diff --git a/Modules/PhotoacousticsLib/include/mitkPASpectralUnmixingFilter.h b/Modules/PhotoacousticsLib/include/mitkPASpectralUnmixingFilter.h index ee5a5671df..5e4b58575d 100644 --- a/Modules/PhotoacousticsLib/include/mitkPASpectralUnmixingFilter.h +++ b/Modules/PhotoacousticsLib/include/mitkPASpectralUnmixingFilter.h @@ -1,94 +1,93 @@ /*=================================================================== 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 MITKPHOTOACOUSTICSPECTRALUNMIXINGFILTER_H #define MITKPHOTOACOUSTICSPECTRALUNMIXINGFILTER_H #include "mitkImageToImageFilter.h" //Includes for smart pointer usage #include "mitkCommon.h" #include "itkLightObject.h" #include #include "mitkPAPropertyCalculator.h" #include // Test with ImagePixelAccessor #include #include namespace mitk { namespace pa { class MITKPHOTOACOUSTICSLIB_EXPORT SpectralUnmixingFilter : public mitk::ImageToImageFilter { public: mitkClassMacro(SpectralUnmixingFilter, mitk::ImageToImageFilter) itkFactorylessNewMacro(Self) //Contains all (so far) possible chromophores enum ChromophoreType { OXYGENATED = 1, DEOXYGENATED = 2 }; //Void to creat m_vector of all chosen chromophores with push back method void SetChromophores(ChromophoreType); std::vector m_Chromophore; //Void to creat m_vector of all wavelengths with push back method void AddWavelength(int wavelength); std::vector m_Wavelength; - void SetDimensions(int dimension); - std::vector m_Dimensions; - + //Void to creat Eigen::Matrix of all absorbtions //@ specific wavelength (columns) of chromophores (rows) Eigen::Matrix AddEndmemberMatrix(); protected: SpectralUnmixingFilter(); virtual ~SpectralUnmixingFilter(); private: virtual void GenerateData(); PropertyCalculator::Pointer m_PropertyCalculator; unsigned int numberofchromophores; unsigned int numberofwavelengths; unsigned int numberOfInputs; unsigned int numberOfOutputs; long length; Eigen::Matrix EndmemberMatrix; //'New': virtual void CheckPreConditions(unsigned int NumberOfInputImages); virtual void InitializeOutputs(); //Eigen::VectorXd OutputVector = (Eigen::VectorXd, Eigen::Matrix); Eigen::VectorXd SpectralUnmixingAlgorithms(Eigen::Matrix EndmemberMatrix, Eigen::VectorXd inputVector); + }; } } #endif // MITKPHOTOACOUSTICSPECTRALUNMIXINGFILTER_H diff --git a/Modules/PhotoacousticsLib/src/SUFilter/mitkPASpectralUnmixingFilter.cpp b/Modules/PhotoacousticsLib/src/SUFilter/mitkPASpectralUnmixingFilter.cpp index 82a7bc34e6..4ff387505b 100644 --- a/Modules/PhotoacousticsLib/src/SUFilter/mitkPASpectralUnmixingFilter.cpp +++ b/Modules/PhotoacousticsLib/src/SUFilter/mitkPASpectralUnmixingFilter.cpp @@ -1,252 +1,244 @@ /*=================================================================== 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 "mitkPASpectralUnmixingFilter.h" -#include -#include - // Includes for AddEnmemberMatrix #include "mitkPAPropertyCalculator.h" #include -// Test with ImagePixelAccessor -#include -#include - +// ImageAccessor #include #include +// for testing reasons: #include mitk::pa::SpectralUnmixingFilter::SpectralUnmixingFilter() { this->SetNumberOfIndexedOutputs(2); for (unsigned int i = 0; iSetNthOutput(i, mitk::Image::New()); } m_PropertyCalculator = mitk::pa::PropertyCalculator::New(); } mitk::pa::SpectralUnmixingFilter::~SpectralUnmixingFilter() { } void mitk::pa::SpectralUnmixingFilter::AddWavelength(int wavelength) { m_Wavelength.push_back(wavelength); } void mitk::pa::SpectralUnmixingFilter::SetChromophores(ChromophoreType chromophore) { m_Chromophore.push_back(chromophore); } void mitk::pa::SpectralUnmixingFilter::GenerateData() { MITK_INFO << "GENERATING DATA.."; + mitk::Image::Pointer input = GetInput(0); + unsigned int xDim = input->GetDimensions()[0]; + unsigned int yDim = input->GetDimensions()[1]; + unsigned int zDim = input->GetDimensions()[2]; - unsigned int xDim = m_Dimensions[0]; - unsigned int yDim = m_Dimensions[1]; - unsigned int zDim = m_Dimensions[2]; + MITK_INFO << "xdim: " << xDim; + MITK_INFO << "ydim: " << yDim; - MITK_INFO << "NumberOfInputImages: " << zDim; + MITK_INFO << "zdim: " << zDim; CheckPreConditions(zDim); InitializeOutputs(); - itk::Index<3> idx; EndmemberMatrix = AddEndmemberMatrix(); + //* IMAGE READ ACCESOR see old SU.cpp + + mitk::ImageReadAccessor readAccess(input); + const float* inputDataArray = ((const float*)readAccess.GetData()); + for (unsigned int x = 0; x < xDim; x++) { - idx[0] = x; for (unsigned int y = 0; y < yDim; y++) { - idx[1] = y; - Eigen::VectorXd inputVector(numberOfInputs); + Eigen::VectorXd inputVector(zDim); for (unsigned int z = 0; z < zDim; z++) { - idx[3] = z; - - //* IMAGE READ ACCESOR see old SU.cpp - mitk::Image::Pointer input = GetInput(z); - mitk::ImageReadAccessor readAccess(input, input->GetVolumeData()); + unsigned int pixelNumber = (xDim*yDim*z)+x*yDim+y; - auto pixel = ((const float*)readAccess.GetData())[pixelNumber];/**/ + //MITK_INFO << pixelNumber; + auto pixel = inputDataArray[pixelNumber];/**/ // --> works with 3x3x3 but not with 1000x1000x3 picture - /* IMAGE PIXEL READ ACCESOR: - // Bsp.: mitkTbssImporter.cpp line 114 - mitk::Image::Pointer data = GetInput(????); - mitk::ImagePixelReadAccessor readAccesor(data, data->GetVolumeData()); - auto pixel = readAccesor.GetPixelByIndex(idx); /**/ - //float pixel = rand(); // dummy value for pixel inputVector[z] = pixel; } Eigen::VectorXd resultVector = SpectralUnmixingAlgorithms(EndmemberMatrix, inputVector); for (int outputIdx = 0; outputIdx < GetNumberOfIndexedOutputs(); ++outputIdx) { auto output = GetOutput(outputIdx); mitk::ImageWriteAccessor writeOutput(output); float* writeBuffer = (float *)writeOutput.GetData(); writeBuffer[x*yDim + y] = resultVector[outputIdx]; } } } MITK_INFO << "GENERATING DATA...[DONE]"; } -// creats vector with x, y, z dimensions as entries -void mitk::pa::SpectralUnmixingFilter::SetDimensions(int Dimension) -{ - m_Dimensions.push_back(Dimension); -} + + // checks if number of Inputs == added wavelengths void mitk::pa::SpectralUnmixingFilter::CheckPreConditions(unsigned int NumberOfInputImages) { if (m_Wavelength.size() != NumberOfInputImages) mitkThrow() << "CHECK INPUTS! WAVELENGTHERROR"; MITK_INFO << "CHECK PRECONDITIONS ...[DONE]"; } // Initialize Outputs void mitk::pa::SpectralUnmixingFilter::InitializeOutputs() { - numberOfInputs = m_Dimensions[2]; + numberOfInputs = GetNumberOfIndexedInputs(); numberOfOutputs = GetNumberOfIndexedOutputs(); //* see MitkPAVolume.cpp 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]; + } Image::Pointer m_InternalMitkImage;/**/ for (unsigned int outputIdx = 0; outputIdx < numberOfOutputs; outputIdx++) { - GetOutput(outputIdx)->Initialize(GetInput(0)); + //GetOutput(outputIdx)->Initialize(GetInput(0)); - /* see MitkPAVolume.cpp :: DOESN'T WORK (TM) + //* see MitkPAVolume.cpp :: DOESN'T WORK (TM) //m_InternalMitkImage = mitk::Image::New(); GetOutput(outputIdx)->Initialize(pixelType, NUMBER_OF_SPATIAL_DIMENSIONS, dimensions);/**/ } } //Matrix with #chromophores rows and #wavelengths columns //so Matrix Element (j,i) contains the Absorbtion of chromophore j @ wavelength i Eigen::Matrix mitk::pa::SpectralUnmixingFilter::AddEndmemberMatrix() { numberofchromophores = m_Chromophore.size(); numberofwavelengths = m_Wavelength.size(); Eigen::Matrix EndmemberMatrix(numberofchromophores, numberofwavelengths); //loop over j