diff --git a/Modules/PhotoacousticsAlgorithms/MitkPABeamformingTool/PABeamformingTool.cpp b/Modules/PhotoacousticsAlgorithms/MitkPABeamformingTool/PABeamformingTool.cpp index 2b2adf2b00..81f0520417 100644 --- a/Modules/PhotoacousticsAlgorithms/MitkPABeamformingTool/PABeamformingTool.cpp +++ b/Modules/PhotoacousticsAlgorithms/MitkPABeamformingTool/PABeamformingTool.cpp @@ -1,228 +1,232 @@ /*=================================================================== 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 +#include #include struct InputParameters { mitk::Image::Pointer inputImage; std::string outputFilename; bool verbose; - int speedOfSound; - int cutoff; + float speedOfSound; + unsigned int cutoff; float angle; - int samples; + unsigned int samples; mitk::BeamformingSettings::BeamformingAlgorithm algorithm; }; InputParameters parseInput(int argc, char* argv[]) { mitkCommandLineParser parser; parser.setCategory("MITK-Photoacoustics"); parser.setTitle("Mitk Photoacoustics Beamforming Tool"); parser.setDescription("Reads a nrrd file as an input and applies a beamforming method as set with the parameters."); parser.setContributor("Computer Assisted Medical Interventions, DKFZ"); parser.setArgumentPrefix("--", "-"); parser.beginGroup("Required parameters"); parser.addArgument( "inputImage", "i", mitkCommandLineParser::InputImage, "Input image (mitk::Image)", "input image (.nrrd file)", us::Any(), false); parser.addArgument( "output", "o", mitkCommandLineParser::OutputFile, "Output filename", "output image (.nrrd file)", us::Any(), false); parser.endGroup(); parser.beginGroup("Optional parameters"); parser.addArgument( "verbose", "v", mitkCommandLineParser::Bool, "Verbose Output", "Whether to produce verbose, or rather debug output. (default: false)"); parser.addArgument( - "speed-of-sound", "sos", mitkCommandLineParser::Int, + "speed-of-sound", "sos", mitkCommandLineParser::Float, "Speed of Sound [m/s]", "The average speed of sound as assumed for the reconstruction in [m/s]. (default: 1500)"); parser.addArgument( "cutoff", "co", mitkCommandLineParser::Int, "cutoff margin on the top of the image [pixels]", "The number of pixels to be ignored for this filter in [pixels] (default: 0)."); parser.addArgument( "angle", "a", mitkCommandLineParser::Float, "field of view of the transducer elements [degrees]", "The field of view of each individual transducer element [degrees] (default: 27)."); parser.addArgument( "samples", "s", mitkCommandLineParser::Int, "samples per reconstruction line [pixels]", "The pixels along the y axis in the beamformed image [pixels] (default: 2048)."); parser.addArgument( "algorithm", "alg", mitkCommandLineParser::String, "one of [\"DAS\", \"DMAS\", \"sDMAS\"]", "The beamforming algorithm to be used for reconstruction (default: DAS)."); parser.endGroup(); InputParameters input; std::map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size() == 0) exit(-1); if (parsedArgs.count("verbose")) { input.verbose = true; } else { input.verbose = false; } MITK_INFO(input.verbose) << "### VERBOSE OUTPUT ENABLED ###"; if (parsedArgs.count("inputImage")) { MITK_INFO(input.verbose) << "Reading input image..."; input.inputImage = mitk::IOUtil::Load(us::any_cast(parsedArgs["inputImage"])); MITK_INFO(input.verbose) << "Reading input image...[Done]"; } else { mitkThrow() << "No input image given."; } if (parsedArgs.count("output")) { input.outputFilename = us::any_cast(parsedArgs["output"]); } else { mitkThrow() << "No output image path given.."; } if (parsedArgs.count("speed-of-sound")) { input.speedOfSound = us::any_cast(parsedArgs["speed-of-sound"]); } else { input.speedOfSound = 1500; } if (parsedArgs.count("cutoff")) { input.cutoff = us::any_cast(parsedArgs["cutoff"]); } else { input.cutoff = 0; } if (parsedArgs.count("angle")) { input.angle = us::any_cast(parsedArgs["angle"]); } else { input.angle = 27; } if (parsedArgs.count("samples")) { input.samples = us::any_cast(parsedArgs["samples"]); } else { input.samples = 2048; } if (parsedArgs.count("algorithm")) { std::string algorithm = us::any_cast(parsedArgs["algorithm"]); MITK_INFO(input.verbose) << "Parsing algorithm: " << algorithm; if (algorithm == "DAS") input.algorithm = mitk::BeamformingSettings::BeamformingAlgorithm::DAS; else if (algorithm == "DMAS") input.algorithm = mitk::BeamformingSettings::BeamformingAlgorithm::DMAS; else if (algorithm == "sDMAS") input.algorithm = mitk::BeamformingSettings::BeamformingAlgorithm::sDMAS; else { MITK_INFO(input.verbose) << "Not a valid beamforming algorithm: " << algorithm << " Reverting to DAS"; input.algorithm = mitk::BeamformingSettings::BeamformingAlgorithm::DAS; } MITK_INFO(input.verbose) << "Sucessfully set algorithm: " << algorithm; } else { input.algorithm = mitk::BeamformingSettings::BeamformingAlgorithm::DAS; MITK_INFO(input.verbose) << "No matching algorithm found. Using DAS."; } return input; } mitk::BeamformingSettings::Pointer ParseSettings(InputParameters &input) { - mitk::BeamformingSettings::Pointer outputSettings = mitk::BeamformingSettings::New(); - - outputSettings->SetAlgorithm(input.algorithm); - outputSettings->SetApod(mitk::BeamformingSettings::Apodization::Box); - outputSettings->SetSpeedOfSound(input.speedOfSound); - outputSettings->SetTimeSpacing(input.inputImage->GetGeometry()->GetSpacing()[1] / 1000000); - outputSettings->SetRecordTime(input.inputImage->GetDimension(1)*input.inputImage->GetGeometry()->GetSpacing()[1] / 1000000); // [s] - outputSettings->SetUseGPU(false); - outputSettings->SetUpperCutoff(input.cutoff); - outputSettings->SetDelayCalculationMethod(mitk::BeamformingSettings::DelayCalc::Spherical); - outputSettings->SetAngle(input.angle); - outputSettings->SetPitch(input.inputImage->GetGeometry()->GetSpacing()[0] / 1000); - outputSettings->SetTransducerElements(input.inputImage->GetDimension(0)); - outputSettings->SetReconstructionLines(input.inputImage->GetDimension(0)); - outputSettings->SetSamplesPerLine(input.samples); - outputSettings->SetIsPhotoacousticImage(true); - outputSettings->SetPartial(false); - outputSettings->SetApodizationArraySize(input.inputImage->GetDimension(0)); - outputSettings->SetUseBP(false); + mitk::BeamformingSettings::Pointer outputSettings = mitk::BeamformingSettings::New( + (float)(input.inputImage->GetGeometry()->GetSpacing()[0] / 1000), + (float)(input.speedOfSound), + (float)(input.inputImage->GetGeometry()->GetSpacing()[1] / 1000000), + input.angle, + true, + input.inputImage->GetDimension(0), + input.cutoff, + false, + (unsigned int*) nullptr, + input.inputImage->GetDimensions(), + false, + mitk::BeamformingSettings::DelayCalc::Spherical, + mitk::BeamformingSettings::Apodization::Box, + input.inputImage->GetDimension(0), + input.algorithm, + false, + 0.0f, + 0.0f); return outputSettings; } int main(int argc, char * argv[]) { auto input = parseInput(argc, argv); MITK_INFO(input.verbose) << "Beamforming input image..."; mitk::PhotoacousticFilterService::Pointer m_BeamformingService = mitk::PhotoacousticFilterService::New(); mitk::BeamformingSettings::Pointer settings = ParseSettings(input); - std::string message = "Test"; + mitk::CastToFloatImageFilter::Pointer castFilter = mitk::CastToFloatImageFilter::New(); + castFilter->SetInput(input.inputImage); + castFilter->Update(); + auto floatImage = castFilter->GetOutput(); - auto output = m_BeamformingService->ApplyBeamforming(input.inputImage, settings, message); + auto output = m_BeamformingService->ApplyBeamforming(floatImage, settings); MITK_INFO(input.verbose) << "Applying BModeFilter to image..."; //output = m_BeamformingService->ApplyBmodeFilter(output, mitk::PhotoacousticFilterService::Abs, false, false, 0.3); MITK_INFO(input.verbose) << "Applying BModeFilter to image...[Done]"; MITK_INFO(input.verbose) << "Saving image..."; mitk::IOUtil::Save(output, input.outputFilename); MITK_INFO(input.verbose) << "Saving image...[Done]"; MITK_INFO(input.verbose) << "Beamforming input image...[Done]"; } diff --git a/Modules/PhotoacousticsAlgorithms/files.cmake b/Modules/PhotoacousticsAlgorithms/files.cmake index 0aeeaf0b4b..80c89f8144 100644 --- a/Modules/PhotoacousticsAlgorithms/files.cmake +++ b/Modules/PhotoacousticsAlgorithms/files.cmake @@ -1,29 +1,30 @@ file(GLOB_RECURSE H_FILES RELATIVE "${CMAKE_CURRENT_SOURCE_DIR}" "${CMAKE_CURRENT_SOURCE_DIR}/include/*") set(CPP_FILES source/filters/mitkBeamformingFilter.cpp + source/filters/mitkBeamformingSettings.cpp source/filters/mitkImageSliceSelectionFilter.cpp source/filters/mitkCastToFloatImageFilter.cpp source/filters/mitkCropImageFilter.cpp source/OpenCLFilter/mitkPhotoacousticBModeFilter.cpp source/utils/mitkPhotoacousticFilterService.cpp source/utils/mitkBeamformingUtils.cpp ) IF(MITK_USE_OpenCL) list(APPEND CPP_FILES source/OpenCLFilter/mitkPhotoacousticOCLBeamformingFilter.cpp source/OpenCLFilter/mitkPhotoacousticOCLUsedLinesCalculation.cpp source/OpenCLFilter/mitkPhotoacousticOCLDelayCalculation.cpp ) ENDIF(MITK_USE_OpenCL) set(RESOURCE_FILES BModeAbs.cl BModeAbsLog.cl UsedLinesCalculation.cl DelayCalculation.cl DMAS.cl DAS.cl sDMAS.cl ) diff --git a/Modules/PhotoacousticsAlgorithms/include/OpenCLFilter/mitkPhotoacousticOCLBeamformingFilter.h b/Modules/PhotoacousticsAlgorithms/include/OpenCLFilter/mitkPhotoacousticOCLBeamformingFilter.h index 25cbeb49e3..ff7d62b1be 100644 --- a/Modules/PhotoacousticsAlgorithms/include/OpenCLFilter/mitkPhotoacousticOCLBeamformingFilter.h +++ b/Modules/PhotoacousticsAlgorithms/include/OpenCLFilter/mitkPhotoacousticOCLBeamformingFilter.h @@ -1,145 +1,145 @@ /*=================================================================== 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 _MITKPHOTOACOUSTICSOCLBEAMFORMER_H_ #define _MITKPHOTOACOUSTICSOCLBEAMFORMER_H_ #include #if defined(PHOTOACOUSTICS_USE_GPU) || DOXYGEN #include "mitkOclDataSetToDataSetFilter.h" #include "mitkPhotoacousticOCLDelayCalculation.h" #include "mitkPhotoacousticOCLUsedLinesCalculation.h" #include "mitkBeamformingSettings.h" #include namespace mitk { /*! * \brief Class implementing a mitk::OclDataSetToDataSetFilter for beamforming on GPU * * The class must be given a configuration class instance of mitk::BeamformingSettings for beamforming parameters through mitk::PhotoacousticOCLBeamformingFilter::SetConfig(BeamformingSettings settings) * Additional configuration of the apodisation function is needed. */ class PhotoacousticOCLBeamformingFilter : public OclDataSetToDataSetFilter, public itk::Object { public: mitkClassMacroItkParent(PhotoacousticOCLBeamformingFilter, itk::Object); mitkNewMacro1Param(Self, BeamformingSettings::Pointer); /** * @brief SetInput Set the input data through an image. Arbitrary images are supported */ void SetInput(Image::Pointer image); /** * brief SetInput Manually set the input data while providing 3 dimensions and memory size of the input data (Bytes per element). */ void SetInput(void* data, unsigned int* dimensions, unsigned int BpE); /** * @brief GetOutput Get a pointer to the processed data. The standard datatype is float. */ void* GetOutput(); /** * @brief GetOutputAsImage Returns an mitk::Image constructed from the processed data */ mitk::Image::Pointer GetOutputAsImage(); /** \brief Update the filter */ void Update(); /** \brief Set the Apodisation function to apply when beamforming */ - void SetApodisation(float* apodisation, unsigned short apodArraySize) + void SetApodisation(const float* apodisation, unsigned short apodArraySize) { m_ApodArraySize = apodArraySize; m_Apodisation = apodisation; } protected: PhotoacousticOCLBeamformingFilter(BeamformingSettings::Pointer settings); virtual ~PhotoacousticOCLBeamformingFilter(); /** \brief Initialize the filter */ bool Initialize(); /** \brief Updated the used data for beamforming depending on whether the configuration has significantly changed */ void UpdateDataBuffers(); /** \brief Execute the filter */ void Execute(); mitk::PixelType GetOutputType() { return mitk::MakeScalarPixelType(); } int GetBytesPerElem() { return sizeof(float); } virtual us::Module* GetModule(); private: /** The OpenCL kernel for the filter */ cl_kernel m_PixelCalculation; unsigned int m_OutputDim[3]; - float* m_Apodisation; + const float* m_Apodisation; unsigned short m_ApodArraySize; unsigned short m_PAImage; BeamformingSettings::Pointer m_Conf; mitk::Image::Pointer m_InputImage; size_t m_ChunkSize[3]; mitk::OCLUsedLinesCalculation::Pointer m_UsedLinesCalculation; mitk::OCLDelayCalculation::Pointer m_DelayCalculation; cl_mem m_ApodizationBuffer; cl_mem m_MemoryLocationsBuffer; cl_mem m_DelaysBuffer; cl_mem m_UsedLinesBuffer; }; } #else namespace mitk { class PhotoacousticOCLBeamformingFilter : public itk::Object { public: mitkClassMacroItkParent(mitk::PhotoacousticOCLBeamformingFilter, itk::Object); itkNewMacro(Self); protected: /** Constructor */ PhotoacousticOCLBeamformingFilter() {} /** Destructor */ ~PhotoacousticOCLBeamformingFilter() override {} }; } #endif #endif diff --git a/Modules/PhotoacousticsAlgorithms/include/mitkBeamformingFilter.h b/Modules/PhotoacousticsAlgorithms/include/mitkBeamformingFilter.h index 667432fff1..834b51dac1 100644 --- a/Modules/PhotoacousticsAlgorithms/include/mitkBeamformingFilter.h +++ b/Modules/PhotoacousticsAlgorithms/include/mitkBeamformingFilter.h @@ -1,102 +1,88 @@ /*=================================================================== 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 MITK_PHOTOACOUSTICS_BEAMFORMING_FILTER #define MITK_PHOTOACOUSTICS_BEAMFORMING_FILTER #include "mitkImageToImageFilter.h" #include #include "./OpenCLFilter/mitkPhotoacousticOCLBeamformingFilter.h" #include "mitkBeamformingSettings.h" #include "mitkBeamformingUtils.h" namespace mitk { /*! * \brief Class implementing an mitk::ImageToImageFilter for beamforming on both CPU and GPU * * The class must be given a configuration class instance of mitk::BeamformingSettings for beamforming parameters through mitk::BeamformingFilter::Configure(BeamformingSettings settings) * Whether the GPU is used can be set in the configuration. * For significant problems or important messages a string is written, which can be accessed via GetMessageString(). */ class BeamformingFilter : public ImageToImageFilter { public: mitkClassMacro(BeamformingFilter, ImageToImageFilter); mitkNewMacro1Param(Self, mitk::BeamformingSettings::Pointer); itkCloneMacro(Self); - /** \brief Sets a new configuration to use - * - * The Filter writes important messages that can be retrieved through this method; if nothing is to be reported, it returns "noMessage". - * @return The message - */ - std::string GetMessageString() - { - return m_Message; - } - /** \brief Sets a callback for progress checking * * An std::function can be set, through which progress of the currently updating filter is reported. * The integer argument is a number between 0 an 100 to indicate how far completion has been achieved, the std::string argument indicates what the filter is currently doing. */ void SetProgressHandle(std::function progressHandle); protected: BeamformingFilter(mitk::BeamformingSettings::Pointer settings); ~BeamformingFilter() override; void GenerateInputRequestedRegion() override; void GenerateOutputInformation() override; void GenerateData() override; //##Description //## @brief Time when Header was last initialized itk::TimeStamp m_TimeOfHeaderInitialization; /** \brief The std::function, through which progress of the currently updating filter is reported. */ std::function m_ProgressHandle; float* m_OutputData; float* m_InputData; float* m_InputDataPuffer; /** \brief Current configuration set */ BeamformingSettings::Pointer m_Conf; /** * The size of the apodization array when it last changed. */ int m_LastApodizationArraySize; /** \brief Pointer to the GPU beamforming filter class; for performance reasons the filter is initialized within the constructor and kept for all later computations. */ mitk::PhotoacousticOCLBeamformingFilter::Pointer m_BeamformingOclFilter; - - /** \brief The message returned by mitk::BeamformingFilter::GetMessageString() - */ - std::string m_Message; }; } // namespace mitk #endif //MITK_PHOTOACOUSTICS_BEAMFORMING_FILTER diff --git a/Modules/PhotoacousticsAlgorithms/include/mitkBeamformingSettings.h b/Modules/PhotoacousticsAlgorithms/include/mitkBeamformingSettings.h index 8028b9ca7c..711710a13b 100644 --- a/Modules/PhotoacousticsAlgorithms/include/mitkBeamformingSettings.h +++ b/Modules/PhotoacousticsAlgorithms/include/mitkBeamformingSettings.h @@ -1,253 +1,251 @@ /*=================================================================== 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 MITK_BEAMFORMING_SETTINGS #define MITK_BEAMFORMING_SETTINGS #include #include -//#include +#include +#include namespace mitk { /*! * \brief Class holding the configuration data for the beamforming filters mitk::BeamformingFilter and mitk::PhotoacousticOCLBeamformingFilter * * A detailed description can be seen below. All parameters should be set manually for successfull beamforming. */ - class BeamformingSettings : public itk::Object + class