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 d72b766f1a..4e9e4be3da 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 @@ -1,378 +1,384 @@ /*=================================================================== 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); } +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") + { + spectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New(); + dynamic_cast(spectralUnmixingFilter.GetPointer()) + ->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::ldlt); + } + + else if (algorithm == "llt") + { + 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 == "test") + { + spectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New(); + dynamic_cast(spectralUnmixingFilter.GetPointer()) + ->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::test); + } + + 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 + int colunm = 0; + int Weight = 1; + while (m_Controls.inputtable->item(1, colunm) && Weight > 0) + { + QString Text = m_Controls.inputtable->item(1, colunm)->text(); + Weight = Text.toInt(); + if (Weight > 0) + spectralUnmixingFilter->AddWeight(Weight); + ++colunm; + } + } + + else if (algorithm == "LS") + { + spectralUnmixingFilter = mitk::pa::SpectralUnmixingFilterVigra::New(); + dynamic_cast(spectralUnmixingFilter.GetPointer()) + ->SetAlgorithm(mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::LS); + } + + else if (algorithm == "vigratest") + { + spectralUnmixingFilter = mitk::pa::SpectralUnmixingFilterVigra::New(); + dynamic_cast(spectralUnmixingFilter.GetPointer()) + ->SetAlgorithm(mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::vigratest); + } + + else if (algorithm == "SimplexMax") + { + spectralUnmixingFilter = mitk::pa::SpectralUnmixingFilterSimplex::New(); + } + + else + mitkThrow() << "404 ALGORITHM NOT FOUND!"; + + return spectralUnmixingFilter; +} + 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(); //Tranfer GUI information(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); - } + mitk::pa::SpectralUnmixingFilterBase::Pointer m_SpectralUnmixingFilter = GetFilterInstance(Algorithm); - else if (Algorithm == "test") - { - m_SpectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New(); - dynamic_cast(m_SpectralUnmixingFilter.GetPointer()) - ->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::test); - } - else if (Algorithm == "NNLARS") - { - m_SpectralUnmixingFilter = mitk::pa::SpectralUnmixingFilterVigra::New(); - dynamic_cast(m_SpectralUnmixingFilter.GetPointer()) - ->SetAlgorithm(mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::LARS); - } - - else if (Algorithm == "NNGoldfarb") - { - 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); - //Tranfer GUI information(Weights) to filter - int colunm = 0; - int Weight = 1; - while (m_Controls.inputtable->item(1, colunm) && Weight > 0) - { - QString Text = m_Controls.inputtable->item(1, colunm)->text(); - Weight = Text.toInt(); - if (Weight > 0) - m_SpectralUnmixingFilter->AddWeight(Weight); - ++colunm; - } - } - - else if (Algorithm == "LS") - { - m_SpectralUnmixingFilter = mitk::pa::SpectralUnmixingFilterVigra::New(); - dynamic_cast(m_SpectralUnmixingFilter.GetPointer()) - ->SetAlgorithm(mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::LS); - } - - 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); //Tranfer GUI information(Wavelength) to filter 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; } //Tranfer GUI information(Chromophores) to filter 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"; m_SpectralUnmixingFilter->AddChromophore( mitk::pa::PropertyCalculator::ChromophoreType::OXYGENATED); } if (DeOxbool) { numberofChromophores += 1; MITK_INFO << "- 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(); int outputCounter = 0; // Write Output images to Data Storage if (Oxbool) { - mitk::Image::Pointer HbO2 = m_SpectralUnmixingFilter->GetOutput(outputCounter); - outputCounter += 1; + mitk::Image::Pointer HbO2 = m_SpectralUnmixingFilter->GetOutput(outputCounter++); 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(outputCounter); - outputCounter += 1; + mitk::Image::Pointer Hb = m_SpectralUnmixingFilter->GetOutput(outputCounter++); 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(outputCounter); - outputCounter += 1; + mitk::Image::Pointer Melanin = m_SpectralUnmixingFilter->GetOutput(outputCounter++); 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(outputCounter); + mitk::Image::Pointer One = m_SpectralUnmixingFilter->GetOutput(outputCounter++); 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 ..."; auto m_sO2 = mitk::pa::SpectralUnmixingSO2::New(); // Oxygen Saturation Setting for (int i = 0; i < 4; ++i) { if (m_Controls.inputtable->item(0, i)) { QString Text = m_Controls.tableSO2->item(0, i)->text(); float value = Text.toFloat(); MITK_INFO << "value: " << value; m_sO2->AddSO2Settings(value); } else m_sO2->AddSO2Settings(0); } // 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(); // 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" + Algorithm); this->GetDataStorage()->Add(dataNodesO2); MITK_INFO << "[DONE]"; } 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/SpectralUnmixing.h b/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/src/internal/SpectralUnmixing.h index ba9fed9c5c..fd57cc12cf 100644 --- a/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/src/internal/SpectralUnmixing.h +++ b/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/src/internal/SpectralUnmixing.h @@ -1,57 +1,60 @@ /*=================================================================== 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 SpectralUnmixing_h #define SpectralUnmixing_h #include #include +#include #include "ui_SpectralUnmixingControls.h" class SpectralUnmixing : public QmitkAbstractView { // this is needed for all Qt objects that should have a Qt meta-object // (everything that derives from QObject and wants to have signal/slots) Q_OBJECT public: static const std::string VIEW_ID; protected: virtual void CreateQtPartControl(QWidget *parent) override; virtual void SetFocus() override; /// \brief called by QmitkFunctionality when DataManager's selection has changed virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer source, const QList &nodes) override; /// \brief Called when the user clicks the GUI button void DoImageProcessing(); virtual void ClearWavelength(); Ui::SpectralUnmixingControls m_Controls; std::vector m_Wavelengths; + mitk::pa::SpectralUnmixingFilterBase::Pointer GetFilterInstance(std::string algorithm); + // Selection of Chromophores bool DeOxbool; bool Oxbool; }; #endif // SpectralUnmixing_h