diff --git a/Modules/PhotoacousticsLib/include/mitkPALinearSpectralUnmixingFilter.h b/Modules/PhotoacousticsLib/include/mitkPALinearSpectralUnmixingFilter.h index 88c4f839b7..0419b70de1 100644 --- a/Modules/PhotoacousticsLib/include/mitkPALinearSpectralUnmixingFilter.h +++ b/Modules/PhotoacousticsLib/include/mitkPALinearSpectralUnmixingFilter.h @@ -1,51 +1,53 @@ /*=================================================================== 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(std::string chosenAlgorithm); 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: + }; } } #endif // MITKLINEARPHOTOACOUSTICSPECTRALUNMIXINGFILTER_H diff --git a/Modules/PhotoacousticsLib/src/SUFilter/mitkPALinearSpectralUnmixingFilter.cpp b/Modules/PhotoacousticsLib/src/SUFilter/mitkPALinearSpectralUnmixingFilter.cpp index efa29231e3..4a03392b43 100644 --- a/Modules/PhotoacousticsLib/src/SUFilter/mitkPALinearSpectralUnmixingFilter.cpp +++ b/Modules/PhotoacousticsLib/src/SUFilter/mitkPALinearSpectralUnmixingFilter.cpp @@ -1,96 +1,100 @@ /*=================================================================== 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(std::string chosenAlgorithm) +{ + MITK_INFO << chosenAlgorithm; +} Eigen::VectorXf mitk::pa::LinearSpectralUnmixingFilter::SpectralUnmixingAlgorithm( Eigen::Matrix EndmemberMatrix, Eigen::VectorXf inputVector) { //test other solvers https://eigen.tuxfamily.org/dox/group__TutorialLinearAlgebra.html int choseSolver = 3; bool relativErrorBool = false; bool tresholdBool = false; int treshold = 0; int defaultValue = -1; Eigen::Vector2f resultVector; if (choseSolver == 0) { resultVector = EndmemberMatrix.colPivHouseholderQr().solve(inputVector); //not working } if (choseSolver == 1) { resultVector = EndmemberMatrix.llt().solve(inputVector); } if (choseSolver == 2) { resultVector = EndmemberMatrix.householderQr().solve(inputVector); } if (choseSolver == 3) { resultVector = EndmemberMatrix.ldlt().solve(inputVector); //until now 'best' algorithm } if (relativErrorBool) { double relativeError = (EndmemberMatrix*inputVector - resultVector).norm() / resultVector.norm(); // norm() is L2 norm MITK_INFO << "rel err: " << relativeError; } //Set threshold and replace with default value if under threshold if (tresholdBool) { for (int i = 0; i < 2; ++i) { if (resultVector[i] < treshold) { resultVector[i] = defaultValue; MITK_INFO << "UNMIXING RESULT N/A"; } } } return resultVector; } diff --git a/Modules/PhotoacousticsLib/src/SUFilter/mitkPASpectralUnmixingFilterBase.cpp b/Modules/PhotoacousticsLib/src/SUFilter/mitkPASpectralUnmixingFilterBase.cpp index 943f52a41e..3b2bcd3112 100644 --- a/Modules/PhotoacousticsLib/src/SUFilter/mitkPASpectralUnmixingFilterBase.cpp +++ b/Modules/PhotoacousticsLib/src/SUFilter/mitkPASpectralUnmixingFilterBase.cpp @@ -1,216 +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 "mitkPASpectralUnmixingFilterBase.h" // Includes for AddEnmemberMatrix #include "mitkPAPropertyCalculator.h" #include // ImageAccessor #include #include // For testing reasons #include mitk::pa::SpectralUnmixingFilterBase::SpectralUnmixingFilterBase() { this->SetNumberOfIndexedOutputs(2); for (unsigned int i = 0; iSetNthOutput(i, mitk::Image::New()); } m_PropertyCalculator = mitk::pa::PropertyCalculator::New(); } mitk::pa::SpectralUnmixingFilterBase::~SpectralUnmixingFilterBase() { } void mitk::pa::SpectralUnmixingFilterBase::AddWavelength(int