rows (Chromophores) for(unsigned int j =0; j < numberofchromophores; ++j) { //loop over i columns (Wavelength) for (unsigned int i = 0; i < numberofwavelengths; ++i) { //writes @ Matrix element (i,j) the absorbtion wavelength of the propertycalculator.cpp EndmemberMatrix(j,i)= m_PropertyCalculator->GetAbsorptionForWavelength( static_cast(m_Chromophore[j]), m_Wavelength[i]); /* Test to see what gets written in the Matrix: MITK_INFO << "map type: " << static_cast(m_Chromophore[j]); MITK_INFO << "wavelength: " << m_Wavelength[i]; MITK_INFO << "Matrixelement: (" << j << ", " << i << ") Absorbtion: " << EndmemberMatrix(j, i);/**/ if (EndmemberMatrix(j, i) == 0) { m_Wavelength.clear(); mitkThrow() << "WAVELENGTH "<< m_Wavelength[i] << "nm NOT SUPPORTED!"; } } } MITK_INFO << "GENERATING ENMEMBERMATRIX SUCCESSFUL!"; return EndmemberMatrix; } // Perform SU algorithm Eigen::VectorXd mitk::pa::SpectralUnmixingFilter::SpectralUnmixingAlgorithms( Eigen::Matrix EndmemberMatrix, Eigen::VectorXd inputVector) { //test "solver" (input = output) - //Eigen::VectorXd resultVector = inputVector; - //return resultVector; + Eigen::VectorXd resultVector = inputVector; + return resultVector; //llt solver - Eigen::VectorXd resultVector = EndmemberMatrix.llt().solve(inputVector); - return resultVector; + //Eigen::VectorXd resultVector = EndmemberMatrix.llt().solve(inputVector); + //return resultVector; //householderqr solver //Eigen::VectorXd resultVector =EndmemberMatrix.householderQr().solve(inputVector); //return resultVector; //test other solvers https://eigen.tuxfamily.org/dox/group__TutorialLinearAlgebra.html // define treshold for relativ error and set value to eg. -1 ;) /*double relative_error = (EndmemberMatrix*inputVector - resultVector).norm() / resultVector.norm(); // norm() is L2 norm MITK_INFO << relative_error;/**/ } /* +++++++++++++++++++++++++++++++++++++++++ OLD CODE: +++++++++++++++++++++++++++++++++++++++++++++++++++ was @ generate data length = GetOutput(0)->GetDimension(0)*GetOutput(0)->GetDimension(1)*GetOutput(0)->GetDimension(2); for (int i = 0; i < length; i++) { Eigen::VectorXd b(numberOfInputs); for (unsigned int j = 0; j < numberOfInputs; j++) { mitk::Image::Pointer input = GetInput(j); mitk::ImageReadAccessor readAccess(input, input->GetVolumeData()); b(j) = ((const float*)readAccess.GetData())[i]; } Eigen::Vector3d x = EndmemberMatrix.householderQr().solve(b); if (i == 0) { MITK_INFO << "for i=0 b(#Inputs)"; MITK_INFO << b; MITK_INFO << "EndmemberMatrix"; MITK_INFO << EndmemberMatrix; MITK_INFO << "x"; MITK_INFO << x; } for (unsigned int outputIdx = 0; outputIdx < numberOfOutputs; outputIdx++) { mitk::Image::Pointer output = GetOutput(outputIdx); mitk::ImageWriteAccessor writeOutput(output, output->GetVolumeData()); double* outputArray = (double *)writeOutput.GetData(); outputArray[i] = x[outputIdx]; } } /**/ 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 ffa0e37da8..9b33b242fa 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 @@ -1,249 +1,212 @@ /*=================================================================== 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 //test mitk image #include #include #include // Include to perform Spectral Unmixing #include "mitkPASpectralUnmixingFilter.