diff --git a/Modules/PhotoacousticsAlgorithms/CMakeLists.txt b/Modules/PhotoacousticsAlgorithms/CMakeLists.txt index 29de53eb58..7eb8df47cd 100644 --- a/Modules/PhotoacousticsAlgorithms/CMakeLists.txt +++ b/Modules/PhotoacousticsAlgorithms/CMakeLists.txt @@ -1,19 +1,19 @@ set(dependencies_list MitkCore MitkAlgorithmsExt) IF(MITK_USE_OpenCL) add_definitions(-DPHOTOACOUSTICS_USE_GPU) set(dependencies_list ${dependencies_list} MitkOpenCL) message("Using OpenCL in PhotoacousticAlgorithms") ENDIF(MITK_USE_OpenCL) MITK_CREATE_MODULE( SUBPROJECTS DEPENDS ${dependencies_list} #AUTOLOAD_WITH MitkCore - INCLUDE_DIRS PUBLIC Algorithms/ITKUltrasound Algorithms Algorithms/OCL + INCLUDE_DIRS PUBLIC include INTERNAL_INCLUDE_DIRS ${INCLUDE_DIRS_INTERNAL} PACKAGE_DEPENDS ITK|ITKFFT+ITKImageCompose+ITKImageIntensity ) add_subdirectory(test) add_subdirectory(MitkPABeamformingTool) diff --git a/Modules/PhotoacousticsAlgorithms/files.cmake b/Modules/PhotoacousticsAlgorithms/files.cmake index 1cfe4eee02..0aeeaf0b4b 100644 --- a/Modules/PhotoacousticsAlgorithms/files.cmake +++ b/Modules/PhotoacousticsAlgorithms/files.cmake @@ -1,26 +1,29 @@ file(GLOB_RECURSE H_FILES RELATIVE "${CMAKE_CURRENT_SOURCE_DIR}" "${CMAKE_CURRENT_SOURCE_DIR}/include/*") set(CPP_FILES - source/mitkPhotoacousticFilterService.cpp - source/mitkPhotoacousticBeamformingFilter.cpp - source/mitkPhotoacousticBeamformingUtils.cpp + source/filters/mitkBeamformingFilter.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 c32bc1fcf0..25cbeb49e3 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 "mitkPhotoacousticBeamformingSettings.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) { 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; 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/OpenCLFilter/mitkPhotoacousticOCLDelayCalculation.h b/Modules/PhotoacousticsAlgorithms/include/OpenCLFilter/mitkPhotoacousticOCLDelayCalculation.h index e35cf5811b..3e60b4ec5c 100644 --- a/Modules/PhotoacousticsAlgorithms/include/OpenCLFilter/mitkPhotoacousticOCLDelayCalculation.h +++ b/Modules/PhotoacousticsAlgorithms/include/OpenCLFilter/mitkPhotoacousticOCLDelayCalculation.h @@ -1,89 +1,89 @@ /*=================================================================== 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 _MITKPHOTOACOUSTICSDELAYCALC_H_ #define _MITKPHOTOACOUSTICSDELAYCALC_H_ #if defined(PHOTOACOUSTICS_USE_GPU) || DOXYGEN #include "mitkOclDataSetToDataSetFilter.h" #include -#include "mitkPhotoacousticBeamformingSettings.h" +#include "mitkBeamformingSettings.h" namespace mitk { /*! * \brief Class implementing a mitk::OclDataSetToDataSetFilter to calculate the delays used for beamforming. * * The class must be given a configuration class instance of mitk::BeamformingSettings for beamforming parameters through mitk::OCLDelayCalculation::SetConfig(BeamformingSettings conf) * Additionally the output of an instance of mitk::OCLUsedLinesCalculation is needed to calculate the delays. */ class OCLDelayCalculation : public OclDataSetToDataSetFilter, public itk::Object { public: mitkClassMacroItkParent(OCLDelayCalculation, itk::Object); mitkNewMacro1Param(Self, mitk::BeamformingSettings::Pointer); void Update(); /** \brief Sets the usedLines buffer object to use for the calculation of the delays. * * @param usedLines An buffer generated as the output of an instance of mitk::OCLUsedLinesCalculation. */ void SetInputs(cl_mem usedLines) { m_UsedLines = usedLines; } protected: OCLDelayCalculation(mitk::BeamformingSettings::Pointer settings); virtual ~OCLDelayCalculation(); /** Initialize the filter */ bool Initialize(); void Execute(); mitk::PixelType GetOutputType() { return mitk::MakeScalarPixelType(); } int GetBytesPerElem() { return sizeof(unsigned short); } virtual us::Module* GetModule(); int m_sizeThis; private: /** The OpenCL kernel for the filter */ cl_kernel m_PixelCalculation; BeamformingSettings::Pointer m_Conf; cl_mem m_UsedLines; unsigned int m_BufferSize; float m_DelayMultiplicatorRaw; char m_IsPAImage; size_t m_ChunkSize[3]; }; } #endif #endif diff --git a/Modules/PhotoacousticsAlgorithms/include/OpenCLFilter/mitkPhotoacousticOCLUsedLinesCalculation.h b/Modules/PhotoacousticsAlgorithms/include/OpenCLFilter/mitkPhotoacousticOCLUsedLinesCalculation.h index bdc7dda056..4394764e23 100644 --- a/Modules/PhotoacousticsAlgorithms/include/OpenCLFilter/mitkPhotoacousticOCLUsedLinesCalculation.h +++ b/Modules/PhotoacousticsAlgorithms/include/OpenCLFilter/mitkPhotoacousticOCLUsedLinesCalculation.h @@ -1,79 +1,79 @@ /*=================================================================== 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 _MITKPHOTOACOUSTICSOCLUSEDLINESCALCULATION_H_ #define _MITKPHOTOACOUSTICSOCLUSEDLINESCALCULATION_H_ #if defined(PHOTOACOUSTICS_USE_GPU) || DOXYGEN #include "mitkOclDataSetToDataSetFilter.h" #include -#include "mitkPhotoacousticBeamformingSettings.h" +#include "mitkBeamformingSettings.h" namespace mitk { /*! * \brief Class implementing a mitk::OclDataSetToDataSetFilter to calculate which lines each sample should use when beamforming. * * The class must be given a configuration class instance of mitk::BeamformingSettings for beamforming parameters through mitk::OCLDelayCalculation::SetConfig(BeamformingSettings conf) */ class OCLUsedLinesCalculation : public OclDataSetToDataSetFilter, public itk::Object { public: mitkClassMacroItkParent(OCLUsedLinesCalculation, itk::Object); mitkNewMacro1Param(Self, mitk::BeamformingSettings::Pointer); void Update(); protected: /** Constructor */ OCLUsedLinesCalculation(mitk::BeamformingSettings::Pointer settings); /** Destructor */ virtual ~OCLUsedLinesCalculation(); /** Initialize the filter */ bool Initialize(); void Execute(); mitk::PixelType GetOutputType() { return mitk::MakeScalarPixelType(); } int GetBytesPerElem() { return sizeof(unsigned short); } virtual us::Module* GetModule(); int m_sizeThis; private: /** The OpenCL kernel for the filter */ cl_kernel m_PixelCalculation; BeamformingSettings::Pointer m_Conf; float m_part; size_t m_ChunkSize[3]; }; } #endif #endif diff --git a/Modules/PhotoacousticsAlgorithms/include/mitkPhotoacousticBeamformingFilter.h b/Modules/PhotoacousticsAlgorithms/include/mitkBeamformingFilter.h similarity index 97% rename from Modules/PhotoacousticsAlgorithms/include/mitkPhotoacousticBeamformingFilter.h rename to Modules/PhotoacousticsAlgorithms/include/mitkBeamformingFilter.h index 7f209ce7fa..667432fff1 100644 --- a/Modules/PhotoacousticsAlgorithms/include/mitkPhotoacousticBeamformingFilter.h +++ b/Modules/PhotoacousticsAlgorithms/include/mitkBeamformingFilter.h @@ -1,102 +1,102 @@ /*=================================================================== 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 "mitkPhotoacousticBeamformingSettings.h" -#include "mitkPhotoacousticBeamformingUtils.