static void CreateMask(Mask::Pointer mask)
{
itk::Size<2> size;
size.Fill(20);
itk::Index<2> start;
start.Fill(0);
itk::ImageRegion<2> region(start,size);
mask->SetRegions(region);
mask->Allocate();
mask->FillBuffer(mask->GetValidValue());
itk::ImageRegionIterator<Mask> iterator(mask, mask->GetLargestPossibleRegion());
while(!iterator.IsAtEnd())
{
if(iterator.GetIndex()[0] > 5 && iterator.GetIndex()[0] < 15 &&
iterator.GetIndex()[1] > 5 && iterator.GetIndex()[1] < 15)
{
mask->SetPixel(iterator.GetIndex(), mask->GetHoleValue());
}
++iterator;
}
}
void Mask::CreateBoundaryImageInRegion(const itk::ImageRegion<2>& region, BoundaryImageType* const boundaryImage,
const HoleMaskPixelTypeEnum& whichSideOfBoundary) const
{
// Create a binary image of the mask
unsigned char holeColor = 255;
unsigned char validColor = 0;
UnsignedCharImageType::Pointer fullBinaryImage = UnsignedCharImageType::New();
CreateBinaryImageInRegion(region, fullBinaryImage, holeColor, validColor);
// Extract the relevant region from the binary image
UnsignedCharImageType::Pointer binaryImage = UnsignedCharImageType::New();
binaryImage->SetRegions(region);
binaryImage->Allocate();
CopyRegion(fullBinaryImage.GetPointer(), binaryImage.GetPointer(), region, region);
// Extract the relevant region from the mask
Mask::Pointer extractedRegionMask = Mask::New();
extractedRegionMask->SetRegions(region);
extractedRegionMask->Allocate();
CopyRegion(this, extractedRegionMask.GetPointer(), region, region);
// Since the hole is white (we have specified this at the beginning of this function),
// we want the foreground value of the contour filter to be black.
// This means that the boundary will be detected in the black pixel region,
// which is on the outside edge of the hole like we want. However,
// The BinaryContourImageFilter will change all non-boundary pixels to the background color,
// so the resulting output will be inverted - the boundary pixels will be black and the
// non-boundary pixels will be white.
// Find the boundary
typedef itk::BinaryContourImageFilter<UnsignedCharImageType, UnsignedCharImageType> binaryContourImageFilterType;
binaryContourImageFilterType::Pointer binaryContourFilter = binaryContourImageFilterType::New();
binaryContourFilter->SetInput(binaryImage);
binaryContourFilter->SetFullyConnected(true);
if(whichSideOfBoundary == HoleMaskPixelTypeEnum::VALID)
{
// we want the boundary pixels to be in the valid region.
binaryContourFilter->SetForegroundValue(validColor);
binaryContourFilter->SetBackgroundValue(holeColor);
}
else if(whichSideOfBoundary == HoleMaskPixelTypeEnum::HOLE)
{
// we want the boundary pixels to be in the hole region.
binaryContourFilter->SetForegroundValue(holeColor);
binaryContourFilter->SetBackgroundValue(validColor);
}
else
{
throw std::runtime_error("An invalid side of the boundary was requested.");
}
binaryContourFilter->Update();
DeepCopy(binaryContourFilter->GetOutput(), boundaryImage);
}
int main(int argc, char*argv[])
{
if(argc < 4)
{
std::cerr << "Required arguments: image mask output" << std::endl;
return EXIT_FAILURE;
}
std::string imageFilename = argv[1];
std::string maskFilename = argv[2];
std::string outputFilename = argv[3];
std::cout << "imageFilename: " << imageFilename << std::endl;
std::cout << "maskFilename: " << maskFilename << std::endl;
std::cout << "outputFilename: " << outputFilename << std::endl;
typedef itk::ImageFileReader<ImageType> ImageReaderType;
