diff --git a/Modules/PhotoacousticsLib/MitkSpectralUnmixing/SpectralUnmixingApp.cpp b/Modules/PhotoacousticsLib/MitkSpectralUnmixing/SpectralUnmixingApp.cpp index 2e560539a3..b95c76182e 100644 --- a/Modules/PhotoacousticsLib/MitkSpectralUnmixing/SpectralUnmixingApp.cpp +++ b/Modules/PhotoacousticsLib/MitkSpectralUnmixing/SpectralUnmixingApp.cpp @@ -1,205 +1,216 @@ /*=================================================================== 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 "mitkPASpectralUnmixingFilterBase.h" #include "mitkPALinearSpectralUnmixingFilter.h" -#include "mitkPASpectralUnmixingSO2.h" +#include "mitkPASpectralUnmixingFilterBase.h" #include "mitkPASpectralUnmixingFilterVigra.h" +#include "mitkPASpectralUnmixingSO2.h" -#include #include -#include #include +#include +#include #include struct InputParameters { - std::string inputPath; - std::string savePath; - int numberOfInputs; -} + std::string inputPath; + std::string savePath; + unsigned int numberOfInputs; +}; -InputParameters parseInput(int argc, char* argv[]) +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.setDescription("Batch processing for spectral unmixing."); parser.setContributor("Computer Assisted Medical Interventions, DKFZ"); parser.setArgumentPrefix("--", "-"); parser.beginGroup("Required parameters"); - parser.addArgument( - "inputPath", "s", mitkCommandLineParser::InputDirectory, - "Input folder (directory)", "input folder", - us::Any(), false); - parser.addArgument( - "savePath", "s", mitkCommandLineParser::InputDirectory, - "Input save folder (directory)", "input save folder", - us::Any(), false); - parser.addArgument( - "numberOfInputs", "s", mitkCommandLineParser::InputDirectory, - "Number of Input files", "number of inputs", - us::Any(), false); + parser.addArgument("inputPath", + "s", + mitkCommandLineParser::InputDirectory, + "Input folder (directory)", + "input folder", + us::Any(), + false); + parser.addArgument("savePath", + "s", + mitkCommandLineParser::InputDirectory, + "Input save folder (directory)", + "input save folder", + us::Any(), + false); + parser.addArgument("numberOfInputs", + "s", + mitkCommandLineParser::InputDirectory, + "Number of Input files", + "number of inputs", + us::Any(), + false); parser.endGroup(); InputParameters input; std::map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size() == 0) exit(-1); if (parsedArgs.count("inputPath")) { - input.saveFolderPath = us::any_cast(parsedArgs["inputPath"]); + input.inputPath = us::any_cast(parsedArgs["inputPath"]); } else { - mitkThrow() << "Error: No inputPath"; + mitkThrow() << "Error: No inputPath"; } if (parsedArgs.count("savePath")) { - input.saveFolderPath = us::any_cast(parsedArgs["savePath"]); + input.savePath = us::any_cast(parsedArgs["savePath"]); } else { - mitkThrow() << "Error: No savePath"; + 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()) + dynamic_cast(spectralUnmixingFilter.GetPointer()) ->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::HOUSEHOLDERQR); } else if (algorithm == "SVD") { spectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New(); - dynamic_cast(spectralUnmixingFilter.GetPointer()) + dynamic_cast(spectralUnmixingFilter.GetPointer()) ->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::JACOBISVD); } else if (algorithm == "LU") { spectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New(); - dynamic_cast(spectralUnmixingFilter.GetPointer()) + dynamic_cast(spectralUnmixingFilter.GetPointer()) ->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::FULLPIVLU); } else if (algorithm == "NNLS") { spectralUnmixingFilter = mitk::pa::SpectralUnmixingFilterVigra::New(); - dynamic_cast(spectralUnmixingFilter.GetPointer()) + dynamic_cast(spectralUnmixingFilter.GetPointer()) ->SetAlgorithm(mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::LARS); } else if (algorithm == "WLS") { spectralUnmixingFilter = mitk::pa::SpectralUnmixingFilterVigra::New(); - dynamic_cast(spectralUnmixingFilter.GetPointer()) + 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]); + + std::vector weigthVec = {39, 45, 47}; + + for (int i; i < 3; ++i) + { + dynamic_cast(spectralUnmixingFilter.GetPointer()) + ->AddWeight(weigthVec[i]); } } - return spectralUnmixingFilter; + return spectralUnmixingFilter; } - -int main(int argc, char * argv[]) +int main(int argc, char *argv[]) { - auto params = parseInput(argc, argv); - - auto inputPathname = params.inputPath; - auto outputPath = params.savePath; - auto numberOfInputs = params.numberOfInputs; - - - 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 (unsigned int filename = 0; filename < numberOfInputs; ++filename) - { - 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(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(); - - auto m_sO2 = mitk::pa::SpectralUnmixingSO2::New(); - m_sO2->Verbose(false); - auto output1 = m_SpectralUnmixingFilter->GetOutput(0); - auto output2 = m_SpectralUnmixingFilter->GetOutput(1); - - std::string unmixingOutputHbO2 = outputPath + '/SUOutput/' + algorithms[alg] + '/HbO2_' + stringvec[filename]; - std::string unmixingOutputHb = outputPath + '/SUOutput/' + algorithms[alg] + '/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()); - - std::string outputSo2 = outputPath + '/So2/' + algorithms[alg] + '/So2_' + stringvec[filename]; - mitk::IOUtil::Save(sO2, outputSo2); - } - } - MITK_INFO << "Spectral Unmixing DONE"; + auto params = parseInput(argc, argv); + + auto inputPathname = params.inputPath; + auto outputPath = params.savePath; + auto numberOfInputs = params.numberOfInputs; + + // 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"}; + + numberOfInputs = 1; + + for (unsigned int filename = 0; filename < numberOfInputs; ++filename) + { + // m_inputImage = mitk::IOUtil::Load(stringvec[filename]); + auto m_inputImage = mitk::IOUtil::Load(inputPathname); + for (unsigned alg = 0; alg < 5; ++alg) + { + mitk::pa::LinearSpectralUnmixingFilter::Pointer m_SpectralUnmixingFilter; + m_SpectralUnmixingFilter = GetFilterInstance(algorithms[alg]); + + 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(); + + auto m_sO2 = mitk::pa::SpectralUnmixingSO2::New(); + m_sO2->Verbose(false); + auto output1 = m_SpectralUnmixingFilter->GetOutput(0); + auto output2 = m_SpectralUnmixingFilter->GetOutput(1); + + std::string unmixingOutputHbO2 = outputPath + "/SUOutput/" + algorithms[alg] + "/HbO2_" + stringvec[filename]; + std::string unmixingOutputHb = outputPath + "/SUOutput/" + algorithms[alg] + "/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()); + + std::string outputSo2 = outputPath + "/So2/" + algorithms[alg] + "/So2_" + stringvec[filename]; + mitk::IOUtil::Save(sO2, outputSo2); + } + } + MITK_INFO << "Spectral Unmixing DONE"; }