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/mitkPhotoacousticBeamformingSettings.h b/Modules/PhotoacousticsAlgorithms/include/mitkBeamformingSettings.h similarity index 87% rename from Modules/PhotoacousticsAlgorithms/include/mitkPhotoacousticBeamformingSettings.h rename to Modules/PhotoacousticsAlgorithms/include/mitkBeamformingSettings.h index 41dd1b5fc8..8028b9ca7c 100644 --- a/Modules/PhotoacousticsAlgorithms/include/mitkPhotoacousticBeamformingSettings.h +++ b/Modules/PhotoacousticsAlgorithms/include/mitkBeamformingSettings.h @@ -1,234 +1,253 @@ /*=================================================================== 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_SETTINGS -#define MITK_PHOTOACOUSTICS_BEAMFORMING_SETTINGS +#ifndef MITK_BEAMFORMING_SETTINGS +#define MITK_BEAMFORMING_SETTINGS #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 { public: mitkClassMacroItkParent(BeamformingSettings, itk::Object) 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 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(Pitch, float) - itkSetMacro(Pitch, float) + 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) { 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->GetPitch() - rhs->GetPitch()) < 0.000001f) && // 0.0001 mm error margin + (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() { } /** \brief Pitch of the used transducer in [m]. */ - float m_Pitch = 0.0003; + float m_PitchInMeters = 0.0003; /** \brief Speed of sound in the used medium in [m/s]. */ float m_SpeedOfSound = 1540; /** \brief The time spacing of the input image */ float m_TimeSpacing = 0.0000000000001; // [s] /** \brief The angle of the transducer elements */ float m_Angle = -1; /** \brief Flag whether processed image is a photoacoustic image or an ultrasound image */ bool m_IsPhotoacousticImage = true; /** \brief How many transducer elements the used transducer had. */ unsigned short m_TransducerElements = 128; /** \brief How many vertical samples should be used in the final image. */ unsigned int m_SamplesPerLine = 2048; /** \brief How many lines should be reconstructed in the final image. */ unsigned int m_ReconstructionLines = 128; /** \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; /** \brief Sets whether only the slices selected by mitk::BeamformingSettings::CropBounds should be beamformed. */ bool m_Partial = false; + /** \brief Sets the first and last slice to be beamformed. */ unsigned int* m_CropBounds; /** \brief Sets the dimensions of the inputImage. */ unsigned int* m_InputDim; /** \brief Decides whether GPU computing should be used */ bool m_UseGPU = false; /** \brief Sets how the delays for beamforming should be calculated. */ DelayCalc m_DelayCalculationMethod = QuadApprox; float* m_ApodizationFunction; /** \brief Sets the used apodization function. */ Apodization m_Apod = Hann; /** \brief Sets the resolution of the apodization array (must be greater than 0). */ int m_ApodizationArraySize = 128; /** \brief Sets the used beamforming algorithm. */ BeamformingAlgorithm m_Algorithm = DAS; /** \brief Sets whether after beamforming a bandpass should be automatically applied */ bool m_UseBP = false; /** \brief Sets the position at which lower frequencies are completely cut off in Hz. */ float m_BPHighPass = 50; /** \brief Sets the position at which higher frequencies are completely cut off in Hz. */ float m_BPLowPass = 50; }; } -#endif +#endif //MITK_BEAMFORMING_SETTINGS diff --git a/Modules/PhotoacousticsAlgorithms/include/mitkPhotoacousticBeamformingUtils.h b/Modules/PhotoacousticsAlgorithms/include/mitkBeamformingUtils.h similarity index 91% rename from Modules/PhotoacousticsAlgorithms/include/mitkPhotoacousticBeamformingUtils.h rename to Modules/PhotoacousticsAlgorithms/include/mitkBeamformingUtils.h index dccf214d63..ead7f821cf 100644 --- a/Modules/PhotoacousticsAlgorithms/include/mitkPhotoacousticBeamformingUtils.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_PHOTOACOUSTICS_BEAMFORMING_FILTER_UTILS -#define MITK_PHOTOACOUSTICS_BEAMFORMING_FILTER_UTILS +#ifndef MITK_BEAMFORMING_FILTER_UTILS +#define MITK_BEAMFORMING_FILTER_UTILS #include "mitkImageToImageFilter.h" #include #include "./OpenCLFilter/mitkPhotoacousticOCLBeamformingFilter.h" -#include "mitkPhotoacousticBeamformingSettings.h" +#include "mitkBeamformingSettings.h" namespace mitk { /*! * \brief Class implementing util functionality for beamforming on CPU * */ - class PhotoacousticBeamformingUtils final + 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); /** \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); /** \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); /** \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); /** \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); /** \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); /** \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: - PhotoacousticBeamformingUtils(); + BeamformingUtils(); - ~PhotoacousticBeamformingUtils(); + ~BeamformingUtils(); }; } // namespace mitk -#endif //MITK_PHOTOACOUSTICS_BEAMFORMING_FILTER_UTILS +#endif //MITK_BEAMFORMING_FILTER_UTILS diff --git a/Modules/PhotoacousticsAlgorithms/include/mitkCastToFloatImageFilter.h b/Modules/PhotoacousticsAlgorithms/include/mitkCastToFloatImageFilter.h new file mode 100644 index 0000000000..7c65d65825 --- /dev/null +++ b/Modules/PhotoacousticsAlgorithms/include/mitkCastToFloatImageFilter.h @@ -0,0 +1,44 @@ +/*=================================================================== + +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_CAST_TO_FLOAT_IMAGE_FILTER +#define MITK_CAST_TO_FLOAT_IMAGE_FILTER + +#include "mitkImageToImageFilter.h" + +namespace mitk { + /*! + * \brief Class implementing an mitk::ImageToImageFilter for casting any mitk image to a float image + */ + + class CastToFloatImageFilter : public ImageToImageFilter + { + public: + mitkClassMacro(CastToFloatImageFilter, ImageToImageFilter); + + itkFactorylessNewMacro(Self); + itkCloneMacro(Self); + + protected: + CastToFloatImageFilter(); + + ~CastToFloatImageFilter() override; + + void GenerateData() override; + }; +} // namespace mitk + +#endif //MITK_CAST_TO_FLOAT_IMAGE_FILTER diff --git a/Modules/PhotoacousticsAlgorithms/include/mitkCropImageFilter.h b/Modules/PhotoacousticsAlgorithms/include/mitkCropImageFilter.h new file mode 100644 index 0000000000..3b052dacb4 --- /dev/null +++ b/Modules/PhotoacousticsAlgorithms/include/mitkCropImageFilter.h @@ -0,0 +1,44 @@ +/*=================================================================== + +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_CROP_IMAGE_FILTER +#define MITK_CROP_IMAGE_FILTER + +#include "mitkImageToImageFilter.h" + +namespace mitk { + /*! + * \brief