diff --git a/Modules/PhotoacousticsLib/MitkSpectralUnmixing/SpectralUnmixingApp.cpp b/Modules/PhotoacousticsLib/MitkSpectralUnmixing/SpectralUnmixingApp.cpp index 275c11fd1d..51a6d1f9ad 100644 --- a/Modules/PhotoacousticsLib/MitkSpectralUnmixing/SpectralUnmixingApp.cpp +++ b/Modules/PhotoacousticsLib/MitkSpectralUnmixing/SpectralUnmixingApp.cpp @@ -1,229 +1,188 @@ /*=================================================================== 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 "mitkPASpectralUnmixingFilterBase.h" #include "mitkPALinearSpectralUnmixingFilter.h" #include "mitkPASpectralUnmixingSO2.h" #include "mitkPASpectralUnmixingFilterVigra.h" #include #include #include #include #include +struct InputParameters +{ + std::string inputPath; + std::string savePath; + +} + InputParameters parseInput(int argc, char* argv[]) { MITK_INFO << "Parsing arguments..."; mitkCommandLineParser parser; parser.setCategory("MITK-Photoacoustics"); parser.setTitle("Mitk Spectral Unmixing App"); parser.setDescription("Batch processing for spectral Unmixing."); parser.setContributor("Computer Assisted Medical Interventions, DKFZ"); parser.setArgumentPrefix("--", "-"); parser.beginGroup("Required parameters"); parser.addArgument( "savePath", "s", mitkCommandLineParser::InputDirectory, "Input save folder (directory)", "input save folder", us::Any(), false); parser.endGroup(); InputParameters input; std::map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size() == 0) exit(-1); - if (parsedArgs.count("empty-volume")) - { - input.empty = us::any_cast(parsedArgs["empty-volume"]); - } - else - { - input.empty = false; - } if (parsedArgs.count("savePath")) { input.saveFolderPath = us::any_cast(parsedArgs["savePath"]); } + else + { + mitkThrow() << "Error: No savePath"; + } + MITK_INFO << "Parsing arguments...[Done]"; return input; } mitk::pa::SpectralUnmixingFilterBase::Pointer GetFilterInstance(std::string algorithm) { mitk::pa::SpectralUnmixingFilterBase::Pointer spectralUnmixingFilter; if (algorithm == "QR") { spectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New(); dynamic_cast(spectralUnmixingFilter.GetPointer()) ->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::HOUSEHOLDERQR); } else if (algorithm == "SVD") { spectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New(); dynamic_cast(spectralUnmixingFilter.GetPointer()) ->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::JACOBISVD); } else if (algorithm == "LU") { spectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New(); dynamic_cast(spectralUnmixingFilter.GetPointer()) ->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::FULLPIVLU); } else if (algorithm == "NNLS") { spectralUnmixingFilter = mitk::pa::SpectralUnmixingFilterVigra::New(); dynamic_cast(spectralUnmixingFilter.GetPointer()) ->SetAlgorithm(mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::LARS); } else if (algorithm == "WLS") { spectralUnmixingFilter = mitk::pa::SpectralUnmixingFilterVigra::New(); dynamic_cast(spectralUnmixingFilter.GetPointer()) ->SetAlgorithm(mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::WEIGHTED); std::vector weigthVec = {39, 45, 47} for (int i; i < 3; ++i) { 3dynamic_cast(spectralUnmixingFilter.GetPointer()) ->AddWeight(weigthVec[i]); } } return spectralUnmixingFilter; } + int main(int argc, char * argv[]) { - std::vector algorithms = {'QR', 'LU', 'SVD', 'NNLS', 'WLS'}, + auto params = parseArguments(argc, argv); + auto inputPathname = params.inputPath); + auto outputPath = params.savePath); + std::vector stringvec + boost::filesystem::path p(inputPathname); + boost::filesystem::directory_iterator start(p); + boost::filesystem::directory_iterator end; + std::transform(start, end, std::back_inserter(stringvec), path_leaf_string()); + + std::vector algorithms = {'QR', 'LU', 'SVD', 'NNLS', 'WLS'}, - for (int i; i < 5; ++i) + for (unsigned int filename = 0; filename < numberOfInputs; ++filename) { - mitk::pa::LinearSpectralUnmixingFilter::Pointer m_SpectralUnmixingFilter; - m_SpectralUnmixingFilter = GetFilterInstance(algorithms[i]); + m_inputImage = mitk::IOUtil::Load(stringvec[filename]); + for (unsigned alg = 0; alg < 5; ++alg) + { + mitk::pa::LinearSpectralUnmixingFilter::Pointer