diff --git a/Modules/PhotoacousticsLib/src/Domain/Volume/mitkPAInSilicoTissueVolume.cpp b/Modules/PhotoacousticsLib/src/Domain/Volume/mitkPAInSilicoTissueVolume.cpp index c6ab1d8e5f..034e1aa585 100644 --- a/Modules/PhotoacousticsLib/src/Domain/Volume/mitkPAInSilicoTissueVolume.cpp +++ b/Modules/PhotoacousticsLib/src/Domain/Volume/mitkPAInSilicoTissueVolume.cpp @@ -1,321 +1,325 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include #include #include #include #include #include #include #include #include mitk::pa::InSilicoTissueVolume::InSilicoTissueVolume(TissueGeneratorParameters::Pointer parameters) { { unsigned int xDim = parameters->GetXDim(); unsigned int yDim = parameters->GetYDim(); unsigned int zDim = parameters->GetZDim(); m_TDim = 4; unsigned int size = xDim * yDim * zDim; double* absorptionArray = new double[size]; double* scatteringArray = new double[size]; double* anisotropyArray = new double[size]; double* segmentationArray = new double[size]; for (unsigned int index = 0; index < size; index++) { absorptionArray[index] = parameters->GetBackgroundAbsorption(); scatteringArray[index] = parameters->GetBackgroundScattering(); anisotropyArray[index] = parameters->GetBackgroundAnisotropy(); segmentationArray[index] = SegmentationType::BACKGROUND; } m_AbsorptionVolume = Volume::New(absorptionArray, xDim, yDim, zDim); m_ScatteringVolume = Volume::New(scatteringArray, xDim, yDim, zDim); m_AnisotropyVolume = Volume::New(anisotropyArray, xDim, yDim, zDim); m_SegmentationVolume = Volume::New(segmentationArray, xDim, yDim, zDim); } m_TissueParameters = parameters; m_PropertyList = mitk::PropertyList::New(); UpdatePropertyList(); } void mitk::pa::InSilicoTissueVolume::UpdatePropertyList() { //Set properties AddIntProperty("mcflag", m_TissueParameters->GetMCflag()); AddIntProperty("launchflag", m_TissueParameters->GetMCLaunchflag()); AddIntProperty("boundaryflag", m_TissueParameters->GetMCBoundaryflag()); AddDoubleProperty("launchPointX", m_TissueParameters->GetMCLaunchPointX()); AddDoubleProperty("launchPointY", m_TissueParameters->GetMCLaunchPointY()); AddDoubleProperty("launchPointZ", m_TissueParameters->GetMCLaunchPointZ()); AddDoubleProperty("focusPointX", m_TissueParameters->GetMCFocusPointX()); AddDoubleProperty("focusPointY", m_TissueParameters->GetMCFocusPointY()); AddDoubleProperty("focusPointZ", m_TissueParameters->GetMCFocusPointZ()); AddDoubleProperty("trajectoryVectorX", m_TissueParameters->GetMCTrajectoryVectorX()); AddDoubleProperty("trajectoryVectorY", m_TissueParameters->GetMCTrajectoryVectorY()); AddDoubleProperty("trajectoryVectorZ", m_TissueParameters->GetMCTrajectoryVectorZ()); AddDoubleProperty("radius", m_TissueParameters->GetMCRadius()); AddDoubleProperty("waist", m_TissueParameters->GetMCWaist()); if (m_TissueParameters->GetDoVolumeSmoothing()) AddDoubleProperty("sigma", m_TissueParameters->GetVolumeSmoothingSigma()); else AddDoubleProperty("sigma", 0); AddDoubleProperty("standardTissueAbsorption", m_TissueParameters->GetBackgroundAbsorption()); AddDoubleProperty("standardTissueScattering", m_TissueParameters->GetBackgroundScattering()); AddDoubleProperty("standardTissueAnisotropy", m_TissueParameters->GetBackgroundAnisotropy()); AddDoubleProperty("airThickness", m_TissueParameters->GetAirThicknessInMillimeters()); AddDoubleProperty("skinThickness", m_TissueParameters->GetSkinThicknessInMillimeters()); } mitk::pa::InSilicoTissueVolume::InSilicoTissueVolume( Volume::Pointer