diff --git a/Modules/PhotoacousticsLib/include/mitkPASpectralUnmixingSO2.h b/Modules/PhotoacousticsLib/include/mitkPASpectralUnmixingSO2.h index 9180e8968a..85bac2c75e 100644 --- a/Modules/PhotoacousticsLib/include/mitkPASpectralUnmixingSO2.h +++ b/Modules/PhotoacousticsLib/include/mitkPASpectralUnmixingSO2.h @@ -1,100 +1,105 @@ /*=================================================================== 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 MITKPHOTOACOUSTICSPECTRALUNMIXINGSO2_H #define MITKPHOTOACOUSTICSPECTRALUNMIXINGSO2_H #include "mitkImageToImageFilter.h" #include //Includes for smart pointer usage #include "mitkCommon.h" #include "itkLightObject.h" namespace mitk { namespace pa { /** * \brief derives out of two identical sized MITK images the oxygen saturation and return one MITK image as result. Furthermore * it is possible to set settings that the result shows just SO2 values above a threshold, or above a input value for Hb, HbO2 to * get just a oxygen saturation image of interessting structures. * * Input: * The input has to be two 3D MITK images. The order of the inputs matter! The first input has to be the Hb image the second input * has to be the HbO2 image. The settings are integer values. The SO2 threshold therefore is percentage value. * * Output: * The output will be one MITK image. Where one can see the oxygen saturation of all pixels above the set threholds. If a pixel is * below a threhold or NAN then the value will be set to zero. */ class MITKPHOTOACOUSTICSLIB_EXPORT SpectralUnmixingSO2 : public mitk::ImageToImageFilter { public: mitkClassMacro(SpectralUnmixingSO2, mitk::ImageToImageFilter); itkFactorylessNewMacro(Self); /** * \brief AddSO2Settings takes integers and writes them at the end of the m_SO2Settings vector. - * @param value has to be a integer + * @param value of the Setting */ - virtual void AddSO2Settings(float value); + virtual void AddSO2Settings(int value); - /* + /** * \brief Verbose gives more information to the console. Default value is false. * @param m_Verbose is the boolian to activate the MITK_INFO logged to the console */ virtual void Verbose(bool verbose); protected: /** * \brief Constructor sets number of input images to two and number of output images to one, respectively. */ SpectralUnmixingSO2(); virtual ~SpectralUnmixingSO2(); std::vector m_SO2Settings; bool m_Verbose = false; private: - /* + /** * \brief Inherit from the "ImageToImageFilter" Superclass. Herain it calls InitializeOutputs and the CheckPreConditions * methods and enables pixelwise access to the inputs to calculate the oxygen saturation via the "calculate SO2" method. */ virtual void GenerateData() override; - /* + /** * \brief Initialized output images with the same size like the input image. The pixel type is set to float. */ virtual void InitializeOutputs(); - /* + /** * \brief Checks if the dimensions of the input images are equal. * @throws if tey are not */ virtual void CheckPreConditions(mitk::Image::Pointer inputHbO2, mitk::Image::Pointer inputHb); - /* - * \brief calculates HbO2 / (Hb + HbO2) and afterwards checks if the result and inputs are above threshold values of the - * settings. If they are not the method returns zero otherwise it returns the calculated result. + /** + * \brief calculates HbO2 / (Hb + HbO2) and afterwards checks if the result is significant (SO2ValueNotSiginificant method). + * If not the method returns zero otherwise it returns the calculated result. * @param pixelHb is the pixel value of the Hb input. * @param pixelHb is the pixel