diff --git a/Modules/PhotoacousticsLib/include/mitkPASpectralUnmixingFilterBase.h b/Modules/PhotoacousticsLib/include/mitkPASpectralUnmixingFilterBase.h index 86e4c610ee..9a9d41d4eb 100644 --- a/Modules/PhotoacousticsLib/include/mitkPASpectralUnmixingFilterBase.h +++ b/Modules/PhotoacousticsLib/include/mitkPASpectralUnmixingFilterBase.h @@ -1,193 +1,194 @@ /*=================================================================== 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. ===================================================================*/ #ifndef MITKPHOTOACOUSTICSPECTRALUNMIXINGFILTERBASE_H #define MITKPHOTOACOUSTICSPECTRALUNMIXINGFILTERBASE_H #include "mitkImageToImageFilter.h" #include //Includes for smart pointer usage #include "mitkCommon.h" #include "itkLightObject.h" // Includes for AddEnmemberMatrix #include "mitkPAPropertyCalculator.h" #include namespace mitk { namespace pa { /** * \brief The spectral unmixing filter base is designed as superclass for several spectral unmixing filter eg. Eigen- or Vigrabased ones. * One can add wavelengths and chromophores and get a unmixed output images out of one MITK input image using algorithms from the subclasses. * * Input: * The unmixing input has to be a 3D MITK image where the XY-plane is a image and the Z-direction represents recordings for different * wavelengths. Herein a XY-plane for a specific Z-direction will be called "image". Every image has to be assigned to a certain wavelength. * The "AddWavelength" uses "push_back" to write float values into a vector. The first wavelength will correspond to the first image!!! * If there a more input images 'I' then added wavelengths 'w' the filter base interprets the next x images as repetition sequence of the same * wavelengths. If I % w !=0 the surplus image(s) will be dropped. * Addtionaly one has to add chromophores from the property calculator class enum "ChromophoreType" with the "AddChromophore" method. * This method as well uses "push_back" but the chosen (arbitary) order will be the order of the outputs. * * Output: * The output will be one MITK image per chosen chromophore. Where the XY-plane is a image and the Z-direction represents recordings for different * sequences. Furthermore it is possible to creat an output image that contains the information about the relative error between unmixing result * and the input image. * * Subclasses: * - mitkPASpectralUnmixingFilterVigra * - mitkPALinearSpectralUnmixingFilter (uses Eigen algorithms) * - mitkPASpectralUnmixingFilterSimplex * * Possible exceptions: * - "PIXELTYPE ERROR! FLOAT 32 REQUIRED": The MITK input image has to consist out of floats. * - "ERROR! REMOVE WAVELENGTHS!": One needs at least the same amount of images (z-dimension) then added wavelengths. * - "ADD MORE WAVELENGTHS!": One needs at least the same amount of wavelengths then added chromophores. * - "WAVELENGTH XXX nm NOT SUPPORTED!": The wavelength is not part of the proptery calculater data base. The data base can be found @ * [...]\mitk\Modules\PhotoacousticsLib\Resources\spectralLIB.dat */ class MITKPHOTOACOUSTICSLIB_EXPORT SpectralUnmixingFilterBase : public mitk::ImageToImageFilter { public: mitkClassMacro(SpectralUnmixingFilterBase, mitk::ImageToImageFilter); /** * \brief AddChromophore takes mitk::pa::PropertyCalculator::ChromophoreType and writes them at the end of the m_Chromophore vector. * The call of the method sets the order of the GetOutput method! * * @param chromophore has to be element of porperty calculater enum chromophore type * @return for wavelength smaller then 300nm and larger then 1000nm the return will be 0, because not at the data base (2018/06/19) */ void AddChromophore(mitk::pa::PropertyCalculator::ChromophoreType chromophore); /** * \brief AddWavelength takes integers and writes them