ImageReaderType::Pointer imageReader = ImageReaderType::New();
imageReader->SetFileName(imageFilename);
imageReader->Update();
Mask::Pointer sourceMask = Mask::New();
sourceMask->Read(maskFilename);
Mask::Pointer targetMask = Mask::New();
targetMask->SetRegions(sourceMask->GetLargestPossibleRegion());
targetMask->Allocate();
ITKHelpers::SetImageToConstant(targetMask.GetPointer(), HoleMaskPixelTypeEnum::VALID);
typedef SSD<ImageType> DistanceFunctorType;
DistanceFunctorType* patchDistanceFunctor = new DistanceFunctorType;
patchDistanceFunctor->SetImage(imageReader->GetOutput());
typedef Propagator<DistanceFunctorType> PropagatorType;
PropagatorType* propagationFunctor = new PropagatorType;
typedef RandomSearch<ImageType, DistanceFunctorType> RandomSearchType;
RandomSearchType* randomSearchFunctor = new RandomSearchType;
typedef PatchMatch<ImageType, PropagatorType, RandomSearchType> PatchMatchType;
PatchMatchType patchMatch;
patchMatch.SetImage(imageReader->GetOutput());
patchMatch.SetPatchRadius(3);
patchMatch.SetPropagationFunctor(propagationFunctor);
patchMatch.SetRandomSearchFunctor(randomSearchFunctor);
patchMatch.Compute();
NNFieldType::Pointer output = patchMatch.GetNNField();
PatchMatchHelpers::WriteNNField(output.GetPointer(), "nnfield.mha");
return EXIT_SUCCESS;
}
void Vector()
{
typedef itk::Image<unsigned char, 2 > ChannelType;
const unsigned int NumberOfChannels = 3;
typedef itk::Image<itk::CovariantVector<unsigned char, NumberOfChannels>, 2 > ImageType;
ImageType::Pointer image = ImageType::New();
itk::Index<2> corner = {{0,0}};
itk::Size<2> imageSize = {{500,500}};
itk::ImageRegion<2> fullRegion(corner, imageSize);
image->SetRegions(fullRegion);
image->Allocate();
for(unsigned int i = 0; i < NumberOfChannels; ++i)
{
itk::RandomImageSource<ChannelType>::Pointer randomImageSource =
itk::RandomImageSource<ChannelType>::New();
randomImageSource->SetNumberOfThreads(1); // to produce non-random results
randomImageSource->SetSize(imageSize);
randomImageSource->Update();
ITKHelpers::SetChannel(image.GetPointer(), i, randomImageSource->GetOutput());
}
itk::Size<2> patchSize = {{21,21}};
// There is nothing magic about these particular patches
itk::Index<2> targetCorner = {{319, 302}};
itk::ImageRegion<2> targetRegion(targetCorner, patchSize);
itk::Index<2> sourceCorner = {{341, 300}};
itk::ImageRegion<2> sourceRegion(sourceCorner, patchSize);
Mask::Pointer mask = Mask::New();
mask->SetRegions(fullRegion);
mask->Allocate();
ITKHelpers::SetImageToConstant(mask.GetPointer(), mask->GetValidValue());
typedef SumSquaredPixelDifference<ImageType::PixelType> PixelDifferenceType;
typedef ImagePatchPixelDescriptor<ImageType> PatchType;
ImagePatchDifference<PatchType, PixelDifferenceType> imagePatchDifference;
PatchType targetPatch(image, mask, targetRegion);
PatchType sourcePatch(image, mask, sourceRegion);
float difference = imagePatchDifference(targetPatch, sourcePatch);
std::cout << "GMHDifference: " << difference << std::endl;
}
void Scalar()
{
typedef itk::Image< unsigned char, 2 > ImageType;
itk::Size<2> imageSize = {{500,500}};
itk::RandomImageSource<ImageType>::Pointer randomImageSource =
itk::RandomImageSource<ImageType>::New();
randomImageSource->SetNumberOfThreads(1); // to produce non-random results
randomImageSource->SetSize(imageSize);
randomImageSource->Update();
ImageType* image = randomImageSource->GetOutput();
itk::Size<2> patchSize = {{21,21}};
