diff --git a/Modules/PhotoacousticsLib/src/SUFilter/mitkPASpectralUnmixingFilterBase.cpp b/Modules/PhotoacousticsLib/src/SUFilter/mitkPASpectralUnmixingFilterBase.cpp index 82e29a6ced..468619d541 100644 --- a/Modules/PhotoacousticsLib/src/SUFilter/mitkPASpectralUnmixingFilterBase.cpp +++ b/Modules/PhotoacousticsLib/src/SUFilter/mitkPASpectralUnmixingFilterBase.cpp @@ -1,225 +1,225 @@ /*=================================================================== 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); + this->SetNumberOfIndexedOutputs(4);// find solution for (unsigned int i = 0; iSetNthOutput(i, mitk::Image::New()); } m_PropertyCalculatorEigen = 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(mitk::pa::PropertyCalculator::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 = CalculateEndmemberMatrix(m_Chromophore, m_Wavelength); //Eigen Endmember Matrix // 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); //Eigen::VectorXf resultVector = SpectralUnmixingAlgorithm(m_Chromophore, 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 HbO2: " << resultVector[0] << "\n Hb: " << 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 colums and #wavelengths rows //so Matrix Element (i,j) contains the Absorbtion of chromophore j @ wavelength i Eigen::Matrix mitk::pa::SpectralUnmixingFilterBase::CalculateEndmemberMatrix( std::vector m_Chromophore, std::vector m_Wavelength) { unsigned int numberOfChromophores = m_Chromophore.size(); //columns unsigned int numberOfWavelengths = m_Wavelength.size(); //rows Eigen::Matrix EndmemberMatrixEigen(numberOfWavelengths, numberOfChromophores); for (unsigned int j = 0; j < numberOfChromophores; ++j) { if (m_Chromophore[j] == mitk::pa::PropertyCalculator::ChromophoreType::OXYGENATED) { for (unsigned int i = 0; i < numberOfWavelengths; ++i) EndmemberMatrixEigen(i, j) = propertyElement(m_Chromophore[j], m_Wavelength[i]); } else if (m_Chromophore[j] == mitk::pa::PropertyCalculator::ChromophoreType::DEOXYGENATED) { for (unsigned int i = 0; i < numberOfWavelengths; ++i) EndmemberMatrixEigen(i, j) = propertyElement(m_Chromophore[j], m_Wavelength[i]); } else if (m_Chromophore[j] == mitk::pa::PropertyCalculator::ChromophoreType::MELANIN) { for (unsigned int i = 0; i < numberOfWavelengths; ++i) + { EndmemberMatrixEigen(i, j) = propertyElement(m_Chromophore[j], m_Wavelength[i]); + MITK_INFO << "MELANIN." << EndmemberMatrixEigen(i, j); + } } else if (m_Chromophore[j] == mitk::pa::PropertyCalculator::ChromophoreType::ONEENDMEMBER) { for (unsigned int i = 0; i < numberOfWavelengths; ++i) EndmemberMatrixEigen(i, j) = 1; } else mitkThrow() << "404 CHROMOPHORE NOT FOUND!"; } //MITK_INFO << "GENERATING ENMEMBERMATRIX [DONE]!"; return EndmemberMatrixEigen; } float mitk::pa::SpectralUnmixingFilterBase::propertyElement(mitk::pa::PropertyCalculator::ChromophoreType Chromophore, int Wavelength) { float value = m_PropertyCalculatorEigen->GetAbsorptionForWavelength(Chromophore, Wavelength); if (value == 0) mitkThrow() << "WAVELENGTH " << Wavelength << "nm NOT SUPPORTED!"; return value; } 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 3adbf7d38d..dae5c5085e 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 @@ -1,310 +1,343 @@ /*=================================================================== 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); } 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(); mitk::pa::SpectralUnmixingFilterBase::Pointer m_SpectralUnmixingFilter; if (Algorithm == "householderQr") { m_SpectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New(); dynamic_cast(m_SpectralUnmixingFilter.GetPointer()) ->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::householderQr); } else if (Algorithm == "ldlt") { m_SpectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New(); dynamic_cast(m_SpectralUnmixingFilter.GetPointer()) ->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::ldlt); } else if (Algorithm == "llt") { m_SpectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New(); dynamic_cast(m_SpectralUnmixingFilter.GetPointer()) ->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::llt); } else if (Algorithm == "colPivHouseholderQr") { m_SpectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New(); dynamic_cast(m_SpectralUnmixingFilter.GetPointer()) ->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::colPivHouseholderQr); } else