void setUp(void)
{
// Load Image Data
m_Image = dynamic_cast<mitk::Image*>(mitk::IOUtil::Load(GetTestDataFilePath("Pic3D.nrrd"))[0].GetPointer());
mitk::CastToItkImage(m_Image,m_ItkImage);
// Create a single mask with only one pixel within the regions
mitk::Image::Pointer mask1 = dynamic_cast<mitk::Image*>(mitk::IOUtil::Load(GetTestDataFilePath("Pic3D.nrrd"))[0].GetPointer());
mitk::CastToItkImage(mask1,m_ItkMask);
m_ItkMask->FillBuffer(0);
MaskType::IndexType index;
index[0]=88;index[1]=81;index[2]=13;
m_ItkMask->SetPixel(index, 1);
MITK_INFO << "Pixel Value: "<<m_ItkImage->GetPixel(index);
mitk::CastToMitkImage(m_ItkMask, m_Mask);
// Create a mask with a covered region
mitk::Image::Pointer lmask1 = dynamic_cast<mitk::Image*>(mitk::IOUtil::Load(GetTestDataFilePath("Pic3D.nrrd"))[0].GetPointer());
mitk::CastToItkImage(lmask1,m_ItkMask1);
m_ItkMask1->FillBuffer(0);
int range=2;
for (int x = 88-range;x < 88+range+1;++x)
{
for (int y=81-range;y<81+range+1;++y)
{
for (int z=13-range;z<13+range+1;++z)
{
index[0] = x;
index[1] = y;
index[2] = z;
//MITK_INFO << "Pixel: " <<m_ItkImage->GetPixel(index);
m_ItkMask1->SetPixel(index, 1);
}
}
}
mitk::CastToMitkImage(m_ItkMask1, m_Mask1);
m_GradientImage=GenerateGradientWithDimXImage<unsigned char>(5,5,5);
m_GradientMask = GenerateMaskImage<unsigned char>(5,5,5);
}
itk::Image<unsigned char, 3>::Pointer pdp::EMClassification::classify(itk::Image<float, 3>::Pointer img, itk::Image<unsigned char, 3>::Pointer mask)
{
typedef itk::Vector< double, 1 > MeasurementVectorType;
typedef itk::Image<unsigned char, 3> MaskType;
typedef itk::Image<float, 3> ImageType;
typedef itk::ImageRegionConstIterator< ImageType > ImageIteratorType;
ImageIteratorType imgIt(img, img->GetLargestPossibleRegion());
typedef itk::ImageRegionConstIterator< MaskType> MaskIteratorType;
MaskIteratorType maskIt( mask, mask->GetLargestPossibleRegion());
MaskType::Pointer correctImage = MaskType::New();
correctImage->CopyInformation(mask);
MaskType::RegionType outputRegion = mask->GetLargestPossibleRegion();
correctImage->SetRegions( outputRegion );
correctImage->Allocate();
typedef itk::ImageRegionIterator<MaskType> IteratorType;
IteratorType outputIt( correctImage, outputRegion);
MeasurementVectorType mv;
for ( imgIt.GoToBegin(), maskIt.GoToBegin(), outputIt.GoToBegin(); !maskIt.IsAtEnd(); ++maskIt, ++imgIt, ++outputIt)
{
if (maskIt.Get() == 255)
{
mv[0] = imgIt.Get();
if (genLabel(mv) == 3)
{
outputIt.Set(255);
}
}
}
return correctImage;
}
typename PatchExtractor<PValue>::MaskType::Pointer PatchExtractor<PValue>::ExtractMask()
{
ContIndexType startIndex;
for(unsigned int i = 0; i < 2; i++)
{
startIndex[i] = m_Center[i] - (m_Size[i] / 2.0);
}
startIndex[2] = 0;
typename ImageType::IndexType properIndex;
for(unsigned int i = 0; i < 3; i++)
{
properIndex[i] = round(startIndex[i]);
}
for(unsigned int i = 0; i < 2; i++)
{
if(properIndex[i] < 0) properIndex[i] = 0;
if((m_Size[i] + properIndex[i]) > (m_Image->GetLargestPossibleRegion().GetSize()[i]-1))
{
m_Size[i] = m_Image->GetLargestPossibleRegion().GetSize()[i]-1-properIndex[i];
}
}
MaskType::RegionType region;
region.SetIndex(properIndex);
m_Size[2] = 1;
region.SetSize(m_Size);
MaskType::Pointer mask = MaskType::New();
mask->SetDirection(m_Image->GetDirection());
mask->SetSpacing(m_Image->GetSpacing());
mask->SetOrigin(m_Image->GetOrigin());
mask->SetRegions(m_Image->GetLargestPossibleRegion());
mask->Allocate();
mask->FillBuffer(0);
itk::ImageRegionIterator<MaskType> imageIt(mask, region);
while(!imageIt.IsAtEnd())
{
imageIt.Set(m_MaskValue);
++imageIt;
}
return mask;
}