diff --git a/Modules/PhotoacousticsLib/include/mitkPASpectralUnmixingFilterBase.h b/Modules/PhotoacousticsLib/include/mitkPASpectralUnmixingFilterBase.h index 1e144b6495..27e193a1d7 100644 --- a/Modules/PhotoacousticsLib/include/mitkPASpectralUnmixingFilterBase.h +++ b/Modules/PhotoacousticsLib/include/mitkPASpectralUnmixingFilterBase.h @@ -1,80 +1,80 @@ /*=================================================================== 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 { class MITKPHOTOACOUSTICSLIB_EXPORT SpectralUnmixingFilterBase : public mitk::ImageToImageFilter { public: - mitkClassMacro(SpectralUnmixingFilterBase, mitk::ImageToImageFilter) + mitkClassMacro(SpectralUnmixingFilterBase, mitk::ImageToImageFilter); // Contains all (so far) possible chromophores enum ChromophoreType { OXYGENATED_HEMOGLOBIN, DEOXYGENATED_HEMOGLOBIN }; // Void to creat m_vector of all chosen chromophores with push back method void AddChromophore(ChromophoreType); // Void to creat m_vector of all wavelengths with push back method void AddWavelength(int wavelength); protected: SpectralUnmixingFilterBase(); virtual ~SpectralUnmixingFilterBase(); std::vector m_Chromophore; std::vector m_Wavelength; virtual Eigen::VectorXf SpectralUnmixingAlgorithm(Eigen::Matrix EndmemberMatrix, Eigen::VectorXf inputVector) = 0; private: // Void checking precondtions possibly throwing exeptions virtual void CheckPreConditions(unsigned int size, unsigned int NumberOfInputImages, const float* inputDataArray); virtual void GenerateData() override; virtual void InitializeOutputs(); // Void to creat Eigen::Matrix of all absorbtions // @ specific wavelength (columns) of chromophores (rows) Eigen::Matrix AddEndmemberMatrix(); PropertyCalculator::Pointer m_PropertyCalculator; }; } } #endif // MITKPHOTOACOUSTICSPECTRALUNMIXINGFILTERBASE_ 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 7646de598e..1d7ce9ad76 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 @@ -1,319 +1,329 @@ /*=================================================================== 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" 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); connect(m_Controls.ButtonAddWavelength, &QPushButton::clicked, this, &SpectralUnmixing::Wavelength); connect(m_Controls.ButtonClearWavelength, &QPushButton::clicked, this, &SpectralUnmixing::ClearWavelength); } // Adds Wavelength @ Plugin with button void SpectralUnmixing::Wavelength() { if (m_Wavelengths.empty()) { size = 0; } unsigned int wavelength = m_Controls.spinBoxAddWavelength->value(); m_Wavelengths.push_back(wavelength); size += 1; // size implemented like this because '.size' is const MITK_INFO << "ALL WAVELENGTHS: "; for (int i = 0; i < size; ++i) { MITK_INFO << m_Wavelengths[i] << "nm"; } } void SpectralUnmixing::ClearWavelength() { m_Wavelengths.clear(); } 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); } 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) mitk::Image *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 << "."; MITK_INFO << message.str(); // Set Algortihm to filter auto qs = m_Controls.QComboBoxAlgorithm->currentText(); std::string Algorithm = qs.toUtf8().constData(); - auto m_SpectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New(); - m_SpectralUnmixingFilter->SetInput(image); + //auto m_SpectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New(); + + mitk::pa::SpectralUnmixingFilterBase::Pointer m_SpectralUnmixingFilter; + + //m_SpectralUnmixingFilter->SetInput(image); if (Algorithm == "householderQr") { - //auto m_SpectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New(); - //m_SpectralUnmixingFilter->SetInput(image); - m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::householderQr); + m_SpectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New(); + dynamic_cast(m_SpectralUnmixingFilter.GetPointer())->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::householderQr); } + //all other enums, if solution adapt to them!: + /* else if (Algorithm == "ldlt") { - //auto m_SpectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New(); + m_SpectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New(); //m_SpectralUnmixingFilter->SetInput(image); m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::ldlt); } else if (Algorithm == "llt") { - //auto m_SpectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New(); + m_SpectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New(); //m_SpectralUnmixingFilter->SetInput(image); m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::llt); } else if (Algorithm == "colPivHouseholderQr") { //auto m_SpectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New(); //m_SpectralUnmixingFilter->SetInput(image); m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::colPivHouseholderQr); } else if (Algorithm == "jacobiSvd") { //auto m_SpectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New(); //m_SpectralUnmixingFilter->SetInput(image); m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::jacobiSvd); } else