at the end of the m_Wavelength vector. The first call of the method then * corresponds to the first input image and so on. * @param wavelength database supports integers between 300 and 1000 nm */ void AddWavelength(int wavelength); /* * \brief Verbose gives more information to the console. Default value is false. * @param verbose is the boolian to activate the MITK_INFO logged to the console */ virtual void Verbose(bool verbose); /** * \brief AddOutputs takes an integer and sets indexed outputs * @param outputs integer correponds to the number of output images */ virtual void AddOutputs(unsigned int outputs); /* * \brief RelativeError returns a image which compare the L2 norm of the input vector with the unmixing result * @param relativeError is the boolian to activate this tool */ virtual void RelativeError(bool relativeError); /** * \brief AddRelativeErrorSettings takes integers and writes them at the end of the m_RelativeErrorSettings vector. * @param value has to be a integer */ virtual void AddRelativeErrorSettings(int value); ofstream myfile; // just for testing purposes; has to be removeed protected: /** * \brief Constructor creats proptery calculater smart pointer new() */ SpectralUnmixingFilterBase(); virtual ~SpectralUnmixingFilterBase(); /** * \brief The subclasses will override the mehtod to calculate the spectral unmixing result vector. * @param endmemberMatrix Matrix with number of chromophores colums and number of wavelengths rows so matrix element (i,j) contains * the absorbtion of chromophore j @ wavelength i taken from the database by PropertyElement method. * @param inputVector Vector containing values of one pixel of XY-plane image with number of wavelength rows (z-dimension of a sequenece) * so the pixelvalue of the first wavelength is stored in inputVector[0] and so on. + * @throws if algorithm implementiation fails (implemented for the algorithms with critical requirements) */ virtual Eigen::VectorXf SpectralUnmixingAlgorithm(Eigen::Matrix endmemberMatrix, Eigen::VectorXf inputVector) = 0; bool m_Verbose = false; bool m_RelativeError = false; std::vector m_Chromophore; std::vector m_Wavelength; std::vector m_RelativeErrorSettings; private: /* * \brief Initialized output images with the same XY-plane size like the input image and total size in z-direction equals number of sequences. * The pixel type is set to float. * @param totalNumberOfSequences = (unsigned int) (numberOfInputImages / numberOfWavelength) >= 1 */ virtual void InitializeOutputs(unsigned int totalNumberOfSequences); /* * \brief Checks if there are a suitable amount of wavelengths and if the input image consists of floats. * @param numberOfInputImages corresponds to the z-dimension of the MITK input image * @param inputDataArray contains every pixel of the MITK input image. Accessable like pseudo multidimensional array, that means * pixel(x,y,z) = (xdim * yDim * z) + x * yDim + y where eg. "xdim" means the total size of the MITK input image in x direction. * @throws if there are more wavelength then images * @throws if there are more chromophores then wavelengths * @throws if the pixel type is not float 32 */ virtual void CheckPreConditions(unsigned int numberOfInputImages, const float* inputDataArray); /* * \brief Inherit from the "ImageToImageFilter" Superclass. Herain it calls InitializeOutputs, CalculateEndmemberMatrix and * CheckPreConditions methods and enables pixelwise access to do spectral unmixing with the "SpectralUnmixingAlgorithm" * method. In the end the method writes the results into the new MITK output images. */ virtual void GenerateData() override; /* * \brief Creats a Matrix with number of chromophores colums and number of wavelengths rows so matrix element (i,j) contains * the absorbtion of chromophore j @ wavelength i. The absorbtion