if (Algorithm == "jacobiSvd") { m_SpectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New(); dynamic_cast(m_SpectralUnmixingFilter.GetPointer()) ->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::jacobiSvd); } else if (Algorithm == "fullPivLu") { m_SpectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New(); dynamic_cast(m_SpectralUnmixingFilter.GetPointer()) ->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::fullPivLu); } else if (Algorithm == "fullPivHouseholderQr") { m_SpectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New(); dynamic_cast(m_SpectralUnmixingFilter.GetPointer()) ->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::fullPivHouseholderQr); } else if (Algorithm == "test") { m_SpectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New(); dynamic_cast(m_SpectralUnmixingFilter.GetPointer()) ->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::test); } - else if (Algorithm == "Lars") + else if (Algorithm == "LARS") { m_SpectralUnmixingFilter = mitk::pa::SpectralUnmixingFilterVigra::New(); dynamic_cast(m_SpectralUnmixingFilter.GetPointer()) ->SetAlgorithm(mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::LARS); } else if (Algorithm == "Goldfarb") { m_SpectralUnmixingFilter = mitk::pa::SpectralUnmixingFilterVigra::New(); dynamic_cast(m_SpectralUnmixingFilter.GetPointer()) ->SetAlgorithm(mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::GOLDFARB); } else if (Algorithm == "weighted") { m_SpectralUnmixingFilter = mitk::pa::SpectralUnmixingFilterVigra::New(); dynamic_cast(m_SpectralUnmixingFilter.GetPointer()) ->SetAlgorithm(mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::WEIGHTED); } else if (Algorithm == "vigratest") { m_SpectralUnmixingFilter = mitk::pa::SpectralUnmixingFilterVigra::New(); dynamic_cast(m_SpectralUnmixingFilter.GetPointer()) ->SetAlgorithm(mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::vigratest); } else if (Algorithm == "SimplexMax") { m_SpectralUnmixingFilter = mitk::pa::SpectralUnmixingFilterSimplex::New(); dynamic_cast(m_SpectralUnmixingFilter.GetPointer()); } else mitkThrow() << "404 ALGORITHM NOT FOUND!"; m_SpectralUnmixingFilter->SetInput(image); // Wavelength implementation ClearWavelength(); 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); ++col; } // Checking which chromophores wanted for SU if none throw exeption! unsigned int numberofChromophores = 0; DeOxbool = m_Controls.checkBoxDeOx->isChecked(); Oxbool = m_Controls.checkBoxOx->isChecked(); + bool Melaninbool = m_Controls.checkBoxMelanin->isChecked(); + bool Onebool = m_Controls.checkBoxAdd->isChecked(); if (DeOxbool || Oxbool) { MITK_INFO << "CHOSEN CHROMOPHORES:"; } if (Oxbool) { numberofChromophores += 1; MITK_INFO << "- Oxyhemoglobin"; // Set chromophore Oxyhemoglobon: m_SpectralUnmixingFilter->AddChromophore( mitk::pa::PropertyCalculator::ChromophoreType::OXYGENATED); } if (DeOxbool) { numberofChromophores += 1; MITK_INFO << "- Deoxygenated hemoglobin"; // Set chromophore Deoxygenated hemoglobin: m_SpectralUnmixingFilter->AddChromophore( mitk::pa::PropertyCalculator::ChromophoreType::DEOXYGENATED); } + if (Melaninbool) + { + numberofChromophores += 1; + MITK_INFO << "- Melanin"; + m_SpectralUnmixingFilter->AddChromophore( + mitk::pa::PropertyCalculator::ChromophoreType::MELANIN); + } + if (Onebool) + { + numberofChromophores += 1; + MITK_INFO << "- Additional Chromophore"; + m_SpectralUnmixingFilter->AddChromophore( + mitk::pa::PropertyCalculator::ChromophoreType::ONEENDMEMBER); + } 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); } + if (Melaninbool) + { + mitk::Image::Pointer Melanin = m_SpectralUnmixingFilter->GetOutput(2); + mitk::DataNode::Pointer dataNodeMelanin = mitk::DataNode::New(); + dataNodeMelanin->SetData(Melanin); + dataNodeMelanin->SetName("Melanin " + Algorithm); + this->GetDataStorage()->Add(dataNodeMelanin); + } + + if (Onebool) + { + mitk::Image::Pointer One = m_SpectralUnmixingFilter->GetOutput(3); + mitk::DataNode::Pointer dataNodeOne = mitk::DataNode::New(); + dataNodeOne->SetData(One); + dataNodeOne->SetName("One " + Algorithm); + this->GetDataStorage()->Add(dataNodeOne); + } + //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]"; } } }