int main()
{
FloatVectorImageType::Pointer image = FloatVectorImageType::New();
Testing::GetBlankImage(image.GetPointer(), 4);
Mask::Pointer mask = Mask::New();
Testing::GetFullyValidMask(mask.GetPointer());
UnsignedCharScalarImageType::Pointer manualPriorityImage = UnsignedCharScalarImageType::New();
Testing::GetBlankImage(manualPriorityImage.GetPointer());
unsigned int patchRadius = 5;
typedef PriorityConfidence ConfidencePriorityType;
ConfidencePriorityType priorityConfidence(mask, patchRadius);
PriorityManual<itk::Index<2>, UnsignedCharScalarImageType, ConfidencePriorityType>
priority(manualPriorityImage, &priorityConfidence);
itk::Index<2> filledPixel = {{0,0}};
priority.Update(filledPixel);
priority.SetManualPriorityImage(manualPriorityImage);
itk::Index<2> queryPixel = {{0,0}};
priority.ComputePriority(queryPixel);
return EXIT_SUCCESS;
}
void TestExtractChannels()
{
typedef itk::VectorImage<float, 2> VectorImageType;
VectorImageType::Pointer image = VectorImageType::New();
itk::Index<2> corner = {{0,0}};
itk::Size<2> size = {{100,100}};
itk::ImageRegion<2> region(corner, size);
image->SetRegions(region);
image->SetNumberOfComponentsPerPixel(3);
image->Allocate();
// Extract the first two channels
std::vector<unsigned int> channels;
channels.push_back(0);
channels.push_back(1);
typedef itk::VectorImage<float, 2> FloatScalarImageType;
FloatScalarImageType::Pointer floatScalarImage = FloatScalarImageType::New();
ITKHelpers::ExtractChannels(image.GetPointer(), channels, floatScalarImage.GetPointer());
typedef itk::VectorImage<unsigned char, 2> UnsignedCharScalarImageType;
UnsignedCharScalarImageType::Pointer unsignedCharScalarImage = UnsignedCharScalarImageType::New();
ITKHelpers::ExtractChannels(image.GetPointer(), channels, unsignedCharScalarImage.GetPointer());
}
int main(int argc, char*argv[])
{
Mask::Pointer mask = Mask::New();
CreateMask(mask);
OutputHelpers::WriteImage(mask.GetPointer(), "mask.png");
UnsignedCharScalarImageType::Pointer image = UnsignedCharScalarImageType::New();
CreateImage(image);
OutputHelpers::WriteImage(image.GetPointer(), "image.png");
FloatScalarImageType::Pointer output = FloatScalarImageType::New();
MaskOperations::MaskedLaplacian(image.GetPointer(), mask.GetPointer(), output.GetPointer());
OutputHelpers::WriteImage(output.GetPointer(), "laplacian.mha");
return EXIT_SUCCESS;
}
void TestExtractChannel()
{
typedef itk::VectorImage<float, 2> VectorImageType;
VectorImageType::Pointer image = VectorImageType::New();
itk::Index<2> corner = {{0,0}};
itk::Size<2> size = {{100,100}};
itk::ImageRegion<2> region(corner, size);
image->SetRegions(region);
image->SetNumberOfComponentsPerPixel(2);
image->Allocate();
typedef itk::Image<float, 2> FloatScalarImageType;
FloatScalarImageType::Pointer floatScalarImage = FloatScalarImageType::New();
ITKHelpers::ExtractChannel(image.GetPointer(), 0, floatScalarImage.GetPointer());
typedef itk::Image<unsigned char, 2> UnsignedCharScalarImageType;
UnsignedCharScalarImageType::Pointer unsignedCharScalarImage = UnsignedCharScalarImageType::New();
ITKHelpers::ExtractChannel(image.GetPointer(), 0, unsignedCharScalarImage.GetPointer());
}
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();
