diff --git a/Modules/PhotoacousticsLib/src/IO/mitkPAIOUtil.cpp b/Modules/PhotoacousticsLib/src/IO/mitkPAIOUtil.cpp index da6c526443..06f2f84d8b 100644 --- a/Modules/PhotoacousticsLib/src/IO/mitkPAIOUtil.cpp +++ b/Modules/PhotoacousticsLib/src/IO/mitkPAIOUtil.cpp @@ -1,240 +1,240 @@ #include "mitkPAIOUtil.h" #include "mitkIOUtil.h" #include "mitkImageReadAccessor.h" #include #include #include #include "mitkPAComposedVolume.h" #include "mitkPASlicedVolumeGenerator.h" #include "mitkPANoiseGenerator.h" #include "mitkPAVolumeManipulator.h" #include #include #include static std::vector splitString(const std::string &s, const char* delim) { std::vector elems; std::stringstream ss(s); std::string item; while (std::getline(ss, item, *delim)) { int numb; std::stringstream(item) >> numb; elems.push_back(numb); } return elems; } bool mitk::pa::IOUtil::DoesFileHaveEnding(std::string const &fullString, std::string const &ending) { if (fullString.length() == 0 || ending.length() == 0 || fullString.length() < ending.length()) return false; return (0 == fullString.compare(fullString.length() - ending.length(), ending.length(), ending)); } mitk::pa::IOUtil::IOUtil() {} mitk::pa::IOUtil::~IOUtil() {} mitk::pa::Volume::Pointer mitk::pa::IOUtil::LoadNrrd(std::string filename, double blur) { if (filename.empty() || filename == "") return nullptr; - mitk::Image::Pointer inputImage = mitk::IOUtil::LoadImage(filename); + mitk::Image::Pointer inputImage = mitk::IOUtil::Load(filename); if (inputImage.IsNull()) return nullptr; auto returnImage = Volume::New(inputImage); VolumeManipulator::GaussianBlur3D(returnImage, blur); return returnImage; } std::map mitk::pa::IOUtil::LoadFluenceContributionMaps(std::string foldername, double blur, int* progress, bool doLog10) { std::map resultMap; itk::Directory::Pointer directoryHandler = itk::Directory::New(); directoryHandler->Load(foldername.c_str()); for (unsigned int fileIndex = 0, numFiles = directoryHandler->GetNumberOfFiles(); fileIndex < numFiles; ++fileIndex) { std::string filename = std::string(directoryHandler->GetFile(fileIndex)); if (itksys::SystemTools::FileIsDirectory(filename)) continue; if (!DoesFileHaveEnding(filename, ".nrrd")) continue; size_t s = filename.find("_p"); size_t e = filename.find("Fluence", s); std::string sub = filename.substr(s + 2, e - s - 2); std::vector coords = splitString(sub, ","); if (coords.size() != 3) { MITK_ERROR << "Some of the data to read was corrupted or did not match the " << "naming pattern *_pN,N,NFluence*.nrrd"; mitkThrow() << "Some of the data to read was corrupted or did not match the" << " naming pattern *_pN,N,NFluence*.nrrd"; } else { MITK_DEBUG << "Extracted coords: " << coords[0] << "|" << coords[1] << "|" << coords[2] << " from string " << sub; Volume::Pointer nrrdFile = LoadNrrd(foldername + filename, blur); if (doLog10) VolumeManipulator::Log10Image(nrrdFile); resultMap[Position{ coords[0], coords[2] }] = nrrdFile; *progress = *progress + 1; } } return resultMap; } int mitk::pa::IOUtil::GetNumberOfNrrdFilesInDirectory(std::string directory) { return GetListOfAllNrrdFilesInDirectory(directory).size(); } std::vector mitk::pa::IOUtil::GetListOfAllNrrdFilesInDirectory(std::string directory, bool keepFileFormat) { std::vector filenames; itk::Directory::Pointer directoryHandler = itk::Directory::New(); directoryHandler->Load(directory.c_str()); for (unsigned int fileIndex = 0, numFiles = directoryHandler->GetNumberOfFiles(); fileIndex < numFiles; ++fileIndex) { std::string filename = std::string(directoryHandler->GetFile(fileIndex)); if (itksys::SystemTools::FileIsDirectory(filename)) continue; if (!DoesFileHaveEnding(filename, ".nrrd")) continue; if (keepFileFormat) { filenames.push_back(filename); } else { filenames.push_back(filename.substr(0, filename.size() - 5)); } } return filenames; } std::vector mitk::pa::IOUtil::GetAllChildfoldersFromFolder(std::string folderPath) { std::vector returnVector; itksys::Directory