absorptionVolume, Volume::Pointer scatteringVolume, Volume::Pointer anisotropyVolume, Volume::Pointer segmentationVolume, TissueGeneratorParameters::Pointer tissueParameters, mitk::PropertyList::Pointer propertyList) { m_AbsorptionVolume = absorptionVolume; m_ScatteringVolume = scatteringVolume; m_AnisotropyVolume = anisotropyVolume; m_SegmentationVolume = segmentationVolume; m_TissueParameters = tissueParameters; m_PropertyList = propertyList; if (m_SegmentationVolume.IsNotNull()) m_TDim = 4; else m_TDim = 3; } void mitk::pa::InSilicoTissueVolume::AddDoubleProperty(std::string label, double value) { m_PropertyList->SetDoubleProperty(label.c_str(), value); mitk::CoreServices::GetPropertyPersistence()->AddInfo(mitk::PropertyPersistenceInfo::New(label)); } void mitk::pa::InSilicoTissueVolume::AddIntProperty(std::string label, int value) { m_PropertyList->SetIntProperty(label.c_str(), value); mitk::CoreServices::GetPropertyPersistence()->AddInfo(mitk::PropertyPersistenceInfo::New(label)); } mitk::Image::Pointer mitk::pa::InSilicoTissueVolume::ConvertToMitkImage() { mitk::Image::Pointer resultImage = mitk::Image::New(); mitk::PixelType TPixel = mitk::MakeScalarPixelType(); unsigned int* dimensionsOfImage = new unsigned int[4]; // Copy dimensions dimensionsOfImage[0] = m_TissueParameters->GetYDim(); dimensionsOfImage[1] = m_TissueParameters->GetXDim(); dimensionsOfImage[2] = m_TissueParameters->GetZDim(); dimensionsOfImage[3] = m_TDim; MITK_INFO << "Initializing image..."; resultImage->Initialize(TPixel, 4, dimensionsOfImage, 1); MITK_INFO << "Initializing image...[Done]"; mitk::Vector3D spacing; spacing.Fill(m_TissueParameters->GetVoxelSpacingInCentimeters()); resultImage->SetSpacing(spacing); MITK_INFO << "Set Import Volumes..."; //Copy memory, deal with cleaning up memory yourself! resultImage->SetImportVolume(m_AbsorptionVolume->GetData(), 0, 0, mitk::Image::CopyMemory); resultImage->SetImportVolume(m_ScatteringVolume->GetData(), 1, 0, mitk::Image::CopyMemory); resultImage->SetImportVolume(m_AnisotropyVolume->GetData(), 2, 0, mitk::Image::CopyMemory); resultImage->SetImportVolume(m_SegmentationVolume->GetData(), 3, 0, mitk::Image::CopyMemory); MITK_INFO << "Set Import Volumes...[Done]"; resultImage->SetPropertyList(m_PropertyList); return resultImage; } mitk::pa::InSilicoTissueVolume::Pointer mitk::pa::InSilicoTissueVolume::New( Volume::Pointer absorptionVolume, Volume::Pointer scatteringVolume, Volume::Pointer anisotropyVolume, Volume::Pointer segmentationVolume, TissueGeneratorParameters::Pointer tissueParameters, mitk::PropertyList::Pointer propertyList) { InSilicoTissueVolume::Pointer smartPtr = new InSilicoTissueVolume( absorptionVolume, scatteringVolume, anisotropyVolume, segmentationVolume, tissueParameters, propertyList); smartPtr->UnRegister(); return smartPtr; } mitk::pa::InSilicoTissueVolume::~InSilicoTissueVolume() { m_AbsorptionVolume = nullptr; m_ScatteringVolume = nullptr; m_AnisotropyVolume = nullptr; m_SegmentationVolume = nullptr; m_TissueParameters = nullptr; m_PropertyList = nullptr; } void mitk::pa::InSilicoTissueVolume::SetVolumeValues(int x, int y, int z, double absorption, double scattering, double anisotropy, SegmentationType segmentType) { if (IsInsideVolume(x, y, z)) { m_AbsorptionVolume->SetData(absorption, x, y, z); m_ScatteringVolume->SetData(scattering, x, y, z); m_AnisotropyVolume->SetData(anisotropy, x, y, z); m_SegmentationVolume->SetData(segmentType, x, y, z); } } bool mitk::pa::InSilicoTissueVolume::IsInsideVolume(int x, int y, int z) { return x >= 0 && x < m_TissueParameters->GetXDim() && y >= 0 && y < m_TissueParameters->GetYDim() && z >= 0 && z < m_TissueParameters->GetZDim(); } mitk::pa::Volume::Pointer mitk::pa::InSilicoTissueVolume::GetAbsorptionVolume() { return m_AbsorptionVolume; } mitk::pa::Volume::Pointer mitk::pa::InSilicoTissueVolume::GetSegmentationVolume() { return m_SegmentationVolume; } void mitk::pa::InSilicoTissueVolume::FinalizeVolume() { AddSkinAndAirLayers(); // If specified, randomize all tissue parameters if (m_TissueParameters->GetRandomizePhysicalProperties()) RandomizeTissueCoefficients(m_TissueParameters->GetUseRngSeed(), m_TissueParameters->GetRngSeed(), m_TissueParameters->GetRandomizePhysicalPropertiesPercentage()); } void mitk::pa::InSilicoTissueVolume::AddSkinAndAirLayers() { //Calculate the index location according to thickness in cm double airvoxel = (m_TissueParameters->GetAirThicknessInMillimeters() / m_TissueParameters->GetVoxelSpacingInCentimeters()) / 10; double skinvoxel = airvoxel + (m_TissueParameters->GetSkinThicknessInMillimeters() / m_TissueParameters->GetVoxelSpacingInCentimeters()) / 10; for (int y = 0; y < m_TissueParameters->GetYDim(); y++) { for (int x = 0; x < m_TissueParameters->GetXDim(); x++) { // Add air from index 0 to airvoxel if (m_TissueParameters->GetAirThicknessInMillimeters() > mitk::eps) { FillZLayer(x, y, 0, airvoxel, m_TissueParameters->GetAirAbsorption(), m_TissueParameters->GetAirScattering(), m_TissueParameters->GetAirAnisotropy(), SegmentationType::AIR); } //Add skin from index airvoxel to skinvoxel if (m_TissueParameters->GetSkinThicknessInMillimeters() > mitk::eps) { FillZLayer(x, y, airvoxel, skinvoxel, m_TissueParameters->GetSkinAbsorption(), m_TissueParameters->GetSkinScattering(), m_TissueParameters->GetSkinAnisotropy(), SegmentationType::SKIN); } } } } void mitk::pa::InSilicoTissueVolume::FillZLayer(int x, int y, double startIdx, double endIdx, double absorption, double scattering, double anisotropy, SegmentationType segmentationType) { for (int z = startIdx; z < endIdx; z++) + { if (IsInsideVolume(x, y, z)) + { if (endIdx - z < 1) { //Simulate partial volume effects m_AbsorptionVolume->SetData((1 - (endIdx - z)) * m_AbsorptionVolume->GetData(x, y, z) + (endIdx - z) * absorption, x, y, z); m_ScatteringVolume->SetData((1 - (endIdx - z)) * m_ScatteringVolume->GetData(x, y, z) + (endIdx - z) * scattering, x, y, z); m_AnisotropyVolume->SetData((1 - (endIdx - z)) * m_AnisotropyVolume->GetData(x, y, z) + (endIdx - z) * anisotropy, x, y, z); if (endIdx - z > 0.5) { //Only put the segmentation label if more than half of the partial volume is the wanted tissue type m_SegmentationVolume->SetData(segmentationType, x, y, z); } } else { m_AbsorptionVolume->SetData(absorption, x, y, z); m_ScatteringVolume->SetData(scattering, x, y, z); m_AnisotropyVolume->SetData(anisotropy, x, y, z); m_SegmentationVolume->SetData(segmentationType, x, y, z); } + } + } } void mitk::pa::InSilicoTissueVolume::RandomizeTissueCoefficients(long rngSeed, bool useRngSeed, double percentage) { std::mt19937 rng; std::random_device randomDevice; if (useRngSeed) { rng.seed(rngSeed); } else { if (randomDevice.entropy() > 0.1) { rng.seed(randomDevice()); } else { rng.seed(std::chrono::duration_cast(std::chrono::high_resolution_clock::now().time_since_epoch()).count()); } } std::normal_distribution<> percentageDistribution(1, percentage / 100); for (int y = 0; y < m_TissueParameters->GetYDim(); y++) { for (int x = 0; x < m_TissueParameters->GetXDim(); x++) { for (int z = 0; z < m_TissueParameters->GetZDim(); z++) { m_AbsorptionVolume->SetData(m_AbsorptionVolume->GetData(x, y, z) * percentageDistribution(rng), x, y, z); m_ScatteringVolume->SetData(m_ScatteringVolume->GetData(x, y, z) * percentageDistribution(rng), x, y, z); } } } } mitk::pa::Volume::Pointer mitk::pa::InSilicoTissueVolume::GetScatteringVolume() { return m_ScatteringVolume; } mitk::pa::Volume::Pointer mitk::pa::InSilicoTissueVolume::GetAnisotropyVolume() { return m_AnisotropyVolume; } diff --git a/Modules/PhotoacousticsLib/src/IO/mitkPAIOUtil.cpp b/Modules/PhotoacousticsLib/src/IO/mitkPAIOUtil.cpp index 99e2260545..6f0b374dfa 100644 --- a/Modules/PhotoacousticsLib/src/IO/mitkPAIOUtil.cpp +++ b/Modules/PhotoacousticsLib/src/IO/mitkPAIOUtil.cpp @@ -1,253 +1,253 @@ #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 +#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); if (inputImage.IsNull()) return nullptr; int xDim = inputImage->GetDimensions()[1]; int yDim = inputImage->GetDimensions()[0]; int zDim = inputImage->GetDimensions()[2]; mitk::ImageReadAccessor readAccess(inputImage, inputImage->GetVolumeData(0)); double* dataArray = new double[xDim*yDim*zDim]; const double* srcData = (const double*)readAccess.GetData(); memcpy(dataArray, srcData, xDim*yDim*zDim * sizeof(double)); auto returnImage = mitk::pa::Volume::New(dataArray, xDim, yDim, zDim); mitk::pa::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 = 2, numFiles = directoryHandler.GetNumberOfFiles(); fileIndex < numFiles; ++fileIndex) { std::string filename = folderPath + "/" + std::string(directoryHandler.GetFile(fileIndex)); if (itksys::SystemTools::FileIsDirectory(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..."; mitk::Image::Pointer inputImage = mitk::IOUtil::LoadImage(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)); double* 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); mitk::ImageReadAccessor readAccess1(inputImage, inputImage->GetVolumeData(1)); double* 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); mitk::ImageReadAccessor readAccess2(inputImage, inputImage->GetVolumeData(2)); double* 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); Volume::Pointer segmentationVolume; if (inputImage->GetDimension() == 4) { mitk::ImageReadAccessor readAccess3(inputImage, inputImage->GetVolumeData(3)); double* 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); } 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::ImageReadAccessor readAccess0(inputImage, inputImage->GetVolumeData(0)); unsigned int xDim = inputImage->GetDimensions()[1]; unsigned int yDim = inputImage->GetDimensions()[0]; unsigned int zDim = inputImage->GetDimensions()[2]; int size = xDim*yDim*zDim; double* fluenceArray = new double[size]; memcpy(fluenceArray, readAccess0.GetData(), size * sizeof(double)); 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 mitk::pa::FluenceYOffsetPair::New(mitk::pa::Volume::New(fluenceArray, xDim, yDim, zDim), yOffset); }