// There is nothing magic about these particular patches
itk::Index<2> targetCorner = {{319, 302}};
itk::ImageRegion<2> targetRegion(targetCorner, patchSize);
itk::Index<2> sourceCorner = {{341, 300}};
itk::ImageRegion<2> sourceRegion(sourceCorner, patchSize);
Mask::Pointer mask = Mask::New();
mask->SetRegions(randomImageSource->GetOutput()->GetLargestPossibleRegion());
mask->Allocate();
ITKHelpers::SetImageToConstant(mask.GetPointer(), mask->GetValidValue());
typedef SumSquaredPixelDifference<ImageType::PixelType> PixelDifferenceType;
typedef ImagePatchPixelDescriptor<ImageType> PatchType;
ImagePatchDifference<PatchType, PixelDifferenceType> imagePatchDifference;
PatchType targetPatch(image, mask, targetRegion);
PatchType sourcePatch(image, mask, sourceRegion);
float difference = imagePatchDifference(targetPatch, sourcePatch);
std::cout << "Difference: " << difference << std::endl;
}
void LidarSegmentationWidget::on_btnErodeSources_clicked()
{
Mask::Pointer sourcesImage = Mask::New();
sourcesImage->SetRegions(this->ImageRegion);
ITKHelpers::IndicesToBinaryImage(this->Sources, sourcesImage);
typedef itk::BinaryBallStructuringElement<Mask::PixelType,2> StructuringElementType;
StructuringElementType structuringElementBig;
structuringElementBig.SetRadius(3);
structuringElementBig.CreateStructuringElement();
typedef itk::BinaryErodeImageFilter<Mask, Mask, StructuringElementType> BinaryErodeImageFilterType;
BinaryErodeImageFilterType::Pointer erodeFilter = BinaryErodeImageFilterType::New();
erodeFilter->SetInput(sourcesImage);
erodeFilter->SetKernel(structuringElementBig);
erodeFilter->Update();
//this->Sources.clear();
this->Sources = ITKHelpers::GetNonZeroPixels(erodeFilter->GetOutput());
UpdateSelections();
}
void TestComputeMaskedImage1DHistogram()
{
// // Single channel
// {
// typedef itk::Image<unsigned char, 2> ImageType;
// ImageType::Pointer image = ImageType::New();
// ImageType::IndexType corner = {{0,0}};
// ImageType::SizeType size = {{100,100}};
// ImageType::RegionType region(corner, size);
// image->SetRegions(region);
// image->Allocate();
// itk::ImageRegionIterator<ImageType> imageIterator(image,region);
// while(!imageIterator.IsAtEnd())
// {
// if(imageIterator.GetIndex()[0] < 70)
// {
// imageIterator.Set(255);
// }
// else
// {
// imageIterator.Set(0);
// }
// ++imageIterator;
// }
// ImageType::PixelType rangeMin = 0;
// ImageType::PixelType rangeMax = 255;
// unsigned int numberOfBins = 10;
// typedef int BinValueType;
// typedef Histogram<BinValueType>::HistogramType HistogramType;
// HistogramType histogram = Histogram<BinValueType>::ComputeImageHistogram1D(image.GetPointer(),
// image->GetLargestPossibleRegion(),
// numberOfBins, rangeMin, rangeMax);
// Histogram<BinValueType>::OutputHistogram(histogram);
// std::cout << std::endl;
// }
// Multi channel VectorImage
{
typedef itk::VectorImage<unsigned char, 2> ImageType;
ImageType::Pointer image = ImageType::New();
ImageType::IndexType corner = {{0,0}};
ImageType::SizeType size = {{100,100}};
ImageType::RegionType region(corner, size);
image->SetRegions(region);
image->SetNumberOfComponentsPerPixel(3);
image->Allocate();
Mask::Pointer mask = Mask::New();
mask->SetRegions(region);
mask->Allocate();
itk::ImageRegionIterator<ImageType> imageIterator(image,region);
while(!imageIterator.IsAtEnd())
{
ImageType::PixelType pixel(image->GetNumberOfComponentsPerPixel());
if(imageIterator.GetIndex()[0] < 70)
{