directoryHandler; directoryHandler.Load(folderPath.c_str()); for (unsigned int fileIndex = 0, numFiles = directoryHandler.GetNumberOfFiles(); fileIndex < numFiles; ++fileIndex) { std::string foldername = std::string(directoryHandler.GetFile(fileIndex)); std::string filename = folderPath + "/" + foldername; if (itksys::SystemTools::FileIsDirectory(filename)) { if (foldername != std::string(".") && foldername != std::string("..")) { MITK_INFO << filename; returnVector.push_back(filename); } continue; } //If there is a nrrd file in the directory we assume that a bottom level directory was chosen. if (DoesFileHaveEnding(filename, ".nrrd")) { returnVector.clear(); returnVector.push_back(folderPath); return returnVector; } } return returnVector; } mitk::pa::InSilicoTissueVolume::Pointer mitk::pa::IOUtil::LoadInSilicoTissueVolumeFromNrrdFile(std::string nrrdFile) { MITK_INFO << "Initializing ComposedVolume by nrrd..."; auto inputImage = mitk::IOUtil::Load(nrrdFile); auto tissueParameters = TissueGeneratorParameters::New(); unsigned int xDim = inputImage->GetDimensions()[1]; unsigned int yDim = inputImage->GetDimensions()[0]; unsigned int zDim = inputImage->GetDimensions()[2]; tissueParameters->SetXDim(xDim); tissueParameters->SetYDim(yDim); tissueParameters->SetZDim(zDim); double xSpacing = inputImage->GetGeometry(0)->GetSpacing()[1]; double ySpacing = inputImage->GetGeometry(0)->GetSpacing()[0]; double zSpacing = inputImage->GetGeometry(0)->GetSpacing()[2]; if ((xSpacing - ySpacing) > mitk::eps || (xSpacing - zSpacing) > mitk::eps || (ySpacing - zSpacing) > mitk::eps) { throw mitk::Exception("Cannot handle unequal spacing."); } tissueParameters->SetVoxelSpacingInCentimeters(xSpacing); mitk::PropertyList::Pointer propertyList = inputImage->GetPropertyList(); mitk::ImageReadAccessor readAccess0(inputImage, inputImage->GetVolumeData(0)); auto* m_AbsorptionArray = new double[xDim*yDim*zDim]; memcpy(m_AbsorptionArray, readAccess0.GetData(), xDim*yDim*zDim * sizeof(double)); auto absorptionVolume = Volume::New(m_AbsorptionArray, xDim, yDim, zDim, xSpacing); mitk::ImageReadAccessor readAccess1(inputImage, inputImage->GetVolumeData(1)); auto* m_ScatteringArray = new double[xDim*yDim*zDim]; memcpy(m_ScatteringArray, readAccess1.GetData(), xDim*yDim*zDim * sizeof(double)); auto scatteringVolume = Volume::New(m_ScatteringArray, xDim, yDim, zDim, xSpacing); mitk::ImageReadAccessor readAccess2(inputImage, inputImage->GetVolumeData(2)); auto* m_AnisotropyArray = new double[xDim*yDim*zDim]; memcpy(m_AnisotropyArray, readAccess2.GetData(), xDim*yDim*zDim * sizeof(double)); auto anisotropyVolume = Volume::New(m_AnisotropyArray, xDim, yDim, zDim, xSpacing); Volume::Pointer segmentationVolume; if (inputImage->GetDimension() == 4) { mitk::ImageReadAccessor readAccess3(inputImage, inputImage->GetVolumeData(3)); auto* m_SegmentationArray = new double[xDim*yDim*zDim]; memcpy(m_SegmentationArray, readAccess3.GetData(), xDim*yDim*zDim * sizeof(double)); segmentationVolume = Volume::New(m_SegmentationArray, xDim, yDim, zDim, xSpacing); } return mitk::pa::InSilicoTissueVolume::New(absorptionVolume, scatteringVolume, anisotropyVolume, segmentationVolume, tissueParameters, propertyList); } mitk::pa::FluenceYOffsetPair::Pointer mitk::pa::IOUtil::LoadFluenceSimulation(std::string fluenceSimulation) { MITK_INFO << "Adding slice..."; - mitk::Image::Pointer inputImage = mitk::IOUtil::LoadImage(fluenceSimulation); + mitk::Image::Pointer inputImage = mitk::IOUtil::Load(fluenceSimulation); auto yOffsetProperty = inputImage->GetProperty("y-offset"); if (yOffsetProperty.IsNull()) mitkThrow() << "No \"y-offset\" property found in fluence file!"; std::string yOff = yOffsetProperty->GetValueAsString(); MITK_INFO << "Reading y Offset: " << yOff; #ifdef __linux__ std::replace(yOff.begin(), yOff.end(), '.', ','); #endif // __linux__ double yOffset = std::stod(yOff); MITK_INFO << "Converted offset " << yOffset; return FluenceYOffsetPair::New(Volume::New(inputImage), yOffset); }