DPH::ImageType::Pointer GetBlurredVectorImage( DPH::ImageType::Pointer vectorImage, double sigma)
{
typedef itk::DiscreteGaussianImageFilter< itk::Image<DPH::DiffusionPixelType, 3 >, itk::Image<DPH::DiffusionPixelType, 3 > > GaussianFilterType;
typedef itk::VectorIndexSelectionCastImageFilter< DPH::ImageType, itk::Image<DPH::DiffusionPixelType, 3 > > IndexSelectionType;
IndexSelectionType::Pointer indexSelectionFilter = IndexSelectionType::New();
indexSelectionFilter->SetInput( vectorImage );
typedef itk::ComposeImageFilter< itk::Image<DPH::DiffusionPixelType, 3>, DPH::ImageType > ComposeFilterType;
ComposeFilterType::Pointer vec_composer = ComposeFilterType::New();
for( unsigned int i=0; i<vectorImage->GetVectorLength(); ++i)
{
GaussianFilterType::Pointer gaussian_filter = GaussianFilterType::New();
indexSelectionFilter->SetIndex( i );
gaussian_filter->SetInput( indexSelectionFilter->GetOutput() );
gaussian_filter->SetVariance( sigma );
vec_composer->SetInput(i, gaussian_filter->GetOutput() );
gaussian_filter->Update();
}
try
{
vec_composer->Update();
}
catch(const itk::ExceptionObject &e)
{
mitkThrow() << "[VectorImage.GaussianSmoothing] !! Failed with ITK Exception: " << e.what();
}
DPH::ImageType::Pointer smoothed_vector = vec_composer->GetOutput();
/*
itk::ImageFileWriter< DPH::ImageType >::Pointer writer =
itk::ImageFileWriter< DPH::ImageType >::New();
writer->SetInput( smoothed_vector );
writer->SetFileName( "/tmp/itk_smoothed_vector.nrrd");
writer->Update();*/
return smoothed_vector;
}
void Difference::ComputeMinAndMaxInAllChannels()
{
std::cout << "ComputeMinAndMaxInAllChannels()" << std::endl;
this->MinimumOfChannels.SetSize(this->Image->GetNumberOfComponentsPerPixel());
this->MaximumOfChannels.SetSize(this->Image->GetNumberOfComponentsPerPixel());
for(unsigned int i = 0; i < this->Image->GetNumberOfComponentsPerPixel(); ++i)
{
typedef itk::VectorIndexSelectionCastImageFilter<ImageType, FloatScalarImageType> IndexSelectionType;
IndexSelectionType::Pointer indexSelectionFilter = IndexSelectionType::New();
indexSelectionFilter->SetIndex(i);
indexSelectionFilter->SetInput(this->Image);
indexSelectionFilter->Update();
typedef itk::MinimumMaximumImageCalculator <FloatScalarImageType> ImageCalculatorFilterType;
ImageCalculatorFilterType::Pointer imageCalculatorFilter = ImageCalculatorFilterType::New();
imageCalculatorFilter->SetImage(indexSelectionFilter->GetOutput());
imageCalculatorFilter->Compute();
this->MinimumOfChannels[i] = imageCalculatorFilter->GetMinimum();
this->MaximumOfChannels[i] = imageCalculatorFilter->GetMaximum();
}
}
bool AppITKImage::LoadAndValidate(const std::string& imagePath)
{
typedef itk::ImageFileReader<AppImageITKType> ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(imagePath);
reader->Update();
if(!m_image)
{
m_image = AppImageITKType::New();
}
// Deep copy
m_image->SetRegions(reader->GetOutput()->GetLargestPossibleRegion());
m_image->SetNumberOfComponentsPerPixel(LfnIc::Image::Pixel::NUM_CHANNELS);
m_image->Allocate();
itk::ImageRegionConstIterator<AppImageITKType> inputIterator(reader->GetOutput(), reader->GetOutput()->GetLargestPossibleRegion());
itk::ImageRegionIterator<AppImageITKType> outputIterator(m_image, m_image->GetLargestPossibleRegion());
while(!inputIterator.IsAtEnd())
{
outputIterator.Set(inputIterator.Get());
++inputIterator;
++outputIterator;
}
#if USE_CHANNEL_WEIGHTING
// Setup channel weights - Uniform weighting - set the weight of each channel so it has the perceived range of 255
// If a channel already has the range 255, the weight is set to 1. If a channel has a range smaller
// than 255, its weight will be > 1. If a channel has a weight larger than 255, its weight will be set to < 1.