for(unsigned int i = 0; i < pixel.GetSize(); ++i)
{
pixel[i] = 255;
}
}
else
{
for(unsigned int i = 0; i < pixel.GetSize(); ++i)
{
pixel[i] = 0;
}
}
imageIterator.Set(pixel);
++imageIterator;
}
// TypeTraits<ImageType::PixelType>::ComponentType rangeMin = 0;
// TypeTraits<ImageType::PixelType>::ComponentType rangeMax = 255;
ImageType::PixelType rangeMins;
rangeMins.SetSize(image->GetNumberOfComponentsPerPixel());
rangeMins.Fill(0);
ImageType::PixelType rangeMaxs;
rangeMaxs.SetSize(image->GetNumberOfComponentsPerPixel());
rangeMaxs.Fill(255);
unsigned int numberOfBinsPerComponent = 10;
typedef int BinValueType;
itk::ImageRegion<2> imageRegion = image->GetLargestPossibleRegion();
itk::ImageRegion<2> maskRegion = image->GetLargestPossibleRegion();
typedef MaskedHistogramGenerator<BinValueType> HistogramGeneratorType;
typedef HistogramGeneratorType::HistogramType HistogramType;
bool allowOutside = false;
HistogramType histogram =
HistogramGeneratorType::ComputeMaskedImage1DHistogram(image.GetPointer(), imageRegion,
mask.GetPointer(), maskRegion,
numberOfBinsPerComponent, rangeMins, rangeMaxs,
allowOutside, HoleMaskPixelTypeEnum::VALID);
histogram.Print();
std::cout << std::endl;
}
// // Multi channel Image<CovariantVector>
// {
// typedef itk::Image<itk::CovariantVector<unsigned char, 3>, 2> ImageType;
// ImageType::Pointer image = ImageType::New();
// ImageType::IndexType corner = {{0,0}};
// ImageType::SizeType size = {{100,100}};
// ImageType::RegionType region(corner, size);
// image->SetRegions(region);
// image->Allocate();
// itk::ImageRegionIterator<ImageType> imageIterator(image,region);
// while(!imageIterator.IsAtEnd())
// {
// ImageType::PixelType pixel(image->GetNumberOfComponentsPerPixel());
// if(imageIterator.GetIndex()[0] < 70)
// {
// for(unsigned int i = 0; i < pixel.GetNumberOfComponents(); ++i)
// {
// pixel[i] = 255;
// }
// }
// else
// {
// for(unsigned int i = 0; i < pixel.GetNumberOfComponents(); ++i)
// {
// pixel[i] = 0;
// }
// }
// imageIterator.Set(pixel);
// ++imageIterator;
// }
// TypeTraits<ImageType::PixelType>::ComponentType rangeMin = 0;
// TypeTraits<ImageType::PixelType>::ComponentType rangeMax = 255;
// unsigned int numberOfBinsPerComponent = 10;
// typedef int BinValueType;
// Histogram<BinValueType>::HistogramType histogram = Histogram<BinValueType>::ComputeImageHistogram1D(image.GetPointer(),
// image->GetLargestPossibleRegion(),
// numberOfBinsPerComponent, rangeMin, rangeMax);
// Histogram<BinValueType>::OutputHistogram(histogram);
// std::cout << std::endl;
// }
}
int main(int argc, char* argv[])
{
// Verify arguments
if(argc < 5)
{
std::cout << "Usage: PatchImage repeatX repeatY outputImage" << std::endl;
return EXIT_FAILURE;
}
// Parse arguments
std::string patchImageFilename = argv[1];
std::stringstream ssRepeatX;
ssRepeatX << argv[2];
unsigned int repeatX = 0;
ssRepeatX >> repeatX;
std::stringstream ssRepeatY;
ssRepeatY << argv[3];
unsigned int repeatY = 0;
ssRepeatY >> repeatY;
std::string outputFilename = argv[4];
// Output arguments
std::cout << "Patch image: " << patchImageFilename << std::endl
<< "Repeat X: " << repeatX << std::endl
<< "Repeat Y: " << repeatY << std::endl
<< "Output image: " << outputFilename << std::endl;
//typedef itk::VectorImage<float, 2> ImageType;
typedef itk::Image<itk::CovariantVector<float, 3>, 2> ImageType;
// Read patch image
typedef itk::ImageFileReader<ImageType> ImageReaderType;
