diff --git a/Modules/PhotoacousticsLib/test/mitkSpectralUnmixingTest.cpp b/Modules/PhotoacousticsLib/test/mitkSpectralUnmixingTest.cpp index e908847a5a..1f276c2d72 100644 --- a/Modules/PhotoacousticsLib/test/mitkSpectralUnmixingTest.cpp +++ b/Modules/PhotoacousticsLib/test/mitkSpectralUnmixingTest.cpp @@ -1,136 +1,247 @@ -///*=================================================================== +//*=================================================================== //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 #include #include #include +#include +#include +#include #include class mitkSpectralUnmixingTestSuite : public mitk::TestFixture { CPPUNIT_TEST_SUITE(mitkSpectralUnmixingTestSuite); - MITK_TEST(testSUAlgorithm); + MITK_TEST(testEigenSUAlgorithm); + MITK_TEST(testVigraSUAlgorithm); + MITK_TEST(testSimplexSUAlgorithm); CPPUNIT_TEST_SUITE_END(); private: mitk::pa::SpectralUnmixingFilterBase::Pointer m_SpectralUnmixingFilter; mitk::Image::Pointer inputImage; std::vector m_inputWavelengths; std::vector m_CorrectResult; float threshold; public: void setUp() override { MITK_INFO << "setUp ... "; //Set empty input image: inputImage = mitk::Image::New(); mitk::PixelType pixelType = mitk::MakeScalarPixelType(); const int NUMBER_OF_SPATIAL_DIMENSIONS = 3; auto* dimensions = new unsigned int[NUMBER_OF_SPATIAL_DIMENSIONS]; dimensions[0] = 1; dimensions[1] = 1; - dimensions[2] = 3; + dimensions[2] = 5; inputImage->Initialize(pixelType, NUMBER_OF_SPATIAL_DIMENSIONS, dimensions); //Set wavelengths for unmixing: m_inputWavelengths.push_back(750); m_inputWavelengths.push_back(800); - m_inputWavelengths.push_back(850); //Set fraction of Hb and HbO2 to unmix: - float fracHb = 0.396579; - float fracHbO2 = 0.594845; + float fracHb = 100; + float fracHbO2 = 300; m_CorrectResult.push_back(fracHbO2); m_CorrectResult.push_back(fracHb); - - //Set threshold 1 digit - threshold = 0.000001; + m_CorrectResult.push_back(fracHbO2 + 10); + m_CorrectResult.push_back(fracHb - 10); + threshold = .01; //Multiply values of wavelengths (750,800,850 nm) with fractions to get pixel values: float px1 = fracHb * 7.52 + fracHbO2 * 2.77; float px2 = fracHb * 4.08 + fracHbO2 * 4.37; - float px3 = fracHb * 3.7 + fracHbO2 * 5.67; + float px3 = (fracHb - 10) * 7.52 + (fracHbO2 + 10) * 2.77; + float px4 = (fracHb - 10) * 4.08 + (fracHbO2 + 10) * 4.37; float* data = new float[3]; data[0] = px1; data[1] = px2; data[2] = px3; + data[3] = px4; + data[5] = 200; inputImage->SetImportVolume(data, mitk::Image::ImportMemoryManagementType::CopyMemory); delete[] data; MITK_INFO << "[DONE]"; } - void testSUAlgorithm() + void testEigenSUAlgorithm() { MITK_INFO << "START FILTER TEST ... "; // Set input image auto m_SpectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New(); m_SpectralUnmixingFilter->SetInput(inputImage); // Set Algortihm to filter //m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::householderQr); //m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::ldlt); //m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::llt); m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::colPivHouseholderQr); //m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::jacobiSvd); //m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::fullPivLu); //m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::fullPivHouseholderQr); //m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::test); //Set wavelengths to filter for (unsigned int imageIndex = 0; imageIndex < m_inputWavelengths.size(); imageIndex++) { unsigned int wavelength = m_inputWavelengths[imageIndex]; m_SpectralUnmixingFilter->AddWavelength(wavelength); } //Set Chromophores to filter m_SpectralUnmixingFilter->AddChromophore( mitk::pa::PropertyCalculator::ChromophoreType::OXYGENATED); m_SpectralUnmixingFilter->AddChromophore( mitk::pa::PropertyCalculator::ChromophoreType::DEOXYGENATED); m_SpectralUnmixingFilter->Update(); + + /*For printed pixel values and results look at: [...]