// A weight should never be negative. There is no magic to scaling to 255, it is just that usually there will be some
// RGB type channels so 255 should make several of the weights close to 1.
std::cout << "Weights: ";
for (int c = 0; c < LfnIc::Image::Pixel::NUM_CHANNELS; c++)
{
typedef itk::Image<LfnIc::Image::Pixel::ChannelType, 2> ScalarImageType;
typedef itk::VectorIndexSelectionCastImageFilter<AppImageITKType, ScalarImageType> IndexSelectionType;
IndexSelectionType::Pointer indexSelectionFilter = IndexSelectionType::New();
indexSelectionFilter->SetIndex(c);
indexSelectionFilter->SetInput(m_image);
indexSelectionFilter->Update();
typedef itk::MinimumMaximumImageCalculator <ScalarImageType> ImageCalculatorFilterType;
ImageCalculatorFilterType::Pointer imageCalculatorFilter = ImageCalculatorFilterType::New();
imageCalculatorFilter->SetImage(indexSelectionFilter->GetOutput());
imageCalculatorFilter->Compute();
// If there is no variation in a channel (take an image with only red (255,0,0) and blue (0,0,255) pixels for example),
// then computing the weight doesn't make sense (and causes a divide by zero).
if( (imageCalculatorFilter->GetMaximum() - imageCalculatorFilter->GetMinimum()) <= 0)
{
m_channelWeights[c] = 1.0f;
}
else
{
m_channelWeights[c] = 255.0f / (imageCalculatorFilter->GetMaximum() - imageCalculatorFilter->GetMinimum());
}
std::cout << m_channelWeights[c] << " ";
}
std::cout << std::endl;
// Now that the weights have been calculated, apply them directly to the image data.
LfnIc::Image::Pixel* pixelPtr = AppITKImage::GetData();
for (int i = 0, n = GetWidth() * GetHeight(); i < n; ++i, ++pixelPtr)
{
LfnIc::Image::Pixel& pixel = *pixelPtr;
for (int c = 0; c < LfnIc::Image::Pixel::NUM_CHANNELS; ++c)
{
pixel.channel[c] *= m_channelWeights[c];
}
}
#endif // USE_CHANNEL_WEIGHTING
return true;
}
void LidarSegmentationWidget::GenerateNeighborSinks()
{
Mask::Pointer sourcesImage = Mask::New();
sourcesImage->SetRegions(this->ImageRegion);
ITKHelpers::IndicesToBinaryImage(this->Sources, sourcesImage);
ITKHelpers::WriteImage(sourcesImage.GetPointer(), "sourcesImage.png");
// Dilate the mask
std::cout << "Dilating mask..." << std::endl;
typedef itk::BinaryBallStructuringElement<Mask::PixelType, 2> StructuringElementType;
StructuringElementType structuringElement;
structuringElement.SetRadius(1);
structuringElement.CreateStructuringElement();
typedef itk::BinaryDilateImageFilter<Mask, Mask, StructuringElementType> BinaryDilateImageFilterType;
BinaryDilateImageFilterType::Pointer dilateFilter = BinaryDilateImageFilterType::New();
dilateFilter->SetInput(sourcesImage);
dilateFilter->SetKernel(structuringElement);
dilateFilter->Update();
// Binary XOR the images to get the difference image
//std::cout << "XORing masks..." << std::endl;
typedef itk::XorImageFilter<Mask> XorImageFilterType;
XorImageFilterType::Pointer xorFilter = XorImageFilterType::New();
xorFilter->SetInput1(dilateFilter->GetOutput());
xorFilter->SetInput2(sourcesImage);
xorFilter->Update();
ITKHelpers::WriteImage(xorFilter->GetOutput(), "boundaryOfSegmentation.png");
// Iterate over the border pixels. If the closest pixel in the original segmentation has
// a depth greater than a threshold, mark it as a new sink. Else, do not.
