diff --git a/Modules/PhotoacousticsLib/MitkSpectralUnmixing/SpectralUnmixingApp.cpp b/Modules/PhotoacousticsLib/MitkSpectralUnmixing/SpectralUnmixingApp.cpp index e2f5cc4a48..c3537c2c01 100644 --- a/Modules/PhotoacousticsLib/MitkSpectralUnmixing/SpectralUnmixingApp.cpp +++ b/Modules/PhotoacousticsLib/MitkSpectralUnmixing/SpectralUnmixingApp.cpp @@ -1,289 +1,289 @@ /*=================================================================== 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 "mitkPALinearSpectralUnmixingFilter.h" #include "mitkPASpectralUnmixingFilterBase.h" #include "mitkPASpectralUnmixingFilterVigra.h" #include "mitkPASpectralUnmixingSO2.h" #include #include #include #include #include #include "mitkPreferenceListReaderOptionsFunctor.h" /* \brief The spectral unmixing mini app (SUMA) is designed to enable batch processing for spectral unmixing. For detailed documentation look into the header files of the included spectral unmixing filters.*/ struct InputParameters { std::string inputFilename; std::string outputFileStruct; // "E:/mydata/awesome_exp_unmixed/a" will be saved as "a_HbO2_SU_.nrrd", "a_Hb_SU_.nrrd" and "a_sO2_.nrrd"; std::string inputAlg; mitkCommandLineParser::StringContainerType inputWavelengths; mitkCommandLineParser::StringContainerType inputWeights; }; 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("inputFilename", "i", mitkCommandLineParser::InputDirectory, "Input Filename (NAME.nrrd)", "input filename", us::Any(), false); parser.addArgument("outputFileStruct", "o", mitkCommandLineParser::OutputDirectory, "Input save name (name without ending!)", "input save name", us::Any(), false); parser.addArgument("inputWavelengths", "l", mitkCommandLineParser::StringList, "Input wavelengths (123 124 125 ... int blank int blank)", "input wavelengths", us::Any(), false); parser.addArgument("inputAlg", "a", mitkCommandLineParser::String, "Input algorithm (string)", "input algorithm", us::Any(), false); parser.addArgument("inputWeights", "w", mitkCommandLineParser::StringList, "Input weights (123 124 125 ... int in % blank int in % blank)", "input weights", us::Any(), true); parser.endGroup(); InputParameters input; std::map parsedArgs = parser.parseArguments(argc, argv); if (argc == 0) exit(-1); for (int i = 0; i < argc; ++i) { MITK_INFO << argv[i]; } if (parsedArgs.count("inputFilename")) { input.inputFilename = us::any_cast(parsedArgs["inputFilename"]); } else { MITK_ERROR << "Error: No input file"; mitkThrow() << "Error: No input file"; } if (parsedArgs.count("outputFileStruct")) { input.outputFileStruct = us::any_cast(parsedArgs["outputFileStruct"]); } else { MITK_ERROR << "Error: No output"; mitkThrow() << "Error: No output"; } if (parsedArgs.count("inputWavelengths")) { input.inputWavelengths = us::any_cast(parsedArgs["inputWavelengths"]); } else { MITK_ERROR << "Error: No wavelengths"; mitkThrow() << "Error: No wavelengths"; } if (parsedArgs.count("inputAlg")) { input.inputAlg = us::any_cast(parsedArgs["inputAlg"]); } else { MITK_ERROR << "Error: No algorithm"; mitkThrow() << "Error: No algorithm"; } if (parsedArgs.count("inputWeights")) { input.inputWeights = us::any_cast(parsedArgs["inputWeights"]); } MITK_INFO << "Parsing arguments...[Done]"; return input; } // Class takes string and sets algorithm for spectral unmixing in the corresponding filter class mitk::pa::SpectralUnmixingFilterBase::Pointer GetFilterInstance(std::string algorithm, std::vector weights = std::vector()) { 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 weightVec = weights; for (unsigned int i = 0; i < weightVec.size(); ++i) { dynamic_cast(spectralUnmixingFilter.GetPointer()) ->AddWeight(weightVec[i]); } } return spectralUnmixingFilter; } int main(int argc, char *argv[]) { auto input = parseInput(argc, argv); std::string algo = input.inputAlg; std::string outputDir = input.outputFileStruct; auto inputWls = input.inputWavelengths; std::vector wavelengths; for (unsigned int s = 0; s < inputWls.size(); ++s) { int wl = std::stoi(inputWls[s]); wavelengths.push_back(wl); MITK_INFO << "Wavelength: " << wl << "\n"; } mitk::pa::SpectralUnmixingFilterBase::Pointer m_SpectralUnmixingFilter; if (algo == "WLS") { auto inputW = input.inputWeights; std::vector Weights; for (unsigned int s = 0; s < inputW.size(); ++s) { int w = std::stoi(inputW[s]); Weights.push_back(w); MITK_INFO << "Weights: " << w << "\n"; } m_SpectralUnmixingFilter = GetFilterInstance(algo, Weights); } else { m_SpectralUnmixingFilter = GetFilterInstance(algo); } m_SpectralUnmixingFilter->Verbose(false); m_SpectralUnmixingFilter->RelativeError(false); m_SpectralUnmixingFilter->AddChromophore(mitk::pa::PropertyCalculator::ChromophoreType::OXYGENATED); m_SpectralUnmixingFilter->AddChromophore(mitk::pa::PropertyCalculator::ChromophoreType::DEOXYGENATED); m_SpectralUnmixingFilter->AddOutputs(2); for (unsigned int wIdx = 0; wIdx < wavelengths.size(); ++wIdx) { m_SpectralUnmixingFilter->AddWavelength(wavelengths[wIdx]); MITK_INFO << wavelengths[wIdx]; } //to add a batch processing: loop for a dir start here; don't forget to set a counter to the three output savenames!!! std::string inputImage = input.inputFilename; auto m_inputImage = mitk::IOUtil::Load(inputImage); m_SpectralUnmixingFilter->SetInput(m_inputImage); m_SpectralUnmixingFilter->Update(); auto output1 = m_SpectralUnmixingFilter->GetOutput(0); auto output2 = m_SpectralUnmixingFilter->GetOutput(1); output1->SetSpacing(m_inputImage->GetGeometry()->GetSpacing()); output2->SetSpacing(m_inputImage->GetGeometry()->GetSpacing()); - std::string unmixingOutputHbO2 = outputDir + "_HbO2_SU_.nrrd"; - std::string unmixingOutputHb = outputDir + "_Hb_SU_.nrrd"; + std::string unmixingOutputHbO2 = outputDir + "_HbO2.nrrd"; + std::string unmixingOutputHb = outputDir + "_Hb.nrrd"; mitk::IOUtil::Save(output1, unmixingOutputHbO2); mitk::IOUtil::Save(output2, unmixingOutputHb); auto m_sO2 = mitk::pa::SpectralUnmixingSO2::New(); m_sO2->Verbose(false); m_sO2->SetInput(0, output1); m_sO2->SetInput(1, output2); m_sO2->Update(); mitk::Image::Pointer sO2 = m_sO2->GetOutput(0); sO2->SetSpacing(m_inputImage->GetGeometry()->GetSpacing()); - std::string outputSo2 = outputDir + "_sO2_.nrrd"; + std::string outputSo2 = outputDir + "_sO2.nrrd"; mitk::IOUtil::Save(sO2, outputSo2); m_sO2 = nullptr; m_SpectralUnmixingFilter = nullptr; //to add a batch processing: loop for a dir end here MITK_INFO << "Spectral Unmixing DONE"; }