MITKPHOTOACOUSTICSALGORITHMS_EXPORT BeamformingSettings : public itk::Object { public: - mitkClassMacroItkParent(BeamformingSettings, itk::Object) + mitkClassMacroItkParent(BeamformingSettings, itk::Object); + mitkNewMacro1Param(BeamformingSettings, std::string); + itkCloneMacro(Self); - itkFactorylessNewMacro(Self) - itkCloneMacro(Self) - - /** \brief Available delay calculation methods: - * - Spherical delay for best results. - * - A quadratic Taylor approximation for slightly faster results with hardly any quality loss. - */ - enum DelayCalc { QuadApprox, Spherical }; + /** \brief Available delay calculation methods: + * - Spherical delay for best results. + * - A quadratic Taylor approximation for slightly faster results with hardly any quality loss. + */ + enum DelayCalc { QuadApprox, Spherical }; /** \brief Available apodization functions: * - Hamming function. * - Von-Hann function. * - Box function. */ enum Apodization { Hamm, Hann, Box }; /** \brief Available beamforming algorithms: * - DAS (Delay and sum). * - DMAS (Delay multiply and sum). */ enum BeamformingAlgorithm { DMAS, DAS, sDMAS }; - itkGetMacro(PitchInMeters, float) - itkSetMacro(PitchInMeters, float) - itkGetMacro(SpeedOfSound, float) - itkSetMacro(SpeedOfSound, float) - itkGetMacro(TimeSpacing, float) - itkSetMacro(TimeSpacing, float) - itkGetMacro(Angle, float) - itkSetMacro(Angle, float) - itkGetMacro(IsPhotoacousticImage, bool) - itkSetMacro(IsPhotoacousticImage, bool) - itkGetMacro(TransducerElements, unsigned short) - itkSetMacro(TransducerElements, unsigned short) - itkGetMacro(SamplesPerLine, unsigned int) - itkSetMacro(SamplesPerLine, unsigned int) - itkGetMacro(ReconstructionLines, unsigned int) - itkSetMacro(ReconstructionLines, unsigned int) - itkGetMacro(UpperCutoff, unsigned int) - itkSetMacro(UpperCutoff, unsigned int) - itkGetMacro(Partial, bool) - itkSetMacro(Partial, bool) - itkGetMacro(CropBounds, unsigned int*) - void SetCropBounds(unsigned int* cropBounds) - { - if (m_CropBounds != nullptr) - { - delete[] m_CropBounds; - } - - m_CropBounds = cropBounds; - } - itkGetMacro(InputDim, unsigned int*) - void SetInputDim(unsigned int* inputDim) - { - if (m_InputDim != nullptr) - { - delete[] m_InputDim; - } - - m_InputDim = inputDim; - } - itkGetMacro(UseGPU, bool) - itkSetMacro(UseGPU, bool) - itkGetMacro(DelayCalculationMethod, DelayCalc) - itkSetMacro(DelayCalculationMethod, DelayCalc) - itkGetMacro(ApodizationFunction, float*) - void SetApodizationFunction(float* function) - { - if (m_ApodizationFunction != nullptr) - { - delete[] m_ApodizationFunction; - } - - m_ApodizationFunction = function; - } - itkGetMacro(Apod, Apodization) - itkSetMacro(Apod, Apodization) - itkGetMacro(ApodizationArraySize, int) - itkSetMacro(ApodizationArraySize, int) - itkGetMacro(Algorithm, BeamformingAlgorithm) - itkSetMacro(Algorithm, BeamformingAlgorithm) - itkGetMacro(UseBP, bool) - itkSetMacro(UseBP, bool) - itkGetMacro(BPHighPass, float) - itkSetMacro(BPHighPass, float) - itkGetMacro(BPLowPass, float) - itkSetMacro(BPLowPass, float) - - /** \brief function for mitk::PhotoacousticOCLBeamformingFilter to check whether buffers need to be updated - * this method only checks parameters relevant for the openCL implementation - */ - static bool SettingsChangedOpenCL(const BeamformingSettings::Pointer lhs, const BeamformingSettings::Pointer rhs) + itkGetConstMacro(PitchInMeters, float); + itkGetConstMacro(SpeedOfSound, float); + itkGetConstMacro(TimeSpacing, float); + itkGetConstMacro(Angle, float); + itkGetConstMacro(IsPhotoacousticImage, bool); + itkGetConstMacro(TransducerElements, unsigned int); + itkGetConstMacro(SamplesPerLine, unsigned int); + itkGetConstMacro(ReconstructionLines, unsigned int); + itkGetConstMacro(UpperCutoff, unsigned int); + itkGetConstMacro(Partial, bool); + itkGetConstMacro(CropBounds, const unsigned int*); + itkGetConstMacro(InputDim, const unsigned int*); + itkGetConstMacro(UseGPU, bool); + itkGetConstMacro(DelayCalculationMethod, DelayCalc); + itkGetConstMacro(ApodizationFunction, const float*); + itkGetConstMacro(Apod, Apodization); + itkGetConstMacro(ApodizationArraySize, int); + itkGetConstMacro(Algorithm, BeamformingAlgorithm); + itkGetConstMacro(UseBP, bool); + itkGetConstMacro(BPHighPass, float); + itkGetConstMacro(BPLowPass, float); + + /** \brief function for mitk::PhotoacousticOCLBeamformingFilter to check whether buffers need to be updated + * this method only checks parameters relevant for the openCL implementation + */ + static bool SettingsChangedOpenCL(const BeamformingSettings::Pointer lhs, const BeamformingSettings::Pointer rhs) { return !((abs(lhs->GetAngle() - rhs->GetAngle()) < 0.01f) && // 0.01 degree error margin (lhs->GetApod() == rhs->GetApod()) && (lhs->GetDelayCalculationMethod() == rhs->GetDelayCalculationMethod()) && (lhs->GetIsPhotoacousticImage() == rhs->GetIsPhotoacousticImage()) && (abs(lhs->GetPitchInMeters() - rhs->GetPitchInMeters()) < 0.000001f) && // 0.0001 mm error margin (lhs->GetReconstructionLines() == rhs->GetReconstructionLines()) && (lhs->GetSamplesPerLine() == rhs->GetSamplesPerLine()) && (abs(lhs->GetSpeedOfSound() - rhs->GetSpeedOfSound()) < 0.01f) && (abs(lhs->GetTimeSpacing() - rhs->GetTimeSpacing()) < 0.00000000001f) && //0.01 ns error margin (lhs->GetTransducerElements() == rhs->GetTransducerElements())); } - protected: - - BeamformingSettings() - { - m_InputDim = new unsigned int[3]{ 1, 1, 1 }; - m_CropBounds = new unsigned int[2]{ 0, 0 }; - m_ApodizationFunction = new float[m_ApodizationArraySize]; - - /*switch (GetApod()) - { - case BeamformingSettings::Apodization::Hann: - SetApodizationFunction(mitk::BeamformingUtils::VonHannFunction(GetApodizationArraySize())); - break; - case BeamformingSettings::Apodization::Hamm: - SetApodizationFunction(mitk::BeamformingUtils::HammFunction(GetApodizationArraySize())); - break; - case BeamformingSettings::Apodization::Box: - SetApodizationFunction(mitk::BeamformingUtils::BoxFunction(GetApodizationArraySize())); - break; - default: - SetApodizationFunction(mitk::BeamformingUtils::BoxFunction(GetApodizationArraySize())); - break; - }*/ - } - ~BeamformingSettings() + static Pointer New(float pitchInMeters, + float speedOfSound, + float timeSpacing, + float angle, + bool isPhotoacousticImage, + unsigned int transducerElements, + unsigned int upperCutoff, + bool partial, + unsigned int* cropBounds, + unsigned int* inputDim, + bool useGPU, + DelayCalc delayCalculationMethod, + Apodization apod, + unsigned int apodizationArraySize, + BeamformingAlgorithm algorithm, + bool useBP, + float BPHighPass, + float BPLowPass) { + Pointer smartPtr = new BeamformingSettings(pitchInMeters, + speedOfSound, + timeSpacing, + angle, + isPhotoacousticImage, + transducerElements, + upperCutoff, + partial, + cropBounds, + inputDim, + useGPU, + delayCalculationMethod, + apod, + apodizationArraySize, + algorithm, + useBP, + BPHighPass, + BPLowPass); + smartPtr->UnRegister(); + return smartPtr; } + protected: + + /** + */ + BeamformingSettings(std::string xmlFile); + + /** + */ + BeamformingSettings(float pitchInMeters, + float speedOfSound, + float timeSpacing, + float angle, + bool isPhotoacousticImage, + unsigned int transducerElements, + unsigned int upperCutoff, + bool partial, + unsigned int* cropBounds, + unsigned int* inputDim, + bool useGPU, + DelayCalc delayCalculationMethod, + Apodization apod, + unsigned int apodizationArraySize, + BeamformingAlgorithm algorithm, + bool useBP, + float BPHighPass, + float BPLowPass + ); + + ~BeamformingSettings(); + /** \brief Pitch of the used transducer in [m]. */ - float m_PitchInMeters = 0.0003; + float m_PitchInMeters; /** \brief Speed of sound in the used medium in [m/s]. */ - float m_SpeedOfSound = 1540; + float m_SpeedOfSound; /** \brief The time spacing of the input image */ - float m_TimeSpacing = 0.0000000000001; // [s] + float m_TimeSpacing; // [s] /** \brief The angle of the transducer elements */ - float m_Angle = -1; + float m_Angle; /** \brief Flag whether processed image is a photoacoustic image or an ultrasound image */ - bool m_IsPhotoacousticImage = true; + bool m_IsPhotoacousticImage; /** \brief How many transducer elements the used transducer had. */ - unsigned short m_TransducerElements = 128; + unsigned int m_TransducerElements; /** \brief How many vertical samples should be used in the final image. */ - unsigned int m_SamplesPerLine = 2048; + unsigned int m_SamplesPerLine; /** \brief How many lines should be reconstructed in the final image. */ - unsigned int m_ReconstructionLines = 128; + unsigned int m_ReconstructionLines; /** \brief Sets how many voxels should be cut off from the top of the image before beamforming, to potentially avoid artifacts. */ - unsigned int m_UpperCutoff = 0; + unsigned int m_UpperCutoff; /** \brief Sets whether only the slices selected by mitk::BeamformingSettings::CropBounds should be beamformed. */ - bool m_Partial = false; + bool m_Partial; /** \brief Sets the first and last slice to be beamformed. */ - unsigned int* m_CropBounds; + const unsigned int* m_CropBounds; /** \brief Sets the dimensions of the inputImage. */ - unsigned int* m_InputDim; + const unsigned int* m_InputDim; /** \brief Decides whether GPU computing should be used */ - bool m_UseGPU = false; + bool m_UseGPU; /** \brief Sets how the delays for beamforming should be calculated. */ - DelayCalc m_DelayCalculationMethod = QuadApprox; + DelayCalc m_DelayCalculationMethod; - float* m_ApodizationFunction; + const float* m_ApodizationFunction; /** \brief Sets the used apodization function. */ - Apodization m_Apod = Hann; + Apodization m_Apod; /** \brief Sets the resolution of the apodization array (must be greater than 0). */ - int m_ApodizationArraySize = 128; + int m_ApodizationArraySize; /** \brief Sets the used beamforming algorithm. */ - BeamformingAlgorithm m_Algorithm = DAS; + BeamformingAlgorithm m_Algorithm; /** \brief Sets whether after beamforming a bandpass should be automatically applied */ - bool m_UseBP = false; + bool m_UseBP; /** \brief Sets the position at which lower frequencies are completely cut off in Hz. */ - float m_BPHighPass = 50; + float m_BPHighPass; /** \brief Sets the position at which higher frequencies are completely cut off in Hz. */ - float m_BPLowPass = 50; + float m_BPLowPass; }; } #endif //MITK_BEAMFORMING_SETTINGS diff --git a/Modules/PhotoacousticsAlgorithms/include/mitkBeamformingUtils.h b/Modules/PhotoacousticsAlgorithms/include/mitkBeamformingUtils.h index ead7f821cf..9060284cfd 100644 --- a/Modules/PhotoacousticsAlgorithms/include/mitkBeamformingUtils.h +++ b/Modules/PhotoacousticsAlgorithms/include/mitkBeamformingUtils.h @@ -1,80 +1,80 @@ /*=================================================================== 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 MITK_BEAMFORMING_FILTER_UTILS #define MITK_BEAMFORMING_FILTER_UTILS #include "mitkImageToImageFilter.h" #include #include "./OpenCLFilter/mitkPhotoacousticOCLBeamformingFilter.h" #include "mitkBeamformingSettings.h" namespace mitk { /*! * \brief Class implementing util functionality for beamforming on CPU * */ class BeamformingUtils final { public: /** \brief Function to perform beamforming on CPU for a single line, using DAS and quadratic delay */ - static void DASQuadraticLine(float* input, float* output, float inputDim[2], float outputDim[2], const short& line, float* apodisation, const short& apodArraySize, const mitk::BeamformingSettings::Pointer config); + static void DASQuadraticLine(float* input, float* output, float inputDim[2], float outputDim[2], const short& line, const mitk::BeamformingSettings::Pointer config); /** \brief Function to perform beamforming on CPU for a single line, using DAS and spherical delay */ - static void DASSphericalLine(float* input, float* output, float inputDim[2], float outputDim[2], const short& line, float* apodisation, const short& apodArraySize, const mitk::BeamformingSettings::Pointer config); + static void DASSphericalLine(float* input, float* output, float inputDim[2], float outputDim[2], const short& line, const mitk::BeamformingSettings::Pointer config); /** \brief Function to perform beamforming on CPU for a single line, using DMAS and quadratic delay */ - static void DMASQuadraticLine(float* input, float* output, float inputDim[2], float outputDim[2], const short& line, float* apodisation, const short& apodArraySize, const mitk::BeamformingSettings::Pointer config); + static void DMASQuadraticLine(float* input, float* output, float inputDim[2], float outputDim[2], const short& line, const mitk::BeamformingSettings::Pointer config); /** \brief Function to perform beamforming on CPU for a single line, using DMAS and spherical delay */ - static void DMASSphericalLine(float* input, float* output, float inputDim[2], float outputDim[2], const short& line, float* apodisation, const short& apodArraySize, const mitk::BeamformingSettings::Pointer config); + static void DMASSphericalLine(float* input, float* output, float inputDim[2], float outputDim[2], const short& line, const mitk::BeamformingSettings::Pointer config); /** \brief Function to perform beamforming on CPU for a single line, using signed DMAS and quadratic delay */ - static void sDMASQuadraticLine(float* input, float* output, float inputDim[2], float outputDim[2], const short& line, float* apodisation, const short& apodArraySize, const mitk::BeamformingSettings::Pointer config); + static void sDMASQuadraticLine(float* input, float* output, float inputDim[2], float outputDim[2], const short& line, const mitk::BeamformingSettings::Pointer config); /** \brief Function to perform beamforming on CPU for a single line, using signed DMAS and spherical delay */ - static void sDMASSphericalLine(float* input, float* output, float inputDim[2], float outputDim[2], const short& line, float* apodisation, const short& apodArraySize, const mitk::BeamformingSettings::Pointer config); + static void sDMASSphericalLine(float* input, float* output, float inputDim[2], float outputDim[2], const short& line, const mitk::BeamformingSettings::Pointer config); /** \brief Pointer holding the Von-Hann apodization window for beamforming * @param samples the resolution at which the window is created */ static float* VonHannFunction(int samples); /** \brief Function to create a Hamming apodization window * @param samples the resolution at which the window is created */ static float* HammFunction(int samples); /** \brief Function to create a Box apodization window * @param samples the resolution at which the window is created */ static float* BoxFunction(int samples); protected: BeamformingUtils(); ~BeamformingUtils(); }; } // namespace mitk #endif //MITK_BEAMFORMING_FILTER_UTILS diff --git a/Modules/PhotoacousticsAlgorithms/include/mitkPhotoacousticFilterService.h b/Modules/PhotoacousticsAlgorithms/include/mitkPhotoacousticFilterService.h index 26bed5e04f..0c017de1ff 100644 --- a/Modules/PhotoacousticsAlgorithms/include/mitkPhotoacousticFilterService.h +++ b/Modules/PhotoacousticsAlgorithms/include/mitkPhotoacousticFilterService.h @@ -1,132 +1,131 @@ /*=================================================================== 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 mitkPhotoacousticFilterService_H_HEADER_INCLUDED #define mitkPhotoacousticFilterService_H_HEADER_INCLUDED #include "itkObject.h" #include "mitkCommon.h" #include "mitkImage.h" #include #include "mitkBeamformingSettings.h" #include "mitkBeamformingFilter.h" #include "MitkPhotoacousticsAlgorithmsExports.h" namespace mitk { /*! * \brief Class holding methods to apply all Filters within the Photoacoustics Algorithms Module * * Implemented are: * - A B-Mode Filter * - A Resampling Filter * - Beamforming on GPU and CPU * - A Bandpass Filter */ class MITKPHOTOACOUSTICSALGORITHMS_EXPORT PhotoacousticFilterService : public itk::Object { public: mitkClassMacroItkParent(mitk::PhotoacousticFilterService, itk::Object); itkFactorylessNewMacro(Self); /** \brief Defines the methods for the B-Mode filter * Currently implemented are an Envelope Detection filter and a simple Absolute filter. */ enum BModeMethod { EnvelopeDetection, Abs }; /** \brief Applies a B-Mode Filter * * Applies a B-Mode filter using the given parameters. * @param inputImage The image to be processed. * @param method The kind of B-Mode Filter to be used. * @param UseGPU Setting this to true will allow the Filter to use the GPU. * @param UseLogFilter Setting this to true will apply a simple logarithm to the image after the B-Mode Filter has been applied. * @param resampleSpacing If this is set to 0, nothing will be done; otherwise, the image is resampled to a spacing of resampleSpacing mm per pixel. * @return The processed image is returned after the filter has finished. */ mitk::Image::Pointer ApplyBmodeFilter(mitk::Image::Pointer inputImage, BModeMethod method = BModeMethod::Abs, bool UseGPU = false, bool UseLogFilter = false, float resampleSpacing = 0.15); // mitk::Image::Pointer ApplyScatteringCompensation(mitk::Image::Pointer inputImage, int