void mitk::ImageLiveWireContourModelFilter::ItkPreProcessImage (const itk::Image<TPixel, VImageDimension>* inputImage)
{
typedef itk::Image< TPixel, VImageDimension > InputImageType;
typedef itk::CastImageFilter< InputImageType, InternalImageType > CastFilterType;
typename CastFilterType::Pointer castFilter = CastFilterType::New();
castFilter->SetInput(inputImage);
castFilter->Update();
m_InternalImage = castFilter->GetOutput();
m_CostFunction->SetImage( m_InternalImage );
m_ShortestPathFilter->SetInput( m_InternalImage );
}
dtkSmartPointer<medAbstractData> itkFiltersComponentSizeThresholdProcess::castToOutputType(medAbstractData* inputData)
{
//we will later label the image so we don't care about precision.
typedef itk::CastImageFilter< InputImageType, OutputImageType > CastFilterType;
typename CastFilterType::Pointer caster = CastFilterType::New();
typename InputImageType::Pointer im = static_cast<InputImageType*>(inputData->data());
caster->SetInput(im);
caster->Update();
dtkSmartPointer<medAbstractData> outputData = medAbstractDataFactory::instance()->createSmartPointer(medUtilitiesITK::itkDataImageId<OutputImageType>());
outputData->setData(caster->GetOutput());
return outputData;
}
void
mitk::ModelSignalImageGenerator::DoPrepareMask(itk::Image<TPixel, VDim>* image)
{
m_InternalMask = dynamic_cast<InternalMaskType*>(image);
if (m_InternalMask.IsNull())
{
MITK_INFO << "Parameter Fit Generator. Need to cast mask for parameter fit.";
typedef itk::Image<TPixel, VDim> InputImageType;
typedef itk::CastImageFilter< InputImageType, InternalMaskType > CastFilterType;
typename CastFilterType::Pointer spImageCaster = CastFilterType::New();
spImageCaster->SetInput(image);
m_InternalMask = spImageCaster->GetOutput();
spImageCaster->Update();
}
}
void PartialVolumeAnalysisClusteringCalculator::InternalQuantify(
const itk::Image< TPixel, VImageDimension > *image,
mitk::Image::Pointer clusteredImage, double* retval, mitk::Image::Pointer mask ) const
{
typedef itk::Image< TPixel, VImageDimension > ImageType;
typedef itk::Image< float, VImageDimension > ProbImageType;
typedef itk::Image< unsigned char, VImageDimension > MaskImageType;
typedef mitk::ImageToItk<ProbImageType> CastFilterType;
typename CastFilterType::Pointer castFilter = CastFilterType::New();
castFilter->SetInput( clusteredImage );
castFilter->Update();
typename ProbImageType::Pointer clusterImage = castFilter->GetOutput();
typename MaskImageType::Pointer itkmask = 0;
if(mask.IsNotNull())
{
typedef mitk::ImageToItk<MaskImageType> CastFilterType2;
typename CastFilterType2::Pointer castFilter2 = CastFilterType2::New();
castFilter2->SetInput( mask );
castFilter2->Update();
itkmask = castFilter2->GetOutput();
}
else
{
itkmask = MaskImageType::New();
itkmask->SetSpacing( clusterImage->GetSpacing() ); // Set the image spacing
itkmask->SetOrigin( clusterImage->GetOrigin() ); // Set the image origin
itkmask->SetDirection( clusterImage->GetDirection() ); // Set the image direction
itkmask->SetRegions( clusterImage->GetLargestPossibleRegion() );
itkmask->Allocate();
itkmask->FillBuffer(1);
}
itk::ImageRegionConstIterator<ImageType>
itimage(image, image->GetLargestPossibleRegion());
itk::ImageRegionConstIterator<ProbImageType>
itprob(clusterImage, clusterImage->GetLargestPossibleRegion());
itk::ImageRegionConstIterator<MaskImageType>
itmask(itkmask, itkmask->GetLargestPossibleRegion());
itimage.GoToBegin();
itprob.GoToBegin();
itmask.GoToBegin();
double totalProb = 0;
double measurement = 0;
double error = 0;
while( !itimage.IsAtEnd() && !itprob.IsAtEnd() && !itmask.IsAtEnd() )
{
double valImag = itimage.Get();
double valProb = itprob.Get();
double valMask = itmask.Get();
typename ProbImageType::PixelType prop = valProb * valMask;
totalProb += prop;
measurement += valImag * prop;
error += valImag * valImag * prop;
++itimage;
++itprob;
++itmask;
}
measurement = measurement / totalProb;
error = error / totalProb;
retval[0] = measurement;
retval[1] = sqrt( error - measurement*measurement );
}
void PartialVolumeAnalysisClusteringCalculator::InternalGenerateRGB( HelperStructRGBChannels *rgbin, mitk::Image::Pointer retval ) const
{
typedef itk::Image< float, VImageDimension > ProbImageType;
typedef itk::Image< typename itk::RGBAPixel<unsigned char>, VImageDimension > RGBImageType;
typedef mitk::ImageToItk<ProbImageType> CastFilterType;
typename CastFilterType::Pointer castFilter = CastFilterType::New();
castFilter->SetInput( rgbin->r );
castFilter->Update();
typename ProbImageType::Pointer r = castFilter->GetOutput();
castFilter = CastFilterType::New();
castFilter->SetInput( rgbin->g );
castFilter->Update();
typename ProbImageType::Pointer g = castFilter->GetOutput();
typename RGBImageType::Pointer rgb = RGBImageType::New();
rgb->SetSpacing( g->GetSpacing() ); // Set the image spacing
rgb->SetOrigin( g->GetOrigin() ); // Set the image origin
rgb->SetDirection( g->GetDirection() ); // Set the image direction
rgb->SetRegions( g->GetLargestPossibleRegion() );
rgb->Allocate();
itk::ImageRegionConstIterator<ProbImageType>
itr(r, r->GetLargestPossibleRegion());
itk::ImageRegionConstIterator<ProbImageType>
itg(g, g->GetLargestPossibleRegion());
itk::ImageRegionIterator<RGBImageType>
itrgb(rgb, rgb->GetLargestPossibleRegion());
itr.GoToBegin();
itg.GoToBegin();
float maxr = 0;
float maxg = 0;
while( !itr.IsAtEnd() )
{
typename ProbImageType::PixelType pr = itr.Get();
typename ProbImageType::PixelType pg = itg.Get();
if(pr > maxr)
{
maxr = pr;
}
if(pg > maxg)
{
maxg = pg;
}
++itr;
++itg;
}
itr.GoToBegin();
itg.GoToBegin();
itrgb.GoToBegin();
while( !itr.IsAtEnd() )
{
typename ProbImageType::PixelType pr = itr.Get();
typename ProbImageType::PixelType pg = itg.Get();
typename RGBImageType::PixelType prgb;
float valr = (pr/maxr)*255.0f;
float valg = (pg/maxg)*255.0f;
float alpha = valr>valg ? valr : valg;
prgb.Set(valr, valg, 0.0f, alpha);
itrgb.Set(prgb);
++itr;
++itg;
++itrgb;
}
retval->InitializeByItk(rgb.GetPointer());
retval->SetVolume(rgb->GetBufferPointer());
}