Class implementing an mitk::ImageToImageFilter for casting any mitk image to a float image + */ + + class CropImageFilter : public ImageToImageFilter + { + public: + mitkClassMacro(CropImageFilter, ImageToImageFilter); + + itkFactorylessNewMacro(Self); + itkCloneMacro(Self); + + protected: + CropImageFilter(); + + ~CropImageFilter() override; + + void GenerateData() override; + }; +} // namespace mitk + +#endif //MITK_CROP_IMAGE_FILTER diff --git a/Modules/PhotoacousticsAlgorithms/include/mitkImageSliceSelectionFilter.h b/Modules/PhotoacousticsAlgorithms/include/mitkImageSliceSelectionFilter.h new file mode 100644 index 0000000000..ac51c1176d --- /dev/null +++ b/Modules/PhotoacousticsAlgorithms/include/mitkImageSliceSelectionFilter.h @@ -0,0 +1,44 @@ +/*=================================================================== + +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_IMAGE_SLICE_SELECTION_FILTER +#define MITK_IMAGE_SLICE_SELECTION_FILTER + +#include "mitkImageToImageFilter.h" + +namespace mitk { + /*! + * \brief Class implementing an mitk::ImageToImageFilter for casting any mitk image to a float image + */ + + class ImageSliceSelectionFilter : public ImageToImageFilter + { + public: + mitkClassMacro(ImageSliceSelectionFilter, ImageToImageFilter); + + itkFactorylessNewMacro(Self); + itkCloneMacro(Self); + + protected: + ImageSliceSelectionFilter(); + + ~ImageSliceSelectionFilter() override; + + void GenerateData() override; + }; +} // namespace mitk + +#endif //MITK_IMAGE_SLICE_SELECTION_FILTER diff --git a/Modules/PhotoacousticsAlgorithms/include/mitkPhotoacousticFilterService.h b/Modules/PhotoacousticsAlgorithms/include/mitkPhotoacousticFilterService.h index dcf6f5fa90..26bed5e04f 100644 --- a/Modules/PhotoacousticsAlgorithms/include/mitkPhotoacousticFilterService.h +++ b/Modules/PhotoacousticsAlgorithms/include/mitkPhotoacousticFilterService.h @@ -1,126 +1,132 @@ /*=================================================================== 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 "mitkPhotoacousticBeamformingSettings.h" -#include "mitkPhotoacousticBeamformingFilter.h" +#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) {}); /** \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 alpha The 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 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 alpha); + 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 alpha); + 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/include/mitkPhotoacousticImage.h b/Modules/PhotoacousticsAlgorithms/include/mitkPhotoacousticImage.h deleted file mode 100644 index 404c814412..0000000000 --- a/Modules/PhotoacousticsAlgorithms/include/mitkPhotoacousticImage.h +++ /dev/null @@ -1,129 +0,0 @@ -/*=================================================================== - -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 mitkPhotoacousticImage_H_HEADER_INCLUDED -#define mitkPhotoacousticImage_H_HEADER_INCLUDED - -#include "itkObject.h" -#include "mitkCommon.h" -#include "mitkImage.h" -#include - -#include "mitkPhotoacousticBeamformingSettings.h" -#include "mitkPhotoacousticBeamformingFilter.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 PhotoacousticImage : public itk::Object - { - public: - mitkClassMacroItkParent(mitk::PhotoacousticImage, 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 config, std::string& message, 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 alpha The 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. - * @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: - PhotoacousticImage(); - ~PhotoacousticImage() 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 /* mitkPhotoacousticImage_H_HEADER_INCLUDED */ diff --git a/Modules/PhotoacousticsAlgorithms/source/OpenCLFilter/mitkPhotoacousticOCLDelayCalculation.cpp b/Modules/PhotoacousticsAlgorithms/source/OpenCLFilter/mitkPhotoacousticOCLDelayCalculation.cpp index 118982ee3b..ec7f6138e3 100644 --- a/Modules/PhotoacousticsAlgorithms/source/OpenCLFilter/mitkPhotoacousticOCLDelayCalculation.cpp +++ b/Modules/PhotoacousticsAlgorithms/source/OpenCLFilter/mitkPhotoacousticOCLDelayCalculation.cpp @@ -1,131 +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. ===================================================================*/ #define _USE_MATH_DEFINES #include #include "./OpenCLFilter/mitkPhotoacousticOCLDelayCalculation.h" #include "usServiceReference.h" #include "mitkImageReadAccessor.h" mitk::OCLDelayCalculation::OCLDelayCalculation(mitk::BeamformingSettings::Pointer settings) : m_PixelCalculation(NULL), m_Conf(settings) { this->AddSourceFile("DelayCalculation.cl"); this->m_FilterID = "DelayCalculation"; m_ChunkSize[0] = 128; m_ChunkSize[1] = 128; m_ChunkSize[2] = 8; this->Initialize(); } mitk::OCLDelayCalculation::~OCLDelayCalculation() { if (this->m_PixelCalculation) { clReleaseKernel(m_PixelCalculation); } } void mitk::OCLDelayCalculation::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::OCLDelayCalculation::Execute() { cl_int clErr = 0; unsigned int gridDim[3] = { m_Conf->GetReconstructionLines() / 2, m_Conf->GetSamplesPerLine(), 1 }; m_BufferSize = gridDim[0] * gridDim[1] * 1; try { this->InitExecNoInput(this->m_PixelCalculation, gridDim, m_BufferSize, sizeof(unsigned short)); } catch (const mitk::Exception& e) { MITK_ERROR << "Caught exception while initializing Delay Calculation filter: " << e.what(); return; } // This calculation is the same for all kernels, so for performance reasons simply perform it here instead of within the kernels if (m_Conf->GetDelayCalculationMethod() == BeamformingSettings::DelayCalc::QuadApprox) m_DelayMultiplicatorRaw = pow(1 / (m_Conf->GetTimeSpacing()*m_Conf->GetSpeedOfSound()) * - m_Conf->GetPitch() * (float)m_Conf->GetTransducerElements() / (float)m_Conf->GetInputDim()[0], 2) / 2; + m_Conf->GetPitchInMeters() * (float)m_Conf->GetTransducerElements() / (float)m_Conf->GetInputDim()[0], 2) / 2; else if (m_Conf->GetDelayCalculationMethod() == BeamformingSettings::DelayCalc::Spherical) m_DelayMultiplicatorRaw = 1 / (m_Conf->GetTimeSpacing()*m_Conf->GetSpeedOfSound()) * - (m_Conf->GetPitch()*(float)m_Conf->GetTransducerElements()); + (m_Conf->GetPitchInMeters()*(float)m_Conf->GetTransducerElements()); // as openCL does not support bool as a kernel argument, we need to buffer this value in a char... m_IsPAImage = m_Conf->GetIsPhotoacousticImage(); unsigned int reconstructionLines = this->m_Conf->GetReconstructionLines(); unsigned int samplesperLine = this->m_Conf->GetSamplesPerLine(); clErr = clSetKernelArg(this->m_PixelCalculation, 1, sizeof(cl_mem), &(this->m_UsedLines)); clErr |= clSetKernelArg(this->m_PixelCalculation, 2, sizeof(cl_uint), &(this->m_Conf->GetInputDim()[0])); clErr |= clSetKernelArg(this->m_PixelCalculation, 