ImageReaderType::Pointer patchImageReader = ImageReaderType::New();
patchImageReader->SetFileName(patchImageFilename);
patchImageReader->Update();
Mask::Pointer mask = Mask::New();
itk::ImageRegion<2> patchRegion = patchImageReader->GetOutput()->GetLargestPossibleRegion();
mask->SetRegions(patchRegion);
mask->Allocate();
itk::Index<2> holeCorner = {{1,1}};
itk::Size<2> holeSize = patchRegion.GetSize();
holeSize[0] -= 2; // Missing one row on the top, and one row on the bottom
holeSize[1] -= 2; // Missing one column on the left, and one column on the right
itk::ImageRegion<2> holeRegion(holeCorner, holeSize);
mask->SetValid(patchRegion);
mask->SetHole(holeRegion);
ImageType::Pointer seamlessPatch = ImageType::New();
ITKHelpers::DeepCopy(patchImageReader->GetOutput(), seamlessPatch.GetPointer());
// Enforce periodic boundary conditions
// Top and bottom
for(int i = 0; i < static_cast<int>(patchRegion.GetSize()[1]); ++i)
{
itk::Index<2> topPixelIndex = {{0, i}};
itk::Index<2> bottomPixelIndex = {{static_cast<int>(patchRegion.GetSize()[0])-1, i}};
ImageType::PixelType topPixelValue = seamlessPatch->GetPixel(topPixelIndex);
ImageType::PixelType bottomPixelValue = seamlessPatch->GetPixel(bottomPixelIndex);
ImageType::PixelType averageValue = (topPixelValue + bottomPixelValue)/2.0f;
seamlessPatch->SetPixel(topPixelIndex, averageValue);
seamlessPatch->SetPixel(bottomPixelIndex, averageValue);
}
// Left and right
for(int i = 0; i < static_cast<int>(patchRegion.GetSize()[0]); ++i)
{
itk::Index<2> leftPixelIndex = {{i, 0}};
itk::Index<2> rightPixelIndex = {{i, static_cast<int>(patchRegion.GetSize()[1])-1}};
ImageType::PixelType leftPixelValue = seamlessPatch->GetPixel(leftPixelIndex);
ImageType::PixelType rightPixelValue = seamlessPatch->GetPixel(rightPixelIndex);
ImageType::PixelType averageValue = (leftPixelValue + rightPixelValue)/2.0f;
seamlessPatch->SetPixel(leftPixelIndex, averageValue);
seamlessPatch->SetPixel(rightPixelIndex, averageValue);
}
typedef PoissonEditingParent::GuidanceFieldType GuidanceFieldType;
std::vector<GuidanceFieldType::Pointer> guidanceFields = PoissonEditingParent::ComputeGuidanceField(patchImageReader->GetOutput());
ImageType::Pointer output = ImageType::New();
FillImage(seamlessPatch.GetPointer(), mask.GetPointer(),
guidanceFields, output.GetPointer(),
patchRegion, seamlessPatch.GetPointer());
// Write output
ITKHelpers::WriteRGBImage(output.GetPointer(), outputFilename);
// Original tiled
ImageType::Pointer originalTiled = ImageType::New();
TilePatch(patchImageReader->GetOutput(), repeatX, repeatY, originalTiled.GetPointer());
ITKHelpers::WriteRGBImage(originalTiled.GetPointer(), "original_tiled.png");
// Seamless tiled
ImageType::Pointer seamlessTiled = ImageType::New();
TilePatch(output.GetPointer(), repeatX, repeatY, seamlessTiled.GetPointer());
ITKHelpers::WriteRGBImage(seamlessTiled.GetPointer(), "seamless_tiled.png");
return EXIT_SUCCESS;
}
int main(int, char*[])
{
// typedef itk::Image<itk::CovariantVector<int, 3>, 2> ImageType;
typedef itk::Image<itk::CovariantVector<unsigned char, 3>, 2> ImageType;
ImageType::PixelType red;
red.Fill(0);
red[0] = 255;
ImageType::PixelType black;
black.Fill(0);
ImageType::PixelType white;
white.Fill(255);
ImageType::PixelType green; // Note this is not 255 because then the magnitude of red and green would be the same,
// which makes debugging hard since the gradient of the magnitude image is used internally (in IntroducedEnergy).
