diff --git a/Modules/PhotoacousticsLib/src/SUFilter/mitkPASpectralUnmixingFilterBase.cpp b/Modules/PhotoacousticsLib/src/SUFilter/mitkPASpectralUnmixingFilterBase.cpp index 614d9f9874..294110db5a 100644 --- a/Modules/PhotoacousticsLib/src/SUFilter/mitkPASpectralUnmixingFilterBase.cpp +++ b/Modules/PhotoacousticsLib/src/SUFilter/mitkPASpectralUnmixingFilterBase.cpp @@ -1,218 +1,218 @@ /*=================================================================== 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 mitk::pa::SpectralUnmixingFilterBase::SpectralUnmixingFilterBase() { m_PropertyCalculatorEigen = mitk::pa::PropertyCalculator::New(); } mitk::pa::SpectralUnmixingFilterBase::~SpectralUnmixingFilterBase() { } void mitk::pa::SpectralUnmixingFilterBase::AddOutputs(unsigned int outputs) { this->SetNumberOfIndexedOutputs(outputs); for (unsigned int i = 0; iSetNthOutput(i, mitk::Image::New()); } 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::Verbose(bool verbose) { m_Verbose = verbose; } void mitk::pa::SpectralUnmixingFilterBase::RelativeError(bool relativeError) { m_RelativeError = relativeError; } void mitk::pa::SpectralUnmixingFilterBase::GenerateData() { MITK_INFO(m_Verbose) << "GENERATING DATA.."; mitk::Image::Pointer input = GetInput(0); unsigned int xDim = input->GetDimensions()[0]; unsigned int yDim = input->GetDimensions()[1]; unsigned int numberOfInputImages = input->GetDimensions()[2]; MITK_INFO(m_Verbose) << "x dimension: " << xDim; MITK_INFO(m_Verbose) << "y dimension: " << yDim; MITK_INFO(m_Verbose) << "z dimension: " << numberOfInputImages; unsigned int sequenceSize = m_Wavelength.size(); unsigned int totalNumberOfSequences = numberOfInputImages / sequenceSize; if (totalNumberOfSequences == 0) //means that more chromophores then wavelengths mitkThrow() << "ERROR! REMOVE WAVELENGTHS!"; MITK_INFO(m_Verbose) << "TotalNumberOfSequences: " << totalNumberOfSequences; InitializeOutputs(totalNumberOfSequences); auto endmemberMatrix = CalculateEndmemberMatrix(m_Chromophore, m_Wavelength); // Copy input image into array mitk::ImageReadAccessor readAccess(input); const float* inputDataArray = ((const float*)readAccess.GetData()); CheckPreConditions(numberOfInputImages, inputDataArray); // test to see pixel values @ txt file myfile.open("SimplexNormalisation.txt"); unsigned int outputCounter = GetNumberOfIndexedOutputs(); std::vector writteBufferVector; - for (int i = 0; i < outputCounter; ++i) + for (unsigned int i = 0; i < outputCounter; ++i) { auto output = GetOutput(i); mitk::ImageWriteAccessor writeOutput(output); float* writeBuffer = (float *)writeOutput.GetData(); writteBufferVector.push_back(writeBuffer); } if (m_RelativeError == true) { // -1 because rel error is output[IndexedOutputs() - 1] and loop over chromophore outputs has to end at [IndexedOutputs() - 2] outputCounter -= 1; } for (unsigned int sequenceCounter = 0; sequenceCounter < totalNumberOfSequences; ++sequenceCounter) { MITK_INFO(m_Verbose) << "SequenceCounter: " << sequenceCounter; //loop over every pixel in XY-plane for (unsigned int x = 0; x < xDim; x++) { for (unsigned int y = 0; y < yDim; y++) { Eigen::VectorXf inputVector(sequenceSize); for (unsigned int z = 0; z < sequenceSize; z++) { /** * 'sequenceCounter*sequenceSize' has to be added to 'z' to ensure that one accesses the * correct pixel, because the inputDataArray contains the information of all sequences and * not just the one of the current sequence. */ unsigned int pixelNumber = (xDim*yDim*(z+sequenceCounter*sequenceSize)) + x * yDim + y; auto pixel = inputDataArray[pixelNumber]; inputVector[z] = pixel; } Eigen::VectorXf resultVector = SpectralUnmixingAlgorithm(endmemberMatrix, inputVector); unsigned int outputCounter = GetNumberOfIndexedOutputs(); if (m_RelativeError == true) { float relativeError = (endmemberMatrix*resultVector - inputVector).norm() / inputVector.norm(); // norm() is L2 norm writteBufferVector[outputCounter][(xDim*yDim * sequenceCounter) + x * yDim + y] = relativeError; } for (unsigned int outputIdx = 0; outputIdx < outputCounter; ++outputIdx) { writteBufferVector[outputIdx][(xDim*yDim * sequenceCounter) + x * yDim + y] = resultVector[outputIdx]; } } } } MITK_INFO(m_Verbose) << "GENERATING DATA...[DONE]"; myfile.close(); } void mitk::pa::SpectralUnmixingFilterBase::CheckPreConditions(unsigned int numberOfInputImages, const float* inputDataArray) { MITK_INFO(m_Verbose) << "CHECK PRECONDITIONS ..."; if (m_Wavelength.size() < numberOfInputImages) MITK_WARN << "NUMBER OF WAVELENGTHS < NUMBER OF INPUT IMAGES"; if (m_Chromophore.size() > m_Wavelength.size()) mitkThrow() << "ADD MORE WAVELENGTHS OR REMOVE ENDMEMBERS!"; if (typeid(inputDataArray[0]).name() != typeid(float).name()) mitkThrow() << "PIXELTYPE ERROR! FLOAT 32 REQUIRED"; MITK_INFO(m_Verbose) << "...[DONE]"; } void mitk::pa::SpectralUnmixingFilterBase::InitializeOutputs(unsigned int totalNumberOfSequences) { MITK_INFO(m_Verbose) << "Initialize Outputs ..."; unsigned int numberOfInputs = GetNumberOfIndexedInputs(); unsigned int numberOfOutputs = GetNumberOfIndexedOutputs(); MITK_INFO(m_Verbose) << "Inputs: " << numberOfInputs << " Outputs: " << numberOfOutputs; mitk::PixelType pixelType = mitk::MakeScalarPixelType(); const int NUMBER_OF_SPATIAL_DIMENSIONS = 3; auto* dimensions = new unsigned int[NUMBER_OF_SPATIAL_DIMENSIONS]; for (unsigned int dimIdx = 0; dimIdx < 2; dimIdx++) dimensions[dimIdx] = GetInput()->GetDimensions()[dimIdx]; dimensions[2] = totalNumberOfSequences; for (unsigned int outputIdx = 0; outputIdx < numberOfOutputs; outputIdx++) GetOutput(outputIdx)->Initialize(pixelType, NUMBER_OF_SPATIAL_DIMENSIONS, dimensions); MITK_INFO(m_Verbose) << "...[DONE]"; } 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) { for (unsigned int i = 0; i < numberOfWavelengths; ++i) endmemberMatrixEigen(i, j) = PropertyElement(m_Chromophore[j], m_Wavelength[i]); } MITK_INFO(m_Verbose) << "GENERATING ENMEMBERMATRIX [DONE]"; return endmemberMatrixEigen; } float mitk::pa::SpectralUnmixingFilterBase::PropertyElement(mitk::pa::PropertyCalculator::ChromophoreType chromophore, int wavelength) { if (chromophore == mitk::pa::PropertyCalculator::ChromophoreType::ONEENDMEMBER) return 1; else { float value = m_PropertyCalculatorEigen->GetAbsorptionForWavelength(chromophore, wavelength); if (value == 0) mitkThrow() << "WAVELENGTH " << wavelength << "nm NOT SUPPORTED!"; else 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 542a6fdd83..4fc454070d 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 @@ -1,440 +1,441 @@ /*=================================================================== 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" #include #include 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(EnableGUIWeight())); connect((QObject*)(m_Controls.checkBoxsO2), SIGNAL(clicked()), this, SLOT(EnableGUISO2())); this->connect(this, SIGNAL(finishSignal()), this, SLOT(storeOutputs())); this->connect(this, SIGNAL(crashSignal()), this, SLOT(crashInfo())); } void SpectralUnmixing::SwitchGUIControls(bool