scatteringCoefficient); /** \brief Resamples the given image * * Resamples an image using the given parameters. * @param inputImage The image to be processed. * @param outputSize An array of dimensions the image should be resampled to. * @return The processed image is returned after the filter has finished. */ mitk::Image::Pointer ApplyResampling(mitk::Image::Pointer inputImage, unsigned int outputSize[2]); /** \brief Beamforms the given image * * Resamples an image using the given parameters. * @param inputImage The image to be processed. * @param config The configuration set to be used for beamforming. - * @param message A string into which potentially critical messages will be written. * @param progressHandle An std::function, through which progress of the currently updating filter is reported. * The integer argument is a number between 0 an 100 to indicate how far completion has been achieved, the std::string argument indicates what the filter is currently doing. * @return The processed image is returned after the filter has finished. */ - mitk::Image::Pointer ApplyBeamforming(mitk::Image::Pointer inputImage, BeamformingSettings::Pointer config, std::string& message, std::function progressHandle = [](int, std::string) {}); + mitk::Image::Pointer ApplyBeamforming(mitk::Image::Pointer inputImage, BeamformingSettings::Pointer config, std::function progressHandle = [](int, std::string) {}); /** \brief Crops the given image * * Crops an image in 3 dimension using the given parameters. * @param inputImage The image to be processed. * @param above How many voxels will be cut from the top of the image. * @param below How many voxels will be cut from the bottom of the image. * @param right How many voxels will be cut from the right side of the image. * @param left How many voxels will be cut from the left side of the image. * @param minSlice The first slice to be present in the resulting image. * @param maxSlice The last slice to be present in the resulting image. * @return The processed image is returned after the filter has finished. For the purposes of this module, the returned image is always of type float. */ mitk::Image::Pointer ApplyCropping(mitk::Image::Pointer inputImage, int above, int below, int right, int left, int minSlice, int maxSlice); /** \brief Applies a Bandpass filter to the given image * * Applies a bandpass filter to the given image using the given parameters. * @param data The image to be processed. * @param recordTime The depth of the image in seconds. * @param BPHighPass The position at which Lower frequencies are completely cut off in Hz. * @param BPLowPass The position at which Higher frequencies are completely cut off in Hz. * @param alphaHighPass The high pass tukey window parameter to control the shape of the bandpass filter: 0 will make it a Box function, 1 a Hann function. alpha can be set between those two bounds. * @param alphaLowPass The low passtukey window parameter to control the shape of the bandpass filter: 0 will make it a Box function, 1 a Hann function. alpha can be set between those two bounds. * @return The processed image is returned after the filter has finished. */ mitk::Image::Pointer BandpassFilter(mitk::Image::Pointer data, float recordTime, float BPHighPass, float BPLowPass, float alphaHighPass, float alphaLowPass); protected: PhotoacousticFilterService(); ~PhotoacousticFilterService() override; /** \brief For performance reasons, an instance of the Beamforming filter is initialized as soon as possible and kept for all further uses. */ mitk::BeamformingFilter::Pointer m_BeamformingFilter; /** \brief Function that creates a Tukey function for the bandpass */ itk::Image::Pointer BPFunction(mitk::Image::Pointer reference, int cutoffFrequencyPixelHighPass, int cutoffFrequencyPixelLowPass, float alphaHighPass, float alphaLowPass); }; } // namespace mitk #endif /* mitkPhotoacousticFilterService_H_HEADER_INCLUDED */ diff --git a/Modules/PhotoacousticsAlgorithms/source/OpenCLFilter/mitkPhotoacousticOCLBeamformingFilter.cpp b/Modules/PhotoacousticsAlgorithms/source/OpenCLFilter/mitkPhotoacousticOCLBeamformingFilter.cpp index 341375c8a7..6a5eb4a76c 100644 --- a/Modules/PhotoacousticsAlgorithms/source/OpenCLFilter/mitkPhotoacousticOCLBeamformingFilter.cpp +++ b/Modules/PhotoacousticsAlgorithms/source/OpenCLFilter/mitkPhotoacousticOCLBeamformingFilter.cpp @@ -1,273 +1,260 @@ /*=================================================================== 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. ===================================================================*/ #if defined(PHOTOACOUSTICS_USE_GPU) || DOXYGEN #include "./OpenCLFilter/mitkPhotoacousticOCLBeamformingFilter.h" #include "usServiceReference.h" mitk::PhotoacousticOCLBeamformingFilter::PhotoacousticOCLBeamformingFilter(BeamformingSettings::Pointer settings) : m_PixelCalculation(NULL), m_InputImage(mitk::Image::New()), m_ApodizationBuffer(nullptr), m_MemoryLocationsBuffer(nullptr), m_DelaysBuffer(nullptr), m_UsedLinesBuffer(nullptr), m_Conf(settings) { + MITK_INFO << "Initializing OCL beamforming Filter..."; this->AddSourceFile("DAS.cl"); this->AddSourceFile("DMAS.cl"); this->AddSourceFile("sDMAS.cl"); this->m_FilterID = "OpenCLBeamformingFilter"; this->Initialize(); unsigned int dim[] = { 128, 2048, 2 }; - mitk::Vector3D spacing; - spacing[0] = 1; - spacing[1] = 1; - spacing[2] = 1; - m_InputImage->Initialize(mitk::MakeScalarPixelType(), 3, dim); - m_InputImage->SetSpacing(spacing); m_ChunkSize[0] = 128; m_ChunkSize[1] = 128; m_ChunkSize[2] = 8; m_UsedLinesCalculation = mitk::OCLUsedLinesCalculation::New(m_Conf); m_DelayCalculation = mitk::OCLDelayCalculation::New(m_Conf); + MITK_INFO << "Initializing OCL beamforming Filter...[Done]"; } mitk::PhotoacousticOCLBeamformingFilter::~PhotoacousticOCLBeamformingFilter() { if (this->m_PixelCalculation) { clReleaseKernel(m_PixelCalculation); } if (m_ApodizationBuffer) clReleaseMemObject(m_ApodizationBuffer); } void mitk::PhotoacousticOCLBeamformingFilter::Update() { //Check if context & program available if (!this->Initialize()) { us::ServiceReference ref = GetModuleContext()->GetServiceReference(); OclResourceService* resources = GetModuleContext()->GetService(ref); // clean-up also the resources resources->InvalidateStorage(); mitkThrow() << "Filter is not initialized. Cannot update."; } else { // Execute this->Execute(); } } void mitk::PhotoacousticOCLBeamformingFilter::UpdateDataBuffers() { /*us::ServiceReference ref = GetModuleContext()->GetServiceReference(); OclResourceService* resources = GetModuleContext()->GetService(ref); cl_ulong globalMemSize = oclGetGlobalMemSize(resources->GetCurrentDevice());*/ //Initialize the Output try { MITK_INFO << "Updating Workgroup size for new dimensions"; size_t outputSize = (size_t)m_Conf->GetReconstructionLines() * (size_t)m_Conf->GetSamplesPerLine() * (size_t)m_Conf->GetInputDim()[2]; m_OutputDim[0] = m_Conf->GetReconstructionLines(); m_OutputDim[1] = m_Conf->GetSamplesPerLine(); m_OutputDim[2] = m_Conf->GetInputDim()[2]; this->InitExec(this->m_PixelCalculation, m_OutputDim, outputSize, sizeof(float)); } catch (const mitk::Exception& e) { MITK_ERROR << "Caught exception while initializing filter: " << e.what(); return; } //TODO FIXME cl_int clErr = 0; MITK_DEBUG << "Updating GPU Buffers for new configuration"; // create the apodisation buffer if (m_Apodisation == nullptr) { MITK_INFO << "No apodisation function set; Beamforming will be done without any apodisation."; - m_Apodisation = new float[1]; - m_Apodisation[0] = 1; + m_Apodisation = new float[1]{ 1 }; m_ApodArraySize = 1; } us::ServiceReference ref = GetModuleContext()->GetServiceReference(); OclResourceService* resources = GetModuleContext()->GetService(ref); cl_context gpuContext = resources->GetContext(); if (m_ApodizationBuffer) clReleaseMemObject(m_ApodizationBuffer); - this->m_ApodizationBuffer = clCreateBuffer(gpuContext, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR, sizeof(float) * m_ApodArraySize, m_Apodisation, &clErr); + this->m_ApodizationBuffer = clCreateBuffer(gpuContext, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR, sizeof(float) * m_ApodArraySize, const_cast(m_Apodisation), &clErr); CHECK_OCL_ERR(clErr); // calculate used lines m_UsedLinesCalculation->Update(); m_UsedLinesBuffer = m_UsedLinesCalculation->GetGPUOutput()->GetGPUBuffer(); // calculate the Delays m_DelayCalculation->SetInputs(m_UsedLinesBuffer); m_DelayCalculation->Update(); m_DelaysBuffer = m_DelayCalculation->GetGPUOutput()->GetGPUBuffer(); //m_ConfOld = m_Conf; } void mitk::PhotoacousticOCLBeamformingFilter::Execute() { cl_int clErr = 0; UpdateDataBuffers(); unsigned int reconstructionLines = this->m_Conf->GetReconstructionLines(); unsigned int samplesPerLine = this->m_Conf->GetSamplesPerLine(); clErr = clSetKernelArg(this->m_PixelCalculation, 2, sizeof(cl_mem), &(this->m_UsedLinesBuffer)); clErr |= clSetKernelArg(this->m_PixelCalculation, 3, sizeof(cl_mem), &(this->m_DelaysBuffer)); clErr |= clSetKernelArg(this->m_PixelCalculation, 4, sizeof(cl_mem), &(this->m_ApodizationBuffer)); clErr |= clSetKernelArg(this->m_PixelCalculation, 5, sizeof(cl_ushort), &(this->m_ApodArraySize)); clErr |= clSetKernelArg(this->m_PixelCalculation, 6, sizeof(cl_uint), &(this->m_Conf->GetInputDim()[0])); clErr |= clSetKernelArg(this->m_PixelCalculation, 7, sizeof(cl_uint), &(this->m_Conf->GetInputDim()[1])); clErr |= clSetKernelArg(this->m_PixelCalculation, 8, sizeof(cl_uint), &(this->m_Conf->GetInputDim()[2])); clErr |= clSetKernelArg(this->m_PixelCalculation, 9, sizeof(cl_uint), &(reconstructionLines)); clErr |= clSetKernelArg(this->m_PixelCalculation, 10, sizeof(cl_uint), &(samplesPerLine)); // execute the filter on a 3D NDRange if (m_OutputDim[2] == 1 || m_ChunkSize[2] == 1) { if (!this->ExecuteKernelChunksInBatches(m_PixelCalculation, 2, m_ChunkSize, 16, 50)) mitkThrow() << "openCL Error when executing Kernel"; } else { if (!this->ExecuteKernelChunksInBatches(m_PixelCalculation, 3, m_ChunkSize, 16, 50)) mitkThrow() << "openCL Error when executing Kernel"; } // signalize the GPU-side data changed m_Output->Modified(GPU_DATA); } us::Module *mitk::PhotoacousticOCLBeamformingFilter::GetModule() { return us::GetModuleContext()->GetModule(); } bool mitk::PhotoacousticOCLBeamformingFilter::Initialize() { MITK_INFO << "Initializing OCL Beamforming Filter..."; bool buildErr = true; cl_int clErr = 0; if (OclFilter::Initialize()) { switch (m_Conf->GetAlgorithm()) { case BeamformingSettings::BeamformingAlgorithm::DAS: { this->m_PixelCalculation = clCreateKernel(this->m_ClProgram, "ckDAS", &clErr); break; } case BeamformingSettings::BeamformingAlgorithm::DMAS: { this->m_PixelCalculation = clCreateKernel(this->m_ClProgram, "ckDMAS", &clErr); break; } case BeamformingSettings::BeamformingAlgorithm::sDMAS: { this->m_PixelCalculation = clCreateKernel(this->m_ClProgram, "cksDMAS", &clErr); break; } default: { MITK_INFO << "No beamforming algorithm specified, setting to DAS"; this->m_PixelCalculation = clCreateKernel(this->m_ClProgram, "ckDAS", &clErr); break; } } buildErr |= CHECK_OCL_ERR(clErr); } CHECK_OCL_ERR(clErr); MITK_INFO << "Initializing OCL Beamforming Filter...[Done]"; return (OclFilter::IsInitialized() && buildErr); } void mitk::PhotoacousticOCLBeamformingFilter::SetInput(mitk::Image::Pointer image) { OclDataSetToDataSetFilter::SetInput(image); - m_InputImage = image; - m_Conf->GetInputDim()[0] = m_InputImage->GetDimension(0); - m_Conf->GetInputDim()[1] = m_InputImage->GetDimension(1); - m_Conf->GetInputDim()[2] = m_InputImage->GetDimension(2); } void mitk::PhotoacousticOCLBeamformingFilter::SetInput(void* data, unsigned int* dimensions, unsigned int BpE) { OclDataSetToDataSetFilter::SetInput(data, dimensions[0] * dimensions[1] * dimensions[2], BpE); - - m_Conf->GetInputDim()[0] = dimensions[0]; - m_Conf->GetInputDim()[1] = dimensions[1]; - m_Conf->GetInputDim()[2] = dimensions[2]; } mitk::Image::Pointer mitk::PhotoacousticOCLBeamformingFilter::GetOutputAsImage() { mitk::Image::Pointer outputImage = mitk::Image::New(); if (m_Output->IsModified(GPU_DATA)) { void* pData = m_Output->TransferDataToCPU(m_CommandQue); const unsigned int dimension = 3; unsigned int dimensions[3] = { (unsigned int)m_OutputDim[0], (unsigned int)m_OutputDim[1], (unsigned int)m_OutputDim[2] }; const mitk::SlicedGeometry3D::Pointer p_slg = m_InputImage->GetSlicedGeometry(); MITK_DEBUG << "Creating new MITK Image."; outputImage->Initialize(this->GetOutputType(), dimension, dimensions); outputImage->SetSpacing(p_slg->GetSpacing()); outputImage->SetImportVolume(pData, 0, 0, mitk::Image::ImportMemoryManagementType::ManageMemory); } MITK_DEBUG << "Image Initialized."; return outputImage; } void* mitk::PhotoacousticOCLBeamformingFilter::GetOutput() { return OclDataSetToDataSetFilter::GetOutput(); } #endif diff --git a/Modules/PhotoacousticsAlgorithms/source/filters/mitkBeamformingFilter.cpp b/Modules/PhotoacousticsAlgorithms/source/filters/mitkBeamformingFilter.cpp index cd63d9df49..c53ea9da18 100644 --- a/Modules/PhotoacousticsAlgorithms/source/filters/mitkBeamformingFilter.cpp +++ b/Modules/PhotoacousticsAlgorithms/source/filters/mitkBeamformingFilter.cpp @@ -1,305 +1,298 @@ /*=================================================================== -mitkPhotoacousticBeamformingFilter +mitkBeamformingFilter 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 "mitkProperties.h" #include "mitkImageReadAccessor.h" #include #include #include #include #include #include "mitkImageCast.h" #include "mitkBeamformingFilter.h" #include "mitkBeamformingUtils.h" mitk::BeamformingFilter::BeamformingFilter(mitk::BeamformingSettings::Pointer settings) : m_OutputData(nullptr), m_InputData(nullptr), - m_Message("noMessage"), m_Conf(settings) { MITK_INFO << "Instantiating BeamformingFilter..."; this->SetNumberOfIndexedInputs(1); this->SetNumberOfRequiredInputs(1); m_ProgressHandle = [](int, std::string) {}; m_BeamformingOclFilter = mitk::PhotoacousticOCLBeamformingFilter::New(m_Conf); MITK_INFO << "Instantiating BeamformingFilter...[Done]"; } void mitk::BeamformingFilter::SetProgressHandle(std::function progressHandle) { m_ProgressHandle = progressHandle; } mitk::BeamformingFilter::~BeamformingFilter() { MITK_INFO << "Destructed BeamformingFilter"; } void mitk::BeamformingFilter::GenerateInputRequestedRegion() { Superclass::GenerateInputRequestedRegion(); mitk::Image* output = this->GetOutput(); mitk::Image* input = const_cast (this->GetInput()); if (!output->IsInitialized()) { return; } input->SetRequestedRegionToLargestPossibleRegion(); } void mitk::BeamformingFilter::GenerateOutputInformation() { mitk::Image::ConstPointer input = this->GetInput(); mitk::Image::Pointer output = this->GetOutput(); if ((output->IsInitialized()) && (this->GetMTime() <= m_TimeOfHeaderInitialization.GetMTime())) return; unsigned int dim[] = { m_Conf->GetReconstructionLines(), m_Conf->GetSamplesPerLine(), input->GetDimension(2) }; output->Initialize(mitk::MakeScalarPixelType(), 3, dim); mitk::Vector3D spacing; spacing[0] = m_Conf->GetPitchInMeters() * m_Conf->GetTransducerElements() * 1000 / m_Conf->GetReconstructionLines(); spacing[1] = (m_Conf->GetTimeSpacing() * m_Conf->GetInputDim()[1]) / 2 * m_Conf->GetSpeedOfSound() * 1000 / m_Conf->GetSamplesPerLine(); spacing[2] = 1; output->GetGeometry()->SetSpacing(spacing); output->GetGeometry()->Modified(); output->SetPropertyList(input->GetPropertyList()->Clone()); m_TimeOfHeaderInitialization.Modified(); } void mitk::BeamformingFilter::GenerateData() { mitk::Image::Pointer input = this->GetInput(); if (!