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 ba8133fdec..b5df5bc14f 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 @@ -1,358 +1,358 @@ /*=================================================================== 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 == "NNLARS") { m_SpectralUnmixingFilter = mitk::pa::SpectralUnmixingFilterVigra::New(); dynamic_cast(m_SpectralUnmixingFilter.GetPointer()) ->SetAlgorithm(mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::LARS); } - else if (Algorithm == "Goldfarb") + 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); } 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(); // 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); } 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]"; } } } 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 a2bfd48a8e..32f2be545a 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 @@ -1,846 +1,842 @@ SpectralUnmixingControls 0 0 398 575 0 0 QmitkTemplate QLabel { color: rgb(255, 0, 0) } Please select an image! Qt::Horizontal Do image processing Perform spectral unmixing Qt::Horizontal 75 true Wavelengths settings 0 75 16777215 75 10 true Qt::SolidLine 42 50 30 30 λ/nm Weights 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 720 755 831 906 942 Qt::Horizontal 75 true Chromophore settings Oxyhemoglobin true true Deoxygenated hemoglobin true true false Melanin Additional Endmember Qt::Horizontal 75 true Unmixing algorithm true MS Shell Dlg 2 false 21 2147483647 ==CHOSE ALGORITHM== - ==EIGEN== + ==QR decomposition== householderQr - ldlt + colPivHouseholderQr - llt - - - - .. + fullPivHouseholderQr - colPivHouseholderQr + ==LU decompositon - jacobiSvd + fullPivLu - fullPivLu + ==Cholesky decompostion== - fullPivHouseholderQr + ldlt - test + llt + + + + .. - ==Vigra== + ==Least squares== - LARS + jacobiSvd - Goldfarb + NNLARS - weighted + NNGoldfarb - vigratest + weighted ==Others== SimplexMax Lagrange - otherstest + ==Test algorithms== + + + + + test + + + + + vigratest Qt::Horizontal 75 true Oxygen saturation calculate sO2 false 380 82 Value Min Hb Min HbO2 Min Sum Min SO2 % 100 200 200 50 Qt::Horizontal - - - - Chrono - - - - - - - Qt::Horizontal - - - Qt::Vertical 20 69