3, sizeof(cl_uint), &(this->m_Conf->GetInputDim()[1])); clErr |= clSetKernelArg(this->m_PixelCalculation, 4, sizeof(cl_uint), &(reconstructionLines)); clErr |= clSetKernelArg(this->m_PixelCalculation, 5, sizeof(cl_uint), &(samplesperLine)); clErr |= clSetKernelArg(this->m_PixelCalculation, 6, sizeof(cl_char), &(this->m_IsPAImage)); clErr |= clSetKernelArg(this->m_PixelCalculation, 7, sizeof(cl_float), &(this->m_DelayMultiplicatorRaw)); CHECK_OCL_ERR(clErr); // execute the filter on a 3D NDRange if (!this->ExecuteKernelChunksInBatches(m_PixelCalculation, 2, m_ChunkSize, 16, 50)) mitkThrow() << "openCL Error when executing Kernel"; // signalize the GPU-side data changed m_Output->Modified(GPU_DATA); } us::Module *mitk::OCLDelayCalculation::GetModule() { return us::GetModuleContext()->GetModule(); } bool mitk::OCLDelayCalculation::Initialize() { bool buildErr = true; cl_int clErr = 0; if (OclFilter::Initialize()) { if (m_Conf->GetDelayCalculationMethod() == BeamformingSettings::DelayCalc::QuadApprox) this->m_PixelCalculation = clCreateKernel(this->m_ClProgram, "ckDelayCalculationQuad", &clErr); if (m_Conf->GetDelayCalculationMethod() == BeamformingSettings::DelayCalc::Spherical) this->m_PixelCalculation = clCreateKernel(this->m_ClProgram, "ckDelayCalculationSphe", &clErr); buildErr |= CHECK_OCL_ERR(clErr); } return (OclFilter::IsInitialized() && buildErr); } diff --git a/Modules/PhotoacousticsAlgorithms/source/OpenCLFilter/mitkPhotoacousticOCLUsedLinesCalculation.cpp b/Modules/PhotoacousticsAlgorithms/source/OpenCLFilter/mitkPhotoacousticOCLUsedLinesCalculation.cpp index a8be7b3aa3..eca19ab074 100644 --- a/Modules/PhotoacousticsAlgorithms/source/OpenCLFilter/mitkPhotoacousticOCLUsedLinesCalculation.cpp +++ b/Modules/PhotoacousticsAlgorithms/source/OpenCLFilter/mitkPhotoacousticOCLUsedLinesCalculation.cpp @@ -1,120 +1,120 @@ /*=================================================================== 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/mitkPhotoacousticOCLUsedLinesCalculation.h" #include "usServiceReference.h" #include "mitkImageReadAccessor.h" mitk::OCLUsedLinesCalculation::OCLUsedLinesCalculation(mitk::BeamformingSettings::Pointer settings) : m_PixelCalculation(NULL), m_Conf(settings) { this->AddSourceFile("UsedLinesCalculation.cl"); this->m_FilterID = "UsedLinesCalculation"; m_ChunkSize[0] = 128; m_ChunkSize[1] = 128; m_ChunkSize[2] = 8; this->Initialize(); } mitk::OCLUsedLinesCalculation::~OCLUsedLinesCalculation() { if (this->m_PixelCalculation) { clReleaseKernel(m_PixelCalculation); } } void mitk::OCLUsedLinesCalculation::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::OCLUsedLinesCalculation::Execute() { cl_int clErr = 0; unsigned int gridDim[3] = { m_Conf->GetReconstructionLines(), m_Conf->GetSamplesPerLine(), 1 }; size_t outputSize = gridDim[0] * gridDim[1] * 3; try { this->InitExecNoInput(this->m_PixelCalculation, gridDim, outputSize, sizeof(unsigned short)); } catch (const mitk::Exception& e) { MITK_ERROR << "Caught exception while initializing UsedLines filter: " << e.what(); return; } // This calculation is the same for all kernels, so for performance reasons simply perform it here instead of within the kernels m_part = (tan(m_Conf->GetAngle() / 360 * 2 * itk::Math::pi) * ((m_Conf->GetSpeedOfSound() * m_Conf->GetTimeSpacing())) / - (m_Conf->GetPitch() * m_Conf->GetTransducerElements())) * m_Conf->GetInputDim()[0]; + (m_Conf->GetPitchInMeters() * m_Conf->GetTransducerElements())) * m_Conf->GetInputDim()[0]; unsigned int reconLines = this->m_Conf->GetReconstructionLines(); unsigned int samplesPerLine = this->m_Conf->GetSamplesPerLine(); clErr = clSetKernelArg(this->m_PixelCalculation, 1, sizeof(cl_float), &(this->m_part)); clErr |= clSetKernelArg(this->m_PixelCalculation, 2, sizeof(cl_uint), &(this->m_Conf->GetInputDim()[0])); clErr |= clSetKernelArg(this->m_PixelCalculation, 3, sizeof(cl_uint), &(this->m_Conf->GetInputDim()[1])); clErr |= clSetKernelArg(this->m_PixelCalculation, 4, sizeof(cl_uint), &(reconLines)); clErr |= clSetKernelArg(this->m_PixelCalculation, 5, sizeof(cl_uint), &(samplesPerLine)); CHECK_OCL_ERR(clErr); // execute the filter on a 2D NDRange if (!this->ExecuteKernelChunksInBatches(m_PixelCalculation, 2, m_ChunkSize, 16, 50)) mitkThrow() << "openCL Error when executing Kernel"; // signalize the GPU-side data changed m_Output->Modified(GPU_DATA); } us::Module *mitk::OCLUsedLinesCalculation::GetModule() { return us::GetModuleContext()->GetModule(); } bool mitk::OCLUsedLinesCalculation::Initialize() { bool buildErr = true; cl_int clErr = 0; if (OclFilter::Initialize()) { this->m_PixelCalculation = clCreateKernel(this->m_ClProgram, "ckUsedLines", &clErr); buildErr |= CHECK_OCL_ERR(clErr); } return (OclFilter::IsInitialized() && buildErr); } #endif diff --git a/Modules/PhotoacousticsAlgorithms/source/mitkPhotoacousticBeamformingFilter.cpp b/Modules/PhotoacousticsAlgorithms/source/filters/mitkBeamformingFilter.cpp similarity index 84% rename from Modules/PhotoacousticsAlgorithms/source/mitkPhotoacousticBeamformingFilter.cpp rename to Modules/PhotoacousticsAlgorithms/source/filters/mitkBeamformingFilter.cpp index 145acd50d0..cd63d9df49 100644 --- a/Modules/PhotoacousticsAlgorithms/source/mitkPhotoacousticBeamformingFilter.cpp +++ b/Modules/PhotoacousticsAlgorithms/source/filters/mitkBeamformingFilter.cpp @@ -1,329 +1,305 @@ /*=================================================================== 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 "mitkPhotoacousticBeamformingFilter.h" -#include "mitkPhotoacousticBeamformingUtils.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); - switch (m_Conf->GetApod()) - { - case BeamformingSettings::Apodization::Hann: - m_Conf->SetApodizationFunction(mitk::PhotoacousticBeamformingUtils::VonHannFunction(m_Conf->GetApodizationArraySize())); - break; - case BeamformingSettings::Apodization::Hamm: - m_Conf->SetApodizationFunction(mitk::PhotoacousticBeamformingUtils::HammFunction(m_Conf->GetApodizationArraySize())); - break; - case BeamformingSettings::Apodization::Box: - m_Conf->SetApodizationFunction(mitk::PhotoacousticBeamformingUtils::BoxFunction(m_Conf->GetApodizationArraySize())); - break; - default: - m_Conf->SetApodizationFunction(mitk::PhotoacousticBeamformingUtils::BoxFunction(m_Conf->GetApodizationArraySize())); - break; - } - 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(); - //GenerateTimeInInputRegion(output, input); } 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; - itkDebugMacro(<< "GenerateOutputInformation()"); - 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->GetPitch() * m_Conf->GetTransducerElements() * 1000 / m_Conf->GetReconstructionLines(); + 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() { - GenerateOutputInformation(); mitk::Image::Pointer input = this->GetInput(); + if (!