void WriteImagePixelsToRGBSpace(const FloatVectorImageType::Pointer image, const std::string& outputFileName)
{
std::cout << "WriteImagePixelsToRGBSpace()" << std::endl;
vtkSmartPointer<vtkPoints> points = vtkSmartPointer<vtkPoints>::New();
vtkSmartPointer<vtkUnsignedCharArray> colors = vtkSmartPointer<vtkUnsignedCharArray>::New();
colors->SetName("Colors");
colors->SetNumberOfComponents(3);
itk::ImageRegionConstIterator<FloatVectorImageType> imageIterator(image, image->GetLargestPossibleRegion());
while(!imageIterator.IsAtEnd())
{
FloatVectorImageType::PixelType pixel = imageIterator.Get();
points->InsertNextPoint(pixel[0], pixel[1], pixel[2]);
// TODO: Narrowing conversion warning
//unsigned char color[3] = {pixel[0], pixel[1], pixel[2]};
unsigned char color[3]; // TODO: Narrowing conversion warning
colors->InsertNextTupleValue(color);
++imageIterator;
}
vtkSmartPointer<vtkPolyData> polyData = vtkSmartPointer<vtkPolyData>::New();
polyData->SetPoints(points);
polyData->GetPointData()->SetScalars(colors);
vtkSmartPointer<vtkVertexGlyphFilter> glyphFilter = vtkSmartPointer<vtkVertexGlyphFilter>::New();
glyphFilter->SetInputData(polyData);
glyphFilter->Update();
vtkSmartPointer<vtkXMLPolyDataWriter> writer = vtkSmartPointer<vtkXMLPolyDataWriter>::New();
writer->SetInputConnection(glyphFilter->GetOutputPort());
writer->SetFileName(outputFileName.c_str());
writer->Write();
}
void WriteClusteredPixelsInRGBSpace(const FloatVectorImageType::Pointer image, const unsigned int numberOfClusters, const std::string& outputFileName)
{
std::cout << "WriteClusteredPixelsInRGBSpace()" << std::endl;
ClusterColorsAdaptive clusterColors;
clusterColors.SetNumberOfColors(numberOfClusters);
clusterColors.ConstructFromImage(image);
vtkSmartPointer<vtkPoints> points = vtkSmartPointer<vtkPoints>::New();
vtkSmartPointer<vtkUnsignedCharArray> colorsVTK = vtkSmartPointer<vtkUnsignedCharArray>::New();
colorsVTK->SetName("Colors");
colorsVTK->SetNumberOfComponents(3);
vtkSmartPointer<vtkUnsignedIntArray> ids = vtkSmartPointer<vtkUnsignedIntArray>::New();
ids->SetName("Ids");
ids->SetNumberOfComponents(1);
ColorMeasurementVectorType queryPoint;
std::vector<ColorMeasurementVectorType> colors = clusterColors.GetColors();
itk::ImageRegionConstIterator<FloatVectorImageType> imageIterator(image, image->GetLargestPossibleRegion());
while(!imageIterator.IsAtEnd())
{
FloatVectorImageType::PixelType pixel = imageIterator.Get();
queryPoint[0] = pixel[0];
queryPoint[1] = pixel[1];
queryPoint[2] = pixel[2];
ClusterColors::TreeType::InstanceIdentifierVectorType neighbors;
clusterColors.GetKDTree()->Search( queryPoint, 1u, neighbors );
points->InsertNextPoint(pixel[0], pixel[1], pixel[2]);
// TODO: Narrowing conversion warning
//unsigned char color[3] = {colors[neighbors[0]][0], colors[neighbors[0]][1], colors[neighbors[0]][2]};
unsigned char color[3]; // TODO: placeholder so it will compile
colorsVTK->InsertNextTupleValue(color);
ids->InsertNextValue(neighbors[0]);
++imageIterator;
}
vtkSmartPointer<vtkPolyData> polyData = vtkSmartPointer<vtkPolyData>::New();
polyData->SetPoints(points);
polyData->GetPointData()->SetScalars(colorsVTK);
polyData->GetPointData()->AddArray(ids);
vtkSmartPointer<vtkVertexGlyphFilter> glyphFilter = vtkSmartPointer<vtkVertexGlyphFilter>::New();
glyphFilter->SetInputData(polyData);
glyphFilter->Update();
vtkSmartPointer<vtkXMLPolyDataWriter> writer = vtkSmartPointer<vtkXMLPolyDataWriter>::New();
writer->SetInputConnection(glyphFilter->GetOutputPort());
writer->SetFileName(outputFileName.c_str());
writer->Write();
}
// Convert a vector ITK image to a VTK image for display
void ITKImagetoVTKRGBImage(FloatVectorImageType::Pointer image, vtkImageData* outputImage)
{
// This function assumes an ND (with N>3) image has the first 3 channels as RGB and extra information in the remaining channels.