(input->GetPixelType().GetTypeAsString() == "scalar (float)" || input->GetPixelType().GetTypeAsString() == " (float)")) { + MITK_ERROR << "Pixel type of input needs to be float for this filter to work."; mitkThrow() << "Pixel type of input needs to be float for this filter to work."; } GenerateOutputInformation(); mitk::Image::Pointer output = this->GetOutput(); if (!output->IsInitialized()) return; auto begin = std::chrono::high_resolution_clock::now(); // debbuging the performance... if (!m_Conf->GetUseGPU()) { int progInterval = output->GetDimension(2) / 20 > 1 ? output->GetDimension(2) / 20 : 1; // the interval at which we update the gui progress bar float inputDim[2] = { (float)input->GetDimension(0), (float)input->GetDimension(1) }; float outputDim[2] = { (float)output->GetDimension(0), (float)output->GetDimension(1) }; for (unsigned int i = 0; i < output->GetDimension(2); ++i) // seperate Slices should get Beamforming seperately applied { mitk::ImageReadAccessor inputReadAccessor(input, input->GetSliceData(i)); m_InputData = (float*)inputReadAccessor.GetData(); m_OutputData = new float[m_Conf->GetReconstructionLines()*m_Conf->GetSamplesPerLine()]; // fill the image with zeros for (int l = 0; l < outputDim[0]; ++l) { for (int s = 0; s < outputDim[1]; ++s) { m_OutputData[l*(short)outputDim[1] + s] = 0; } } std::thread *threads = new std::thread[(short)outputDim[0]]; // every line will be beamformed in a seperate thread if (m_Conf->GetAlgorithm() == BeamformingSettings::BeamformingAlgorithm::DAS) { if (m_Conf->GetDelayCalculationMethod() == BeamformingSettings::DelayCalc::QuadApprox) { for (short line = 0; line < outputDim[0]; ++line) { threads[line] = std::thread(&BeamformingUtils::DASQuadraticLine, m_InputData, - m_OutputData, inputDim, outputDim, line, m_Conf->GetApodizationFunction(), - m_Conf->GetApodizationArraySize(), m_Conf); + m_OutputData, inputDim, outputDim, line, m_Conf); } } else if (m_Conf->GetDelayCalculationMethod() == BeamformingSettings::DelayCalc::Spherical) { for (short line = 0; line < outputDim[0]; ++line) { threads[line] = std::thread(&BeamformingUtils::DASSphericalLine, m_InputData, - m_OutputData, inputDim, outputDim, line, m_Conf->GetApodizationFunction(), - m_Conf->GetApodizationArraySize(), m_Conf); + m_OutputData, inputDim, outputDim, line, m_Conf); } } } else if (m_Conf->GetAlgorithm() == BeamformingSettings::BeamformingAlgorithm::DMAS) { if (m_Conf->GetDelayCalculationMethod() == BeamformingSettings::DelayCalc::QuadApprox) { for (short line = 0; line < outputDim[0]; ++line) { threads[line] = std::thread(&BeamformingUtils::DMASQuadraticLine, m_InputData, - m_OutputData, inputDim, outputDim, line, m_Conf->GetApodizationFunction(), - m_Conf->GetApodizationArraySize(), m_Conf); + m_OutputData, inputDim, outputDim, line, m_Conf); } } else if (m_Conf->GetDelayCalculationMethod() == BeamformingSettings::DelayCalc::Spherical) { for (short line = 0; line < outputDim[0]; ++line) { threads[line] = std::thread(&BeamformingUtils::DMASSphericalLine, m_InputData, - m_OutputData, inputDim, outputDim, line, m_Conf->GetApodizationFunction(), - m_Conf->GetApodizationArraySize(), m_Conf); + m_OutputData, inputDim, outputDim, line, m_Conf); } } } else if (m_Conf->GetAlgorithm() == BeamformingSettings::BeamformingAlgorithm::sDMAS) { if (m_Conf->GetDelayCalculationMethod() == BeamformingSettings::DelayCalc::QuadApprox) { for (short line = 0; line < outputDim[0]; ++line) { threads[line] = std::thread(&BeamformingUtils::sDMASQuadraticLine, m_InputData, - m_OutputData, inputDim, outputDim, line, m_Conf->GetApodizationFunction(), - m_Conf->GetApodizationArraySize(), m_Conf); + m_OutputData, inputDim, outputDim, line, m_Conf); } } else if (m_Conf->GetDelayCalculationMethod() == BeamformingSettings::DelayCalc::Spherical) { for (short line = 0; line < outputDim[0]; ++line) { threads[line] = std::thread(&BeamformingUtils::sDMASSphericalLine, m_InputData, - m_OutputData, inputDim, outputDim, line, m_Conf->GetApodizationFunction(), - m_Conf->GetApodizationArraySize(), m_Conf); + m_OutputData, inputDim, outputDim, line, m_Conf); } } } // wait for all lines to finish for (short line = 0; line < outputDim[0]; ++line) { threads[line].join(); } output->SetSlice(m_OutputData, i); if (i % progInterval == 0) m_ProgressHandle((int)((i + 1) / (float)output->GetDimension(2) * 100), "performing reconstruction"); delete[] m_OutputData; m_OutputData = nullptr; m_InputData = nullptr; } } #if defined(PHOTOACOUSTICS_USE_GPU) || DOXYGEN else { try { // first, we check whether the data is float, other formats are unsupported if (!(input->GetPixelType().GetTypeAsString() == "scalar (float)" || input->GetPixelType().GetTypeAsString() == " (float)")) { MITK_ERROR << "Pixel type is not float, abort"; return; } unsigned long availableMemory = m_BeamformingOclFilter->GetDeviceMemory(); unsigned int batchSize = 16; unsigned int batches = (unsigned int)((float)input->GetDimension(2) / batchSize) + (input->GetDimension(2) % batchSize > 0); unsigned int batchDim[] = { input->GetDimension(0), input->GetDimension(1), batchSize }; unsigned int batchDimLast[] = { input->GetDimension(0), input->GetDimension(1), input->GetDimension(2) % batchSize }; // the following safeguard is probably only needed for absurdly small GPU memory for (batchSize = 16; (unsigned long)batchSize * ((unsigned long)(batchDim[0] * batchDim[1]) * 4 + // single input image (float) (unsigned long)(m_Conf->GetReconstructionLines() * m_Conf->GetSamplesPerLine()) * 4) // single output image (float) > availableMemory - (unsigned long)(m_Conf->GetReconstructionLines() / 2 * m_Conf->GetSamplesPerLine()) * 2 - // Delays buffer (unsigned short) (unsigned long)(m_Conf->GetReconstructionLines() * m_Conf->GetSamplesPerLine()) * 3 * 2 - // UsedLines buffer (unsigned short) 50 * 1024 * 1024; // 50 MB buffer for local data, system purposes etc --batchSize) { } if (batchSize < 1) { MITK_ERROR << "device memory too small for GPU beamforming"; return; } mitk::ImageReadAccessor copy(input); for (unsigned int i = 0; i < batches; ++i) { m_ProgressHandle(input->GetDimension(2) / batches * i, "performing reconstruction"); mitk::Image::Pointer inputBatch = mitk::Image::New(); + unsigned int num_Slices = 1; if (i == batches - 1 && (input->GetDimension(2) % batchSize > 0)) { inputBatch->Initialize(mitk::MakeScalarPixelType(), 3, batchDimLast); - m_Conf->GetInputDim()[2] = batchDimLast[2]; + num_Slices = batchDimLast[2]; } else { inputBatch->Initialize(mitk::MakeScalarPixelType(), 3, batchDim); - m_Conf->GetInputDim()[2] = batchDim[2]; + num_Slices = batchDim[2]; } inputBatch->SetSpacing(input->GetGeometry()->GetSpacing()); inputBatch->SetImportVolume(&(((float*)copy.GetData())[input->GetDimension(0) * input->GetDimension(1) * batchSize * i])); m_BeamformingOclFilter->SetApodisation(m_Conf->GetApodizationFunction(), m_Conf->GetApodizationArraySize()); m_BeamformingOclFilter->SetInput(inputBatch); m_BeamformingOclFilter->Update(); void* out = m_BeamformingOclFilter->GetOutput(); - for (unsigned int slice = 0; slice < m_Conf->GetInputDim()[2]; ++slice) + for (unsigned int slice = 0; slice < num_Slices; ++slice) { output->SetImportSlice( &(((float*)out)[m_Conf->GetReconstructionLines() * m_Conf->GetSamplesPerLine() * slice]), batchSize * i + slice, 0, 0, mitk::Image::ImportMemoryManagementType::CopyMemory); } } } catch (mitk::Exception &e) { std::string errorMessage = "Caught unexpected exception "; errorMessage.append(e.what()); MITK_ERROR << errorMessage; float* dummyData = new float[m_Conf->GetReconstructionLines() * m_Conf->GetSamplesPerLine() * m_Conf->GetInputDim()[2]]; - output->SetImportVolume(dummyData, 0, 0, mitk::Image::ImportMemoryManagementType::ManageMemory); - - m_Message = "An openCL error occurred; all GPU operations in this and the next session may be corrupted."; + output->SetImportVolume(dummyData, 0, 0, mitk::Image::ImportMemoryManagementType::CopyMemory); } } #endif m_TimeOfHeaderInitialization.Modified(); auto end = std::chrono::high_resolution_clock::now(); MITK_INFO << "Beamforming of " << output->GetDimension(2) << " Images completed in " << ((float)std::chrono::duration_cast(end - begin).count()) / 1000000 << "ms" << std::endl; } diff --git a/Modules/PhotoacousticsAlgorithms/source/filters/mitkBeamformingSettings.cpp b/Modules/PhotoacousticsAlgorithms/source/filters/mitkBeamformingSettings.cpp new file mode 100644 index 0000000000..1b6313ffa0 --- /dev/null +++ b/Modules/PhotoacousticsAlgorithms/source/filters/mitkBeamformingSettings.cpp @@ -0,0 +1,119 @@ +/*=================================================================== +mitkBeamformingSettings +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 "mitkBeamformingSettings.h" +#include "mitkBeamformingUtils.h" +#include "itkMutexLock.h" + +mitk::BeamformingSettings::BeamformingSettings(std::string xmlFile) +{ + MITK_ERROR << "Not implemented yet."; + mitkThrow() << "Not implemented yet."; +} + +mitk::BeamformingSettings::BeamformingSettings(float pitchInMeters, + float speedOfSound, + float timeSpacing, + float angle, + bool isPhotoacousticImage, + unsigned int transducerElements, + unsigned int upperCutoff, + bool partial, + unsigned int* cropBounds, + unsigned int* inputDim, + bool useGPU, + DelayCalc delayCalculationMethod, + Apodization apod, + unsigned int apodizationArraySize, + BeamformingAlgorithm algorithm, + bool useBP, + float BPHighPass, + float BPLowPass +) : + m_PitchInMeters(pitchInMeters), + m_SpeedOfSound(speedOfSound), + m_TimeSpacing(timeSpacing), + m_Angle(angle), + m_IsPhotoacousticImage(isPhotoacousticImage), + m_TransducerElements(transducerElements), + m_UpperCutoff(upperCutoff), + m_Partial(partial), + m_CropBounds(cropBounds), + m_UseGPU(useGPU), + m_DelayCalculationMethod(delayCalculationMethod), + m_Apod(apod), + m_ApodizationArraySize(apodizationArraySize), + m_Algorithm(algorithm), + m_UseBP(useBP), + m_BPHighPass(BPHighPass), + m_BPLowPass(BPLowPass) +{ + if (inputDim == nullptr) + { + MITK_ERROR << "No input dimension given."; + mitkThrow() << "No input dimension given."; + } + + switch (GetApod()) + { + case BeamformingSettings::Apodization::Hann: + m_ApodizationFunction = mitk::BeamformingUtils::VonHannFunction(GetApodizationArraySize()); + break; + case BeamformingSettings::Apodization::Hamm: + m_ApodizationFunction = mitk::BeamformingUtils::HammFunction(GetApodizationArraySize()); + break; + case BeamformingSettings::Apodization::Box: + default: + m_ApodizationFunction = mitk::BeamformingUtils::BoxFunction(GetApodizationArraySize()); + break; + } + + if (m_CropBounds == nullptr) + m_CropBounds = new unsigned int[2]{ 0, 0 }; + + m_InputDim = new unsigned int[2]{ inputDim[0], inputDim[1] }; + + m_SamplesPerLine = m_InputDim[1]; + m_ReconstructionLines = m_InputDim[0]; +} + +mitk::BeamformingSettings::~BeamformingSettings() +{ + MITK_INFO << "Destructing beamforming settings..."; + //Free memory + if (m_ApodizationFunction != nullptr) + { + MITK_INFO << "Deleting apodization function..."; + delete[] m_ApodizationFunction; + MITK_INFO << "Deleting apodization function...[Done]"; + } + + if (m_CropBounds != nullptr) + { + MITK_INFO << "Deleting crop bounds..."; + delete[] m_CropBounds; + MITK_INFO << "Deleting crop bounds...[Done]"; + } + + if (m_InputDim != nullptr) + { + MITK_INFO << "Deleting input dim..."; + delete[] m_InputDim; + MITK_INFO << "Deleting input dim...[Done]"; + } + + MITK_INFO << "Destructing beamforming settings...[Done]"; +} diff --git a/Modules/PhotoacousticsAlgorithms/source/filters/mitkCastToFloatImageFilter.cpp b/Modules/PhotoacousticsAlgorithms/source/filters/mitkCastToFloatImageFilter.cpp index b8d6e8e995..4809971115 100644 --- a/Modules/PhotoacousticsAlgorithms/source/filters/mitkCastToFloatImageFilter.cpp +++ b/Modules/PhotoacousticsAlgorithms/source/filters/mitkCastToFloatImageFilter.cpp @@ -1,91 +1,92 @@ /*=================================================================== mitkCastToFloatImageFilter 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 "mitkCastToFloatImageFilter.h" #include "mitkImageReadAccessor.h" #include "mitkImageWriteAccessor.h" mitk::CastToFloatImageFilter::CastToFloatImageFilter() { MITK_INFO << "Instantiating CastToFloatImageFilter..."; SetNumberOfIndexedInputs(1); SetNumberOfIndexedOutputs(1); MITK_INFO << "Instantiating CastToFloatImageFilter...[Done]"; } mitk::CastToFloatImageFilter::~CastToFloatImageFilter() { MITK_INFO << "Destructed CastToFloatImageFilter."; } template float* CastData(const void* inputArray, unsigned long length) { float* outputArray = new float[length]; for (unsigned long i = 0; i < length; ++i) { outputArray[i] = (float)((TPixelType*)inputArray)[i]; } return outputArray; } void mitk::CastToFloatImageFilter::GenerateData() { mitk::Image::Pointer inputImage = GetInput(); mitk::Image::Pointer outputImage = GetOutput(); std::string type = inputImage->GetPixelType().GetTypeAsString(); if (type == "scalar (float)" || type == " (float)") { outputImage->Initialize(mitk::MakeScalarPixelType(), inputImage->GetDimension(), inputImage->GetDimensions()); outputImage->SetSpacing(inputImage->GetGeometry()->GetSpacing()); outputImage->SetImportVolume(mitk::ImageWriteAccessor(inputImage).GetData(), 0, 0, mitk::Image::ImportMemoryManagementType::RtlCopyMemory); MITK_INFO << "Input is already float type. Nothing to do here."; return; } if (outputImage.IsNull()) { outputImage = mitk::Image::New(); } unsigned long length = 1; for (unsigned int i = 0, limit = inputImage->GetDimension(); i < limit; ++i) length *= inputImage->GetDimensions()[i]; float* outputData; mitk::ImageReadAccessor readAccess(inputImage); if (type == "scalar (short)" || type == " (short)") outputData = CastData(readAccess.GetData(), length); else if (type == "scalar (unsigned short)" || type == " (unsigned short)" || type == " (unsigned_short)" || type == "scalar (unsigned_short)") outputData = CastData(readAccess.GetData(), length); else if (type == "scalar (int)" || type == " (int)") outputData = CastData(readAccess.GetData(), length); else if (type == "scalar (unsigned int)" || type == " (unsigned int)" || type == " (unsigned_int)" || type == "scalar (unsigned_int)") outputData = CastData(readAccess.GetData(), length); else if (type == "scalar (double)" || type == " (double)") outputData = CastData(readAccess.GetData(), length); else if (type == "scalar (long)" || type == " (long)") outputData = CastData(readAccess.GetData(), length); else mitkThrow() << "The given image has a datatype that is not yet supported. Given datatype: " << type; outputImage->Initialize(mitk::MakeScalarPixelType(), inputImage->GetDimension(), inputImage->GetDimensions()); outputImage->SetSpacing(inputImage->GetGeometry()->GetSpacing()); - outputImage->SetImportVolume(outputData, 0, 0, mitk::Image::ImportMemoryManagementType::ManageMemory); + outputImage->SetImportVolume(outputData, 0, 0, mitk::Image::ImportMemoryManagementType::RtlCopyMemory); + delete[] outputData; } diff --git a/Modules/PhotoacousticsAlgorithms/source/filters/mitkCropImageFilter.cpp b/Modules/PhotoacousticsAlgorithms/source/filters/mitkCropImageFilter.cpp index 5ab767a9bd..7f04518e91 100644 --- a/Modules/PhotoacousticsAlgorithms/source/filters/mitkCropImageFilter.cpp +++ b/Modules/PhotoacousticsAlgorithms/source/filters/mitkCropImageFilter.cpp @@ -1,111 +1,112 @@ /*=================================================================== mitkCropImageFilter 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 "mitkCropImageFilter.h" #include #include mitk::CropImageFilter::CropImageFilter() : m_XPixelsCropEnd(0), m_YPixelsCropEnd(0), m_ZPixelsCropEnd(0), m_XPixelsCropStart(0), m_YPixelsCropStart(0), m_ZPixelsCropStart(0) { MITK_INFO << "Instantiating CropImageFilter..."; SetNumberOfIndexedInputs(1); SetNumberOfIndexedOutputs(1); MITK_INFO << "Instantiating CropImageFilter...[Done]"; } mitk::CropImageFilter::~CropImageFilter() { MITK_INFO << "Destructed CastToFloatImageFilter."; } void mitk::CropImageFilter::SanityCheckPreconditions() { mitk::Image::Pointer inputImage = GetInput(); std::string type = inputImage->GetPixelType().GetTypeAsString(); if (!