green.Fill(0);
green[1] = 122;
ImageType::PixelType blue;
blue.Fill(0);
blue[2] = 255;
ImageType::Pointer image = ImageType::New();
itk::Index<2> imageCorner = {{0,0}};
itk::Size<2> imageSize = {{100,100}};
itk::ImageRegion<2> region(imageCorner,imageSize);
image->SetRegions(region);
image->Allocate();
Mask::Pointer mask = Mask::New();
mask->SetRegions(region);
mask->Allocate();
itk::ImageRegionIteratorWithIndex<Mask> initializeMaskIterator(mask, mask->GetLargestPossibleRegion());
while(!initializeMaskIterator.IsAtEnd())
{
if(initializeMaskIterator.GetIndex()[0] < 55)
{
initializeMaskIterator.Set(mask->GetHoleValue());
}
else
{
initializeMaskIterator.Set(mask->GetValidValue());
}
++initializeMaskIterator;
}
ITKHelpers::WriteImage(mask.GetPointer(), "mask.png");
// Create a red image
itk::ImageRegionIterator<ImageType> initializeIterator(image, image->GetLargestPossibleRegion());
while(!initializeIterator.IsAtEnd())
{
initializeIterator.Set(red);
++initializeIterator;
}
// Setup source and target patch
itk::Size<2> patchSize = {{10,10}};
itk::Index<2> sourceCorner = {{10,10}};
itk::ImageRegion<2> sourceRegion(sourceCorner, patchSize);
itk::Index<2> targetCorner = {{50,50}};
itk::ImageRegion<2> targetRegion(targetCorner, patchSize);
itk::Index<2> perfectSourceCorner = {{75,75}};
itk::ImageRegion<2> perfectSourceRegion(perfectSourceCorner, patchSize);
// Make the source patch green
itk::ImageRegionIterator<ImageType> sourceRegionIterator(image, sourceRegion);
while(!sourceRegionIterator.IsAtEnd())
{
sourceRegionIterator.Set(green);
++sourceRegionIterator;
}
ITKHelpers::WriteImage(image.GetPointer(), "image.png");
{
ImageType::Pointer regionHighlightImage = ImageType::New();
ITKHelpers::DeepCopy(image.GetPointer(), regionHighlightImage.GetPointer());
ITKHelpers::OutlineRegion(regionHighlightImage.GetPointer(), sourceRegion, white);
ITKHelpers::OutlineRegion(regionHighlightImage.GetPointer(), targetRegion, black);
ITKHelpers::OutlineRegion(regionHighlightImage.GetPointer(), perfectSourceRegion, blue);
ITKHelpers::WriteImage(regionHighlightImage.GetPointer(), "regions.png");
}
IntroducedEnergy<ImageType> introducedEnergy;
introducedEnergy.SetDebugImages(true);
// Bad match
{
std::cout << "Bad match:" << std::endl;
float patchBoundaryEnergy = introducedEnergy.ComputeIntroducedEnergyPatchBoundary(image, mask, sourceRegion, targetRegion);
std::cout << "patchBoundaryEnergy: " << patchBoundaryEnergy << std::endl;
float maskBoundaryEnergy = introducedEnergy.ComputeIntroducedEnergyMaskBoundary(image, mask, sourceRegion, targetRegion);
std::cout << "maskBoundaryEnergy: " << maskBoundaryEnergy << std::endl;
float totalEnergy = introducedEnergy.ComputeIntroducedEnergy(image, mask, sourceRegion, targetRegion);
std::cout << "totalEnergy: " << totalEnergy << std::endl;
}
// Perfect match
{
std::cout << "Perfect match:" << std::endl;
// IntroducedEnergy<ImageType> introducedEnergy;
typedef IntroducedEnergy<ImageType> IntroducedEnergyType;
float patchBoundaryEnergy = introducedEnergy.ComputeIntroducedEnergyPatchBoundary(image, mask, perfectSourceRegion, targetRegion);
std::cout << "patchBoundaryEnergy: " << patchBoundaryEnergy << std::endl;
float maskBoundaryEnergy = introducedEnergy.ComputeIntroducedEnergyMaskBoundary(image, mask, perfectSourceRegion, targetRegion);
std::cout << "maskBoundaryEnergy: " << maskBoundaryEnergy << std::endl;
float totalEnergy = introducedEnergy.ComputeIntroducedEnergy(image, mask, perfectSourceRegion, targetRegion);
std::cout << "totalEnergy: " << totalEnergy << std::endl;
}
return EXIT_SUCCESS;
}
int main(int argc, char *argv[])
{
unsigned int t = time(NULL);
srand(t);
itk::Size<2> size;
size.Fill(100);
itk::Index<2> index;
index.Fill(0);
itk::ImageRegion<2> region(index, size);
/*
// Generate a random image (this method doesn't work with VectorImage)
