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; }