(type == "scalar (float)" || type == " (float)")) { + MITK_ERROR << "This filter can currently only handle float type images."; mitkThrow() << "This filter can currently only handle float type images."; } if (m_XPixelsCropStart + m_XPixelsCropEnd >= inputImage->GetDimension(0)) mitkThrow() << "X Crop area too large for selected input image"; if (m_YPixelsCropStart + m_YPixelsCropEnd >= inputImage->GetDimension(1)) mitkThrow() << "Y Crop area too large for selected input image"; if (inputImage->GetDimension() == 3) { if (m_ZPixelsCropStart + m_ZPixelsCropEnd >= inputImage->GetDimension(2)) { mitkThrow() << "Z Crop area too large for selected input image"; } } else { if (m_ZPixelsCropStart + m_ZPixelsCropEnd > 0) { mitkThrow() << "Z Crop area too large for selected input image"; } } } void mitk::CropImageFilter::GenerateData() { mitk::Image::Pointer inputImage = GetInput(); mitk::Image::Pointer outputImage = GetOutput(); SanityCheckPreconditions(); unsigned int* outputDim; unsigned int* inputDim = inputImage->GetDimensions(); if (inputImage->GetDimension() == 2) outputDim = new unsigned int[2]{ inputImage->GetDimension(0) - m_XPixelsCropStart - m_XPixelsCropEnd, inputImage->GetDimension(1) - m_YPixelsCropStart - m_YPixelsCropEnd }; else outputDim = new unsigned int[3]{ inputImage->GetDimension(0) - m_XPixelsCropStart - m_XPixelsCropEnd, inputImage->GetDimension(1) - m_YPixelsCropStart - m_YPixelsCropEnd, inputImage->GetDimension(2) - m_ZPixelsCropStart - m_ZPixelsCropEnd }; outputImage->Initialize(mitk::MakeScalarPixelType(), inputImage->GetDimension(), outputDim); outputImage->SetSpacing(inputImage->GetGeometry()->GetSpacing()); ImageReadAccessor accR(inputImage); const float* inputData = (const float*)(accR.GetData()); ImageWriteAccessor accW(outputImage); float* outputData = (float*)(accW.GetData()); unsigned int zLength = inputImage->GetDimension() == 3 ? outputDim[2] : 0; for (unsigned int sl = 0; sl < zLength; ++sl) { for (unsigned int l = 0; l < outputDim[0]; ++l) { for (unsigned int s = 0; s < outputDim[1]; ++s) { outputData[l + s*outputDim[0] + sl*outputDim[0] * outputDim[1]] = inputData[(l + m_XPixelsCropStart) + (s + m_YPixelsCropStart)*inputDim[0] + (sl + m_ZPixelsCropStart)*inputDim[0] * inputDim[1]]; } } } delete[] outputDim; } diff --git a/Modules/PhotoacousticsAlgorithms/source/utils/mitkBeamformingUtils.cpp b/Modules/PhotoacousticsAlgorithms/source/utils/mitkBeamformingUtils.cpp index 76ae7a34b5..f805227198 100644 --- a/Modules/PhotoacousticsAlgorithms/source/utils/mitkBeamformingUtils.cpp +++ b/Modules/PhotoacousticsAlgorithms/source/utils/mitkBeamformingUtils.cpp @@ -1,537 +1,548 @@ /*=================================================================== mitkPhotoacousticBeamformingFilter 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 "mitkProperties.h" #include "mitkImageReadAccessor.h" #include #include #include #include #include #include "mitkImageCast.h" #include "mitkBeamformingUtils.h" mitk::BeamformingUtils::BeamformingUtils() { } mitk::BeamformingUtils::~BeamformingUtils() { } float* mitk::BeamformingUtils::VonHannFunction(int samples) { float* ApodWindow = new float[samples]; for (int n = 0; n < samples; ++n) { ApodWindow[n] = (1 - cos(2 * itk::Math::pi * n / (samples - 1))) / 2; } return ApodWindow; } float* mitk::BeamformingUtils::HammFunction(int samples) { float* ApodWindow = new float[samples]; for (int n = 0; n < samples; ++n) { ApodWindow[n] = 0.54 - 0.46*cos(2 * itk::Math::pi*n / (samples - 1)); } return ApodWindow; } float* mitk::BeamformingUtils::BoxFunction(int samples) { float* ApodWindow = new float[samples]; for (int n = 0; n < samples; ++n) { ApodWindow[n] = 1; } return ApodWindow; } void mitk::BeamformingUtils::DASQuadraticLine( float* input, float* output, float inputDim[2], float outputDim[2], - const short& line, float* apodisation, const short& apodArraySize, - const mitk::BeamformingSettings::Pointer config) + const short& line, const mitk::BeamformingSettings::Pointer config) { + const float* apodisation = config->GetApodizationFunction(); + const short apodArraySize = config->GetApodizationArraySize(); float& inputS = inputDim[1]; float& inputL = inputDim[0]; float& outputS = outputDim[1]; float& outputL = outputDim[0]; short AddSample = 0; short maxLine = 0; short minLine = 0; float delayMultiplicator = 0; float l_i = 0; float s_i = 0; float part = 0; float tan_phi = std::tan(config->GetAngle() / 360 * 2 * itk::Math::pi); float part_multiplicator = tan_phi * config->GetTimeSpacing() * config->GetSpeedOfSound() / config->GetPitchInMeters() * inputL / config->GetTransducerElements(); float apod_mult = 1; short usedLines = (maxLine - minLine); //quadratic delay l_i = line / outputL * inputL; for (short sample = 0; sample < outputS; ++sample) { s_i = (float)sample / outputS * inputS / 2; part = part_multiplicator*s_i; if (part < 1) part = 1; maxLine = (short)std::min((l_i + part) + 1, inputL); minLine = (short)std::max((l_i - part), 0.0f); usedLines = (maxLine - minLine); apod_mult = (float)apodArraySize / (float)usedLines; delayMultiplicator = pow((1 / (config->GetTimeSpacing()*config->GetSpeedOfSound()) * (config->GetPitchInMeters()*config->GetTransducerElements()) / inputL), 2) / s_i / 2; for (short l_s = minLine; l_s < maxLine; ++l_s) { AddSample = delayMultiplicator * pow((l_s - l_i), 2) + s_i + (1 - config->GetIsPhotoacousticImage())*s_i; if (AddSample < inputS && AddSample >= 0) output[sample*(short)outputL + line] += input[l_s + AddSample*(short)inputL] * apodisation[(short)((l_s - minLine)*apod_mult)]; else --usedLines; } output[sample*(short)outputL + line] = output[sample*(short)outputL + line] / usedLines; } } void mitk::BeamformingUtils::DASSphericalLine( float* input, float* output, float inputDim[2], float outputDim[2], - const short& line, float* apodisation, const short& apodArraySize, - const mitk::BeamformingSettings::Pointer config) + const short& line, const mitk::BeamformingSettings::Pointer config) { + const float* apodisation = config->GetApodizationFunction(); + const short apodArraySize = config->GetApodizationArraySize(); + float& inputS = inputDim[1]; float& inputL = inputDim[0]; float& outputS = outputDim[1]; float& outputL = outputDim[0]; short AddSample = 0; short maxLine = 0; short minLine = 0; float l_i = 0; float s_i = 0; float part = 0.07 * inputL; float tan_phi = std::tan(config->GetAngle() / 360 * 2 * itk::Math::pi); float part_multiplicator = tan_phi * config->GetTimeSpacing() * config->GetSpeedOfSound() / config->GetPitchInMeters() * inputL / (float)config->GetTransducerElements(); float apod_mult = 1; short usedLines = (maxLine - minLine); //exact delay l_i = (float)line / outputL * inputL; for (short sample = 0; sample < outputS; ++sample) { s_i = (float)sample / outputS * inputS / 2; part = part_multiplicator*s_i; if (part < 1) part = 1; maxLine = (short)std::min((l_i + part) + 1, inputL); minLine = (short)std::max((l_i - part), 0.0f); usedLines = (maxLine - minLine); apod_mult = (float)apodArraySize / (float)usedLines; for (short l_s = minLine; l_s < maxLine; ++l_s) { AddSample = (int)sqrt( pow(s_i, 2) + pow((1 / (config->GetTimeSpacing()*config->GetSpeedOfSound()) * (((float)l_s - l_i)*config->GetPitchInMeters()*(float)config->GetTransducerElements()) / inputL), 2) ) + (1 - config->GetIsPhotoacousticImage())*s_i; if (AddSample < inputS && AddSample >= 0) output[sample*(short)outputL + line] += input[l_s + AddSample*(short)inputL] * apodisation[(short)((l_s - minLine)*apod_mult)]; else --usedLines; } output[sample*(short)outputL + line] = output[sample*(short)outputL + line] / usedLines; } } void mitk::BeamformingUtils::DMASQuadraticLine( float* input, float* output, float inputDim[2], float outputDim[2], - const short& line, float* apodisation, const short& apodArraySize, - const mitk::BeamformingSettings::Pointer config) + const short& line, const mitk::BeamformingSettings::Pointer config) { + const float* apodisation = config->GetApodizationFunction(); + const short apodArraySize = config->GetApodizationArraySize(); + float& inputS = inputDim[1]; float& inputL = inputDim[0]; float& outputS = outputDim[1]; float& outputL = outputDim[0]; short maxLine = 0; short minLine = 0; float delayMultiplicator = 0; float l_i = 0; float s_i = 0; float part = 0.07 * inputL; float tan_phi = std::tan(config->GetAngle() / 360 * 2 * itk::Math::pi); float part_multiplicator = tan_phi * config->GetTimeSpacing() * config->GetSpeedOfSound() / config->GetPitchInMeters() * inputL / (float)config->GetTransducerElements(); float apod_mult = 1; float mult = 0; short usedLines = (maxLine - minLine); //quadratic delay l_i = line / outputL * inputL; for (short sample = 0; sample < outputS; ++sample) { s_i = sample / outputS * inputS / 2; part = part_multiplicator*s_i; if (part < 1) part = 1; maxLine = (short)std::min((l_i + part) + 1, inputL); minLine = (short)std::max((l_i - part), 0.0f); usedLines = (maxLine - minLine); apod_mult = (float)apodArraySize / (float)usedLines; delayMultiplicator = pow((1 / (config->GetTimeSpacing()*config->GetSpeedOfSound()) * (config->GetPitchInMeters()*config->GetTransducerElements()) / inputL), 2) / s_i / 2; //calculate the AddSamples beforehand to save some time short* AddSample = new short[maxLine - minLine]; for (short l_s = 0; l_s < maxLine - minLine; ++l_s) { AddSample[l_s] = (short)(delayMultiplicator * pow((minLine + l_s - l_i), 2) + s_i) + (1 - config->GetIsPhotoacousticImage())*s_i; } float s_1 = 0; float s_2 = 0; for (short l_s1 = minLine; l_s1 < maxLine - 1; ++l_s1) { if (AddSample[l_s1 - minLine] < inputS && AddSample[l_s1 - minLine] >= 0) { for (short l_s2 = l_s1 + 1; l_s2 < maxLine; ++l_s2) { if (AddSample[l_s2 - minLine] < inputS && AddSample[l_s2 - minLine] >= 0) { s_2 = input[l_s2 + AddSample[l_s2 - minLine] * (short)inputL]; s_1 = input[l_s1 + AddSample[l_s1 - minLine] * (short)inputL]; mult = s_2 * apodisation[(int)((l_s2 - minLine)*apod_mult)] * s_1 * apodisation[(int)((l_s1 - minLine)*apod_mult)]; output[sample*(short)outputL + line] += sqrt(fabs(mult)) * ((mult > 0) - (mult < 0)); } } } else --usedLines; } output[sample*(short)outputL + line] = output[sample*(short)outputL + line] / (float)(pow(usedLines, 2) - (usedLines - 1)); delete[] AddSample; } } void mitk::BeamformingUtils::DMASSphericalLine( float* input, float* output, float inputDim[2], float outputDim[2], - const short& line, float* apodisation, const short& apodArraySize, - const mitk::BeamformingSettings::Pointer config) + const short& line, const mitk::BeamformingSettings::Pointer config) { + const float* apodisation = config->GetApodizationFunction(); + const short apodArraySize = config->GetApodizationArraySize(); + float& inputS = inputDim[1]; float& inputL = inputDim[0]; float& outputS = outputDim[1]; float& outputL = outputDim[0]; short maxLine = 0; short minLine = 0; float l_i = 0; float s_i = 0; float part = 0.07 * inputL; float tan_phi = std::tan(config->GetAngle() / 360 * 2 * itk::Math::pi); float part_multiplicator = tan_phi * config->GetTimeSpacing() * config->GetSpeedOfSound() / config->GetPitchInMeters() * inputL / (float)config->GetTransducerElements(); float apod_mult = 1; float mult = 0; short usedLines = (maxLine - minLine); //exact delay l_i = (float)line / outputL * inputL; for (short sample = 0; sample < outputS; ++sample) { s_i = (float)sample / outputS * inputS / 2; part = part_multiplicator*s_i; if (part < 1) part = 1; maxLine = (short)std::min((l_i + part) + 1, inputL); minLine = (short)std::max((l_i - part), 0.0f); usedLines = (maxLine - minLine); apod_mult = (float)apodArraySize / (float)usedLines; //calculate the AddSamples beforehand to save some time short* AddSample = new short[maxLine - minLine]; for (short l_s = 0; l_s < maxLine - minLine; ++l_s) { AddSample[l_s] = (short)sqrt( pow(s_i, 2) + pow((1 / (config->GetTimeSpacing()*config->GetSpeedOfSound()) * (((float)minLine + (float)l_s - l_i)*config->GetPitchInMeters()*(float)config->GetTransducerElements()) / inputL), 2) ) + (1 - config->GetIsPhotoacousticImage())*s_i; } float s_1 = 0; float s_2 = 0; for (short l_s1 = minLine; l_s1 < maxLine - 1; ++l_s1) { if (AddSample[l_s1 - minLine] < inputS && AddSample[l_s1 - minLine] >= 0) { for (short l_s2 = l_s1 + 1; l_s2 < maxLine; ++l_s2) { if (AddSample[l_s2 - minLine] < inputS && AddSample[l_s2 - minLine] >= 0) { s_2 = input[l_s2 + AddSample[l_s2 - minLine] * (short)inputL]; s_1 = input[l_s1 + AddSample[l_s1 - minLine] * (short)inputL]; mult = s_2 * apodisation[(int)((l_s2 - minLine)*apod_mult)] * s_1 * apodisation[(int)((l_s1 - minLine)*apod_mult)]; output[sample*(short)outputL + line] += sqrt(fabs(mult)) * ((mult > 0) - (mult < 0)); } } } else --usedLines; } output[sample*(short)outputL + line] = output[sample*(short)outputL + line] / (float)(pow(usedLines, 2) - (usedLines - 1)); delete[] AddSample; } } void mitk::BeamformingUtils::sDMASQuadraticLine( float* input, float* output, float inputDim[2], float outputDim[2], - const short& line, float* apodisation, const short& apodArraySize, - const mitk::BeamformingSettings::Pointer config) + const short& line, const mitk::BeamformingSettings::Pointer config) { + const float* apodisation = config->GetApodizationFunction(); + const short apodArraySize = config->GetApodizationArraySize(); + float& inputS = inputDim[1]; float& inputL = inputDim[0]; float& outputS = outputDim[1]; float& outputL = outputDim[0]; short maxLine = 0; short minLine = 0; float delayMultiplicator = 0; float l_i = 0; float s_i = 0; float part = 0.07 * inputL; float tan_phi = std::tan(config->GetAngle() / 360 * 2 * itk::Math::pi); float part_multiplicator = tan_phi * config->GetTimeSpacing() * config->GetSpeedOfSound() / config->GetPitchInMeters() * inputL / (float)config->GetTransducerElements(); float apod_mult = 1; float mult = 0; short usedLines = (maxLine - minLine); //quadratic delay l_i = line / outputL * inputL; for (short sample = 0; sample < outputS; ++sample) { s_i = sample / outputS * inputS / 2; part = part_multiplicator*s_i; if (part < 1) part = 1; maxLine = (short)std::min((l_i + part) + 1, inputL); minLine = (short)std::max((l_i - part), 0.0f); usedLines = (maxLine - minLine); apod_mult = (float)apodArraySize / (float)usedLines; delayMultiplicator = pow((1 / (config->GetTimeSpacing()*config->GetSpeedOfSound()) * (config->GetPitchInMeters()*config->GetTransducerElements()) / inputL), 2) / s_i / 2; //calculate the AddSamples beforehand to save some time short* AddSample = new short[maxLine - minLine]; for (short l_s = 0; l_s < maxLine - minLine; ++l_s) { AddSample[l_s] = (short)(delayMultiplicator * pow((minLine + l_s - l_i), 2) + s_i) + (1 - config->GetIsPhotoacousticImage())*s_i; } float s_1 = 0; float s_2 = 0; float sign = 0; for (short l_s1 = minLine; l_s1 < maxLine - 1; ++l_s1) { if (AddSample[l_s1 - minLine] < inputS && AddSample[l_s1 - minLine] >= 0) { s_1 = input[l_s1 + AddSample[l_s1 - minLine] * (short)inputL]; sign += s_1; for (short l_s2 = l_s1 + 1; l_s2 < maxLine; ++l_s2) { if (AddSample[l_s2 - minLine] < inputS && AddSample[l_s2 - minLine] >= 0) { s_2 = input[l_s2 + AddSample[l_s2 - minLine] * (short)inputL]; mult = s_2 * apodisation[(int)((l_s2 - minLine)*apod_mult)] * s_1 * apodisation[(int)((l_s1 - minLine)*apod_mult)]; output[sample*(short)outputL + line] += sqrt(fabs(mult)) * ((mult > 0) - (mult < 0)); } } } else --usedLines; } output[sample*(short)outputL + line] = output[sample*(short)outputL + line] / (float)(pow(usedLines, 2) - (usedLines - 1)) * ((sign > 0) - (sign < 0)); delete[] AddSample; } } void mitk::BeamformingUtils::sDMASSphericalLine( float* input, float* output, float inputDim[2], float outputDim[2], - const short& line, float* apodisation, const short& apodArraySize, - const mitk::BeamformingSettings::Pointer config) + const short& line, const mitk::BeamformingSettings::Pointer config) { + const float* apodisation = config->GetApodizationFunction(); + const short apodArraySize = config->GetApodizationArraySize(); + float& inputS = inputDim[1]; float& inputL = inputDim[0]; float& outputS = outputDim[1]; float& outputL = outputDim[0]; short maxLine = 0; short minLine = 0; float l_i = 0; float s_i = 0; float part = 0.07 * inputL; float tan_phi = std::tan(config->GetAngle() / 360 * 2 * itk::Math::pi); float part_multiplicator = tan_phi * config->GetTimeSpacing() * config->GetSpeedOfSound() / config->GetPitchInMeters() * inputL / (float)config->GetTransducerElements(); float apod_mult = 1; float mult = 0; short usedLines = (maxLine - minLine); //exact delay l_i = (float)line / outputL * inputL; for (short sample = 0; sample < outputS; ++sample) { s_i = (float)sample / outputS * inputS / 2; part = part_multiplicator*s_i; if (part < 1) part = 1; maxLine = (short)std::min((l_i + part) + 1, inputL); minLine = (short)std::max((l_i - part), 0.0f); usedLines = (maxLine - minLine); apod_mult = (float)apodArraySize / (float)usedLines; //calculate the AddSamples beforehand to save some time short* AddSample = new short[maxLine - minLine]; for (short l_s = 0; l_s < maxLine - minLine; ++l_s) { AddSample[l_s] = (short)sqrt( pow(s_i, 2) + pow((1 / (config->GetTimeSpacing()*config->GetSpeedOfSound()) * (((float)minLine + (float)l_s - l_i)*config->GetPitchInMeters()*(float)config->GetTransducerElements()) / inputL), 2) ) + (1 - config->GetIsPhotoacousticImage())*s_i; } float s_1 = 0; float s_2 = 0; float sign = 0; for (short l_s1 = minLine; l_s1 < maxLine - 1; ++l_s1) { if (AddSample[l_s1 - minLine] < inputS && AddSample[l_s1 - minLine] >= 0) { s_1 = input[l_s1 + AddSample[l_s1 - minLine] * (short)inputL]; sign += s_1; for (short l_s2 = l_s1 + 1; l_s2 < maxLine; ++l_s2) { if (AddSample[l_s2 - minLine] < inputS && AddSample[l_s2 - minLine] >= 0) { s_2 = input[l_s2 + AddSample[l_s2 - minLine] * (short)inputL]; mult = s_2 * apodisation[(int)((l_s2 - minLine)*apod_mult)] * s_1 * apodisation[(int)((l_s1 - minLine)*apod_mult)]; output[sample*(short)outputL + line] += sqrt(fabs(mult)) * ((mult > 0) - (mult < 0)); } } } else --usedLines; } output[sample*(short)outputL + line] = output[sample*(short)outputL + line] / (float)(pow(usedLines, 2) - (usedLines - 1)) * ((sign > 0) - (sign < 0)); delete[] AddSample; } } diff --git a/Modules/PhotoacousticsAlgorithms/source/utils/mitkPhotoacousticFilterService.cpp b/Modules/PhotoacousticsAlgorithms/source/utils/mitkPhotoacousticFilterService.cpp index e519762011..ffa3db3902 100644 --- a/Modules/PhotoacousticsAlgorithms/source/utils/mitkPhotoacousticFilterService.cpp +++ b/Modules/PhotoacousticsAlgorithms/source/utils/mitkPhotoacousticFilterService.cpp @@ -1,442 +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. ===================================================================*/ #include "mitkPhotoacousticFilterService.h" #include "../ITKFilter/ITKUltrasound/itkBModeImageFilter.h" #include "../ITKFilter/itkPhotoacousticBModeImageFilter.h" #include "mitkImageCast.h" #include "mitkITKImageImport.h" #include "mitkBeamformingFilter.h" #include #include #include #include "./OpenCLFilter/mitkPhotoacousticBModeFilter.h" #include "mitkConvert2Dto3DImageFilter.h" #include // itk dependencies #include "itkImage.h" #include "itkResampleImageFilter.h" #include "itkCastImageFilter.h" #include "itkCropImageFilter.h" #include "itkRescaleIntensityImageFilter.h" #include "itkIntensityWindowingImageFilter.h" #include #include "itkMultiplyImageFilter.h" #include "itkBSplineInterpolateImageFunction.h" #include // needed itk image filters #include "mitkITKImageImport.h" #include "itkFFTShiftImageFilter.h" #include "itkMultiplyImageFilter.h" #include "itkComplexToModulusImageFilter.h" #include #include "../ITKFilter/ITKUltrasound/itkFFT1DComplexConjugateToRealImageFilter.h" #include "../ITKFilter/ITKUltrasound/itkFFT1DRealToComplexConjugateImageFilter.h" mitk::PhotoacousticFilterService::PhotoacousticFilterService() { MITK_INFO << "[PhotoacousticFilterService] created filter service"; } mitk::PhotoacousticFilterService::~PhotoacousticFilterService() { MITK_INFO << "[PhotoacousticFilterService] destructed filter service"; } mitk::Image::Pointer mitk::PhotoacousticFilterService::ApplyBmodeFilter(mitk::Image::Pointer inputImage, BModeMethod method, bool UseGPU, bool UseLogFilter, float resampleSpacing) { // the image needs to be of floating point type for the envelope filter to work; the casting is done automatically by the CastToItkImage typedef itk::Image< float, 3 > itkFloatImageType; typedef itk::IdentityTransform TransformType; if (method == BModeMethod::Abs) { mitk::Image::Pointer input; mitk::Image::Pointer out; if (inputImage->GetPixelType().GetTypeAsString() == "scalar (float)" || inputImage->GetPixelType().GetTypeAsString() == " (float)") input = inputImage; else input = ApplyCropping(inputImage, 0, 0, 0, 0, 0, 0); if (!UseGPU) { PhotoacousticBModeFilter::Pointer filter = PhotoacousticBModeFilter::New(); filter->SetParameters(UseLogFilter); filter->SetInput(input); filter->Update(); out = filter->GetOutput(); if (resampleSpacing == 0) return out; } #ifdef PHOTOACOUSTICS_USE_GPU else { PhotoacousticOCLBModeFilter::Pointer filter = PhotoacousticOCLBModeFilter::New(); filter->SetParameters(UseLogFilter); filter->SetInput(input); filter->Update(); out = filter->GetOutput(); if (resampleSpacing == 0) return out; } #endif typedef itk::ResampleImageFilter < itkFloatImageType, itkFloatImageType > ResampleImageFilter; ResampleImageFilter::Pointer resampleImageFilter = ResampleImageFilter::New(); itkFloatImageType::Pointer itkImage; mitk::CastToItkImage(out, itkImage); itkFloatImageType::SpacingType outputSpacing; itkFloatImageType::SizeType inputSize = itkImage->GetLargestPossibleRegion().GetSize(); itkFloatImageType::SizeType outputSize = inputSize; outputSpacing[0] = itkImage->GetSpacing()[0]; outputSpacing[1] = resampleSpacing; outputSpacing[2] = itkImage->GetSpacing()[2]; outputSize[1] = inputSize[1] * itkImage->GetSpacing()[1] / outputSpacing[1]; typedef itk::IdentityTransform TransformType; resampleImageFilter->SetInput(itkImage); resampleImageFilter->SetSize(outputSize); resampleImageFilter->SetOutputSpacing(outputSpacing); resampleImageFilter->SetTransform(TransformType::New()); resampleImageFilter->UpdateLargestPossibleRegion(); return mitk::GrabItkImageMemory(resampleImageFilter->GetOutput()); } else if (method == BModeMethod::EnvelopeDetection) { typedef itk::BModeImageFilter < itkFloatImageType, itkFloatImageType > BModeFilterType; BModeFilterType::Pointer bModeFilter = BModeFilterType::New(); // LogFilter typedef itk::PhotoacousticBModeImageFilter < itkFloatImageType, itkFloatImageType > PhotoacousticBModeImageFilter; PhotoacousticBModeImageFilter::Pointer photoacousticBModeFilter = PhotoacousticBModeImageFilter::New(); // No LogFilter typedef itk::ResampleImageFilter < itkFloatImageType, itkFloatImageType > ResampleImageFilter; ResampleImageFilter::Pointer resampleImageFilter = ResampleImageFilter::New(); itkFloatImageType::Pointer itkImage; mitk::CastToItkImage(inputImage, itkImage); itkFloatImageType::Pointer bmode; if (UseLogFilter) { bModeFilter->SetInput(itkImage); bModeFilter->SetDirection(1); bmode = bModeFilter->GetOutput(); } else { photoacousticBModeFilter->SetInput(itkImage); photoacousticBModeFilter->SetDirection(1); bmode = photoacousticBModeFilter->GetOutput(); } // resampleSpacing == 0 means: do no resampling if (resampleSpacing == 0) { return mitk::GrabItkImageMemory(bmode); } itkFloatImageType::SpacingType outputSpacing; itkFloatImageType::SizeType inputSize = itkImage->GetLargestPossibleRegion().GetSize(); itkFloatImageType::SizeType outputSize = inputSize; outputSpacing[0] = itkImage->GetSpacing()[0]; outputSpacing[1] = resampleSpacing; outputSpacing[2] = itkImage->GetSpacing()[2]; outputSize[1] = inputSize[1] * itkImage->GetSpacing()[1] / outputSpacing[1]; resampleImageFilter->SetInput(bmode); resampleImageFilter->SetSize(outputSize); resampleImageFilter->SetOutputSpacing(outputSpacing); resampleImageFilter->SetTransform(TransformType::New()); resampleImageFilter->UpdateLargestPossibleRegion(); return mitk::GrabItkImageMemory(resampleImageFilter->GetOutput()); } return nullptr; } mitk::Image::Pointer mitk::PhotoacousticFilterService::ApplyResampling(mitk::Image::Pointer inputImage, unsigned int outputSize[2]) { typedef itk::Image< float, 3 > itkFloatImageType; typedef itk::ResampleImageFilter < itkFloatImageType, itkFloatImageType > ResampleImageFilter; ResampleImageFilter::Pointer resampleImageFilter = ResampleImageFilter::New(); typedef itk::LinearInterpolateImageFunction T_Interpolator; itkFloatImageType::Pointer itkImage; mitk::CastToItkImage(inputImage, itkImage); itkFloatImageType::SpacingType outputSpacingItk; itkFloatImageType::SizeType inputSizeItk = itkImage->GetLargestPossibleRegion().GetSize(); itkFloatImageType::SizeType outputSizeItk = inputSizeItk; outputSizeItk[0] = outputSize[0]; outputSizeItk[1] = outputSize[1]; outputSizeItk[2] = inputSizeItk[2]; outputSpacingItk[0] = itkImage->GetSpacing()[0] * (static_cast(inputSizeItk[0]) / static_cast(outputSizeItk[0])); outputSpacingItk[1] = itkImage->GetSpacing()[1] * (static_cast(inputSizeItk[1]) / static_cast(outputSizeItk[1])); outputSpacingItk[2] = itkImage->GetSpacing()[2]; typedef itk::IdentityTransform TransformType; T_Interpolator::Pointer _pInterpolator = T_Interpolator::New(); resampleImageFilter->SetInput(itkImage); resampleImageFilter->SetSize(outputSizeItk); resampleImageFilter->SetOutputSpacing(outputSpacingItk); resampleImageFilter->SetTransform(TransformType::New()); resampleImageFilter->SetInterpolator(_pInterpolator); resampleImageFilter->UpdateLargestPossibleRegion(); return mitk::GrabItkImageMemory(resampleImageFilter->GetOutput()); } mitk::Image::Pointer mitk::PhotoacousticFilterService::ApplyCropping(mitk::Image::Pointer inputImage, int above, int below, int right, int left, int zStart, int zEnd) { mitk::CropImageFilter::Pointer cropImageFilter = mitk::CropImageFilter::New(); cropImageFilter->SetInput(inputImage); cropImageFilter->SetXPixelsCropStart(left); cropImageFilter->SetXPixelsCropEnd(right); cropImageFilter->SetYPixelsCropStart(above); cropImageFilter->SetYPixelsCropEnd(below); cropImageFilter->SetZPixelsCropStart(zStart); cropImageFilter->SetZPixelsCropEnd(zEnd); cropImageFilter->Update(); return cropImageFilter->GetOutput(); } mitk::Image::Pointer mitk::PhotoacousticFilterService::ApplyBeamforming(mitk::Image::Pointer inputImage, - BeamformingSettings::Pointer config, std::string& message, std::function progressHandle) + BeamformingSettings::Pointer config, std::function progressHandle) { Image::Pointer processedImage = mitk::Image::New(); if (inputImage->GetDimension() != 3) { mitk::Convert2Dto3DImageFilter::Pointer dimensionImageFilter = mitk::Convert2Dto3DImageFilter::New(); dimensionImageFilter->SetInput(inputImage); dimensionImageFilter->Update(); processedImage = dimensionImageFilter->GetOutput(); } - - config->GetInputDim()[0] = processedImage->GetDimension(0); - config->GetInputDim()[1] = processedImage->GetDimension(1); - config->GetInputDim()[2] = processedImage->GetDimension(2); + else + { + processedImage = inputImage; + } // perform the beamforming m_BeamformingFilter = mitk::BeamformingFilter::New(config); m_BeamformingFilter->SetInput(processedImage); m_BeamformingFilter->SetProgressHandle(progressHandle); m_BeamformingFilter->UpdateLargestPossibleRegion(); processedImage = m_BeamformingFilter->GetOutput(); - message = m_BeamformingFilter->GetMessageString(); return processedImage; } mitk::Image::Pointer mitk::PhotoacousticFilterService::BandpassFilter(mitk::Image::Pointer data, float recordTime, float BPHighPass, float BPLowPass, float alphaHighPass, float alphaLowPass) { bool powerOfTwo = false; int finalPower = 0; for (int i = 1; pow(2, i) <= data->GetDimension(1); ++i) { finalPower = i; if (pow(2, i) == data->GetDimension(1)) { powerOfTwo = true; } } if (!powerOfTwo) { unsigned int dim[2] = { data->GetDimension(0), (unsigned int)pow(2,finalPower + 1) }; data = ApplyResampling(data, dim); } MITK_INFO << data->GetDimension(0); // do a fourier transform, multiply with an appropriate window for the filter, and transform back typedef float PixelType; typedef itk::Image< PixelType, 3 > RealImageType; RealImageType::Pointer image; mitk::CastToItkImage(data, image); typedef itk::FFT1DRealToComplexConjugateImageFilter ForwardFFTFilterType; typedef ForwardFFTFilterType::OutputImageType ComplexImageType; ForwardFFTFilterType::Pointer forwardFFTFilter = ForwardFFTFilterType::New(); forwardFFTFilter->SetInput(image); forwardFFTFilter->SetDirection(1); try { forwardFFTFilter->UpdateOutputInformation(); } catch (itk::ExceptionObject & error) { std::cerr << "Error: " << error << std::endl; MITK_WARN << "Bandpass could not be applied"; return data; } float singleVoxel = 1 / (recordTime / data->GetDimension(1)) / 2 / 1000; float cutoffPixelHighPass = std::min(BPHighPass / singleVoxel, (float)data->GetDimension(1) / 2); float cutoffPixelLowPass = std::min(BPLowPass / singleVoxel, (float)data->GetDimension(1) / 2 - cutoffPixelHighPass); RealImageType::Pointer fftMultiplicator = BPFunction(data, cutoffPixelHighPass, cutoffPixelLowPass, alphaHighPass, alphaLowPass); typedef itk::MultiplyImageFilter< ComplexImageType, RealImageType, ComplexImageType > MultiplyFilterType; MultiplyFilterType::Pointer multiplyFilter = MultiplyFilterType::New(); multiplyFilter->SetInput1(forwardFFTFilter->GetOutput()); multiplyFilter->SetInput2(fftMultiplicator); /*itk::ComplexToModulusImageFilter::Pointer toReal = itk::ComplexToModulusImageFilter::New(); toReal->SetInput(forwardFFTFilter->GetOutput()); return GrabItkImageMemory(toReal->GetOutput()); return GrabItkImageMemory(fftMultiplicator); *///DEBUG typedef itk::FFT1DComplexConjugateToRealImageFilter< ComplexImageType, RealImageType > InverseFilterType; InverseFilterType::Pointer inverseFFTFilter = InverseFilterType::New(); inverseFFTFilter->SetInput(multiplyFilter->GetOutput()); inverseFFTFilter->SetDirection(1); return GrabItkImageMemory(inverseFFTFilter->GetOutput()); } itk::Image::Pointer mitk::PhotoacousticFilterService::BPFunction(mitk::Image::Pointer reference, int cutoffFrequencyPixelHighPass, int cutoffFrequencyPixelLowPass, float alphaHighPass, float alphaLowPass) { float* imageData = new float[reference->GetDimension(0)*reference->GetDimension(1)]; float width = reference->GetDimension(1) / 2.0 - (float)cutoffFrequencyPixelHighPass - (float)cutoffFrequencyPixelLowPass; float center = (float)cutoffFrequencyPixelHighPass / 2.0 + width / 2.0; for (unsigned int n = 0; n < reference->GetDimension(1); ++n) { imageData[reference->GetDimension(0)*n] = 0; } for (int n = 0; n < width; ++n) { imageData[reference->GetDimension(0)*n] = 1; if (n <= (alphaHighPass*(width - 1)) / 2.0) { if (alphaHighPass > 0.00001) { imageData[reference->GetDimension(0)*(int)(n + center - (width / 2))] = (1 + cos(itk::Math::pi*(2 * n / (alphaHighPass*(width - 1)) - 1))) / 2; } else { imageData[reference->GetDimension(0)*(int)(n + center - (width / 2))] = 1; } } else if (n >= (width - 1)*(1 - alphaLowPass / 2)) //??? { if (alphaLowPass > 0.00001) { imageData[reference->GetDimension(0)*(int)(n + center - (width / 2))] = (1 + cos(itk::Math::pi*(2 * n / (alphaLowPass*(width - 1)) + 1 - 2 / alphaLowPass))) / 2; } else { imageData[reference->GetDimension(0)*(int)(n + center - (width / 2))] = 1; } } //MITK_INFO << "n:" << n << " is " << imageData[reference->GetDimension(0)*(int)(n + center - (width / 2))]; } MITK_INFO << "width: " << width << ", center: " << center << ", alphaHighPass: " << alphaHighPass << ", alphaLowPass: " << alphaLowPass; // mirror the first half of the image for (unsigned int n = reference->GetDimension(1) / 2; n < reference->GetDimension(1); ++n) { imageData[reference->GetDimension(0)*n] = imageData[(reference->GetDimension(1) - (n + 1)) * reference->GetDimension(0)]; } // copy and paste to all lines for (unsigned int line = 1; line < reference->GetDimension(0); ++line) { for (unsigned int sample = 0; sample < reference->GetDimension(1); ++sample) { imageData[reference->GetDimension(0)*sample + line] = imageData[reference->GetDimension(0)*sample]; } } typedef itk::Image< float, 3U > ImageType; ImageType::RegionType region; ImageType::IndexType start; start.Fill(0); region.SetIndex(start); ImageType::SizeType size; size[0] = reference->GetDimension(0); size[1] = reference->GetDimension(1); size[2] = reference->GetDimension(2); region.SetSize(size); ImageType::SpacingType SpacingItk; SpacingItk[0] = reference->GetGeometry()->GetSpacing()[0]; SpacingItk[1] = reference->GetGeometry()->GetSpacing()[1]; SpacingItk[2] = reference->GetGeometry()->GetSpacing()[2]; ImageType::Pointer image = ImageType::New(); image->SetRegions(region); image->Allocate(); image->FillBuffer(itk::NumericTraits::Zero); image->SetSpacing(SpacingItk); ImageType::IndexType pixelIndex; for (unsigned int slice = 0; slice < reference->GetDimension(2); ++slice) { for (unsigned int line = 0; line < reference->GetDimension(0); ++line) { for (unsigned int sample = 0; sample < reference->GetDimension(1); ++sample) { pixelIndex[0] = line; pixelIndex[1] = sample; pixelIndex[2] = slice; image->SetPixel(pixelIndex, imageData[line + sample*reference->GetDimension(0)]); } } } delete[] imageData; return image; } diff --git a/Modules/PhotoacousticsAlgorithms/test/mitkPAFilterServiceTest.cpp b/Modules/PhotoacousticsAlgorithms/test/mitkPAFilterServiceTest.cpp index 139492343d..6bf86cfb2f 100644 --- a/Modules/PhotoacousticsAlgorithms/test/mitkPAFilterServiceTest.cpp +++ b/Modules/PhotoacousticsAlgorithms/test/mitkPAFilterServiceTest.cpp @@ -1,95 +1,111 @@ /*=================================================================== 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 // us #include #include #include #include #include #include #include class mitkPAFilterServiceTestSuite : public mitk::TestFixture { CPPUNIT_TEST_SUITE(mitkPAFilterServiceTestSuite); MITK_TEST(testRunning); CPPUNIT_TEST_SUITE_END(); private: mitk::PhotoacousticFilterService::Pointer m_PhotoacousticFilterService; public: void setUp() override { m_PhotoacousticFilterService = mitk::PhotoacousticFilterService::New(); } - mitk::BeamformingSettings::Pointer CreateBeamformingSettings() + mitk::BeamformingSettings::Pointer CreateEmptyBeamformingSettings() + { + mitk::BeamformingSettings::Pointer config = mitk::BeamformingSettings::New(); + return config; + } + + mitk::BeamformingSettings::Pointer CreateFunctionalBeamformingSettings() { mitk::BeamformingSettings::Pointer config = mitk::BeamformingSettings::New(); return config; } void testRunning() { int xDim = 3; int yDim = 3; int length = yDim * xDim; - int* testArray = new int[length]; + float* testArray = new float[length]; for (int i = 0; i < length; ++i) { testArray[i] = 0; } + unsigned int NUMBER_OF_SPATIAL_DIMENSIONS = 2; - auto* dimensions = new unsigned int[NUMBER_OF_SPATIAL_DIMENSIONS]; + unsigned int* dimensions = new unsigned int[NUMBER_OF_SPATIAL_DIMENSIONS]; dimensions[0] = yDim; dimensions[1] = xDim; - mitk::PixelType pixelType = mitk::MakeScalarPixelType(); + mitk::PixelType pixelType = mitk::MakeScalarPixelType(); mitk::Image::Pointer testImage = mitk::Image::New(); testImage->Initialize(pixelType, NUMBER_OF_SPATIAL_DIMENSIONS, dimensions); - testImage->SetImportSlice(testArray, 0, 0, 0, mitk::Image::ImportMemoryManagementType::ManageMemory); - std::string message = "Es ist egal. Das taucht nicht auf!"; - mitk::BeamformingSettings::Pointer config = CreateBeamformingSettings(); - auto output = m_PhotoacousticFilterService->ApplyBeamforming(testImage, config, message); + testImage->SetImportSlice(testArray, 0, 0, 0, mitk::Image::ImportMemoryManagementType::RtlCopyMemory); + delete[] testArray; + + mitk::ImageReadAccessor readAccessInput(testImage); + const float* inputArray = (const float*)readAccessInput.GetData(); + + for (int i = 0; i < length; ++i) + { + CPPUNIT_ASSERT_MESSAGE(std::string("Input array already not correct: " + std::to_string(inputArray[i])), abs(inputArray[i]) < 1e-5f); + } + + mitk::BeamformingSettings::Pointer config = CreateEmptyBeamformingSettings(); + auto output = m_PhotoacousticFilterService->ApplyBeamforming(testImage, config); - mitk::ImageReadAccessor readAccess(output, output->GetVolumeData()); - const int* outputArray = (const int*)readAccess.GetData(); + mitk::ImageReadAccessor readAccess(output); + const float* outputArray = (const float*)readAccess.GetData(); for (int i = 0; i < length; ++i) { - CPPUNIT_ASSERT(outputArray[i] == 0); + CPPUNIT_ASSERT_MESSAGE(std::string("Ouput