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 4723d2171a..eb0ee2243f 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 @@ -1,373 +1,374 @@ /*=================================================================== 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); m_Controls.tableWeight->hide(); m_Controls.tableSO2->hide(); connect((QObject*)(m_Controls.QComboBoxAlgorithm), SIGNAL(currentIndexChanged(int)), this, SLOT(ChangeGUIWeight())); connect((QObject*)(m_Controls.checkBoxsO2), SIGNAL(clicked()), this, SLOT(ChangeGUISO2())); } void SpectralUnmixing::ChangeGUIWeight() { auto qs = m_Controls.QComboBoxAlgorithm->currentText(); std::string Algorithm = qs.toUtf8().constData(); if (Algorithm == "weighted") m_Controls.tableWeight->show(); else m_Controls.tableWeight->hide(); } void SpectralUnmixing::ChangeGUISO2() { if (m_Controls.checkBoxsO2->isChecked()) m_Controls.tableSO2->show(); else m_Controls.tableSO2->hide(); } void SpectralUnmixing::SetVerboseMode(mitk::pa::SpectralUnmixingFilterBase::Pointer m_SpectralUnmixingFilter, bool PluginVerbose) { m_SpectralUnmixingFilter->Verbose(PluginVerbose); } void SpectralUnmixing::SetWavlength(mitk::pa::SpectralUnmixingFilterBase::Pointer m_SpectralUnmixingFilter) { 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); MITK_INFO(PluginVerbose) << "Wavelength: " << Wavelength << "nm \n"; } ++col; } } void SpectralUnmixing::SetChromophore(mitk::pa::SpectralUnmixingFilterBase::Pointer m_SpectralUnmixingFilter, std::vector boolVec, std::vector chromophoreNameVec) { unsigned int numberofChromophores = 0; std::vector m_ChromoType = { mitk::pa::PropertyCalculator::ChromophoreType::OXYGENATED, mitk::pa::PropertyCalculator::ChromophoreType::DEOXYGENATED, mitk::pa::PropertyCalculator::ChromophoreType::MELANIN, mitk::pa::PropertyCalculator::ChromophoreType::ONEENDMEMBER}; for (unsigned int chromo = 0; chromo < m_ChromoType.size(); ++chromo) { if (boolVec[chromo] == true) { MITK_INFO(PluginVerbose) << "Chromophore: " << chromophoreNameVec[chromo]; m_SpectralUnmixingFilter->AddChromophore(m_ChromoType[chromo]); numberofChromophores += 1; } } if (numberofChromophores == 0) mitkThrow() << "PRESS 'IGNORE' AND CHOOSE A CHROMOPHORE!"; } 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 == "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; + unsigned int colunm = 0; int Weight = 1; while (m_Controls.tableWeight->item(0, colunm) && Weight > 0) { QString Text = m_Controls.tableWeight->item(0, colunm)->text(); Weight = Text.toInt(); if (Weight > 0) { dynamic_cast(spectralUnmixingFilter.GetPointer()) ->AddWeight(Weight); MITK_INFO(PluginVerbose) << "Weight: " << Weight; } ++colunm; } } else if (algorithm == "LS") { spectralUnmixingFilter = mitk::pa::SpectralUnmixingFilterVigra::New(); dynamic_cast(spectralUnmixingFilter.GetPointer()) ->SetAlgorithm(mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::LS); } else if (algorithm == "SimplexMax") { spectralUnmixingFilter = mitk::pa::SpectralUnmixingFilterSimplex::New(); } else mitkThrow() << "404 ALGORITHM NOT FOUND!"; return spectralUnmixingFilter; } void SpectralUnmixing::SetSO2Settings(mitk::pa::SpectralUnmixingSO2::Pointer m_sO2) { for (unsigned 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(PluginVerbose) << "SO2 setting value: " << value; m_sO2->AddSO2Settings(value); } else m_sO2->AddSO2Settings(0); } } void SpectralUnmixing::CalculateSO2(mitk::pa::SpectralUnmixingFilterBase::Pointer m_SpectralUnmixingFilter, std::vector boolVec) { MITK_INFO(PluginVerbose) << "CALCULATE OXYGEN SATURATION ..."; if (!boolVec[0]) mitkThrow() << "SELECT