change) { m_Controls.inputtable->setEnabled(change); m_Controls.checkBoxOx->setEnabled(change); m_Controls.checkBoxDeOx->setEnabled(change); m_Controls.checkBoxMelanin->setEnabled(change); m_Controls.checkBoxAdd->setEnabled(change); m_Controls.QComboBoxAlgorithm->setEnabled(change); m_Controls.tableWeight->setEnabled(change); m_Controls.checkBoxsO2->setEnabled(change); m_Controls.tableSO2->setEnabled(change); m_Controls.checkBoxVerbose->setEnabled(change); m_Controls.checkBoxChrono->setEnabled(change); m_Controls.buttonPerformImageProcessing->setEnabled(change); m_Controls.checkBoxError->setEnabled(change); } void SpectralUnmixing::EnableGUIWeight() { 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::EnableGUISO2() { 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 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::Settings(mitk::Image::Pointer image) { boolVec = { m_Controls.checkBoxOx->isChecked(), m_Controls.checkBoxDeOx->isChecked(), m_Controls.checkBoxMelanin->isChecked(), m_Controls.checkBoxAdd->isChecked() }; outputNameVec = { "HbO2", "Hb", "Melanin", "Static Endmember" }; sO2Bool = (m_Controls.checkBoxsO2->isChecked()); //Read GUI information(algorithm) auto qs = m_Controls.QComboBoxAlgorithm->currentText(); Algorithm = qs.toUtf8().constData(); m_SpectralUnmixingFilter = GetFilterInstance(Algorithm); SetVerboseMode(m_SpectralUnmixingFilter, PluginVerbose); m_SpectralUnmixingFilter->RelativeError(m_Controls.checkBoxError->isChecked()); m_SpectralUnmixingFilter->SetInput(image); SetWavlength(m_SpectralUnmixingFilter); SetChromophore(m_SpectralUnmixingFilter, boolVec, outputNameVec); boolVec.push_back(m_Controls.checkBoxError->isChecked()); outputNameVec.push_back("Relative Error"); m_SpectralUnmixingFilter->AddOutputs(std::accumulate(boolVec.begin(), boolVec.end(), 0)); MITK_INFO(PluginVerbose) << "Number of indexed outputs: " << std::accumulate(boolVec.begin(), boolVec.end(), 0); } void SpectralUnmixing::storeOutputs() { int outputCounter = 0; mitk::Image::Pointer m_Output; for (unsigned int chromophore = 0; chromophore < outputNameVec.size(); ++chromophore) { if (boolVec[chromophore] != false) { m_Output = m_SpectralUnmixingFilter->GetOutput(outputCounter++); m_Output->SetSpacing(image->GetGeometry()->GetSpacing()); WriteOutputToDataStorage(m_Output, outputNameVec[chromophore] + Algorithm); } } if (sO2Bool) CalculateSO2(m_SpectralUnmixingFilter, boolVec); mitk::RenderingManager::GetInstance()->InitializeViewsByBoundingObjects(this->GetDataStorage()); MITK_INFO(PluginVerbose) << "Adding images to DataStorage...[DONE]"; std::chrono::steady_clock::time_point _end(std::chrono::steady_clock::now()); MITK_INFO(m_Controls.checkBoxChrono->isChecked()) << "Time for image Processing: " << std::chrono::duration_cast>(_end - _start).count(); SwitchGUIControls(true); } void SpectralUnmixing::WorkingThreadUpdateFilter(mitk::pa::SpectralUnmixingFilterBase::Pointer m_SpectralUnmixingFilter) { SwitchGUIControls(false); try { m_SpectralUnmixingFilter->Update(); emit finishSignal(); } catch (const mitk::Exception& e) { SwitchGUIControls(true); - MITK_ERROR << e.GetDescription(); + errorMessage = e.GetDescription(); emit crashSignal(); } } void SpectralUnmixing::crashInfo() { - QMessageBox::information(nullptr, "Template", "ERROR! For more information have a look at the console."); + const char *error = errorMessage.c_str(); + QMessageBox::information(nullptr, "Template", error); } 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) 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 << "."; _start = std::chrono::steady_clock::now(); PluginVerbose = m_Controls.checkBoxVerbose->isChecked(); MITK_INFO(PluginVerbose) << message.str(); try { Settings(image); MITK_INFO(PluginVerbose) << "Updating Filter..."; QtConcurrent::run(this, &SpectralUnmixing::WorkingThreadUpdateFilter, m_SpectralUnmixingFilter); } catch (const mitk::Exception& e) { QMessageBox::information(nullptr, "Template", e.GetDescription()); } } } } 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 1e7da6d7eb..ce8ae58d5c 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 @@ -1,187 +1,188 @@ /*=================================================================== 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 #include "ui_SpectralUnmixingControls.h" /** * \brief The spectral unmixing plugin provides a GUI tool to perform spectral unmixing of multispectral MITK images. * It was designed to unmix beamformed photoacoustic imgaes. The outputs are as well MITK images for every chosen absorber * (endmember). Furthermore it is possible to calculate the oxygen saturation of the multispectral input if the endmembers * oxy- and deoxyhemoglobin are selected in the GUI. * * For further information look at the documentation of the mitkPASpectralUnmixingFilterBase.h * * @exeption if the GenerateOutput method throws a exception the plugin will show a QMessageBox with the exception * message at the GUI */ 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. Checks if the selected data is an image. Then passen on the GUI * information using the Settings method. Afterwards it performs spectral unmixing via the WorkingThreadUpdateFilter * method in a own thread. The spectral unmixing is based on the spectral unmixing filter base and its subclasses. * @exception if nothing is selected. Inform the user and return * @exception if settings fails. Informs with the mitkthorw information of the filter as QMessageBox */ void DoImageProcessing(); /** * \brief slots are there to show/hide input tables for weights- and SO2 settings ig they are not needed */ public slots: void EnableGUIWeight(); void EnableGUISO2(); /** * \brief slot waits for finishSignal of the working thread and starts storeOutputs */ public slots: /** * \brief slot does the image post processing * - GetOutput from m_SpectralUnmixingFilter * - calles WriteOutputToDataStorage * - if (true) calls CalculateSO2 * - does the rendering * - if (true) shows the chrono result * - switches the GUI back on */ void storeOutputs(); signals: void finishSignal(); /** - * \brief slot waits for crashSignal and if neccessary ends working thread + * \brief slot waits for crashSignal and if neccessary ends working thread and shows QMessageBox with the error message */ public slots: void crashInfo(); signals: void crashSignal(); protected: Ui::SpectralUnmixingControls m_Controls; /** * \brief passes the algorithm information from the GUI on to the spectral unmixing filter base subclass method * "SetAlgortihm" and initializes the subclassFilter::Pointer. * @param algorithm has to be a string which can be assigned to the mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType * @throws if the algorithm string doesn't match to an implemented algorithm */ mitk::pa::SpectralUnmixingFilterBase::Pointer GetFilterInstance(std::string algorithm); bool PluginVerbose = true; mitk::pa::SpectralUnmixingFilterBase::Pointer m_SpectralUnmixingFilter; std::vector outputNameVec; std::vector boolVec; std::string Algorithm; bool sO2Bool; mitk::Image *image; std::chrono::steady_clock::time_point _start; + std::string errorMessage; private: /* * \brief thread * - disables GUI * - tries Filter->Update() method * - gives finishSignal which calls storeOutputs * - cathes by enables GUI and gives crashSignal */ void WorkingThreadUpdateFilter(mitk::pa::SpectralUnmixingFilterBase::Pointer m_SpectralUnmixingFilter); /** * \brief takes an MITK image as input and performs spectral unmixing based on the spectral unmixing filter base and its subclasses. * Therefor it first passes all information from the GUI into the filter by using the "set"methods of the plugin, which then are calling * the "add" methods of the filter(base). * @param image has to be an MITK image (pointer). For the request on the image look at the docu of the mitkPASpectralUnmixngFilterBase.h */ virtual void Settings(mitk::Image::Pointer image); /* * \brief The method takes a image pointer and a file name which then will get to the data storage. * @param m_Image is a mitk_::Image::Pointer pointing at the output which one wants to get stored * @param name has to be a string and will be the file name */ virtual void WriteOutputToDataStorage(mitk::Image::Pointer m_Image, std::string name); /** * \brief passes the algorithm information if verbose mode is requested from the GUI on to the spectral unmixing filter * @param m_SpectralUnmixingFilter is a pointer of the spectral unmixing filter base * @param PluginVerbose is the GUI information bool */ virtual void SetVerboseMode(mitk::pa::SpectralUnmixingFilterBase::Pointer m_SpectralUnmixingFilter, bool PluginVerbose); /* * \brief passes the wavelength information from the GUI on to the spectral unmixing filter base method "AddWavelength". * @param m_SpectralUnmixingFilter is a pointer of the spectral unmixing filter base */ virtual void SetWavlength(mitk::pa::SpectralUnmixingFilterBase::Pointer m_SpectralUnmixingFilter); /* * \brief passes the chromophore information from the GUI on to the spectral unmixing filter base method "AddChromophore". * @param m_SpectralUnmixingFilter is a pointer of the spectral unmixing filter base * @param boolVec is a vector which contains the information which chromophore was checked in the GUI * @param chromophoreNameVec contains the names of all chromophores as strings * @throws "PRESS 'IGNORE' AND CHOOSE A CHROMOPHORE!" if no chromophore was chosen */ virtual void SetChromophore(mitk::pa::SpectralUnmixingFilterBase::Pointer m_SpectralUnmixingFilter, std::vector boolVec, std::vector chromophoreNameVec); /** * \brief passes the SetSO2Settings information from the GUI on to the spectral unmixing SO2 filter method "AddSO2Settings". * @param m_sO2 is a pointer of the spectral unmixing SO2 filter */ virtual void SetSO2Settings(mitk::pa::SpectralUnmixingSO2::Pointer m_sO2); /** * \brief calcultes out of two identical sized MITK images the oxygen saturation and stores the result in an image. Herein the two * input images are the output for oxy- and deoxyhemoglobin from the GenerateOutput method (spectral unmixing filter results). * @param m_SpectralUnmixingFilter is a pointer of the spectral unmixing filter base to get the filter output images as sO2 input * @param boolVec is a vector which contains the information which chromophore was checked in the GUI * @throws if oxy- or deoxyhemoglobin was not selected in the GUI */ virtual void CalculateSO2(mitk::pa::SpectralUnmixingFilterBase::Pointer m_SpectralUnmixingFilter, std::vector boolVec); /** * \brief enables/disables GUI * @param change true means GUI buttons enabled, false disabled respectively */ virtual void SwitchGUIControls(bool change); }; #endif // SpectralUnmixing_h