//std::cout << "ITKImagetoVTKRGBImage()" << std::endl;
if(image->GetNumberOfComponentsPerPixel() < 3)
{
std::stringstream ss;
ss << "The input image has " << image->GetNumberOfComponentsPerPixel() << " components, but at least 3 are required.";
throw std::runtime_error(ss.str());
}
// Setup and allocate the image data
outputImage->SetNumberOfScalarComponents(3);
outputImage->SetScalarTypeToUnsignedChar();
outputImage->SetDimensions(image->GetLargestPossibleRegion().GetSize()[0],
image->GetLargestPossibleRegion().GetSize()[1],
1);
outputImage->AllocateScalars();
// Copy all of the input image pixels to the output image
itk::ImageRegionConstIteratorWithIndex<FloatVectorImageType> imageIterator(image,image->GetLargestPossibleRegion());
imageIterator.GoToBegin();
while(!imageIterator.IsAtEnd())
{
unsigned char* pixel = static_cast<unsigned char*>(outputImage->GetScalarPointer(imageIterator.GetIndex()[0],
imageIterator.GetIndex()[1],0));
for(unsigned int component = 0; component < 3; component++)
{
pixel[component] = static_cast<unsigned char>(imageIterator.Get()[component]);
}
++imageIterator;
}
}
// Convert a vector ITK image to a VTK image for display
void ITKImagetoVTKMagnitudeImage(FloatVectorImageType::Pointer image, vtkImageData* outputImage)
{
std::cout << "ITKImagetoVTKMagnitudeImage()" << std::endl;
// Compute the magnitude of the ITK image
typedef itk::VectorMagnitudeImageFilter<
FloatVectorImageType, FloatScalarImageType > VectorMagnitudeFilterType;
// Create and setup a magnitude filter
VectorMagnitudeFilterType::Pointer magnitudeFilter = VectorMagnitudeFilterType::New();
magnitudeFilter->SetInput( image );
magnitudeFilter->Update();
// Rescale and cast for display
typedef itk::RescaleIntensityImageFilter<
FloatScalarImageType, UnsignedCharScalarImageType > RescaleFilterType;
RescaleFilterType::Pointer rescaleFilter = RescaleFilterType::New();
rescaleFilter->SetOutputMinimum(0);
rescaleFilter->SetOutputMaximum(255);
rescaleFilter->SetInput( magnitudeFilter->GetOutput() );
rescaleFilter->Update();
// Setup and allocate the VTK image
outputImage->SetNumberOfScalarComponents(1);
outputImage->SetScalarTypeToUnsignedChar();
outputImage->SetDimensions(image->GetLargestPossibleRegion().GetSize()[0],
image->GetLargestPossibleRegion().GetSize()[1],
1);
outputImage->AllocateScalars();
// Copy all of the scaled magnitudes to the output image
itk::ImageRegionConstIteratorWithIndex<UnsignedCharScalarImageType> imageIterator(rescaleFilter->GetOutput(), rescaleFilter->GetOutput()->GetLargestPossibleRegion());
imageIterator.GoToBegin();
while(!imageIterator.IsAtEnd())
{
unsigned char* pixel = static_cast<unsigned char*>(outputImage->GetScalarPointer(imageIterator.GetIndex()[0],
imageIterator.GetIndex()[1],0));
pixel[0] = imageIterator.Get();
++imageIterator;
}
}
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;
}
void PartialPatchVectorComparison()
{
std::cout << "PartialPatchVectorComparison()" << std::endl;
const unsigned int dimension = 3;
FloatVectorImageType::Pointer vectorImage = FloatVectorImageType::New();
Testing::GetBlankImage<FloatVectorImageType>(vectorImage, dimension);
// Make the left half of the image (0,0,0) and the right half (5,6,7)
itk::ImageRegionIterator<FloatVectorImageType> imageIterator(vectorImage, vectorImage->GetLargestPossibleRegion());
itk::VariableLengthVector<float> leftHalfPixel;
leftHalfPixel.SetSize(dimension);
leftHalfPixel.Fill(0);
itk::VariableLengthVector<float> rightHalfPixel;
rightHalfPixel.SetSize(dimension);
rightHalfPixel[0] = 5;
rightHalfPixel[1] = 6;
rightHalfPixel[2] = 7;
while(!imageIterator.IsAtEnd())
{
if(imageIterator.GetIndex()[0] < static_cast<int>(vectorImage->GetLargestPossibleRegion().GetSize()[0]/2))
{
imageIterator.Set(leftHalfPixel);
}
else
{
imageIterator.Set(rightHalfPixel);