array not correct: " + std::to_string(abs(outputArray[i]))), abs(outputArray[i]) < 1e-5f); } } void tearDown() override { m_PhotoacousticFilterService = nullptr; } }; MITK_TEST_SUITE_REGISTRATION(mitkPAFilterService) diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/src/internal/PAImageProcessing.cpp b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/src/internal/PAImageProcessing.cpp index b5827dcdab..10a65f5d17 100644 --- a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/src/internal/PAImageProcessing.cpp +++ b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/src/internal/PAImageProcessing.cpp @@ -1,1160 +1,1161 @@ /*=================================================================== 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 "PAImageProcessing.h" // Qt #include #include #include #include //mitk image #include #include "mitkPhotoacousticFilterService.h" +#include "mitkCastToFloatImageFilter.h" #include "mitkBeamformingFilter.h" //other #include #include #include const std::string PAImageProcessing::VIEW_ID = "org.mitk.views.paimageprocessing"; PAImageProcessing::PAImageProcessing() : m_ResampleSpacing(0), m_UseLogfilter(false), m_FilterBank(mitk::PhotoacousticFilterService::New()) { qRegisterMetaType(); qRegisterMetaType(); } void PAImageProcessing::SetFocus() { m_Controls.buttonApplyBModeFilter->setFocus(); } void PAImageProcessing::CreateQtPartControl(QWidget *parent) { BFconfig = mitk::BeamformingSettings::New(); // create GUI widgets from the Qt Designer's .ui file m_Controls.setupUi(parent); connect(m_Controls.buttonApplyBModeFilter, SIGNAL(clicked()), this, SLOT(StartBmodeThread())); connect(m_Controls.DoResampling, SIGNAL(clicked()), this, SLOT(UseResampling())); connect(m_Controls.Logfilter, SIGNAL(clicked()), this, SLOT(UseLogfilter())); connect(m_Controls.ResamplingValue, SIGNAL(valueChanged(double)), this, SLOT(SetResampling())); connect(m_Controls.buttonApplyBeamforming, SIGNAL(clicked()), this, SLOT(StartBeamformingThread())); connect(m_Controls.buttonApplyCropFilter, SIGNAL(clicked()), this, SLOT(StartCropThread())); connect(m_Controls.buttonApplyBandpass, SIGNAL(clicked()), this, SLOT(StartBandpassThread())); connect(m_Controls.UseImageSpacing, SIGNAL(clicked()), this, SLOT(UseImageSpacing())); connect(m_Controls.ScanDepth, SIGNAL(valueChanged(double)), this, SLOT(UpdateImageInfo())); connect(m_Controls.SpeedOfSound, SIGNAL(valueChanged(double)), this, SLOT(UpdateImageInfo())); connect(m_Controls.SpeedOfSound, SIGNAL(valueChanged(double)), this, SLOT(ChangedSOSBeamforming())); connect(m_Controls.BPSpeedOfSound, SIGNAL(valueChanged(double)), this, SLOT(ChangedSOSBandpass())); connect(m_Controls.Samples, SIGNAL(valueChanged(int)), this, SLOT(UpdateImageInfo())); connect(m_Controls.UseImageSpacing, SIGNAL(clicked()), this, SLOT(UpdateImageInfo())); connect(m_Controls.boundLow, SIGNAL(valueChanged(int)), this, SLOT(LowerSliceBoundChanged())); connect(m_Controls.boundHigh, SIGNAL(valueChanged(int)), this, SLOT(UpperSliceBoundChanged())); connect(m_Controls.Partial, SIGNAL(clicked()), this, SLOT(SliceBoundsEnabled())); connect(m_Controls.BatchProcessing, SIGNAL(clicked()), this, SLOT(BatchProcessing())); connect(m_Controls.StepBeamforming, SIGNAL(clicked()), this, SLOT(UpdateSaveBoxes())); connect(m_Controls.StepCropping, SIGNAL(clicked()), this, SLOT(UpdateSaveBoxes())); connect(m_Controls.StepBandpass, SIGNAL(clicked()), this, SLOT(UpdateSaveBoxes())); connect(m_Controls.StepBMode, SIGNAL(clicked()), this, SLOT(UpdateSaveBoxes())); UpdateSaveBoxes(); m_Controls.DoResampling->setChecked(false); m_Controls.ResamplingValue->setEnabled(false); m_Controls.progressBar->setMinimum(0); m_Controls.progressBar->setMaximum(100); m_Controls.progressBar->setVisible(false); m_Controls.UseImageSpacing->setToolTip("Image spacing of y-Axis must be in us, x-Axis in mm."); m_Controls.UseImageSpacing->setToolTipDuration(5000); m_Controls.ProgressInfo->setVisible(false); m_Controls.UseBP->hide(); m_Controls.UseGPUBmode->hide(); #ifndef PHOTOACOUSTICS_USE_GPU m_Controls.UseGPUBf->setEnabled(false); m_Controls.UseGPUBf->setChecked(false); m_Controls.UseGPUBmode->setEnabled(false); m_Controls.UseGPUBmode->setChecked(false); #endif UseImageSpacing(); } void PAImageProcessing::ChangedSOSBandpass() { m_Controls.SpeedOfSound->setValue(m_Controls.BPSpeedOfSound->value()); } void PAImageProcessing::ChangedSOSBeamforming() { m_Controls.BPSpeedOfSound->setValue(m_Controls.SpeedOfSound->value()); } std::vector splitpath( const std::string& str , const std::set delimiters) { std::vector result; char const* pch = str.c_str(); char const* start = pch; for (; *pch; ++pch) { if (delimiters.find(*pch) != delimiters.end()) { if (start != pch) { std::string str(start, pch); result.push_back(str); } else { result.push_back(""); } start = pch + 1; } } result.push_back(start); return result; } void PAImageProcessing::UpdateSaveBoxes() { if (m_Controls.StepBeamforming->isChecked()) m_Controls.SaveBeamforming->setEnabled(true); else m_Controls.SaveBeamforming->setEnabled(false); if (m_Controls.StepCropping->isChecked()) m_Controls.SaveCropping->setEnabled(true); else m_Controls.SaveCropping->setEnabled(false); if (m_Controls.StepBandpass->isChecked()) m_Controls.SaveBandpass->setEnabled(true); else m_Controls.SaveBandpass->setEnabled(false); if (m_Controls.StepBMode->isChecked()) m_Controls.SaveBMode->setEnabled(true); else m_Controls.SaveBMode->setEnabled(false); } void PAImageProcessing::BatchProcessing() { QFileDialog LoadDialog(nullptr, "Select Files to be processed"); LoadDialog.setFileMode(QFileDialog::FileMode::ExistingFiles); LoadDialog.setNameFilter(tr("Images (*.nrrd)")); LoadDialog.setViewMode(QFileDialog::Detail); QStringList fileNames; if (LoadDialog.exec()) fileNames = LoadDialog.selectedFiles(); QString saveDir = QFileDialog::getExistingDirectory(nullptr, tr("Select Directory To Save To"), "", QFileDialog::ShowDirsOnly | QFileDialog::DontResolveSymlinks); DisableControls(); std::set delims{ '/' }; bool doSteps[] = { m_Controls.StepBeamforming->isChecked(), m_Controls.StepCropping->isChecked() , m_Controls.StepBandpass->isChecked(), m_Controls.StepBMode->isChecked() }; bool saveSteps[] = { m_Controls.SaveBeamforming->isChecked(), m_Controls.SaveCropping->isChecked() , m_Controls.SaveBandpass->isChecked(), m_Controls.SaveBMode->isChecked() }; for (int fileNumber = 0; fileNumber < fileNames.size(); ++fileNumber) { m_Controls.progressBar->setValue(0); m_Controls.progressBar->setVisible(true); m_Controls.ProgressInfo->setVisible(true); m_Controls.ProgressInfo->setText("loading file"); QString filename = fileNames.at(fileNumber); auto split = splitpath(filename.toStdString(), delims); std::string imageName = split.at(split.size() - 1); // remove ".nrrd" imageName = imageName.substr(0, imageName.size() - 5); mitk::Image::Pointer image = mitk::IOUtil::Load(filename.toStdString().c_str()); UpdateBFSettings(image); // Beamforming if (doSteps[0]) { std::function progressHandle = [this](int progress, std::string progressInfo) { this->UpdateProgress(progress, progressInfo); }; m_Controls.progressBar->setValue(100); - std::string errorMessage = ""; - image = m_FilterBank->ApplyBeamforming(image, BFconfig, errorMessage, progressHandle); + image = m_FilterBank->ApplyBeamforming(image, BFconfig, progressHandle); if (saveSteps[0]) { std::string saveFileName = saveDir.toStdString() + "/" + imageName + " beamformed" + ".nrrd"; mitk::IOUtil::Save(image, saveFileName); } } // Cropping if (doSteps[1]) { m_Controls.ProgressInfo->setText("cropping image"); image = m_FilterBank->ApplyCropping(image, m_Controls.CutoffAbove->value(), m_Controls.CutoffBelow->value(), 0, 0, 0, 0); if (saveSteps[1]) { std::string saveFileName = saveDir.toStdString() + "/" + imageName + " cropped" + ".nrrd"; mitk::IOUtil::Save(image, saveFileName); } } // Bandpass if (doSteps[2]) { m_Controls.ProgressInfo->setText("applying bandpass"); float recordTime = image->GetDimension(1)*image->GetGeometry()->GetSpacing()[1] / 1000 / m_Controls.BPSpeedOfSound->value(); // add a safeguard so the program does not chrash when applying a Bandpass that reaches out of the bounds of the image float maxFrequency = 1 / (recordTime / image->GetDimension(1)) * image->GetDimension(1) / 2 / 2 / 1000; float BPHighPass = 1000000 * m_Controls.BPhigh->value(); // [Hz] float BPLowPass = maxFrequency - 1000000 * m_Controls.BPlow->value(); // [Hz] if (BPLowPass > maxFrequency && m_Controls.UseBP->isChecked()) { QMessageBox Msgbox; Msgbox.setText("LowPass too low, disabled it."); Msgbox.exec(); BPLowPass = 0; } if (BPLowPass < 0 && m_Controls.UseBP->isChecked()) { QMessageBox Msgbox; Msgbox.setText("LowPass too high, disabled it."); Msgbox.exec(); BPLowPass = 0; } if (BPHighPass > maxFrequency && m_Controls.UseBP->isChecked()) { QMessageBox Msgbox; Msgbox.setText("HighPass too high, disabled it."); Msgbox.exec(); BPHighPass = 0; } if (BPHighPass > maxFrequency - BFconfig->GetBPLowPass()) { QMessageBox Msgbox; Msgbox.setText("HighPass higher than LowPass, disabled both."); Msgbox.exec(); BPHighPass = 0; BPLowPass = 0; } image = m_FilterBank->BandpassFilter(image, recordTime, BPHighPass, BPLowPass, m_Controls.BPFalloffHigh->value(), m_Controls.BPFalloffLow->value()); if (saveSteps[2]) { std::string saveFileName = saveDir.toStdString() + "/" + imageName + " bandpassed" + ".nrrd"; mitk::IOUtil::Save(image, saveFileName); } } // Bmode if (doSteps[3]) { m_Controls.ProgressInfo->setText("applying bmode filter"); bool useGPU = m_Controls.UseGPUBmode->isChecked(); if (m_Controls.BModeMethod->currentText() == "Absolute Filter") image = m_FilterBank->ApplyBmodeFilter(image, mitk::PhotoacousticFilterService::BModeMethod::Abs, useGPU, m_UseLogfilter, m_ResampleSpacing); else if (m_Controls.BModeMethod->currentText() == "Envelope Detection") image = m_FilterBank->ApplyBmodeFilter(image, mitk::PhotoacousticFilterService::BModeMethod::EnvelopeDetection, useGPU, m_UseLogfilter, m_ResampleSpacing); if (saveSteps[3]) { std::string saveFileName = saveDir.toStdString() + "/" + imageName + " bmode" + ".nrrd"; mitk::IOUtil::Save(image, saveFileName); } } m_Controls.progressBar->setVisible(false); } EnableControls(); } void PAImageProcessing::StartBeamformingThread() { QList nodes = this->GetDataManagerSelection(); if (nodes.empty()) return; mitk::DataStorage::Pointer storage = this->GetDataStorage(); mitk::DataNode::Pointer node = nodes.front(); if (!node) { // Nothing selected. Inform the user and return QMessageBox::information(NULL, "Template", "Please load and select an image before starting image processing."); return; } 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) { UpdateBFSettings(image); std::stringstream message; std::string name; message << "Performing beamforming for image "; if (node->GetName(name)) { // a property called "name" was found for this DataNode message << "'" << name << "'"; m_OldNodeName = name; } else m_OldNodeName = " "; message << "."; MITK_INFO << message.str(); m_Controls.progressBar->setValue(0); m_Controls.progressBar->setVisible(true); m_Controls.ProgressInfo->setVisible(true); m_Controls.ProgressInfo->setText("started"); m_Controls.buttonApplyBeamforming->setText("working..."); DisableControls(); BeamformingThread *thread = new BeamformingThread(); connect(thread, &BeamformingThread::result, this, &PAImageProcessing::HandleBeamformingResults); connect(thread, &BeamformingThread::updateProgress, this, &PAImageProcessing::UpdateProgress); - connect(thread, &BeamformingThread::message, this, &PAImageProcessing::PAMessageBox); connect(thread, &BeamformingThread::finished, thread, &QObject::deleteLater); thread->setConfig(BFconfig); thread->setInputImage(image); thread->setFilterBank(m_FilterBank); MITK_INFO << "Started new thread for Beamforming"; thread->start(); } } } void PAImageProcessing::HandleBeamformingResults(mitk::Image::Pointer image) { MITK_INFO << "Handle Beamforming results"; auto newNode = mitk::DataNode::New(); newNode->SetData(image); // name the new Data node std::stringstream newNodeName; newNodeName << m_OldNodeName << " "; if (BFconfig->GetAlgorithm() == mitk::BeamformingSettings::BeamformingAlgorithm::DAS) newNodeName << "DAS bf, "; else if (BFconfig->GetAlgorithm() == mitk::BeamformingSettings::BeamformingAlgorithm::DMAS) newNodeName << "DMAS bf, "; if (BFconfig->GetDelayCalculationMethod() == mitk::BeamformingSettings::DelayCalc::QuadApprox) newNodeName << "q. delay"; if (BFconfig->GetDelayCalculationMethod() == mitk::BeamformingSettings::DelayCalc::Spherical) newNodeName << "s. delay"; newNode->SetName(newNodeName.str()); // update level window for the current dynamic range mitk::LevelWindow levelWindow; newNode->GetLevelWindow(levelWindow); levelWindow.SetAuto(image, true, true); newNode->SetLevelWindow(levelWindow); // add new node to data storage this->GetDataStorage()->Add(newNode); // disable progress bar m_Controls.progressBar->setVisible(false); m_Controls.ProgressInfo->setVisible(false); m_Controls.buttonApplyBeamforming->setText("Apply Beamforming"); EnableControls(); // update rendering mitk::RenderingManager::GetInstance()->InitializeViews(image->GetGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void PAImageProcessing::StartBmodeThread() { QList nodes = this->GetDataManagerSelection(); if (nodes.empty()) return; mitk::DataStorage::Pointer storage = this->GetDataStorage(); mitk::DataNode::Pointer node = nodes.front(); if (!node) { // Nothing selected. Inform the user and return QMessageBox::information(NULL, "Template", "Please load and select an image before starting image processing."); return; } 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) { UpdateBFSettings(image); std::stringstream message; std::string name; message << "Performing image processing for image "; if (node->GetName(name)) { // a property called "name" was found for this DataNode message << "'" << name << "'"; m_OldNodeName = name; } else m_OldNodeName = " "; message << "."; MITK_INFO << message.str(); m_Controls.buttonApplyBModeFilter->setText("working..."); DisableControls(); BmodeThread *thread = new BmodeThread(); connect(thread, &BmodeThread::result, this, &PAImageProcessing::HandleBmodeResults); connect(thread, &BmodeThread::finished, thread, &QObject::deleteLater); bool useGPU = m_Controls.UseGPUBmode->isChecked(); if (m_Controls.BModeMethod->currentText() == "Absolute Filter") thread->setConfig(m_UseLogfilter, m_ResampleSpacing, mitk::PhotoacousticFilterService::BModeMethod::Abs, useGPU); else if (m_Controls.BModeMethod->currentText() == "Envelope Detection") thread->setConfig(m_UseLogfilter, m_ResampleSpacing, mitk::PhotoacousticFilterService::BModeMethod::EnvelopeDetection, useGPU); thread->setInputImage(image); thread->setFilterBank(m_FilterBank); MITK_INFO << "Started new thread for Image Processing"; thread->start(); } } } void PAImageProcessing::HandleBmodeResults(mitk::Image::Pointer image) { auto newNode = mitk::DataNode::New(); newNode->SetData(image); // name the new Data node std::stringstream newNodeName; newNodeName << m_OldNodeName << " "; newNodeName << "B-Mode"; newNode->SetName(newNodeName.str()); // update level window for the current dynamic range mitk::LevelWindow levelWindow; newNode->GetLevelWindow(levelWindow); auto data = newNode->GetData(); levelWindow.SetAuto(dynamic_cast(data), true, true); newNode->SetLevelWindow(levelWindow); // add new node to data storage this->GetDataStorage()->Add(newNode); // disable progress bar m_Controls.progressBar->setVisible(false); m_Controls.buttonApplyBModeFilter->setText("Apply B-mode Filter"); EnableControls(); // update rendering mitk::RenderingManager::GetInstance()->InitializeViews( dynamic_cast(data)->GetGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void PAImageProcessing::StartCropThread() { QList nodes = this->GetDataManagerSelection(); if (nodes.empty()) return; mitk::DataStorage::Pointer storage = this->GetDataStorage(); mitk::DataNode::Pointer node = nodes.front(); if (!node) { // Nothing selected. Inform the user and return QMessageBox::information(NULL, "Template", "Please load and select an image before starting image cropping."); return; } 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) { UpdateBFSettings(image); std::stringstream message; std::string name; message << "Performing image cropping for image "; if (node->GetName(name)) { // a property called "name" was found for this DataNode message << "'" << name << "'"; m_OldNodeName = name; } else m_OldNodeName = " "; message << "."; MITK_INFO << message.str(); m_Controls.buttonApplyCropFilter->setText("working..."); DisableControls(); CropThread *thread = new CropThread(); connect(thread, &CropThread::result, this, &PAImageProcessing::HandleCropResults); connect(thread, &CropThread::finished, thread, &QObject::deleteLater); thread->setConfig(m_Controls.CutoffAbove->value(), m_Controls.CutoffBelow->value(), 0, image->GetDimension(2) - 1); thread->setInputImage(image); thread->setFilterBank(m_FilterBank); MITK_INFO << "Started new thread for Image