values are taken from the "PropertyElement" method. * @param m_Chromophore is a vector of "PropertyCalculator::ChromophoreType" containing all selected chromophores for the unmixing * @param m_Wavelength is a vector of integers containing all wavelengths of one sequence */ virtual Eigen::Matrix CalculateEndmemberMatrix( std::vector m_Chromophore, std::vector m_Wavelength); /* * \brief "PropertyElement" is the tool to access the absorbtion values out of the database using mitk::pa::PropertyCalculator::GetAbsorptionForWavelengt * and checks if the requested wavelength is part of the database (not zero values). The "ONEENDMEMBER" is a pseudo absorber with static absorbtion 1 * at every wavelength and is therefor not part of the database. If this one is the selected chromophore the return value is 1 for every wavelength. * @param wavelength has to be integer between 300 and 1000 nm * @param chromophore has to be a mitk::pa::PropertyCalculator::ChromophoreType * @throws if mitk::pa::PropertyCalculator::GetAbsorptionForWavelengt returns 0, because this means that the delivered wavelength is not in the database. */ virtual float PropertyElement(mitk::pa::PropertyCalculator::ChromophoreType, int wavelength); /* * \brief calculates the relative error between the input image and the unmixing result in the L2 norm * @param endmemberMatrix is a Eigen matrix containing the endmember information * @param inputVector is a Eigen vector containing the multispectral information of one pixel * @param resultVector is a Eigen vector containing the spectral unmmixing result */ float CalculateRelativeError(Eigen::Matrix endmemberMatrix, Eigen::VectorXf inputVector, Eigen::VectorXf resultVector); PropertyCalculator::Pointer m_PropertyCalculatorEigen; }; } } #endif // MITKPHOTOACOUSTICSPECTRALUNMIXINGFILTERBASE_ diff --git a/Modules/PhotoacousticsLib/src/SUFilter/mitkPALinearSpectralUnmixingFilter.cpp b/Modules/PhotoacousticsLib/src/SUFilter/mitkPALinearSpectralUnmixingFilter.cpp index 8a8e013550..feb1b59449 100644 --- a/Modules/PhotoacousticsLib/src/SUFilter/mitkPALinearSpectralUnmixingFilter.cpp +++ b/Modules/PhotoacousticsLib/src/SUFilter/mitkPALinearSpectralUnmixingFilter.cpp @@ -1,74 +1,84 @@ /*=================================================================== 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 "mitkPALinearSpectralUnmixingFilter.h" // Testing algorithms #include // ImageAccessor #include #include mitk::pa::LinearSpectralUnmixingFilter::LinearSpectralUnmixingFilter() { } mitk::pa::LinearSpectralUnmixingFilter::~LinearSpectralUnmixingFilter() { } void mitk::pa::LinearSpectralUnmixingFilter::SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType inputAlgorithmName) { algorithmName = inputAlgorithmName; } Eigen::VectorXf mitk::pa::LinearSpectralUnmixingFilter::SpectralUnmixingAlgorithm( Eigen::Matrix endmemberMatrix, Eigen::VectorXf inputVector) { Eigen::VectorXf resultVector; if (mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::HOUSEHOLDERQR == algorithmName) resultVector = endmemberMatrix.householderQr().solve(inputVector); else if (mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::LDLT == algorithmName) { - mitkThrow() << "algorithm not working"; - resultVector = endmemberMatrix.ldlt().solve(inputVector); + Eigen::LLT lltOfA(endmemberMatrix); + if (lltOfA.info() == Eigen::NumericalIssue) + { + mitkThrow() << "Possibly non semi-positive definitie endmembermatrix!"; + } + else + resultVector = endmemberMatrix.ldlt().solve(inputVector); } else if (mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::LLT == algorithmName) { - mitkThrow() << "algorithm not working"; - resultVector = endmemberMatrix.llt().solve(inputVector); + Eigen::LLT lltOfA(endmemberMatrix); + if (lltOfA.info() == Eigen::NumericalIssue) + { + mitkThrow() << "Possibly