension > TImageType;
typedef itk::ImageFileWriter< TImageType > WriterType;
typename WriterType::Pointer simpleWriter = WriterType::New();
simpleWriter->SetFileName( fileName );
simpleWriter->SetInput( itkImage );
try
{
simpleWriter->Update();
}
catch( itk::ExceptionObject &e)
{
std::cerr << "Caught exception while writing image with composite type: \n" << e.what();
}
}
void ForegroundBackgroundSegmentMask::
Write(const std::string& filename,
const ForegroundPixelValueWrapper<TPixel>& foregroundValue,
const BackgroundPixelValueWrapper<TPixel>& backgroundValue)
{
typedef itk::Image<TPixel, 2> ImageType;
typename ImageType::Pointer image = ImageType::New();
image->SetRegions(this->GetLargestPossibleRegion());
image->Allocate();
itk::ImageRegionConstIteratorWithIndex<ForegroundBackgroundSegmentMask>
maskIterator(this,
this->GetLargestPossibleRegion());
while(!maskIterator.IsAtEnd())
{
if(maskIterator.Get() == ForegroundBackgroundSegmentMaskPixelTypeEnum::FOREGROUND)
{
image->SetPixel(maskIterator.GetIndex(),
foregroundValue.Value);
}
else if(maskIterator.Get() == ForegroundBackgroundSegmentMaskPixelTypeEnum::BACKGROUND)
{
image->SetPixel(maskIterator.GetIndex(), backgroundValue.Value);
}
++maskIterator;
}
typedef itk::ImageFileWriter<ImageType> WriterType;
typename WriterType::Pointer writer = WriterType::New();
writer->SetFileName(filename);
writer->SetInput(image);
writer->Update();
}
void DemonsRegistration::GenerateData2(const itk::Image<TPixel, VImageDimension>* itkImage1)
{
typedef typename itk::Image< TPixel, VImageDimension > FixedImageType;
typedef typename itk::Image< TPixel, VImageDimension > MovingImageType;
typedef float InternalPixelType;
typedef typename itk::Image< InternalPixelType, VImageDimension > InternalImageType;
typedef typename itk::CastImageFilter< FixedImageType,
InternalImageType > FixedImageCasterType;
typedef typename itk::CastImageFilter< MovingImageType,
InternalImageType > MovingImageCasterType;
typedef typename itk::Image< InternalPixelType, VImageDimension > InternalImageType;
typedef typename itk::Vector< float, VImageDimension > VectorPixelType;
typedef typename itk::Image< VectorPixelType, VImageDimension > DeformationFieldType;
typedef typename itk::DemonsRegistrationFilter<
InternalImageType,
InternalImageType,
DeformationFieldType> RegistrationFilterType;
typedef typename itk::WarpImageFilter<
MovingImageType,
MovingImageType,
DeformationFieldType > WarperType;
typedef typename itk::LinearInterpolateImageFunction<
MovingImageType,
double > InterpolatorType;
typedef TPixel OutputPixelType;
typedef typename itk::Image< OutputPixelType, VImageDimension > OutputImageType;
typedef typename itk::CastImageFilter<
MovingImageType,
OutputImageType > CastFilterType;
typedef typename itk::ImageFileWriter< OutputImageType > WriterType;
typedef typename itk::ImageFileWriter< DeformationFieldType > FieldWriterType;
typename FixedImageType::Pointer fixedImage = FixedImageType::New();
mitk::CastToItkImage(m_ReferenceImage, fixedImage);
typename MovingImageType::ConstPointer movingImage = itkImage1;
if (fixedImage.IsNotNull() && movingImage.IsNotNull())
{
typename RegistrationFilterType::Pointer filter = RegistrationFilterType::New();
this->AddStepsToDo(4);
typename itk::ReceptorMemberCommand<DemonsRegistration>::Pointer command = itk::ReceptorMemberCommand<DemonsRegistration>::New();
command->SetCallbackFunction(this, &DemonsRegistration::SetProgress);
filter->AddObserver( itk::IterationEvent(), command );
typename FixedImageCasterType::Pointer fixedImageCaster = FixedImageCasterType::New();
fixedImageCaster->SetInput(fixedImage);
filter->SetFixedImage( fixedImageCaster->GetOutput() );
typename MovingImageCasterType::Pointer movingImageCaster = MovingImageCasterType::New();
movingImageCaster->SetInput(movingImage);
filter->SetMovingImage(movingImageCaster->GetOutput());
filter->SetNumberOfIterations( m_Iterations );
filter->SetStandardDeviations( m_StandardDeviation );
filter->Update();
typename WarperType::Pointer warper = WarperType::New();
typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
warper->SetInput( movingImage );
warper->SetInterpolator( interpolator );
warper->SetOutputSpacing( fixedImage->GetSpacing() );
warper->SetOutputOrigin( fixedImage->GetOrigin() );
warper->SetOutputDirection( fixedImage->GetDirection());
warper->SetDisplacementField( filter->GetOutput() );
warper->Update();
Image::Pointer outputImage = this->GetOutput();
mitk::CastToMitkImage( warper->GetOutput(), outputImage );
typename WriterType::Pointer writer = WriterType::New();
typename CastFilterType::Pointer caster = CastFilterType::New();
writer->SetFileName( m_ResultName );
caster->SetInput( warper->GetOutput() );
writer->SetInput( caster->GetOutput() );
if(m_SaveResult)
{
writer->Update();
}
if (VImageDimension == 2)
{
typedef DeformationFieldType VectorImage2DType;
typedef typename DeformationFieldType::PixelType Vector2DType;
typename VectorImage2DType::ConstPointer vectorImage2D = filter->GetOutput();
typename VectorImage2DType::RegionType region2D = vectorImage2D->GetBufferedRegion();
typename VectorImage2DType::IndexType index2D = region2D.GetIndex();
typename VectorImage2DType::SizeType size2D = region2D.GetSize();
typedef typename itk::Vector< float, 3 > Vector3DType;
typedef typename itk::Image< Vector3DType, 3 > VectorImage3DType;
typedef typename itk::ImageFileWriter< VectorImage3DType > WriterType;
typename WriterType::Pointer writer3D = WriterType::New();
typename VectorImage3DType::Pointer vectorImage3D = VectorImage3DType::New();
typename VectorImage3DType::RegionType region3D;
typename VectorImage3DType::IndexType index3D;
typename VectorImage3DType::SizeType size3D;
index3D[0] = index2D[0];
index3D[1] = index2D[1];
index3D[2] = 0;
size3D[0] = size2D[0];
size3D[1] = size2D[1];
size3D[2] = 1;
region3D.SetSize( size3D );
region3D.SetIndex( index3D );
typename VectorImage2DType::SpacingType spacing2D = vectorImage2D->GetSpacing();
typename VectorImage3DType::SpacingType spacing3D;
spacing3D[0] = spacing2D[0];
spacing3D[1] = spacing2D[1];
spacing3D[2] = 1.0;
vectorImage3D->SetSpacing( spacing3D );
vectorImage3D->SetRegions( region3D );
vectorImage3D->Allocate();
typedef typename itk::ImageRegionConstIterator< VectorImage2DType > Iterator2DType;
typedef typename itk::ImageRegionIterator< VectorImage3DType > Iterator3DType;
Iterator2DType it2( vectorImage2D, region2D );
Iterator3DType it3( vectorImage3D, region3D );
it2.GoToBegin();
it3.GoToBegin();
Vector2DType vector2D;
Vector3DType vector3D;
vector3D[2] = 0; // set Z component to zero.
while( !it2.IsAtEnd() )
{
vector2D = it2.Get();
vector3D[0] = vector2D[0];
vector3D[1] = vector2D[1];
it3.Set( vector3D );
++it2;
++it3;
}
writer3D->SetInput( vectorImage3D );
m_DeformationField = vectorImage3D;
writer3D->SetFileName( m_FieldName );
try
{
if(m_SaveField)
{
writer3D->Update();
}
}
catch( itk::ExceptionObject & excp )
{
MITK_ERROR << excp << std::endl;
}
}
else
{
typename FieldWriterType::Pointer fieldwriter = FieldWriterType::New();
fieldwriter->SetFileName(m_FieldName);
fieldwriter->SetInput( filter->GetOutput() );
m_DeformationField = (itk::Image<itk::Vector<float, 3>,3> *)(filter->GetOutput());
if(m_SaveField)
{
fieldwriter->Update();
}
}
this->SetRemainingProgress(4);
}
}
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;
}
void
mitk::TeemDiffusionTensor3DReconstructionImageFilter<D,T>
::Update()
{
// save input image to nrrd file in temp-folder
char filename[512];
srand((unsigned)time(0));
int random_integer = rand();
sprintf( filename, "dwi_%d.nhdr",random_integer);
typedef mitk::NrrdDiffusionImageWriter<D> WriterType;
typename WriterType::Pointer nrrdWriter = WriterType::New();
nrrdWriter->SetInput( m_Input );
//nrrdWriter->SetDirections(m_Input->GetDirections());
//nrrdWriter->SetB_Value(m_Input->GetB_Value());
nrrdWriter->SetFileName(filename);
try
{
nrrdWriter->Update();
}
catch (itk::ExceptionObject e)
{
std::cout << e << std::endl;
}
file_replace(filename,"vector","list");
// build up correct command from input params