value of the Hb input. * @warn if the HbO2 value is NAN (in patricular if Hb == -HbO2), but result will be set to zero */ - float calculateSO2(float pixelHb, float pixelHbO2); + float CalculateSO2(float pixelHb, float pixelHbO2); + + /** + * \brief return true if SO2 result is not significant by checking if the input values are above the threshold of the settings + */ + bool SO2ValueNotSiginificant(float Hb, float HbO2, float result); }; } } #endif // MITKPHOTOACOUSTICSPECTRALUNMIXINGSO2_ diff --git a/Modules/PhotoacousticsLib/src/SUFilter/mitkPASpectralUnmixingSO2.cpp b/Modules/PhotoacousticsLib/src/SUFilter/mitkPASpectralUnmixingSO2.cpp index 47cfcb208d..6ce14c6efd 100644 --- a/Modules/PhotoacousticsLib/src/SUFilter/mitkPASpectralUnmixingSO2.cpp +++ b/Modules/PhotoacousticsLib/src/SUFilter/mitkPASpectralUnmixingSO2.cpp @@ -1,153 +1,155 @@ /*=================================================================== 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 "mitkPASpectralUnmixingSO2.h" // ImageAccessor #include #include mitk::pa::SpectralUnmixingSO2::SpectralUnmixingSO2() { this->SetNumberOfIndexedInputs(2); this->SetNumberOfIndexedOutputs(1); this->SetNthOutput(0, mitk::Image::New()); } mitk::pa::SpectralUnmixingSO2::~SpectralUnmixingSO2() { } void mitk::pa::SpectralUnmixingSO2::Verbose(bool verbose) { m_Verbose = verbose; } void mitk::pa::SpectralUnmixingSO2::GenerateData() { MITK_INFO(m_Verbose) << "GENERATING DATA.."; // Get input image mitk::Image::Pointer inputHbO2 = GetInput(0); mitk::Image::Pointer inputHb = GetInput(1); CheckPreConditions(inputHbO2, inputHb); unsigned int xDim = inputHbO2->GetDimensions()[0]; unsigned int yDim = inputHbO2->GetDimensions()[1]; unsigned int zDim = inputHbO2->GetDimensions()[2]; InitializeOutputs(); mitk::ImageReadAccessor readAccessHbO2(inputHbO2); mitk::ImageReadAccessor readAccessHb(inputHb); const float* inputDataArrayHbO2 = ((const float*)readAccessHbO2.GetData()); const float* inputDataArrayHb = ((const float*)readAccessHb.GetData()); auto output = GetOutput(0); mitk::ImageWriteAccessor writeOutput(output); float* writeBuffer = (float *)writeOutput.GetData(); for (unsigned int x = 0; x < xDim; x++) { for (unsigned int y = 0; y < yDim; y++) { for (unsigned int z = 0;z < zDim; z++) { unsigned int pixelNumber = (xDim*yDim * z) + x * yDim + y; float pixelHb = inputDataArrayHb[pixelNumber]; float pixelHbO2 = inputDataArrayHbO2[pixelNumber]; - float resultSO2 = calculateSO2(pixelHb, pixelHbO2); + float resultSO2 = CalculateSO2(pixelHb, pixelHbO2); writeBuffer[(xDim*yDim * z) + x * yDim + y] = resultSO2; } } } MITK_INFO(m_Verbose) << "GENERATING DATA...[DONE]"; } void mitk::pa::SpectralUnmixingSO2::CheckPreConditions(mitk::Image::Pointer inputHbO2, mitk::Image::Pointer inputHb) { unsigned int xDimHb = inputHb->GetDimensions()[0]; unsigned int yDimHb = inputHb->GetDimensions()[1]; unsigned int zDimHb = inputHb->GetDimensions()[2]; unsigned int xDimHbO2 = inputHbO2->GetDimensions()[0]; unsigned int yDimHbO2 = inputHbO2->GetDimensions()[1]; unsigned int zDimHbO2 = inputHbO2->GetDimensions()[2]; if (xDimHb != xDimHbO2 || yDimHb != yDimHbO2 || zDimHb != zDimHbO2) mitkThrow() << "DIMENTIONALITY ERROR!"; MITK_INFO(m_Verbose) << "CHECK PRECONDITIONS ...