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); } // Add Wavelength is working, BUT in the Plugin! Not with same implementation at the filter // probably because the m_wavelengths vector is created new every time and not 'saved'. void SpectralUnmixing::Wavelength() { if (m_Wavelengths.empty()) { size = 0; } wavelength = m_Controls.spinBoxAddWavelength->value(); m_Wavelengths.push_back(wavelength); MITK_INFO << "ADD WAVELENGTH: " << wavelength << "nm"; 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 (SOON)"; + 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::SpectralUnmixingFilter::New(); - for (unsigned int i = 0; i < 3; i++) - { - m_SpectralUnmixingFilter->SetDimensions(image->GetDimension(i)); - } + m_SpectralUnmixingFilter->SetInput(image); // Checking which chromophores wanted for SU if none throw exeption! 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->SetChromophores( - mitk::pa::SpectralUnmixingFilter::ChromophoreType(1)); + mitk::pa::SpectralUnmixingFilter::ChromophoreType::OXYGENATED); } if (DeOxbool) { numberofChromophores += 1; MITK_INFO << "- Deoxygenated hemoglobin"; // Set chromophore Deoxygenated hemoglobin: m_SpectralUnmixingFilter->SetChromophores( - mitk::pa::SpectralUnmixingFilter::ChromophoreType(2)); + mitk::pa::SpectralUnmixingFilter::ChromophoreType::DEOXYGENATED); } if (numberofChromophores == 0) { mitkThrow() << "PRESS 'IGNORE' AND CHOOSE A CHROMOPHORE!"; } // Checking if number of wavelengths >= number of chromophores if (numberofChromophores > size) { mitkThrow() << "PRESS 'IGNORE' AND ADD MORE WAVELENGTHS!"; } //code recreaction from "old" SU.cpp MITK_INFO << "GENERATING DATA..."; unsigned int numberOfInputs = size; unsigned int numberOfOutputs = numberofChromophores; - MITK_INFO << "Inputs: " << numberOfInputs << " Outputs: " << numberOfOutputs; - - mitk::DataStorage::Pointer storage = this->GetDataStorage(); - - mitk::DataNode::Pointer node = nodes.front(); - - mitk::Image* inputImage = dynamic_cast(data); - - const unsigned int dimensions[]{ - inputImage->GetDimension(0), - inputImage->GetDimension(1), - 1 }; // just the first sequence for starters TODO GENERALIZE - unsigned int dimension = 3; - mitk::PixelType TPixel = mitk::MakeScalarPixelType(); + MITK_INFO << "Inputs: " << numberOfInputs << " Outputs: " << numberOfOutputs; // additional wavelength implementation into fiter vector; needs "above" one for (unsigned int imageIndex = 0; imageIndex < numberOfInputs; imageIndex++) { - mitk::Image::Pointer fooImage = mitk::Image::New(); - fooImage->Initialize(TPixel, dimension, dimensions); wavelength = m_Wavelengths[imageIndex]; MITK_INFO << wavelength; m_SpectralUnmixingFilter->AddWavelength(wavelength); - mitk::ImageReadAccessor inputAcc(inputImage, inputImage->GetSliceData(imageIndex)); - fooImage->SetSlice(inputAcc.GetData(), 0); - m_SpectralUnmixingFilter->SetInput(imageIndex, fooImage); + } MITK_INFO << "Updating Filter..."; m_SpectralUnmixingFilter->Update(); mitk::Image::Pointer HbO2 = m_SpectralUnmixingFilter->GetOutput(0); - - //* - HbO2->GetGeometry()->SetIndexToWorldTransform(inputImage->GetGeometry()->GetIndexToWorldTransform()); - - mitk::ImageWriteAccessor writeOutputHbO2(HbO2, HbO2->GetVolumeData()); - double* outputArrayHbO2 = (double *)writeOutputHbO2.GetData();/**/ - mitk::DataNode::Pointer dataNodeHbO2 = mitk::DataNode::New(); dataNodeHbO2->SetData(HbO2); dataNodeHbO2->SetName("HbO2"); this->GetDataStorage()->Add(dataNodeHbO2); mitk::Image::Pointer Hb = m_SpectralUnmixingFilter->GetOutput(1); - - //* - Hb->GetGeometry()->SetIndexToWorldTransform(inputImage->GetGeometry()->GetIndexToWorldTransform()); - - mitk::ImageWriteAccessor writeOutputHb(Hb, Hb->GetVolumeData()); - double* outputArrayHb = (double *)writeOutputHb.GetData();/**/ - mitk::DataNode::Pointer dataNodeHb = mitk::DataNode::New(); dataNodeHb->SetData(Hb); dataNodeHb->SetName("Hb"); this->GetDataStorage()->Add(dataNodeHb); mitk::RenderingManager::GetInstance()->InitializeViewsByBoundingObjects(this->GetDataStorage()); MITK_INFO << "Adding images to DataStorage...[DONE]"; } } }