wavelength) { m_Wavelength.push_back(wavelength); } void mitk::pa::SpectralUnmixingFilterBase::AddChromophore(ChromophoreType chromophore) { m_Chromophore.push_back(chromophore); } void mitk::pa::SpectralUnmixingFilterBase::GenerateData() { MITK_INFO << "GENERATING DATA.."; // Get input image mitk::Image::Pointer input = GetInput(0); unsigned int xDim = input->GetDimensions()[0]; unsigned int yDim = input->GetDimensions()[1]; unsigned int zDim = input->GetDimensions()[2]; unsigned int size = xDim * yDim * zDim; MITK_INFO << "x dimension: " << xDim; MITK_INFO << "y dimension: " << yDim; MITK_INFO << "z dimension: " << zDim; InitializeOutputs(); auto EndmemberMatrix = AddEndmemberMatrix(); // Copy input image into array mitk::ImageReadAccessor readAccess(input); const float* inputDataArray = ((const float*)readAccess.GetData()); CheckPreConditions(size, zDim, inputDataArray); /* READ OUT INPUTARRAY MITK_INFO << "Info Array:"; int numberOfPixels= 6; for (int i=0; i< numberOfPixels; ++i) MITK_INFO << inputDataArray[i];/**/ // test to see pixel values @ txt file ofstream myfile; myfile.open("PASpectralUnmixingPixelValues.txt"); //loop over every pixel @ x,y plane for (unsigned int x = 0; x < xDim; x++) { for (unsigned int y = 0; y < yDim; y++) { Eigen::VectorXf inputVector(zDim); for (unsigned int z = 0; z < zDim; z++) { // Get pixel value of pixel x,y @ wavelength z unsigned int pixelNumber = (xDim*yDim*z) + x * yDim + y; auto pixel = inputDataArray[pixelNumber]; //MITK_INFO << "Pixel_values: " << pixel; // dummy values for pixel for testing purposes //float pixel = rand(); //write all wavelength absorbtion values for one(!) pixel to a vector inputVector[z] = pixel; } Eigen::VectorXf resultVector = SpectralUnmixingAlgorithm(EndmemberMatrix, inputVector); // write output for (int outputIdx = 0; outputIdx < GetNumberOfIndexedOutputs(); ++outputIdx) { auto output = GetOutput(outputIdx); mitk::ImageWriteAccessor writeOutput(output); float* writeBuffer = (float *)writeOutput.GetData(); writeBuffer[x*yDim + y] = resultVector[outputIdx]; } myfile << "Input Pixel(x,y): " << x << "," << y << "\n" << inputVector << "\n"; myfile << "Result: " << "\n Hb: " << resultVector[0] << "\n HbO2: " << resultVector[1] <<"\n"; } } MITK_INFO << "GENERATING DATA...[DONE]"; myfile.close(); } void mitk::pa::SpectralUnmixingFilterBase::CheckPreConditions(unsigned int size, unsigned int NumberOfInputImages, const float* inputDataArray) { // Checking if number of Inputs == added wavelengths if (m_Wavelength.size() != NumberOfInputImages) mitkThrow() << "CHECK INPUTS! WAVELENGTHERROR"; // Checking if number of wavelengths >= number of chromophores if (m_Chromophore.size() > m_Wavelength.size()) mitkThrow() << "PRESS 'IGNORE' AND ADD MORE WAVELENGTHS!"; // Checking if pixel type is float int maxPixel = size; for (int i = 0; i < maxPixel; ++i) { if (typeid(inputDataArray[i]).name() != typeid(float).name()) { mitkThrow() << "PIXELTYPE ERROR! FLOAT 32 REQUIRED"; } else continue; } MITK_INFO << "CHECK PRECONDITIONS ...