static void ApplyTransforms(const mxArray *In, mxArray *Out) { double *Input = mxGetPr(In); double *Output = mxGetPr(Out); size_t nPixels = GetNumberOfPixels(In);; cmsDoTransform(hColorTransform, Input, Output, nPixels ); }
std::vector<cleaver::AbstractScalarField*> NRRDTools::loadNRRDFiles(std::vector<std::string> files, double sigma) { std::vector<cleaver::AbstractScalarField*> fields; size_t num = 0; for (auto file : files) { // read file using ITK if (file.find(".nrrd") != std::string::npos) { itk::NrrdImageIOFactory::RegisterOneFactory(); } else if (file.find(".mha") != std::string::npos) { itk::MetaImageIOFactory::RegisterOneFactory(); } ReaderType::Pointer reader = ReaderType::New(); reader->SetFileName(file); reader->Update(); //do some blurring GaussianBlurType::Pointer blur = GaussianBlurType::New(); blur->SetInput(reader->GetOutput()); blur->SetVariance(sigma * sigma); blur->Update(); ImageType::Pointer img = blur->GetOutput(); //convert the image to a cleaver "abstract field" auto region = img->GetLargestPossibleRegion(); auto numPixel = region.GetNumberOfPixels(); float *data = new float[numPixel]; auto x = region.GetSize()[0], y = region.GetSize()[1], z = region.GetSize()[2]; fields.push_back(new cleaver::FloatField(data, x, y, z)); auto beg = file.find_last_of("/") + 1; auto name = file.substr(beg, file.size() - beg); fields[num]->setName(name); itk::ImageRegionConstIterator<ImageType> imageIterator(img, region); size_t pixel = 0; while (!imageIterator.IsAtEnd()) { // Get the value of the current pixel float val = static_cast<float>(imageIterator.Get()); ((cleaver::FloatField*)fields[num])->data()[pixel++] = val; ++imageIterator; } ((cleaver::FloatField*)fields[num])->setScale(cleaver::vec3(1., 1., 1.)); num++; } return fields; }
std::vector<cleaver::AbstractScalarField*> NRRDTools::segmentationToIndicatorFunctions(std::string filename, double sigma) { // read file using ITK if (filename.find(".nrrd") != std::string::npos) { itk::NrrdImageIOFactory::RegisterOneFactory(); } else if (filename.find(".mha") != std::string::npos) { itk::MetaImageIOFactory::RegisterOneFactory(); } ReaderType::Pointer reader = ReaderType::New(); reader->SetFileName(filename); reader->Update(); ImageType::Pointer image = reader->GetOutput(); //determine the number of labels in the segmentations ImageCalculatorFilterType::Pointer imageCalculatorFilter = ImageCalculatorFilterType::New(); imageCalculatorFilter->SetImage(reader->GetOutput()); imageCalculatorFilter->Compute(); auto maxLabel = static_cast<size_t>(imageCalculatorFilter->GetMaximum()); auto minLabel = static_cast<size_t>(imageCalculatorFilter->GetMinimum()); std::vector<cleaver::AbstractScalarField*> fields; //extract images from each label for an indicator function for (size_t i = minLabel, num = 0; i <= maxLabel; i++, num++) { //pull out this label ThreshType::Pointer thresh = ThreshType::New(); thresh->SetInput(image); thresh->SetOutsideValue(0); thresh->ThresholdOutside(static_cast<double>(i) - 0.001, static_cast<double>(i) + 0.001); thresh->Update(); //change the values to be from 0 to 1 MultiplyImageFilterType::Pointer multiplyImageFilter = MultiplyImageFilterType::New(); multiplyImageFilter->SetInput(thresh->GetOutput()); multiplyImageFilter->SetConstant(1. / static_cast<double>(i)); multiplyImageFilter->Update(); //do some blurring GaussianBlurType::Pointer blur = GaussianBlurType::New(); blur->SetInput(multiplyImageFilter->GetOutput()); blur->SetVariance(sigma * sigma); blur->Update(); //find the average value between ImageCalculatorFilterType::Pointer calc = ImageCalculatorFilterType::New(); calc->SetImage(blur->GetOutput()); calc->Compute(); float mx = calc->GetMaximum(); float mn = calc->GetMinimum(); auto md = (mx + mn) / 2.f; //create a distance map with that minimum value as the levelset DMapType::Pointer dm = DMapType::New(); dm->SetInput(blur->GetOutput()); dm->SetInsideValue(md + 0.1f); dm->SetOutsideValue(md -0.1f); dm->Update(); //MultiplyImageFilterType::Pointer mult = // MultiplyImageFilterType::New(); //mult->SetInput(blur->GetOutput()); //mult->SetConstant(-20. / (mx - mn)); //mult->Update(); /*SubtractImageFilterType::Pointer subtractFilter = SubtractImageFilterType::New(); subtractFilter->SetInput1(mult->GetOutput()); subtractFilter->SetConstant2(1.); subtractFilter->Update();*/ //convert the image to a cleaver "abstract field" auto img = dm->GetOutput(); auto region = img->GetLargestPossibleRegion(); auto numPixel = region.GetNumberOfPixels(); float *data = new float[numPixel]; auto x = region.GetSize()[0], y = region.GetSize()[1], z = region.GetSize()[2]; fields.push_back(new cleaver::FloatField(data, x, y, z)); auto beg = filename.find_last_of("/") + 1; auto name = filename.substr(beg, filename.size() - beg); auto fin = name.find_last_of("."); name = name.substr(0, fin); std::stringstream ss; ss << name << i; fields[num]->setName(ss.str()); itk::ImageRegionConstIterator<ImageType> imageIterator(img, region); size_t pixel = 0; while (!imageIterator.IsAtEnd()) { // Get the value of the current pixel float val = static_cast<float>(imageIterator.Get()); ((cleaver::FloatField*)fields[num])->data()[pixel++] = -val; ++imageIterator; } auto spacing = img->GetSpacing(); ((cleaver::FloatField*)fields[num])->setScale( cleaver::vec3(spacing[0], spacing[1], spacing[2])); //NRRDTools::saveNRRDFile(fields[num], "a" + std::to_string(num)); } return fields; }