void Mask::FindBoundary(UnsignedCharScalarImageType* boundaryImage) const
{
// Compute the "outer" boundary of the region to fill. That is, we want the boundary pixels to be in the source region.
//HelpersOutput::WriteImageConditional<Mask>(this->CurrentMask, "Debug/FindBoundary.CurrentMask.mha", this->DebugImages);
//HelpersOutput::WriteImageConditional<Mask>(this->CurrentMask, "Debug/FindBoundary.CurrentMask.png", this->DebugImages);
// Create a binary image (throw away the "dont use" pixels)
Mask::Pointer holeOnly = Mask::New();
holeOnly->DeepCopyFrom(this);
itk::ImageRegionIterator<Mask> maskIterator(holeOnly, holeOnly->GetLargestPossibleRegion());
// This should result in a white hole on a black background
while(!maskIterator.IsAtEnd())
{
itk::Index<2> currentPixel = maskIterator.GetIndex();
if(!holeOnly->IsHole(currentPixel))
{
holeOnly->SetPixel(currentPixel, holeOnly->GetValidValue());
}
++maskIterator;
}
//HelpersOutput::WriteImageConditional<Mask>(holeOnly, "Debug/FindBoundary.HoleOnly.mha", this->DebugImages);
//HelpersOutput::WriteImageConditional<Mask>(holeOnly, "Debug/FindBoundary.HoleOnly.png", this->DebugImages);
// Since the hole is white, 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 <Mask, Mask> binaryContourImageFilterType;
binaryContourImageFilterType::Pointer binaryContourFilter = binaryContourImageFilterType::New();
binaryContourFilter->SetInput(holeOnly);
binaryContourFilter->SetFullyConnected(true);
binaryContourFilter->SetForegroundValue(holeOnly->GetValidValue());
binaryContourFilter->SetBackgroundValue(holeOnly->GetHoleValue());
binaryContourFilter->Update();
//HelpersOutput::WriteImageConditional<Mask>(binaryContourFilter->GetOutput(), "Debug/FindBoundary.Boundary.mha", this->DebugImages);
//HelpersOutput::WriteImageConditional<Mask>(binaryContourFilter->GetOutput(), "Debug/FindBoundary.Boundary.png", this->DebugImages);
// Since we want to interpret non-zero pixels as boundary pixels, we must invert the image.
typedef itk::InvertIntensityImageFilter <Mask> InvertIntensityImageFilterType;
InvertIntensityImageFilterType::Pointer invertIntensityFilter = InvertIntensityImageFilterType::New();
invertIntensityFilter->SetInput(binaryContourFilter->GetOutput());
invertIntensityFilter->SetMaximum(255);
invertIntensityFilter->Update();
//this->BoundaryImage = binaryContourFilter->GetOutput();
//this->BoundaryImage->Graft(binaryContourFilter->GetOutput());
ITKHelpers::DeepCopy<UnsignedCharScalarImageType>(invertIntensityFilter->GetOutput(), boundaryImage);
//HelpersOutput::WriteImageConditional<UnsignedCharScalarImageType>(this->BoundaryImage, "Debug/FindBoundary.BoundaryImage.mha", this->DebugImages);
}
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 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;
}
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;
}