}
++imageIterator;
}
itk::Size<2> patchSize;
patchSize.Fill(10);
// Full patches differ
std::cout << "Full patch different test." << std::endl;
{
itk::Index<2> sourceCorner;
sourceCorner.Fill(0);
itk::ImageRegion<2> sourceRegion(sourceCorner, patchSize);
ImagePatchPixelDescriptor<FloatVectorImageType> sourcePatch(vectorImage, sourceRegion, true);
itk::Index<2> targetCorner;
targetCorner.Fill(vectorImage->GetLargestPossibleRegion().GetSize()[0]/2 + 4); // No magic about 4, just want a patch on the right side of the image
itk::ImageRegion<2> targetRegion(targetCorner, patchSize);
ImagePatchPixelDescriptor<FloatVectorImageType> targetPatch(vectorImage, targetRegion, true);
PatchPair<FloatVectorImageType> patchPair(&sourcePatch, targetPatch);
PatchDifferencePixelWiseSum<FloatVectorImageType, PixelDifference> vector_patchDifferencePixelWiseSum;
vector_patchDifferencePixelWiseSum.SetImage(vectorImage);
float difference = vector_patchDifferencePixelWiseSum.Difference(patchPair);
float correctDifference = targetRegion.GetNumberOfPixels() * 18; // 18 = 5+6+7, the sum of the elements of 'rightHalfPixel'
if(difference != correctDifference)
{
std::stringstream ss;
ss << "Difference " << difference << " does not match correctDifference " << correctDifference;
throw std::runtime_error(ss.str());
}
}
// Full patches identical
std::cout << "Identical patch test." << std::endl;
{
itk::Index<2> sourceCorner;
sourceCorner.Fill(5);
itk::ImageRegion<2> sourceRegion(sourceCorner, patchSize);
ImagePatchPixelDescriptor<FloatVectorImageType> sourcePatch(vectorImage, sourceRegion, true);
itk::Index<2> targetCorner;
targetCorner.Fill(5);
itk::ImageRegion<2> targetRegion(targetCorner, patchSize);
ImagePatchPixelDescriptor<FloatVectorImageType> targetPatch(vectorImage, targetRegion, true);
PatchPair<FloatVectorImageType> patchPair(&sourcePatch, targetPatch);
PatchDifferencePixelWiseSum<FloatVectorImageType, PixelDifference> vector_patchDifferencePixelWiseSum;
vector_patchDifferencePixelWiseSum.SetImage(vectorImage);
float difference = vector_patchDifferencePixelWiseSum.Difference(patchPair);
float correctDifference = 0;
if(difference != correctDifference)
{
std::stringstream ss;
ss << "Difference " << difference << " does not match correctDifference " << correctDifference;
throw std::runtime_error(ss.str());
}
}
}
int main(int argc, char *argv[])
{
unsigned int t = time(NULL);
srand(t);
itk::Size<2> size;
size.Fill(10);
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] = RandomFloat();
pixel[1] = RandomFloat();
pixel[2] = RandomFloat();
imageIterator.Set(pixel);
++imageIterator;
}
}
// 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();
// Write the mask
itk::ImageFileWriter<Mask>::Pointer maskWriter =
itk::ImageFileWriter<Mask>::New();
maskWriter->SetFileName("mask.png");
maskWriter->SetInput(mask);
maskWriter->Update();
unsigned int patchRadius = 1;
// Create source patches
itk::ImageRegionConstIterator<FloatVectorImageType> imageIterator(image, image->GetLargestPossibleRegion());
std::vector<itk::ImageRegion<2> > sourcePatches;
while(!imageIterator.IsAtEnd())
{
itk::Index<2> currentPixel = imageIterator.GetIndex();
itk::ImageRegion<2> region = GetRegionInRadiusAroundPixel(currentPixel, patchRadius);
if(image->GetLargestPossibleRegion().IsInside(region))
{
sourcePatches.push_back(region);
}
++imageIterator;
}
itk::Size<2> targetSize;
targetSize.Fill(patchRadius * 2 + 1);
itk::Index<2> targetIndex;
targetIndex.Fill(3);
itk::ImageRegion<2> targetRegion(targetIndex, targetSize);
SelfPatchCompare patchCompare;
patchCompare.SetImage(image);
patchCompare.SetMask(mask);
patchCompare.SetSourceRegions(sourcePatches);
patchCompare.SetTargetRegion(targetRegion);
patchCompare.ComputeOffsets();
//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;
}