m_SpectralUnmixingFilter; + m_SpectralUnmixingFilter = GetFilterInstance(algorithms[alg]); - m_SpectralUnmixingFilter->SetInput(inputImage); - m_SpectralUnmixingFilter->AddOutputs(2); - m_SpectralUnmixingFilter->Verbose(false); - m_SpectralUnmixingFilter->RelativeError(false); - m_SpectralUnmixingFilter->AddWavelength(757); - m_SpectralUnmixingFilter->AddWavelength(797); - m_SpectralUnmixingFilter->AddWavelength(847); - m_SpectralUnmixingFilter->AddChromophore(mitk::pa::PropertyCalculator::ChromophoreType::OXYGENATED); - m_SpectralUnmixingFilter->AddChromophore(mitk::pa::PropertyCalculator::ChromophoreType::DEOXYGENATED); + m_SpectralUnmixingFilter->SetInput(m_inputImage); + m_SpectralUnmixingFilter->AddOutputs(2); + m_SpectralUnmixingFilter->Verbose(false); + m_SpectralUnmixingFilter->RelativeError(false); + m_SpectralUnmixingFilter->AddWavelength(757); + m_SpectralUnmixingFilter->AddWavelength(797); + m_SpectralUnmixingFilter->AddWavelength(847); + m_SpectralUnmixingFilter->AddChromophore(mitk::pa::PropertyCalculator::ChromophoreType::OXYGENATED); + m_SpectralUnmixingFilter->AddChromophore(mitk::pa::PropertyCalculator::ChromophoreType::DEOXYGENATED); - m_SpectralUnmixingFilter->Update(); + m_SpectralUnmixingFilter->Update(); - auto m_sO2 = mitk::pa::SpectralUnmixingSO2::New(); - m_sO2->Verbose(false); - auto output1 = m_SpectralUnmixingFilter->GetOutput(0); - auto output2 = m_SpectralUnmixingFilter->GetOutput(1); + auto m_sO2 = mitk::pa::SpectralUnmixingSO2::New(); + m_sO2->Verbose(false); + auto output1 = m_SpectralUnmixingFilter->GetOutput(0); + auto output2 = m_SpectralUnmixingFilter->GetOutput(1); - # save outputs! - - - m_sO2->SetInput(0, output1); - m_sO2->SetInput(1, output2); + std::string unmixingOutputHbO2 = outputPath + '/SUOutput/HbO2_' + stringvec[filename]; + std::string unmixingOutputHb = outputPath + '/SUOutput/Hb_' + stringvec[filename]; + + mitk::IOUtil::Save(output1, unmixingOutputHbO2); + mitk::IOUtil::Save(output2, unmixingOutputHb); + + m_sO2->SetInput(0, output1); + m_sO2->SetInput(1, output2); - m_sO2->Update(); - - mitk::Image::Pointer sO2 = m_sO2->GetOutput(0); - sO2->SetSpacing(output1->GetGeometry()->GetSpacing()); - WriteOutputToDataStorage(sO2, "sO2"); - - # save output!! - + m_sO2->Update(); + + mitk::Image::Pointer sO2 = m_sO2->GetOutput(0); + sO2->SetSpacing(output1->GetGeometry()->GetSpacing()); + + std::string outputSo2 = outputPath + '/So2/So2_' + stringvec[filename]; + mitk::IOUtil::Save(sO2, outputSo2); + } } - - - - - - - - - - - - auto input = parseInput(argc, argv); - auto parameters = CreatePhantom_04_04_18_Parameters(); - if (input.empty) - { - parameters->SetMaxNumberOfVessels(0); - parameters->SetMinNumberOfVessels(0); - } - MITK_INFO(input.verbose) << "Generating tissue.."; - auto resultTissue = InSilicoTissueGenerator::GenerateInSilicoData(parameters); - MITK_INFO(input.verbose) << "Generating tissue..[Done]"; - - auto inputfolder = std::string(input.saveFolderPath + "input/"); - auto outputfolder = std::string(input.saveFolderPath + "output/"); - if (!itksys::SystemTools::FileIsDirectory(inputfolder)) - { - itksys::SystemTools::MakeDirectory(inputfolder); - } - if (!itksys::SystemTools::FileIsDirectory(outputfolder)) - { - itksys::SystemTools::MakeDirectory(outputfolder); - } - - std::string savePath = input.saveFolderPath + "input/Phantom_" + input.identifyer + - ".nrrd"; - mitk::IOUtil::Save(resultTissue->ConvertToMitkImage(), savePath); - std::string outputPath = input.saveFolderPath + "output/Phantom_" + input.identifyer + - "/"; - - resultTissue = nullptr; - - if (!itksys::SystemTools::FileIsDirectory(outputPath)) - { - itksys::SystemTools::MakeDirectory(outputPath); - } - - outputPath = outputPath + "Fluence_Phantom_" + input.identifyer; - - MITK_INFO(input.verbose) << "Simulating fluence.."; - - int result = -4; - - std::string cmdString = std::string(input.exePath + " -i " + savePath + " -o " + - (outputPath + ".nrrd") + - " -yo " + "0" + " -p " + input.probePath + - " -n 10000000"); - - MITK_INFO << "Executing: " << cmdString; - - result = std::system(cmdString.c_str()); - - MITK_INFO << result; - MITK_INFO(input.verbose) << "Simulating fluence..[Done]"; + MITK_INFO << "Spectral Unmixing DONE"; }