char command[4096];
sprintf( command, "tend estim -i %s -B kvp -o tensors_%d.nhdr -knownB0 true",
filename, random_integer);
//m_DiffusionImages;
if(m_EstimateErrorImage)
{
sprintf( command, "%s -ee error_image_%d.nhdr", command, random_integer);
}
if(m_Sigma != -19191919)
{
sprintf( command, "%s -sigma %f", command, m_Sigma);
}
switch(m_EstimationMethod)
{
case TeemTensorEstimationMethodsLLS:
sprintf( command, "%s -est lls", command);
break;
case TeemTensorEstimationMethodsMLE:
sprintf( command, "%s -est mle", command);
break;
case TeemTensorEstimationMethodsNLS:
sprintf( command, "%s -est nls", command);
break;
case TeemTensorEstimationMethodsWLS:
sprintf( command, "%s -est wls", command);
break;
}
sprintf( command, "%s -wlsi %d", command, m_NumIterations);
if(m_ConfidenceThreshold != -19191919.0)
{
sprintf( command, "%s -t %f", command, m_ConfidenceThreshold);
}
sprintf( command, "%s -soft %f", command, m_ConfidenceFuzzyness);
sprintf( command, "%s -mv %f", command, m_MinPlausibleValue);
// call tend estim command
std::cout << "Calling <" << command << ">" << std::endl;
int success = system(command);
if(!success)
{
MITK_ERROR << "system command could not be called!";
}
remove(filename);
sprintf( filename, "dwi_%d.raw", random_integer);
remove(filename);
// change kind from tensor to vector
sprintf( filename, "tensors_%d.nhdr", random_integer);
file_replace(filename,"3D-masked-symmetric-matrix","vector");
// read result as mitk::Image and provide it in m_Output
typedef itk::ImageFileReader<VectorImageType> FileReaderType;
typename FileReaderType::Pointer reader = FileReaderType::New();
reader->SetFileName(filename);
reader->Update();
typename VectorImageType::Pointer vecImage = reader->GetOutput();
remove(filename);
sprintf( filename, "tensors_%d.raw", random_integer);
remove(filename);
typename ItkTensorImageType::Pointer itkTensorImage = ItkTensorImageType::New();
itkTensorImage->SetSpacing( vecImage->GetSpacing() ); // Set the image spacing
itkTensorImage->SetOrigin( vecImage->GetOrigin() ); // Set the image origin
itkTensorImage->SetDirection( vecImage->GetDirection() ); // Set the image direction
itkTensorImage->SetLargestPossibleRegion( vecImage->GetLargestPossibleRegion() );
itkTensorImage->SetBufferedRegion( vecImage->GetLargestPossibleRegion() );
itkTensorImage->SetRequestedRegion( vecImage->GetLargestPossibleRegion() );
itkTensorImage->Allocate();
itk::ImageRegionIterator<VectorImageType> it(vecImage,
vecImage->GetLargestPossibleRegion());
itk::ImageRegionIterator<ItkTensorImageType> it2(itkTensorImage,
itkTensorImage->GetLargestPossibleRegion());
it2 = it2.Begin();
//#pragma omp parallel private (it)
{
for(it=it.Begin();!it.IsAtEnd(); ++it, ++it2)
{
//#pragma omp single nowait
{
VectorType vec = it.Get();
TensorType tensor;
for(int i=1;i<7;i++)
tensor[i-1] = vec[i] * vec[0];
it2.Set( tensor );
}
} // end for
} // end ompparallel
m_OutputItk = mitk::TensorImage::New();
m_OutputItk->InitializeByItk(itkTensorImage.GetPointer());
m_OutputItk->SetVolume( itkTensorImage->GetBufferPointer() );
// in case: read resulting error-image and provide it in m_ErrorImage
if(m_EstimateErrorImage)
{
// open error image here
}
}
int changeOrientationMethod(string inputFilename, string outputFilename, OrientationType orientation, bool changeOrientation, bool displayInitialOrientation, bool displayAvailableOrientation)
{
typedef itk::Image< TPixelType, N > ImageType;
typedef itk::ImageFileReader<ImageType> ReaderType;
typedef itk::ImageFileWriter<ImageType> WriterType;
typename ReaderType::Pointer reader = ReaderType::New();
itk::NiftiImageIO::Pointer io = itk::NiftiImageIO::New();
reader->SetImageIO(io);
reader->SetFileName(inputFilename);
OrientImage<ImageType> orientationFilter;
orientationFilter.setInputImage(reader->GetOutput());
if (displayInitialOrientation)
{
try {
io->SetFileName(inputFilename);
io->ReadImageInformation();
//reader->Update();
} catch( itk::ExceptionObject & e ) {
std::cerr << "Exception caught while reading input image " << std::endl;
