diff --git a/Modules/PhotoacousticsLib/include/mitkPALinearSpectralUnmixingFilter.h b/Modules/PhotoacousticsLib/include/mitkPALinearSpectralUnmixingFilter.h index 5d99dc0c68..ace3e74ad9 100644 --- a/Modules/PhotoacousticsLib/include/mitkPALinearSpectralUnmixingFilter.h +++ b/Modules/PhotoacousticsLib/include/mitkPALinearSpectralUnmixingFilter.h @@ -1,59 +1,62 @@ /*=================================================================== 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 MITKLINEARPHOTOACOUSTICSPECTRALUNMIXINGFILTER_H #define MITKLINEARPHOTOACOUSTICSPECTRALUNMIXINGFILTER_H #include #include namespace mitk { namespace pa { class MITKPHOTOACOUSTICSLIB_EXPORT LinearSpectralUnmixingFilter : public SpectralUnmixingFilterBase { public: mitkClassMacro(LinearSpectralUnmixingFilter, SpectralUnmixingFilterBase) itkFactorylessNewMacro(Self) void mitk::pa::LinearSpectralUnmixingFilter::SetAlgorithm(int SetAlgorithmIndex); enum AlgortihmType { + householderQr, ldlt, llt, colPivHouseholderQr, - householderQr, + jacobiSvd, + fullPivLu, + fullPivHouseholderQr, test }; protected: LinearSpectralUnmixingFilter(); virtual ~LinearSpectralUnmixingFilter(); // Test algorithm for SU --> later a new class should be set up virtual Eigen::VectorXf SpectralUnmixingAlgorithm(Eigen::Matrix EndmemberMatrix, Eigen::VectorXf inputVector) override; private: mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType algorithmIndex; }; } } #endif // MITKLINEARPHOTOACOUSTICSPECTRALUNMIXINGFILTER_H diff --git a/Modules/PhotoacousticsLib/src/SUFilter/mitkPALinearSpectralUnmixingFilter.cpp b/Modules/PhotoacousticsLib/src/SUFilter/mitkPALinearSpectralUnmixingFilter.cpp index 5ac1d3fe9e..1719db394e 100644 --- a/Modules/PhotoacousticsLib/src/SUFilter/mitkPALinearSpectralUnmixingFilter.cpp +++ b/Modules/PhotoacousticsLib/src/SUFilter/mitkPALinearSpectralUnmixingFilter.cpp @@ -1,108 +1,107 @@ /*=================================================================== 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" // Includes for AddEnmemberMatrix #include "mitkPAPropertyCalculator.h" #include // Testing algorithms #include // ImageAccessor #include #include mitk::pa::LinearSpectralUnmixingFilter::LinearSpectralUnmixingFilter() { } mitk::pa::LinearSpectralUnmixingFilter::~LinearSpectralUnmixingFilter() { } void mitk::pa::LinearSpectralUnmixingFilter::SetAlgorithm(int SetAlgorithmIndex) { algorithmIndex = static_cast(SetAlgorithmIndex); } Eigen::VectorXf mitk::pa::LinearSpectralUnmixingFilter::SpectralUnmixingAlgorithm( Eigen::Matrix EndmemberMatrix, Eigen::VectorXf inputVector) { //test other solvers https://eigen.tuxfamily.org/dox/group__TutorialLinearAlgebra.html - bool relativErrorBool = false; - bool tresholdBool = false; - int treshold = 0; - int defaultValue = -1; - Eigen::Vector2f resultVector; if (mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::colPivHouseholderQr == algorithmIndex) { resultVector = EndmemberMatrix.colPivHouseholderQr().solve(inputVector); //works :) } if (mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::llt == algorithmIndex) { resultVector = EndmemberMatrix.llt().solve(inputVector); //works with negativ values (no correct unmixing) } if (mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::householderQr == algorithmIndex) { resultVector = EndmemberMatrix.householderQr().solve(inputVector); //works :) } if (mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::ldlt == algorithmIndex) { mitkThrow() << "not working"; - resultVector = EndmemberMatrix.ldlt().solve(inputVector); //not working because matrix not quadratic(?) } - //testing new algorithms: - if (mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::test == algorithmIndex) + if (mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::jacobiSvd == algorithmIndex) { - mitkThrow() << "nothing implemented"; + mitkThrow() << "not working"; + resultVector = EndmemberMatrix.jacobiSvd().solve(inputVector); //not working } - if (relativErrorBool) + if (mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::fullPivLu == algorithmIndex) { - double relativeError = (EndmemberMatrix*inputVector - resultVector).norm() / resultVector.norm(); // norm() is L2 norm - MITK_INFO << "rel err: " << relativeError; + resultVector = EndmemberMatrix.fullPivLu().solve(inputVector); //works :) } - //Set threshold and replace with default value if under threshold - if (tresholdBool) + if (mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::householderQr == algorithmIndex) { - for (int i = 0; i < 2; ++i) - { - if (resultVector[i] < treshold) - { - resultVector[i] = defaultValue; - MITK_INFO << "UNMIXING RESULT N/A"; - } - } + resultVector = EndmemberMatrix.householderQr().solve(inputVector); //works :) + } + + if (mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::fullPivHouseholderQr == algorithmIndex) + { + resultVector = EndmemberMatrix.fullPivHouseholderQr().solve(inputVector);//works :) + } + + //testing new algorithms: + if (mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::test == algorithmIndex) + { + mitkThrow() << "nothing implemented"; } - bool resultIsApprox = inputVector.isApprox(EndmemberMatrix*resultVector); - MITK_INFO << "IS APPROX RESULT: " << resultIsApprox; + double relativeError = (EndmemberMatrix*resultVector - inputVector).norm() / inputVector.norm(); // norm() is L2 norm + //MITK_INFO << "relativ error: " << relativeError; + float accuracyLevel = .1; + bool resultIsApprox = inputVector.isApprox(EndmemberMatrix*resultVector, accuracyLevel); + //MITK_INFO << "IS APPROX RESULT: " << resultIsApprox; return resultVector; } diff --git a/Modules/PhotoacousticsLib/test/mitkSpectralUnmixingTest.cpp b/Modules/PhotoacousticsLib/test/mitkSpectralUnmixingTest.cpp index f2a4ea7343..17c20cdd80 100644 --- a/Modules/PhotoacousticsLib/test/mitkSpectralUnmixingTest.cpp +++ b/Modules/PhotoacousticsLib/test/mitkSpectralUnmixingTest.cpp @@ -1,50 +1,49 @@ ///*=================================================================== //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 class mitkSpectralUnmixingTestSuite : public mitk::TestFixture { CPPUNIT_TEST_SUITE(mitkSpectralUnmixingTestSuite); MITK_TEST(testSUAlgorithm); CPPUNIT_TEST_SUITE_END(); private: mitk::pa::SpectralUnmixingFilterBase::Pointer m_SpectralUnmixingFilter; public: void setUp() override { } void testSUAlgorithm() { // INSERT TEST HERE? MITK_INFO << "TEST TEST"; - } void tearDown() override { m_SpectralUnmixingFilter = nullptr; } }; MITK_TEST_SUITE_REGISTRATION(mitkSpectralUnmixing) 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 3236b12b0c..e3ef04c10a 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 @@ -1,194 +1,200 @@ /*=================================================================== 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" 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(); auto m_SpectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New(); m_SpectralUnmixingFilter->SetInput(image); // Set Algortihm to filter int SetAlgorithmIndex = m_Controls.QComboBoxAlgorithm->currentIndex(); m_SpectralUnmixingFilter->SetAlgorithm(SetAlgorithmIndex); // 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( mitk::pa::SpectralUnmixingFilterBase::ChromophoreType::DEOXYGENATED_HEMOGLOBIN); } if (numberofChromophores == 0) { mitkThrow() << "PRESS 'IGNORE' AND CHOOSE A CHROMOPHORE!"; } MITK_INFO << "Updating Filter..."; m_SpectralUnmixingFilter->Update(); - mitk::Image::Pointer Hb = m_SpectralUnmixingFilter->GetOutput(0); - mitk::DataNode::Pointer dataNodeHb = mitk::DataNode::New(); - dataNodeHb->SetData(Hb); - dataNodeHb->SetName("Hb"); - this->GetDataStorage()->Add(dataNodeHb); - - mitk::Image::Pointer HbO2 = m_SpectralUnmixingFilter->GetOutput(1); - mitk::DataNode::Pointer dataNodeHbO2 = mitk::DataNode::New(); - dataNodeHbO2->SetData(HbO2); - dataNodeHbO2->SetName("HbO2"); - this->GetDataStorage()->Add(dataNodeHbO2); + if (DeOxbool) + { + mitk::Image::Pointer Hb = m_SpectralUnmixingFilter->GetOutput(0); + mitk::DataNode::Pointer dataNodeHb = mitk::DataNode::New(); + dataNodeHb->SetData(Hb); + dataNodeHb->SetName("Hb"); + this->GetDataStorage()->Add(dataNodeHb); + } + + if (Oxbool) + { + mitk::Image::Pointer HbO2 = m_SpectralUnmixingFilter->GetOutput(1); + mitk::DataNode::Pointer dataNodeHbO2 = mitk::DataNode::New(); + dataNodeHbO2->SetData(HbO2); + dataNodeHbO2->SetName("HbO2"); + this->GetDataStorage()->Add(dataNodeHbO2); + } mitk::RenderingManager::GetInstance()->InitializeViewsByBoundingObjects(this->GetDataStorage()); MITK_INFO << "Adding images to DataStorage...[DONE]"; } } } diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/src/internal/SpectralUnmixingControls.ui b/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/src/internal/SpectralUnmixingControls.ui index 50771f5cfd..db554dbecc 100644 --- a/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/src/internal/SpectralUnmixingControls.ui +++ b/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/src/internal/SpectralUnmixingControls.ui @@ -1,233 +1,248 @@ SpectralUnmixingControls 0 0 222 399 0 0 QmitkTemplate QLabel { color: rgb(255, 0, 0) } Please select an image! Qt::Vertical 20 40 Do image processing Perform spectral unmixing Oxyhemoglobin true true Deoxygenated hemoglobin true true false Add Wavelength [nm] Qt::Vertical 2000 Clear all Wavelengths + + + householderQr + + ldlt llt colPivHouseholderQr - householderQr + jacobiSvd + + + + + fullPivLu + + + + + fullPivHouseholderQr test Qt::Horizontal Qt::Horizontal 75 true Wavelengths settings Qt::Horizontal Qt::Horizontal 75 true Chromophore settings Qt::Horizontal 75 true Unmixing algorithm