(input->GetPixelType().GetTypeAsString() == "scalar (float)" || input->GetPixelType().GetTypeAsString() == " (float)")) + { + 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)); - - // first, we check whether the dara is float, other formats are unsupported - if (input->GetPixelType().GetTypeAsString() == "scalar (float)" || input->GetPixelType().GetTypeAsString() == " (float)") - { - m_InputData = (float*)inputReadAccessor.GetData(); - } - else - { - MITK_INFO << "Pixel type is not float, abort"; - return; - } + 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(&PhotoacousticBeamformingUtils::DASQuadraticLine, m_InputData, + threads[line] = std::thread(&BeamformingUtils::DASQuadraticLine, m_InputData, m_OutputData, inputDim, outputDim, line, m_Conf->GetApodizationFunction(), m_Conf->GetApodizationArraySize(), m_Conf); } } else if (m_Conf->GetDelayCalculationMethod() == BeamformingSettings::DelayCalc::Spherical) { for (short line = 0; line < outputDim[0]; ++line) { - threads[line] = std::thread(&PhotoacousticBeamformingUtils::DASSphericalLine, m_InputData, + threads[line] = std::thread(&BeamformingUtils::DASSphericalLine, m_InputData, m_OutputData, inputDim, outputDim, line, m_Conf->GetApodizationFunction(), m_Conf->GetApodizationArraySize(), 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(&PhotoacousticBeamformingUtils::DMASQuadraticLine, m_InputData, + threads[line] = std::thread(&BeamformingUtils::DMASQuadraticLine, m_InputData, m_OutputData, inputDim, outputDim, line, m_Conf->GetApodizationFunction(), m_Conf->GetApodizationArraySize(), m_Conf); } } else if (m_Conf->GetDelayCalculationMethod() == BeamformingSettings::DelayCalc::Spherical) { for (short line = 0; line < outputDim[0]; ++line) { - threads[line] = std::thread(&PhotoacousticBeamformingUtils::DMASSphericalLine, m_InputData, + threads[line] = std::thread(&BeamformingUtils::DMASSphericalLine, m_InputData, m_OutputData, inputDim, outputDim, line, m_Conf->GetApodizationFunction(), m_Conf->GetApodizationArraySize(), 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(&PhotoacousticBeamformingUtils::sDMASQuadraticLine, m_InputData, + threads[line] = std::thread(&BeamformingUtils::sDMASQuadraticLine, m_InputData, m_OutputData, inputDim, outputDim, line, m_Conf->GetApodizationFunction(), m_Conf->GetApodizationArraySize(), m_Conf); } } else if (m_Conf->GetDelayCalculationMethod() == BeamformingSettings::DelayCalc::Spherical) { for (short line = 0; line < outputDim[0]; ++line) { - threads[line] = std::thread(&PhotoacousticBeamformingUtils::sDMASSphericalLine, m_InputData, + threads[line] = std::thread(&BeamformingUtils::sDMASSphericalLine, m_InputData, m_OutputData, inputDim, outputDim, line, m_Conf->GetApodizationFunction(), m_Conf->GetApodizationArraySize(), 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(); if (i == batches - 1 && (input->GetDimension(2) % batchSize > 0)) { inputBatch->Initialize(mitk::MakeScalarPixelType(), 3, batchDimLast); m_Conf->GetInputDim()[2] = batchDimLast[2]; } else { inputBatch->Initialize(mitk::MakeScalarPixelType(), 3, batchDim); m_Conf->GetInputDim()[2] = 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) { 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."; } } #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/mitkCastToFloatImageFilter.cpp b/Modules/PhotoacousticsAlgorithms/source/filters/mitkCastToFloatImageFilter.cpp new file mode 100644 index 0000000000..11612f35a9 --- /dev/null +++ b/Modules/PhotoacousticsAlgorithms/source/filters/mitkCastToFloatImageFilter.cpp @@ -0,0 +1,34 @@ +/*=================================================================== +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" + +mitk::CastToFloatImageFilter::CastToFloatImageFilter() +{ + MITK_INFO << "Instantiating CastToFloatImageFilter..."; + SetNumberOfIndexedInputs(1); + SetNumberOfIndexedOutputs(1); + MITK_INFO << "Instantiating CastToFloatImageFilter...[Done]"; +} + +mitk::CastToFloatImageFilter::~CastToFloatImageFilter() +{ + MITK_INFO << "Destructed CastToFloatImageFilter."; +} + +void mitk::CastToFloatImageFilter::GenerateData() +{ +} diff --git a/Modules/PhotoacousticsAlgorithms/source/filters/mitkCropImageFilter.cpp b/Modules/PhotoacousticsAlgorithms/source/filters/mitkCropImageFilter.cpp new file mode 100644 index 0000000000..0e46c8d494 --- /dev/null +++ b/Modules/PhotoacousticsAlgorithms/source/filters/mitkCropImageFilter.cpp @@ -0,0 +1,34 @@ +/*=================================================================== +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" + +mitk::CropImageFilter::CropImageFilter() +{ + MITK_INFO << "Instantiating CropImageFilter..."; + SetNumberOfIndexedInputs(1); + SetNumberOfIndexedOutputs(1); + MITK_INFO << "Instantiating CropImageFilter...[Done]"; +} + +mitk::CropImageFilter::~CropImageFilter() +{ + MITK_INFO << "Destructed CastToFloatImageFilter."; +} + +void mitk::CropImageFilter::GenerateData() +{ +} diff --git a/Modules/PhotoacousticsAlgorithms/source/filters/mitkImageSliceSelectionFilter.cpp b/Modules/PhotoacousticsAlgorithms/source/filters/mitkImageSliceSelectionFilter.cpp new file mode 100644 index 0000000000..b90b5a726e --- /dev/null +++ b/Modules/PhotoacousticsAlgorithms/source/filters/mitkImageSliceSelectionFilter.cpp @@ -0,0 +1,34 @@ +/*=================================================================== +mitkImageSliceSelectionFilter +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 "mitkImageSliceSelectionFilter.h" + +mitk::ImageSliceSelectionFilter::ImageSliceSelectionFilter() +{ + MITK_INFO << "Instantiating CropImageFilter..."; + SetNumberOfIndexedInputs(1); + SetNumberOfIndexedOutputs(1); + MITK_INFO << "Instantiating CropImageFilter...[Done]"; +} + +mitk::ImageSliceSelectionFilter::~ImageSliceSelectionFilter() +{ + MITK_INFO << "Destructed CastToFloatImageFilter."; +} + +void mitk::ImageSliceSelectionFilter::GenerateData() +{ +} diff --git a/Modules/PhotoacousticsAlgorithms/source/mitkphotoacousticbeamformingfilterutils.cpp b/Modules/PhotoacousticsAlgorithms/source/mitkphotoacousticbeamformingfilterutils.cpp deleted file mode 100644 index b447706ece..0000000000 --- a/Modules/PhotoacousticsAlgorithms/source/mitkphotoacousticbeamformingfilterutils.cpp +++ /dev/null @@ -1,468 +0,0 @@ -/*=================================================================== -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 "mitkPhotoacousticBeamformingUtils.h" - -mitk::PhotoacousticBeamformingUtils::PhotoacousticBeamformingUtils() -{ -} - -mitk::PhotoacousticBeamformingUtils::~PhotoacousticBeamformingUtils() -{ -} - -void mitk::PhotoacousticBeamformingUtils::DASQuadraticLine(float* input, float* output, float inputDim[2], float outputDim[2], const short& line, float* apodisation, const