if (Algorithm == "fullPivLu") { //auto m_SpectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New(); //m_SpectralUnmixingFilter->SetInput(image); m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::fullPivLu); } else if (Algorithm == "fullPivHouseholderQr") { //auto m_SpectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New(); - //m_SpectralUnmixingFilter->SetInput(image); + m_SpectralUnmixingFilter->SetInput(image); m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::fullPivHouseholderQr); } else if (Algorithm == "test") { - //auto m_SpectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New(); - //m_SpectralUnmixingFilter->SetInput(image); + auto m_SpectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New(); + m_SpectralUnmixingFilter->SetInput(image); m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::test); } - + else if (Algorithm == "Lars") { auto m_SpectralUnmixingFilter = mitk::pa::SpectralUnmixingFilterVigra::New(); - //m_SpectralUnmixingFilter->SetInput(image); + m_SpectralUnmixingFilter->SetInput(image); m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::LARS); } else if (Algorithm == "Goldfarb") { auto m_SpectralUnmixingFilter = mitk::pa::SpectralUnmixingFilterVigra::New(); - //m_SpectralUnmixingFilter->SetInput(image); + m_SpectralUnmixingFilter->SetInput(image); m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::GOLDFARB); } else if (Algorithm == "weighted") { auto m_SpectralUnmixingFilter = mitk::pa::SpectralUnmixingFilterVigra::New(); - //m_SpectralUnmixingFilter->SetInput(image); + m_SpectralUnmixingFilter->SetInput(image); m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::WEIGHTED); } - - else if (Algorithm == "vigratest") + */ // all other enums + + else if (Algorithm == "test") { - auto m_SpectralUnmixingFilter = mitk::pa::SpectralUnmixingFilterVigra::New(); - //m_SpectralUnmixingFilter->SetInput(image); - m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::vigratest); + m_SpectralUnmixingFilter = mitk::pa::SpectralUnmixingFilterVigra::New(); + dynamic_cast(m_SpectralUnmixingFilter.GetPointer())->SetAlgorithm(mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::LARS); } else mitkThrow() << "ALGORITHM ERROR!"; + m_SpectralUnmixingFilter->SetInput(image); + + //itk::SmartPointer m_SpectralUnmixingFilterBase; + //m_SpectralUnmixingFilterBase->mitk::pa::SpectralUnmixingFilterBase::New(); + + // Wavelength implementation into filter for (unsigned int imageIndex = 0; imageIndex < m_Wavelengths.size(); imageIndex++) { unsigned int wavelength = m_Wavelengths[imageIndex]; m_SpectralUnmixingFilter->AddWavelength(wavelength); } // Checking which chromophores wanted for SU if none throw exeption! unsigned int numberofChromophores = 0; DeOxbool = m_Controls.checkBoxDeOx->isChecked(); Oxbool = m_Controls.checkBoxOx->isChecked(); if (DeOxbool || Oxbool) { MITK_INFO << "CHOSEN CHROMOPHORES:"; } if (Oxbool) { numberofChromophores += 1; MITK_INFO << "- Oxyhemoglobin"; // Set chromophore Oxyhemoglobon: m_SpectralUnmixingFilter->AddChromophore( mitk::pa::SpectralUnmixingFilterBase::ChromophoreType::OXYGENATED_HEMOGLOBIN); } if (DeOxbool) { numberofChromophores += 1; MITK_INFO << "- Deoxygenated hemoglobin"; // Set chromophore Deoxygenated hemoglobin: - m_SpectralUnmixingFilter->AddChromophore( + m_SpectralUnmixingFilter->AddChromophore( mitk::pa::SpectralUnmixingFilterBase::ChromophoreType::DEOXYGENATED_HEMOGLOBIN); } if (numberofChromophores == 0) { mitkThrow() << "PRESS 'IGNORE' AND CHOOSE A CHROMOPHORE!"; } MITK_INFO << "Updating Filter..."; m_SpectralUnmixingFilter->Update(); // Write Output images to Data Storage if (Oxbool) { mitk::Image::Pointer HbO2 = m_SpectralUnmixingFilter->GetOutput(0); mitk::DataNode::Pointer dataNodeHbO2 = mitk::DataNode::New(); dataNodeHbO2->SetData(HbO2); dataNodeHbO2->SetName("HbO2 " + Algorithm); this->GetDataStorage()->Add(dataNodeHbO2); } if (DeOxbool) { mitk::Image::Pointer Hb = m_SpectralUnmixingFilter->GetOutput(1); mitk::DataNode::Pointer dataNodeHb = mitk::DataNode::New(); dataNodeHb->SetData(Hb); dataNodeHb->SetName("Hb " + Algorithm); this->GetDataStorage()->Add(dataNodeHb); } //Calculate oxygen saturation bool sO2bool = m_Controls.checkBoxsO2->isChecked(); if (sO2bool) { if (!DeOxbool) mitkThrow() << "SELECT CHROMOPHORE DEOXYHEMOGLOBIN!"; if (!Oxbool) mitkThrow() << "SELECT CHROMOPHORE OXYHEMOGLOBIN!"; MITK_INFO << "CALCULATE OXYGEN SATURATION ..."; // Initialize pipeline from SU filter class to SO2 class auto m_sO2 = mitk::pa::SpectralUnmixingSO2::New(); 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(); // Write Output images to Data Storage mitk::Image::Pointer sO2 = m_sO2->GetOutput(0); mitk::DataNode::Pointer dataNodesO2 = mitk::DataNode::New(); dataNodesO2->SetData(sO2); dataNodesO2->SetName("sO2"); this->GetDataStorage()->Add(dataNodesO2); MITK_INFO << "[DONE]"; } mitk::RenderingManager::GetInstance()->InitializeViewsByBoundingObjects(this->GetDataStorage()); MITK_INFO << "Adding images to DataStorage...[DONE]"; } } }