}
bool TestExtractChannel()
{
// VectorImage
{
typedef itk::VectorImage<float, 2> VectorImageType;
VectorImageType::Pointer image = VectorImageType::New();
itk::Index<2> corner = {{0,0}};
itk::Size<2> size = {{100,100}};
itk::ImageRegion<2> region(corner, size);
image->SetRegions(region);
image->SetNumberOfComponentsPerPixel(2);
image->Allocate();
typedef itk::Image<float, 2> FloatScalarImageType;
FloatScalarImageType::Pointer floatScalarImage = FloatScalarImageType::New();
ITKHelpers::ExtractChannel(image.GetPointer(), 0, floatScalarImage.GetPointer());
typedef itk::Image<unsigned char, 2> UnsignedCharScalarImageType;
UnsignedCharScalarImageType::Pointer unsignedCharScalarImage = UnsignedCharScalarImageType::New();
ITKHelpers::ExtractChannel(image.GetPointer(), 0, unsignedCharScalarImage.GetPointer());
}
// VectorImage different output type
{
typedef itk::VectorImage<float, 2> VectorImageType;
VectorImageType::Pointer image = VectorImageType::New();
itk::Index<2> corner = {{0,0}};
itk::Size<2> size = {{100,100}};
itk::ImageRegion<2> region(corner, size);
image->SetRegions(region);
image->SetNumberOfComponentsPerPixel(2);
image->Allocate();
typedef itk::Image<unsigned char, 2> UnsignedCharScalarImageType;
UnsignedCharScalarImageType::Pointer unsignedCharScalarImage = UnsignedCharScalarImageType::New();
ITKHelpers::ExtractChannel(image.GetPointer(), 0, unsignedCharScalarImage.GetPointer());
}
// Scalar Image
{
typedef itk::Image<float, 2> VectorImageType;
VectorImageType::Pointer image = VectorImageType::New();
itk::Index<2> corner = {{0,0}};
itk::Size<2> size = {{100,100}};
itk::ImageRegion<2> region(corner, size);
image->SetRegions(region);
image->Allocate();
typedef itk::Image<float, 2> FloatScalarImageType;
FloatScalarImageType::Pointer floatScalarImage = FloatScalarImageType::New();
ITKHelpers::ExtractChannel(image.GetPointer(), 0, floatScalarImage.GetPointer());
typedef itk::Image<unsigned char, 2> UnsignedCharScalarImageType;
UnsignedCharScalarImageType::Pointer unsignedCharScalarImage = UnsignedCharScalarImageType::New();
ITKHelpers::ExtractChannel(image.GetPointer(), 0, unsignedCharScalarImage.GetPointer());
}
// Image<CovariantVector>
{
typedef itk::Image<itk::CovariantVector<float, 3>, 2> VectorImageType;
VectorImageType::Pointer image = VectorImageType::New();
itk::Index<2> corner = {{0,0}};
itk::Size<2> size = {{100,100}};
itk::ImageRegion<2> region(corner, size);
image->SetRegions(region);
image->Allocate();
typedef itk::Image<float, 2> FloatScalarImageType;
FloatScalarImageType::Pointer floatScalarImage = FloatScalarImageType::New();
ITKHelpers::ExtractChannel(image.GetPointer(), 0, floatScalarImage.GetPointer());
}
// Image<Vector>
{
typedef itk::Image<itk::Vector<float, 3>, 2> VectorImageType;
VectorImageType::Pointer image = VectorImageType::New();
itk::Index<2> corner = {{0,0}};
itk::Size<2> size = {{100,100}};
itk::ImageRegion<2> region(corner, size);
image->SetRegions(region);
image->Allocate();
typedef itk::Image<float, 2> FloatScalarImageType;
FloatScalarImageType::Pointer floatScalarImage = FloatScalarImageType::New();
ITKHelpers::ExtractChannel(image.GetPointer(), 0, floatScalarImage.GetPointer());
}
return true;
}