non semi-positive definitie endmembermatrix!"; + } + else + resultVector = endmemberMatrix.llt().solve(inputVector); } else if (mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::COLPIVHOUSEHOLDERQR == algorithmName) resultVector = endmemberMatrix.colPivHouseholderQr().solve(inputVector); else if (mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::JACOBISVD == algorithmName) resultVector = endmemberMatrix.jacobiSvd(Eigen::ComputeFullU | Eigen::ComputeFullV).solve(inputVector); else if (mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::FULLPIVLU == algorithmName) resultVector = endmemberMatrix.fullPivLu().solve(inputVector); else if (mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::FULLPIVHOUSEHOLDERQR == algorithmName) resultVector = endmemberMatrix.fullPivHouseholderQr().solve(inputVector); else mitkThrow() << "404 VIGRA ALGORITHM NOT FOUND"; return resultVector; } diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/src/internal/SpectralUnmixing.cpp b/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/src/internal/SpectralUnmixing.cpp index 88c3e7fbf4..9cdb2f6293 100644 --- a/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/src/internal/SpectralUnmixing.cpp +++ b/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/src/internal/SpectralUnmixing.cpp @@ -1,469 +1,471 @@ /*=================================================================== 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. ===================================================================*/ // Blueberry #include #include // Qmitk #include "SpectralUnmixing.h" // Qt #include // mitk image #include // Include to perform Spectral Unmixing #include "mitkPASpectralUnmixingFilterBase.h" #include "mitkPALinearSpectralUnmixingFilter.h" #include "mitkPASpectralUnmixingSO2.h" #include "mitkPASpectralUnmixingFilterVigra.h" #include "mitkPASpectralUnmixingFilterLagrange.h" #include "mitkPASpectralUnmixingFilterSimplex.h" #include #include const std::string SpectralUnmixing::VIEW_ID = "org.mitk.views.spectralunmixing"; void SpectralUnmixing::SetFocus() { m_Controls.buttonPerformImageProcessing->setFocus(); } void SpectralUnmixing::CreateQtPartControl(QWidget *parent) { // create GUI widgets from the Qt Designer's .ui file m_Controls.setupUi(parent); connect(m_Controls.buttonPerformImageProcessing, &QPushButton::clicked, this, &SpectralUnmixing::DoImageProcessing); m_Controls.tableWeight->hide(); m_Controls.tableSO2->hide(); m_Controls.tableError->hide(); connect((QObject*)(m_Controls.QComboBoxAlgorithm), SIGNAL(currentIndexChanged(int)), this, SLOT(EnableGUIWeight())); connect((QObject*)(m_Controls.checkBoxsO2), SIGNAL(clicked()), this, SLOT(EnableGUISO2())); connect((QObject*)(m_Controls.checkBoxError), SIGNAL(clicked()), this, SLOT(EnableGUIError())); this->connect(this, SIGNAL(finishSignal()), this, SLOT(storeOutputs())); this->connect(this, SIGNAL(crashSignal()), this, SLOT(crashInfo())); } void SpectralUnmixing::SwitchGUIControls(bool change) { m_Controls.inputtable->setEnabled(change); m_Controls.checkBoxOx->setEnabled(change); m_Controls.checkBoxDeOx->setEnabled(change); m_Controls.checkBoxMelanin->setEnabled(change); m_Controls.checkBoxAdd->setEnabled(change); m_Controls.QComboBoxAlgorithm->setEnabled(change); m_Controls.tableWeight->setEnabled(change); m_Controls.checkBoxsO2->setEnabled(change); m_Controls.tableSO2->setEnabled(change); m_Controls.checkBoxVerbose->setEnabled(change); m_Controls.checkBoxChrono->setEnabled(change); m_Controls.buttonPerformImageProcessing->setEnabled(change); m_Controls.checkBoxError->setEnabled(change); } void SpectralUnmixing::EnableGUIWeight() { auto qs = m_Controls.QComboBoxAlgorithm->currentText(); std::string Algorithm = qs.toUtf8().constData(); if (Algorithm == "weighted") m_Controls.tableWeight->show(); else