[DONE]"; } void mitk::pa::SpectralUnmixingSO2::InitializeOutputs() { unsigned int numberOfInputs = GetNumberOfIndexedInputs(); unsigned int numberOfOutputs = GetNumberOfIndexedOutputs(); 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; dimIdxGetDimensions()[dimIdx]; } for (unsigned int outputIdx = 0; outputIdx < numberOfOutputs; outputIdx++) { GetOutput(outputIdx)->Initialize(pixelType, NUMBER_OF_SPATIAL_DIMENSIONS, dimensions); } } -float mitk::pa::SpectralUnmixingSO2::calculateSO2(float Hb, float HbO2) +float mitk::pa::SpectralUnmixingSO2::CalculateSO2(float Hb, float HbO2) { - float MinHb = m_SO2Settings[0]; - float MinHbO2 = m_SO2Settings[1]; - float MinSum = m_SO2Settings[2]; - float MinSO2 = m_SO2Settings[3]; float result = HbO2 / (Hb + HbO2); - float zero = 0.0; if (result != result) { MITK_WARN(m_Verbose) << "SO2 VALUE NAN! WILL BE SET TO ZERO!"; - return zero; + return 0; } else { - if (MinHb != 0 && MinHb > Hb) - return zero; - else if (MinHbO2 != 0 && MinHbO2 > HbO2) - return zero; - else if (MinSum != 0 && MinSum > Hb + HbO2) - return zero; - else if (MinSO2 != 0 && 100 * result > MinSO2) - return result; - else if (MinSO2 != 0 && result < MinSO2) - return zero; - else - return result; + if (SO2ValueNotSiginificant(Hb, HbO2, result)) + return 0; + else return result; } } -void mitk::pa::SpectralUnmixingSO2::AddSO2Settings(float value) +void mitk::pa::SpectralUnmixingSO2::AddSO2Settings(int value) { m_SO2Settings.push_back(value); } + +bool mitk::pa::SpectralUnmixingSO2::SO2ValueNotSiginificant(float Hb, float HbO2, float result) +{ + std::vector significant; + significant.push_back(HbO2); + significant.push_back(Hb); + significant.push_back(HbO2 + Hb); + significant.push_back(100*(result)); + + for (unsigned int i = 0; i < m_SO2Settings.size(); ++i) + { + if (m_SO2Settings[i] >= significant[i]) + return true; + } + return false; +} 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 395f8fbafb..88c3e7fbf4 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 @@ -1,469 +1,469 @@ /*=================================================================== 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(); m_Controls.tableError->hide(); connect((QObject*)(m_Controls.QComboBoxAlgorithm), SIGNAL(currentIndexChanged(int)), this, SLOT(EnableGUIWeight())); connect((QObject*)(m_Controls.checkBoxsO2), SIGNAL(clicked()), this, SLOT(EnableGUISO2())); connect((QObject*)(m_Controls.checkBoxError), SIGNAL(clicked()), this, SLOT(EnableGUIError())); 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::EnableGUIError() { if (m_Controls.checkBoxError->isChecked()) m_Controls.tableError->show(); else m_Controls.tableError->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)) + if (m_Controls.tableSO2->item(0, i)) { QString Text = m_Controls.tableSO2->item(0, i)->text(); - float value = Text.toFloat(); + int value = Text.toInt(); MITK_INFO(PluginVerbose) << "SO2 setting value: " << value; m_sO2->AddSO2Settings(value); } else m_sO2->AddSO2Settings(0); } } void SpectralUnmixing::SetRelativeErrorSettings(mitk::pa::SpectralUnmixingFilterBase::Pointer m_SpectralUnmixingFilter) { for (unsigned int i = 0; i < 2; ++i) { if (m_Controls.tableError->item(0, i)) { QString Text = m_Controls.tableError->item(0, i)->text(); int value = Text.toInt(); MITK_INFO(PluginVerbose) << "Relative error setting value: " << value; m_SpectralUnmixingFilter->AddRelativeErrorSettings(value); } else m_SpectralUnmixingFilter->AddRelativeErrorSettings(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"); if (m_Controls.checkBoxError->isChecked()) SetRelativeErrorSettings(m_SpectralUnmixingFilter); 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); errorMessage = e.GetDescription(); emit crashSignal(); } } void SpectralUnmixing::crashInfo() { 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()); } } } }