short& apodArraySize) -{ - 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 = 0.07 * inputL; - float tan_phi = std::tan(m_Conf.Angle / 360 * 2 * itk::Math::pi); - float part_multiplicator = tan_phi * m_Conf.TimeSpacing * m_Conf.SpeedOfSound / m_Conf.Pitch * inputL / m_Conf.TransducerElements; - 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 / (m_Conf.TimeSpacing*m_Conf.SpeedOfSound) * (m_Conf.Pitch*m_Conf.TransducerElements) / 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 - m_Conf.isPhotoacousticImage)*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::PhotoacousticBeamformingUtils::DASSphericalLine(float* input, float* output, float inputDim[2], float outputDim[2], const short& line, float* apodisation, const short& apodArraySize) -{ - 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(m_Conf.Angle / 360 * 2 * itk::Math::pi); - float part_multiplicator = tan_phi * m_Conf.TimeSpacing * m_Conf.SpeedOfSound / m_Conf.Pitch * inputL / (float)m_Conf.TransducerElements; - 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 / (m_Conf.TimeSpacing*m_Conf.SpeedOfSound) * (((float)l_s - l_i)*m_Conf.Pitch*(float)m_Conf.TransducerElements) / inputL), 2) - ) + (1 - m_Conf.isPhotoacousticImage)*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::PhotoacousticBeamformingUtils::DMASQuadraticLine(float* input, float* output, float inputDim[2], float outputDim[2], const short& line, float* apodisation, const short& apodArraySize) -{ - 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(m_Conf.Angle / 360 * 2 * itk::Math::pi); - float part_multiplicator = tan_phi * m_Conf.TimeSpacing * m_Conf.SpeedOfSound / m_Conf.Pitch * inputL / (float)m_Conf.TransducerElements; - 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 / (m_Conf.TimeSpacing*m_Conf.SpeedOfSound) * (m_Conf.Pitch*m_Conf.TransducerElements) / 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 - m_Conf.isPhotoacousticImage)*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::PhotoacousticBeamformingUtils::DMASSphericalLine(float* input, float* output, float inputDim[2], float outputDim[2], const short& line, float* apodisation, const short& apodArraySize) -{ - 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(m_Conf.Angle / 360 * 2 * itk::Math::pi); - float part_multiplicator = tan_phi * m_Conf.TimeSpacing * m_Conf.SpeedOfSound / m_Conf.Pitch * inputL / (float)m_Conf.TransducerElements; - 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 / (m_Conf.TimeSpacing*m_Conf.SpeedOfSound) * (((float)minLine + (float)l_s - l_i)*m_Conf.Pitch*(float)m_Conf.TransducerElements) / inputL), 2) - ) + (1 - m_Conf.isPhotoacousticImage)*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::PhotoacousticBeamformingUtils::sDMASQuadraticLine(float* input, float* output, float inputDim[2], float outputDim[2], const short& line, float* apodisation, const short& apodArraySize) -{ - 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(m_Conf.Angle / 360 * 2 * itk::Math::pi); - float part_multiplicator = tan_phi * m_Conf.TimeSpacing * m_Conf.SpeedOfSound / m_Conf.Pitch * inputL / (float)m_Conf.TransducerElements; - 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 / (m_Conf.TimeSpacing*m_Conf.SpeedOfSound) * (m_Conf.Pitch*m_Conf.TransducerElements) / 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 - m_Conf.isPhotoacousticImage)*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::PhotoacousticBeamformingUtils::sDMASSphericalLine(float* input, float* output, float inputDim[2], float outputDim[2], const short& line, float* apodisation, const short& apodArraySize) -{ - 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(m_Conf.Angle / 360 * 2 * itk::Math::pi); - float part_multiplicator = tan_phi * m_Conf.TimeSpacing * m_Conf.SpeedOfSound / m_Conf.Pitch * inputL / (float)m_Conf.TransducerElements; - 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 / (m_Conf.TimeSpacing*m_Conf.SpeedOfSound) * (((float)minLine + (float)l_s - l_i)*m_Conf.Pitch*(float)m_Conf.TransducerElements) / inputL), 2) - ) + (1 - m_Conf.isPhotoacousticImage)*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/mitkPhotoacousticBeamformingUtils.cpp b/Modules/PhotoacousticsAlgorithms/source/utils/mitkBeamformingUtils.cpp similarity index 88% rename from Modules/PhotoacousticsAlgorithms/source/mitkPhotoacousticBeamformingUtils.cpp rename to Modules/PhotoacousticsAlgorithms/source/utils/mitkBeamformingUtils.cpp index 72d882ff53..76ae7a34b5 100644 --- a/Modules/PhotoacousticsAlgorithms/source/mitkPhotoacousticBeamformingUtils.cpp +++ b/Modules/PhotoacousticsAlgorithms/source/utils/mitkBeamformingUtils.cpp @@ -1,537 +1,537 @@ /*=================================================================== 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 "mitkPhotoacousticBeamformingUtils.h" +#include "mitkBeamformingUtils.h" -mitk::PhotoacousticBeamformingUtils::PhotoacousticBeamformingUtils() +mitk::BeamformingUtils::BeamformingUtils() { } -mitk::PhotoacousticBeamformingUtils::~PhotoacousticBeamformingUtils() +mitk::BeamformingUtils::~BeamformingUtils() { } -float* mitk::PhotoacousticBeamformingUtils::VonHannFunction(int samples) +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::PhotoacousticBeamformingUtils::HammFunction(int samples) +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::PhotoacousticBeamformingUtils::BoxFunction(int samples) +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::PhotoacousticBeamformingUtils::DASQuadraticLine( +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) { 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->GetPitch() * inputL / config->GetTransducerElements(); + 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->GetPitch()*config->GetTransducerElements()) / inputL), 2) / s_i / 2; + (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::PhotoacousticBeamformingUtils::DASSphericalLine( +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) { 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->GetPitch() * inputL / (float)config->GetTransducerElements(); + 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->GetPitch()*(float)config->GetTransducerElements()) / inputL), 2) + (((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::PhotoacousticBeamformingUtils::DMASQuadraticLine( +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) { 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->GetPitch() * inputL / (float)config->GetTransducerElements(); + 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->GetPitch()*config->GetTransducerElements()) / inputL), 2) / s_i / 2; + (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::PhotoacousticBeamformingUtils::DMASSphericalLine( +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) { 