\mitk-superbuild\MITK-build\Modules\PhotoacousticsLib\test\*/ + ofstream myfile; + myfile.open("EigenTestResult.txt"); + for (int i = 0; i < 2; ++i) + { + mitk::Image::Pointer output = m_SpectralUnmixingFilter->GetOutput(i); + mitk::ImageReadAccessor readAccess(output); + const float* inputDataArray = ((const float*)readAccess.GetData()); + auto pixel = inputDataArray[0]; + auto pixel2 = inputDataArray[1]; + + myfile << "Output "<SetInput(inputImage); + + m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::LARS); + //m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::GOLDFARB); + //m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::WEIGHTED); //ADD WIEGHTS! + //m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::LS); + //m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::vigratest); + + //Set wavelengths to filter + for (unsigned int imageIndex = 0; imageIndex < m_inputWavelengths.size(); imageIndex++) + { + unsigned int wavelength = m_inputWavelengths[imageIndex]; + m_SpectralUnmixingFilter->AddWavelength(wavelength); + } + + //Set Chromophores to filter + m_SpectralUnmixingFilter->AddChromophore( + mitk::pa::PropertyCalculator::ChromophoreType::OXYGENATED); + m_SpectralUnmixingFilter->AddChromophore( + mitk::pa::PropertyCalculator::ChromophoreType::DEOXYGENATED); + + m_SpectralUnmixingFilter->Update(); + + + /*For printed pixel values and results look at: [...]\mitk-superbuild\MITK-build\Modules\PhotoacousticsLib\test\*/ + ofstream myfile; + myfile.open("VigraTestResult.txt"); for (int i = 0; i < 2; ++i) { mitk::Image::Pointer output = m_SpectralUnmixingFilter->GetOutput(i); mitk::ImageReadAccessor readAccess(output); const float* inputDataArray = ((const float*)readAccess.GetData()); auto pixel = inputDataArray[0]; - /*For printed pixel values and results look at: [...]\mitk-superbuild\MITK-build\Modules\PhotoacousticsLib\test\*/ + auto pixel2 = inputDataArray[1]; + + myfile << "Output " << i << ": " << "\n" << inputDataArray[0] << "\n" << inputDataArray[1] << "\n"; + myfile << "Correct Result: " << "\n" << m_CorrectResult[i] << "\n" << m_CorrectResult[i + 2] << "\n"; + + CPPUNIT_ASSERT(std::abs(pixel - m_CorrectResult[i])SetInput(inputImage); + + //Set wavelengths to filter + for (unsigned int imageIndex = 0; imageIndex < m_inputWavelengths.size(); imageIndex++) + { + unsigned int wavelength = m_inputWavelengths[imageIndex]; + m_SpectralUnmixingFilter->AddWavelength(wavelength); + } + + //Set Chromophores to filter + m_SpectralUnmixingFilter->AddChromophore( + mitk::pa::PropertyCalculator::ChromophoreType::OXYGENATED); + m_SpectralUnmixingFilter->AddChromophore( + mitk::pa::PropertyCalculator::ChromophoreType::DEOXYGENATED); + + m_SpectralUnmixingFilter->Update(); + + + /*For printed pixel values and results look at: [...]\mitk-superbuild\MITK-build\Modules\PhotoacousticsLib\test\*/ + ofstream myfile; + myfile.open("SimplexTestResult.txt"); + for (int i = 0; i < 2; ++i) + { + mitk::Image::Pointer output = m_SpectralUnmixingFilter->GetOutput(i); + mitk::ImageReadAccessor readAccess(output); + const float* inputDataArray = ((const float*)readAccess.GetData()); + auto pixel = inputDataArray[0]; + auto pixel2 = inputDataArray[1]; + + myfile << "Output " << i << ": " << "\n" << inputDataArray[0] << "\n" << inputDataArray[1] << "\n"; + myfile << "Correct Result: " << "\n" << m_CorrectResult[i] << "\n" << m_CorrectResult[i + 2] << "\n"; + CPPUNIT_ASSERT(std::abs(pixel - m_CorrectResult[i])