std::cerr << e << std::endl;
}
typename ImageType::DirectionType direction;
vector<double> dir0 = io->GetDirection(0);
for (int i=0; i<dir0.size(); i++)
direction(i,0) = dir0[i];
vector<double> dir1 = io->GetDirection(1);
for (int i=0; i<dir1.size(); i++)
direction(i,1) = dir1[i];
vector<double> dir2 = io->GetDirection(2);
for (int i=0; i<dir2.size(); i++)
direction(i,2) = dir2[i];
cout << direction << endl;
cout << "Input image orientation : " << FlagToString(orientationFilter.getOrientationFromDirection(direction)) << endl;
}
if (changeOrientation)
{
try {
io->SetFileName(inputFilename);
io->ReadImageInformation();
//reader->Update();
} catch( itk::ExceptionObject & e ) {
std::cerr << "Exception caught while reading input image " << std::endl;
std::cerr << e << std::endl;
}
orientationFilter.orientation(orientation);
typename WriterType::Pointer writer = WriterType::New();
writer->SetImageIO(io);
writer->SetFileName(outputFilename);
writer->SetInput(orientationFilter.getOutputImage());
try {
writer->Write();
} catch( itk::ExceptionObject & e ) {
std::cerr << "Exception caught while writing output image " << std::endl;
std::cerr << e << std::endl;
}
}
return EXIT_SUCCESS;
}
void operator()( const Parameter ¶m )
{
OSLM_DEBUG( "itk::ImageSeriesWriter with PIXELTYPE "<< fwTools::DynamicType::string<PIXELTYPE>() );
::fwData::Image::sptr image = param.m_dataImage;
// VAG attention : ImageFileReader ne notifie AUCUNE progressEvent mais son ImageIO oui!!!! mais ImageFileReader ne permet pas de l'atteindre
// car soit mis a la mano ou alors construit lors de l'Update donc trop tard
// Il faut dont creer une ImageIO a la mano (*1*): affecter l'observation sur IO (*2*) et mettre le IO dans le reader (voir *3*)
// Reader IO (*1*)
typename itk::ImageIOBase::Pointer imageIOWrite = itk::ImageIOFactory::CreateImageIO( "image.jpg", itk::ImageIOFactory::WriteMode);
assert( imageIOWrite.IsNotNull() );
// create writer
typedef itk::Image< PIXELTYPE, 3> itkImageType;
typedef itk::Image< unsigned char, 2 > Image2DType;
typedef typename itk::ImageSeriesWriter< itkImageType, Image2DType > WriterType;
typename WriterType::Pointer writer = WriterType::New();
// set observation (*2*)
itk::LightProcessObject::Pointer castHelper= (itk::LightProcessObject *)(imageIOWrite.GetPointer());
assert( castHelper.IsNotNull() );
Progressor progress(castHelper, param.m_fwWriter, param.m_filename);
// create itk Image
typename itkImageType::Pointer itkImage = ::fwItkIO::itkImageFactory<itkImageType>( image );
typedef ::itk::IntensityWindowingImageFilter< itkImageType, itkImageType > RescaleFilterType;
typename RescaleFilterType::Pointer rescaleFilter = RescaleFilterType::New();
double min, max;
::fwData::Composite::sptr poolTF;
poolTF = image->getField< ::fwData::Composite>( ::fwComEd::Dictionary::m_transferFunctionCompositeId );
if(poolTF)
{
::fwData::Composite::iterator iter = poolTF->find(::fwData::TransferFunction::s_DEFAULT_TF_NAME);
if(iter != poolTF->end())
{
::fwData::TransferFunction::sptr tf;
tf = ::fwData::TransferFunction::dynamicCast(iter->second);
min = tf->getWLMinMax().first;
max = tf->getWLMinMax().second;
}
}
else
{
::fwComEd::fieldHelper::MedicalImageHelpers::getMinMax(image, min, max);
}
rescaleFilter->SetWindowMinimum( min );
rescaleFilter->SetWindowMaximum( max );
rescaleFilter->SetOutputMinimum( 0 );
rescaleFilter->SetOutputMaximum( 255 );
rescaleFilter->InPlaceOff();
rescaleFilter->SetInput( itkImage );
rescaleFilter->Update();
writer->SetInput( rescaleFilter->GetOutput() );
typedef itk::NumericSeriesFileNames NameGeneratorType;
NameGeneratorType::Pointer nameGenerator = NameGeneratorType::New();
std::string format = param.m_filename;
format += "/%04d.jpg";
nameGenerator->SetSeriesFormat( format.c_str() );
nameGenerator->SetStartIndex( 1 );
nameGenerator->SetEndIndex( image->getSize()[2] );
nameGenerator->SetIncrementIndex( 1 );
writer->SetFileNames( nameGenerator->GetFileNames() );
writer->SetImageIO( imageIOWrite );
// save image;
writer->Update();
}