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->GetPitch() * inputL / (float)config->GetTransducerElements(); + 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->GetPitch()*(float)config->GetTransducerElements()) / inputL), 2) + (((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::PhotoacousticBeamformingUtils::sDMASQuadraticLine( +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) { 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->GetPitch() * inputL / (float)config->GetTransducerElements(); + 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->GetPitch()*config->GetTransducerElements()) / inputL), 2) / s_i / 2; + (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::PhotoacousticBeamformingUtils::sDMASSphericalLine( +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) { 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->GetPitch() * inputL / (float)config->GetTransducerElements(); + 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->GetPitch()*(float)config->GetTransducerElements()) / inputL), 2) + (((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/mitkPhotoacousticFilterService.cpp b/Modules/PhotoacousticsAlgorithms/source/utils/mitkPhotoacousticFilterService.cpp similarity index 96% rename from Modules/PhotoacousticsAlgorithms/source/mitkPhotoacousticFilterService.cpp rename to Modules/PhotoacousticsAlgorithms/source/utils/mitkPhotoacousticFilterService.cpp index 4e11f43d2d..652c2aedb6 100644 --- a/Modules/PhotoacousticsAlgorithms/source/mitkPhotoacousticFilterService.cpp +++ b/Modules/PhotoacousticsAlgorithms/source/utils/mitkPhotoacousticFilterService.cpp @@ -1,502 +1,502 @@ /*=================================================================== 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 "mitkPhotoacousticBeamformingFilter.h" +#include "mitkBeamformingFilter.h" #include #include #include #include "./OpenCLFilter/mitkPhotoacousticBModeFilter.h" #include "mitkConvert2Dto3DImageFilter.h" // 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, inputImage->GetDimension(2) - 1); 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 minSlice, int maxSlice) { unsigned int inputDim[3] = { inputImage->GetDimension(0), inputImage->GetDimension(1), inputImage->GetDimension(2) }; unsigned int outputDim[3] = { inputImage->GetDimension(0) - left - right, inputImage->GetDimension(1) - (unsigned int)above - (unsigned int)below, (unsigned int)maxSlice - (unsigned int)minSlice + 1 }; void* inputData; float* outputData = new float[outputDim[0] * outputDim[1] * outputDim[2]]; ImageReadAccessor acc(inputImage); inputData = const_cast(acc.GetData()); // convert the data to float by default // as of now only float, short, double are used at all. if (inputImage->GetPixelType().GetTypeAsString() == "scalar (float)" || inputImage->GetPixelType().GetTypeAsString() == " (float)") { // copy the data into the cropped image for (unsigned short sl = 0; sl < outputDim[2]; ++sl) { for (unsigned short l = 0; l < outputDim[0]; ++l) { for (unsigned short s = 0; s < outputDim[1]; ++s) { outputData[l + s*(unsigned short)outputDim[0] + sl*outputDim[0] * outputDim[1]] = (float)((float*)inputData)[(l + left) + (s + above)*(unsigned short)inputDim[0] + (sl + minSlice)*inputDim[0] * inputDim[1]]; } } } } else if (inputImage->GetPixelType().GetTypeAsString() == "scalar (short)" || inputImage->GetPixelType().GetTypeAsString() == " (short)") { // copy the data to the cropped image for (unsigned short sl = 0; sl < outputDim[2]; ++sl) { for (unsigned short l = 0; l < outputDim[0]; ++l) { for (unsigned short s = 0; s < outputDim[1]; ++s) { outputData[l + s*(unsigned short)outputDim[0] + sl*outputDim[0] * outputDim[1]] = (float)((short*)inputData)[(l + left) + (s + above)*(unsigned short)inputDim[0] + (sl + minSlice)*inputDim[0] * inputDim[1]]; } } } } else if (inputImage->GetPixelType().GetTypeAsString() == "scalar (double)" || inputImage->GetPixelType().GetTypeAsString() == " (double)") { // copy the data to the cropped image for (unsigned short sl = 0; sl < outputDim[2]; ++sl) { for (unsigned short l = 0; l < outputDim[0]; ++l) { for (unsigned short s = 0; s < outputDim[1]; ++s) { outputData[l + s*(unsigned short)outputDim[0] + sl*outputDim[0] * outputDim[1]] = (float)((double*)inputData)[(l + left) + (s + above)*(unsigned short)inputDim[0] + (sl + minSlice)*inputDim[0] * inputDim[1]]; } } } } else { MITK_INFO << "Could not determine pixel type"; } mitk::Image::Pointer output = mitk::Image::New(); output->Initialize(mitk::MakeScalarPixelType(), 3, outputDim); output->SetSpacing(inputImage->GetGeometry()->GetSpacing()); output->SetImportVolume(outputData, 0, 0, mitk::Image::CopyMemory); delete[] outputData; return output; } mitk::Image::Pointer mitk::PhotoacousticFilterService::ApplyBeamforming(mitk::Image::Pointer inputImage, BeamformingSettings::Pointer config, std::string& message, 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->SetRecordTime(config->GetRecordTime() - (float)(config->GetUpperCutoff()) / // (float)inputImage->GetDimension(1) * config->GetRecordTime()); // adjust the recorded time lost by cropping //progressHandle(0, "converting image"); //if (!config->GetPartial()) //{ // config->GetCropBounds()[0] = 0; // config->GetCropBounds()[1] = inputImage->GetDimension(2) - 1; //} //processedImage = ApplyCropping(inputImage, config->GetUpperCutoff(), 0, 0, 0, config->GetCropBounds()[0], config->GetCropBounds()[1]); config->GetInputDim()[0] = processedImage->GetDimension(0); config->GetInputDim()[1] = processedImage->GetDimension(1); config->GetInputDim()[2] = processedImage->GetDimension(2); // 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) + 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) + 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; + (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; + (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/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/src/internal/PAImageProcessing.cpp b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/src/internal/PAImageProcessing.cpp index de9bd6c176..7e413d3e5a 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 +1,1160 @@ /*=================================================================== 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 "mitkPhotoacousticBeamformingFilter.