diff --git a/Modules/PhotoacousticsLib/include/mitkPASpectralUnmixingSO2.h b/Modules/PhotoacousticsLib/include/mitkPASpectralUnmixingSO2.h index c5d15fa6a0..c710493743 100644 --- a/Modules/PhotoacousticsLib/include/mitkPASpectralUnmixingSO2.h +++ b/Modules/PhotoacousticsLib/include/mitkPASpectralUnmixingSO2.h @@ -1,47 +1,48 @@ /*=================================================================== 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 { class MITKPHOTOACOUSTICSLIB_EXPORT SpectralUnmixingSO2 : public mitk::ImageToImageFilter { public: - mitkClassMacro(SpectralUnmixingSO2, mitk::ImageToImageFilter) + mitkClassMacro(SpectralUnmixingSO2, mitk::ImageToImageFilter); + itkFactorylessNewMacro(Self); protected: SpectralUnmixingSO2(); virtual ~SpectralUnmixingSO2(); private: virtual void GenerateData() override; virtual void InitializeOutputs(); virtual void CheckPreConditions(mitk::Image::Pointer inputHbO2, mitk::Image::Pointer inputHb); float calculateSO2(float pixelHb, float pixelHbO2); }; } } #endif // MITKPHOTOACOUSTICSPECTRALUNMIXINGSO2_ diff --git a/Modules/PhotoacousticsLib/src/SUFilter/mitkPASpectralUnmixingSO2.cpp b/Modules/PhotoacousticsLib/src/SUFilter/mitkPASpectralUnmixingSO2.cpp index 08676a25bb..8cf17bc8de 100644 --- a/Modules/PhotoacousticsLib/src/SUFilter/mitkPASpectralUnmixingSO2.cpp +++ b/Modules/PhotoacousticsLib/src/SUFilter/mitkPASpectralUnmixingSO2.cpp @@ -1,117 +1,117 @@ /*=================================================================== 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->SetNumberOfIndexedInputs(2); this->SetNumberOfIndexedOutputs(1); this->SetNthOutput(0, mitk::Image::New()); } mitk::pa::SpectralUnmixingSO2::~SpectralUnmixingSO2() { } void mitk::pa::SpectralUnmixingSO2::GenerateData() { MITK_INFO << "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 size = xDim * yDim; MITK_INFO << "x dimension: " << xDim; MITK_INFO << "y dimension: " << yDim; InitializeOutputs(); // Copy input image into array mitk::ImageReadAccessor readAccessHbO2(inputHbO2); mitk::ImageReadAccessor readAccessHb(inputHb); const float* inputDataArrayHbO2 = ((const float*)readAccessHbO2.GetData()); const float* inputDataArrayHb = ((const float*)readAccessHb.GetData()); for (unsigned int x = 0; x < xDim; x++) { for (unsigned int y = 0; y < yDim; y++) { unsigned int pixelNumber = x * yDim + y; float pixelHb = inputDataArrayHb[pixelNumber]; float pixelHbO2 = inputDataArrayHbO2[pixelNumber]; float resultSO2 = calculateSO2(pixelHb, pixelHbO2); auto output = GetOutput(0); mitk::ImageWriteAccessor writeOutput(output); float* writeBuffer = (float *)writeOutput.GetData(); writeBuffer[x*yDim + y] = resultSO2; } } MITK_INFO << "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 xDimHbO2 = inputHbO2->GetDimensions()[0]; unsigned int yDimHbO2 = inputHbO2->GetDimensions()[1]; if (xDimHb != xDimHbO2 || yDimHb != yDimHbO2) mitkThrow() << "DIMENTIONALITY ERROR!"; MITK_INFO << "CHECK PRECONDITIONS ...[DONE]"; } void mitk::pa::SpectralUnmixingSO2::InitializeOutputs() { unsigned int numberOfInputs = GetNumberOfIndexedInputs(); unsigned int numberOfOutputs = GetNumberOfIndexedOutputs(); // Set dimensions (2) and pixel type (float) for output mitk::PixelType pixelType = mitk::MakeScalarPixelType(); const int NUMBER_OF_SPATIAL_DIMENSIONS = 2; auto* dimensions = new unsigned int[NUMBER_OF_SPATIAL_DIMENSIONS]; for(unsigned int dimIdx=0; dimIdxGetDimensions()[dimIdx]; } // Initialize numberOfOutput pictures with pixel type and dimensions 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 result = HbO2 / (Hb + HbO2); return result; } 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 5eb88b8443..eb57a06479 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 @@ -1,294 +1,292 @@ /*=================================================================== 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" 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); connect(m_Controls.ButtonAddWavelength, &QPushButton::clicked, this, &SpectralUnmixing::Wavelength); connect(m_Controls.ButtonClearWavelength, &QPushButton::clicked, this, &SpectralUnmixing::ClearWavelength); } // Adds Wavelength @ Plugin with button void SpectralUnmixing::Wavelength() { if (m_Wavelengths.empty()) { size = 0; } unsigned int wavelength = m_Controls.spinBoxAddWavelength->value(); m_Wavelengths.push_back(wavelength); size += 1; // size implemented like this because '.size' is const MITK_INFO << "ALL WAVELENGTHS: "; for (int i = 0; i < size; ++i) { MITK_INFO << m_Wavelengths[i] << "nm"; } } 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(); auto