itk::RandomImageSource<FloatVectorImageType>::Pointer imageSource =
itk::RandomImageSource<FloatVectorImageType>::New();
imageSource->SetNumberOfThreads(1); // to produce non-random results
imageSource->SetSize(size);
imageSource->SetMin(0);
imageSource->SetMax(100);
imageSource->Update();
FloatVectorImageType::Pointer image = imageSource->GetOutput();
*/
// Generate a random image
FloatVectorImageType::Pointer image = FloatVectorImageType::New();
image->SetRegions(region);
image->SetNumberOfComponentsPerPixel(3);
image->Allocate();
{
itk::ImageRegionIterator<FloatVectorImageType> imageIterator(image, image->GetLargestPossibleRegion());
while(!imageIterator.IsAtEnd())
{
FloatVectorImageType::PixelType pixel;
pixel.SetSize(3);
pixel[0] = drand48();
pixel[1] = drand48();
pixel[2] = drand48();
imageIterator.Set(pixel);
++imageIterator;
}
}
// Generate a random membership image
IntImageType::Pointer membershipImage = IntImageType::New();
membershipImage->SetRegions(region);
membershipImage->Allocate();
membershipImage->FillBuffer(0);
{
itk::ImageRegionIterator<IntImageType> membershipImageIterator(membershipImage, membershipImage->GetLargestPossibleRegion());
while(!membershipImageIterator.IsAtEnd())
{
IntImageType::PixelType pixel;
pixel = rand() / 1000;
membershipImageIterator.Set(pixel);
++membershipImageIterator;
}
}
// Write the image
itk::ImageFileWriter<FloatVectorImageType>::Pointer imageWriter =
itk::ImageFileWriter<FloatVectorImageType>::New();
imageWriter->SetFileName("image.mha");
imageWriter->SetInput(image);
imageWriter->Update();
// // Generate a random mask
// itk::RandomImageSource<Mask>::Pointer maskSource = itk::RandomImageSource<Mask>::New();
// maskSource->SetNumberOfThreads(1); // to produce non-random results
// maskSource->SetSize(size);
// maskSource->SetMin(0);
// maskSource->SetMax(255);
// maskSource->Update();
//
// // Threshold the mask
// //typedef itk::ThresholdImageFilter <UnsignedCharImageType> ThresholdImageFilterType;
// typedef itk::BinaryThresholdImageFilter <Mask, Mask> ThresholdImageFilterType;
// ThresholdImageFilterType::Pointer thresholdFilter = ThresholdImageFilterType::New();
// thresholdFilter->SetInput(maskSource->GetOutput());
// thresholdFilter->SetLowerThreshold(0);
// thresholdFilter->SetUpperThreshold(122);
// thresholdFilter->SetOutsideValue(1);
// thresholdFilter->SetInsideValue(0);
// thresholdFilter->Update();
// Mask::Pointer mask = thresholdFilter->GetOutput();
std::cout << "Creating mask..." << std::endl;
Mask::Pointer mask = Mask::New();
mask->SetRegions(region);
mask->Allocate();
{
itk::ImageRegionIterator<Mask> maskIterator(mask, mask->GetLargestPossibleRegion());
while(!maskIterator.IsAtEnd())
{
int randomNumber = rand()%10;
//std::cout << "randomNumber: " << randomNumber << std::endl;
if(randomNumber > 5)
{
maskIterator.Set(mask->GetHoleValue());
}
else
{
maskIterator.Set(mask->GetValidValue());
}
++maskIterator;
}
}
std::cout << "Writing mask..." << std::endl;
// Write the mask
itk::ImageFileWriter<Mask>::Pointer maskWriter = itk::ImageFileWriter<Mask>::New();
maskWriter->SetFileName("mask.png");
maskWriter->SetInput(mask);
maskWriter->Update();
std::cout << "Creating source patches..." << std::endl;
unsigned int patchRadius = 10;
// Create source patches
itk::ImageRegionConstIterator<FloatVectorImageType> imageIterator(image, image->GetLargestPossibleRegion());
std::vector<Patch> sourcePatches;
while(!imageIterator.IsAtEnd())
{
itk::Index<2> currentPixel = imageIterator.GetIndex();
itk::ImageRegion<2> region = Helpers::GetRegionInRadiusAroundPixel(currentPixel, patchRadius);
if(image->GetLargestPossibleRegion().IsInside(region))
{
sourcePatches.push_back(Patch(region));
}
++imageIterator;
}
std::cout << "Source patches: " << sourcePatches.size() << std::endl;
itk::Size<2> targetSize;
targetSize.Fill(patchRadius * 2 + 1);