m_Controls.tableWeight->hide(); } void SpectralUnmixing::EnableGUISO2() { if (m_Controls.checkBoxsO2->isChecked()) m_Controls.tableSO2->show(); else m_Controls.tableSO2->hide(); } void SpectralUnmixing::EnableGUIError() { if (m_Controls.checkBoxError->isChecked()) m_Controls.tableError->show(); else m_Controls.tableError->hide(); } void SpectralUnmixing::SetVerboseMode(mitk::pa::SpectralUnmixingFilterBase::Pointer m_SpectralUnmixingFilter, bool PluginVerbose) { m_SpectralUnmixingFilter->Verbose(PluginVerbose); } void SpectralUnmixing::SetWavlength(mitk::pa::SpectralUnmixingFilterBase::Pointer m_SpectralUnmixingFilter) { int col = 0; int Wavelength = 1; while (m_Controls.inputtable->item(0, col) && Wavelength > 0) { QString Text = m_Controls.inputtable->item(0, col)->text(); Wavelength = Text.toInt(); if (Wavelength > 0) { m_SpectralUnmixingFilter->AddWavelength(Wavelength); MITK_INFO(PluginVerbose) << "Wavelength: " << Wavelength << "nm \n"; } ++col; } } void SpectralUnmixing::SetChromophore(mitk::pa::SpectralUnmixingFilterBase::Pointer m_SpectralUnmixingFilter, std::vector boolVec, std::vector chromophoreNameVec) { unsigned int numberofChromophores = 0; std::vector m_ChromoType = { mitk::pa::PropertyCalculator::ChromophoreType::OXYGENATED, mitk::pa::PropertyCalculator::ChromophoreType::DEOXYGENATED, mitk::pa::PropertyCalculator::ChromophoreType::MELANIN, mitk::pa::PropertyCalculator::ChromophoreType::ONEENDMEMBER}; for (unsigned int chromo = 0; chromo < m_ChromoType.size(); ++chromo) { if (boolVec[chromo] == true) { MITK_INFO(PluginVerbose) << "Chromophore: " << chromophoreNameVec[chromo]; m_SpectralUnmixingFilter->AddChromophore(m_ChromoType[chromo]); numberofChromophores += 1; } } if (numberofChromophores == 0) mitkThrow() << "PRESS 'IGNORE' AND CHOOSE A CHROMOPHORE!"; } void SpectralUnmixing::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*source*/, const QList &nodes) { // iterate all selected objects, adjust warning visibility foreach (mitk::DataNode::Pointer node, nodes) { if (node.IsNotNull() && dynamic_cast(node->GetData())) { m_Controls.labelWarning->setVisible(false); m_Controls.buttonPerformImageProcessing->setEnabled(true); return; } } m_Controls.labelWarning->setVisible(true); m_Controls.buttonPerformImageProcessing->setEnabled(false); } mitk::pa::SpectralUnmixingFilterBase::Pointer SpectralUnmixing::GetFilterInstance(std::string algorithm) { mitk::pa::SpectralUnmixingFilterBase::Pointer spectralUnmixingFilter; if (algorithm == "householderQr") { spectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New(); dynamic_cast(spectralUnmixingFilter.GetPointer()) ->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::HOUSEHOLDERQR); } else if (algorithm == "ldlt") { + MITK_WARN << "Unfortunaly algorithm is likley to fail!"; spectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New(); dynamic_cast(spectralUnmixingFilter.GetPointer()) ->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::LDLT); } else if (algorithm == "llt") { + MITK_WARN << "Unfortunaly algorithm is likley to fail!"; spectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New(); dynamic_cast(spectralUnmixingFilter.GetPointer()) ->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::LLT); } else if (algorithm == "colPivHouseholderQr") { spectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New(); dynamic_cast(spectralUnmixingFilter.GetPointer()) ->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::COLPIVHOUSEHOLDERQR); } else if (algorithm == "jacobiSvd") { spectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New(); dynamic_cast(spectralUnmixingFilter.GetPointer()) ->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::JACOBISVD); } else if (algorithm == "fullPivLu") { spectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New(); dynamic_cast(spectralUnmixingFilter.GetPointer()) ->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::FULLPIVLU); } else if (algorithm == "fullPivHouseholderQr") { spectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New(); dynamic_cast(spectralUnmixingFilter.GetPointer()) ->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::FULLPIVHOUSEHOLDERQR); } else if (algorithm == "NNLARS") { spectralUnmixingFilter = mitk::pa::SpectralUnmixingFilterVigra::New(); dynamic_cast(spectralUnmixingFilter.GetPointer()) ->SetAlgorithm(mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::LARS); } else if (algorithm == "NNGoldfarb") { spectralUnmixingFilter = mitk::pa::SpectralUnmixingFilterVigra::New(); dynamic_cast(spectralUnmixingFilter.GetPointer()) ->SetAlgorithm(mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::GOLDFARB); } else if (algorithm == "weighted") { spectralUnmixingFilter = mitk::pa::SpectralUnmixingFilterVigra::New(); dynamic_cast(spectralUnmixingFilter.GetPointer()) ->SetAlgorithm(mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::WEIGHTED); //Tranfer GUI information(Weights) to filter unsigned int colunm = 0; int Weight = 1; while (m_Controls.tableWeight->item(0, colunm) && Weight > 0) { QString Text = m_Controls.tableWeight->item(0, colunm)->text(); Weight = Text.toInt(); if (Weight > 0) { dynamic_cast(spectralUnmixingFilter.GetPointer()) ->AddWeight(Weight); MITK_INFO(PluginVerbose) << "Weight: " << Weight; } ++colunm; } } else if (algorithm == "LS") { spectralUnmixingFilter = mitk::pa::SpectralUnmixingFilterVigra::New(); dynamic_cast(spectralUnmixingFilter.GetPointer()) ->SetAlgorithm(mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::LS); } else if (algorithm == "SimplexMax") { spectralUnmixingFilter = mitk::pa::SpectralUnmixingFilterSimplex::New(); } else mitkThrow() << "404 ALGORITHM NOT FOUND!"; return spectralUnmixingFilter; } void SpectralUnmixing::SetSO2Settings(mitk::pa::SpectralUnmixingSO2::Pointer m_sO2) { for (unsigned int i = 0; i < 4; ++i) { if (m_Controls.tableSO2->item(0, i)) { QString Text = m_Controls.tableSO2->item(0, i)->text(); int value = Text.toInt(); MITK_INFO(PluginVerbose) << "SO2 setting value: " << value; m_sO2->AddSO2Settings(value); } else m_sO2->AddSO2Settings(0); } } void SpectralUnmixing::SetRelativeErrorSettings(mitk::pa::SpectralUnmixingFilterBase::Pointer m_SpectralUnmixingFilter) { for (unsigned int i = 0; i < 2; ++i) { if (m_Controls.tableError->item(0, i)) { QString Text = m_Controls.tableError->item(0, i)->text(); int value = Text.toInt(); MITK_INFO(PluginVerbose) << "Relative error setting value: " << value; m_SpectralUnmixingFilter->AddRelativeErrorSettings(value); } else m_SpectralUnmixingFilter->AddRelativeErrorSettings(0); } } void SpectralUnmixing::CalculateSO2(mitk::pa::SpectralUnmixingFilterBase::Pointer m_SpectralUnmixingFilter, std::vector boolVec) { MITK_INFO(PluginVerbose) << "CALCULATE OXYGEN SATURATION ..."; if (!boolVec[0]) mitkThrow() << "SELECT CHROMOPHORE DEOXYHEMOGLOBIN!"; if (!boolVec[1]) mitkThrow() << "SELECT CHROMOPHORE OXYHEMOGLOBIN!"; auto m_sO2 = mitk::pa::SpectralUnmixingSO2::New(); m_sO2->Verbose(PluginVerbose); SetSO2Settings(m_sO2); // Initialize pipeline from SU filter class to SO2 class auto output1 = m_SpectralUnmixingFilter->GetOutput(0); auto output2 = m_SpectralUnmixingFilter->GetOutput(1); 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"); MITK_INFO(PluginVerbose) << "[DONE]"; } void SpectralUnmixing::WriteOutputToDataStorage(mitk::Image::Pointer m_Image, std::string name) { mitk::DataNode::Pointer dataNodeOutput = mitk::DataNode::New(); dataNodeOutput->SetData(m_Image); dataNodeOutput->SetName(name); this->GetDataStorage()->Add(dataNodeOutput); } void SpectralUnmixing::Settings(mitk::Image::Pointer