Cropping"; thread->start(); } } } void PAImageProcessing::HandleCropResults(mitk::Image::Pointer image) { auto newNode = mitk::DataNode::New(); newNode->SetData(image); // name the new Data node std::stringstream newNodeName; newNodeName << m_OldNodeName << " "; newNodeName << "Cropped"; newNode->SetName(newNodeName.str()); // update level window for the current dynamic range mitk::LevelWindow levelWindow; newNode->GetLevelWindow(levelWindow); auto data = newNode->GetData(); levelWindow.SetAuto(dynamic_cast(data), true, true); newNode->SetLevelWindow(levelWindow); // add new node to data storage this->GetDataStorage()->Add(newNode); m_Controls.buttonApplyCropFilter->setText("Apply Crop Filter"); EnableControls(); // update rendering mitk::RenderingManager::GetInstance()->InitializeViews( dynamic_cast(data)->GetGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void PAImageProcessing::StartBandpassThread() { QList nodes = this->GetDataManagerSelection(); if (nodes.empty()) return; mitk::DataStorage::Pointer storage = this->GetDataStorage(); mitk::DataNode::Pointer node = nodes.front(); if (!node) { // Nothing selected. Inform the user and return QMessageBox::information(NULL, "Template", "Please load and select an image before starting image cropping."); return; } 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) { UpdateBFSettings(image); std::stringstream message; std::string name; message << "Performing Bandpass filter on image "; if (node->GetName(name)) { // a property called "name" was found for this DataNode message << "'" << name << "'"; m_OldNodeName = name; } else m_OldNodeName = " "; message << "."; MITK_INFO << message.str(); m_Controls.buttonApplyBandpass->setText("working..."); DisableControls(); BandpassThread *thread = new BandpassThread(); connect(thread, &BandpassThread::result, this, &PAImageProcessing::HandleBandpassResults); connect(thread, &BandpassThread::finished, thread, &QObject::deleteLater); float recordTime = image->GetDimension(1)*image->GetGeometry()->GetSpacing()[1] / 1000 / m_Controls.BPSpeedOfSound->value(); // add a safeguard so the program does not chrash when applying a Bandpass that reaches out of the bounds of the image float maxFrequency = 1 / (recordTime / image->GetDimension(1)) * image->GetDimension(1) / 2 / 2 / 1000; float BPHighPass = 1000000 * m_Controls.BPhigh->value(); // [Hz] float BPLowPass = maxFrequency - 1000000 * m_Controls.BPlow->value(); // [Hz] if (BPLowPass > maxFrequency && m_Controls.UseBP->isChecked()) { QMessageBox Msgbox; Msgbox.setText("LowPass too low, disabled it."); Msgbox.exec(); BPLowPass = 0; } if (BPLowPass < 0 && m_Controls.UseBP->isChecked()) { QMessageBox Msgbox; Msgbox.setText("LowPass too high, disabled it."); Msgbox.exec(); BPLowPass = 0; } if (BPHighPass > maxFrequency && m_Controls.UseBP->isChecked()) { QMessageBox Msgbox; Msgbox.setText("HighPass too high, disabled it."); Msgbox.exec(); BPHighPass = 0; } if (BPHighPass > maxFrequency - BFconfig->GetBPLowPass()) { QMessageBox Msgbox; Msgbox.setText("HighPass higher than LowPass, disabled both."); Msgbox.exec(); BPHighPass = 0; BPLowPass = 0; } thread->setConfig(BPHighPass, BPLowPass, m_Controls.BPFalloffLow->value(), m_Controls.BPFalloffHigh->value(), recordTime); thread->setInputImage(image); thread->setFilterBank(m_FilterBank); MITK_INFO << "Started new thread for Bandpass filter"; thread->start(); } } } void PAImageProcessing::HandleBandpassResults(mitk::Image::Pointer image) { auto newNode = mitk::DataNode::New(); newNode->SetData(image); // name the new Data node std::stringstream newNodeName; newNodeName << m_OldNodeName << " "; newNodeName << "Bandpassed"; newNode->SetName(newNodeName.str()); // update level window for the current dynamic range mitk::LevelWindow levelWindow; newNode->GetLevelWindow(levelWindow); auto data = newNode->GetData(); levelWindow.SetAuto(dynamic_cast(data), true, true); newNode->SetLevelWindow(levelWindow); // add new node to data storage this->GetDataStorage()->Add(newNode); m_Controls.buttonApplyBandpass->setText("Apply Bandpass"); EnableControls(); // update rendering mitk::RenderingManager::GetInstance()->InitializeViews( dynamic_cast(data)->GetGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void PAImageProcessing::SliceBoundsEnabled() { if (!m_Controls.Partial->isChecked()) { m_Controls.boundLow->setEnabled(false); m_Controls.boundHigh->setEnabled(false); return; } else { m_Controls.boundLow->setEnabled(true); m_Controls.boundHigh->setEnabled(true); } } void PAImageProcessing::UpperSliceBoundChanged() { if (m_Controls.boundLow->value() > m_Controls.boundHigh->value()) { m_Controls.boundLow->setValue(m_Controls.boundHigh->value()); } } void PAImageProcessing::LowerSliceBoundChanged() { if (m_Controls.boundLow->value() > m_Controls.boundHigh->value()) { m_Controls.boundHigh->setValue(m_Controls.boundLow->value()); } } void PAImageProcessing::UpdateProgress(int progress, std::string progressInfo) { if (progress < 100) m_Controls.progressBar->setValue(progress); else m_Controls.progressBar->setValue(100); m_Controls.ProgressInfo->setText(progressInfo.c_str()); qApp->processEvents(); } void PAImageProcessing::PAMessageBox(std::string message) { if (0 != message.compare("noMessage")) { QMessageBox msgBox; msgBox.setText(message.c_str()); msgBox.exec(); } } void PAImageProcessing::UpdateImageInfo() { QList nodes = this->GetDataManagerSelection(); if (nodes.empty()) return; mitk::DataNode::Pointer node = nodes.front(); if (!node) { // Nothing selected return; } 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) { // beamforming configs if (m_Controls.UseImageSpacing->isChecked()) { m_Controls.ElementCount->setValue(image->GetDimension(0)); m_Controls.Pitch->setValue(image->GetGeometry()->GetSpacing()[0]); } m_Controls.boundLow->setMaximum(image->GetDimension(2) - 1); m_Controls.boundHigh->setMaximum(image->GetDimension(2) - 1); UpdateBFSettings(image); std::stringstream frequency; float maxFrequency = (1 / BFconfig->GetTimeSpacing()) * image->GetDimension(1) / 2 / 2 / 1000; frequency << maxFrequency / 1000000; //[MHz] frequency << "MHz"; m_Controls.BPhigh->setMaximum(maxFrequency / 1000000); m_Controls.BPlow->setMaximum(maxFrequency / 1000000); frequency << " is the maximal allowed frequency for the selected image."; m_Controls.BPhigh->setToolTip(frequency.str().c_str()); m_Controls.BPlow->setToolTip(frequency.str().c_str()); m_Controls.BPhigh->setToolTipDuration(5000); m_Controls.BPlow->setToolTipDuration(5000); } } } void PAImageProcessing::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.buttonApplyBModeFilter->setEnabled(true); m_Controls.labelWarning2->setVisible(false); m_Controls.buttonApplyCropFilter->setEnabled(true); m_Controls.labelWarning3->setVisible(false); m_Controls.buttonApplyBandpass->setEnabled(true); m_Controls.labelWarning4->setVisible(false); m_Controls.buttonApplyBeamforming->setEnabled(true); UpdateImageInfo(); return; } } m_Controls.labelWarning->setVisible(true); m_Controls.buttonApplyBModeFilter->setEnabled(false); m_Controls.labelWarning2->setVisible(true); m_Controls.buttonApplyCropFilter->setEnabled(false); m_Controls.labelWarning3->setVisible(true); m_Controls.buttonApplyBandpass->setEnabled(false); m_Controls.labelWarning4->setVisible(true); m_Controls.buttonApplyBeamforming->setEnabled(false); } void PAImageProcessing::UseResampling() { if (m_Controls.DoResampling->isChecked()) { m_Controls.ResamplingValue->setEnabled(true); m_ResampleSpacing = m_Controls.ResamplingValue->value(); } else { m_Controls.ResamplingValue->setEnabled(false); m_ResampleSpacing = 0; } } void PAImageProcessing::UseLogfilter() { m_UseLogfilter = m_Controls.Logfilter->isChecked(); } void PAImageProcessing::SetResampling() { m_ResampleSpacing = m_Controls.ResamplingValue->value(); } void PAImageProcessing::UpdateBFSettings(mitk::Image::Pointer image) { if ("DAS" == m_Controls.BFAlgorithm->currentText()) BFconfig->SetAlgorithm(mitk::BeamformingSettings::BeamformingAlgorithm::DAS); else if ("DMAS" == m_Controls.BFAlgorithm->currentText()) BFconfig->SetAlgorithm(mitk::BeamformingSettings::BeamformingAlgorithm::DMAS); else if ("sDMAS" == m_Controls.BFAlgorithm->currentText()) BFconfig->SetAlgorithm(mitk::BeamformingSettings::BeamformingAlgorithm::sDMAS); if ("Quad. Approx." == m_Controls.DelayCalculation->currentText()) { BFconfig->SetDelayCalculationMethod(mitk::BeamformingSettings::DelayCalc::QuadApprox); } else if ("Spherical Wave" == m_Controls.DelayCalculation->currentText()) { BFconfig->SetDelayCalculationMethod(mitk::BeamformingSettings::DelayCalc::Spherical); } if ("Von Hann" == m_Controls.Apodization->currentText()) { BFconfig->SetApod(mitk::BeamformingSettings::Apodization::Hann); } else if ("Hamming" == m_Controls.Apodization->currentText()) { BFconfig->SetApod(mitk::BeamformingSettings::Apodization::Hamm); } else if ("Box" == m_Controls.Apodization->currentText()) { BFconfig->SetApod(mitk::BeamformingSettings::Apodization::Box); } BFconfig->SetPitchInMeters(m_Controls.Pitch->value() / 1000); // [m] BFconfig->SetSpeedOfSound(m_Controls.SpeedOfSound->value()); // [m/s] BFconfig->SetSamplesPerLine(m_Controls.Samples->value()); BFconfig->SetReconstructionLines(m_Controls.Lines->value()); BFconfig->SetTransducerElements(m_Controls.ElementCount->value()); BFconfig->SetApodizationArraySize(m_Controls.Lines->value()); BFconfig->SetAngle(m_Controls.Angle->value()); // [deg] BFconfig->SetUseBP(m_Controls.UseBP->isChecked()); BFconfig->SetUseGPU(m_Controls.UseGPUBf->isChecked()); if (m_Controls.UseImageSpacing->isChecked()) { BFconfig->SetTimeSpacing(image->GetGeometry()->GetSpacing()[1] / 1000000); MITK_INFO << "Calculated Scan Depth of " << (image->GetDimension(1)*image->GetGeometry()->GetSpacing()[1] / 1000000) * BFconfig->GetSpeedOfSound() * 100 / 2 << "cm"; } else { BFconfig->SetTimeSpacing((2 * m_Controls.ScanDepth->value() / 1000 / BFconfig->GetSpeedOfSound()) / image->GetDimension(1)); } if ("US Image" == m_Controls.ImageType->currentText()) { BFconfig->SetIsPhotoacousticImage(false); } else if ("PA Image" == m_Controls.ImageType->currentText()) { BFconfig->SetIsPhotoacousticImage(true); } BFconfig->SetPartial(m_Controls.Partial->isChecked()); BFconfig->GetCropBounds()[0] = m_Controls.boundLow->value(); BFconfig->GetCropBounds()[1] = m_Controls.boundHigh->value(); } void PAImageProcessing::EnableControls() { m_Controls.BatchProcessing->setEnabled(true); m_Controls.StepBeamforming->setEnabled(true); m_Controls.StepBandpass->setEnabled(true); m_Controls.StepCropping->setEnabled(true); m_Controls.StepBMode->setEnabled(true); UpdateSaveBoxes(); m_Controls.DoResampling->setEnabled(true); UseResampling(); m_Controls.Logfilter->setEnabled(true); m_Controls.BModeMethod->setEnabled(true); m_Controls.buttonApplyBModeFilter->setEnabled(true); m_Controls.CutoffAbove->setEnabled(true); m_Controls.CutoffBelow->setEnabled(true); m_Controls.buttonApplyCropFilter->setEnabled(true); m_Controls.BPSpeedOfSound->setEnabled(true); m_Controls.buttonApplyBandpass->setEnabled(true); m_Controls.Partial->setEnabled(true); m_Controls.boundHigh->setEnabled(true); m_Controls.boundLow->setEnabled(true); m_Controls.BFAlgorithm->setEnabled(true); m_Controls.DelayCalculation->setEnabled(true); m_Controls.ImageType->setEnabled(true); m_Controls.Apodization->setEnabled(true); m_Controls.UseBP->setEnabled(true); #ifdef PHOTOACOUSTICS_USE_GPU m_Controls.UseGPUBf->setEnabled(true); m_Controls.UseGPUBmode->setEnabled(true); #endif m_Controls.BPhigh->setEnabled(true); m_Controls.BPlow->setEnabled(true); m_Controls.BPFalloffLow->setEnabled(true); m_Controls.BPFalloffHigh->setEnabled(true); m_Controls.UseImageSpacing->setEnabled(true); UseImageSpacing(); m_Controls.Pitch->setEnabled(true); m_Controls.ElementCount->setEnabled(true); m_Controls.SpeedOfSound->setEnabled(true); m_Controls.Samples->setEnabled(true); m_Controls.Lines->setEnabled(true); m_Controls.Angle->setEnabled(true); m_Controls.buttonApplyBeamforming->setEnabled(true); } void PAImageProcessing::DisableControls() { m_Controls.BatchProcessing->setEnabled(false); m_Controls.StepBeamforming->setEnabled(false); m_Controls.StepBandpass->setEnabled(false); m_Controls.StepCropping->setEnabled(false); m_Controls.StepBMode->setEnabled(false); m_Controls.SaveBeamforming->setEnabled(false); m_Controls.SaveBandpass->setEnabled(false); m_Controls.SaveCropping->setEnabled(false); m_Controls.SaveBMode->setEnabled(false); m_Controls.DoResampling->setEnabled(false); m_Controls.ResamplingValue->setEnabled(false); m_Controls.Logfilter->setEnabled(false); m_Controls.BModeMethod->setEnabled(false); m_Controls.buttonApplyBModeFilter->setEnabled(false); m_Controls.CutoffAbove->setEnabled(false); m_Controls.CutoffBelow->setEnabled(false); m_Controls.buttonApplyCropFilter->setEnabled(false); m_Controls.BPSpeedOfSound->setEnabled(false); m_Controls.buttonApplyBandpass->setEnabled(false); m_Controls.Partial->setEnabled(false); m_Controls.boundHigh->setEnabled(false); m_Controls.boundLow->setEnabled(false); m_Controls.BFAlgorithm->setEnabled(false); m_Controls.DelayCalculation->setEnabled(false); m_Controls.ImageType->setEnabled(false); m_Controls.Apodization->setEnabled(false); m_Controls.UseBP->setEnabled(false); #ifdef PHOTOACOUSTICS_USE_GPU m_Controls.UseGPUBf->setEnabled(false); m_Controls.UseGPUBmode->setEnabled(false); #endif m_Controls.BPhigh->setEnabled(false); m_Controls.BPlow->setEnabled(false); m_Controls.BPFalloffLow->setEnabled(false); m_Controls.BPFalloffHigh->setEnabled(false); m_Controls.UseImageSpacing->setEnabled(false); m_Controls.ScanDepth->setEnabled(false); m_Controls.Pitch->setEnabled(false); m_Controls.ElementCount->setEnabled(false); m_Controls.SpeedOfSound->setEnabled(false); m_Controls.Samples->setEnabled(false); m_Controls.Lines->setEnabled(false); m_Controls.Angle->setEnabled(false); m_Controls.buttonApplyBeamforming->setEnabled(false); } void PAImageProcessing::UseImageSpacing() { if (m_Controls.UseImageSpacing->isChecked()) { m_Controls.ScanDepth->setDisabled(true); } else { m_Controls.ScanDepth->setEnabled(true); } } #include void BeamformingThread::run() { mitk::Image::Pointer resultImage = mitk::Image::New(); mitk::Image::Pointer resultImageBuffer; - std::string errorMessage = ""; std::function progressHandle = [this](int progress, std::string progressInfo) { emit updateProgress(progress, progressInfo); }; - - resultImageBuffer = m_FilterBank->ApplyBeamforming(m_InputImage, m_BFconfig, errorMessage, progressHandle); + mitk::CastToFloatImageFilter::Pointer castToFloatImageFilter = mitk::CastToFloatImageFilter::New(); + castToFloatImageFilter->SetInput(m_InputImage); + castToFloatImageFilter->Update(); + m_InputImage = castToFloatImageFilter->GetOutput(); + mitk::IOUtil::Save(m_InputImage, "G:/castedImage.nrrd"); + resultImageBuffer = m_FilterBank->ApplyBeamforming(m_InputImage, m_BFconfig, progressHandle); mitk::ImageReadAccessor copy(resultImageBuffer); resultImage->Initialize(resultImageBuffer); resultImage->SetSpacing(resultImageBuffer->GetGeometry()->GetSpacing()); resultImage->SetImportVolume(const_cast(copy.GetData()), 0, 0, mitk::Image::CopyMemory); emit result(resultImage); - emit message(errorMessage); } void BeamformingThread::setConfig(mitk::BeamformingSettings::Pointer BFconfig) { m_BFconfig = BFconfig; } void BeamformingThread::setInputImage(mitk::Image::Pointer image) { m_InputImage = image; } void BmodeThread::run() { mitk::Image::Pointer resultImage; resultImage = m_FilterBank->ApplyBmodeFilter(m_InputImage, m_Method, m_UseGPU, m_UseLogfilter, m_ResampleSpacing); emit result(resultImage); } void BmodeThread::setConfig(bool useLogfilter, double resampleSpacing, mitk::PhotoacousticFilterService::BModeMethod method, bool useGPU) { m_UseLogfilter = useLogfilter; m_ResampleSpacing = resampleSpacing; m_Method = method; m_UseGPU = useGPU; } void BmodeThread::setInputImage(mitk::Image::Pointer image) { m_InputImage = image; } void CropThread::run() { mitk::Image::Pointer resultImage; resultImage = m_FilterBank->ApplyCropping(m_InputImage, m_CutAbove, m_CutBelow, 0, 0, 0, 0); emit result(resultImage); } void CropThread::setConfig(unsigned int CutAbove, unsigned int CutBelow, unsigned int CutSliceFirst, unsigned int CutSliceLast) { m_CutAbove = CutAbove; m_CutBelow = CutBelow; m_CutSliceLast = CutSliceLast; m_CutSliceFirst = CutSliceFirst; } void CropThread::setInputImage(mitk::Image::Pointer image) { m_InputImage = image; } void BandpassThread::run() { mitk::Image::Pointer resultImage; resultImage = m_FilterBank->BandpassFilter(m_InputImage, m_RecordTime, m_BPHighPass, m_BPLowPass, m_TukeyAlphaHighPass, m_TukeyAlphaLowPass); emit result(resultImage); } void BandpassThread::setConfig(float BPHighPass, float BPLowPass, float TukeyAlphaHighPass, float TukeyAlphaLowPass, float recordTime) { m_BPHighPass = BPHighPass; m_BPLowPass = BPLowPass; m_TukeyAlphaHighPass = TukeyAlphaHighPass; m_TukeyAlphaLowPass = TukeyAlphaLowPass; m_RecordTime = recordTime; } void BandpassThread::setInputImage(mitk::Image::Pointer image) { m_InputImage = image; }