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); 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, image->GetDimension(2) - 1); 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()); + 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->SetPitch(m_Controls.Pitch->value() / 1000); // [m] + 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::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, m_CutSliceFirst, m_CutSliceLast); 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; } diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/src/internal/PAImageProcessing.h b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/src/internal/PAImageProcessing.h index be16b6df22..029b34a0b5 100644 --- a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/src/internal/PAImageProcessing.h +++ b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/src/internal/PAImageProcessing.h @@ -1,252 +1,252 @@ /*=================================================================== 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 PAImageProcessing_h #define PAImageProcessing_h #include #include #include #include #include "ui_PAImageProcessingControls.h" -#include "mitkPhotoacousticBeamformingFilter.h" -#include "mitkPhotoacousticBeamformingSettings.h" +#include "mitkBeamformingFilter.h" +#include "mitkBeamformingSettings.h" Q_DECLARE_METATYPE(mitk::Image::Pointer) Q_DECLARE_METATYPE(std::string) /*! * \brief Plugin implementing an interface for the Photoacoustic Algorithms Module * * Beamforming, Image processing as B-Mode filtering, cropping, resampling, as well as batch processing can be performed using this plugin. */ class PAImageProcessing : public QmitkAbstractView { // this is needed for all Qt objects that should have a Qt meta-object // (everything that derives from QObject and wants to have signal/slots) Q_OBJECT public: static const std::string VIEW_ID; PAImageProcessing(); protected slots: void UpperSliceBoundChanged(); void LowerSliceBoundChanged(); void SliceBoundsEnabled(); void UseResampling(); void UseLogfilter(); void SetResampling(); void UseImageSpacing(); void UpdateImageInfo(); /** \brief Method called when the beamforming thread finishes; * it adds the image to a new data node and registers it to the worbench's data storage */ void HandleBeamformingResults(mitk::Image::Pointer image); /** \brief Beamforming is being performed in a separate thread to keep the workbench from freezing. */ void StartBeamformingThread(); /** \brief Method called when the B-mode filter thread finishes; * it adds the image to a new data node and registers it to the worbench's data storage */ void HandleBmodeResults(mitk::Image::Pointer image); /** \brief B-mode filtering is being performed in a separate thread to keep the workbench from freezing. */ void StartBmodeThread(); /** \brief Method called when the Cropping thread finishes; * it adds the image to a new data node and registers it to the worbench's data storage */ void HandleCropResults(mitk::Image::Pointer image); /** \brief Cropping is being performed in a separate thread to keep the workbench from freezing. */ void StartCropThread(); /** \brief Method called when the bandpass thread finishes; * it adds the image to a new data node and registers it to the worbench's data storage */ void HandleBandpassResults(mitk::Image::Pointer image); /** \brief Bandpassing is being performed in a separate thread to keep the workbench from freezing. */ void StartBandpassThread(); void UpdateProgress(int progress, std::string progressInfo); void PAMessageBox(std::string message); void BatchProcessing(); void UpdateSaveBoxes(); void ChangedSOSBandpass(); void ChangedSOSBeamforming(); protected: virtual void CreateQtPartControl(QWidget *parent) override; virtual void SetFocus() override; /** \brief called by QmitkFunctionality when DataManager's selection has changed. * On a change some parameters are internally updated to calculate bounds for GUI elements as the slice selector for beamforming or * the bandpass filter settings. */ virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer source, const QList& nodes) override; /** \brief Instance of the GUI controls */ Ui::PAImageProcessingControls m_Controls; float m_ResampleSpacing; bool m_UseLogfilter; std::string m_OldNodeName; /** \brief The settings set which is used for beamforming, updated through this class. */ mitk::BeamformingSettings::Pointer BFconfig; /** \brief Method for updating the BFconfig by using a selected image and the GUI configuration. */ void UpdateBFSettings(mitk::Image::Pointer image); void EnableControls(); void DisableControls(); /** \brief Class through which the filters are called. */ mitk::PhotoacousticFilterService::Pointer m_FilterBank; }; class BeamformingThread : public QThread { Q_OBJECT void run() Q_DECL_OVERRIDE; signals: void result(mitk::Image::Pointer); void updateProgress(int, std::string); void message(std::string); public: void setConfig(mitk::BeamformingSettings::Pointer BFconfig); void setInputImage(mitk::Image::Pointer image); void setFilterBank(mitk::PhotoacousticFilterService::Pointer filterBank) { m_FilterBank = filterBank; } protected: mitk::BeamformingSettings::Pointer m_BFconfig; mitk::Image::Pointer m_InputImage; int m_Cutoff; mitk::PhotoacousticFilterService::Pointer m_FilterBank; }; class BmodeThread : public QThread { Q_OBJECT void run() Q_DECL_OVERRIDE; signals: void result(mitk::Image::Pointer); public: enum BModeMethod { ShapeDetection, Abs }; void setConfig(bool useLogfilter, double resampleSpacing, mitk::PhotoacousticFilterService::BModeMethod method, bool useGPU); void setInputImage(mitk::Image::Pointer image); void setFilterBank(mitk::PhotoacousticFilterService::Pointer filterBank) { m_FilterBank = filterBank; } protected: mitk::Image::Pointer m_InputImage; mitk::PhotoacousticFilterService::BModeMethod m_Method; bool m_UseLogfilter; double m_ResampleSpacing; bool m_UseGPU; mitk::PhotoacousticFilterService::Pointer m_FilterBank; }; class CropThread : public QThread { Q_OBJECT void run() Q_DECL_OVERRIDE; signals: void result(mitk::Image::Pointer); public: void setConfig(unsigned int CutAbove, unsigned int CutBelow, unsigned int CutSliceFirst, unsigned int CutSliceLast); void setInputImage(mitk::Image::Pointer image); void setFilterBank(mitk::PhotoacousticFilterService::Pointer filterBank) { m_FilterBank = filterBank; } protected: mitk::Image::Pointer m_InputImage; unsigned int m_CutAbove; unsigned int m_CutBelow; unsigned int m_CutSliceLast; unsigned int m_CutSliceFirst; mitk::PhotoacousticFilterService::Pointer m_FilterBank; }; class BandpassThread : public QThread { Q_OBJECT void run() Q_DECL_OVERRIDE; signals: void result(mitk::Image::Pointer); public: void setConfig(float BPHighPass, float BPLowPass, float TukeyAlphaHighPass, float TukeyAlphaLowPass, float recordTime); void setInputImage(mitk::Image::Pointer image); void setFilterBank(mitk::PhotoacousticFilterService::Pointer filterBank) { m_FilterBank = filterBank; } protected: mitk::Image::Pointer m_InputImage; float m_BPHighPass; float m_BPLowPass; float m_TukeyAlphaHighPass; float m_TukeyAlphaLowPass; float m_RecordTime; mitk::PhotoacousticFilterService::Pointer m_FilterBank; }; #endif // PAImageProcessing_h