itk::Index<2> targetIndex;
targetIndex.Fill(3);
itk::ImageRegion<2> targetRegion(targetIndex, targetSize);
Patch targetPatch(targetRegion);
CandidatePairs pairs(targetPatch);
pairs.AddPairFromPatch(targetPatch);
itk::ImageRegion<2> adjacentRegion = targetRegion;
itk::Index<2> adjacentIndex;
adjacentIndex[0] = targetIndex[0] + 1;
adjacentIndex[1] = targetIndex[1] + 1;
adjacentRegion.SetIndex(adjacentIndex);
Patch adjacentPatch(adjacentRegion);
pairs.AddPairFromPatch(adjacentPatch);
//pairs.AddPairFromPatch(sourcePatches[0]);
SelfPatchCompare patchCompare;
patchCompare.SetPairs(&pairs);
patchCompare.SetImage(image);
patchCompare.SetMask(mask);
patchCompare.SetNumberOfComponentsPerPixel(3);
patchCompare.SetMembershipImage(membershipImage);
patchCompare.FunctionsToCompute.push_back(boost::bind(&SelfPatchCompare::SetPatchMembershipDifference,&patchCompare,_1));
patchCompare.ComputeAllSourceDifferences();
std::cout << "pairs: " << pairs.size() << std::endl;
for(unsigned int i = 0; i < pairs.size(); ++i)
{
std::cout << "MembershipDifference: " << pairs[i].DifferenceMap[PatchPair::MembershipDifference] << std::endl;
}
//unsigned int bestMatchSourcePatchId = patchCompare.FindBestPatch();
//std::cout << "bestMatchSourcePatchId: " << bestMatchSourcePatchId << std::endl;
/*
unsigned int patchId = 1;
float slowPatchDifference = patchCompare.SlowDifference(sourcePatches[patchId]);
std::cout << "slowPatchDifference: " << slowPatchDifference << std::endl;
float fastPatchDifference = patchCompare.PatchDifference(sourcePatches[patchId]);
std::cout << "fastPatchDifference: " << fastPatchDifference << std::endl;
unsigned int iterations = 1e6;
itk::TimeProbe slowTimer;
slowTimer.Start();
for(unsigned int i = 0; i < iterations; ++i)
{
float slowPatchDifference = patchCompare.SlowDifference(sourcePatches[patchId]);
}
slowTimer.Stop();
std::cout << "Slow Total: " << slowTimer.GetTotal() << std::endl;
itk::TimeProbe fastTimer;
fastTimer.Start();
for(unsigned int i = 0; i < iterations; ++i)
{
float fastPatchDifference = patchCompare.PatchDifference(sourcePatches[patchId]);
}
fastTimer.Stop();
std::cout << "Fast Total: " << fastTimer.GetTotal() << std::endl;*/
return EXIT_SUCCESS;
}
int main(int argc, char*argv[])
{
if(argc != 6)
{
std::cerr << "Required arguments: image output R G B" << std::endl;
return EXIT_FAILURE;
}
std::vector<int> values(3,0);
std::stringstream ss;
unsigned int counter = 0;
for(int i = 3; i < argc; ++i)
{
ss << argv[i] << " ";
counter++;
}
for(int i = 0; i < 3; ++i)
{
ss >> values[i];
}
// itk::RGBPixel<unsigned char> color;
// color.SetRed(values[0]);
// color.SetGreen(values[1]);
// color.SetBlue(values[2]);
Color color;
color.r = values[0];
color.g = values[1];
color.b = values[2];
std::string imageFilename = argv[1];
std::string outputMaskFilename = argv[2];
std::cout << "Reading image: " << imageFilename << std::endl;
std::cout << "outputMaskFilename: " << outputMaskFilename << std::endl;
std::cout << "Color: " << static_cast<int>(values[0]) << " " << static_cast<int>(values[1]) << " " << static_cast<int>(values[2]) << std::endl;
//typedef itk::Image<float, 2> ImageType;
typedef itk::Image<itk::CovariantVector<unsigned char, 3>, 2> ImageType;
ImageType::PixelType pixelColor;
pixelColor[0] = color.r;
pixelColor[1] = color.g;
pixelColor[2] = color.b;
typedef itk::ImageFileReader<ImageType> ImageReaderType;
ImageReaderType::Pointer imageReader = ImageReaderType::New();
imageReader->SetFileName(imageFilename.c_str());
imageReader->Update();
Mask::Pointer mask = Mask::New();
mask->SetRegions(imageReader->GetOutput()->GetLargestPossibleRegion());
mask->Allocate();
mask->CreateFromImage(imageReader->GetOutput(), pixelColor);
OutputHelpers::WriteImage(mask.GetPointer(), outputMaskFilename);
return EXIT_SUCCESS;
}
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();
}