m_SpectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New(); m_SpectralUnmixingFilter->SetInput(image); // Set Algortihm to filter auto qs = m_Controls.QComboBoxAlgorithm->currentText(); std::string Algorithm = qs.toUtf8().constData(); if (Algorithm == "householderQr") m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::householderQr); else if (Algorithm == "ldlt") m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::ldlt); else if (Algorithm == "llt") m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::llt); else if (Algorithm == "colPivHouseholderQr") m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::colPivHouseholderQr); else if (Algorithm == "jacobiSvd") m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::jacobiSvd); else if (Algorithm == "fullPivLu") m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::fullPivLu); else if (Algorithm == "fullPivHouseholderQr") m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::fullPivHouseholderQr); else if (Algorithm == "test") m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::test); else mitkThrow() << "ALGORITHM ERROR!"; // Wavelength implementation into filter for (unsigned int imageIndex = 0; imageIndex < m_Wavelengths.size(); imageIndex++) { unsigned int wavelength = m_Wavelengths[imageIndex]; m_SpectralUnmixingFilter->AddWavelength(wavelength); } // Checking which chromophores wanted for SU if none throw exeption! unsigned int numberofChromophores = 0; DeOxbool = m_Controls.checkBoxDeOx->isChecked(); Oxbool = m_Controls.checkBoxOx->isChecked(); if (DeOxbool || Oxbool) { MITK_INFO << "CHOSEN CHROMOPHORES:"; } if (Oxbool) { numberofChromophores += 1; MITK_INFO << "- Oxyhemoglobin"; // Set chromophore Oxyhemoglobon: m_SpectralUnmixingFilter->AddChromophore( mitk::pa::SpectralUnmixingFilterBase::ChromophoreType::OXYGENATED_HEMOGLOBIN); } if (DeOxbool) { numberofChromophores += 1; MITK_INFO << "- Deoxygenated hemoglobin"; // Set chromophore Deoxygenated hemoglobin: m_SpectralUnmixingFilter->AddChromophore( mitk::pa::SpectralUnmixingFilterBase::ChromophoreType::DEOXYGENATED_HEMOGLOBIN); } if (numberofChromophores == 0) { mitkThrow() << "PRESS 'IGNORE' AND CHOOSE A CHROMOPHORE!"; } MITK_INFO << "Updating Filter..."; m_SpectralUnmixingFilter->Update(); 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); } mitk::RenderingManager::GetInstance()->InitializeViewsByBoundingObjects(this->GetDataStorage()); //*++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ //FRAGE zu SetInput: reicht es dort einen image pointer anzugeben? //wenn ja zweite Variante wenn nein dann erste. funktioniern aber leider beide nicht:/ bool sO2bool = m_Controls.checkBoxsO2->isChecked(); //1: /* mitk::Image::Pointer HbO2 = m_SpectralUnmixingFilter->GetOutput(0); mitk::DataNode::Pointer dataNodeHbO2 = mitk::DataNode::New(); dataNodeHbO2->SetData(HbO2); mitk::BaseData *dataHbO2 = dataNodeHbO2->GetData(); mitk::Image *imageHbO2 = dynamic_cast(dataHbO2); mitk::Image::Pointer Hb = m_SpectralUnmixingFilter->GetOutput(1); mitk::DataNode::Pointer dataNodeHb = mitk::DataNode::New(); dataNodeHb->SetData(Hb); mitk::BaseData *dataHb = dataNodeHb->GetData(); mitk::Image *imageHb = dynamic_cast(dataHb); auto m_sO2 = mitk::pa::SpectralUnmixingSO2::New(); m_sO2->SetInput(0,imageHbO2); m_sO2->SetInput(1,imageHb); m_sO2->Update(); 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);/**/ //2: - /* + //* if (sO2bool) { - if (DeOxbool) - { - if (Oxbool) - { - MITK_INFO << "CALCULATE OXYGEN SATURATION ..."; - auto m_sO2 = mitk::pa::SpectralUnmixingSO2::New(); - m_sO2->SetInput(0, m_SpectralUnmixingFilter->GetOutput(0)); - m_sO2->SetInput(1, m_SpectralUnmixingFilter->GetOutput(1)); - - //http://docs.mitk.org/nightly/PipelineingConceptPage.html - //m_SpectralUnmixingFilter->Update(); - //m_sO2->SetInput(m_SpectralUnmixingFilter->GetOutput()); - - m_sO2->Update(); - - 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]"; - } - else - mitkThrow() << "SELECT CHROMOPHORE OXYHEMOGLOBIN!"; - } - else + if (!DeOxbool) mitkThrow() << "SELECT CHROMOPHORE DEOXYHEMOGLOBIN!"; + if (!Oxbool) + mitkThrow() << "SELECT CHROMOPHORE OXYHEMOGLOBIN!"; + + MITK_INFO << "CALCULATE OXYGEN SATURATION ..."; + auto m_sO2 = mitk::pa::SpectralUnmixingSO2::New(); + auto output1 = m_SpectralUnmixingFilter->GetOutput(0); + auto output2 = m_SpectralUnmixingFilter->GetOutput(1); + + m_sO2->SetInput(0, output1); + m_sO2->SetInput(1, output2); + + //http://docs.mitk.org/nightly/PipelineingConceptPage.html + //m_SpectralUnmixingFilter->Update(); + //m_sO2->SetInput(m_SpectralUnmixingFilter->GetOutput()); + + m_sO2->Update(); + + 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]"; } } }