[DONE]"; } void mitk::pa::SpectralUnmixingFilterBase::InitializeOutputs() { unsigned int numberOfInputs = GetNumberOfIndexedInputs(); unsigned int numberOfOutputs = GetNumberOfIndexedOutputs(); //MITK_INFO << "Inputs: " << numberOfInputs << " Outputs: " << numberOfOutputs; // Set dimensions (2) and pixel type (float) for output mitk::PixelType pixelType = mitk::MakeScalarPixelType(); const int NUMBER_OF_SPATIAL_DIMENSIONS = 2; auto* dimensions = new unsigned int[NUMBER_OF_SPATIAL_DIMENSIONS]; for(unsigned int dimIdx=0; dimIdxGetDimensions()[dimIdx]; } // Initialize numberOfOutput pictures with pixel type and dimensions for (unsigned int outputIdx = 0; outputIdx < numberOfOutputs; outputIdx++) { GetOutput(outputIdx)->Initialize(pixelType, NUMBER_OF_SPATIAL_DIMENSIONS, dimensions); } } //Matrix with #chromophores rows and #wavelengths columns //so Matrix Element (i,j) contains the Absorbtion of chromophore i @ wavelength j Eigen::Matrix mitk::pa::SpectralUnmixingFilterBase::AddEndmemberMatrix() { unsigned int numberOfChromophores = m_Chromophore.size(); //rows unsigned int numberOfWavelengths = m_Wavelength.size(); //columns Eigen::Matrix EndmemberMatrix(numberOfChromophores, numberOfWavelengths); //loop over i rows (Chromophores) for(unsigned int i = 0; i < numberOfChromophores; ++i) { //loop over j columns (Wavelengths) for (unsigned int j = 0; j < numberOfWavelengths; ++j) { //writes @ Matrix element (i,j) the absorbtion wavelength of the propertycalculator.cpp //'i+1' because MapType is defined different then ChromophoreType EndmemberMatrix(i,j)= m_PropertyCalculator->GetAbsorptionForWavelength( static_cast(m_Chromophore[i]+1), m_Wavelength[j]); - //* Tests to see what gets written in the Matrix: + /* Tests to see what gets written in the Matrix: auto testtype = m_PropertyCalculator->GetAbsorptionForWavelength( static_cast(m_Chromophore[i]+1), m_Wavelength[j]); MITK_INFO << "TEST_TYPE Matrix: " << typeid(EndmemberMatrix(i,j)).name(); MITK_INFO << "map type: " << static_cast(m_Chromophore[i]+1); MITK_INFO << "wavelength: " << m_Wavelength[j]; MITK_INFO << "Matrixelement: (" << i << ", " << j << ") Absorbtion: " << EndmemberMatrix(i, j);/**/ if (EndmemberMatrix(i, j) == 0) { m_Wavelength.clear(); mitkThrow() << "WAVELENGTH "<< m_Wavelength[j] << "nm NOT SUPPORTED!"; } } } MITK_INFO << "GENERATING ENMEMBERMATRIX [DONE]!"; return EndmemberMatrix; } 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 b072bba50c..fe63271301 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 @@ -1,190 +1,195 @@ /*=================================================================== 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); - // Wavelength implementation into fiter + // Set Algortihm to filter + QString fooChosenAlgorithm = m_Controls.QComboBoxAlgorithm->currentText(); + std::string chosenAlgorithm = fooChosenAlgorithm.toLocal8Bit().constData(); + m_SpectralUnmixingFilter->SetAlgorithm(chosenAlgorithm); + + // 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); 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 73093ff3d6..50771f5cfd 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 @@ -1,151 +1,233 @@ SpectralUnmixingControls 0 0 222 399 0 0 QmitkTemplate - - - - true - - - Deoxygenated hemoglobin - - - true - - - true - - - false - - - 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 - + + + + + ldlt + + + + + llt + + + + + colPivHouseholderQr + + + + + householderQr + + + + + test + + + + + Qt::Horizontal - + Qt::Horizontal - + + + + + 75 + true + + + + Wavelengths settings + + + + Qt::Horizontal + + + + Qt::Horizontal + + + + + + + + 75 + true + + + + Chromophore settings + + + + + + + Qt::Horizontal + + + + + + + + 75 + true + + + + Unmixing algorithm + + +