image) { boolVec = { m_Controls.checkBoxOx->isChecked(), m_Controls.checkBoxDeOx->isChecked(), m_Controls.checkBoxMelanin->isChecked(), m_Controls.checkBoxAdd->isChecked() }; outputNameVec = { "HbO2", "Hb", "Melanin", "Static Endmember" }; sO2Bool = (m_Controls.checkBoxsO2->isChecked()); //Read GUI information(algorithm) auto qs = m_Controls.QComboBoxAlgorithm->currentText(); Algorithm = qs.toUtf8().constData(); m_SpectralUnmixingFilter = GetFilterInstance(Algorithm); SetVerboseMode(m_SpectralUnmixingFilter, PluginVerbose); m_SpectralUnmixingFilter->RelativeError(m_Controls.checkBoxError->isChecked()); m_SpectralUnmixingFilter->SetInput(image); SetWavlength(m_SpectralUnmixingFilter); SetChromophore(m_SpectralUnmixingFilter, boolVec, outputNameVec); boolVec.push_back(m_Controls.checkBoxError->isChecked()); outputNameVec.push_back("Relative Error"); if (m_Controls.checkBoxError->isChecked()) SetRelativeErrorSettings(m_SpectralUnmixingFilter); m_SpectralUnmixingFilter->AddOutputs(std::accumulate(boolVec.begin(), boolVec.end(), 0)); MITK_INFO(PluginVerbose) << "Number of indexed outputs: " << std::accumulate(boolVec.begin(), boolVec.end(), 0); } void SpectralUnmixing::storeOutputs() { int outputCounter = 0; mitk::Image::Pointer m_Output; for (unsigned int chromophore = 0; chromophore < outputNameVec.size(); ++chromophore) { if (boolVec[chromophore] != false) { m_Output = m_SpectralUnmixingFilter->GetOutput(outputCounter++); m_Output->SetSpacing(image->GetGeometry()->GetSpacing()); WriteOutputToDataStorage(m_Output, outputNameVec[chromophore] + Algorithm); } } if (sO2Bool) CalculateSO2(m_SpectralUnmixingFilter, boolVec); mitk::RenderingManager::GetInstance()->InitializeViewsByBoundingObjects(this->GetDataStorage()); MITK_INFO(PluginVerbose) << "Adding images to DataStorage...[DONE]"; std::chrono::steady_clock::time_point _end(std::chrono::steady_clock::now()); MITK_INFO(m_Controls.checkBoxChrono->isChecked()) << "Time for image Processing: " << std::chrono::duration_cast>(_end - _start).count(); SwitchGUIControls(true); } void SpectralUnmixing::WorkingThreadUpdateFilter(mitk::pa::SpectralUnmixingFilterBase::Pointer m_SpectralUnmixingFilter) { SwitchGUIControls(false); try { m_SpectralUnmixingFilter->Update(); emit finishSignal(); } catch (const mitk::Exception& e) { SwitchGUIControls(true); errorMessage = e.GetDescription(); emit crashSignal(); } } void SpectralUnmixing::crashInfo() { const char *error = errorMessage.c_str(); QMessageBox::information(nullptr, "Template", error); } void SpectralUnmixing::DoImageProcessing() { QList nodes = this->GetDataManagerSelection(); if (nodes.empty()) return; mitk::DataNode *node = nodes.front(); if (!node) { // Nothing selected. Inform the user and return QMessageBox::information(nullptr, "Template", "Please load and select an image before starting image processing."); return; } // here we have a valid mitk::DataNode // a node itself is not very useful, we need its data item (the image) mitk::BaseData *data = node->GetData(); if (data) { // test if this data item is an image or not (could also be a surface or something totally different) image = dynamic_cast(data); if (image) { std::stringstream message; std::string name; message << "PERFORMING SPECTRAL UNMIXING "; if (node->GetName(name)) { // a property called "name" was found for this DataNode message << "'" << name << "'"; } message << "."; _start = std::chrono::steady_clock::now(); PluginVerbose = m_Controls.checkBoxVerbose->isChecked(); MITK_INFO(PluginVerbose) << message.str(); try { Settings(image); MITK_INFO(PluginVerbose) << "Updating Filter..."; QtConcurrent::run(this, &SpectralUnmixing::WorkingThreadUpdateFilter, m_SpectralUnmixingFilter); } catch (const mitk::Exception& e) { QMessageBox::information(nullptr, "Template", e.GetDescription()); } } } }