std::cout << "Determining which boundary pixels should be declared background..." << std::endl;
//std::cout << "There should be " << Helpers::CountNonZeroPixels(xorFilter->GetOutput())
// << " considered." << std::endl;
typedef std::vector<itk::Index<2> > VectorOfPixelsType;
VectorOfPixelsType newSinks;
typedef itk::VectorIndexSelectionCastImageFilter<ImageType, FloatScalarImageType> IndexSelectionType;
IndexSelectionType::Pointer indexSelectionFilter = IndexSelectionType::New();
indexSelectionFilter->SetIndex(3);
indexSelectionFilter->SetInput(this->Image);
indexSelectionFilter->Update();
FloatScalarImageType::Pointer depthImage = indexSelectionFilter->GetOutput();
//float sameObjectThreshold = 0.1f;
VectorOfPixelsType consideredPixels;
itk::ImageRegionIterator<Mask> imageIterator(xorFilter->GetOutput(),
xorFilter->GetOutput()->GetLargestPossibleRegion());
while(!imageIterator.IsAtEnd())
{
if(imageIterator.Get()) // If the current pixel is in question
{
consideredPixels.push_back(imageIterator.GetIndex());
}
++imageIterator;
}
std::cout << "There are " << consideredPixels.size() << " potential new sink pixels." << std::endl;
for(VectorOfPixelsType::const_iterator iter = consideredPixels.begin(); iter != consideredPixels.end(); ++iter)
{
//std::cout << "Considering pixel " << consideredCounter << " (index "
// << imageIterator.GetIndex() << ")" << std::endl;
ImageType::PixelType currentPixel = this->Image->GetPixel(*iter);
unsigned int radius = this->txtBackgroundCheckRadius->text().toUInt();
ImageType::RegionType desiredRegion = ITKHelpers::GetRegionInRadiusAroundPixel(*iter, radius);
//std::cout << "desiredRegion: " << desiredRegion << std::endl;
itk::ImageRegionIterator<Mask> sourcesImageIterator(sourcesImage, desiredRegion);
std::vector<float> nonForegroundDepths;
std::vector<float> foregroundDepths;
while(!sourcesImageIterator.IsAtEnd())
{
if(sourcesImageIterator.Get())
{
foregroundDepths.push_back(depthImage->GetPixel(sourcesImageIterator.GetIndex()));
}
else
{
nonForegroundDepths.push_back(depthImage->GetPixel(sourcesImageIterator.GetIndex()));
}
++sourcesImageIterator;
}
if(nonForegroundDepths.size() < 1)
{
}
float nonForegroundMedian = Helpers::VectorMedian(nonForegroundDepths);
float foregroundMedian = Helpers::VectorMedian(foregroundDepths);
float difference = fabs(foregroundMedian - nonForegroundMedian);
if(difference > this->txtBackgroundThreshold->text().toFloat())
{
//std::cout << "Difference was " << difference << " so this is a sink pixel." << std::endl;
newSinks.push_back(*iter);
}
else
{
//std::cout << "Difference was " << difference << " so this is NOT a sink pixel." << std::endl;
}
} // end loop over considered pixels
unsigned char blue[3] = {0, 0, 255};
// ImageType::PixelType blue(3);
// blue[0] = 0;
// blue[1] = 0;
// blue[2] = 255;
ITKVTKHelpers::SetPixels(this->SourceSinkImageData.GetPointer(), consideredPixels, blue);
this->SourceSinkImageData->Modified();
this->Refresh();
// Save the new sink pixels for inspection
UnsignedCharScalarImageType::Pointer newSinksImage = UnsignedCharScalarImageType::New();
newSinksImage->SetRegions(this->Image->GetLargestPossibleRegion());
newSinksImage->Allocate();
ITKHelpers::IndicesToBinaryImage(newSinks, newSinksImage);
ITKHelpers::WriteImage(newSinksImage.GetPointer(), "newSinks.png");
//std::cout << "Out of " << consideredCounter << " pixels considered, "
// << backgroundCounter << " were declared background." << std::endl;
// Set the new sinks
std::cout << "Setting " << newSinks.size() << " new sinks." << std::endl;
// Modify the list of sinks so it can be retrieved by the MainWindow after the segmentation is finished
this->Sinks.insert(this->Sinks.end(), newSinks.begin(), newSinks.end());
UpdateSelections();
}