CHROMOPHORE DEOXYHEMOGLOBIN!"; if (!boolVec[1]) mitkThrow() << "SELECT CHROMOPHORE OXYHEMOGLOBIN!"; auto m_sO2 = mitk::pa::SpectralUnmixingSO2::New(); m_sO2->Verbose(PluginVerbose); SetSO2Settings(m_sO2); // 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(); mitk::Image::Pointer sO2 = m_sO2->GetOutput(0); - + sO2->SetSpacing(output1->GetGeometry()->GetSpacing()); WriteOutputToDataStorage(sO2, "sO2"); MITK_INFO(PluginVerbose) << "[DONE]"; } void SpectralUnmixing::WriteOutputToDataStorage(mitk::Image::Pointer m_Image, std::string name) { mitk::DataNode::Pointer dataNodeOutput = mitk::DataNode::New(); dataNodeOutput->SetData(m_Image); dataNodeOutput->SetName(name); this->GetDataStorage()->Add(dataNodeOutput); } 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 << "."; PluginVerbose = m_Controls.checkBoxVerbose->isChecked(); MITK_INFO(PluginVerbose) << message.str(); GenerateOutput(image); } } } void SpectralUnmixing::GenerateOutput(mitk::Image::Pointer image) { std::vector boolVec = { m_Controls.checkBoxOx->isChecked(), m_Controls.checkBoxDeOx->isChecked(), m_Controls.checkBoxMelanin->isChecked(), m_Controls.checkBoxAdd->isChecked() }; std::vector chromophoreNameVec = { "HbO2", "Hb", "Melanin", "Static Endmember" }; //Read GUI information(algorithm) auto qs = m_Controls.QComboBoxAlgorithm->currentText(); std::string Algorithm = qs.toUtf8().constData(); mitk::pa::SpectralUnmixingFilterBase::Pointer m_SpectralUnmixingFilter = GetFilterInstance(Algorithm); SetVerboseMode(m_SpectralUnmixingFilter, PluginVerbose); m_SpectralUnmixingFilter->SetInput(image); SetWavlength(m_SpectralUnmixingFilter); SetChromophore(m_SpectralUnmixingFilter, boolVec, chromophoreNameVec); MITK_INFO(PluginVerbose) << "Updating Filter..."; m_SpectralUnmixingFilter->Update(); int outputCounter = 0; mitk::Image::Pointer m_Output; for (unsigned int chromophore = 0; chromophore < chromophoreNameVec.size(); ++chromophore) { if (boolVec[chromophore] != false) { m_Output = m_SpectralUnmixingFilter->GetOutput(outputCounter++); + m_Output->SetSpacing(image->GetGeometry()->GetSpacing()); WriteOutputToDataStorage(m_Output, chromophoreNameVec[chromophore] + Algorithm); } } if (m_Controls.checkBoxsO2->isChecked()) CalculateSO2(m_SpectralUnmixingFilter, boolVec); mitk::RenderingManager::GetInstance()->InitializeViewsByBoundingObjects(this->GetDataStorage()); MITK_INFO(PluginVerbose) << "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 095f4ba348..af319acd6b 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 @@ -1,997 +1,997 @@ SpectralUnmixingControls 0 0 398 - 607 + 620 0 0 QmitkTemplate QLabel { color: rgb(255, 0, 0) } Please select an image! Qt::Horizontal 75 true Wavelengths settings 0 75 16777215 75 10 true Qt::SolidLine 42 50 30 30 λ [nm] 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 + Chromophore selection Oxyhemoglobin true true Deoxygenated hemoglobin true true false Melanin Static Endmember Qt::Horizontal 75 true Unmixing algorithm true MS Shell Dlg 2 false 21 2147483647 ==CHOSE ALGORITHM== ==QR decomposition== householderQr colPivHouseholderQr fullPivHouseholderQr ==LU decompositon fullPivLu ==Cholesky decompostion== ldlt llt .. ==Least squares== LS jacobiSvd NNLARS NNGoldfarb weighted ==Others== SimplexMax true 0 75 380 81 false false Weights [%] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 20 60 85 90 69 52 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 75 true Additional Settings Verbose Mode (additional console outputs) Do image processing Perform spectral unmixing Qt::Horizontal Qt::Vertical 20 40